E. Pauwels

Density-functional study of S2- defects in alkali halides

F. Stevens, H. Vrielinck, F. Callens, E. Pauwels, M. Waroquier
Physical Review B
66 (13), 134103
2002
A1

Abstract 

Density-functional methods, as implemented in the Amsterdam Density Functional program, are used to calculate the electron paramagnetic resonance (EPR) and electron nuclear double resonance (ENDOR) parameters of the S2- defect in a halide monovacancy in various alkali halides (MZ:M=Na, K, Rb and Z=Cl, Br, I) lattices. The calculations were performed on cluster in vacuo models for the defect and its lattice surroundings, involving up to 88 atoms in order to limit boundary effects. For all MZ lattices, the calculated g and 33S hyperfine tensors of the S2- molecular ion are in very good agreement with the available EPR data, explicitly supporting the monovacancy model for the defect. In addition, computational results for the principal superhyperfine and quadrupole values and axes of the nearest shells of M+ and Z- ions are compared with experimental ENDOR data. The merits and shortcomings of the applied cluster in the vacuo method are critically evaluated.

Tentative Structures for the Radiation-Induced Radicals in Crystalline β-d-Fructose Using Density Functional Theory

E. Pauwels, P. Lahorte, G. Vanhaelewyn, F. Callens, F. De Proft, P. Geerlings, M. Waroquier
Journal of Physical Chemistry A
106 (51), 12370-12375
2002
A1

Abstract 

In this study, density functional theory calculations were used to identify the structure of the radiation-induced radicals in solid state β-d-fructose, using a single molecule approach. Four model radicals were proposed, and the electron paramagnetic resonance (EPR) parameters were calculated for the optimized geometries. These calculated parameters were subsequently compared with those of two radical species, observed in an experimental EPR and electron nuclear double resonance study on irradiated fructose (Vanhaelewyn, G.; Lahorte, P.; De Proft, F.; Mondelaers, W.; Geerlings, P.; Callens, F. Phys. Chem. Chem. Phys. 2001, 3, 1729). On the basis of this preliminary comparison, three model structures were rejected. By varying the main degree of freedom of the remaining model, a number of conformations were obtained that yielded isotropic and anisotropic hyperfine tensor components in close agreement with experimental results. To disentangle between these possible conformers, a detailed study was made of the hyperfine tensor eigenvectors. One conformation was found to be in close agreement with the experimental measurement of the hyperfine tensor of the two observed radical species. It was concluded that these experimental species are in fact manifestations of one and the same radical, with a structure conforming to our model but with slightly altered conformations.

Density Functional Calculations on Alanine-Derived Radicals:  Influence of Molecular Environment on EPR Hyperfine Coupling Constants

E. Pauwels, V. Van Speybroeck, P. Lahorte, M. Waroquier
Journal of Physical Chemistry A
105 (38), 8794–8804
2001
A1

Abstract 

The amino acid l-α-alanine and its associated radiation-induced radicals display particular characteristics in solid-state that make it very appropriate for use in Electron Paramagnetic Resonance (EPR) dosimetry. In contrast to the number of experimental studies, relatively few theoretical studies have been published concerning the EPR parameters of these radicals. However, these studies inadequately account for the molecular environment of the alanine radicals in the crystalline lattice. Here, we present Density Functional Theory (DFT) calculations on one of the stable radiation-induced radicals of l-α-alanine both in molecular cluster models and in periodic models. An extensive investigation is presented on the various geometrical ingredients which have a substantial impact on the hyperfine coupling constants as the planarity of the radical backbone and the internal rotations of the final methyl and amino group vary. It is found that the accurate modeling of the hydrogen bonds with neighboring molecules is of utmost importance for an adequate reproduction of the experimental data.

Oxidation and Reduction Products of X Irradiation at 10 K in Sucrose Single Crystals: Radical Identification by EPR, ENDOR, and DFT

H. De Cooman, E. Pauwels, H. Vrielinck, E. Sagstuen, M. Waroquier, F. Callens
Journal of Physical Chemistry B
114 (1), 666–674
2010
A1

Abstract 

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.

