Adenine−Hydrogen Peroxide System: DFT and MP2 Investigation

Complexes of hydrogen peroxide molecules with DNA nucleic bases

The analysis of complexes formation of hydrogen peroxide molecule with DNA nucleic bases is carried out using methods of quantum chemistry. Optimized geometries of complexes are determined and the interaction energies that lead to complex formation are calculated. Comparison with the same calculations for water molecule is made. It is shown that complexes with hydrogen peroxide molecule are energetically more stable than the same complexes with water molecule. Such energetic advantage is achieved particularly due to geometrical properties of hydrogen peroxide molecule, especially presence of dihedral angle. Position of hydrogen peroxide molecule in close vicinity to DNA could lead to blocking of its recognition by proteins or direct damage via hydroxyl radical formation. These results can have significant impact in understanding of mechanisms of cancer therapy.Communicated by Ramaswamy H. Sarma.

Nature and role of the weak intermolecular bond in enantiomeric conformations of H2O2–noble gas adducts: a chiral prototypical model

The role and nature of the weak intermolecular bond in the H₂O₂–noble gas enantiomeric conformations are presented. Charge transfer associated with the formation of a weak intermolecular hydrogen bond tends to stabilize the cis-barrier conformation.

Theoretical Investigation on H2O2-Ng (He, Ne, Ar, Kr, Xe, and Rn) Complexes Suitable for Stereodynamics: Interactions and Thermal Chiral Rate Consequences

Although molecular collisions of noble gases (Ng) can be theoretically used to distinguish between the enantiomers of hydrogen peroxide - H₂O₂ (HP), little is known about the effects of HP-Ng interactions on the chiral rate. In this work, the chiral rate as a function of temperature (CRT) between enantiomeric conformations of HP and Ng (Ng=He, Ne, Ar, Kr, Xe, and Rn) are presented at MP2(full)/aug-cc-pVTZ level of theory through a fully basis set superposition error (BSSE) corrected potential energy surface. The results show that: (a) the CRT is highly affected even at a small decrease in the height of trans-barrier; (b) its smallest values occur with Ne for all temperatures between 100 and 4,000 K; (c) that the decrease of CRT shows an inverse correlation with respect to the average valence electron energy of the Ng and (d) Ne and He may be the noble gases more suitable for study the oriented collision dynamics of HP. In addition to binding energies, the electron density ρ and its Laplacian ∇²ρ topological analyses were also performed within the atoms in molecules (AIM) theory in order to determine the nature of the HP-Ng interactions. The results of this work provide a more complete foundation on experiments to study HP's chirality using Ng in crossed molecular beams without a light source.

Benchmarking sampling methodology for calculations of Rayleigh light scattering properties of atmospheric molecular clusters

We present four different computational methods for benchmarking the sampling and Rayleigh light scattering of hydrogen bonded atmospheric molecular clusters.

Interaction of Refractory Dibenzothiophenes and Polymerizable Structures

We carried out first principles calculations to show that polymerizable structures containing hydroxyl (alcoholic chain) and amino groups are suitable to form stable complexes with dibenzothiophene (DBT) and its alkyl derivates. These sulfur pollutants are very difficult to eliminate through traditional catalytic processes. Spontaneous and exothermic interactions at 0 K primarily occur through the formation of stable complexes of organosulfur molecules with monomeric structures by hydrogen bonds. The bonds are formed between the sulfur atom and the hydrogen of the hydroxyl group; additional hydrogen bonds are formed between the hydrogen atoms of the organosulfur molecule and the nitrogen atoms of the monomers. We vary the number of methylene groups in the alcoholic chain containing the hydroxyl group of the monomer and find that the monomeric structure with four methylene groups has the best selectivity towards the interaction with the methyl derivates with reference to the interaction with DBT. Even this study does not consider solvent and competitive adsorption effects; our results show that monomeric structures containing amino and hydroxyl groups can be used to develop adsorbents to eliminate organosulfur pollutants from oil and its derivates.

