Molecular dynamics and phase transitions in phospholipid monolayers at liquid-liquid interfaces

Stablen-hexadecane/water andn-tetradecane/water macroemulsions containing monolayers of natural (egg yolk lecithin, EY) and synthetic (dimyristoylphosphatidylcholine, DMPC) phospholipids at liquid-liquid interfaces were prepared. The existence of the monolayers was proved by studying the reduction kinetics of a surface-active spin probe with ascorbate anions. Spin labeled derivatives of stearic acid in which the nitroxide group is locared at different distances from the polar head (5-, 12-, and 16-doxylstearic acids) were used to study the temperature dependences of the molecular ordering, rotational mobility, and local polarity in the monolayers in emulsions and also in bilayers in liposomes obtained from the same lipids. In the EY monolayers, the degree of spin probe solubilization is higher, while the order parameters (S) and rotational correlation times (τ) are lower than those in EY bilayers. The differences between these parameters for mono- and bilayers increase with an increase in the distance of the reporter group from the aqueous phase. In the DMPC monolayers, a first-order phase transition was detected by measuring the temperature dependences ofS and τ. The temperature region of the phase transition in monolayers is shifted to lower temperatures with respect to that for bilayers and depends on the nature of the oil phase. It was concluded that the phospholipid monolayers in emulsions incorporate hydrocarbon molecules, whose concentration in the DMPC monolayers increases on going from the low-temperature (gel) to the high-temperature (liquid crystal) phase. Translated fromIzvestiya Akademii Nauk. Seriya Khimicheskaya, No. 3, pp. 418–425, March, 1998.     

Pressure-induced phase transitions in multiferroic RbFe(MoO4)2—Raman scattering study

High pressure Raman scattering experiments were performed on RbFe(MoO₄)₂. These experiments revealed that two phase transitions take place in RbFe(MoO₄)₂ at very low pressures, i.e. between ambient pressure and 0.2 GPa and between 0.4 and 0.7 GPa. Raman results showed that at the first phase transition the room temperature P3?m1 phase transforms into the P3? phase, which is also observed at ambient pressure below 190 K. The second pressure-induced phase transition occurs into a low symmetry phase of unknown symmetry. The performed lattice dynamics calculations for the P3?m1 phase and ab initio calculation of the structural changes under hydrostatic pressure helped us to get better insights into the mechanism of the observed phase transitions.     

Molecular dynamics and phase behavior of polystyrene/poly(vinyl methyl ether) blend in the presence of nanosilica

The variation of phase morphology, critical temperature of demixing, and molecular dynamics for polystyrene/poly(vinyl methyl ether)(PS/PVME) blends induced by hydrophilic nanosilica(A200) or hydrophobic nanosilica(R974) was investigated. With the phase separation of blend matrix, A200 migrated into PVME-rich phase due to strong interaction between A200 and PVME, while R974 moved into PS-rich phase. The thermodynamic miscibility and concentration fluctuation during phase separation of blend matrix were remarkably retarded by A200 nanoparticles due to the surface adsorption of PVME on A200, verified by the correlation length ξ near the critical region from rheological measurement and the weakened increment of reversing heat capacity(ΔC_p) during glass transition via modulated differential scanning calorimetry(MDSC). The restricted chain diffusion induced by nanosilica still occurred despite no influence of A200 and R974 on the segmental dynamics of homogenous blend matrix. The interactions between nanosilica and polymer components could restrict the terminal relaxation of blend matrix and further manipulate their phase behavior.     

The pressure induced B1-B2 phase transition of alkaline halides and alkaline earth chalcogenides. A first principles investigation

In this work, we considered the pressure induced B1-B2 phase transition of AB compounds. The DFT calculations were carried out for 11 alkaline halides, 11 alkaline earth chalcogenides and the lanthanide pnictide CeP. For both the B1 and the B2 structures of each compound, the energy was calculated as a function of the cell volume. The transition pressure, the bulk moduli and their pressure derivatives were obtained from the corresponding equations of state. The transition path of the Buerger mechanism was described using roots of the transition matrix. We correlated the computed enthalpies of activation to some structure defining properties of the compounds. A fair correlation to Pearsons hardness of the ions was observed.     

