Center for Molecular Modeling - H. De Cooman

Solved? The reductive radiation chemistry of alanine

michel — Tue, 22 Oct 2013 15:16:29 +0000

E. Pauwels, H. De Cooman, M. Waroquier, E. Hole, E. Sagstuen

Physial Chemistry Chemical Physics

16(6), 2475-2482

2014

Abstract

The structural changes throughout the entire reductive radiation-induced pathway of l-α-alanine are solved on an atomistic level with the aid of periodic DFT and nudged elastic band (NEB) simulations. This yields unprecedented information on the conformational changes taking place, including the protonation state of the carboxyl group in the "unstable" and "stable" alanine radicals and the internal transformation converting these two radical variants at temperatures above 220 K. The structures of all stable radicals were verified by calculating EPR properties and comparing those with experimental data. The variation of the energy throughout the full radiochemical process provides crucial insight into the reason why these structural changes and rearrangements occur. Starting from electron capture, the excess electron quickly localizes on the carbon of a carboxyl group, which pyramidalizes and receives a proton from the amino group of a neighboring alanine molecule, forming a first stable radical species (up to 150 K). In the temperature interval 150-220 K, this radical deaminates and deprotonates at the carboxyl group, the detached amino group undergoes inversion and its methyl group sustains an internal rotation. This yields the so-called "unstable alanine radical". Above 220 K, triggered by the attachment of an additional proton on the detached amino group, the radical then undergoes an internal rotation in the reverse direction, giving rise to the "stable alanine radical", which is the final stage in the reductive radiation-induced decay of alanine.

Open Access version available at UGent repository

DOI

http://dx.doi.org/10.1039/c3cp54441a

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14_PCCP_16(6)2475_Pauwels.pdf

14_PCCP_preprint_Pauwels.pdf

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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13_chemphyschem_15,9615_Aalbergsjo.pdf

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

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

Early-Stage Evolution of the EPR Spectrum of Crystalline Sucrose at Room Temperature after High-Dose X Irradiation

wim — Mon, 03 Oct 2011 12:10:40 +0000

H. Vrielinck, H. De Cooman, Y. Karakirova, N.D. Yordanov, F. Callens

Radiation Research

172 (2), 226-233

2009

Abstract

X irradiation of sucrose single crystals at room temperature leads to the production of stable radicals, which give rise to the dosimetric electron paramagnetic resonance (EPR) signal. In the first few hours after irradiation, however, the shape of the EPR spectrum changes drastically. Based on two-dimensional field-frequency electron nuclear double resonance (FF-ENDOR) measurements, we demonstrate that, after high-dose (5 kGy) and high-dose-rate irradiation, several species with limited stability at room temperature are produced next to the stable radicals. For two of these species, the main characteristics could be determined. Analysis of the time evolution of the FF-ENDOR and room-temperature EPR spectra in the first few hours after irradiation leads to the conclusion that these meta-stable radicals mainly recombine into diamagnetic species, while transformation into stable radicals is at most a marginal process.

DOI

http://dx.doi.org/10.1667/RR1746.1

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09 rad. res 172(2)226 vrielinck.pdf

Determination of the g Tensors for the Dominant Stable Radicals in X-Irradiated β-d-Fructose Single Crystals

wim — Mon, 03 Oct 2011 11:59:27 +0000

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

Journal of Physical Chemistry A

113 (28), 7994-8000

2009

Abstract

In spite of recent successful identifications of radicals produced after X-ray irradiation at 10 and 77 K in β-d-fructose, the structure of the two stable radicals dominating the electron paramagnetic resonance (EPR) spectrum after room temperature irradiation is still unclear. Based on the agreement between proton hyperfine (HF) tensors obtained in electron nuclear double resonance (ENDOR) experiments and the results of single molecule density functional calculations, a model for these radicals, involving OH abstraction at the C2 ring position, had previously been proposed, but this assignment could not be confirmed when the radical was embedded in a crystal environment. In this paper, we therefore provide additional experimental information for these radicals. First, their g tensors are determined from angular dependent ENDOR-induced EPR experiments. The relatively large anisotropy of these tensors is indicative of delocalization of the unpaired electron onto a neighboring oxygen atom. Second, EPR spectra of fructose powders, selectively enriched in 13C on various ring positions, are presented, demonstrating that the HF interaction with the carbon atom C3 is larger than with the C2. Combining the g tensor, proton and 13C HF data, we conclude that the structure of the stable radicals differs strongly from that of intact molecules and that further advanced quantum chemical modeling will be required to fully identify them.

DOI

http://dx.doi.org/10.1021/jp9017019

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09 j. phys. chem. A 113(28)7994 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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09 phys. chem. chem. phys 11(7)1105 de cooman.pdf

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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08 j. mag. res. 195(2)196 vlierick.pdf

Radiation-Induced Radicals in Glucose-1-phosphate. I. Electron Paramagnetic Resonance and Electron Nuclear Double Resonance Analysis of in situ X-Irradiated Single Crystals at 77 K

wim — Mon, 03 Oct 2011 09:50:56 +0000

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

Journal of Physical Chemistry B

112 (47), 15045-15053

2008

Abstract

Electron magnetic resonance analysis of radiation-induced defects in dipotassium glucose-1-phosphate dihydrate single crystals in situ X-irradiated and measured at 77 K shows that at least seven different carbon-centered radical species are trapped. Four of these (R1−R4) can be fully or partly characterized in terms of proton hyperfine coupling tensors. The dominant radical (R2) is identified as a C1-centered species, assumedly formed by a scission of the sugar−phosphate junction and the concerted formation of a carbonyl group at the neighboring C2 carbon. This structure is chemically identical to a radical recently identified in irradiated sucrose single crystals. Radical species R1 and R4 most likely are C3- and C6-centered species, respectively, both formed by a net hydrogen abstraction. R3 is suggested to be chemically similar to but geometrically different from R4. Knowledge of the identity of the sugar radicals present at 77 K provides a first step in elucidating the formation mechanism of the phosphoryl radicals previously detected after X-irradiation at 280 K. In paper II, the chemical identity, precise conformation, and possible formation mechanisms of these radical species are investigated by means of DFT calculations and elementary insight into the radiation chemistry of sugar and sugar derivatives is obtained.

DOI

http://dx.doi.org/10.1021/jp804290e

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08 phys. chem. B 112 (47)15045 de cooman.pdf