Schlegel Research Group

Department of Chemistry, Wayne State University 
5101 Cass Av., Detroit, Michigan, USA, 48202-3489

Rooms 371, 379, Chemistry Bldg.
Phone: Office (313) 577-2562, Student Office (313) 577-2546, Fax: (313) 577-8822

Software


The Schlegel Research Group has developed a variety of programs and Mathematica tools that are freely available for scientific research. Usage of this software, including any modified variant, must be properly acknowledged by the denoted references. This software is offered with no guarantees or warranties, express or implied, about the functionality of the works.

Programs

  • Electronic Structure Perl Toolkit (ESPT) - The electronic structure Perl toolkit is a suite of object-oriented Perl modules designed to facilitate quick and easy access to data located in Electronic Structure Suites (ESS) output files.

  • FreeNodes - FreeNodes parses the output from pbsnodes and returns a list of the available computing resources on a Beowulf cluster running PBS. FreeNodes requires a working version of PBS.

  • GTable - GTable is designed to extract data from Gaussian log files and return it in text files suitable for importing into Excel. It is particularly well suited for tabulating benchmarking data in which the same molecular system is run at a variety of basis sets and theory levels. GTable requires a working installation of the ESPT.

  • TAO (Toolkit to Assist Oniom calculations) is a set of tools to facilitate QM/MM calculation of biochemical systems using the ONIOM method in Gaussian. A collection of files used in the TAO tutorial is also available.

  • Tlogger - Tlogger is a summary and extraction tool for ESS output files. It summarizes the results in an ESS output file and displays cannonical Molecular Orbital diagrams in a simple, compact form. Tlogger requires a working installation of the ESPT.



Mathematica Tools

  • Archive Reader - A Mathematica 6.0 and later notebook for reading data from the archive entry located at the end of a Gaussian log file.

  • DG-EVB Examples - The EVB toolkit must already be installed in Mathematica 5.2 or later for these examples to work.

    • Claisen - Claisen reaction of allyl vinyl ether using 61 internal coordinates

      Reference: Jason L. Sonnenberg and H. Bernhard Schlegel, Mol. Phys., 2007, 105, 2719-2729.

    • HCN - HCN → CNH isomerization reaction using five internal coordinates

      Reference: H. Bernhard Schlegel and Jason L. Sonnenberg, J. Chem. Theory Comput., 2006, 2, 905-911.

    • Malonaldehyde - Malonaldehyde intramolecular proton transfer using 35 internal coordinates

      Reference:

    • Pentadiene - Pentadiene intramolecular proton transfer using 59 internal coordinates

      Reference:

    • 2-Pyridone Tautomerization - 2-Pyridone → 2-Hydroxypyridine tautomerization reaction using 56 internal coordinates

      Reference: Jason L. Sonnenberg and H. Bernhard Schlegel, Mol. Phys., 2007, 105, 2719-2729.

      Reference: Jason L. Sonnenberg, Kim Wong, Gregory A. Voth, and H. Bernhard Schlegel, J. Chem. Theory Comput., 2009.

    • 2-Pyridone Tautomerization + H2O - 2-Pyridone → 2-Hydroxypyridine tautomerization reaction catalyzed by one proton-shuttling water using 67 internal coordinates

      Reference: Jason L. Sonnenberg, Kim Wong, Gregory A. Voth, and H. Bernhard Schlegel, J. Chem. Theory Comput., 2009.

  • Empirical Valence Bond (EVB) Toolkit - The EVB Toolkit is a series of Mathematica modules implementing the core routines necessary for a Distributed Gaussian (DG) EVB surface fit. All modules are compatible with versions 5.2 and 6.0 of Mathematica. To install the toolkit, decompress the .zip file and place the resulting Chemistry folder into AddOns/ExtraPackages inside of Mathematica's base directory.

    Reference: Jason L. Sonnenberg, Kim Wong, Gregory A. Voth, and H. Bernhard Schlegel, J. Chem. Theory Comput., 2009.

    • Constants.nb - Useful conversion factors: Bohr2Angstrom, Calorie2Joule, Hartree2Kcalmol, Radian2Degree

    • EVB.nb - All of the core EVB routines including V11(q), V22(q), and V122(q)

    • fchk.nb - A full compliment of data extraction routines for Gaussian fchk files

    • Glib.nb - A library package contains common functions for the Gaussian file modules

    • Glog.nb - A full compliment of data extraction routines for Gaussian log files

    • GMRES.nb - An implementation of the Generalized Minimum Residual (aka DIIS) solver

    • InternalCoordinates.nb - General internal coordinate manipulation routines for bonds, angles and dihedrals
  • Fractional Coordinate Converter - A Mathematica 6.0 and later notebook for generating Cartesian coordinates from crystal structure fractional coordinates.

  • Intrinsic Reaction Coordinate - A Mathematica 6.0 and later notebook containing the Muller-Brown, Serpentine, and Whirlpool surfaces used in method development.

    Reference: Carlos Gonzalez, H. Bernhard Schlegel, J. Chem. Phys., 1991, 95, 5853-5860.

    Reference: H. Bernhard Schlegel, J. Chem. Soc. Faraday Trans., 1994, 90, 1569-1574.

  • Optimization on a Seam - A Mathematica 6.0 and later notebook for optimizing on a seam of intersection between two different spin states. This notebook requires a working installation of the EVB toolkit.

  • Spin Projection - A Mathematica 6.0 and later notebook for computing Yamaguchi's spin projected energies, gradients and Hessians. This notebook requires a working installation of the EVB toolkit.

  • TD-CIS - This Mathematica 6.0 or later notebook can be used to simulate the electronic optical response of a molecule in an intense laser pulse. The notebook reads the results of a CIS calculation from a Gaussian output file and integrates the time dependent Schrodinger equation in the space of single excitations under the influence of a time varying electric field.

    Reference: H. Bernhard Schlegel, Stan M. Smith, and Xiaosong Li, J. Chem. Phys., 2007, 126, 244110-244123.