Pressure-induced Structural Changes Research Articles

Pressure Effect on the Secondary Structure of Peptides Studied by Generalized-Ensemble Molecular Dynamics Simulations

Pressure effect on the structure of proteins and peptides has recently been studied theoretically and experimentally. Some proteins are denatured under high pressure conditions while some peptides are more stable in the folded state than in the random coil state at high pressure. It is important to understand the molecular mechanism of pressure-induced structural changes of proteins and peptides.We studied pressure effect on the structure of peptides by using molecular dynamics simulations. Molecular simulations often get trapped in the local minimum states of the free energy. In order to overcome such difficulty, we used a generalized-ensemble algorithm, which gives more efficient sampling in a molecular simulation.We performed molecular dynamics simulations with a generalized-ensemble algorithm for helical peptides in explicit water molecules. We found that the population of the secondary structure of the peptides changes as pressure increases. We also calculated the free energy as a function of pressure. The detail molecular mechanism of the structural change induced by pressure will be shown in the meeting.

Under Pressure That Splits a Family in Two. The Case of Lipocalin Family

The lipocalin family is typically composed of small proteins characterized by a range of different molecular recognition properties. Odorant binding proteins (OBPs) are a class of proteins of this family devoted to the transport of small hydrophobic molecules in the nasal mucosa of vertebrates. Among OBPs, bovine OBP (bOBP) is of great interest for its peculiar structural organization, characterized by a domain swapping of its two monomeric subunits. The effect of pressure on unfolding and refolding of native dimeric bOBP and of an engineered monomeric form has been investigated by theoretical and experimental studies under pressure. A coherent model explains the pressure-induced protein structural changes: i) the substrate-bound protein stays in its native configuration up to 330 MPa, where it loses its substrate; ii) the substrate-free protein dissociates into monomers at 200 MPa; and iii) the monomeric substrate-free form unfolds at 120 MPa. Molecular dynamics simulations showed that the pressure-induced tertiary structural changes that accompany the quaternary structural changes are mainly localized at the interface between the monomers. Interestingly, pressure-induced unfolding is reversible, but dimerization and substrate binding can no longer occur. The volume of the unfolding kinetic transition state of the monomer has been found to be similar to that of the folded state. This suggests that its refolding requires relatively large structural and/or hydrational changes, explaining thus the relatively low stability of the monomeric form of this class of proteins.

Synchrotron x-ray spectroscopy studies of valence and magnetic state in europium metal to extreme pressures

In order to probe the changes in the valence state and magnetic properties of Eu metal under extreme pressure, x-ray absorption near-edge spectroscopy, x-ray magnetic circular dichroism, and synchrotron M\"ossbauer spectroscopy experiments were carried out. The M\"ossbauer isomer shift exhibits anomalous pressure dependence, passing through a maximum near 20 GPa. Density functional theory has been applied to give insight into the pressure-induced changes in both Eu's electronic structure and M\"ossbauer isomer shift. Contrary to previous reports, Eu is found to remain nearly divalent to the highest pressures reached (87 GPa) with magnetic order persisting to at least 50 GPa. These results should lead to a better understanding of the nature of the superconducting state found above 75 GPa and of the sequence of structural phase transitions observed to 92 GPa.

Effects of High Hydrostatic Pressure Treatment on Physicochemical Characteristics of Sea Cucumber

The effects of high hydrostatic pressure (HHP) treatment on sea cucumber qualities, such as shelf-life, autoenzyme, total volatile basic nitrogen (TVB-N), mucopolysaccha ride and protein, were investigated experimentally. The shelf-life of sea cucumber was greatly prolonged by HHP treatment. High pressure treatment of sea cucumber significantly reduced the activity of autoenzyme at 550 MPa. The TVB-N content was 8.4 mg/100 g in the HHP-treated samples after 38 days' storage at 4 °C, while it had already reached 11.2 mg/100 g in the untreated ones after 5 days' storage under the same condition. The relative mucopolysaccharide content of the HHP-treated samples was 94.3%, while that of the heat-treated ones was only 35.5%. The sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE), Differential scanning calorimetric (DSC), ANS fluorescence probe method and fourier-transform infrared (FTIR) spectroscopy results indicated some changes in protein subunits, denaturation, surface hydrophobicity and secondary structure of sea cucumber protein. This study has provided complementary information of pressure-induced structural changes on both the molecular and the sub-molecular level of sea cucumber protein.

