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P C Mishra

Publications and source records attributed to P C Mishra.

At least 19 recordsLinked to original sources
PubMed2006

Binding of gold clusters with DNA base pairs: a density functional study of neutral and anionic GC-Aun and AT-Aun (n = 4, 8) complexes.

Binding of clusters of gold atoms (Au) with the guanine-cytosine (GC) and adenine-thymine (AT) Watson-Crick DNA base pairs was studied using the density functional theory (DFT). Geometries of the neutral GC-Au(n) and AT-Au(n) and the corresponding anionic (GC-Au(n))(-1) and (AT-Au(n))(-1) (n = 4, 8) complexes were fully optimized in different electronic states, that is, singlet and triplet states for the neutral complexes and doublet and quartet states for the anionic complexes, using the B3LYP density functional method. The 6-31+G basis set was used for all atoms except gold. For gold atoms, the Los Alamos effective core potential (ECP) basis set LanL2DZ was employed. Vibrational frequency calculations were performed to ensure that the optimized structures corresponded to potential energy surface minima. The gold clusters around the neutral GC and AT base pairs have a T-shaped structure, which satisfactorily resemble those observed experimentally and in other theoretical studies. However, in anionic GC and AT base pairs, the gold clusters have extended zigzag and T-shaped structures. We found that guanine and adenine have high affinity for Au clusters, with their N3 and N7 sites being preferentially involved in binding with the same. The calculated adiabatic electron affinities (AEAs) of the GC-Au(n)complexes (n = 4, 8) were found to be much larger than those of the isolated base pairs.

Adenine↗
PubMed2005

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.

Binding, Competitive↗
PubMed2005

Adiabatic electron affinities of the polyhydrated adenine-thymine base pair: a density functional study.

Adiabatic electron affinities (AEAs) of the adenine-thymine (AT) base pair surrounded by 5 and 13 water molecules have been studied by density functional theory (DFT). Geometries of neutral AT x nH2O and anionic (AT x nH2O)- complexes (n = 5 and 13) were fully optimized, and vibrational frequency analysis was performed at the B3LYP/6-31+G** level of theory. The optimized structures of the neutral (AT x nH2O) and (AT x nH2O)- complexes were found to be somewhat nonplanar. Some of the water molecules are displaced away from the AT ring plane and linked with one another by hydrogen bonds. The optimized structures of the complexes are found to be in a satisfactory agreement with the observed experimental and molecular dynamics simulation results. In the optimized anionic complexes, the thymine (T) moiety was found to be puckered, whereas the adenine (A) moiety remained almost planar. Natural population analysis (NPA) performed using the B3LYP/6-31+G** method shows that the thymine moiety in the anionic (AT x nH2O)- complexes (n = 5 and 13) has most of the excess electronic charge, i.e., approximately -0.87 and approximately -0.81 (in the unit of magnitude of the electronic charge), respectively. The zero-point energy corrected adiabatic electron affinities of the hydrated AT base pair were found to be positive both for n = 5 and 13 and have the values of 0.97 and 0.92 eV, respectively, which are almost three times the AEA of the AT base pair. The results show that the presence of water molecules appreciably enhances the EA of the base pair.

Adenine↗
PubMed2005

Dust accumulation and leaf pigment content in vegetation near the national highway at Sambalpur, Orissa, India.

An investigation on the seasonal variation in dust accumulation on leaves and leaf pigment content of six plant species of mixed habits was carried out at the side of the National Highway (NH 6) at Sambalpur, Orissa, India. The plants selected for study were Pongamia pinnata, Tabernaemontana divaricata, Ipomea carnea, Ficus relogiosa, Ficus benghalensis, and Quisqualis indica. The observed trend of dust accumulation was in the order T. divaricata>I. carnea>P. pinnata>F. religiosa>F. benghalensis>Q. indica. One-way analysis of variance showed significant difference in dust accumulation among plant species (F1 = 4.674, P < 0.01) and between seasons (F2 = 9.240, P < 0.01). It was seen that dust load increases with increasing number of vehicles using the highway (major emission source). The result shows significant correlation (negative) between dust load and pigment content in summer and rainy season.

Dust↗
PubMed2005

Contamination of water due to major industries and open refuse dumping in the steel city of Orissa--a case study.

