Category Archives: Models

Atoms in Molecules (QTAIM) – Flash lesson


As far as population analysis methods goes, the Quantum Theory of Atoms in Molecules (QTAIM) a.k.a Atoms in Molecules (AIM) has become a popular option for defining atomic properties in molecular systems, however, its calculation is a bit tricky and maybe not as straightforward as Mulliken’s or NBO.

Personally I find AIM a philosophical question since, after the introduction of the molecule concept by Stanislao Cannizzaro in 1860 (although previously developed by Amadeo Avogadro who was dead at the time of the Karlsruhe congress), the questions of whether or not an atom retains its identity when bound to others? where does an atom end and the next begins? What are the connections between atoms in a molecule? are truly interesting and far deeper than we usually consider because it takes a big mental leap to think about how matter is organized to give rise to substances. Particularly I’m very interested with the concept of a Molecular Graph which in turn is concerned with the way we “draw lines” to form conceptual molecules. Perhaps in a different post we can go into the detail of the method, which is based in the Laplacian operator of the electron density, but today, I just want to collect the basic steps in getting the most basic AIM answers for any given molecule. Recently, my good friend Pezhman Zarabadi-Poor and I have used rather extensively the following procedure. We hope to have a couple of manuscripts published later on. Therefore, I’ve asked Pezhman to write a sort of guest post on how to run AIMALL, which is our selected program for the integration algorithm.

The first thing we need is a WFN or WFX file, which contains the wavefunction in a Fortran unformatted file on which the Laplacian integration is to be performed. This is achieved in Gaussian09 by incluiding the keyword output=wfn or output=wfx in the route section and adding a name for this file at the bottom line of the input file, e.g.

filename.wfn

(NOTE: WFX is an eXtended version of  WFN; particularly necessary when using pseudopotentials or ECP’s)

Analyzing this file requires the use of a third party software such as AIMALL suite of programs, of which the standard version is free of charge upon registration to their website.

OpenAIMStudio (the accompanying graphical interface) and select the AIMQB program from the run menu as shown in figure 1.

 

Figure 1

Figure 1

Select your WFN/WFX file on which the calculation is to be run. (Figure 2)

 

Figure 2

Figure 2

You can control several options for the integration of the Laplacian of the electron density as well as other features. If your molecules are simple enough, you may go through with a successful and meaningful calculation using the default settings. After the calculation is finished, several result files are obtained. We’ll work in this tutorial only with *.mpgviz (which contains information about the molecular graph, MG) and *.sum (which contains all of  needed numerical data).

Visualization of the MG yields different kinds of critical points, such as: 1) Nuclear Attractor Critical Points (NACP); 2) Bond Critical Points (BCP); 3) Ring CP’s (RCP); and 4) Cage CP’s (CCP).

Of the above, BCP are the ones that indicate the presence of a chemical bond between two atoms, although this conclusion is not without controversy as pointed out by Foroutan-Njead in his paper: C. Foroutan-Nejad, S. Shahbazian and R. Marek, Chemistry – A European Journal, 2014, 20, 10140-10152. However, at a first approximation, BCP’s can help us to explore chemical interactions.

Now, let’s go back to visualizing those MGs (in our examples we’ve used methane and ethylene and acetylene). We open the corresponding *.mpgviz file in AIMStudio and export the image from the file menu and using the save as picture option (figure 3).

Figure 3

Figure 3

The labeled atoms are NACP’s while the green dots correspond to BCP’s. Multiplicity of a bond cannot be discerned within the MG; in order to find out whether a bond is a single, double or triple bond we have to look into the *.sum file, in which we’ll take a look at the bond orders between pairs of atoms in the section labeled “Diatomic Electron Pair Contributions and Delocalization Data” (Figure 4).

Figure 4

Figure 4

Delocalization indexes, DI’s, show the approximate number of electrons shared between two atoms. From the above examples we get the following DI(C,C) values: 1.93 for C2H4 and 2.87 for C2H2; on the other hand, DI(C,H) values are  0.98 for CH4, 0.97 in C2H4 and 0.96 in C2H2. These are our usual bond orders.