Pressure-induced structural change of intermediate-range order in poly(4-methyl-1-pentene) melt

High-pressure in situ x-ray diffraction and specific-volume measurements on isotactic poly(4-methyl-1-pentene) melt have uncovered abrupt changes in the pressure dependence of microscopic structure as well as that of macroscopic density. The first sharp diffraction peak of the polymer melt, which is related to the intermediate-range order and is explained as resulting from the correlations between main chains, is suppressed at pressures less than 1 kbar. These changes in intermediate-range order show similarities to those seen in liquid-liquid or amorphous-amorphous transitions in simpler small molecule based systems, suggesting that this kind of phenomenon may occur in a wide range of materials.

High-pressure single-crystal XRD and magnetic study of a octacyanoniobate-based magnetic sponge

In the present study we report the structural and magnetic response of the 3-D cyano-bridged magnetic sponge-like system {[MnII(pydz)(H2O)2][MnII(H2O)2][NbIV(CN)8]·3H2O}nA to external pressure up to 1.8 GPa using single-crystal crystallography and magnetic measurements. The observed pressure-induced structural changes: shrinkage of the Nb–C bonds and bending of Mn–NC–Nb linkages are responsible for the strengthening of the antiferromagnetic interactions between Mn and Nb centers and consequently for the substantial increase of the magnetic ordering temperature from 43 K to 51 K under 0.57 GPa. The observed magneto-structural response to external pressure is similar in nature to the removal of guest molecules and confirms the significant susceptibility of molecular magnetic sponges to mechanical stress.

DAC基盤技術の開発と元素の構造相転移の研究および状態方程式の決定

Development of DAC and related basic technologies are described, including a high-pressure gas-loading apparatus. Pressure-induced phase transitions and structural change of the elements under high pressure are reviewed, focusing on the molecular dissociation of iodine and electronic topological transition in zinc. Importance of hydrostaticity for the determination of accurate equation of states is discussed.

放射光を用いた液体・アモルファスの高圧力下の研究

High pressure research of liquids and amorphous using synchrotron radiation is reviewed. From the systematic research of various liquids, the difference of pressure-induced structural change between liquids and solids has been observed. The phase transitions between meta-stable phases are also reviewed from the experiments under low temperatures and high pressures.

Reversal of Hall–Petch Effect in Structural Stability of PbTe Nanocrystals and Associated Variation of Phase Transformation

Using an in situ synchrotron X-ray diffraction technique, a pressure-induced phase transformation of PbTe nanocrystals with sizes of 13 and 5 nm up to ∼20 GPa was studied. Upon an increase of pressure, we observed that the 13 nm PbTe nanocrystals start a phase transformation from rocksalt structure to an intermediate orthorhombic structure and finally CsCl-type structure at 8 GPa, which is 2 GPa higher than that in bulk PbTe. In contrast, the 5 nm PbTe nanocrystals do not display the same type of transition with a further increased transition pressure as expected. Instead of orthorhombic or CsCl-type structure, the 5 nm PbTe nanocrystals turn to amorphous phase under a similar pressure (8 GPa). Upon a release of pressure, the 13 nm PbTe nanocrystals transform from high pressure CsCl-type structure directly to rocksalt structure, whereas the 5 nm PbTe nanocrystals remain their amorphous phase to ambient conditions. The structure stability of rocksalt-type PbTe shows a significant reversal of Hall-Petch effect. On the basis of such an observation with a critical size determination of ∼9 nm, PbTe nanocrystals appear as the first class of material that demonstrates a pressure-induced structural change from order to disorder. By sharing the insight of this reversed Hall-Petch effect with associated transition types, we tuned our experimental protocol and successfully synthesized a sample with "high-pressure metastable structure", amorphous phase at ambient pressure. This integrative study provides a feasible pathway to understand nucleation mechanism as a function of particle size and to explore novel materials with high-pressure metastable structure and unique properties under lab-accessible conditions.

Structural state of relaxor ferroelectrics PbSc0.5Ta0.5O3and PbSc0.5Nb0.5O3at high pressures up to 30 GPa

