Comp Chem 02

(4/10/20, bes)

Previous pages:

Computational Chemistry 1

In the previous discussion you were taught how to submit a WebMO/Gaussian job and analyze results related to measuring of bond length and angles, viewing molecular orbitals, and determining the rotation barrier energy about a carbon-carbon bond. We will continue to use WebMO/Gaussian to develop chemistry insights, but first we must discuss further the nature of the calculations that were done in the previous exercises.

Review

WebMo is an excellent tool (graphical interface) to build an input file for the Gaussian engine. WebMO assisted in the construction of the input file; you are familiar with the figure on the left where you select your job/calculation parameters. The middle figure is generated if you choose to "preview" the job parameters, and the figure to the right shows how Gaussian interpreted the WebMO input file. The figure on the right is an excerpt from the "Raw output" "Actions" item accessed through the "View Job" window.

Job Options

As shown above, the user must specify certain job options. Each of these options will be discussed briefly.

Calculation

Molecular Energy

This option calculates the energy, or "single-point (SP) energy" of the structure "as drawn" in the Build Molecule window. After building a molecule, structures are "cleaned up" and default bond lengths and bond angles are used. This calculation can be used to see how the energy changes as bond lengths/angles are changes. Overall, this is not a very useful type of calculation.

Geometry Optimization

This option requests that a geometry optimization (OPT) be performed. The geometry (all bond length and bond angles) will be adjusted until the lowest energy configuration is found. There are multiple ways to adjust the geometry and there are multiple ways to evaluate when the lowest energy has been found, more on this later. This is probably the most used calculation option.

Vibrational Frequencies

This option computes force constants and the resulting vibrational frequencies (FREQ).

Optimize + Vib Freq

Because it is often necessary to optimize geometry (OPT) prior to doing a vibrational frequency (FREQ) analysis, an option exists to do these operations in series.

Excited States and UV-Vis

For now, the name says a lot...calculates UV-Vis spectrum.

NMR

Calculates the expected NMR spectrum. This does not work real well unless you use a very high level of theory. Please note that there are many NMR "simulation" packages...these use empirical (experimental) data to make an educated guess at the NMR spectrum. The math used to simulate is different than the math (QM) used in computational approaches.

Coordinate Scan

A coordinate scan carries out a set of calculations on a molecule that differ in a single "coordinate," like bond angle. In the previous Exercise 3 - Study of Rotation Barrier Energy about Carbon-Carbon Bonds we performed a coordinate scan to show how the energy is dependent on the "torsion angle" of the central C-C bond.

Bond Orders

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Molecular Orbitals

Everybody knows about atomic orbitals, 1s, 2s, 2p, 3s, 3p, 3d, 4s, 4p, 4d, 4f, --> 7f, and we have even plotted the hydrogen atom atomic orbitals using Mathematica (or at least shown in the text). Again, i hate to be the bearer of bad news, but when a second electron is added to the picture, ie. helium, these well loved atomic orbitals (solutions to the Schrodinger Equation) are no longer valid. When two elements come together to form a bond, the resulting molecule orbitals (solutions to the Schrodinger Equation) look nothing like the atomic orbitals. We did do an introductory molecular orbital calculation in Lab 1, titled Exercise 2 - Study of the Molecular Orbitals in Ethene, CH₂CH₂.

Natural Bond Orders

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Transition State Optimization

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Saddle Calculation

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IRC Calculation

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CBS-QB3 High Accuracy Energy

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Other

WebMO has the above "common" calculation types hard-wired into the drop down menus. Gaussian can do many other, less common calculations and if you wish to do these you need to find the "keyword" to enter here.

Theory