About me
Personal Info
Name: Joaquin Barroso-Flores
Born: March 15th, 1978 Mexico City
Education:
- Chemistry Faculty, National Autonomous University of Mexico (UNAM). Chemist (graduated with honors, 2001)
- Chemistry Faculty, National Autonomous University of Mexico (UNAM). PhD in chemistry (2001 – 2005)
Download CV’s: Barroso CV (English)
Current work: Associate researcher at the Joint Center for Research in Sustainable Chemistry (CCIQS), which is part of the Institute of Chemistry from the National Autonomous University of Mexico (UNAM). This center is located at the city of Toluca, 100 km west from Mexico City. (Link to official site on Instituto de Química)
Current projects: Molecular dynamics calculations on calixarene systems as drug delivery agents.
Professional Experience:
- Associate Researcher at Instituto de Química, UNAM. Mexico. (May 2010 – present)
- Postdoc researcher at Facultatea de Chemie si Ingenieria Chimica, Universitatea Babes-Bolyai; Cluj-Napoca, Romania. Click on the following link to find out more about the MOLSEN project, currently under development by our team at Babes-Bolyai. (Dec. 2008 – Jan 2010)
- Associate Research Fellow at Centro de Investigacion en Polimeros (COMEXgroup) (2006 – 2008)
- TA electromagnetism with Prof. Dr. Germund Hojer at the Chemistry Faculty, UNAM (2003 – 2005)
- High School Chemistry teacher at Escuela Preparatoria Logos (Chemistry I & II) (2002 – 2003)
Research interests: Theoretical chemistry; Computational chemistry; Description of molecular properties in weakly interacting systems through assessment of electron density distribution.
Published papers:
- Joaquín Barroso-Flores, Raymundo Cea-Olivares, Rubén A. Toscano, J. A. Cogordan, “Synthesis of the anisobidentate compound bis(2-amino-cyclopent-1-ene-carbodithioate)diethyltin (IV). Experimental and theoretical study” Journal of Organometallic Chemistry 689 (2004) 2096-2102.
- Óscar Baldovino-Pantaleón, Joaquín Barroso-Flores, J.A. Cogordan, Simón Hernández-Ortega, Rubén A. Toscano, David Morales-Morales, “Phosphane-free C-C Heck couplings catalyzed by Pd(II) fluorinated aniline complexes of the type trans-[PdCl2(NH2ArF)2]” Journal of Molecular Catalysis A. Chemical 247 (2005) 65-72.
- Joaquín Barroso-Flores, J. A. Cogordan “Influence of Intramolecular Sn-Chalcogen interactions on the conformational preferences for three Diorganotin (IV) Xanthates.” Journal of Organometallic Chemistry 691 (2006) 4937-4944.
- Jocelyn Alcántara-García, Vojtech Jancik, Joaquín Barroso, Raymundo Cea-Olivares, Mónica Moya-Cabrera, “Coordination Diversity of Aluminum centers Molded by Triazole Based Chalcogen Ligands” Inorganic Chemistry (2009) 48, 13 5545-5558.
- Joaquín Barroso-Flores, J. A. Cogordan”A theoretical approach on the secondary interactions formed in common organotellurium (IV) compounds. Uncommon geometries explained.” In writing.
Languages: English, Romanian, German, Spanish
Apreciado Joaquin: Conozco algunos de los próceres que mencionas en el Bolg. Cea Olivares, e algunosde los vampiritos. Haiduc tal vez. Estuve varias veces en México, una de ellas convidaddo por Jacobo Gomez Lara, ya fallecido, otras por Victor Castaño. bueno..
mi pregunta esla siguiente como buen novato. Estudiando el complexo bis-dietilditiocarbamato de Cu(II) enconbtré transferencia de carga entre:
Donador ACEEPTOR ENERGIA
85 LP(2) S8 LP* Cu1 31.14
esto está muy padre y pudeo visualizar el orbital 85
en Gaussian View y en el Chemcraft. Como visualizao el orbital 83? Si es antiligante deve estar arriba de l LUMO y no abajo del HOMO.
