Two forms of Pf1 Inovirus: X-ray diffraction studies on a structural phase transition and a calculated libration normal mode of the asymmetric unit

Inovirus is a helical array of alpha-helical protein asymmetric units surrounding a DNA core. X-ray fibre diffraction studies show that the Pf1 species of Inovirus can undergo a reversible temperature-induced transition between two similar structural forms having slightly different virion helix parameters. Molecular models of the two forms show no evidence for altered interactions between the protein and either the solvent or the viral DNA; but there are significant differences in the shape and orientation of the protein asymmetric unit, related to the changes in the virion parameters. Normal modes involving libration of whole asymmetric units are in a frequency range with appreciable entropy of libration, and the structural transition may be related to changes in libration.

An infrared spectroscopic study of the orientational phase transitions of C70

Infrared spectroscopic studies of C70 films show variation in absorbance and linewidth of the bands across the orientational phase transitions around 280 and 340 K. There is some evidence for the coexistence of phases in the 210–270 K region and for the occurrence of another transition below 200 K.

Two forms of PF1 INOVIRUS: X-ray diffraction studies on a structural phase transition and a calculated libration normal mode of the assymetric unit

Inovirus is a helical array of agr-helical protein asymmetric units surrounding a DNA core. X-ray fibre diffraction studies show that the Pf1 species of Inovirus can undergo a reversible temperature-induced transition between two similar structural forms having slightly different virion helix parameters. Molecular models of the two forms show no evidence for altered interactions between the protein and either the solvent or the viral DNA; but there are significant differences in the shape and orientation of the protein asymmetric unit, related to the changes in the virion parameters. Normal modes involving libration of whole asymmetric units are in a frequency range with appreciable entropy of libration, and the structural transition may be related to changes in libration.

Orientational phase transitions in C70: A Raman spectroscopic investigation

Raman investigations of C70 films in the 14-370-K range show significant changes across the orientational phase transitions around 270 and 330 K. Seven of the Raman modes of C70 soften smoothly across the transitions, the magnitude of the decrease in frequencies being in the range of 2-5 cm-1. Linewidths of the bands increase in the transition region over and above the anharmonic contributions.

Spectroscopic investigations of phase transitions in complex solids

Spectroscopic methods have provided information of seminal importance in understanding phase transitions in solids. After briefly examining some fundamental concept related to phase transitions, we shall discuss several case studies particularly involving the use of vibrational (IR and Raman) spectroscopy. Examples will include both order-disorder and displacive transitions. Under the former are included transitions in nitrates, ammonium halides, alkylammonium salts, plastic state of C60 and superionic conductors (specially CsHSO4). In addition, we shall discuss some aspects of incommensurate phase transitions, the glass transition and electronic phase transitions. Transitions of phosphonitrilic halide tetramers and alkane dicarboxylic acids are also examined

Orientational ordering in C70. Evidence for three distinct phase transitions

Variable-temperature X-ray diffraction studies of C70 suggest the occurrence of two phase transitions around 350 and 280 K where the high-temperature phase is fcc and the low-temperature phase is monoclinic, best described as a distorted hcp structure with a doubled unit cell; two like-phases (possibly hcp) seem to coexist in the 280-350 K range. Application of pressure gives rise to three distinct transitions associated with characteristic pressure coefficients, the extrapolated values of the transition temperatures at ambient pressure being around 340, 325 and 270 K. Pressure delineates closely related phases Of C70 just as in the case Of C60 which exhibits two orientational phase transitions at high pressures.

Phase transitions in triammonium hydrogen disulphate: Crystal structure of an intermediate stable phase at-90 degrees C

Triammonium hydrogen disulphate, (NH4)(3)H(SO4)(2), belongs to the family of crystal structures M3H(XO4)(2) (with M = NH4, K, Rb, Cs, and X = S, Se) which display super protonic phases at elevated temperatures, while at room temperature these are relatively poor proton conductors. The crystal structure of triammonium hydrogen disulphate has been determined by X-ray diffraction at -90 degrees C and the variation in the characteristics of the hydrogen bond is discussed in comparison with that of the structures at -110 degrees C and room temperature. It is concluded that the mechanics involving the proton migration in such systems is realised in terms of the variations in the hydrogen bond features with temperature.

