Methods and molecular modeling

The reaction cycle discussed is generally accepted for unmodified cobalt and unmodified rhodium catalysts. But it has to be stressed here that to date no one has been able to prove the single steps conclusively it is still a subject of research, with modern techniques like in situ spectroscopic methods and molecular modeling in conjunction with kinetic investigations. 

Bain A D, Duns G J, Ternieden S, Ma J and Werstiuk N H 1994 The barrier to internal rotation and chemical exchange in N-acetyipyrroie. A study based on novei NMR methods and molecular modelling J. Phys. Chem. 98 7458-63... 

Study impact of BSA type used on zinc deposition morphology via electrochemical methods and molecular modelling... 

Abstract This review summarizes computational studies devoted to interactions of metal cations with nucleobases, nucleotides, and short oligonucleotides considered as DNA/RNA models. Since this topic is complex, basically only the results obtained using ab initio and DFT methods are discussed. Part 1 focuses mainly on the interactions of the isolated bases with metal cations in bare, hydrated, and ligated forms. First, interactions of bare cations with nucleobases in gas phase approach are mentioned. Later, solvation effects using polarizable continuum models are analyzed and a comparison with explicitly hydrated ions is presented. In Part II, adducts of alkali metal, metal of alkaline earth, and zinc group metal cations with canonical base pairs are discussed. A separate section is devoted to platinum complexes related to anticancer treatment. Stacked bases and larger systems are discussed in last section. Here, semiempirical methods and molecular modeling are also discussed due to extensive size of studied complexes. 

Specific solute-solvent interactions involving the first solvation shell only can be treated in detail by discrete solvent models. The various approaches like point charge models, siipennoleciilar calculations, quantum theories of reactions in solution, and their implementations in Monte Carlo methods and molecular dynamics simulations like the Car-Parrinello method are discussed elsewhere in this encyclopedia. Here only some points will be briefly mentioned that seem of relevance for later sections. 

Gilson, M. K. Multiple-site titration and molecular modeling Two rapid methods for computing energies and forces for ionizable groups in proteins. Proteins Struct. Punct. Genet. 15 (1993) 266-282. 

There is a lot of confusion over the meaning of the terms theoretical chemistry, computational chemistry and molecular modelling. Indeed, many practitioners use all three labels to describe aspects of their research, as the occasion demands "Theoretical chemistry is often considered synonymous with quantum mechanics, whereas computational chemistry encompasses not only quantum mechanics but also molecular mechaiucs, minimisation, simulations, conformational analysis and other computer-based methods for understanding and predicting the behaviour of molecular systems. Molecular modellers use all of these methods and so we shall not concern ourselves with semantics but rather shall consider any theoretical or computational tecluiique that provides insight into the behaviour of molecular systems to be an example of molecular modelling. If a distinction has to be... 

E. San2,J. Giraldo, andE. lsl. 2ia2LU., QSAR and Molecular Modeling Concepts, Computational Methods and Biological Applications,]. R. Prous Science Pubhshers,... 

Robust peptide-derived approaches aim to identify a small drug-like molecule to mimic the peptide interactions. The primary peptide molecule is considered in these approaches as a tool compound to demonstrate that small molecules can compete with a given interaction. A variety of chemical, 3D structural and molecular modeling approaches are used to validate the essential 3D pharmacophore model which in turn is the basis for the design of the mimics. The chemical approaches include in addition to N- and C-terminal truncations a variety of positional scanning methods. Using alanine scans one can identify the key pharmacophore points D-amino-acid or proline scans allow stabilization of (i-turn structures cyclic scans bias the peptide or portions of the peptide in a particular conformation (a-helix, (i-turn and so on) other scans, like N-methyl-amino-acid scans and amide-bond-replacement (depsi-peptides) scans aim to improve the ADME properties." ... 

Many researchers have put a considerable amount of effort into studies of the chiral recognition mechanisms (using, e.g., NMR and molecular modeling), but yet the choice of chiral selector or chiral phase for a new compound is often based on trial and error. Different strategies for chiral method development have been presented by many of the retailers of chiral columns as a service for the customers. In addition to the information supplied by these retailers, another source of knowledge is Chirbase, a database that contains more than 50,000 HPLC separations of more than 15,000 different chiral substances [61], which also can provide guidance to the analytical chemist. 

Tian, J. et al., Probing the binding of scutellarin to human serum albumin by circular dichroism, fluorescence spectroscopy, FTIR, and molecular modeling method. Biomacromolecules, 5, 1956, 2004. 

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