Strain Energies in Homoatomic Nitrogen Clusters N(4), N(6), and N(8)

Strain energies and resonance energies can be obtained as the energy changes for appropriate homodesmotic reactions using ab initio calculated total energies as the energies of the reactants and products involved. Homodesmotic reactions conserve bond types and preserve valence environments at all atoms, requirements that favor the cancellation of basis set and electron correlation errors in the ab initio energies. In this paper we calculate strain energies and resonance energies for N(4), N(6), and N(8) clusters in a number of chemically significant but, for nitrogen, hypothetical structural forms. The nitrogen cluster strain energies are generally of the same order of magnitude as those of isostructural hydrocarbon clusters, and individual differences can be explained by using the ring strain additivity rule and recognizing the effect of the presence of lone pairs of electrons on nitrogen clusters but not on the hydrocarbons. Resonance energies of the nitrogen clusters are much smaller than those of the comparable aromatic hydrocarbons. The differences can be rationalized by considering the relative strengths of CC and NN single and double bonds. Strain and resonance energies of nitrogen clusters are compared with those previously reported for homoatomic clusters of phosphorus and arsenic. Trends through the series are remarkably similar, but strain energies for clusters from lower periods are progressively smaller. Strain and resonance have been important organizing concepts in organic chemistry for many years. Estimates of corresponding parameters for inorganic analogs are only now becoming available.     

Surface layering in ionic liquids: an X-ray reflectivity study

The surface structure and thermodynamics of two ionic liquids, based on the 1-alkyl-3-methylimidazolium cations, were studied by X-ray reflectivity and surface tensiometry. A molecular layer of a density approximately 18% higher than that of the bulk is found to form at the free surface of these liquids. In common with surface layering in liquid metals and surface freezing in melts of organic chain molecules, this effect is induced by the lower dimensionality of the surface. The concentrations of the oppositely charged ions within the surface layer are determined by chemical substitution of the anion. The temperature-dependent surface tension measurements reveal a normal, negative-slope temperature dependence. The different possible molecular arrangements within the enhanced-density surface layer are discussed.     

Charge calculations in molecular mechanics. Part 8 Partial atomic charges from classical calculations

Summary The CHARGE2 programme, which involves the classical calculation of both the inductive and resonance contributions to the partial atomic charges in molecules is described, and the charges and electrostatic potentials obtained presented for some illustrative examples.In substituted methanes (CH₃X, CF₃X, CCl₃X) the effects of varying the electronegativity of the substituents and the - and -substituent contributions are clearly illustrated for a variety of substituent groups X.The problems involved in the inclusion of silicon into this scheme are detailed, together with the methods of overcoming them. The partial atomic charges ( and contributions) and electrostatic potentials for some silicon oxygen compounds are presented and discussed.The partial atomic charges from CHARGE2 for all the natural amino acids as their N-acetyl, N-methyl-amides are given and compared with those obtained from the AMBER and ECEPP/2 force fields. Considerable differences in these figures are observed, with the AMBER charges consistently much larger than those from the other two methods.The CHARGE2 partial atomic charges and electrostatic potentials for the four common nucleic acids, adenine, cytosine, guanine and thymine, are given and compared with those derived from other calculations. Again there is general similarity but also there are considerable differences, with those from the AMBER force field somewhat larger than the other methods.For previous parts in this series, see Refs. 1-7.     

Exact rotamer optimization for protein design

Computational methods play a central role in the rational design of novel proteins. The present work describes a new hybrid exact rotamer optimization (HERO) method that builds on previous dead-end elimination algorithms to yield dramatic performance enhancements. Measured on experimentally validated physical models, these improvements make it possible to perform previously intractable designs of entire protein core, surface, or boundary regions. Computational demonstrations include a full core design of the variable domains of the light and heavy chains of catalytic antibody 48G7 FAB with 74 residues and 10(128) conformations, a full core/boundary design of the beta1 domain of protein G with 25 residues and 10(53) conformations, and a full surface design of the beta1 domain of protein G with 27 residues and 10(60) conformations. In addition, a full sequence design of the beta1 domain of protein G is used to demonstrate the strong dependence of algorithm performance on the exact form of the potential function and the fidelity of the rotamer library. These results emphasize that search algorithm performance for protein design can only be meaningfully evaluated on physical models that have been subjected to experimental scrutiny. The new algorithm greatly facilitates ongoing efforts to engineer increasingly complex protein features.     

Intrinsic folding of small peptide chains: spectroscopic evidence for the formation of beta-turns in the gas phase

Laser desorption of model peptides coupled to laser spectroscopic techniques enables the gas-phase observation of genuine secondary structures of biology. Spectroscopic evidence for the formation of beta-turns in gas-phase peptide chains containing glycine and phenylalanine residues establishes the intrinsic stability of these forms and their ability to compete with other stable structures. The precise characterization of local minima on the potential energy surface from IR spectroscopy constitutes an acute assessment for the state-of-the-art quantum mechanical calculations also presented. The observation of different types of beta-turns depending upon the residue order within the sequence is found to be consistent with the residue propensities in beta-turns of proteins, which suggests that the prevalence of glycine in type II and II' turns stems essentially from an energetic origin, already at play under isolated conditions.