pp 11-12 January 2012 Structure, Reactivity and Dynamics
Susanta Mahapatra Sanjay Kumar
pp 13-19 January 2012 Structure, Reactivity and Dynamics
The quantum dynamics of intramolecular H-atom transfer in malonaldehyde is investigated with a model two-dimensional Hamiltonian constructed with the help of available ab initio theoretical data on the relevant portion of the potential energy surface. At zero temperature, the H-atom transfer takes place by tunnelling leading to cis-cis isomerization while the cis-trans channel remains closed. Local excitation of the cis-trans mode by an external field is predicted to quench cis-cis tunnelling isomerization while excitation of the cis-cis mode is found to enhance the isomerization by tunnelling.
pp 21-28 January 2012 Structure, Reactivity and Dynamics
Shape change as entropic phase transition: A study using Jarzynski relation
Moupriya Das Debasish Mondal Deb Shankar Ray
A Brownian particle in a confined space with varying cross-section, experiences an effective entropic potential in reduced dimension. We modulate the shape of the confinement and examine the nature of dynamical transition between two distinct thermalized entropic states corresponding to different shapes of the enclosure, using Jarzynski relation on the basis of work-distribution over non-equilibrium paths. Our analysis reveals that modulating the shape of the boundaries of the enclosure makes the resident Brownian particles feel an entropic phase transition.
pp 29-34 January 2012 Structure, Reactivity and Dynamics
Fitness landscapes in natural rocks system evolution: A conceptual DFT treatment
Soma Duley Jean-Louis Vigneresse Pratim Kumar Chattaraj
The chemical reactivity descriptors, such as electronegativity, hardness and electrophilicity of major oxides computed from density functional theory are reported in this paper. These parameters are plotted within a fitness landscape diagram, showing that the principles of minimum electrophilicity (MEP) and maximum hardness (MHP) act as guides towards the region of higher stability. The diagrams indicate the trends and the parameters that control the evolution of natural rocks. Application of the principle S-bearing copper compounds shows the possible and preferred combinations of elements, that give rise to compounds observed during ore formation.
pp 35-42 January 2012 Structure, Reactivity and Dynamics
A Subha Mahadevi Y Indra Neela G Narahari Sastry
Application of quantum chemical calculations is vital in understanding hydrogen bonding observed in formamide clusters, a prototype model for motifs found in protein secondary structure. DFT calculations have been performed on four arrangements of formamide clusters [HCONH_{2}]$_n$, ($n = 1 − 10$) linear, circular, helical and stacked forms. These studies reveal the maximum cooperativity in the stacked arrangement followed by the circular, helical and linear arrangements and is based on interaction energy per monomer. In all these arrangements as we increase cluster size, an increasing trend in cooperativity of hydrogen bonding is observed. Atoms-in-molecule analysis establishes the nature of bonding between the formamide monomers on the basis of electron density values obtained at the bond critical point (BCP).
pp 43-50 January 2012 Structure, Reactivity and Dynamics
By employing an intense microwave laser of wavelength 116.65 𝜇m with intensities $1 \times 10^{13}$ and $5 \times 10^{18}$Wcm^{−2}, respectively, the conclusion is reached theoretically and computationally that it is possible to dissociate the CO molecule, modelled as a Morse oscillator. It is predicted that for above-threshold dissociation (ATD), the molecule should absorb 1044 photons of the given wavelength in order to reach the lowest edge of the vibrational continuum. A consistent analysis of the predicted dissociation process is provided though the time-dependent probability density, dissociation probability, norm, potential function, HHG and ATD spectra, obtained by numerically solving the time-dependent vibrational Schödinger equation.
pp 51-58 January 2012 Structure, Reactivity and Dynamics
Subhankar Sardar Satrajit Adhikari
We have performed a nuclear dynamics simulation to calculate photoelectron spectra and population profiles of benzene radical cation (C_{6}H$^+_6$) employing the parallelized Time Dependent Discrete Variable Representation (TDDVR) approach. For this purpose, we have considered two multi-state multi-mode model Hamiltonians of C_{6}H$^+_6$ with degeneracy among the electronic states: (a) One consists of three states and eight modes, which in turn leads to a five state thirteen mode Hamiltonian ($X^2$E$_{1g}$-$B^2$E$_{2g}$-$C^2$A$_{2u}$) due to the degeneracy; and (b) The other is constituted of three states and thirteen modes which is basically a five state twenty mode Hamiltonian ($B^2$E$_{2g}$-$D^2$E$_{1u}$-$E^2$B$_{2u}$) for the same reason. Since these electronic states are interconnected by several conical intersections in the vicinity of the Franck Condon region, it will be challenging to pursue such large dynamical calculation in the presence of nonadiabaticity among the electronic states. The spectral as well as population profiles calculated with the advent of TDDVR approach show reasonably good agreement with the results obtained by the Multi Configuration Time Dependent Hartree (MCTDH) methodology.
