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Gaussian Guide. Section 1. Optimization and

Frequency Calculations

Technical Report · September 2015

DOI: 10.13140/RG.2.1.4695.6007

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 AUTONOMOUS UNIVERSTY OF BARCELONA

Gaussian09 and
GaussView05 Guide.
Section 1. Optimization and
Frequency Calculations

Joaquim Maria Rius Bartra

Graduate in Chemistry. Mention in Industrial Chemistry and Environmental.
Autonomous University of Barcelona. Spain

*This guide is writing with permission of Gaussian, Inc. but there is not connection or
approval from Gaussian, Inc.

*This guide does not have any commercial purpose.

*The complete guide will be composed by different documents corresponding on

sections.

This guide provides common technical steps concerning to the utilization of Gaussian
software.
 Gaussian09 and GaussView05 Guide
Section 1. Optimization and Frequency Calculations

1. Introduction.

The most important and basic types of calculations in computational chemistry are
the optimization and the frequency calculations. These methods offer the essential
parameters of thermodynamic and kinetic parameters to characterize a chemical
reaction.
The first step always must include an optimization of the initial structure in order to
generate a geometry suitable to the method used, meaning that any other calculation
type is performed in a minima o maxima of the PES. An example of a PES could be the
figure 1.
Figure 1. Energy Potential Surface

In computational chemistry usually is very complex to study the entire surface, also
taking into account that not all points are interesting. For this reason and for the
simplicity of working on 2D the required points for a reaction are the minima, maxima
and saddle points. The optimization calculus finds these special points but for their
evaluation, it is necessary to perform the frequency calculation. In addition, the
frequencies allow calculating the thermodynamic parameters of the point by calculating
the second derivatives of the optimized system matrix.
An important fact to solve chemical reaction is draw or imagines an “approximate”
PES of the system with the objective to start with better structures, predict complex or
the specific chemical properties or extract all the information possible from the results.

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Section 1. Optimization and Frequency Calculations

2. Initial Geometry.

The first step of any calculation is drawing the initial structure or importing a
structure form database or other program. An example of this database is the NIST
web page. There you could have access to different data. For example, searching the
CH3OH you can find a table with many data for different methods of calculations and
basis sets. Selecting one of them appears the information related to them and it gives
access to the coordination matrix (I will focus in draw the matrix because in
supplementary information of studies it is used). As in Figure appears, to introduce this
matrix in GView you must select Edit>Atoms list…

In this option, all geometric information can be included with different objectives, as
Molecular Mechanics, ONIOM levels or freeze. Even so, other option can be used to do
these options.

In this case, in order to draw the geometry of the matrix is better to use the
Cartesian coordinates, the Z-matrix is useful in some methods as CCSD(T).

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 Gaussian09 and GaussView05 Guide
Section 1. Optimization and Frequency Calculations

Before introducing the matrix a drawn molecules can be observed. This structure
does not show the bonds. An important and recurrent question about, is which is the
means of the drawn bonds? The answer depends on the level of theory that you are
working. In MM or semi-empirical is extremely necessary to specify the bonds (and in
input, let the command “geom=connectivity”). Even so, in QM the bonds do not show
definition explicitly and all parameters a defined by the matrix coordinates or Z-matrix in
numerical integrations.

The GView draw the bonds from predefined distances, being singles, double in
shorter distances, triple… In addition, you can modify this visualization by selecting the
bond modifier.

For example with these options, you can modify distances, angles and dihedral
angles. There are some tricks to draw very complex structures, for example using a
multi-coordination atoms such metals and later replace the metal for the atom of
interest. Even so, these three parameters are very useful to draw and the dihedral
angle is the most powerful tool for draw a very complex structures but the less intuitive.

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Section 1. Optimization and Frequency Calculations

In addition, GView includes a library with organic rings, organic functional groups,
amino acids and nucleotides. With selecting an atom, as in formyl group, you can
attach it by the selected atom (also very useful for draw structures).