Environmental Effects on the Enhancement in Natural and Damaged DNA Nucleobase Acidity Because of Discrete Hydrogen-Bonding Interactions

The present study uses density functional theory to carefully consider the effects of the environment on the enhancement in (natural and damaged) DNA nucleobase acidities because of multiple hydrogen-bonding interactions. Although interactions with one small molecule can increase the acidity of the nucleobases by up to 60 kJ mol-1 in the gas phase, the maximum increase in enzymatic-like environments is expected to be approximately 40 kJ mol-1, which reduces to approximately 30 kJ mol-1 in water. Furthermore, the calculated (simultaneous) effects of two, three, or four molecules are increasingly less than the sum of the individual (additive) effects with an increase in the number and acidity of the small molecules bound or the dielectric constant of the solvent. Regardless of these trends, our calculations reveal that additional hydrogen-bonding interactions will have a significant effect on nucleobase acidity in a variety of environments, where the exact magnitude of the effect depends on the properties of the small molecule bound, the nucleobase binding site, and the solvent. The maximum increase in nucleobase acidity because of interactions with up to four small molecules is approximately 80 kJ mol-1 in enzymatic-like environments (or 65 kJ mol-1 in water). These results suggest that hydrogen-bonding interactions likely play an important role in many biological processes by changing the physical and chemical properties of the nucleobases.

Interaction of Peroxyformic Acid with Water Molecules: A First-Principles Study

The present article comprises a theoretical study of structures and energetics of the lowest energy conformers of peroxyformic acid (PFA) and its hydrated variants, viz. PFA...(H2O)n (n = 1-4), at the molecular level. We have employed two different ab initio quantum chemical methods, viz. restricted Hartree-Fock (RHF) and the second-order Møller-Plesset (MP2) perturbation theory with the basis sets 6-31G(d,p) and 6-311++G(2d,2p). Modifications in the structure as well as vibrational frequencies of PFA brought about by successive addition of H2O molecules are also discussed. Cooperativity of hydrogen bonding in these clusters can be gauged through a detailed many body interaction energy analysis.

Effect of additional hydrogen peroxide to H2O2⋯(H2O)n, n=1 and 2 complexes: Quantum chemical study

Hydrogen peroxide, H2O2, acts as a particularly strong reactant in aqueous environment. It has been demonstrated earlier that agglomerates with a single peroxide interacting with one and two water molecules manifest in several stable conformers within a narrow energy range. In the present study we seek structural changes brought out by adding an extra H2O2 to these systems at molecular level employing ab initio quantum chemical methods, viz., restricted Hartree-Fock and the second order Moller-Plesset perturbation theory. These clusters exhibit consistent trends in energy hierarchy at both the levels. Further, a many body interaction energy analysis quantifies the strength and cooperativity of hydrogen bonding in the (H2O2)2...(H2O)n, (n=1 and 2) clusters, bringing out structuring/destructuring effects attributed to attachment of water and hydrogen peroxide molecules.

Mechanisms of Formation of 8-Oxoguanine Due To Reactions of One and Two OH• Radicals and the H2O2 Molecule with Guanine: A Quantum Computational Study

Mechanisms of formation of the mutagenic product 8-oxoguanine (8OG) due to reactions of guanine with two separate OH* radicals and with H2O2 were investigated at the B3LYP/6-31G, B3LYP/6-311++G, and B3LYP/AUG-cc-pVDZ levels of theory. Single point energy calculations were carried out with the MP2/AUG-cc-pVDZ method employing the optimized geometries at the B3LYP/AUG-cc-pVDZ level. Solvent effect was treated using the PCM and IEF-PCM models. Reactions of two separate OH* radicals and H2O2 with the C2 position of 5-methylimidazole (5MI) were investigated taking 5MI as a model to study reactions at the C8 position of guanine. The addition reaction of an OH* radical at the C8 position of guanine is found to be nearly barrierless while the corresponding adduct is quite stable. The reaction of a second OH* radical at the C8 position of guanine leading to the formation of 8OG complexed with a water molecule can take place according to two different mechanisms, involving two steps each. According to one mechanism, at the first step, 8-hydroxyguanine (8OHG) complexed with a water molecule is formed ,while at the second step, 8OHG is tautomerized to 8OG. In the other mechanism, at the first step, an intermediate complexed (IC) with a water molecule is formed, the five-membered ring of which is open, while at the second step, the five-membered ring is closed and a hydrogen bonded complex of 8OG with a water molecule is formed. The reaction of H2O2 with guanine leading to the formation of 8OG complexed with a water molecule can also take place in accordance with two different mechanisms having two steps each. At the first step of one mechanism, H2O2 is dissociated into two OH* groups that react with guanine to form the same IC as that formed in the reaction with two separate OH* radicals, and the subsequent step of this mechanism is also the same as that of the reaction of guanine with two separate OH* radicals. At the first step of the other mechanism of the reaction of guanine with H2O2, the latter molecule is dissociated into a hydrogen atom and an OOH* group which become bonded to the N7 and C8 atoms of guanine, respectively. At the second step of this mechanism, the OOH* group is dissociated into an oxygen atom and an OH* group, the former becomes bonded to the C8 atom of guanine while the latter abstracts the H8 atom bonded to C8, thus producing 8OG complexed with a water molecule. Solvent effects of the aqueous medium on certain reaction barriers and released energies are appreciable. 5MI works as a satisfactory model for a qualitative study of the reactions of two separate OH* radicals or H2O2 occurring at the C8 position of guanine.