pp 59-63 January 2012 Structure, Reactivity and Dynamics
Understanding proton affinity of tyrosine sidechain in hydrophobic confinement
T G Abi T Karmakar S Taraphder
Tyrosine is an important amino acid residue that plays a key role in several biochemical transformations such as, abstraction/donation of proton from/by its sidechain. We present here a density functional study on the proton affinity of tyrosine sidechain suspended inside the core of a single walled carbon nanotube that mimics the environment of protein structural pores and molecular channels. Tyrosine is found to exhibit a lower reactivity on confinement and unlike several other polar amino acid sidechains, its reactivity does not respond to hydrogen bonding with neighbouring hydroxyl groups.
pp 65-73 January 2012 Structure, Reactivity and Dynamics
Full dimensional quantum scattering study of the H_{2} + CN reaction
S Bhattacharya A Kirwai Aditya N Panda H-D Meyer
Exact wave packet calculations are carried out to investigate the effect of vibrational excitation of the reagent bonds on the dynamics of the CN + H_{2} → HCN + H process using the multiconfiguration time-dependent Hartree algorithm. The results are compared to the approximate theoretical and the available experimental results. The differences between the results of the theoretical studies are discussed from the point of view of an approximate or exact kinetic energy operator used in the quantum mechanical studies. Deviations between exact theoretical and experimental results points to the inaccuracies of the potential energy surface used.
pp 75-81 January 2012 Structure, Reactivity and Dynamics
Dynamics of atomic clusters in intense optical fields of ultrashort duration
Intense laser pulses have been generated that last for only 10 fs, long enough to accommodate only 3 optical cycles of 800 nm light. Upon focussing such pulses, intensities in the 10^{15} W cm^{−2} range are readily generated. At such intensities, the magnitude of the optical field begins to match intra-atomic Coulombic fields. Consequently, exposure of atoms and molecules to such intense pulses inevitably leads to single and multiple ionization. We report here results of experiments that we have conducted that involve irradiation of gas-phase Ar15,000 clusters by such intense, few-cycle laser pulses. The clusters become multiply ionized and undergo Coulomb explosion, giving rise to ejection of fast Ar-ions. Results show that the strong-field dynamics in the few-cycle domain differ significantly from those that occur in the longer pulse (> 30 fs) regime. Manifestations of these differences are presented in the form of angle-dependent ion energy and ion yield functions.
pp 83-91 January 2012 Structure, Reactivity and Dynamics
B Jayaram Priyanka Dhingra Bharat Lakhani Shashank Shekhar
Protein folding, considered to be the holy grail of molecular biology, remains intractable even after six decades since the report of the first crystal structure. Over 70,000 X-ray and NMR structures are now available in protein structural repositories and no physico-chemical solution is in sight. Molecular simulation methodologies have evolved to a stage to provide a computational solution to the tertiary structures of small proteins. Knowledge base driven methodologies are maturing in predicting the tertiary structures of query sequences which share high similarities with sequences of known structures in the databases. The void region thus seems to be medium (> 100 amino acid residues) to large proteins with no sequence homologs in the databases and hence which has become a fertile ground for the genesis of hybrid models which exploit local similarities together with ab initio models to arrive at reasonable predictions.We describe here the development of Bhageerath an ab initio model and Bhageerath-H a hybrid model and present a critique on the current status of prediction of protein tertiary structures.
pp 93-97 January 2012 Structure, Reactivity and Dynamics
Domenico Caruso Mario Tacconi Franco A Gianturco Ersin Yurtsever
Quantum dynamics of superelastic collisions involving vibrational levels of MgH^{+}(X^{1}$\sum^+$) ions in cold traps, interacting with ^{4}He(^{1}S) as a buffer gas at relative temperatures down to millikelvins, is discussed using an ab initio computed potential energy surface. The relative efficiency of collisional cooling with respect to collisional quenching of the internal vibrations is examined from the results of the relative sizes of the relevant cross sections in relation to predicting actual behaviour in cold traps. The present study indicates the feasibility of cooling vibrationally `hot’, trapped ions with the buffer gas.
