Center for Molecular Modeling - FWO Callens (3G007008)

Structural specificity of alkoxy radical formation in crystalline carbohydrates

wim — Tue, 26 Feb 2013 10:39:21 +0000

S.G. Aalbergsjø, E. Pauwels, H. De Cooman, E.O. Hole, E. Sagstuen

Physical Chemistry Chemical Physics (PCCP)

15(24), 9615-9619

2013

Abstract

A DFT study of radiation induced alkoxy radical formation in crystalline α-l-rhamnose has been performed to better understand the processes leading to selective radical formation in carbohydrates upon exposure to ionizing radiation at low temperatures. The apparent specificity of radiation damage to carbohydrates is of great interest for understanding radiation damage processes in the ribose backbone of the DNA molecule. Alkoxy radicals are formed by deprotonation from hydroxyl groups in oxidized sugar molecules. In α-l-rhamnose only one alkoxy radical is observed experimentally even though there are four possible sites for alkoxy radical formation. In the present work, the origin of this apparently specific action of radiation damage is investigated by computationally examining all four possible deprotonation reactions from oxygen in the oxidized molecule. All calculations are performed in a periodic approach and include estimates of the energy barriers for the deprotonation reactions using the Nudged Elastic Band (NEB) method. One of the four possible radical sites is ruled out due to the lack of a suitable proton acceptor. For the other three possible sites, the reaction paths and energy profiles from primary cationic radicals to stable, neutral alkoxy radicals are compared. It is found that deprotonation from one site (corresponding to the experimentally observed radical) differs from the others in that the reaction path is less energy demanding. Hence, it is suggested that the alkoxy radical formation is not necessarily site specific, but that the observed radical is formed in much greater abundance than the others due to the different energetics of the processes and reaction products.

DOI

http://dx.doi.org/10.1039/c3cp50789k

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Dominant stable radicals in irradiated sucrose: g tensors and contribution to the powder electron paramagnetic resonance spectrum

michel — Thu, 03 Jan 2013 09:40:32 +0000

H. De Cooman, J. Keysabyl, J. Kusakovskij, A. Van Yperen-De Deyne, M. Waroquier, F. Callens, H. Vrielinck

Journal of Physical Chemistry B

117 (24), 7169–7178

2013

Abstract

Ionizing radiation induces a composite, multiline electron paramagnetic resonance (EPR) spectrum in sucrose, that is stable at room temperature and whose intensity is indicative of the radiation dose. Recently, the three radicals which dominate this spectrum were identified and their proton hyperfine tensors were accurately determined. Understanding the powder EPR spectrum of irradiated sucrose, however, also requires an accurate knowledge of the g tensors of these radicals. We extracted these tensors from angular dependent electron nuclear double resonance-induced EPR measurements at 110 K and 34 GHz. Powder spectrum simulations using this completed set of spin Hamiltonian parameters are in good agreement with experimentally recorded spectra in a wide temperature and frequency range. However, as-yet nonidentified radicals also contribute to the EPR spectra of irradiated sucrose in a non-negligible way.

DOI

http://dx.doi.org/10.1021/jp400053h

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13_jphyschemB_117_7169_DeCooman.pdf

Ti-functionalized NH2-MIL-47: an effective and stable epoxidation catalyst

wim — Tue, 07 Aug 2012 11:18:13 +0000

K. Leus, G. Vanhaelewyn, T. Bogaerts, Y-Y Liu, F. Esquivel, F. Callens, G.B. Marin, V. Van Speybroeck, H. Vrielinck, P. Van der Voort

Catalysis Today

208, 97-105

2013

Abstract

In this paper, we describe the post-functionalization of a V-containing Metal-organic framework with TiO(acac)2 to create a bimetallic oxidation catalyst. The catalytic performance of this V/Ti-MOF was examined for the oxidation of cyclohexene using molecular oxygen as oxidant in combination with cyclohexanecarboxaldehyde as co-oxidant. A significantly higher cyclohexene conversion was observed for the bimetallic catalyst compared to the non-functionalized material. Moreover, the catalyst could be recycled at least 3 times without loss of activity and stability. No detectable leaching of V or Ti was noted. Electron paramagnetic resonance measurements were performed to monitor the fraction of V-ions in the catalyst in the +IV valence state. A reduction of this fraction by ∼17% after oxidation catalysis is observed, in agreement with the generally accepted mechanism for this type of reaction.