Puede usted ayudarme co la ayuda? Apreciaria enormemente.
Un abrazo extensivo a L. Haiduc.
Calduio Téllez
Apreciado Joaquin: Conozco algunos de los próceres que mencionas en el Blog. Cea Olivares, e algunos de los vampiritos. Haiduc tal vez. Estuve varias veces en México, una de ellas convidado por Jacobo Gomez Lara, ya fallecido, otras por Victor Castaño. bueno..
mi pregunta es la siguiente como buen novato. Estudiando el complexo bis-dietilditiocarbamato de Cu(II) encontré transferencia de carga entre:
Donador ACEPTOR ENERGIA
85 LP(2) S8 LP* Cu1 31.14
esto está muy padre y puedo visualizar el orbital 85
en Gaussian View y en el Chemcraft. Como visualizo el orbital 83? Si es antiligante deve estar arriba de l LUMO y no abajo del HOMO.
Puede usted ayudarme con mi duda? Apreciaria enormemente.
Un abrazo extensivo a L. Haiduc.
(texto corrigido!)
Claudio Téllez
Apreciado Claudio
Me da gusto saber que a través del blog has viajado mentalmente a México nuevamente, por supuesto que pasaré tus saludos al Dr. Haiduc en breve.
En cuanto a tu pregunta: Creo que hay un error de interpretación; según entiendo las lineas que me pones corresponden al análisis de perturbaciones a segundo orden (el cual se obtiene por default o con la opción E2PERT según el programa que uses). En esta sección el número 85 NO hace referencia al orbital, sino a la interacción (la interacción perturbativa número 85 que pasó el umbral -threshold- de 0.5 kCal/mol para ser impreso). Si estás graficando el ORBITAL NATURAL 85 quien sabe que sea lo que estás viendo, pero no corresponde a la interacción que describes. Lo que podrías hacer (asumiendo que etiendo tu intención) es buscar a que NBO corresponde el LP(2) del S8, es decir buscar su número en donde se encuentra la descripción de todos los NBO’s (ve mi post sobre el análisis de resultados NBO), graficarlo y hacer lo mismo para el LP* de Cu1. Molekel y Gaussview pueden presentar superficies simultaneamente (OJO! no es lo mismo que sumar las superficies, esto es completamente distinto). Así graficadas puedes analizar como se están traslapando ambos NBOs. Desconozco el resto de tu archivo pero me imagino que esta interacción es importante en la formación de tu complejo (¿tiolato?),revisa que no tengas interacciones perturbativas con mayores energías que pudieran ser más importantes que esta.
Espero que te sea de ayuda. No dudes en contactarme por este medio o por mail para cualquier otra duda.
Saludos hasta allá
I’m post graduated chemsitry student and I’m trying to learn gaussian, I use gaussian 03 for win. I am studying on TD DFT study a dinitrile compound. After 6 days processing, because of electricity
cutting, my gaussian job is terminated and computer is closed. I want to resumption my job but I dont know how to do it. is it possible? or should I open
latest out file and restart process.
I tried “Geom=check guess=read” functions but I thought I didnt manage
My input file;
%chk=C:/Users/TURKR/Desktop/tddft50trs.chk
%mem=100MW
%nproc=1
#p td=(singlets,nstates=50) b3lyp/6-311+g(d) guess=save geom=connectivity
pop=full gfinput
final part of my out file;
Cannot handle 2e integral symmetry, ISym2E=1.
CISAX: IP= 1 NPass= 3 NMax= 34.
CISAX will form 34 AO SS matrices at one time.
NMat= 34 NSing= 34.
NMat= 34 NSing= 34.
NMat= 32 NSing= 32.
Cannot handle 2e integral symmetry, ISym2E=1.
CISAX: IP= 1 NPass= 3 NMax= 34.
