Dynamics of activationless reactions in solution

Recent picosecond and subpicosecond laser spectroscopy experiments have revealed several chemically and biologically important reactions in solution in which the reaction potential surface does not present a barrier to the motion along the reaction coordinate.The dynamics of these reactions display diverse and interesting behavior. They include the dependence of relaxation rate on the solvent viscosity, the solvent polarity, the temperature, and the wavelength of the exciting light. In this article we review the recent developments in the theoretical description of activationless processes in solution and compare them with the available experimental results

Dynamics of charge transfer in the excited amine complexes of the fullerenes C60 and C70.: A picosecond laser flash photolysis study

In benzene solution, C60 and C70 interact weakly in the ground state with amines having favourable oxidation potentials. Picosecond time-resolved absorption measurements show that on photoexcilation, the weak complexes undergo charge separation to produce ion pairs which in turn undergo fast geminate recombination either to produce the triplet state of the fullerenes or give back the ground slate of the complex, depending on the oxidation potential of the amine. Free-ion yield is generally negligible.

Molecular dynamics simulations on parallel and antiparallel C.G*G triplexes

Molecular dynamics (MD) studies have been carried out on the Hoogsteen hydrogen bonded parallel and the reverse Hoogsteen hydrogen banded antiparallel C.G*G triplexes. Earlier, the molecular mechanics studies had shown that the parallel structure was energetically more favourable than the antiparallel structure. To characterize the structural stability of the two triplexes and to investigate whether the antiparallel structure can transit to an energetically more favourable structure, due to the local fluctuations in the structure during the MD simulation, the two structures were subjected to 200ps of constant temperature vacuum MD simulations at 300K. Initially no constraints were applied to the structures and it was observed that for the antiparallel tripler, the structure showed a large root mean square deviation from the starting structure within the first 12ps and the N4-H41-O6 hydrogen bond in the WC duplex got distorted due to a high propeller twist and a moderate increase in the opening angle in the basepairs. Starting from an initial value of 30 degrees, helical twist of the average structure from this simulation had a value of 36 degrees, while the parallel structure stabilized at a twist of 33 degrees. In spite of the hydrogen bond distortions in the antiparallel tripler, it was energetically comparable to the parallel tripler. To examine the structural characteristics of an undistorted structure, another MD simulation was performed on the antiparallel tripler by constraining all the hydrogen bonds. This structure stabilized at an average twist of 33 degrees. In the course of the dynamics though the energy of the molecule - compared to the initial structure - improved, it did not become comparable to the parallel structure. Energy minimization studies performed in the presence of explicit water and counterions also showed the two structures to be equally favourable energetically Together these results indicate that the parallel C.G*G tripler with Hoogsteen hydrogen bonds also represents a stereochemically and energetically favourable structure for this class of triplexes.

Sequence Independent Recombination Triple Helices: A Molecular Dynamics Study

Recent experimental studies have shown that the Rec-A mediated homologous recombination reaction involves a triple helical intermediate, in which the third strand base forms hydrogen bonds with both the bases in the major groove of the Watson-Crick duplex. Such 'mixed' hydrogen bonds allow formation of sequence independent triplexes. DNA triple helices involving 'mixed' hydrogen bonds have been studied, using model building, molecular mechanics (MM) and molecular dynamics (MD). Models were built for a tripler comprising all four possible triplets viz., G.C*C, C.G*G, A.T*T and T.A*A. To check the stability of all the 'mixed' hydrogen bonds in such triplexes and the conformational preferences of such tripler structures, MD studies were carried out starting from two structures with 30 degrees and 36 degrees twist between the basepairs. It was observed that though the two triplexes converged towards a similar structure, the various hydrogen bonds between the WC duplex and the third strand showed differential stabilities. An MD simulation with restrained hydrogen bonds showed that the resulting structure was stable and remained close to the starting structure. These studies help us in defining stable hydrogen bond geometries involving the third strand and the WC duplex. It was observed that in the C.G*G triplets the N7 atom of the second strand is always involved in hydrogen bonding. In the G.C*C triplets, either N3 or O2 in the third strand cytosine can interchangeably act as a hydrogen bond acceptor.

