Molecular modeling case studies

In the case of nanojunctions, an exponential law is also predicted [91], and was very recently amenable to an experimental verification [5c]. This confirms the relationship between molecular model systems studied in solution, and actual devices involving an electrical connection to the outside world. 

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]. 

The second group of studies tries to explain the solvent effects on enantioselectivity by means of the contribution of substrate solvation to the energetics of the reaction [38], For instance, a theoretical model based on the thermodynamics of substrate solvation was developed [39]. However, this model, based on the determination of the desolvated portion of the substrate transition state by molecular modeling and on the calculation of the activity coefficient by UNIFAC, gave contradictory results. In fact, it was successful in predicting solvent effects on the enantio- and prochiral selectivity of y-chymotrypsin with racemic 3-hydroxy-2-phenylpropionate and 2-substituted 1,3-propanediols [39], whereas it failed in the case of subtilisin and racemic sec-phenetyl alcohol and traws-sobrerol [40]. That substrate solvation by the solvent can contribute to enzyme enantioselectivity was also claimed in the case of subtilisin-catalyzed resolution of secondary alcohols [41]. 

In recent years it has been realized that molecular modeling studies of the alkaloidal molecules having different pharmacological activities are highly important in order to explain their mechanisms, at least partially in some cases. This chapter presents and critically reviews some examples of molecular modeling studies of alkaloids, based on their different biological properties or sometimes performed in parallel to explain their biochemical effects. 

Pietrzyk, P., Gil, B. and Sojka, Z. (2007) Combining computational and in situ spectroscopies joint with molecular modeling for determination of reaction intermediates of deNOx process -CuZSM-5 catalyst case study, Catal. Today. doi 10.1016/j.cattod.2006.09.033. 

Another hypothesis was provided by Mikio Shimitso (1982) on the basis of studies of steric effects in molecular models. It had been noted years previously that the fourth nucleotide at the 3 end of the tRNA molecules (referred to as the discrimination base) might have a recognition function. In the case of certain amino acids (i.e., their tRNA-amino acid complexes) this base pair, in combination with the anticodon of the tRNA molecule, can select the amino acid corresponding to the tRNA species in question this is done on the basis of the stereochemical properties of the molecule. Since the anticodon of a tRNA molecule and the fourth nucleotide of the acceptor stem are far apart in space, two tRNA molecules must complex in a head-to-tail manner. The pocket thus formed can then fit specifically to the corresponding amino acid. 

Muller and Stock [227] used the vibronic coupling model Hamiltonian, Section III.D, to compare surface hopping and Ehrenfest dynamics with exact calculations for a number of model cases. The results again show that the semiclassical methods are able to provide a qualitative, if not quantitative, description of the dynamics. A large-scale comparison of mixed method and quantum dynamics has been made in a study of the pyrazine absorption spectrum, including all 24 degrees of freedom [228]. Here a method related to Ehrenfest dynamics was used with reasonable success, showing that these methods are indeed able to reproduce the main features of the dynamics of non-adiabatic molecular systems. 

It is remarkable that in the same year, 1934, two independent approaches, those of Stoll et al. and of Kuhn, led to the definition of two quantities which are conceptually quite similar and can be practically identical in many actual cases. In either case the intramolecular reaction is compared to a corresponding intermolecular process. This is the dimerisation reaction of the bifunctional reactant in the definition of the cyclisation constant C in the case of the effective concentration Crff Winter must be determined with the aid of an inter-molecular model reaction, the choice of which is not always obvious and can possibly lead to conceptual as well as experimental difficulties. It is also worth noting that although these early workers established a firm basis for interpretation of physical as well as of preparative aspects of intramolecular reactions, no extensive use of quantities C and Qff appears to have been made in the chemical literature over more than three decades after their definition. This is in spite of the enormous development of studies in the field of... 

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