pp 99-104 January 2012 Structure, Reactivity and Dynamics
Sitansh Sharma Gabriel G Balint-Kurti Harjinder Singh
Optimal control theory in combination with time-dependent quantum dynamics is employed to design laser pulses which can perform selective vibrational and rotational excitations in a heteronuclear diatomic system. We have applied the conjugate gradient method for the constrained optimization of a suitably designed functional incorporating the desired objectives and constraints. Laser pulses designed for several excitation processes of the $HF$ molecule were able to achieve predefined dynamical goals with almost 100% yield.
pp 105-113 January 2012 Structure, Reactivity and Dynamics
M Vinothkumar G Nandhini M V Sangaranarayanan
The partition function for two-dimensional nearest neighbour Ising model in a non-zero magnetic field have been derived for a finite square lattice of 16, 25, 36 and 64 sites with the help of
pp 115-120 January 2012 Structure, Reactivity and Dynamics
An extended Longuet-Higgins formalism recently utilized to obtain generalized Born-Oppenheimer equations including the geometrical phase effect has been used to study a three-fold pseudo-Jahn-Teller type electronic degeneracy. The results of dynamics calculations carried out with the novel formalism are compared with Born-Oppenheimer (geometrical phase ignored), extended Born-Oppenheimer, and coupled three-state ones for the same system. The theory shows unprecedented simplicity while depicting all features.
pp 121-129 January 2012 Structure, Reactivity and Dynamics
Optimal control of the initiation of a pericyclic reaction in the electronic ground state
Pericyclic reactions in the electronic ground state may be initiated by down-chirped pump-dump sub-pulses of an optimal laser pulse, in the ultraviolet (UV) frequency and sub-10 femtosecond (fs) time domain. This is demonstrated by means of a quantum dynamics model simulation of the Cope rearrangement of Semibullvalene. The laser pulse is designed by means of optimal control theory, with detailed analysis of the mechanism. The theoretical results support the recent experimental initiation of a pericyclic reaction. The present approach provides an important step towards monitoring asynchronous electronic fluxes during synchronous nuclear pericyclic reaction dynamics, with femto-to-attosecond time resolution, as motivated by the recent prediction of our group.
pp 131-139 January 2012 Structure, Reactivity and Dynamics
Montu K Hazra Moitrayee Mukherjee V Ramanathan Tapas Chakraborty
Laser-induced fluorescence spectra of a 2:1 complex between 7-azaindole and water, known as `non-reactive dimer’ of the molecule, have been measured in a supersonic jet expansion. The dispersed fluorescence spectrum of the electronic origin band of the complex shows a very large number of low-frequency vibrational features corresponding to different intermolecular modes of the complex in the ground electronic state. Geometries of several possible isomeric structures of the complex and their vibrational frequencies at harmonic approximation were calculated by electronic structure theory method at MP2/6-31G^{∗∗} level. An excellent agreement is observed between the measured and calculated intermolecular vibrational mode frequencies for the energetically most favoured structure of the complex, where the water molecule is inserted within one of the two N$\cdots$H-N hydrogen bonds of the 7AI dimer.
pp 141-148 January 2012 Structure, Reactivity and Dynamics
Bhavesh K Shandilya Manabendra Sarma Satrajit Adhikari Manoj K Mishra
Vibrational excitation cross-sections $\sigma_{v_f \leftarrow v_i}$(𝐸) in resonant e-F_{2} and HCl scattering are calculated from transition matrix elements $T_{v_f \leftarrow v_i}$(𝐸) obtained using Fourier transform of the cross correlation function $\langle \phi_{v_f} (R) | \Phi_{v_i} (R, t) \rangle$. where $\Psi_{v_i} (R,t) \approx e^{i \hbar H_{AB^-}(R)t} \phi_{v_i} (R)$. Time evolution under the influence of the resonance anionic Hamiltonian H$_{AB^-}$ (AB=F_{2}/HCl) is effected using Lanczos reduction technique followed by fast Fourier transform and the target (AB) vibrational eigenfunctions $\phi_{ν_i}$ (𝑅) and $\phi_{v_f}$ (𝑅) are calculated using Fourier grid Hamiltonian method applied to potential energy (PE) curve of the neutral target. The resulting vibrational excitation cross-sections provide reasonable agreement with experimental and other theoretical results.