The pressure-induced structural changes in perovskite-type (ABO${}_{3}$) Pb-based relaxor ferroelectrics are studied on the basis of in situ single-crystal synchrotron x-ray diffraction and Raman scattering experiments on PbSc${}_{0.5}$Ta${}_{0.5}$O${}_{3}$ and PbSc${}_{0.5}$Nb${}_{0.5}$O${}_{3}$ conducted under hydrostatic conditions up to 30 GPa. Complementary density functional theory calculations have been performed to compare the stability of various atomic configurations for both compounds at high pressures. By combining the experimental and theoretical results, the following sequence of structural transformations is proposed. At a characteristic pressure ${p}_{1}^{\ensuremath{\star}}$ the mesoscopic polar order is violated and a local antipolar order of Pb atoms as well as quasidynamical long-range order of antiphase octahedral tilts is developed. These structural changes facilitate the occurrence of a continuous phase transition at ${p}_{c1}g{p}_{1}^{\ensuremath{\star}}$ from cubic to a nonpolar rhombohedral structure comprising antiphase octahedral tilts of equal magnitude (${a}^{\ensuremath{-}}{a}^{\ensuremath{-}}{a}^{\ensuremath{-}}$). At a characteristic pressure ${p}_{2}^{\ensuremath{\star}}g{p}_{c1}$ the octahedral tilts around the cubic [100], [010], and [001] directions become different from each other on the mesoscopic scale. The latter precedes a second phase transition at ${p}_{c2}$, which involves long-range order of Pb antipolar displacements along cubic $[uv0]$ directions and a compatible mixed tilt system (${a}^{+}{b}^{\ensuremath{-}}{b}^{\ensuremath{-}}$) or long-range ordered antiphase tilts with unequal magnitudes (${a}^{0}{b}^{\ensuremath{-}}{b}^{\ensuremath{-}}$) without Pb displacement ordering. The phase-transition pattern at ${p}_{c2}$ depends on the fine-scale degree of chemical B-site order in the structure.

Pressure-induced Structural and Hydration Changes of Proteins in Aqueous Solutions

The effects of elevated hydrostatic pressure on four representative proteins, lysozyme, human serum albumin, ubiquitin and RNase A, were investigated by using Fourier transform infrared (FTIR) spectroscopy, by principal component analysis (PCA) and by moving-window two-dimensional (MW2D) correlation analysis. In addition, we revealed the pressure-induced changes of secondary structure elements using curve fitting. With pressure increase, the amide I band shifted to lower wavenumbers, with a transition at 200 MPa, which was indicative of hydration enhancement. Moreover, the pressure-induced behavior of pure water was studied, similar transition pressure was observed with protein in aqueous solution, suggesting that structure change of water around 200 MPa caused a hydration enhancement of protein. Under pressure higher than 200 MPa, the structural changes of the four proteins were obviously different except for the common features shifting to lower wavenumbers with pressure, basically due to the distinct structural differences among them.

Effect of Network Polymerization on the Pressure-Induced Structural Changes in Sodium Aluminosilicate Glasses and Melts: 27Al and 17O Solid-State NMR Study

Probing the pressure-induced structural changes and the extent of disorder in aluminosilicate glasses and melts at high pressure remains a challenge in modern physical and chemical sciences. With an aim of establishing a systematic relationship between pressure, composition, and glass structures, we report 27Al and 17O 3QMAS NMR spectra for sodium aluminosilicate glasses [Na2O:Al2O3:SiO2 = 1.5:0.5:2n with n = 1 (NAS150520, XSiO2 = 0.5), 2 (NAS150540, XSiO2 = 0.67), and 3 (NAS150560, XSiO2 = 0.75)], quenched from melts at pressures up to 8 GPa. We also explore the stability of the [4]Al–O–[4]Al cluster in the highly depolymerized, NAS150520, glass at high pressure. For given glass composition, the [5,6]Al peak intensity increases with increasing pressure. The population of [5,6]Al increases linearly with XSiO2 from NAS150520 (XSiO2 = 0.5) to NAS150560 glass (XSiO2 = 0.75) at both 6 and 8 GPa. The [5,6]Al/XSiO2 ratio also tends to increase with pressure, indicating a possible relationship between [5,6]Al fr...

Pressure-induced changes in the electronic structure of americium metal

We have conducted electronic-structure calculations for Am metal under pressure to investigate the behavior of the 5$f$-electron states. Density-functional theory (DFT) does not reproduce the experimental photoemission spectra for the ground-state phase where the 5$f$ electrons are localized, but the theory is expected to be correct when 5$f$ delocalization occurs under pressure. The DFT prediction is that peak structures of the 5$f$ valence band will merge closer to the Fermi level during compression indicating the presence of itinerant 5$f$ electrons. Existence of such 5$f$ bands is argued to be a prerequisite for the phase transitions, particularly to the primitive orthorhombic AmIV phase, but does not agree with modern dynamical-mean-field theory (DMFT) results. Our DFT model further suggests insignificant changes of the 5$f$ valence under pressure in agreement with recent resonant x-ray emission spectroscopy, but in contradiction to the DMFT predictions. The influence of pressure on the 5$f$ valency in the actinides is discussed and is shown to depend in a nontrivial fashion on 5$f$-band position and occupation relative to the $spd$ valence bands.

