Ultrafast solvation dynamics in water: Isotope effects and comparison with experimental results

A detailed theoretical study of solvation dynamics in water is presented. The motivation of the present study comes from the recent experimental observation that the dynamics of solvation of an ion in water is ultrafast and the solvation time correlation function decays with a time constant of about 55 fs. The slower decay in the long time can be described by a sum of two exponentials with time constants equal to 126 and 880 fs. The molecular theory (developed earlier) predicts a time constant equal to 52 fs for the initial Gaussian decay and time constants equal to 134 and 886 fs for the two exponential components at the long time. This nearly perfect agreement is obtained by using the most detailed dynamical information available in the literature. The present study emphasizes the importance of the intermolecular vibrational band originating from the O...O stretching mode of the O�H...O units in the initial dynamics and raises several interesting questions regarding the nature of the decay of this mode. We have also studied the effects of isotope substitution on solvation dynamics. It is predicted that a significant isotope effect may be observed in the long time. The experimental results have also been compared with the prediction of the dynamic mean spherical approximation (DMSA); the agreement is not satisfactory at the long time. It is further found that the molecular theory and the DMSA lead to virtually identical results if the translational modes of the solvent molecules are neglected in the former. DMSA has also been used to investigate the dynamics of solvation of a dipolar solute in water. It is found that the dynamics of dipolar solvation exhibit features rather different from those of ion solvation. © 1995 American Institute of Physics.

Mutagenic significance of proton acidities in methylated guanine and thymine bases and deoxynucleosides: A theoretical study

Proton changes have been advanced as being the key molecular basis for the mutagenecity of alkylated DNA bases and nucleosides, leading to questions as to which protons are involved and whether the protic changes are tautomeric shifts or abstractions. This semiempirical molecular orbital study seeks to clarify the issue by examining the various possibilities open for these protic changes in a number of methylated guanines and thymines and their deoxynucleosides. Proton shifts leading to tautomer formation are not predicted as being thermodynamically favourable in most cases. The most feasible proton abstractions are predicted to involve the Watson-Crick protons in all cases, which corroborates Watson-Crick proton loss as providing the key molecular basis for the induction of point mutations. The calculated proton acidities correlate well with experimental data. The gas-phase deprotonation enthalpies for a number of alkylated nucleosides are found to correlate linearly with the solvent-phase pK(a) values. The theoretically calculated enthalpies in a simulated aqueous solvent phase of the deprotonation reactions of various nucleic acid bases are also found to have good linear correlations with experimental pK(a) values. The consensus of these calculations is that O-6-alkyldeoxyguanosines, and O-2- and O-4-alkyldeoxythymidines would be mutagenic while N-7-alkyldeoxyguanosines would not be mutagenic (as experiment indicates). The untested N-3-methyldeoxyguanosine is predicted to be mutagenic. (C) 1997 Elsevier Science B.V.

Prediction of separation factor in foam separation of proteins

A phenomenological model has been developed for predicting separation factors obtained in concentrating protein solutions using batch-foam columns. The model considers the adsorption of surface active proteins onto the air-water interface of bubbles, and drainage of liquid from the foam, which are the two predominant processes responsible for separation in foam columns. The model has been verified with data collected on casein and bovine serum albumin (BSA) solutions, for which adsorption isotherms are available in the literature. It has been found that an increase in liquid pool height above the gas distributor and the time allowed for drainage result in a better separation. Further, taller foam columns yield poorer separation at constant time of drainage. The model successfully predicts the observed results. (C) 1997 Elsevier Science Ltd.

Prediction of the senses of helical amphiphilic assemblies from effective intermolecular pair potential: Studies on chiral monolayers and bilayers

It is well-known that the senses (or the handedness) of the helical assemblies formed from compressed monolayers and bilayers of chiral amphiphiles are highly specific about the chirality of the monomers concerned. We present here a molecular approach that can successfully predict the senses of such helical morphologies. The present approach is based on a reduced tractable description in terms of an effective pair potential (EPP) which depends on the distance of separation and the relative orientations of the two amphiphiles. This approach explicitly considers the pairwise intermolecular interactions between the groups attached to the chiral centers of the two neighboring amphiphiles. It is found that for a pair of the same kind of enantiomers the minimum energy configuration favors a twist angle between molecules and that this twist from neighbor to neighbor gives rise to the helicity of the aggregate. From the known twist angles at the minimum energy configuration the successive arrangement of an array of molecules can be predicted. Therefore, the sense of the helicity can be predicted from the molecular interactions. The predicted senses of the helical structures are in complete agreement with all known experimental results.