pp 149-158 January 2012 Structure, Reactivity and Dynamics
Tailoring approach for obtaining molecular orbitals of large systems
Anuja P Rahalkar Shridhar R Gadre
Molecular orbitals (MO’s) within Hartree-Fock (HF) theory are of vital importance as they provide preliminary information of bonding and features such as electron localization and chemical reactivity. The contemporary literature treats the Kohn-Sham orbitals within density functional theory (DFT) equivalently to the MO's obtained within HF framework. The high scaling order of ab initio methods is the main hurdle in obtaining the MO's for large molecular systems. With this view, an attempt is made in the present work to employ molecular tailoring approach (MTA) for obtaining the complete set of MO's including occupied and virtual orbitals, for large molecules at HF and B3LYP levels of theory. The energies of highest occupied and lowest unoccupied molecular orbitals, and hence the band gaps, are accurately estimated by MTA for most of the test cases benchmarked in this study, which include 𝜋-conjugated molecules. Typically, the root mean square errors of valence MO's are in range of 0.001 to 0.010 a.u. for all the test cases examined. MTA shows a time advantage factor of 2 to 3 over the corresponding actual calculation, for many of the systems reported.
pp 159-166 January 2012 Structure, Reactivity and Dynamics
Srinivasa R Varanasi S Yashonath
A molecular dynamics study of the dependence of diffusivity of the cation on ionic radii in molten AgI is reported.We have employed modified Parinello-Rahman-Vashistha interionic pair potential proposed by Shimojo and Kobayashi. Our results suggest that the diffusivity of the cation exhibits an increase followed by a decrease as the ionic radius is increased. Several structural and dynamical properties are reported.
pp 167-176 January 2012 Structure, Reactivity and Dynamics
Dhurairajan Senthilnathan Rajadurai Vijay Solomon Ponnambalam Venuvanalingam
Imidozirconocene complex is known for its bifunctional reactivity and catalytic ability and this complex mediates ring cleavage of epoxides. Cyclooctene oxide (1) Norbornene oxide (2) and 2,5-dimethyl cyclohexene oxide (3) undergo ring cleavage in the presence of imidozirconocene complex. Epoxide 1 has accessible 𝛽-hydrogens (type I) while epoxide 2 and 3 do not have them (type II). Normally type I epoxides undergo elimination while type II epoxides prefer insertion. All the insertion reactions lead to five-membered metallacycle formation and elimination results in thermodynamically stable allyl-alkoxy product. The insertion is a two-step process following either diradical or zwitterionic pathway, while elimination is a one-step concerted reaction. DFT (density functional theory) modelling of these reactions at B3LYP/LANL2DZ level show that epoxide 1 undergoes elimination in agreement with experiment. However, calculations indicate that epoxide (2) proceeds through diradical intermediate in contrast to experimental observations. Surprisingly, epoxide (3) that has both the 𝛽 positions blocked by methyl groups undergoes elimination rather than insertion. AIM and EDA analyses offer further insights on the reaction mechanism and bifunctional reactivity of imidozirconozene complex.
pp 177-186 January 2012 Structure, Reactivity and Dynamics
Basic principles of ultrafast Raman loss spectroscopy
N K Rai A Y Lakshmanna V V Namboodiri S Umapathy
When a light beam passes through any medium, the effects of interaction of light with the material depend on the field intensity. At low light intensities the response of materials remain linear to the amplitude of the applied electromagnetic field. But for sufficiently high intensities, the optical properties of materials are no longer linear to the amplitude of applied electromagnetic field. In such cases, the interaction of light waves with matter can result in the generation of new frequencies due to nonlinear processes such as higher harmonic generation and mixing of incident fields. One such nonlinear process, namely, the third order nonlinear spectroscopy has become a popular tool to study molecular structure. Thus, the spectroscopy based on the third order optical nonlinearity called stimulated Raman spectroscopy (SRS) is a tool to extract the structural and dynamical information about a molecular system. Ultrafast Raman loss spectroscopy (URLS) is analogous to SRS but is more sensitive than SRS. In this paper, we present the theoretical basis of SRS (URLS) techniques which have been developed in our laboratory.
pp 187-192 January 2012 Structure, Reactivity and Dynamics
Hydrogenoid orbitals revisited: From Slater orbitals to Coulomb Sturmians
Danilo Calderini Simonetta Cavalli Cecilia Coletti Gaia Grossi Vincenzo Qquilanti
The simple connection between the Slater orbitals, venerable in quantum chemistry, and the Coulomb Sturmian orbitals, more recently employed in atomic and molecular physics, is pointed out explicitly in view of the renewed interest in both as basis sets in applied quantum mechanics. Research in Slater orbitals mainly concerns multicentre, many-body integrals, whereas that on Sturmians exploits their orthonormality and completeness with no need of continuum states. An account of recent progress is outlined, also with reference to relationships between the two basis sets, and with the momentum space and hyperspherical harmonics representations.
