Spartan

Molecular mechanics is presently the only practical method for calculations on very large molecules or for conformational searching on highly flexible molecules. MMFF94, in particular, has proven to be a reliable and fast tool for conformational analysis. There are no atom limits for molecular mechanics calculations.

Both the SYBYL and MMFF94 force fields are supported. SYBYL extends throughout the entire Periodic Table while MMFF94 has been specifically parameterized to reproduce geometries and conformations of organic molecules and biopolymers. Additionally, an MMFFaq option applies an aqueous solvent energy correction to energy data, of special utility in ranking conformers.

Semi-empirical models are the simplest of the quantum chemical schemes, and are useful for equilibrium and transition-state structure calculations. PM3, in particular, has proven to be a reliable tool for geometry calculations on transition metal inorganic and organometallic compounds.

MNDO, AM1, RM1, PM3, and PM6 methods are supported. MNDO/d extensions for heavy main-group elements have been implemented and PM3 parameters for most transition metals are available.

The RM1 (Recife Model 1) reparameterization of AM1 is new in Spartan'06. In most cases RM1 yields superior results to both AM1 and PM3 (for organic molecules).

Hartree-Fock models useful for predicting structure, energy and property calculations, in particular for organic molecules.

A variety of standard basis sets are supported: STO-3G, 3-21G, 6-31G*, 6-311G*, cc-pVDZ, cc-pVTZ and cc-pVQZ, with extensions including (d), (d,p), (2d), (2d,2p), (2df, 2dp), (3d, 3p), (3df, 3dp) and diffuse functions and/or additional polarization functions. Also supported are a variety of pseudopotentials for calculations on molecules incorporating heavy elements. Spartan allows for the import of additional basis sets, and for the construction of user-created basis sets. Additionally, a new dual basis set procedure is is available, allowing the approximation of basis set extension using perturbation theory (for improved precision and performance).

Determine total energy (Hartree-Fock, density functional, Møller-Plesset, advanced correlated), heat of formation (semi-empirical or thermochemical recipes) or strain energy (molecular mechanics).

Determines local energy minimum.

Determine transition-state geometry, with the option to calculate the intrinsic reaction coordinate (IRC).

All methods except MP3, MP4 and advanced correlated. Needed to establish validity of transition states.

Chemical shifts from Hartree-Fock and DFT models.

Hartree-Fock/CIS and DFT/TDDFT models.

Search conformation space to determine either lowest-energy conformer or diverse set of low-energy conformers. Additional procedure for generating a conformational library of the minimal set of conformers required to span conformational space (used in conjunction with Similarity Analysis).

Define and calculated energies for user specified geometrical coordinates. Useful to locate a transition state along a reaction coordinate and to analyze conformational energy changes. Includes the ability to provide grid scanning to concurrently drive two geometric coordinates.

Assess and quantify similarity between molecules or molecules and pharmacophore models. Similarity based on molecular structure or chemical function descriptors is available. A scoring function based on rms deviations is available (and automatically adjusts to account for unfavorable intramolecualr interactions).

Mulliken and Natural Bond Orbital Charges are available as are charges based on fits to electrostatic potentials.

Enthalpies, entropies and free energies as well as isotope effects, based on calculated geometries and IR vibrational frequencies.

Dipole, quadrapole and higher moments, polarizabilities (including alpha, beta, and gamma terms).

Weight, Area, Volume, Symmetry Group, HOMO and LUMO Energies, Polar Surface Area, LogP, Ovality, Q-Minus, Q-Plus, Electronegativity and Hardness.

Vibrational spectra available from IR calculations including plotting and animation of vibrational modes.

Aqueous solvation energies from SM6, SM5.4 or SM50R models. An additional continuum solvation model is also included.

Chemical shift calculations for Hartree-Fock and DFT models, and, new in Spartan'10, a correction scheme for the EDF2 model for chemical shifts with accuracy of 1.7-1.8 ppm.

Vertical excitation spectra based using either CIS/CIS(D) or Time Dependent DFT models is provided.

Access and retrieve/replace constructed or imported structures from a library of 150,000* molecules, pre-calculated at up to 5 quantum theory levels: HF/3-21G, HF/6-31G*, EDF1/6-31G*, B3LYP/6-31G*, and MP2/6-31G* models. Retrieved data includes: the name, equilibrium geometry, gas-phase energy, estimated (aqueous) solvation energy, HOMO and LUMO energies, dipole moments, electrostatic-fit atomic charges, surface area, polar surface area, volume, weight, symmetry, and spectra data.

*Spartan'10 includes a subset of >6,000 molecules. The full SMD (and SSPD) is available for purchase. Customers with Maintenance receive the full SMD at no additional charge.

The SSPD is a collection of >75,000 molecules that includes highly accurate structures, energies, properties, and IR and NMR spectra as well as the molecule's wavefunction for auto-generation of graphical surfaces.

Access to exact and substructure searching of the Spartan Reaction Database of more than 1500 reaction types for providing initial structure guesses for transition state geometry calculations.

Accesses the Cambridge Structural Database (CSD)* of over 440,000 experimental X-ray crystal structures for organic and organometallic molecules, together with their literature references. Spartan optionally adds hydrogens and refines hydrogen positions.

*CSD may be licensed from the Cambridge Crystallographic Data Centre or one of its distributors.

Spartan can retrieve (based on PDB ID) entries from RCSB PDB (provided your computer has current internet connectivity). The Protein Data Bank includes more than 50,000 x-ray crystal and NMR structures of proteins and nucleic acids. Band ligands may be extracted.

Spartan automatically processes files comprising lists of molecules. In general, operations applicable to a single molecule may be applied to lists of molecules. Spartan is optimized to operate on lists of hundreds of molecules (not thousands or tens of thousands).

NOE data can be applied to conformational searching as a post-processing filter.

If your computer has internet connectivity, Spartan'10 can retrieve and plot experimental IR (~ 14,000 molecules) and UV/Vis (~ 1,500) spectra from the NIST Chemistry Webbook.

If your computer has internet connectivity, Spartan'10 can retrieve and plot experimental NMR Chemical Shifts (~ 15,000 molecules) from the NMR database maintained by the University of Cologne.

Spartan'10 can optionally extract bound ligands and their environment from protein (PDB) files, along with customizable chemical function descriptors (CFD's).

Geometry optimization and conformational analysis are available subject to user specified constraints (of distance, angle, or torsion angle) and/or frozen atoms.

Parallel to the Spartan Molecular Database (SMD) and Spartan Specta and Properties Database (SSPD), users can save Spartan data in the .spentry format (Spartan Molecular Database format) and construct custom databases, extend the computational models, and the number of molecules available from within Spartan.