This is the first part of a crash tutorial on AIM, in my opinion this is the very basics anyone needs to get started with this interesting and widespread method. Thanks to all who asked about QTAIM, now you have your long answer.

Thanks a lot to my good friend Dr Pezhman Zarabadi-Poor for providing this contribution to the blog, we hope you all find it helpful. Please share and comment.

Elements4D – Exploring Chemistry with Augmented Reality


A bit outside the scope of this blog (maybe), but just too cool to overlook. Augmented reality in chemistry education.

Science and Stuff - Sciencebase.com

This is a guest post from Samantha Morra of EdTechTeacher.org, an advertiser on FreeTech4Teachers.com. 

Augmented Reality (AR) blurs the line between the physical and digital world. Using cues or triggers, apps and websites can “augment” the physical experience with digital content such as audio, video and simulations. There are many benefits to using AR in education such as giving students opportunities to interact with items in ways that spark inquiry, experimentation, and creativity. There are a quite a few apps and sites working on AR and its application in education.

Elements4D, an AR app from Daqri, allows students explore chemical elements in a fun way while learning about real-life chemistry. To get started, download Elements4D and print the cubes.

There are 6 physical paper cubes printed with different symbols from the periodic table. It takes a while to cut out and put together the cubes, but it…

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Transition State Search (QST2 & QST3) and IRC with Gaussian09


Theoretical evaluation of a reaction mechanism is all about finding the right transition states (TS) but there are no guarantees within the available methods to actually find the one we need. Chemical intuition in the proposal of a mechanism is paramount. Let’s remember that a TS is a critical point on a Potential Energy Surface (PES) that is a minimum in every dimension but one. For a PES with more than two degrees of freedom, a hyper-surface, envisioning the location of a TS is a bit tricky, in the case of a three dimensional PES (two degrees of freedom) the saddle point constitutes the location of the TS as depicted in figure 1 by a section of a revolution hyperboloid.

400px-Saddle_point

Fig1. Saddle point on a surface (min in one direction; max in the other)

Fig 1a Pringles chips -Yuck-. They exhibit a maximum on the direction parallel to the screen and a minimum on the direction perpendicular to the screen at the same point.

Fig 1a Pringles chips -Yuck-. They exhibit a maximum on the direction parallel to the screen and a minimum on the direction perpendicular to the screen at the same point.

The following procedure considers gas phase calculations. Nevertheless, the use of the SCRF keyword activates the implicit solvent calculation of choice in order to evaluate to some degree the solvent influence on the reaction energetics at different temperatures with the use of the temperature keyword.

The first step consists of a high level optimization of all minimums involved, such as reagents, products and intermediates, with a subsequent frequency analysis that includes no imaginary eigenvalues.

In order to find the structures of the transition states we use in Gaussian the Synchronous Transit-guided Quasi-Newton method [1] through the keywords QST2 or QST3. In the former case, coordinates for the reagents and products are needed as input; for the latter keyword, coordinates for the TS structure guess is needed also.

QST2)

%chk=file.chk
%nprocshared=n
%mem=nGB

#p opt=(qst2,redundant) m062x/6-31++G(d,p) freq=noraman Temperature=373.15 SCRF=(Solvent=Water)

Title card for reagents

Q M
Cartesian Coordinates for reagents
blank line
Title card for products

Q M
Cartesian Coordinates for products
blank line

QST3)

%chk=file.chk
%nprocshared=n
%mem=nGB

#p opt=(qst3,redundant) m062x/6-31++G(d,p) freq=noraman Temperature=373.15 SCRF=(Solvent=Water)

Title Card for reagents

Q M
Cartesian Coordinates for reagents
blank line
Title card for products

Q M
Cartesian Coordinates for products
blank line–
Title card for TS
Q M
Cartesian Coordinates for TS
blank line

NOTE: It is fundamental that the numbering order is kept constant throughout the molecular specifications of all two, or three, input structures. Hence, I recommend to build a set of molecules, save their structure, and then modified the coordinates on the same file to produce the following structure, that way the number for every atom will remain the same for every step.

