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- aggregation classification "D1".
- aggregation creator person.
- aggregation date "2004".
- aggregation format "application/pdf".
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- aggregation language "eng".
- aggregation publisher "".
- aggregation rights "I have retained and own the full copyright for this publication".
- aggregation subject "Chemistry".
- aggregation title "First-principles study of radiation-induced radicals in solid-state amino acids and sugars: confrontation of density-functional calculations with experimental results".
- aggregation abstract "In this work, we present an extensive computational study of several radiationinduced radicals of biomolecules. In particular, two specific types of molecular systems will be highlighted: amino acids and sugars. Both systems are abundantly present in the natural world and are vital to the existence of life in all its forms. Amino acids are the building blocks of polypeptides and proteins, which are involved in nearly all biochemical processes. Sugars (or carbohydrates) also play a key role, not merely as sweeteners but rather as essential components in the biological energy storage and transport systems of animals and as chief structural material in plants. As can be expected, the radical adducts of these compounds have an equal importance in biochemistry. These radicals can arise in chemical reactions or can be induced as the result of radiation damage. Such species are normally very shortliving in gas phase or solution. In crystals on the other hand, the radicals become “trapped” inside the amino-acid or carbohydrate lattice and their reactivity will be sharply reduced. The solid state therefore offers the opportunity to extensively study the nature and structure of the (radiation-)induced organic radicals using various experimental techniques, of which Electron Paramagnetic Resonance spectroscopy (EPR) can be favoured as it can access an abundance of structural information about the radical. However, this technique does not provide the information as such, instead it has to be deduced from the EPR spectroscopic parameters, an analysis that is often complex and open to ambiguity. In addition, the radiation chemistry of sugars and especially amino acids in the solid state is an elaborate field of study and requires a profound understanding of the different physical and chemical processes taking place inside the crystal. This area of interest has received considerable attention in view of interesting applications in EPR dosimetry. Within this respect, we refer to the success of the alanine dosimeter for reference- and routine dosimetry in radiation therapy, biological research and industrial high-dose irradiation facilities. However, it was only after the publication of a detailed EPR study on this amino acid that an enhanced understanding of its radiation chemistry was established. Three radical species were in this way identified as contributing significantly to the observed composite spectrum and hence also to the overall dosimetric characteristics of the alanine system. As a result of the often-cumbersome analysis of the EPR parameters and the complexity of the associated radiation chemistry, the experimentalist is faced with a delicate task to propose appropriate models for the paramagnetic species present in the crystals. Over the last few years, it has become increasingly popular to rely on ab-initio molecular modeling techniques for this purpose. This success is in part due to the spectacular expansion of recent computer capabilities but is not in the least a result of the ongoing development of theoretical models and numerical algorithms in the field of quantum chemistry. Especially since the introduction of Density Functional Theory (DFT), a sharp quantitative as well as qualitative increase of theoretical calculations has been witnessed. The effectiveness of DFT can be largely attributed to a better incorporation of electron correlation as compared to more conventional ab-initio methods (such as e.g. Hartree Fock). Furthermore, this DFT algorithm does not require considerably more computer time as compared to conventional HF calculations but, in contrast, is significantly faster in comparison with other high-level correlation calculations (e.g. post HF), which renders it a very cost-effective method. Not only can these types of ab-initio calculations identify and verify proposed radical structures with the aid of optimization routines, predictions can also be made founded on entirely theoretical grounds. In addition, these methods offer the possibility to reproduce EPR quantities based on first principles. Evidently this presents a powerful tool to the experimentalist for the interpretation and analysis of EPR spectra. By now comparing measured and predicted spectroscopic parameters with each other, the true identity of an experimentally observed paramagnetic species can be linked directly to the structural characteristics of a theoretical model proposed for the specified radical. In this work, we will specifically make use of the link with experiment to characterize the radiation-induced radicals of amino acids and sugars from a theoretical point of view. A general computational strategy is reported, which outlines a basic procedure for the theoretical treatment and simulation of radicals in a solid state. This strategy is composed of four main steps. In an initial step, one or more radical models are proposed that might be consistent with the experimental EPR data of an observed paramagnetic species. The structures of these radical models are subsequently optimized within a well-defined model space, in either a DFT or semi-empirical framework. A third step concerns the determination of EPR parameters for the optimized structures, adopting an ab-initio level of theory. The results of these EPR calculations can also be sensitive to the used model space. In the final step, a conclusive analysis between calculated and measured EPR parameters is then possible. Applied on amino-acid and sugar systems, the drafted procedure will enable us to formulate specific conclusions with regard to the nature and identity of the radiation induced radicals, on the condition that an appropriate approximation is made for the solid-state environment of the radical. The extent of the model space during the optimization and EPR calculations is therefore of particular importance. In this work, it is examined what effect the size of the model space and the applied level of theory have on the calculated structural and spectroscopic properties of a simulated radical. This is achieved by introducing several model space approaches – classified from “single molecule”, over “cluster” to “periodic” – which incorporate an increasing amount of intermolecular interactions between the radical and its crystalline environment. Eventually, it is argued that the model space indeed plays a considerable role for the determination of a radical geometry and its associated EPR parameters. This aspect must therefore be carefully considered when initiating a computational study of radicals in the solid state. This work is organized in two main sections. The first section contains chapters 2 to 4 and outlines the conceptual framework of this thesis. In chapter 2, a concise overview is presented of some general principles in molecular modeling that are relevant to this work. The subsequent chapter deals with the basic concepts and theory of EPR spectroscopy. In the fourth chapter, we will introduce a general computational strategy that will be followed in the applications-section to determine EPR parameters on theoretical grounds. In the second, applied section (chapters 5 to 10), several investigations are made of radiation-induced radicals in solid-state systems. Chapters 5 and 6 deal with the amino-acid systems, alanine and glycine, respectively. After a general introduction into the applications and occurrence of radicals in sugar crystals (chapter 7), a report is given on the radicals in β-D-fructose (chapter 8), α-D-glucose (chapter 9) and α-L-sorbose (chapter 10). In the final chapter, some general conclusions are formulated.".
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