Molecule is a program for generating, editing and displaying molecular
structures on an Apple Macintosh
computer or on a PC running
ARDI's Executor. Originally written as
a simple tool for checking Ampac inputs and visualizing calculated
structures as simple "wireframes", Molecule has been extended and improved
and is now available as a versatile tool for computational chemistry.
The program offers the following features :
- it can read many computational chemistry file formats (Ampac, Mopac, and
Gaussian input and archive files,
Spartan inputs,
MacSpartan files,
Gamess-US outputs,
various cartesian coordinates formats, fractional crystallographic coordinates,
etc.);
- it can generate input files for a number of popular computational chemistry
programs:
Gaussian,
Mopac, Ampac,
Spartan and MacSpartan,
ADF,
Gamess-US,
PS-GVB,
offering easy-to-use interfaces, and for the freeware
Persistence of Vision
raytracing program;
- it includes an interactive molecule builder, a freehand drawing tool
and several editors for the generation of molecular structures;
- it allows the definition of template structures for frequently used
functional groups (a number of common ones are included with the program);
- definition of a "Z-Matrix" internal coordinate description of the
molecule, including automatic generation of a sensible Z-matrix starting
from cartesian coordinates;
- it offers tools for handling molecular symmetry, including the
generation of symmetry-dependent atoms and symmetrization of a Z-matrix;
- it can generate high-quality pictures, including elementary colors,
of molecular structures, with extensive user-control over style, plot type,
atom and bond sizes and labels, atom shading, etc. Look
here, here, or
here for some examples;
- it can display molecular orbitals in schematic form, with the size of
the atomic orbitals representing the AO coefficients in the MOs. Display
of d-orbitals is included. Several styles are available. Two examples are
shown here.
- it can animate vibrational normal modes;
- it can interpolate between two isomeric structures;
- it offers interactive display of geometrical parameters (distances,
angles, dihedral angles), results from quantum chemical computations
(atomic charges, bond orders, nuclear shieldings/chemical shifts) and
derived information (H-H coupling constants based on the Karplus equation);
- it can estimate atomic charges and bond energies, based on
electronegativity equalization;
- it includes a "quick-and-dirty" force field module for pre-optimizing
structures generated with the freehand-drawing tool or using standard
structural parameters. An example is given here;
- it is possible to add user-written modules ("Plug-ins") for extra
functionality (input and output formats, display, editor, and calculation
modules);
- up to 40 molecules of up to 320 atoms each can be handled, depending
on the amount of memory available to the program;
- it was written "as compatible as possible", so that it runs on any
Macintosh, ranging from the Mac Plus to the PowerMacs (the present version
is not yet "native"), as well as on a PC under
ARDI's Executor. No color display or
math coprocessor is necessary;
- it is "speed-optimized", so that it runs reasonably fast even on
low-end machines;
- it runs, and has extensively been tested, under MacOS (6.0.8 to 9.2.2) AND
MacOS X (in the Classic environment). A native MacOS X version is in preparation.
In response to the comments of many users of older versions, Molecule is
designed to be an easy-to-use program. Full control over all program
features is available through the standard Macintosh user interface,
via pull-down menus.
Shortcuts are available for some frequently-used commands.
A utility program, "makexyz", is freely available for non-commercial use.
Click here to download the Fortran source (7kb).
This program reads a Gaussian 94 or Gaussian 98 output file, extracts
- the last set of cartesian coordinates;
- the first three vibrational normal modes;
- the 5 highest occupied and 5 lowest virtual orbitals, which are combined
to an easy-to-read minimal basis set format;
and writes this data to a file which can be read directly by Molecule. In
addition, MSC's XMol and R.Sayle's
RasMol
can also read the structure information.
Molecule is being made available through site licenses. For academic and
educational groups, the license fee depends on the size of the group, as
follows:
- Regular license fee : 275.00 Euro
- Reduced license fee for small groups, up to 5 members : 175.00 Euro
- Additional fee for "classroom" use : 100.00 Euro
Fees for industrial licenses are available from the author upon request.
The license allows installation of the program on all computers belonging
to the research group or institution that licensed Molecule, including
installation on file-servers, and use of the program by all members of the
group. In addition, group members are allowed to install the program on
their private machines, e.g. for use at home.
A user manual will be available in electronic form. The manual may be reproduced
for use by all group members.
An extension of the license is available for "classroom use". This allows
installation of the program on a file-server for a teaching laboratory.
Students are allowed to install and use the program on their private
machines for the duration of the course.
Contact
Nico van Eikema Hommes, the author of Molecule, via email
or send a letter to the following address:
Dr. N.J.R. van Eikema Hommes
Computer-Chemie-Centrum,
Universitaet Erlangen-Nuernberg
Naegelsbachstrasse 25
91052 Erlangen, Germany
Fax: +49(0)-9131-8526565
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