Spartan is a

molecular modelling Molecular modelling encompasses all methods, theoretical and computational, used to model or mimic the behaviour of molecules. The methods are used in the fields of computational chemistry, drug design, computational biology and materials sci ...

and computational chemistry application from Wavefunction. It contains code for

molecular mechanics Molecular mechanics uses classical mechanics to model molecular systems. The Born–Oppenheimer approximation is assumed valid and the potential energy of all systems is calculated as a function of the nuclear coordinates using Force field (chemi ...

, semi-empirical methods, ''ab initio'' models, density functional models,

post-Hartree–Fock In computational chemistry, post-Hartree–Fock methods are the set of methods developed to improve on the Hartree–Fock (HF), or self-consistent field (SCF) method. They add electron correlation which is a more accurate way of including the repu ...

models, and thermochemical recipes including G3(MP2) and T1. Quantum chemistry calculations in Spartan are powered by

Q-Chem Q-Chem is a general-purpose electronic structure package featuring a variety of established and new methods implemented using innovative algorithms that enable fast calculations of large systems on various computer architectures, from laptops and ...

. Primary functions are to supply information about structures, relative stabilities and other properties of isolated molecules.

Molecular mechanics Molecular mechanics uses classical mechanics to model molecular systems. The Born–Oppenheimer approximation is assumed valid and the potential energy of all systems is calculated as a function of the nuclear coordinates using Force field (chemi ...

calculations on complex molecules are common in the chemical community. Quantum chemical calculations, including

Hartree–Fock method In computational physics and chemistry, the Hartree–Fock (HF) method is a method of approximation for the determination of the wave function and the energy of a quantum many-body system in a stationary state. The Hartree–Fock method often ...

molecular orbital calculations, but especially calculations that include

electronic correlation Electronic correlation is the interaction between electrons in the electronic structure of a quantum system. The correlation energy is a measure of how much the movement of one electron is influenced by the presence of all other electrons. Atom ...

, 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 state In chemistry, the transition state of a chemical reaction is a particular configuration along the reaction coordinate. It is defined as the state corresponding to the highest potential energy along this reaction coordinate. It is often marked ...

s, or based on

Hammond's postulate Hammond's postulate (or alternatively the Hammond–Leffler postulate), is a hypothesis in physical organic chemistry which describes the geometric structure of the transition state in an organic chemical reaction A chemical reaction is a pro ...

, 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 Quantitative may refer to: * Quantitative research, scientific investigation of quantitative properties * Quantitative analysis (disambiguation) * Quantitative verse, a metrical system in poetry * Statistics, also known as quantitative analysis ...

(QSAR) analyses, and intermolecular potentials for

and

molecular dynamics Molecular dynamics (MD) is a computer simulation method for analyzing the physical movements of atoms and molecules. The atoms and molecules are allowed to interact for a fixed period of time, giving a view of the dynamic "evolution" of t ...

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 Nuclear magnetic resonance (NMR) is a physical phenomenon in which nuclei in a strong constant magnetic field are perturbed by a weak oscillating magnetic field (in the near field) and respond by producing an electromagnetic signal with ...

, IR, Raman, and UV-visible spectra, molecular (and atomic) properties, reactivity, and selectivity.

Computational abilities

This software provides the

, Merck Molecular Force Field (MMFF), (for validation test suite), MMFF with extensions, and SYBYL, force fields calculation, Semi-empirical calculations,

MNDO MNDO, or Modified Neglect of Diatomic Overlap is a semi-empirical method for the quantum calculation of molecular electronic structure in computational chemistry. It is based on the Neglect of Diatomic Differential Overlap integral approximation. ...

/MNDO(D),

Austin Model 1 Austin Model 1, or AM1, is a semi-empirical method for the quantum calculation of molecular electronic structure in computational chemistry. It is based on the Neglect of Differential Diatomic Overlap integral approximation. Specifically, it is a ...

(AM1), PM3, Recife Model 1 (RM1) PM6. *'' Hartree–Fock,

self-consistent field In classical deductive logic, a consistent theory is one that does not lead to a logical contradiction. The lack of contradiction can be defined in either semantic or syntactic terms. The semantic definition states that a theory is consistent ...

