Reinout Declerck

Influence of protein environment on the electron paramagnetic resonance properties of flavoprotein radicals: a QM/MM study.

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 g(y) 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 g(y) 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 g(x) and the g(y) 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.

Evidence for a Grotthuss-like mechanism in the formation of the rhamnose alkoxy radical based on periodic DFT calculations.

Abstract Pauwels, E., Declerck, R., Van Speybroeck, V. and Waroquier, M. Evidence for a Grotthuss-Like Mechanism in the Formation of the Rhamnose Alkoxy Radical Based on Periodic DFT Calculations. Radiat. Res. 169, 8–18 (2008). Molecular modeling adopting a periodic approach based on density functional theory (DFT) indicates that a Grotthuss-like mechanism is active in the formation of the radiation-induced alkoxy radical in α-l-rhamnose. Starting from an oxidized crystal structure, a hydroxyl proton is transferred along an infinite hydrogen bond chain pervading the entire crystal. The result of this proton shuttling mechanism is a stable radical species dubbed RHop. Only after several reorientations of crystal waters and hydroxyl groups, the more stable radical form RO4 is obtained, which differs in structure from the former by the absence of only one hydrogen bond. Calculations of the energetics associated with the mechanism as well as simulated spectroscopic properties reveal that different variants of the rhamnose alkoxy radical can be observed depending on the temperature of irradiation and consecutive EPR measurement. Cluster calculations on both radical variants provide hyperfine coupling and g tensors that are in good agreement with two independent experimental measurements at different temperatures.

Insight into the Solvation and Isomerization of 3‐Halo‐1‐azaallylic Anions from Ab Initio Metadynamics Calculations and NMR Experiments

In organic synthesis, it is observed experimentally that the nature of the solvent can influence tremendously the reactivity and overall product selectivity. In this communication, we report on the E/Z isomerization of a typical solvated species, that is, the stable lithiated 3-chloro-3-methyl-1azaallylic anion readily accessible from the N-isopropylACHTUNGTRENNUNGimine of a-chloropropiophenone, from a theoretical and a subsequent NMR study. To date, the configurational properties of these 3-chloro-3-methyl-1-azaallylic anions are poorly understood. Our main emphasis is devoted to the monomeric species as these are believed to be the most important for further reactivity studies (see below). It will be shown that the investigated species is a particular example in which the inclusion of the solvent in the modeling study is of the utmost importance to determine the proper chemical ACHTUNGTRENNUNGbehavior. The 3-chloro-3-methyl-1-azaallylic anion was chosen as a model compound to obtain a deeper insight into the structural features of 3-halo-1-azaallylic anions and to get a better understanding, and eventually a better control, of the stereochemical outcome of the reactions in which these anions are involved. Since their first use in the early 1960s, non-halogenated 1-azaallylic anions have gained a predominant role in organic synthesis due to their ability to form new C C bonds with a lack of side products. The chemistry of 1-azaallylic anions leads to basic heterocyclic systems such as aziridines, azetidines, pyrrolidines, pyrroles, piperidines, oxiranes, oxolanes, and higher functionalized ring systems, currently of interest for pharmaceutical chemistry and agrochemistry. The application of certain halogenated counterparts, that is, the 3-chloro-3-methyl-1azaallylic anions, in particular by the group of De Kimpe and more general by the group of Florio, which incorporated the 3-chloro-3-methyl-1-azaallylic moiety into heterocyclic structures, has led to the synthesis of various important classes of compounds such as cyclopropanes, tetrahydrofurans, tetrahydropyrans, oxiranes, aziridines, chloroimines, pyrroles and pyridines, steroids, alkenylheterocycles, and oxazetidines. As mentioned, 3-chloro3-methyl-1-azaallylic anions can be used for the synthesis of functionalized oxiranes and aziridines since the former anions behave as nucleophiles in Darzensand aza-Darzenstype reactions with carbonyl compounds and imines. One of the determining factors in the stereochemical outcome of these Darzens-type reactions is the E/Z stereochemistry of the starting 1-azaallylic anion. Therefore, it is important to know and understand the configurational properties of 3chloro-3-methyl-1-azaallylic anions in order to perform aldoland Mannich-type reactions with these intermediates in a stereocontrolled manner. NMR investigation and semiempirical calculations on the stereochemistry of (2-(a-chloroethyl)benzothiazolyl)lithium and (4,4-dimethyl-2-(a-chloroethyl)oxazolinyl)lithium have demonstrated that internal coordination between lithium and chlorine stabilizes the corresponding isomer with nitrogen and chlorine at the same side of the C=C double bond. The lack of such structural investigations on 3chloro-3-methyl-1-azaallylic anions in sensu stricto urged us to study their stereochemical properties. The E/Z isomerism for non-halogenated 1-azaallylic anions has been observed and investigated quite frequently. The facile carbon carbon bond rotation in simple lithiated 1-azaallylic anions was investigated using H NMR spectros[a] Dr. R. Declerck, B. De Sterck, T. Verstraelen, Prof. Dr. M. Waroquier, Prof. Dr. V. Van Speybroeck Center for Molecular Modeling, Ghent University Proeftuinstraat 86, 9000 Gent (Belgium) Fax: (+32) 9-264-6697 E-mail : Veronique.VanSpeybroeck@UGent.be [b] Dr. G. Verniest, Dr. S. Mangelinckx, J. Jacobs, Prof. Dr. N. De Kimpe Department of Organic Chemistry, Faculty of Bioscience Engineering Ghent University, Coupure links 653, 9000 Gent (Belgium) Fax: (+32) 9-264-6243 E-mail : Norbert.DeKimpe@UGent.be Supporting information for this article is available on the WWW under http://dx.doi.org/10.1002/chem.200800948.

Molecular Environment and Temperature Dependence of Hyperfine Interactions in Sugar Crystal Radicals from First Principles

The effect of the molecular environment and the temperature dependence of hyperfine parameters in first principles calculations in alpha-d-glucose and beta-d-fructose crystal radicals have been investigated. More specifically, we show how static (0 K) cluster in vacuo hyperfine calculations, commonly used today, deviate from more advanced molecular dynamics calculations at the experimental temperature using periodic boundary conditions. From the latter approach, more useful information can be extracted, allowing us to ascertain the validity of proposed molecular models.