Software News and Updates

Gabedit—A Graphical User Interface for Computational

Chemistry Softwares

ABDUL-RAHMAN ALLOUCHE1,2,3
1
Universite´ de Lyon, F-69622 Lyon, France
2
Universite´ Lyon 1, Villeurbanne, France
3
CNRS, UMR 5579, LASIM, France

Received 22 October 2009; Revised 8 April 2010; Accepted 10 May 2010

DOI 10.1002/jcc.21600
Published online 6 July 2010 in Wiley Online Library (wileyonlinelibrary.com).

Abstract: Gabedit is a freeware graphical user interface, offering preprocessing and postprocessing adapted (to
date) to nine computational chemistry software packages. It includes tools for editing, displaying, analyzing, convert-
ing, and animating molecular systems. A conformational search tool is implemented using a molecular mechanics or
a semiempirical potential. Input files can be generated for the computational chemistry software supported by Gabe-
dit. Some molecular properties of interest are processed directly from the output of the computational chemistry pro-
grams; others are calculated by Gabedit before display. Molecular orbitals, electron density, electrostatic potential,
nuclear magnetic resonance shielding density, and any other volumetric data properties can be displayed. It can dis-
play electronic circular dichroism, UV–visible, infrared, and Raman-computed spectra after a convolution. Gabedit
can generate a Povray file for geometry, surfaces, contours, and color-coded planes. Output can be exported to a
selection of popular image and vector graphics file formats; the program can also generate a series of pictures for
animation. Quantum mechanical electrostatic potentials can be calculated using the partial charges on atoms, or by
solving the Poisson equation using the multigrid method. The atoms in molecule charges can also be calculated.
Gabedit is platform independent. The code is distributed under free open source X11 style license and is available at
http://gabedit.sourceforge.net/.
q 2010 Wiley Periodicals, Inc. J Comput Chem 32: 174–182, 2011

Key words: GUI; computational chemistry softwares; animation; charge distribution; electrostatic potential; molecu-
lar density; visualization

Introduction The quantum chemistry softwares are also used increasingly in

education. Having a GUI, Gabedit is easy to use, and is, therefore,
The continuous speedup of computer hardware has made quan- well suited as an introduction for students learning to prepare data
tum chemistry programs very valuable tools in fields as diverse files (which are often quite complex), to start calculating and learn-
as drug design, planning, synthesis, and materials science. Pre- ing to analyze the results. Gabedit is a teaching aid, in this context.
dictions from quantum chemistry methods can be considered as Gabedit provides a package to assemble and modify molecu-
complementary to other investigation. However, non-specialists lar structures in a simple and powerful application. It can gener-
are often discouraged from using these tools due to the use of ate input files for the most popular CCS including Gamess-US,1
unfamiliar concepts or complex user interfaces. Experienced Gaussian,2 Molcas,3 Molpro,4 MPQC,5 Open Mopac,6 Orca,7 PC
computational chemistry software (CCS) users, as well as non- Gamess,8 and QChem,9 then run the appropriate CCS and
specialists, could benefit from a user-friendly interface that sim- finally, analyze the results of these calculations.
plifies this step, and then distills important and relevant output The default settings make Gabedit readily accessible to
from CCS calculations into a convenient format. Some CCS pro- beginners and students, but the default settings can of course be
viders simplify the use of their product by developing a specific custom-tailored to suit the more experienced user.
graphical user interface (GUI). In many instances, optimum The remainder of the article is organized as follows: a
study of a given system requires the use of several quantum description of the general capabilities of Gabedit is followed by
chemistry softwares, so Gabedit as a single GUI able to assist
the user to manage multiple calculations using various quantum
chemistry softwares is practical and advantageous. Correspondence to: A.-R. Allouche; e-mail: [email protected]

q 2010 Wiley Periodicals, Inc.

