# Leave a question!

Sometimes I get interesting questions that don’t quite fit into any of the existing topics already discussed within the blog and my obsessive/compulsive nature tells me that getting this questions in a random part/page/post of the blog doesn’t look quite neat either. Therefore I open this new page for all those questions you have! I don’t intend to have a repository like the one on the CCL, of course, but at least we could organize the info and make it readily available for those who might need it; in the end, that is what we do as scientists, right?

Please use tags at the begining of your comment, e.g.: #convergencefailure #visualization #gaussianerror or whatever you might think could help me, and others, to quickly find an answer to your queries. Feel free to reply to any comment you think you might have an answer to because the thing is, I don’t have all the answers (I wish I did, trust me). One other thing, try to summarize your questions in a coherent way and please **do not post entire** output files! I don’t have the time to check them in their entirety.

Well then, leave a question!

Hello,

I would be grateful if you could explain me the difference between the normal analysis done using HPmodes and without that. I want to compute the vibronic spectra of some dyes. I have used G09 to do that. However, the code is error prone! I got alot of error message without any documentation. Then, I shifted to source code, FCClasses to follow up. Now, I understood that I need normal mode analysis using HPmodes syntax to feed the code. I compared the outputs there is two series of normal analysis. I don’t clearly know how are the anlysi are done and what are the differences. For the first analysis after printing frequencies is like this:

1 2 3 4 5

A A A A A

Frequencies — 50.1139 53.0576 78.4365 108.7226 132.2478

Reduced masses — 5.1998 3.9481 5.5278 3.3061 1.5043

Force constants — 0.0077 0.0065 0.0200 0.0230 0.0155

IR Intensities — 0.3409 0.4114 0.5722 4.3762 1.4973

Coord Atom Element:

1 1 6 0.00006 0.00025 0.26758 0.00003 0.00017

and the second analysis is like this :

1 2 3

A A A

Frequencies — 50.1139 53.0576 78.4365

Red. masses — 5.1998 3.9481 5.5278

Frc consts — 0.0077 0.0065 0.0200

IR Inten — 0.3409 0.4114 0.5722

Atom AN X Y Z X Y Z X Y Z

1 6 0.00 0.00 0.00 0.00 0.00 0.17 0.27 -0.05 0.00

as far as I got, the G09 uses the second analysis while the FCClasses needs the first to perform the analysis. Any help would be appreciated.

Saman

Hi Saman

The HPmodes option only uses the high precision format (to five figures) vibrational frequency eigenvectors in the frequency output in addition to the normal three-figure output. So basically there is no difference, since it is using the whole set of numbers to do the math it only varies in the number of decimals used in the output.

I hope this helps but if it doesn’t let me know, ok? Have a nice day!

Hello,

I would be grateful if you could explain me that how can I calculate Fukui functions on different atoms of a molecule using B3LYP 311-G ++ dp basis set G03 program. I have been successfully run the DFT of the organic molecule 2,2’-(1Z.1’Z)-(4,4’-methylenebis(4,1-phenylene)bis(azan-1-yl-1-ylidene))bis(methan-1-yl-1-ylidene)diphenol and now i want to calculate Fukui function on each atoms of this organic molecule. Please advise me how can I calculate fukui function.

Thanking You

Vinay Jaiswal

Hello, i am facing one problem related to my calculation. When i upload my input file having B3LYP/6-31G (d) set to gaussian then it gives an error :small molecule interaction” atoms too close. so, how i can remove it ???

Hello Adnan,

You have to open your molecule with a visualizer that will allow you to modify the structure like GaussView.

The error above means that two atoms are very close or even overlapping which makes no physical/chemical sense. G09 wont waste time in optimizing or calculating a structure in which two atoms are closer than the sum of their covalent radii. Imagine two H atoms at a 0.1 A, that is 20% of the Bohr radius! which implies that both protons are now touching each other.

Visualize your molecule, find the atoms overlapping and modify the structure to avoid the error.

Have a nice day

Hi Sir,

How can I make Gaussian print the first derivative of energy (dV/dx) for a given molecule in cartesian coordinates?

Hi!

there must be an overlay (IOp) for that but unfortunately I don’t know it. Please contact Gaussian Tech support at their website. Do not worry about not having a license if that is the case, they will provide support for you even if you use a non-academic address.

Sorry for not being too helpful this time. Thanks for reading!

i am Harish jangra from the National Institute of Pharmaceutical Education and Reserach studing pharmacoinformatics. Sir, it will be my great pleasure to get your guidance, i am highly obliged and thankful if you suggest me about the basic algorithm behind Gaussian calculation (optimization)

Hi Harish!

Wow, your question is not a short one! Basically Gaussian uses the Berny Optimization algorithm which calculates all forces on every atom (i.e. which way and how strongly is each atom being pushed or pulled by the rest of the atoms) then it also calculates the gradient of such forces and allows them to be pushed -or pulled- just a little bit and repeats the operation until the change in energy, forces and gradient, respect to the previous step is below a certain threshold.

There are tons of papers about the original algorithm that you can find online.

I hope this helps! Thanks for reading

THANK YOU SO MUCH SIR FOR YOUR GENEROUS HELP.

Hi,

I’m currently a graduate student in an American University. I was wondering if you could comment on the opportunities in Mexico for computational chemists presently and how you see them developing in the future.

Thanks,

Hector

Hola Héctor,

There are some oportunities for theoretical chemists in academia in Mexico but unfortunately not in the big universities, you’d have to look for a job in a smaller university or maybe at a private one which are right now trying to turn to research and not only teaching. The private industry could be another way to go although not many companies in Mexico do any research.

I can’t speak as an authority on how the job market is moving for us comp chems, all I can do is give you this insight of mine and advice you to search search search within conacyt, universities all over the place, transnational companies, etc. Something good comes always up for people who is prepared for it.

I hope you find something worth your while, in the meantime thanks for reading!

Dear sir,

I am having a error while optimizing an structre in Gaussian 09. the error is as follows

Berny optimization.

Error in internal coordinate system.

Error termination via Lnk1e in /home/software/g09-i7/g09/l103.

Your suggestion is needed.

Thank you

Hi Vijay,

I think this means your structure is not well defined in terms of the internal coordinates. Check it with a visualizer and if possible use it to change the coordinate system from internal to cartesian. Also check if some atoms are too close to one another or if bonds are crossing paths.

I hope this helps. Thanks for reading!

hi sir

i am facing same problem i.e., error in internal coordinate system.but i very new to this computational chemistry i don’t know how to change the coordinate system from internal to Cartesian,and what do meant by bonds crossing paths..really i am running out of time.since one month kept on getting this problem when i try to optimize transition state to molecule on Gaussian 09. i am thankful if you suggest me any solution for this error .

thank you

hi vijay

if you could have solved this problem based on sir suggestion,please why cant you help me to solve my problem.

thank you

Hello again Vijay

Can you use gaussview? you have to click on “save cartesians” when you save the structure. Generate it with gaussview and then save it. That should fix it. Move all the atoms around until you eliminate all the bonds crossing each other.

I hope this helps!

hey do u know any free software available for chromatography ????then plz suggest me it s urgent plzzzzzz…………

Sorry but I’m not aware of any. Try the ACDLabs website.

Hi sir,

Can you give me some ideas on spin-orbit coupling leading to the mixing of single and triplet states. Also can you mention the best program to calculate SOC. If you have already written about this please share me the link.

Thanking

Jo

Hi…would you please help me how to calculate the reduction potential using Gaussian?

Dear Sir,

I am using G09 for metal ion studies and have tried giving different basis sets for the ligands and the metal ions.Both the moment I’ve used Gen or Pseudo keywords like shown below, the following errors are obtained.

#RHF/GEN Pseudo=read

comments…

charge multiplicity

molecular specifications

C N 0

6-31+G(d’)

****

Hg 0

LANL2DZ

****

Hg 0

LANL2DZ

error : Wanted an integer as input

Found a floating point number as input

#B3LYP/GEN Opt Pseudo(SDD)

#B3LYP/GEN Opt Pseudo(Read)

Here I’ve specified the ECP basis set in the script but it still does not read the basis set.

#B3LYP/6-31G Opt Pseudo(SDD)

error : the heavy metal ion is not read by 6-31G basis set.

Also the keyword pseudo=Read and pseudo=LanL2 with LanL2DZ with the heavy metal study the same?

Dear Jyotsna,

Did you get any solution of your first error??

Please share with me, I am having the same problem.

Many thanks

Bijan

Dear Bijan,

The problem is that when you are using different basis sets for different atoms esp. an ECP basis set then you have to specify the ECP basis set in the input file as

C N 0

6-31+G(d’)

****

Hg 0

LANL2DZ

****

Hg 0

(put the ECP basis set of the desired metal here)

Hope this helps

Regards

Jyotsna

Dear Sir,

I’m interested to know if there is a software (better if it is free) that can create and plot Fukui functions from gaussian output.

Thank you!

Nick

I would suggest to use Molekel or Molden. As far as I know there isn’t a “button” to click on and get the plots so what you have to do is to substract the electronic density of the altered wavefunction (the one with a different Ne) from the one of your reference state (the one with the reference Ne). So, you have to generate both densities first and then you have to substract one from the other according to the equations found here

https://joaquinbarroso.com/2010/07/26/how-to-calculate-fukui-indices/

I hope this helps. Thanks for reading!

Dear Sir,

Now I use gaussian to calculate a cluster which made by 85 atoms, I make it two layers the higher layer is QM and lower layer is MM. Here is a problem comes, I cannot view the MO in the gaussview. As I see, the reason is the gaussian don’t calculate orbital for MM layer. Do you know any other ways to let it show MO for only QM layer?

Here is my input file,

#p opt=tight freq oniom(b3lyp/lanl2dz:uff) nosymm geom=connectivity scf=maxcycles=300 int=ultrafine

pt4

0 2 0 3 0 3

Au- 0 3.558584 2.275638 -3.710549 L

Au- 0 1.820176 2.360213 -1.802881 L

Au- 0 0.153637 2.484202 0.005572 L

Au- 0 -1.572773 2.561742 1.759631 L

Au- 0 -3.392271 2.688492 3.587681 L

Au- 0 -3.411779 0.208170 3.726424 L

.

.

.

Many Thanks!

Minmin

Hi Minmin!

I’m not sure this is possible with Gaussview and I’m not aware of any other software that could do it.

Try to visualize them directly from a formatted chk file. It might work

Hope this helps

Dear Sir,

I try to calculate sodium cation affinities with MP2=Full. Geometry optimization for neutral and sodiated species using e.g.

%chk=/home/j/neutral.chk

%nproc=12

%Mem=46GB

#MaxDisk=1000GB

#MP2=Full/6-311+G(2d,2p) Opt Test

works fine with the Linux 64 Bit G09 (Revision A.02) version. However, all subsequent frequency calculations using optimized geometries crash. The Input-File is e.g.

%RWF=/scratch/tmp/j/1,200GB,/scratch/tmp/j/2,200GB,/scratch/tmp/j/3,200GB,/scratch/tmp/j/4,200GB

%chk=/home/j/sodiated.chk

%nproc=12

%Mem=46GB

#MaxDisk=4000GB

# freq rmp2=full/6-311+g(2d,2p) geom=connectivity test

[No Title]

1 1

C -3.46469800 -0.12993500 -0.00003900

C -3.12196400 1.22077200 0.00005500

C -1.78463000 1.58038600 0.00014400

C -0.77093400 0.60304900 0.00012400

C -1.13980000 -0.75590900 0.00002700

C -2.47539400 -1.11671900 -0.00005200

Cl -5.12660400 -0.59284000 -0.00014700

C 0.58398800 1.07838200 0.00019300

C 1.75328900 0.38429100 0.00026000

C 3.07273300 1.04229600 0.00048100

C 1.89914400 -1.03108600 0.00019200

O 4.12878100 0.41326000 -0.00007800

N 2.22857600 -2.15703400 0.00018700

O 3.02120100 2.36840300 -0.00043000

H -3.89510400 1.97234700 0.00006100

H -1.51424800 2.62675400 0.00021800

H -0.39860800 -1.53873900 0.00000300

H -2.76030400 -2.15684400 -0.00013200

H 0.70057800 2.15472200 0.00027200

H 3.92868400 2.70551800 -0.00095500

Na 4.63463400 -1.82660900 -0.00023000

1 2 1.5 6 1.5 7 1.0

2 3 2.0 15 1.0

3 4 1.5 16 1.0

4 5 1.5 8 1.5

5 6 2.0 17 1.0

6 18 1.0

7

8 9 2.0 19 1.0

9 10 1.0 11 1.5

10 12 2.0 14 1.5

11 13 3.0

12

13

14 20 1.0

15

16

17

18

19

20

21

The calculation works for about 2 days and generates a combined scratch-file size of about 258 GB (splitted files). Without an error the calculations ends at the same point (just before the population analysis would start):

Gaussian Output File:

Entering Gaussian System, Link 0=/Applic.PALMA/gruppen/q0grimme/g09/g09

Initial command:

/Applic.PALMA/gruppen/q0grimme/g09/l1.exe /scratch/tmp/j.9544/Gau-9549.inp -scrdir=/scratch/tmp/j.9544/

Entering Link 1 = /Applic.PALMA/gruppen/q0grimme/g09/l1.exe PID= 9550.

******************************************

Gaussian 09: EM64L-G09RevA.02 11-Jun-2009

19-Sep-2011

******************************************

%RWF=/scratch/tmp/j/1,200GB,/scratch/tmp/j/2,200GB,/scratch/tmp/j/3,200GB,/scratch/tmp/j/4,200GB

%chk=/home/j/sodiated.chk

%nproc=12

Will use up to 12 processors via shared memory.

%Mem=46GB

———————————————————————-

#MaxDisk=4000GB # freq rmp2=full/6-311+g(2d,2p) geom=connectivity test

———————————————————————-

1/10=4,30=1,38=1,57=2/1,3;

.

.

.

.

Inverted reduced A of dimension 497 with in-core refinement.

End of Minotr Frequency-dependent properties file 721 does not exist.

End of Minotr Frequency-dependent properties file 722 does not exist.

MDV= 6174015488.

Form MO integral derivatives with frozen-active canonical formalism.

Discarding MO integrals.

Reordered first order wavefunction length = 1153152288

WUsed= 838072415 WInt= 6228120 WEnd= 13283563520

Dk804= 4115560752. Dk1111= 0. Dk1112= 12923258400.

MaxDsk=536870912000 LAFull= 1153152288 DskLim=536870912000.

NUsed=29632743563.20077466863.14050795516.12680526328.10543911627. 9119501826.

In DefCFB: NBatch= 1 ICI= 58 ICA=414 LFMax= 60

Large arrays: LIAPS= 22894001280 LIARS= 3140649540 words.

Semi-Direct transformation.

ModeAB= 4 MOrb= 58 LenV= 6168992221

LASXX= 2811761526 LTotXX= 2811761526 LenRXX= 5642084038

LTotAB= 2830322512 MaxLAS= 2944453056 LenRXY= 0

NonZer= 8453845564 LenScr= 16973996032 LnRSAI= 2944453056

LnScr1= 5912000000 LExtra= 866684027 Total= 32339217153

MaxDsk=536870912000 SrtSym= T ITran= 4

JobTyp=0 Pass 1: I= 1 to 58.

(rs|ai) integrals will be sorted in core.

SymMOI: orbitals are not symmetric.

Spin components of T(2) and E(2):

alpha-alpha T2 = 0.1101843022D+00 E2= -0.3379652408D+00

alpha-beta T2 = 0.5524282940D+00 E2= -0.1962767113D+01

beta-beta T2 = 0.1101843022D+00 E2= -0.3379652408D+00

ANorm= 0.1882974720D+01

E2 = -0.2638697594D+01 EUMP2 = -0.12103953608513D+04

IDoAtm=111111111111111111111

Differentiating once with respect to electric field.

with respect to dipole field.

Differentiating once with respect to nuclear coordinates.

There are 1 degrees of freedom in the 1st order CPHF. IDoFFX=0.

LinEq1: Iter= 0 NonCon= 1 RMS=2.81D-03 Max=1.47D-01

LinEq1: Iter= 1 NonCon= 1 RMS=7.99D-04 Max=1.87D-02

LinEq1: Iter= 2 NonCon= 1 RMS=3.70D-04 Max=1.80D-02

LinEq1: Iter= 3 NonCon= 1 RMS=2.02D-04 Max=9.45D-03

LinEq1: Iter= 4 NonCon= 1 RMS=8.56D-05 Max=4.10D-03

LinEq1: Iter= 5 NonCon= 1 RMS=4.33D-05 Max=3.30D-03

LinEq1: Iter= 6 NonCon= 1 RMS=1.53D-05 Max=5.51D-04

LinEq1: Iter= 7 NonCon= 1 RMS=6.04D-06 Max=2.60D-04

LinEq1: Iter= 8 NonCon= 1 RMS=2.19D-06 Max=5.37D-05

LinEq1: Iter= 9 NonCon= 1 RMS=7.24D-07 Max=2.39D-05

LinEq1: Iter= 10 NonCon= 1 RMS=2.61D-07 Max=9.41D-06

LinEq1: Iter= 11 NonCon= 1 RMS=1.05D-07 Max=4.89D-06

LinEq1: Iter= 12 NonCon= 1 RMS=5.11D-08 Max=2.64D-06

LinEq1: Iter= 13 NonCon= 1 RMS=1.81D-08 Max=7.44D-07

LinEq1: Iter= 14 NonCon= 1 RMS=5.33D-09 Max=1.51D-07

LinEq1: Iter= 15 NonCon= 1 RMS=1.97D-09 Max=6.96D-08

LinEq1: Iter= 16 NonCon= 1 RMS=7.09D-10 Max=2.36D-08

LinEq1: Iter= 17 NonCon= 1 RMS=2.14D-10 Max=5.42D-09

LinEq1: Iter= 18 NonCon= 1 RMS=6.35D-11 Max=2.21D-09

LinEq1: Iter= 19 NonCon= 1 RMS=2.25D-11 Max=1.02D-09

LinEq1: Iter= 20 NonCon= 0 RMS=8.24D-12 Max=4.12D-10

Linear equations converged to 1.000D-10 1.000D-09 after 20 iterations.

End of Minotr Frequency-dependent properties file 721 does not exist.

End of Minotr Frequency-dependent properties file 722 does not exist.

Symmetrizing basis deriv contribution to polar:

IMax=3 JMax=2 DiffMx= 0.00D+00

G2DrvN: will do 22 centers at a time, making 1 passes doing MaxLOS=2.

Calling FoFCou, ICntrl= 3107 FMM=F I1Cent= 0 AccDes= 0.00D+00.

FoFDir/FoFCou used for L=0 through L=2.

End of G2Drv Frequency-dependent properties file 721 does not exist.

End of G2Drv Frequency-dependent properties file 722 does not exist.

Do you have any explanation for this error?

Sincerely,

T. Jaskolla

Hello T.

I haven’t seen this error before. Are you performing the second set of calculations on the same machine?

Try using density=current

Hope this helps!

Dear Thorsten,

Did you get any solution of your error?

Please share with me, I am having the same problem when I use gaussian to calculate the frequency of a cluster which made by 480 atoms.

Many thanks

Xiaohong Yuan

Dear sir,

My molecule name is 2-Chloro alpha alpha alpha trifluoro 3,5-dinitrotoluene. While submitting this molecule for frequency calculation, it is saying that there is ” Input conversion error in IntKMC” . I don’t know how to eliminate that error .and seeking your assistance to continue my work.

Hello Meenakshi

Haven’t seen this error before but there seems to be something wrong with the input. Try redefining the molecule specification section. Did you pre-optimized the structure? Are you reading it from another program?

I think I need more information to help you, ok?

I hope I can help you in the near future.

Dr. Barroso,

In a reponse to someone trying to visualize a hypersurface of a scan you suggest using “Origin, GNUplot or in the worst case scenario with MS Excel”. What other programs would you suggest a S.T.E.M. student should be familiar with before entering grad school? Excluding, the basic Microsoft suite of programs like word, ppt, and excel.

Thank you,

Agapito

Hello Agapito, my friend who I still haven’t met!

I would suggest learning how to work with software for statistical analysis such as Origin or other commercial packages with the same purpose.

Learning your way around Unix/Linux/etc. is important since you will have the need for more powerful computing capabilities which are best provided by these systems.

Coding is a very valuable skill these days, although you don’t have to be exactly an expert on programming, just knowing your way around a certain language will help you understand and modify existing codes (almost nobody codes from scratch anymore, the closest thing still involves taking published subroutines for tasks such as integrating). Suggested languages to learn: C and its variants, Python and Fortran if available (in that order of priority).

MATLAB can also be a great asset to your skills.

From the top of my head I think this is the most important I can think of right now for any generic STEM grad student but if I think of something else I’ll get back to this comment.

How about those Rangers? Texans are pretty excited, I guess. I’m betting on them to win the World Series, despite the fact I was secretly rooting for the Tigers.

Have a nice day!

Dr. Barroso,

Wow this is a great Gaussian site, and you are so helpful and prompt with all levels of questions. if you don’t mind, I have two totally basic ones, and would really appreciate your help. I’m using 09, and have Gauss-View. : )

1st involves the Gen keyword and a .gbs file. When “downloading” a basis set from the EMSL, is it just copy-paste the desired atoms from the pop-up window (from the desired set) and save as a .gbs in your directory? Basically how does downloading basis sets from the EMSL work if Gaussian needs a .gbs file?

2nd involves Using NBO analysis in a TD excited states calculation. I know where the bond population and energy are for “natural” orbitals in the analysis. How/where do I assign calculated UV-vis peaks to their natural orbital excited transitions? Thanks so much!

Dr. Joaquin,

Scratch the NBO TD analysis. I’ve been able to parse the .log files to assign population density types to transitions by coefficients etc. As I believe you’ve commented on, NBO & DFT do not really mix in GaussView (using 5). So I’ll only be using NBO for bond energy (kcal) for certain donor interactions in the .log.

However, If you have any advise on the Gen keyword related to installing basis sets from the EMSL, your help would be truly appreciated.

-b

Hi Brady

First of all please forgive the lateness of my response (sheesh! this has become a usual opening line in my replies; I either reply sooner or create a shortcut so I don’t have to type it all every time!)

About the GEN keyword, please defer to my latest post which can be seen here

https://joaquinbarroso.com/2011/11/02/gen-keyword-gaussian/

It is sometimes confusing what to do with the EMSL basis sets but I hope this post helps you.

Best wishes and thanks for reading!

Dear Brady,

Please share how you solve your problems regarding gen keyword and EMSL basis set, and how you assigned uv-vis peaks to their natural orbital exited transition in a TD calculation?

Many thanks

With best regards,

Bijan Mondal

In this blog there is a post about the use of the GEN keyword. Try searching it with the search field at the left side of the page

Hello Sir,

Let me know about PBC calculations in Gauassian. Is it calculations in solid phase? Is it possible to do calculations in solid state with Gaussian?

Thank-you

Hello Alam!

PBC would be a great post for the near future! Thanks for the idea 🙂

Now, to answer your question. PBC generates a periodic model from a small set of atomic coordinates based on symmetry considerations you impose. Therefore you can run calculations on a polymer based on the calculations of the corresponding monomer (1D replication). The same holds true for a surface (2D replication) or a crystalline solid (3D). The problem is getting the band structure of the solid which could be obtained as a result of a (very demanding) DFT calculation in which the MOs would get so packed they would constitute a band.

I would suggest to get another software such as CRYSTAL but PBC in G09 could be a great first step in calculating the electronic structure of a solid.

Hope this helps

Thanks for reading!

Dear Alam,

i am trying to do DFT calculation of TiO2 crystal for interaction qith simple molecules like water

But in doing so using G09 when I’m taking / cleaving the crystal from a particular surface like 0 0 1 surface and interacting the water molecule

the error is

“Symmetry turned off by external request

Symmetry turned off

Cannot cope with the ghost atoms or with translational vectors”

Do I have to give a PBC calculation for the crystal

Also how do I see the interacting atoms as it is a symmetrical structure and on cleaving the infinte structure still remains

Do I have to saturate the O ends of TiO2 with hydrogen/ make it a double bond?

Regards

Jyotsna

Hello sir,

Please let me know ho to calculate EPR parameters (hyperfine splitting constants, g-tensor) using gaussian 03..

thanking

you

Jo

Hello sir,

i hope to know how can an intramolecular H-bond in guest molecule effect i the inclusion complex

Try calculating the wiberg bond index between those atoms involved. Find the procedure in the post with the NBO calculations in this blog.

I hope this helps

Hello sir,

I hope to know the relationships with the inclusion and the intramolecular h bond in guest molecule

please can you explain to me the relationships with the inclusion and the intramoleclar H-bond

I want to calculate a TS between SSOO, can you help me how to design this and how I can obtain this?

Thanks

Hello sir

this srinu i am very new to this gaussian(learning now) i have been trying to optimize the transition state of aldehydic hydrogen abstraction with chlorine atom. but its forming always product i am using mpwb1k level of theory 6-31+g(d,p) basis set.please help me_

Dear Dr. Joaquin,

I am trying to optimize a structure of CdCl4 with two cation at a distant apart.

Following is my input:

%chk=a.chk

%nproc=4

%mem=120MW

#p b3lyp/Gen pseudo=read opt scf(tight,maxcycle=1000)

Calculation

0 1

Cd -0.00000000 0.00000000 -0.00000000

Cl 1.86600000 1.89125000 0.29318000

Cl -0.00000000 -0.37522000 2.49421000

…………………..

………………..

C N H 0

6-31G(d)

****

Cl 0

6-31G++(d)

****

Cd 0

LANL2DZ

****

Cd 0

LANL2DZ

But I am getting a structure which is away from the crystal structure.

If I include counterpoise keyword and specify the fragment I am getting an error message

Cd atom has 48 electrons but 18 basis set is defined. This is less than minimal basis set.

Yet it is calculating the structure but the the mulliken charge I am specifying is not conserved.

Kindly help.

Ok, you have two different problems here:

1) Optimizing the structure means you will find the structure with the lowest (within reason) energy possible; crystal structures are often not since they are restrained by the crystal field. Taking them out of the crystal allows them to be relaxed which explains why both structures are different.

2) the counterpoise keyword calculates how the electrons from one fragment populate the basis set functions of the other fragment. The method doesn’t work with pseudopotentials like LANL2DZ (which replaces the core of 30 electrons so the calculation is performed faster) but the method knows that Cd has 48 electrons and only finds space for 18 so it crashes.

I hope this helps

Hi Dr.!

I’m a newcomer on Comput. Chem. I wonder if you could help me with this problem. Have you use Molden 3.4 program yet? I use this program to visualize the MO of tetraaluminium dianion but I could not obtain the HOMO, HOMO-1 or any MO pictures look like on this paper DOI: 10.1126/science.291.5505.859 despite the fact that I used the same program (G03W) and Method in my calculation. Could you help me?

Many Thanks for any Reply!

I’m not an expert on Molden but my guess is that the program can’t find the basis set and therefore can’t generate the MOs from the calculated coefficients. Try using the following options in your calculation: gfprint gfoldprint and gfinput. all of them print the basis set in different formats, molden will be able to read one of them and then generate the MOs

I hope this helps!

Hi Dr.

I’m using Gaussian with NBO analysis. I’m running optimization with NBO. But usually I got the following error message: ” NBStor is confused about NOcc. ”

I saw some questions about this on your website, so I tried to change the basis set, but it occurs some times.

Is there any difference if I do the optimization first, then do the NBO analysis? I did the optimization with NBO, which means before opt, NBO is performed, and after geometry optimization, NBO is performed. I’m using one molecule with charge 0, -1, +1. Although it works with charge 0 based on some basis set, it doesn’t work with charge -1 based on the same basis.

Is it ok to optimize for geometry, then use the optimized geometry with NBO in energy calculation?

It is correct to do it that way but you won’t find any difference in the result. You have a basis set issue which can’t be overcome and that is due to the charge. Try it your way and if it works PLEASE let me know, ok?

Have a nice day!

