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.
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 Hammond's postulate,[9] 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 quantitative structure-activity relationship (QSAR)[10] analyses, and intermolecular potentials for molecular mechanics and molecular dynamics calculations.
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-visiblespectra, molecular (and atomic) properties, reactivity, and selectivity.
The calculated T1[7] heat of formation (y axis) relative to the experimental heat of formation (x axis) for a set of >1800 diverse organic molecules from the NIST thermochemical database[30] with mean absolute and RMS errors of 8.5 and 11.5 kJ/mol, respectively.
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.
Equilibrium conformer[72] – Locates lowest-energy conformation. Often performed before calculating structure 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).
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]
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).
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]
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]
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.
The calculated (DFT/EDF2/6-31G*) IR spectra (red), scaled and optimized to the experimental FT-IR spectra (blue) of phenyl 9-acridinecarboxylate (below).
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:
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.
Larry A. Curtiss; Paul C. Redfern; Krishnan Raghavachari; Vitaly Rassolov & John A. Pople (1998). "Gaussian-3 theory using reduced Møller-Plesset order". The Journal of Chemical Physics. 110 (10). The American Institute of Physics: 4703–4710. Bibcode:1999JChPh.110.4703C. doi:10.1063/1.478385.
Ohlinger, William S.; Philip E. Klunzinger; Bernard J. Deppmeier; Warren J. Hehre (2009). "Efficient Calculation of Heats of Formation". The Journal of Physical Chemistry A. 113 (10). ACS Publications: 2165–2175. Bibcode:2009JPCA..113.2165O. doi:10.1021/jp810144q. PMID19222177.
Hammond, G. S. (1955). "A Correlation of Reaction Rates". Journal of the American Chemical Society. 77 (2). ACS Publications: 334–338. doi:10.1021/ja01607a027.
Matthew Clark; Richard D. Cramer III & Nicole Van Opdenbosch (1989). "Validation of the general purpose tripos 5.2 force field". Journal of Computational Chemistry. 10 (8): 982–1012. doi:10.1002/jcc.540100804. S2CID97743988.
Michael J. S. Dewar & Walter Thiel (1977). "Ground states of molecules. 38. The MNDO method. Approximations and parameters". Journal of the American Chemical Society. 99 (15). ACS Publications: 4899–4907. doi:10.1021/ja00457a004.
Michael J. S. Dewar; Eve G. Zoebisch; Eamonn F. Healy; James J. P. Stewart (1985). "Development and use of quantum molecular models. 75. Comparative tests of theoretical procedures for studying chemical reactions". Journal of the American Chemical Society. 107 (13). ACS Publications: 3902–3909. doi:10.1021/ja00299a024.
James J. P. Stewart (1989). "Optimization of parameters for semiempirical methods I. Method". The Journal of Computational Chemistry. 10 (2): 209–220. doi:10.1002/jcc.540100208. S2CID36907984.
James J. P. Stewart (1989). "Optimization of parameters for semiempirical methods II. Applications". The Journal of Computational Chemistry. 10 (2): 221–264. doi:10.1002/jcc.540100209. S2CID98850840.
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. 10 (2). Springer Berlin-Heidelberg: 155–164. doi:10.1007/s00894-004-0183-z. PMID14997367. S2CID11617476.
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. 27 (10): 1101–1111. doi:10.1002/jcc.20425. PMID16691568. S2CID9017673.
Aleksandr V. Marenich; Ryan M. Olson; Casey P. Kelly; Christopher J. Cramer & Donald G. Truhlar (2007). "Self-Consistent Reaction Field Model for Aqueous and Nonaqueous Solutions Based on Accurate Polarized Partial Charges". Journal of Chemical Theory and Computation. 3 (6). ACS Publications: 2011–2033. doi:10.1021/ct7001418. PMID26636198.
John P. Perdew (1986). "Density-functional approximation for the correlation energy of the inhomogeneous electron gas". Physical Review B. 33 (12). American Physical Society: 8822–8824. Bibcode:1986PhRvB..33.8822P. doi:10.1103/PhysRevB.33.8822. PMID9938299.
P. J. Stephens; F. J. Devlin; C. F. Chabalowski; M. J. Frisch (1994). "Ab Initio Calculation of Vibrational Absorption and Circular Dichroism Spectra Using Density Functional Force Fields". The Journal of Physical Chemistry. 98 (45). ACS Publications: 11623–11627. doi:10.1021/j100096a001. S2CID97035345.
Peter M. W. Gill, Yeh Lin Ching and Michael W. George (2004). "EDF2: A density functional for predicting molecular vibrational frequencies". Australian Journal of Chemistry. 57 (4). Commonwealth Scientific and Industrial Research Organization: 365–370. doi:10.1071/CH03263.
John P. Perdew & Yue Wang (1992). "Accurate and simple analytic representation of the electron-gas correlation energy". Physical Review B. 45 (23). The American Physical Society: 13244–13249. Bibcode:1992PhRvB..4513244P. doi:10.1103/PhysRevB.45.13244. PMID10001404.
