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Theoretical study on thermolysis of a group of beta-hydroxyl aldehydes is reported, with emphasis on activation energies and rate constants obtained using conventional transition state theory. The results showed that thermolysis of beta-hydroxyl aldehydes are slower than the thermolysis of similar beta-hydroxyl ketones.

A report is presented on several weak interactions in nucleic acids, which collectively can make a noneligible contribution to the structure and stability of these molecules. A study characterizes the pi-stacking interaction between the nearest neighbor stacked bases, the interactions that a given nuclease has with the backbone and the interactions within the backbone itself.

The ubiquity of the fluorine-fluorine bonding interaction for a systematic examination is reported. Teh bond path is shown to persist for a range of internuclear distances (2.3-2.8 angstrom) and a range of relative orientations of the two C-F internuclear axes.

This paper explores the atomic contributions to the electronic vibrationless bond dissociation enthalpy (BDE) at 0 K of the central C–C bond in straight-chain alkanes (CnH2n+2) and trans-alkenes (CnH2n) with an even number of carbon atoms, where n=2, 4, 6, 8. This is achieved using the partitioning of the total molecular energy according to the quantum theory of atoms in molecules by comparing the atomic energies in the intact molecule and its dissociation products. The study is conducted at the MP2(full)/6-311++G(d,p) level of theory. It is found that the bulk of the electronic energy necessary to sever a single C–C bond is not supplied by these two carbon atoms (the α-carbons) but instead by the atoms directly bonded to them. Thus, the burden of the electronic part of the BDE is primarily carried by the two hydrogens attached to each of the α-carbons and by the β-carbons. The effect drops off rapidly with distance along the hydrocarbon chain. The situation is more complex in the case of the double bond in alkenes, since here the burden is shared between the α-carbons as well as the atoms directly bonded to them, namely, again the α-hydrogens and the β-carbons. These observations may lead to a better understanding of the bond dissociation process and should be taken into account when locally dense basis sets are introduced to improve the accuracy of BDE calculations. [ABSTRACT FROM AUTHOR]

The aim was to investigate the relationship between the bond length and the electron density at the bond critical point in homonuclear X&bond;X and Z&bond;Z and heteronuclear C&bond;Z bonds (X = Li-F, Z = Na-Cl). The d,ρc pairs were obtained from 472 target bonds in DFT-optimized (B3LYP/6-311+G(d,p)) small molecular species. These species were selected arbitrarily but with a view to maximize the range widths WR for each atom combination. It was found that (i) with one clear exception, the d(A - A) means (A = X or Z) correlate linearly with the bond lengths d(A2) of the respective diatomic molecules; (ii) the d(A - A) means correlate parabolically with n, the formal number of valence electrons in the atoms of the bond; and (iii) with increasing sample size N the ratio WR(ρc)/WR(d) appears to converge toward a representation f [WR(ρc)/WR(d)]N→∞ characteristic of A. Detailed analysis of the d,ρc relationship has shown that by and large simple power regression accounts best for the DFT data. The regression coefficients of d = aρc-b and ρc = αd-β (b, β > 0) vary with n in a seemingly irregular manner but one that is consistent with simple chemical notions. The d(A2) can be approximated in terms of multilinear MO electron occupancies. © 2007 Wiley Periodicals, Inc. J Comput Chem, 2008 [ABSTRACT FROM AUTHOR]

A molecular dynamics (MD) investigation on a series of oligo-α-arabinofuranosides (1-8) using the AMBER force field and the GLYCAM carbohydrate parameter set is reported. The validation of the method was carried out by direct comparison of experimental vicinal proton-proton coupling constants ((3)JH,H) with those obtained by using an empirically determined Karplus equation and density functional theory (DFT)-derived relationships specifically tailored for α-arabinofuranosyl systems. A simple code was developed to implement the determination of (3)JH,H by applying these relationships to the probability distributions of rotamers and ring conformations displayed by the simulations. The empirical Karplus relationship and the DFT-derived equations yielded, in most cases, the same trend as experiment for intra-ring (3)JH,H values. This direct comparison circumvents additional sources of errors that may arise from the assumptions introduced by the deconvolution procedures often used to calculate population of rotamers and ring conformations from experimental (3)JH,H.

A number of lower organisms (bacteria, fungi, and parasites) produce glycoconjugates that contain furanose rings. Of particular interest to our group are cell wall polysaccharides from mycobacteria, including the human pathogen, Mycobacterium tuberculosis , which contain a large number of arabinofuranose resides. As part of a larger project on the conformational analysis of these molecules, we report here molecular dynamics simulations on methyl α-D-arabinofuranoside ( 1 ) using the AMBER force field and the GLYCAM carbohydrate parameter set. We initially studied the ability of this method to predict rotamer populations about the hydroxymethyl group (C4-C5) bond. Importantly, we show that simulation times of up to 200 ns are required in order to obtain convergence of the rotamer populations for this ring system. We also propose a new charge derivation approach that accounts for the flexibility of the furanoside ring by taking an average of the charges from a large number of conformers across the psuedorotational itinerary. The approach yields rotamer populations that are in good agreement with available NMR data and, in addition, provides insight into the nature of the puckering angle and amplitude in 1 .

A mechanism involving a six-membered cyclic transition state where the hydrogen of the hydroxyl group interacts with the oxygen of the carbonyl group has been proposed previously to describe the thermolysis of many beta-hydroxyl compounds. In this paper, the proposed mechanism is studied for a series of beta-hydroxyl aldehydes. Rate constants and activation energies are reported as well as a study of the influence of tunneling on the reaction rates. The electron density at the ring critical points, population analyses by the theory of atoms in molecules (AIM) and the natural bond orbital (NBO) method, as well as atomic energy analyses are used to gain insight into this interesting mechanism and into the effects of substituents.

This paper describes a new empirical approach for the evaluation of fluorine-fluorine spin-spin coupling constants (J(FF)) in aromatic compounds. The correlations between J(FF) and the delocalization index calculated within the framework of the theory of atoms in molecules (AIM) and with the fluorine-fluorine internuclear separation are investigated. Both the internuclear separation and the delocalization index are found to be highly correlated with J(FF). A regression model in which the experimental J(FF) coupling constant is fitted exponentially to the internuclear separation and linearly to the delocalization index yields a squared correlation coefficient as high as 0.96 for a data set consisting of 33 coupling constants spread over a range of 85 Hz.