pp 193-202 January 2012 Structure, Reactivity and Dynamics
The role of C-H$\ldots \pi$ interaction in the stabilization of benzene and adamantane clusters
R Mahesh Kumar M Elango R Parthasarathi Dolly Vijay V Subramanian
In this investigation, a systematic attempt has been made to understand the interaction between adamantane and benzene using both ab initio and density functional theory methods. C-H$\ldots \pi$ type of interaction between C-H groups of adamantane and 𝜋 cloud of benzene is found as the important attraction for complex formation. The study also reveals that the methylene (-CH_{2}) and methine (-CH) groups of adamantane interact with benzene resulting in different geometrical structures. And it is found that the former complex is stronger than the later. The diamondoid structure of adamantane enables it to interact with a maximum of four benzene molecules, each one along the four faces. The stability of the complex increases with increase in the number of benzene molecules. The energy decomposition analysis of adamantane-benzene complexes using DMA approach shows that the origin of the stability primarily arises from the dispersive interaction. The theory of atoms in molecules (AIM) supports the existence of weak interaction between the two systems. The electrostatic topography features provide clues for the mode of interaction of adamantane with benzene.
pp 203-207 January 2012 Structure, Reactivity and Dynamics
Density functional studies of endosulphan and its interaction with glycine and GABA
C N Ramachandran Brijesh Kumar Mishra Ashwani Kumar Tiwari
Density functional theoretic (DFT) methods are employed to study the interactions between endosulphan and two amino acids, namely glycine and 𝛾 -aminobutyric acid (GABA). Two conformers of each isomer 𝛼- and 𝛽-endosulphan are considered in the study. The DFT methods B3LYP, M05, M05-2X, M06 and M06-2X in conjunction with the basis set 6-31++G^{∗∗} are used. The complexes of 𝛼- and 𝛽-endosulphan with amino acids are stabilized by a strong hydrogen bond. In addition, there are several weak C-H…O interactions present between the two moieties. Among the DFT methods used, M06-2X method shows the highest stabilization energy for all the complexes. The M06-2X/6-31++G^{∗∗} method predicts that among the four conformers of endosulphan, the 𝛼 conformer in which the S=O points up, forms the most stable complex with both glycine and GABA, with stabilization energies −15.24 kcal/mol and −14.39 kcal/mol, respectively. The 𝛽 conformer in which the S=O points down, forms the least stable complex with both amino acids with stabilization energies −7.14 and −7.85 kcal/mol, respectively.
pp 209-214 January 2012 Structure, Reactivity and Dynamics
Variation of kinetic isotope effect in multiple proton transfer reactions
Recently, we had suggested that the motion along the promoter mode in the first part of the IRC of proton transfer reaction enhances the delocalization of $n_\sigma$ electrons on the acceptor atom into the $\sigma^\ast$ orbital of the donor-hydrogen covalent bond, and as a consequence weakens it. This leads to a reduction of the barrier to the proton transfer as well as the stretching frequency of donor-hydrogen bond. An extension of this to the concerted multiple proton transfer reactions implies that the kinetic isotope effect in such reaction depends exponentially on the number of protons that are being transferred. Computational evidence on three systems, (HF)_{3}, formic acid dimer, and (H_{2}O)$_n$ clusters is provided to support this assertion.
pp 215-221 January 2012 Structure, Reactivity and Dynamics
Bhabani S Mallik Amalendu Chandra
We present an ab initio molecular dynamics study of vibrational spectral diffusion and hydrogen bond dynamics in aqueous solution of acetone at room temperature. It is found that the frequencies of OD bonds in the acetone hydration shell have a higher stretch frequency than those in the bulk water. Also, on average, the frequencies of hydration shell OD modes are found to increase with increase in the acetone-water hydrogen bond distance. The vibrational spectral diffusion of the hydration shell water molecules reveals three time scales: A short-time relaxation (∼80 fs) corresponding to the dynamics of intact acetone-water hydrogen bonds, a slower relaxation (∼1.3 ps) corresponding to the lifetime of acetone-water hydrogen bonds and another longer time constant (∼12 ps) corresponding to the escape dynamics of water from the solute hydration shell. The present first principles results are compared with those of available experiments and classical simulations.