CISAX will form 34 AO SS matrices at one time.
NMat= 34 NSing= 34.
NMat= 34 NSing= 34.
NMat= 32 NSing= 32.
Root 1 has converged.
Root 2 has converged.
Root 3 has converged.
Root 4 has converged.
Root 5 has converged.
Root 6 has converged.
Root 7 has converged.
Root 8 has converged.
Root 9 has converged.
Root 10 has converged.
Root 11 has converged.
Root 12 has converged.
Root 13 not converged, maximum delta is 0.001146383849072
Root 14 not converged, maximum delta is 0.001076901825947
Root 15 has converged.
Root 16 has converged.
Root 17 has converged.
Root 18 has converged.
Root 19 has converged.
Root 20 has converged.
Root 21 has converged.
Root 22 has converged.
Root 23 has converged.
Root 24 has converged.
Root 25 has converged.
Root 26 has converged.
Root 27 has converged.
Root 28 not converged, maximum delta is 0.001298203075257
Root 29 has converged.
Root 30 has converged.
Root 31 has converged.
Root 32 not converged, maximum delta is 0.001487599984012
Root 33 not converged, maximum delta is 0.002130187054738
Root 34 not converged, maximum delta is 0.009687228977448
Root 35 not converged, maximum delta is 0.014708674044360
Root 36 has converged.
Root 37 not converged, maximum delta is 0.001056178564194
Root 38 not converged, maximum delta is 0.001307476560090
Root 39 not converged, maximum delta is 0.001281081401660
Root 40 has converged.
Root 41 not converged, maximum delta is 0.001061548241041
Root 42 not converged, maximum delta is 0.001573623655971
Root 43 has converged.
Root 44 has converged.
Root 45 has converged.
Root 46 has converged.
Root 47 not converged, maximum delta is 0.001567486009780
Root 48 not converged, maximum delta is 0.005544365303514
Root 49 not converged, maximum delta is 0.015140942251070
Root 50 not converged, maximum delta is 0.016487405708613
Excitation Energies [eV] at current iteration:
Root 1 : 3.097975009587616 Change is -0.000001105943253
Root 2 : 3.583514852565895 Change is -0.000007448515000
Root 3 : 3.617241820182027 Change is -0.000021813870515
Root 4 : 3.991502586858061 Change is -0.000023174927667
Root 5 : 4.138876536189863 Change is -0.000007145969739
Root 6 : 4.211283026540273 Change is -0.000007302963600
Root 7 : 4.270327709174773 Change is -0.000012531626331
Root 8 : 4.368328284874000 Change is -0.000005937553695
Root 9 : 4.445535867701103 Change is -0.000032779976579
Root 10 : 4.540640063389401 Change is -0.000002225280201
Root 11 : 4.656404960218242 Change is -0.000023209382109
Root 12 : 4.714797549284374 Change is -0.000019602079988
Root 13 : 4.754991510970658 Change is -0.00001
Hi Turker
I’m catching up with my email and my blog comments today and I saw you already asked the CCL community. To restart a job you have to use the keywords geom=check guess=check but also you have to allocate the checkpoint file in the default location. NOW! you have to also type %NoSave below the %chk=filename.chk line, that way it will read it and wont write it! Be careful because if you don’t write that line then you will loose your checkpoint. I think the idea of copying and renaming it is a good one, try it but also use the %NoSave option I write about here.
Have a nice day!
Hello I’m surfing the net and I found you are know everything about gaussian03.
I have some problems and don’t know how can solve my problems.
In my thesis I being involved to find HOMO and LOMO wave function but I found HOMO only in wfn file
Please help to find LOMO wave function
Please
We are carrying out our calculations using G03W and GVW3.09.I have recently purchased G09W. But it is not possible now to submit the job from G03W to G09W.
Can you kindly guide me in this direction?
If I understand correctly you have GaussView installed along G03 and now you changed to G09 and as a consequence you cant link GaussView with G09. It has to do with the way Gaussview is installed so:
1) uninstall everything!!
