Computational studies structure prediction

The fully unsaturated dicyclopenta[cd,g/z]pentalene 4 (Fig. 7) remains elusive. Several attempts at generating 4 have been made, but so far all available knowledge about the system rests on computational studies which predict the structure and properties of this highly strained 7r-system [35]. In contrast to computational results for pentalene 2 and acepentalene 3, calculations for 4 predict an aromatic singlet ground state with a delocalized 7r-system. While the dianion of 4 is calculated to also be aromatic, the dication 42+ should be antiaromatic [35]. 

CsPuF6 was prepared and verified to be isostructural with corresponding compounds of uranium and neptunium. Its decomposition was studied in an inert gas atmosphere and in vacuum. Its spectrum has been measured in the region 400-2000 nm. The energy level structure of Pu5+ in the trigonally distorted octahedral CsPuF6 site was computed from a predictive model and compared with the observed spectrum. 

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... 

As seen above, /3-deprotonation implies a six-center transition state. Recent computational studies show an important variation of the H —C—C—O dihedral angle from reactant to transition state . Thus, the ground state geometry of the oxirane cannot be used to predict its reactivity. However, for structural reasons, some oxiranes cannot adopt a suitable conformation for -deprotonation and furnish exclusively a-deprotonation products. This concept is well illustrated by the norbornene oxide 17, which gives exclusively the transannular 1,3 insertion product 18 in the presence of lithium amide (Scheme 5) . 

Computational quantum chemistry has emerged in recent years as a viable tool for the elucidation of molecular structure and molecular properties, especially for the prediction of geometrical parameters, kinetics and thermodynamics of highly labile compounds such as nitrosomethanides. However, they are difficult objects for both experimental (high toxicity, redox lability, high reactivity, explosive character etc.) and computational studies, even with today s sophisticated techniques (e.g. NO compounds are often species with open-shell biradical character which requires the application of multi-configuration methods). 

Summary. We recently developed an all-atom free energy force field (PFFOl) for protein structure prediction with stochastic optimization methods. We demonstrated that PFFOl correctly predicts the native conformation of several proteins as the global optimum of the free energy surface. Here we review recent folding studies, which permitted the reproducible all-atom folding of the 20 amino-acid trp-cage protein, the 40-amino acid three-helix HIV accessory protein and the sixty amino acid bacterial ribosomal protein L20 with a variety of stochastic optimization methods. These results demonstrate that all-atom protein folding can be achieved with present day computational resources for proteins of moderate size. 

We note that a computational study of the dimer features is involved. It must account for the anisotropy of the interaction as this was done for the pure rotational bands of hydrogen pairs [355, 357], Whereas a treatment based on the isotropic potential approximation may be expected to predict nearly correct total intensities of the free-bound, bound-free, and bound-bound transitions involving the (H2)2 van der Waals molecule (and, of course, the free-free transitions which make up more than 90% of the observed intensities), the anisotropy of the interaction causes elaborate fine structure that is of considerable interest for the measurement of the anisotropy [248]. 

According to the torquoelectronic theory [34—37], this should result in less energetic transition structures if the largest substitution is electron-releasing. In contrast, if this substituent is electron-withdrawing, the 3-inward position should be favored. This prediction was verified by computational studies carried out both in the gas phase and in dichloromethane solution. Table 1 shows some significant results [50-52],... 

Whilst these difficulties do not invalidate application of molecular mechanics methods to such systems, they do mean that the interpretation of the results must be different from what is appropiate for small-molecule systems. For these reasons, the real value of molecular modeling of macromolecule systems emerges when the models are used to make predictions that can be tested experimentally or when the modeling is used as an adjunct to the interpretation of experiments. Alternatively, the relatively crude molecular mechanics models, while not of quantitative value, are an excellent aid to the visualization of problems not readily accessible in any other way. Molecular dynamics is needed, especially for large molecules, to scan the energy surface and find low-energy minima. The combination of computational studies with experimental data can help to assign the structure. 

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