P. C. Mishra

An ab initio study of excited states of guanine in the gas phase and aqueous media: Electronic transitions and mechanism of spectral oscillations

Ground state geometries of the four tautomeric forms keto‐N9H, keto‐N7H, enol‐N9H, and enol‐N7H of guanine were optimized in the gas phase at the RHF level using a mixed basis set consisting of the 4‐31G basis set for all the atoms except the nitrogen atom of the amino group for which the 6‐311+G* basis set was used. These calculations were also extended to hydrogen‐bonded complexes of three water molecules with each of the keto‐N9H (G9‐3W) and keto‐N7H (G7‐3W) forms of guanine. Relative stabilities of the four above‐mentioned tautomers of guanine as well as those of G9‐3W and G7‐3W complexes in the ground state in the gas phase were studied employing the MP2 correlation correction. In aqueous solution, relative stabilities of these systems were studied using the MP2 correlation correction and polarized continuum model (PCM) or the isodensity surface polarized continuum model (IPCM) of the self‐consistent reaction field (SCRF) theory. Geometry optimization in the gas phase at the RHF level using the 6‐31+G* basis set for all atoms and the solvation calculations in water at the MP2 level using the same basis set were also carried out for the nonplanar keto‐N9H and keto‐N7H forms of guanine. Thus, it is shown that among the different tautomers of guanine, the keto‐N7H form is most stable in the gas phase, while the keto‐N9H form is most stable in aqueous solution. It appears that both the keto‐N9H and keto‐N7H forms of guanine would be present in the ground state, particularly near the aqueous solution–air interface. Vertical excitation and excited state geometry optimization calculations were performed using configuration interaction involving single electron excitation (CIS). It is found that the absorption spectrum of guanine would arise mainly due to its keto‐N9H form but the keto‐N7H form of the same would also make some contribution to it. The enol‐N9H and enol‐N7H forms of the molecule are not expected to occur in appreciable abundance in the gas phase or aqueous media. The normal fluorescence spectrum of guanine in aqueous solution with a peak near 332 nm seems to originate from the lowest singlet excited state of the keto‐N7H form of the molecule while the fluorescence of oxygen‐rich aqueous solutions of guanine with a peak near 450 nm appears to originate from the lowest singlet excited state of the keto‐N9H form of the molecule. The origin of the slow damped spectral oscillation observed in the absorption spectrum of guanine has been explained.

Electronic spectra of adenine and 2-aminopurine: an ab initio study of energy level diagrams of different tautomers in gas phase and aqueous solution

Ground and lowest two singlet excited state geometries of four tautomeric forms (N9H, N7H, N3H and N1H) of each of adenine and 2-aminopurine (2AP) were optimized using an ab initio approach employing a mixed basis set (6-311 + G* on the nitrogen atom of the amino group and 4-31G basis set on the other atoms). Excited states were generated employing configuration interaction involving single electron excitations (CIS). Subsequently, the different species were solvated in water employing the self-consistent reaction field (SCRF) approach along with the corresponding gas phase optimized geometries. Thus the observed absorption and fluorescence spectra of adenine and 2AP have been explained successfully. It is concluded that both the N9H and N7H forms of 2AP would contribute to absorption and fluorescence spectra. Further, the fluorescence of 2AP would be absorbed by its cation in which both the N9 and N7 atoms are protonated, the fluorescence of which can have an anti-Stokes component. Among the different tautomers of adenine, the N9H form would be present dominantly in the ground state in aqueous solutions but the N7H form would be produced by energy transfer and subsequent fluorescence. The N3H form of adenine appears to be responsible for the observed absorption near 300 nm by its solutions intermittently exposed to ultraviolet radiation. The rings of the different species related to 2AP and adenine remain almost planar in the pi-pi* and n-pi* singlet excited states as in the ground state. The pyramidal character of the amino group is usually less in the pi-pi* excited states than that in the corresponding ground or n-pi* excited states. Molecular electrostatic potential (MEP) maps of the molecules provide useful clues regarding phototautomerism.

Urocanic acid as an efficient hydroxyl radical scavenger: a quantum theoretical study

