Sequence Of Structural Transitions Research Articles

Watching a signaling protein function: What has been learned over four decades of time-resolved studies of photoactive yellow protein.

Photoactive yellow protein (PYP) is a signaling protein whose internal p-coumaric acid chromophore undergoes reversible, light-induced trans-to-cis isomerization, which triggers a sequence of structural changes that ultimately lead to a signaling state. Since its discovery nearly 40 years ago, PYP has attracted much interest and has become one of the most extensively studied proteins found in nature. The method of time-resolved crystallography, pioneered by Keith Moffat, has successfully characterized intermediates in the PYP photocycle at near atomic resolution over 12 decades of time down to the sub-picosecond time scale, allowing one to stitch together a movie and literally watch a protein as it functions. But how close to reality is this movie? To address this question, results from numerous complementary time-resolved techniques including x-ray crystallography, x-ray scattering, and spectroscopy are discussed. Emerging from spectroscopic studies is a general consensus that three time constants are required to model the excited state relaxation, with a highly strained ground-state cis intermediate formed in less than 2.4 ps. Persistent strain drives the sequence of structural transitions that ultimately produce the signaling state. Crystal packing forces produce a restoring force that slows somewhat the rates of interconversion between the intermediates. Moreover, the solvent composition surrounding PYP can influence the number and structures of intermediates as well as the rates at which they interconvert. When chloride is present, the PYP photocycle in a crystal closely tracks that in solution, which suggests the epic movie of the PYP photocycle is indeed based in reality.

Epigenetic regulator RNF20 underlies temporal hierarchy of gene expression to regulate postnatal cardiomyocyte polarization

Differentiated cardiomyocytes (CMs) must undergo diverse morphological and functional changes during postnatal development. However, the mechanisms underlying initiation and coordination of these changes remain unclear. Here, we delineate an integrated, time-ordered transcriptional network that begins with expression of genes for cell-cell connections and leads to a sequence of structural, cell-cycle, functional, and metabolic transitions in mouse postnatal hearts. Depletion of histone H2B ubiquitin ligase RNF20 disrupts this gene network and impairs CM polarization. Subsequently, assay for transposase-accessible chromatin using sequencing (ATAC-seq) analysis confirmed that RNF20 contributes to chromatin accessibility in this context. As such, RNF20 is likely to facilitate binding of transcription factors at the promoters of genes involved in cell-cell connections and actin organization, which are crucial for CM polarization and functional integration. These results suggest that CM polarization is one of the earliest events during postnatal heart development and provide insights into how RNF20 regulates CM polarity and the postnatal gene program.

Phase transitions in a polycrystalline compound Ho0.1Mn0.9S

Sequence of structural transitions in the magnetically ordered region and a displacement-type structural transition at T = 220 K accompanied by the variation in the thermal expansion coefficient, ultrasound attenuation coefficient, g factor, and polarization current in the polycrystalline compound Ho0.1Mn0.9S was found. The electronic transitions above room temperature were established on the basis of the measurements of the conductivity, ultrasound attenuation maxima, and IR spectra.

Electropositive core in electronegative magnetized capacitive radio frequency plasmas

The magnetized drift-ambipolar (‘m-DA’) electron power absorption mode and a sequence of structural transitions, including the formation of an electropositive core where the electron density is much higher than the negative ion density, are identified in a magnetized capacitive Radio-Frequency (RF) plasma of a strongly electronegative gas, CF4. The m-DA mode is caused by a magnetic enhancement of the bulk electric field due to the attenuation of the electron transport and plasma conductivity across the magnetic field. This leads to the formation of ionization maxima at distinct axial positions and a local trapping of electrons by the magnetic field as a function of its strength.

