Semiempirical Software

The PRDDO (partial retention of diatomic differential overlap) method is an attempt to get the optimal ratio of accuracy to CPU time. It has been parameterized for the periodic elements through Br, including the 3rd row transition metals. It was parameterized to reproduce ah initio results. PRDDO has been used primarily for inorganic compounds, organometallics, solid-state calculations, and polymer modeling. This method has seen less use than other methods of similar accuracy mostly due to the fact that it has not been incorporated into the most widely used semiempirical software. 

CIS calculations from the semiempirical wave function can be used for computing electronic excited states. Some software packages allow Cl calculations other than CIS to be performed from the semiempirical reference space. This is a good technique for modeling compounds that are not described properly by a single-determinant wave function (see Chapter 26). Semiempirical Cl... 

One very popular technique is an adaptation of the Born model for orbital-based calculations by Cramer and Truhlar, et. al. Their solvation methods (denoted SMI, SM2, and so on) are designed for use with the semiempirical and ah initio methods. Some of the most recent of these methods have a few parameters that can be adjusted by the user in order to customize the method for a specific solvent. Such methods are designed to predict ACsoiv and the geometry in solution. They have been included in a number of popular software packages including the AMSOL program, which is a derivative of AMPAC created by Cramer and Truhlar. 

Some of these software packages also have semiempirical or molecular mechanics functionality. However, the primary strength of each is ah initio calculation. There are also ah initio programs bundled with the Unichem, Spartan, and Hyperchem products discussed previously in this appendix. 

GAMESS stands for general atomic and molecular electronic structure system (we reviewed a version dated Dec. 2, 1998). It is an ah initio and semiempirical program, and has seen the most widespread use for ah initio calculations. The ASCII input hie format is usable but somewhat more lengthy than some other programs. The fact that GAMESS is a free, high-quality software makes it a favorite of many academic researchers. 

The Prandtl mixing length concept is useful for shear flows parallel to walls, but is inadequate for more general three-dimensional flows. A more complicated semiempirical model commonly used in numerical computations, and found in most commercial software for computational fluid dynamics (CFD see the following subsection), is the A — model described by Launder and Spaulding (Lectures in Mathematical Models of Turbulence, Academic, London, 1972). In this model the eddy viscosity is assumed proportional to the ratio /cVe. 

Many other approaches for finding a correct structural model are possible. A short description of ab-initio, density functional, and semiempirical methods are included here. This information has been summarized from the paperback book Chemistry with Computation An Introduction to Spartan. The Spartan program is described in the Computer Software section below.65 Another description of computational chemistry including more mathematical treatments of quantum mechanical, molecular mechanical, and statistical mechanical methods is found in the Oxford Chemistry Primers volume Computational Chemistry,52... 

The semiempirical molecular orbital (MO) methods of quantum chemistry [1-12] are widely used in computational studies of large molecules. A number of such methods are available for calculating thermochemical properties of ground state molecules in the gas phase, including MNDO [13], MNDOC [14], MNDO/d [15-18], AMI [19], PM3 [20], SAMI [21,22], OM1 [23], OM2 [24,25] MINDO/3 [26], SINDOl [27,28], and MSINDO [29-31]. MNDO, AMI, and PM3 are widely distributed in a number of software packages, and they are probably the most popular semiempirical methods for thermochemical calculations. We shall therefore concentrate on these methods, but shall also address other NDDO-based approaches with orthogonalization corrections [23-25],... 

The decision of which quantum mechanical model to use boils down to what size molecule you want to calculate, how reliable an answer you want, and how much time are you willing to wait for the results. Fortunately, as software and hardware improve, the tipping point of the balance weighing the pros and cons of semiempirical vs. DFT vs. ab initio is shifting such that larger molecules can be handled by the better methods. In special situations, a molecule with a couple of hundred atoms can be treated by an ab initio method (46,47), but the typical molecule of interest to theorists, spectrosco-pists, and physicists is smaller than what a pharmaceutical chemist usually wants to treat. Large molecular systems are often best left to one of the FF approaches (see next section). 

The procedure is called MetaSite (Site of Metabolism prediction) [25]. The MetaSite procedure is fully automated and does not require any user assistance. All the work can be handled and submitted in a batch queue. The molecular interaction fields for CYPs obtained from the GRID package are precomputed and stored inside the software. The semiempirical calculations, phaimacophoric recognition, descriptor handling, similarity computation, and reactivity computation are carried out automatically once the structures of the compounds are provided. The complete calculation is performed in a few seconds in IRIX SGI machines, and is even faster in the Linux or Windows environment. For example, processing a database of 100 compounds, starting from 3D molecular structures, takes about three minutes at full resolution with a... 

The models are all available in the semiempirical package AMSOL.339 They have also been implemented in commercial software packages.299.34o... 

A search for Oxford Molecular Ltd., which produces a variety of software for sequence alignment, molecular modeling of antibodies, QSAR, semiempirical molecular orbital calculations, and so on, yielded five hits in CJACS through 1993. A search for CompuDrug produced a total of two hits, one in 1990 and one in 1992. 

Sixt, S., Altschuh, I and Brtiggemann, R. (1996). Estimation of pka for Qrganic Oxyacids Using Semiempirical Quantum Chemical Methods. In Software Development in Chemistry - Vol. 10 (Gasteiger, J., ed.), Fachgruppe Chemie-Information-Computer (CIC), Frankfurt am Main (Germany), pp. 147-153. 

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