Computational studies structure

Free Energy Computational Studies Structure Refinement with Sparse Restraints... 

Biological membranes provide the essential barrier between cells and the organelles of which cells are composed. Cellular membranes are complicated extensive biomolecular sheetlike structures, mostly fonned by lipid molecules held together by cooperative nonco-valent interactions. A membrane is not a static structure, but rather a complex dynamical two-dimensional liquid crystalline fluid mosaic of oriented proteins and lipids. A number of experimental approaches can be used to investigate and characterize biological membranes. However, the complexity of membranes is such that experimental data remain very difficult to interpret at the microscopic level. In recent years, computational studies of membranes based on detailed atomic models, as summarized in Chapter 21, have greatly increased the ability to interpret experimental data, yielding a much-improved picture of the structure and dynamics of lipid bilayers and the relationship of those properties to membrane function [21]. 

Empirical energy functions can fulfill the demands required by computational studies of biochemical and biophysical systems. The mathematical equations in empirical energy functions include relatively simple terms to describe the physical interactions that dictate the structure and dynamic properties of biological molecules. In addition, empirical force fields use atomistic models, in which atoms are the smallest particles in the system rather than the electrons and nuclei used in quantum mechanics. These two simplifications allow for the computational speed required to perform the required number of energy calculations on biomolecules in their environments to be attained, and, more important, via the use of properly optimized parameters in the mathematical models the required chemical accuracy can be achieved. The use of empirical energy functions was initially applied to small organic molecules, where it was referred to as molecular mechanics [4], and more recently to biological systems [2,3]. 

BW Beck, Q Xie, T Ichiye. Computational study of S—H S hydrogen bonds m [4Ee-4S]-type ferredoxm x-ray and NMR structures Characterization and implications for redox potentials. Protein Sci, submitted. 

Computational studies of nucleic acids offer the possibility to enliance and extend the infonnation available from experimental work. Computational approaches can facilitate the experimental detennination of DNA and RNA structures. Dynamic information. 

Many computational studies in heterocyclic chemistry deal with proton transfer reactions between different tautomeric structures. Activation energies of these reactions obtained from quantum chemical calculations need further corrections, since tunneling effects may lower the effective barriers considerably. These effects can either be estimated by simple models or computed more precisely via the determination of the transmission coefficients within the framework of variational transition state calculations [92CPC235, 93JA2408]. 

A few computational studies focus on the saturated analog of 4//-l,4-oxazine, i.e., morpholine [98JCS(P2)1223, 00JCS(P2)1619, 00TL5077]. These cover the structure of lithium morpholide, cycloaddition reactions, and molecular complexes with genistein. 

Finally, metalated epoxides undergo isomerization processes characteristic of traditional carbenoids (Scheme 5.2, Path C). The structure of a metalated epoxide is intermediate in nature between the structures 2a and 2b (Scheme 5.2). The existence of this intermediacy is supported by computational studies, which have shown that the a-C-O bond of oxirane elongates by -12% on a-lithiation [2], Furthermore, experimentally, the a-lithiooxycarbene 4a (Scheme 5.3) returned cydo-pentene oxide 7 among its decomposition products indeed, computational studies of singlet 4a suggest it possesses a structure in the gas phase that is intennediate in nature between an a-lithiocarbene and the lithiated epoxide 4b [3],... 

No detailed structural studies have been carried out experimentally on T4 derivatives but a number of computational studies have been undertaken as part of the drive to understand the fundamental nature of silicate structures, many of which are made up of small polyhedral units. 

There have a number of computational studies of hypothetical RMMR species [10-13, 40, 411. The simplest compounds are the hydrides HMMH. Some calculated structural parameters and energies of the linear and trans-bent metal-metal bonded forms of the hydrides are given in Table 1. It can be seen that in each case the frans-bent structure is lower in energy than the linear configuration. However, these structures represent stationary points on the potential energy surface, and are not the most stable forms. There also exist mono-bridged, vinylidene or doubly bridged isomers as shown in Fig. 2... 

The structures and conformational properties of a simple hemicarcerand, created earlier by Cram, see <96JA5590>, as well as the complexation and decomplexation with guest molecules have been computationally studied <96JA8056>. 

Because of fhe planar nafure of the cormterflow flame and the relatively high Reynolds number associated with the flow, the flame/flow configuration can be considered to be "aerodynamically clean," where the quasi-one-dimensional and bormdary-layer simplifications can be implemented in either analytical or computational studies. Useful insights into the thermochemical structure... 

With the development of accurate computational methods for generating 3D conformations of chemical structures, QSAR approaches that employ 3D descriptors have been developed to address the problems of 2D QSAR techniques, that is, their inability to distinguish stereoisomers. Examples of 3D QSAR include molecular shape analysis (MSA) [26], distance geometry,and Voronoi techniques [27]. The MSA method utilizes shape descriptors and MLR analysis, whereas the other two approaches apply atomic refractivity as structural descriptor and the solution of mathematical inequalities to obtain the quantitative relationships. These methods have been applied to study structure-activity relationships of many data sets by Hopfinger and Crippen, respectively. Perhaps the most popular example of the 3D QSAR is the com-... 

Due to their demanding synthesis, diamondoids are helpful models to study structure-activity relationships in carbocations and radicals, to develop empirical computational methods for hydrocarbons, and to investigate orientational disorders in molecular crystals as well [5,32]. 

In one of the very first realistic computational studies of PECD effects, performed for the amino acid alanine [51], it was noted that different results were obtained at each of three fixed geometries corresponding to low lying conformations identified in previous structure investigations [69-71]. A later combined experimental-theoretical study of PECD in 3-hydroxytetrahydrofuran [61] further looked at the influence of presumed conformation and concluded that while the predicted cross-section, a, and p parameters were mildly affected by conformation, the chiral parameters were much more strongly... 

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