Center for Molecular Modeling - E. Sagstuen

Automated generation of radical species in crystalline carbohydrate using ab initio MD simulations

michel — Mon, 16 Jun 2014 19:21:40 +0000

S.G. Aalbergsjø, E. Pauwels, A. Van Yperen-De Deyne, V. Van Speybroeck, E. Sagstuen

Physical Chemistry Chemical Physics (PCCP)

16 (32), 17196-17205

2014

Abstract

As the chemical structures of radiation damaged molecules may vary greatly from their undamaged counterparts, investigation and description of radiation damaged structures is commonly biased by the researcher. Radical formation from ionizing radiation in crystalline α-L-rhamnose monohydrate has been investigated using a new method where the selection of radical structures is unbiased by the researcher. The method is based on using ab initio molecular dynamics (MD) studies to investigate how ionization damage can form, change and move. Diversity in the radical production is gained by using different points on the potential energy surface of the intact crystal as starting points for the ionizations and letting the initial velocities of the nuclei after ionization be generated randomly. 160 ab initio MD runs produced 12 unique radical structures for investigation. Out of these, 7 of the potential products have never previously been discussed, and 3 products are found to match with radicals previously observed by electron magnetic resonance experiments

Open Access version available at UGent repository

DOI

http://dx.doi.org/10.1039/C4CP02179G

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paper2.pdf

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

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

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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08 phys. chem. B 112 (47)15054 pauwels.pdf

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

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

wim — Mon, 03 Oct 2011 08:46:46 +0000

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

Journal of Physical Chemistry A

112 (17) , 3898-3905

2008

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.

DOI

http://dx.doi.org/10.1021/jp7119284

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08 j. phys. chem. A 112(17)3898 tarpan.pdf