Monte Carlo and molecular dynamics simulation of argon clusters andn-alkanes in the confined regions of zeolites

Geometry and energy of argon clusters confined in zeolite NaCaA are compared with those of free clusters. Results indicate the possible existence of magic numbers among the confined clusters. Spectra obtained from instantaneous normal mode analysis of free and confined clusters give a larger percentage of imaginary frequencies for the latter indicating that the confined cluster atoms populate the saddle points of the potential energy surface significantly. The variation of the percentage of imaginary frequencies with temperature during melting is akin to the variation of other properties. It is shown that confined clusters might exhibit inverse surface melting, unlike medium-to-large-sized free clusters that exhibit surface melting. Configurational-bias Monte Carte (CBMC) simulations of n-alkanes in zeolites Y and A are reported. CBMC method gives reliable estimates of the properties relating to the conformation of molecules. Changes in the conformational properties of n-butane and other longer n-alkanes such as n-hexane and n-heptane when they are confined in different zeolites are presented. The changes in the conformational properties of n-butane and n-hexane with temperature and concentration is discussed. In general, in zeolite Y as well as A, there is significant enhancement of the gauche population as compared to the pure unconfined fluid.

Temperature dependence of the levitation effect - Implications for separation of multicomponent mixtures

Sufficiently long molecular dynamics simulations have been carried out on spherical monatomic sorbates in NaY zeolite, interacting via simple Lennard-Jones potentials, to investigate the dependence of the levitation effect on the temperature. Simulations carried out in the range 100-300 K suggest that the anomalous peak in the diffusion coefficient (observed when the levitation parameter, gamma, is near unity) decreases in intensity with increase in temperature. The rate of cage-to-cage migrations also exhibits a similar trend. The activation energy obtained from Arrhenius plots is found to exhibit a minimum when the diffusion coefficient is a maximum, corresponding to the gamma approximate to 1 sorbate diameter. In the linear or normal regime, the activation energy increases with increase in sorbate diameter until it shows a sharp decrease in the anomalous regime. Locations and energies of the adsorption sites and their dependence on the sorbate size gives interesting insight into the nature of the underlying potential-energy surface and further explain the observed trend in the activation energy with sorbate size. Cage residence times, tau(c), show little or no change with temperature for the sorbate with diameter corresponding to gamma approximate to 1, whereas there is a significant decrease in tau(c) with increase in temperature for sorbates in the linear regime. The implications of the present study for the separation of mixtures of sorbates are discussed.

Irreversibility-to-reversibility crossover in transient response of an optically trapped particle

We study the transient response of a colloidal bead which is released from different heights and allowed to relax in the potential well of an optical trap. Depending on the initial potential energy, the system's time evolution shows dramatically different behaviors. Starting from the short-time reversible to long-time irreversible transition, a stationary reversible state with zero net dissipation can be achieved as the release point energy is decreased. If the system starts with even lower energy, it progressively extracts useful work from thermal noise and exhibits an anomalous irreversibility. In addition, we have verified the Transient Fluctuation Theorem and the Integrated Transient Fluctuation Theorem even for the non-ergodic descriptions of our system. Copyright (C) EPLA, 2011

Nonlinear dynamics and chaotic motions in feedback-controlled two- and three-degree-of-freedom robots

The dynamics of a feedback-controlled rigid robot is most commonly described by a set of nonlinear ordinary differential equations. In this paper we analyze these equations, representing the feedback-controlled motion of two- and three-degrees-of-freedom rigid robots with revolute (R) and prismatic (P) joints in the absence of compliance, friction, and potential energy, for the possibility of chaotic motions. We first study the unforced or inertial motions of the robots, and show that when the Gaussian or Riemannian curvature of the configuration space of a robot is negative, the robot equations can exhibit chaos. If the curvature is zero or positive, then the robot equations cannot exhibit chaos. We show that among the two-degrees-of-freedom robots, the PP and the PR robot have zero Gaussian curvature while the RP and RR robots have negative Gaussian curvatures. For the three-degrees-of-freedom robots, we analyze the two well-known RRP and RRR configurations of the Stanford arm and the PUMA manipulator respectively, and derive the conditions for negative curvature and possible chaotic motions. The criteria of negative curvature cannot be used for the forced or feedback-controlled motions. For the forced motion, we resort to the well-known numerical techniques and compute chaos maps, Poincare maps, and bifurcation diagrams. Numerical results are presented for the two-degrees-of-freedom RP and RR robots, and we show that these robot equations can exhibit chaos for low controller gains and for large underestimated models. From the bifurcation diagrams, the route to chaos appears to be through period doubling.

