Exorga, Inc. - Consultants in Chemistry, Molecular Modeling, and the Environment
A
company of consultants in chemistry and chemical engineering, actively involved
in computational, experimental, and environmental organic chemistry.
An anthraquinone intercalated into a DNA double
helix, from the x-ray coordinate data.
Find out about STR3DI32's molecular models, how you can generate them, and how you can use them in your daily tasks, presentations, reports and publications.
THE STR3DI MOLECULAR
MODELERS
STR3DI32
generates the best molecular simulations of single molecules and docked
molecular clusters, of any molecular mechanics program currently available.
The
advanced structure analytical algorithms of STR3DI32 are tried and tested, and
shown to be vastly superior to others, in detecting subtle stereo-electronic
effects embedded in diffraction generated coordinate data, like aromaticity and
anomeric effects.
If
you are examining diffraction (x-ray, etc) coordinate data for accuracy and
reliability, then only STR3DI32’s proven and superior structure analytical
algorithms will ensure you of accurate analysis.
The
new version 5.2.0.x has -
·
A new utility, Str3Dinv.Exe, now prompts Str3Di32 to automatically
perform a complete inventory of all .SXS and .XXS files in the \Str3Di
directory, and to use the data to update the MOLECULE.LOG and MOLECULE.HTM
database files. If you have
several thousand structure files, the way we do, and might need to refresh
functional group data in the MOLECULE.LOG, then this is VERY useful.
·
A new parent directory name - \Str3Di. The parent/working directory for
STR3DI32 must now be named \Str3Di.
New users and upgraders can use the utility app Str3DiUtil1
to facilitate the renaming process.
·
An improved molecular database. STR3DI32 records and monitors data (including a functional
group analysis) on newly simulated molecules in it’s MOLECULE.LOG and
MOLECULE.HTM database files.
Invalid/outdated entries are automatically flagged and deleted. An improved method for searching the
log/database is now available.
·
An extended set of structure drawing tools and
options. Now the structures of new
molecules can be created and modified using the recently updated CONSTRUCTION -
CREATE/MODIFY a MOLECULE routine, AND the structures
of existing molecules can be modified using the recently updated CONSTRUCTION -
ADD ATOM/H/lp routine.
·
Accommodates organic-ligand-chelated metal atoms up to
coordination number 8.
·
In version 4.6.0.24 we finally release the entirety of the
totally revamped structure-energy minimization routine, to provide more
accurate energy minima, faster than before. This new module will enable STR3DI32 to perform the energy
minimizations at almost the same speed, regardless of the molecule’s size.
·
A routine for calculating the molar enthalpies of formation
of simple small molecules. This
routine will be improved in future versions.
·
A totally reworked routine for automatically importing
molecules of any size, up to 7168 atoms and lone pairs. No user input is necessary to adjust
the programme’s limits, etc.
·
A totally new scaling algorithm for changing molecule
sizes, that enables the program to automatically display molecules of all
sizes, when in “autosize” mode. An
optional “autozoom” feature that lets you watch the structure size adjustments.
·
A new algorithm to detect bonds that are not shown in x-ray
crystallography due to atom coordinate errors (leading to an atom being
slightly displaced beyond bonding distance).
·
The Move/Measure routine automatically shows the energy of
the molecule, if it is fully valence elaborated with hydrogens and lone pairs.
·
The file importer FILECONV now works totally transparently,
and automatically, with STR3DI32, and it is a joy.
·
Crystallographers and unit cell constructors will
appreciate the new features.
·
As of version 4.5.0.6, STR3DI32 will insert the molecule’s
functional groups into the database, molecule.log/molecule.htm, in addition to
your own (VERY BRIEF) molecular description. This evolving feature will enhance your ability to search
for molecules with special features.
·
Atom coordinate data is saved, once again, in single
precision numbers, so making the data files even smaller.
·
And, if you like sound effects, now we’ve got some. Feel free to suggest, or substitute,
ones you like.
Meeting
More Challenges
Most
C-H, O-H and N-H bonds in x-ray crystal structures are too short! In fact, based on the covalent radii of
the atoms involved, in most instances the bond lengths would correspond to bond
orders of 2! This is such a
widespread problem that we tweaked STR3DI32 to handle these errors. We also tweaked the graphics to enhance
the viewing of multiple bonds in molecules, and the clipboard routine to give
more options in copying images.
The jump from version 4.2.0.x to version 4.5.0.x embraced several nice
changes.
Then,
there is the totally unfathomable reluctance of the PDB group to require that
element symbols be written as required in all of the rest of chemistry (Ca, Pb,
Sb, etc, while PDB files use CA, PB, SB).