Contamination of ground water is common in the areas surrounded by industrial refuse dumping sites and the probability of contamination is more where dumping is done in low lying areas and the rate of percolation through the soil is high. In order to assess the ground water pollution by leachate around the refuse dumping site, eighteen wells were selected for study. Few wells are nearer to the dumps, few are far away and others are in between. Also an attempt has been made to evaluate the effect of industrial effluents on the ground and surface water due to Integrated Rourkela Steel Plant and other major industries. From the analytical data of physico-chemical parameters, it is indicated that the river water is contaminated mainly due to the industrial and municipal effluents and the ground water of some of the analyzed areas is contaminated due to municipal and industrial solid waste dumping.

Cities↗
PubMed2004

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.

Adenine↗
PubMed2004

Electronic transitions of guanine tautomers, their stacked dimers, trimers and sodium complexes.

Planar and nonplanar geometries of the keto-N9H and keto-N7H tautomers of the guanine base of DNA as well as the hydrogen bonded complexes of these species with three water molecules each were optimized using the density functional theory at the B3LYP/6-31G** level. Geometries of the isolated bases were also optimized using the ab initio approach at the MP2/6-31G** level. The isolated keto-N9H and keto-N7H tautomers as well as their hydrogen bonded complexes with three water molecules each were solvated in bulk water employing the polarized continuum model (PCM) of the self-consistent reaction field theory (SCRF). Stacked dimers and trimers of both the tautomers of guanine were generated by placing the planar forms of the species at a fixed distance of 3.5 A from the neighboring one and rotating one molecule with respect to the other by 110 degrees for the keto-N9H form and 90 degrees for the keto-N7H form which corresponded to total energy minima at the B3LYP/6-31G** level. Geometry optimization for the cation of the monomer of guanine was performed at the same level of theory, and its solvation in bulk water was treated using the PCM model of the SCRF theory. The geometries of complexes of the two tautomers of guanine with a Na+ ion each were optimized at the B3LYP/6-31G** level, and the Na+ ion is predicted to bind with the keto-N9H tautomer preferentially. While the complex of the keto-N7H form of guanine with three water molecules in gas phase is slightly more stable than the corresponding complex of the keto-N9H form of guanine, the reverse is true in bulk water. Stacking interactions enhance the relative stability of the keto-N9H tautomer over that of the keto-N7H tautomer, suggesting that in bulk solutions, the former would be dominant. Electronic spectra of the isolated tautomers of guanine, those of their complexes with three water molecules each, the (keto-n9h and keto-n7h) cation of guanine, the complexes of the tautomers with a Na+ ion each, the stacked dimers and trimers of the two tautomers were calculated using configuration interaction involving single electron excitations (CIS). The relative absorption intensities of the two tautomers of guanine near 275 and 248 nm in the monomer, dimer, and trimer are predicated to be in the opposite order. Thus the absorption intensity oscillation observed using a guanine aqueous solution can be explained in terms of oscillation of relative populations of the two tautomers of the molecule. The 248 nm absorption peak would be appreciably red-shifted on formation of the cation of guanine. Binding of the Na+ ion with the two tautomers of guanine reduces intensities of their transitions appreciably and also it causes large red-shifts in the same.

Dimerization↗
PubMed2003

An ab initio study of microsolvation of LiF in water: structures and properties of LiF-Wn, n = 1-9 complexes.

Geometries of clusters of water molecules (W(n)) and those of the LiF-W(n) (n = 1-9) complexes were optimized using the B3LYP/6-31+G** method. Geometries of the complexes up to n = 7 were also optimized using the MP2/6-31+G** approach. Only one structure of each of W(n), n = 1-5 was considered to generate the complexes with LiF while two structures, one of a cage type and the other of a prism type, were considered for n = 6-9. The LiF-W(2) complex is found to be most stable among the various complexes. The LiF-W(6) complex, where W(6) is of a cage type, is predicted to be substantially less stable than that where W(6) is of a prism type. Certain existing ambiguities regarding the most stable structures of the LiF-W(n) (n = 1-3) complexes have been resolved. The LiF molecule seems to divide the W(n) clusters in the LiF-W(n) (n = 3-6) complexes into different fragments where at least one W(2)-like fragment is present. In LiF-W(6) (cage), there is one W(2)-like fragment while in LiF-W(6) (prism), there are three W(2)-like fragments. The LiF bond length is substantially increased in going from the gas phase to the different complexes, this increase being most prominent in LiF-W(6), where W(6) is of the cage or prism type. The LiF molecule, however, does not acquire the ionic structure Li(+)F(-) in any of the complexes studied here. An appreciable amount of electronic charge is transferred from LiF to the water molecules involved in the different complexes. In this process, the Li atom gains electronic charge in some cases, while the F atom considered separately, as well as the Li and F atoms taken together, lose the same in most cases.

