The idea behind MOZYME was conceived on a fishing boat on the way back from the Gothenberg Archepeligo during a conference at Aspenas. Prof. Allinger had given some very enjoyable talks on molecular mechanics, and it was singularly frustrating to be aware that we could never hope to run such large systems using conventional matrix algebra.
Near the end of an afternoon excursion, during which there was a little too much to drink, the idea of using Lewis structures as an alternative to matrix algebra was born. Of course, the idea itself was not novel, but perhaps the way in which the idea was rendered as method and then as FORTRAN code is novel.
Anyhow, from the start of method development, in May 1993, until now, May 1996, the project has matured into the program MOZYME. The first stage was to do a feasibility study - that took about one entire year! After that came the extension of the original concept so that it would work for a wide range of systems, and to include the dull but essential features such as restarts, data-checking routines, and output routines. Finally, the method was published, and many test cases were run, and a distribution tape made, so that researchers could reproduce the calculations described in the publications.
MOZYME is copyrighted software. Fujitsu is the copyright owner. Researchers interested in getting a copy of MOZYME should contact Fujitsu. No version of MOZYME will be placed in the public domain for the forseeable future.
MOZYME has a limited range of functionalities. Among these are:
MOZYME is a semiempirical quantum chemical program for the study of large systems. The methods in MOZYME are similar to those in MOPAC. The fundamental difference is that, whereas MOPAC uses matrix algebra for the solution of the self-consistent field equations, MOZYME uses localized molecular orbitals. Examples of MOZYME calculations
Examples of systems that have been run successfully using MOZYME are
Grignard reagent Methyl magnesium bromide can be drawn as a Lewis
structure as Me(-) Mg(++) Br(-).
Benzaldehyde Using localized orbitals, delocalized systems can be
modeled.
Crambin The geometry of a small cross-linked protein is optimized.
Poly paraphenylenebenzobisthiazole A highly delocalized
one-dimensional
polymer.
Boron Nitride A simple two-dimensional layer system.
DiamondA simple three-dimensional solid
A Protein from the Brookhaven Protein Data Bank
Rhizomucor miehei Lipase A large protein.
Examples of Data
Grignard Reagent
A single-point calculation of Methyl Magnesium Bromide demonstrates that
quite complicated Lewis structures can
readily be handled.
Examples of Data
Benzaldehyde
Examination of the 3 dimensional structure of benzaldehyde shows the
following Lewis structural elements:
6 C-H single bonds.
6 C-C sigma bonds in the aromatic ring.
1 C-C sigma bond to the carbon of the aldehyde group.
1 C-O sigma bond.
3 C=C pi-bonds in the aromatic ring.
1 C=O pi bond.
2 lone pairs on the oxygen.
There are thus 18 bonds and 2 lone pairs - these form the occupied set
of
localized molecular orbitals. For every
bond there is an antibond, therefore there are 18 antibonds. These form
the virtual set of LMOs.
The results of a MOZYME run show that the electronic structure is the
same
as that from MOPAC. In both these
calculations, the starting points were the same. For this calculation,
MOZYME took about 70 seconds to MOPAC's
13 seconds. Much of the extra time can be accounted for because MOZYME
geometry optimizer is less efficient...
Examples of Data
Crambin
Crambin is a 46 residue protein found in Abbysinian cabbage seed. From
the
PDB file the 3 dimensional structure
shows that crambin is highly compact. A 1SCF calculation shows that 7
residues are ionized.
The heat of formation of the optimized geometry is -XXXX kcal/mol.
Examples of Data
Poly-paraphenylenebenzobisthiazole
Like
MOPAC, MOZYME can model high polymers with large unit cells. Thus PBT, a
system with a three ringed
heterocyclic fragment and one para-phenyl ring per unit cell is best
represented in the calculation by three fundamental
unit cells. The elastic modulus of such a system can be calculated using
Hook's law - stretch the unit cell, and monitor
how the heat of formation changes.
Examples of Data
Boron Nitride
Boron nitride illustrates a two-dimensional layer system. For this
calculation, 49 fundamental unit cells were used as
the unit cell. In the calculation, each unit cell is surrounded by 8 =
(3**N)-1 other unit cells, where N is the
dimensionality of the system. After geometry optimization, a 1SCF
calculation gives the final electronic structure.
Examples of Data
Diamond
Like MOPAC, MOZYME can calculate the electronic structure of
three-dimensional systems. A good test case is
diamond: every atom is in the same environment and any differences in
the
electronic structure of the atoms is an
indication of errors in the method. Using a cluster of 216 atoms, the
results of a 1SCF calculation show that all the
atoms are, indeed, identical. Making the unit cell bigger, to 512 atoms,
did not result in any significant change in the
electronic structure.
Examples of Data
Rhizomucor miehei Lipase
This system has 4,054 atoms. As with crambin, the 3 dimensional
structure
shows that the protein is highly compact.
A 1SCF calculation shows that 7 residues are ionized.
Limits of MOZYME
As distributed, MOZYME is configured to run systems of up to 10,000 atoms. If a very small system is run, then the size of the running executable is a little less than 2.5 megabytes. The extra memory required for larger systems is proportional to the square of the size. This is a result of the electrostatics, which involve every pair of atoms. The largest system run during the testing phase was just over 4,000 atoms, and that ran in about 400 megabytes.
Comments to
James J. P. Stewart
URL:
http://home.att.net/~MrMOPAC/mozdesc.htm