 Graphical User Interface for CCS 175

more in-depth discussions of the geometry builder, the CCS Table 1. LIST of File Formats Supported by Gabedit.
input generator, and CCS output visualization. Finally, a com-
parison between capabilities of Gabedit and those of other soft- Operation List of files formats
wares is provided.
Read geometry Output file of any of nine computational chemistry
softwares (CCS) supported by Gabedit:
Program Overview Gamess-US, Gaussian, Molcas, Molpro, MPQC,
Open Mopac, Orca, PC Gamess and Q-Chem.
Gabedit is a GUI developed 1) to facilitate the production of Input file of Gaussian, Molcas, MPQC, Open
results from quantum chemistry methods through various CCS Mopac, Orca, PC Gamess and Q-Chem.
and 2) to provide a thorough analysis of these results. It con- Gabedit, Molden, XMol XYZ, Hyperchem,
structs a molecular geometry, from which an input file for any Tinker, Mol, Mol2 and Protein Data Bank
one of the Gabedit-supported CCS packages can be made. It (PDB), OpenMopac aux, Gamess, and PC
Gamess IRC files.
then runs the chosen CCS and provides an analysis of corre-
Save geometry Input file of any of nine CCS supported by Gabedit.
sponding output.
Gabedit, XYZ, Hyperchem, Mol2, Tinker, PDB,
Gabedit can build the molecule atom by atom, or fragment by Mopac Z-matrix or Gaussian Z-matrix.
fragment. It can also read the geometry from a variety of file for- Read volumetric Gaussian cube file (orbitals, density, potential,
mats, as discussed in the section on the geometry builder. Once data Laplacian), Molpro cube file (orbitals, density,
geometry has been established, the user can create an input data potential, Laplacian), Gabedit cube file, ADF
file for any CCS supported by Gabedit. Gabedit contains a text ASCII tape 41 (orbitals and density), Grid
editor and the input CCS data require modification. The user can ASCII Molcas file, and Q-Chem grid file.
run the CCS job from the graphical interface of Gabedit, either Export the image Geometry, surfaces, contours, color-coded planes,
on the local computer or on a remote host server. in vectorial file electric dipole, principal axes, XYZ axes, labels,
format spectrum can be exported in EPS, PDF, SVG
The most powerful features of Gabedit are associated with the
files formats.
analysis it performs on the CCS output files. Appropriate visualiza-
Save the screen Any window of Gabedit (Draw geometry, OpenGL
tion can be a critical aid to the proper interpretation of the results, in file window, Curves window) can be saved in PNG,
and also offers a valuable educational tool. Gabedit is tuned to pro- JPEG, BMP, PPM files format.
vide real-time visualization with modest hardware requirements,
so that the program can run on a standard laptop computer to pres-
ent results at scientific meetings, or be used in classroom environ-
ments for educational demonstrations. Gabedit can produce output all be altered. The values of distances, angles, and dihedral are
in a variety of formats suitable for both hardcopy and Web-based recalculated automatically after any change of the connectivities.
publication as well as screen-based visual formats. These options Gabedit can optimize the structure by a molecular mechanics
are described in detail in the section on the output file analysis. (MM) calculation implemented in it, using Amber parameters. It
Visualization options include simple structures, series of struc- can also optimize the structure, interactively, through a semiem-
tures, normal modes of vibration, molecular orbitals, total electron pirical method using Open Mopac or PC Gamess. The user can
densities, density differences, molecular electrostatic potentials perform a molecular dynamics (MD) simulation using a MM
(MEPs), and any other volumetric data properties that can be read potential implemented in Gabedit or a semiempirical potential
from a variety of file formats recorded in Table 1. The openGL using Open Mopac or PC Gamess. Conformational searches
library furnishes 3D hardware graphics acceleration. based on a MD simulation followed by an optimization of struc-
tures selected during the MD simulation can be performed with
Gabedit. The potential used during the simulation can be a MM
Geometry Builder or a semiempirical potential.
Most computational chemistry softwares are able to freeze
Gabedit allows the user to construct a molecule and to examine some atoms of the molecule during the geometry optimization
it in three dimensions (see Fig. 1). procedure. Gabedit allows doing this using a ‘‘click to select"
Various possibilities are offered by Gabedit to build the ge- operation to specify which atoms are to be frozen.
ometry of a molecule. From Gabedit one can build molecules Gaussian can perform ONIOM10 calculations, where the mo-
atom by atom, from fragments, or using the tools implemented lecular system under investigation is divided into two or three
in Gabedit for building linear molecules, cyclic molecules, mole- layers which are treated at different levels of sophistication.
cules with an axis of symmetry, polypeptides, polynucleic acids, Gabedit accepts a selection of atoms to be considered at a given
polysaccharides, and nanotubes. The structure of a molecule can level, and then the desired level of calculation (low, medium, or
be imported from an existing file (the file formats supported by high). This facilitates Gaussian ONIOM calculations.
Gabedit are listed in Table 1). Gabedit is able to modify the ge- The user-defined geometry can be saved in various file for-
ometry of the molecule in 3D. An XYZ editor included in Gabe- mats, which are indicated in Table 1. This image can be
dit can be used to change the coordinates. Gabedit can convert exported in any of the vectorial formats and on a Povray format.
the XYZ format to a Z-matrix format. The Z-matrix can then be Gabedit can also save a screen capture of the geometry to a file.
modified using an editor with which the distance between atoms, The image can equally be copied to clipboard, to include it in
angles, dihedral angles, and the connectivity between atoms can another program such as MS-word, open office, or gimp.