The photoisomerization of urocanic acid (UCA)—which is present in human skin epidermis, where it acts as a sunscreen—from its trans isomer to its cis isomer upon exposure to UV-B radiation is known to cause immunosuppression. In recent years, the antioxidant properties of UCA (it acts as a hydroxyl radical scavenger) have also been recognized. In view of this, the mechanisms of stepwise reactions of trans-UCA with up to four hydroxyl radicals were investigated. The molecular geometries of the different species and complexes involved in the reactions (reactant, intermediate and product complexes, as well as transition states) were optimized via density functional theory in the gas phase. Solvation in aqueous media was treated with single point energy calculations using DFT and the polarizable continuum model. Single point energy calculations in the gas phase and aqueous media were also carried out using second-order Møller–Plesset perturbation theory (MP2). The AUG-cc-pVDZ basis set was employed in all calculations. Corrections for basis set superposition error (BSSE) were applied. Vibrational frequency analysis was performed for each optimized structure to ensure the validity of the optimized transition states. It was found that the binding of the first OH· radical to UCA involves a positive energy barrier, while subsequent reactions of OH· radicals are exergonic. Transition states were successfully located, even in those cases where the barrier energies were found to be negative. The cis–trans isomerization barrier energy of UCA and that of the first OH· radical addition to UCA are comparable, meaning that both processes can occur simultaneously. It was found that UCA could serve as an antioxidant in the form of an efficient OH· radical scavenger.

A theoretical study of structures and electron affinities of radical anions of guanine-cytosine, adenine-thymine, and hypoxanthine-cytosine base pairs

Adiabatic electron affinities (AEA) and structural perturbations due to addition of an excess electron to each of the neutral guanine‐cytosine (G‐C), adenine‐thymine (A‐T), and hypoxanthine‐cytosine (HX‐C) base pairs were studied using the self‐consistent charge, density functional tight‐binding (SCC‐DFTB‐D) method, augmented by the empirical London dispersion energy term. Performance of the SCC‐DFTB‐D method was examined by comparing the calculated results using it with those obtained from experiment as well as ab initio and other different density functional theoretical studies. An excellent agreement between the SCC‐DFTB‐D results and those obtained by the other calculations regarding the structural modifications, hydrogen bonding, and dissociation energies of the neutral and radical anion base pairs was found. It is shown that adiabatic electron affinity can be better predicted by considering reaction enthalpies of formation of the respective neutral and anionic base pairs from their respective molecular components instead of taking the difference between their total energies. The calculated AEAs of the base pairs were compared with those obtained by the bracketing method from Schaefer and coworkers, where a satisfactory agreement was found. It shows applicability of the SCC‐DFTB‐D method to study charged DNA models at a highly economical computational cost.

Electronic spectra of 2-aminopurine and 2,6-diaminopurine: phototautomerism and fluorescence reabsorption

Abstract Ultraviolet absorption, fluorescence and excitation spectra of 2-aminopurine (2AP) and 2,6-diaminopurine (2,6DAP) have been studied using aqueous solutions at different pH values. The molecules are found to fluoresce most efficiently near the neutral pH. It is also found that the fluorescence caused by the solutions of these compounds is partly reabsorbed. Molecular orbital calculations on 2AP, its tautomers, anion and cation, and excited state life-time measurements corresponding to the emissions of 2AP and 2,6DAP near 370 and 342 nm, respectively, have been carried out, and have been found to be useful in the interpretation of the experimental observations.

Scavenging mechanism of curcumin toward the hydroxyl radical: a theoretical study of reactions producing ferulic acid and vanillin.

Curcumin is known to be an antioxidant, as it can scavenge free radicals from biological media. A sequence of H-abstraction and addition reactions involving up to eight OH radicals and curcumin or its degradation products leading to the formation of two other antioxidants, namely, ferulic acid and vanillin, was studied. Single electron transfer from curcumin to an OH radical was also studied. All relevant extrema on the potential energy surfaces were located by optimizing geometries of the reactant and product complexes, as well as those of the transition states, at the BHandHLYP/6-31G(d,p) level of density functional theory in the gas phase. Single-point energy calculations were also performed in the gas phase at the BHandHLYP/aug-cc-pVDZ and B3LYP/aug-cc-pVDZ levels of theory. Solvent effects in aqueous media were treated by performing single-point energy calculations at all of the above-mentioned levels of theory employing the polarizable continuum model and the geometries optimized at the BHandHLYP/6-31G(d,p) level in the gas phase. A few reaction steps were also studied by geometry optimization in aqueous media, and the thus-obtained Gibbs free energy barriers were similar to those obtained by corresponding single-point energy calculations. Our calculations show that the hydrogen atom of the OH group attached to the phenol moiety of curcumin would be most efficiently abstracted by an OH radical, in agreement with experimental observations. Further, our study shows that OH addition would be most favored at the C10 site of the heptadiene chain. It was found that curcumin can serve as an effective antioxidant.

ELECTRONIC SPECTRA, STRUCTURE AND PHOTOISOMERIZATION OF UROCANIC ACID

Abstract Electronic absorption and fluorescence spectra of urocanic acid are studied in aqueous solution at different pH. The observed results are explained using molecular orbital geometry optimization calculations for the ground states of a number of tautomers of urocanic acid including those of its anion, followed by calculation of electronic transitions. The isomers of urocanic acid which would strongly absorb UV-B radiation have thus been identified. Further, the possible mechanisms of isomerization of urocanic acid from the trans - to cis -form which is related to its role in immunosuppression and UV-B induced skin cancer have been suggested.

