This section first outlines the goals which have guided, and continue to guide, the development of Spartan. Following this is a brief discussion of Spartan's architecture, in particular, the connectivity of its graphics and compute components, and how this architecture relates to the intended use of the program. Spartan's present capabilities and limitations are then enumerated. A listing of hardware and operating systems on which Spartan's modules are available is provided.
Section 1.1: Spartan
Calculations, in particular molecular mechanics calculations1 and quantum chemical calculations,2-4 play a multiple role in modern-day computational chemistry. Traditionally, they have served to supply information about the structures, relative stabilities and other properties of isolated molecules. Because of their inherent simplicity, molecular mechanics calculations on complex molecules may even be performed on personal computers and, probably because of this, have spread widely throughout the chemical community. Quantum chemical calculations, even semi-empirical molecular orbital calculations, but especially ab initio molecular orbital calculations and density functional calculations, are much more time demanding. Only recently, with the availability of fast workstations and efficient graphics-based programs, have these methods begun to be widely applied.
Quantum chemical methods have also been called on to furnish information about the mechanisms and product distributions of chemical reactions, either directly by calculations on transition states, or indirectly by modeling the steric and electronic demands of the reactants. Quantitative quantum chemical calculations, leading to information about reaction mechanisms, will become more common with increasing knowledge about the geometries of transition states, while qualitative models will still be needed for systems too large to be subjected to the more rigorous treatments.
Quantum chemical calculations are also able to supply information needed as input for other techniques, for example, atomic charges for QSAR analyses. Ab initio Hartree-Fock and correlated molecular orbital calculations, and density functional calculations, in particular, are also able to provide accurate intra and intermolecular potentials. This kind of information is required both by molecular mechanics and by molecular dynamics techniques used to describe a wide variety of phenomena, ranging from interactions between an enzyme and a drug to the physical properties of polymeric materials. All of these tasks are too complex now to be treated using quantum chemical models, even semi-empirical models. Non-empirical quantum chemical methods may also provide the best means of parameterizing next-generation, semi-empirical molecular orbital models, extending the range of application of quantum chemical techniques beyond that currently practical using ab initio and/or density functional methods.
The expanding role of molecular mechanics and quantum chemical calculations in chemistry and biochemistry and closely related fields, together with truly explosive developments in computer hardware and software technologies and with the rapidly changing makeup of the user community, prompted the development of Spartan, a program embracing molecular mechanics as well as ab initio and semi-empirical molecular orbital and density functional methods. Spartan is intended to provide a convenient environment to carry out individual molecular mechanics calculations, as well as semi-empirical and ab initio Hartree-Fock and correlated molecular orbital calculations and density functional calculations on diverse molecular systems. It also serves to facilitate processing of large numbers of closely-related calculations as might be required to map a conformational energy profile, to screen a set of compounds for a particular property or structural characteristic, or to parameterize a potential function for later use in a molecular mechanics or molecular dynamics calculation. Spartan is intended to be utilized by chemists, primarily experimental chemists, who may have little or no background in molecular mechanics or quantum chemical methods, but who want to use calculations much in the same way as experimental techniques such as NMR spectroscopy. With this in mind, particular attention has been paid to the interface linking Spartan to the user. Modern computer graphics techniques have been extensively employed, not only to greatly reduce the drudgery and possibility of error associated with the construction of program input, but also to guide the interpretation of program output.
Spartan presently comprises seven independent program modules: a graphical user interface and ab initio, density functional, semi-empirical, mechanics, properties and graphics modules. Different modules may reside on the same or on different computers, and communicate with each other via the transfer of files without user intervention. In addition, Spartan's graphical user interface may also provide input for, execute and retrieve output from the Gaussian 94 electronic structure program,5 thereby extending its capability in a completely transparent manner.
The figure below illustrates the interconnectivity of Spartan's modules.