2) install G09W
3) Install GaussView
I hope this helps
We are carrying out our calculations using G03W and GV3.09. I have recently purchased G09W. But it is not possible now to submit the job from GV3.09 to G09W.
Can you kindly guide me in this direction?
I think you need to reinstall GaussView, or just re-link it. I’m afraid you need to contact Gaussian Inc for this one or maybe your local IT guy can fix you up.
Have a nice day!
Hi Dr. Joaquin
I am trying to optimize metal complexes of phthalocyanine derivatives by using ONIOM method. I completed optimization of Zn-Phthalocyanine and calculated IR and UV. But I couldn’t optimize Cu-Pht and Co-Pht and I haven’t tried Ni-Pht yet. I met an error message in optimization of Cu-Pht. I think that For metal complex, ONIOM method is more complicated than general single layer methods.
Could you help me, please
Best Regards
Command line my out file:
#p opt=(tight,maxcycle=512,gdiis) freq=noraman oniom(b3lyp/6-31g:pm3mm) geom=connectivity int=ultrafine scf=maxcycle=512
Error message:
Warning! Cu atom 209 has 11 valence electrons but only 4 basis functions.This is less than a minimal basis set!
IExCor= 0 DFT=F Ex=HF Corr=None ExCW=0 ScaHFX= 1.000000ScaDFX= 1.000000 1.000000 1.000000 1.000000IRadAn= 5 IRanWt= -1 IRanGd= 0 ICorTp=0NAtoms= 209 NActive= 209 NUniq= 209 SFac= 1.00D+00 NAtFMM= 60 Big=TLeave Link 301 at Thu Nov 25 11:42:58 2010, MaxMem= 104857600 cpu: 0.0
(Enter C:\G03W\l401.exe)Simple Huckel Guess.NBasis= 620 NMin= 625 so simple Huckel guess is impossible.Error termination via Lnk1e in C:\G03W\l401.exe at Thu Nov 25 11:43:02 2010.Job cpu time: 0 days 0 hours 0 minutes 12.0 seconds.File lengths (MBytes): RWF= 52 Int= 0 D2E= 0 Chk= 1 Scr= 1
Hi Turker
Your basis set is just too small, try changing it for 6-311G(d,p) perhaps, or get one with a pseudopotential such as SDD or LANL2DZ. Check Gaussian’s manual for a wider variety of basis sets available for Cu and the other metallic ions you are studying.
Hi Dr. Joaquin
I am appriciated for your advices. You are right, I think semiemprical method isn’t suitable for Cu, Co and Ni atoms. LANL2DZ is good but too slow for the compound, so I have tried ONIOM method (DFT631G:PM3MM). I also tried LANL2DZ:PM3MM and only PM3MM. Results were same. One more interesting point; when I used molecular mechanics instead of PM3MM (for example ONIOM631G:UFF), I didn’t meet an error.