Effects of Hydrogen Bonding on the Acidity of Adenine, Guanine, and Their 8-Oxo Derivatives

Complexes between ammonia, water, or hydrogen fluoride and adenine, guanine, or their 8-oxo derivatives are investigated using density-functional theory. The binding strengths of the neutral and (N9) anionic complexes are considered for a variety of purine binding sites. The effects of hydrogen-bonding interactions on the (N9) acidity of the purine derivatives are considered as a function of the molecule bound and the binding site. It is found that hydrogen-bonding interactions with one molecule can increase the acidity of purine derivatives by up to 60 kJ mol(-1). The (calculated) simultaneous effects of up to four molecules on the acidity of the purine derivatives are also considered. Our data suggest that the effects of more than one molecule on the acidity of the purines are generally less than the sum of the individual (additive) effects, where the magnitude of the deviation from additivity increases with the number, as well as the acidity, of molecules bound. Nevertheless, the increase in the acidity due to additional hydrogen-bonding interactions is significant, where the effect of two, three, or four hydrogen-bonding interactions can be as large as approximately 95, 115, and 130 kJ mol(-1), respectively. The present study provides a greater fundamental understanding of hydrogen-bonding interactions involving the natural purines, as well as those generated through oxidative DNA damage, which may aid the understanding of important biological processes.

Structures, Energetics, and Vibrational Spectra of H2O2···(H2O)n,n= 1−6 Clusters: Ab Initio Quantum Chemical Investigations

Hydrogen-bonded heteroclusters of H(2)O(2)...(H(2)O)(n)(), with n varying from 1 through 6, have been investigated herein employing ab initio quantum chemical methods. For a given n, several energetically comparable conformers emerge as local minima on the potential energy surface (PES). All of the conformers obtained at restricted Hartree-Fock (RHF) and Møller-Plesset second-order perturbation (MP2) levels of theory exhibit parallel trends in energy hierarchy. The effect of clustering by water on the modification in the vibrational frequencies has also been investigated and further, a many-body interaction-energy analysis is carried out providing insights into cooperativity in H(2)O(2)...(H(2)O)(n)() clusters.

Matrix Isolation and Ab Initio Study of the Hydrogen-Bonded H2O2-CO Complex

The structure, energetics, and infrared spectrum of the H2O2-CO complex have been studied computationally with the use of ab initio calculations and experimentally by FTIR matrix isolation techniques. Computations predict two stable conformations for the H2O2-CO complex, both of which show almost linear hydrogen bonds between the subunits. The carbon-attached HOOH-CO complex is the lower-energy form, and it has an interaction energy of -9.0 kJmol(-1) at the CCSD(T)/6-311++G(3df,3pd)// MP2/6-311++G(3df,3pd) level. The higher-energy form, HOOH-OC, has an interaction energy of 4.7 kJmol(-1) at the same level of theory. Experimentally, only the lower-energy form, HOOH-CO, was observed in Ar, Kr, and Xe matrices, and the hydrogen bonding results in substantial perturbations of the observed vibrational modes of both complex subunits. UV photolysis of the complex species primarily produces a complex between water and carbon dioxide, but minor amounts of HCO and trans-HOCO were found as well.