Semi-empirical molecular models

All of the so-called semi-empirical molecular models can now be recog-... 

Nooruddin NS, Wahlbeck PG, Carper WR (2009) Semi-Empirical molecular modeling of ionic liquid tribology ionic liquid-hydroxylated silicon surface interactions. Tribol Lett 36 147-156... 

However, the non-transitional Zn ion would rather prefer either a tetrahedral or a five-coordinate stereochemistry (in the latter case, a solvent molecule would complete the coordination polyhedron). Figure 18 shows the CPK model for the tetrahedral arrangement, as calculated by a semi-empirical molecular model. In this situation, the nitrogen atom of the donor group is only 5.1 A distant from the closest... 

Templeton et al 30) used semi-empirical molecular modeling calculations and x-ray crystal structures of novolac oligomeric residues to show that ortho-ortho linkages in novolac result in an extensive network of intramolecular hydrogen bonding. Templeton proposed that this hydrogen bonding causes the phenols to form... 

In all these examples, the importance of good simulation and modeling cannot be stressed enough. A variety of methods have been used in this field to simulate the data in the cases studies described above. Blander et al. [4], for example, used a semi-empirical molecular orbital method, MNDO, to calculate the geometries of the free haloaluminate ions and used these as a basis for the modeling of the data by the RPSU model [12]. Badyal et al. [6] used reverse Monte Carlo simulations, whereas Bowron et al. [11] simulated the neutron data from [MMIM]C1 with the Empirical Potential Structure Refinement (EPSR) model [13]. 

Semi-empirical molecular orbital calculations have been carried out on the model phosphorane HaPiCHa. Besides the expected transfer of charge, the inclusion of the phosphorus 2>d orbitals showed a significant hyperconjugative interaction between the CHg orbitals and a 2>d orbital of appropriate symmetry on phosphorus. Calculations on cyclopropylidene-phosphorane revealed a similar interaction between the Walsh orbitals of the ring and an in-plane phosphorus 2>d orbital. 

The absorption bands measured by the flash spectrographic method are often assigned by (a) comparison with known singlet-singlet absorption spectra, (b) comparison of the lifetime of the species responsible for the absorption with the phosphorescence lifetime, (c) comparison with calculated energies and intensities of the various possible absorptions by semi-empirical molecular orbital methods, and (d) comparison with published triplet absorption spectra and decay kinetics of model compounds. 

Semi-empirical molecular orbital, MO, theory uses a combination of experimental data and quantum mechanical MO methods to model the valence electronic structure of molecules. In the MNDO (8) method each atom is parameterized using experimental data. This calculation provides molecular orbital descriptions of the valence electrons, as well as effective charges of each atom in the molecule. 

The basis of molecular modeling is that all important molecular properties, i. e., stabilities, reactivities and electronic properties, are related to the molecular structure (Fig. 1.1). Therefore, if it is possible to develop algorithms that are able to calculate a structure with a given stoichiometry and connectivity, it must be possible to compute the molecular properties based on the calculated structure, and vice versa. There are many different approaches and related computer programs, including ab-initio calculations, various semi-empirical molecular orbital (MO) methods, ligand field calculations, molecular mechanics, purely geometrical approaches, and neural networks, that can calculate structures and one or more additional molecular properties. 

The MPE/MCSCF approach has been employed to study the interplay of solvent and conformation effects on the spin-spin coupling constants in methanol and methylamine [72], The simulated solvent effects are noticeable for the one-bond coupling constants and for some of the geminal coupling constants but negligible for 3/ee. The dielectric continuum effects have been found to depend considerably on the molecular conformation in the case of and 27ece. It is worth noting here that the MCSCF results have confirmed the conclusions drawn in ref. [80] from semi-empirical continuum model calculations. 

Warne, M.S., Boyd, M.A., Meharg, E.M., Osbom, D., Killham, D., Lindon, J.C. and Nicholson, J.K. (1999a). Quantitative Stmcture-Toxicity Relationships for Halobenzenes in Two Species of Bioluminescent Bacteria, Pseudomonas fluorescens and Vibrio fischeri. Using an Atom-Centered Semi-Empirical Molecular-Orbital Based Model. SAR QSAR Environ.Res., 10, 17-38. 

Figure 18 The ball-and-stick model of the Zn" complex of the disubstituted tetramine 11, as calculated through a semi-empirical molecular orbital method. Hydrogen atoms have been omitted for clarity. The Zn" centre (black ball) chose a tetrahedral stereochemistry. Five-coordination (including a solvent molecule) is possible, too. Both stereochemical arrangements put the A/ A -dimethylaniline and anthracene subunits at a distance favourable to the occurrence of a donor-to-fluorophore eT process.

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