E. Pauwels

Electron paramagnetic resonance (EPR), electron nuclear double resonance (ENDOR), and ENDOR-induced EPR (EIE) measurements on sucrose single crystals at 10 K after in situ X irradiation at this temperature reveal the presence of at least nine different radical species. Nine proton hyperfine coupling tensors were determined from ENDOR angular variations and assigned to six of these species (R1−R6) using EIE. Spectral simulations indicate that four of those (R1−R3 and R6) dominate the EPR absorption. Assisted by periodic density functional theory (DFT) calculations, R1 and R2 are identified as H-abstracted C1- and C5-centered radicals, R3 is tentatively assigned to an H-abstracted C6-centered radical, and R6 is identified as an alkoxy radical where the abstracted hydroxy proton has migrated to a neighboring OH group via intermolecular proton transfer. The latter radical had been characterized and identified in a previous study, but the present DFT calculations provide additional insight into its conformation and particular properties. This study provides the first step in unraveling the formation mechanism of the stable sucrose radicals detected after room-temperature irradiation and contributes to the understanding of the initial stages of radiation damage to solid-state carbohydrates.

The properties and functions of (bio)molecules are closely related to their molecular conformations. A variety of methods are available to sample the conformational space at a relatively low level of theory. If a higher level of theory is required, the computational cost can be reduced by selecting a uniformly distributed set of conformations from the ensemble of conformations generated at a low level of theory and by optimizing this selected set at a higher level. The generation of conformers is performed using molecular dynamics runs which are analyzed using the MD-Tracks code [ J. Chem. Inf. Model. 2008, 48, 2414]. This article presents a Kennard−Stone-based algorithm, with a distance measure based on the distance matrix, for the selection of the most diverse set of conformations. The method has been successfully applied to macrocyclic alkenes. The correct thermodynamic stability of the double-bond isomers of a flexible macrocyclic alkene containing two chiral centers is reproduced. The double-bond configuration has a limited effect on the conformation of the whole macrocycle. The chirality of the stereocenters has a larger effect on the molecular conformations.

The crystal structures of eight cyclodipeptides are determined, incorporating pipecolic acid or proline and phenylalanine or N-methyl phenylalanine. This set of structures allows the evaluation of the effects on molecular conformation and crystal packing of imino acid ring-size, relative configuration of the two amino acids, and N-methylation. In the non-methylated compounds, hydrogen-bonding interactions form one-dimensional motifs that dominate the packing arrangement. Three compounds have more than one symmetry-independent molecule in the asymmetric unit (Z' > 1), indicative of a broad and shallow molecular energy minimum. Density functional theory calculations reveal the interplay between inter- and intramolecular factors in the crystals. Only for the N-methylated compounds do simulations of the molecules in the isolated state succeed to reproduce the observed crystallographic conformations. Puckering of the diketopiperazine ring and the deviation from planarity of the amide bonds are not reproduced in the remaining compounds. Cluster in vacuo calculations with a central cyclodipeptide molecule surrounded by hydrogen-bound molecules establish that hydrogen bonding is of major importance but that other intermolecular interactions must also contribute substantially to the crystal structure. More advanced periodic calculations, incorporating the crystallographic environment to the full extent, are necessary to correctly describe all the conformational features of these cyclodipeptide crystals.

The neutral and anionic semiquinone radicals of the flavin adenine dinucleotide (FAD) cofactor noncovalently bound in glucose oxidase from A. niger are examined with the aid of QM/MM molecular modeling methods, enabling complete inclusion of the protein environment. Recently, the electron paramagnetic resonance (EPR) characteristics, the anisotropic g tensor and all the significant hyperfine couplings, of these flavoprotein radicals were determined at high resolution (J. Phys. Chem. B 2008, 112, 3568). A striking difference between the neutral and anionic radical forms was found to be a shift in the gy principal value. Within the QM/MM framework, geometry optimization and molecular dynamics simulations are combined with EPR property calculations, employing a recent implementation by some of the authors in the CP2K software package. In this way, spectroscopic characteristics are computed on the fly during the MD simulations of the solvated protein structure, mimicking as best as possible the experimental conditions. The general agreement between calculated and experimental EPR properties is satisfactory and on par with those calculated with other codes (Gaussian 03, ORCA). The protonation state of two histidines (His559 and His516) at the catalytic site of this flavoprotein is found to have a remarkable influence on the isotropic hyperfine coupling of one of the methyl groups on the neutral FAD radical, which is consistent with experimental findings in other flavoproteins (J. Biol. Chem. 2007, 282, 4738). Furthermore, the shift in the gy principal values between the neutral and anionic radicals is well reproduced by QM/MM simulations. Incorporation of at least the nearest protein environment of the cofactor radicals proves to be vital for a correct reproduction, indicating that this shift is a global feature of the protein rather than a local one. In addition, QM/MM techniques are used to make a prediction of relative angles between important spectroscopic principal directions, which are not readily determined by conventional EPR experiments. Significantly, the directions of the gx and the gy components of the g-tensor that lie in the plane of the isoalloxazine moiety are rotated by approximately 59° between the neutral and the anionic radicals.