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.

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.

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.

Solvation dynamics in a Brownian dipolar lattice. Comparison between computer simulation and various molecular theories of solvation dynamics

Several recent theoretical and computer simulation studies have considered solvation dynamics in a Brownian dipolar lattice which provides a simple model solvent for which detailed calculations can be carried out. In this article a fully microscopic calculation of the solvation dynamics of an ion in a Brownian dipolar lattice is presented. The calculation is based on the non‐Markovian molecular hydrodynamic theory developed recently. The main assumption of the present calculation is that the two‐particle orientational correlation functions of the solid can be replaced by those of the liquid state. It is shown that such a calculation provides an excellent agreement with the computer simulation results. More importantly, the present calculations clearly demonstrate that the frequency‐dependent dielectric friction plays an important role in the long time decay of the solvation time correlation function. We also find that the present calculation provides somewhat better agreement than either the dynamic mean spherical approximation (DMSA) or the Fried–Mukamel theory which use the simulated frequency‐dependent dielectric function. It is found that the dissipative kernels used in the molecular hydrodynamic approach and in the Fried–Mukamel theory are vastly different, especially at short times. However, in spite of this disagreement, the two theories still lead to comparable results in good agreement with computer simulation, which suggests that even a semiquantitatively accurate dissipative kernel may be sufficient to obtain a reliable solvation time correlation function. A new wave vector and frequency‐dependent dissipative kernel (or memory function) is proposed which correctly goes over to the appropriate expressions in both the single particle and the collective limits. This form is expected to lead to better results than all the existing descriptions.

Solvation dynamics in liquid water. A novel interplay between librational and diffusive modes

A microscopic calculation of the solvation dynamics of an ion in liquid water is presented. The calculated solvation time correlation function shows an ultrafast Gaussian decay which carries about 70%–90% of the strength followed by a biexponential decay with time constants equal to 250 fs and 1 ps. These results are in excellent agreement with the computer simulations of Maroncelli and Fleming and also with the experimental findings of Barbara and Jarzeba. In addition, we find that both the rotational librations and the intermolecular translational vibrational modes of water contribute significantly to the initial Gaussian decay.

Sorbate properties and cage-to-cage diffusion of argon in NaCaA: a molecular dynamics study

Detailed molecular dynamics simulations of argon in zeolite NaCaA are reported. Thermodynamic, structural, and dynamical properties of the sorbate as a function of temperature have been obtained. The properties calculated include various site-site radial distribution functions, different energy distribution functions, selfdiffusion coefficients, the power spectra, and properties relating to cage-to-cage diffusion. The results suggest that sorbate is delocalized above 300 K. Both modes of cage-to-cage diffusion-the surface-mediated and centralized diffusion-are associated with negative barrier heights. Surprisingly, rate of cage-to-cage diffusion is associated with negative and positive activation energies below and above 500 K. The observed differences in the behavior of the rate of cage-to-cage diffusion between Xe-NaY and Ar-NaCaA systems and the nature of the potential energy surface are discussed. Presence of sorbatezeolite interactions results in significant enhancement in the rate of cage-to-cage diffusion and rate of cage visits. It is shown that properties dependent on the long-time behavior such as the diffusion coefficient and the rate of cages visited exhibit the expected Arrhenius dependence on temperature.

Impact of climate change on Indian forests: a dynamic vegetation modeling approach

We make an assessment of the impact of projected climate change on forest ecosystems in India. This assessment is based on climate projections of the Regional Climate Model of the Hadley Centre (HadRM3) and the dynamic global vegetation model IBIS for A2 and B2 scenarios. According to the model projections, 39% of forest grids are likely to undergo vegetation type change under the A2 scenario and 34% under the B2 scenario by the end of this century. However, in many forest dominant states such as Chattisgarh, Karnataka and Andhra Pradesh up to 73%, 67% and 62% of forested grids are projected to undergo change. Net Primary Productivity (NPP) is projected to increase by 68.8% and 51.2% under the A2 and B2 scenarios, respectively, and soil organic carbon (SOC) by 37.5% for A2 and 30.2% for B2 scenario. Based on the dynamic global vegetation modeling, we present a forest vulnerability index for India which is based on the observed datasets of forest density, forest biodiversity as well as model predicted vegetation type shift estimates for forested grids. The vulnerability index suggests that upper Himalayas, northern and central parts of Western Ghats and parts of central India are most vulnerable to projected impacts of climate change, while Northeastern forests are more resilient. Thus our study points to the need for developing and implementing adaptation strategies to reduce vulnerability of forests to projected climate change.

Synthesis, Reactivity, Structural Aspects, and Solution Dynamics of Cyclopalladated Compounds of N,N `,N `'-Tris(2-anisyl)guanidine