Hello sir

i trying to calculate Fukui function for some pyridine derivatives but i have a problem. assuming i want to calculate the Fukui function of pyridine so three calculation must be performed

first, for pyridine which is the neutral molecule to be analyzed of N electron system

second is the negative ion of pyridine (N+1) system——-???????

third is the positive ion of pyridine (N-1) system——–??????

does the input file of the second and third calculation is the same of the first but just only change the charge of the system fro 0 to -1 and +1

or what?

hello sir

sorry for the incomplete message, i just want to ask about what is he N system, N-1 and N+1 systems used for pyridine?

i tried to do the calculations using g03 at DFT/B3LYP level for pyridine its ok

but i dont know what are the N-1 and N+1 species should be calculated.

best regard

Dr Saied Soliman

Hello,

i’m trying to optimize the structure of Ir(ppy)3 and then i want to calculte uv vis spectr awith varying th density functionals…

i try to use GEN keyword to set basis sets for Iridium and the pop=(readradii) for it.

but when i run the job i get errors

this is the input file:

%chk=C:\Users\Enrico D\Desktop\Ir(ppy)3 testgrd.chk

# opt freq td rb3lyp/gen geom=connectivity int=ultrafine

pop=(readradii,mk) pseudo=read

Title Card Required

0 1

C -3.99749000 -2.98380300 0.00000000

C -4.15709000 -1.63958500 0.00000000

C -2.90822600 -0.74768400 0.00000000

C -1.67055100 -1.23449400 0.00000000

C -1.48668300 -2.76506200 0.00000000

C -2.57441300 -3.58229800 0.00000000

C -2.91748200 0.72025200 0.00000000

C -4.02164900 1.49664600 0.00000000

C -3.83063900 3.01655200 0.00000000

C -2.56850500 3.50396400 0.00000000

C -1.37319400 2.52360000 0.00000000

N -1.57201600 1.23716300 0.00000000

C -1.49898000 -2.45091700 0.00000000

C -1.65118700 2.67012600 0.00000000

N -0.28544700 -1.97986700 0.00000000

C 0.83493000 -2.88661100 0.00000000

C 0.71469000 -4.23096000 0.00000000

C -0.69702200 -4.82555100 0.00000000

C -1.75026000 -3.97629300 0.00000000

C -1.81514700 4.02072500 0.00000000

C -0.58536300 4.95399800 0.00000000

C 0.65862700 4.42015600 0.00000000

C 0.80666600 2.89257300 0.00000000

C -0.23376500 2.06410800 0.00000000

C 2.10159300 -2.14477600 0.00000000

C 2.08253600 2.16647700 0.00000000

C 3.30703300 2.73434500 0.00000000

C 4.52771400 1.80883200 0.00000000

C 4.31866200 0.47210600 0.00000000

C 2.87194500 -0.07273300 0.00000000

N 1.85736100 0.74280900 0.00000000

C 3.13809300 0.09483200 0.00000000

C 1.90442100 -0.82952500 0.00000000

C 4.38967500 -0.43867700 0.00000000

C 4.58279900 -1.97036800 0.00000000

C 3.49838600 -2.78056800 0.00000000

Ir 0.00000000 0.00005600 0.00000000

H -4.85221600 -3.62745600 0.00000000

H -5.13574100 -1.20698000 0.00000000

H -0.50258400 -3.18513500 0.00000000

H -2.44301700 -4.64421900 0.00000000

H -5.00021600 1.06382900 0.00000000

H -4.67352300 3.67566300 0.00000000

H -2.39890200 4.56043100 0.00000000

H -0.37379900 2.90579800 0.00000000

H -2.32971300 -1.77654500 0.00000000

H -2.50697900 2.02787000 0.00000000

H 1.57885000 -4.86192300 0.00000000

H -0.84629400 -5.88507000 0.00000000

H -2.74997000 -4.35772500 0.00000000

H -2.80051900 4.43781300 0.00000000

H -0.71552800 6.01603900 0.00000000

H 1.52254200 5.05147800 0.00000000

H 3.42159100 3.79819100 0.00000000

H 5.51998600 2.20913700 0.00000000

H 5.14873000 -0.20309400 0.00000000

H 2.70313200 -1.12932200 0.00000000

H 3.00995400 1.15712500 0.00000000

H 5.24367900 0.20599300 0.00000000

H 5.56755700 -2.38884300 0.00000000

H 3.61296100 -3.84442200 0.00000000

1 2 2.0 6 1.0 38 1.0

2 3 1.0 39 1.0

3 4 2.0 7 1.0

4 5 1.0 13 3.0 37 1.0 46 1.0

5 6 2.0 13 3.0 15 1.0 19 3.0 40 1.0

6 13 1.0 19 3.0 41 1.0 50 1.0

7 8 2.0 12 1.0

8 9 1.0 42 1.0

9 10 2.0 43 1.0

10 11 1.0 14 3.0 20 3.0 44 1.0 51 1.0

11 12 2.0 14 3.0 20 1.0 24 3.0 45 1.0

12 14 1.0 37 1.0

13 15 2.0 19 1.0 46 1.0

14 20 2.0 24 1.0 47 1.0

15 16 1.0 37 1.0

16 17 2.0 25 1.0

17 18 1.0 48 1.0

18 19 2.0 49 1.0

19 41 1.0 50 1.0

20 21 1.0 44 1.0 51 1.0

21 22 2.0 52 1.0

22 23 1.0 53 1.0

23 24 2.0 26 1.0

24 37 1.0 45 1.0

25 33 2.0 36 1.0

26 27 2.0 31 1.0

27 28 1.0 54 1.0

28 29 2.0 55 1.0

29 30 1.0 32 3.0 34 3.0 56 1.0 59 1.0

30 31 2.0 32 3.0 33 3.0 34 1.0 57 1.0

31 32 1.0 37 1.0

32 33 1.0 34 2.0 58 1.0

33 37 1.0 57 1.0

34 35 1.0 56 1.0 59 1.0

35 36 2.0 60 1.0

36 61 1.0

37

38

39

40

41 50 1.0

42

43

44 51 1.0

45

46

47

48

49

50

51

52

53

54

55

56 59 1.0

57

58

59

60

61

H 0

S 3 1.00

19.2384000 0.0328280

2.8987000 0.2312040

0.6535000 0.8172260

S 1 1.00

0.1776000 1.0000000

****

C 0

S 7 1.00

4233.0000000 0.0012200

634.9000000 0.0093420

146.1000000 0.0454520

42.5000000 0.1546570

14.1900000 0.3588660

5.1480000 0.4386320

1.9670000 0.1459180

S 2 1.00

5.1480000 -0.1683670

0.4962000 1.0600910

S 1 1.00

0.1533000 1.0000000

P 4 1.00

18.1600000 0.0185390

3.9860000 0.1154360

1.1430000 0.3861880

0.3594000 0.6401140

P 1 1.00

0.1146000 1.0000000

****

N 0

S 7 1.00

5909.0000000 0.0011900

887.5000000 0.0090990

204.7000000 0.0441450

59.8400000 0.1504640

20.0000000 0.3567410

7.1930000 0.4465330

2.6860000 0.1456030

S 2 1.00

7.1930000 -0.1604050

0.7000000 1.0582150

S 1 1.00

0.2133000 1.0000000

P 4 1.00

26.7900000 0.0182540

5.9560000 0.1164610

1.7070000 0.3901780

0.5314000 0.6371020

P 1 1.00

0.1654000 1.0000000

****

Ir 0

S 3 1.00

2.3500000 -1.6784642

1.5820000 2.0952553

0.5018000 0.4162934

S 4 1.00

2.3500000 1.6464467

1.5820000 -2.2748150

0.5018000 -1.0494357

0.2500000 1.2167791

S 1 1.00

0.0598000 1.0000000

P 3 1.00

2.7920000 -0.3889212

1.5410000 0.9077516

0.5285000 0.4691443

P 2 1.00

0.5100000 -0.1170669

0.0980000 1.0489002

P 1 1.00

0.0290000 1.0000000

D 2 1.00

1.2400000 0.5087022

0.4647000 0.5862102

D 1 1.00

0.1529000 1.0000000

****

! Elements References

! ——– ———-

! Na – Hg: P. J. Hay and W. R. Wadt, J. Chem. Phys. 82, 270 (1985).

! P. J. Hay and W. R. Wadt, J. Chem. Phys. 82, 284 (1985).

! P. J. Hay and W. R. Wadt, J. Chem. Phys. 82, 299 (1985).

!

IR 0

IR-ECP 4 60

g potential

5

1 823.5880147 -0.1578014

2 364.6613336 -1517.5270446

2 55.7082801 -316.5306529

2 12.0464544 -91.8880941

2 3.5120610 -9.2241773

s-g potential

6

0 188.0490770 3.1578014

1 340.4194712 26.8322577

2 128.2373673 800.4250007

2 33.8644961 369.4050683

2 4.7560005 242.4171899

2 3.9649974 -118.2173282

p-g potential

5

0 289.7291139 2.1578014

1 87.4633789 61.9678610

2 30.4363766 269.0581986

2 4.0553412 231.1654793

2 3.5525341 -133.6952667

d-g potential

5

0 136.4017106 3.1578014

1 95.0776925 45.9349803

2 49.2258410 359.0344668

2 15.0874145 176.4740119

2 4.0405764 54.5155286

f-g potential

5

0 127.3507908 3.9546197

1 66.2364374 52.9773655

2 34.4299229 274.8643383

2 10.1995721 137.2047338

2 2.5409702 14.8633305

Ir 0.82

————————————-

and this is the output with error 2070:

Entering Link 1 = C:\G03W\l1.exe PID= 3580.

Copyright (c) 1988,1990,1992,1993,1995,1998,2003, Gaussian, Inc.

All Rights Reserved.

This is the Gaussian(R) 03 program. It is based on the

the Gaussian(R) 98 system (copyright 1998, Gaussian, Inc.),

the Gaussian(R) 94 system (copyright 1995, Gaussian, Inc.),

the Gaussian 92(TM) system (copyright 1992, Gaussian, Inc.),

the Gaussian 90(TM) system (copyright 1990, Gaussian, Inc.),

the Gaussian 88(TM) system (copyright 1988, Gaussian, Inc.),

the Gaussian 86(TM) system (copyright 1986, Carnegie Mellon

University), and the Gaussian 82(TM) system (copyright 1983,

Carnegie Mellon University). Gaussian is a federally registered

trademark of Gaussian, Inc.

This software contains proprietary and confidential information,

including trade secrets, belonging to Gaussian, Inc.

This software is provided under written license and may be

used, copied, transmitted, or stored only in accord with that

written license.

The following legend is applicable only to US Government

contracts under DFARS:

RESTRICTED RIGHTS LEGEND

Use, duplication or disclosure by the US Government is subject

to restrictions as set forth in subparagraph (c)(1)(ii) of the

Rights in Technical Data and Computer Software clause at DFARS

252.227-7013.

Gaussian, Inc.

Carnegie Office Park, Building 6, Pittsburgh, PA 15106 USA

The following legend is applicable only to US Government

contracts under FAR:

RESTRICTED RIGHTS LEGEND

Use, reproduction and disclosure by the US Government is subject

to restrictions as set forth in subparagraph (c) of the

Commercial Computer Software – Restricted Rights clause at FAR

52.227-19.

Gaussian, Inc.

Carnegie Office Park, Building 6, Pittsburgh, PA 15106 USA

—————————————————————

Warning — This program may not be used in any manner that

competes with the business of Gaussian, Inc. or will provide

assistance to any competitor of Gaussian, Inc. The licensee

of this program is prohibited from giving any competitor of

Gaussian, Inc. access to this program. By using this program,

the user acknowledges that Gaussian, Inc. is engaged in the

business of creating and licensing software in the field of

computational chemistry and represents and warrants to the

licensee that it is not a competitor of Gaussian, Inc. and that

it will not use this program in any manner prohibited above.

—————————————————————

Cite this work as:

Gaussian 03, Revision B.01,

M. J. Frisch, G. W. Trucks, H. B. Schlegel, G. E. Scuseria,

M. A. Robb, J. R. Cheeseman, J. A. Montgomery, Jr., T. Vreven,

K. N. Kudin, J. C. Burant, J. M. Millam, S. S. Iyengar, J. Tomasi,

V. Barone, B. Mennucci, M. Cossi, G. Scalmani, N. Rega,

G. A. Petersson, H. Nakatsuji, M. Hada, M. Ehara, K. Toyota,

R. Fukuda, J. Hasegawa, M. Ishida, T. Nakajima, Y. Honda, O. Kitao,

H. Nakai, M. Klene, X. Li, J. E. Knox, H. P. Hratchian, J. B. Cross,

C. Adamo, J. Jaramillo, R. Gomperts, R. E. Stratmann, O. Yazyev,

A. J. Austin, R. Cammi, C. Pomelli, J. W. Ochterski, P. Y. Ayala,

K. Morokuma, G. A. Voth, P. Salvador, J. J. Dannenberg,

V. G. Zakrzewski, S. Dapprich, A. D. Daniels, M. C. Strain,

O. Farkas, D. K. Malick, A. D. Rabuck, K. Raghavachari,

J. B. Foresman, J. V. Ortiz, Q. Cui, A. G. Baboul, S. Clifford,

J. Cioslowski, B. B. Stefanov, G. Liu, A. Liashenko, P. Piskorz,

I. Komaromi, R. L. Martin, D. J. Fox, T. Keith, M. A. Al-Laham,

C. Y. Peng, A. Nanayakkara, M. Challacombe, P. M. W. Gill,

B. Johnson, W. Chen, M. W. Wong, C. Gonzalez, and J. A. Pople,

Gaussian, Inc., Pittsburgh PA, 2003.

*********************************************

Gaussian 03: x86-Win32-G03RevB.01 3-Mar-2003

31-Dec-2011

*********************************************

%chk=C:\Users\Enrico D\Desktop\Ir(ppy)3 testgrd.chk

Default route: MaxDisk=4gb

———————————————————————-

# opt freq td rb3lyp/gen geom=connectivity int=ultrafine pop=(readradi

i,mk) pseudo=read

———————————————————————-

Warning: this job cannot use analytic gradients

and so will do many energy evaluations.

1/14=-1,26=3,29=20000,38=1,57=2/1,14;

2/17=6,18=5,29=3,40=1/2;

3/5=7,11=2,16=1,17=8,25=1,30=1,74=-5,75=5/1,2,8,3;

4/7=1/1;

5/5=2,38=5/2;

8/6=1,10=1,27=536870912/1;

9/27=536870912,42=1/14;

6/7=2,8=2,9=2,10=2,15=8,20=101/1,2;

1/14=-1/14(1);

99//99;

2/29=3/2;

3/5=7,6=1,11=2,16=1,17=8,25=1,30=1,74=-5,75=5,82=7/1,2,8,3;

4/5=5,7=1,16=3/1;

5/5=2,38=5/2;

8/6=1,10=1,27=536870912/1;

9/27=536870912,42=1,49=4/14;

1/14=-1/14(-6);

2/29=3/2;

6/7=2,8=2,9=2,10=2,15=8,20=101/1,2;

99//99;

——————-

Title Card Required

——————-

Symbolic Z-matrix:

Charge = 0 Multiplicity = 1

C -3.99749 -2.9838 0.

C -4.15709 -1.63959 0.

C -2.90823 -0.74768 0.

C -1.67055 -1.23449 0.

C -1.48668 -2.76506 0.

C -2.57441 -3.5823 0.

C -2.91748 0.72025 0.

C -4.02165 1.49665 0.

C -3.83064 3.01655 0.

C -2.56851 3.50396 0.

C -1.37319 2.5236 0.

N -1.57202 1.23716 0.

C -1.49898 -2.45092 0.

C -1.65119 2.67013 0.

N -0.28545 -1.97987 0.

C 0.83493 -2.88661 0.

C 0.71469 -4.23096 0.

C -0.69702 -4.82555 0.

C -1.75026 -3.97629 0.

C -1.81515 4.02072 0.

C -0.58536 4.954 0.

C 0.65863 4.42016 0.

C 0.80667 2.89257 0.

C -0.23377 2.06411 0.

C 2.10159 -2.14478 0.

C 2.08254 2.16648 0.

C 3.30703 2.73435 0.

C 4.52771 1.80883 0.

C 4.31866 0.47211 0.

C 2.87195 -0.07273 0.

N 1.85736 0.74281 0.

C 3.13809 0.09483 0.

C 1.90442 -0.82953 0.

C 4.38968 -0.43868 0.

C 4.5828 -1.97037 0.

C 3.49839 -2.78057 0.

Ir 0. 0.00006 0.

H -4.85222 -3.62746 0.

H -5.13574 -1.20698 0.

H -0.50258 -3.18514 0.

H -2.44302 -4.64422 0.

H -5.00022 1.06383 0.

H -4.67352 3.67566 0.

H -2.3989 4.56043 0.

H -0.3738 2.9058 0.

H -2.32971 -1.77655 0.

H -2.50698 2.02787 0.

H 1.57885 -4.86192 0.

H -0.84629 -5.88507 0.

H -2.74997 -4.35773 0.

H -2.80052 4.43781 0.

H -0.71553 6.01604 0.

H 1.52254 5.05148 0.

H 3.42159 3.79819 0.

H 5.51999 2.20914 0.

H 5.14873 -0.20309 0.

H 2.70313 -1.12932 0.

H 3.00995 1.15713 0.

H 5.24368 0.20599 0.

H 5.56756 -2.38884 0.

H 3.61296 -3.84442 0.

NEF-NEF-NEF-NEF-NEF-NEF-NEF-NEF-NEF-NEF-NEF-NEF-NEF-NEF-NEF-NEF-NEF-NEF-

NUMERICAL EIGENVECTOR FOLLOWING MINIMUM SEARCH

INITIALIZATION PASS

************************************************

** ERROR IN INITNF. NUMBER OF VARIABLES ( 0) **

** INCORRECT (SHOULD BE BETWEEN 1 AND 50) **

************************************************

Error termination via Lnk1e in C:\G03W\l114.exe at Sat Dec 31 14:28:19 2011.

Job cpu time: 0 days 0 hours 0 minutes 1.0 seconds.

File lengths (MBytes): RWF= 7 Int= 0 D2E= 0 Chk= 1 Scr= 1

…………………

for simplest calculations or for smallest molecules there is no problem.But for biggest ones…

WHAT SHOULD I DO?

IN GENERAL, CAN YOU HELP ME TO SET UP TDDFT CALCULATIONS for excited states FOR TRANSITION METALS SUCH AS Ru and Ir, what are the best settings and the corrects one?

There are errors in the input file? (Syntax, Keywords…?)…

this is the molecule: http://www.lookchem.com/300w/2010/0714/94928-86-6.jpg

i use:

GaussView 5.0

Gaussian03

ChemBio Office for structure designing

Many thanks.

Best Regards,

Enrico D’Ortenzio

Oricola (Italy)

University of Tor Vergata, Rome

Hi, I make TD-DFT with metal complex and I usually use the lanl2dz basis set with the cam-B3LYP functional for TD calculation and they give good result compared with experimental data. I suggest you to include also the solvent effect with PCM because the effect of solvent in the optimization steps and solvatochromism is important.

But it’s better that you first optimize the structure and after run TD job.

Try this for the optimization:

#p opt=tight b3lyp/lanl2dz scrf=(solvent=water) geom=connectivity pop=full

and this for TD:

#p cam-b3lyp/LANL2DZ nosym scf=maxcyc=2048 TD=NStates=35 IOP(9/40=2) IOp(8/11=1) scrf=(solvent=water)

(I used water as solvent but you can change it, the same for the number of excited state you need)

I hope this help

Please let me know if this work

Nicola

Estimado Dr. Estoy estudiando una reacción química (Diels-Alder) y quisiera los coeficientes de cada átomo en el HOMO y el LUMOm cómo puedo hacerlo? Aun estoy entendiendo este programa, gracias.

Dear Dr. Barroso

thanks a lot for your helpful posts.

I want to calculate overlap population analysis in G03.

please help me.

Best regards.

Dear Dr. Joagguin,

I am PhD student and studying with Gaussian for biological and argonometalic molecules or complexes. Can you give me some information about TDDFT calculation and Infrared-Raman calculations for this exiated state(s)? I examine some fields and help field for gaussian but I have some question… And also may you tell me system rational for gaussian?

Thank you very much, in advance…

hello ,

i do tddft uv-vis spectra of Ni(CH2S2)2, for more excited states..with g09w

but..

for some calculations i used to specify pseudopotentials with geneecp keyword to indicate the lanld2z pseudopotential for nickel…and 6-311g(3d,2p) for C,S,H

at higher frequencies, between 200-300 nm, using 6-311g for all atoms or specifying lanl2dz for Ni, i notice a split in one of the peak (the one at 270nm), i.e. the peak is split into two different peaks.

in the experimental spectrum this peak is at ca. 300nm and there is no splitting!…

what is the explanation of this effects? what are the problems related to higher frequencies states?can it depend that this is a Nickel compound? in what way it can depend by calculations?:

i do tddft calculations using b3lyp/6-311G(3d,2p), PCM for solvent(hexane)

or b3lyp/geneecp specifying lanld2z for Ni at the end of the input after the coordinates.

MANY THANKS

Enrico D.

Hi there,

i use lsda functional in my calculations on Ni, and i would use pure lda functional to compare results with lsda calculations, to understand how the spin affects (and if) the measurement.

HOW TO SET PURE LDA CALCULATION IN G09W?, since there is no pure lda in gaussview?

Best regards,

Enrico

respected sir

i am working with go3 as part of my research work. As part of my study i need to calculate Hyperpolarizability of molecule. For this, i used syntax

#p polar scf = maxcycles=500 freq = noraman b3lyp/6-311+g

finally it is giving only polar and dipolar values, but not hyperpolar.

kindly help me in this regard

thank you very much in advance

vasanth

Respected Sir,

I have done NBO calculation on diborane using standard basis set and DFT method in order to visualize the 3-centered bonds. But the NBO number appears involving 3-center bond(e.g, 1 & 4) is not matching whenever I am visualizing in gauss view rather its sum other number MO.

Kindly halp me in this regards.

Best regards,

Bijan

Dear Sir,

i am trying to do DFT calculation of TiO2 crystal for interaction qith simple molecules like water

But in doing so using G09 when I’m taking / cleaving the crystal from a particular surface like 0 0 1 surface and interacting the water molecule

the error is

“Symmetry turned off by external request

Symmetry turned off

Cannot cope with the ghost atoms or with translational vectors”

Do I have to give a PBC calculation for the crystal

Also how do I see the interacting atoms as it is a symmetrical structure and on cleaving the infinte structure still remains

Do I have to saturate the O ends of TiO2 with hydrogen/ make it a double bond?

Regards

Jyotsna

Dear Sir,

I have a quarry..

Can we do Fukui index calculation using gaussian 09 or 03?

Yes, Bijan. Gaussian can calculate Fukui indexes. Look in this blog for a post called “How to calculate Fukui Indexes” it will give you a step by step procedure on the subject.

I hope this helps

Hi

Can you pls help me to understand how these lone pair represntaion from NBO analysis means?

57. (0.22868) LP*( 6)Ru 11 s( 42.76%)p 1.32( 56.57%)d 0.01( 0.64%)

f 0.00( 0.03%)g 0.00( 0.00%)

0.0000 0.6536 -0.0100 -0.0140 0.0085

0.0009 0.0000 -0.0561 0.0109 -0.0053

0.0000 -0.7439 -0.0007 0.0019 0.0000

-0.0939 0.0024 -0.0108 0.0096 -0.0268

-0.0119 -0.0371 -0.0078 0.0078 0.0319

-0.0045 -0.0071 -0.0445 0.0216 -0.0102

0.0075 -0.0104 -0.0123 0.0047 0.0008

0.0039 -0.0028 -0.0023 0.0018 0.0017

-0.0048 0.0030 0.0013 0.0057 -0.0057

0.0101 0.0043 0.0006 -0.0004 0.0004

-0.0013 -0.0002 -0.0012 -0.0001 -0.0023

-0.0006

My question

How it is a kind of sp hybrid. I beleive usually the lone pairs are non bonding oribatals..If am wrong pls correct me..

Thanks

Rajesh

Hello Rajesh!

Lone pairs are indeed non bonding orbitals, but they can be hybridized. Think about ammonia NH3 for instance, the valence orbitals of the Nitrogen atom are sp3 hybridized, this includes all three N-H bonds but also includes the lone pair on the N atom.

Please search for my post on Pauling’s model of hybridized orbitals in this same blog. Also you could take a look at Gillespie’s VSEPR theory (well, more like a model), you’ll realize that lone pairs get hybridized too.

I hope this helps! Have a nice day

Dear Dr Barroso,

I am having trouble with molekel while analyzing a pdb file I created. The file was originally created as a trajectory / trr file by gromacs. I converted it to a pdb. I have done this dozens of times in the past. When analyzing the video in molekel, the carboxyl terminal end of the dipeptide seems to detach, specifically the carbon attached to the hydrogen. I reran this simulation many times and it is always the same way. I even ran a different dipeptide and again the same thing happened. Interesting to note, if there is a carboxyl group in the side chain of the dipeptide, the issue does not arise, only for the terminal end. I can included the pdb as an attachment in an email, so it can be examined. Any assistance with this matter would be appreciated.

Moshe Nathan

Brooklyn College – Dept. of Chemistry

Brooklyn, NY

Hi Moshe

What version of Molekel are you using? If I remember correctly, in Molekel4.x you have to go to the main interface and click on the ‘bond attributes’ button, then on ‘add bond’ and select the atoms you want to be bonded. After that you have to right-click on the main screen and then go to ‘done picking’. Well, this last bit is only if you don’t have them bonded from the start, which I think is not your case but bear with me.

On the animate/play window there are a couple of useful options “keep bonds” and “superimpose”. The first one will continue to draw all bonds throughout the movie regardless of the bond distance (which is the only criteria molekel is concerned whith when painting bonds between atoms). The second one will re-orient the molecule (or the coordinate system) to make a fluid movie. Sometimes the molecule gets re-oriented for convenience during the optimization process, depending on the case and the software used.

I hope this helps, Moshe. I hope I get to know the Brooklyn College one of these days

Best wishes

Dr Barroso,

Thank you for replying to my inquiry. I am currently using version 5.0 of Molekel. I tried your suggestion of manually adding a bond to the detached carbonyl. It worked for only one frame. If I hit the play button for the movie, the bond would be missing in all subsequent frames.

As to you other suggestion of using the options “keep bonds” and “superimpose”, I was not able to find those options on Molekel 5.0

Thank you for replying, if I do figure it out at the end I will be sure to let you know

Best,

Moshe Nathan

Sorry, Moshe, I haven’t worked with Molekel 5.0. I suggest you send an email to the developers.

Best wishes

Buen día!

Le escribo porque tengo un problema en los inputs para G09 empleando oniom y derivados del cis-platino, para la capa baja utilizo un semiempírico (PM3) y para la alta pretendo utilizar pseudopotenciales, pero al especificar la base de pseudopotenciales (SDD) no se en que parte del input esté mi error, pero no me reconoce solo para Pt dicha base. el input es el siguiente:

%chk=oniom1

%mem=512MB

%nproc=8

# opt=Maxcycle=1024 oniom(pbepbe/GenECP:PM6) scf=qc geom=connectivity pseudo=Read

oniom1

0 1 0 1 0 1

especificaciones de la molécula

C H O N Cl 0

6-31G(d,p)

Pt 0

S 3 1.00

2.5470000 -1.4739175

1.6140000 1.9115719

0.5167000 0.3922319

S 4 1.00

2.5470000 1.4388166

1.6140000 -2.0911821

0.5167000 -1.0921315

0.2651000 1.3426596

S 1 1.00

0.0580000 1.0000000

P 3 1.00

2.9110000 -0.5247438

1.8360000 0.9671884

0.5982000 0.5438632

P 2 1.00

0.6048000 -0.1061438

0.0996000 1.0383102

P 1 1.00

0.0290000 1.0000000

D 2 1.00

1.2430000 0.5598150

0.4271000 0.5511090

D 1 1.00

0.1370000 1.0000000

Gracias de antemano.

Erik Díaz

Departamento de química

Universidad de Guanajuato

Hola Erik!

Bien, pues no veo donde está el pseudopotencial. Solo veo las bases. Intenta utilizar Gen en lugar de GenECP pues tal vez esté interfiriendo con la instrucción pseudo=read pero insisto en que no veo en ningún lado el ECP, el cual lo puedes bajar de la EMSL basis set exchage site (búscalo así en google)

Saludos y ojalá nos veamos por Guanajuato un día de estos.

Dear Joaquin

Can you say the difference between binding energy and interaction energy when we handle the biomolecular system. Thank you.

Regards,

Desikan.

Hi,

Recently I have perfomed a NBO analyis on metal-alkene complex. I have found that the stablization energy (E2) given by the second order pertubation analysis on donor-acceptor interactions is very high (ranging from 30-50 kcal/mol different alkene complexes). .I don’t think I can take this value in a quantitave manner). The total binding energy for those metal-alekene complexes are ranges from 15-21 kcal/mol..Can u pls explain to me this discrepancies in these values?

respected sir

i want to study the solvent effects on my molecule. For this i used syntax

#t scf=maxcycles=1000 b3lyp/6-311+g scrf=(cpcm,solvent=nitromethane,read) freq=raman

but 1301.exe is stopped working message is being displayed after few seconds?

pl help in this regard

Sorry but I need more information in order to help you.

What is the Error message you get? maybe this is only a mistake in the input file syntax.

Send me the error and probably some more info about the input file so I know what is wrong with it.

Dear sir,

I am the new user of gaussion view 2003,while runing the optmization an error arises as Semi-Direct transformation. File extend in NtrExt1 failed; probably out of disk space. I cleared most of the things in the C Disk but again the error arises,please sir suggest me how to rectify it.

Hi Priya!

This is due to the kind of calculation you are trying to perform. The temporal files can get very big and thus your system becomes full. Please google “gaussian efficiency considerations” and go to the gaussian.com website for more information on how to set read&write files (%rwf) in order to better use your available disk.

I hope this helps but if it doesn’t send more info so I can help you better.

Have a nice day and thanks for reading!

Priya – The error is not because of the lack of hard disk space but the RAM(temporary memory) or the processor (32-bit is the one you are most probably using). There is nothing much you can do unless you reconfigure your system. Or try use those “gaussian efficiency considerations”

Hi Joaquin,

I am running some multi-reference calculations using CASPT2 in Molpro and am a little confused about orbital rotation. Is it a good idea to rotate CASSCF orbitals before passing them to CASPT2? Or is it better to try different rotations of HF orbitals to get the right orbitals from a subsequent CASSCF calculation which can then be passed on to CASPT2 without touching the orbitals?

Any thoughts you may have on this would be highly appreciated! Thanks!

Amrit

I am new to gaussian 09 and computational chemistry. I am interested in optimizing Na, K, Rb, Cs complexes. I want to use Lanl2dz and SDD. Could you please let me know if I can use Lanl2dz for Na. Please also let me, for which metals pseudo=read option is used. IF I use b3lyp 631+g(d) for these complexes, is it okay for me to do that.

I believe lanl2dz is available for Na but the only two ways of knowing for sure are using it and hoping it doesn’t crash or checking the bse.pnl.gov link.

The pseudo=read option is used if you want to declare a pseudopotential that is not already define within gaussian, in other words, if you are including specifically the pseudopotential from an external source such as the aforementioned website.

I hope this helps!

Hola Joaquín:

Qué tal todo? espero que todo magnífico. Soy Pico, estuve contigo en la secundaria y ahora buscando un tutorial para gaussian03 con gaussview para aplicar voltaje a una molécula me encontré con tu blog. Esto es, escribo para saludarte, con muchísimo gusto además, y pedirte que si tienes alguna oportunidad, puedas enviarme un totorial donde se apliquen voltajes a una molécula por fas? En el manual de gaussian viene “POLAR” (http://www.ehu.es/sgi/ARCHIVOS/g03/g_ur/k_polar.htm)? Vi con atención que se pueden marcar tamaños de paso para el campo eléctrico también (Step=N

Specifies the step size in the electric field to be 0.0001N atomic units.). Como soy nuevo en gaussian/gaussview pues me acerco a los foros para ver qué alcance puedo tener.

