Spartan (chemistry software)
Developer(s) | Wavefunction, Inc.[1] & Q-Chem |
---|---|
Initial release | 1991 |
Stable release | Spartan'20 v.1.1
/ 2021 |
Written in | OS X, Linux |
Platform | x86-64 |
Available in | English |
Type | Molecular modelling, computational chemistry |
License | Proprietary commercial software |
Website | www |
Spartan is a
Primary functions are to supply information about structures, relative stabilities and other properties of isolated molecules. Molecular mechanics calculations on complex molecules are common in the chemical community. Quantum chemical calculations, including Hartree–Fock method molecular orbital calculations, but especially calculations that include electronic correlation, are more time-consuming in comparison.
Spartan applies computational chemistry methods (theoretical models) to many standard tasks that provide calculated data applicable to the determination of molecular shape conformation, structure (equilibrium and transition state geometry), NMR, IR, Raman, and UV-visible spectra, molecular (and atomic) properties, reactivity, and selectivity.
Computational abilities
This software provides the
- Coupled cluster methods.
- Møller–Plesset methods.
- Excited state methods.
- Time-dependent density functional theory (TDDFT)[63][64]
- Configuration interaction: CIS,[65] CIS(D),[66] QCIS(D),[67] quadratic configuration interaction (QCISD(T)),[67] RI-CIS(D)[68]
- Quantum chemistry composite methods, thermochemical recipes.
Tasks performed
Available computational models provide molecular, thermodynamic, QSAR, atomic, graphical, and spectral properties. A calculation dialogue provides access to the following computational tasks:
- Energy[71] – For a given geometry, provides energy and associated properties of a molecule or system. If quantum chemical models are employed, the wave function is calculated.
- Equilibrium molecular geometry[72] - Locates the nearest local minimum and provides energy and associated properties.
- Transition state geometry[72] - Locates the nearest first-order saddle point (a maximum in a single dimension and minima in all others) and provides energy and associated properties.
- using a quantum chemical model.
- Conformer distribution[71] – Obtains a selection of low-energy conformers. Commonly used to identify the shapes a specific molecule is likely to adopt and to determine a Boltzmann distribution for calculating average molecular properties.
- Conformer library[71] – Locates lowest-energy conformer and associates this with a set of conformers spanning all shapes accessible to the molecule without regard to energy. Used to build libraries for similarity analysis.
- Energy profile[71] – Steps a molecule or system through a user defined coordinate set, providing equilibrium geometries for each step (subject to user-specified constraints).
- Similarity analysis[71] – 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). Quantifies likeness of a molecule (and optionally its conformers) to a pharmacophore.
Graphical user interface
The software contains an integrated graphical user interface. Touch screen operations are supported for Windows 7 and 8 devices. Construction of molecules in 3D is facilitated with molecule builders (included are organic, inorganic, peptide, nucleotide, and substituent builders). 2D construction is supported for organic molecules with a 2D sketch palette. The Windows version interface can access ChemDraw; which versions 9.0 or later may also be used for molecule building in 2D. A calculations dialogue is used for specification of task and computational method. Data from calculations are displayed in dialogues, or as text output. Additional data analysis, including linear regression, is possible from an internal spreadsheet.[71]
Graphical models
Graphical models, especially molecular orbitals, electron density, and electrostatic potential maps, are a routine means of molecular visualization in chemistry education.[73][74][75][76][77]
- Surfaces:
- Molecular orbitals (highest occupied, lowest unoccupied, and others)
- Electron density – The 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 density may be portrayed in terms of an isosurface (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 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.[72]
- Van der Waals radius (surface)
- Solvent accessible surface area
- Electrostatic potential – The 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.
- Composite surfaces (maps):
- Electrostatic potential map (electrophilic indicator) – The most commonly employed property map is the electrostatic potential map. This gives the potential at locations on a particular surface, most commonly a surface of electron density corresponding to overall molecular size.[71]
- 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.
Spectral calculations
Available spectra data and plots for:
- Infrared spectroscopy (IR) spectra
- Fourier transform spectroscopy (FT-IR)[78]
- Raman spectroscopy (IR)[79]
- Nuclear magnetic resonance (NMR) spectra
- 1H chemical shifts[80][81] and coupling constants (empirical)
- 13C DEPT spectra
- 2D H vs H Spectra
- COSY[82]plots
- 2D C vs H Spectra
Experimental spectra may be imported for comparison with calculated spectra: IR and UV/vis spectra in Joint Committee on Atomic and Molecular Physical Data (JCAMP)[86] (.dx) format and NMR spectra in Chemical Markup Language (.cml) format. Access to public domain spectral databases is available for IR, NMR, and UV/vis spectra.
Databases
Spartan accesses several external databases.
- Quantum chemical calculations databases:
- Spartan Spectra & Properties Database (SSPD) – a set of about 252,000 molecules, with structures, energies, NMR and IR spectra, and wave functions calculated using the EDF2[27] density functional theory with the 6-31G* basis set.[87]
- Spartan Molecular Database (SMD) – a set of about 100,000 molecules calculated from following models:
- Hartree–Fock with 3-21G, 6-31G*, and 6-311+G** basis sets[87]
- B3LYP[25] density functional with 6-31G* and 6-311+G** basis sets
- EDF1[26] density functional with 6-31G* basis set
- MP2[55] with 6-31G* and 6-311+G** basis sets
- G3(MP2)[6]
- T1[7]
- Experimental databases:
- NMRShiftDB[88] – an open-source database of experimental 1H and 13C chemical shifts.
- Cambridge Structural Database (CSD)[89] - a large repository of small molecule organic and inorganic experimental crystal structures of about 600,000 entries.
- NIST database[30] of experimental IR and UV/vis spectra.
Major release history
- 1991 Spartan version 1 Unix
- 1993 Spartan version 2 Unix
- 1994 Mac Spartan Macintosh
- 1995 Spartan version 3 Unix
- 1995 PC Spartan Windows
- 1996 Mac Spartan Plus Macintosh
- 1997 Spartan version 4 Unix
- 1997 PC Spartan Plus Windows
- 1999 Spartan version 5 Unix
- 1999 PC Spartan Pro Windows
- 2000 Mac Spartan Pro Macintosh
- 2002 Spartan'02 Unix, Linux, Windows, Mac
Windows, Macintosh, Linux versions
- 2004 Spartan'04
- 2006 Spartan'06
- 2008 Spartan'08
- 2010 Spartan'10
- 2013 Spartan'14
- 2016 Spartan'16
- 2018 Spartan'18
- 2021 Spartan'20
See also
- Q-Chem quantum chemistry software
- Molecular design software
- Molecule editor
- Comparison of software for molecular mechanics modeling
- List of software for Monte Carlo molecular modeling
- Quantum chemistry composite methods
- List of quantum chemistry and solid state physics software
References
- ^ Wavefunction, Inc.
- ^ Computational Chemistry, David Young, Wiley-Interscience, 2001. Appendix A. A.1.6 pg 330, Spartan
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- ^ a b c d e f g Spartan Tutorial & User's Guide Hehre, Warren J.; Ohlinger, William S. (2013). Spartan'14 Tutorial and User's Guide. Irvine, California: Wavefunction, Inc.
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External links
- Official website, Wavefunction, Inc.