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Spartan

Molecular Modelling und 3D-Visualisierung per Mausklick

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	New in Spartan08 Graphical User Interface Computational Enhancements Tasks Performed Computational Methods Methods Molecular Properties Additional Features

Spartan ist ein quantenchemisches Modellierungspaket mit einem ausgezeichneten grafischen Interface für den Einsatz in der Chemie, Biochemie, Pharmazeutischen Chemie und verwandten Wissenschaften. Es vereinfacht die Forschung gleichermaßen für den erfahrenen "Computational Chemist", wie für den Laborchemiker, bei einem überraschend geringen Zeitaufwand. Die mühsame Erstellung von Eingabedateien und das aufwendige Herausschreiben von berechneten Ergebnissen aus den Ausgabedateien entfällt bei Spartan völlig. Mit Hilfe des Spartan Builders können sowohl organische, anorganische und metallorganische Verbindungen, als auch Polypeptide und Polynukleotide schnell und effizient erstellt werden.

Die Auswahl, ob nun molekulare Eigenschaften, Reaktionspfade oder Übergangszustände berechnet werden sollen, wie auch die Auswahl der Rechenmethode selbst, geschieht über das grafische Interface. Statt sich Programmbefehle zu merken, kann sich insbesondere der Laborchemiker ausschließlich auf das chemische Problem konzentrieren.

New in Spartan08

Graphical User Interface Features: (RED items not available in Essential Edition)

• New Reactions Dialogue provides tool for calculation reaction and activation energies
• Improved File Structure allows for embedding external data files in native Spartan file format
• Improved proton NMR plotting, new COSY and NOSY plotting now available
• Import of experimental NMR and IR in JCAMP file format
• Export of calculated NMR and IR in JCAMP file format
• Expanded Transition State Library to more than 2000 reaction types
• Discrete Property Maps for display of composite calculated surfaces (ESP Maps, for example)
• Electron density surface optionally displayed as a % of total electron density (vs. isovalue)
• New "Tumble" feature for display of molecule in rotation
• Import/Export of multi-molecule MOL2 or SDF Files (including atomic charge data)
• Substituent Definitions can now be used in SMD database searching
• 2D Thumbnails may now be included in Spartan spreadsheet
• Vector quantities may now be stored in Spartan spreadsheet (and plotted)

Computational Enhancements: (RED items not available in Essential Edition)

• Solvation Models
  SM6 and SS(V)PE continuum models now available.
• RI-CIS(D)
  Resolution of the Image CIS(D) available with an order of magnitude speed increase for energy and a factor of 3 speed increase for structure [over CIS(D)].
• New DFT Functionals
  Non-empirical GGA functional PBE has been implemented. ?B97X-D, M05, M06, Slater-Dirac, Vokso-Wilk-Nusair, Perdew-Zunger, Wigner, Becke88, Gill96, Gilber-Gill99, Lee-Yang-Parr, Perdew86, GGA91, BMK, EDF1, and EDF2 are now available. Additionally, custom specification of exchange and correlation is included.
• Thermochemical Recipes
  The T1 procedure has been improved to provide heats of formation within 2 kJ/mol (RMSD) of G3(MP2) with speed and performance enhancements enabling routine calculations on molecules up to ~ 500 amu.
• NMR
  Improvements in the form of correction factors to C13 chemical shifts has been implemented reducing the mean absolute error to within ~ 2ppm.

Tasks Performed by Spartan'08 for Windows: (Items in RED are not available on Spartan'08 Essential Edition.)

• Energy
  Determine total energy (Hartree-Fock, density functional, Møller-Plesset, advanced correlated), heat of formation (semi-empirical or thermochemical recipes) or strain energy (molecular mechanics).
• Equilibrium Geometry
  Determines local energy minimum.
• Transition State Geometry
  Determine transition-state geometry, with the option to calculate the intrinsic reaction coordinate (IRC).
• Calculate and Plot IR Spectra
  All methods except MP3, MP4 and advanced correlated. Needed to establish validity of transition states.
• Calculate and Plot NMR Spectra
  Chemical shifts from Hartree-Fock and DFT models.
• Calculate and Plot UV/vis Spectra
  Hartree-Fock/CIS and DFT/TDDFT models.
• Conformational Analysis
  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).
• Energy Profile
  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.
• Similarity Analysis
  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).

Dies-Alder-Reaktion

The Spartan 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).

Reaktion zwischen Cyanid und Methyliodid

Spartan Molecular Properties: In addition to energies, equilibrium and transition-state geometries and frequencies, Spartan'08 provides a number of valuable properties. (Items in RED are not available in Spartan'08 Essential Edition.)

• Atomic Charges
  Mulliken and Natural Bond Orbital Charges are available as are charges based on fits to electrostatic potentials.
• Thermodynamics
  Enthalpies, entropies and free energies as well as isotope effects, based on calculated geometries and IR vibrational frequencies.
• Electrical
  Dipole, quadrapole and higher moments, polarizabilities (including alpha, beta, and gamma terms).
• Additional Properties
  Weight, Area, Volume, Symmetry Group, HOMO and LUMO Energies, Polar Surface Area, LogP, Ovality, Q-Minus, Q-Plus, Electronegativity and Hardness
• IR Spectra
  Vibrational spectra available from IR calculations including plotting and animation of vibrational modes.
• Solvation
  Aqueous solvation energies from SM6, SM5.4 or SM50R models. An additional continuum solvation model is also included.
• NMR Calculations
  Chemical shift calculations are now available for Hartree-Fock and DFT models, and new in Spartan'08, an empirical model for coupling constants.
• UV/vis Spectra
  Vertical excitation spectra based using either CIS/CIS(D) or Time Dependent DFT models is provided.

Additional Spartan'08 Features:

• List processing
  Spartan automatically processes files comprising lists of molecules, in general operations applicable to a single molecule may be appplied to lists of molecules. Spartan is optimized to operate on lists of a hundreds of molecules (not thousands or tens of thousands).
• NOEs
  NOE data can be applied to confomrational searching as a post-processing filter.
• On-line Infrared and UV/vis data
  If your computer has internet connectivity, Spartan'08 can retieve and plot experimental IR (~ 14,000 molecules) and UV/Vis (~ 1,500) spectra from the NIST Chemistry Webbook.
• On-line NMR Chemical Shift data
  If your computer has internet connectivity, Spartan'08 can retieve and plot experimental NMR Chemical Shifts (~ 15,000 molecules) from the NMR database maintained by the University of Cologne.
• Ligand and Binding Site Extraction
  Spartan'08 can optionally extract bound ligands and their envrionment from protein (PDB) files, along with customizeable chemical function descriptors (CFD's).
• Constraints and Frozen Atoms
  Geometry optimization and conformational analysis are available subject to user specified constraints (of distance, angle, or torsion angle) and/or frozen atoms.
• User Generated Database
  Parallel to the Spartan Molecular Database, user's can save Spartan data in the .spentry format (Spartan Molecular Database format) and construct custom databases, extend the computational models, and number of molecules available from within Spartan.

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