Structure and phase transitions of a liquid crystalline polymer

Summary The structures, textures as well as thermodynamic properties of a side chain polymer exhibiting a liquid crystalline phase in addition to a partially crystalline state and the isotropic fluid state were investigated. Furthermore the kinetics of phase transitions between these states were analyzed. It was found that the properties of this polymer are intermediate between that of low molecular weight liquid crystals and common polymers. In particular it was observed that the relation between the liquid crystalline texture and the structure is different from that of low molecular weight liquid crystals and that the properties of the crystalline and liquid crystalline state depend strongly on the tacticity of the polymer.

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Zusammenfassung Für ein Seitenkettenpolymeres, das zusätzlich zum teilkristallinen Zustand und zur isotropen Schmelze einen flüssig-kristallinen Zustand aufweist, wurden die Strukturen und Texturen untersucht sowie thermodynamische Eigenschaften. Außerdem wurde die Kinetik der Phasenumwandlungen analysiert. Es zeigt sich, daß die Eigenschaften zwischen denen üblicher Polymerer und denen von niedrigmolekularen flüssigen Kristallen liegen. Insbesondere zeigte sich, daß die Beziehung zwischen molekularer Struktur und Textur von der bei niedrigmolekularen flüssigen Kristallen abweicht, und daß die Taktizität der Kette einen starken Einfluß auf die Eigenschaften nicht nur der kristallinen Phase sondern auch der flüssig-kristallinen Phase ausübt.

     

Atomistic in situ investigation of the morphogenesis of grains during pressure-induced phase transitions: molecular dynamics simulations of the B1-B2 transformation of RbCl

The mechanistic details of the pressure-induced B1-B2 phase transition of rubidium chloride are investigated in a series of transition path sampling molecular dynamics simulations. The B2→B1 transformation proceeds by nucleation and growth involving several, initially separated, nucleation centers. We show how independent and partially correlated nucleation events can function within a global mechanism and explore the evolution of phase domains during the transition. From this, the mechanisms of grain boundary formation are elaborated. The atomic structure of the domain-domain interfaces fully support the concept of Bernal polyhedra. Indeed, the manifold of different grain morphologies obtained from our simulations may be rationalized on the basis of essentially only two different kinds of Bernal polyhedra. The latter also play a crucial role for the B1→B2 transformation and specific grain boundary motifs are identified as preferred nucleation centers for this transition.     

Crystal structures and phase transitions of Sr2CrSbO6

Sr₂CrSbO₆ was synthesized by the conventional solid-state reaction process. X-ray powder diffraction (XRPD) and neutron powder diffraction (NPD) has been used to reinvestigate the structure at room temperature and to study the phase transitions at high- and low-temperature. Rietveld analysis revealed that Sr₂CrSbO₆ crystallizes at room temperature in a monoclinic system having a space group I2/m, with a=5.5574(1) Å; b=5.5782(1) Å; c=7.8506(2) Å and β=90.06(2), no P2₁/n space group as was previously reported. The high-temperature study (300-870 K) has shown that the compound presents the following temperature induced phase-transition sequence: I2/m-I4/m-Fm-3m. The low-temperature study (100-300 K) demonstrated that the room-temperature I2/m monoclinic symmetry seems to be stable down to 100 K.     