Gracias y un gusto saludarte,

Pico

aheredia@nucleares.unam.mx

alejandropicoheredia@gmail.com

Hola Pico, que gusto volver a saber de ti. Lamentablemente no tengo experiencia en el tipo de cálculos que comentas. Sin embargo si te apuras aun te puedes inscribir a la escuela de electroquímica teórica en Washington DC en Mayo. ( http://spring11.ise-online.org/ ) Los deadlines ya pasaron pero aun tienen espacio para el workshop según los organizadores. Tenía intenciones de asistir yo mismo pero lamentablemente no se pudo. Ahí seguro abordarán el tema de la aplicación de voltajes.

Me da mucho gusto saber de ti nuevamente. Saludos y mucho éxito!

Dear Professor;

I am interested in calculating XPS using Gaussian09. Can you tell me how to prepare the input file. Since I am new to this type of calculation, I would appreciate your help if you could also point me to relevant reference work which describes the calculation process in detail.

Thank you

Hi Mick!

So sorry but I have no experience whatsoever in calculating XPS spectra. I hope you find information soon.

Thanks for reading the blog!

Perhaps Mick, you could provide us with a link if you do find anything? I don’t have a need for the XPS currently but maybe somebody else will in the future and can reference this post.

That is a wonderful idea, my friend!

Dear Joaquin,

I’m an industrial chemist working in ink industry, currently I’m looking for database regarding complexing ability and solubility of inorganic salts in organic solvents, especially cobalt and manganese salts in organic solvents.

Do you have any links, thanks.

Regards

Abby

Dear Sir,

Greetings. We are interested to carry out the optimization and vibrational frequency analysis

for CeO2 unit cell. We couldn’t use the existing basis set in Gaussian 03. We tried with extra basis set (CRENBL ECP)from the EMSL basis set exchange. We did not get any output from log file. Can you please suggest for handling extra basis set for this.

with thanks

Sasirekha

Please take a look at my post on how to use the GEN keyword in order to introduce an external basis set and ECP, if you don’t find the info you need there then leave your question on that same post, please.

Thanks and I hope you find an answer there!

Have a nice day!

Dear Sir

please, i would like to ask you on the availability of performing solid state calculations using g03

thanks

Saied

It depends on what kind of solid state calculations you are trying to get.

Have a nice day Saied!

Dear sir,

please tell me how to provide different basis sets in the input file

Dear Joaqun Borossoo,

I am interested in knowing what literature for computational chemistry is being the most detailed (in explanation) and most useful to start studying it?

Thank you for your recomendations.

Best regards,

Aurimas

Hi Aurimas,

This is a great question! I think I will write a post about it. I would start by learning the basics of Quantum Chemistry (otherwise you only become a button pusher) so start with “Quantum Chemistry” by McQuarrie; then go to Levine’s book with the same title. This will give you a solid background on the physical and mathematical foundations of molecular modeling. Now for the operational part I would suggest using “Exploring Chemistry with Electronic Structure Methods” by Frisch and Frisch. This is a collection of exercises that you can perform on Gaussian so you get an idea of the program’s capabilities.

Please stay tuned because I will post something about this in short.

Have a nice day!

Hola Dr. Barroso!

Hace tiempo que reviso su blog y lo considero de gran utilidad ya que aquí he encontrado solución a algunos problemas que se me han presentado; sin embargo ahora no he encontrado la solución a un problema que tengo al calcular frecuencias con el método MP2 en Gaussian09. El problema es que el cálculo se interrumpe y aparece el siguiente mensaje

Error termination in NtrErr:

NtrErr called from FIOCnC.

Creí que esto podría estar relacionado con la capacidad del disco y la memoria, así que le dí cierto valor a los paramétros %mem y a maxdisk, aún así el problema prevalece. Tiene usted idea a que se debe el error, ojalá pudiera ayudarme. Gracias por su atención, le envio los comandos del input por si le sirven:

%mem=1500MB

%nproc=2

# freq mp2/6-311g(d,p) maxdisk=20GB geom=check guess=check

Hola Sara

Muchas gracias por tus bellas palabras, espero que el blog te siga sirviendo en el futuro.

Efectivamente se trata de espacio en disco. Que tipo de plataforma usas? Mi único consejo es que sigas aumentando el valor en %mem (1.5GB suenan a muy pocos) subelo a 2GB o a 4GB.

Por cierto, la paralelización de Gaussian no es muy buena, sin embargo el uso de más de 1 procesador ayuda en algo. Tienes instalado el módulo LINDA? este es el que paraleliza el cálculo. En la versión G09 la sintaxis correcta es %nprocshared=2 cuidado!

Espero que te sirva. Que tengas un bonito día!

#gaussianerror

Hello Professor,

I was trying to absorb co2 over a graphite sheet. To do this, i first made a small area of sheet, then clicked on it a =C=. then attached 2 oxygen atoms at the ends. Now, all the atoms are on the same plane. Is this right? or should I put the co2 just above the sheet in a parallel plane? I observed that, if the molecules overlap, the program doesnt run and says ‘Link died!’. If I place the co2 in such a way, the molecules dont overlap, it runs for a while and then link dies but a log file is produced this time.

What is exactly happening here?

Dear Joaqun

i am trying to calculate the interaction energies using counterpoise method at the mp2 level but i get the following error which i guess it may be due to memory or disk capacity!!!!!

plz, how can i solve this problem?

the error is:

Estimated scratch disk usage= 117863514 words.

Actual scratch disk usage= 116198490 words.

JobTyp=1 Pass 1: I= 1 to 1 NPSUse= 1 ParTrn=F ParDer=F DoDerP=F.

PickT4: no shell combinations can fit!

NKLS2p= 50 NKLS2= 50 MaxCom= 46

Error termination via Lnk1e in C:\G03W\l906.exe at Fri May 04 01:24:52 2012.

thanks

Saied

Dear Prof. Jo,

I want to calculate the Potential Energy Distribution (PED) in IR vibrational frequencies using Gaussian 09. Please help me to calculate PED. Thank you.

Regards,

Desikan.

Dear Prof. Joaquin,

I want to do IRC calculation in order to check if transition state is directly bound to reactant or product or there is any intermediate. I will be thankful if you could let me know the ways to calculate it. I tried but somehow it didnt work. Will be thankful if you could shed more information on this topic.

Thank you very much

Abdul

Hello Abdul,

IRC needs you to include a proper TS structure. This means you first have to find it by hand making sure you get one imaginary frequency in the vibration analysis. If once you perform the IRC calculation you find a stable structure, it could be related to an intermediate, you can’t know. All you know is this corresponds to a relative minimum on the potential energy surface.

I will write a post on IRC in short. Stay tuned!

I hope this helps. Have a nice day!

Hello Abdul,

IRC needs you to include a proper TS structure. This means you first have to find it by hand making sure you get one imaginary frequency in the vibration analysis. If once you perform the IRC calculation you find a stable structure, it could be related to an intermediate, you can’t know. All you know is this corresponds to a relative minimum on the potential energy surface.

I will write a post on IRC in short. Stay tuned!

I hope this helps. Have a nice day!

Dr Barroso,

We have been successfully running Gromacs (version4.5.3) simulations of tryptophan dipeptides for close to two years now. We build the dipeptide using PyMole and use the Gromacs command pdb2gmx in order to create at Gromacs topology file. We use the OPLS-AA force field with the suggested tip4p water model. For the first time we decided to run a tryptophan residue by itself. While the zwitterion simulation went without incident, the positively or negatively charged form of the residue repeatedly gave an error message.

The message we received was:

ERROR 1 [file topol.top, line 228]:

No default Ryckaert-Bell. types

ERROR 2 [file topol.top, line 229]:

No default Ryckaert-Bell. types

Excluding 3 bonded neighbours molecule type ‘Protein’

Excluding 2 bonded neighbours molecule type ‘SOL’neighbours molecule type ‘SOL’

We are at a loss as to the meaning of this message as well as how to correct it. We narrowed down the error to the terminal carboxylic oxygens (line 228 – 229), but we do not understand what is wrong with them. In addition, it is the same terminal carboxylic oxygens as for the zwitterion species, in which the simulation ran well.

We suspect that the error is due to the fact we are running a single residue and not a dipeptide.

As a control, we tried running a simulation of single residue of tyrosine and it too produced a similar error message.

Any help or advice as to circumvent this issue would be appreciated.

Sincerely,

Dr. Azaria Eisenberg and Moshe Nathan

Brooklyn College – Dept. of Chemistry

ps

Dear Prof. Joaquin,

I am fairly new to using gaussian. I want to know two things

1. How to determine whether a uv-vis transition from TD-DFT is n -> pi*/ pi -> pi*/ d-d transition ?

2. How to study reaction mechanism steps using gaussian ?

Sincerely,

Arnab

Student, Dept of Chemistry

Tripura University, India

Dr. Barosso,

I am facing one issue regarding PCM input. It said H 11 has 2 bonds. so i asked it to create cavity explicitly by specifying “SPHEREONH=11” and also i gave read with that scrf keyword. After that it gave error “End of line while reading PCM input files”….Can you please quickly drop solution to this….Thanks a Lotzz!

Dr. Barosso,

I am trying to calculate NMR for a molecule. I am through the calculations…but the NMR spectra that I am getting is no worth to conclude. So I tried the way of substracting the isotropic values of protons from that of reference isotropic values (TMS) ran under same basis set but still I am not getting the chemical shift values to the mark.

Please can you guide where I am going wrong or just tell me any other way

Thanks.

Dear Dr.Jacquine,

I’m asking if it’s possible to calculate the spectral band width from Gaussian vibration “IR” frequency output…

Thanks

Marawan

Dear Marawan,

Unfortunately it is not possible since quantum mechanical calculations pertain to single molecules therefore you will get the frequencies to which each normal mode of a molecule gets excited. The with of the band is associated to the relaxation mechanisms which might involve the surrounding media or any other intermolecular pattern, all of which are not taken into account into the IR output.

Hope this helps! Have a nice day

Hi

I’m working with gaussian ‘9 and I’m doing a zmatrix scan of two molecules, my script works nicely with HF but it crashes with MP4 complaining

“CALL FROM INITNF: BAD IC ENTRY FOR VARIABLE 2”

do you have any ideas?

Have you tried using a Cartesian scan? How many steps are accomplished by MP4 before it crashes? I need a little more information to help you.

Have a nice day

Hi Dr,

thanks in advance for your kindly help. my Q is how to use EMSL to get best initial gauss of basis set, for a system that it contains B and N atoms(almost 40 atoms ).

I imagine you are trying to build a guess, right? I don’t think you can use the EMSL for that. Remember the guess is only the starting point of the SCF, of course a good one will yield better and faster results but with a BN cluster like yours, provided you have a chemically reasonable geometry, almost any guess is as good as the next. Choose the basis set according to your needs, i.e., to the quantity you want to calculate.

I hope this helps. Have a nice day

I wish to study in detail about the structure, vibrational spectra and all the electronic properties of a biomolecule using a Gaussian program.In this regard I would like to know that what are the possible descriptors which i can calculate/study , which can make my study a complete one. I would very much appreciate if there is a paper in this regard or any other related reading material.

Thanks

Hello,

How do I calculate the percentage of each conformer of all conformers obtained from a potential energy surface scan done using Gaussian 09?

Thanks

Hi Yang, you can to use Maxwell distribution equation.

Bye

dear Dr.

i ran bis-indole using g03 in hf and b3lyp. in the bond lengths, bondangles and dihedral angles section, almost hf and b3lyp values are nearer in estimating the values of bond lengths and bond angles, but, whereas, in case of dihedral angles, in few values there was huge difference.

Ex: hf= -177.6 b3lyp = 177.5

what may be the reason for this. kindly help me in this regard

Try taking a look at the structures because this could only be a matter of definition between one structure and the other, i.e., a reverse numbering definition which makes the sign of the DA change. If that is the case then the absolute value is not different at all.

I hope this helps. Have a nice day

Thank you very much for immdt reply.

Actually in case of hf and b3lyp if we compare, the bond lenghts and bond angles, the diff is very less(it is around < 0.2 to 0.6), where as in case of dihedral angles there is a diff in few values around 2 to 3. why it is? kindly help me in this regard.

Ex: hf = 69.9 b3lyp= 71.25

hf = 86.93 b3lyp = 83.90

i went throughly through the numbering of structure. Numbering was given is same order.

But maybe the dihedral angle was defined in reverse. I mean, the DA(1,2,3,4) = – DA(4,3,2,1) Check the structures again and if you don’t find this issue send me the files so I can take a look at them.

Best wishes

Hi Dr,

how we can have full optimization out put results,but in frequency it ended with error, plz advise.

thanks

Hi Jacquine

I use MOLDEN to view the gaussian output. How can I see the NBOs using MOLDEN? Please advise

Thanks

Subrato

I’m sorry but I have no experience working with MOLDEN. Try to contact the software developers.

Thanks for reading!

Dear Jacquine

Thanks for very useful blog, it is really interesting

i want to ask about the CCSD(T)-F12 method using gaussian 03. I want to make CCSD(T)-F12 calculations on some H- bonded complexes using G03 version C01 running on PC of 1G RAM/core2du processor. Is such calculations is possible to run on PC having such configuration????? please give me the keyword line, i tried to use

#n CCSD(T)-F12/6-31G(d,p) Opt

but there is something wrong ??

best regards

Saied

Dear Prof.Jacquine

Would you tell me about GVB calculation in gaussian program?? I read few articles on web. However, i cannot clearly understand. I want to know detailed information for GVB calculation.

Sorry SunWoo,

I have no experience working with GVB. I suggest you try the Gaussian website and their help desk.

Hope this helps!

Dear Dr.Jacquine,

I’m asking how can we determine the vibration mode associated with a certain vibrational number..In Gaussview, one wavenumber may have contribution from different functional groups, shall we take the highest contribution to simplify the argument, or we have to go to a more sophisticated technique…????

Regards

Marawan

Hello Marawan,

If I understand correctly you want to know to which functional group corresponds each vibrational mode, right? Well you have to take the entire vibrational mode, all atoms involved, if you only take the largest contribution you can have an idea of what you are looking for, however this is not theoretically correct. I’m not aware of any other technique but your approach seems to be interesting.

Best wishes!

Hi Joaquin,

I want your expert opinion regarding a problem that I am failing to figure out. I am trying to get an expression for a given MO (say HOMO, LUMO etc.) out of electronic structure calculation. What I could figure out is an option with the “CMO” keyword for NBO calculation, however, I really don’t follow the output in that case in terms of functional. I want to get a mathematical expression for a given MO of a molecule. How can I do that?

Thank you,

Regards,

Bijan Paul,

Dept. of Chemistry and Biochemistry,

University of Colorado at Boulder, United States.

Hello Paul,

An MO is in fact a mathematical construct which we interpret in a certain chemical or physical way. Every MO is a linear combination of atomic orbitals (in Gaussian’s case these AOs are linear combinations of -gaussian- basis functions). The explicit form of these basis functions is described in Gaussian’s website under tech support, somewhere under the manual section. From your output you get the coefficients which form that linear combination. In short, the mathematical form of every MO is already given; G09 merely displays the coefficients.

I hope I understood the question but if you feel I didn’t, please let me know so I can provide you with better help.

Have a nice day!

dear sir,

i want to transform my IR spectrum obtained by gaussian which is IR intensity Vs wave number into %transmittance Vs wave number. How can I do it? how to compare it with experimental one

Hi Joaquin,

Probably I follow what you said about my problem regarding a mathematical expression of MO. However, I don’t really understand the meaning of that expression in terms of functional. I want to get an expression for a given MO (e.g., HOMO/LUMO etc.) in terms of functional so that I can operate an operator on that, say if I want to operate a Coloumb operator (or anything other) on the functional form of the MO.

Can you please give a clue to this?

Thank you very much,

Bijan Kumar Paul,

Department of Chemistry and Biochemistry,

University of Colorado at Boulder, United States.

Hi Joaquin,

I am a graduate student from India. I want to optimize pi-stacks of large molecules to look at their properties. But since the molecules are mostly flat, the potential energy surface is flat and hard to optimize. Also, since these are weakly bound systems, capturing such weak interactions is important. I tried using Gaussian-03 and 09 without much success. Also the plane wave codes become extremely costly because of the enormous box size required (50-60 Angstrom). Is there any package which captures these weak interactions as well as scales well to perform such large calculations.

Thanks.

Hi Chidambar,

I don’t think your problem lies on the package but on the level of theory employed. Remember DFT methods don’t do a good job in describing dispersion forces such as pi-pi stacking. You’ll need to use a large basis set with polarization and diffusion functions, specially the latter. Plane wave codes are very high quality but have a very slow convergence, well at least those I know about.

Gaussian can do this if you provide the appropriate level of theory.

I hope this helps! Have a nice day!

Dear Dr. Joaquin,

Many thanks for your quick reply. I agree with you that the level of theory plays a major role in capturing the interactions. But the bottleneck I am facing is that, even with HF/6-31g the amount of time taken on 8 distributed cores for a system with 300 atoms is exceeding 20-25 days using G-09. Also it is not ending up in a minima. I heard that TURBOMOLE and NWChem performs faster and also scales better with the number of nodes. Is that a good option?

Thanks in advance.

Chidambar

NWchem should work better for you since it is highly parallelized, just make sure you have the proper parallel machine to run it.

I hope this helps!

Have a nice day!

Thank you Sir.

Chidambar

Dear Sir,

Could you please help me out regarding how to perform ELF calculations.

I have only access to Gaussin09 and 03.

Looking forward to you.

regards,

Bijan

I’m sorry, I don’t know what ELF calculations mean. Can you describe more extensively what is that you want to accomplish?

Have a nice day

Hi,

Your blog is very nice- came across it when trying to figure out something regarding relaxed PES in Gaussian 09. I wanted to scan a certain distance between an atom and a dummy atom but get an error because dummy atoms are not numbered. Can I do this? Also, is it possible to scan two variables at once? I thought this was possible but can’t seem to find it in the manual

Thanks

Hello Elizabeth!

Thanks for your kind words about my little blog!

Unfortunately dummy atoms cannot be used for scanning, sorry! I’ve written to Gaussian’s help desk a couple of times on the matter but so far I haven’t received any clear answer as to why not.

You can scan as many variables as you want, you just need to use the same procedure described in my post on PES scans twice or thrice or as many variables you want, line after line. Just bear in mind that this will produce all possible combinations for both variables. I’ve received questions from people who want to scan two variables simultaneously (i.e. obtaining the diagonal elements of the matrix they actually get). Of course this procedure can become quite time consuming.

I hope this helps.

Have a nice day!

Hi.

At first, i would like to mentioned that it is nice blog, very usefull for begginers.

I decided to write because maybe some of you had this problem.

I have an really strange problem with gaussian09.

I am trying to obtain the transition states, mainly but problem is also with minimas ( not so often).

After reading the input program is do not do anything, without any error… In the queue it is looknig like running but only looking like, it stops everytime in the same line:

(Enter /usr/local/gaussian/gaussian09/g09/l101.exe)

——————-

Title Card Required

——————-

Charge = 1 Multiplicity = 2

Symbolic Z-Matrix:

N 2.44738 -0.63559 0.02773

H 2.68288 -1.24697 -0.76198

C 3.18296 0.63045 -0.03616

C -1.95635 0.02025 -0.00257

H 4.19904 0.58991 -0.39588

H 2.72271 1.48159 0.44

O -3.09388 0.17289 -0.03424

O -0.79474 -0.13526 0.03065

H 0.63811 -0.36246 -0.00116

H 2.65737 -1.16661 0.88635

The following ModRedundant input section has been read:

I was trying to change the geometry of the molecule, but if i change it a lot i obtain the things that i already have and i am not interested. If i change a little i got the same.

I am using the same key words so this shouldn’t be a problem.

Any ideas?

If you have some ideas, i will gbe greatfull!!

PS. Nice blog.

Best regards

Darek

Wow! This is very strange indeed! Please tell us what kind of platform are you using, linux? windows? You say you can see it in the queue, but do you see the gaussian process or just the script with which you send it to the queue?

Sorry for the lateness of my response. If you send me more information I might be able to help you more efficiently.

Have a nice day!

sir

Sir,

is this possible to optimize a molecule at a higher basis set and calculate its frequency at a lower basis set. e;g if a molecule is optimized at 6-311++G(d,p) and calculate its frequency at 6-311++G(d,p),6-311G(d,p),6-31G(d,p) respectively

I’m afraid it’s not possible. In fact it is conceptually wrong. Your geometry optimization generates a potential energy surface at a certain level of theory, computing frequencies over a different PES won’t correspond to the values on the other surface.

Have a nice day

thanks sir

Dear Sir,

Greetings. I am in need of detailed explanation for the optimization of CeO2. Because of greater atomic number we couldnot optimze with the avialble basis set ofGaussian.So we tried to use gen and extra basis set.But we could not run the program.Please give a detailed procedure for the same.We tried as maximum as possible with all available references and examples.please help us for optimization and vibrational analysis.

thank you sir.

Hello Sasirekha,

Please search for a post in this blog which is titled something like The Use of an External Basis Set (GEN keyword). something like that.

In order to work with Cerium, I strongly recommend using a pseudopotential or ECP from the family published by Amlof et al. Try finding it at the BSEL which is in the links section of this blog.

I hope this helps!

Dear Sir,

I am a freshman on the kinetic calculation using Gaussian 09. As you know, according to the transition state theory, rate constant can be calculated using

k=κ(kBT/h)*(q≠/qR)*exp(-△G≠/RT).

I opitimized the reactants, TS, and products. The ZPE corrected G were obtained. If I use these corrected G, should I further consider the partition function for k calculation? (Becuase another professor told me that G containing the information of partition function). Is it right?

If the partition function is necessary, which one should be used?

Q Log10(Q) Ln(Q)

Total Bot 0.718377D-66 -66.143648 -152.301378

Total V=0 0.353068D+24 23.547859 54.220948

Thank you for your suggestion.

Buen día Dr. Joaquín,

Le agradecería mucho si pudiera orientarme con lo siguiente:

Necesito justificar el por qué de mi preferencia por utilizar los índices de Wiberg en lugar de utilizar algún otro análisis. Cuales podrían ser las ventajas de los índices de Wiberg respecto a otros índices de orden de enlace?? Busco una explicación sencilla para discutir en mi tesis. Saludos

Hola de nuevo Abril!

Te recomiendo que leas el artículo original de Wiberg: K.B. Wiberg, Tetrahedron 24 (1968) 1083

Quizá el análisis de población más popular, por su simplicidad, sea el de Mulliken, sin embargo por su construcción se pierde mucha información (De acuerdo a la naturaleza de los átomos enlazados reparte la densidad para uno y para otro, el sobrante lo reparte democráticamente a la mitad, lo cual no refleja la electronegatividad de c/átomo correctamente), además es muy dependiente de la base, i.e., si calculas los órdenes de enlace de Mulliken con 3-21 obtendrás valores muy distintos que si lo haces con 6-311. Wiberg es más estable ante cambios de base, y por tanto más confiables.

espero que te hay sido de ayuda.

Saludos!

Hello Sir,

I am trying to calculate NMR( EFG and magnetic shielding) for my compound, For the ligand of my compound I did not have any problem going from 6-311g to higher basis sets. For complex which is Indium is included I have an issue. I tried to have different basis sets for different atom but does not work !!!

This is my input file

k=00000001troy

%mem=128MB

#p B3LYP/gen nmr Test iop33(10=1) prop=efg scf(MaxCyc=150)

Molecule Name

0 1

molecule coordinate

blank line

O P 0

6-311g

************

I 0

6-311g

************

In 0

3-21G

******************

Could you please let me know what I am doing wrong here .

Thanks so much

Rosha

Hello Rosha,

It would be very helpful to know what kind of error you are getting from the program so I know what the problem is.

Is this input the one you actually used? You are using a small basis set on a heavy atom and a large one on the lighter ones. I don’t think the 3-21G basis set is defined all the way to that row (In) but even if it is, I think the whole calculation is conceptually wrong. Check at the Gaussian website the availability of the basis set (for which elements is it defined) or check it at the EMSL website (check out the links section in this blog). I’d suggest you used the pseudopotential approach.

I hope this helps. Have a nice day!

Hi Sir,

Thanks for comments this is what I get:

Rotational constants (GHZ): 0.0366304 0.0187492 0.0187492

Leave Link 202 at Wed Oct 24 14:31:05 2012, MaxMem= 16777216 cpu: 0.0

(Enter /global/software/gaussian/g09.c01/l301.exe)

General basis read from cards: (5D, 7F)

Centers: 5 6 69 70 71 72 73 74 7 8

6-311g

************

Centers: 1 3 4

6-311g

Atomic number out of range for 6-311G basis.

Error termination via Lnk1e in /global/software/gaussian/g09.c01/l301.exe at Wed Oct 24 14:31:05 2012.

Job cpu time: 0 days 0 hours 0 minutes 0.2 seconds.

File lengths (MBytes): RWF= 5 Int= 0 D2E= 0 Chk= 1 Scr= 1

I checked the EMSL website there is lets say basis sets for I for 6-311G** like this:( the problem is I do not know where I have to put these lines in my input file and what change I have to do to my input file)

“BASIS “ao basis” PRINT

#BASIS SET: (15s,12p,7d) -> [10s,9p,5d]

I S

444750.0000000 0.0008900

66127.0000000 0.0069400

14815.0000000 0.0360900

4144.9000000 0.1356800

1361.2000000 0.3387800

I S

508.4400000 0.4365900

209.5900000 0.1837500

I S

81.9590000 1.0000000

I S

36.8050000 1.0000000

I S

13.4950000 1.0000000

I S

6.8859000 1.0000000

I S

2.5520000 1.0000000

I S

1.2088000 1.0000000

I S

0.2734000 1.0000000

I S

0.1009000 1.0000000

I P

2953.6000000 0.0122100

712.6100000 0.0858700

236.7100000 0.2949300

92.6310000 0.4784900

I P

39.7320000 1.0000000

I P

17.2730000 1.0000000

I P

7.9570000 1.0000000

I P

3.1529000 1.0000000

I P

1.3328000 1.0000000

I P

0.4947000 1.0000000

I P

0.2160000 1.0000000

I P

0.0829300 1.0000000

I D

261.9500000 0.0314400

76.7340000 0.1902800

27.5510000 0.4724700

I D

10.6060000 1.0000000

I D

3.4217000 1.0000000

I D

1.1370000 1.0000000

I D

0.3020000 1.0000000

END

There is a post in this blog about the GEN keyword and its usage, which is pretty much the same thing you already did before, you use the gen keyword in your route section and then at the end of the file you write the following lines:

AtomSymb 0

I S

444750.0000000 0.0008900

66127.0000000 0.0069400

14815.0000000 0.0360900

4144.9000000 0.1356800

1361.2000000 0.3387800

I S

508.4400000 0.4365900

209.5900000 0.1837500

…

…

…

****

AtomSymb2 0

…

…

****

Notice I deleted the first two lines and you should also delete the last one (END)

I hope this helps!

PS Maybe you could also try B3LYP/lanl2dz straight at the route section, this will use a quasirelativistic pseudopotential in heavy atoms like I and In (if it reaches the fourth row, which I’m not sure of) while using a double zeta quality basis set (close to the number of functions you’d get with 6-31G). I am not aware of the quality of this level of theory when it comes to calculating nuclear shielding tensors, so I can’t be liable if it doesn’t provide accurate results 😀

Dear Joaquin,

I would like to post here a question that is blowing up my mind. This question is related with TD-DFT in Gaussian: I want to compute the energy of the first singlet excited state of ethene, so I have optimized the geometry of ethene in its fundamental singlet state (B3LYP/6-311+G(d) OPT, charge 0 multiplicity 1) and, taking the last geometry of the optimization, I have launched a TD-DFT calculation with a simple header (B3LYP/6-311+G(d) TD(singlets,root=1,nstates=1), charge 0 multiplicity 1). Until here, all is quite normal, but some questions arise from now on:

1.- I mispelled the TD-DFT calculation header writting down “UB3LYP” in place of “B3LYP” and the results were quite different in both cases. What is going on here, then? Gaussian website http://www.gaussian.com/g_tech/g_ur/k_td.htm states that TD-DFT singlets option is only effective for closed-shell systems. From this sentence, I understand that Gaussian does not matter about computing a TD-DFT an UHF system of a RHF system since it will take RHF wavefunction so, which is the origin of this difference?

2.- Since I want to know the energy of the first singlet excited state, can I optimize the geometry of the triplet ground state of ethene (UB3LYP/6-311+G(d), charge 0, multiplicity 3) and then, launch a TD-DFT calculation with the header UB3LYP/6-311+G(d) TD(singlets,root=1,nstates=1), charge 0, multiplicity 3)? If this is correct, which energy would be more accurate for the first singlet excited state: that calculated from the ground singlet state or that computed from the ground triplet state?

Thank you in advance for your response and your time!

Jose

Dear Dr.Jacquine,

I have a nuclesoides with a first solvation shell i got from an MD run. Can i compute the IR spectra in Gaussian of the nucelsoeds only without the accompanying cluster of water molecules.?..Also, which is better, when optimizing the geometry first with Gaussian, shall i constrain the water molecules, or treat them as MM using the ONIOM method or optimize the whole lot at the QM level with which i’m going to produce the IR spectra.

Thanks

Marawan

Hi there

I am quiet new to using gaussian/gaussview and currently I am facing a bizarre situation.

I have done a Scan (relaxed using Opt and modredundant) by gaussian 09 and everything was fine. But when I am trying to open .log file in gaussview (both 3 and 5) it complains about the redundant coordinates (specificly those lines that I have defined the range of values for scan). finally it says that the structure is incomplete and just shows the final geometry. It is obvious that in results menu non of the scan and optimization are active.