Journal of Computational Chemistry DOI 10.1002/jcc

176 Allouche • Vol. 32, No. 1 • Journal of Computational Chemistry

Figure 1. The Gabedit geometry builder window in action.

Once the molecule building step is performed, the user can the graphical interface of Gabedit. Figure 3 illustrates the sub-
easily generate an input file for any of the nine CCS supported mission step of a CCS (Orca in this example) job via Gabedit.
by Gabedit to date. If the user accepts the default settings, Gabedit builds a script
file (sh under Unix, bat under Windows) and submit a monopro-
cessor calculation, on the local machine or on a remote machine,
Input Generation following user’s choice. However, the user can use his own
script file to submit his job with one or more processors. The
Gabedit incorporates an input generator to help construct CCS user script can accept any number of parameters, but the last pa-
input files. Figure 2 illustrates the interface of the input builder rameter must be the name of the input file. With the Gabedit
for Gaussian software. The input groups that are present enable source files, it includes scripts (sh) for the most common batch
the user to specify the type of wavefunction, basis set, type of systems, such as load sharing facility, LoadLeveler, portable
run (optimization, internal reaction coordinate, saddle point batch system, and sun grid engine. The user can use these scripts
search, etc.), molecular parameters (charge, multiplicity, symme- to run his favorite CCS but the user should ensure that these
try, etc.), and various other options that affect how the CCS will scripts appear in his PATH.
run the calculations. To submit a CCS job under Windows, the user must specify
The constraints on the geometry optimization, defined during the locations of the directories where the CCS routines are in-
the geometry-building step are taken into account when creating stalled, using the settings/preferences options in the Gabedit
the input CCS file. For some CCS, like Gamess, Molcas, and menu.
PCGames, one can define the symmetry group in the input file.
Gabedit can detect the symmetry and it can remove the atoms
that are generated by the CCS according to symmetry group. Result Analysis

Gabedit processes numerical information produced by CCS. This

Submitting a CCS Job processing can result in direct visualization, if all the necessary
information is available directly. If it is not, additional visualiza-
Having created an appropriate input file, the user can run the tion information may be calculated via Gabedit in an intermedi-
CCS job on the local computer or on a remote host server via ate computational step.

Journal of Computational Chemistry DOI 10.1002/jcc

 Graphical User Interface for CCS 177

Figure 2. An example to generate input for Gaussian.

Figure 3. Submission job window.

