NBO Java Applications
Java is a full-featured, general-purpose programming language that can be used to develop standalone applications across platforms on servers, desktops, and mobile devices. The Java programming language was released by Sun Microsystem in 1996 and still today, it remains one of the most widely used object-oriented programming language.
Java is normally compiled to the bytecode instruction set and binary format defined in the Java Virtual Machine Specification. As such, compiled Java code can be run on any platform that has a Java interpreter. A desktop application can use a graphical user interface (GUI) or a console to display output and get user input. The Java Development Kit (JDK) required to develop and test Java programs is free to download and use.
To make analysis and interpretation of NBO results even more accessible to a wide variety of users on different platforms, this site presents several GUI applications that are free to download and use.
NboScan (Windows, Linux)
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.
NboScan is a java-based GUI application which:
- Reads Gaussian output files containing geometries and energies of the PES run (output of coordinate driving with keyword Opt).
- Generates multiple Gaussian input files (.gjf) containing custom route card, comments, geometries, and NBO keylists and keywords.
- Generates a plot view of energy profile along the scanned coordinate.
- Creates Gaussian batch list file (.bcf) for processing multiple input (.gjf) files.
Review the sequence of steps in the workflow by pointing mouse over the Figure 1 and download the application and related files in the resource section below.
Figure 1. Interaction of donor-acceptor pairs from E2Pert analysis.
NboScan code is available at overview is at GitHub and has its own blog page with manual and more details. The GUI was optimized both for Windows7 and Linux (Ubuntu, SuSe). Each OS has its own download below. Core functionality has been also provided in the Python script PesScan featured in the corresponding section of these pages.
Gennbo Helper (Windows, Linux)
is a Java-based GUI application which offers a simple way of generating:
- Keylists and the corresponding keywords for standalone program GenNBO5/6 (processing of existing archive files (FILE47))
- Keylists and the corresponding keywords for ESS-linked or "embedded" NBO modules
- Input files with nbo keywords for two ESS/NBO programs, namely Gaussian09 and PC-GAMESS/Firefly
- Batch processing of archive (FILE47) files by the GenNbo program to generate the corresponding .nbo files
Gennbo Helper assists with syntax of NBO keylists and keywords and formats them for input into standalone Gennbo program. It works directly with local NBO6 gennbo.i4.exe to process .47 archive files. Gennbo Helper can also generate basic input files for electronic structure system (ESS) programs with either included or linked NBO modules. In its specific adaptation, input files are formatted for Gaussian09 (G09, G09W) and PC-GAMESS/Firefly (FF).
Figure 2. Basic keyword panel in Gennbo Helper application.
Jmol-NBO Visualization Helper v2.1 (Windows, Linux)
Jmol NBO Visualization Helper
Jmol-Nbo Visualization Helper is a Java application that generates sets of Jmol .macro files that assist with generating orbital images in Jmol molecular viewer. Besides the .macro files, the application has additional option to generate scripts that assist with writing 3-D file formats, such as .x3d and .jvxl. Specific NBOs and NBO-NBO* pairs can be easily visualized and their interactions analyzed. Additional features include options to write .macro files into the default Jmol directory and to inspect source .nbo files for the key properties associated with NBO orbitals. The application has also options for visualization of 2-D contour images in customizable planes and an option to generate imagery for spin-polarized unrestricted solutions (alpha and beta spin orbitals). Java app GUI has been adapted to run both under Windows and Linux systems. Linux version actually looks great on both systems.
Figure 3. Main user interface in the Jmol-NBO Visualization application.