As I wrote above, there are no guarantees of finding the right TS so many attempts are probably needed. Once we have the optimized structures for all the species involved in our mechanistic proposal we can plot their energies very simply with MS Excel the way we’ve previously described in this blog (reblogged from eutactic.wordpress.com)

Once we’ve succeeded in finding the structure of our TS we may run an Internal Reaction Coordinate (IRC) calculation. This calculation will connect the TS structure to those of the products and the reagents. Initial constant forces are required and these are commonly retrieved from the TS calculation checkpoint file through the RCFC keyword.

%chk=QST3_2p.chk
%nprocshared=8

#p m062x/6-31++G(d,p) IRC=(Maxpoints=50,RCFC,phase=(2,1))Temperature=373.15 SCRF=(Solvent=Water) geom=allcheck

Title Card

Q M
blank line

Finally, the IRC path can be visualized with GaussView from the Results menu. A successful IRC will link both structures along a single reaction coordinate proving that both reagents and products are linked by the obtained TS.

Hat tip to Howard Diaz who has become quite skillful in calculating these mechanisms as proven by his recent poster at the XII RMFQT a couple of weeks back. And as usual thanks to everyone who reads, comments, likes, recommends, rates and shares my silly little posts.

Natural Bond Orbitals (NBO) Visualization with Chemcraft


It’s been a long time since I last posted something and so many things have happened in our research group! I should catch up with them in short but times have just been quite hectic.

I’m glad to publicly thank Prof. Frank Weinhold’s gesture to include this blog in the bibliography section of the new NBO6.0 website under the NBO-Related Websites tab.

Here is a contribution from Igor Marques at the University of Aveiro in Portugal (Group Website); the original text can be found as a comment in the original NBO Visualization post but it is pretty much the same thing you can find in this post. Here is a link to Chemcraft’s website. Thanks for sharing this, Igor!

=> Examples provided by Igor Marques used Chemcraft Version 1.7, build 365 <=

In the Gaussian input, with the NBORead option included under the population keyword, we should include the PLOT option as illustrated below. The gfoldprint keyword will print the basis set to the output file in the old G03 format. Some visualization programs require a certain format of the basis set to be printed to the output file in order to plot orbitals and other surfaces like the electron density; therefore, if you want to play safe, use gfoldprint, gfprint and gfinput in the same line. gfprint will print the basis set as a list but in the new G09 format, whereas gfinput will print the basis set using Gaussian’s own input format. (The used level of theory and number of shared processors are shown as illustrations only; also the Opt keyword is not fundamental to the visualization of the NBO’s)

%chk=filename.chk
%nprocshared=8

#P b3lyp/6-311++g** Opt pop=(full,nboread) gfoldprint 
filename

0 1
molecular coordinates
$NBO BNDIDX PLOT $END

this will generate files from *.31 to *.41
For the visualization of NBOs, you’ll need FILE.31 and FILE.37. Open FILE.31 from chemcraft. It will automatically detect FILE.37 (if in the same directory).

Tools > Orbitals > Render molecular orbitals

select the NBOs of interest (whcih are in the same order of the output),

Adjust settings > OK

On the left side of the window, select the NBO of interest and then click on ‘show isosurface’. Adjust the remaining settings. To represent another orbital, click on ‘keep this surface’ and then select another orbital from the rendered set and follow the previous steps.

Some Considerations:

> It’s possible to open a formated checkpoint file, containing the NBOs, in chemcraft.
Gaussian input:

%Chk=filename.chk
%nprocshared=4
#P b3lyp/6-311++g** Opt pop=(full,nboread,savenbo) gfoldprint 
filename

0 1
molecular coordinates
$NBO BNDIDX $END

the procedure is identical, but it is only necessary to read the *fchk file and then render the desired orbitals.
However, two problems might arise:
a) Orbitals in the checkpoint are reordered, thus requiring some careful inspection of the output.
b) Sometimes, for a larger molecule, the checkpoint might not be properly saved and the Gaussian job (as previously reported – http://goo.gl/DrSgA ) will end with:

Failed in SchOr1 in NBStor.
Error termination via Lnk1e in /data/programs/g09/l607.exe at Wed Mar 6 15:27:33 2013.