Systematic structural study in praseodymium compressed in a neon pressure medium up to 185 GPa

Angle-dispersive x-ray powder diffraction experiments have been performed on praseodymium metal compressed in a soft pressure-transmitting medium at ambient temperature up to 185 GPa. We observe the previously reported high-pressure structural transition sequence up to 20 GPa and the coexistence of body-centered orthorhombic (bco) Pr and \ensuremath{\alpha}-U Pr from $\ensuremath{\sim}20$ up to $\ensuremath{\sim}38\phantom{\rule{0.16em}{0ex}}\mathrm{GPa}$. The \ensuremath{\alpha}-U structure of Pr is stable from 20 to 185 GPa, and no evidence of the proposed transition to a primitive orthorhombic phase $>147\phantom{\rule{0.16em}{0ex}}\mathrm{GPa}$ was observed. With density functional theory (DFT), we calculated the lattice parameters and $y$ coordinate for \ensuremath{\alpha}-U Pr and found good agreement between our calculations and experimental measurements. The obtained DFT energies of the proposed primitive orthorhombic $(P{2}_{1}{2}_{1}{2}_{1})$ and the \ensuremath{\alpha}-uranium phases at $\ensuremath{\sim}150\phantom{\rule{0.16em}{0ex}}\mathrm{GPa}$ show that the \ensuremath{\alpha}-uranium phase is lower in energy. Hence, neither our experimental data nor our DFT results support the transition to a primitive orthorhombic phase $>150\phantom{\rule{0.16em}{0ex}}\mathrm{GPa}$. DFT suggests, however, that Pr may transform to the $P{2}_{1}{2}_{1}{2}_{1}$ phase above $\ensuremath{\sim}220\phantom{\rule{0.16em}{0ex}}\mathrm{GPa}$. We also compare the axial ratios and lattice parameters of praseodymium to \ensuremath{\alpha}-uranium structured Nd, Ce, and U.

Comparative study of the high-pressure behavior of ZnV2O6, Zn2V2O7, and Zn3V2O8

Abstract We report a study of the high-pressure structural behavior of ZnV2O6, Zn2V2O7, and Zn3V2O8, which has been explored by means of synchrotron powder x-ray diffraction. We found that ZnV2O6 and Zn3V2O8 remain in the ambient-pressure structure up to 15 GPa. In contrast, in the same pressure range, Zn2V2O7 undergoes three phase transitions at 0.7, 3.0, and 10.8 GPa, respectively. Possible crystal structures for the first and second high-pressure phases are proposed. Reasons for the distinctive behavior of Zn2V2O7 are discussed. The compressibility of the different polymorphs has been determined. The response to pressure is found to be anisotropic in all the considered compounds and the room-temperature equations of state have been determined. The bulk moduli of ZnV2O6 (129(2) GPa) and Zn3V2O8 (120(2) GPa) are consistent with a structural framework composed of compressible ZnO6 octahedra and uncompressible VO4 tetrahedra. In contrast, Zn2V2O7 is highly compressible with a bulk modulus of 58(9) GPa, which is almost half of the bulk modulus of the other two vanadates. The large compressibility of Zn2V2O7 and its sequence of structural transitions are related to the fact that this material is less dense than the other zinc vanadates and to the penta-coordination of Zn atoms by oxygen atoms in Zn2V2O7. A comparison to the high-pressure behavior of related compounds is presented.

Structural transitions and bilayer formation of CTAB aggregates

Controlled CTAB self-assembly is an essential prerequisite for the formation of gold nanorods with tailored shape and monodispersity. In this paper, we exploit the use of salt concentration and co-surfactant decanol for the preparation of CTAB aggregates with different morphologies. To this end we use a model of CTAB recently developed by ourselves, and perform electronic structure calculations in order to improve current point charge parametrization of decanol. Using molecular dynamics simulations with the new models, we find a sequence of structural transitions of CTAB aggregates induced by salt concentration and added cosurfactant. In pure solutions, CTAB aggregates form spherical micelles with a compact ionic shell and a diffuse double layer that can be qualitatively described with Poisson–Boltzmann theory. Addition of decanol as a cosurfactant induces a sequence of dramatic structural transitions at low surfactant concentration and allows the stabilization of compact ordered bilayers in a well defined range of intermediate decanol/CTAB ratios. At low and high decanol/CTAB ratios spherical micelles are transformed into wormlike cylindrical micelles. At intermediate decanol/CTAB ratios, fully formed bilayers are observed, with surfactants exhibiting a compact structure with strong positional and orientational order. We discuss how the controlled self-assembly of compact CTAB bilayers at low global CTAB concentration can pave the way for the selective passivation of gold facets and the controlled formation of monodisperse gold nanorods.

