Spartan (software)

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Spartan'10 Software
Spartan10WinMacLinuxLogo.svg
Spartan08 Screen Shot.PNG
Spartan Graphical User Interface
Developer(s) Wavefunction & Q-Chem
Initial release 1991; 21 years ago (1991)
Stable release 1.1.0 / March 22, 2011; 11 months ago (2011-03-22)
Development status Active
Written in C, C++, Fortran, Qt
Platform Cross-platform
Type Molecular Modeling Software
License Wavefunction, Inc. EULA
Website Wavefunction

SPARTAN is a molecular modeling and computational chemistry application from Wavefunction, Inc.[1] It contains code for molecular mechanics, semi-empirical methods, ab initio models,[2] density functional models,[3] post-Hartree-Fock models,[4] and thermochemical recipes including T1.[5]

Molecular mechanics calculations and quantum chemical calculations play an ever-increasing role in modern chemistry. Primary functions are to supply information about structures, relative stabilities and other properties of isolated molecules. Because of their inherent simplicity, molecular mechanics calculations on complex molecules are widespread throughout the chemical community. Quantum chemical calculations, including Hartree-Fock molecular orbital calculations, but especially calculations that include electron correlation, are much more time demanding. Only recently, have fast enough computers become widely available to make their application routine among mainstream chemists.

Quantum chemical calculations are also called upon to furnish information about mechanisms and product distributions of chemical reactions, either directly by calculations on transition states, or based on the Hammond Postulate,[6] by modeling the steric and electronic demands of the reactants. Quantitative calculations, leading directly to information about the geometries of transition states, and about reaction mechanisms in general, are increasingly common, while qualitative models are still needed for systems that are too large to be subjected to more rigorous treatments. Quantum chemical calculations can supply information to complement existing experimental data or replace it altogether, for example, atomic charges for QSAR[7] analyses, and intermolecular potentials for molecular mechanics and molecular dynamics calculations.

SPARTAN is a modern molecular modeling program, while its developmental roots stretch back to the beginning of computational chemistry programs,[8] current versions are designed to apply computational chemistry methods (theoretical models) to a number of a standard tasks that provide chemists with calculated data applicable to the determination of molecular shape (conformation), structure (equilibrium and transition state geometry), spectral properties, molecular (and atomic) properties, reactivity and selectivity.

Contents

[edit] Computational Capabilities

According to the most recent SPARTAN[9] manual,[10] the software provides the following computational approaches[11]:

The calculated T1[5] heat of formation (y axis) compared to the experimental heat of formation (x axis) for a set of >1800 diverse organic molecules from the NIST thermochemical database[32] with mean absolute and RMS errors of 8.5 and 11.5 kJ/mol, respectively.

[edit] Tasks Performed

Several computational models are available, providing molecular, thermodynamic, QSAR, atomic, graphical and spectral properties. The SPARTAN calculation dialogue provides access to the following standard computational tasks:

  • Energy[10] - For a given geometry, provides energy and associated properties of a molecule or system. If quantum chemical models are employed, the wavefunction is calculated.
  • Equilibrium Geometry[11] - Locates the nearest local minimum and provides energy and associated properties.
  • Transition State Geometry[11] - Locates the nearest first-order saddle point (a maximum in a single dimension and minima in all others) and provides energy and associated properties.
  • Equilibrium Conformer[11] - Replaces the submitted molecule with its lowest-energy conformation. Often performed prior to calculating structure using a quantum chemical model.
  • Conformer Distribution[10] - Creates a new file consisting of a selection of low-energy conformers. Commonly used to identify the shapes a specif molecule is likely to adopt and to determine a Boltzmann distribution for calculating average molecular properties.
  • Conformer Library[10] - Replaces the submitted molecule with its lowest-energy conformer and attaches the coordinates of a set of conformers spanning all shapes accessible to the molecule without regard to energy. Used to build libraries for similarity analysis.
  • Energy Profile[10] - Steps a molecule or system through a user defined coordinate set, providing equilibrium geometries for each step (subject to user-specified constraints).
  • Similarity Analysis[10] - quantifies the likeness of molecules (and optionally their conformers) based on either structure or chemical function (Hydrogen Bond Acceptors/Donors, Positive/Negative Ionizables, Hydrophobes, Aromatics). Also quantifies likeness of a molecule (and optionally its conformers) to a pharmacophore.