Spartan provides tight interconnectivity between compute and graphical components. Without leaving the graphical interface, the user can build a complex molecular structure and refine its geometry using molecular mechanics, then specify a task, e.g., geometry optimization, and level of quantum chemical calculation, e.g., AM1 semi-empirical. Following this, the user can designate any graphical surfaces, e.g., a surface of constant total electron density, and/or any graphical volumes from which isosurfaces and/or 2D slices can later be constructed, e.g., a volume of points corresponding to the electrostatic potential, for later display, specify properties of interest, e.g., charges based on fits to electrostatic potentials, and then submit the calculation either to the local workstation or to a server somewhere on the network. Once the calculation has completed, the user can view and/or print text and/or graphical output. Requests for additional molecular mechanics or quantum chemical calculations and/or additional graphical and property output may be made following completion. Spartan keeps track of what has already been done and will not repeat calculations unnecessarily. While one (or more) job is running, input for another job can be constructed or output corresponding to yet another examined. These jobs may be derivative, i.e., based on information resulting from earlier jobs, or completely independent. In short, the graphical user interface is a window into Spartan, allowing convenient access to its many features.
Spartan's architecture makes a clear separation between tasks and methods. Tasks indicate what is to be done, e.g., perform a geometry optimization or search conformation space, while methods dictate how the tasks are to be done, e.g., use MMFF molecular mechanics or the PM3 semi-empirical method. Both tasks and methods are specified in the graphical user interface, while the actual calculations are performed in the outlying modules. In principle, any task can be handled by any method and, while practical considerations may prove limiting in some cases, e.g., full conformation searches using high-level ab initio or correlated techniques are probably impractical at present, the notion that tasks and methods are independent is fundamental in the design of Spartan. Technology developments will continue to push the limits of what is practical.
SPARTAN's graphical user interface provides a number of functions, among them:
Spartan's ab initio, density functional and semi-empirical modules each serve five primary functions:
Spartan's mechanics module serves four primary functions:
Spartan's properties module serves five primary functions:
Spartan's graphics module is responsible for the actual calculation (but not the display) of volumes and surfaces and properties mapped onto those surfaces, based on ab initio, density functional, or semi-empirical wavefunctions. These include electron and spin densities and electrostatic and polarization potentials, as well as the molecular orbitals. Difference plots may be prepared from these data in the graphical user interface.
Below are described the present capabilities and limitations of Spartan's ab initio, density functional, semi-empirical and mechanics modules.
Spartan's ab initio module provides for calculation of the energy and wavefunction for a given nuclear configuration, of equilibrium or transition-state geometries and of normal-mode vibrational frequencies. It also allows for searching of conformation space both for acyclic systems as well as for molecules incorporating rings. The module is presently limited to Hartree-Fock and MP2 correlated models,3,6 for both closed-shell and open-shell systems (UHF and UMP2 methods only). Internally stored basis sets include STO-3G, 3-21G, 6-31G and 6-311G, and extensions to include one or more sets of polarization functions and/or diffuse basis functions.7 Input of an arbitrary basis set, comprising s, p and d-type Gaussians, is permitted.
Spartan's ab initio module provides both in-memory and direct techniques. In- memory techniques are very fast but are limited in their range of application. Hartree-Fock calculations for closed-shell systems comprising up to approximately 90 basis functions are practical with 64 mbytes of available memory, and up to approximately 105 basis functions with 128 mbytes of memory. In-memory, closed-shell MP2 calculations are limited to approximately 75 and 90 basis functions for 64 and 128 mbytes of memory, respectively. Memory requirements for open-shell molecules are greater.
Direct Hartree-Fock and MP2 methods incur significant additional computation cost, but may be extended to much larger systems with quite low memory demands. Hartree-Fock calculations involving 300-550 basis functions are practical with even modest amounts of memory, e.g., 32 mbytes. Memory demands for direct MP2 calculations are greater; calculations on systems with 150-200 basis functions are practical.
Preset limits within Spartan's ab initio module are enumerated below.