Drug-drug co-crystals: Temperature-dependent proton mobility in the molecular complex of isoniazid with 4-aminosalicylic acid

Two drug-drug co-crystals of the anti-tuberculosis drugs isoniazid (INH), pyrazinamide (PYR) and 4-aminosalicylic acid (PAS) are reported. The first is the 1 : 1 molecular complex of INH and PAS. The second is the monohydrate of the 1 : 1 complex of PYR and PAS. The crystal structures of both co-crystals are characterized by a number of hydrogen bonded synthons. Hydrogen bonding of the COOH center dot center dot center dot N-pyridine type is found in both cases. In the INH : PAS co-crystal, there are two symmetry independent COOH center dot center dot center dot center dot N-pyridine hydrogen bonds. In one of these, the H-atom is located on the carboxylic group and is indicative of a co-crystal. In the second case, partial proton transfer occurs across the hydrogen bond, and the extent of proton transfer depends on the temperature. This is more indicative of a salt. Drug-drug co-crystals may have some bearing in the treatment of tuberculosis.

Investigation of short-time isomerization dynamics in p-nitroazobenzene from resonance Raman intensity analysis

Resonance Raman (RR) spectra are presented for p-nitroazobenzene dissolved in chloroform using 18 excitation Wavelengths, covering the region of (1)(n --> pi*) electronic transition. Raman intensities are observed for various totally symmetric fundamentals, namely, C-C, C-N, N=N, and N-O stretching vibrations, indicating that upon photoexcitation the excited-state evolution occurs along all of these vibrational coordinates. For a few fundamentals, interestingly, in p-nitroazobenzene, it is observed that the RR intensities decrease near the maxima of the resonant electronic (1)(n --> pi*) transition. This is attributed to the interference from preresonant scattering due to the strongly allowed (1)(pi --> pi*) electronic transition. The electronic absorption spectrum and the absolute Raman cross section for the nine Franck-Condon active fundamentals of p-nitroazobenzene have been successfully modeled using Heller's time-dependent formalism for Raman scattering. This employs harmonic description of the lowest energy (1)(n --> pi*) potential energy surface. The short-time isomerization dynamics is then examined from a priori knowledge of the ground-state normal mode descriptions of p-nitroazobenzene to convert the wave packet motion in dimensionless normal coordinates to internal coordinates. It is observed that within 20 fs after photoexcitation in p-nitroazobenzene, the N=N and C-N stretching vibrations undergo significant changes and the unsubstituted phenyl ring and the nitro stretching vibrations are also distorted considerably.

On the importance of backbone loop and peptide flip in the Walker sequence in F-1-ATPase action

The Walker sequence, GXXXXGKT, present in all the six subunits of F-1-ATPase exists in a folded form, known as phosphate-binding loop (P-loop). Analysis of the Ramachandran angles showed only small RMS deviation between the nucleotide-bound and nucleotide-free forms. This indicated a good overlap of the backbone loops. The catalytic beta-subunits (chains D, E and F) showed significant changes in the Ramachandran angles and the side chain torsion angles, but not the structural alpha-subunits (chains A, B and C). Most striking among these are the changes associated with Val160 and Gly161 corresponding to a flip in the peptide unit between them when a nucleotide is bound (chains D or F compared to nucleotide-free chain E). The conformational analysis further revealed a hitherto unnoticed hydrogen bond between amide-N of the flipped Gly161 and terminal phosphate-O of the nucleotide. This assigns a role for this conserved amino acid, otherwise ignored, of making an unusual direct interaction between the peptide backbone of the enzyme protein and the incoming nucleotide substrate. Significance of this interaction is enhanced, as it is limited only to the catalytic subunits, and also likely to involve a mechanical rotation of bonds of the peptide unit. Hopefully this is part of the overall events that link the chemical hydrolysis of ATP with the mechanical rotation of this molecule, now famous as tiny molecular motor.

Through ring umbrella inversion of a molecular rattle

We report theoretical investigations on some [Ring]Li--(+) compounds, which can exhibit a through ring umbrella like inversion. Our studies predict cyclononatetraenyllithium to be molecular rattle, in which such inversions can occur. The potential energy for the motion is a double well, with an activation barrier of 11.50 kcal/mol. We find that the lithium should go through the ring easily by an excitation to nu = 17 vibrational level. (C) 2002 Elsevier Science B.V. All rights reserved.

