Molecular modeling semiempirical calculations

These are all empirical measurements, so the model of the harmonic oscillator, which is pur ely theoretical, becomes semiempirical when experimental information is put into it to see how it compares with molecular vibration as determined spectroscopically. In what follows, we shall refer to empirical molecular models such as MM, which draw heavily on empirical information, ab initio molecular models such as advanced MO calculations, which one strives to derive purely from theory without any infusion of empirical data, and semiempirical models such as PM3, which are in between (see later chapters). 

The most severe limitation of ah initio methods is the limited size of the molecule that can be modeled on even the largest computers. Semiempirical calculations can be used for large organic molecules, but are also too computation-intensive for most biomolecular systems. If a molecule is so big that a semiempirical treatment cannot be used elfectively, it is still possible to model its behavior avoiding quantum mechanics totally by using molecular mechanics. 

Section 2 mainly focuses on the current efforts to improve the accuracy of quantum calculations using simplified empirical model forms. McNamara and Hillier, in Chapter 5, summary their work on improving the description of the interactions in biological systems via their optimized semiempirical molecular models. Piquemal and co-workers present recent advances in the classical molecular methods, aiming at better reproduction of high-level quantum descriptions of the electtostatic interactions in Chapter 6. In Chatper 7, Cui and Elstner describe a different semiempir-... 

Fu et al. [16] analyzed a set of 57 compounds previously used by Lombardo and other workers also. Their molecular geometries were optimized using the semiempirical self-consistent field molecular orbital calculation AMI method. Polar molecular surface areas and molecular volumes were calculated by the Monte Carlo method. The stepwise multiple regression analysis was used to obtain the correlation equations between the log BB values of the training set compounds and their structural parameters. The following model was generated after removing one outlier (Eq. 50) ... 

Dynamic NMR gives information on the number and symmetries of conformations present in solution and on the energy barriers separating these conformations. This is particularly true for systems with barriers between about 25 and 90 kJ mol-1, a situation which often occurs in the medium ring. The interpretation of the NMR data can be carried out by the examination of molecular models, but this is a relatively crude and sometimes misleading method. Empirical force field (or molecular mechanics) calculations are much superior, even though the parametrization of heteroatoms may be open to question. Quantum mechanical calculations are not very suitable the semiempirical type, e.g. MINDO, do not reproduce conformational properties of even cyclohexane satisfactorily, and the ab initio... 

In this paper, we make use of molecular modelling techniques, particularly the AMI semiempirical molecular orbital method, to study the intermolecular interactions that are important for determining the manner in which crystal formation takes place. We are particularly inter ested in compounds that can potentially exhibit nonlinear optical properties. The calculational techniques are directed towards providing insight into the manner in which the desired nonlinear optical properties can be op timized in the macromolecular crystal state.(1)... 

Tel. 800-424-9737, fax 415-491-8311 (U.S.A.), tel. 41-38-337633 (U.K.) Model building, display, charge density, electrostatic potential, and molecular orbital plots. Stick, sphere, and dot surface display. 2D to 3D conversion. Protein and DNA fragment libraries. MM+, BIO+ (implementations of MM2 and CHARMM, respectively), OPLS, and AMBER molecular mechanics and dynamics. Solvent box. Semiempirical calculations by Extended Hiickel, CNDO, INDO, MINDO/3, MNDO, AMI, and PM3. Originated at Hypercube, Inc. (Dr. N. Ostlund et al.), of Ontario, Canada. Runs under Windows on a 386 or 486 PC and under Motif on a Silicon Graphics workstation. 

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. 

Tel. 703-658-4854, fax 703-658-4887, e-mail syazdi presto.ig.com Desktop molecular modeling. NEMESIS SAMPLER for simple modeling. PRO-EXPLORE for sequence analysis and biomolecular modeling. PRO-SIMULATE for molecular simulations with GROMOS, AMBER, and BOSS via a graphical interface. PRO-QUANTUM for semiempirical (MOPAC, extended Hiickel) and ab initio (CADPAC) calculations via a graphical interface. FDCALC and ESCALC for electrostatics calculations. N-DEE for analysis of NMR data. PC-PROT-I- (sequence analysis), PC-TAMMO-I- (protein—lipid modeling), and MASCA (statistics). Macintosh, PCs, and UNIX workstations. 

---