Molecular computations for reactions and phase transitions: applications to protein stabilization, hydrates and catalysis

In this work we have made significant contributions in three different areas of interest: therapeutic protein stabilization, thermodynamics of natural gas clathrate-hydrates, and zeolite catalysis. In all three fields, using our various computational techniques, we have been able to elucidate phenomena that are difficult or impossible to explain experimentally. More specifically, in mixed solvent systems for proteins we developed a statistical-mechanical method to model the thermodynamic effects of additives in molecular-level detail. It was the first method demonstrated to have truly predictive (no adjustable parameters) capability for real protein systems. We also describe a novel mechanism that slows protein association reactions, called the “gap effect.” We developed a comprehensive picture of methioine oxidation by hydrogen peroxide that allows for accurate prediction of protein oxidation and provides a rationale for developing strategies to control oxidation. The method of solvent accessible area (SAA) was shown not to correlate well with oxidation rates. A new property, averaged two-shell water coordination number (2SWCN) was identified and shown to correlate well with oxidation rates. Reference parameters for the van der Waals Platteeuw model of clathrate-hydrates were found for structure I and structure II. These reference parameters are independent of the potential form (unlike the commonly used parameters) and have been validated by calculating phase behavior and structural transitions for mixed hydrate systems. These calculations are validated with experimental data for both structures and for systems that undergo transitions from one structure to another. This is the first method of calculating hydrate thermodynamics to demonstrate predictive capability for phase equilibria, structural changes, and occupancy in pure and mixed hydrate systems. We have computed a new mechanism for the methanol coupling reaction to form ethanol and water in the zeolite chabazite. The mechanism at 400°C proceeds via stable intermediates of water, methane, and protonated formaldehyde.

Spin-canted antiferromagnetic phase transitions in alternating phenoxo- and carboxylato-bridged Mn(III)-salen complexes

Three new MnIII complexes, {[Mn-2(salen)(2)(OCn)](ClO4)}(n) (1), {[Mn-2(salen)(2)(OPh)](ClO4)}(n) (2) and {[Mn-2(salen)(2)(OBz)](ClO4)}(2) (3) (where salen = N,N'-bis(salicylidene)-1,2-diaminoethane dianion, OCn = cinnamate, OPh = phenylacetate and OBz = benzoate), have been synthesized and characterized structurally and magnetically. The crystal structures reveal that all three structures contain syn-anti carboxylatebridged dimeric [Mn-2(salen)(2)(OOCR)](+) cations (OOCR = bridging carboxylate) that are joined together by weak Mn center dot center dot center dot O(phenoxo) interactions to form infinite alternating chain structures in 1 and 2, but the relatively long Mn center dot center dot center dot O(phenoxo) distance [3.621(2)angstrom] in 3 restricts this structure to tetranuclear units. Magnetic studies showed that 1 and 2 exhibited magnetic long-range order at T-N = 4.0 and 4.6 K (T-N = Neel transition temperature), respectively, to give spin-canted antiferromagnetic structures. Antiferromagnetic coupling was also observed in 3 but no peaks were recorded in the field-cooled magnetization (FCM) or zero-field-cooled magnetization (ZFCM) data, indicating that 3 remained paramagnetic down to 2 K. This dominant antiferromagnetic coupling is attributed to the carboxylate bridges. The ferromagnetic coupling expected due to the Mn-O(phenoxo)center dot center dot center dot Mn bridge plays an auxiliary role in the magnetic chain, but is an essential component of the bulk magnetic properties of the material.

Response of the northern stratospheric polar vortex to the seasonal alignment of QBO phase transitions

This study considers the strength of the Northern Hemisphere Holton-Tan effect (HTE) in terms of the phase alignment of the quasi-biennial oscillation (QBO) with respect to the annual cycle. Using the ERA-40 Reanalysis, it is found that the early winter (Nov–Dec) and late winter (Feb–Mar) relation between QBO phase and the strength of the stratospheric polar vortex is optimized for subsets of the 44-year record that are chosen on the basis of the seasonality of QBO phase transitions at the 30 hPa level. The timing of phase transitions serves as a proxy for changes in the vertical structure of the QBO over the whole depth of the tropical stratosphere. The statistical significance of the Nov–Dec (Feb–Mar) HTE is greatest when 30 hPa QBO phase transitions occur 9–14 (4–9) months prior to the January of the NH winter in question. This suggests that there exists for both early and late winter a vertical structure of tropical stratospheric winds that is most effective at influencing the interannual variability of the polar vortex, and that an early (late) winter HTE is associated with an early (late) progression of QBO phase towards that structure. It is also shown that the seasonality of QBO phase transitions at 30 hPa varies on a decadal timescale, with transitions during the first half of the calendar year being relatively more common during the first half of the tropical radiosonde wind record. Combining these two results suggests that decadal changes in HTE strength could result from the changing seasonality of QBO phase transitions. Citation: Anstey, J. A., and T. G. Shepherd (2008), Response of the northern stratospheric polar vortex to the seasonal alignment of QBO phase transitions, Geophys. Res. Lett., 35, L22810, doi:10.1029/2008GL035721.