3. Optimization of the initial structure.

With the objective to simplify the guide, in this section 1, the topic of methods and
basis sets will not be explained but it will appear in future sections.
After obtain initial guess of “equilibrium structures” the next step is optimizing it.
There are two options as calculation refers, only optimize or combines in same calculus
the optimization and frequency calculation. In this guide it will be done separately but
the opt+freq calculus imply the combination of both methods explained. The key words
for OPT can be found in: http://www.gaussian.com/g_tech/g_ur/k_opt.htm

1) For the reaction proposed the first step is optimize the reactants and products
taking care of multiplicity and charge.
The first option to see is the objective of the calculus; in this case localize a
minimal. The next option helps to optimize program, the interesting of this option in this
guide is that improves the convergence of the energy. For simple calculations, it could
be not necessary, but for some issues it could be necessary. The observed results that
offers is that increase the time-cost but it is possible to reduce the number of steps if
“once” is selected. The option “always” will imply an increase of total time-cost.
The option RFO is default when it is necessary, so for the moment it is not
necessary. In addition, it could be useful if some convergence problem appears.

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 Gaussian09 and GaussView05 Guide
Section 1. Optimization and Frequency Calculations

2) The next step is selecting a method. In this tab you can introduce the “total”
charge of the system (GView offer a multiplicity automatically, but in other kind of
studies or reactions the multiplicity must be different than ground state). The options of
this tab will be treated in further sections. For this example, an easy methodology is the
presented in the next figure.

3) The last tab for this example is the Link 0. Here the technical options must be
introduced. It depends of every computer used. For normal pc with 8Gb of RAM the
maxima capacity for memory is 200 MWords but for cluster calculations a good relation
is 4cpu X 5GB RAM. Even so, the more RAM given the faster the calculation can be
completed.
Other option to take into account is the “checkpoint file”. This file is where
Gaussian allocated the “internal” results, such matrix, force constants, etc. It is
employed to restart calculations, recalculate energies at different temperatures and
others. It will be useful for further calculations.

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 Gaussian09 and GaussView05 Guide
Section 1. Optimization and Frequency Calculations

The last point is the number of CPU. In this case the more cpu the faster it is. With
PC usually are built as, for example, 4 cpu cores and 4 logic cpu in total 8 cpu. For the
computational calculations this situation it is not valid, taking into account that logic cpu
are much slower than cpu cores. The optimized numbers of cpu to add in these cases
are 4 cpu in order to use cores.
Finally, the input has been prepared and the “Edit” option or “Submit” if it is a local
version in a PC. The edit option opens the input, which is a good option to be sure that
all the commands are correct. With open the .log file, you will be able to see the result
in the options bar and the graph of the energy of the different structures generated.

4. Frequency calculations

One time all structures have been calculated it is necessary for study all chemical
properties to run a “freq” calculus. To perform the freq it must be used the structure
from optimization result with the same method and basis set in order to describe the
same point of the same PES. The key words of freq calculation can be found:
http://www.gaussian.com/g_tech/g_ur/k_freq.htm
The frequency calculus has two important objectives:
-Obtain de frequencies, which are the diagonal of matrix. With this information,
it is possible to ensure if the structure obtained is a minimal or TS.
-Perform optical calculation such IR or Raman.
-Calculate the thermodynamic of a structure: E+zpe, Eº, Hº and Gº.
In other section, the spectroscopy studies will be done together with UV-vis
spectra.

In chemical reactivity, the Raman calculus is not useful but it is a calculation that
requires moderate time to be performed. For this reason is important in order to
improve the time-cost that the option stay disable or with the command
“freq=noraman”.
The reaction of example will be studied completely below, from minima structures
to localize the TS. Also, in this case, the job will be opt+freq together with the entire
feature explained above.

