Interaction of adenine adducts with thymine: a computational study

The existence of DNA adducts bring the danger of carcinogenesis because of mispairing with normal DNA bases. 1,N6-ethenoadenine adducts (epsilonA) and 1,N6-ethanoadenine adducts (EA) have been considered as DNA adducts to study the interaction with thymine, as DNA base. Several different stable conformers for each type of adenine adduct with thymine, [epsilonA(1)-T(I), epsilonA(2)-T(I), epsilonA(3)-T(I) and EA(1)-T(I), EA(2)-T(I), EA(3)-T(I)] and [epsilonA(1)-T(II), epsilonA(2)-T(II), epsilonA(3)-T(II) and EA(1)-T(II), EA(2)-T(II), EA(3)-T(II)], have been considered with regard to their interactions. The differences in their geometrical structures, energetic properties, and hydrogen-bonding strengths have also been compared with Watson-Crick adenine-thymine base pair (A-T). Single-point energy calculations at MP2/6-311++G** levels on B3LYP/6-31+G* optimized geometries have also been carried out to better estimate the hydrogen-bonding strengths. The basis set superposition error corrected hydrogen-bonding strength sequence at MP2/6-311++G**//B3LYP/6-31+G* for the most stable complexes is found to be EA(2)-T(I) (15.30 kcal/mol) > EA(1)-T(II) (14.98 kcal/mol) > EA(3)-T(II) (14.68 kcal/mol) > epsilonA(2)-T(I) (14.54 kcal/mol) > epsilonA(3)-T(II) (14.22 kcal/mol) > epsilonA(3)-T(II) (13.64 kcal/mol) > A-T (13.62 kcal/mol). The calculated reaction enthalpy value for epsilonA(2)-T(I) is 10.05 kcal/mol, which is the highest among the etheno adduct-thymine complexes and about 1.55 kcal/mol more than those obtained for Watson-Crick A-T base pair and the reaction enthalpy value for EA(1)- T(II) is 10.22 kcal/mol, which is highest among the ethano addcut-thymine complexes and about 1.72 kcal/mol more than those obtained for Watson-Crick A-T base pair. The aim of this research is to provide fundamental understanding of adenine adduct and thymine interaction at the molecular level and to aid in future experimental studies toward finding the possible cause of DNA damage.     

CS2O+ and CS2O in the gas phase: an experimental and computational study

The CS2O+ ion and CS2O molecule were prepared and structurally characterized by mass spectrometric techniques as isolated species in the gas phase. The theoretical analysis, performed by B3LYP and CCSD(T) computational methods, predicted different CS2O+ isomers, SSCO+, O(CS2)+, SCSO+, SCOS+ and S(COS)+, and structurally related singlet and triplet CS2O. Experiment and theory agree in identifying the obtained CS2O+ ions as a mixture of SCSO+ and SCOS+ isomers. CS2O neutral species, prepared by neutralization-reionization mass spectrometry, were directly characterized as intact, long-lived species with a lifetime tau > or =2 micros.     

Electron transfer to protonated beta-alanine N-methylamide in the gas phase: an experimental and computational study of dissociation energetics and mechanisms

Ammonium radicals derived from protonated beta-alanine N-methyl amide (BANMA) were generated by femtosecond collisional electron transfer to gas-phase cations prepared by chemical ionization and electrospray. Regardless of the mode of precursor ion preparation, the radicals underwent complete dissociation on the time scale of 5.15 micros. Deuterium isotope labeling and product analysis pointed out several competitive and convergent dissociation pathways that were not completely resolved by experiment. Ab initio calculations, which were extrapolated up to the CCSD(T)/6-311++G(3df,2p) level of theory, provided the proton affinity and gas-phase basicity of BANMA as PA = 971 kJ mol-1 and GB = 932 kJ mol-1 to form the most stable ion structure 1c+ in which the protonated ammonium group was internally solvated by hydrogen bonding to the amide carbonyl. Ion 1c+ was calculated to have an adiabatic recombination energy of 3.33 eV to form ammonium radical 1c*. The potential energy surface for competitive and consecutive isomerizations and dissociations of 1c* was investigated at correlated levels of theory and used for Rice-Ramsperger-Kassel-Marcus (RRKM) calculations. RRKM unimolecular rate constants suggested that dissociations starting from the ground electronic state of radical 1c* were dominated by loss of an ammonium hydrogen atom. In contrast, dissociations starting from the B excited state were predicted to proceed by reversible isomerization to an aminoketyl radical (1f*). The latter can in part dissociate by N-Calpha bond cleavage leading to the loss of the amide methyl group. This indicates that apparently competitive dissociations observed for larger amide and peptide radicals, such as backbone cleavages and losses of side-chain groups, may originate from different electronic states and proceed on different potential energy surfaces.     

