Gaussian is a commercial computational chemistry package for molecular structure and property calculations. The user can predict equilibrium and transition state structures, NMR spectra, IR frequencies, and other properties tied to the electronic wavefunction.
While a lifetime’s worth of theory exists underneath the hood, you only need a few practical tips to get started making an impact in your field. In this post, I’ll run you through the GUI, showing you the basics of setting up and running QM calculations.
Table of Contents
- How Can Beginners Learn Gaussian?
- Calculation Setup in GaussView
- Understanding Gaussian Output
- Visualizing Molecules with Other Applications
How Can Beginners Learn Gaussian?
Start With GaussView For Visual Learning
GaussView, the graphical user interface for Gaussian, simplifies the processes of building molecular structures, visualizing results, and running calculations without needing to write complex input files. Detailed, helpful documentation and examples exist online for mastering GaussView, but can be somewhat overwhelming to new users in my opinion. I’ll break it down with simple cases to get you started.
First, the user must either build or import a molecule. The quality of this input structure is highly important, as outlined in a post on geometry optimization. The options for providing a structure include:
- Constructing a 3D structure in the Molecule Builder window
- Import molecules, including Sybyl (.mol2), MDL (.sdf) and PDB (.pdb)
- SMILES (.smi) must first be converted to 2D or 3D before import
I license ChemDraw for drawing 2D molecular graphs or creating SMILES for new molecules, but PubChem Sketcher is a free online tool that can export SMILES and other compatible formats.
Building Cycloheptane Two Ways
Let’s generate input structures for cycloheptane using the PubSketcher Tool and the GaussView editor.
- Importing from PubSketcher
The exported file is ‘sketcher.sdf’, which you can (and should) change to a more specific name. I’ll use ‘cycloheptane_pubsketcher.sdf’. GaussView will ask if you want to add hydrogens when you import. The initial structure is 2D, so click the ‘Clean’ button to generate 3D coordinates and minimize with molecular mechanics. Your structure is ready for Calculation Setup.
- Building in GaussView
Alternatively, you can build cycloheptane directly in the molecular editor within GaussView. Much like 2D sketchers, there are windows for choosing the element, functional group, or ring you would like to add. The point of connection used during building will be colored light blue in the Preview Pane.
The builder is intuitive to use. For our purposes, we’ll choose the cycloheptane ring fragment and click in the Editor window. A 3D structure appears similar to the imported and cleaned SMILES file. You’re now ready for setting up a calculation or two.
Calculation Setup in GaussView
Next, it’s time to setup a calculation for our input structure. There are three ways to bring up the window for editing the Gaussian input file within the main GUI:
- Shortcut icon
- Opening the ‘Calculate’ tab
- Keyboard shortcut ‘Ctrl+G’
Within the Gaussian Calculation Setup window, the user is able to specify:
- Job Type – geometry optimization, energy, etc.
- Method – theory (DFT, HF, etc.) and basis set.
- Job Title
- Link 0 – computational resources like memory
- Guess – option for mixing orbitals
- Pop – calculate atomic charges and bonding orbitals
- Solvation – implicit models for modeling solvent
Geometry optimizations and frequency calculations (for enthalpy and Gibbs free energy) are the most common types. I use them in drug discovery campaigns to compute ligand strain, as an example. Let’s see how to do this using our cycloheptane input structure.
Once you’ve specified the job type, it is time to choose the ab initio method. Entire volumes have been written on appropriate choices, and ultimately it depends on the character of the system you are studying. Choices include:
- Semi-empirical methods (PM6) – combine QM with empirical parameters
- Wavefunction-based – HF, MP2/MP4, and CCSD
- DFT – B3LYP, M06-2X, etc.
- Excited-states: CASSCF
For the interested reader, one of the best recent reviews on best practices for DFT methods is here. We won’t get bogged down too much by the theory. Instead, I’ll give you some recommendations I have found useful in the context of organic chemistry.
A small benchmark set I used to test thermochemical precision shows comparable performance among various methods. I computed rotational energy barriers of biaryl rings and compared my results with experiment. The values are root-mean-square errors in kcal/mol (smaller is better).
To identify the method used, choose a density functional on the left and combine with a basis set on the bottom, e.g. B3LYP/6-31G*. These are all “double-zeta” basis sets, but their performance is decent for most purposes.