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Section 1. Optimization and Frequency Calculations

5. Procedure for a Chemical Reaction.

1st Step: As a general procedure and exhaustive study of the experimental

chemistry around the reaction of interest must be done. This point is important to know
which compounds are (intermediates, dimers or monomers of the compound,
stereochemistry, coherent properties or unexpected, etc…). With this all equilibrium
structures of the reaction can be draw it.
2nd Step: The first kind of chemical properties to calculate are the thermodynamic
of the global reaction. In any suggested mechanism, before study the kinetics, their
energy must be calculated because, if a reaction will not react for thermodynamic laws,
it will not do it by kinetics. Then, thermodynamics can modify the kinetic perspective of
the reaction. To calculate this properties a OPT+FREQ calculation must be done. From
here, different results are obtained and must be evaluated:
a) See the frequencies to ensure that all of them are positive, meaning that the
structure is a minimal and ensure that the job has been finished properly by
going on the last lines in output.
b) See the electronic energy of the system. This is important to compare with
other methods or basis sets or detect if the methodology is inconsistent with
the system (very common with DFT calculations).
c) Calculate ∆E+zpe, ∆Eº, ∆Hº and ∆Gº.

The results for the CH3OH molecule are:

a) Frequencies, as you can see all freq are positive (or diagonal values of matrix
are positives). Then this structure is a minimal.

b) To see the electronic energy there are two ways. In Results>Summary or in

output. To find it in a fast way you can search the words “SCF Done“ and
going to the last one.

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Section 1. Optimization and Frequency Calculations

c) Below the electronic energy in the output, the thermodynamic results can be
found (searching “Thermochemistry “):

With these results of all structures of reaction, the properties can be calculated
with the equation:
∆𝑋𝑖𝑗 = ∑[𝑋𝑖 (𝑝𝑟𝑜𝑑𝑢𝑐𝑡𝑠)] − ∑[𝑋𝑗 (𝑟𝑒𝑎𝑔𝑒𝑛𝑡𝑠)]
𝑖 𝑗
Where X refers to the property, for example enthalpy or Gibbs energy, i and j are
the compound of products or reagents.

3rd Step: With all thermodynamic calculated, the kinetics of the reaction can be
calculated. In order to determine these features, the TS must be located. There are
different theories to apply but the easiest are the TST (Transition State Theory).
To search the TS there are 3 different strategies.
1) Use an approximate structure form bibliography or similar reactions (draw
the structure, freeze+OPT and finally, TS search.
2) Scan PES of the coordinate of interest (for example, the approximation of
the reactants).
3) QTS2 or QTS3 extrapolations from reactants and products and/or similar
TS.
The search of TS will be made in the independent section below with the example
of reaction.

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 Gaussian09 and GaussView05 Guide
Section 1. Optimization and Frequency Calculations

4th Step: Evaluate the transition state energy in TST. In this case, the transition
structure has the equivalent thermodynamic information than in equilibrium structures.
Even so, the first step in this part is ensuring the localization of TS. To make this there
are two option: The first frequency must be negative and perform an IRC calculation.
Sometime in frequencies appears two negatives frequencies, that means that the
structure obtained are in a saddle point of 2nd order but it do not have any function in
chemistry. To solve this problem select the manual displacement of the one negative
frequency and move it to one of the two directions (taking into account a chemical
meaning). Then save the structure and run a TS calculation.

The result of this is a movement on one direction of the 2nd order saddle point to a
near saddle point as appears in the next figure.

The other option of the IRC (intrinsic reaction coordinate) is based on starting from
a transition structure and finding the two minima (products and reactants). To perform
this calculation you must choose different option depending on the system and interest.
For example, you can choose the direction (to products or to reactants). The number of
points usually should move from 20 to 50 or more depending on interest. Each point
will be a structure extrapolated from the TS.
In addition, this calculation sometimes implies an error due to the correction
algorism. For this reason you can modify it in “recorrect steps” (see the link above
about IRC).