Penta- and hexa-coordinated beryllium and phosphorus in high-pressure modifications of CaBe2P2O8

Beryllium oxides have been extensively studied due to their unique chemical properties and important technological applications. Typically, in inorganic compounds beryllium is tetrahedrally coordinated by oxygen atoms. Herein based on results of in situ single crystal X-ray diffraction studies and ab initio calculations we report on the high-pressure behavior of CaBe2P2O8, to the best of our knowledge the first compound showing a step-wise transition of Be coordination from tetrahedral (4) to octahedral (6) through trigonal bipyramidal (5). It is remarkable that the same transformation route is observed for phosphorus. Our theoretical analysis suggests that the sequence of structural transitions of CaBe2P2O8 is associated with the electronic transformation from predominantly molecular orbitals at low pressure to the state with overlapping electronic clouds of anions orbitals.

Stable group-IIB elements —Zn, Cd and Hg at terapascal pressures

The group-IIB elements, including zinc (Zn), cadmium (Cd), and mercury (Hg) are studied at multi-TPa pressures using first-principle electronic structure calculations coupled to an efficient structural prediction method. The experimental structural transition sequence with increasing pressure is successfully reproduced, and most metallic elements structures, for instance, simple cubic (sc), body-centered cubic (bcc) and samarium-type (Sm-type) are not stable at terapascal pressures of the group-IIB elements. In addition, the high-pressure hexagonal-close-packed (hcp) phase of Zn, Cd and Hg, can remain up to 6 TPa, and double hexagonal-close-packed (dhcp) and faced-centered cubic (fcc) phases transitions have been observed in Zn and Cd. Hg transforms directly from hcp to fcc, with dhcp absent. The calculated results also show that the c/a ratios of Zn and Cd have a similar transformation, and Hg goes towards the ideal value of 1.633 for a hexagonal close packing at high pressures. The calculated electronic properties indicate that Zn are high-pressure electrides with some of the electrons localized at interstitial sites enclosed by the surrounding atoms. The structural changes from hcp to dhcp and fcc are associated with a dynamical instability, and the soft mode phase transition mainly corresponds to the phase transition mechanism.

Unraveling the Hidden Martensitic Phase Transition in BaClF and PbClF under High Pressure Using an Ab Initio Evolutionary Approach.

We predict crystal structures of MClF (M = Ba and Pb) compounds by performing an ab initio evolutionary simulation at ambient as well as high pressure. We propose a structural transition sequence in MClF compounds as follows: P4/ nmm → Pmcn → P63/ mmc below 100 GPa. The predicted ambient and intermediate phases are consistent with X-ray and Raman spectroscopic measurements, while the newly proposed high pressure P63/ mmc phase is thermodynamically more favorable than the previously proposed monoclinic ( P21/ m) phase. It is found that the P4/ nmm → Pmcn transition is first order in nature, while the Pmcn → P63/ mmc transition is a martensitic phase transition, which is accompanied by a slight volume change and is of a displacive nature. The austenite and martensite phases coexist in a wide pressure range, especially for PbClF. The martensite phase transition is mainly driven by (1) tilting and transformation of distorted heptahedron to pentahedron environment of MCl6, which leads to negative area compressibility, and (2) cooperative displacive movement of F- ions to form a trigonal bypyramidal (MF5) structure around a metal cation. Overall, the metal cation coordination increases from 9 (MF4Cl5- P4/ nmm) to 10 (MF4Cl6- Pmcn) and, further, to 11 (MF5Cl6- P63/ mmc) under high pressure. The predicted ambient and high pressure phases are mechanically and dynamically stable under the studied pressure range. Electronic structure, bonding, and optical properties are calculated and discussed using new parametrization of Tran Blaha modified Becke Johnson potential. We find nearly isotropic optical properties (except for the ambient phase of PbClF), even though all the predicted ambient and high pressure phases are structurally anisotropic.