pp 223-232 January 2012 Structure, Reactivity and Dynamics
Lalitha Ravichandran Debarati Bhattacharya Nayana Vaval Sourav Pal
Dipole moment calculations of SF and ClO radicals have been carried out using the recently developed partial triples correction to Fock-space multi-reference coupled cluster method. Theoretical calculation of the doublet SF and ClO radicals is useful due to their importance in atmospheric chemistry. The dipole moments of these radicals are extremely sensitive to correlation effects. A brief insight to the way the triples correction has been implemented is presented. We compare the results obtained from our analytic response treatment with that of restricted open Hartree-Fock (ROHF) calculations. Results are presented for both relaxed and non-relaxed approach in the ROHF method. Results suggest the importance of triples corrections. The effects of orbital relaxation are also analysed from the results.
pp 233-240 January 2012 Structure, Reactivity and Dynamics
Excitation energy transfer from dye molecules to doped graphene
Recently, we have reported theoretical studies on the rate of energy transfer from an electronically excited molecule to graphene. It was found that graphene is a very efficient quencher of the electronically excited states and that the rate $\alpha z^{−4}$. The process was found to be effective up to 30 $nm$ which is well beyond the traditional FRET limit. In this report, we study the transfer of an amount of energy $\hbar \Omega$ from a dye molecule to doped graphene. We find a crossover of the distance dependence of the rate from $z^{−4}$ to exponential as the Fermi level is increasingly shifted into the conduction band, with the crossover occurring at a shift of the Fermi level by an amount $\hbar \Omega/2$.
pp 241-245 January 2012 Structure, Reactivity and Dynamics
Using dimensional analyses, the scaling properties of the Heisenberg uncertainty relationship as well as the various information theoretical uncertainty-like relationships are derived for the bound states corresponding to the superposition of the power potential of the form $V(r) = Zr^n + \sum_i Z_ir^{n_i}$, where 𝑍, $Zi$, 𝑛, $n_i$ are parameters, in the free state as well as in the additional presence of a spherical penetrable boundary wall located at radius 𝑅 The uncertainty product and all other net information measures are shown here to depend only on the parameters [$s_i$] defined by the ratios $Z_i/Z^{(n_i+2)/(n+2)}$. Introduction of a finite potential, $V_c$ at the radial distance $r ≥ R$ results in a complete set of scaling parameters given by [$s_i$, $t_1$, $t_2$], where $t_1$ is given by $RZ^{1/(n+2)}$ and $t_2 = V_c/(Z)^{2/(n+2)}$.
pp 247-253 January 2012 Structure, Reactivity and Dynamics
Quantum dynamical study of low-energy photoelectron bands of 2-phenylethyl-$N,N$-dimethylamine
Susana Gómez-Carrasco Horst Köppel
The first three photoelectron bands of 2-phenylethyl-$N,N$-dimethylamine (PENNA) are investigated theoretically, paying particular attention to the vibrational structure and to possible nonadiabatic coupling effects. A substantial vibronic interaction is established between the first and second excited cationic states (corresponding to the second and third photoelectron bands). Their coupling to the cationic ground state is found to be rather weak. This is tentatively attributed to the well-known fact that the latter carries a hole at the amine site, while the former two have the electron removed from benzene-type orbitals. The interaction between the two excited cationic states is characterized by a `hidden’ or local symmetry at the phenyl moiety. Preliminary dynamic calculations with two interacting electronic states and four vibrational modes are reported. The computed spectra are compared to experimental results of Weinkauf et al.
pp 255-260 January 2012 Structure, Reactivity and Dynamics
Computational investigation of hydrogen adsorption in silicon-lithium binary clusters
Naresh K Jena K Srinivasu Swapan K Ghosh
Theoretical studies on hydrogen adsorption properties of silicon-lithium binary clusters are carried out. We have considered three different clusters viz., Si_{5}Li$^{−5}$, Si_{5}Li^{6} and Si_{5}Li$^+_7$ and for each cluster, the geometries of different possible isomers are optimized. In all the minimum energy isomers of the three clusters considered, two of the lithium atoms are found to be situated in the axial positions and the remaining lithium atoms are in the equatorial position in the Si_{5} plane. The lithium atoms which are in Si_{5} plane are bonded to the Si-Si edge through a bridged bond instead of a corner in the Si5 ring. From the calculated atomic charges, it is found that there is a charge transfer from lithium to silicon leaving a partial positive charge on the Li atoms and the axial lithium atoms are more charged as compared to the remaining lithium atoms. In the case of Si_{5}Li_{6} and Si_{5}Li$^+_7$, the Li sites can trap a total of 14 and 17 H_{2} molecules, respectively, with each bridge bonded Li site adsorbing three H_{2} molecules and each axial Li adsorbing one H_{2} molecule which corresponds to a gravimetric density of 13.33 wt% and 15.25 wt%, respectively.
