S.G. Aalbergsjø

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

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

A1

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

Structural specificity of alkoxy radical formation in crystalline carbohydrates

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

Physical Chemistry Chemical Physics (PCCP)

15(24), 9615-9619

2013

A1

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.