Center for Molecular Modeling - E.O. Hole

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

Private attachment

13_chemphyschem_15,9615_Aalbergsjo.pdf

On the identity of the radiation-induced stable alanine radical

wim — Tue, 13 Sep 2011 11:57:38 +0000

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

Physical Chemistry Chemical Physics (PCCP)

12, 8733-8736

2010

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.

DOI

http://dx.doi.org/10.1039/C004380J

Private attachment

10 phys. chem. chem. phys 12(31)8733 pauwels.pdf

Seeing the molecules - using DFT calculations and periodic boundary conditions

ewald — Mon, 27 Feb 2012 22:15:41 +0000

S.G. Aalbergsjø, E. Pauwels, E.O. Hole, E. Sagstuen

Talk

Conference / event / venue

Kongsvold Biophysics Meeting 2012

Kongsvold, Norway

Thursday, 15 March, 2012 to Saturday, 17 March, 2012

Abstract (private)

kongsvold_abst_dft2012.pdf

Elucidation of radiation induced processes in alanine using DFT calculations

wim — Tue, 18 Oct 2011 07:30:31 +0000

E. Pauwels, E. Sagstuen, E.O. Hole, M. Waroquier

Poster

Conference / event / venue

Radiation Chemistry Conference

Waterville Valley, NH, US

Sunday, 6 July, 2008 to Friday, 11 July, 2008

Which role do excited states play in radiation damage to organic solid-state compounds?

wim — Mon, 17 Oct 2011 14:14:26 +0000

H. De Cooman, S.G. Aalbergsjø, E. Pauwels, E. Sagstuen, E.O. Hole, F. Callens, M. Waroquier

Poster

Conference / event / venue

Quantum Chemistry in Belgium 9th edition

Louvain-la-Neuve, Belgium

Tuesday, 26 January, 2010

Abstract

2010 QCB9_Abstract_HendrikDeCooman.pdf

Elucidation of radiation-induced processes using DFT calculations

wim — Mon, 17 Oct 2011 10:02:49 +0000

E. Pauwels, E. Sagstuen, E.O. Hole, M. Waroquier

Talk

Conference / event / venue

11th International Workshop on Electron Magnetic Resonance Of Disordered Systems (EMARDIS)

Sofia-Boyana, Bulgaria

Thursday, 11 June, 2009 to Wednesday, 17 June, 2009

Abstract

Abstract_EMARDIS2009.pdf

Elucidation of radiation-induced processes using DFT calculations

wim — Mon, 17 Oct 2011 09:45:46 +0000

E. Pauwels, E. Sagstuen, E.O. Hole, M. Waroquier

Talk

Conference / event / venue

RRS: 55th Annual Meeting of the Radiation Research Society

Savannah, Georgia, United States

Saturday, 3 October, 2009 to Wednesday, 7 October, 2009

Abstract

Abstract_EMARDIS2009.pdf