E. Pauwels

Combined Electron Magnetic Resonance and Density Functional Theory Study of 10 K X-Irradiated β-d-Fructose Single Crystals

M.A. Tarpan, E. Sagstuen, E. Pauwels, H. Vrielinck, M. Waroquier, F. Callens
Journal of Physical Chemistry A
112 (17) , 3898-3905
2008
A1

Abstract 

Primary free radical formations in fructose single crystals X-irradiated at 10 K were investigated at the same temperature using X-band Electron Paramagnetic Resonance (EPR), Electron Nuclear Double Resonance (ENDOR) and ENDOR induced EPR (EIE) techniques. ENDOR angular variations in the three principal crystallographic planes and a fourth skewed plane allowed the unambiguous determination of five proton hyperfine coupling tensors. From the EIE studies, these hyperfine interactions were assigned to three different radicals, labeled T1, T1* and T2. For the T1 and T1* radicals, the close similarity in hyperfine coupling tensors suggests that they are due to the same type of radical stabilized in two slightly different geometrical conformations. Periodic density functional theory calculations were used to aid the identification of the structure of the radiation-induced radicals. For the T1/T1* radicals a C3 centered hydroxyalkyl radical model formed by a net H abstraction is proposed. The T2 radical is proposed to be a C5 centered hydroxyalkyl radical, formed by a net hydrogen abstraction. For both radicals, a very good agreement between calculated and experimental hyperfine coupling tensors was obtained.

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

E. Pauwels, R. Declerck, V. Van Speybroeck, M. Waroquier
Radiation Research
169 (1), 8-18
2008
A1

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 alpha-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.

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

R. Declerck, E. Pauwels, V. Van Speybroeck, M. Waroquier
Journal of Physical Chemistry B
112 (5), 1508 -1514
2008
A1

Abstract 

The effect of the molecular environment and the temperature dependence of hyperfine parameters in first principles calculations in α-d-glucose and β-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.

First-principles calculations of hyperfine parameters with the Gaussian and augmented-plane-wave method: Application to radicals embedded in a crystalline environment

R. Declerck, E. Pauwels, V. Van Speybroeck, M. Waroquier
Physical Review B
74 (24), 245103
2006
A1

Abstract 

A method for the calculation of hyperfine parameters in extended systems under periodic boundary conditions is presented, using the Gaussian and augmented-plane-wave density functional method, and implemented in QUICKSTEP. In order to increase the efficiency in larger systems, a hybrid scheme is proposed, in which an all-electron treatment for the nuclei of interest and a pseudopotential approximation for the remaining atoms in the simulation cell are combined. The method is validated first by comparing the hyperfine parameters for a selection of atoms and small molecules (using a supercell technique) with other theoretical methods and experimental data from literature. As a typical example of a periodic system where our hybrid method can be applied, the hyperfine parameters of the well-characterized R2 L-α-alanine derived radical are evaluated, yielding results in excellent agreement with the available experimental data.

Study of Rhamnose Radicals in the Solid State Adopting a Density Functional Theory Cluster Approach

E. Pauwels, V. Van Speybroeck, M. Waroquier
Journal of Physical Chemistry A
110 (14) , 6504-6513
2006
A1

Abstract 

A theoretical study is performed on the radiation-induced radicals in crystalline α-l-rhamnose, using density functional theory (DFT) calculations. Irrespective of earlier structural assignments, a host of possible radical models is examined in search for a structure that accurately reproduces experimental electron paramagnetic resonance (EPR) properties. A cluster approach is followed, incorporating all hydrogen bond interactions between radical and crystalline environment. Hyperfine coupling tensors as well as g tensors are determined and a comparison is made with available experimental data. Three carbon-centered hydroxyalkyl radicals are validated, in accordance with experimental suggestions for their structure. The occurrence of a carbon-centered oxygen anion radical for one of the radical species is rejected on theoretical grounds, and instead an altered hydroxyalkyl structure is suggested. Our cluster calculations are able to determine g and hyperfine tensors for the oxygen-centered alkoxy radical in rhamnose, in accordance with one of the two measurements for this species. For all radical models, quantitative agreement with experimental hyperfine tensors is obtained by performing full cluster DFT calculations. The inclusion of the molecular environment for the determination of this EPR property proved to be essential.

X- (X = O, S) Ions in Alkali Halide Lattices through Density Functional Calculations. 1. Substitutional Defect Models

F. Stevens, H. Vrielinck, V. Van Speybroeck, E. Pauwels, F. Callens, M. Waroquier
Journal of Physical Chemistry B
110 (16), 8204–8212
2006
A1

Abstract 

Monoatomic X- (X = O, S) chalcogen centers in MZ (M = Na, K, Rb and Z = Cl, Br, I) alkali halide lattices are investigated within the framework of density functional theory with the principal aim to establish defect models. In electron paramagnetic resonance (EPR) experiments, X- defects with tetragonal, orthorhombic, and monoclinic g-tensor symmetry have been observed. In this paper, models in which X- replaces a single halide ion, with a next nearest neighbor and a nearest neighbor halide vacancy, are validated for the X- centers with tetragonal and orthorhombic symmetry, respectively. As such defect models are extended, the ability to reproduce experimental data is a stringent test for various computational approaches. Cluster in vacuo and embedded cluster schemes are used to calculate energy and EPR parameters for the two vacancy configurations. The final assignment of a defect structure is based on the qualitative and quantitative reproduction of experimental g and (super)hyperfine tensors.