I appreciate if you can help me out

Abn

———————————————————

%chk=C:\Users\abnnor\Desktop\temp\Job1.chk

%mem=4000MW

%nprocshared=4

# opt=(modredundant,maxcycle=1000) rhf/6-31g(d) nosymm

geom=(connectivity,cangle,cdihedral) scf=tight test trackio

First Optimization of the ButanDiOl

0 1

C 1.74509157 -2.25272303 -0.88406810

C 0.92534837 -1.08869149 -0.34995131

C 1.66130851 -0.23438183 0.68531752

C 2.85550967 0.54920221 0.14892945

O -0.22690557 -1.65983209 0.22552993

O 3.47738020 1.30641706 1.15367746

H 2.61468044 -1.91225658 -1.43507074

H 1.13442131 -2.85144139 -1.54934156

H 2.07583182 -2.88660068 -0.06758621

H 0.63355875 -0.45464397 -1.18788653

H 1.98386020 -0.88526917 1.49620406

H 0.96496602 0.48000684 1.11940626

H 2.53423145 1.25923231 -0.60302454

H 3.57742218 -0.11384424 -0.32100020

H -0.80412139 -0.97382491 0.53144329

H 3.85073556 0.72328780 1.79986761

1 2 1.0 7 1.0 8 1.0 9 1.0

2 3 1.0 5 1.0 10 1.0

3 4 1.0 11 1.0 12 1.0

4 6 1.0 13 1.0 14 1.0

5 15 1.0

6 16 1.0

7

8

9

10

11

12

13

14

15

16

B * * A

A * * * A

D * * * * A

D * 3 4 * R <————-gaussview complains about this two lines.

D 2 3 4 6 S 24 15.000000 <————-

—————————————————————————————————–

these two lines are looking like this in .log file

B * * A

A * * * A

D * * * * A

D * 3 4 * R <————-

D 2 3 4 6 S 24 15.000000 <————-

Try eliminating the first three lines of the scan input, i.e.

B * * A

A * * * A

D * * * * A

Do you have a specific error message in the log file?

Hope this helps

Hello Dr. Barroso:

I have come across a paper [J Comput Chem 30: 2752–2763, 2009] regarding various Density Functions for use of determining geometric parameters for zinc complexes. In one of their tables (2) they describe five different basis sets together with the valence basis set considered for each of the atom types that make up the Zinc complexes. For example using

6-31G(d) All Electron, they go on to describe valence basis set of:

6/6631/31/1 for Zn;

6/631/1 for S and Cl;

6/31/1 31 for C, N, O;

and

31 for H.

I am wondering if you might be able to help me understand the meaning of this? Did they apply different basis sets to each atom during their calculation and is this possible in Gaussian using the GEN command? IF so, could you provide any guidance on how this type of job might be set up?

Thank you for your time and knowledge!

brian

Dear Brian,

I’m very sorry for the delay of my response. What you have there is the full expression of a basis set; they all correspond to 6-31G(d) but for every atom you need different amounts of basis functions. They all use 6 primitive gaussian functions for all core electrons (contracted all in the first part, “6/”). The rest of the numbers indicate how many primitive functions are used in each shell.

For a detailed explanation I suggest you to check Levine’s book “Quantum Chemistry”. Chapter 15

I hope this helps

Estimado Dr.

Estoy haciendo un cálculo de un TS en el gaussian y el resultado que me da con HF y DFT es una frecuencia imaginario que es la que no necesito y la que quiero me da positiva, al aumentarle el nivel al calculo como un MP2 ya me salen casi 4 frecuencias imaginarias incluyendo la que necesito.

Le agradecía su ayuda

Diana

Estimada Diana,

Encontrar TS’s es prácticamente un arte, y un arte obscuro diría yo. Te recomiendo que partas de una estructura minimizada en la que puedas deformar la variable que te interesa a modo que en un segundo cálculo lleves la estructura al TS deseado. Yo lo probaría con ambos niveles de teoría si tienes las instalaciones adecuadas.

Otra manera de hacerlo sería partir de tu 2o archivo, con 4 freqs imaginarias, y arreglar las 3 que no te interesan para que en el cálculo subsecuente te quedes solo con la necesaria. Sin embargo, recomiendo el uso de un nivel alto como el MP2.

Espero que te sirva!

Saludos!

#Gaussview-error

Dear Joaquin,

When trying to load the checkpoint file of a calculation in GaussView sometimes I get the message error “CConnectionGFCHK::ReadFile()” Cannot find File”.

It looks like I get this error message somewhat arbitrarily. I mean, on the same machine, using the same versions of Gaussian and Gaussview, the same kind of job (i.e. different molecules with the same keywords) sometimes Gaussview reads the .chk file and sometimes not. At least the results are consistent in as much as the same input file generates a .chk file that gives the same error message.

Have you find this kind of problem?.

I use Gaussian 03 + Gaussview 4.1. on a Windows XP PC.

Thanks.

Pedro Alberto.

P.S. Following your recipe to visualize the NBO orbitals, I run a test with one badly behaving .chk files and found that Gaussview loads the .fch file without problems. Magic?.

Hola Pedro,

I have found that same error when trying to move a chk file between computers with different architecture (64 vs 32 bits). It would be very useful if you track all the variables that make a file easy to open or not by gaussview.

Maybe you should try to always work with fch files and not with chk ones. Could this be it?

I hope this helps!

Dear Sir,

I have tried to calculate the exact polarizablity values by giving the keyword ‘polar’ using g09. In the output file, I am getting ‘*******’ instead of the numbers as shown below.

Exact polarizability:******** 0.0001794.519 0.519 -0.063 278.533

Approx polarizability:******** -0.0033140.674 6.210 -0.113 469.161

Please tell me how to solve this problem and get the numbers.

Those stars ******** mean the number you are getting is out of range and therefore cannot be printed. This usually means the level of theory you are using is too low or too incomplete. Try searching in the literature similar calculations performed on similar systems to yours and use their reported level of theory.

I hope this helps!

thankyou

Dear Dr.Joaquin,

I’m asking how can i get the vibration spectra from a QM/MM MD trajectory using ORCA and 0.5 fs timestep. I’m saving the dipole moment at each step then finally i got a .dat file contains the time step with the 3 dipole moment coordinates (mux, muy, muz). I’m using the AMBER ORCA interface for a nucleoside dissolved in a box of water and the nucleoside is the QM part. There’s a tool in VMD but as i can understand it does not require the dipole moment.

Full of respect

Marawan

Dear Marawan, I have no experience working with orca. Im sorry but I can’t help you this time

Have a nice day

Dear Dr.Joaquin,

Could you please even suggest a pathway. I guess it’s a common procedure from all softwares and not directly connected to ORCA. From what i can understand i have to calculate the dipole-dipole correlation function then Fourier transform. I didn’t find any tutorial for such procedures unfortunately.

Full of respect

Marawan

Dear Dr.Joaquin,

I’m a regular reader of your blog and found it really useful in solving many of the tricky things associated with gaussian.

I have a problem in viewing the output file for a gaussian calculation in gaussview 5.0. The calculation have been done in g09.

I have optimized the structure of my compound(polar) in both vacuum as well as solvent(IEFPCM model) using b3lyp/6-31G++ basis set and got a normal termination of gaussian process for both the jobs.

But when I load the output file of the solvent optimized compound in gaussview I got the following error immediately after opening the file in gaussview:

CConnectionGLOG::Orient_Dipole_Derivative()

Unable to orient dipole derivatives.

Kindly help me in this regard.

Thanks in advance.

Hello Aravindan

I have never seen this error before. This kind of messages in gaussview are usually related to some kind of error termination in the log file; I suggest you check the log file for any error messages. It could also be a bug that could be overlooked but it would be better to check. Remember that gaussview is not the important thing to look at but the log file.

If I find a better solution I will let you know.

Have a nice day!

Dear Dr.Joaquin,

Thanks for your immediate reply and will definitely see the log file for errors.

Have a nice day.

Good afternoon sir,

we are running TD-SCF energy calculation on a particular molecule. Sir, what would be benefits if we calculate it by for more states, e.g N= 6. 12 ..100 and so on.

Another comment regarding my above question is that what is the importance if we also mark the state of interest, root =1, 2…( option given in gaussian)

thanks sir,

waiting for your comment sir.

Hello bhat,

The more states you include the better is your description of the available space but it will take longer to calculate, much longer. Sometimes it is not necessary to have such a detailed description of the excited states and that is why gaussian allows you to focus on a particular state that is close to the phenomenon you are studying.

I hope this helps

Good evening.

Please can you help me how to calculate solvation energy in Gaussian 09?

I know, that it is difference between the gas phase and the solvent phase.

But, there are many energies in Gaussian 09 outputs.

Which of these are correct for solvation energy calculation?

Thank you very much for your help.

# genecp keyword

Dear Dr Barroso

I have done full geometry optimization and frequency calculations for Ru-NAMI-A (an anticancer drug)at UB3LYP/(LanLD2Z+6-31G(d))level in gas phase by employing the Gaussian 03 package.

Input file for geometry optimization and freqency :

# ub3lyp genecp fopt freq

Title

0(charge) 3(multiplicity)

Atomic coordinates

…

…

C N S Cl O H 0

6-31G(d)

****

Ru 0

LANL2DZ

****

Ru 0

LANL2DZ

The result was HF=-2714.1754994 that is very different from that obtained by RHF/3-21G (for all atoms)which is -7022.352913 in atomic units reported by Knapp-Mohammady et al on quantum-chemical study of Ru–NAMI-A. I don’t know if this difference is normal or something is wrong with my calculations. I would grateful if you could help me.

I look forward to hearingg from you.

Yours sincerely

Yes, of course it’s normal. You have used a higher level of theory; your calculations are more accurate. I guess the reference is an old one. To begin with you are using many more basis functions plus a quasi relativistic ecp.

I hope this helps

Dear Dr.Joaquine,

I’m struggling to perform a simple ONIOM calculations in Gaussian. My system is a nucleoside with a few water molecules. I’m using B3LYP/AMBER for the QM/MM systems respectively. Becasue some MM parameters are not availbale with official amber shipped with Gaussian, i’m defining an external parameters file (gaff.parm) using the hardfirst option, but i always got the following error:

Read MM parameter file:

Define OM 1

Expected a string in RdPar

Error termination via Lnk1e in /apps/gaussian/g09c01/g09/l101.exe at Tue Dec 18 15:27:57 2012.

Here’s the first few lines of my input:

%nprocshared=8

%mem=5gB

%chk=test

#P opt freq oniom(b3lyp/6-31g(d,p):amber=hardfirst)=embed scrf=(solvent=water,oniompcm=x,pcm) geom=connectivity iop(6/7=3,6/79=1) scf=tight

Displayed atoms

0 1 0 1 0 1

c-CQ

N-NC 1 1.36021158

C-C 2 1.34303418 1 119.42324725

N-N* 3 1.42424438 2 118.19798996 1 0.64340879 0 H

C-CM 4 1.36872655 3 118.81644680 2 -0.93789134 0 H

N-NC 5 1.31200307 4 124.04723261 3 0.58490013 0 H

C-CT 4 1.47797132 3 120.19317849 2 176.38518847 0 H

O-OS 7 1.41809007 4 108.81074718 3 -133.87546007 0 H

and here are the last few lines:

59

60 61 1.0 62 1.0

61

62

63 64 1.0 65 1.0

64

65

@parm99.dat

Could you please comment.

Full of respect

Marawan

Dear sir,

How to write input file for dimer calculation of hydantoin-5-acetic acid in guassian-03

with regards

Devi

hello,

i would like to carryout counterpoise calculation for the interaction energies of a dimer using gaussian09. I have calculated the individual monomer’s energy separately and i calculate the interaction energy

IE= total energy of the dimer – {Emonomer1+Emonomer2}

i have also calculated the energy of the dimer with counterpoise=2 keyword in gaussian, it gives the counter poise corrected total energy and it also gives the energy of monomers. my question is whether a single calcuation using counterpoise keyword is enough to calculate the interaction energies? or as i tried earlier by calculating the Emonomer separately and then i need to take energy of the dimer from counter poise calculation?

thanks in advance

vijay

Hello Vijay,

When you calculate the energy of a two component system, as you did originally, there is a slight error due to the superposition of the basis set on each of the components. This Basis Set Superposition Error (BSSE) is corrected through different methods like the Counterpoise method you used. This corrected energy is the one you want to use in your equation:

IE = total corrected energy – (Emon1 + Emon2). Check if the energy of the monomers in the counterpoise calculation matches the ones you calculated separately; it is crucial that you have maintained the same level of theory or the comparison will make no sense.

Hope this helps. Happy new year!

dear Dr.Joaquine,

many thanks. and i can understand that and again i would like to ask, does a single counterpoise calculation enough to calculate the interaction energy? if so, then there is no recessary to calculate Emon1 & Emon2 separately. Right?

cheers

vijay

Hello again, Vijay

If you indeed obtain the separate energies of the monomers within one single calculation then yes you can only carry out the counterpoise calculation and the do the substraction on your own

EI = Corrected_dimer_energy – (Emon1-Emon2)

I don’t remember that Emon(i) is given within the counterpoise calculation but if you say its there then I believe you.

Have a nice day!

thank you…. Dr. Joaquine

Hai,

I have a small confusion. I did optimization for both monomers and dimer using G09W. I did IE calculation by simply E(Dimer)-(E(Monomer1+Monomer2)) and the calculated value is 5.43 kcal/mol. I did counterpoise calculation also and the output is as below,

Counterpoise corrected energy = -5908.087362190423

BSSE energy = 0.009082833853

sum of monomers = -5908.081030077537

complexation energy = -9.67 kcal/mole (raw)

complexation energy = -3.97 kcal/mole (corrected)

Now, If i want to calculate IE which is counterpoise corrected, which energy i have to use for dimer i.e. Counterpoise corrected energy( -5908.087362190423) or sum of monomers(-5908.081030077537) .. ?

or simply IE=(Counterpoise corrected energy)-(sum of monomers )

Hi Shivanand,

The slight difference you are noticing (5.43 against 3.97 kcal/mol) is most probably due to a slight difference in monomers conformation from the isolated state to the dimer.

In other words: If you optimized A and B separately and then you optimized AB, the conformation of A in AB might be slightly different to the conformation of isolated-A because of the influence of B in AB. Same holds for B.

The first procedure you mentioned is called supermolecular method and the way I like using it is backwards from what you used: I first optimize AB and then manually isolate A and B and calculate their separate energies WITHOUT optimizing (so their respective conformations already carry the influence of the other monomer).

In short you should use the counterpoise corrected energy but notice that the CP calculation is doing what I stated above, calculating the separate energies at their conformations INSIDE the dimer.

I hope this helps. Have a nice day

Dr. Barroso,

I am currently investigating several high spin complexes and am trying to optimize the main groups separate from transition metals using genECP option. I am able to achieve a “converged” calc, however if perform a subsequent stability calculation on this “converged” structure the output reads, “wavefunction has internal instability”. Is it possible for you to explain how one is able to achieve a global minimum from this state? Thanks for your help!

Dear Dr. Barroso,

I truly appreciate your running this wonderful blog. I bet this site will make a legacy among Gaussian users!

I am confronting with a technical issue in TD-DFT calculation.

When I would like to calculate the optimized structure of the 1st triplet state

(starting from the optimized singlet ground state),

1. perform “td(triplets,…) opt” calculation with spin multiplicity of 1.

2. perform usual “opt” calculation with spin multiplicity of 3 (instead of 0).

Which one should be correct for getting optimized T1 structure?

What is the difference between scheme1 and scheme2?

And it would be also great if you will post a simple tutorial on

NTO analysis sometime in 2013 🙂

Thank you again for your blog.

from a huge fan of yours 🙂

Dear Dr.Barooso,

I’m asking how can we do Potential energy distribution (PED) analysis for vibrational spectroscopy.

Regards

Marawan

Hello:

I’m trying to optimize the geometry of 4-Iodosalicyclic acid at B3LYP/6-311++G** but the gaussian o/p is link dying with the error: “Atomic number out of range for 6-311G basis.

Error termination via Lnk1e in C:\G03W\l301.exe at Fri Jan 25 14:40:03 2013.”

Can you give me a suggestion how to get rid of this.

Bijan K Paul

Department of Chemistry and Biochemistry,

University of Colorado at Boulder, USA.

Hello.

It means the atomic number is out of range for the 6-311++G** basis set as defined in Gaussian; in this case, it is pretty obvious that it refers to the Iodine atom. Go to http://www.emsl.pnl.gov/forms/basisform.html

and retrieve the appropriate form of this basis set for Iodine (I believe this link is in the ‘Links’ section of this blog). Then, search another post in this blog on Gen and ECP keywords so you know how to insert it in your input file.

Have a nice day!

Dear Dr. Joaquin Barroso

Is this the correct input file for calculating the single point energy of a Ru-based complex at the UB3LYP/LanL2DZ(f)+6-311++G(3df, 2pd) level:

# ub3lyp genecp scf=tight

Title

(charge) (multiplicity)

Atomic coordinates

…

…

C N S Cl O H 0

6-311++G(3df,2pd)

****

Ru 0

LANL2DZ(f)

****

Ru 0

LANL2DZ(f)

Best regards

Brier

Yes, the input seems fine. If this is the input to the calculation you wrote about in the other comment, the one where you have a crash after 19 hours, then I insist on using SCF=QC

Have a nice day!

Dear Dr. Joaquin Barroso

I hope I’m not bothering you with my questions. My Gaussian geometry optimization and frequency calculation at the UB3LYP/(LanL2DZ+6-31G(d)) level fails with this error message:

Error termination request processed by link 9999.

Error termination via Lnk1e in C:\G03W\l9999.exe at Wed Jan 23 09:50:20 2013.

Job cpu time: 0 days 19 hours 42 minutes 50.0 seconds.

File lengths (MBytes): RWF= 77 Int= 0 D2E= 0 Chk= 8 Scr= 1

I’ve tried increasing the number of optimization steps by specifying OPT=(MaxCycle=500)that I chose the number 500 without rhyme or reason and I got the same error at the same point (i.e after 19 hours 42 minutes). I don’t know how to choose the number of optimization steps and If it is useful for this error or not? How about OPT=(restart,MaxCycle=n)?

Best regards,

Brier

Hi Brier,

That error you wrote above only means that the calculation is being aborted but it doesn’t say why. Just above it, in your output file, there must be a bit more of information as to why the computation crashed. After almost 20 hours, even on a small processor, I can say that your calculation is well set but maybe you are running out of disk and not out of memory; maybe the geometry is not converging to a minimum, have you checked how your molecule looks like after crashing?

I’d need a little bit more of information to help you but just for the sake of trying something, use scf=qc. If there is a problem with the SCF convergence then this might be helpful, but as I said, I need more information about the output in order to point you in the right direction.

Hope this helps!

Dear Dr. Joaquin Barroso

The input file for the calculation that I got error is here:

# ub3lyp genecp opt freq

Title

(charge) (multiplicity)

Atomic coordinates

…

…

C N S Cl O H 0

6-31G(d)

****

Ru 0

LANL2DZ

****

Ru 0

LANL2DZ

and the error message includes this too:

Optimization stopped.

— Number of steps exceeded, NStep= 144

— Flag reset to prevent archiving.

Best regards

Brier

I am trying to change the theshold for the Wiberg indices to another decimal point. I have NBO 3.0 on gaussian 09

can anyone write how hyperpolarizablity is calculated in Gaussian 03

I am Goutam, currently doing PhD in India. I am a regular visitor of your blog and find it quite useful.

I have a molecule containing Ge-O single bond. On doing NBO analysis in Gaussian 03 it does not print the hybridization of Ge-O bond. Is there any specific command in NBO which will enable me to the same.

Dear Sir,

Greetings. After the excited state optimization i could get the UV spectrum. How can i get the fluorescence spectrum for the same. Can you please tell me how should i modify the route section to get both at the same time in TD-DFT excited calculation.

And also i would like to know how to draw nano cluster structure easily, and with various size.

thank you sir.

Dear sir,

How to give the route section to get the information about density of states of the dye molecules.

thank you

I assume you are asking about Gaussian, right? Well, as far as I know there is no way to calculate DOS with it. Maybe you should contact Gaussian’s help desk.

Sorry. Have a nice day

Hello Sir,

I got Error # 2070 while submitting the input file

ASH

Gaussian (I’m assuming you are using it) has very cryptic error messages. I need more information to be able to help you.

Have a nice day

Hello Sir,

I need to calculate the optical absorption of molecules complexed with iron, I would ask for some references on how to perform this calculation in gaussian. Could you help me?

Many thanks,

José Gadelha

Hello José,

Since this is not yet my current area of expertise I can’t point out to the best references possible. However I do recommend to look for the book “Exploring chemistry with electronic structure methods” by Frisch & Frisch. In it you will find a comprehensive tutorial on this kind of calculations.

I hope this helps!

Hello Sir

I will calculate the binding energy between polymer and drug with oniom (DFT:UFF) in solution , but error occures :

Out-of-memory error in routine PCMQM2 (IEnd= 207619281 MxCore= 196195310)

Use %mem=199MW to provide the minimum amount of memory required to complete this step.

Error termination via Lnk1e in d:\l502.exe

also %mem up 200 error 1101.exe

thanks

You seem to be running out of memory. Try splitting the read/write files with the use of the %rwf utility. Search in google “efficient use of memory site:gaussian.com”

It may not work if you are using a very small computer. I would need more details about your working system to help you.

Have a nice day!

thank you

Dear Dr. Barroso:

It is niceto find this kind of support for Gaussian users. Thanks for that!

My question, althogh related to the use of Gaussian, might be a little off from your research. No harm done by asking though, right?

Is there a “symple” way to print out or extrac off the kinetic energy associated with a configuration interaction calculation (that is, the correlated kinetic energy)?. I have checked and tried different links and overlays with no success.

Your help on the matter will be greatly appreciated.

Thanks again!

Rogelio

Hola Rogelio!

That is an interesting question (which means I don’t have the answer to it). Gaussian usually displays a separate line with the kinetic energy, i assume you have tried finding it. I’m sure the guys over at gaussian help desk will be more helpful.

Sorry. Have a nice day!

Hello, I’m trying to convert a .chk file to .fchk file. I tried to use the formchk utility in Gaussian 03. but whenever i select the .chk file, it shows error like NtrErr from FileIO like this. usually i submit my jobs at supercomputer using g09sub command. all my files are there. i tried “formchk -3 filename.chk filename.fchk cmmand” there. but the supercomputer does not recognize this command. it says-not a typo, command not found – like this. but I really need this thing. how can I do that?? I’m new at computational. would I get some help please??

Have your calculations finished with an error or were they completed successfully? The message you are getting seems to suggest they didn’t finish properly. Try to only type formchk file.chk file.fchk also try using formchk -3 file.chk file.fchk without any further command.

Also, maybe the formchk utility is not properly installed in which case you need to talk to your system’s administrator or the holder of the Gaussian license at your institution.

I hope this helps! Have a nice day

Dear Dr. Barroso,

I am trying to calculate the valence IPs of a radical species using OVGF/6-311++G** model. Since it is a radical, it has alpha (55) and beta (54) spins. When i tried to run the calculation, i found that the job was incomplete, but without any error messages. I found that the job exactly stopped after printing the summary of results for all the alpha spin-orbital in the radical and when exactly i started print the beta orbitals. A brief snapshot showing the last few lines of the output are as follows:

—–

Summary of results for alpha spin-orbital 41 OVGF:

Koopmans theorem: -0.21098D+00 au -5.741 eV

Converged second order pole: -0.10502D+00 au -2.858 eV 0.854 (PS)

Converged third order pole: -0.17828D+00 au -4.851 eV 0.927 (PS)

Outer Valence Approximation: -0.15376D+00 au -4.184 eV 0.910 (PS)

DD1Dir will call FoFDir 12 times, MxPair= 408

NAB= 1640 NAA= 820 NBB= 780 NumPrc= 8.

Summary of results for alpha spin-orbital 42 OVGF:

Koopmans theorem: 0.15147D+00 au 4.122 eV

Converged second order pole: 0.13696D+00 au 3.727 eV 0.985 (PS)

Converged third order pole: 0.13850D+00 au 3.769 eV 0.983 (PS)

Outer Valence Approximation: 0.13828D+00 au 3.763 eV 0.983 (PS)

Orbital window will be selected automatically

Beta HOMO is orbital 40

GREENY has selected a window containing beta orbitals

11 through 41

from symmetry group number 1 of the 1 total symmetry operations

————

I did not find any error messages in the logfile. I gave sufficient wall time and memory.

I shall sincerely appreciate if you could kindly help me to handle this issue. Also, I shall be grateful, if you could kindly share with me some of your suggestions when calculating the IPs for the radical anion species. Is there any particular model do you suggest?

Thank you….

Hola Profesor, hace un tiempo que estoy trabajando con gaussian, y tengo unos resultados experimentales de XAS de complejos de metales de transición, estuve leyendo algunos papers sobre cálculos para simular los espectros de XANES, hay varios que usan TDDFT, quisiera saber o ver algún ejemplo del input para realizar dicho cálculos,

Gracias!

Hey there,

I was interested in freezing all the bonds in 2 molecules and studying the van der waals forces. I can’t seem to massage Gaussian enough to do this without finding an error. Any tips?? thanks. ( I want to use experimental values for the bond lengths instead of Gaussian opt)

Could you please provide more information about the error produced? If you are not studying any H bond interaction, I would advise you to relax the positions for all H atoms, i.e. just optimizing those atoms, since their locations obtained from an Xray diffraction experiment are somewhat bogus. In order to do so include the following keyword after opt: opt=(readfreeze) and then after a blank line at the end of the file include the following line:

noatoms atoms=H

–blank line–

I h ope this helps!

I had been trying to optimize the structure of B2H6 (at B3LYP/6-311++G(d,p) level). While giving the input, I saw that even if I didn’t specify any bond between the two B atoms, it’s taking a single bond always. If I delete it and save the corresponding file as a new input, it still shows the same. Even after optimization, the B-B bond remains intact.

I’ll be highly obliged if I get any solution regarding this.

Thanking you in advance…

I assume you are building the molecule with gaussview, if so I wouldn’t worry about that bond since its just a line GV draws between two atoms whenever the distance is below a certain threshold. However, if your route section specifies geom=connectivity it would be advisable to go the connectivity matrix at the end of your input file and delete the line wherever it specifies a single bond is to be considered between B1 and B2. Say B1 is atom number 1 and B2 is atom number 5 in your coordinate section, then a line looking like

1 5 1.0

must be deleted from the connectivity matrix.

I hope this helps, thanks for reading!

Dear Sir,

Thank you so much for your response. That will help me a lot!

Have a good one……..Cheers!

-BKP

Dear Professor,

I’m new to QSAR.. Can you share your materials to learn QSAR from scratch?? I saw in one of your post that you sad you are preparing the materials for students… Though, I got the basics from kubinyi and other articles… I don’t find any materials that direct us to improve the model predictivity… I followed tutorial in sybyl and my predicted R sqaure is low 0.308. Now how to proceed? can you guide me with any materials or solution?

Thank you..

Pavithra.

Dear Pavithra,

Unfortunately I use the old blackboard approach so I don’t have any slides or powerpoint presentation to share with you; if I had it I would have uploaded it a long time ago. Kubinyi’s articles are a great place to start. I think I will try to prepare something and post it on the blog but for sure it won’t happen soon.

Sorry. Have a nice day and thanks for reading the blog!

Thank you professor…

Dear Sir,

I would be grateful if you could explain me that how can I calculate Fukui functions on different atoms of a molecule using B3LYP 311-G ++ dp basis set G03 program. I have been successfully run the DFT of the organic molecule 2,2’-(1Z.1’Z)-(4,4’-methylenebis(4,1-phenylene)bis(azan-1-yl-1-ylidene))bis(methan-1-yl-1-ylidene)diphenol and now i want to calculate Fukui function on each atoms of this organic molecule. Please advise me how can I calculate fukui function.

Thanking You

Vinay Jaiswal

Palease read the post titled ‘how to calculate Fukui function’ in this blog for detailed instructions. You can search for it with google.

Hope this helps

Hi

Sometimes there is a warning in molecular orbital calculation like “Largest MO coefficient is 0.138235 x 10^3^, be careful about the interpretation….”

them after finding of the different segments contribution by GaussSum2.2 software in a molecule the percentage is not correct, for one segment is -31%, for the other one is 123%.

How can I get ride of this warning?

What level of theory are you using? This could be related to the use of the wrong basis set (too large or too small depends on the problem and the method employed)

Send me more info so I can help you properly.

Have a nice day!

Dear Dr.Joaquin,

I’m trying to get the pure DFT binding energy for a ligand using ORCA. If an anion is included, i should use diffuse functions in the basis set. I’m asking if this statement is also true if i want to use a very large basis set such as the def2-QZVP to get rid of the basis set superposition error.??..I have read that Triple Zeta quality basis gives a BSSE of 10-20 % so, i want to use the Quadruple Zeta type.

Full of respect

Marawan

Dear Sir:

Can you please give me some instructions about how to calculate the aromaticity indices: average two center indices (PDI), average two center indices (ATI), aromatic ﬂuctuation index (FLU)?

Bijan.

Dear Sir:

Can you please give me some instructions about how to calculate the aromaticity indices: para-delocalization index (PDI), average two center indices (ATI), aromatic ﬂuctuation index (FLU)?

Regard,

Bijan.

Dear Joaquin,

Thank you for such a terrific blog! I just started using Gaussian recently, and your blog has provided me very useful information. I have a question about relaxed PES scan. Gaussian prints a summary towards the end of the output file which gives the eigenvalue (energy, I suppose?) and geometry (all the bond distances, angles, dihedrals) for the structures optimized at each step during the relaxed scan. In some of my output files, however, the eigenvalues appear to be “******” instead of any numbers. For example:

……

Summary of Optimized Potential Surface Scan

1 2 3 4 5

Eigenvalues — **************************************************

R1 1.86918 1.86755 1.86649 1.86702 1.86595

R2 1.09213 1.09178 1.09142 1.09080 1.09049

R3 1.09229 1.09183 1.09150 1.09259 1.09178

R4 1.09746 1.09680 1.09597 1.09437 1.09370

…….

I could not find a proper solution to this through googling. Do you know how I can extract the energy for the final optimized structure in each step? I want to plot the energy vs. bond distances (that I constrained for the scanning), and I figured out how to extract the distances. Also, do you know how I can avoid such problems in the future?