DOI

http://dx.doi.org/10.1016/j.cattod.2012.09.037

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13_catalysis_today_208_97_Leus.pdf

Room Temperature Radiation Products in Trehalose Single Crystals: EMR and DFT analysis

michel — Mon, 06 Aug 2012 20:24:36 +0000

H. De Cooman, M. Tarpan, H. Vrielinck, M. Waroquier, F. Callens

Radiation Research

179 (3), 313-322

2013

Abstract

Radicals generated in trehalose single crystals by X radiation at room temperature were investigated by electron paramagnetic resonance (EPR), electron nuclear double resonance (ENDOR) and ENDOR-induced EPR measurements, together with periodic density functional theory calculations. In the first days after irradiation, three radical species (I1, I2 and I3) were detected, two of which (I1 and I2) dominate the EPR spectrum and could be identified as H-abstracted species centered at C3′ (I1) and C2 (I2), the latter with additional formation of a carbonyl group at C3. Annealing the sample at 40°C for 3 days or storing it in ambient conditions for three months resulted in another, more stable EPR spectrum. Two major species could be characterized in this stage (S1 and S2), only one of which was tentatively identified as an H-abstracted, C2-centered species (S1). Our findings disagree with a previous EPR study [Gräslund and Löfroth (23)] on several accounts. This work stresses the need for caution when interpreting composite EPR spectra and thermally induced spectral changes of radiation-induced species, even in these relatively simple carbohydrates. It also provides further evidence that the pathways for radiation damage critically depend on the specific conformation of a molecule and its environment, but also that carbonyl group formation is a common process in the radiation chemistry of sugars and related compounds.

DOI

http://dx.doi.org/10.1667/RR3179.1

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13_radiation_res_179_313_DeCooman.pdf

Radiation Products at 77 K in Trehalose Single Crystals: EMR and DFT Analysis

michel — Wed, 29 Feb 2012 19:38:27 +0000

M. Tarpan, H. De Cooman, E. Hole, M. Waroquier, F. Callens

Journal of Physical Chemistry A

116 (13), 3377-3387

2012

Abstract

The radicals obtained in trehalose dihydrate single crystals after 77 K X-irradiation have been investigated at the same temperature using X-band electron paramagnetic resonance (EPR), electron nuclear double resonance (ENDOR), and ENDOR-induced EPR (EIE) techniques. Five proton hyperfine coupling tensors were unambiguously determined from the ENDOR measurements and assigned to three carbon-centered radical species (T1, T1*, and T2) based on the EIE spectra. EPR angular variations revealed the presence of four additional alkoxy radical species (T3 to T6) and allowed determination of their g tensors. Using periodic density functional theory (DFT) calculations, T1/T1*, T2, and T3 were identified as H-loss species centered at C4, C1′, and O2′, respectively. The T4 radical is proposed to have the unpaired electron at O4, but considerable discrepancies between experimental and calculated HFC values indicate it is not simply the (net) H-loss species. No suitable models were found for T5 and T6. These exhibit a markedly larger g anisotropy than T3 and T4, which were not reproduced by any of our DFT calculations.

DOI

http://dx.doi.org/10.1021/jp300979g

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12 j. phys.chem A 116, 3377 Tarpan.pdf

ENDOR and HYSCORE analysis and DFT-assisted identification of the third major stable radical in sucrose single crystals X-irradiated at room temperature

wim — Mon, 03 Oct 2011 10:17:30 +0000

H. De Cooman, E. Pauwels, H. Vrielinck, E. Sagstuen, S. Van Doorslaer, F. Callens, M. Waroquier

Physical Chemistry Chemical Physics (PCCP)

11 (7), 1105-1114

2009

Abstract

Recently, the chemical structure of two of the three major stable radicals (T2 and T3) produced in sucrose single crystals by X-irradiation at room temperature was identified by comparing Density Functional Theory (DFT) calculations of Electron Magnetic Resonance parameters with experimental results [H. De Cooman, E. Pauwels, H. Vrielinck, E. Sagstuen, F. Callens and M. Waroquier, J. Phys. Chem. B, 2008, 112, 7298–7307]. Ambiguities concerning an unusual proton hyperfine coupling (HFC) tensor prevented the identification of the third major stable radical (T1). In the present work, experimental results of continuous wave Electron Nuclear Double Resonance experiments on sucrose single crystals and Hyperfine Sublevel Correlation Spectroscopy experiments on sucrose powder are presented that lift these remaining ambiguities. Using the final set of experimental HFC tensors and employing advanced DFT calculations, the chemical structure of the T1 radical is established: an allylic-type radical with approximately half of the spin density localised on the C2′ carbon of the fructose unit, involving glycosidic bond cleavage at the fructose side and a concerted formation of a carbonyl group at the C1′ carbon. The electronic structure of the T1 radical is discussed in more detail by means of additional DFT calculations, yielding a better understanding of the peculiar properties of the unusual proton HFC tensor mentioned above.

DOI

http://dx.doi.org/10.1039/B816641B

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Schonland ambiguity in the electron nuclear double resonance analysis of hyperfine interactions: Principles and practice