pp 261-269 January 2012 Structure, Reactivity and Dynamics
B Shadrack Jabes Manish Agarwal Charusita Chakravarty
Molecular dynamics simulations are performed to study the structure and dynamics of the LiF-BeF_{2} system over a range of compositions using the transferable rigid-ion model (TRIM). The densities obtained with the TRIM potential are approximately 17-20% lower than the experimental values while polarizable ion models (PIM) give densities within 5% of the experimental value. The TRIM and PIM potentials give essentially identical radial distribution functions (RDFs) for Li-F and Be-F ion pairs though the Be-Be pair correlations differ significantly and reflect the corresponding density differences. The variation in the radial distribution functions with concentration, particularly the anion-anion pair correlation function, reflects the reorganization of the fluoride ions as the addition of BeF_{2} in the mixture promotes the formation of the tetrahedral fluoroberyllate network. Along the 67 mol% LiF isopleth, diffusivities and Nernst-Einstein ionic conductivities from simulations using the PIM and TRIM potentials are in good agreement for temperatures up to 925 K. The viscosity data using the PIM model is also found to be in good agreement with the TRIM results presented here along the 873K isotherm for compositions ranging from 0 to 50 mol% BeF_{2}. The main conclusion from this study is that the non-polarizable, TRIM provides reasonable results for the structural correlations and transport properties of the LiF-BeF_{2} system in comparison with first-principles-based, PIM.
pp 271-279 January 2012 Structure, Reactivity and Dynamics
N Bhargava Ram Vaibhav S Prabhudesai E Krishnakumar
The dynamics of the formation and decay of negative ion resonance of A_{1} symmetry at 8.5 eV electron energy in the dissociative electron attachment (DEA) process in H_{2}O and D_{2}O are investigated using the velocity slice imaging technique. While the highest energy hydride ions formed by DEA show angular distributions characteristic to the A_{1} symmetry, those formed with low-kinetic energy show considerably different angular distributions indicating changes in the orientation of the dissociating bond due to bending mode vibrations. Our observations are quite different from the recently reported measurements, but consistent with the fully quantum calculations.
pp 281-289 January 2012 Structure, Reactivity and Dynamics
Exploring control parameters of two photon processes in solutions
Two-photon microscopy depends extensively on the two-photon absorption cross-sections of biologically relevant chromophores. High repetition rate (HRR) lasers are essential in multiphoton microscopy for generating satisfactory signal to noise at low average powers. However, HRR lasers generate thermal distortions in samples even with the slightest single photon absorption. We use an optical chopper with HRR lasers to intermittently `blank’ irradiation and effectively minimize thermal effects to result in a femtosecond z-scan setup that precisely measures the two-photon absorption (TPA) cross-sections of chromophores. Though several experimental factors impact such TPA measurements, a systematic effort to modulate and influence TPA characteristics is yet to evolve. Here, we present the effect of several control parameters on the TPA process that are independent of chromophore characteristics for femtosecond laser pulse based measurements; and demonstrate how the femtosecond laser pulse repetition rate, chromophore environment and incident laser polarization can become effective control parameters for such nonlinear optical properties.
pp 291-300 January 2012 Structure, Reactivity and Dynamics
On the nature of highly vibrationally excited states of thiophosgene
In this work an analysis of the highly vibrationally excited states of thiophosgene (SCCl_{2}) is made in order to gain insights into some of the experimental observations and spectral features. The states analysed here lie in a spectrally complex region where strong mode mixings are expected due to the overlap of several strong anharmonic Fermi resonances. Two recent techniques, a semiclassical angle space representation of the eigenstates and the parametric variation of the eigenvalues (level-velocities) are used to identify eigenstate sequences exhibiting common localization characteristics. Preliminary results on the influence of highly excited out-of-plane bending modes on the nature of the eigenstates suggest a possible bifurcation in the system.
