• Volume 119, Issue 5

September 2007,   pages  333-579

• Foreword

• Time-dependent quantum fluid density functional theory of hydrogen molecule under intense laser fields

A time-dependent generalized non-linear Schrödinger equation (GNLSE) of motion was earlier derived in our laboratory by combining density functional theory and quantum fluid dynamics in threedimensional space. In continuation of the work reported previously, the GNLSE is applied to provide additional knowledge on the femtosecond dynamics of the electron density in the hydrogen molecule interacting with high-intensity laser fields. For this purpose, the GNLSE is solved numerically for many time-steps over a total interaction time of 100 fs, by employing a finite-difference scheme. Various time-dependent (TD) quantities, namely, electron density, ground-state survival probability and dipole moment have been obtained for two laser wavelengths and four different intensities. The high-order harmonics generation (HHG) is also examined. The present approach goes beyond the linear response formalism and, in principle, calculates the TD electron density to all orders of change.

• Orientational dynamics and energy landscape features of thermotropic liquid crystals: An analogy with supercooled liquids

Recent optical kerr effect (OKE) studies have revealed that orientational relaxation of rodlike nematogens near the isotropic-nematic (I-N) phase boundary and also in the nematic phase exhibit temporal power law decay at intermediate times. Such behaviour has drawn an intriguing analogy with supercooled liquids. Here, we have investigated the single-particle and collective orientational dynamics of a family of model system of thermotropic liquid crystals using extensive computer simulations. Several remarkable features of glassy dynamics are on display including non-exponential relaxation, dynamical heterogeneity, and non-Arrhenius temperature dependence of the orientational relaxation time. Over a temperature range near the I-N phase boundary, the system behaves like a fragile glass-forming liquid. Using proper scaling, we construct the usual relaxation time versus inverse temperature plot and explicitly demonstrate that one can successfully define a density dependent fragility of liquid crystals. The fragility of liquid crystals shows a temperature and density dependence which is remarkably similar to the fragility of glass forming supercooled liquids. Energy landscape analysis of inherent structures shows that the breakdown of the Arrhenius temperature dependence of relaxation rate occurs at a temperature that marks the onset of the growth of the depth of the potential energy minima explored by the system.

• Retarded Boson-Fermion interaction in atomic systems

The retarded interaction between an electron and a spin-0 nucleus, that has been derived from electro-dynamical perturbation theory is discussed here. A brief account of the derivation is given. The retarded form is correct through order $v^2/c^2$. Use of the relative coordinates leads to an effective oneelectron operator that can be used through all orders of perturbation theory. A few unitary transformations give rise to the interaction that is valid in the non-relativistic limit.

• Quantum electron transfer processes induced by thermo-coherent state

When the reactant surface is not in a thermal equilibrium, but in a thermo-coherent state we have derived the rate and discussed about the quantum features of the rate. In the limit of very low and very high temperature the expressions are derived analytically and compared with the case of thermal distribution. We have investigated the dependence of temperature on the rate due to displacement, distortion of the harmonic potential energy surfaces of the reactant and product manifold.

• Filled and empty states of carbon nanotubes in water: Dependence on nanotube diameter, wall thickness and dispersion interactions

We have carried out a series of molecular dynamics simulations of water containing a narrow carbon nanotube as a solute to investigate the filling and emptying of the nanotube and also the modifications of the density and hydrogen bond distributions of water inside and also in the vicinity of the outer surfaces of the nanotube. Our primary goal is to look at the effects of varying nanotube diameter, wall thickness and also solute-solvent interactions on the solvent structure in the confined region also near the outer surfaces of the solute. The thickness of the walls is varied by considering single and multi-walled nanotubes and the interaction potential is varied by tuning the attractive strength of the 12-6 pair interaction potential between a carbon atom of the nanotubes and a water molecule. The calculations are done for many different values of the tuning parameter ranging from fully Lennard-Jones to pure repulsive pair interactions. It is found that both the solvation characteristics and hydrogen bond distributions can depend rather strongly on the strength of the attractive part of the solute-water interaction potential. The thickness of the nanotube wall, however, is found to have only minor effects on the density profiles, hydrogen bond network and the wetting characteristics. This indicates that the long range electrostatic interactions between water molecules inside and on the outer side of the nanotube do not make any significant contribution to the overall solvation structure of these hydrophobic solutes. The solvation characteristics are primarily determined by the balance between the loss of energy due to hydrogen bond network disruption, cavity repulsion potential and offset of the same by attractive component of the solute-water interactions. Our studies with different system sizes show that the essential features of wetting and dewetting characteristics of narrow nanotubes for different diameter and interaction potentials are also present in relatively smaller systems consisting of about five hundred molecules.