I am an amateur, I am studying and studying
thanks, happy new years
Dear Dr. Barroso:
I am trying to optimize a structure in which Zn is octahedrally coordinated with two citrate molecules. When I optimize this structure the bonding between Zn and the two citrate molecules dissapears. I know this complex is possible since I got the structure from the authors of a published crystallography paper. This is my input:
%chk=octacomplex.chk
%mem=70MW
%nprocshared=2
# opt rb3lyp/6-311+g(d,p) guess=(local,save) geom=connectivity
Title Card Required
-4 1
C 0.00000000 0.00000000 0.00000000
O 0.00000000 0.00000000 1.44957233
H 0.84063190 0.00000000 1.70043798
C -1.45846423 -0.22289327 -0.45896769
O -2.29631461 -0.61293155 0.41986215
O -1.72466070 -0.03349046 -1.65301136
C 0.88489416 -1.13110147 -0.54914157
H 0.78695471 -1.14345589 -1.51425010
H 1.80867833 -0.90423719 -0.35833379
O -0.35546025 -2.74486386 0.71897856
C 0.55671496 1.33042743 -0.51066400
H 1.47945129 1.40232696 -0.21933614
H 0.56235260 1.30216071 -1.48011487
C -0.17273032 2.58702456 -0.08041309
O -1.40015281 2.55436371 0.08757794
O 0.51874797 3.64592327 0.04721742
C -2.70592252 -3.08341975 4.08248350
O -2.70592252 -3.08341975 2.63291117
H -3.54664302 -3.08346576 2.38205127
C -1.24759139 -2.86049159 4.54141854
O -0.40960791 -2.47048821 3.66262135
O -0.98130632 -3.04984838 5.73545646
C -3.59086117 -1.95223738 4.63158667
H -3.49287722 -1.93996386 5.59673360
H -4.51473395 -2.17914766 4.44078464
C -3.34303653 -0.55032925 4.12272545
O -2.35059538 -0.33852100 3.36347229
O -4.12000079 0.34887973 4.48811035
C -3.26277058 -4.41381229 4.59311486
H -4.18537380 -4.48574672 4.30181964
H -3.26836372 -4.38562647 5.56260412
C -2.53332530 -5.67040942 4.16286395
O -1.30581420 -5.63770256 3.99486717
O -3.22475909 -6.72938904 4.03527183
Zn -1.35300556 -1.54173288 2.04124462
C 0.63698091 -2.53305560 -0.04027460
O 1.42338885 -3.44322386 -0.41004057
1 2 1.0 4 1.0 7 1.0 11 1.0
2 3 1.0 35 1.0
3
4 5 1.0 6 2.0
5 35 1.0
6
7 8 1.0 9 1.0 36 1.0
8
9
10 36 1.0 35 1.0
11 12 1.0 13 1.0 14 1.0
12
13
14 15 2.0 16 2.0
15
16
17 18 1.0 20 1.0 23 1.0 29 1.0
18 19 1.0 35 1.0
19
20 21 2.0 22 2.0
21 35 1.0
22
23 24 1.0 25 1.0 26 1.0
24
25
26 27 1.0 28 2.0
27 35 1.0
28
29 30 1.0 31 1.0 32 1.0
30
31
32 33 2.0 34 2.0
33
34
35
36 37 2.0
37
1 2 1.0 4 1.0 7 1.0 11 1.0
2 3 1.0 35 1.0
3
4 5 1.5 6 2.0
5 35 1.0
6
7 8 1.0 9 1.0 36 1.0
8
9
10 36 1.5 35 1.0
11 12 1.0 13 1.0 14 1.0
12
13
14 15 2.0 16 2.0
15
16
17 18 1.0 20 1.0 23 1.0 29 1.0
18 19 1.0 35 1.0
19
20 21 1.5 22 2.0
21 35 1.0
22
23 24 1.0 25 1.0 26 1.0
24
25
26 27 1.5 28 2.0
27 35 1.0
28
29 30 1.0 31 1.0 32 1.0
30
31
32 33 2.0 34 2.0
33
34
35
36 37 2.0
37
Any help would be greatly appreciated.
Best regards,
Gabriela Arias
Hola Gabriela!
What do you mean it disappears? If you mean you can no longer see it in a visualizer such as GaussView then you have nothing to worry about, sometimes visualizers have different thresholds for painting a bond or not.
Your initial bond lengths (Zn-O) where taken from the crystallographic data, right? How much longer are those bonds after optimization?
Take a look on the bond indexes to assert that the bond is lost or if it is just an artifact from the visualizer.
I need more information to help you out but I hope this sets you on the right path.
Happy holidays!
Dear Dr. Barroso:
Thanks for your quick response. In the optimized structure, Zn is no longer coordinated with the citrate molecules, so it is not a visualization problem. The distance between Zn and the binding sites in the optimized structure is about 0.10 longer than in the crystallographic data.
Happy Christmas,
Gabriela Arias
Hola de nuevo Gabriela!