A computational study on the capability of borane‐cyclic boryl anion adducts to act as hydrogen atom donors

According to our theoretical approaches, a cyclic boryl anion can act as a Lewis base like its isoelectronic counterpart N‐heterocyclic carbene, reducing the homolytic bond dissociation energy of B? H in BH₃. However, the donating efficiency is affected by the counter cation in both gas phase and nonpolar solvents. Moreover, we also predict the seven‐membered ring boryl anion 5 , although it has not yet synthesized, to be the most efficient reagent to reduce the bond dissociation energy of a B? H bond in BH₃. This study may thus pave another avenue toward Lewis base induced hydrogen atom abstraction in BH₃. © 2010 Wiley Periodicals, Inc. J Comput Chem, 2010     

1,2-Chlorine atom migration in 3-chloro-2-butyl radicals: a computational study

The structure as well as several unimolecular reaction pathways of the 3-chloro-2-butyl radical 1 have been studied at several different theoretical levels (B3LYP/aug-cc-pVDZ, BHLYP/aug-cc-pVDZ, G3(ROMP2)B3). The symmetrically chlorine-bridged structure is a transition state at all levels of theory and the most favorable ground state structure is the unbridged beta-chloroalkyl radical. Reaction barriers for the 1,2-chlorine migration process are higher than those for rotation around the central C-C bond. 1,2-migration of the chlorine atom is accompanied by an increase in chlorine negative charge as well as chlorine spin density. This hybrid homo-/heterolytic process is well known from rearrangement reactions in beta-(dialkoxyphosphoryloxy)alkyl radicals and suggests that chlorine migration can be influenced by polar substituent effects.     

Silylium-arene adducts: an experimental and theoretical study

The solvent-coordinated [Me(3)Si·arene][B(C(6)F(5))(4)] salts (arene = benzene, toluene, ethylbenzene, n-propylbenzene, isopropylbenzene, o-xylene, m-xylene, p-xylene, 1,2,3-trimethylbenzene, 1,2,4-trimethylbenzene, 1,3,5-trimethylbenzene) are prepared and fully characterized. As an interesting decomposition product the formation of bissilylated fluoronium ion [Me(3)Si-F-SiMe(3)](+) was observed and even cocrystallized with [Me(3)Si·arene][B(C(6)F(5))(4)] (arene = benzene and toluene). Investigation of the degradation of [Me(3)Si·arene][B(C(6)F(5))(4)] reveals the formation of fluoronium salt [Me(3)Si-F-SiMe(3)][B(C(6)F(5))(4)], B(C(6)F(5))(3), and a reactive "C(6)F(4)" species which could be trapped with CS(2). Upon addition of CS(2), the formation of a formal S-heterocyclic carbene adduct, C(6)F(4)CS(2)-B(C(6)F(5))(3), was observed. The structure and bonding of substituted [Me(3)Si·arene][B(C(6)F(5))(4)] with arene = R(n)C(6)H(6-n) (R = H, Me, Et, Pr, and Bu; n = 0-6) is discussed on the basis of experimental and theoretical data. X-ray data of [Me(3)Si·arene][B(C(6)F(5))(4)] salts reveal nonplanar arene species with significant cation···anion interactions. As shown by different theoretical approaches (charge transfer, partial charges, trimethylsilyl affinity values) stabilizing inductive effects occur; however, the magnitude of such effects differs depending on the degree of substitution and the substitution pattern.     

