Molecular modeling ab initio

Keywords Halogen bond Crystallography Molecular modeling ab initio ... 

Michal Ksawery Cyrailski was born in Warsaw, Poland (1970). In 1994 received his M.Sc. degree and in 1999 his Ph.D. degree, both at the Chemistry Department of Warsaw University. In 1997 he was a holder of the Foundation for Polish Science grant in 1998 he received the distinction of the Kemula Reward (by the Polish Chemical Society) and in 1999 the Kolos Reward for the best Ph.D. work (by the Department of Chemistry of Warsaw University). In 1998-2000 he was a secretary of the Executive Committee of the Polish Chemical Society (elected). His main scientific interests are the structural chemistry of small organic compounds, crystallochemistry, molecular modeling (ab initio), structural aspects of aromatic character of r-electron systems, and definition of aromaticity. So far, he has published over 30 original papers and 5 reviews and presented 5 lectures and over 30 poster and oral communications. His hobby is classical music, especially by J. S. Bach, and singing in a professional choir. 

The estimation of properties from molecular structures is the task of deriving specific chemical, physical, and thermodynamic properties, for a chemical compound or a mixture of chemical compounds, under a specific set of conditions (usually temperature, pressure, and phase), based primarily on information about the molecular structures of the compounds involved (and the composition, in the case of a mixture). While many modem techniques (including molecular modeling, ab initio or semiempirical quantum-chemical computations of molecular orbitals, and density functional theory) involve substantial computational effort for any one system (molecule or simple mixture) they study, other methods involve direct correlations between property values and particular features of the molecular structures involved. The latter methods involve regression of a model with experimental data over a class of compounds these methods favor empirical approximations and arguments over fundamental models. 

Chemists seeking to use computational chemistry to support experimental efforts now have three generd theoretical tools available to them force field or molecular mechanics models, ab initio molecular orbital (MO) models and semiempirical MO models (1). Each of these tools have strengths and weaknesses which must be evaluated to determine which is most appropriate for a given applications. 

The existing structural models are overwhelmingly of the reconstructive type, in which the model is constructed based on experimental structural data. This is a result of the complex and poorly understood synthesis of the carbons. Mimetic simulation methods, in which the synthesis is modeled using molecular or ab initio simulations, have been successfully used for some other porous materials. 

Molecular calculations. Molecular relativistic ab initio DF codes with electron correlation are still in development (see, for example. Refs. 86,87 and the corresponding chapters in this issue). Correlation effects are included there at the Cl [88], MBPT (the seccmd order Moller-Plesset, MP2 [89,90]), or the CCSD levels [91,92]. They are too computer time intensive and still not sufficiently economic to be applied to the heaviest element systems in a routine manner, especially to those studied experimentally. DF molecular codes, some without correlation, were recently used for small molecules of the heaviest elements. The main aim of those calculations was to study relativistic and correlation effects on some model systems like lllH, 117H, 113H, (113)2 or II4H4 [93-99]. Some pioneer calculations by PyykkO for Rfitt and SgHe using the one-center expansion DF method should also be mentioned here [100-102]. 

A. Quantitative Model Ab Initio Molecular Orbital Theory... 

There are many large molecules whose mteractions we have little hope of detemiining in detail. In these cases we turn to models based on simple mathematical representations of the interaction potential with empirically detemiined parameters. Even for smaller molecules where a detailed interaction potential has been obtained by an ab initio calculation or by a numerical inversion of experimental data, it is usefid to fit the calculated points to a functional fomi which then serves as a computationally inexpensive interpolation and extrapolation tool for use in fiirtlier work such as molecular simulation studies or predictive scattering computations. There are a very large number of such models in use, and only a small sample is considered here. The most frequently used simple spherical models are described in section Al.5.5.1 and some of the more common elaborate models are discussed in section A 1.5.5.2. section Al.5.5.3 and section Al.5.5.4. 

The approach is ideally suited to the study of IVR on fast timescales, which is the most important primary process in imimolecular reactions. The application of high-resolution rovibrational overtone spectroscopy to this problem has been extensively demonstrated. Effective Hamiltonian analyses alone are insufficient, as has been demonstrated by explicit quantum dynamical models based on ab initio theory [95]. The fast IVR characteristic of the CH cliromophore in various molecular environments is probably the most comprehensively studied example of the kind [96] (see chapter A3.13). The importance of this question to chemical kinetics can perhaps best be illustrated with the following examples. The atom recombination reaction... 

Ultimately we may want to make direct comparisons with experimental measurements made on specific materials, in which case a good model of molecular interactions is essential. The aim of so-called ab initio molecular dynamics is to reduce the amount of fitting and guesswork in this process to a minimum. On the other hand, we may be interested in phenomena of a rather generic nature, or we may simply want to discriminate between good and bad theories. When it comes to aims of this kind, it is not necessary to have a perfectly realistic molecular model one that contains the essential physics may be quite suitable. 

Molecular dipole moments are often used as descriptors in QPSR models. They are calculated reliably by most quantum mechanical techniques, not least because they are part of the parameterization data for semi-empirical MO techniques. Higher multipole moments are especially easily available from semi-empirical calculations using the natural atomic orbital-point charge (NAO-PC) technique [40], but can also be calculated rehably using ab-initio or DFT methods. They have been used for some QSPR models. 

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