Modeling Radiation-Damage Processes in Organic Solids via DFT Calculations of EMR Parameters

High-energy radiation induces radicals in organic materials. When created in biological macromolecules such as DNA, these can cause harm to living organisms. This detrimental effect is also exploited for the sterilisation of e.g. foodstuffs, and radiation-induced radicals are used for dosimetry purposes. Knowledge of the structure of the radicals and their formation mechanisms is therefore of fundamental importance. In particular, radiation-induced radicals in solid sugars are studied (i) as model systems to gain insight into the precise role of the deoxyribose unit in the radiation chemistry of DNA and (ii) because of their potential as (emergency) dosimeters. X-irradiation typically gives rise to a variety of primary radicals in these systems, which then transform into stable radicals or diamagnetic species via one or more radical reactions. A prerequisite for unraveling the formation mechanisms is the identification of the different intermediate (semistable) radicals. Experimentally, solid-state sugar radicals can be characterised in detail by electron magnetic resonance (EMR) experiments. These allow determination of EMR parameters which describe the interaction of the unpaired-electron spin with its lattice environment, e.g. with (nearby) nuclear spins. Theoretical calculations of EMR parameters with DFT codes are increasingly being used to help clarify, interpret and explain experimental results. Recently we have managed, in a combined experimental and theoretical approach, to identify the structure of the major radiation-induced stable radicals in solid sucrose [1,2,3] (see Figure). We currently are investigating their formation mechanism, also via both EMR experiments and DFT modeling. A summary of the results obtained so far are presented

Radiation-induced radical formation in solid state sugars: a review of recent EMR and DFT results

Carbohydrates are important constituents of several biological systems, including DNA, and elucidating their radiation chemistry is therefore of general importance. In particular, sugar radicals play a crucial role in radiation-induced single and double strand breaks in DNA, which can lead to mutations and, finally, cancer. Certain sugars such as sucrose (table sugar) are also promising dosimetric materials. An advanced knowledge of the radiation-induced processes in carbohydrates may therefore provide better insight into the DNA radiation chemistry and aid in establishing reliable sugar dosimetry protocols. The first step in acquiring such knowledge is identification of the radical structures. Electron Magnetic Resonance (EMR) experiments on irradiated sugar single crystals allow a very detailed characterisation of the radicals via the g-tensor and the hyperfine interactions between the unpaired electron spin and the nuclear spins in the lattice. Single crystals also offer the advantage of mimicking to some extent the compact structure of chromosomal DNA. Numerous EMR studies on single crystals of sugars and sugar derivatives have been performed the last decades, but radical identification by EMR experiments alone is often ambiguous and sometimes not feasible. The last few years, highly accurate Density Functional Theory (DFT) calculations on extended organic solid state systems have become possible. These provide a powerful tool to help clarify and interpret experimental results and enable unambiguous structural identifications that were not possible before. In this talk, an overview will be given of recently identified radiation-induced radicals in single crystals of sugars (e.g. sucrose,1,2,3 fructose4) and sugar derivatives (e.g. glucose 1-phosphate5,6). The results pertain to primary as well as intermediate and stable species and the identifications are mainly based on the agreement, both in principal values and directions, between experimentally determined and DFT calculated proton hyperfine tensors. Common structural features are highlighted and possible commonly operative formation mechanisms are discussed

Combined Electron Magnetic Resonance and Density Functional Theory Study of Thermally Induced Free Radical Reactions in Fructose and Trehalose Single Crystals

Both as models for studying the effects of radiation on the DNA sugar unit and for applications in dosimetry, radiation-induced defects in sugars have in the past few decades been intensively studied with electron magnetic resonance (EMR) techniques, often with considerable success. However, irradiation generally gives rise to a large variety of free radicals, resulting in strongly composite Electron Paramagnetic Resonance (EPR) spectra. This complexity makes studying them quite a challenge. Despite considerable efforts, little is still known about the identity of the radicals and even less about the radical formation and transformation processes and mechanisms. At room temperature (RT) the primary radiation products, which may be stabilized upon low temperature (LT) irradiation, transform into stable radicals via multistep reaction mechanisms. While the species formed at LT are expected to be formed by simple processes, the molecular structure and geometry of the stable radicals may differ considerably from that of the intact molecule even in the solid state (crystals). Studying the intermediate radicals in the reactions occurring after LT irradiation helps elucidating the formation and identity of the stable radicals. The structural identification of these radicals is in most cases the result of a combination of EPR, Electron Nuclear Double Resonance (ENDOR) and ENDOR Induced EPR (EIE) experiments and advanced quantum chemistry calculations based on Density Functional Theory (DFT). In the present study a summary is given of the experimental EMR results obtained so far on radiation-induced radicals at different temperatures in fructose and trehalose single crystals and powders. “In situ” X-irradiation at LT (10 K) without annealing, leads to spectra strongly different from those observed after RT irradiation and offers the possibility to study and characterize the primary radiation products [1]. Performing EMR measurements on samples irradiated and/or annealed at various temperatures between LT (10 K or 77 K) and RT allows us to study the intermediate products, and such studies therefore have the potential to devise mechanistic links between the primary radicals and the stable radicals. In the present work, our own measurements are compared with results reported in the EMR literature. An outline at future experimental (EMR) and theoretical (DFT) research will also be given