****

As usual, thanks to all for reading/commenting/rating this and other posts in this blog!

Delta G of solvation in Gaussian09


How to calculate the Delta G of solvation? This is a question that I get a lot in this blog, so it is about time I wrote a (mini)post on it, and at the same time put an end to this posting drought which has lasted for quite a few months due to a lot of pending work with which I’ve had to catch up. Therefore, this is another post in the series of SCRF calculations that are so popular in this blog. For the other posts on this subjects remember to click here and here.

SMD

SMD is the keyword you want to use when performing a Self Consistent Reaction Field (SCRF) calculation with G09. This keyword was only made available in this last version of the program and it corresponds to Truhlar’s and coworkers solvation model which is recommended by Gaussian itself as the preferred model to calculate Delta G of solvation. The syntax used is the standard way used in any other Gaussian input files as follows:

# 'route section keywords' SCRF=SMD

Separately, we must either perform a gas phase calculation or use the DoVacuum keyword within the same SCRF input, and then take the energy difference between gas phase and solvated models.

# 'route section keywords' SCRF=(SMD,DoVacuum)

No solvation or cavity model should be defined since, by definition, SMD will use the IEFPCM model which is a synonym for PCM.

As opposed to the previous versions of Gaussian, the output energy already contains all corrections, this is why we must take the difference between both values (remember to calculate them both at the same level of theory if calculated separately!). Nevertheless, when using the SMD keyword we get a separate line, just below the energy, stating the SMD-CDS non electrostatic value in kCal/mol.

The radii were also defined in the original paper by Truhlar; I’m not sure if using the keyword RADII with any of its options yields a different result or if it even ends in an error. Its worth the try!

Some calculation variations are not available when using SMD, such as Dis (calculation of the solute-solvent dispersion interaction energy), Rep (solute-solvent repulsion interaction energy) and Cav (inclusion of the solute cavitation energy in the total energy). I guess the reason for this might be that the SMD model is highly parametrized.

Have you found any issue with any item listed above? Pleases share your thoughts in the comments section below. As usual I hope this post was useful and that you all rate it, like it and comment.

References

A. V. Marenich, C. J. Cramer, and D. G. Truhlar, “Universal solvation model based on solute electron density and a continuum model of the solvent defined by the bulk dielectric constant and atomic surface tensions,” J. Phys. Chem. B, 113 (2009) 6378-96.

The Local Bond Order, LBO (Barroso et al. 2004)


I don’t know why I haven’t written about the Local Bond Order (LBO) before! And a few days ago when I thought about it my immediate reaction was to shy away from it since it would constitute a blatant self-promotion attempt; but hell! this is my blog! A place I’ve created for my blatant self-promotion! So without further ado, I hereby present to you one of my own original contributions to Theoretical Chemistry.

During the course of my graduate years I grew interested in weakly bonded inorganic systems, namely those with secondary interactions in bidentate ligands such as xanthates, dithiocarboxylates, dithiocarbamates and so on. Description of the resulting geometries around the central metallic atom involved the invocation of secondary interactions defined purely by geometrical parameters (Alcock, 1972) in which these were defined as present if the interatomic distance was longer than the sum of their covalent radii and yet smaller than the sum of their van der Waals radii. This definition is subject to a lot of constrictions such as the accuracy of the measurement, which in turn is related to the quality of the monocrystal used in the X-ray difraction experiment; the used definition of covalent radii (Pauling, Bondi, etc.); and most importantly, it doesn’t shed light on the roles of crystal packing, intermolecular contacts, and the energetics of the interaction.

This is why in 2004 we developed a simple yet useful definition of bond order which could account for a single molecule in vacuo the strength and relevance of the secondary interaction, relative to the well defined covalent bonds.

Barroso-Flores, J. et al. Journal of Organometallic Chemistry 689 (2004) 2096–2102
http://dx.doi.org/10.1016/j.jorganchem.2004.03.035,

Let a Molecular Orbital be defined as a wavefunction ψi which in turn may be constructed by a linear combination of Atomic Orbitals (or atom centered basis set functions) φj

We define ζLBO in the following way, where we explicitly take into account a doubly occupied orbital (hence the multiplication by 2) and therefore we are assuming a closed shell configuration in the Restricted formalism.

