SPARTAN 5.0 (UNIX Only) Features Overview

This page describes SPARTAN 5.0, Wavefunction's flagship modeling software for UNIX workstations. This text-based summary is complemented by a set of software feature
Options: I. Graphical User Interface IV. Properties Calculated
II. Computational Methods V. Additional Features
III. Tasks Performed

I. The SPARTAN 5.0 Graphical User Interface

Introduction: SPARTAN has a single, fully-featured GUI that many consider to be the best in the business. In very little time, you can build and manipulate molecules, display computed graphics, and see the answers to your most complex chemistry questions.

Builders: Molecules can be constructed in minutes using graphical "builders" that provide fast and easy access to a wide range of elements and hybridizations.

Entry (Organics) Builder. Uses 20 basic atomic fragments (e.g., sp 3 carbon) to allow building of most common organic structures. Included with the Entry builder is a selection of molecular fragments divided into Groups (e.g., "Ester") and Rings (e.g., "Phenanthryl") to make building even easier.

Peptide Builder. Access to 20 natural amino acids and their stereoisomers for rapid construction of polypeptide chains.

Expert Builder. Adding to the power of the Entry and Peptide builders, the Expert builder facilitates rapid building of inorganic and organometallic molecules. Includes modifiable hybridizations, a library of Ligands (e.g., "Cyclopentadienyl"), rapid bond editing, and more.

Nucleotide Builder. This new builder allows for the rapid building of single and double-stranded DNA and RNA helices with just a few clicks of the mouse. Related displays will (in SPARTAN 5.1) include ribbon graphics for easier viewing of large strands.

Library Builder. SPARTAN 5.0 builders can access your own libraries of molecules and molecular fragments. This makes building easier and faster than ever before. Included is a library of transition states for common organic reactions.

Combinatorial Builder. A new tool to rapidly assemble sets of molecules which differ by substitution.

Transition States Builder. Automatic transition state guesses using the Linear Synchronous Transit method

Crystal/Solids Builder (SPARTAN 5.1).

Minimization: Fast Minimization. Molecular mechanics minimization for preliminary structure refinement using either the SYBYL or the Merck Molecular Force Field (MMFF).

Displays:
Spreadsheet Analysis Tools. New spreadsheets for output and analysis of molecules and molecular groups.
    1. Wide variety of properties for QSAR analysis.

    2. Property plots along x and y axes, which may incorporate related molecular graphics.

    3. Standard statistical analysis, including linear regression.

    4. Import/Export of spreadsheet tables to Microsoft Excel and as tab-delimeted text.

Multiple Model Display Styles Properties. Display of calculated properties, including geometrical parameters, volumes and surface areas, dipole moments, and atomic charges.

Surfaces. Display of isosurfaces including electron densities, spin densities, electrostatic and polarization potentials, and molecular orbitals. Each surface can be viewed in a variety of style Slices The best slices since sliced bread. Display all properties listed under "Surfaces" as single or multiple 2D countours or slices.

Texture Mapping In addition to continuous surface property maps, SPARTAN 5.0 allows you to texture map discrete bands of information to surfaces.

Reaction Animation. Molecular and graphical models generated and animated along reaction coordinates for a list of molecules.

Properties Mapping Mapping of one property to an isosurface of another property, which means that one property is color-coded by another. Two beautiful examples are a map of the electrostatic potential of Urea to an electron density surface, and a map of the spin density of 4-Pentynel Radical on its electron density surface.

Vibration Animation. Molecular and graphical models animated along vibrational coordinates for a list of molecules.

Stereo 3D Display graphics in stereo 3D using colored glasses.

Multiple Molecules. Have as many molecules in the main viewing window as you want. Manipulate singly or in concert.

Interfaces. Seamless access to Gaussian92 and Gaussian94.

Other GUI Features: Import and Export. Rapid conversion of PDB, and SYBYL Mol., SYBYL Mol2, and MACROMODEL molecular structure files.

PICT Graphics. Export of rgb formatted graphics files.

OSF/Motif Toolkit. SPARTAN makes use of the OSF/Motif toolkit, the most widely used toolkit for X-Windows programs. This makes the user interface easy to use, reliable, and easier to learn for users of other common X-Windows programs.

X-Windows Support. Remote GUIs (sold separately) provide complete 3-D visualization through X-windows as well as GL and OPENGL. This allows any machine that has an X server to display SPARTAN graphics, including PCs and Macintoshes. The X-Window system will even perform stereo rendering compatible with the colored lens glasses.


II. SPARTAN 5.0 Computational Methods

Introduction: SPARTAN 5.0 provides a wide range of computational methods in order to address the needs of educators, bench chemists, and professional molecular modelers. All methods are easily accessed via the seamless graphical interface, putting real computationl power just a few clicks away.

Methods: Molecular Mechanics. Use of the SYBYL and Merck Molecular Mechanics Force Fields. The Merck MFF is parameterized for major classes of organic and bio-organic molecules. A new minimizer has been implemented for faster treatment of 1,000+ atom molecules.

Semi-Empirical. Methods Including MNDO/d, AM1, PM3, and PM3(tm) for Transition Metals. AM1-SMX methods are available for treatment of molecules in water.

Ab Initio. Included are a variety of basis sets for Hartree-Fock and MP2 methods.

Density Functional Theory (DFT). Local (VWN) and Non-Local Becke-Perdew (BP86 and pBP86). The latter is new to SPARTAN 5.0 and promises to be more than ten times faster than Hartree-Fock methods for medium-to-large molecules.
Other: Properties Calculations. Including QSAR Descriptors and Vibrational Frequencies.

Torsion-Angle-Only Optimization.

Extended QSAR descriptors.


III. Tasks Performed by SPARTAN 5.0

Examples: Coordinate Driving To simulate chemical reactions.

Molecular Alignment Previously called "Similarity and Superposition Analysis", this feature allows manual and automatic graphical comparisons between molecules.

Conformational Analysis. Systematic, Osawa, Monte Carlo, and Genetic Algorithm.

Energies. Calculate heats of formation or strain energies.

Geometries. Determine equilibrium geometries.

Transition States. Determine transition state geometries.

Normal Modes. Calculate normal-mode vibrational frequencies.


IV. Properties Calculated by SPARTAN 5.0

Properties: Charges. Mulliken and electrostatic-fit charges.

Orbital Charges. Natural bond orbital charges.

Bader Charges. SPARTAN 5.1.

Dipole Moments.

Other. Enthalpies, entropies, and free energies.


V. Additional Features in SPARTAN 5.0

Miscellaneous: Optimization. All of SPARTAN 5.0's back-end codes have been fully optimized for the MIPS R5000 and R10000 processors, and for SGI's new O2 and Octane workstations.

"Basket" submission. Remote submissions work one machine or a list ("basket") of machines. This means that if a Conformational Analysis generates ten conformers, and you have ten workstations licensed with SPARTAN, you can distribute the calculations over all ten workstations.


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