[edit] Graphical Models

A "cut-away" view of the Electrostatic Potential Map of fullerene (C60), the blue area inside the molecule is an area of positive charge (relative to the superstructure, providing a pictorial explanation for fullerene's ability to encapsulate negatively charged species).

SPARTAN is commonly employed to calculate and display a number of graphical models. Use of graphical models, especially molecular orbitals, electron density, and electrostatic potential maps, has become a routine means of molecular visualization in chemistry education.[72][73][74][75][76]

  • Surfaces:
    • Molecular Orbitals (Highest Occupied, Lowest Unoccupied, and others.)
    • Electron Density - The electron density, ρ(r), is a function of the coordinates r, defined such that ρ(r)dr is the number of electrons inside a small volume dr. This is what is measured in an X-ray diffraction experiment. The electron density may be portrayed in terms of an isosurface (an isodensity surface) with the size and shape of the surface being given by the value (or percentage of enclosure) of the electron density.
    • Spin Density - The spin density, ρspin(r), is defined as the difference in electron density formed by electrons of α spin, ρα(r), and the electron density formed by electrons of β spin, ρβ(r). For closed-shell molecules (in which all electrons are paired), the spin density is zero everywhere. For open-shell molecules (in which one or more electrons are unpaired), the spin density indicates the distribution of unpaired electrons. Spin density is an indicator of reactivity of radicals.[11]
    • Van der Waals surface
    • Solvent Accessible surface
    • Electrostatic Potential - The electrostatic potential, εp, is defined as the energy of interaction of a positive point charge located at p with the nuclei and electrons of a molecule. A surface for which the electrostatic potential is negative (a negative potential surface) delineates regions in a molecule which are subject to electrophilic attack.
    • Polarization Potential - The polarization potential,εp´ is the next term (beyond the electrostatic potential) in the expansion of the energy of interaction of a point positive charge with the nuclei and electrons of a molecule. It provides the energy due to electronic reorganization of the molecule as a result of its interaction with a point positive charge. The sum of the electrostatic and polarization potentials provides a better account of the energy of interaction of a point positive charge than available from the electrostatic potential alone. As evidence, it properly orders the proton affinities of trimethylamine, dimethyl ether and fluoromethane.[11]
  • Composite Surfaces (Maps):
    • Electrostatic Potential Map (Electrophilic indicator) - The most commonly employed property map is the electrostatic potential map. This gives the electrostatic potential at locations on a particular surface, most commonly a surface of electron density corresponding to overall molecular size.[10]
    • Local Ionization Potential Map - Is defined as the sum over orbital electron densities, ρi(r) times absolute orbital energies, ∈i , and divided by the total electron density, ρ(r). The local ionization potential reflects the relative ease of electron removal (“ionization”) at any location around a molecule. For example, a surface of “low” local ionization potential for sulfur tetrafluoride demarks the areas which are most easily ionized.
    • LUMO Map (Nucleophilic indicator) - Maps of molecular orbitals may also lead to graphical indicators. For example, the “LUMO map”, wherein the (absolute value) of the lowest-unoccupied molecular orbital (the LUMO) is mapped onto a size surface (again, most commonly the electron density), providing an indication of nucleophilic reactivity.

[edit] Spectral Calculations

The calculated (DFT/EDF2/6-31G*) IR spectra (red), scaled and optimized to the experimental FT-IR spectra (blue) of phenyl 9-acridinecarboxylate (below).
2D rendering
3D rendering
The molecule phenyl 9-acridinecarboxylate.