Structural changes of a simple peptide—Trpzip-1—in aqueous solutions and the corresponding hydration phenomena under the influence of temperature

Trpzip-1, a simple β-hairpin, is a rare example of peptide with stable secondary structure and can be a convenient model to study temperature-related processes that potential prion or amyloid proteins undergo. Although its sequence is simple, the exact processes which the peptide undergoes in aqueous solutions are quite complex and not well understood. The selection of well-established experimental (DSC, FTIR) and theoretical methods allowed to describe, on the molecular level, the sequence of Trpzip-1 structural transitions. Our results we can indicate and explain peculiarities concerning initial oligomerization and two-step denaturation mechanism. The analysis of water structure surrounding the peptide at various temperatures reveals that the hydration sphere of its monomeric, oligomeric, and unfolded states is enhanced in comparison to the “bulk” water, but in each case, it exhibits different properties. Our observations may be of general nature in terms of structural changes of peptides and accompanying phenomena in solutions.

The giant strain response mechanism in textured Mn-modified 0.925(Bi0.5Na0.5)TiO3-0.075BaTiO3 relaxor ferroelectric ceramics

This work highlights structural and domain evolution, orbital hybridization, and giant strain in the textured [(Bi1/2Na1/2)0.925Ba0.075](Ti0.998Mn0.002)O3 (BNT-7.5BT-0.2%Mn) ceramics. The as-sintered textured specimens reveal a predominant tetragonal P4bm (fraction∼94.4%) phase with a minor rhombohedral R3c (fraction∼1.4%) phase. X-ray absorption spectra indicate reduced hybridization between the O 2p and the Na 3sp/Bi 6sp/Ti 3d orbitals, implying decreased atomic bonding due to Mn doping. A mixture of Mn2+, Mn3+, and Mn4+ valence states was identified in the ceramic matrix. In-situ electric (E)-field dependent XRD results show a reversible E-field-induced phase transition, suggesting an ergodic relaxor ferroelectric. An E-field-induced giant strain of ∼0.495% at room temperature is attributed to the oriented relaxor ferroelectric P4bm phase and decreased bonding strength, which facilitate a transition from relaxor to ferroelectric phase. The poled specimen at E = 60 kV/cm shows a structural transition sequence of tetragonal P4bm + rhombohedral R3c→∼220°C tetragonal P4bm→∼483°C cubic.

Magnetic and Structural Phase Transitions in Thulium under High Pressures and Low Temperatures

The nature of 4f electrons in many rare earth metals and compounds may be broadly characterized as being either “localized” or “itinerant”, and is held responsible for a wide range of physical and chemical properties. The pressure variable has a very dramatic effect on the electronic structure of rare earth metals which in turn drives a sequence of structural and magnetic transitions. We have carried out four-probe electrical resistance measurements on rare earth metal Thulium (Tm) under high pressures to 33 GPa and low temperatures to 10 K to monitor the magnetic ordering transition. These studies are complemented by angle dispersive x-ray diffraction studies to monitor crystallographic phase transitions at high pressures and low temperatures. We observe an abrupt increase in magnetic ordering temperature in Tm at a pressure of 17 GPa on phase transition from ambient pressure hcp-phase to α-Sm phase transition. In addition, measured equation of state (EOS) at low temperatures show anomalously low thermal expansion coefficients likely linked to magnetic transitions.

Prediction of Novel High-Pressure Structures of Magnesium Niobium Dihydride.

On the basis of a combination of the particle-swarm optimization technique and density functional theory (DFT), we explore the crystal structures of MgH2, NbH2, and MgNbH2 under high pressure. The enthalpy-pressure (H-P) diagrams indicate that the structural transition sequence of MgH2 is α → γ → δ → ε → ζ and that NbH2 transforms from the Fm3̅m phase to the Pnma phase at 47.80 GPa. However, MgNbH2 is unstable when the pressure is too low or too high. Two novel MgNbH2 structures, the hexagonal P6̅m2 phase and the orthorhombic Cmcm phase, are discovered, which are stable in the pressure ranges of 13.24-128.27 GPa and 128.27-186.77 GPa, respectively. The P6̅m2 phase of MgNbH2 consists of alternate layers of polymetric NbH6 and MgH6 triangular prisms, while the Cmcm phase contains distorted MgH6 trigonal prisms. The calculated elastic constants and phonon dispersions confirm that both phases are mechanically and dynamically stable. The analyses of density of states (DOS), electron localization function (ELF), and Bader charge demonstrate that a combination of ionic and metallic bonds exist in both P6̅m2 and Cmcm phases. We hope the newly predicted magnesium niobium dihydrides with desirable electronic properties will promote future experimental and theoretical studies on mixed main group-transition metal hydrides.