A kinetic study of the reactions of the hydrogen atom with the cyclohexadiene isomers in the gas phase

Absolute values of the rate constants for the reaction of hydrogen atoms with cyclic olefins in the gas phase have been measured in a discharge-flow system under 3.5, 16, and 22 torr Ar at 23°C. The attenuation of hydrogen atom concentration in the reaction tube in the presence of a large excess of olefin was measured with an ESR spectrometer, and the products were analyzed by gas chromatography. Cyclic C₆ hydrocarbons were the only significant products obtained when the hydrogen atom concentration was 2.6 × 10^?10 mole/1., the olefin concentration was in the range of 9 to 22 × 10^?8 mole/1., and the pressure was 16 torr Ar. The values for the rate constants for reaction with cyclohexadiene-1,3, cyclohexadiene-1,4, and cyclohexene are, respectively, (9 ± 2) × 10⁸, (12 ± 1) × 10⁸, and (6 ± 1) × 10⁸ l./mole-sec, and they are not changed significantly by a sixfold change in total pressure. The fraction of the total interaction that proceeds by addition is 84% in the cyclohexadiene-1,3 system, but only 18% in the cyclohexadiene-1,4 system, and the cyclohexadienyl radical is therefore the dominant radical species in the latter system. The pattern of interaction between the hydrogen atom and the cyclohexadienyl radical was determined, and comprises 65% of disproportionation, and 13% and 23% of combination to yield cyclohexadiene-1,3 and cyclohexadiene-1,4, respectively. These results are consistent with the general patterns of reactivity emerging from studies of the reactions between free radicals and olefins in related systems.     

Acidity of adenine and adenine derivatives and biological implications. A computational and experimental gas-phase study

The gas-phase acidities of adenine, 9-ethyladenine, and 3-methyladenine have been investigated for the first time, using computational and experimental methods to provide an understanding of the intrinsic reactivity of adenine. Adenine is found to have two acidic sites, with the N9 site being 19 kcal mol(-1) more acidic than the N10 site; the bracketed acidities are 333 +/- 2 and 352 +/- 4 kcal mol(-1), respectively. Because measurement of the less acidic site can be problematic, we benchmarked the adenine N10 measurement by bracketing the acidity of 9-ethyladenine, which has the N9 site blocked and allows for exclusive measurement of the N10 site. The acidity of 9-ethyladenine brackets to 352 +/- 4 kcal mol(-1), comparable to that of the N10 site of the parent adenine. Calculations and experiments with 3-methyladenine, a harmful mutagenic nucleobase, uncovered the surprising result that the most commonly written tautomer of 3-methyladenine is not the most stable in the gas phase. We have found that the most stable tautomer is the "N10 tautomer" 10, as opposed to the imine tautomer 3. The bracketed acidity of 10 is 347 +/- 4 kcal mol(-1). Since 10 is not a viable species in DNA, 3 is a likely tautomer; calculations indicate that this form has an extremely high acidity (320-323 kcal mol(-1)). The biological implications of these results, particularly with respect to enzymes that cleave alkylated bases from DNA, are discussed.     

Mass spectrometric and computational study of SnPb in the gas phase

The SnPb molecule has been identified in a Knudsen effusion mass spectrometry experiment. The direct dissociation reaction and two isomolecular exchange reactions involving the Sn(2) and Pb(2) molecules have been studied, in the 1426-1705 K range of temperatures, using both second and third law procedures. The D(degree)0(SnPb,g) has been derived, for the first time, as (122.6+/-4.0) kJ mol(-1). Density functional and ab initio calculations up to the coupled clusters level of theory were also performed. In addition, the anion dissociation energy D(degree)0(SnPb(-),g) of (179.2+/-4.2) kJ mol(-1) was determined using the D(degree)0(SnPb,g) mass spectrometric value derived in this investigation and literature data.     