Radiation-induced radicals in alpha-D-glucose: Comparing DFT cluster calculations with magnetic resonance experiments

E. Pauwels, V. Van Speybroeck, M. Waroquier
Spectrochimica Acta Part A (Mol. & biomol.)
63 (4), 795-801
2006
A1

Abstract 

Using density functional theory (DFT) calculations, an enhanced theoretical examination was made of the radiation-induced radicals in alpha-d-glucose. For the carbon-centred radicals in this sugar, the effect of the model space on the radical geometry as well as on the calculated radical hyperfine coupling tensors was examined. The findings were compared with previously published tensors, as determined by electron paramagnetic resonance (EPR) experiments and single molecule DFT calculations. A cluster approach was adopted, in which intermolecular interactions (predominantly hydrogen bonds) between the radical species and its environment were explicitly incorporated. This substantially improved the correspondence with experimental findings in comparison with single molecule calculations of an earlier examination. In a direct comparison between both computational methods for the glucose radicals, it was shown that the extent of the model space plays an important part in the determination of the radical geometry. Furthermore, the model space also has an impact on the calculated hyperfine coupling tensors. Full cluster EPR calculations, in which the paramagnetic properties are calculated for the entire model space of the cluster, give an excellent agreement with the experimental EPR measurements.

Open Access version available at UGent repository

X- (X = O, S, Se) Ions in Alkali Halide Lattices through Density Functional Calculations. 2. Interstitial Defect Models

V. Van Speybroeck, F. Stevens, E. Pauwels, H. Vrielinck, F. Callens, M. Waroquier
Journal of Physical Chemistry B
110 (16), 8213-8218
2006
A1

Abstract 

Density functional theory techniques are used to investigate the defect structure of X- (X = O, S, Se) ions in MZ (M = Na, K, Rb and Z = Cl, Br) alkali halides which exhibit monoclinic-I g-tensor symmetry, using cluster in vacuo, embedded cluster, and periodic embedding schemes. Although a perturbed interstitial defect model was suggested from electron paramagnetic resonance experiments (EPR), the nature of the perturbation is still unknown. An appropriate defect model is developed theoretically by comparing structural and energetical properties of various defect configurations. Further validation is achieved by cross referencing experimental and computed EPR data. On the basis of the computational results, the following defect model is proposed:  the X- ion is located interstitially with a charge compensating halide vacancy in its first coordination shell.

Q-Band EPR and ENDOR of Low Temperature X-Irradiated β-d-Fructose Single Crystals

G. Vanhaelewyn, E. Pauwels, F. Callens, M. Waroquier, E. Sagstuen, P. Matthys
Journal of Physical Chemistry A
110 (6), 2147–2156
2006
A1

Abstract 

β-d-Fructose single crystals were in situ X-irradiated at 80 K and measured using electron paramagnetic resonance (EPR), electron nuclear double resonance (ENDOR) and ENDOR-induced EPR (EIE) techniques at Q-band (34 GHz) microwave frequencies. The measurements revealed the presence of at least four carbon-centered radicals stable at 80 K. By means of ENDOR angular variations in the three principal crystallographic planes, six proton hyperfine coupling tensors could be determined and were assigned to four different radicals by the aid of EIE. Two of the radicals exhibit only β-proton hyperfine couplings and reveal almost identical EIE spectra. For the other two radicals, the major hyperfine splitting originates from a single α-proton hyperfine coupling and their EIE spectra were also quite similar. The similarity of the EIE spectra and hyperfine tensors led to the assumption that there are only two essentially different radical structures. The radical exhibiting only β-proton hyperfine couplings was assigned to a C3 centered radical arising from H3 abstraction and the other radical suggested to be an open-ring species with a disrupted C2−C3 bond and a double C2−O2 bond. A possible formation mechanism for the latter open-ring radical is presented. By means of cluster density functional theory (DFT) calculations, the structures of the two radicals were determined and a fairly good agreement between the calculated and experimental hyperfine tensors was found.

Rules for Generating Conformers and Their Relative Energies in n-Alkanes with a Heteroelement O or S:  Ethers and Alcohols, or Sulfides and Thiols

P. Vansteenkiste, E. Pauwels, V. Van Speybroeck, M. Waroquier
Journal of Physical Chemistry A
109 (42), 9617–9626
2005
A1

Abstract 

With the aid of density functional theory calculations, all conformers of several single-chain alcohols, thiols, ethers, and sulfides are investigated. Starting from earlier computational works on n-alkanes, we construct an extended set of general rules for predicting the number and occurrence of conformers in these oxygen- or sulfur-containing compounds. In alcohols and thiols, it is found that only the conformers generated by internal rotations in the HXCH2CH2CH2 (X = O or S) top are distinctive from those in n-alkanes. In ethers and sulfides, the primary influence of the heteroelement also extends up to three internal rotations, but many more conformers are possible. However, a number of double gauche sequences are forbidden, and therefore, several conformers can be eliminated. These exclusions in particular make up a set of rules for eventually deducing all possible conformers. Furthermore, on the basis of only an exact calculation of these gg conformations in addition to single gauche conformers, it is possible to make an accurate estimate of the relative energy. This two-dimensional approximation scheme constitutes an effective tool for adequately describing the relative energies of all possible conformers at a minimal computational cost.

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