Site-specific spin crossover in Fe2TiO4 post-spinel under high pressure up to nearly a megabar

X-ray diffraction studies to ~90 GPa at room temperature show that Fe$_{2}$TiO$_{4}$ ferrous inverse spinel undergoes the following sequence of structural transitions : cubic (Fd3m) to tetragonal (I41/amd)to orthorhombic(Cmcm) to orthorhombic(Pmma),at the indicated onset transition pressures. Within the Cmcm phase, site-specific spin crossover is initiated and involves only highly distorted octahedral sites constituting ~25% of all Fe locations. This is manifest as a steeper volume decrease of dV/V0 ~ 3.5% beyond ~40 GPa and an emergent diamagnetic component discerned in 57Fe M\"ossbauer spectroscopy at variable cryogenic temperatures. A subsequent Cmcm to Pmma Fe/Ti disorder-order reconfiguration is facilitated at 6-fold coordinated (octahedral) sites. The rest of the high-spin Fe in 6-fold and 8-fold coordinated sites (~75% abundance) in the Pmma phase exhibit average saturation internal magnetic fields of H$_{hf}$ ~ 42 T to ~90 GPa, typical of spin-only (orbitally quenched) Fermi-contact values. By contrast average H$_{hf}$ ~ 20 T values, signifying unquenched orbital moments, occur below the 40-45 GPa spin-crossover initiation regime in the Cmcm phase. Therefore site-specific spin crossover invokes a cooperative lattice response and polyhedral distortions at the rest of the high-spin Fe sites, translating to 3d level (sub-band) changes and consequential orbital moment quenching. Near ~90 GPa Fe$_{2}$TiO$_{4}$ is a partially spin-converted chemically ordered Pmma post-spinel structure having a persistent charge gap of ~100 meV. Despite structural symmetry changes, partial spin crossover and lattice compressibility resulting in a ~33% total reduction in unit-cell volume and corresponding 3d bandwidth broadening, strong electron correlations persist at high densification.

Comparative study of structural phase transitions in bulk and powdered Fe–27Ga alloy by real-time neutron thermodiffractometry

Phase transformations in an iron–gallium alloy have been analyzed by in situ real-time neutron diffraction in the temperature range from 293 to 1223 K. Two compositionally identical samples were studied: the first was in the as-cast bulk state, and the second was ground into a powdered state. In both samples, the same sequence of structural transitions was recorded on heating with a constant heating rate (D03 → A2 → L12 → D019 → A2), and the same structural state (D03 + L12) was recorded after slow cooling to room temperature. Owing to strong texture in the bulk sample, only diffraction patterns of the powdered sample were treated with the Rietveld method to determine the volume fractions of the coexisting phases, the coefficients of thermal expansion, and the thermal and static atomic disorder parameters. The occupancy of Ga positions and the ordered iron magnetic moment were refined at selected temperatures. The level of microstrain in the crystallites in the initial as-quenched state is small, but it sharply increases in the course of phase transitions when the alloy is heated. The microstrains are high and strongly anisotropic after slow cooling. Generally, phase transformations occur similarly in the powdered and bulk samples, but with a noticeable difference in details. The fulfilled analysis of the bulk and powdered samples allowed the real possibilities of the quantitative neutron diffraction analyses of phase transitions in ferromagnetic ordered alloys to be assessed.

Spin-lattice coupling phase transition and phonon anomalies in bismuth ferrite BiFeO3

Phase transition, phonon vibration, and magnetization in (100) BiFeO3 (BFO) multiferroic single crystals have been characterized as functions of temperature. The BFO single crystal exhibits a weak ferromagnetic hysteresis loop possibly due to appearance of ferromagnetic FeOFe orderings and a modulation of the FeOFe bond. Zero-field-cooled (ZFC) and field-cooled (FC) magnetic susceptibilities suggest a weak spin-glass behavior below ∼200 K. High-resolution transmission electron microscopy (HRTEM) suggests a rhombohedral R3c symmetry (with tilted FeO6 octahedra) and lattice distortion in the surface layer. The BFO crystal undergoes a structural transition sequence of rhombohedral−tetragonal−orthorhombic− cubic at ∼620–640, ∼1000, and ∼1100 K, respectively. The spin-lattice coupling accounts for the rhombohedraltetragonal transition upon approaching the Néel temperature (TN). The low-frequency Raman-active modes ψ4,II, E(1), A1(1), and A1(2) reveal clear softening anomalies in frequency shifts and broad peaks in full-width-at-half-maximum (FWHM) around 450 K, which is attributed to the FeOFe ordering transition without change of structural symmetry.