Journal of Computational Chemistry DOI 10.1002/jcc

178 Allouche • Vol. 32, No. 1 • Journal of Computational Chemistry

this case, the atomic orbitals must be supplied via a Gabedit file.
Gabedit can calculate the MEP from volumetric electronic den-
sities, by solving the Poisson equation numerically, using the
multigrid method.12 Gabedit can also calculate the MEP using
the partial atomic charges. Isosurface contours for a chosen vol-
umetric property can be color coded using any other volumetric
property (Fig. 5). More options are available to manipulate a
volumetric property. For example, Gabedit can square, scale,
apply a restriction, compute the gradient, compute the Laplacian
(generally used to compute the Laplacian of the electronic den-
sity, an important property in the atoms in molecule (AIM)
Bader’s theory13) for the volumetric property (read from a file
or calculated by Gabedit). Gabedit can take the difference
between one volumetric calculation and another; this feature is
generally used to analyze the consequence of electronic excita-
tion.
Figure 4. Vibration vectors for a selected mode of the benzene Using the electronic density, Gabedit can calculate the AIM
molecule. charges via the method proposed by Tang et al.14 There are sev-
eral different approaches to calculate Bader volumes. Early algo-
rithms were implemented for quantum chemistry calculations of
small molecules, in which the gradient of the charge density can
Animation of Computation Results be calculated from derivatives of an analytic wavefunction,
using a linear combination of Gaussian basis sets.13,15 The
Gabedit is able to animate computation results. This includes the method has been criticized as being computationally expensive
animation of normal modes as well as any multiframe computa- for large systems. The grid-based algorithm of Tang et al. has
tion from CCS. Gabedit displays normal modes as a series of been implemented in Gabedit. This method is highly efficient,
geometries. The starting geometry is gradually distorted by scal- scales linearly with system size, and is robust to complex bond-
ing the atomic displacement vectors that make up a normal ing topology found in condensed systems and is not limited to
mode. Gabedit allows the animation to be saved in the form of a wavefunctions where the Gaussian basis sets are used.
series of image files (cf. Table 1). These can be converted by Using the gl2ps library, Gabedit is able to export all visual-
external programs (such as ‘‘Convert’’ from ImageMagik) to a ized properties in a 2D vector graphic files formats (Table 1).
.gif or .png animated file. The animation can also be saved in a Gabedit can also export the scene, without the labels, in a Pov-
series of Povray files to obtain a high quality animated file. ray file. A screen capture can be saved in a file (Table 1).
Gabedit also indicates the vibration vectors (Fig. 4). The minor
components can be excluded to avoid cluttering the picture.
Gabedit can read the normal modes from the output files of the
nine CCS supported by Gabedit, from a Gabedit file, or from a
Molden11 file.
Gabedit can animate reaction paths from internal reaction
coordinate calculations, MD trajectories, optimization, and sad-
dle runs.

Analysis of Volumetric Data Properties

Gabedit can visualize any volumetric data properties in a user-

defined plane either as a 2D contour map or 2D color-coded
plane. It can also visualize these data in a 3D isosurface. Most
of the volumetric data file formats can be read by Gabedit. Sev-
eral volumetric data properties can also be calculated by Gabedit
using the molecular orbitals and the atomic basis sets taken
from the output files produced by the Gabedit-supported CCS
packages. Gabedit can also read the orbitals and the atomic basis
sets from a Molden file and (naturally) from a Gabedit format
file. Using the orbitals and the atomic basis sets, Gabedit can
calculate the following volumetric properties: molecular orbitals,
electronic density, electron-localized function, solvent-accessible
surface, and spin density. It can also compute the molecular Figure 5. Electronic density isosurface, color-coded with the spin
electronic density minus the atomic electronic densities, but in density of C6H5NO2 anion, calculated at the UHF/6-31G* level.

Journal of Computational Chemistry DOI 10.1002/jcc

 Graphical User Interface for CCS 179

Figure 6. A calculated B3LYP/6-311G* IR spectrum of benzene molecule, compared to an experi-

mental one (read from a JDX file format).