Indian Ocean Dipole: Processes and impacts

Equatorial Indian Ocean is warmer in the east, has a deeper thermocline and mixed layer, and supports a more convective atmosphere than in the west. During certain years, the eastern Indian Ocean becomes unusually cold, anomalous winds blow from east to west along the equator and southeastward off the coast of Sumatra, thermocline and mixed layer lift up and the atmospheric convection gets suppressed. At the same time, western Indian Ocean becomes warmer and enhances atmospheric convection. This coupled ocean-atmospheric phenomenon in which convection, winds, sea surface temperature (SST) and thermocline take part actively is known as the Indian Ocean Dipole (IOD). Propagation of baroclinic Kelvin and Rossby waves excited by anomalous winds, play an important role in the development of SST anomalies associated with the IOD. Since mean thermocline in the Indian Ocean is deep compared to the Pacific, it was believed for a long time that the Indian Ocean is passive and merely responds to the atmospheric forcing. Discovery of the IOD and studies that followed demonstrate that the Indian Ocean can sustain its own intrinsic coupled ocean-atmosphere processes. About 50% percent of the IOD events in the past 100 years have co-occurred with El Nino Southern Oscillation (ENSO) and the other half independently. Coupled models have been able to reproduce IOD events and process experiments by such models – switching ENSO on and off – support the hypothesis based on observations that IOD events develop either in the presence or absence of ENSO. There is a general consensus among different coupled models as well as analysis of data that IOD events co-occurring during the ENSO are forced by a zonal shift in the descending branch of Walker cell over to the eastern Indian Ocean. Processes that initiate the IOD in the absence of ENSO are not clear, although several studies suggest that anomalies of Hadley circulation are the most probable forcing function. Impact of the IOD is felt in the vicinity of Indian Ocean as well as in remote regions. During IOD events, biological productivity of the eastern Indian Ocean increases and this in turn leads to death of corals over a large area.Moreover, the IOD affects rainfall over the maritime continent, Indian subcontinent, Australia and eastern Africa. The maritime continent and Australia suffer from deficit rainfall whereas India and east Africa receive excess. Despite the successful hindcast of the 2006 IOD by a coupled model, forecasting IOD events and their implications to rainfall variability remains a major challenge as understanding reasons behind an increase in frequency of IOD events in recent decades.

Temperature-dependent chirped coherent phonon dynamics in Bi2Te3 using high-intensity femtosecond laser pulses

Degenerate pump-probe reflectivity experiments have been performed on a single crystal of bismuth telluride (Bi2Te3) as a function of sample temperature (3 K to 296 K) and pump intensity using similar to 50 femtosecond laser pulses with central photon energy of 1.57 eV. The time-resolved reflectivity data show two coherently generated totally symmetric A(1g) modes at 1.85 THz and 3.6 THz at 296 K which blue-shift to 1.9 THz and 4.02 THz, respectively, at 3 K. At high photoexcited carrier density of similar to 1.7 x 10(21) cm(-3), the phonon mode at 4.02 THz is two orders of magnitude higher positively chirped (i.e the phonon time period decreases with increasing delay time between the pump and the probe pulses) than the lower-frequency mode at 1.9 THz. The chirp parameter, beta is shown to be inversely varying with temperature. The time evolution of these modes is studied using continuous-wavelet transform of the time-resolved reflectivity data. Copyright (C) EPLA, 2010

Deformation dynamics of SS-316 Between 1023-K TO 1223-K In The Framework of Cottrell-Stokes Law

Kocks' formalism for analysing steady state deformation data for the case where Cottrell-Stokes law is valid is extended to incorporate possible back stresses from solution and/or precipitation hardening, and dependence of pre-exponential factor on the applied stress. A simple graphical procedure for exploiting these equations is demonstrated by analyzing tensile steady state data for a type 316 austentic stainless steel for the temperature range 1023 to 1223 K. In this instance, the computed back stress values turned out to be negative, a physically meaningless result. This shows that for SS 316, deformation in this temperature regime can not be interpreted in terms of a mechanism that obeys Cottrell-Stokes law.

Dielectric friction and solvation dynamics: Novel results on relaxation in dipolar liquids

In this article we present a new, general but simple, microscopic expression for time-dependent solvation energy of an ion. This expression is surprisingly similar to the expression for the time-dependent dielectric friction on a moving ion. We show that both the Chandra-Bagchi and the Fried-Mukamel formulations of solvation dynamics can be easily derived from this expression. This expression leads to an almost perfect agreement of the theory with all the available computer simulation results. Second, we show here for the first time that the mobility of a light solute ion can significantly accelerate its own solvation, specially in the underdamped limit. The latter result is also in excellent agreement with the computer simulations.

