Master Computational Chemistry Simulations with Gaussian

Learn how to access and install Gaussian and GaussView via university licenses, set up the software, and validate a ready-to-use environment for research publication.

Learn to troubleshoot Gaussian and Gaussview in computational chemistry, contact the instructor with error screenshots or output files, and expect updates or added videos to address missing calculations.

Adjust GaussView display format to set background color, window size, hydrogen visibility, labels, bonds, stereochemistry, and symbols, then choose ball-and-stick or wireframe rendering with chosen colors and text size.

Survey software like Gaussian for quantum calculations and Vasp for bulk simulations, and classify methods into force field, ab initio, semi-empirical, density functional theory, and molecular dynamics.

Draw n-hexane in Gaussview, the graphical interface for Gaussian, by selecting carbon tetrahedral, using the periodic table to set bonding modes, and carefully bonding through the correct atom.

Learn to build binaphthyl by joining two naphthalene rings, adjust dihedral angle to separate rings, and add ethyl and O-H groups, noting coordinates drive quantum calculations over drawn bonds.

Learn to adjust bond and dihedral angles by selecting four atoms and rotating either groups or one end, keeping the other fixed to avoid distortion.

Demonstrate drawing a cobalt octahedral complex with six water ligands in Gaussview, converting O-H groups to water by adding valency to each oxygen to form coordinate covalent bonds.

Discover how to draw nitrobenzene by attaching a nitro group to benzene in Gaussian, using R group fragments and bonding through nitrogen rather than oxygen.

Select biological fragments, especially amino acids, to design an oligopeptide and explore bonding styles. Choose alanine as central, amino terminal, or carboxyl terminal fragment to build termini and extend bonding.

Learn to build nucleosides and fragments in Gaussview, including central, terminal, and free nucleosides, with acetyl and n-methyl amine groups, and copy structures with the clipboard.

Explore ghost and dummy atoms in Gaussian, using dummy 'x' and ghost 'bq' elements for specific calculations like NMR, and recap drawing of ring fragments and functional groups.

Convert a CIF to a readable mol file via Mercury, then import into GaussView to visualize and identify the structure.

Extract Cartesian coordinates from the published manuscript's supporting information and copy them into a Gaussian input file, ensuring correct charge and multiplicity, to reproduce optimized structures for simulations.

Learn to draw a complex natural product like morphine by building from phenanthrene in Gaussview, switching aromatic carbons to sp3, and exploring stereochemistry and dihedral orientations for optimal, lowest-energy conformations.

Learn to set up a methane optimization in Gaussian by choosing job type, method, basis set, and link zero parameters, then submit and review the log and gjf input files.

Open and analyze a methane optimization input file for Gaussian, detailing link zero and root lines, the Hartree-Fock with a 3-1 basis set, cartesian coordinates, and connectivity.

Learn the components of a Gaussian input file, including link zero commands, the root section, title, charge and multiplicity, and Cartesian or z matrix coordinates for a water molecule optimization.

Learn to locate information in Gaussian output by opening the log file, enabling read intermediate geometries, and interpreting optimization steps to assess if the methane geometry is near equilibrium.

Analyze optimization results in GaussView by tracking energy changes across steps, noting energy drop from structure one to two and near-constant from two to three, with restricted Hartree-Fock, no solvent.

Describe how Gaussian defines convergence in geometry optimization using thresholds for maximum and RMS forces and displacements, and explain why exact minima are unattainable, stopping when derivatives are small.

Learn how Gaussian convergence criteria guide geometry optimization, tracking SCF energy across steps and applying four thresholds—maximum force, RMS force, maximum displacement, and RMS displacement—to achieve true optimization.

Extract atomic charges and multipole values, including dipole, quadrupole, octupole, and hexa décapole, from the Gaussian log file and gaussview, noting the zero dipole moment and hf energy.

The lecture explains a frequency calculation in Gaussian on methane to identify minima by positive frequencies. It shows transition states by one imaginary frequency and Raman, VCD, and harmonic corrections.

Explore methane vibrational analysis in Gaussian by viewing normal modes and frequencies, with IR and Raman activity, demonstrating CH bending and asymmetric stretch with animated mode previews and spectrum saving.