Comparative study of various normal mode analysis techniques based on partial Hessians

A. Ghysels, V. Van Speybroeck, E. Pauwels, S. Catak, B.R. Brooks, D. Van Neck, M. Waroquier
Journal of Computational Chemistry
31 (5), 994-1007
2010
A1

Abstract 

Standard normal mode analysis becomes problematic for complex molecular systems, as a result of both the high computational cost and the excessive amount of information when the full Hessian matrix is used. Several partial Hessian methods have been proposed in the literature, yielding approximate normal modes. These methods aim at reducing the computational load and/or calculating only the relevant normal modes of interest in a specific application. Each method has its own (dis)advantages and application field but guidelines for the most suitable choice are lacking. We have investigated several partial Hessian methods, including the Partial Hessian Vibrational Analysis (PHVA), the Mobile Block Hessian (MBH), and the Vibrational Subsystem Analysis (VSA). In this article, we focus on the benefits and drawbacks of these methods, in terms of the reproduction of localized modes, collective modes, and the performance in partially optimized structures. We find that the PHVA is suitable for describing localized modes, that the MBH not only reproduces localized and global modes but also serves as an analysis tool of the spectrum, and that the VSA is mostly useful for the reproduction of the low frequency spectrum. These guidelines are illustrated with the reproduction of the localized amine-stretch, the spectrum of quinine and a bis-cinchona derivative, and the low frequency modes of the LAO binding protein. © 2009 Wiley Periodicals, Inc. J Comput Chem, 2010

Conformational Sampling of Macrocyclic Alkenes Using a Kennard−Stone-Based Algorithm

D.D. Claeys, T. Verstraelen, E. Pauwels, C.V. Stevens, M. Waroquier, V. Van Speybroeck
Journal of Physical Chemistry A
114 (25), 6879–6887
2010
A1

Abstract 

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.

On the identity of the radiation-induced stable alanine radical

E. Pauwels, H. De Cooman, M. Waroquier, E.O. Hole, E. Sagstuen
Physical Chemistry Chemical Physics (PCCP)
12, 8733-8736
2010
A1

Abstract 

Using periodic DFT calculations, it is concluded that the stable radiation-induced alanine radical most probably is the result of reductive deamination and protonation of the detached amino group, yielding an NH4+ ammonium ion and a negatively charged radical.

Structures of cyclic dipeptides: an X-ray and computational study of cis- and trans-cyclo(Pip-Phe), cyclo(Pro-Phe) and their N-methyl derivatives

M. Budesinsky, I. Cisarova, J. Podlaha, F. Borremans, J.C. Martins, M. Waroquier, E. Pauwels
Acta Crystallographica Section B Structural Science
B66, 662-677
2010
A1

Abstract 

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.

Electron Magnetic Resonance and Density Functional Theory Study of Room Temperature X-Irradiated β-d-Fructose Single Crystals

M.A. Tarpan, E. Pauwels, H. Vrielinck, M. Waroquier, F. Callens
Journal of Physical Chemistry A
114 (47), 12417–12426
2010
A1

Abstract 

Stable free radical formation in fructose single crystals X-irradiated at room temperature was investigated using Q-band electron paramagnetic resonance (EPR), electron nuclear double resonance (ENDOR), and ENDOR induced EPR (EIE) techniques. ENDOR angular variations in the three main crystallographic planes allowed an unambiguous determination of 12 proton HFC tensors. From the EIE studies, these hyperfine interactions were assigned to six different radical species, labeled F1−F6. Two of the radicals (F1 and F2) were studied previously by Vanhaelewyn et al. [Vanhaelewyn, G. C. A. M.; Pauwels, E.; Callens, F. J.; Waroquier, M.; Sagstuen, E.; Matthys, P. J. Phys. Chem. A 2006, 110, 2147.] and Tarpan et al. [Tarpan, M. A.; Vrielinck, H.; De Cooman, H.; Callens, F. J. J. Phys. Chem. A 2009, 113, 7994.]. The other four radicals are reported here for the first time and periodic density functional theory (DFT) calculations were used to aid their structural identification. For the radical F3 a C3 carbon centered radical with a carbonyl group at the C4 position is proposed. The close similarity in HFC tensors suggests that F4 and F5 originate from the same type of radical stabilized in two slightly different conformations. For these radicals a C2 carbon centered radical model with a carbonyl group situated at the C3 position is proposed. A rather exotic C2 centered radical model is proposed for F6.

Influence of Protein Environment on the Electron Paramagnetic Resonance Properties of Flavoprotein Radicals: A QM/MM Study

E. Pauwels, R. Declerck, T. Verstraelen, B. De Sterck, C.W.M. Kay, V. Van Speybroeck, M. Waroquier
Journal of Physical Chemistry B
114 (49), 16655–16665
2010
A1

Abstract 

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.

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