N,N',N `'-Tris(2-anisyl)guanidine, (ArNH)(2)C=NAr (Ar = 2-(MeO)C6H4), was cyclopallaclated with Pd(OC(O)R)(2) (R = Me, CF3) in toluene at 70 degrees C to afford palladacycles Pd{kappa(2)(C,N)-C6H3-(OMe)-3(NHC(NHAr)(=NAr))-2}(mu-OC(O)R)](2)(R = Me (1a) and CF3 (1b)) in 87% and 95% yield, respectively. Palladacycle 1a was subjected to a metathetical reaction with LiBr in aqueous ethanol at 78 degrees C to afford palladacycle Pd{kappa(2)(C,N)-C6H3(OMe)-3(NHC(NHAr)(=NAr))-2}(mu-Br)](2) (2) in 90% yield. Palladacycle 2 was subjected to a bridge-splitting reaction with Lewis bases in CH2Cl2 to afford the monomeric palladacycles Pd{kappa(2)(C,N)-C6H3(OMe)-3(NHC(NHAr)(=NAr))-2}Br(L)] (L = 2,6-Me2C5H3N (3a), 2,4-Me2C5H3N (3b), 3,5-Me2C5H3N (3c), XyNC (Xy = 2,6-Me2C6H3; 4a), (BuNC)-Bu-t (4b), and PPh3 (5)) in 87-95% yield. Palladacycle 2 upon reaction with 2 equiv of XyNC in CH2Cl2 afforded an unanticipated palladacycle, Pd{kappa(2)(C,N)-C(=NXy)(C6H3(OMe)-4)-2(N=C-(NH Ar)(2))-3} Br(CNXy)] (6) in 93% yield, and the driving force for the formation of 6 was ascribed to a ring contraction followed by amine-imine tautomerization. Palladacycles 1 a,b revealed a dimeric transoid in-in conformation with ``open book'' framework in the solid state. In solution, 1 a exhibited a fluxional behavior ascribed to the six-membered ``(C,N)Pd'' ring inversion and partly dissociates to the pincer type and kappa(2)-O,O'-OAc monomeric palladacycles by an anchimerically assisted acetate cleavage process as studied by variable-temperature H-1 NMR data. Palladacycles 3a,b revealed a unique trans configuration around the palladium with lutidine being placed trans to the Pd-C bond, whereas cis stereochemistry was observed between the Pd-C bond and the Lewis base in 4a (as determined by X-ray diffraction data) and 5 (as determined by P-31 and C-13 NMR data). The aforementioned stereochemical difference was explained by invoking relative hardness/softness of the donor atoms around the palladium center. In solution, palladacycles 3a-c exist as a mixture of two interconverting boat conformers via a planar intermediate without any bond breaking due to the six-membered ``(C,N)Pd'' ring inversion, whereas palladacycles 4a,b and 5 exist as a single isomer, as deduced from detailed H-1 NMR studies.

A Molecular Dynamics Study of Atomic Correlations in Glassy BzS3t

Glassy B&, the parent compound of the superionic conductor LiI-Li&B& has been studied by the molecular dynamics technique using a new potential model. The results suggest that the glass is made up of local units of four-membered B2S2 rings bridged by sulfur atoms, leading to a chainlike structure. Various pair correlation functions have been analyzed, and the B2Sz rings have been found to be planar. The calculated neutron structure factor shows a peak at 1.4 A-' which has been attributed to B-B correlations at 5.6 A. The glass transition temperature of the simulated system has been calculated to be around 800 K.

Analysis of Hydrogen Bonding and Stability of Protein Secondary Structures in Molecular Dynamics Simulation

Molecular Dynamics (MD) simulations provide an atomic level account of the molecular motions and have proven to be immensely useful in the investigation of the dynamical structure of proteins. Once an MD trajectory is obtained, specific interactions at the molecular level can be directly studied by setting up appropriate combinations of distance and angle monitors. However, if a study of the dynamical behavior of secondary structures in proteins becomes important, this approach can become unwieldy. We present herein a method to study the dynamical stability of secondary structures in proteins, based on a relatively simple analysis of backbone hydrogen bonds. The method was developed for studying the thermal unfolding of beta-lactamases, but can be extended to other systems and adapted to study relevant properties.

1H NMR study of molecular dynamics and phase transition in (NH4)2ZnBr4

The proton second moment (M2) and spin-lattice relaxation time (T1) have been measured in (NH4)2ZnBr4 in the range 77-300 K. The room-temperature spectrum shows a structure which disappears around 243 K. The signal is strong and narrow even at 77 K. Proton T1 shows a maximum at 263 K, caused by spin rotation interaction and decreases with decreasing temperature till 235 K, where it shows a sudden increase. Below 235 K, again it decreases and shows a slope change around 216.5 K (reported Tc). From 216.5 K, T1 decreases continuously without exhibiting any minimum down to 77 K. The narrow line at 77 K, and absence of a T1 minimum down to 77 K indicate the possibility of quantum mechanical tunnelling in this system. Motional parameters such as activation energy and pre-exponential factor have been evaluated for the reorientational motion of the NH+4 ion.

E. C. G. Sudarshan and Symmetry in Classical Dynamics, Optics and Quantum Mechanics

We review work initiated and inspired by Sudarshan in relativistic dynamics, beam optics, partial coherence theory, Wigner distribution methods, multimode quantum optical squeezing, and geometric phases. The 1963 No Interaction Theorem using Dirac's instant form and particle World Line Conditions is recalled. Later attempts to overcome this result exploiting constrained Hamiltonian theory, reformulation of the World Line Conditions and extending Dirac's formalism, are reviewed. Dirac's front form leads to a formulation of Fourier Optics for the Maxwell field, determining the actions of First Order Systems (corresponding to matrices of Sp(2,R) and Sp(4,R)) on polarization in a consistent manner. These groups also help characterize properties and propagation of partially coherent Gaussian Schell Model beams, leading to invariant quality parameters and the new Twist phase. The higher dimensional groups Sp(2n,R) appear in the theory of Wigner distributions and in quantum optics. Elegant criteria for a Gaussian phase space function to be a Wigner distribution, expressions for multimode uncertainty principles and squeezing are described. In geometric phase theory we highlight the use of invariance properties that lead to a kinematical formulation and the important role of Bargmann invariants. Special features of these phases arising from unitary Lie group representations, and a new formulation based on the idea of Null Phase Curves, are presented.