• Selective control of HOD photodissociation using CW lasers

Selective control of HOD photodissociation (H-O + D $\leftarrow$ HOD → H + O-D) has been theoretically investigated using CW lasers with appropriate carrier frequency and |0, 0$\rangle$, |0, 1$\rangle$ and |0, 2$\rangle$ with zero quantum of excitation in the O-H bond and zero, one and two quanta of excitation in the O-D bond as the initial states. Results indicate that the O-H bond in HOD can be selectively dissociated with a maximum flux of 87% in the H + O-D channel from the ground vibrational state |0, 0$\rangle$. For the O-D bond dissociation, it requires two quanta of excitation (|0, 2$\rangle$) in the O-D mode to obtain 83% flux in the H-O + D channel. Use of a two colour laser set-up in conjunction with the field optimized initial state (FOIST) scheme to obtain an optimal linear combination of |0, 0$\rangle$ and |0, 1$\rangle$ vibrational states as the initial state provides an additional 7% improvement to flux in the H-O + D channel as compared to that from the pure |0, 1$\rangle$ state.

• Calculation of vibrational excitation cross-sections in resonant electron-molecule scattering using the time-dependent wave packet (TDWP) approach with application to the ${}^2\Pi$ CO- shape resonance

Results from application of a new implementation of the time-dependent wave packet (TDWP) approach to the calculation of vibrational excitation cross-sections in resonant e-CO scattering are presented to examine its applicability in the treatment of e-molecule resonances. The results show that the SCF level local complex potential (LCP) in conjunction with the TDWP approach can reproduce experimental features quite satisfactorily.

• Non-ideality in Born-free energy of solvation in alcohol-water and dimethylsulfoxide-acetonitrile mixtures: Solvent size ratio and ion size dependence

Recent extension of mean spherical approximation (MSA) for electrolyte solution has been employed to investigate the non-ideality in Born-free energy of solvation of a rigid, mono-positive ion in binary dipolar mixtures of associating (ethanol-water) and non-associating (dimethylsulfoxide-acetonitrile) solvents. In addition to the dipole moments, the solvent size ratio and ion size have been treated in a consistent manner in this extended MSA theory for the first time. The solvent-solvent size ratio is found to play an important role in determining the non-ideality in these binary mixtures. Smaller ions such as Li+ and Na+ show stronger non-ideality in such mixtures compared to bigger ions (for example, Cs+ and Bu4N+). The partial solvent polarization densities around smaller ions in tertiary butanol (TBA)-water mixture is found to be very different from that in other alcohol-water mixtures as well as to that for larger ions in aqueous solutions of TBA. Non-ideality is weaker in mixtures consisting of solvent species possessing nearly equal diameters and dipole moments and is reflected in the mole fraction dependent partial solvent polarization densities.

• Reactive chemical dynamics through conical intersections

Reaction dynamics of prototypical, D + H2 and Cl (2P) + H2, chemical reactions occurring through the conical intersections of the respective coupled multi-sheeted potential energy surfaces is examined here. In addition to the electronic coupling, nonadiabatic effects due to relativistic spin-orbit coupling are also considered for the latter reaction. A time-dependent wave packet propagation approach is undertaken and the quantum dynamical observables viz., energy resolved reaction probabilities, integral reaction cross-sections and thermal rate constants are reported.

• Diabatic potential energy surfaces of H+ + CO

Ab initio adiabatic and diabatic surfaces of the ground and the first excited electronic states have been computed for the H+ + CO system for the collinear ($\gamma = 0^\circ$) and the perpendicular (γ = 90°) geometries employing the multi-reference configuration interaction method and Dunning's 𝑐𝑐-𝑝VTZ basis set. Other properties such as mixing angle before coupling potential and before coupling matrix elements have also been obtained in order to provide an understanding of the coupling dynamics of inelastic and charge transfer process.