J. P. Perdew & A. Zunger (1986). "Self-interaction correction to density-functional approximations for many-electron systems". Physical Review B. 33 (12). The American Physical Society: 8822–8824. Bibcode:1986PhRvB..33.8822P. doi:10.1103/PhysRevB.33.8822. PMID9938299.
Yan Zhao; Nathan E. Schultz & Donald G. Truhlar (2006). "Design of Density Functionals by Combining the Method of Constraint Satisfaction with Parameterization for Thermochemistry, Thermochemical Kinetics, and Noncovalent Interactions". Journal of Chemical Theory and Computation. 2 (2). ACS Publications: 364–382. doi:10.1021/ct0502763. PMID26626525.
Yan Zhao & 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. 125 (19). American Institute of Physics: 194101–194119. Bibcode:2006JChPh.125s4101Z. doi:10.1063/1.2370993. PMID17129083.
Yan Zhao & 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. 110 (49). ACS Publications: 13126–13130. Bibcode:2006JPCA..11013126Z. doi:10.1021/jp066479k. PMID17149824.
George D. Purvis & Rodney J. Bartlett (1982). "A full coupled-cluster singles and doubles model: The inclusion of disconnected triples". The Journal of Chemical Physics. 76 (4). The American Institute of Physics: 1910–1919. Bibcode:1982JChPh..76.1910P. doi:10.1063/1.443164.
Krishnan Raghavachari; Gary W. Trucks; John A. Pople and; Martin Head-Gordon (1989). "A fifth-order perturbation comparison of electron correlation theories". Chemical Physics Letters. 157 (6). Elsevier Science: 479–483. Bibcode:1989CPL...157..479R. doi:10.1016/S0009-2614(89)87395-6.
Troy Van Voorhis & Martin Head-Gordon (2001). "Two-body coupled cluster expansions". The Journal of Chemical Physics. 115 (11). The American Institute of Physics: 5033–5041. Bibcode:2001JChPh.115.5033V. doi:10.1063/1.1390516.
C. David Sherrill; Anna I. Krylov; Edward F. C. Byrd & Martin Head-Gordon (1998). "Energies and analytic gradients for a coupled-cluster doubles model using variational Brueckner orbitals: Application to symmetry breaking in O+ 4". The Journal of Chemical Physics. 109 (11). The American Institute of Physics: 4171–4182. Bibcode:1998JChPh.109.4171S. doi:10.1063/1.477023.
Steven R. Gwaltney & Martin Head-Gordon (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. 323 (1–2). Elsevier: 21–28. Bibcode:2000CPL...323...21G. doi:10.1016/S0009-2614(00)00423-1.
Anna I. Krylov; C. David Sherrill; Edward F. C. Byrd & Martin Head-Gordon (1998). "Size-consistent wave functions for nondynamical correlation energy: The valence active space optimized orbital coupled-cluster doubles model". The Journal of Chemical Physics. 109 (24). The American Institute of Physics: 10669–10678. Bibcode:1998JChPh.10910669K. doi:10.1063/1.477764.
Pople, J. A.; Seeger, R.; Krishnan, R. (1977). "Variational configuration interaction methods and comparison with perturbation theory". International Journal of Quantum Chemistry. 12 (S11): 149–163. doi:10.1002/qua.560120820.
Pople, John A.; Binkley, J. Stephen; Seeger, Rolf (1976). "Theoretical models incorporating electron correlation". International Journal of Quantum Chemistry. 10 (S10): 1–19. doi:10.1002/qua.560100802.
Krishnan Raghavachari & John A. Pople (1978). "Approximate fourth-order perturbation theory of the electron correlation energy". International Journal of Quantum Chemistry. 14 (1): 91–100. doi:10.1002/qua.560140109.
Martin Feyereisena, George Fitzgeralda & Andrew Komornickib (1993). "Scaled Second-Order Perturbation Corrections to Configuration Interaction Singles: Efficient and Reliable Excitation Energy Methods". Chemical Physics Letters. 208 (5–6). Elsevier: 359–363. Bibcode:1993CPL...208..359F. doi:10.1016/0009-2614(93)87156-W.
Florian Weigend & Marco Häser (1997). "RI-MP2: first derivatives and global consistency". Theoretical Chemistry Accounts. 97 (1–4). Springer Berlin / Heidelberg: 331–340. doi:10.1007/s002140050269. S2CID97649855.
Robert A. Distasio J.R.; Ryan P. Steele; Young Min Rhee; Yihan Shao & Martin Head-Gordon (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. 28 (5): 839–856. doi:10.1002/jcc.20604. PMID17219361. S2CID8438511.
Erich Runge & E. K. U. Gross (1984). "Density-Functional Theory for Time-Dependent Systems". Physical Review Letters. 52 (12). American Physical Society: 997–1000. Bibcode:1984PhRvL..52..997R. doi:10.1103/PhysRevLett.52.997.