So PDB files, as now written, can confuse users between calcium (written
CA in PDB files) and carbon-alfa (also written CA in PDB files). Talk about nightmares. We’ll just have to keep making FileConv
smarter, and we have, but get with the times PDB!
More
Modern
Exorga,
Inc. has developed
STR3DI32, “the next generation of molecular modelers”. Based on
the new QVBMM molecular mechanics force
field, this high-level molecular modeling tool has re-defined
the standards for molecular mechanics programs. STR3DI32 will enable you to tackle theoretical problems in
organic chemistry that are outside of the reach of all other molecular
mechanics based force fields.
You'll also be able to explore some problems that cannot be fully
resolved by the currently available molecular orbital-based methods.
For
example, acetals show unusual conformational preferences that have puzzled
theoreticians for many years, and this phenomenon has been called the Anomeric
Effect. In 1998, following a study
of saccharides and other simple acetals, using STR3DI32 and data from the
Cambridge Crystallographic Database, Vernon. G. S. Box published (Heterocycles)
a landmark paper in which the roles of C-H hydrogen bonding, and lone pair
interactions, were definitively used to rationalize the Anomeric Effect, and
the Reverse Anomeric Effect. At
that time, MO calculations were unable to simulate these stereo-electronic
effects. It was only in 2007 that
MO studies by O. Takahashi, et al., were able to corroborate the roles of C-H
hydrogen bonding in the Anomeric Effect (Carbohydrate Research).
More
Versatile
No
substructure templates used in energy minimization
Have
you ever wondered how the MM2, MM3, MM4, MMX programs manage to perform such
fast structure energy minimizations?
Well, these programmes use a massive set of “functional group templates”
to squish the molecular model into, rather than to truly search for a minimum
energy structure. So MM3 and MM4
have templates for 46 kinds of oxygens, 21 kinds of nitrogen, 16 kinds of
carbon, 9 kinds of sulfur, etc.
You might as well use an elaborate set of mechanical models that has 46
types oxygen atoms, 16 types of carbons, etc, and you would get the same data
as that from MM3 and MM4, with less hassle.
STR3DI32
has one set of parameters that are widely used for each hybridization state,
for each of the common atoms, just the way nature does it. There are only two situations in which
STR3DI32 uses special parameters, and these are for cyclopropane carbons and
for thiophenes sulfurs. STR3DI32
executes a thorough search for minimum energy structures, no fiddles or
artificial templates are used, and the results are the most reliable. This fundamentally different type
of search for structure energy minima takes a bit longer than using templates,
but is much more congruent with true scientific principles, and much more
reliable.
Incidentally,
MM4 was released in 2003 and started to try to use polarized bonds, the way
STR3DI32 did seventeen – 17 - years before!
Versatile
cluster creation and handling
We
all know about the great importance of molecular associations and
clusters. Whether we are
considering simple dimers, trimers, or other oligomers, or the more complex
cases of molecular clusters like solvated species. The potential energies of molecules can vary dramatically if
they are associated with other atoms of molecules, as opposed to if they are
isolated. The same applies to the
energies of the conformations of molecules. So, it is obvious that occasionally you will wish to study
molecular complexes.
STR3DI32
can handle molecular complexes.
Most of the other molecular mechanics programs, MM2, MM3, MM4, MMX,
PCModel, and others, simply cannot minimize the structures of molecular
clusters. The algorithms that
these programs use to generate rapid, and sometimes erroneous, minimizations
would not allow them to handle molecular clusters properly.
Easy
“trapping” of high energy conformers
Have
you ever wished to stop the structure minimization process at some point that
is not a minimum, in order to examine the molecule’s parameters? STR3DI32 allows you to do that. You can’t do this if you are using
other molecular modeling programs, especially if you don’t want to place
artificial geometrical constraints on your molecule.
Easy
importation of data in several data file formats
The
utility program FILECONV was specifically developed to convert molecular
modeling file formats into those native to STR3DI32 and can be executed from
within STR3DI32. FILECONV can also
be used as a stand-alone program.
Thus, STR3DI32, in conjunction with FILECONV, will read files written in
the following formats and for the following programs - Alchemy, Cambridge
Crystallographic Data Centre (CIF, CMF and CSD), M3D, MDL, MM2, MM3, INP, MMX,
MOL, MOL2, MOPAC, PCModel, PDB, Schakal, XYZ as well as its native files (MXS,
SXS, XCC and XXS). FILECONV, can
be used as a stand-alone program, and is also automatically activated from
within STR3DI32.