Phase transitions in the anchored organic bilayers of long-chain alkylammonium lead iodides (CnH2n+1NH3)(2)PbI4; n=12, 16, 18

The single perovskite slab alkylammonium lead iodides (CnH2n+1NH3)(2)PbI4, n = 12, 16, 18, display two phase transitions, just above room temperature, associated with changes in the alkylammonium chains. We have followed these two phase transitions using scanning calorimetry, X-ray powder diffraction, and IR and Raman spectroscopies. We find the first phase transition to be associated with symmetry changes arising from a dynamic rotational disordering of the ammonium headgroup of the chain whereas the second transition, the melting of the chains in two dimensions, is characterized by an increased conformational disorder of the methylene units of the alkyl chains. We examine these phase transitions in light of the interesting optical properties of these materials, as well as the relevance of these systems as models for phase transitions in lipid bilayers.

Infrared studies of the phase transitions of alkylammonium halides, RNH3X, and bis-(alkylammonium) tetrahalogenometallates(II), (RNH3)2MX4, (R = alkyl, M = metal, X = Cl or Br)

Internal vibration modes of bis-(alkylammonium) tetrachlorometallates(II) and the corresponding alkylammonium chlorides have been studied through their phase transitions using infrared spectroscopy. The studies show that the vibrational states of alkylammonium ions change markedly through the phase transitions. Spectra of the analogous tetrabromometallates and alkylammonium bromides also confirm this behaviour. There is appreciable motion of the alkylammonium ions in the high-temperature phases; thus, CH3NH+3 ions are essentially undistorted in these phases. The low-temperature, ordered phases show evidence of stronger hydrogen bonding of the cations and for the presence of C—N torsional modes.

Anomalous phase transitions in soft colloid-polymer binary mixtures

We have shown earlier [1] that these PGNPs resemble star polymers or spherical brushes in terms of their morphology in the melt. However, these particles show dynamics in melt which is quite different from other soft colloidal particles. Since most of the work on soft colloidal particles have been performed in solutions we have now explored the phase behavior of the PGNPs in good solvent using microscopic structural and dynamical measurements on binary mixtures of homopolymers and soft colloids consisting of polymer grafted nanoparticles. We observe anomalous structural and dynamical phase transitions of these binary mixtures, including appearance of spontaneous orientational alignment and logarithmic structural relaxations, as a function of added homopolymers of different molecular weights. Our experiments points to the possibility of exploiting the phase space in density and homopolymer size, of such hybrid systems, to create new materials with unique properties.

Evidence for phase transitions and pseudospin phonon coupling in K-0.9(NH4)(0.1)H2AsO4

This work reports a detailed temperature dependent Raman study on the mixed crystals of K-0.9(NH4)(0.1)H2AsO4 (KADA) from 5K to 300K in the spectral range of 60-1200cm(-1), covering tetragonal to orthorhombic structural phase transition accompanied by paraelectric to ferroelectric transition at T-c* similar to 60K. Multiple phase transitions below transition temperature (Tc* similar to 60K) are marked by the appearance of new modes, splitting of existing ones as well as anomalies in the self-energy parameters (i.e. mode frequencies and damping coefficient) of the phonon modes. Temperature independent behaviour of damping coefficient and abrupt jump in the mode frequency of some of the internal vibrations of AsO4 tetrahedra as well as external vibrations clearly signal long range ferroelectric ordering and proton ordering below T-c*. In addition, we observed that temperature dependence of many prominent phonon modes diverges significantly from their normal anharmonic behaviour below T-c* suggesting potential coupling between pseudospins and phonons. (C) 2015 Author(s).

FRENKEL-KONTOROVA DOMAIN-WALL PHASE-TRANSITIONS IN AN ADSORBED LAYER - POTASSIUM ON CO(10(1)OVER-BAR-0)

As the potassium fractional coverage of a cobalt {1010BAR} surface is increased over the range 0.2 to 0.6 monolayer the adlayer passes through a series of phase transitions. A commensurate phase is formed at exactly 0.5 monolayer, and corresponds to adatoms bonded in high-symmetry hollow sites on the unreconstructed cobalt surface, with an effective adatom radius lying between the ionic and covalent radii of potassium. A detailed structural study shows that the structural transitions can be characterised within a one-dimensional Frenkel-Kontorova model, with small lateral displacements of adatoms away from hollow sites in the low and high coverage phases. The low coverage phases progress from a distributed vacancy structure to a low density domain-wall structure; while the high coverage phase formed above half a monolayer is a high density asymmetric domain-wall structure.

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.