SPARTAN calculates and provides spectra plots for:

Experimental spectra may be imported for comparison with calculated spectra: IR and UV/vis spectra in JCAMP[84] (.dx) format and NMR spectra in Chemical Markup Language (.cml) format. Access to public domain spectral databases is available for:

  • FT-IR Spectra[32]
  • 1H and 13C NMR spectra[85]
  • UV/vis spectra[32]

[edit] Major Release history

[edit] See also

[edit] References

  1. ^ Computational Chemistry, David Young, Wiley-Interscience, 2001. Appendix A. A.1.6 pg 330, SPARTAN
  2. ^ Hehre, Warren J.; Leo Radom, Paul v.R. Schleyer, and John A. Pople (1986). AB INITIO Molecular Orbital Theory. John Wiley & Sons. ISBN 0-471-81241-2. 
  3. ^ Hohenberg, Pierre; Walter Kohn (1964). "Inhomogeneous electron gas". Physical Review 136 (3B): B864–B871. Bibcode 1964PhRv..136..864H. doi:10.1103/PhysRev.136.B864. 
  4. ^ Cramer, Christopher J. (2002). Essentials of Computational Chemistry. John Wiley & Sons. ISBN 0-470-09182-1. 
  5. ^ a b c Ohlinger, William S.; Philip E. Klunzinger, Bernard J. Deppmeier, and Warren J. Hehre (January 2009). "Efficient Calculation of Heats of Formation". The Journal of Physical Chemistry A (ACS Publications) 113 (10): 2165–2175. doi:10.1021/jp810144q. PMID 19222177. 
  6. ^ Hammond, G. S. (1955). "A Correlation of Reaction Rates". The Journal of the American Chemical Society (ACS Publications) 77 (2): 334–338. doi:10.1021/ja01607a027. 
  7. ^ Leach, Andrew R. (2001). Molecular modelling: principles and applications. Englewood Cliffs, N.J: Prentice Hall. ISBN 0-582-38210-6. 
  8. ^ W. J. Hehre, W. A. Lathan, R. Ditchfield, M. D. Newton, and J. A. Pople, Gaussian 70 (Quantum Chemistry Program Exchange, Program No. 237, 1970)
  9. ^ [1] There are several Spartan versions, this comparison chart documents major differences.
  10. ^ a b c d e f g Spartan Tutorial & User's Guide Hehre, Warren J.; William Sean Ohlinger (2010). Spartan'10 Tutorial and User's Guide. Irvine, CA: Wavefunction, Inc.. ISBN ISBN 1-890661-41-4. 
  11. ^ a b c d e f [2] An assessment of most computational models is available. Hehre, Warren J. (2003). A Guide to Molecular Mechanics and Quantum Chemical Calculations. Irvine, California: Wavefunction, Inc.. ISBN 1-890661-06-6. 
  12. ^ Thomas A. Halgren (1996). "Merck molecular force field. I. Basis, form, scope, parameterization, and performance of MMFF94". Journal of Computational Chemistry (Wiley InterScience) 17 (5-6) (5–6): 490–519. doi:10.1002/(SICI)1096-987X(199604)17:5/6<490::AID-JCC1>3.0.CO;2-P. 
  13. ^ MMFF94 on Computational Chemistry List
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  18. ^ James J. P. Stewart (1989). "Optimization of parameters for semiempirical methods II. Applications". The Journal of Computational Chemistry (Wiley InterScience) 10 (2): 221–264. doi:10.1002/jcc.540100209. 
  19. ^ James J. P. Stewart (1991). "Optimization of parameters for semiempirical methods. III Extension of PM3 to Be, Mg, Zn, Ga, Ge, As, Se, Cd, In, Sn, Sb, Te, Hg, Tl, Pb, and Bi". The Journal of Computational Chemistry (Wiley InterScience) 12 (3): 320–341. doi:10.1002/jcc.540120306. 
  20. ^ James J. P. Stewart (2004). "Optimization of parameters for semiempirical methods IV: extension of MNDO, AM1, and PM3 to more main group elements". The Journal of Molecular Modeling (Springer Berlin / Heidelberg) 10 (2): 155–164. doi:10.1007/s00894-004-0183-z. 
  21. ^ Gerd B. Rocha, Ricardo O. Freire, Alfredo M. Simas, James J. P. Stewart (2006). "RM1: A reparameterization of AM1 for H, C, N, O, P, S, F, Cl, Br, and I". The Journal of Computational Chemistry (Wiley InterScience) 27 (10): 1101–1111. doi:10.1002/jcc.20425. 