• Effective Floquet Hamiltonian for spin 𝐼 = 1 in magic angle spinning NMR using contact transformation

Contact transformation is an operator transformation method in time-independent perturbation theory which is used successfully in molecular spectroscopy to obtain an effective Hamiltonian. Floquet theory is used to transform the periodic time-dependent Hamiltonian, to a time-independent Floquet Hamiltonian. In this article contact transformation method has been used to get the analytical representation of Floquet Hamiltonian for quadrupolar nuclei with spin 𝐼 = 1 in the presence of an RF field and first order quadrupolar interaction in magic angle spinning NMR experiments. The eigenvalues of contact transformed Hamiltonian as well as Floquet Hamiltonian have been calculated and a comparison is made between the eigenvalues obtained using the two Hamiltonians.

• Non-adiabatic collisions in H+ + O2 system: An 𝑎𝑏 initio study

An $ab$ initio study on the low-lying potential energy surfaces of H+ + O2 system for different orientations (𝛾) of H+ have been undertaken employing the multi-reference configuration interaction (MRCI) method and Dunning's $cc-p$VTZ basis set to examine their role in influencing the collision dynamics. Nonadiabatic interactions have been analysed for the $2 \times 2$ case in two dimensions for 𝛾 = 0°, 45° and 90°, and the corresponding diabatic potential energy surfaces have been obtained using the diabatic wavefunctions and their CI coefficients. The characteristics of the collision dynamics have been analysed in terms of vibrational coupling matrix elements for both inelastic and charge transfer processes in the restricted geometries. The strengths of coupling matrix elements reflect the vibrational excitation patterns observed in the state-to-state beam experiments.

• Quantum control of vibrational excitations in a heteronuclear diatomic molecule

Optimal control theory is applied to obtain infrared laser pulses for selective vibrational excitation in a heteronuclear diatomic molecule. The problem of finding the optimized field is phrased as a maximization of a cost functional which depends on the laser field. A time dependent Gaussian factor is introduced in the field prior to evaluation of the cost functional for better field shape. Conjugate gradient method$^{21,24}$ is used for optimization of constructed cost functional. At each instant of time, the optimal electric field is calculated and used for the subsequent quantum dynamics, within the dipole approximation. The results are obtained using both Morse potential as well as potential energy obtained using ab initio calculations.

• Controlling dynamics in diatomic systems

Controlling molecular energetics using laser pulses is exemplified for nuclear motion in two different diatomic systems. The problem of finding the optimized field for maximizing a desired quantum dynamical target is formulated using an iterative method. The method is applied for two diatomic systems, HF and OH. The power spectra of the fields and evolution of populations of different vibrational states during transitions are obtained.

• Integrated rate expression for the production of glucose equivalent in C4 green plant and the effect of temperature

A temperature-dependent integrated kinetics for the overall process of photosynthesis in green plants is discussed. The C4 plants are chosen and in these plants, the rate of photosynthesis does not depend on the partial pressure of O2. Using some basic concepts like chemical equilibrium or steady state approximation, a simplified scheme is developed for both light and dark reactions. The light reaction rate per reaction center ($R'_1$) in thylakoid membrane is related to the rate of exciton transfer between chlorophyll neighbours and an expression is formulated for the light reaction rate $R'_1$. A relation between $R'_1$ and the NADPH formation rate is established. The relation takes care of the survival probability of the membrane. The CO2 saturation probability in bundle sheath is also taken into consideration. The photochemical efficiency (𝜙) is expressed in terms of these probabilities. The rate of glucose production is given by $R_{\text{glucose}} = (8/3)(R'_1v_L)\phi(T)g(T)$ ([G3P]/[$P_i$]$^2_{\text{leaf}}$)$_{SS}$Q$_{\text{G3P} \rightarrow \text{glucose}}$ where 𝑔 is the activity quotient of the involved enzymes, and G3P represent glycealdehyde-3-phosphate in steady state. A Gaussian distribution for temperaturedependence and a sigmoid function for de-activation are incorporated through the quotient 𝑔. In general, the probabilities are given by sigmoid curves. The corresponding parameters can be easily determined. The theoretically determined temperature-dependence of photochemical efficiency and glucose production rate agree well with the experimental ones, thereby validating the formalism.

