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The Spartan Graphical User Interface. A single, integrated, easy-to-use GUI. In little time, one can build/import/and augment molecules and systems, run molecular mechanics and quantum chemical calculations, and analyze results with Spartan graphics, property dialogs, integrated spreadsheets, data and spectra plots, and text output.
Build/Import/Export/Embed
Organic
Accesses a builder for common organic fragments (e.g., "sp3 carbon"), functional groups and rings for easy construction of organic molecules.
Inorganic
Extends building throughout the entire Periodic Table. Includes groups, rings and a library of common ligands.
Peptide
Accesses a builder with amino acids for construction of polypeptides as helices, sheets or in user-defined conformations.
Nucleotide
Accesses a builder of nucleotide bases for construction of single or double stranded DNA or RNA as A or B helices or in user-defined conformations.
Substituen
t A new builder for generating groups of substituted molecules.
2D Building
Seamless access to 2-D building via ChemDraw (must be licensed separately from CambridgeSoft). Requires ChemDraw 10 or later.
Custom
Access an included (and customizable) library of additional functional groups, rings and ligands.
Clipboard
Access to any molecule or molecular fragment which has previously been constructed.
Import
Spartan, SYBYL MOL and MOL2, PDB, MacroModel, smiles, XYZ, SDF, TGF, SKC, CIF, CDX, and JCAMP files.
Export
Spartan, SYBYL MOL and MOL2, PDB, MacroModel, smiles, and XYZ molecule files, graphics as JPG, PNG, BMP files, and animations, and Spectra as JCAMP files.
Embed
Spartan can embed external files (Word, Excel, PDF, etc.) into native Spartan files for improved organization of molecular data.
Refinement and Analysis:
Structure Refinement
Energy (strain energy) minimization with MMFF94 molecular mechanics force field, provides fast structure clean-up and assists in building molecules.
Chirality Inversion
Assignment of R/S chirality and user specified inversion of both chiral centers and absolute configuration.
Structure Query
Measure, post to spreadsheet (and optionally constrain) any distance, angle or dihedral (torsion) angle. Surface area, polar surface area, and molecular volumes may be measured and data posted to Spartan's spreadsheet.
Align Molecules
Instant alignment of multiple conformers or molecules based on either molecular structure or chemical function descriptors with alignment scores (rms values) available in dialoques and the Spartan Spreadsheet.
Data Organization
Post a full range of calculated molecular properties, or, optionally copy/paste directly to/from other cell-based data organization tools. Tabulated data in Spartan Spreadsheets is available for Linear Regression Analysis.
Plotting Features
2D and 3D plots are available for all data tabulated in Spartan's spreadsheet.
Graphical Displays
Molecular Models
Structures may be displayed in several styles, including: line, wire, ball-and-wire, tube, ball-and-spoke, and space-filling models. User-defined points and planes may be added to the models. Atoms, bonds, and molecules may be custom colored to emphasize specific features, or for highlighting superposition. An arrow may be displayed with the model, indicating the sign and direction of the calculated dipole moment.
Biopolymer Models
Display options for polypeptides and polynucleotides, include: ribbons, lines, or beads, with the option to customize color based on secondary structure, strand or residue type. PDB files with explicitly specified ligands will be automatically rendered in ribbon style with ligands displayed. Ligands are available for extraction, along with their environment.
Hydrogen Bonds
Optionally displays graphical indicator of inter/intra molecular hydrogen bonds.
Surfaces and Maps
Electron densities, van der Waals surfaces, spin densities, molecular orbitals, electrostatic potentials (and esp from charges) and local ionization potentials may be displayed as isosurfaces or color mapped on top of isosurfaces. Maps are available with continuous color gradient, or discrete bands.
Surfaces and maps may be displayed as opaque or translucent solids, meshes, or as a series of "dots". Area and volume of a displayed surface may be measured and property value at a selected surface location may be measured and posted to Spartan's spreadsheet.
Accessible surface regions may be optionally highlighted, and an alternate definition of polar surface area (termed polar area) based on the value of the electrostatic potential above and below a user-defined lipophilic range is also provided.
Slices
Electron densities, spin densities, molecular orbitals, electrostatic potentials and local ionization potentials may be displayed as contour plots.
Animations
Molecular models and associated surfaces, maps and slices for molecules contained within a list may be displayed in sequence. This allows visualizing changes in property throughout a chemical reaction or conformational motion. A "special case", involving motion along the normal mode, is useful for establishing whether a transition state smoothly connects reactants and products. Animations can be exported.
Stereo 3D
Molecular models and associated graphics can be displayed in 3D using color filtration techniques or via true unassisted stereo display available from SHARP 3D.
Multiple Molecules
As many molecules as desired may be displayed simultaneously on screen, together with any associated graphics.
