Introduction
NBO analysis of orbital interactions is a powerful approach to understanding molecular properties. Subtle interactions can be often revealed by studying the NBO-derived properties at the potential energy surface (PES). By plotting the potential energy changes along the defined molecular coordinate (atom distance, angle, dihedral), one can get a better appreciation of different components of the total energy.

In this post, we will explore a typical workflow utilizing Gaussian09W ESS to generate multiple molecular structures at the PES. We will introduce a new Java application that processes the Gaussian PES output files (*.out) and creates formatted Gaussian input files to perform a single point NBO analysis (Figure 1). In the simplest case, Gaussian Scan keyword performs a series of single point calculations at various geometries. This, so called rigid PES scan performs evaluations over a rectangular grid involving selected internal coordinates. The molecular structure must be defined in Z-matrix coordinates. To avoid potential troubles with a poorly constructed Z-matrix, NboScan app can only read output files generated by the relaxed PES scan initiated with the keyword Opt=ModRedundant. In such case, the keyword requests that a geometry optimization (Opt) be performed in redundant internal coordinate that may include scan and constraint information [2]. The latter option requires a separate input section to activate, freeze, and scan PES. Initial geometry can be supplied as Cartesian coordinates or as Z-matrix. Results are recorded in the job output file. Each PES output file contains table of "Initial Parameters", which indicate the name and the value of Scanned and Frozen coordinates. Atom coordinates together with the corresponding energy at each coordinate increment are all part of the output file. Efficient retrieval of all requested values is often challenging task, certainly not error proof. It is where the NboScan app comes handy.

To avoid potential troubles with a poorly constructed Z-matrix, this app can only read output files generated by the the relaxed PES scan initiated with the keyword Opt=ModRedundant.

Fig. 1. A typical workflow for PES calculation using NboScan.

N-Methyl Formamide Example

We will start with an example of rigid rotation of the methyl group in cis-N-methylformamide (CH3NHCHO, cis-NMF). Results can be compared to the example discussed in the excellent book of Frank Weinhold and Clark R. Landis [1] on pages 141-142. The molecule of formamide was evaluated at HF B3LYP/6-311++G** level of theory. Gaussian09W was used for the relaxed PES evaluation with additional constraints. The input .gjf file is shown in Figure 2. All discussed files can be downloaded from the Download section at the bottom of this post.

Fig. 2. Gaussian input in Cartesian coordinates with added redundant coordinates.

%chk=Formamide_rot_recoor.chk
# rhf/6-311++G(d,p) opt=modredundant nosymm

RHF/6-311++G(d,p) (MeHNCHO) Me rot 2-1-6-7= 0 to 60

0 1
N 0.00000000 0.00000000 -1.36100000
C 0.00000000 0.00000000 0.00000000
O 0.99400000 0.00000000 0.69340000
H -0.85910000 0.00000000 -1.88640000
H -1.02320000 0.00000000 0.42260000
C 1.28045663 0.00000000 -2.08303243
H 2.08663777 0.00000000 -1.37948999
H 1.34338205 -0.87365131 -2.69758412
H 1.34338270 0.87365135 -2.69758400

6 * F Freeze bond lengths around the atom 6
1 * F Freeze bond lengths around the atom 1
* 1 * F Freeze bond angles around the atom 1
* 2 * F Freeze bond angles around the atom 2
* 1 6 * R Relax coordinates passing through atoms 1-6 (dihedral)
D 2 1 6 7 S 12 5.0 Scan dihedral 2-1-6-7 in 12 steps of 5 deg

Upon completion of the run, results of the nearly rigid methyl group rotation are written into the corresponding .out file.

Extracting coordinates and energy data:

In the next step, we will launch the NboScan app by double-clicking the NboScan.jar file and load the above created .out file (Figure 3).

Fig. 3. Main window of the NboScan application.

Click on button 1. Browse Dir to locate the file. Set the output directory for newly created Gaussian input files (.gjf) using the 2. Set Dir button. Alternatively, check the Use input Dir box to direct output into the same directory (Figure 4).

Fig. 4. Loading files for processing and setting the output directory.

Set parameters for the following single point energy calculation in the section 3. Those include the level of theory, basis set (pull-down menus) and additional comments and keywords to the route card. Alternatively, type in the custom level of theory and basis set.

Fig. 5. Entering parameters for single point energy calculation at a given geometry.

Optionally, check the Plot profile box to output the energy profile along the scanned coordinate (Figure 6). This will plot the total electronic energies at different dihedral angles (0-60 deg).

Fig. 6. Energy profile along the scanned coordinate (dihedral 7-6-1-2).

Enable/disable additional options at the bottom of the window. Energy values at calculated points can be retrieved by pointing the mouse at the blue diamond. Axis values can be toggled between horizontal/vertical.

Section 4. involves entering NBO keywords or selecting the preset NBO properties (Figure 7). For more complex keyword lists, use the GennboHelper application described earlier and the Enter custom keywords. The latest version of the GennboHelper can be downloaded from the app’s website.

Fig. 7. Setting NBO keywords and Gaussian-NBO options.

Choosing the PLOT files only option will generate the corresponding NBO keywords necessary to create PLOT files for each scanned geometry. The last option, Set user 1, allows entering custom keywords that are retrieved next time when running the application.

Instructions to Gaussian program on how to perform NBO calculations are selected on line 5.

G03 option uses older NBO3 module compiled as part of Gaussian 03 package.
G09-link-NBO6 option adds keywords “EXTERNAL” and “pop=nbo6read” into the G09w route card and links NBO6 Windows binaries to G09w (revision D.01) [DEFAULT]. This option requires having gaunbo6.bat file (part of the NBO6 package) in the main Gaussian directory (e.g., C:\G09W\gaunbo6.bat).
G09-NBO option adds NBO6 specific keywords (pop=nbo6read) into the route card of G09w, which had NBO6 compiled together with G09w binaries.
.47 file only option instructs ESS to generate .47 archive file for later analysis by GENNBO5/6. This is equivalent to NBO keywords ARCHIVE FILE=xxx.

The message window at the bottom provides information related to the key scan parameters, such as, name of the scanned coordinate, its description in the output file, number of extracted geometries, and total number of atoms in the molecule. Path to files created by NboScan application is also part of the output.

To facilitate the next step, that is, evaluation of each geometry with specified NBO keywords, Gaussian batch file (*.bcf) is created at the end of the run. Just drop the batch file into the main Gaussian09w window and click the “run” triangle icon (Figure 8).

Fig. 8. Starting the batch process in main interface of Gaussian09w.

Files created after the run are shown in Figure 9. Each created file has a suffix indicating value of the scanned coordinate.

Fig. 9. List of input and output files.

A representative example of the newly created series of .gjf files is shown in Figure 10. Note the comment field referring to discrete geometry and the value of scanned coordinate (_10_, _20_, etc.).