• Quantum chemical investigation of the reaction of O(${}^3P_2$) with certain hydrocarbon radicals

The reaction of ground-state atomic oxygen [O(${}^3P_2$)] with methyl, ethyl, 𝑛-propyl and isopropyl radicals has been studied using the density functional method and the complete basis set model. The energies of the reactants, products, reaction intermediates and various transition states as well as the reaction enthalpies have been computed. The possible product channels and the reaction pathways are identified in each case. In the case of methyl radical the minimum energy reaction pathway leads to the products CO + H2 + H. In the case of ethyl radical the most facile pathway leads to the products, methanal + CH3 radical. For propyl radical (𝑛- and iso-), the minimum energy reaction pathway would lead to the channel containing ethanal + methyl radical.

• Insertion of singlet chlorocarbenes across C-H bonds in alkanes: Evidence for two phase mechanism

Transition states for the insertion reactions of singlet mono and dichlorocarbenes (1CHCl and 1CCl2) into C-H bonds of alkanes (methane, ethane, propane and 𝑛-butane) have been investigated at MP2 and DFT levels with 6-31g (𝑑 , 𝑝) basis set. The $p_\pi$ of 1CHCl and 1CCl2 may interact with alkane’s filled fragment orbital of either 𝜎 or 𝜋 symmetry. So chlorocarbenes insertion reactions have been investigated for both (𝜎/𝜋) approaches. The 𝜎 approach has been adjudicated to be the minimum energy path over the 𝜋 approach both at the MP2 and DFT levels. Mulliken, NPA and ESP derived charge analyses have been carried out along the minimal energy reaction path using the IRC method for 1CHCl and 1CCl2 insertions into the primary and secondary C-H bonds of propane. The occurrence of TSs either in the electrophilic or nucleophilic phase has been identified through NBO charge analyses in addition to the net charge flow from alkane to the carbene moiety.

• An atom counting and electrophilicity based QSTR approach

Quantitative-structure-toxicity-relationship (QSTR) models are developed for predicting the toxicity (pIGC50) of 252 aliphatic compounds on Tetrahymena pyriformis. The single parameter models with a simple molecular descriptor, the number of atoms in the molecule, provide reasonable results. Better QSTR models with two parameters result when global electrophilicity is used as the second descriptor. In order to tackle both charge- and frontier-controlled reactions the importance of the local electro (nucleo) philicities and atomic charges is also analysed.

• Reactivity descriptors and electron density analysis for ligand chemistry: A case study of 2,2'-bipyridine and its analogues

In this paper, we study the reactivity of diimines like 2,2'-bipyridine and its analogues using reactivity descriptors. We discuss evaluation of local descriptors using relaxed as well as frozen approximation and characterize the 𝜎/𝜋 acceptance/donor characteristics of the above ligands. The intermolecular reactivity sequence for the same systems is examined by the global and local philicity index. In addition, electron density analysis has been carried out to highlight the possible strengths of interaction of the bipyridine and its analogues with metal ions.

• Theoretical investigation of redox species in condensed phase

We give a detailed description of the use of explicit as well as implicit solvation treatments to compute the reduction potentials of biomolecules in a medium. The explicit solvent method involves quantum mechanical/molecular mechanics (QM/MM) treatment of the solvated moiety followed by a Monte-Carlo (MC) simulation of the primary solvent layer. The QM task for considerably large biomolecules is normally carried out by density functional treatment (DFT) along with the MM-assisted evaluation of the most stable configuration for the primary layer and biomolecule complex. The MC simulation accounts for the dynamics of the associated solvent molecules. Contributions of the solvent molecules of the bulk towards the absolute free energy change of the reductive process are incorporated in terms of the Born energy of ion-dielectric interaction, the Onsager energy of dipole-dielectric interaction and the Debye-Hückel energy of ion-ionic cloud interaction. In the implicit solvent treatment, one employs the polarizable continuum model (PCM). Thus the contribution of all the solvent molecules towards the free energy change are incorporated by considering the whole solvent as a dielectric continuum.