Structure and dynamics of water at water|Pt interface as seen by molecular dynamics computer simulation

Five molecular dynamics computer simulations were performed to study the structural and dynamical properties of water next to uncharged and charged Pt surfaces. The results show that the structure of a water layer adsorbed on the metal surface is very sensitive to the details of the water–metal potential. While patches of short-living hexagonal ice-like structure are observed in the adsorbed water layer next to the uncharged Pt(111) surface, a square lattice solid-like structure is seen for the layer on top of the uncharged Pt(100) surface. The orientational ordering for the following two layers of water next to uncharged Pt is displaying a preference towards the orientations that are characteristic of hexagonal ice-I, while water is liquid-like in these layers. In the presence of a high value external electric field water reorients and undergoes a layering transition.     

Molecular dynamics simulation of the water|nitrobenzene interface

The structure and dynamics of the neat water|nitrobenzene liquid|liquid interface are studied at 300 K using molecular dynamics computer simulations. The water is modeled using the flexible SPC potential, and the nitrobenzene is modeled using an empirically determined nitrobenzene potential energy function. Although nitrobenzene is a polar liquid with a large dielectric constant, the structure of the interface is similar to other water|non-polar organic liquid interfaces. Among the main structural features we describe are an enhancement of interfacial water hydrogen bonds, the specific orientation of water dipoles and nitrobenzene molecules, and a rough surface that is locally sharp. Surface roughness is also characterized dynamically. The dynamics of molecular reorientation are shown to be only mildly modified at the interface. The effect due to the polarizable many-body potential energy functions of both liquids is investigated and is found to affect only mildly the above results.     

Structure formation and dynamics of water in strong external electric fields

We have performed molecular dynamics computer simulations of water in homogeneous external electric fields which were varied in a wide range of field strengths. The dielectric response is found to be linear up to fields E₀≈0.01 V/Å from where dielectric saturation effects become important. At fields of E₀≈3 V/Å a phase transition into an ordered, ice-like structure is observed, which is stabilized through hydrogen-bonds. With an increasing external electric field, the frequency spectrum of the water dynamics shows a remarkable red shift of the intramolecular modes and a blue shift of the librational motions, where the frequency varies quadratically with the field strength. A simple analytical model is discussed which reproduces the observed behavior.     

Molecular modeling and dynamics of neuropeptide Y

Summary A combination of molecular modeling and molecular dynamics (MD) is used to determine a theoretical structure for neuropeptide Y (NPY). Starting with the X-ray structure for avian pancreatic polypeptide (APP), the substituted amino acids were mutated, the side chains oriented to local potential energy minima, and the entire structure minimized and subjected to an MD simulation. Comparison of the resulting NPY structure with APP X-ray and MD results showed secondary structural elements to be maintained and RMS fluctuations to be similar, although differences in both were observed. The approach presented offers a means to study the structure-function relationships of NPY and other similar polypeptides when combined with pharmacological measurements.Abbreviations NPY Neuropeptide Y - APP Avian pancreatic polypeptide - ABNR Adopted-basis Newton Raphson - MD Molecular dynamics     

Phase transitions of LiAlO2 at high pressure and high temperature

This work presents a comprehensive study on phase transitions in LiAlO₂ system at high pressures and temperatures (0.5-5.0 GPa and 300-1873 K, respectively), as well as the phase stability for polymeric phases of LiAlO₂ in the studied P-T space by X-ray diffraction (XRD). Besides the previously described polymorphic hexagonal α-phase, orthorhombic β-phase and tetragonal δ-phase, a possible new phase of LiAlO₂ was observed after the tetragonal γ-LiAlO₂ sample was treated at 5.0 GPa and 389 K. The stable regimes of these high-pressure phases were defined through the observation of coexistence points of the polymeric phases. Our results revealed that LiAlO₂ could experience structural phase transitions from γ-LiAlO₂ to its polymorphs at lower pressures and temperatures compared to the reported results. Hexagonal α-LiAlO₂ with highly (003) preferential orientation was prepared at 5.0 GPa and 1873 K.     