So Hirata & 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. 302 (5–6). Elsevier: 375–382. Bibcode:1999CPL...302..375H. doi:10.1016/S0009-2614(99)00137-2.
David Maurice & Martin Head-Gordon (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. 96 (10). Taylor & Francis: 1533–1541. Bibcode:1999MolPh..96.1533M. doi:10.1080/00268979909483096.
John A. Pople; Martin Head-Gordon & Krishnan Raghavachari (1987). "Quadratic configuration interaction. A general technique for determining electron correlation energies". The Journal of Chemical Physics. 87 (10). American Institute of Physics: 5968–35975. Bibcode:1987JChPh..87.5968P. doi:10.1063/1.453520.
Larry A. Curtiss; Krishnan Raghavachari; Paul C. Redfern; Vitaly Rassolov & John A. Pople (1998). "Gaussian-3 (G3) theory for molecules containing first and second-row atoms". The Journal of Chemical Physics. 109 (18). The American Institute of Physics: 7764–7776. Bibcode:1998JChPh.109.7764C. doi:10.1063/1.477422.
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. ISBN1-890661-06-6.
Alan J. Shusterman & Gwendolyn P. Shusterman (1997). "Teaching Chemistry with Electron Density Models". The Journal of Chemical Education. 74 (7). ACS Publications: 771–775. Bibcode:1997JChEd..74..771S. doi:10.1021/ed074p771.
Kimberly J. Linenberger; Renee S. Cole & Somnath Sarkar (2011). "Looking Beyond Lewis Structures: A General Chemistry Modeling Experiment Focusing on Physical Properties and Geometry". The Journal of Chemical Education. 88 (7). ACS Publications: 962–965. Bibcode:2011JChEd..88..962L. doi:10.1021/ed100727r.
Hyosub Kim; Segun Sulaimon; Sandra Menezes; Anne Son & Warren J. C. Menezes (2011). "A Comparative Study of Successful Central Nervous System Drugs Using Molecular Modeling". The Journal of Chemical Education. 88 (10). ACS Publications: 1389–1393. Bibcode:2011JChEd..88.1389K. doi:10.1021/ed100824u.
Anthony P. Scott & Leo Radom (1996). "Harmonic Vibrational Frequencies: An Evaluation of Hartree−Fock, Møller−Plesset, Quadratic Configuration Interaction, Density Functional Theory, and Semiempirical Scale Factors". The Journal of Physical Chemistry. 100 (41). ACS Publications: 16502–16513. doi:10.1021/jp960976r.
Benny G. Johnson & Jan Florián (1995). "The prediction of Raman spectra by density functional theory. Preliminary findings". Chemical Physics Letters. 47 (1–2). Elsevier: 120–125. Bibcode:1995CPL...247..120J. doi:10.1016/0009-2614(95)01186-9.
Jorg Kussman & Christian Ochsenfeld (2007). "Linear-scaling method for calculating nuclear magnetic resonance chemical shifts using gauge-including atomic orbitals within Hartree-Fock and density-functional theory". The Journal of Chemical Physics. 127 (5). American Institute of Physics: 054103. Bibcode:2007JChPh.127e4103K. doi:10.1063/1.2749509. PMID17688330.
Krzysztof Wolinski; James F. Hinton; Peter Pulay (1990). "Efficient implementation of the gauge-independent atomic orbital method for NMR chemical shift calculations". Journal of the American Chemical Society. 112 (23). ACS Publications: 8251–8260. doi:10.1021/ja00179a005.
Silverstein, Robert M.; Francis X. Webster; David J. Kiemle (2005). Spectroscopy Identification of Organic Compounds. John Wiley & Sons, Inc. pp.250–254, 259, 267. ISBN978-0-471-39362-7.
Silverstein, Robert M.; Francis X. Webster; David J. Kiemle (2005). Spectroscopy Identification of Organic Compounds. John Wiley & Sons, Inc. pp.254–263. ISBN978-0-471-39362-7.
John A. Pople; Martin Head-Gordon & Krishnan Raghavachari (1987). "Quadratic configuration interaction. A general technique for determining electron correlation energies". The Journal of Chemical Physics. 87 (10). American Institute of Physics: 5968–35975. Bibcode:1987JChPh..87.5968P. doi:10.1063/1.453520.
McDonald, R. S.; Paul A. Wilks (1988). "JCAMP-DX: A Standard Form for Exchange of Infrared Spectra in Computer Readable Form". Applied Spectroscopy. 42 (1). Society for Applied Spectroscopy: 151–162. Bibcode:1988ApSpe..42..151M. doi:10.1366/0003702884428734. S2CID97461751.
Ditchfield, R; Hehre, W.J; Pople, J. A. (1971). "Self-Consistent Molecular-Orbital Methods. IX. An Extended Gaussian-Type Basis for Molecular-Orbital Studies of Organic Molecules". J. Chem. Phys. 54 (2): 724–728. Bibcode:1971JChPh..54..724D. doi:10.1063/1.1674902.