Addition of hot hydrogen atoms to 1-butene in the gas phase and dissociation of excited butyl radicals

The reaction of hot hydrogen atoms originating from 253.7- and 228.8-nm photolyses of hydrogen sulfide with 1-butene was investigated. Of the hydrogen atoms undergoing addition a substantial part undergoes it in a first collision (37 and 48% at 253.7 and 228.8 nm, respectively) yielding highly excited butyl radicals. The ratio of nonterminal to terminal addition is 0.5 and practically does not depend on the energy of the hydrogen atoms over the range of 15–33 kcal/mol. Comparing the results of 229- and 254-nm photolyses of hydrogen sulfide with those of 313- and 334-nm photolyses of hydrogen iodide with the use of the decomposition rate constants of n-butyl radicals calculated by the RRKM methods, the conclusion is reached that the hydrogen atom from H₂S photodissociation has 90–95% of the available energy.     

Selectivity in Garratt-Braverman cyclization: an experimental and computational study

Bispropargyl sulfones equipped with aromatic rings of dissimilar nature were synthesized. Under basic conditions, these sulfones isomerized to the bisallenic sulfones, creating a competitive scenario between two alternate Garratt-Braverman (GB) cyclization pathways. The observed product distribution ruled out the involvement of any ionic intermediate and supported the diradical mechanism with greater involvement of the electron-rich aromatic ring via the more nucleophilic radical. DFT-based calculations supported the diradical mechanism along with the observed selectivity.     

Structure of radicals from X-irradiated guanine derivatives: an experimental and computational study of sodium guanosine dihydrate single crystals

In sodium guanosine dihydrate single crystals, the guanine moiety is deprotonated at N1 due to growth from high-pH (>12) solutions. Electron paramagnetic resonance (EPR) and electron-nuclear double resonance (ENDOR) studies of crystals X-irradiated at 10 K detected evidence for three radical forms. Radical R1, characterized by two proton and two nitrogen hyperfine interactions, was identified as the product of net hydrogenation at N7 of the N1-deprotonated guanine unit. R1 exhibited an unusually distorted structure leading to net positive isotropic components of the hydrogen alpha-couplings. Radical R2, characterized by one proton and one nitrogen hyperfine coupling, was identified as the primary electron-loss product. This product is equivalent to that of deprotonation at N1 by the guanine cation and represents the first ENDOR characterization of that product. Radical R3, characterized by a single hydrogen hyperfine coupling, was identified as the product of net dehydrogenation at C1' of the ribose moiety. The identification of radicals R1-R3 was supported by density functional theory (DFT) calculations on several possible structures using the B3LYP/6-311G(2df,p)//6-31G(d,p) approach. Radical R4, detected after warming the crystals to room temperature, was identified as the well-known product of net hydrogenation of C8 of the (N1-deprotonated) guanine component. Radical R1, evidently formed by protonation of the primary electron addition product, was present as roughly 60% of the total radicals detected at 10 K. Radical R2 was present as roughly 27% of the total yield, and the concentration of R3 contributed the remaining 13%. R3 is evidently the product of one-electron oxidation followed by deprotonation; thus, the balance of oxidation and reduction products is approximately equal within experimental uncertainty.     

Adding water to sugar: a spectroscopic and computational study of alpha- and beta-phenylxyloside in the gas phase

The gas phase structures of phenyl alpha- and beta-d-xylopyranoside (alpha- and beta-pXyl) and their mono-hydrates have been investigated using a combination of resonant two-photon ionization (R2PI), ultra-violet hole-burning and resonant infrared ion dip spectroscopy, coupled with density functional theory (DFT) and ab initio computation. The hole-burning experiments indicate the population of a single conformer only, in each of the two anomers. Their experimental and calculated infrared spectra are both consistent with a conformational assignment corresponding to the computed global minimum configuration. All three OH groups are oriented towards the oxygen atom (O1) on the anomeric carbon atom to form an all trans(ttt) counter-clockwise chain of hydrogen bonds. The mono-hydrates, alpha- and beta-pXyl(H(2)O) each populate two distinct structures in the molecular beam environment, with the water molecule inserted between OH4 and OH3 or between OH3 and OH2 in alpha-pXyl(H2O), and between OH2 and O1 in either of two alternative orientations, in beta-pXyl(H2O). In all of the mono-hydrated xyloside complexes, the water molecule inserts into the weakest link of the sugar molecules' hydrogen-bonded chain of hydroxy groups, creating a single extended chain, strengthened by co-operativity. The all-trans configuration of the xylose moiety is retained and the mono-hydrate structures correspond to those calculated to lie at the lowest relative energies.     