  22. ^ >James J. P. Stewart (2007). "Optimization of Parameters for Semiempirical Methods V: Modification of NDDO Approximations and Application to 70 Elements". The Journal of Molecular Modeling (Springer) 13 (12): 1173–1213. doi:10.1007/s00894-007-0233-4. ISBN 0089400702334. 
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  30. ^ a b c Yan Zhao and Donald G. Truhlar (2008). "The M06 suite of density functionals for main group thermochemistry, thermochemical kinetics, noncovalent interactions, excited states, and transition elements: two new functionals and systematic testing of four M06-class functionals and 12 other functionals". Theoretical Chemistry Accounts (Springer Berlin / Heidelberg) 120 (1-3): 215–241. doi:10.1007/s00214-007-0310-x. 
  31. ^ a b J. D. Chai and Martin Head-Gordon (2008). "Long-range corrected hybrid density functionals with damped atom-atom dispersion corrections". Physical Chemistry Chemical Physics (RSC Publishing) 10 (44): 6615–66120. doi:10.1039/b810189b. PMID 18989472. 
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  36. ^ John P. Perdew and Yue Wang (1992). "Accurate and simple analytic representation of the electron-gas correlation energy". Physical Review B (American Physical Society) 45 (23): 13244–13249. Bibcode 1992PhRvB..4513244P. doi:10.1103/PhysRevB.45.13244. 
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  41. ^ John P. Perdew, Kieron Burke, and Matthias Ernzerhof (October 1996). "Generalized Gradient Approximation Made Simple". Physical Review Letters (American Physical Society) 77 (18): 3865–3868. Bibcode 1996PhRvL..77.3865P. doi:10.1103/PhysRevLett.77.3865. PMID 10062328. 
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  44. ^ a b Yan Zhao, Nathan E. Schultz, and Donald G. Truhlar (2006). "Design of Density Functionals by Combining the Method of Constraint Satisfaction with Parameterization for Thermochemistry, Thermochemical Kinetics, and Noncovalent Interactions". The Journal of Chemical Theory and Computation (ACS Publications) 2 (2): 364–382. doi:10.1021/ct0502763. 
  45. ^ Yan Zhao and Donald G. Truhlar (2008). "A new local density functional for main-group thermochemistry, transition metal bonding, thermochemical kinetics, and noncovalent interactions". The Journal of Chemical Physics (American Institute of Physics) 125 (8) (19): 194101–194119. doi:10.1063/1.2370993. 
  46. ^ Yan Zhao and Donald G. Truhlar (2008). "Density Functional for Spectroscopy: No Long-Range Self-Interaction Error, Good Performance for Rydberg and Charge-Transfer States, and Better Performance on Average than B3LYP for Ground States". The Journal of Physical Chemistry A (ACS Publications) 110 (49): 13126–13130. doi:10.1021/jp066479k. 
  47. ^ a b Jeng-Da Chai and Martin Head-Gordon (2006). "Systematic optimization of long-range corrected hybrid density functionals". The Journal of Chemical Physics (American Institute of Physics) 128 (8): 084106–084121. doi:10.1063/1.2834918. 
  48. ^ George D. Purvis and Rodney J. Bartlett (1982). "A full coupled‐cluster singles and doubles model: The inclusion of disconnected triples". The Journal of Chemical Physics (The American Institute of Physics) 76 (4): 1910–1919. Bibcode 1982JChPh..76.1910P. doi:10.1063/1.443164. 
  49. ^ Krishnan Raghavachari, Gary W. Trucks, John A. Pople and, Martin Head-Gordon (March 24, 1989). "A fifth-order perturbation comparison of electron correlation theories". Chemical Physics Letters (Elsevier Science) 157 (6): 479–483. Bibcode 1989CPL...157..479R. doi:10.1016/S0009-2614(89)87395-6. 
  50. ^ Troy Van Voorhis and Martin Head-Gordon (June 19, 2001). "Two-body coupled cluster expansions". The Journal of Chemical Physics (The American Institute of Physics) 115 (11): 5033–5041. Bibcode 2001JChPh.115.5033V. doi:10.1063/1.1390516. 