Wouldn’t this mean your bonding is mainly ionic in nature? I mean, if the distances are so similar after the opt procedure and the bond order is so low then there is probably no covalent bond there to begin with! Try running a bond order calculation (I suggest NBO with BNDIDX keyword for a Wiberg analysis)on the initial and final structures just to make sure. Also employing Generalize Valence Bond theory could throw some light on to why are your bonds disappearing in the gas phase. Thanks for stopping by.
Have a great year!
Hi Dr. Barboso
I’m facing some troubles trying to visualize NBOs. I’ve optimized some molecules using g09 and then I made a single point calculation for each one and added some keywords for a NBO analysis. The problem is: when I try to visualize the NBO orbitals using GV 5.0, only the the usual MOs show up.
The CMO, NRT and other default analysis performed by NBO were in the .log file as they should be. The only problem is visualizing the orbitals.
I used the following keywords:
——-
#T M062X/cc-pvtz sp Pop=(NBORead,savenbos)
…
$NBO NRT CMO plot file=job $END
——-
I appreciate any help you can provide me.
With regards,
Italo
Hi Italo
I assume you already read my post (in this same blog) about how to visualize NBO’s with GaussView. Maybe there is something about the 5.0 version. I don’t know if I have it available but if I do I will run some tests and will let you know.
In the mean time I hope you have a nice day
Dear Italo,
Did you get solution for your error?
Kindly share with me, I am having the same kind of error.
Many thanks,
Bijan
I am trying to visualize the HOMO and LUMO of a compound on MOLDEN of which I ran gaussian calculations on. I read an article online that says that for MOLDEN to find all required information in the output file, I need to run a single point calculation at the desired level of theory including the pop=full and gfinput keywords. I entered the above in my input file and the following is my input:
%chk=Chlorin-1_b3lyp_go
%mem=23000mb
%nprocshared=8
# b3lyp/6-31G(d) sp scf=tight pop=full gfinput maxdisk=50gb
b3lyp geometry optimization using Gaussian
Chlorin-sp-1
The mem value in the run script is 23500mb and maxdisk=50gb. However, when I run this job, an error message comes up which says: ‘galloc: cannot allocate memory.’ I tried increasing the memory on the run script to 24000mb but I keep getting the message ‘Requested node configuration unavailable.’ I do not know what the problem is. Is there a problem with my input file or what else do you think I should do. I am sorry if I did not do a good job expalaining the problem; I am new to this. Thanks a lot for your anticipated response.
Hi Tijesunimi!
If your chlorin molecule is too big then perhaps you can run it with %mem=300MB or something. Asking for 23GB just wont work 
Sorry for the delay in my response. The error is very simple, you are trying to allocate A LOT of memory in the %mem part of your link0!
I don’t know what kind of processor are you using but if you already have the optimized structure and you only want to plot the orbitals then run this job (at the SAME level of theory than your opt) but get rid of those options (I mean %mem and maxdisk) let the program use the defaults. Also you can drop the %nprocshared=8 Gaussian will never use them all efficiently anyway. I hope this helps, please try it and PLEASE LET ME KNOW how it went ok?
I see you are working in photosynthesis, interesting because I’ve been thinking on doing that myself
Take care and thanks for reading!
Joaquin, primero que todo, mis mas sinceras y grandes felicitaciones por tu blog, y tu esmero por ayudar a lagente a tra ves de el.
Segundo quisiera saber si existe alguna manera usando Gaussian 03 de hacer el calculo de un “ground state” pero “quitando” el lone pair de el nitrogeno, o los dos lone pairs del oxigeno y asi obtener un nuevo “ground state” donde estos lone pairs no son tenidos en cuenta y ver la diferencia entre estructuras….mil gracias por cualquier ayuda que me puedas dar
Hola Henry
Mil perdones por la tardanza de mi respuesta. Muchas gracias por tus palabras acerca del blog, espero que pueda seguir a la altura por mucho tiempo (contestar prontamente podría ser una buena manera de empezar).