The Tevatron Higgs exclusion limits and theoretical uncertainties: A critical appraisal

We examine the exclusion limits set by the CDF and D0 experiments on the Standard Model Higgs boson mass from their searches at the Tevatron in the light of large theoretical uncertainties on the signal and background cross sections. We show that when these uncertainties are consistently taken into account, the sensitivity of the experiments becomes significantly lower and the currently excluded mass range M-H = 158-175 GeV could be entirely reopened. The necessary luminosity required to recover the current sensitivity is found to be a factor of two higher than the present one. (C) 2011 Elsevier B.V. All rights reserved.

Theoretical analysis of x-ray-absorption near-edge fine structure at the O and metal K edges of LaFeO3 and LaCoO3

We present experimental x-ray-absorption spectra at the oxygen and 3d transition-metal K edges of LaFeO3 and LaCoO3. We interpret the experimental results in terms of detailed theoretical calculations based on multiple-scattering theory. Along with providing an understanding of the origin of various experimental features, we investigate the effects of structural distortions and the core-hole potential in determining the experimental spectral shape. The results indicate that the core-hole potential as well as many-body effects within the valence electrons do not have any strong effect on the spectra suggesting that the spectral features can be directly interpreted in terms of the electronic structure of such compounds.

Halogen Bonding in 2,5-Dichloro-1,4-benzoquinone: Insights from Experimental and Theoretical Charge Density Analysis

Experimental charge density distribution in 2, 5-dichloro-1, 4-benzoquinone has been carried out using high resolution X-ray diffraction data at 90 K to quantitatively evaluate the nature of C-Cl center dot center dot center dot O=C halogen bond in molecular crystals. Additionally, the halogen bond is studied from geometrical point of view and the same has been visualized using Hirshfeld surface analysis. The obtained results from experimental charge density analysis are compared with periodic quantum calculations using B3LYP 6-31G(d,p) level of theory. The topological values at bond critical point, three-dimensional static deformation density features and electrostatic potential isosurfaces unequivocally establish the attractive nature of C-Cl center dot center dot center dot O=C halogen bond in crystalline lattice.

[n]peristylanes and [n]oxa[n]peristylanes (n = 3-6): A theoretical study

Theoretical studies at the HF and Becke3LYP levels using 6-31G* basis sets were carried out on a series of [n]peristylanes and [n]oxa[n]peristylanes (n = 3-6) to understand their structure and energetics. The structures of the [3]- and [4]peristylanes (1, 2) and their era-derivatives (5, 6) were calculated to have the anticipated high symmetry, C-nv. In contrast, a C-s structure (9) at HF/6-31G* and another (25) at the Becke3LYP/6-31G* level were calculated for the [5]oxa[5]peristylane. The energy difference between them is extremely small even though there are major differences in the structures indicating every soft potential energy surface: On the other hand, the potential energy surface of [6]oxa[6]peristylane is not as soft. Similar structures were also calculated for the top rings. Calculations on the seco-compounds 11-14 and 15-19 (Table 4) indicate that there is no unusual strain involved in the formation of 27 from 19. The Li+ interaction energies of the [n]oxa[n]peristylanes are 61.7 (n = 3), 72.8 (n = 4), 84.2 (n = 5) and 91.7 (n = 6) kcal mol(-1) at the Becke3LYP/6-3IG* level. Dramatic differences between the C-C bond lengths obtained from the solid state X-ray diffraction studies and those from the calculations for the [n]oxa[n]peristylanes were also observed.

A game theoretical multiple resource interaction approach to resource allocation in an air campaign

In this paper we propose a multiple resource interaction model in a game-theoretical framework to solve resource allocation problems in theater level military campaigns. An air raid campaign using SEAD aircraft and bombers against an enemy target defended by air defense units is considered as the basic platform. Conditions for the existence of saddle point in pure strategies is proved and explicit feedback strategies are obtained for a simplified model with linear attrition function limited by resource availability. An illustrative example demonstrates the key features.