Other Properties in the source files. Gabedit is able to export the curves in a 2D
vector graphic file formats (Table 1). A screen capture of the 2D
Repulsion integrals can be calculated analytically or numerically window can be saved in a file (Table 1).
by solving the Poisson equation using the multigrid technique.
Permanent electronic dipoles can be calculated using the partial
charges or from the volumetric electronic density. The transition Comparisons with Other Softwares
matrix between orbitals can be calculated by Gabedit.
The density of states can be calculated (convolution using Some distributors of computational chemistry programs have
Lorentzian or Gaussian line shapes) and shown in 2D plotting developed a customized graphical interface to facilitate the use
window, implemented in Gabedit. The half-width at half-maxi- of their product. For example, GaussView20 is a GUI for Gaus-
mum, used in the convolution can be changed by the user. The sian,2 MacMolPlt21 is a GUI for Gamess-US,1 and CCP122 is a
electronic circular dichroism, ultraviolet-visible, infrared, and GUI for Gamess-UK.23 Each of these interfaces supports only
Raman spectra calculated as peaks by the CCS can be also con- one CCS. Theoretically, to study a given system, the use of sev-
voluted by Gabedit, using Lorentzian or Gaussian line shapes. eral quantum chemistry softwares is often necessary and then a
The spectra as peaks and after convolution are shown in the 2D graphical interface that supports the majority of CCS is useful.
plotting window of Gabedit, where several options are available Several freeware programs have been developed for this aim.
to edit the curve; scaling, shifting, saving of data on a text The visualization of results is the main objective of some of
file to be used by other graphics softwares, changing of the line these programs, such as Molekel,24 Jmol,25 and Molden,26
style, and more others options. The user can also measure the whereas editing the geometry used in CCS is the main objective
distance between two points of the 2D window. One can add of other softwares such as Ghemical27 and Avogadro.28 As an
curve by reading a text multiple columns file, JDX format16–18 application, Gabedit provides a freeware GUI enabling the edi-
file, and JMRui19 text file (Fig. 6). Using the chemical shift and tion of the geometry, the creation of input files, the submitting
indirect spin–spin coupling parameters, Gabedit can simulate nu- of a CCS job, the computation of several properties, and the vis-
clear magnetic resonance spectra. The program currently handles ualization of the results for nine softwares, among the most pop-
a maximum of 10 spin groups to economize computational ular ones in the field of quantum chemistry. Table 2 gives an
effort, but the number of spin groups can easily be augmented overview of the capabilities of Gabedit compared to the Molden

Journal of Computational Chemistry DOI 10.1002/jcc

180 Allouche • Vol. 32, No. 1 • Journal of Computational Chemistry

Table 2. Comparison Between Gabedit, Molden (Version 4.8 under Linux) and Avogadro
(Version 1.0.0 Under Windows).

Operation Gabedit Molden Avogadro

Tools for building Z-matrix editor. XYZ editor. Draw molecule Z-matrix editor. XYZ editor. Draw molecule atom
geometry atom by atom. Build polypeptides: 24 by atom. Build polypeptides:
conformations are available, polynucleic three conformations are available.
acids, polysaccharides and nanotubes. Build Build molecule fragment by
molecule fragment by fragment: about 200 fragment: implemented but no
fragments in the database, the user can add fragments are available in the
his personal fragments. Optimization of database. Optimization of
geometry by MM or semi-empirical geometry by MM.
methods. Conformational search based on Conformational search (based on
molecular dynamics simulation, using a MM openbabel) limited to very small
or semi-empirical potential. molecules.
Creation of input Gabedit has a tool to create input file for: Mopac7: no control of Avogadro has a tool to create input
file Gamess-US, Gaussian, Molcas, Molpro, consistency between file for Gamess-US, and
computational MPQC, Open Mopac, Orca, PC Gamess and charge and Molden has a Gaussian. No control of
chemistry Q-Chem. The consistency between charge tool to create input file for consistency between charge and
softwares and spin multiplicity is controlled by Gamess-UK, Gaussian, spin multiplicity. The symmetry
Gabedit. The constraints on the geometry and spin multiplicity. The is not computed by Avogadro and
optimization, defined during the building symmetry is not computed the input geometry is for a C1
molecule step are taken into account when by Molden and the input group.
creating the input CCS file. For some CCS, geometry is for a C1
like Gamess, Molcas and PCGames, one can group.
define the symmetry group in the input file.
Gabedit can detect the symmetry and it can
remove the atoms that are generated by the
CCS using the symmetry group. Gabedit can
create an input file for ONIOM Gaussian
calculation.
Run a CCS Gabedit can run any of the nine CCS Molden can run Gamess-UK, Not implemented.
supported, locally or on a remote machine. Gaussian, Mopac7 locally.
The output file of the CCS can be got from
the remote machine by one click.
Quantities Molecular electrostatic potential (MEP), MEP, orbitals, electronic Orbitals, electronic density.
calculated orbitals, electronic density, difference density, difference density,
before density, Laplacian of the density, AIM Laplacian of the density
visualization charges, Fukui functions, ELF, SAS, and SAS. The peak IR
Coulomb integrals, transition matrix and Raman spectra can be
elements. Volumetric data can be scaled, convoluted with a
squared or subtracted. The peak IR, UV, Gaussian or a Lorentzian
Raman, ECD spectra can be convoluted with profile.
a Gaussian or a Lorentzian profile. NMR
spectra can be calculated from chemical
shift and spin–spin coupling constants.
Gabedit can calculate the ro-vibrational
correction to chemical shifts and to spin–
spin couplings. The isotope distribution for a
molecule can be calculated by Gabedit.
Visualization of Gabedit can visualize the geometry, volumetric Molden can visualize the Avogadro can visualize the
results data as surface, contours or plans color- geometry, volumetric data geometry, volumetric data as
coded form. It can animate the vibration. as surface or as contours surface form. It can animate the
The IR, Raman, UV, ECD, NMR spectra form. It can animate the vibration. The IR, Raman, UV
(with or without a convolution) can be vibration. The IR and and CD spectra can be plotted as
plotted and compared to other data (a full Raman spectra (with a peak form (without a
2D plotting tool is implemented). convolution) can be convolution).
plotted.