(SCF) methods'', available with

implicit solvent Implicit solvation (sometimes termed continuum solvation) is a method to represent solvent as a continuous medium instead of individual “explicit” solvent molecules, most often used in molecular dynamics simulations and in other applications of ...

(SM8). ** Restricted, unrestricted, and

restricted open-shell Hartree–Fock Restricted open-shell Hartree–Fock (ROHF) is a variant of Hartree–Fock method for open shell molecules. It uses doubly occupied molecular orbitals as far as possible and then singly occupied orbitals for the unpaired electrons. This is the sim ...

*''

Density functional theory Density-functional theory (DFT) is a computational quantum mechanical modelling method used in physics, chemistry and materials science to investigate the electronic structure (or nuclear structure) (principally the ground state) of many-body ...

(DFT) methods'', available with

(SM8). **''Standard functionals'': BP, BLYP, B3LYP, EDF1, EDF2, M06, ωB97X-D T1 vs NIST Expiremental Heat of Formation

**''Exchange functionals'': HF, Slater-Dirac, Becke88, Gill96, GG99, B(EDF1), PW91 **''Correlation functionals'': VWN, LYP, PW91, P86, PZ81, PBE. **''Combination or

hybrid functional Hybrid functionals are a class of approximations to the exchange–correlation energy functional in density functional theory (DFT) that incorporate a portion of exact exchange from Hartree–Fock theory with the rest of the exchange–correla ...

s'': B3PW91, B3LYP, B3LYP5, EDF1, EDF2, BMK *** Truhlar group functionals: M05, M05-2X, M06, M06-L M06-2X, M06-HF *** Head-Gordon group functionals: ωB97, ωB97X, ωB97X-D *''

Coupled cluster Coupled cluster (CC) is a numerical technique used for describing many-body systems. Its most common use is as one of several post-Hartree–Fock ab initio quantum chemistry methods in the field of computational chemistry, but it is also used in ...

methods''. **CCSD, CCSD(T), CCSD(2), OD, OD(T), OD(2), QCCD, VOD, VOD(2), VQCCD *'' Møller–Plesset methods''. **MP2, MP3, MP4, RI-MP2 *'' Excited state methods''. **''

Time-dependent density functional theory Time-dependent density-functional theory (TDDFT) is a quantum mechanical theory used in physics and chemistry to investigate the properties and dynamics of many-body systems in the presence of time-dependent potentials, such as electric or magne ...

(TDDFT) **''

Configuration interaction Configuration interaction (CI) is a post-Hartree–Fock linear variational method for solving the nonrelativistic Schrödinger equation within the Born–Oppenheimer approximation for a quantum chemical multi-electron system. Mathematical ...

'': CIS, CIS(D), QCIS(D),

quadratic configuration interaction Quadratic configuration interaction (QCI) is an extension of configuration interaction that corrects for size-consistency errors in single and double excitation CI methods (CISD). Size-consistency means that the energy of two non-interacting (i. ...

(QCISD(T)), RI-CIS(D) *''

Quantum chemistry composite methods Quantum chemistry composite methods (also referred to as thermochemical recipes) are computational chemistry methods that aim for high accuracy by combining the results of several calculations. They combine methods with a high level of theory and ...

, thermochemical recipes''. **T1, G2, G3, G3(MP2)

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 In physics, energy (from Ancient Greek: ἐνέργεια, ''enérgeia'', “activity”) is the quantitative property that is transferred to a body or to a physical system, recognizable in the performance of work and in the form of hea ...

Spartan Tutorial & User's Guide
– For a given geometry, provides energy and associated properties of a molecule or system. If quantum chemical models are employed, the

wave function A wave function in quantum physics is a mathematical description of the quantum state of an isolated quantum system. The wave function is a complex-valued probability amplitude, and the probabilities for the possible results of measurements ...

is calculated. * Equilibrium

molecular geometry Molecular geometry is the three-dimensional arrangement of the atoms that constitute a molecule. It includes the general shape of the molecule as well as bond lengths, bond angles, torsional angles and any other geometrical parameters that dete ...