Journal Article↗
PubMed2003

Quality of water for drinking and agriculture in and around a mines in Keonjhar District, Orissa.

For optimum utilization of water resources, it is necessary to know both the quantity as well as quality of water. This paper describes the assessment of the quality of water of a mining area in the Keonjhar district of Orissa for drinking and agricultural purpose. The water quality for drinking purposes and for agricultural purposes was found to be suitable, however to give the final conclusion it requires the study of biological parameters.

Agriculture↗
PubMed2002

An ab initio theoretical study of electronic structure and properties of 2'-deoxyguanosine in gas phase and aqueous media.

Molecular geometries of two structural forms of 2'-deoxyguanosine (keto-N9R and keto-N7R, R = the sugar moiety) considering both the C2'-endo and C3'-endo conformations of the sugar ring and those of the complexes of these species with two water molecules each were optimized employing the ab initio RHF procedure. A mixed basis set consisting of the 6-311+G* basis set for the nitrogen atom of the amino group and the 4-31G basis set for all the other atoms was used. The RHF calculations were followed by correlation correction of the total energy at the MP2 level. Both the structural forms of 2'-deoxyguanosine were solvated using the polarized continuum model (PCM) of the self-consistent reaction field (SCRF) theory and the corresponding RHF optimized geometries at the RHF and MP2 levels. Geometry optimization was also performed in aqueous media using the Onsager model at the RHF level using the above-mentioned mixed basis set, and subsequently, using the reoptimized geometries, single-point MP2 calculations were performed. It is found that both the keto-N9R and keto-N7R forms of 2'-deoxyguanosine as well as their complexes with two water molecules each would occur, particularly at the water-air interface. Though the normal Watson-Crick-type base pairing would not be possible with the keto-N7R form of 2'-deoxyguanosine(G*), two other (G*-C and G*-T) base pairing schemes may occur with this form of the nucleoside, which may cause mutation. The present calculated geometry of the keto-N9R form of the anti-conformation of 2'-deoxyguanosine including the dihedral angle chi(CN) agree satisfactorily with the available crystallographic results. The present results also agree satisfactorily with those obtained by other authors earlier for the keto-N9R form of 2'-deoxyguanosine using B3LYP and MP2 methods employing the 6-31G* basis set. Using transition state calculations, it is shown that tautomerism of guanine and other similar molecules where the tautomers would coexist would be facilitated by the occurrence of the H(+) and OH(-) fragments of water molecules. Further, this coexistence of the two tautomers appears to make the C8 carbon atom located between the N7 and N9 nitrogen atoms susceptible to attack by the OH(-) group. Thus, an explanation is obtained for the efficient formation of the reaction product 8-hydroxy-2'-deoxyguanosine, which serves as a biomarker for oxidative damage to DNA in biological systems.

8-Hydroxy-2'-Deoxyguanosine↗
PubMed2001

Soil biochemical activity and growth response of rice Oryza sativa in flyash amended soil.

Soil amended with different proportions of flyash, a solid waste generated from coal-fired thermal power plants, was evaluated as a soil conditioner and nutrient supplement during a field study on the growth of rice, Oryza sativa. Generally, pH and organic carbon (OC) content did not increase significantly (P > 0.05) in flyash amended soil, but significant increases (P < 0.05) in soil conductivity (32%), available phosphorus (48%) and organic matter (OM, 29%) were observed during harvest at the 20 t ha-1 flyash application rate. Amylase, invertase, dehydrogenase and protease activities, and CO2 evolution increased in flyash amended soil over the control. The pigment (chl-a, chl-b, and carotenoid) content in rice plants did not vary significantly (P > 0.05) between different flyash amendments. Total plants biomass and aboveground biomass increased (P < 0.05) significantly (17% and 25%, respectively) at the 20 t ha-1 flyash application. However, there was a retarded growth of underground biomass. Grain and straw yield increased by 21% and 18%, respectively, at 17.5 t ha-1 flyash amendment when compared to the control. Although, a significant increase (P < 0.05) in plant biomass and grain yield in flyash amended soil is encouraging from the point of waste disposal and management, elucidation of reasons for retarded growth in underground biomass will require additional research based on long-term studies.

Amylases↗
PubMed2001

An ab initio study of electronic structure and spectra of 8-bromoguanine: a comparative study with guanine.

