Free energy of WALP23 dimer association in DMPC, DPPC, and DOPC bilayers.

The MARTINI coarse-grained model is used to gain insight into the association of WALP23 helices in three different lipid membranes: DMPC, DPPC and DOPC. Potentials of mean force describing the association of two WALP23 helices embedded in different lipid bilayers indicate no barrier of association and a stabilization of more than 20 kJ mol(-1) of the associated state relative to the fully dissociated state. Association is strongest in DMPC, followed by DPPC and DOPC.

Chemical rescue of enzymes: proton transfer in mutants of human carbonic anhydrase II.

In human carbonic anhydrase II (HCA II), the mutation of position 64 from histidine to alanine (H64A) disrupts the rate limiting proton transfer (PT) event, resulting in a reduction of the catalytic activity of the enzyme as compared to the wild-type. Potential of mean force (PMF) calculations utilizing the multistate empirical valence bond (MS-EVB) methodology for H64A HCA II yields a PT free energy barrier significantly higher than that found in the wild-type enzyme. This high barrier, determined in the absence of exogenous buffer and assuming no additional ionizable residues in the PT pathway, indicates the likelihood of alternate enzyme pathways that utilize either ionizable enzyme residues (self-rescue) and/or exogenous buffers (chemical rescue).

The effect of multiplicity on the size of iron(II) and the structure of iron(II) porphyrins.

The displacement of the iron(II) atom from the porphyrin plane in iron(II) porphyrin complexes is investigated with respect to the spin state of iron(II) employing density functional theory. In this study the quantum theory of atoms in molecules (QTAIM) is used to show that the atomic volume of iron is smaller in the quintet state of imidazolium ligated iron(II) porphyrin than in the triplet state. This is consistent with what has been found for free atoms and contradicts the original interpretation of structural studies with X-rays, which assumed that the out-of-plane displacement of iron from the porphyrin ring in the quintet state is due to the increased spatial size of the high-spin iron atom.

Conformational Analysis of Arabinofuranosides: Prediction of (3)JH,H Using MD Simulations with DFT-Derived Spin-Spin Coupling Profiles.

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.

Conformational Studies of Methyl β-d-Arabinofuranoside Using the AMBER/GLYCAM Approach.

Furanosides are important constituents of a number of glycoconjugates from many microorganisms. The highly flexible nature of these furanosyl moieties is believed to contribute significantly to their role in biological processes. Therefore, an understanding of the conformational preferences of these molecules is an important area of research.

Approach for the Simulation and Modeling of Flexible Rings: Application to the α-D-Arabinofuranoside Ring, a Key Constituent of Polysaccharides from .

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, , 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 () using the AMBER force field and the GLYCAM carbohydrate parameter set.

Bond length and the electron density at the bond critical point: X--X, Z--Z, and C--Z bonds (X = Li-F, Z = Na-Cl).

The aim was to investigate the relationship between the bond length and the electron density at the bond critical point in homonuclear X--X and Z--Z and heteronuclear C--Z bonds (X = Li-F, Z = Na-Cl). The d,rho(c) 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.

Atomic contributions to bond dissociation energies in aliphatic hydrocarbons.

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 (C(n)H(2n+2)) and trans-alkenes (C(n)H(2n)) 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.

Characterization of a closed-shell fluorine-fluorine bonding interaction in aromatic compounds on the basis of the electron density.

A bond path linking two saturated fluorine atoms is found to be ubiquitous in crowded difluorinated aromatic compounds. The bond path is shown to persist for a range of internuclear distances (2.3-2.

Theoretical study of the thermolysis of beta-hydroxyl aldehydes.

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.

An Atoms in Molecules Study of the Halogen Resonance Effect.

We report a detailed study by means of the theory of atoms in molecules (AIM) of the resonance effect exhibited in systems where a halogen is adjacent to a carbon-carbon double bond. Moreover, we have carried out a comparable study of the respective saturated halohydrocarbons and hydrocarbons, as well as the related unsaturated hydrocarbons. The valence shell charge concentration (VSCC) of the atoms in systems that exhibit the halogen resonance effect is considerably different from that of the systems where only the electron withdrawing inductive effect is present.

Extended weak bonding interactions in DNA: pi-stacking (base-base), base-backbone, and backbone-backbone interactions.

We report on several weak interactions in nucleic acids, which, collectively, can make a nonnegligible contribution to the structure and stability of these molecules. Fragments of DNA were obtained from previously determined accurate experimental geometries and their electron density distributions calculated using density functional theory (DFT). The electron densities were analyzed topologically according to the quantum theory of atoms in molecules (AIM).

Fluorine-fluorine spin-spin coupling constants in aromatic compounds: correlations with the delocalization index and with the internuclear separation.

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).