Journal of Computational Chemistry DOI 10.1002/jcc

 Graphical User Interface for CCS 181

and Avogadro programs, which are among the softwares closest Gill, P. M. W.; Johnson, B.; Chen, W.; Wong, M. W.; Gonzalez, C.;
to Gabedit. Pople, J. A. Gaussian 03, Revision C. 02; Gaussian Inc.: Walling-
ford, CT, 2004.
3. Karlström, G.; Lindh, R.; Malmqvist, P.; Roos, B. O.; Ryde, U.;
Conclusion Veryazov, V.; Widmark, P.; Cossi, M.; Schimmelpfennig, B.; Neo-
grady, P.; Seijo, L. Comput Mater Sci 2003, 28, 222.
Gabedit provides an easy-to-user interface for most computa- 4. Werner, H.; Knowles, P. J.; Lindh, R.; Manby, F. R.; Schütz, M.;
tional chemistry packages, offering a range of features appealing Celani, P.; Korona, T.; Mitrushenkov, A.; Rauhut, G.; Adler, T. B.;
Amos, R. D.; Bernhardsson, A.; Berning, A.; Cooper, D. L.; Deegan,
to the novice as well as the veteran user. Gabedit provides to
M. J. O.; Dobbyn, A. J.; Eckert, F.; Goll, E.; Hampel, C.; Hetzer,
CCS users a wide range of tools that facilitate the use of these
G.; Hrenar, T.; Knizia, G.; Koppl, C.; Liu, Y.; Lloyd, A. W.; Mata,
softwares: very powerful and easy to use builder geometry, a R. A.; May, A. J.; McNicholas, S. J.; Meyer, W.; Mura, M. E.;
tool to create the input files for the CCS, a tool to facilitate the Nicklass, A.; Palmieri, P.; Pfluger, K.; Pitzer, R.; Reiher, M.; Schu-
run of the CCS job, and varied tools to analyze at the best the mann, U.; Stoll, H.; Stone, A. J.; Tarroni, R.; Thorsteinsson, T.;
calculation results. Wang, M.; Wolf, A. MOLPRO, Version 2008.3, A Package of Ab
Gabedit produces high-quality graphics output, suitable for Initio Programs; Molpro: University of Birmingham, UK, 2008.
publication. It also supports the most popular formats for the 5. Janssen, C. L.; Nielsen, I. B.; Leininger, M. L.; Valeev, E. F.;
publication of results on the Web, such as jpeg, png, and ani- Kenny, J. P.; Seidl, E. T. The Massively Parallel Quantum Chemis-
mated png or gif. Gabedit has already established a sizable user try Program (MPQC); Sandia National Laboratories: Livermore, CA,
base worldwide; 20% of which is used in teaching applications. 2004.
6. Stewart, J. J. P. MOPAC2009; Stewart Computational Chemistry:
Many enhancements are planned for future versions of Gabe-
Colorado Springs, CO, 2009.
dit. Among these are plans to support several other CCS not
7. Neese, F. ORCA, An Ab Initio, Density Functional, and Semiempiri-
presently supported by Gabedit, including PSI3,29 DFTB1,30 cal Program Package; Max-Planck-Institut für Bioanorganische
and NWChem31. Several other tools will evolve to enhance the Chemie: Mülheim an der Ruhr, Germany, 2009.
analytical capacity of the package, for example, a tool to locate 8. Granovsky, A. A. PC GAMESS/Firefly. Available at: http://classic.
and visualize the critical points of the electronic density (AIM chem.msu.su/gran/gamess/index.html. (accessed September 3, 2009).
Bader theory) and a tool to search the basins of ELF32 and to 9. Shao, Y.; Molnar, L. F.; Jung, Y.; Kussmann, J.; Ochsenfeld, C.;
integrate the electronic density for each basin. Brown, S. T.; Gilbert, A. T.; Slipchenko, L. V.; Levchenko, S. V.;
O’Neill, D. P.; DiStasio, R. A., Jr.; Lochan, R. C.; Wang, T.; Beran,
G. J.; Besley, N. A.; Herbert, J. M.; Lin, C. Y.; Van Voorhis, T.;
