Molecular modeling calculations

Molecular modelling calculations using values of smaller than 3 Angstrom units for these proton-proton distances can be performed to obtain an optimized picture of the molecule. But this exceeds the scope of this book. 

One problem in molecular modelling calculations is that large powers of 10 tend to appear in all the calculated quantities. Thus, for example, molecules have... 

Table 0.1 shows such atomic units . The accepted values of the SI constants are themselves subject to minor experimental improvements, so authors generally report (he results of molecular modelling calculations as (e.g.) R = 50aa and give the conversion factor to SI somewhere in their paper, usually as a footnote. 

This chemistry was mechanistically interesting, and in order to rationalize the observed diastereoselectivities, molecular modeling calculations were conducted on the proposed oxonium ion intermediates.4 There are E- and Z-oxonium ion conformers. Since the major Z-oxonium ion conformers (86, 87) from these calculations were approximately 3 kcalmol-1 higher in energy, these conformers most likely did not significantly contribute to the stereochemical outcome of the reaction (Figure 7.3). 

It has been observed that cobalt may undergo large-scale reconstruction under a synthesis gas environment.27 Reconstruction is a thermodynamically driven process that results in the stabilization of less reactive surfaces. Recent molecular modeling calculations have shown that atomic carbon can induce the clock reconstruction of an fee cobalt (100) surface.28 It has also been postulated and shown with in situ x-ray adsorption spectroscopy (XAS) on cobalt supported on carbon nanofibers that small particles (<6 nm) undergo a reconstruction during FTS that can result in decreased activity.29... 

This scenario for molecular packing leading to biased chiral symmetrybreaking is quite speculative. However, it makes an important point for molecular modeling of lipid membranes The unusual feature of diacetylenic lipids does not have to be associated with the stereocenter of the molecules but rather may be a broken symmetry in the packing of the kinks in the acyl chains. This speculation needs to be investigated by detailed molecular modeling calculations. 

Molecular modeling calculations give important insight into the origin of such a large enantioselectivity. Unlike the rigid /3-CD, the hnear maltoheptaose allows each enantiomer of phenylalanine to find the most favorable conformation. The phenyl group of L-phenylalanine is oriented towards the C6 center of the hosts, while that of D-phenylalanine is oriented towards the C2 and C3 centers of the hosts. 

The basis for the further assignment of the bands to specific vibrations is the assignment of the benzene bands given by Whiffen (1955) on the basis of an exact molecular model calculation. 

Molecular modeling calculations atteiqpt to predict physical... 

Molecular modeling calculations may allow one, in the ideal case, to compute in a reasonable time and rather precisely the energy and structure of intermolecular complexes of biomedical, pharmaceutical, and chemical relevance. 

Further systematic studies are required to establish overall patterns suitable for application in molecular modeling calculations. 

Molecular modeling calculations using ab initio methods (MP2/6-31+G ) predict that spiro-(3-lactam of type M adopt a (3-tum secondary structure [50] which is very close to the ideal type-III (3-tums. Thus, these spiro-(3-lactams are the important members of the core for the preparation of different types of peptidomimetics using well-established chemistry. They combine the structural features required for inducing (3-tum motif. 

Molecular modeling calculations were conducted on the methyl viologen derivative 8 and methyl viologen (MVZ+) to generate the dihedral angles for the dicationic (fully oxidized) and monocationic (one-electron reduced) species <2005TL7291>. 

Molecular modeling calculations performed on the regio- and stereoselective intramolecular cycloaddition of 5 to give the bridged-ring cycloadduct 6 show that the transoid-conformation of acryloyl pendant in 5 is more suitable for the cycloaddition than the cisoid one (Scheme 1) <2001H(55)1987>. 

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