Ab initio molecular orbital calculations of the infrared spectra of interacting water molecules. Part 4. Interaction energies and band intensities of the complexes of water with carbon dioxide and nitrous oxide

The molecular structures and infrared band wavenumbers of a number of different isomers of the binary complexes formed between water and carbon dioxide, and water and nitrous oxide, have been predicted by means of ab initio molecular orbital theory. The results are discussed in the light of high resolution gas phase infrared and microwave, and matrix isolation infrared spectroscopic studies, and of theoretical calculations on these and on a wide variety of similar complexes containing carbon dioxide and nitrous oxide.

Abstract

Ab initio study of energies, structures and vibrational spectra of the complexes of water with carbon oxysulfide and nitrous oxide

Methylmalonyl-CoA mutase is an adenosylcobalamin-dependent enzyme that catalyzes the 1,2 rearrangement of methylmalonyl-CoA to succinyl-CoA. This reaction results in the interchange of a carbonyl-CoA group and a hydrogen atom on vicinal carbons. The crystal structure of the enzyme reveals the presence of an aromatic cluster of residues in the active site that includes His-244, Tyr-243, and Tyr-89 in the large subunit. Of these, His-244 is within hydrogen bonding distance to the carbonyl oxygen of the carbonyl-CoA moiety of the substrate. The location of these aromatic residues suggests a possible role for them in catalysis either in radical stabilization and/or by direct participation in one or more steps in the reaction. The mechanism by which the initially formed substrate radical isomerizes to the product radical during the rearrangement of methylmalonyl-CoA to succinyl-CoA is unknown. Ab initio molecular orbital theory calculations predict that partial proton transfer can contribute significantly to the lowering of the barrier for the rearrangement reaction. In this study, we report the kinetic characterization of the H244G mutant, which results in an acute sensitivity of the enzyme to oxygen, indicating the important role of this residue in radical stabilization. Mutation of His-244 leads to an approximately 300-fold lowering in the catalytic efficiency of the enzyme and loss of one of the two titratable pK(a) values that govern the activity of the wild type enzyme. These data suggest that protonation of His-244 increases the reaction rate in wild type enzyme and provides experimental support for ab initio molecular orbital theory calculations that predict rate enhancement of the rearrangement reaction by the interaction of the migrating group with a general acid. However, the magnitude of the rate enhancement is significantly lower than that predicted by the theoretical studies.

Ab initio molecular orbital calculations of the infrared spectra of interacting water molecules part 2. complexes of water with carbon monoxide and nitrogen

In this project we have proposed several mechanisms for radiation damage to DNA and its constituents, and have detailed a series of experiments utilizing electron spin resonance spectroscopy, HPLC, GC-mass spectroscopy and ab initio molecular orbital calculations to test the proposed mechanisms. The results from these various techniques have resulted in an understanding of consequences of radiation damage to DNA from the early ionization event to the production of non-radical lesions (discussed in detail in Comprehensive Report). In this year`s work we have found the hydroxyl radical in DNA`s hydration layer. This is an important result which impacts the hole transfer hypothesis and the understanding of the direct vs. indirect effect in DNA. Further we have found the first ESR evidence for sugar radicals as a result of direct radiation damage to DNA nucleotides in an aqueous environment. This is significant as it impacts the biological endpoint of radiation damage to DNA and suggests future work in DNA. Work with DNA-polypeptides show clear evidence for electron transfer to DNA from the polypeptide which we believe is a radioprotective mechanism. Our work with ab initio molecular orbital theory has gain insight into the initial events of radiation damage to DNA. Ab initio calculations have provided an understanding of the energetics involved in anion and cation formation, ion radical transfer in DNA as well as proton transfer with DNA base pair radical ions. This has been extended in this year`s work to new, more accurate values for the electron affinities of the DNA bases, understanding of the relative stability of all possible sugar radicals formed by hydrogen abstraction on the deoxyribose group, hydration effects on, thiol radioprotectors, and an ongoing study of radical intermediates formed from initial DNA ion radicals. During this fiscal year five articles have been published, three are in press, two are submitted and several more are in preparation.

In this project we have proposed several mechanisms for radiation damage and recently radiation protection to DNA and its constituents, and have detailed a series of experiments utilizing electron spin resonance spectroscopy, HPLC, GC-mass spectroscopy and ab initio molecular orbital calculations to test the proposed mechanisms. In this years work we have performed experiments which elucidate the role of hydration water on DNA radiation damage, continued the investigation of the localization of the initial charges on DNA and employed ab initio molecular orbital theory to gain insight into the initial events of radiation damage to DNA. Ab initio calculations have provided an understanding of the energetics envolved in anion and cation formation, ion radical transfer in DNA as well as proton transfer with DNA base pair radical ions. This information has aided the formation of new radiation models for the effect of radiation on DNA. During this fiscal year four articles have been published, two are in press, two are submitted and several more are in preparation. Six papers have been presented at scientific meetings. This years effort includes a review article on the Chemical Consequences of Radiation Damage to DNA''. This review presents an overview of this field at this time.