wim — Mon, 03 Oct 2011 09:55:14 +0000

H. Vrielinck, H. De Cooman, M.A. Tarpan, E. Sagstuen, M. Waroquier, F. Callens

Journal of Magnetic Resonance

195 (2), 196-205

2008

Abstract

For the analysis of the angular dependence of electron paramagnetic resonance (EPR) spectra of low-symmetry centres with S = 1/2 in three independent planes, it is well-established—but often overlooked—that an ambiguity may arise in the best-fit tensor result. We investigate here whether a corresponding ambiguity also arises when determining the hyperfine coupling (HFC) tensor for nuclei with I = 1/2 from angular dependent electron nuclear double resonance (ENDOR) measurements. It is shown via a perturbation treatment that for each set of MS ENDOR branches two best-fit tensors can be derived, but in general only one unique solution simultaneously fits both. The ambiguity thus only arises when experimental data of only one MS multiplet are used in analysis or in certain limiting cases. It is important to realise that the ambiguity occurs in the ENDOR frequencies and therefore the other best-fit result for an ENDOR determined tensor depends on various details of the ENDOR experiment: the MS state of the fitted transitions, the microwave frequency (or static magnetic field) in the ENDOR measurements and the rotation planes in which data have been collected. The results are of particular importance in the identification of radicals based on comparison of theoretical predictions of HFCs with published literature data. A procedure for obtaining the other best-fit result for an ENDOR determined tensor is outlined.

DOI

http://dx.doi.org/10.1016/j.jmr.2008.09.017

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Radiation-Induced Radicals in Glucose-1-phosphate. II. DFT Analysis of Structures and Possible Formation Mechanisms

wim — Mon, 03 Oct 2011 09:48:58 +0000

E. Pauwels, H. De Cooman, G. Vanhaelewyn, E. Sagstuen, F. Callens, M. Waroquier

Journal of Physical Chemistry B

112 (47), 15054-15063

2008

Abstract

Four radiation-induced carbon-centered radicals in dipotassium glucose-1-phosphate dihydrate single crystals are examined with DFT methods, consistently relying on a periodic computational scheme. Starting from a set of plausible radical models, EPR hyperfine coupling tensors are calculated for optimized structures and compared with data obtained from EPR/ENDOR measurements, which are described in part I of this work. In this way, an independent structural identification is made of all the radicals that were observed in the experiments (R1−R4) and tentative reaction schemes are proposed. Also, the first strong evidence for conformational freedom in sugar radicals is established: two species are found to have the same chemical composition but different conformations and consequently different hyperfine coupling tensors. Analysis of the calculated energies for all model compounds suggests that the radiation chemistry of sugars, in general, is kinetically and not necessarily thermodynamically controlled.

DOI

http://dx.doi.org/10.1021/jp804287c

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Identification and Conformational Study of Stable Radiation-Induced Defects in Sucrose Single Crystals using Density Functional Theory Calculations of Electron Magnetic Resonance Parameters

wim — Mon, 03 Oct 2011 09:16:30 +0000

H. De Cooman, E. Pauwels, H. Vrielinck, E. Sagstuen, F. Callens, M. Waroquier

Journal of Physical Chemistry A

112 (24), 7298-7307

2008

Abstract

One of the major stable radiation-induced radicals in sucrose single crystals (radical T2) has been identified by means of density functional theory (DFT) calculations of electron magnetic resonance parameters. The radical is formed by a net glycosidic bond cleavage, giving rise to a glucose-centered radical with the major part of the spin density residing at the C1 carbon atom. A concerted formation of a carbonyl group at the C2 carbon accounts for the relatively small spin density at C1 and the enhanced g factor anisotropy of the radical, both well-known properties of this radical from several previous experimental investigations. The experimentally determined and DFT calculated proton hyperfine coupling tensors agree very well on all accounts. The influence of the exact geometrical configuration of the radical and its environment on the tensors is explored in an attempt to explain the occurrence and characteristics of radical T3, another major species that is most likely another conformation of T2. No definitive conclusions with regard to the actual structure of T3 could be arrived at from this study. However, the results indicate that, most likely, T3 is identical in chemical structure to T2 and that changes in the orientation of neighboring hydroxy groups or changes in the configuration of the neighboring fructose ring can probably not account for the type and size of the discrepancies between T2 and T3.

DOI

http://dx.doi.org/10.1021/jp712004g

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08 j. phys. chem. A 112(24)7298 de cooman.pdf

Radiation-induced defects in sucrose single crystals, revisited: A combined electron magnetic resonance and density functional theory study

wim — Mon, 03 Oct 2011 08:48:49 +0000

H. De Cooman, E. Pauwels, H. Vrielinck, A. Dimitrova, N.D. Yordanov, E. Sagstuen, M. Waroquier, F. Callens

Spectrochimica Acta Part A (Mol. & biomol.)

69 (5), 1372-1383

2008

Abstract

The results are presented of an electron magnetic resonance analysis at 110 K of radiation-induced defects in sucrose single crystals X-irradiated at room temperature, yielding a total of nine 1H hyperfine coupling tensors assigned to three different radical species. Comparisons are made with results previously reported in the literature. By means of electron paramagnetic resonance and electron nuclear double resonance temperature variation scans, most of the discrepancies between the present 110 K study and a previous 295 K study by Sagstuen and co-workers are shown to originate from the temperature dependence of proton relaxation times and hyperfine coupling constants. Finally, radical models previously suggested in the literature are convincingly refuted by means of quantum chemical density functional theory calculations.

DOI

http://dx.doi.org/10.1016/j.saa.2007.09.033

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08 spect. acta A 69(5)1372 de cooman.pdf