Ground state geometries of the four tautomeric forms keto-N9H, keto-N7H, enol-N9H and enol-N7H of 8-bromoguanine (8BG) were optimized using the ab initio RHF procedure employing a mixed basis set consisting of the 6-311 + G* basis set for the nitrogen atom of the amino group and the bromine atom, and the 4-31G basis set for all other atoms. These calculations were followed by correlation correction of the total energy at the MP2 level using the same basis set. The different tautomeric forms of 8BG in the ground state were solvated using the isodensity surface polarized continuum model (IPCM) of the SCRF theory both at the RHF and MP2 levels. Excited states were generated employing configuration interaction among singly excited configurations (CIS) obtained using a limited window of filled and empty molecular orbitals. Formation of hydrogen-bonded complexes between 8BG and three water molecules in the ground and excited states was considered in order to account for solvent effects approximately. Excited state geometry was optimized in each case for the lowest singlet excited state which was found to be of pi-pi* type. Vibrational frequency analysis was performed in order to ensure that the stationary points located on the potential energy surfaces by geometry optimization were minima. It is found that 8BG would occur in the ground state dominantly in the keto-N7H form both at the aqueous solution-air interface and inside the bulk liquid. The observed absorption and fluorescence spectra of 8BG can be explained satisfactorily considering only the keto-N7H form of the molecule. The enol tautomers of 8BG do not appear to be important from the point of view of ground state properties or electronic spectra. The observed differences between the behaviors of guanine and 8BG can be easily explained on the basis of the results obtained.

DNA↗
PubMed2000

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.

2-Aminopurine↗
PubMed1999

A geometry optimization and molecular electrostatic potential mapping study of structure-activity relationship for some anti-Alzheimer agents.

Molecular geometries of some substituted (pyrroloamino)pyridines which possess anti-Alzheimer activity were optimized and potential-derived CHelpG point charges were computed using ab initio SCF molecular orbital approach employing the 3-21G basis set. AM1 molecular orbital calculations were performed using these optimized geometries and thus optimized Hybridization. Displacement Charges (HDC) combined with Löwdin charges continuously distributed in three dimension were obtained. Molecular electrostatic potential (MEP) maps of the molecules were obtained in two ways: (i) using the HDC-based model with the help of which MEP minima near the molecules were located, and (ii) using the CHelpG point charges, MEP values on the van der Waals surfaces of the molecules were computed. The MEP maps computed using both the methods have negative MEP regions near the pyridine nitrogen atom which appears to be the main binding site of the molecules with the appropriate receptor. Both electrostatic interaction and lipophilic association between these molecules and the receptor appear to contribute to biological activity.

Alzheimer Disease↗
PubMed1998

Haematological characteristics and bone fluoride content in Bufo melanostictus from an aluminium industrial site.

Fluoride concentration in bones and differential haemotological characteristics (RBC, haemoglobin, haematocrit, mean corpusclar haemoglobin and mean corpuscular volume) were measured in amphibians, Bufo melanostictus, collected from fluoride-contaminated and -uncontaminated areas. The average haemoglobin content, total RBC count and haematocrit (%) in blood samples were found to be significantly reduced, while mean corpuscular concentration and volume were significantly elevated in individuals from the contaminated area in comparison to those from the uncontaminated area. Fluoride concentration was approximately 11 times greater in the bones of toads from the contaminated area.

Journal Article↗
PubMed1997

Electric field mapping and structure-activity relationship for cardiotonic activities of medorinone and some of its analogs.

Medorinone 5-methyl-1,6-napthyridin-2(1H)-one and some of its analogs having varying degrees of cardiotonic potency have been studied by molecular orbital and electric field mapping methods. Ground state geometries of the molecules were optimized using the MNDO molecular orbital method. Hybridization displacement charges (HDC) combined with Löwdin charges as well as Mulliken charges were used for electric field mapping around the molecules. Electric fields near the O2 site of medorinone and its analogs correlate well with their observed cardiotonic potencies. This result is in agreement with certain pharmacological models for cardiotonics.

Cardiotonic Agents↗
PubMed1996

Molecular electrostatic potential mapping and structure-activity relationship for 3-methoxy flavones.

Molecular electrostatic potential (MEP) maps of certain 3-methoxy flavone derivatives having different anti-picornavirus activities have been studied. Geometries of the molecules were optimised and charge distributions computed using the AM1 molecular orbital method. Hybridization displacement charges (HDC) were combined with the Löwdin charge distributions to compute the MEP maps. Reliability of the method of computing MEP maps was tested by studying certain other molecules for which ab initio MEP results are available. The anti-picornavirus activities of the flavones have been shown to be related with negative MEP values in two regions, one near the 3-methoxy group and another in a diagonally opposite region near the substituent attached to the C7 atom of the molecules.

Antiviral Agents↗