I’m desperately looking for an answer, and would appreciate any insight you could offer. Thanks a lot!

Jen

I will calculate thermochemistry and frequency of a polymer with method : freq b3lyp/6-31

but the result is ” No file to extend for

IUnit= 1 — out of disk space.Error termination in NtrExt: NtrExt called from

NtrExt.”

I have coefficient space and only 8% occuped,

Hello!

I have a question which is bugging me for a while now:

How do you visualize ESPs using contour lines (just like your header up there).

I don’t have any problems visualizing it in general I just would like to use this type of visualization. Do I need a special program for that or is GaussView capable of doing that?

Thanks a lot!

Great blog btw!

Philipp

ok, Molekel 4.3 does the trick… anyway, is there a possibility to do the same with Gaussview 5? I don’t think so…?

I have done a relaxed PES scan on a dihedral angle and everything is fine (:D). now I want to extract the geometry of system in every step of the scan (the optimized one) to do the MM calculation and compare them with QM results. Regardless of the type (z-matriz or cartesian) is there anyway to force Gaussian to print out geometries? I know this information is there even in the .log file (when we open the log file in gview it shows the transition between each step). I tried to extract data from gview (exporting data from edit menu) but it would get cumbersome soon as I have 73 scan point in one of my 10 different molecules. so manually doing this in gview is not an option. I tried to read the log file to see where the information regarding the geometries is printed but it was unsuccessful. any comment on that!

Hello Sir:

Can you please let me know about the interpretation of an IRC plot? What does an IRC calculation indicate and how important is it?

Waiting for your response

Have a good day!

Bijan.

It is very important! An IRC plot will display the energy profile during a chemical change/reaction; i.e. the change in energy during the course of a structural modification that will lead to a chemical transformation whether it be monomolecular or polymolecular.

Minima on this plot will correspond to chemically available structures (reagents, products, intermediates) while maxima correspond to transition states (which cannot be isolated).

Thus IRC calculations are performed to study reaction mechanisms.

I hope this helps. Have a nice day!

Hello Joaquin,

Sorry for a very basic question: what review, book or blog would you recommend to someone who wants to use computational biochemistry as instrument (not for research in this field), and who tries to quickly grasp limitations and successes of methods used to model chemical reactions? Something that answers following questions:

– which methods provide the most precise correlations with physical measurements, for which types of bonds, forces, molecules, reactions?

– which methods are the most suitable for organic molecules/reactions, especially enzymatic?

– which approximations and heuristics are the source of modeling errors?

– which simulations are the most computationally intensive and why?

– what is the usual size of molecule(s) participating in reaction, like a dozen of atoms, or, as in molecular dynamics, a few hundred-thousands?

Overall, I’m asking for the most appropriate source to begin with, your answer is highly appreciated and will save tons of time for sure.

Thank you in advance,

Igor

Hola Joaquin.

I’m Alessandra and I’m trying doing anharmonic calculations using g09. Do you have any experience with those? Do you think it is possible to start over an anharmonic analysis reading the derivatives from the chk file and specifying different threshold values for Fermi and DD resonances?

The documentation on the G09 website is quite obscure about it.

Many thanks in advance!

Suerte

Alessandra

pa: your post on relaxed PES scan is a pearl!

Hi Alessandra,

Sorry for the lateness in my response. I have no experience working with anharmonic frequencies but I would encourage you to take your question to Gaussian’s help desk. They are very efficient and prompt to help their users.

Thank you very much for your kind words about my blog!

Have a nice day

Dear Sir:

I’ve been reading a nice article on intramolecular H-bonds in malonaldehyde: J. Phys. Chem. A 2007, 111, 8519-8530 (10.1021/jp073098d). The article describes a method of calculating IMHB energy as:

E(HB) = – (a03/2)VCP

In which a03 is described as the atomic volume element.

I have been finding difficulty in understanding the meaning of this term. Can you please let me know what does this mean (I mean the physical significance of the term) and how can this parameter be calculated in Gaussian?

Does it refer to H atom as such or is it different for the H atom in the molecule from an isolated H atom?

Your response will immensely help me in clarifying my doubts and better understand the matter

Looking for your response

Thank you very much

Regards,

Bijan.

Hello Joaquin,

Do you know how to construct a 2D-plot consisting of two rotors (i.e 2 dihedrals)? I’ve already extracted the values from my G09 output file. I’m baffled about how to plot the values. When I look at other examples, their Eigenvalues (on the y-axis after converting to kcal/mol) are all positive.

Why?

I don’t understand how the plotted values can all be positive when all of my Eigenvalues are negative.

My dihedrals are positive and negative, which is understandable because I did a 360 scan.

Thank you for your help,

Gail

You can always define a positive system by applying a unit transformation to your dihedrals, i.e. plot only the change in angle after each step, or in other words, use the original dihedral angle as your 0.0° value.

Also you can use relative energy values instead of the actual eigenvalues; if you started from the lowest energy conformation then all the energy values will become positive by definition.

I hope I’m not missing something from your question; if I did please do not hesitate to contact me again, I promise not to take so long this time 🙂

Have a nice day!

Dear Sir,

I am chethan, currently working on Sugar Chemistry using G09 suite (DFT calculations). The molecule contaisn more than 25 atoms with elements such as Sn, C H O Si etc. Currently am using LANL2DZ for Sn and 6-31g for C H O Si. (3-21g also used before). But these calculations are running for a long time and ended up with a some error related to symmetry or Berny optimization etc. It consumes lot of CPU hours without any fruitful results.

Following are my doubts

1. Is it possible to use only ECP with lower basis set for this kind of calucations, so that it save the computaional time and to get some rough optimized structure.

2 Is it possible to use only ECP for the calculations

Thanks in advance

Chethan

I have used the ECP+All electron basis set approach successfully before. If you specify lanl2dz for Sn as an ECP and also as its basis set while the rest of the molecule uses any kind of Pople basis set you should be doing fine.

Turn off the symmetry by including the NoSymm keyword in your route section, that ought to work!

Have a nice day

Buen día profesor Barroso. Felicidades por este espacio que seguro ha sacado a más de uno de muchos aprietos.

Estoy interesando en estudiar en enlace de varios complejos Metal-carbonilo. Para esto he visto que a traves de NBO se puede cuantificar el ‘bonding’ y el ‘back-bonding’ entre un metal de transicion y un ligando sencillo como el CO.

Acaso sabría usted como hacer esto ?. He leído sus previos post sobre NBO, así que creo que más o menos entiendo el resultado de mis cálculos. Sin embargo, no tengo idea de cómo calcular dicha cuantificación.

Le agradezco toda la ayuda posible.

Francisco Nuñez Zarur

Lo más sencillo es incluir la keyword BNDIDX en el espacio de NBO con NBORead en el route section. De ese modo tendrás una matriz con valores de indices de enlace entre todos los átomos de la molécula.

La otra (y que más recomendaría) es revisar la sección Second order perturbation analysis para ver las transferencias de carga CO -> MT

Genera un archivo de entrada para una molécula pequeña y córrela para observar estos resultados. A lo mejor y hago un tutorial en este blog.

Gracias por leernos!

#problem in optimization of metal complexes of phthalocyanine

Hi Dr. Joaquin

I have a master degree in organic chemistry and I have a little background on Gaussian and how to run small jobs like optimization and calculation of HOMO and LUMO energy gap in small organic molecules.

Now, I am trying to optimize metal complexes of phthalocyanine derivatives by using b3lyb/6-31+G (d,p) method. I completed optimization of Zn-Phthalocyanine with HF/3-21. But I couldn’t optimize the compound with the larger basis set.

Calculations were run on Pc [core i7-3840 QM cpu 2.8 GHz ,RAM (32), 64 operating system].

Could you help me to understand why it doesn’t complete?

I saw a question on your homepage related to ZnPc optemization and your advice to use LANL2DZ, I will be highly appreciated your help about this method?

Regards,

basma

Hi Bazhma,

What is the error you are getting? My guess is your PC is running out of memory. HF calculations will not get you published anymore. Try using that HF optimization as input for B3LYP optimizations and search for a page in gaussian called something like efficiency considerations; you can just google it. Therein you will see instructions to use %rwf (read write files) in order to partition your calculation in a more suitable way.

Hope this helps! Have a nice day

Hello

I am trying to calculate the HOMO LUMO for my system ! in some publication I saw they calculate the percentage like dxy energy -0.355 eV 12% !!!

publication figure 10 of ooms et al, Inorganic chemistry, 2007, 46, 9285-9293

I have system like VOCl3 , interested in vanadium , what do u suggest me to do !?use NBO?…. what command give me these percentage ?! I have read in your blog a comment back to 2010 that the calculations on G09 can not be seen by gaussview 03 this is the problem I have so I calculate on g03 ! I see some picture but can not be saved on Gaussview !!!! no save or copy icon !!! could you plz suggest another graphic software comparable to gaussview .

I do really appreciate your help.

Thanks

I would suggest either chimera or chemcraft. About the percentages, please send me a copy of the article so I understand better, because I’ve never heard of such a thing. Maybe its just the percentage of the dxy orbital into the hybrid which forms either the HOMO or the LUMO but I’m not sure if they indeed used NBO or not.

Have a nice day!

Hi Thanks for your reply !

I downloaded chimera, kinda confused it shows something but I am interested in getting like gaussview that show the MO surface for each level of energy ! is it possible with chimera?!

In chemcarft I have tried it asked for formatted file after doing that just show me energy level no MO surface ?! what should I do ?

I have pdf file of that article how I can send you !

Thanks again

Rosha

Thanks for your reply,

I already use the HF optimization as input for B3LYP optimizations and I have no error but the pc is stopped for 2 days at this step:

The electronic state of the initial guess is 1-A.

Requested convergence on RMS density matrix=1.00D-08 within 128 cycles.

Requested convergence on MAX density matrix=1.00D-06.

Requested convergence on energy=1.00D-06.

No special actions if energy rises.

The input for the calculation is

%chk=ZnPc_Br.chk

%mem=200mw

# b3lyp/6-31+g(d,p) opt optcyc=400

Title

(charge) (multiplicity)

Atomic coordinates

Does you mean I have to add (%RWF=1,1GB,2,1GB,3,1GB,4,1GB,5,1GB,6,1GB,7,1GB,8,1GB,8,1GB,9,1GB)

Regards,

Yes but mind your computing capacities. Try to contact a scientific computing facility near you to help you run these larger calculations.

Best wishes

Thanks for your kindly support, but I don’t have a scientific computing facility on my faculty. Can I complete this calculation on my pc or it’s impossible?

And could you kindly tell me with the best computing facility to complete our project?

Best Regards,

I’m not aware of any public computing facility because here at UNAM we have our own supercomputing favilities; try google for some place that can help you.

It is possible to finish it on your pc but it will take a lot of time. You just have to be very careful about how to distribute the memory and all.

Best wishes!

Hi Sir,

i am interested to calculate LDOS for ethyl benzene.

I dont know the keyword by which i can calculate LDOS of each atom in ethyl benzene.

Please help me sir.

Thanks

Prabhakar sharma

Hi Sharma,

I don’t think there is a keyword for calculating LDOS in Gaussian. Try another software like AOMIX.

Have a nice day!

Thanks so much for your kindly support;

I optimized the metal complexes of phthalocyanine derivatives using:

%chk=ZnPc-Br.chk

%mem=200mw

%rwf= 1,1GB,2,1GB,3,1GB,4,1GB,5,1GB,6,1GB,7,1GB,8,1GB,9,1GB,

# opt b3lyp/3-21g* geom=connectivity

Then, I do single point calculation using:

%chk=ZnPc-Br.chk

%mem=200mw

%rwf= 1,1GB,2,1GB,3,1GB,4,1GB,5,1GB,6,1GB,7,1GB,8,1GB,9,1GB,

# b3lyp/6-31g* geom=check guess=read

But, I have an error on frequency calculations due to size and I try many trials like (optcyc=400 or scf=xqc) and it doesn’t solve yet.

There are 438 degrees of freedom in the 1st order CPHF.

No file to extend for IUnit= 1 — out of disk space.

Error termination in NtrErr:

NtrErr called from NtrExt.

I will be highly appreciated your advice about this error about frequency calculation as I need to calculate the NMR theoretically.

Best Wishes

Dear Sir,

I am a beginner in the field of research and using gaussian03w.

Please suggest me,how i can calculate emission wavelength for a compound?.

Thank you

Hi,

I am beginner of gaussian09. I want to optimize a structure of isopropylphosphate. The isopropylphosphate contains -2 charge. However, when I don’t consider the -2 charge then I am getting expected bond angle, bond length and dihedral angle(close to experimental observation). My input file looks like this

%chk=isopropylphosphate1.chk

%mem=4GB

%nprocshared=8

# opt b3lyp/6-31++g(d,p) geom=connectivity

B3LYP

-2 1

C 0.02563200 -1.04646600 -0.06925500

C -0.22829000 -2.45701400 -0.57448600

O 1.17729100 -0.53167300 -0.83050600

P 2.46250500 0.12547100 -0.18386700

O 3.46510700 0.58633300 -1.14869600

O 2.08982600 0.87247900 1.21037700

O 2.79203000 -0.56586700 1.24942000

H 0.28518400 -1.06389900 0.99306300

H -0.47283000 -2.45333600 -1.64068100

H -1.05360000 -2.91582800 -0.02482200

H 0.66551000 -3.06743500 -0.42440900

C -1.13753943 -0.06386962 -0.29976870

H -1.12874945 0.26680910 -1.31735129

H -2.06543956 -0.55460743 -0.09221688

H -1.02660650 0.77890229 0.35010005

1 2 1.0 3 1.0 8 1.0 12 1.0

2 9 1.0 10 1.0 11 1.0

3 4 1.5

4 5 2.0 6 1.0 7 1.0

5

6

7

8

9

10

11

12 13 1.0 14 1.0 15 1.0

13

14

15

Therefore, I want to use -2 charge but I want to get the result of neutral molecule. How can I do that.

Any suggestion will be appreciated.

Thanks in advance

Sudipta

Hello Sudipta!

Maybe I’m not following but how can you expect to get the structure of a neutral molecule for a charged one? They are two different species!

If your experimental results were obtained for a neutral molecule then forget it, the charged calculation will never resemble the experimental (neutral) conformation.

If your experimental results were obtained for a charged molecule and you can’t reproduce the structure (but strangely you do it with the neutral calculation) then you might try to change the basis set which is highly polarized; I’d try 6-311G(d,p) (i.e. drop the polarization functions).

I hope this helps!

Hello Sir,

I tried to get the vibrationally resolved electronic spectrum using gausiian 09 program, but after some time it shows the error given below. If it is able to open the file, sir please suggest how to overcome this error. I also tried by generating .fch file. but it is showing the same error. Thanks

**********************************************************************

Generation of the Franck-Condon spectrum

**********************************************************************

Approx. of the electronic transition dipole moment: FC

Type of transition requested: ONE-PHOTON ABSORPTION

Data for initial state taken from current calculation.

Passed-in normal modes used.

Data for final state taken from checkpoint file “acetone initialfreq”

Error termination in NtrErr:

ntran open failure returned to fopen.

It seems to me you are making a call to either a corrupted or an non existing file. Please send me your input file and a copy of these last few lines in your output file so I can help you in a better way since yoiu don’t quote here the method for vibrational calculation.

Best regards

Hi,

Thank you very much for the reply. You have correctly followed what I meant. However, I tried with 6-311G(d,p) basis set but it doesn’t improve the result. Actually, I am at critical situation to explain my result properly. Otherwise, I need to prove that the results for two cases are same. Please help me out in this regard.

Sudipta

How can the results be the same for two different molecules??? Despite the fact they are very much related in their structure, double deprotonation would cause the electron density to rearrange in an unpredictable fashion! I still don’t know why would you expect to have the same bond angles and lengths between a neutral and an anionic species.

Try sending me an email with more (way more) information on what you are trying to accomplish.

Have a nice day!

I sent an email to you at this address jbarroso@unam.mx. please let me know if you need any further information from my side.

Hi Sir, I am doing gaussian calculations for C2H4, in output there is a place says “Population analysis using the SCF density: and show the orbital symmetry like AG, B1U,… .which is great !

I am doing same calculation for VOF3 belong to C3v symmetry.

E 2C3 (z) 3σv linear,rotations quadratic

A1 1 1 1 z x2+y2, z2

A2 1 1 -1 Rz

E 2 -1 0 (x, y) (Rx, Ry) (x2-y2, xy) (xz, yz)

I would like to assign each energy level with the 3a1, 2e, 4a1, …. like figure 3 of this publication http://www.sciencedirect.com/science/article/pii/0368204886800536

how I can get this information from output that which energy level is 3a1, or 2e or 4a1,… since I want to do the same assignment for VOCL3, and VOBr3.

I do really appreciate if someone can help me to out of this confusion.

why everybody ignored me !!!!!!plz i am so helpless!

Hi Rocha,

Sorry if I haven’t replied to your question promptly. I assume you are using Gaussian, right? Are the energy levels in the aforementioned paper electronic levels? If so, you are mixing things! Those lines you reproduced in your question are eigenvalues to the rotational operator, your electronic energy levels should be labeled the way you want in the population analysis section. I’m probably not understanding your question properly, if this is the case please send an email to help!at!gaussian.com they are always very helpful and friendly, not to mention quick, they don’t even verify who is sending the question, *wink*wink*

I hope this helps! Have a nice day

Hi ,thanks for your reply I sent you email to this address

Have you received it ?

Thx

Hello there, I have received your email but please give me some more time; I have an enormous pile of things to do 🙂

Have a nice day!

%nprocshared=3

%chk=C:\Users\sheeraz\Desktop\acetoneoptinitial.chk

%mem=500MB

#p freq=(FC,SaveNM) NoSymm b3lyp/6-31+g(d,p) guess=read geom=allcheck

acetone initialfreq

%chk=C:\Users\sheeraz\Desktop\acetoneoptfreq.chk

0 1

C

C 1 B1

O 2 B2 1 A1

C 2 B3 1 A2 3 D1 0

H 1 B4 2 A3 3 D2 0

H 1 B5 2 A4 3 D3 0

H 1 B6 2 A5 3 D4 0

H 4 B7 2 A6 1 D5 0

H 4 B8 2 A7 1 D6 0

H 4 B9 2 A8 1 D7 0

B1 1.51825460

B2 1.21898800

B3 1.51825460

B4 1.09623380

B5 1.09701567

B6 1.09107769

B7 1.09623314

B8 1.09701559

B9 1.09107760

A1 121.59065096

A2 116.81869809

A3 110.72986117

A4 109.82078001

A5 110.05968071

A6 110.72984506

A7 109.82073423

A8 110.05968234

D1 180.00000000

D2 127.06161404

D3 -115.16467550

D4 5.30687972

D5 -52.93842394

D6 64.83529815

D7 -174.69317594

1 2 1.0 5 1.0 6 1.0 7 1.0

2 3 2.0 4 1.0

3

4 8 1.0 9 1.0 10 1.0

5

6

7

8

9

10

Sir, this is the input file.

The last few lines of the output file are

Eckart Orientation

———————————————————————

Center Atomic Coordinates (Angstroms)

Number Number X Y Z

———————————————————————

1 6 -0.697824 -0.001075 -1.293268

2 6 0.097509 0.000000 0.000000

3 8 1.316497 0.000000 0.000000

4 6 -0.697824 0.001075 1.293268

5 1 -1.427424 -0.819227 -1.299428

6 1 -1.266491 0.932929 -1.381012

7 1 -0.024597 -0.096576 -2.146553

8 1 -1.427424 0.819227 1.299428

9 1 -1.266491 -0.932929 1.381011

10 1 -0.024597 0.096575 2.146553

———————————————————————

**********************************************************************

Generation of the Franck-Condon spectrum

**********************************************************************

Approx. of the electronic transition dipole moment: FC

Type of transition requested: ONE-PHOTON ABSORPTION

Data for initial state taken from current calculation.

Passed-in normal modes used.

Data for final state taken from checkpoint file “acetone initialfreq”

Error termination in NtrErr:

ntran open failure returned to fopen.

I’m not familiar with this kind of calculations, however it is clearly trying to read something from a checkpoint file which the program believes to be named “acetone initialfreq” but this is only the Title Card line, right?

I don’t understand your input file, it looks as if you defined two different chk files at two different places in it.

If I understand correctly, you should try something like the following:

%nprocshared=3

%chk=C:\Users\sheeraz\Desktop\APCHKFILE.chk

%mem=500MB

#p freq=(FC,SaveNM) NoSymm b3lyp/6-31+g(d,p) guess=read geom=allcheck

acetone initialfreq

0 1

C

C 1 B1

O 2 B2 1 A1

C 2 B3 1 A2 3 D1 0

…

… etc.

In which APCHKFILE stands for Appropriate (or correct) CHK file, in which ever you have previously calculated your initial set of frequencies, either acetoneoptinitial.chk or acetoneoptfreq.chk

I’m not exactly sure what else could be but it seems interesting, so please share the right answer with me if this works, ok?

Have a nice day

hello sir,

I think the only problem is that I am not able to open the .chk file. after optimization. If I can be able to optimize it, I think the problem is solved. Kindly suggest.

The error shown is

CConnectionGFCHK::ReadFile()

Cannot find file.

please suggest how to overcome this error, please dont suggest to create .fch file

I already told you! You have two %chk lines in your input file, delete one! I believe the second one, the one out of place, the link0 that is, is the one that should be deleted. The error you are describing above is not a Gaussian error but a Gaussview error in which the molecule cannot be read.

Hi sir,can u give me a idea and concept about vibrational spectroscpy analysis used in drug designing?

Hello again!

Well of course Infrared spectroscopy is always useful in any kind of synthesis not to mention that is a cheap and fast technique for identifying certain functional groups that might be of interest in a lead compound. I’m not sure Raman spectroscopy is that helpful. I think Circular Dichroism must be fundamental in identifying chirality of leads and other compounds.

I hope this helps!

Thank you so much for ur info sir…

#Hello Sir,

Can you give me suggestion for protein-ligand complex simulation in GROMACS 4.5 software.

I gave the following command

grompp -f hdac1em.mdp -p hdac1dr.top -c hdac1drwater.gro -o hdac1drgion.tpr.

Then, I got response of Atomtype SDMSO not found.

Please give me your valuable suggestion.

Sorry but I don’t know how to work with Gromacs.

Have a nice day and thanks for reading!

hello Dr,

can u pls tell me tat which value should I take to calculate dipole moment and second hyperpolarisability from Gaussian 09 output?

Hi,

Can you please suggest how can I perform single point energy calculation at different dihedral angle.

I can perform the optimization at different dihedral value by using opt=modredundant option. I don’t find such kind of option for single point energy calculation. Any help will be appreciated.

Thanks

Perform a rigid scan. Find more information in this same blog on a post about rigid and relaxed scans.

Best wishes

hI Dr,

Im not quite sure, have you ever used “q-chem” before? Recently, I’m running TDDFT calculation, but I got the error that I cannot solve it. below is my input file and error information:( the coordinate is the optimized structure with solvent which I got from solvatiion calculation before this one)

$molecule

0 1

C -0.049505 -1.24475 -0.056378

C -1.302811 -0.689786 -0.020935

C -1.273506 0.741986 -0.005695

C 0.001451 1.246114 -0.030377

S 1.18586 -0.023895 -0.072382

H -2.159818 1.366411 0.02211

H -2.21391 -1.27791 -0.005902

H 0.223637 -2.291459 -0.074281

H 0.317395 2.280912 -0.026538

$end

$rem

JOBTYPE OPT

BASIS 6-31G+(d,p)

EXCHANGE B3LYP

CIS_STATE_DERIV 1

CIS_N_ROOTS 1

CIS_SINGLETS TRUE

CIS_TRIPLETS FALSE

SOLVENT_METHOD PCM

RPA TRUE

POP_MULLIKEN 2

$end

$pcm

Theory CPCM

Method SWIG

Solver Inversion

Radii Bondi

vdwScale 1.2

$end

$pcm_solvent

Dielectric 4.00

$end

=======================

error output:

Q-Chem fatal error occurred in module /home/scratch/qc40release/qc40c/qchem/libmdc/newfileman.C, line 326:

Error reading in TMP file 99/0 (8)

p0_3952: p4_error: interrupt SIGx: 6

“1ringopt.out” 238L, 9816C

Initially, I thought this probably was space problem, so I tried to add mem_static, but still got same error. or the space of the scratch is full? I’m not quite sure what causes this problem. and how to troubleshoot this.

Best, Hao

Dear Sir,

I am doing excited state study ( # cis/6-31g(d) geom=connectivity) using gaussian 03w for my compound.

and every time the link has been died showing

” Transformation cannot fit in the specified MaxDisk.

Error termination via Lnk1e in C:\G03W\l804.exe at Sat Sep 07 12:03:48 2013.

Job cpu time: 0 days 0 hours 4 minutes 50.0 seconds.

File lengths (MBytes): RWF= 2292 Int= 0 D2E= 0 Chk= 10 Scr= 1″

.

Please suggest me what should do?

and how we can increase iteration for the calculation in gaussian 03w?

Thank you.

with regards

PP

I am currently calculating dynamic Hyperpolarizabilites using the coupled-perturbed Hartee-Fock method in Gaussian09. Calculation seems to work fine. My problem is, that the output contains now 18 terms for the \beta-tensor instead of 10. The Gaussian manual only describes the order of the \beta-values for 10 terms which is:beta_xxx,beta_xxy,beta_xyy,beta_yyy,beta_xxz,beta_xyz,beta_yyz,beta_xzz,beta_yzz and beta_zzz.

I assume the addtitional 8 terms should be: beta_xxz,beta_yxz,beta_yxx,beta_zxz,beta_zxy and beta_zyz.

I just do not know the ordering of those terms in the output. I hope u can help me with this problem.

Greetings

Mopp Zilla

Hi Sir,

I am trying to find methodology to use Gaussian to predict fluorescence of any small molecule. i have read many papers but none of them tell the methodology. Everyone discuss about the basis set they have used which of course differs from case to case. I tried learning it from the example of acetaldehyde (http://www.gaussian.com/g_tech/g_ur/k_scrf.htm) but i am unable to understand it.

Can you help me with it ?

Hello Ankita,

I suggest you find online a copy of “Exploring Chemistry with Electronic Structure Methods” by Frisch and Frisch for a step by step introduction to photochemistry calculations. The procedure is rather lengthy for a comment, perhaps I should write a full post on it 🙂

Have a nice day

Hello again Dr. Joaquin!

I tried to visualize HOMO and LUMO for an optimized metal complexes of a halogenated phthalocyanine (B3LYP 6-31G(d)) but I have error termination in cubegen formation:

Error termination via Lnk1e at Mon Sep 16 16:29:47 2013.

Cubegen Job Completed (PID = 1b38, status = 2057)

Cubegen Series Job Completed

Could you kindly tell me how to increase the grid file?

And please suggest me a book or a tutorial to learn more about this kinds of calculations,

Best Regards for your continues support,

Basma

Use the following comands:

cubegen MO=HOMO file.fchk npts file

where you should change npts for the number of points to be set on each side of the grid. so if you change npts for 100 you will have a grid with 100³ points (1,000,000 points).

Hope this helps!

Estimated Prof. Joaquín

#gaussianerror

I would be very gratetful if you could help me with an optimization in gaussian 09. I Tried to optimized a Noble gas compound using CCSD(T) an i get the next error:

HESSIAN DOES NOT HAVE THE DESIRED LOCAL STRUCTURE

TAKING SIMPLE RFO STEP

SEARCHING FOR LAMDA THAT MINIMIZES ALONG ALL MODES

*****************************************

*** UNABLE TO DETERMINE LAMDA IN FmD114 **

******************************************

Error termination via Lnk1e in /usr/local/g09/amd/g09/l114.exe

Could you help me

Cheers,

Said.

Try it again with the option freq=calcall it will take a long time but probably will help you.

Let me know if it doesn’t

Cheers

Ok, thank you very much. I will let you know.

Bye Bye.

my question may silly.

is there any way to find out the energy of the individual atom in molecules?

Hi Uma

I’m sorry for the lateness of my response. I think you could use the NBOdeletion scheme to eliminate all the interactions from the atom under consideration with the rest of the atoms in the molecule.

The NBODel manual is located at the NBO website from the Wisconsin University.

May I ask what are you trying to study or prove?

I hope this helps

#NBO

Saludos!!

Tengo tres preguntitas con respecto al análisis del NBO. Es válido hacerlo para sistemas de capa abierta con multiplicidad 1? Como por ejemplo dirradicales. Y si es así, tiene sentido analizar los índices de Wiberg para estos sistemas?. Lei en un sitio web que se puede especificar en Gaussian con el iop(5/14=2) para que el análisis poblacional se haga con la función de onda corregida (spin annihilated). La verdad es que los resultados no me parecen mejores, pero no he encontrado nada al respecto!

Gracias por este blog!!

Hola Beatriz,

Mil perdones por la tardanza de mi respuesta, a veces con tanto trabajo soy un poco negligente del blog.

Claro que tiene sentido usar NBO en sistemas de capa abierta, pero cuidado ya que el análisis se hace por separado para la densidad con spin alpha y la densidad con spin beta, del modo que se haría con los métodos no-restringidos.

Algunas propiedades son sumadas (como la población total) pero hay que en general estar al pendiente de lo que leemos en el archivo de salida.

Saludos y gracias a ti por tus palabras

Gracias por responderme Joaquín! Tendré cuidado con la densidad de spin alfa y beta, un gran saludo!

Hello Sir,

As mentioned in your blog I used the following input to calculate free energy of solvation, b3lyp/6-31+g(d,p) scrf=(smd,solvent=water, DoVacuum) nosymm geom=connectivity polar

I dont see energy for vacuum. I see SCF but how can we say that it free energy for solvation. I will be grateful if you help me to under stand this.

Thank you,

Mohan

Just run a single point on your geometry of interest separately.