An assessment of most computational models is available. - Locates the nearest local minimum and provides energy and associated properties. *

Transition state In chemistry, the transition state of a chemical reaction is a particular configuration along the reaction coordinate. It is defined as the state corresponding to the highest potential energy along this reaction coordinate. It is often marked ...

geometry - 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 – Locates lowest-energy conformation. Often performed before calculating structure using a quantum chemical model. * Conformer distribution – 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 In statistical mechanics and mathematics, a Boltzmann distribution (also called Gibbs distribution Translated by J.B. Sykes and M.J. Kearsley. See section 28) is a probability distribution or probability measure that gives the probability th ...

for calculating average molecular properties. * Conformer library – 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 – Steps a molecule or system through a user defined coordinate set, providing equilibrium geometries for each step (subject to user-specified constraints). * Similarity analysis – quantifies the likeness of molecules (and optionally their conformers) based on either structure or chemical function ( Hydrogen bond acceptors–donors, positive–negative ionizables,

hydrophobe In chemistry, hydrophobicity is the physical property of a molecule that is seemingly repelled from a mass of water (known as a hydrophobe). In contrast, hydrophiles are attracted to water. Hydrophobic molecules tend to be nonpolar and, ...

aromatics Aromatic compounds, also known as "mono- and polycyclic aromatic hydrocarbons", are organic compounds containing one or more aromatic rings. The parent member of aromatic compounds is benzene. The word "aromatic" originates from the past groupin ...

). Quantifies likeness of a molecule (and optionally its conformers) to a

pharmacophore 300px, An example of a pharmacophore model. A pharmacophore is an abstract description of molecular features that are necessary for molecular recognition of a ligand by a biological macromolecule. IUPAC defines a pharmacophore to be "an ensemble o ...

Graphical user interface

The software contains an integrated

graphical user interface The GUI ( "UI" by itself is still usually pronounced . or ), graphical user interface, is a form of user interface that allows users to interact with electronic devices through graphical icons and audio indicator such as primary notation, inst ...

. Touch screen operations are supported for

Windows 7 Windows 7 is a major release of the Windows NT operating system developed by Microsoft. It was released to manufacturing on July 22, 2009, and became generally available on October 22, 2009. It is the successor to Windows Vista, released nearly ...

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 Windows is a group of several proprietary graphical operating system families developed and marketed by Microsoft. Each family caters to a certain sector of the computing industry. For example, Windows NT for consumers, Windows Server for ser ...

version interface can access

ChemDraw ChemDraw is a molecule editor first developed in 1985 by David A. Evans and Stewart Rubenstein (later by the cheminformatics company CambridgeSoft). The company was sold to PerkinElmer in the year 2011. ChemDraw, along with Chem3D and ChemFinde ...

; 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.

Graphical models

Graphical models, especially molecular orbitals, electron density, and electrostatic potential maps, are a routine means of molecular visualization in chemistry education. *''Surfaces'': **

Molecular orbital In chemistry, a molecular orbital is a mathematical function describing the location and wave-like behavior of an electron in a molecule. This function can be used to calculate chemical and physical properties such as the probability of findin ...

s (highest occupied, lowest unoccupied, and others) **

Electron density In quantum chemistry, electron density or electronic density is the measure of the probability of an electron being present at an infinitesimal element of space surrounding any given point. It is a scalar quantity depending upon three spatial va ...

– The density, ρ(''r''), is a function of the coordinates ''r'', defined such that ρ(''r'')d''r'' is the number of electrons inside a small volume d''r''. 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, ρ^spin(''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. **

Van der Waals radius The van der Waals radius, ''r'', of an atom is the radius of an imaginary hard sphere representing the distance of closest approach for another atom. It is named after Johannes Diderik van der Waals, winner of the 1910 Nobel Prize in Physics, ...

(surface) **Solvent

accessible surface area The accessible surface area (ASA) or solvent-accessible surface area (SASA) is the surface area of a biomolecule that is accessible to a solvent. Measurement of ASA is usually described in units of square angstroms (a standard unit of measurement ...

Electrostatic potential Electrostatics is a branch of physics that studies electric charges at rest ( static electricity). Since classical times, it has been known that some materials, such as amber, attract lightweight particles after rubbing. The Greek word for ambe ...