Learn to read Gaussian frequency outputs, extract reduced masses and infrared and Raman data, and apply zero-point and thermal corrections to electronic energy to obtain enthalpy and Gibbs free energy.

Learn to plot the infrared spectrum in GaussView, convert absorbance to transmittance by inverting axes, and export spectral data as csv or txt for plotting in Excel or Origin.

Master the z matrix, an internal coordinate system using bond lengths, angles, and dihedrals to define atom positions, with an ethylene example and guidance on connectivity and variable labeling.

Learn how a rigid scan in ethane fixes all geometry except the carbon-carbon bond, mapping energies on the potential energy surface from 1 to 7 angstrom with 0.1 angstrom steps.

Explore the rigid scan in Gaussview to locate the lowest-energy ethane structure between 1.5 and 1.6 angstroms, using 0.1 (or 0.01) steps to guide optimization toward the equilibrium bond length.

Explore the potential energy surface of N2 by scanning the nitrogen-nitrogen bond distance, showing a minimum near 1 angstrom and illustrating a PES scan with translation, rotation, and vibration.

Compute the potential energy surface of the nitrogen molecule (N2) by building a z-matrix, performing a scan with 50 points at 0.1 angstrom steps, and analyzing the Gaussian results.

Explore the potential energy surface for ozone to isozone, with two degrees of freedom, bond lengths and angles, and a reaction coordinate linking reactants, products, and a transition state.

Explore a Gaussian-based potential energy surface analysis of ozone and isoozone, adjusting B1/B2 bond lengths and the O–O–O angle to locate minima and a transition state near 90 degrees.

Explore relaxed scans that optimize non-scanned variables while fixed scanned ones map a series of structures on the potential energy surface for transition-state discovery, using z-matrix input for keto–enol tautomerization.

Learn to perform a relaxed scan in Gaussian to map keto to enol tautomerization, using z-matrix variables and atom renumbering to define proton shift and track energies along the path.

Optimize a transition state for keto-enol tautomerization using the highest-energy structure from the relaxed scan, apply a force constant at the first step, and run Gaussian with opt=no icon.

Characterize a transition state by inspecting the imaginary frequency and animating the associated normal mode. Check that its energy exceeds reactants and products, and confirm with intrinsic reaction coordinate calculations.

Locate and confirm a transition state by performing a frequency calculation, identify the imaginary frequency, and visualize keto–enol interconversion via axis displacement between reactants and products.

Locate the SN2 transition state of chloromethane with bromide using chemical intuition, forming a trigonal bipyramidal arrangement with partial bonds, then verify via Gaussian optimization and frequency in gas phase.

Explore a negative frequency normal mode representing the SN2 transition state as carbon moves from chlorine to bromine, showing bond formation and cleavage between chloromethane and bromide.

Locate a transition state using the Quest2 method in Gaussian, aligning reactant-product numbering for a sigmatropic hydrogen shift in 1,3-pentadiene, and verify with a negative frequency.

Compute the methane UV visible spectrum from an optimized structure using time dependent Hartree-Fock, performing excited-state calculations with singlet and triplet states and selecting multiple states.

Customize UV-visible and ECD spectra in Gaussian, adjust axes, range, titles, and appearance, and save data while interpreting excited states with energies, wavelengths, oscillator strength, and orbital contributions.

Learn how to compute pyridine's NMR spectrum with Gaussian, using an optimized structure, select Hartree-Fock 3-1 NMR methods, assess shielding values, and convert to chemical shifts with a reference.

Perform Gaussian-based calculations to obtain benzene molecular orbitals after optimizing its structure, focusing on pi orbitals; save all orbitals by choosing full pop to show homo and lumo.

Analyze benzene orbitals by loading the check file, viewing homo and lumo pi-type surfaces, adjusting iso values, and saving orbital images in tiff or other formats.

Compare restricted open-shell and unrestricted Hartree-Fock methods, linking multiplicity to unpaired electrons and orbital pairing, and explain how alpha and beta orbitals define orbital counts.

Compare RHF, ROHF, and UHF energies for twisted ethene and show that HOMO-LUMO mixing in UHF lowers energy, despite spin contamination.

Calculate spin contamination from s^2 values in Gaussian outputs, interpret singlet and triplet states, and understand mixed-state examples with unpaired electrons.