Chemical Function
Desctiptors
Spartan optionally displays and makes use of CFDs in either alignment or similarity analysis. CFD's are based on standard pharmacophore definitions (hydrogen bond acceptors/donors, positive/negative ionizable centers, aromatic centers, hydrophobic centers, and excluded volume centers, but may also be further customized or user-defined.
Dialogs:
Calculations
A single dialog allows for easy specification of all aspects of a molecular mechanics or quantum chemical calculation. A "surface" dialog allows specification of surfaces, property maps and slices.
Output
Individual dialogs are available for standard text output.
Properties
Dialogs display calculated properties (energies, dipole moments and atomic charges, among other quantities) without having to examine "text" output.
Spreadsheet
A spreadsheet is available to collect calculated quantities for molecules contained in a list. 2D and 3D plots are available using this data.
Surfaces
A single, user friendly dialog for requesting and displaying graphical indicators as molecular surfaces.
Similarities
A dialog for screening and review of similarity analysis results, includes similarity score (rms value), visualization of aligned and superimposed similarity pair (template and library entry), conformer number (from conformer libraries) as well indication of enantiomer. Includes the ability to retrieve any 'hit' to main Spartan interface.
Reactions
A reactions dialog provides an easy-to-use tool for calculation of user-defined reaction energies from either calculated data of the Spartan Molecular Database.
Database
Provides GUI tool for screening results from searches of the Spartan Molecular Database (SMD), Spartan Reaction Database (SRD), Cambridge Structural Database (CSD), and Protein Data Bank (PDB).
Spartan includes access to a number of highly useful molecular databases, including: The Spartan Molecular Database, Spartan Reaction Database, Cambridge Structural Database* and Protein Data Bank**.
*CSD must be licensed separately. **PDB access requires internet connectivity.
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Spartan Molecular Database
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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'08 includes a subset of >10,000 molecules. The full SMD is available for purchase. Customers with Maintenance receive the full SMD at no additional charge.
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Spartan Reaction Database
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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.
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Cambridge Structural Database
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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.
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Protein Data Bank
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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.
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Computational Methods. Spartan'08 provides a wide range of computational methods, addressing the needs of educators, bench chemists, and professional modelers. All methods are easily accessed via Spartan's seamless graphical interface.
Methods: (Items in RED are not available in the Spartan'08 Essential Edition)
Molecular Mechanics
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 Molecular Orbital
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 and PM3 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 an PM3 (for organic molecules), comparisons to MNDO were not available at the time of Spartan'06 release.
Hartree-Fock Molecular Orbital
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).
Density Functional
Density functional models typically provide results of a quality comparable to conventional correlated models such as MP2, but at a cost only slightly greater than that of Hartree-Fock models. As such, they are particularly useful for high-quality structure, energy and property calculations, including calculations on transition-metal inorganic and organometallic compounds.
Local density models and BP, BLYP, EDF1, EDF2, and B3LYP models are supported with the same basis sets and pseudopotentials as available for Hartree-Fock models. The non-empirical GGA functional PBE has been implemented. Both M05, 5 and M06, 7 suites of meta-GGA functionals from the Truhlar group have also been implemened. Additionally, a wider range of functionals is available as calculation options with the ability to specify model and percentages for exchange and correlation (these include Slater-Dirac), Vokso-Wilk-Nusair, Perdew-Zunger, Wigner, Becke88, Gill96, Gilbert-Gill99, Lee-Yang-Parr, Perdew86, GGA91, BMK, EDF1 and EDF2).
Møller-Plesset
MP2 is perhaps the simplest model to take reasonable account of electron correlation, and generally provides accurate descriptions of equilibrium structure, conformation and energetics of a variety of chemical reactions, including reactions where chemical bonds are broken. MP methods are supported for the same basis sets and pseudopotentials available for Hartree-Fock and density functional models.
The RI-MP2 model, providing nearly identical results to MP2 but with significant performance improvements: energy calculations an order of magnitude faster and structure calculations a factor of 3 times faster than conventional MP2.
MP3 and MP4 models are available for single-point energy calculations only, as is a fast localized orbital variant of MP2. The same basis sets and pseudopotentials supported for Hartree-Fock are available.
Thermochemical Recipes
Several recipes for obtaining highly accurate heats of formation are available, including the new T1 recipe that provides results within 2 kJ/mol of the (also available) G3(MP2) approach, but with performance several orders of magnitude faster than G3(MP2). Additional recipes include G2, G3.
Advanced Correlated
A number of high-order correlated models are available for energy calculations only. These include CCSD, CCSD(T), OD, OD(T), QCISD, QCISD(T), QCCD, and QCCD(T) models, with the same basis sets and pseudopotentials available for Hartree-Fock, density functional and Møller-Plesset calculations.
Excited-State Methods
Calculations on excited states may be performed using CIS, CIS(D), RI-CIS(D) and TDDFT models in addition to the entire range of density functional models. The same basis sets and pseudopotentials supported for ground-state calculations are available. |
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