Center for Molecular Modeling - S.G. Aalbergsjø

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

Private attachment

paper2.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

Private attachment

13_chemphyschem_15,9615_Aalbergsjo.pdf

Radiation induced damage in biomolecules. An ab initio molecular dynamics study on crystalline α-L-rhamnose

Bernadette — Fri, 13 Jun 2014 06:33:21 +0000

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

ISBN/ISSN:

Talk

Conference / event / venue

FemEx-Oslo conference

Oslo, Norway

Friday, 13 June, 2014 to Monday, 16 June, 2014

Abstract (private)

aalbergsjo_siv_oral.pdf

A method for investigating radiation damage

wim — Thu, 03 Apr 2014 12:39:37 +0000

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

ISBN/ISSN:

Talk

Conference / event / venue

Semi-Annual Norwegian Biophysics meeting

Oslo, Norway

Thursday, 6 March, 2014 to Friday, 7 March, 2014

Abstract (private)

14_abstract_aalbergsjo.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

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

DFT and TDDFT studies of deprotonation from oxygen in rhamnose cations

wim — Mon, 17 Oct 2011 08:52:53 +0000

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

Talk

Conference / event / venue

Quantum Chemistry beyond the Arctic Circle

Sommarøy-Tromsø, Norway

Wednesday, 23 June, 2010 to Saturday, 26 June, 2010

Abstract

Abstract_AalbergsjoS_Polar2010.pdf