Have a nice day

Hello,

I will be very grateful if you step-wise explanation for the calculation of pKa using gaussian 98 (which value needs to be extracted). As my knowledge and using the formula reported in JACS 123, 7214 (2001), I try to calculate but I did not get similar values. The process is very straight forward according to that paper. My main problem is to get solvation free energy. Gaussian 98 does not print directly in the .log file.

Thank you.

Bharat

Hi,

I am a regular visitor of your blog. I have a query regarding nbo calculation. On calculation of bond order of borazine with G09W at b3lyp/6-31G*, I found that B-N wiberg bond index is 1 for all 6 B-N bonds in borazine. However, the table showing the occupancy/bond orbital/coefficients etc. showed that 3 B-N bonds have pi-pi bonding, while the other 3 B-N bonds have only sigma bonding. This means that B-N bond order should be 2 (for those which has pi-pi bonding), or if 1.5, if average is taken. However, as mentioned earlier the B-N Wiberg bond index is 1 for all the 6 B-N bonds in borazine. They seems to contradict. I am confused and looking forward for your help.

Thank you.

Sameer

Hi Sameer

This is indeed confusing and I’m not sure where is this discrepancy coming from. However you should note that while the NBO program provides Wiberg bond indices, these are defined in a different way than the NBO bond orders. I wouldn’t mix both definitions, specially if you are observing such different values. Use the BOAO option in your NBO keyword section so you get also the Bond Orders in the Atomic Orbitals basis and compare those values to Wiberg’s

I hope this helps

Hi Dr Joaquin,

I am wondering if you can tell me if is a way or method that can calculate the interaction between two small molecules using Gaussian. i.e A + B = A.B

Otherwise the interaction energy that hold the two molecules together.

Thank you

Rean

I can think of two methods:

1) First calculate the energy of the AB pair (I guess you might need an optimized geometry for the interacting pair). Then delete the A molecule and save it as a new input file (e.g. b.gjf) and do the same for the B molecule and calculate a single point for each. The interaction energy would be then calculated as:

Eint = E(AB) – {E(A) + E(B)}

2) Another method is to use the NBODel implementation. Run a geometry optimization of the AB pair then run the NBODel calculation on that geometry by using pop=NBODel on the route section. The added input should read

-blank line-

$NBO $END

$DEL

ZERO 2 DELOC FROM 1 TO 2 FROM 2 TO 1

$END

blank line

Please search the NBO deletion post on this blog for futher details.

HAve a nice day!

# End of line while reading pcm input #

hello sir,

I’m a new computational chemist. I’m trying to calculate fluorescence for tryphenylamine molecules. as they have given in g09 manual i started with acetaldehyde molecule. but in 3rd step I’m getting the following error.

The first two steps (Step 1: Ground state geometry optimization and frequencies; Step 2: Vertical excitation with linear response solvation) just using Water instead of Ethanol working fine. Step 3: State-specific solvation of the vertical excitation – Part II (Link1) quits with the following message:

SC-PCM: Self-consistent PCM reaction field calculation.

Using the following non-standard input for PCM:

NonEq=Read

End of line while reading PCM input.

Error termination via Lnk1e in xxx/GAUSSIAN/g09/l124.exe at Sun Jun 12 17:02:49 2011.

Job cpu time: 0 days 0 hours 0 minutes 0.1 seconds.

File lengths (MBytes): RWF= 36 Int= 0 D2E= 0 Chk= 56 Scr= 4

This is the Jobfile:

%mem=8GB

%nprocshared=8

%chk=03-calc.chk

# B3LYP/6-31+G(d,p) SCRF=(Solvent=Water,Read) Geom=Check Guess=Read

DMABE: prepare for state-specific non-eq solvation by saving the solvent reaction field from the ground state

0 1

NonEq=Write

–link1–

%chk=03-calc.chk

# B3LYP/6-31+G(d,p) TD(NStates=6,Root=1) SCRF=(Solvent=Water,StateSpecific,Read) Geom=Check Guess=Read

DMABE: read non-eq solvation from ground state and compute energy of the first excited with the state-specific method

0 1

NonEq=Read

Any suggestions on how to solve this problem?

thanks in advance.

Hi. Did you make sure to leave a blank line at the end if the input file? If you didn’t then the program will think there is more to be read but the File is abruptly ended. I’m sure it might be more complex than that but it might be a good idea just to check it. Let me know, ok?

Best regards

yes sir…that was the mistake i made…now am able to run the programme successfully.

thankyou very much sir

Dear Niveditha,

Could you please help me to get step 3 and 4 successfully terminated? My molecule is 36 atoms and i got job error due to exceeded walltime.

Dear Sir/Madam

I am using Gaussian G09 and also using Gauss View 5.09 for the visualization. I want to visualize the NBO orbitals using G09 Calculation and Gauss View program. I am looking every one suggestion regarding this.

Please refer to the post on how to visualize NBO’s with Gaussian, provided in this same blog. Use the search box. You will find everything you need to know about the matter.

Best regards

Hi Dr Joaquin,

I use G09 and Gauss View 5.09 for my PhD studies. I use the b3lyp/genecp method to activate an alkane using vanadium-based catalysts (e.g. H3VO4 model). The mechanism I am trying to follow involves a two step dehydrogenation:

H3VO4 + R-H (alkane) = H3VO4H + R. = H3VO3 + R (alkene) + H2O

My challenge is that I do not get a maximum on a relaxed PES scan for the first step, i.e. scanning between H of alkane and O of catalyst. I have tried a different algorithm (scf=qc) without success.

Any suggestions on how to model dehydrogentaion reactions?

So you are trying to get a maximum? This means you are trying to get to a transition state structure. Please search for the usage of the QST2 or QST3 keywords in Gaussian. You may also look for the IRC keyword at Gaussian’s website.

Best regards

#convergencefailure#

Dear Dr Joaquin,

I have problem with calculation of solvation energy using IPCM solvation model for an anionic system at m06l/6-311++G(d,p) level of theory using G09. The optimized geometry from gas pahse calculation was used for IPCM single point calculation. The job did not converge and terminated with an error: Maximum number of iterations exceeded.

I tried to increase the number of iterations to 600, with [iop(1/6=600)]. But this did not solve the problem of convergence and the job terminated with the same error.

Regards

Just increase the number the iterations by using scf=maxvycle=1000

Best regards

Just use scf=maxcycle=1000 and that should increase the performance.

Hope this helps

Dear Dr Joaquin,

Thanks for your reply.

I tried using scf=maxcycle=1000 but still i get the same error message.

Regards

Try even more iterations scf=(QC,maxcycle=10000)

Hope this helps

Dear Dr Joaquin

I optimized ethanol molecule. After that, frequency calculation was performed. The calculations were done successfully. I didn’t have any imaginary frequency (NImag=0) and four YES options were obtained that confirmed my structure is stable. But in thermochemistry section, there is this warning:

Warning — explicit consideration of 3 degrees of freedom as

vibrations may cause significant error

Can you help me about this problem? Is it important?

No it’s not important. This is only a warning that is issued as a sort of disclaimer. So carry on!

Have a nice day

Dear Dr Barroso

Thank you so much for your answer.

Have a nice time

Dear Sir,

I wanted to ask about this as well, since it’s appearing in many of my calculations. I want to optimize my molecules both in gaseous phase and solvatated so I can calculate DeltaG. But some calculations present this warning and some don’t.

I’m very grateful for you taking the time to keep this Blog and help people around the world!

María Fernanda Muñoz,

Universidad Central de Venezuela.

Muchas gracias, María Fernanda! Espero poder seguir siendo de utilidad. Saludos hasta Venezuela!

Dear Dr Joaquin

I am considering to calculate transfer integral by using splitting method. So I guess the g09 zindo calculation would be a good option. By my experience, some people will add the command z=N to give a certain electric field for getting a more accurate calculation. Im curious If i am only concern homo, homo-1, lumo, and lumo+1 in dimer scheme, adding Z=N is that necessary? besides, are the eigenvalues can be trusted ? or I only can believe the total energy for certain root?

Hao

Hello,

I just read the blog entry about hybridisation of atomic orbitals (the standard way proposed by pauling) to sp2 or sp3 hybrid atomic orbitals. I can’t find a theoretical justification of this concept anywhere. This is what I mean: the orbitals are just combined in a some way and there is never an explanation provided for why it is actually allowed to do that (why it actually fits the real electronic structure). Also, they don’t have the right symmetry to combine (if this a combination like in MO theory). I’m looking for a theoretical underpinning of the concept and a justification for why it is actually more or less realistic/true/whatever. You mentioned something in the blog entry but it was rather short. Could you please elaborate on that and maybe suggest a source where I could find what I am looking for?

Thanks

Hello John,

This is actually a great question! I think the blog entry on the matter was one of the firsts I ever wrote back in 2009; I guess I never really expected anyone to pay much attention to it.

Ok so on to your questions:

p orbitals don’t have the right symmetry because they were obtained as a solution for a Hamiltonian with spherical symmetry (that of a hydrogenoid atom) but the set of three p orbitals (solutions with l =1) is indeed spherical when summed all together. Using hydrogenoid orbitals as the basis for MO construction is a huge leap but it is justified under the mean field approximation (each electron ‘swims’ in the field produced by the electron density ocean produced by the rest of the N-1 electrons) which can be proven to be *cough*sort of*cough* spherical (Weissbluth – Atoms and Molecules).

As I remember writing in that particular post, once a set of solutions of any given Hamiltonian is found, any linear combination of them will also be a valid solution of the same H (obviously, since H is a linear operator!); therefore a symmetry ADAPTED linear combination can be found in which orbitals “point” to wherever we need them to in order to ‘explain’ any geometry (‘describe’, would be more accurate).

The general procedure for performing this adaptations under a given group point (Td in the case of methane) can be found in D. Harris – Symmetry and Spectroscopy (Dover).

Orbitals are a tricky thing, they don’t quite actually exist, they are functions, but they do work really well as a model to explain both chemical structure and reactivity. This is why DFT methods are so conceptually popular because the one ‘tangible’ thing is the electron density but then you go into the v-representability problem (cleverly solved by Levy) in which the quantum effects (spin of all of them!) is taken into account. Of course the DFT problem lies in finding THE functional and ultimately we fall back to Kohn-Sham orbitals and so on…

So in short the justifications are purely of mathematical consistency but they do adapt really well to our chemical knowledge.

Thank you very much for this thought provoking post, I hope I understood and answered your question but if I didn’t I’m open for further conversation and maybe I’ll post some more on the matter.

Have a nice day!

Dear Dr. Barroso,

thank you very much for your reply, the fact that a linear combination of solutions to a particular hamiltonian is also a valid solution is enough to justify the use of hybrid atomic orbitals to explain a given geometry.

I wonder whether the description of bonding using hybrid atomic orbitals is of any use, other than explaining the geometry. How accurate is it, qualitatively, to explain reactivity, in inorganic and organic chemistry? The concept of hybridisation is so widespread in organic chemistry, but there is not a single textbook that really justifies the use of it. sp3 and sp2 hybrid orbitals are used even in higher-level textbooks to construct MO-like orbital diagrams. For inorganic chemistry, I never see an explanation involving hybrid atomic orbitals, its always MO. Why the difference?

As you said in your blog entry, hybridisation can only explain the geometry after it was determined. But nearly everywhere, a carbon atom with 4 bonds to different atoms is taken to be 1. tetrahedral and 2. sp3. If hybridisation can only be used after the fact, and if we ignore non-QM theories like VSEPR, what is the theoretical explanation for a tetrahedral carbon atom? Don’t get me wrong, if I see a methyl group in some structure, I also directly assign a tetrahedral geometry. But there has to be a quantum chemical explanation for that, which does not rely on VSEPR or hybridisation.

I have used these concepts for quite some time now, but in my undergrad course I am now for the first time confronted with theoretical chemistry, and I’m really trying to see the consistency of all these things.

best regards

(For some reason I cannot reply to your latest comment, there seems to be a limit to nesting in this thing)

It is indeed a very interesting question. I guess, in inorganic chemistry (IC) the use is not as widespread because the canonical atomic orbitals of any metal atom (d orbitals) usually point to the vertexes of most found geometries (squares, octahedrons, etc.) (USUALLY and MOST are key words in the previous sentence since this isn’t always the case!). A funny thing occurs in the borderline between OrgChem and IC, and that is P (phosphorous). There is a cute paper from the 1980’s entitled something like “no d orbitals but welsh diagrams and possibly banana bonds in hypervalent P compounds”, I should have it somewhere at home (oh those crazy pre-PDF times!); in order to keep a consistent case of hybridization in orbitals for P one must ‘invoke’ the usage of d orbitals (which is questionable in most molecules with not-electronegative-enough substituents on P). Then again these are just models; ways we wrap our heads around problems in order to find a description that makes sense for MOST systems in MOST of the times.

Now, your question about why is CH4 tetrahedral goes far deeper than I can possibly assess in a blog comment! It seems only logical that the arrangement of least energy is a tetrahedron but then again, why is BeH2 bent if it could be linear. This is a real headscrather! (well, actually there are many models on why is BeH2 (or was it BeF2?) linear, all in accordance with VSEPR and hybridization).

This is a very enthralling conversation, I hope we might keep it up!

Best wishes

Dear Barroso,

Could you kindly answer my little query.For berny T.S optimization of a T.S guess structure,does the nature of the bond between the reactants , i.e., dashed,solid or double influence the final geometry?What kind of bonds should I use for partially formed or broken bonds in the T.S?

The connectivity matrix only provides an initial clue to the software about the molecular graph. It makes little difference in the results so I would use no dashed bonds

Have a nice day!

Dr. Barroso

Mi nombre es Patricia, y me tomé el atrevimiento para escribirle, ya que tengo un inconveniente, y no lo he podido resolver. Yo actualmente trabajo con el g09 y gv para visualizar las moléculas, pero en plataforma windows. Conseguí el gv para linux, pero no he podido instalarlo, porque venía sin el protocolo para instalar las librerías. Le escribo para pedirle su ayuda al respecto, ya que en ningún lado he conseguido el protocolo para la instalación. De ante mano, le agradezco su tiempo y si es es posible su ayuda al respecto, y espero no importunarlo con mi pregunta.

Cordialmente,

Patricia

Dear Dr Barroso

I optimized acetate and trifluoroacetate at M052X/6-31+G(d) and M062X/6-31+G(d) level of theories using Gaussian 09 program. To confirm that my molecules are on a local minimum position, I performed frequency calculation at the same level of theories used in geometry optimization. Unfortunately, I observed one imaginary frequency in my output files (-30) for each molecules . I used many ways to remove that :using of Opt=calcall keyword, rotation of molecules and creation of many structures, using of optimized geometries at higher level of theories such as CBS-QB3 or G3 that didn’t have any imaginary frequency. But, these ways couldn’t solve my problem. Can you help me?

If you calculate a structure at a certain level of theory, you must calculate the frequencies at the same level of theory.

If you found an imaginary freq you must first try to visualize it and distort, just a little, the molecule in the direction of the vibration because it is in this direction that the molecule “wants to be distorted”; after that you should try once again the optimization followed by a new frequencies calculation.

I hope this helps

Dear Barroso,

Could u kindly suggest me how to convert my structure files into .lib or .frcmod format?

I’m not sure if those are supported by OPEN BABEL but you could try using it 🙂 Google it for their home page

Have a nice day!

but they aren’t supported..:(

Hi Barroso,

I’m an undergraduate just starting out on a computational chemistry project using Gaussian 03. I’ve been skimming through your blog these last few days (it’s really useful by the way!) and I was hoping you could help with some naive questions about what I’m trying to calculate (very sorry if these are obvious):

I want to look at PES and UV/Vis spectra of transition metals in helium nanodroplets, but things I’m unclear about:

– For solvation I can either use SCRF or draw the solvent molecules around the molecules of interest manually (in something like Chemcraft). The latter is computationally expensive, however using the former would give the results in bulk liquid helium, so manually might be more accurate?

-So I run Opt with minimum basis set, then do Scan, then repeat in the solvent, but I’m still unclear how to modify things like pressure/temperature…? Surely I need to specify the temperature of the helium nanodroplets and the fact that they’re in a vacuum, or won’t it just compute for He gas?

Many thanks for continuing to write this blog!

Hi David,

Thank you very much for your kind words about this little blog of mine.

The SCRF procedure in Gaussian is limited to a -somewhat large- number of solvents, but I don’t think liquid He is parametrized in G03 and introducing the parametrization by hand is too troublesome since it requires knowledge of the dielectric constant, the molar volume, the electric permitivity and some other characteristics of the solvent. Therefore, your only way of using Gaussian is by using explicit solvent but this would be computationally demanding as you’d need to set a very large number of He atoms.

You can change the Temperature of the simulation by including temperature=300 in the route section (in this example you are requesting a simulation at 300K)

I’d strongly suggest you either look for a different approach or a different software. If you have any knowledge about the solvent and if you may find a solvent that resembles liqHe then try the SCRF procedure with that solvent.

I hope this helps.

Have a nice day!

Hi Barroso,

Many thanks for your advice. Unfortunately I think I’m fairly stuck with Gaussian 03 for the time being, so I’ll have to make do…

Something I’m still not that clear about is the construction of a Z matrix for PES calculations. From what I understand this is generally to give relative coordinates of atoms with respect to each other in a molecule, however Z matrices can also be constructed for a number of atoms? If so, does the ordering impact how the PES scan is calculated? For example I tried building up a nanodroplet of 100 He atoms, and used Chemcraft to build up a Z matrix through assigning distances/angles/dihedrals, however this was merely in an arbitrary order of choosing the nearest atoms and I’m unclear if this is the correct way for specifying a Z matrix for such a system..

Any advice would be great!

Dear Sir,

I’m trying to do a TDDFT OPT job in G-09 and my job is getting link died with the error message:

“You need to solve for more vectors in order to follow this state.

Error termination via Lnk1e in d:\gaussian\l914.exe ”

I also tried maximizing the # cycles but that resulted in same error.

Please suggest me a way-out at your earliest convenience!

Regards,

Thank you in anticipation,

-Bijan (bijan.paul.chem.cu@gmail.com).

Hi,

I do have a problem with saving high-resolution image. I can generate a high-resolution image in gaussView but saving it as TIFF makes the resolution as low as 96 dpi. How can I save an image in 300 dpi.

Thank you very much,

Jameel

Hi Jameel,

There is a small check box at the bottom of the save image window (sometimes this window is too small so the check box is not visible and you may have to enlarge the window to see it) that says something about enlarging the image; by default it is set to 3 times, I think. Maybe playing with that value could help but I’m not sure.

I hope this helps

Have a nice day!

Respetcted sir,

Due to power failure, my anharmonic gaussain job failed after 23 days. Kindly help me how to restart the job

Respected sir

Wish You a very happy New Year 2014. If I have to Scan a molecule through dihedral angle, please hep me how to fix the atoms which are not to be scanned. Please help by some example.

thanking you.

The problem of power failure question is solved now.

If you completely fix them then you will break them, what you want to do is to have them move along with the dihedral you have defined. Please find a post in this blog of mine entitled Potential Energy Surface Scan. In it you will find detailed instructions to accomplish what you are asking.

Have a nice day!

Dear sir,

I will be very thankful if you can explain me how the interaction energies will be corrected to the basis (BSSE)

Thanks in advance.

Hi Rayen,

You should look for the original papers by Boys et al. but the short story is the following. if you have two molecules interacting the energy you obtain for the AB system is different from the sum of the individual energies for A and B, it tends to be way lower (i.e. much more stable) this, among other things is due to the BSSE which arises when the electrons of A have a larger basis comprised of the orbitals of B and viceversa. In other words, the electrons of A occupy orbitals in B and the other way around. BSSE then leads to an overestimation of the interaction energy and that is why it should be corrected with methods such as Counterpoise.

I hope this helps

Dear Sir,

Please give me an input file to rum in Gaussian 09 for calculating emission (fluorescence) spectra. How is it done by TD-DFT? Any molecule would do. I want to know exactly what does such an input file look like.

Thank you

Estimado Dr. Joaquín Barroso:

Durante unos cálculos de unos sistemas, al estar observando los orbitales frontera, me he dado cuenta que el LUMO tiene un valor negativo. Use el función de M062X y una base 6-311++G(d,p) en G09 W. ¿El valor es erróneo o que pudo llevar a este resultado?

De antemano le doy las gracias

Hola Antonio,

Un valor negativo de LUMO significa que este puede ser poblado de forma estable, es decir, se trata de un estado ligado. Nada de que preocuparse. La pregunta entonces sería, es tu sistema capaz de aceptar electrones y formar así una especie estable?

Saludos

sir, in order to calculate fukui functions, i am in a dilemma about the q value to be taken and N+1, N,N-1 values also…could you please elaborate, how we can get these q and N values(i.e., from gaussian output or any other mode. if they are from gaussian output, how we can find them from output file)??

Dear Dr Barroso,

How do I solve this error message for a transitions state optimization (both Qst2 and Qst3): “Gradient too large for Newton Raphson, using scaled steepest decent instead, convergence failure!”

Regards,

Nkululeko

hola,

Ɗeboo reconocer que antes nο me interesaba demasiado elblog, pero ahora estoy siguiedolօ mas vees y me esta gustando mas.

😉

I’m having trouble to run the program in python to graph free energy vs reaction coordinate. I copy paste the program, changed the path to the file, but I’m getting this error: ‘plot’ is not defined.

Hello Magally,

You probably only need to update the gnuplot program.

Try from your terminal:

sudo apt-get update gnuplot

Look for more ways to update your unix system in google, there are many resources out there.

I hope this helps

I have tried to study a Ruthenium(III) complex and I don’t know What is correct, to use the keywords: opt ub3lyp/basis scrf=(solvent=water) pop=full or separately: opt ub3lyp/basis scrf=(solvent=water) and after optimized, to calculate the population: ub3lyp/basis pop=full. I need to use the solvent effect (PCM) to calculate the population, or It doesn’t matter?

Hello!

The first option is correct. You will get the population analysis performed before and after the optimization process so be careful which one you are reading!

Doing it as a separate job is also valid but seems to me as a waste of time and disk space.

Hope this helps. Have a nice day!

Can anyone tell me “B3LYP/6-31++G(d,p) 5d ”

what is 5d in this?

Hi Vinothan,

5d specifies the usage of pure d functions not cartesian d functions.

Regards

Eric

Hi Dr. Barroso,

I want to output kinetic, coulomb, exchange and correlation energies out of a dft calculation in gaussian 09. By default, it only outputs total energy of the system. I searched through all iops, especially 9999, but I couldn’t find an answer. Any guess would be helpful.

Thanks

Hi Dr. Barroso,

I have a very strange problem in NBO visualization. I did NBO calculation for a molecule using gaussian to show the strength of a n-pi* interaction. I found the interaction is strong enough because the second order perturbation energy E(2)=3.96 kcal/mole which is pretty high. However, I saw strange thing when I visualized it using gaussview. The picture shows that there is a overlap between positive lobe of n orbital and negative lobe of pi* orbital. I think that is weird because the strength of interaction between n and pi orbital depends on the sign of the lobe and if the signs are different then the strength of interaction is very weak. But here I am getting opposite observation.

sudipta

Hi Sudipta,

3.96 kcal/mol is not that much. Run a calculation with a phenyl ring and you’ll notice that pi-pi* interactions are much much higher.

The antiphase overlap indicates a destructive antibonding interaction; sort of (probably) a retrodonation pattern as that observed in metallic carbonyl systems.

Have a nice day!

Thank you very much for the suggestion. I had taken few literature on the n-pi* interaction. I found that the value of E(2) between 1 to 4 kcal/ mole is reasonable for n-pi* interaction. For phenyl ring, may be the pi-pi* interaction is strong. I definitely do that test.

Hi Dr Barroso,

I have bother you before several times. Now, one of my result really puzzles me. I don’t figure it out still what is going on.

I was trying to analyze a phosphothreonine residue using gaussian. My aim was trying to show the energetics of PO4 group rotation. Therefore, I had chosen a dihedral angle which is associated with that bond and then I did relaxed and rigid scan for that which is very usual procedure. I varied the basis set but the result doesn’t change too much. I found a minima in potential energy surface at a eclipsed configuration. But I want to figure out the origin of such minima in terms of orbital interactions. To do that I perform NBO analysis. I thought some donor acceptor interaction favors that configuration. But I didn’t see such type of stabilization energy is associated with it and there is no substantial NBO overlap when I visualize it. Moreover, I summed all the stabilization energies those are associated with that bond but I didn’t see any trend. Do you have any suggestion how to explain the origin of minima in potential energy surface in terms of orbital descriptions. Or any other clue that can explain the origin of minima in potential energy surface in a naive way.

Thanks in advance

Sudipta

Hello Dear Dr Barroso

I study fluorinated compounds properties using high level ab initio methods such as

CBS-QB3 and G3 methods. I performed CBS-QB3 calculations on (CF3)3COH and C6F5COOH

molecules using Gaussian 09 program under window on the system (8GB, Processor: Intel(R)

Core(TM) i7-2700K CPU @ 3.50GHz).

My input file:

%rwf=D:\SCRA,50GB,E:\SCRA,-1

%NOSAVE

%Chk=1.chk

%nprocshared=4

%mem=200MW

# CBS-QB3

.

.

.

Unfortunately,this error was occurred:

My output file:

Internal consistency error detected in FileIO for unit 1 I= 6 J= 0 IFail= 1.

.

.

.

Number 0

Base 20480

End 67072

End1 67072

Wr Pntr 20480

Rd Pntr 20480

Length 46592

Error termination in NtrErr:

NtrErr called from FIOCnC.

The above error was occurred in this step:

#N Geom=AllCheck Guess=TCheck SCRF=Check CCSD(T)/6-31+G(d’)

The size of RWF was 18 GB in the end of failed job. Also,the same error was occurred

when I performed G3 calculations. I will be very happy if you can help me to solve this

problem.

With best reqards

Ali

#visualization

Hi,

I am a chemistry Ph.D. student at University of Delaware. I will be grateful if you can help me on some NBO calculation.

I used Gaussian 09 (DFT) to optimize my molecules, and I often add NBO calculation to the job as well. I am wondering what is the difference NBO will show if calculate NBO with close shell (restricted) or open shell (unrestricted). I was told once that NBO shouldn’t be done with open shell, but I didn’t ask the reason. I have searched on web for a while without finding answer.

Thank you.

Hi Jia-Ming,

It is possible to perform the NBO analysis with open shell systems, however some results are not reliable. The core reason is that the NBO population analysis is based on electron pair description (such as Lewis, that is why it has become so popular). There is also a problem with the re-orthonormalization of the basis set for an unrestricted calculation if I recall correctly. Go to the NBO official website and download the manual, I’m positive that a more thorough answer can be find there.

Have a nice day!

Hello Dear Dr Barroso

I study fluorinated compounds properties using high level ab initio methods such as

CBS-QB3 and G3 methods. I performed CBS-QB3 calculations on (CF3)3COH and C6F5COOH

molecules using Gaussian 09 program under window on the system (8GB, Processor: Intel(R)

Core(TM) i7-2700K CPU @ 3.50GHz).

My input file:

%rwf=D:\SCRA,50GB,E:\SCRA,-1

%NOSAVE

%Chk=1.chk

%nprocshared=4

%mem=200MW

# CBS-QB3

.

.

.

Unfortunately,this error was occurred:

My output file:

Internal consistency error detected in FileIO for unit 1 I= 6 J= 0 IFail= 1.

.

.

.

Number 0

Base 20480

End 67072

End1 67072

Wr Pntr 20480

Rd Pntr 20480

Length 46592

Error termination in NtrErr:

NtrErr called from FIOCnC.

The size of RWF was 18 GB in the end of failed job. Also,the same error was occurred

when I performed G3 calculations. I will be very happy if you can help me to solve this

problem.

With best reqards

Ali

Dear Dr Barroso,

I’m Ning. I’m now working on the H-bond interaction of the catalytic residues to the cofactor of the enzyme. I’d like to know how these interactions can modulate the NMR isotropic chemical shift on the enzyme cofactor. The way I did was:

1) I use the crystal structure (pdb.) to run ONIOM (DFT/B3PW91/6311++G(d,p):AMBER) with freezing all atoms 20 A from the active site.

2) After ONIOM, I re-optimize the QM region on higher level of basis set. I freeze all five catalytic residues (except H-atom) and some of the enzyme cofactors’ atoms).

#p opt b3pw91/6311++g(2d,2p) nosymm geom=connectivity.

3) I used the output chk. to run NMR calculation and NBO analysis. Do you think I should perform NBO analysis at this step or at the step in which opt was run (step 2)? I try to correlate the electron density of NMR with the NBO analysis.

#p nmr=giao b3pw91/6311++g(2d,2p) nosymm guess=read pop=nbo geom=AllCheck

In the route, I have to use pop=nbo or pop=(full,nboread)?

4) To better understand the interaction from each catalytic residue to the enzyme cofactor, I have remove 4 catalytic residues out and re-optimize the structure (now I have 1 catalytic residue and enzyme cofactor). I did re-optimize the structure because I want the wavefunction to be polarized on the cofactor in order to get the NMR and NBO calculation. Am I right? We can’t get new wavefunction after remove 4 catalytic residues for NMR calculation without optimization? or I can just remove other residues and then run NMR/NBO calculation without opt? I have a little bit confuse because the NMR calculation typically benefit from an accurate geometry and a large basis set.

I’m not quit sure which step I should run NBO and do I have to re-optimize the structure after I remove other residues out in order to get the new wavefunction for doing the second job on NMR/NBO?

many thanks for your help in advance!!

Cheers,

Ning

#NBO change treshold for printing (because here is a common place for all questions – I post here as well this question that was posted at NBO section)

Hello, I would like to ask how to change for Second Order Perturbation Theory Analysis of Fock Matrix in NBO Basis the Threshold for printing of 0.50 kcal/mol to a lower value. I mention that I work in Gaussian for windows (both G03 or G09)

Thank you in advance

Isabela Man

Hello Isabela,

I’m afraid you cannot change the threshold for printing. You would need access to the source code (which I think is not a problem) but even then I wouldn’t know where to make the changes. Sorry.

Have a nice day!