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

Ionizing radiation induces radicals in organic materials. When such species are created in biological macromolecules like DNA, they harm living organisms. This detrimental effect is explicitly exploited for the sterilisation of e.g. foodstuffs, and radiation-induced radicals are quantitatively used for radiation dosimetry purposes. For understanding radiation actions at different levels of molecular and cellular organisation, knowledge of the radical structures and their formation mechanisms is of fundamental importance. In this context, radiation-induced processes in solid sugars are studied, among others, to gain insight into the role of the deoxyribose unit in the radiation chemistry of DNA. X-irradiation typically gives rise to a variety of primary radicals in these systems, which transform into stable radicals or diamagnetic species via one or more radical reactions. By combining electron magnetic resonance experiments and density functional theory (DFT) calculations, we recently identified the major stable [1,2], as well as the major primary [3] radiation-induced radicals in solid sucrose (see figure). We are currently investigating how the primary radicals transform into the stable ones. A general but important observation is that in sucrose and similar carbohydrates, e.g. rhamnose, the primary radical formation (typically by way of net H-abstraction) is selective: it preferentially takes place at particular carbons and oxygens. This selectivity apparently cannot be explained simply on thermodynamical grounds. It may be hypothesised that, after the initial oxidation event (leaving the radical cation in an excited state), the hole ‘migrates’ to a particular carbon or oxygen, after which de-excitation and deprotonation processes yield a neutral radical. It is our goal to examine factors possibly explaining the experimentally observed selectivity. So far we have made some preliminary ground-state calculations on energy profiles of deprotonation reactions in rhamnose single crystals, as well as time-dependent DFT calculations of excited states in this system

Direct-effect radiation chemistry of solid-state carbohydrates using EMR and DFT

To contribute to a mechanistic understanding of radical reaction pathways in the sugar-phosphate backbone of DNA, we are investigating primary radicals induced by X-rays, as well as their transformation into stable radicals or diamagnetic products, in crystalline sugar and sugar derivatives. Radicals are identified and characterized mainly via the hyperfine interactions of the electron spin with protons in the molecular environment. These interactions are determined experimentally with electron magnetic resonance (EMR) techniques and compared to theoretical ab initio calculations based on density functional theory in a periodic approach. Different stages of the radiation-induced processes are investigated by irradiating in situ at various temperatures and controlled annealing experiments. Here, results obtained in single crystals of the dipotassium salt of glucose 1-phosphate (K2G1P) and the disaccharides sucrose and trehalose are presented. The dominant radical in K2G1P after irradiation at 77 K exhibits a broken phospho-ester bond and is chemically identical to one of the major stable sucrose radicals, the latter all being characterized by a broken glycosidic bond. This suggests that the ester bond is radiation sensitive and that the phosphate group is not essential for the reaction pathway leading to this scission. Surprisingly, however, no evidence for glycosidic bond scission has so far been observed in trehalose. Rather, a simple H-abstraction alkyl radical is remarkably stable in this system. In all three compounds, dominant radicals are formed with one or several concerted carbonyl group formations. Extended studies are necessary to establish how and to which extent structural or geometrical factors determine the radiation chemistry, but certain general principles are starting to emerge

Electron magnetic resonance study of primary free radicals in trehalose single crystals