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 Gaussian09 and GaussView05 Guide
Section 1. Optimization and Frequency Calculations

The result that offers the IRC is the entire reaction path, for example the figure
below.

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 Gaussian09 and GaussView05 Guide
Section 1. Optimization and Frequency Calculations

6. Transition Structure Search

Strategy 1 and 2: The first strategy is to reuse or adapt the structure from
bibliography. Even so, the methodology, structures or atom usually are much different
in our structure. For example, studying a hypothetic TS with metal complex of [FeCN6]3-
and [RuCN6]4- the structure in GView is very similar but if you have the first structure
easily you can build the new structure by changing Fe for Ru (with corrects multiplicity
and charge in method tab). Even so, the “approximated” structure of Ru can be far from
the equilibrium but the TS pre-complex could be similar. For this reason is useful to
freeze the TS pre-complex and let other atoms achieve the equilibrium.
The faster way to freeze successfully the atoms of interest is Edit>Atom Groups…

The principle idea is to add the number of the level to be frozen in (YES). Also
selecting highlight can help with big system to identify the frozen atoms. To add the
atoms only write their “number level” separated with comma as in the example:

After prepare the atoms to be frozen, run a normal OPT (freq calculation do not
have sense here) and adding this command “ opt=modredun “ to activate freeze option.

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 Gaussian09 and GaussView05 Guide
Section 1. Optimization and Frequency Calculations

With the optimized structure, then a TS calculation can be performed. The first
option to calculate TS is using only one structure, which must be near to TS in the PES
that you are studying.
Other possibility to stay near of this point is performing a SCAN calculation. In this
option you can evaluate automatically different structures with a changed parameter
(also you can perform it manually by using the frozen atoms) and changing a distance
for example).
To prepare the input for scan you must go Edit> Redundant coordinates… There
you can scan different types of properties like distances, dihedral angles, etc… Also
you can prepare a more complex scan by adding different steps with its actuation but it
require a very prepared strategy. In addition, this calculation is evaluating a PES,
meaning that more parameters to study, higher is the space function you study. The
easier is use one parameters to obtain a potential curve but it is possible to perform
higher space evaluations.
An example of preparation is the study of a SN2 reaction by scanning the distance
C···Cl- and eliminating the Br-.

The curve obtained is E(elec) vs Distance of the selected parameters. All

structures are optimized, meaning that the “maxima” that appears are not really TS but
they are near points. With the structure of these maxima, you can perform the TS
calculation to obtain the real transition structure with its frequencies.

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 Gaussian09 and GaussView05 Guide
Section 1. Optimization and Frequency Calculations

The interpretation of this curve from 2.5 is a point near to breaking of the bond
C-Br and the next point at 2.4 is the geometry corresponding to the TS with C(sp2).
From 2.4 to 1.8 is the approximation of C to Cl until the formation of the CH3Cl. As in
the input the last distance is 1.5 you can observe the inter-atomic repulsion between
the C and Cl.
Finally to localize the TS you must run the OPT+FREQ calculation as in the image.
The Raman option is better if it is disabled to reduce the time-cost. The option to
calculate TS from a single structure is the TS(Berny) as appear in the example. In
future sections the importance of the method and basis set will be explained.
Sometimes the calculation can imply some problems. If the program needs more
cycle of the opt you can add the command: “opt=maxcycles=300”. In addition, other
command interesting is the “opt=noeigentest” which is very useful. The command
disable the test of the curvature of Berny but this test is independent if the energy have
been converged, meaning that you structure could be correct but it gives you error.
Other command is the opt=tight or integral=ultrafine (for DFT). This option increase
the number of steps, and it is very useful when there are similar structures with similar
energies or some convergence problems.