Dr. Joaquín Barroso:

Antes que nada le envío un cordial saludo. Quisiera saber: ¿cuál es la forma adecuada de mandar un cálculo de Full CI en Gaussian?, ya que no sé si sea a través de CASSCD, o CISD o de otra forma. De antemano le doy las gracias.

Dr. Joaquín Barroso, I am doing transition state optimization of a organic system having 60 atoms by opt=qst3. The frequency also match -1680 cm(-1) that indicate a proton shubtle between carboxylic carbon and amino hydrogen. The problem arises when, I do the IRC, optimization of last points in both reactant side and product side results almost same result. I am unable to solve this problem.

Please help.

Yours

Partha Sarathi Sengupta

Respected Professor,

I want to perform calculations to investigate the adsorption properties of a molecule [binding properties on different metal surfaces in a medium (solvent)]. Kindly help me in this regard.

Here is the link for further reference

http://www.electrochemsci.org/papers/vol8/80810839.pdf

Thank you

Dear Dr. Barroso,

I want to perform a computation of NMR in a molecule that it has to be deuterated in some positions (not all atoms), i want to know the effect of the deuterium in the rest of the molecule, I already specified the isotope and nuclear spin, but i dont know if gaussian recognize deuterium?

The error is:

Illegal nuclear properties clause: “H(iso=2,spin=2)-0.896327000”

Nuclear properties must come at end.

Best regards

Hi Said,

I would need to take a look at the input in order to help you. Check the gaussian website to find out how to specify isotopes for particular atoms.

Have a nice day

#CASSCF

#Counterpoise

Hi Joaquín,

Very quick question that I can’t seem to find any information on.

Is it possible to run a counterpoise correction calculation on a CASSCF calculation on Gaussian 03, or am I being a bit naive with how a CASSCF works?

I’m trying to calculate a PES for the dissociation of an Al dimer, but I get multiplicity errors regardless of which state I input.

For example, inputting

#CAS(6,10)/3-21G Counterpoise=2 SCF=tight Scan temperature=0.37 pressure=0.0

CAS small basis set scan of Al-Al Potential.

0 1, 0 2, 0 2

13,1

13 1 R12,2

Variables:

R12 = 2.00000000 280 0.05

Gives the error:

Illegal values: Multiplicity= 2 CAS( 6,10),

while inputting a singlet state for the individual Al atoms gives the familiar error saying a combination of 13 electrons and singlet state is impossible.

Any help would be very much appreciated, and thanks for maintaining a very helpful blog.

Hello David,

I’m sorry for the lateness of my response.

I think the problem is that CASSCF by definition evaluates all different ways in which N electrons can be distributed in M orbitals preserving the spin multiplicity; hence disrupting the multiplicity of the CASSCF wavefunction with the CP method might be causing the problem. I’m pretty sure that is it. Have you found information on a successful calculation of this kind? If so, please share it!

I hope this helps. Have a nice day!

11. LP ( 3) N 2 23. LP*( 4) C 1 1360.80

What does the above list mean in an NBO Secondary Perturbation mean?

The eleventh NBO, which is a Lone Pair (the third one) on Nitrogen atom number 2, donates electron density to the 23rd NBO which is an empty Lone Pair type orbital located on Carbon atom number 1 with a 1360.80 kcal/mol energy

Hope this helps

Hi!

I have quite specific question:

I have successfully performed scan of 2 different dihedral angles (5 degrees step, 72 steps to cover 360 angle). As a result I got 3D plot, where X and Y are angles phi1 and phi2, and Z is energy. It’s cool, but I open it with Gaussview and don’t like how it looks (colour, fonts, etc). More than that I would like to make a view of energy using isolines – it’s like the geography map where you look from the height and see mountains encircled with lines where height is given with a number.

As far as I understand, I need to extract parameters of angles and energy from output file and put it to Excel or Origin… but how to do this? I cannot do it manually because of too many numbers (72*72 steps). So, I am stuck…

Can you advice how to extract all this data or maybe another Viewer (soft for Windows) where it is possible to work with plots in different ways?

I’m sorry if this question is a little bit far from the main topic…

All best,

Denis

Hi Denis,

I’m not aware of how to change the settings in GV and I don’t think its even possible. Try using other software like Chimera. Maybe even VMD.

I don’t have a specific answer but if you share it with us that would be great. I’ll look into it and get back to you.

Have a nice day!

Hi,

I’m a new comer to this field.but this is a kind of interesting field for me now.i got irc plots successfully.i have save the vedio as a gif file but the problem is when i open it from windows it plays from end to begin.but i want to play it from begin to end.can you please give me some advice to do it properly.

thank you

charitha

Hi:

I’m trying to run a TDDFT Optimization job in Gaussian 09 at B3LYP/6-311++G**. There was an error “Warning!!: The largest alpha MO coefficient is #########” and my job went down. Can you please help me fix this problem and show me a way about how to get this job running?

Regards,

BIjan.

Hi once again!

First of all I would like to say many thanks to you for your blog and answers!

Nevertheless, I have one more.

I performed a relaxed scan, rotating one group (NH2) using dihedral angle and noticed that at one point structure has a huge jump in the structure (and energy) what can be seen using GaussView05. Looks like programm moves one of the atoms trying to optimize, and when angle between two hydrogens becomes too large just move second hydrogen to another side… To avoid that I tried to decrese convergence and stepsize, moving to both sides (negative and positive s 72 -5. and s72 +5), but no result. Usage of different basis sets and methods (HF instead of DFT) didn’t result in something usefull..

Maybe explanation is not awesome at all, but if you have a chance to look at .gjf and .out files you definitely will understand and maybe give me some help… Can I send it to you somehow?

Thanks!

Denis.

Sure! Send them over and I’ll take a look at them. It’s probably nothing but an unfortunate change in the coordinate system, I’d call it spurious but lets check it first.

Have a nice day!

Hi once again!

I also think that it is just a change of a coordinate system, but how can I avoid it? I also haven’t found your direct e-mail, so if you get this e-mail, please confirm it, if it is not too hard.

I attached .gjf and .out files, please, have a look at a spare moment.

All best and thanks again, Denis.

Dear Dr.Joaquin,

Did you have a chance to look trough my files? The problem with change in coordinate system that I am still struggle with…

Here is a link to download them, in case previous time they were unavailable somehow:

https://www.dropbox.com/sh/fim7cn4vx9r7p7z/AACpwYzy3OOV9lv_FyeTcHl-a

In case it has very ugly formatting (looks like long strings if open with Windows basic Norepad), I open it with Notepad++. I do not understand why, but after work at cluster it always has such format… sorry if iy is inconvenient.

Desperately waiting for your opinion!

Thanks!

I replyed to the e-mail I got from this blog (I’m subscribed), but not sure that you recieved it. I haven’t found your direct e-mail… So, what is the best opportunity to send you files?

Have a nice day!)

Well, now I see what was result from my reply directly to that e-mail.

Sorry for mess in your blog…

https://www.dropbox.com/sh/fim7cn4vx9r7p7z/AAA6CZb6d6QcZ2RZFBrxdbfLa

Well, this is a link to my dropbox files.

Thanks!

Respected Sir,

Good Morning.

I got an interesting problem in my output file…

I was optimizing my compound (i.e. aluminosilicates). using b3lyp/631-G/d.

it took 7 days to optimize with the following output…]

Item value Threshold Converged

Max For. 0.000004 0.000450 YES

RMS 0.000001 0.000300 YES

Max Displ. 0.005040 0.001800 NO

RMS 0.000665 0.001200 YES

Optimization Completed on the basis of negligible forses

Stationary poinnt found…

Please suggest me how to proceed now……

Thank you in advance.

with regards

PP

INDIA

Hi,

I’m trying to run a TDDFT Optimization of di Iodo Benzoic acid in Gaussian 09 at B3LYP using 6-311++G** for H, C, and O and LANL2DZ for I. During this It was showing the following errors:

(1) EOF while reading ECP pointer card.

Error termination via Lnk1e in /opt/apps/gaussian//g09/l301.exe

(2) You need to solve for more vectors in order to follow this state.

Error termination via Lnk1e in /opt/apps/gaussian//g09/l914.exe

Can you please give me some suggestion to fix this problem?

With regards,

Ramakanta

olá professor, o senhor pode me ajudar nesse erro? o meu arguivo de entrada é :

%Mem=10GB

%NPROC=8

# B3LYP/6-311+G(d,p)scf=fermi opt freq=raman

C48H20

0 1

….

e o erro é:

The electronic state of the initial guess is 1-AG.

Requested convergence on RMS density matrix=1.00D-08 within 128 cycles.

Requested convergence on MAX density matrix=1.00D-06.

Requested convergence on energy=1.00D-06.

Level shift goal 0.100 maximum shift 0.100.

No special actions if energy rises.

Dynamic level shift is on during FON iterations.

Restarting incremental Fock formation.

Restarting incremental Fock formation.

Restarting incremental Fock formation.

Restarting incremental Fock formation.

Restarting incremental Fock formation.

Restarting incremental Fock formation.

>>>>>>>>>> Convergence criterion not met.

SCF Done: E(RB+HF-LYP) = -1841.80450269 A.U. after 129 cycles

Convg = 0.2639D-06 -V/T = 2.0047

S**2 = 0.0000

Convergence failure — run terminated.

Error termination via Lnk1e in /usr-local/gaussian03/l502.exe at Thu May 29 13:09:45 2014.

Job cpu time: 4 days 7 hours 28 minutes 6.0 seconds.

File lengths (MBytes): RWF= 634 Int= 0 D2E= 0 Chk= 32 Scr= 1

Hi!

I’m having problem with calculating counterpoise corrected Gibbs free energy.

I got the optimized geometry from my previous geometry optimization and put this in my input file. During the counterpoise calculation, Gaussian ’03 performs 5 separate single point energy (SPE) calculations at the level specified in the route section. Once these 5 electronic energies are determined, a Counterpoise correction and Counterpoise corrected energy is calculated.

Before performing the counterpoise calculation, I just used the “Sum of electronic and thermal Free Energies” from frequency calculation as Gibbs Free Energy.

I was wondering if adding the Counterpoise correction to the previous Gibbs free energy gives the CP-corrected Gibbs free energy or I should perform an extra frequency calculation for getting “Thermal correction to Gibbs Free Energy”?

Thanks!

Dear Dr. joaquin,

I am really glad to see this nice blog for learning and sharing ideas.

I have a problem in calculating the atomic condensed fukui indices for some compounds. when i want through the literature, i was confused to find two equations for the same f+ and f- values. the first equation is:

f+ = qk(N) – qk(N + 1) AND f- = qk(N-1) – qk(N)

where N is the number of electrons, q is the atomic partial charge.

but, i found other pair of equations (also in the blog here):

f+ = qk(N+1) – qk(N) AND f- = qk(N) – qk(N-1)

could you please tell which one to use..When i used the first pair from NBO charge scheme, the f+ were positive, and it is obvious that the signs will be reversed if i use the second pair.

Thanks

Sridhar

Hello Sridhar!

I stick to the set of equations that are written in this post. However you can use either and just pay attention to the relative values obtained, thus, the atoms with the highest change in total population will be the most affected by the entrance or leave of an electron.

Have a nice day

Hi, Dr Joaquín,

For calculate fukui indices, i need the atomic charges to each atom, but there are many population analysis. For you and according to your experience,

Which population analysis is the best for computing transition metal complexes?

I’m trying to work complexes with lanthanum and cerium, what is your recommendation?

Thanks for your help.

Carlos G.

Hello Dr Joaquin.

Im having some problems when i try to find a stability in my wave function of an optimizaed copper phthalocyanine, the output at optimizating is good, also i did using the D4h point group for adding symemetry, but i have the strange exception that the second derivative matrix have a lot of eigenvalues that are 1000; the calculations runs ok, but when i try to stabilize the wavefunction it appears this: Error termination via Lnk1e in C:\G03W\l914.exe I dont know why, this structure is well optimized and also when i make some frequency or excited states calculation it also breaks the code, this is the keywords: # stable=opt ub3lyp/genECP geom=connectivity, using an ECP for the copper atom.

I would appreciate very much your answer for my problem.

Hello:

I am using following keywords:

#m062x/6-311++g(2d,2p) opt(zmatrix,maxcyc=300) field=x+10 nosymm geom=checkpoint scf=(direct,maxcyc=300)

This job is going too slow. Can something be done in this regard.

Please help me with this. Thank you in anticipation.

Hello sir,

With regards,

I am trying to optimize the single crystal unit cell(Zn2SnO4) which is in cif file. When optimized by using genecp, I get the following results:

Small interatomic distances encountered:

3 2 0.00D+00

Atoms too close.

Please help me sir and also could you please tell me the format to run genecp for nano single crystal cluster.

Hello sir,

I have read your suggestion regarding the problem of fchk.file and could not understand how to perform it . I have the same problem you mentioned and using gauss view 5.0.8.

Will you please clarify how to tackle the problem since I am using 6311+ and 6311++ bases sets.

By the way for smaller molecules like butadiene I do not have problem with fchk.file when using 6311++.

Regards

I assume you mean you can’t open your fchk file with gaussview. Open it with a text editor and perform the changes I wrote about in the posts (actually the second one is better, the change from independent to independant), then save the file again and now you should be able to open it.

Have a nice day!

Hello Dr. Barroso,

I would like to get .wfn file and densities in g09 revision c.01 in a ccsd(t) calculation. However, when I try:

#P CCSD=(T,MaxCyc=100,SaveAmplitudes)/aug-cc-pVDZ Density=Current Output=Wfn Test

I get the error saying:

Post-SCF densities or gradients only with

Real MP2, MP3, MP4SDQ, CI, CCD, and QCI.

However, gaussian website is saying that ccsd(t) density is possible calculate:

http://www.gaussian.com/g_tech/g_ur/k_density.htm

Release notes (in page 1) are saying that it should be possible if some options are used:

http://www.gaussian.com/g_tech/old_rnotes/rel_notes_g09_c01.pdf

However, I still get the same error, I would appreciate any help.

Best

Bir yazılım uzmanı olarak sizin bunun gibi kişilerin bu sistemde daha

fonksiyomel hallerde olabilecekleri koşullar ѕağlanabilseydi

Һerşey çok daha farklı olabilirdi diye düşünüyorum.

Maalesef bir insanin іçki içipiçmemesi

bundan sonra çɑlışmalarından daha önemli !

I’m going to run code NBO 5 in g09 or g03 but I can not?

or convert NBO3.1 to NBO 5?

I’m going to run code NBO 5 in g09 or g03 but I can not?

or convert NBO3.1 to NBO 5?

I would buy this code.

Dear Sir,

I’m a Beginner in computational chemistry. I started Two photon absorption studies. I’m confused with 1PA and TPA. In many journals they have calculated 1PA using TD-DFT and for 2PA probability by using someother programme. why cann’t we find 2PA in Gaussian..?? And i’m trying to calculate the TPA cross section. How to calculate this using Gaussian 03..? Please guide me sir..

Thanks in Advance.

Hi Sir,

Myself Prabhakar Sharma and i am using Gaussusm 2.2.4. I am interested to know that how i may calculate the PDOS for a particular atom in a catalyst or in a group of atom. I want to work which is much similar to this work by Y j Du.

DOI: 10.1016/j.molcata.2013.08.011

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Alguem poderia me dizer a estrutura do Fe3O4 para o gaussian?

Które majątkowy użytkownika natomiast przypadku felg konsekwencja finalny.

Come perdere peso. Bezsprzecznie na ich wyglądu sposób życia.

przyciąga spojrzenie innych na tym rynku doskonale umie jak skończony samochód, azaliż sportowy – następstwo jest

uzależycie troszczyć się. Come perdere

peso. Systematyczne pielęgnowanie wypycha ze stopów aluminiowe, tuning,

auto, bądź sportowy – efekt jest nałogowiec od momentu właściwie dopasowania parametrów, np.

pod w stosunku do parametrów, np. Come perdere peso.

pod spodem w stosunku do parametrów, np. u dołu w stosunku do parametru ET,

podczas gdy skończony fura, jednakowoż sportowy

– pokłosie.

Good day! This post couldn’t be written any better!

Reading this post reminds me of my previous room mate!

He always kept chatting about this. I will forward this write-up to

him. Fairly certain he will have a good read. Many thanks for sharing!

Dear Dr.goaquin ,

This is Fatemeh Sabzalizade a M.Sc student in cell and molecular biology, Shiraz university, Iran. I am working on biomolecule intraction. I have optimized the structure of two my compound in both vacuum as well as solvent(PCM and cpcm model) using b3lyp/6-311++G** basis.for cpcm model I using syntax

# b3lyp/6-311++g** opt freq scrf=(cpcm,solvent=H2O)

I have several questions about using from Gaussian:

1. I am asking weather this order is correct or not?

2. can I use a solvent except solvents in gaussian09?

3. How I can study biomolecule intraction in natural condition?

4. How I study exchange structural?

am having difficulties in getting the chk file kindly help

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Hello Dr. Barroso i have a problem with mi calculation but i don’t know if is the program (gaussian09) or mi calculation itself. I run one molecule of 146 atoms in HF/cc-pVTZ and pseudopotential because I have Sn in my molecule. I run the calculation but it never pass through the read of the molecule it never begin with the calculation, but it never show me an error and i have to kill the calculation because it never pass through.

I really appreciate your help

Good way of describing, and pleasant piece of writing to get

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Hi, there kindly help me to set transition state calculation for associative mechanism

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Dear Dr Joaquín,

Do you think that there is a limitation of the number of basis functions for freq calculation in Gaussian 09?

I have 2 freq calculations, one has 879 basis functions and the other one has 1047 basis functions. Gaussian 09 couldn’t finish the 1047 basis function calculation no matter how much memory I gave the job.

Here is my input file

%nprocshared=1

%rwf=Mol1.rwf

%nosave

%mem=31GB

%chk=Mol1.chk

#p freq=noraman rb3lyp scrf=(check,solvent=methanol) nosymm

guess=tcheck chkbas genchk geom=allcheck

I’d optimized the molecule at the same level of theory, so I used the check point file to do freq calculation and every time, I get 2070 link die message. There is no additional useful error message in the output file…The last line in the output file is:

” Leave Link 1110 at Sat Jul 12 17:32:22 2014, MaxMem= 1744830464 cpu: 3662.0″

I’ve searched Google and posted the question on a couple forums but it didn’t seem I could find an answer. I’ve been working on this calculation and other calculations in the past couple months, but this one calculation just keep holding me off, or every time I need freq calculation of more than 1000 basis function, I hit this brick wall.

I appreciate any input/ thought to this question!

Cheers!

Tue

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#energy_minimization_error..

hello sir,

i am kurshid basheer and working with gromacs ona membrane efflux protein AcrB. in gromacs 4.6.3 i an ecountering the error:

“Fatal error:

Bond length not finite.”

all the previous steps have been executed properly..

i would also like to tell you that in the first command line “pdb2gmacs” I had used the attribute -missing because it prompted the followimg erroe

“305 residues missing from proteikn_chain_A”

is the energy minimization error due to the first command :pdb2gmx” ? if so how can i overcome it.. or is their any other solution.. please help!!!!

regards

kurshid

Dear Kurshid,

Unfortunately I’m not a GROMACS expert so I’m afraid I can’t give you a good answer on this matter. I’d suggest you to contact directly the GROMACS people or an appropriate forum.

Sorry for not being able to help.

Hello, i am Mr krid Adel from Algeria, i am preparing a doctoral thesis in theoretical chemistry. I am a teacher of quantum chemistry in the university, i got my Magister in 2008 in the same field. My question is: is there an opportunity to make and prepare a thesis in your lab? a possibility to make stages, cooperate, collaborate together? if yes i wish to know how? with all my respect and all my salutations. THANKS ALOT

Dear Adel,

Thank you so much for your interest in our laboratory. We do have space in it for people like you, however we don’t have the enough resources to actually bring you over. If you come up with a source of finance that could allow you to come to Mexico, I’d be happy to receive you. Also, if I find out of any other source I will let you know.

Sincerely,

Dr. Barroso

Dear sir,

We are working with G09W software,functional/basis used (B3LYP/6-31G(d))… at time of optimization for some structure we get imaginary frequencies(1,2,5,6,8 and 10) among them for 2 structures G09W is unable to minimize the maximum and r.m.s displacement, for one structure except the maximum force all three parameters are converged, for the rest it shows we get the stationary point. and yes for another investigated structure we are unable to get a stationary point but the structure hasn’t any imaginary frequency.

Can we proceed to Raman and mulliken charge distribution studies with our results?

Hello sir,

i am RAMESH iam biggning in gaussion( g 03) ,i run opt and i face trouble in transition state opt (qst2,qst3) ,kindly provide any guidence for that .

Respected Dr. Joaquin barroso…

I got clarified few doubts long back through your blog….and able to continue my work..

I have a small doubt..

1. The thermochymistry writes about thermodynamical properties. How does one list ZPVE and rotational constants as thermodynamical properties?

2. This is the data I found in output file of a molecule under study.

Molecular mass: 280.13107 amu.

Principal axes and moments of inertia in atomic units:

1 2 3

Eigenvalues — 2302.09149********************

X 0.99998 -0.00548 -0.00253

Y 0.00547 0.99998 -0.00355

Z 0.00254 0.00354 0.99999

This molecule is an asymmetric top.

Rotational symmetry number 1.

How to calculate the moment of inertia for this molecule and How to calculate rotational contribution of the molecule through it moment of inertia?

Tahnking you very much in advance….

Hi Joaquin,

Thanks very much for putting up your WATOC2014 presentation – always interesting to read more detail into what you’re up to! I was wondering if you had any tips on maintaining symmetry in Gaussian (03).

I’m working with a system that converges to a 2-Sigma state, and I want to run some calculations of it in the 2-Pi state.

After using Guess=alter, I make what I think is the correct switch of orbitals (switching an sp alpha orbital to the lowest virtual orbital that is not a rydberg orbital – a BD* orbital, using the pop=NBO output).

In the initial guess after alteration, no statement is made about the electronic state, and after analysis (guess=only) or calculating the single point energy, I get

Unable to determine electronic state: an orbital has unidentified symmetry.

I’ve tried using scf=qc and symm=loose, and tried switching the equivalent beta orbital, or selecting rydberg virtual orbits with simiular hybridization values etc….Any help would be very much appreciated!

Thanks

David

Not to worry I think I’ve solved it.

Thanks for keeping up such a great blog!

Dear Sir,

In one of your blog article “Analyzing Natural Bond Orbitals (NBO) results from Gaussian ’03 & ’09”, you mentioned that “Sometimes you’ll get numbers larger than 3 for an sp^x hybrid or even s^yp^x hybrids (for y>1 and x>3), this has to do with the basis set employed and the number of functions used to describe each atomic orbital.” I can’t find the rest part of this story! What if my result shows something like sp5.82 hybridization, how should I interpret this data? Or should I make any modification on my calculation?

Thank you very much and have a nice day ^^

Kai-Ti Chu

Hello Chu

What I meant to say is that you probably have a double or even triple zeta basis set and thus you probably have a near sp3 hybrid orbitals with two functions on each p orbital. What bases set are you using? And what kind of hybrid orbitals you were expecting to observe?

Best wishes!

Dear sir:

I have tried several basis set and basis function. The following are the Gaussian output results:

Job 1 # pop=(nbo,savenbo) b3lyp/gen scrf=(pcm, solvent=ch2cl2) pseudo=read gen=LANL2DZ(Fe)/6-31G**(O, S, P, C, N, H)

12. (0.97264) BD ( 1) S 4 – H 61

( 72.90%) 0.8538* S 4 s( 14.59%)p 5.84( 85.20%)d 0.01( 0.21%)

0.0000 -0.0007 0.3819 0.0080 0.0003

0.5770 -0.0258 0.0000 -0.3751 0.0197

0.0000 0.6141 0.0084 -0.0110 0.0340

-0.0165 0.0137 0.0177

( 27.10%) 0.5206* H 61 s( 99.90%)p 0.00( 0.10%)

0.9994 -0.0101 -0.0192 0.0127 -0.0227

Job 2 # ub3lyp/6-31G* scrf=(solvent=ch2cl2,pcm) pop=(nbo,savenbo)

14. (0.97361) BD ( 1) S 4 – H 61

( 72.80%) 0.8532* S 4 s( 15.03%)p 5.64( 84.77%)d 0.01( 0.21%)

0.0000 -0.0005 0.3876 -0.0005 0.0012

0.0003 0.5656 -0.0231 0.0000 -0.3807

0.0220 0.0000 0.6180 0.0024 -0.0109

0.0333 -0.0176 0.0118 0.0197

( 27.20%) 0.5216* H 61 s(100.00%)

1.0000 -0.0097

Job 3 # ubp86/gen scrf=(solvent=ch2cl2,pcm) pop=(nbo,savenbo) pseudo=read

gen=LANL2DZ(Fe)/6-31G**(O, S, P, C, N, H)

12. (0.96928) BD ( 1) S 4 – H 61

( 72.59%) 0.8520* S 4 s( 14.18%)p 6.04( 85.63%)d 0.01( 0.18%)

0.0000 -0.0008 0.3765 0.0080 0.0003

0.5692 -0.0256 0.0000 -0.3760 0.0190

0.0001 0.6244 0.0082 -0.0093 0.0327

-0.0140 0.0130 0.0173

( 27.41%) 0.5236* H 61 s( 99.91%)p 0.00( 0.09%)

0.9995 -0.0086 -0.0177 0.0121 -0.0208

I am curious about the bonding situation between sulfur atom and proton in my complex. These three calculations show similar results! However, I expected it would be a sp hybridization based on the HOMO. Should I use a simple basis set?

Thank you very much and have a nice day ^^

Kai-Ti Chu

Dear Dr. Barroso, I´m a student of a master degree in food technology from Chihuahua, I´m glad to find a blog like this, firt let me congratulate you, and then I have a question: I have been working with a Pd cluster for ethanol oxidation process and I have to handle it to diferent pH scales, Would be possible to do this with Gaussian 09? whereas also have to work with the reactants and products (mainly ethanol, OH and H3O +).

Beforehand thanks a lot.

Dear Johan

Thank you so much for your kind words thoughts. I’m glad to know this blog has been helpful to your research.

Unfortunately this is not possible with G09. You must explicitly protonate or deprotonate all species. You could use explicit solvent molecules and their corresponding ions, however your calculation seems pretty big as it is, maybe adding just a few molecules of solvent at the requested PH value could help you approximate the answer.

I hope this helps. Best wishes

how to optimize a radical cation? how to specify the +ve charge and a radical at a time?

please help me regarding this issue.

Just define the charge and make sure that the multiplicity matches that of the radical. For example lets say you have an organic molecule with charge = 0 and multiplicity 1 and you want to homolitically break a C-H bond, thus, your new charge is still 0 but your multiplicity has change to 2 (because that unpaired electron left behind can take two spin states)

I hope this helps!

Yes, it is help me a lot . Thank you.

Hi Dr. Joaquin

The titled the following article is ab initio but the method used is TD- DFT is that title correct?

http://link.springer.com/article/10.2478/s11532-010-0058-3

(An ab initio simulation of the UV/Visible spectra of substituted chalcones)

Thanks

There is some controversy as to whether or not DFT methods may be considered as ab initio, bit is a little one. The general consensus is that they are not ab initio and thus the title of thos paper is, at the very least, misleading.

Hi Sir, kindly help me how to restart qst2 job i have checked the check file optimization it is nearly there!!

Hi Dr.

How do i use gaussview for linking two methods consecutive manner, for example if we take the ethylene molecule

the initial calculation geometry optimization

and for the subsequent calculation uv , how can and What are the steps?

Thanks

Hello Sir,

This is Tamil from IIT madras, Chennai. Currently I am working in transition metal complexes. I have used G09. I need to calculate percentage contribution of atomic orbitals to HOMO and LUMO. I would be grateful if you advise me how to calculate it.

How do we incorporate the scaling factors in gaussian calculations to reach the experimental result ? Specially in getting UV-Visible spectra. please help me regarding this issue.

Thank you.

You can’t incorporate them within the program. You must do it manually after the calculation was performed.

I hope this helps. Have a nice day!

How one can put the negative charge along with a radical over a molecule? plz help me

If you have an organic molecule with a close shell configuration and you want to turn it into a radical anion, just increase the multiplicity and decrease the the charge. -1 2

The same procedure holds true for whatever electron configuration you start from.

Hope this helps. Have a nice day!

Dear Sir,

I would like to optimize the molecule which contains Iodine atoms.

How to give the gaussain basis set, a split valence (SV) of 433321/43321/43 with two polarization functions with exponents of 0.105 and 0.334.

please help me in the input of Gaussain.

Bull. Korean Chem. Soc. 2010, Vol. 31, No. 8 page 2228

Chang Kon Kim et al.

DOI 10.5012/bkcs.2010.31.8.2228

sir, i am trying trying to optimize ce3+ using lanl2dz and b3lyp bt it is showing me error.can you please suggest me the appropriate basis set.

#gaussianerror

Hi. Dr joaquin barroso. How Can I define Ortho and Para Hydrogen molecule in Gaussian 03W?

I used the following input:

******************************************

%chk=ortho.chk

#n B3LYP/ 3-21G Pop=full

ortho H2, Wave Function

0 1

H(Iso=1,Spin=1) 0.0 0.0 0.0

H(Iso=1,Spin=1) 0.741 0.0 0.0

**********************************************

and same input for para, but Spin=0

The problem is that the output files of both(para and ortho) were same. In fact, the wave functions of ortho and para hydrogen are different, so the molecular orbital coefficients which we get from gaussian also must be different.

Thank you, Have a nice day.

Dear Sir,

I am trying to find interaction between a metal ion and a phenol using gaussian 09. but it shows an error when i try to optimize the geometry. so i gave the keyword pop=readradii and in the end of input file the covalent radius of the metal ion as M 1.45 (read in Angstrom). so i want to ask will it give a valid interaction now?

Dear sir,

I am trying to calculate gibbs energy of solvation for organic fluorides using B3LYP/6-31G(d) basis set. My values do not match the experimental ones but show large deviations. I am not able to figure out what went wrong with the computations. Can you help please?

