Spartan 5.1 has improved, added, changed, or removed a number of
features and functions. Among the more important are the following.
1. The Graphical User Interface:
- What's New?
- Virtual Reality Mark-up Language (VRML) graphics
files, for display and manipulation of 3D molecular structures on the
Internet, can now be exported (from Export under File menu).
- The new Spartan Exchange and Collection
files, used in conjunction with SpartanView, can now be imported and
exported (from Export under File menu)
A SPARTAN Exchange file contains molecule information and all graphics
displayed for a single molecule, while a SPARTAN Collection file contains
the same information and graphics for the entire collection of molecules
shown on screen.
- SPARTAN 5.1 can import and display FDAT crystal structures such as those
provided by the Cambridge
Crysallographic Database (CCDB). SPARTAN can also produce expanded
(periodic) structures from the unit cells.
- A "Polyhedra" display mode has been added to the Model menu
draws shaded polyhedra around atomic centers surrounded by
O, F, Cl, Br, or I (or any combination of these elements).
Elements may be added to or subtracted from this list by editing
"Vertex Elements:" under "Polyhedra:" in the Preferences dialog (Preferences
under the menu).
- A new function, "Annotate", has been added to the Model menu. This
allows the user to specify one or more alternative names (aliases), provide
a heat of formation, or make comments. This information is added to the
input file and is presently accessible only through Annotate. (Future
developments will allow information to be entered into database.)
- "Freeze Center" has been modified (Geometry Menu) to allow automatic
freezing of heavy atoms only. The primary use of this is to facilitate
optimization of hydrogen positions (only) in X-Ray crystal structures.
- "Report Chirality" has been added to the Geometry Menu. Selection results
in R/S designation of all chiral centers.
- Bond making between two atoms, and between an atom and a free
valence (in addition to bond making between two free valences), is now
available in the builders. This leads to an increase in coordination
number of the atoms involved.
- A new bond type has been added to the expert Model Kit. In conjunction
with the new bond making capability mentioned above, this can be used to
designate weakly-bonded interactions (e.g., hydrogen bonds).
- A new function, "Grow Hydrogens", has been added to the Edit menu (in the
builders). The primary use of this is to add hydrogens which might be
missing from X-Ray crystal structure data.
- What's Improved?
- Conformational searching has been completely reworked. Bonds are
marked for rotation and rings for "rotation" automatically without user
intervention. A search method ("Systematic" or "Monte-Carlo") is
automatically chosen as that which leads to the smaller number of "moves".
Bond and ring selections can be altered, the extent of bond rotations
(3-fold, 4-fold, etc.) adjusted, and the search method changed by selecting
Conformer Search from the Build menu.
- Molecule alignment has been completely reworked. It is no longer
necessary to relabel atoms in the individual molecules, as common
substructures are now automatically identified wherever possible.
Relabeling is still possible and will override the automatic
assignments. Operation is as before: First, select a "parent molecule" (the
molecule to which other members of the list are to be aligned), then
select Align coordinates from the molecule menu in the spreadsheet.
Click on atoms to be aligned (at least three atoms, but preferably
no more than six) and click on Align.
2. Computational Methods:
- What's New?
- Density Functional. Overall numerical stability has been
significantly improved without
adversely affecting overall performance. In addition, an "extra fine"
integration grid is available (invoked using the keyword expression
"grid=xf" or "mesh=xf"). This leads to a factor of two increase in time
(less as system size increases), but significant reduction in numerical
"noise". The extra fine grid may be important for accurately establishing
small energy differences such as conformation energy differences.
- Semi-Empirical. Analytical gradients and second derivatives have
been implemented following: S. Patchkovskii and W. Thiel, J. Computational
Chem., 17, 1318 (1996). Together with other improvements (in initial
wavefunction guesses and memory allocation) the 5.1 code is approximately
twice as fast as the 5.0 code for geometry (transition-state geometry)
optimization and frequency calculations for non-d-function cases, and 2-4
times faster where d-functions are involved (MNDO/d and PM3 for transition
metals). Analytical gradients are used by default but may be overridden by
the "numerical" keyword. Analytical second derivatives are used by default
provided that sufficient memory is available, and may be overridden by the
"numerical" keyword. "freq=analytical" forces calculation of second
derivatives by analytical methods irrespective of available memory.
- Semi-Empirical. The SM5.4 solvation model: C. C. Chambers, G. D.
Hawkins, C. J. Cramer and D. G. Truhlar, J. Phys. Chem,., 100, 16385
(1996), is available for both AM1 and PM3 wavefunctions
(SM5.4a and SM5.4p). It may be invoked using the keyword expression
solvent=SM54. (Attempt to use SM5.4 method with MNDO or
MNDO/d will result in an error.) Like the other solvent models, SM5.4 is
rapid for single calculations but VERY SLOW for geometry (transition-state
geometry) optimizations. SM5.4 is also accessible from the Property Module.
- What's Improved?
Spartan's implementation of MMFF94 has been tested against and yields the
correct results for all 753 molecules contained in the
- Mechanics and Semi-Empirical.
Optimization (transition-state optimization) has been improved to recognize
convergence earlier than in version 5.0.
- All Modules.
Selection of "Global" inside the mechanics, Semi-Empirical, Ab Initio and
Density Functional dialog (as well as inside the setup dialog for Gaussian)
no longer applies to Title, Total Charge and Multiplicity entries.
3. Properties Module:
- What's New?
- The SM5.4 solvation model: C. C. Chambers, G. D. Hawkins, C. J. Cramer and
D. G. Truhlar, J. Phys. Chem., 100, 16385 (1996) is available for both AM1
and PM3 wavefunctions (SM5.4a and SM5.4p). These may be invoked using
keyword expressions "solvent=SM54A" and "solvent=SM54P", respectively.
- Polarizabilities and hyperpolarizabilities from semi-empirical
wavefunctions: J. J. P. Stewart and K. M. Dieter, J. Computational Chem.
11, 82 (1990), are available and may be invoked by the keyword "polar".
Calculation requires approximately 20 times the amount of time than for a