pp 301-310 January 2012 Structure, Reactivity and Dynamics
Avinash L Puyad Ch Ramesh Kumar K Bhanuprakash
The adsorption of model croconate dyes on the stoichiometric TiO_{2} anatase (101) surface has been studied by means of periodic density functional calculations to understand the adsorption of the diketo (-COCO-) groups. Past experimental and theoretical results have shown the strong binding ability of the acid group (-COOH) to the TiO_{2} surface but here the theoretical studies predicts the binding strength of the diketo group to be also significant and comparable with that of the -COOH group. This may cause a competitive binding between the keto groups and the acid groups on the TiO_{2} surface in the case of croconate dyes and cause a reduction in the efficiency of the DSSC.
pp 311-316 January 2012 Structure, Reactivity and Dynamics
Quantum dynamics of the Cl+H_{2} reaction at ultracold temperatures
Quantum calculations are reported for the reaction between vibrationally excited H_{2} molecules and Cl atoms at energies ranging from the ultracold to thermal regimes. It is found that chemical reaction leading to vibrationally excited HCl molecules dominates over non-reactive vibrational quenching. The product HCl molecule is found to be formed predominantly in the $v = 1$ vibrational level with appreciable rotational excitation. A spin-orbit uncorrected value of $1.86 \times 10^{−12}$ cm^{3} molecule^{-1} s^{-1} is predicted for the rate coefficient in the zero-temperature limit, which is about two orders of magnitude larger than the thermal rate coefficient of the Cl+H_{2} reaction at 300 K.
pp 317-325 January 2012 Structure, Reactivity and Dynamics
Hydration dynamics of protein molecules in aqueous solution: Unity among diversity
Biman Jana Subrata Pal Biman Bagchi
Dielectric dispersion and NMRD experiments have revealed that a significant fraction of water molecules in the hydration shell of various proteins do not exhibit any slowing down of dynamics. This is usually attributed to the presence of the hydrophobic residues (HBR) on the surface, although HBRs alone cannot account for the large amplitude of the fast component. Solvation dynamics experiments and also computer simulation studies, on the other hand, repeatedly observed the presence of a non-negligible slow component. Here we show, by considering three well-known proteins (lysozyme, myoglobin and adelynate kinase), that the fast component arises partly from the response of those water molecules that are hydrogen bonded with the backbone oxygen (BBO) atoms. These are structurally and energetically less stable than those with the side chain oxygen (SCO) atoms. In addition, the electrostatic interaction energy distribution (EIED) of individual water molecules (hydrogen bonded to SCO) with side chain oxygen atoms shows a surprising two peak character with the lower energy peak almost coincident with the energy distribution of water hydrogen bonded to backbone oxygen atoms (BBO). This two peak contribution appears to be quite general as we find it for lysozyme, myoglobin and adenylate kinase (ADK). The sharp peak of EIED at small energy (at less than 2 $k_{B}T$) for the BBO atoms, together with the first peak of EIED of SCO and the HBRs on the protein surface, explain why a large fraction (∼ 80%) of water in the protein hydration layer remains almost as mobile as bulk water. Significant slowness arises only from the hydrogen bonds that populate the second peak of EIED at larger energy (at about 4 k$_B$T). Thus, if we consider hydrogen bond interaction alone, only 15-20% of water molecules in the protein hydration layer can exhibit slow dynamics, resulting in an average relaxation time of about 5-10 ps. The latter estimate assumes a time constant of 20-100 ps for the slow component. Interestingly, relaxation of water molecules hydrogen bonded to back bone oxygen exhibit an initial component faster than the bulk, suggesting that hydrogen bonding of these water molecules remains frustrated. This explanation of the heterogeneous and non-exponential dynamics of water in the hydration layer is quantitatively consistent with all the available experimental results, and provides unification among diverse features.
pp 327-332 January 2012 Structure, Reactivity and Dynamics
Subodh C Tiwari Timir Hajari Ashish Sharma B L Tembe
Constrained molecular dynamics is used to calculate the potentials of mean force for the exo and endo dissociation of 2-norbornyl chlorides in two solvents, namely water and dimethyl sulphoxide (DMSO). The gas phase potential energy curves for the 2-norbornyl chlorides are computed by ab initio methods and these curves are fitted into a 12-6-1 potential for use in classical molecular dynamics simulations. The gas phase potential energy curves indicate a greater barrier for the dissociation of the endo 2-norbornyl chloride (than the exo). The potentials of mean force (PMF) in DMSO and water indicate the locations and the magnitudes of the activation barriers in these solutions and are sensitive functions of the fitted gas phase potentials.
Volume 132, 2020
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