Availability Chien, S. H.; Sodt, A.; Steele, R. P.; Rassolov, V. A.; Maslen, P. E.;
Korambath, P. P.; Adamson, R. D.; Austin, B.; Baker, J.; Byrd, E.
Gabedit is available free of charge to all users, on an open F. C.; Dachsel, H.; Doerksen, R. J.; Dreuw, A.; Dunietz, B. D.;
Dutoi, A. D.; Furlani, T. R.; Gwaltney, S. R.; Heyden, A.; Hirata,
source license. To obtain Gabedit please refer to the Web address:
S.; Hsu, C.; Kedziora, G.; Khalliulin, R. Z.; Klunzinger, P.; Lee, A.
http://gabedit.sourceforge.net/. Complete system requirements,
M.; Lee, M. S.; Liang, W.; Lotan, I.; Nair, N.; Peters, B.; Proynov,
feature lists, user manual, several tutorials as well as the program E. I.; Pieniazek, P. A.; Rhee, Y. M.; Ritchie, J.; Rosta, E.; Sherrill,
itself can be found at that site. C. D.; Simmonett, A. C.; Subotnik, J. E.; Woodcock, H. L., III;
Zhang, W.; Bell, A. T.; Chakraborty, A. K. Phys Chem Chem Phys
2006, 8, 3172.
References 10. Dapprich, S.; Komaromi, I.; Byun, K. S.; Morokuma, K.; Frisch, M.
J. J Mol Struct THEOCHEM 1999, 461, 1.
1. Schmidt, M. W.; Baldridge, K. K.; Boatz, J. A.; Elbert, S. T.; Gor- 11. Schaftenaar, G.; Noordik, J. H. J Comput Aided Mol Des 2000, 14,
don, M. S.; Jensen, J. H.; Koseki, S.; Matsunaga, N.; Nguyen, K. 123.
A.; Su, S.; Windus, T. L.; Dupuis, M.; Montgomery, J. A., Jr. J 12. Briggs, E. L.; Sullivan, D. J.; Bernholc, J. Phys Rev B 1996, 54,
Comput Chem 1993, 14, 1347. 14362.
2. Frisch, M. J.; Trucks, G. W.; Schlegel, H. B.; Scuseria, G. E.; Robb, 13. Bader, R. F. W.; Gangi, R. A. J Am Chem Soc 1971, 93, 1831.
M. A.; Cheeseman, J. R.; Montgomery, J.; Vreven, T.; Kudin, K. 14. Tang, W.; Sanville, E.; Henkelman, G. J Phys: Condens Matter
N.; Burant, J. C.; Millam, J. M.; Iyengar, S. S.; Tomasi, J.; Barone, 2009, 21, 084204.
V.; Mennucci, B.; Cossi, M.; Scalmani, G.; Rega, N.; Petersson, G. 15. Stefanov, B. R.; Cieslowski, J. J Comput Chem 1995, 16, 1394.
A.; Nakatsuji, H.; Hada, M.; Ehara, M.; Toyota, K.; Fukuda, R.; 16. Baumbach, J. I.; Davies, A. N.; Lampen, P.; Schmidt, H. Pure Appl
Hasegawa, J.; Ishida, M.; Nakajima, T.; Honda, Y.; Kitao, O.; Chem 2001, 73, 1765.
Nakai, H.; Klene, M.; Li, X.; Knox, J. E.; Hratchian, H. P.; Cross, J. 17. Davies, A.; Lampen, P. Appl Spectrosc 1993, 47, 1093.
B.; Bakken, V.; Adamo, C.; Jaramillo, J.; Gomperts, R.; Stratmann, 18. Lampen, P.; Hillig, H.; Davies, A.; Linscheid, M. Appl Spectrosc
R. E.; Yazyev, O.; Austin, A. J.; Cammi, R.; Pomelli, C.; Ochterski, 1994, 48, 1545.
J. W.; Ayala, P. Y.; Morokuma, K.; Voth, G. A.; Salvador, P.; Dan- 19. Stefan, D.; Di Cesare, F.; Andrasescu, A.; Popa, E.; Lazariev, A.;
nenberg, J. J.; Zakrzewski, V. G.; Dapprich, S.; Daniels, A. D.; Vescovo, E.; Strbak, O.; Williams, S.; Starcuk, Z.; Cabanas, M.; van
Strain, M. C.; Farkas, O.; Malick, D. K.; Rabuck, A. D.; Raghava- Ormondt, D.; Graveron-Demilly, D. Meas Sci Technol 2009, 20,
chari, K.; Foresman, J. B.; Ortiz, J. V.; Cui, Q.; Baboul, A. G.; Clif- 104035.
ford, S.; Cioslowski, J.; Stefanov, B. B.; Liu, G.; Liashenko, A.; Pis- 20. Nielsen, A.; Holder, A. GaussView 3.0 User’s Reference; Gaussian,
korz, P.; Komaromi, I.; Martin, R. L.; Fox, D. J.; Keith, T.; Al- Inc.: Pittsburgh, PA 2003.
Laham, M. A.; Peng, C. Y.; Nanayakkara, A.; Challacombe, M.; 21. Bode, B. M.; Gordon, M. S. J Mol Graph Model 1998, 16, 133.