– The potential, ''ε_p'', 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. **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 The electron ( or ) is a subatomic particle with a negative one elementary electric charge. Electrons belong to the first generation of the lepton particle family, and are generally thought to be elementary particles because they have no ...

density), providing an indication of nucleophilic reactivity.

Spectral calculations

Available spectra data and plots for: *''

Infrared spectroscopy Infrared spectroscopy (IR spectroscopy or vibrational spectroscopy) is the measurement of the interaction of infrared radiation with matter by absorption, emission, or reflection. It is used to study and identify chemical substances or function ...

(IR) spectra'' ** Fourier transform spectroscopy (FT-IR) ** Raman spectroscopy (IR) *''

Nuclear magnetic resonance Nuclear magnetic resonance (NMR) is a physical phenomenon in which nuclei in a strong constant magnetic field are perturbed by a weak oscillating magnetic field (in the near field) and respond by producing an electromagnetic signal with a ...

(NMR) spectra'' **¹H

chemical shift In nuclear magnetic resonance (NMR) spectroscopy, the chemical shift is the resonant frequency of an atomic nucleus relative to a standard in a magnetic field. Often the position and number of chemical shifts are diagnostic of the structure o ...

s and coupling constants (empirical) **¹³C

s, Boltzmann averaged shifts, and ¹³C

DEPT spectra Carbon-13 (C13) nuclear magnetic resonance (most commonly known as carbon-13 NMR spectroscopy or 13C NMR spectroscopy or sometimes simply referred to as carbon NMR) is the application of nuclear magnetic resonance (NMR) spectroscopy to carbon. It is ...

**2D H vs H Spectra *** COSY plots **2D C vs H Spectra *** Heteronuclear single-quantum correlation spectroscopy (HSQC) spectra *** HMBC spectra *'' UV/vis 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 The Joint Committee on Atomic and Molecular Physical Data (JCAMP) defined several JCAMP-DX (JCAMP-data exchange) file formats in chemistry. IUPAC The International Union of Pure and Applied Chemistry (IUPAC ) is an international federation of ...

(JCAMP) (.dx) format and NMR spectra in Chemical Markup Language (.cml) format. Access to

public domain The public domain (PD) consists of all the creative work to which no exclusive intellectual property rights apply. Those rights may have expired, been forfeited, expressly waived, or may be inapplicable. Because those rights have expired, ...

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

density functional theory Density-functional theory (DFT) is a computational quantum mechanical modelling method used in physics, chemistry and materials science to investigate the electronic structure (or nuclear structure) (principally the ground state) of many-body ...

with the 6-31G* basis set. **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 ***B3LYP density functional with 6-31G* and 6-311+G** basis sets ***EDF1 density functional with 6-31G* basis set *** MP2 with 6-31G* and 6-311+G** basis sets ***G3(MP2) ***T1 *''Experimental databases:'' **NMRShiftDB
NMRShiftDB. – an open-source database of experimental ¹H and ¹³C chemical shifts. **

Cambridge Structural Database The Cambridge Structural Database (CSD) is both a repository and a validated and curated resource for the three-dimensional structural data of molecules generally containing at least carbon and hydrogen, comprising a wide range of organic, metal- ...

(CSD) - a large repository of small molecule organic and inorganic experimental crystal structures of about 600,000 entries. **NIST database of experimental IR and UV/vis spectra.

Major release history

*1991 Spartan version 1

Unix Unix (; trademarked as UNIX) is a family of multitasking, multiuser computer operating systems that derive from the original AT&T Unix, whose development started in 1969 at the Bell Labs research center by Ken Thompson, Dennis Ritchie, an ...

*1993 Spartan version 2 Unix *1994 Mac Spartan

Macintosh The Mac (known as Macintosh until 1999) is a family of personal computers designed and marketed by Apple Inc. Macs are known for their ease of use and minimalist designs, and are popular among students, creative professionals, and software en ...

*1995 Spartan version 3 Unix *1995 PC Spartan

*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

References

External links

* , Wavefunction, Inc. {{Chemistry software Molecular modelling software Computational chemistry software Electronic structure methods Monte Carlo molecular modelling software