One-dimensional zinc phosphates with linear chain structure

Three one-dimensional zinc phosphates, [C5N2H14][Zn(HPO4)2], I, [C10N4H26][Zn(HPO4)2].2H2O II, and [C4N2H6]2[Zn(HPO4)], III, have been prepared employing hydro/solvothermal methods in the presence of organic amines. While I and II consist of linear chains of corner-shared four-membered rings, III is a polymeric wire where the amine molecule is directly bonded to the metal center. The wire, as well as the chain in these structures, are held together by hydrogen bond interactions involving the amine and the framework oxygens. The polymeric zinc phosphate with wire-like architecture, III, is only the second example of such architecture. Crystal data: I, monoclinic, P21/c (no. 14), a=8.603(2), b=13.529(2), c=10.880(1) ��, ��=94.9(1)��, V=1261.6(1) ��3, Z=4, ��calc.=1.893 gcm���3, ��(MoK��)=2.234 mm���1, R1=0.032, wR2=0.086, [1532 observed reflections with I>2��(I)], II, orthorhombic, Pbca (no. 61), a=8.393(1), b=15.286(1), c=22.659(1) ��, V=2906.9(2) ��3, Z=8, ��calc.=1.794 gcm���3, ��(MoK��)=1.957 mm���1, R1=0.055, wR2=0.11, [1565 observed reflections with I>2��(I) and III, monoclinic, P21/c (no. 14), a=8.241(1), b=13.750(2), c=10.572(1) ��, ��=90.9(1)��, V=1197.7(2) ��3, Z=4, ��calc.=1.805 gcm���3, ��(MoK��)=2.197 mm���1, R1=0.036, wR2=0.10, [1423 observed reflections with I>2��(I)].

Towards the concept of hydrodynamic cavitation control

A careful study of the existing literature available in the field of cavitation reveals the potential of ultrasonics as a tool for controlling and, if possible, eliminating certain types of hydrodynamic cavitation through the manipulation of nuclei size present in a flow. A glass venturi is taken to be an ideal device to study the cavitation phenomenon at its throat and its potential control. A piezoelectric transducer, driven at the crystal resonant frequency, is used to generate an acoustic pressure field and is termed an ������ultrasonic nuclei manipulator (UNM)������. Electrolysis bubbles serve as artificial nuclei to produce travelling bubble cavitation at the venturi throat in the absence of a UNM but this cavitation is completely eliminated when a UNM is operative. This is made possible because the nuclei, which pass through the acoustic field first, cavitate, collapse violently and perhaps fragment and go into dissolution before reaching the venturi throat. Thus, the potential nuclei for travelling bubble cavitation at the venturi throat seem to be systematically destroyed through acoustic cavitation near the UNM. From the solution to the bubble dynamics equation, it has been shown that the potential energy of a bubble at its maximum radius due to an acoustic field is negligible compared to that for the hydrodynamic field. Hence, even though the control of hydrodynamic macro cavitation achieved in this way is at the expense of acoustic micro cavitation, it can still be considered to be a significant gain. These are some of the first results in this direction.

Some salient features of the atmosphere observed over the north Bay of Bengal during BOBMEX

This paper describes the near surface characteristics and vertical variations based on the observations made at 17.5degreesN and 89degreesE from ORV Sagar Kanya in the north Bay of Bengal during the Bay of Bengal Monsoon Experiment (BOBMEX) carried out in July-August 1999. BOBMEX captured both the active and weak phases of convection. SST remained above the convection threshold throughout the BOBMEX. While the response of the SST to atmospheric forcing was clearly observed, the response of the atmosphere to SST changes was not clear. SST decreased during periods of large scale precipitation, and increased during a weak phase of convection. It is shown that the latent heat flux at comparable wind speeds was about 25-50% lower over the Bay during BOBMEX compared to that over the Indian Ocean during other seasons and tropical west Pacific. On the other hand, the largest variations in the surface daily net heat flux are observed over the Bay during BOBMEX. SST predicted using observed surface fluxes showed that 1-D heat balance model works sometime but not always, and horizontal advection is important. The high resolution Vaisala radiosondes launched during BOBMEX could clearly bring out the changes in the vertical structure of the atmosphere between active and weak phases of convection. Convective Available Potential Energy of the surface air decreased,by 2-3 kJ kg(-1) following convection, and recovered in a time period of one or two days. The mid tropospheric relative humidity and water vapor content, and wind direction show the major changes between the active and weak phases of convection.