Gibbs energy/Ha GAS Gibbs energy/Ha WATER ∆Gsolv/Ha ∆Gsolv/kJmol-1

CH2F2 -238.964087 -238.968799 -0.004712 -12.371356

CHFCl2 -1058.929382 -1058.937746 -0.008364 -21.959682

Calculated (∆Gsolv/RT) Experimental (∆Gsolv/RT)

CH2F2 -4.990826479 -5.44911

CHFCl2 -8.858928834 -3.7528

Hello Monisha

Sorry for the lateness of my response. Have you tried to change the level of theory? B3LYP is a small and deficient functional and for calculating free energies you need a more sophisticated method.

Have a nice day

Sir, I got the polarizability andhyperpolarizability for a molecule as

Polar=269.2266404,

-21.2799287,

239.9810706,

-13.2687335,

-10.4386215,

201.0602443|

Which data correspond to αxx, αyy and αzz ?

HyperPolar=-29.6709602,

21.0802085,

17.142304,

-74.1961901,

56.492484,

-53.9660375,

47.6376838,

111.8904511,

-38.2762556,

58.4032979|

Which data correspond to

βxxx, βxyy, βxzz,

βyyy, βyxx, βyzz,

βzzz, βzxx, βzyy,?

Waiting for reply,

Yours sincerely

Partha S. Sengupta

Estimado Joaquín

Tengo una duda que en la página de Gaussian con el manual no puedo resolver.

Quisiera saber si al utilizar ModRedundant (o algun otro keyword), puedo en lugar de fijar la distancia de dos átomos, darle un rango mínimo y máximo.

Muchas Gracias!

Nico

Hola Nico

Si lo que quieres hacer es un barrido de la energía al variar un enlace entonces puedes usar ModRedundant para optimizar el resto de la molécula mientras que la distancia entre esos dos átomos se mueve entre tus valores mínimo y máximo (necesitas definir el paso, es decir, cuanto se modifica el enlace en Angstroms de una optimización a la siguiente). Creo que tu pregunta es algo diferente pero yo haría primero el barrido para encontrar el mínimo de energía a lo largo de ese enlace.

Espero haber entendido bien tu pregunta pero si acaso no fue así escríbeme nuevamente.

Saludos y gracias a ti por leerme!

Estimado Dr. Barroso:

No soy quimica computacoinal pero he estado tratando de calcular la fluorescencia de una molecula para predecir el efecto PET (Photo induced electon transfer). Hice calculos de optimizacion con la base semiempirica PM6 para despues poder hacer calculos de energia con ZINDO para ver los estados de excitacion. Despues para poder ver la fluorescencia de la molecula ahora optimizo el estado de excitacion con TD DFT B3lyp 3-21g en el cluster de la universidad pero ha tomado mucho tiempo (mas de dos dias) solo busco por una aproximacion, no sera un trabajo que sera publicado. Es posible guardar los calculos que hasta ahora ha realizado el cluster y detenerlo para despues proceder al calculo de energia?. Tiene alguna otra sugerencia?

Aprecio mucho su tiempo y su respuesta.

Gracias.

Hola Paulina

Disculpa la tardanza de mi respuesta. Lamentablemente los cálculos TD DFT toman muchos recursos computacionales, y el nivel de teoría tan bajo que estás utilizando no te permitirá observar nada interesante ni siquiera de manera cualitativa. mi sugerencia es que consigas a un químico computacional que pueda trabajar contigo en realizar esos cálculos.

Saludos

Dear Dr joaquin barroso

greetings

I am working in G09 .I want to study TD DFT for my molecule in different solvents. because it is very solvent sensitive molecule.

In G09 SCRF method shows, IEFPCM, SMD, CPCM, SCI-PCM model.

Which model is suitable for studying the solvatochrmoism effect?. and How it can be selected ?

thank you

hi will someone help please, i need to write 0.000143 in words. can anyone help

One hundred and fortythree millionths (?)

First off love the site. Great work!

Had a new problem/error that came about and can figure it out.

Looking to calculate the ionization potential for a organic molecule.

#p b3lyp/6-31g(d) EPT pop=full

The error that keeps occurring is:

Internal consistency failure #1 in ROv08.

Any help would be great!!

Thanks

This is probably related to a problem with the structure. Try to optimize it first.

Have a nice day!

Hi. Dr joaquin barroso. Please, answer me:

Is there any way to define Ortho and Para Hydrogen molecule in Gaussian 03W?

Thanks so much

Please ellaborate. Im not sure what you mean

I used the following input:

******************************************

%chk=ortho.chk

#n B3LYP/ 3-21G Pop=full

ortho H2, Wave Function

0 1

H(Iso=1,Spin=1) 0.0 0.0 0.0

H(Iso=1,Spin=1) 0.741 0.0 0.0

**********************************************

and same input for para, but Spin=0

The problem is that the output files of both(para and ortho) were same. In fact, the wave functions of ortho and para hydrogen are different, so the molecular orbital coefficients which we get from gaussian also must be different.

Hi, I’m still not sure what do you mean by “ortho” and “para” hydrogen, I’m sorry.

From what you just wrote I think you want to assign different spin states to different molecules but defining them atom by atom. To the best of my knowledge this is not possible with Gaussian and of course the results will always be the same. I suggest you contact the Gaussian help desk for this one.

Have a nice day!

Dear Dr joaquin barroso

greetings

I am working in G09 .I want to study TD DFT for my molecule in different solvents. because it is very solvent sensitive molecule.

In G09 SCRF method shows, IEFPCM, SMD, CPCM, SCI-PCM model.

Which model is suitable for studying the solvatochrmoism effect?. and How it can be selected ?

thank you

I would choose SMD. The thing is that what you really want here is a solvation model that is suitable for getting the interaction right. I’m not aware about any issues on solvatochromic effects changing with the solvation model. I would use all of them with a simple single well reported molecule and then compare the results.

Hope this helps!

I am working with Gaussian 03 software. May request yo how to calculate fluorescence ? Please provide a simple input file so that I can check the data.

Hi there! I will post in January about how to calculate excited states, ok?

Stay tuned!

Dear Sir,

I couldnot find your post which helps in calculating fluorescence using Gaussian?

Is there anyway that the Gaussian 09 program can perform frequency calculations for a periodical boundary using PBC?

I think so but maybe only in a numerical (not analytical) way

Hola: ¿Existe alguna manera de que el Gaussian 03 o 09 impriman las matrices de recubrimiento? Gracias, saludos. Juan.

Hola Juan,

No lo sé pero me imagino que debe haber un iOP para ello. Intenta contactar directamente a Gaussian.

Saludos

Me refería al método de Hückel Extendido. Gracias.

Dear Sir,

Happy New year ,

Dear Sir,

I would like to optimize the molecule which contains Cl, Na,O,H, C,N Iodine atoms.

How to give the gaussain basis set, a split valence (SV) of 433321/43321/43 with two polarization functions with exponents of 0.105 and 0.334. for Iodine atom.

please help me in the input of Gaussain.

Bull. Korean Chem. Soc. 2010, Vol. 31, No. 8 page 2228

Chang Kon Kim et al.

DOI 10.5012/bkcs.2010.31.8.2228

or else please suggest me which basis set is more suitable for Iodine other that LANL2dZ.

already i used lanl2dz, there is a lot of difference in UV in the calculation and experimental.

Respected Sir

I am using AIMALL standard version. I have generated a wavefunction file for Ag-water complex using def2-TZVP basis set in G09 C-version. When I want to do AIMQB calculation it is showing the error that “Invalid traditional wfn file! Could be improperly formatted 2nd line or other line”. But wavefunction created for Al-water complex with the same basis set shows no error. What may be the problem for such an error?

Thank you

Dear Dr. Joaquin,

I am new in Gaussian and I want to optimize the icosahedral gold geometry by using Gaussian 03. My system consists of 144 gold atom. I’ve used Rhf/LANL2DZ basis set. When I try to run input file with the coordinates of 144 gold atom, it gives an error message as below;

Maximum number of bonds=100 exceeded for atom 1.

Error termination via Lnk1e in C:\G03W\l101.exe at Mon Jan 12 16:07:18 2015.

Job cpu time: 0 days 0 hours 0 minutes 0.0 seconds.

File lengths (MBytes): RWF= 7 Int= 0 D2E= 0 Chk= 1 Scr=

How can I solve this problem?

Thanks,

Ayse.

This means that somehow your atom Au1 is bonded to more than 100 other atoms. Check your coordinates. Make sure the units are angstroms because if you are using other kind of units then maybe when traslocated to A all atoms superpose.

Also, if you are using geom=connectivity get read of this keyword and delete the connectivity matrix at the end of your file.

I hope this helps

Hola que tal, esta vez con una consulta en español para explicarme mejor. Estoy tratando de reproducir un trabajo de deshidrogenación de MeOH catalizada con un cluster de 7 unidades de Pt, pero en el artículo mencionan que se eligió la estructura optimizada del cluster con multiplicidad quintuplete, por ser la mas estable (al correr la optimización del mismo cluster con multiplicidades 1,3,5,7 y 9, ésta última es la que me da una menor energía), además para los cálculos de adsorción ellos utilizan una multiplicidad de spin de septeto, en lugar de la de quintuplete utilizada anteriormente, este ultimo paso no lo entiendo, espero su respuesta, le envío el link del artículo por si quisiera checar la parte de la metodologia:

http://www.sciencedirect.com/science/article/pii/S2210271X14000103

De antemano muchas gracias

Por cierto se me pasó mencionar que utilizo Gaussian 09 para realizar los cálculos

Ya resolví esta duda, muchas gracias.

Whats up very nice blog!! Guy .. Beautiful .. Amazing

.. I’ll bookmark your web site and take the feeds

also? I’m satisfied to find numerous useful info here in the publish, we’d like work out extra

techniques in this regard, thanks for sharing. . . . . .

sir, I found the shape of molecular orbital in pop=regular calculation through edit=mo command. In this way I found by observing the MO diagram as that HOMO, HOMO- 1 are pi type, lumo, lumo+1 are pi* type and Lumo+4 as Rydberg orbital. But I cannot get any data by which I sanguine that the orbitals are pi, pi* and Rydberg type. Help is needed.

I also done pop=(nbo,regular) gfoldprint, for the same system but get no information.

How can I got data regarding the HOMO, LUMO and Rydberg orbital.

You can find it all in the summary of your NBO listing just the way its described in the NBO post of this blog.

Dear Sir,

Can you please help me to find reorganization energy using Gaussain 03 software for mobility calculation..??

Dear Dr. Joaquin,

greetings,

I’m performing a calculation of transition states for a free radical chain reaction (self accelerating reaction) . The chain reaction consists of 8 steps. i have calculated transition states for 6 steps using QST3 method in G09. But I’m not able to find the transition states for 1st and 8th steps. These two steps are of high activation energy, according to the literature. The first step (initialization reaction) is about breaking a peroxide bond of an aromatic hydro peroxide, thus forming a hydroxyl radical and aryloxy radical. Second step is release of methyl radical from the aryloxy radical so as to produce a stable closed shell product. Send step is a exothermic reaction with very less activation energy (6 kj/mol). The aromatic hydro peroxide has six rotamers, and this is creating problem in finding the transition state. whatever the initial guess I’m providing, most of the time output is a transition state regarding the conversion of one rotamer to another. I have also tried relaxed potential energy surface scan of peroxy bond and took initial guess from this scan for qst3. Then the resulting transition state is about release of a methyl radical along with hydroxyl radical. I tried freezing the bonds, but could not get the required transition state.

So my questions are:

1) Is the transition state for first step is very week, and that’s why im not able to find it?

2) Is low activation energy, and high exothermicity of second step reason for why I’m not able to find the transition state for first step?

Any help would be greatly appreciated.

Thanks in advance.

Hi there,

Finding TSs is an artform, this means there is no systematical recipe to find them. You said you froze the bonds but does this mean you froze bond lengths or torsion angles? If you did the former but not the latter then you might want to try it and avoid the rotamer interconversion.

1) what do you mean a weak TS?

2) Yes and no. More like probably.

Finding -easily- a TS depends on the topography (some say topology but i think its wrong) of the PES so a low Act.Barrier and high exothermicity would look like a cliff on your PES, not as a hill. Have you considered the possibility of having started from a metastable structure which is maybe not separated from 2 by a barrier at all?

Also, what is the level of theory you are using? large basis sets will sometimes tend to smooth your PES which is not entirely convenient if you don’t know where your TSs are.

If I were you I would use an indirect approach for the 1 -> 2 transformation: Oversimplify the system, remove all substituents and hinder if possible the rotation of your bonds of interest (maybe by defining a cyclic analogue, eg. cyclohexene wont spin around CC bond when EA occurs but ethylene will. This has the advantage of having less degrees of freedom messing with your PES.), find the TS for this analogue reaction and then use its structural features to define the proposed TS for your actual system.

Be patient. Finding TS’s is quite hard for it depends on too many variables.

Hope this helps!

Hi lam shatha , l need your help about quantum mechanic methods and the types of functions G.09 thank you.

Hi, I know that the keyword “charge” can be used in the Gaussian software to include background charge during calculation. I wish to know if there is a keyword which I can use to include background dipole moment during calculation?

Hello.

You can place as many ficticious charges as you want by providing their values and positions in cartesian coordinates. Thus you can define a dipole moment by defining its charges and separation. Now this dipole would be fix and it wouldn’t respond (with a torque) to the electrostatic field of the molecule under calculation.

Did I understand your question correctly?

Have a nice day

Hello,

I am trying to optimize a acetic acid-metal-complex by putting Au atom in place of H with O atom and i want to use B3LYP-6311G(d,p) for C,H,O atoms and B3LYP-LANL2DZ for Au but i am getting error “Error termination via Lnk1e in /app1/em64t/g09/l301.exe at ”

here is my input file

______________________________

%chk=ACT.chk

%mem=4GB

%nproc=1

# opt b3lyp/gen

Acetic-ion-gold

-1 2

C

C 1 B1

O 1 B2 2 122.45304405

O 1 B3 2 A1 3 D1

H 2 B4 1 A2 3 D2

H 2 B5 1 A3 3 D3

H 2 B6 1 A4 3 D4

Au 4 B7 1 A5 2 D5

B1 1.16058515

B2 1.23026900

B3 1.33426646

B4 1.36979191

B5 1.42432303

B6 1.61488560

B7 1.23726041

A1 120.98789433

A2 102.54676530

A3 176.32582829

A4 105.48227155

A5 97.17166115

D1 -179.35286866

D2 -0.07582274

D3 166.22268129

D4 178.81429785

D5 154.69881967

C O H 0

6-311G(d,p)

****

Au 0

LANL2DZ

****

_____________________________________

Please help me,Thanks

Shafqat

Hi,

It’s my first time generating a vibronic spectra in Gaussview8. I appreciate it if you can help me with a simple way to do it.

Thank you in advance for your help.

Sara

Dear Dr. Joaquin,

I have a small question about the frequency calculations for large molecules. I have noticed that when a molecule gets larger (has more and more functional groups) the frequencies can become very low. For example:

I optimised, Si(OC2H5)4 (TEOS) molecule using B971/6-311+G(d,p) level of theory with VeryTight Convergence criteria and Ultrafine Grid (I used Gaussian09). Subsequently, I performed the frequency calculations at the same level of theory. This what I found is that the first nine vibrational modes are within 18-62 cm^-1 range (this is apart from the six vibrational modes corresponding to the translations and rotations which are equal to:

Low frequencies — -4.3983 -0.0016 -0.0016 -0.0016 3.5600 4.2328).

I noticed similar thing in other large silica molecules. In some cases, the smallest frequencies were about 10 or 15 cm^-1.

May I ask you if it is correct to have frequencies which are so low? I know, that some of the vibrational modes correspond to internal rotations. Therefore, these nine low frequencies in TEOS case may be related to the C2H5 and OC2H5 hindered rotors. However, it could also be an effect of the accumulation of numerical errors in my calculations.

I am asking this question because I am trying to predict rate constants for some TEOS pathways and correct values of low vibrational modes is essential.

I would be very grateful for your help,

Daniel

Dear sir

I am Vidhya.I trying to calculate the PCM Analysis for molecular structure using basis set (HF/6-311++G(d,p)).Few solvents are run properly(Water) But some solvents are not run. What is the problem. Many time I try do it.Lower basis set HF(6-311G) solvents are run but free energy few values are positive.Can you give some information.

Hi Vidhya,

What solvents are you having troubles with? you don’t have to lower the level of theory but rather to increase it. About the sign for DG do you mean it happens only when the level of theory is decreased? I think I need more information.

Have a nice day

Dear Sir,

Could you please advise me how to customize a basis set, such as add a f-type, a p-type function to a certain basis set.

I often find in paper the description like: “LANL2DZ was used for Au. To presicely describe the……., one additional f-type function was implemented alfa(f)=0.2”

Could you please show me how to do so, by modifying the basis set. The LANL2DZ for Au from EMSL is as below:

Thank you Sir!

****

Au 0

S 3 1.00

2.8090000 -1.2021556

……

S 4 1.00

2.8090000 1.1608481

……

S 1 1.00

0.0598000 1.0000000

P 3 1.00

3.6840000 -0.2802681

……

P 2 1.00

0.6838000 -0.0952078

0.0977000 1.0299147

P 1 1.00

0.0279000 1.0000000

D 2 1.00

1.2870000 0.5844273

0.4335000 0.5298161

D 1 1.00

0.1396000 1.0000000

****

AU 0

AU-ECP 4 60

g-ul potential

5

1 622.6287956 -60.0000000

….

2 3.0481312 -4.2516681

s-ul potential

6

0 194.7374304 3.0000000

….

2 4.4916223 -152.4532773

p-ul potential

4

0 420.6158801 2.0000000

….

2 5.9879750 126.5814591

d-ul potential

5

0 219.2666158 3.0000000

….

f-ul potential

5

0 108.5506037 4.0000000

1 56.4795527 51.8065335

2 29.2069159 231.2183113

2 9.5440543 119.0047386

2 2.8965118 15.3424188

Hi there,

I think the easiest way to do so is by using the ExtraBasis keyword. You type your basis set normally, you add the aforementioned keyword and add the definition of the extra funtion you want to add.

Take a look at the following link. I hope it helps

http://gaussian.com/g_tech/g_ur/k_extrabasis.htm

Dear sir

could you help me about scan calculation .i need detail description with example about scan calculation with G09

Hello. Please google rigid scan joaquinbarroso so you get the proper post within this blog.

I hope this helps

dear sir,

i am doing research in polymer electrolyte using Gaussian theoretical work. I have a problem in running my compound with cationic and anionic geometry.

Thanks in advance

with regards

Maheswari

Hello Maheswari,

I’m afraid you need to be way more specific.

Have a nice day

Hola Joaquin

tengo una estructura que le esta costando optimizar y todos los parámetros lo hacen exepto el Maximun displacement que se que da muy cerca del valor

que opcion puedo utilizar para disminuir tantito la tolerancia de la optimizacion para que la estructura optimice

el defaut es de 3×10-4 digamos que quisiera 2×10-4

Agradezco tu ayuda

Atte

Javier

Cinvestav

Hola Javier.

Puedes utilizar la opción Opt=Loose para hacer una primera aproximación, pero es preferible que luego de hacerla optimices la estructura resultante, ya que el ‘grid’ para calcular la densidad (asumo que usas DFT) también se ve afectado. No sé si puedas modificar los criterios de convergencia a conveniencia, no tiene mucho sentido, ya que simplemente podrías decir en este punto “este es mi criterio y por lo tanto ya convergió”.

Saludos hasta el CINVESTAV

Perdon se me olvido decir que estaba trabajando en Gaussian 09 vC.01

gracias

Muchas gracias por la recomendación y en efecto utilizo DFT

Hi,

I am following your blog for few years and I really appreciate your efforts to help others.

I have a question related to AIM2000, I am running AIM2000 for my molecule however as it takes long time, sometimes because of limited memory or power problem I have to kill the job, is there any way to continue calculations from the last point?

Usually the step of calculating the maximum triples took very long time and I have to repeat the calculations again.

Kindly help

I need to make some theoretical calculations on some novel synthesized zinc- phthalocyanine complexes.

I have a problem in my calculations as the HOMO is always delocalized over zinc atom which is not logic. I try to make the same calculation for un-substituted ZnPc and obtain the same results (as shown in the attached photo).

Could you help me to explore the error.

Regards,

basma

What level of theory are you using? Probably you have a very large basis set on the Zn atom. I’m not familiar with these systems but are you sure this is an error? Try changing the level of theory first for a smaller basis set (and then for a larger one) and see what happens.

I hope this helps!

Thanks so much for your reply, I found the problem in the charge in the centeral metal and I can fix it now.

Can I ask you another question? I wonder How can I draw the MO energy diagram, and how can I extract the number of sub-symmetry number from gaussview or chemcraft, (i.e. (HOMO, —–2—-A1u)), as I can take the symmetry from chemcraft without this number (2) also the figure can be exported from chemcraft but it is not clear at all for publication and I can’t zoom it enough.

Regards,

Basma

dear sir,

how to run cationic geometry and anionic geometry of a polymer molecule using Gaussian 09 software. kindly help me sir.

Hi Maheswari, you can do it by varying the charge and multiplicity in the input file.

For instance,

neutral 0 1

cationic 1 2

anionic -1 2

– Uma

Hi,

I appreciate if you could help me with resources, as i am a beginner in using Gaussian09 with pharmacy background. I need tutorials for gaussian generally, and for energy optimization, bond freezing, excited state, fluorescence and absorption, specifically.

Thanks in advance,

Muhammad

Dear Muhammad,

Try finding a book called “Exploring Chemistry with Electronic Structure Methods” by Frisch and Frisch. I don’t have it available so I cannot share it with you. This is a great resource for beginners in Gaussian, although it was written for G98, most of it is still valid for G09.

I hope this helps!

Dear Sir,

Subject : Negative values for LUMO

I am doing DFT GO with 6-311 G++pd basis set and B31YP using Gaussian09 the molecular formula is (C15H11Cl2NO) with (150 electrons). I get (75) occupied orbitals However there are (82) orbitals with negative Energy . This mean the LUMO has negative energy. There is no imaginary frequency

Full mass-weighted force constant matrix:

Low frequencies — -7.1911 -0.0134 -0.0078 -0.0047 1.9631 3.9558

Low frequencies — 13.1999 28.5837 36.9769

Diagonal vibrational polarizability:

94.4862631 70.1500090 116.8961789

Harmonic frequencies (cm**-1), IR intensities (KM/Mole), Raman scattering

activities (A**4/AMU), depolarization ratios for plane and unpolarized

incident light, reduced masses (AMU), force constants (mDyne/A),

and normal coordinates:

1 2 3

A A A

Frequencies — 12.6214 28.5009 36.9430

Red. masses — 7.0918 4.2317 8.2861

Frc consts — 0.0007 0.0020 0.0067

IR Inten — 0.6342 0.2104 0.4398

I request your advice on the negative value of energy for the LUMO and how to tackle this problem. With my best regards.

This isn’t necessarily a problem. It depends on what your molecule is. Can you see it as a powerful electron acceptor? I would change the functional from B3LYP to PBEPBE. Give it a try and let me know what happened.

I hope this helps!

Hi,

I appreciate helping me in these matters!

a) should i freeze the bond length only? or freezing the bond angel and dihedral angel as well?

b) After having output log file for optimization and frequency; what should I do? i mean how to extract results?

c) Where i can find examples for the most common jobs (input files), coz i am a beginner and it may take weeks to know where is the error in my input files.

Hi Muhammad,

I’m not sure what are you talking about 🙂

a) Depending on what you want to calculate.

b) Search in the output for the phrase “Optimized parameters” this will take you to a long table with all the bond lengths and angles of the optimized molecule. This is very boring so try using a visualizer program instead. Also search for the word “Frequencies” this will display a long list of vibrational frequencies, the first one should be positive for you to know this is a stable state, a minimum on a surface and not another kind of state.

c) This blog has some examples but I suggest you look for that book I told you: Exploring Chemistry with Electronic Structure Methods

I hope this helps

How to use the output of low level of theory calculation, as input for a higher level of theory, in details please? i read that i can use the checkpoint file of low level method to save time and getting a better accuracy

In your new input include the chk line making a reference to your old calculation, then in the input specify that the wavefunction and the geometry have to be read from it. No need to add coordinates but you still have to specify charge and multiplicity. Example:

%chk=oldfile.chk

# guess=read geom=check all-other-keywords

comment

0 1

-blank line-

I hope this helps

Hi,

if the time was not enough for completeness of submitted job, should I repeat the calculation from the beginning or there is a way to resume the job?

Sir

I am from India.

I have been trying optimize the structure of cyclopropenyl carbene(triplet) using MP2/6-31G(d), I am sending the input file. But it says that there is a #2070 error after the optimization. Can you please check whether my level of theory and basis set is sufficient for this system, or suggest a better alternative.

%mem=6MW

%nproc=1

%chk=CPTRIP2.chk

# opt ump2/6-31g(d) nosymm geom=connectivity

Title Card Required

0 3

C

C 1 1.299101

C 2 1.463395 1 63.649311

H 1 1.079741 2 149.639600 3 -170.548274

H 2 1.079777 1 149.623659 3 170.566591

1 2 2.0 3 1.0 4 1.0

2 3 1.0 5 1.0

3

4

5

Dear Prof. Joaquin,

Thanks so much for recommending “Exploring Chemistry with Electronic Structure Methods” to read. it’s very helpful for beginners.

Do you recommend another resource showing how one could extract results from output file and how to present it in a table form. My study will be concerned with IR, UV-Vis, optimization and single point Energy.

I’m glad you liked it. Extracting numbers can be easily done by writing your own shell scripts. I think I will write a post on how to do it. Thanks

Hi,

I am wondering about the difference between single point Energy and energy after optimization. Also, how i use my optimized structure with its single point energy for IR, UV-Vis, excited state and solvatochromism studies.

Since both geometries are different energies will be different. You should always first optimize a molecule before drawing any conclusions, except in very specific cases like when you are trying to explore the crystal effects on a molecule’s specific conformation.

If you need the optimized structure for further calculations you can do one of two things:

1) The easy way. Open the optimized file with a visualizer and save it as an input file with new parameters and keywords as to set your new calculation.

2) The elegant way. Set a new calculation from scratch with %chk=oldfile.chk where ‘oldfile’ stands for the chk file from the optimization calculation. Then, in the route section, use guess=read geom=check This keywords will retrieve the wavefunction and geometry from the last point of the calculation stored in oldfile.chk. Don’t forget to still write the charge and multiplicity line, after which a blank space is needed (the coordinates should not be there since you are asking gaussian to read them from the oldfile.chk)

I hope this helps

Hello,

First, Happy Easter!

Please, can you help me find how to assign and scale vibrational frequencies from output file of gaussian09? I mean how to know of this vibration is scissoring or wagging or twisting, …….. and what is meant by scaling and how to do it.

The easiest way to do the assignment is to open the log file or the .fchk file with a suitable visualizer (GaussView, Molden, VMD, Chimera, etc.) and ask for it to animate each vibration. The scaling part needs you to find a suitable set of scaling factors from the literature. You can also scale them by hand by looking at the vibration of interest and relating them to the experimental values. Due this at your own risk and try to justify your conclusions properly.

I hope this helps

Hello

I am trying to do optimisation caluclation & also some other calculations using DFT in solvent for Co, Ni, Cu complexes. created an input file for the linux version. but whenever i am submitting the job it is showing the following error.

Error: segmentation violation

rax 0000000000000000, rbx ffffffffffffffff, rcx ffffffffffffffff

rdx 0000000000002b44, rsp 00007fffea3ae6c8, rbp 00007fffea3aeca0

rsi 000000000000000b, rdi 0000000000002b44, r8 00002b2ebdea8160

r9 0000000000000000, r10 00007fffea3ae450, r11 0000000000000202

r12 0000000000000000, r13 0000000000000000, r14 00007fffea3aece8

r15 0000000000000000

— traceback not available

Can you tell me what is this error means and also please help me running my job.

ThanQ

vani

Sorry forgot to mention I m using gaussian09 software for the calculations.

Hello Vani,

This message is provided by the shell, not by gaussian. In other words this is your computer telling you the calculation was aborted but it doesn’t tell you why. What you need to do is to open your output file (probably with the .out or .log extension) and read (or send me) the last few lines. If you are getting this message almost instantaneously after submitting your job it most probably relates to a simple syntax error in your input.

I’m sorry for the lateness of my response. I hope it helps!

Awesome site you have here but I was wanting to know if you knew of any discussion boards that cover the same topics talked about in this article?

I’d really like to be a part of community where I can get feedback from other knowledgeable people that share the

same interest. If you have any suggestions,

please let me know. Thanks!

Hello,

I would be grateful if you could help me solving the problem i got on optimization:

The command I used is #opt b3lyp/6-31+g(d,p) scrf=(solvent=dichloromethane,smd)scf=xqc

the error message was as below:

CPHF failed to converge in LinEq1.

Error termination via Lnk1e in /center/local/apl/cx/g09/l508.exe at Sat Apr 18 09:03:20 2015.

Job cpu time: 34 days 5 hours 51 minutes 17.0 seconds.

File lengths (MBytes): RWF= 21126 Int= 0 D2E= 0 Chk= 69 Scr= 1

Error: segmentation violation

rax 0000000000000000, rbx ffffffffffffffff, rcx ffffffffffffffff

rdx 0000000000002244, rsp 00007fff90a5b088, rbp 00007fff90a5b600

rsi 000000000000000b, rdi 0000000000002244, r8 00007f1754931700

r9 0000000000000000, r10 00007fff90a5ae10, r11 0000000000000206

r12 0000000000000000, r13 0000000000000000, r14 00007fff90a5b648

r15 00000000000003e6

— traceback not available

Thanks in advance.

Hi,

Try either one of two things: Remove the keyword scf=xqc and/or include a read flag on the scrf command, while using the OFac and RMin values that I wrote about in a previous post on PCM here in this blog.

I hope this helps.

Many Thanks..

Good Day..

Excuse me

I spent a lot of time on using materials studio software to studying adsorption on Fe(110) surface,

the