In this project the author has proposed several mechanisms for radiation damage to DNA and its constituents, and has detailed a series of experiments utilizing electron spin resonance spectroscopy, HPLC, GC-mass spectroscopy and ab initio molecular orbital calculations to test the proposed mechanisms. In this years work he has completed several experiments on the role of hydration water on DNA radiation damage, continued the investigation of the localization of the initial charges and their reactions on DNA, investigated protonation reactions in DNA base anions, and employed ab initio molecular orbital theory to gain insight into the initial events of radiation damage to DNA. Ab initio calculations have provided an understanding of the energetics evolved in anion and cation formation, ion radical transfer in DNA as well as proton transfer with DNA base pair radical ions. This has been extended in this years work to a consideration of ionization energies of various components of the DNA deoxyribose backbone and resulting neutral sugar radicals. This information has aided the formation of new radiation models for the effect of radiation on DNA. During this fiscal year four articles have been published, four are in press, one is submitted and several more are in preparation. Four papers have been presented at scientific meetings. This years effort will include another review article on the {open_quotes}Electron Spin Resonance of Radiation Damage to DNA{close_quotes}.

In this project we have proposed several mechanisms for radiation damage and recently radiation protection to DNA and its constituents, and have detailed a series of experiments utilizing electron spin resonance spectroscopy, HPLC, GC-mass spectroscopy and ab initio molecular orbital calculations to test the proposed mechanisms. In this years work we have performed experiments which elucidate the role of hydration water on DNA radiation damage, continued the investigation of the localization of the initial charges on DNA and employed ab initio molecular orbital theory to gain insight into the initial events of radiation damage to DNA. Ab initio calculations have provided an understanding of the energetics envolved in anion and cation formation, ion radical transfer in DNA as well as proton transfer with DNA base pair radical ions. This information has aided the formation of new radiation models for the effect of radiation on DNA. During this fiscal year four articles have been published, two are in press, two are submitted and several more are in preparation. Six papers have been presented at scientific meetings. This years effort includes a review article on the ``Chemical Consequences of Radiation Damage to DNA``. This review presents an overview of this field atmore » this time.« less

The infrared band intensities and other properties of the homodimers of the methyl and silyl halides: An ab initio study

A study of the kinetics and mechanisms involved in the atmospheric degradation of bromoform by atomic chlorine

This review summarizes the results of recent ab initio molecular orbital calculations performed on DNA constituents that attempt to further our understanding of the radiation-induced damage to DNA. The results reviewed include calculations performed on the four individual DNA bases, the base pairs in gas phase and modelled aqueous phase, the deoxyribose moiety, and a portion of the sugar-phosphate backbone. The emphasis is on the electron affinities and ionization potentials of the radical species calculated under various conditions (i.e. gas phase, aqueous phase, proton transfer, base stacking), as it has been shown that the initial ion radical distribution is largely a function of these two properties. Theoretical studies of the electronic excited states of the individual bases and radioprotection of the biomolecule by various thiol compounds are also reviewed. Finally, a summary is provided to allow for further elaboration of the current model for radiation damage to DNA and to show the present advantages and limitations of ab initio theory in the investigation of such processes.

High level ab initio molecular orbital theory calculations have been used to study the geometries and thermochemistry of molecules and free radicals substituted by BH2, BHCH3, and B(CH3)2. The heats of formation and RR'B—X bond strengths (RR' = H, H; H, CH3; CH3, CH3 and X = CH3, NH2, OH, F, SiH3, PH2, SH, and Cl) together with those for the open-shell systems RR'B—Y· (RR' = H, H; H, CH3; CH3, CH3 and Y = CH2, NH, O, SiH2, PH, and S) have been calculated at the G3 level of theory. The trends observed for the homolytic bond strengths in the closed-shell systems are those expected from electronegativity arguments, i.e., as the difference in electronegativity between the two atoms in the B—X bond increases, the bond strength increases. Methyl substitution on B in the closed- and open-shell species increases the ionic contribution to the bond thereby decreasing the bond strength. The lowest possible homolytic dissociation energy for the free radicals RR'BY· is lower than those of their closed-shell counterparts, yet the B—Y· bonds are shorter. This is due to the demands of spin conservation in the dissociation of the radicals favouring the formation of higher energy products.Key words: ab initio calculations, bond dissociation energy, organoboron compounds, thermochemistry.

The application of ab initio molecular orbital theory to the anomeric effect. A comparison of theoretical predictions and experimental data on conformations and bond lengths in some pyranoses and methyl pyranosides

The effects of para substituents (OH, F, Me, CHO, CN, and NO2) on the barrier to rotation about the C–O bond in phenol as determined by ab initio molecular orbital calculations and far i.r. spectroscopic measurements are generally in close agreement; substituents which are π-electron donors lower the observed barrier while π-electron acceptors raise the barrier.