N-centered radicals in self-terminating radical cyclizations: experimental and computational studies

Intermolecular addition of photochemically generated N-centered aminium and amidyl radicals 13a-d and 16a,b, respectively, to the cyclic alkyne 1 initiates a radical translocation/cyclization cascade, followed by an oxidative termination step that eventually leads to formation of the bicyclic ketones 7a and 8a. Computational studies were performed to gain insight into the mechanism of these reactions, which are an interesting modification of the recently discovered concept of self-terminating radical cyclizations.     

A computational study of nicotine conformations in the gas phase and in water

The conformational preferences of nicotine in three protonation states and in the gas phase as well as aqueous solution are investigated using several computational procedures. Conformational aspects emphasized are N-methyl stereochemistry, relative rotation of the pyridine and pyrrolidine rings, and pyrrolidine ring conformation. All methods consistently predicted that the N-methyl trans species are most stable for all protonation states in both gas phase and in water. However, the cis/trans energy gap is significantly reduced in water. Additionally, the two pyridine ring rotamers, which are energetically equivalent in the gas phase, experience different solvation energies in water.     

Computational studies of intramolecular hydrogen atom transfers in the beta-hydroxyethylperoxy and beta-hydroxyethoxy radicals

The beta-hydroxyethylperoxy (I) and beta-hydroxyethoxy (III) radicals are prototypes of species that can undergo hydrogen atom transfer across their intramolecular hydrogen bonds. These reactions may play an important role in both the atmosphere and in combustion systems. We have used density functional theory and composite electronic structure methods to predict the energetics of these reactions, RRKM/master equation simulations to model the kinetics of chemically activated I, and variational transition state theory (TST) to predict thermal rate constants for the 1,5-hydrogen shift in I (Reaction 1) and the 1,4-hydrogen shift in III (Reaction 2). Our multi-coefficient Gaussian-3 calculations predict that Reaction 1 has a barrier of 23.59 kcal/mol, and that Reaction 2 has a barrier of 22.71 kcal/mol. These predictions agree rather well with the MPW1K and BB1K density functional theory predictions but disagree with predictions based on B3LYP energies or geometries. Our RRKM/master equation simulations suggest that almost 50% of I undergoes a prompt hydrogen shift reaction at pressures up to 10 Torr, but the extent to which I is chemically activated is uncertain. For Reaction 1 at 298 K, the variational TST rate constant is approximately 30% lower than the conventional TST result, and the microcanonical optimized multidimensional tunneling (muOMT) method predicts that tunneling accelerates the reaction by a factor of 3. TST calculations on Reaction 2 reveal no variational effect and a 298 K muOMT transmission coefficient of 10(5). The Eckart method overestimates transmission coefficients for both reactions.     

A new high pressure phase of sodium formate dihydrate; an experimental and computational study

As part of an on-going programme to study the high pressure structural behaviour of hydrated small molecular systems, sodium formate dihydrate has been studied using high pressure single crystal X-ray and neutron powder diffraction methods. A new phase was initially identified at 17 kbar by X-ray diffraction and high level quantum mechanical calculations completed the structure, allowing definitive hydrogen atom positioning. The resulting structure compared favourably with that found subsequently by high pressure neutron diffraction. The neutron diffraction study also revealed that the deuterated form, NaDCO(2).2D(2)O, is stable in a different structural form to that of the non-deuterated material at ambient pressure. The structure of this phase is related to that of the high pressure phase via a simple translation of the molecular layers.