Journal of Computational Chemistry DOI 10.1002/jcc

182 Allouche • Vol. 32, No. 1 • Journal of Computational Chemistry

22. Sherwood P.; van Dam H. J. J.; Thomas J. The CCP1 GUI Project. Margraf, T.; Niehaus, C.; Ochsenreither, S.; Vandermeersch, T.;
Available at: http://www.cse.scitech.ac.uk/ccg/software/ccp1gui/. Avogadro. Version 1.0.0. Available at: http://www.avogadro.open-
(accessed September 3, 2009). molecules.net. (accessed February 3, 2010).
23. Guest, M. F.; Bush, I. J.; Van Dam, H. J. J.; Sherwood, P.; Thomas, 29. Crawford, T. D.; Sherrill, C. D.; Valeev, E. F.; Fermann, J. T.;
J. M. H.; Van Lenthe, J. H.; Havenith, R. W. A.; Kendrick, J. Mol King, R. A.; Leininger, M. L.; Brown, S. T.; Janssen, C. L.;
Phys 2005, 103, 719. Seidl, E. T.; Kenny, J. P.; Allen, W. D. J Comput Chem 2007,
24. Varetto, U. Molekel; Swiss National Supercomputing Centre: 28, 1610.
Manno, Switzerland. Available at: http://molekel.cscs.ch. (accessed
30. Aradi, B.; Hourahine, B.; Frauenheim, T. J Phys Chem A 2007, 111,
September 3, 2009).
5678.
25. Jmol: an open-source Java viewer for chemical structures in 3D.
Available at: http://www.jmol.org/. (accessed October 8, 2009). 31. Kendall, R. A.; Apra, E.; Bernholdt, D. E.; Bylaska, E. J.; Dupuis,
26. Schaftenaar, G.; Noordik, J. H. J Comput Aided Mol Des 2000, 14, 123. M.; Fann, G. I.; Harrison, R. J.; Ju, J. L.; Nichols, J. A.; Nieplocha,
27. Hassinen, T.; Perakyla, M. J Comput Chem 2001, 22, 1229. J.; Straatsma, T. P.; Windus, T. L.; Wong, A. T. Comput Phys Com-
28. Ali, S.; Banck, M.; Braithwaite, R.; Bunt, J.; Curtis, D.; Fox, N.; mun 2000, 128, 260.
Hanwell, M.; Hutchison, G.; Jacob, B.; Lonie, D.; Mantha, J.; 32. Savin, A.; Silvi, B.; Colonna, F. Can J Chem 1996, 74, 1088.

Journal of Computational Chemistry DOI 10.1002/jcc