Revisiting the Mechanism of the Triosephosphate Isomerase Reaction: The Role of the Fully Conserved Glutamic Acid 97 Residue

An analysis of 503 available triosephosphate isomerase sequences revealed nine fully conserved residues. Of these, four residues-K12, H95, E97 and E165-are capable of proton transfer and are all arrayed around the dihydroxyacetone phosphate substrate in the three-dimensional structure. Specific roles have been assigned to the residues K12, H95 and E165, but the nature of the involvement of E97 has not been established. Kinetic and structural characterization is reported for the E97Q and E97D mutants of Plasmodium falciparum triosephosphate isomerase (Pf TIM). A 4000-fold reduction in k(cat) is observed for E97Q, whereas the E97D mutant shows a 100-fold reduction. The control mutant, E165A, which lacks the key catalytic base, shows an approximately 9000-fold drop in activity. The integrity of the overall fold and stability of the dimeric structure have been demonstrated by biophysical studies. Crystal structures of E97Q and E97D mutants have been determined at 2.0 angstrom resolution. In the case of the isosteric replacement of glutamic acid by glutamine in the E97Q mutant a large conformational change for the critical K12 side chain is observed, corresponding to a trans-to-gauche transition about the C gamma-C delta (chi(3)) bond. In the E97D mutant, the K12 side chain maintains the wild-type orientation, but the hydrogen bond between K12 and D97 is lost. The results are interpreted as a direct role for E97 in the catalytic proton transfer cycle. The proposed mechanism eliminates the need to invoke the formation of the energetically unfavourable imidazolate anion at H95, a key feature of the classical mechanism.

Microwave spectrum and structure of C(6)H(5)CCH center dot center dot center dot H(2)S complex

Rotational spectra of C(6)H(5)CCH center dot center dot center dot H(2)S, C(6)H(5)CCH center dot center dot center dot H(2)(34)S, C(6)H(5)CCH center dot center dot center dot HDS, C(6)H(5)CCH center dot center dot center dot D(2)S and C(6) H(5)CCD center dot center dot center dot H(2)S complexes have been observed using a pulsed nozzle Fourier transform microwave spectrometer. The observed spectrum is consistent with a structure in which hydrogen sulfide is located over the phenyl ring pi cloud and the distance between the centers of masses of the two monomers is 3.74 +/- 0.01 angstrom. In the complex, the H(2)S unit is shifted from the phenyl ring center towards the acetylene group. The vibrationally averaged structure has an effective Cs symmetry. Ab initio calculations were performed at MP2/aug-cc-pVDZ level of theory to locate the possible geometries of the complex. The calculations reveal the experimentally observed structure to be more stable than a coplanar arrangement of the monomers, which was observed for the C(6)H(5)CCH center dot center dot center dot H(2)O complex. Atoms in molecule theoretical analysis shows the presence of S-H center dot center dot center dot pi hydrogen bond. For the parent isotopologue, each transition frequency was found to split into two resulting from an interchange of the equivalent hydrogens of H(2)S unit in the complex. (C) 2011 Elsevier Inc. All rights reserved.

2-{[{2-Hydroxy-3-[2-methyl-5-(propan-2-yl)phenoxy]propyl}(pyridin -2-ylmethyl)amino]methyl}phenol

In the title racemic compound, C(26)H(32)N(2)O(3), an intramolecular O-H center dot center dot center dot N hydrogen bond is formed between the phenolic OH group and the tertiary amine N atom. Another O-H center dot center dot center dot N hydrogen bond that is formed between the OH group and the pyridine N atom links the molecules into a polymeric chain extending along the a axis. The structure is further stabilized by intramolecular and intermolecular C-H center dot center dot center dot O interactions.

Dynamic and thermodynamic anomalies of water at low temperatures: from bulk water to reverse micelles and DNA hydration layer

Liquid water is known to exhibit remarkable thermodynamic and dynamic anomalies, ranging from solvation properties in supercritical state to an apparent divergence of the linear response functions at a low temperature. Anomalies in various dynamic properties of water have also been observed in the hydration layer of proteins, DNA grooves and inside the nanocavity, such as reverse micelles and nanotubes. Here we report studies on the molecular origin of these anomalies in supercooled water, in the grooves of DNA double helix and reverse micelles. The anomalies have been discussed in terms of growing correlation length and intermittent population fluctuation of 4- and 5-coordinated species. We establish correlation between thermodynamic response functions and mean squared species number fluctuation. Lifetime analysis of 4- and 5-coordinated species reveals interesting differences between the role of the two species in supercooled and constrained water. The nature and manifestations of the apparent and much discussed liquid-liquid transition under confinement are found to be markedly different from that in the bulk. We find an interesting `faster than bulk' relaxation in reverse micelles which we attribute to frustration effects created by competition between the correlations imposed by surface interactions and that imposed by hydrogen bond network of water.