Radiation-induced radicals in sugars have recently gained considerable interest with respect to both fundamental and applied research. A number of studies are available that focus on the dosimetric characteristics of sugar systems. Other studies, like ours, aim to understand the identity and the structural properties of the involved radicals, and the radical reactions in which the primary or secondary products can be linked to the stable radicals. Furthermore, carbohydrates represent extremely suitable model systems in which primary radiation-induced events may be studied. For instance, the detection of a trapped electron center in organic solids was first made in carbohydrate single crystals1,2 and the nature of alkoxy radicals is readily investigated in these systems 3. We present here experimental results obtained for low temperature radiation-induced radicals in trehalose single crystals. After 10 K in situ X-irradiation of trehalose single crystals four dominant radicals are present. Two radical species, labeled R1 and R2 are characterized by anisotropic g factors typical for the alkoxy type radicals. The R1 EPR spectrum is a broad singlet for most orientations, indicating only small proton hyperfine couplings. The direction of the maximum g value (gmax) indicates that O4’ is the most likely site for the unpaired electron. R2 mainly exhibits a quartet EPR spectrum and the gmax direction favours O2 as the site of the unpaired electron. The other two radicals, R3 and R4, are characterized by a rather isotropic g tensor typical of alkyl radicals. R3 is characterized by a rather isotropic triplet in EPR which suggests two almost equivalent β proton hyperfine interactions. It is obtained by a net hydrogen abstraction from the C3’ position. The second alkyl radical has most likely the unpaired electron localized at the C2 position. A major purpose of this study is to compare the obtained results with the results reported by De Cooman et al4 for 10 K X-irradiated sucrose single crystals. Trehalose and sucrose have a close structural similarity: they both are disaccharides composed of two units linked by a glycosidic oxygen bridge between their two anomeric carbon atoms, C1 and C1’. The study of very similar products may lead to a better general understanding of the radiation chemistry of carbohydrates

Deep level transient spectroscopy (DLTS) study of P3HT:PCBM organic solar cells

The electronic structure of an organic photovoltaic bulk heterojunction cell strongly deviates from the typical textbook examples of a single sided junction used to explain electrical characterisation of defects in semiconductors. Therefore it is not so straightforward to assign the capacitance of this device or the charge in it to the presence of a depleted layer within this structure. However, conventional electronic spectroscopic techniques could give useful information to understand the electronic behaviour of the device. Therefore, in this work capacitance and charge DLTS have been performed on P3HT:PCBM solar cells. At 1MHz only negligible variation in the capacitance as a function of temperature and bias has been observed. As a result no spectrum could be recorded using a standard DLTS setup, registering the capacitance at this high frequency. To avoid this parasitic effect low frequency capacitance DLTS (40 kHz) has been performed, showing an anomalous signal with negative amplitude and an activation energy of 160meV, and a complementary positive signal could be observed altering the biases. Charge DLTS clearly revealed that both signals transients, conventional and with altered bias have the same time constants. A recent study has shown that such behaviour cannot be explained by the thermodynamic properties of capture and emission of carriers by a defect in bulk semiconductor. The validity of alternative explanations, including interface states, non-ideal ohmic contacts and effects of carrier hopping on charge mobility, will discussed

A stochastic movement simulator improves estimates of landscape connectivity

Acknowledgments This publication issued from the project TenLamas funded by the French Ministère de l'Energie, de l'Ecologie, du Développement Durable et de la Mer through the EU FP6 BiodivERsA Eranet; by the Agence Nationale de la Recherche (ANR) through the open call INDHET and 6th extinction MOBIGEN to V. M. Stevens, M. Baguette, and A. Coulon, and young researcher GEMS (ANR-13-JSV7-0010-01) to V. M. Stevens and M. Baguette; and by a VLIR-VLADOC scholarship awarded to J. Aben. L. Lens, J. Aben, D. Strubbe, and E. Matthysen are grateful to the Research Foundation Flanders (FWO) for financial support of fieldwork and genetic analysis (grant G.0308.13). V. M. Stevens and M. Baguette are members of the “Laboratoire d'Excellence” (LABEX) entitled TULIP (ANR-10-LABX-41). J. M. J. Travis and S. C. F. Palmer also acknowledge the support of NERC. A. Coulon and J. Aben contributed equally to the work.Peer reviewedPublisher PD

Micro-Capsules in Shear Flow

This paper deals with flow-induced shape transitions of elastic capsules. The state of the art concerning both theory and experiments is briefly reviewed starting with dynamically induced small deformation of initially spherical capsules and the formation of wrinkles on polymerized membranes. Initially non-spherical capsules show tumbling and tank-treading motion in shear flow. Theoretical descriptions of the transition between these two types of motion assuming a fixed shape are at variance with the full capsule dynamics obtained numerically. To resolve the discrepancy, we expand the exact equations of motion for small deformations and find that shape changes play a dominant role. We classify the dynamical phase transitions and obtain numerical and analytical results for the phase boundaries as a function of viscosity contrast, shear and elongational flow rate. We conclude with perspectives on timedependent flow, on shear-induced unbinding from surfaces, on the role of thermal fluctuations, and on applying the concepts of stochastic thermodynamics to these systems.Comment: 34 pages, 15 figure