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Section 1. Optimization and Frequency Calculations

The first to see with the result of a structure is the frequencies and its
“displacement”. The first negative frequency implies a saddle point and it is a good
candidate to be a TS. The frequency is high, more than |100cm-1|, which can be
suitable for this kind of atoms. The blue vector indicates that C move along Y-axis,
going and coming back from Br to Cl. A way to see that is animate it and verify that the
frequency have a CHEMICAL MEANING. For example, imagine that the negative
frequency is a bending where C move along the X-axis. In the intuitive chemical point
of view, the atoms are not approximating or it is not a collision. Other way to see that is
to compare directly with reactants and products. If you select “manual displacement”,
you should be able to see two structures “product-like” and “reactant-like”.

*In the Resources of the document, there will be an animated GIF and the inputs
and outputs of the calculations. If some problem to see or obtain them, I invite to
contact me via ResearchGate.

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Section 1. Optimization and Frequency Calculations

Strategy 3: The third strategy is performing an extrapolation of the TS with the

products and reactants (QTS2) and with similar TS structure (QTS3).
To prepare the QTS2 input you must open two windows of with the option “Add to
molecule group”. In the first windows, you must draw the reactants and the second one
the products, all each other. For example, Br-C(H)3····Cl- in the first one
and Cl-C(H3)····Br-. The next step is to connect both windows. For this use the tool
Edit>Connection…

Usually if you use “copy-paste” to draw the second complex with “enable
autofixing” should be enough. Even so, it is possible that atoms do not match. To solve
this, select on atom with left mouse and change their number level with other with right
mouse button. Also in Z-Matrix tools you have the option to “Reorder” which recount all
atoms and it try to match them. As bigger is the system, more difficult to match could
be. In addition, find the word “Valid structure found” after prepare the calculation to
avoid the fail of the calculation. Finally, select QTS2 to run with the usual features
explained above.

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Section 1. Optimization and Frequency Calculations

In the QTS3, the molecule group must be composed by three windows, reactants,
products and near TS structure. This option is useful if you know the mechanism, for
example that in this case the C is sp2. Also other option is use the SCAN structure or
similar reactions where the TS are already defined. In the next figure, the third complex
is the obtained with the SCAN above.

There are different problems that can happen with match. For example, that two
atoms exchange the labels. Other is the bonds connection, in this draws the bonds are
important to indicate to the program the structures to find. In this example, if you add
an extra bond in the products between Cl-C-Br says that there is a match problem and
it can imply an error.

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 Gaussian09 and GaussView05 Guide
Section 1. Optimization and Frequency Calculations

With the transition structure found and with their properties, a kinetic study can be
performed. From the frequency calculation you are available to calculate the activation
enthalpy, activation Gibbs energy, energy barrier, rate constants, Arrhenius parameters
and activation energy.
The most usual and easy formula to calculate the rate constant is the Eyring-
Polanyi equation in the last form with ∆G‡ which is:

K B T RT −∆r G‡
k= · · e RT
h P°
In order to change the temperature to calculate Arrhenius equation or evaluate the
reaction at higher temperature you must save the .chk file. To recalculate the
thermodynamic parameters at different temperatures you must add the next
commands: “freq=readfc”, “guess=read” and temperature=X where X is the
temperature. In addition, you must specify the direction where the previous chk file was
saved. For example:
%chk=/users/yourname/checks/yourpreviousfreqcalc.chk
With the rate constant at different temperatures, you could plot the Arrhenius
equation to compare the results with experimental ones and obtain the Ea and A. Also
there are other formula to calculate an approximate Ea which is: Ea=∆H‡ +RT

7. Author’s Comments

This guide is illustrative and some specific uses have been avoided. Even so, I
recommend using the key words of Gaussian page (linked during the text).
I invite anyone interested to send to me corrections, comments, questions or
suggestions about this guide. This is the first section that I have made but there are
other methods, calculation and interesting uses of Gaussian that I want to introduce it.
In addition I would like to invite any researcher/professor/scientist specialized to
participate with me in the production of this guide to help and introduce the
computational chemistry to the students and researchers new in this interesting area.
Other interesting uses can be the use of this guide for academic purpose, such
auxiliary material for students in their computational practices.

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