Spartan's density functional module provides for calculation of
energies, equilibrium and transition-state geometries and normal-mode
vibrational frequencies. At the present time it supports local density calculations using
the SVWN functional,4 and non-local density functional calculations using
the BP864,8 functional. Two different implementations of the latter have
been provided, one in which non-local corrections are introduced in a
self-consistent manner, and the other (less expensive) in which they are introduced
perturbatively. Three different numerical basis sets are available: DN, DN* and DN**.
While they are roughly equivalent in "size" to the 6-31G, 6-31G* and 6-31G**
Gaussian basis sets, respectively, experience suggests that they yield results closer to
much larger Gaussian basis sets.1b Note, that because density functional methods
are correlated methods, basis sets need to include functions of higher angular
quantum number than required for description of atomic ground states. DN* which includes
Spartan's density functional module does not make significant use of intermediate disk storage, and in addition makes only modest memory demands. Calculations on molecules comprising 300-550 basis functions require on the order of 32 mbytes of memory.
Preset limits within Spartan's density functional module are enumerated below.
Spartan's semi-empirical module provides for the calculation of heats of formation, equilibrium and transition-state geometries and normal-mode vibrational frequencies, as well as for searching of conformation space of both acyclic and cyclic molecules. The MNDO,9 AM110 and PM311 models are supported, as is the MNDO/d method of Thiel.12
Also available is a semi-empirical method for transition metals called PM3 (tm).13 This is related to Thiel's MNDO/d model, and describes each transition metal in terms of both d-type as well as s and p-type valence atomic orbitals. It is distinct from previous semi-empirical parameterizations available for Group IIB transition metals (Zn, Cd, Hg), in that it explicitly incorporates d functions. PM3 (tm) is intended to be used in conjunction with PM3 for non-transition metals.
Any of these semi-empirical methods may be used as the basis for singles and doubles CI, although the limits of CI calculations may be dictated by time and memory demands.
Corrections for aqueous solvation using the SM1, SM1a and SM2 models developed by Cramer and Truhlar14 may be obtained using AM1 wavefunctions. The Cramer/Truhlar SM3 model for water14 may be used with the PM3 method. Also incorporated into Spartan, are solvation models for both water and hexadecane developed by Dixon, Leonard and Hehre.15 These have been specifically parameterized for the MNDO, AM1 and PM3 methods (six parameterizations in total). They are computationally superior to the Cramer/Truhlar models as implemented in AMSOL,16 and generally produce solvation energies in better agreement with experiment.
While the memory requirements of semi-empirical molecular orbital methods are far less than those for ab initio models, they can still be significant for large molecules. The demand goes as approximately 100 times the square of the number of heavy atoms, and between 10 to 20 times the square of the number of basis functions. With 32 mbytes of memory, calculations are limited in practice to molecules comprising no more than 100 heavy atoms; 128 mbytes of available memory effectively doubles this limit.
Preset limits for Spartan's semi-empirical module are enumerated below.
Spartan's mechanics module presently provides for the calculation of equilibrium geometries, strain energies and normal-mode vibrational frequencies, as well as for searching of conformation space for both cyclic and acyclic molecules. The SYBYL force field17 from Tripos, Inc., and the recently introduced MMFF9418 are supported.
Spartan's properties module provides text output printing, population analyses (Mulliken,19 natural bond orbital20 and based on fits to molecular electrostatic potentials21), normal-mode analysis and evaluation of thermodynamic quantities (enthalpy, entropy and free energy), and calculation of the dipole moment. These functions apply to semi-empirical, density functional and ab initio wavefunctions from Spartan's modules, as well as to wavefunctions obtained from Gaussian 92/94/98. It also supports solvation energy calculations in water, hexadecane and in octanol and LogP calculations.
Spartan's graphics module provides data preparation associated with the
display as isosurfaces, or as 2D slices of molecular orbitals, electron densities,
spin densities and electrostatic and polarization potentials, as well as arbitrary
sums and differences of these quantities. Graphics functions apply to
semi-empirical, density functional and ab
initio wavefunctions obtained from
Spartan's modules as well as wavefunctions obtained from Gaussian 94.
Computers on which SPARTAN's modules are available are enumerated below.