The summation is carried over all the orbitals which belong to atom A1 and those of atom A2.
Simplifying we yield,

where Sjk is the overlap integral for the φj and φk functions.

By summing over all i MOs we have accomplished with this definition to project all the MO’s onto the space of those functions centered on atoms A1 and A2. This definition is purely quantum mechanical in nature and is independent from any geometric requirement of such interacting atoms (i.e. interatomic distance) thus can be used as a complement to the internuclear distance argument to assess the interaction between them. This definition also results very simple and easy to calculate for all you need are the coefficients to the LCAO expansion and the respective overlap integrals.

Unfortunately, the Local Bond Order hasn’t found much echo, partly due to the fact that it is hidden in a missapropriate journal. I hope someone finds it interesting and useful; if so, don’t forget to cite it appropriately 😉

Polarizability and Hyperpolarizability in Gaussian


Calculating both Polarizability and the Hyperpolarizability in Gaussian is actually very easy and straightforward. However, interpreting the results requires a deeper understanding of the underlying physics of such phenomena. Herein I will try to describe the most common procedures for calculating both quantities in Gaussian09 and the way to interpret the results; if possible I will also try to address some of the most usual problems associated with their calculation.

Introduction

The dipole moment of a molecule changes when is placed under a static electric field, and this change can be calculated as

pe = pe,0 + α:E + (1/2) β:EE + … (1)

where pe,0 is the dipole moment in the absence of an electric field; α is a second rank tensor called the polarizability tensor and β is the first in an infinite series of dipole hiperpolarizabilities. The molecular potential energy changes as well with the influence of an external field in the following way

U = U0 – pe.E – (1/2) α:EE – (1/6) β:EEE – … (2)

.

Route Section Keyword: Polar

This keyword requests calculation of the polarizability and, if available, hyperpolarizability for the molecule under study. This keyword is both available for DFT and HF methods. Hyperpolarizabilities are NOT available for methods that lack analytic derivatives, for example CCSD(T), QCISD, MP4 and other post Hartree-Fock methods.

Frequency dependent polarizabilities may be calculated by including CPHF=RdFreq in the route section and then specifying the frequency (expressed in Hartrees!!!) to which the calculation should be performed, after the molecule specification preceded by a blank line. Example:

#HF/6-31G(d) Polar CPHF=RdFreq

Title Section

Charge Multiplicity
Molecular coordinates
==blank line==
0.15

In this example 0.15 is the frequency in Hartrees to which the calculation is to be performed. By default the output file will also include the static calculation, that is, ω = 0.0. Below you can find an example of the output when the CPHF=RdFreq is employed (taken from Gaussian’s website) Notice that the second section is performed at ω = 0.1 Ha

 SCF Polarizability for W=    0.000000:
                1             2             3
      1  0.482729D+01
      2  0.000000D+00  0.112001D+02
      3  0.000000D+00  0.000000D+00  0.165696D+02
 Isotropic polarizability for W=    0.000000       10.87 Bohr**3.
 SCF Polarizability for W=    0.100000:
                1             2             3
      1  0.491893D+01
      2  0.000000D+00  0.115663D+02
      3  0.000000D+00  0.000000D+00  0.171826D+02

 Isotropic polarizability for W=    0.100000       11.22 Bohr**3.

You may have noticed now that the polarizabilities are expressed in volume units (Bohr^3) and the reason is the following:

Consider the simplest case of an atom with nuclear charge Q, radius r, and subjected to an electric field, E, which creates a force QE, and displaces the nucleus by a distance d. According to Gauss’ law this latter force is given by:

(dQ^2)/(4πεr^3) = QE      (Hey! WordPress! I could really use an equation editor in here!)

if the polarizability is defined by Qd/E then we can rearrange the previous equation and yield

α = 4πεr^3 which in atomic units yields volume units, r^3, since 4πε = 1. This is why polarizabilities are usually referred to as ‘polarizability volumes’.