Vi que pusiste esta misma pregunta en CCL pero ya no vi que respuestas obtuviste.
Sugiero que le entres al esquema NBODel, este método elimina interacciones particulares (elementos de la Matriz de Fock) y calcula la nueva función de onda con las condiciones dadas.
la forma de usarlo sería poner en el route section pop=NBODel y al final de la molécula
$NBO $END
$DEL
delete n orbitals
i
j
k
$END
donde n es el numero de orbitales a eliminar e ijk son las etiquetas NBO de cada uno. Corre un calculo NBO inicial (pop=NBO) luego localiza los pares libre etiquetados como LP, copia los números y ahora sí corres el cálculo con NBODel. Busca en este mismo blog el post sobre como interpretar NBO para más ayuda.
Espero que te haya servido Henry! Gracias por tus comentarios y por leer este blog!
Cheers!
Send me the details of calculating first order hyperpolarizability from G03output usning freq=raman keyword.
Thanking you
Dear Dr. Barroso,
thank you for your illuminative blog!
Perhaps you have a quick answer to my question:
I managed to display the HOMO of a molecule in GaussView 5.04 – but I can’t do two things:
- change the orbital colors to anything other than red and green;
- export the surface as an image file (preferably a vector image, of course)
Do you know how to do this?
Thanks a million!
David
Hi David!
Thank you very much for your kind words. About your questions: 1) I don’t think you can change the colors, I haven’t tried. Probably you need to do it externally with photoshop or something.
2) you can save it as a picture file (gif, tiff, jpg, etc.) but not as a vector file.
GaussView is not the best solution for this sort of high performance rendering you are trying to achieve. Let me suggest VMD, I believe that could be more up your alley
Thanks for reading!
Hi,
I was actually looking for some hints on the internet about changing the orbital colours in Gaussview and ended up with this blog. Though, I was not able to get the answer here, I had a play around Gaussview and finally found the way to change orbital colours. Go to File—Preferences—Colors—Surface Colors. You should be able to change the colors there. I hope this is useful.
Thanks
Shanthi
Hi Dr. Barroso,
Sorry, I would like to ask a simple question. I ran a basic job as follow from a Gaussian textbook.
#T RHF/6-31G(d) Pop=Full Test
Formaldehyde Single Point
0 1
C 0.0 0.0 0.0
O 0.0 1.22 0.0
H 0.94 -0.54 0.0
H -0.94 -0.54 0.0
But, an error message showed up saying,
galloc: could not allocate memory.: Cannot allocate memory
galloc: could not allocate memory.
I saw one of your previous reply, but I don’t have %mem in the input.
Could you please tell me where has gone wrong?
Thanks a lot,
jovis
Hi Jovis
Include the %mem line at the top of your input file and then set it accordingly to your available computation resources, say
%mem=128MW
#T RHF…
Check this link for more info http://gaussian.com/g_tech/g_ur/m_eff.htm
I hope this helps and thanks for reading!
Dear Dr. Barroso, I have a problems with my input file for G03W
here is my input
%mem=100MB
%chk=dai.chk
#n pop=(NBO,savenbo)density=current rmp2/aug-cc-pvdz scf=tight
NBO-HF at MP2 wfn
0 1
S,0.,0.,0.5909815593
C,0.,0.,-1.0398818668
H,0.,0.9356771308,-1.6155519262
H,0.,-0.9356771308,-1.6155519262
but when I was running programme I got the error with
Sorting of NBOs: 48 30 47 45 46 64 56 29 28 44
Sorting of NBOs: 43 42 27 26 25 41 63 55 40 62
Sorting of NBOs: 54 24 23 22 53 61 60 52 59 51
Sorting of NBOs: 21 39 38 37 36 58 50 20 57 49
Sorting of NBOs: 35 34 33 19 18 17 32 16 31 15
Sorting of NBOs: 14 13 65 67 68 66 12 2 1 11
Sorting of NBOs: 3 4 6 10 9 7 8 5
NBStor is confused about NOcc.