We
have seen the true range of human folly in the way people put together
structure data files. Even with
strong standards for files like CIF, or PDB, the guys sometimes even omit the
name of the molecule under study.
These errors can stymie FILECONV, and if they do, then you might need to
go familiarize yourself with the proper file format, adjust the one you wish to
work with, and then reuse FILECONV.
Sorry about that, but until we have self-critical scientists, the problem
will remain.
Better
Data
We
have generated, and structure-energy minimized, molecular simulations using
MM2, MM3, MMX, and PCModel, and then subjected these to structure-energy
minimizations using STR3DI32. In
every case, STR3DI32 generated better, more geometrically accurate when
compared to x-ray diffraction data, minimum energy structures.
Some
people seem to be bothered by the time it takes for STR3DI32 to minimize the
structure energy of a molecular model.
You should be aware that STR3DI32 will generate a structure that is
within 0.2 kcals/mol of the closest energy minimum within two minimization
cycles. If you want a “quick and
dirty” structure, then you can stop the minimization process at any time, or
you could have used one of the other molecular modeling programs. On the other hand, if you let STR3DI32
alone, it will do the most thorough search of the molecule’s potential energy
surface that any molecular modeling program can do, and that takes time. Further, you should be aware that when
a structure energy minimization process is being launched, you do have the
option of going for a quick minimization.
Better
Data Analysis
Data
from diffraction studies (x-ray crystallography, etc) are only as useful as the
method that converts the data into realistic molecular structural
information. Often diffraction
derived coordinate data have errors that are overlooked by crystallographers
that use inferior molecular modeling programs, because these programs cannot
draw the experimenter’s attention to these errors. STR3DI32 will immediately draw its user’s attention to these
errors.
The
other molecular modeling methods, which rely on a user generated atom
connectivity file to construct the molecular model, will often display
structures that have ridiculous bond lengths, as normal structures.
These
errors are not apparent in the structure unless the user of these other
programmes goes measuring all of the bond lengths. There are thousands of instances of coordinate data for
molecules, available on the WWW, and from the scientific literature, that have
these errors. So, do you know what
you are really looking at? We have
a large collection of coordinate data, from all kinds of sources that show
molecules with some single bonds having the lengths of triple bonds.
Other
molecular modeling programs don’t attract the user’s attention to this kind of
data error, but STR3DI32 does.
STR3DI32 will always show the user a displayed structure that is
consistent with the implied bond data (lengths and angles), and if there are
errors, then these errors will be very visible onscreen.
More
Updates
We are always trying to develop new algorithms that will
enable STR3DI32 to generate better molecular simulations. Sometime these efforts bomb, but
sometimes they work! We think that
it is good science to try to develop new algorithms since they might offer
subtle insights into the way things really work.
The 2.00X versions of STR3DI32 will no longer be supported,
and will be replaced by the newly updated version 3.000.N.X.
The
3.000.1.X versions of STR3DI32 were tweaked to better handle cyclopropanes,
cyclobutanes and thiophenes, to make many features more user friendly, and to
completely eradicate some long-standing problems.
The
new 3.000.2.X versions of STR3DI32 build upon the successes of the past
versions, and have totally revamped structure-energy minimization routines to
provide better minimum energy structures.
The “user friendliness” of the program has also been significantly
enhanced.
Version
3.000.3.X has important new algorithms to handle memory usage, structure data
importation and display, and updated user prompting with hints.
Version
4.0.0.X has further refinements to improve user-friendliness, user error
control, improved help file access, and added sound effects.
More
Support
Current
STR3DI32 users should keep abreast of new developments in the STR3DI molecular
modelers by visiting the STR3DI TEMPLATES SITE, the STR3DI UPDATE NEWS SITE., and the STR3DI NEWS SITE. When you are there, remember to check
out the TIPS and HINTS help page.
We have worked on eradicating installation problems by now offering
a download of a zipped folder of a “newly installed” \STR directory. Many people will find this easier than
downloading STR32D, even though this file offers a more versatile installation
method. We do apologize for any
installation inconveniences you’ve had.
Windows Vista users should watch out for security issues
when installing and running any new program.
For more details about STR3DI32 jump to STR3DI32 details.and STR3DI32
feature list
What
Do You NEED To Do?
Accept
the challenge! Run molecular
simulations using STR3DI32, and then using any other molecular mechanics
program that you wish, and see which program produces the best simulation. STR3DI32 gives you complete control of
your molecular modeling experiences.
EXORGA
INC. - Consultants in ALL areas of organic chemistry and Custom chemistry
software producers!
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