Salt Effects on the Thermodynamics of a Frameshifting RNA Pseudoknot under Tension

Because of the potential link between −1 programmed ribosomal frameshifting and response of a pseudoknot (PK) RNA to force, a number of single-molecule pulling experiments have been performed on PKs to decipher the mechanism of programmed ribosomal frameshifting. Motivated in part by these experiments, we performed simulations using a coarse-grained model of RNA to describe the response of a PK over a range of mechanical forces (fs) and monovalent salt concentrations (Cs). The coarse-grained simulations quantitatively reproduce the multistep thermal melting observed in experiments, thus validating our model. The free energy changes obtained in simulations are in excellent agreement with experiments. By varying f and C, we calculated the phase diagram that shows a sequence of structural transitions, populating distinct intermediate states. As f and C are changed, the stem–loop tertiary interactions rupture first, followed by unfolding of the 3′-end hairpin (I⇌F). Finally, the 5′-end hairpin unravels, producing an extended state (E⇌I). A theoretical analysis of the phase boundaries shows that the critical force for rupture scales as (logCm)α with α=1(0.5) for E⇌I (I⇌F) transition. This relation is used to obtain the preferential ion–RNA interaction coefficient, which can be quantitatively measured in single-molecule experiments, as done previously for DNA hairpins. A by-product of our work is the suggestion that the frameshift efficiency is likely determined by the stability of the 5′-end hairpin that the ribosome first encounters during translation.

Mechanical Force and Salt Effects on the Thermodynamics of a Frameshifting RNA Pseudoknot

Mechanical resistance of pseudoknot (PK) in mRNA deemed relevant in stimulating programmed ribosomal frameshifting (PRF) has lead to a number of single molecule pulling experiments in order to decipher the PRF mechanism. Motivated by these studies, we performed simulations to describe the response of a Beet Western Yellow Virus (BWYV) PK over a range of mechanical forces (fs) and monovalent salt concentrations (Cs) using a coarse-grained model. The simulations based on the model quantitatively reproduces the three-stage thermal melting of BWYV PK and the stability of the folded state (F) with respect to the unfolded state (U) inferred in ensemble experiments setting the stage for making testable predictions. The predicted phase diagram in the [C, f] plane shows that a sequence of structural transitions populating intermediates occur as f and C are changed. The least stable tertiary interactions rupture first followed by unfolding of the 3′-end hairpin. Finally, the most stable 5′-end hairpin unravels producing a stretched state. A theoretical analysis of the phase boundaries, separating the F and an intermediate state (I), and I and U states shows that the critical force for rupture scales as (log Cm)α with α=1 (=0.5) for U−I (I−F) transition. This relation is used to obtain the ion-preferential coefficients, which suggests that ion-RNA interactions can be quantitatively measured using laser optical tweezers experiments. We predict that −1 PRF efficiency should be determined by the stability of the 5′ hairpin that the ribosome first encounters. A good correlation between the increase in −1 PRF efficiency and increase in the stability of 5′ hairpin supports this prediction.

Boundaries for martensitic transition of (7)Li under pressure.

Physical properties of lithium under extreme pressures continuously reveal unexpected features. These include a sequence of structural transitions to lower symmetry phases, metal-insulator-metal transition, superconductivity with one of the highest elemental transition temperatures, and a maximum followed by a minimum in its melting line. The instability of the bcc structure of lithium is well established by the presence of a temperature-driven martensitic phase transition. The boundaries of this phase, however, have not been previously explored above 3 GPa. All higher pressure phase boundaries are either extrapolations or inferred based on indirect evidence. Here we explore the pressure dependence of the martensitic transition of lithium up to 7 GPa using a combination of neutron and X-ray scattering. We find a rather unexpected deviation from the extrapolated boundaries of the hR3 phase of lithium. Furthermore, there is evidence that, above ∼3 GPa, once in fcc phase, lithium does not undergo a martensitic transition.