Differential stability of beta-sheets and alpha-helices in beta-lactamase: a high temperature molecular dynamics study of unfolding intermediates

Beta-Lactamase, which catalyzes beta-lactam antibiotics, is prototypical of large alpha/beta proteins with a scaffolding formed by strong noncovalent interactions. Experimentally, the enzyme is well characterized, and intermediates that are slightly less compact and having nearly the same content of secondary structure have been identified in the folding pathway. In the present study, high temperature molecular dynamics simulations have been carried out on the native enzyme in solution. Analysis of these results in terms of root mean square fluctuations in cartesian and [phi, psi] space, backbone dihedral angles and secondary structural hydrogen bonds forms the basis for an investigation of the topology of partially unfolded states of beta-lactamase. A differential stability has been observed for alpha-helices and beta-sheets upon thermal denaturation to putative unfolding intermediates. These observations contribute to an understanding of the folding/unfolding processes of beta-lactamases in particular, and other alpha/beta proteins in general.

Effect of constraints by threonine on proline containing αa-helix—A molecular dynamics approach

Proline plays an important role in the secondary structure of proteins. In the pursuit of understanding its structural role, Proline containing helices with constraints have been studied by employing molecular dynamics (MD) technique. In the present study, the constraint introduced is a threonine residue, whose sidechain has intramolecular hydrogen bond interaction with the backbone oxygen atom. The three systems that have been chosen for characterization are: (1) Ace-(Ala)12−Thr-Pro-(Ala)10−NHMe, (2) Ace-(Ala)13-Pro-Ala-Thr- (Ala)8-NHMe and (3) Ace-(Ala)13-Pro-(Ala)3-Thr-(Ala)6-NHMe. The equilibrium structures and structural transitions have been identified by monitoring the backbone dihedral angles, bend related parameters and the hydrogen bond interactions. The MD averages and root mean square (r.m.s.) fluctuations are compared and discussed. Energy minimization has been carried out on selected MD simulated points in order to analyze the characteristics of different conformations.

Mechanisms of variability and predictability of the tropical coupled ocean-atmosphere system

A conceptual model is proposed to explain the observed aperiodicity in the short term climate fluctuations of the tropical coupled ocean-atmosphere system. This is based on the evidence presented here that the tropical coupled ocean-atmosphere system sustains a low frequency inter-annual mode and a host of higher frequency intra-seasonal unstable modes. At long wavelengths, the low frequency mode is dominant while at short wavelengths, the high frequency modes are dominant resulting in the co-existence of a long wave low frequency mode with some short wave intra-seasonal modes in the tropical coupled system. It is argued that due to its long wavelength, the low frequency mode would behave like a linear oscillator while the higher frequency short wave modes would be nonlinear. The conceptual model envisages that an interaction between the low frequency linear oscillator and the high frequency nonlinear oscillations results in the observed aperiodicity of the tropical coupled system. This is illustrated by representing the higher frequency intra-seasonal oscillations by a nonlinear low order model which is then coupled to a linear oscillator with a periodicity of four years. The physical mechanism resulting in the aperiodicity in the low frequency oscillations and implications of these results on the predictability of the coupled system are discussed.

Molecular theory of ion solvation dynamics in water, acetonitrile and methanol: A unified microscopic description of collective dynamics in dipolar liquids

A recently developed microscopic theory of solvation dynamics in real dipolar liquids is used to calculate, for the first time, the solvation time correlation function in liquid acetonitrile, water and methanol. The calculated results are in excellent agreement with known experimental and computer simulation studies.

Normal mode sound propagation in an ocean with random narrow-band surface waves

Normal mode sound propagation in an isovelocity ocean with random narrow-band surface waves is considered, assuming the root-mean-square wave height to be small compared to the acoustic wavelength. Nonresonant interaction among the normal modes is studied straightforward perturbation technique. The more interesting case of resonant interaction is investigated using the method of multiple scales to obtain a pair of stochastic coupled amplitude equations which are solved using the Peano-Baker expansion technique. Equations for the spatial evolution of the first and second moments of the mode amplitudes are also derived and solved. It is shown that, irrespective of the initial conditions, the mean values of the mode amplitudes tend to zero asymptotically with increasing range, the mean-square amplitudes tend towards a state of equipartition of energy, and the total energy of the modes is conserved.

Proton NMR study of molecular dynamics in ammonium tribromo stannate (NH4SnBr3)

The proton second moment M2 and spin-lattice relaxation time T1 have been measured in ammonium tribromo stannate (NH4SnBr3) in the temperature range 77–300 K, to determine the ammonium dynamics. The continuous wave signal is strong and narrow at 77 and 300 K but has revealed an interesting intensity anomaly between 210 and 125 K. T1 shows a maximum (13 s) around 220 K. No minimum in the T1 vs 1000/T plot was observed down to 77 K. M2 and T1 results are interpreted in terms of NH+4 ion dynamics. The activation energy Ea for NH+4 ion reorientation is estimated to be 1.4 kcal mol−1.