First-order-reversal-curve analysis of Pr-Fe-B-based exchange spring magnets

Ribbons of nominal composition (Pr(9.5)Fe(84.5)B(6))(0.96)Cr(0.01)(TiC)(0.03) were produced by arc-melting and melt-spinning the alloys on a Cu wheel. X-ray diffraction (XRD) reveals two main phases, one based upon alpha-Fe and the other upon Pr(2)Fe(14)B. The ribbons show exchange spring behavior with H (c) = 12.5 kOe and (BH)(max) = 13.6 MGOe when these two phases are well coupled. Transmission electron microscopy revealed the coupled behavior is observed when the microstructure consists predominantly of alpha-Fe grains (diameter similar to 100 nm.) surrounded by hard material containing Pr(2)Fe(14)B. The microstructure is discussed in terms of a calculation by Skomski and Coey. A first-order-reversal-curve (FORC) analysis was performed for both a well-coupled sample and a poorly coupled sample. The FORC diagrams show two strong peaks for both the poorly coupled sample and for the well-coupled material. In both cases, the localization of the FORC probability suggests magnetizing interactions between particles. Switching field distributions were calculated and are consistent with the sample microstructure.

First-order-reversal-curve analysis of Pr-Fe-B-based nanocomposites

Ribbons of nominal composition (Pr(9.5)Fe(84.5)B(6))(0.96)Cr(0.01)(TiC)(0.03) were produced by arc-melting and melt-spinning the alloys on a Cu wheel. X-ray diffraction reveals two main phases, one based upon alpha-Fe and the other upon Pr(2)Fe(14)B. The ribbons show exchange spring behavior with H(c)=12.5 kOe and (BH)(max)= 13.6 MGOe when these two phases are well coupled. Transmission electron microscopy revealed that the coupled behavior is observed when the microstructure consists predominantly of alpha-Fe grains(diameter similar to 100 nm.) surrounded by hard material containing Pr(2)Fe(14)B. A first-order-reversal-curve (FORC) analysis was performed for both a well-coupled sample and a partially-coupled sample. The FORC diagrams show two strong peaks for both the partially-coupled sample and for the well coupled material. In both cases, the localization of the FORC probability suggests demagnetizing interactions between particles. Switching field distributions were calculated and are consistent with the sample microstructure. (C) 2009 Elsevier B.V. All rights reserved.

Two phase transitions in (s+id)-wave Bardeen-Cooper-Schrieffer superconductivity

We establish universal behaviour in the temperature dependencies of some observables in (s + id)-wave BCS superconductivity in the presence of a weak a wave. We find also a second second-order phase transition. As temperature is lowered-past the usual critical temperature T-c, a less ordered superconducting phase is created in the d wave, which changes to a more ordered phase in a (s + id) wave at T-c1 (phase transitions is manifested by the two jumps in the specific heat at T-c and T(c)1. The temperature dependencies of the susceptibility, penetration depth, and thermal conductivity also confirm the existence of the new phase transition.

First-order actions: A new view

We analyse systems described by first-order actions using the Hamilton-Jacobi (HJ) formalism for singular systems. In this study we verify that generalized brackets appear in a natural way in HJ approach, showing us the existence of a symplectic structure in the phase space of this formalism.

Numerical approximation of the Ginzburg-Landau equation with memory effects in the dynamics of phase transitions

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Resonance and chaos .1. First-order interior resonances

Analytical models for studying the dynamical behaviour of objects near interior, mean motion resonances are reviewed in the context of the planar, circular, restricted three-body problem. The predicted widths of the resonances are compared with the results of numerical integrations using Poincare surfaces of section with a mass ratio of 10(-3) (similar to the Jupiter-Sun case). It is shown that for very low eccentricities the phase space between the 2:1 and 3:2 resonances is predominantly regular, contrary to simple theoretical predictions based on overlapping resonance. A numerical study of the 'evolution' of the stable equilibrium point of the 3:2 resonance as a function of the Jacobi constant shows how apocentric libration at the 2:1 resonance arises; there is evidence of a similar mechanism being responsible for the centre of the 4:3 resonance evolving towards 3:2 apocentric libration. This effect is due to perturbations from other resonances and demonstrates that resonances cannot be considered in isolation. on theoretical grounds the maximum libration width of first-order resonances should increase as the orbit of the perturbing secondary is approached. However, in reality the width decreases due to the chaotic effect of nearby resonances.