In situ X-ray diffraction study on pressure-induced structural changes in hydrous forsterite and enstatite melts

We investigated the pressure-induced structural changes in hydrous forsterite and enstatite melts using in situ synchrotron X-ray diffraction. Diffraction data was collected up to 6.9 GPa at superliquidus temperatures. At pressures below 3 GPa, the first sharp diffraction peak ( FSDP), which reflects the silicate network ordering in the silicate melts that consist of … Si O Si … linkages, is shifted notably toward higher Q (scattering vector [Å − 1 ]) in both melt compositions. This observation indicates that water has a depolymerizing effect on the silicate network below 3 GPa, which means that … Si O Si … linkages are partially disrupted by hydroxyl species (Si-OH units). In contrast, the peaks move to lower Q at pressures above 3 GPa in spite of the compression, which indicates lengthening of the silicate network ordering (i.e., polymerization of silicate network). This observation indicates that water changes to have a polymerizing effect on the silicate network above 3 GPa by a new free hydroxyl group such as Mg-OH, which was previously proposed in the study on hydrous silicate glasses structure. In fact, the structural changes in the present study are more pronounced in the hydrous Mg 2SiO 4 melt, suggesting that the MgO component has an important influence on the polymerization of hydrous melt structure at 3–5 GPa. The present structural change, re-polymerization at high pressure, in hydrous silicate melt can influence the viscosity. Such a relatively high-viscosity hydrous magma may be able to stay (or be decreased in the rising velocity) at a depth of 100–180 km, which can enhance the decrease in a seismological wave velocity in the Earth's asthenosphere as proposed in previous seismological observations.

Transformation processes in relaxor ferroelectric PbSc0.5Ta0.5O3heavily doped with Nb and Sn

The effect of a third type of B-site cation on the temperature-and pressure-induced structural changes in ABO3-type relaxors has been studied by in-situ Raman scattering and X-ray diffraction on 0.72PbSc 0.5Ta0.5O3-0.28PbSc0.5Nb 0.5O3 (PSTN) and 0.78PbSc0.5Ta 0.5O3-0.22PbSnO3 (PSTS). The incorporation of Nb into the PST matrix is an isovalent substitution for Ta5+ on the ferroelectrically active B-site, whereas the incorporation of Sn4+ is a coupled aliovalent substitution for both types of B-cations in the host system. Both PSTN and PSTS exhibit the characteristic temperature T*, which for PSTS is shifted to slightly lower temperatures. The incorporation of Nb and Sn into the PST matrix smears the transformation processes near and below T* and suppresses the ferroelectric long-range order at low temperatures. Both PSTN and PSTS exhibit a continuous pressure-induced phase transition. The high-pressure phases have the same structural features as for pure PST: suppressed B-cation off-centre shifts, enhancement of coupled Pb-O ferroic species, and long-range order of anti-phase tilts of the BO6 octahedra. Nb-doping shifts the critical pressure pc from 1.9 GPa for pure PST to 2.5 GPa, whereas Sn-doping lowers pc to 1.3 GPa. The incorporation of both Nb and Sn decreases the degree of the overall pressure-induced structural distortion, with the effect of Sn being more pronounced than Nb. The dilution of the B-site cation system with Sn4+ results in local electric and elastic fields which reduce the coherence between nanoregions with anti-phase octahedral tilting and shifts the pressure at which long-range order of the tilts occurs to ∼ 4 GPa.

High pressure cell for neutron reflectivity measurements up to 2500 bar

The design of a high pressure (HP) cell for neutron reflectivity experiments is described. The cell can be used to study solid-liquid interfaces under pressures up to 2500 bar (250 MPa). The sample interface is based on a thick silicon block with an area of about 14 cm(2). This area is in contact with the sample solution which has a volume of only 6 cm(3). The sample solution is separated from the pressure transmitting medium, water, by a thin flexible polymer membrane. In addition, the HP cell can be temperature-controlled by a water bath in the range 5-75°C. By using an aluminum alloy as window material, the assembled HP cell provides a neutron transmission as high as 41%. The maximum angle of incidence that can be used in reflectivity experiments is 7.5°. The large accessible pressure range and the low required volume of the sample solution make this HP cell highly suitable for studying pressure-induced structural changes of interfacial proteins, supported lipid membranes, and, in general, biomolecular systems that are available in small quantities, only. To illustrate the performance of the HP cell, we present neutron reflectivity data of a protein adsorbate under high pressure and a lipid film which undergoes several phase transitions upon pressurization.