A study on determining the theoretical dispersion curve for Rayleigh wave propagation

A method has been presented to establish the theoretical dispersion curve for performing the inverse analysis for the Rayleigh wave propagation. The proposed formulation is similar to the one available in literature, and is based on the finite difference formulation of the governing partial differential equations of motion. The method is framed in such a way that it ultimately leads to an Eigen value problem for which the solution can be obtained quite easily with respect to unknown frequency. The maximum absolute value of the vertical displacement at the ground surface is formed as the basis for deciding the governing mode of propagation. With the proposed technique, the numerical solutions were generated for a variety of problems, comprising of a number of different layers, associated with both ground and pavements. The results are found to be generally satisfactory. (C) 2011 Elsevier Ltd. All rights reserved.

Quantum theoretical study of molecular mechanisms of mutation and cancer - A review

Several endogenous and exogenous chemical species, particularly the so-called reactive oxygen species (ROS) and reactive nitrogen oxide species (RNOS), attack deoxyribonucleic acid (DNA) in biological systems producing DNA lesions which hamper normal cell functioning and cause various diseases including mutation and cancer. The guanine (G) base of DNA among all the bases is most susceptible and certain modified guanines get involved in mispairing with other bases during DNA replication. The biological system repairs the abnormal base pairs, but those that are still left cause mutation and cancer. Anti-oxidants present in biological systems can scavenge the ROS and RNOS. Thus three types of molecular events occur in biological media: (i) DNA damage, (ii) DNA repair, and (iii) prevention of DNA damage by scavenging ROS and RNOS. Quantum mechanical methods may be used to unravel molecular mechanisms of such phenomena. Some recent quantum theoretical results obtained on these problems are reviewed here.

Multivariate nonlinear ensemble prediction of daily chaotic rainfall with climate inputs

The basic characteristic of a chaotic system is its sensitivity to the infinitesimal changes in its initial conditions. A limit to predictability in chaotic system arises mainly due to this sensitivity and also due to the ineffectiveness of the model to reveal the underlying dynamics of the system. In the present study, an attempt is made to quantify these uncertainties involved and thereby improve the predictability by adopting a multivariate nonlinear ensemble prediction. Daily rainfall data of Malaprabha basin, India for the period 1955-2000 is used for the study. It is found to exhibit a low dimensional chaotic nature with the dimension varying from 5 to 7. A multivariate phase space is generated, considering a climate data set of 16 variables. The chaotic nature of each of these variables is confirmed using false nearest neighbor method. The redundancy, if any, of this atmospheric data set is further removed by employing principal component analysis (PCA) method and thereby reducing it to eight principal components (PCs). This multivariate series (rainfall along with eight PCs) is found to exhibit a low dimensional chaotic nature with dimension 10. Nonlinear prediction employing local approximation method is done using univariate series (rainfall alone) and multivariate series for different combinations of embedding dimensions and delay times. The uncertainty in initial conditions is thus addressed by reconstructing the phase space using different combinations of parameters. The ensembles generated from multivariate predictions are found to be better than those from univariate predictions. The uncertainty in predictions is decreased or in other words predictability is increased by adopting multivariate nonlinear ensemble prediction. The restriction on predictability of a chaotic series can thus be altered by quantifying the uncertainty in the initial conditions and also by including other possible variables, which may influence the system. (C) 2011 Elsevier B.V. All rights reserved.

DNA Free Energy-Based Promoter Prediction and Comparative Analysis of Arabidopsis and Rice Genomes

The cis-regulatory regions on DNA serve as binding sites for proteins such as transcription factors and RNA polymerase. The combinatorial interaction of these proteins plays a crucial role in transcription initiation, which is an important point of control in the regulation of gene expression. We present here an analysis of the performance of an in silico method for predicting cis-regulatory regions in the plant genomes of Arabidopsis (Arabidopsis thaliana) and rice (Oryza sativa) on the basis of free energy of DNA melting. For protein-coding genes, we achieve recall and precision of 96% and 42% for Arabidopsis and 97% and 31% for rice, respectively. For noncoding RNA genes, the program gives recall and precision of 94% and 75% for Arabidopsis and 95% and 90% for rice, respectively. Moreover, 96% of the false-positive predictions were located in noncoding regions of primary transcripts, out of which 20% were found in the first intron alone, indicating possible regulatory roles. The predictions for orthologous genes from the two genomes showed a good correlation with respect to prediction scores and promoter organization. Comparison of our results with an existing program for promoter prediction in plant genomes indicates that our method shows improved prediction capability.