As an example, the QM(DFT)/MM/MC-Born/Onsager/Debye-Hückel corrections yielded the oneelectron reduction potential of Pheophytin-a in the solvent DMF as $−0.92 \pm 0.27$ V and the two-electron reduction potential as $−1.34 \pm 0.25$ V at 298.15 K while the DFT-DPCM method yielded the corresponding values as $−1.03 \pm 0.17$ V and $−1.30 \pm 0.17$ V, respectively. The calculated values more or less agree with the observed mid-point potentials of −0.90 V and −1.25 V, respectively. Moreover, a numerical finite difference Poisson-Boltzmann solution along with the DFT-DPCM methodology was employed to calculate the reduction potential of Pheophytin-a within the thylakoid membrane. The calculated reduction potential value of −0.58 V is in agreement with the reported value of −0.61 V that appears in the socalled 𝑍-scheme and is considerably different from the value in vitro.

• Metal ion binding with dehydroannulenes - Plausible two-dimensional molecular sieves

Theoretical investigations have been carried out at B3LYP/6-311++G∗∗ level of theory to study the binding interaction of various metal ions, Li+, Na+ and K+ with dehydroannulene systems. The present study reveals that alkali metal ions bind strongly to dehydroannulenes and the passage through the central cavity is controlled by the size of metal ion and dimension of dehydroannulene cavity.

• Chiral discrimination in biomimetic systems: Phenylalanine

Chiral discrimination and recognition is important in peptide biosynthesis, amino acid synthesis and drug designing. Detailed structural information is available about the peptide synthesis in ribosome. However, no detailed study is available about the discrimination in peptide synthesis. We study the conformational energy variation of neutral methoxy phenyl alanine molecule as a function of its different dihedral angle to locate the minimum energy conformation using quantum chemical theory. We compared the intermolecular energy surfaces of phenyl alanine molecule in its neutral and zwitterionic state using quantum chemical theory as a function of distance and mutual orientation. The energy surfaces are studied with rigid geometry by varying the distance and orientation. The potential energy surfaces of 𝐿-𝐿 and 𝐷-𝐿 pairs are found to be dissimilar and reflect the underlying chirality of the homochiral pair and racemic nature of the heterochiral pair. The intermolecular energy surface of homochiral pair is more favourable than the corresponding energy surface of heterochiral pair.

• Base pairing in RNA structures: A computational analysis of structural aspects and interaction energies

The base pairing patterns in RNA structures are more versatile and completely different as compared to DNA. We present here results of ab-initio studies of structures and interaction energies of eight selected RNA base pairs reported in literature. Interaction energies, including BSSE correction, of hydrogen added crystal geometries of base pairs have been calculated at the HF/6-31G∗∗ level. The structures and interaction energies of the base pairs in the crystal geometry are compared with those obtained after optimization of the base pairs. We find that the base pairs become more planar on full optimization. No change in the hydrogen bonding pattern is seen. It is expected that the inclusion of appropriate considerations of many of these aspects of RNA base pairing would significantly improve the accuracy of RNA secondary structure prediction.

• Reaction mechanism of 𝑂-acylhydroxamate with cysteine proteases

The gas-phase reaction mechanism of 𝑂-acylhydroxamate with cysteine proteases has been investigated using ab initio and density functional theory. On the irreversible process, after breakdown of tetrahedral intermediate (INT1), small 1-2 anionotropic has been formed and rearranged to give stable by-products sulfenamide (P1) and thiocarbamate (P2) with considerable energy loss. While, on the reversible part of this reaction mechanism, intermediate (INT2) breaks down on oxidation, to form a stable product (P3). Topological and AIM analyses have been performed for hydrogen bonded complex in this reaction profile. Intrinsic reaction coordinates [IRC, minimum-energy path (MEP)] calculation connects the transition state between R-INT1, INT1-P1 and INT1-P2. The products P1, P2 and P3 are energetically more stable than the reactant and hence the reaction enthalpy is found to be exothermic.

• Effect of electrostatic interactions on the formation of proton transfer pathways in human carbonic anhydrase II

We report here a theoretical study on the effect of electrostatic interactions on the formation of dynamical, proton-conducting hydrogen-bonded networks in the protein HCA II. The conformational fluctuations of His-64 is found to contribute crucially to the mechanism of such path formation irrespective of the way electrostatic interactions are modelled.