Soda-lime silicate glass under hydrostatic pressure and indentation: a micro-Ramanstudy

Raman micro-spectroscopy is used to analyse the plastic behaviour of window glass (asoda-lime silicate glass) under high hydrostatic pressure and Vickers indentation.We show pressure-induced irreversible structural changes, notably an increase ofQ2 species at theexpense of Q3. For the first time, a very accurate calibration curve has been established. Local density variations of a Vickers indentedwindow glass have been characterized by micro-Raman mapping using a highspatial resolution device. The effects of glass depolymerization on indentation andhydrostatic compression are discussed. Differences between window glass and pureSiO2 glass behaviour under high stresses are also highlighted and analysed at a local scale.

Structural instability of unfilled skutterudite compounds TSb3 (T=Co, Rh and Ir) under high pressure

Filled skutterudite compounds attracted many researchers' interest as strongly correlated electron systems. The skutterudite family includes binary, unfilled skutterudite compounds. We have studied the powder x-ray diffraction of unfilled skutterudite compounds TSb3 (T=Rh and Ir) under high pressure up to around 40 GPa, using synchrotron radiation. Pressure-induced irreversible structural changes of TSb3 (T=Rh and Ir) have been observed. Structural instability of the unfilled skutterudite compounds TSb3 (T=Co, Rh and Ir) under high pressure is discussed.

Chemical and Hydrostatic Pressure in Natrolites: Pressure-Induced Hydration of an Aluminogermanate Natrolite

The ambient structure and pressure-induced structural changes of a synthetic sodium aluminogermanate with a natrolite (NAT) framework topology (Na−AlGe-NAT) were characterized by using Rietveld refinements of high-resolution synchrotron X-ray powder diffraction data at ambient and high pressures. Unlike a previously established model for Na8Al8Ge12O40·8H2O based on a single-crystal study, the ambient structure of the Na−AlGe-NAT is found to adopt a monoclinic space group Cc (or Fd) with a ca. 6% expanded unit cell. The refined ambient structure of Na8Al8Ge12O40·12H2O indicates an increased water content of 50%, compared to the single-crystal structure. The unit-cell volume and water-content relationships observed between the two Na−AlGe-NAT structures at ambient conditions with 8 and 12 H2O respectively seem to mirror the ones found under hydrostatic pressure between the Na8Al8Si12O40·8H2O and the parantrolite phase Na8Al8Si12O40·12H2O. Under hydrostatic pressures mediated by a pore-penetrating alcohol and water mixture, the monoclinic Na−AlGe-NAT exhibits a gradual decrease of the unit-cell volume up to ca. 2.0 GPa, where the unit-cell volume then contracts abruptly by ca. 4.6%. This is in marked contrast to what is observed in the Na−AlSi-NAT and Na−GaSi-NAT systems, where one observes a pressure-induced hydration and volume expansion due to the auxetic nature of the frameworks. Above 2 GPa, the monoclinic phase of Na−AlGe-NAT transforms into a tetragonal structure with the unit-cell composition of Na8Al8Ge12O40·16H2O, revealing pressure-induced hydration and a unit cell volume contraction. Unlike in the Na−Al,Si-paranatrolite phase, however, the sodium cations in the Na−AlGe-NAT maintain a 6-fold coordination in the monoclinic structure and only become 7-fold coordinated at higher pressures in the tetragonal structure. When comparing the pressure-induced hydration in the observed natrolite-type zeolites, Na−AlGe-NAT appears to have a nonauxetic framework and reveals the highest onset pressure for complete superhydration.

Crystal and Electronic Structure of FeSe at High Pressure and Low Temperature

We have investigated the high-pressure crystal and electronic structures of superconducting FeSe by high-resolution synchrotron powder X-ray diffraction and density functional theory (DFT) calculations at ambient and at low temperatures down to 8 K. Ambient nuclear resonant inelastic X-ray scattering (NRIXS) experiments were performed on FeSe to understand the partial phonon density of states (PDOS) of the high-pressure phases. On the basis of our experimental results and DFT calculations, we demonstrate a pressure-induced distortion of the low-temperature Cmma phase at around 1.6 GPa and the appearance of a high-pressure Pbnm phase. Upon increasing the pressure above 9 GPa, the orthorhombic phase becomes the major phase, and a mixed-phase region exists up to 26 GPa. The pressure-induced structural changes in this system and its connection to T(c) enhancement are discussed.