I might catch a lot of criticism for this, but I tend to use B3LYP most frequently. Is it the best? No. Does it work. Mostly.
Alternatively, I like the Minnesota functionals (M06-2X, MN12SX, etc.) with the Ahlrichs basis sets (def2-SVP, def2-TZVP). Benchmark a few to see which works best in your context.
Heavier elements, e.g. iodine or palladium, typically require split basis sets with effective core potentials for relativistic effects. While we won’t address specialized cases here, the LANL2DZ basis set is decent for this purpose.
Finally, you can set the memory allocation and number of processors to utilize parallel computing under the ‘Link 0’ tab. You may use the default memory limit of 800MB, which is suitable for most basic calculations. I typically set this value to 1-2GB and the number of processors to 16-20.
With that, your calculation is setup. If you want, you may submit the calculation directly from this window. Don’t forget to click “Retain” before you save the file to retain your settings. If you want to submit your calculation later from a command line interface, simply navigate to the directory of your file and type:
g16 < cycloheptane.com > cycloheptane.logUnderstanding Gaussian Output
The output file cycloheptane.log contains information on:
- Calculation input parameters
- Atomic coordinates
- Charges
- Forces
- SCF convergence criteria
- Energies / Enthalpies / Free energies
- Calculation time
You can view the text of the output file from your terminal or use GaussView to load it. Optimization convergence critera, plots, and vibrational frequencies can be visualized in GaussView, making this method preferred for the beginner.
Open GaussView and import the cycloheptane.log file. The ‘Results’ tab contains the data we’re interested in:
Gaussian Results: Summary Tab
I typically look at ‘Summary’, ‘Vibrations’, and ‘Optimization’ as shown above. However, the information in ‘Summary’ is adequate enough for most purposes.
Convergence criteria (did the calculation complete properly?) and thermochemistry results are found within the Opt and Thermo tabs, respectively. An error message will pop up on import if the job has not completed properly, but it’s a good idea to check for yourself.
All energies and thermal corrections are reported in Hartrees. For comparison with other molecules, the difference must be converted to kcal/mol or kJ/mol. Here’s a simple case comparing cis- and trans-butene:
The computed energy difference favors the trans isomer in agreement with experiment:
cis – trans = (-157.224774 – (-157.226910)) * 627.5095 = +1.3 kcal/mol
Visualizing Molecules with Other Applications
You’ve run your calculations and now it’s time to make a sweet presentation to show your colleagues. You could take a screenshot of your structure in the GaussView window, but is there a more elegant way?
Yes. More than one. Please never use a screenshot from GaussView.
It’s as easy as saving your output structure ‘cycloheptane.log’ as a molecule file, e.g. SDF or MOL2. After that, you’re free to use your 3D molecule viewer of choice to export high-quality images:
- Molecular Operating Environment (MOE)
- Flare
- Maestro
- Avogadro
- PyMOL
- etc.
If you prefer, you may use a command line interface to get a file of the optimized 3D structure using a Gaussian utility called newzmat. One caveat: the file types we’ve discussed aren’t supported. Here is a simple workaround with Bash to process all output files in a given directory (dependency on OpenBabel):
#!/bin/bash
module load gaussian
module load openbabel
for file in *.chk; do
base="$(basename ${file} | cut -d. -f1)"
newzmat -ichk ${file} -opdb ${base}.pdb
obabel -ipdb ${base}.pdb -osdf -O ${base}_opt.sdf
rm ${base}.pdb
doneSave this as a script, e.g. newzmat_sdf_conversion.sh, and use to convert cycloheptane.chk to cycloheptane_opt.sdf
> chmod 777 newzmat_sdf_conversion.sh
> ./newzmat_sdf_conversion.shLastly, there is one more free option for displaying Gaussian log files directly that I really like: CYLView. Simply download the program and load in your log files for snazzy images you might see in publications by Houk et al.
Closing Remarks
You’ve done it! You’re ready to run basic (but useful) calculations using GaussView, the GUI of Gaussian. Like I mentioned at the beginning, there is a lot of theory to understand in quantum mechanical methods. But following my recommendations at first and learning more as you go is a decent starting point.
Know anyone who might benefit from this content? Interested in learning more or have requests for specific content? Pass it along, and let’s connect!
Until Next Time,
Avery
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