  51. ^ C. David Sherrill, Anna I. Krylov, Edward F. C. Byrd, and Martin Head-Gordon (June 11, 1998). "Energies and analytic gradients for a coupled-cluster doubles model using variational Brueckner orbitals: Application to symmetry breaking in O4+". The Journal of Chemical Physics (The American Institute of Physics) 109 (11): 4171–4182. doi:10.1063/1.477023. 
  52. ^ Steven R. Gwaltney and Martin Head-Gordon (June 9, 2000). "A second-order correction to singles and doubles coupled-cluster methods based on a perturbative expansion of a similarity-transformed Hamiltonian". Chemical Physics Letters (Elsevier) 323 (1-2): 21–28. Bibcode 2000CPL...323...21G. doi:10.1016/S0009-2614(00)00423-1. 
  53. ^ Troy Van Voorhis and Martin Head-Gordon (November 17, 2000). "The quadratic coupled cluster doubles model". Chemical Physics Letters (Elsevier) 330 (5-6) (5–6): 585–594. Bibcode 2000CPL...330..585V. doi:10.1016/S0009-2614(00)01137-4. 
  54. ^ a b c Anna I. Krylov, C. David Sherrill, Edward F. C. Byrd, and Martin Head-Gordon (September 15, 1998). "Size-consistent wave functions for nondynamical correlation energy: The valence active space optimized orbital coupled-cluster doubles model". The Journal of Chemical Physics (The American Institute of Physics) 109 (24): 10669–10678. doi:10.1063/1.477764. 
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  60. ^ Martin Feyereisena, George Fitzgeralda and Andrew Komornickib (May 10, 1993). "Scaled Second-Order Perturbation Corrections to Configuration Interaction Singles: Efficient and Reliable Excitation Energy Methods". Chemical Physics Letters (Elsevier) 208 (5-6) (5–6): 359–363. doi:10.1016/0009-2614(93)87156-W. 
  61. ^ Florian Weigend and Marco Häser (October 13, 1997). "RI-MP2: first derivatives and global consistency". Theoretical Chemistry Accounts (Springer Berlin / Heidelberg) 97 (1-4): 331–340. doi:10.1007/s002140050269. 
  62. ^ Robert A. Distasio JR., Ryan P. Steele, Young Min Rhee, Yihan Shao, and Martin Head-Gordon (April 15, 2007). "An improved algorithm for analytical gradient evaluation in resolution-of-the-identity second-order Møller-Plesset perturbation theory: Application to alanine tetrapeptide conformational analysis". Journal of Computational Chemistry (Wiley InterScience) 28 (5): 839–856. doi:10.1002/jcc.20604. 
  63. ^ a b Erich Runge and E. K. U. Gross (October 1984). "Density-Functional Theory for Time-Dependent Systems". Physical Review Letters (American Physical Society) 52 (12): 997–1000. Bibcode 1984PhRvL..52..997R. doi:10.1103/PhysRevLett.52.997. 
  64. ^ a b So Hirata and Martin Head-Gordon (1999). "Time-dependent density functional theory for radicals: An improved description of excited states with substantial double excitation character". Chemical Physics Letters (Elsevier) 302 (5-6) (5–6): 375–382. Bibcode 1999CPL...302..375H. doi:10.1016/S0009-2614(99)00137-2. 
  65. ^ a b David Maurice and Martin Head-Gordon (May 10, 1999). "Analytical second derivatives for excited electronic states using the single excitation configuration interaction method: theory and application to benzo[a]pyrene and chalcone". Molecular Physics (Taylor & Francis) 96 (10): 1533–1541. Bibcode 1999MolPh..96.1533M. doi:10.1080/00268979909483096. 
  66. ^ a b Martin Head-Gordon, Rudolph J. Rico, Manabu Oumi, and Timothy J. Lee (1994). "A doubles correction to electronic excited states from configuration interaction in the space of single substitutions". Chemical Physics Letters (Elsevier) 219 ((1-2)): 21–29. Bibcode 1994CPL...219...21H. doi:10.1016/0009-2614(94)00070-0. 
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