 

****THIS POST IS STILL IN PROGRESS. WILL COMPLETE IT IN SHORT. SORRY FOR ANY INCONVENIENCE****

 

The use of double zeta quality basis sets is paramount but it also makes these calculations more time consuming. Polarization functions on the basis set functions are a requirement for good results.

As usual, please rate/comment/share this post if you found it useful or if you think someone else might find it useful. Thanks for reading!


This is the first time I reblog a post from a fellow computational chemist and the reason why I do it is because of its beautiful simplicity and usefulness. Given the scope this blog has taken I think this post becomes most appropriate. This post will show you how to create an energy level diagram using nothing but MS Excel.
Kudos to ‘Eutactic’, from Australia, for coming up with a nice solution to this problem. Check out his blog at eutactic.wordpress.com.
Thanks for letting me repost it 🙂

eutactic

I worked out a very quick and easy way to generate level schemes in Excel, based on a query from one of the other students in the group. Normally I would resort to something like the astonishing TikZ for this sort of task, however our group is very much a Microsoft Office ‘What You See Is A Metaphor For Cosmic Horror‘ group and recommending that a colleague learns two new markup languages to produce a figure is probably not helpful in the short term. One of the issues with charting energy levels in Excel is that levels are typically represented by horizontal bars connected at their vertices with lines representing transitions. Whilst Excel does have a horizontal bar as a marker, it possesses two show-stopping limitations:

  1. It is only uniformly scalable, and can only be scaled so far – we cannot make it anywhere near wide and…

View original post 222 more words

The Gen keyword in Gaussian. Adding an external basis set.


I am frequently asked how to include an extra set of basis functions in a calculation or how to use an entirely external basis set. Sometimes this question also implies the explicit declaration of an external pseudopotential or Effective Core Potential (ECP).

New basis sets and ECPs are published continuously in specialized journals all the time. The same happens with functionals for DFT calculations. The format in which they are published is free and usually only a list of coefficients and exponents are shown and one has to figure out how to introduce it in ones calculation. The EMSL Basis Set Exchange site helps you get it right! It has a clickable periodic table and a list of many (not all) different basis sets at the left side. Below the periodic table there is a menu from which one can select which program we want our basis set for; finally we click on “get basis set” and a pop-up window shows the result in the selected format along with the corresponding references for citation. A multiple query can be performed by selecting more than one element on the table, which generates a list that almost sure can be used as input without further manipulations. Dr. David Feller is to be thanked for leading the creation of this repository. More on the history and mission of the EMSL can be found on their About page. Because of my experience, the rest of the post addresses the inclusion of external basis sets in Gaussian, other programs such as NwChem will be addressed in a different post soon.

The correct format for inclusion of an external basis set is exemplified below with the inclusion of the 3-21G basis set for Carbon as obtained from the EMSL Basis Set Exchange site (blank lines are marked explicitly just to emphasize their location:

spin multiplicity
Molecular coordinates
- blank line -
C     0
S   3   1.00
    172.2560000              0.0617669
     25.9109000              0.3587940
      5.5333500              0.7007130
SP   2   1.00
      3.6649800             -0.3958970              0.2364600
      0.7705450              1.2158400              0.8606190
SP   1   1.00
      0.1958570              1.0000000              1.0000000
****
- blank line -

The use of four stars ‘****’ is mandatory to indicate the end of the basis set specification for any given atom. If a basis set is to be declared for a second atom, it should be included after the **** line without any blank line in between.

WARNING! Sometimes we can find more than one basis set in a single file this is due to different representations, spherical or cartesian basis sets. Gaussian by default uses cartesian (5D,7F) functions. Pure gaussian use 6 functions for d-type orbitals and 10 for f-type orbitals (6D, 10F). Calculations must be consistent throughout, hence all basis functions should be either cartesian or pure.