• Docking of B-cell epitope antigen to specific hepatitis B antibody

The interaction of pres1 region of hepatitis B virus B-cell epitope antigen with specific hepatitis B neutralizing monoclonal antibody was examined by docking study. We modelled the 3D complex structure of B-cell epitope antigen residues CTTPAQGNSMFPSCCCTKPTDGNCY by homology modelling and docked it with the crystal structure of monoclonal antibody specific for the pres1 region of the hepatitis B virus. At the optimized docked conformation, the interactions between the amino acids of antigen and antibody were examined. It is found that the docked complex is stabilized by 59.3 kcal/mol. The stability of the docked antigen-antibody complex is due to hydrogen bonding and van der Waals interactions. The amino acids of the antigen and antibody responsible for the interaction were identified.

• On the analysis of the virulence nature of TIGR4 and R6 strains of Streptococcus pneumoniae using genome comparison tools

Comparative genome sequence analysis is a powerful technique for gaining insights into any genome of interest. Streptococcus pneumoniae is a human pathogen, which causes life-threatening diseases, such as pneumoniae, bacteremia, meningitis, etc. After the whole genome of two strains of S. pneumoniae, the virulent TIGR4 and non-pathogenic R6 were sequenced; there is a hope that comparing the genomes will allow an identification of the genes responsible for its virulence and thus the development of treatment and control. Many antimicrobial drugs have diminished the risk from pneumococcal disease because of its multi-drug resistance nature. Several pneumococcal proteins are also being investigated, as virulence factors as potential vaccine or drug targets. Structural and biochemical studies of these pneumococcal virulence factors have facilitated the development of novel antibiotics or protein antigen-based vaccines for the treatment of pneumococcal disease. Here we describe the comparison between the genomes of two strains of S. pneumoniae with few existing genomics databases and tools available in the public domain websites. By comparing nucleotide and protein sequences of the two strains, we investigate the existing differences and similarities. Mainly we focus on the virulence factors and its encoding genes in TIGR4 and how do they differ from R6 strain.

• Phenylalkylamines as calcium channel blockers

In this study we present ab initio Hartree Fock molecular orbital calculations with complete geometry optimizations on some phenylalkylamines (PAAs) that are clinically used as antiarrhythmic drugs. Pharmacophoric features of PAAs have been derived. An explanation of potency regulation in PAAs has been suggested based on ion capturing vs. ion holding by the drug. Ion capturing by the drug is always electrostatically highly favourable but has to be analysed in terms of conformational changes required and physiological accessibility of the situation. Our results also seem to offer an explanation for inhibitory effect of Ca2+ ion concentration on binding affinity of PAAs.

• In silico characterization of antifreeze proteins using computational tools and servers

In this paper, seventeen different fish Antifreeze Proteins (AFPs) retrieved from Swiss-Prot database are analysed and characterized using In silico tools. Primary structure analysis shows that most of the AFPs are hydrophobic in nature due to the high content of non-polar residues. The presence of 11 cysteines in the rainbow smelt fish and sea raven fish AFPs infer that these proteins may form disulphide (SS) bonds, which are regarded as a positive factor for stability. The aliphatic index computed by Ex-Pasy’s ProtParam infers that AFPs may be stable for a wide range of temperature. Secondary structure analysis shows that most of the fish AFPs have predominant α-helical structures and rest of the AFPs have mixed secondary structure. The very high coil structural content of rainbow smelt fish and sea raven fish AFPs are due to the rich content of more flexible glycine and hydrophobic proline amino acids. Proline has a special property of creating kinks in polypetide chains and disrupting ordered secondary structure. SOSUI server predicts one transmembrane region in winter flounder fish and atlantic cod and two transmembrane regions in yellowtail flounder fish AFP. The predicted transmembrane regions were visualized and analysed using helical wheel plots generated by EMBOSS pepwheel tool. The presence of disulphide (SS) bonds in the AFPs Q01758 and P05140 are predicted by CYS_REC tool and also identified from the three-dimensional structure using Rasmol tool. The disulphide bonds identified from the three-dimensional structure using the Rasmol tool might be correct as the evaluation parameters are within the acceptable limits for the modelled 3D structures.

• # Journal of Chemical Sciences

Volume 132, 2020
All articles
Continuous Article Publishing mode

• # Editorial Note on Continuous Article Publication

Posted on July 25, 2019