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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 objectoriented 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.

DGEVB
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, 27192729.

HCN
 HCN → CNH
isomerization reaction using five internal coordinates
Reference:
H. Bernhard
Schlegel and Jason L. Sonnenberg, J. Chem. Theory Comput.,
2006, 2,
905911.

Malonaldehyde
 Malonaldehyde intramolecular proton transfer using 35 internal
coordinates
Reference:

Pentadiene
 Pentadiene intramolecular proton transfer using 59 internal
coordinates
Reference:

2Pyridone
Tautomerization  2Pyridone → 2Hydroxypyridine
tautomerization reaction using 56 internal coordinates
Reference:
Jason L.
Sonnenberg and H. Bernhard Schlegel, Mol. Phys., 2007,
105, 27192729.
Reference:
Jason L. Sonnenberg, Kim Wong, Gregory A. Voth, and H. Bernhard
Schlegel, J. Chem. Theory Comput., 2009.

2Pyridone
Tautomerization + H_{2}O  2Pyridone
→ 2Hydroxypyridine tautomerization reaction catalyzed by one
protonshuttling 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 V_{11}(q),
V_{22}(q), and V_{12}^{2}(q)
fchk.nb
 A full compliment of data extraction routines for Gaussian
fchk files
 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 MullerBrown,
Serpentine, and Whirlpool surfaces used in method development.
Reference:
Carlos
Gonzalez, H. Bernhard Schlegel, J. Chem. Phys., 1991,
95, 58535860.
Reference:
H. Bernhard
Schlegel, J. Chem. Soc. Faraday Trans., 1994,
90, 15691574.
 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.
 TDCIS  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,
244110244123.