First-order-like transition in salt-induced macroion-polyelectrolyte desorption

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Resonance and chaos: I. First-order interior resonances

Analytical models for studying the dynamical behaviour of objects near interior, mean motion resonances are reviewed in the context of the planar, circular, restricted threebody problem. The predicted widths of the resonances are compared with the results of numerical integrations using Poincaré surfaces of section with a mass ratio of 10-3 (similar to the Jupiter-Sun case). It is shown that for very low eccentricities the phase space between the 2:1 and 3:2 resonances is predominantly regular, contrary to simple theoretical predictions based on overlapping resonance. A numerical study of the 'evolution' of the stable equilibrium point of the 3:2 resonance as a function of the Jacobi constant shows how apocentric libration at the 2:1 resonance arises; there is evidence of a similar mechanism being responsible for the centre of the 4:3 resonance evolving towards 3:2 apocentric libration. This effect is due to perturbations from other resonances and demonstrates that resonances cannot be considered in isolation. On theoretical grounds the maximum libration width of first-order resonances should increase as the orbit of the perturbing secondary is approached. However, in reality the width decreases due to the chaotic effect of nearby resonances.

First-order perturbed Korteweg-de Vries solitons

We consider the Korteweg-de Vries equation with a perturbation arising naturally in many physical situations. Although being asymptotically integrable, we show that the corresponding perturbed solitons do not have the usual scattering properties. Specifically, we show that there is a solution, correct up to O(ε), where ε is the perturbative parameter, consisting, at t→ -∞ of two superposed deformed solitons characterized by wave numbers k1 and k2 that give rise, for t→ +∞, to the same but phase-shifted superposed solitons plus a coupling term depending on k1, and k2. We also find the condition on the original equation for which this coupling vanishes.

A DFT Study of Structural and Electronic Properties of ZnS Polymorphs and its Pressure-Induced Phase Transitions

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Phase transition from a d(x(2)-y(2)) to d(x(2)-y(2))+id(xy) superconductor

The temperature dependencies of specific heat and spin susceptibility of a coupled dx2-y2 + idxy superconductor in the presence of a weak dxy component are investigated in the tight-binding model (1) on square lattice and (2) on a lattice with orthorhombic distortion. As the temperature is lowered past the critical temperature Tc, first a less ordered dx2-y2 superconductor is created, which changes to a more ordered dx2-y2 + idxy superconductor at Tcl(< Tc). This manifests in two second order phase transitions identified by two jumps in specific heat at Tc and Tc1. The temperature dependencies of the superconducting observables exhibit a change from power-law to exponential behavior as temperature is lowered below Tc1 and confirm the new phase transition. © 1998 Published by Elsevier Science B.V. All rights reserved.

Effect of alkyl chain length of alcohols on nematic uniaxial-to-biaxial phase transitions in a potassium laurate/alcohol/K2SO4/water lyotropic mixture

Lyotropic liquid crystalline quaternary mixtures of potassium laurate (KL), potassium sulphate (K2SO4)/alcohol (n-OH)/water, with the alcohols having different numbers of carbon atoms in the alkyl chain (n), from 1-octanol to 1-hexadecanol, were investigated by optical techniques (optical microscopy and laser conoscopy). The biaxial nematic phase domain is present in a window of values of n = n(KL) +/- 2, where n(KL) = 11 is the number of carbon atoms in the alkyl chain of KL. The biaxial phase domain became smaller and the uniaxial-to-biaxial phase transition temperatures shifted to relatively higher temperatures upon going from 1-nonanol to 1-tridecanol. Moreover, compared with other lyotropic mixtures these new mixtures present high birefringence values, which we expect to be related to the micellar shape anisotropy. Our results are interpreted assuming that alcohol molecules tend to segregate in the micelles in a way that depends on the relative value of n with respect to nKL. The larger the value of n, the more alcohol molecules tend to be located in the curved parts of the micelle, favoring the uniaxial nematic calamitic phase with respect to the biaxial and uniaxial discotic nematic phases.