Inclusion of a pseudopotential allows for more computational resources to be used for calculation of the electronic structure of the valence shell by replacing the inner electrons for a set of functions which simulate the presence of these and their effect (such as shielding) on the valence electrons. There are full core pseudopotentialas, which replace the entire core (kernel). There are also medium core pseudopotentials which only replace the previous kernel to the full one, allowing for the outermost core electrons to be explicitly calculated. The correct inclusion of a pseudopotential is shown below exemplified by the LANL2DZ ECP by Hay and Wadt for the Chlorine atom.

spin multiplicity
Molecular coordinates
- blank line -
basis set for atom1
****
basis set for atom2 (if there is any)
****
- blank line -
CL     0
CL-ECP     2     10
d   potential
  5
1     94.8130000            -10.0000000
2    165.6440000             66.2729170
2     30.8317000            -28.9685950
2     10.5841000            -12.8663370
2      3.7704000             -1.7102170
s-d potential
  5
0    128.8391000              3.0000000
1    120.3786000             12.8528510
2     63.5622000            275.6723980
2     18.0695000            115.6777120
2      3.8142000             35.0606090
p-d potential
  6
0    216.5263000              5.0000000
1     46.5723000              7.4794860
2    147.4685000            613.0320000
2     48.9869000            280.8006850
2     13.2096000            107.8788240
2      3.1831000             15.3439560

If a second ECP is to be introduced, it should be placed right after the first one without any blank line! If a blank line is detected then the program will assume it’s done reading all ECPs and Basis Sets.

Finally, here is an example of a combination of both keywords. If a second ECP was needed then we’d place it at the end of the first one without a blank line. The molecule is any given chlorinated hydrocarbon (H, C and Cl atoms exclusively)

#P B3LYP/gen pseudo=read ADDITIONAL-KEYWORDS
- blank line -
0 1
Molecular Coordinates
- blank line -
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
****
Cl     0
S   2   1.00
      2.2310000             -0.4900589
      0.4720000              1.2542684
S   1   1.00
      0.1631000              1.0000000
P   2   1.00
      6.2960000             -0.0635641
      0.6333000              1.0141355
P   1   1.00
      0.1819000              1.0000000
****
- blank line -
CL     0
CL-ECP     2     10
d   potential
  5
1     94.8130000            -10.0000000
2    165.6440000             66.2729170
2     30.8317000            -28.9685950
2     10.5841000            -12.8663370
2      3.7704000             -1.7102170
s-d potential
  5
0    128.8391000              3.0000000
1    120.3786000             12.8528510
2     63.5622000            275.6723980
2     18.0695000            115.6777120
2      3.8142000             35.0606090
p-d potential
  6
0    216.5263000              5.0000000
1     46.5723000              7.4794860
2    147.4685000            613.0320000
2     48.9869000            280.8006850
2     13.2096000            107.8788240
2      3.1831000             15.3439560
- blank line -

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Polarizable Continuum Model (PCM) in G09 (Part II)


One of the most successful posts this blog has ever published was on certain nuances of the solvation calculations on PCM in G03. However there are some differences in the SCRF modules between G09 and G03 and I here present some of them as well as some tips to work with the new version.

The SCFVAC keyword used to calculate the Gibbs Solvation Energy change is no longer available. It is now replaced by DoVacuum which should be included in the SCRF options as SCRF=(DoVacuum,etc.). However, the absolute solvation energy now requires a gas-phase optimization along with a frequency calculation followed by the same calculations with the SCRF=SMD option in the desired solvent and with the appropriate variables.

Gaussian 03 used to calculate and report non-electrostatic contributions to the solvation energy, however they were not included in the total energy nor during optimization procedures. These non-electrosatic interactions are no longer calculated in the default. In order to include these terms during the SCF procedure, and to have them reported separately, the SCRF=SMD option should be used.

My previous post on PCM mentioned the usage of the options OFac=0.8 & RMin=0.5 as part of the additional input. These ‘magic numbers’ (I hate the term) were used to modify the way by which the overlapping spheres were treated in order to create the surface which in turn defined the cavity. G09 uses a new algorithm to make the overlaps generate a smoother surface. I recommend to use the default values before including ‘magic parameters’.

All the default values which G03 used can be retrieved with the G03Defaults keyword, but it is strongly suggested to use it only for comparison with calculations previously done with the older version.

As with some other so-called ‘white papers’ this post will be further improved as more information arises during my own calculations. Thanks for reading! Please comment/like/share this post, as well as others in the blog, if you found useful the information within.

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