Error termination via Lnk1e in C:\G03W\l607.exe at Mon Jul 18 07:45:50 2011
Please tell me why? And could you help me to fix it?
Many thanks to you!
Regards!
Dai.
Hello Dai
I get this question a lot and I still haven’t found a right solution, I need to work on it a little bit more. This has to do with a warning that NBO sends you if the occupation of each orbital doesn’t follow the aufbau principle, i.e., the energy and the population don’t follow the same order. Try the following:
1) Make sure you are working with a minimum of the PES by performing a vibrational frequency analysis (you probably already did but its better to be sure)
2) Change your basis set. Although NBO is not so sensitive to change in basis set there could be a reorthonormalization problem with the particular one you are using.
Hope this works. Thanks for reading
Hi Dr.!
I guess I’ve just found that my problem depends on my program,, that is G03 doesn’t include NBO5.G so I can’t perform NBO analysis with MP2 wavefunction (keyword: density=current). DO you agree with me?
Regards!
Dai
I think its a good idea, Dai! Calculate the mp2 wavefunction and then perform the nbo on it, it might work. Try it and please let me know how it goes ok?
Have a nice day and keep coming back!
It’s ok but I used G09, not G03. You can’t perform NBO on G03, you only perform NBO analysis from HF-wfn. I’ve just know that.
Thank for you kind, Dr.!
Regards!
p.s: you dont mind if I will have questions for you in the future?
Of course I don’t mind!!! I’m glad I can be of help and I like to interact with other comp.chemists from around the world.
Have a nice day!
Dear Dr. Barroso,
I have performed two calculations using Nosymm keyword with G09. I know that in this way all calculation are performed in the Input Orientation. However in one calculations I obteined a Z-Matrix orientation, while for the other I have an Input Orientation.
I ckecked the output, in both cases the symmetry was turned off. The only difference between the calculations is the size of the system, for the system with 61 atoms I have Z-Matrix Orientation , for smaller system I have Input Orientation (In both cases the command used where the same).
Do you where these differences come from. Is there some way to control it?
Thanks in advance.
Hello Fernanda
First I appologize for the lateness of my response. As far as I know there is no way to control this since the program will re-orientate the molecule to where its best suited even if the symmetry is turned off. the symmetry option is more related to the symmetry of the wavefunction, which is a consequence of the symetry of the molecule; a molecule could be symetric and the wavefunction can be made non-symetric with this option. However orientations are a bit harder to control.
Hope this helps!
dear Dr Barroso.
please help me to know how i can calculate bond order in NBO (G03).
I know how can i calculate wiberg bond index, are these two parameters equal?
Hello Mohamad!
They are definitely not the same thing since their definitions are diferent. If you run a full population analysis with nbo pop=(full,nboread) and then you use bndidx in the line:
$NBO BNDIDX NAO $END
you will find both bond orders (Wiberg bond index and Bond Order in the NAO basis)
I hope this helps
Have a nice day
what should be the input file for the optimization of metal complex of phthalocyanine in g03w rather than using oniom calculations?
Hi, Dr. I research in computational chemistry with use Gaussian 03/gaussview 05 software . so , I need a more tutorial or learning in field .please guide me for useful link, literature, book and journal particular commends in Gaussian program. thanks
Hello Fardin!
Go to http://www.gaussian.com and look for tutorials under the Technical Support page. Also try to find a book called “Exploring Chemistry with Electronic Structure Methods” by Frisch and Frisch. This book is very illuminating about how to work with Gaussian
I hope this helps
Hello Fardin!
Go to http://www.gaussian.com and look for tutorials under the Technical Support page. Also try to find a book called “Exploring Chemistry with Electronic Structure Methods” by Frisch and Frisch. This book is very illuminating about how to work with Gaussian
I hope this helps
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