An ab initio study of water clusters in gas phase and bulk aqueous media: (H2O)n, n=1–12

Geometries of several clusters of water molecules including single minimum energy structures of n-mers (n=1–5), several hexamers and two structures of each of heptamer to decamer derived from hexamer cage and hexamer prism were optimized. One structural form of each of 11-mer and 12-mer were also studied. The geometry optimization calculations were performed at the RHF/6-311G* level for all the cases and at the MP2/6-311++G** level for some selected cases. The optimized cluster geometries were used to calculate total energies of the clusters in gas phase employing the B3LYP density functional method and the 6-311G* basis set. Frequency analysis was carried out in all the cases to ensure that the optimized geometries corresponded to total energy minima. Zero-point and thermal free energy corrections were applied for comparison of energies of certain hexamers. The optimized cluster geometries were used to solvate the clusters in bulk water using the polarized continuum model (PCM) of the self-consistent reaction field (SCRF) theory, the 6-311G* basis set, and the B3LYP density functional method. For the cases for which MP2/6-311++G** geometry optimization was performed, solvation calculations in water were also carried out using the B3LYP density functional method, the 6-311++G** basis set, and the PCM model of SCRF theory, besides the corresponding gas-phase calculations. It is found that the cage form of water hexamer cluster is most stable in gas phase among the different hexamers, which is in agreement with the earlier theoretical and experimental results. Further, use of a newly defined relative population index (RPI) in terms of successive total energy differences per water molecule for different cluster sizes suggests that stabilities of trimers, hexamers, and nonamers in gas phase and those of hexamers and nonamers in bulk water would be favored while those of pentamer and decamer in both the phases would be relatively disfavored.

Protection Against Radiation-Induced DNA Damage by Amino Acids : A DFT Study

Direct and indirect radiation-induced DNA damage is associated with the formation of radical cations (G(+)) and radical anions (G(-)) of guanine, respectively. Deprotonation of G(+) and dehydrogenation of G(-) generate guanine neutral radical [G(-H)] and guanine anion [G(-H)(-)], respectively. These products are of worrisome concern, as they are involved in reactions that are related to certain lethal diseases. It has been observed that guanyl radicals can be repaired by amino acids having strong reducing properties that are believed to be the residues of DNA-bound proteins such as histones. As a result, repair of G(-H) and G(-H)(-) by the amino acids cysteine and tyrosine has been studied here in detail by density functional theory in both the gas phase and aqueous medium using the polarized continuum and Onsager solvation models of self-consistent reaction field theory. Solvation in aqueous medium using three explicit water molecules was also studied. Four equivalent tautomers of each the above radical and anion that will be formed through proton and hydrogen loss from all of the nitrogen centers of guanine radical cation and guanine radical anion, respectively, were considered in the present study. It was found that in both the gas phase and aqueous medium, normal guanine can be retrieved from its radical-damaged form by a hydrogen-atom-transfer (HT) mechanism. Normal guanine can also be retrieved from its anionic damaged form in both the gas phase and aqueous medium through a two-electron-coupled proton-transfer (TECPT) mechanism or a one-step hydrogen-atom- and electron-transfer (OSHET) mechanism. The present results are discussed in light of the experimental findings.

Formation of 8‐nitroguanine and 8‐oxoguanine due to reactions of peroxynitrite with guanine

Reactions of peroxynitrite with guanine were investigated using density functional theory (B3LYP) employing 6‐31G** and AUG‐cc‐pVDZ basis sets. Single point energy calculations were performed at the MP2/AUG‐cc‐pVDZ level. Genuineness of the calculated transition states (TS) was tested by visually examining the vibrational modes corresponding to the imaginary vibrational frequencies and applying the criterion that the TS properly connected the reactant and product complexes (PC). Genuineness of all the calculated TS was further ensured by intrinsic reaction coordinate (IRC) calculations. Effects of aqueous media were investigated by solvating all the species involved in the reactions using the polarizable continuum model (PCM). The calculations reveal that the most stable nitro‐product complex involving the anion of 8‐nitroguanine and a water molecule i.e. 8NO2G− + H2O can be formed according to one reaction mechanism while there are two possible reaction mechanisms for the formation of the oxo‐product complex involving 8‐oxoguanine and anion of the NO2 group i.e. 8OG + NO2−. The calculated relative stabilities of the PC, barrier energies of the reactions and the corresponding enthalpy changes suggest that formation of the complex 8OG + NO2− would be somewhat preferred over that of the complex 8NO2G− + H2O. The possible biological implications of this result are discussed.