Molecular dynamics simulations of the isolated domain 1 of annexin I

Annexin molecules consist of a symmetrical arrangement of four domains of identical folds but very different sequences. Nuclear magnetic resonance (NMR) experiments on the isolated domains of annexin I in aqueous solution have indicated that domain 1 retains its native structure whereas domain 2 unfolds. Therefore these two domains constitute interesting models for comparative simulations of structural stability using molecular dynamics. Here we present the preliminary results of molecular dynamics simulations of the isolated domain 1 in explicit water at 300 K, using two different simulation protocols. For the first, domain 1 was embedded in a 46 ? cubic box of water. A group-based non-bonded cut-off of 9 ? with a 5–9 ? non-bonded switching function was used and a 2 fs integration step. Bonds containing hydrogens were constrained with the SHAKE algorithm. These conditions led to unfolding of the domain within 400 ps at 300 K. In the second protocol, the domain was embedded in a 62 ? cubic box of water. An atom-based non-bonded cut-off of 8–12 ? using a force switching function for electrostatics and a shifting function for van der Waals interactions were used with a 1 fs integration step. This second protocol led to a native-like conformation of the domain in accord with the NMR data which was stable over the whole trajectory (∼2 ns). A small, but well-defined relaxation of the structure, from that observed for the same domain in the entire protein, was observed. This structural relaxation is described and methodological aspects are discussed. Received: 10 May 1998 / Accepted: 4 August 1998 / Published online: 2 November 1998     

Magnetic phase transitions in nanostructures induced by shear stress under high pressure

Magnetic phase transitions of the first and second order were revealed by Mössbauer spectroscopy in nanosystems of - and -ferric oxides and metallic europium subjected to shear stress (240°) under high pressure (20 kbar). For - and -ferric oxide nanoclusters, the Curie (Neel) points decreased to 300 K, whereas for nanostructured europium the Neel point increased from 90 to 100 K. The thermodynamic model of magnetic phase transitions predicting a change in the character of magnetic phase transitions and a decrease (increase) in the critical Neel (Curie) points in nanoclusters was developed. The type of magnetic phase transitions and the change in the critical points were caused by defects in nanoclusters, whose maximum concentration was observed for the clusters with the 20—50 nm size range.     

Molecular dynamics simulation of the aggregation of colloidal particles

The spontaneous time evolution of systems containing N colloidal particles (N = 12, 24, 100) in a spherical cell of volume V at a constant volume fraction φ=0.1 was studied by a molecular dynamics method in the NVT ensemble. The starting velocities of the particles are allocated according to the Maxwell distribution at T=273 K.

Pairwise interaction of the particles was specified by molecular, electrostatic and elastic forces. The changes in the potential energy of the systems were calculated during the establishment of dynamic equilibrium. Coagulation takes place at sufficiently high values of the Hamaker constant. The value of the coefficient of Brownian diffusion, which is calculated from the half-time of coagulation, is found to be close to the known value for aqueous dispersions. The inclusion of electrostatic forces prevents coagulation.

The results obtained are in agreement with those obtained using theories of aggregate formation. Some structural characteristics of aggregates and stable systems are discussed.     

High-pressure phase transitions of Cu2O

In the present study, we extensively explored the crystal structures of Cu₂O on increasing the pressure from 0 GPa to 24 GPa using the first-principles density functional calculations. A series of pressure-induced structure phase transitions of Cu₂O are examined. The calculated results show that the phase transitions (Pn-3m phase → R-3m phase → P-3m1 phase) occur at 5 GPa and 12 GPa, respectively. The P-3m1 phase is found to be the metallic phase via band-gap closure under high pressure.     

Spectroscopic modifications of Pippard relations: first-order and second-order phase transitions in NH4Cl

In this study we introduce the spectroscopic modifications of Pippard relations and apply them to the disorder-induced Raman modes of NH₄Cl in the first-order (P=0) and second-order (2.8 kbar) phase regions in this crystalline system. We obtain linear variations of the specific heat C_P with our observed frequency shifts [(1/ν)(∂ν/∂T)_P] of those Raman modes studied for the first-order and second-order phase transitions in NH₄Cl. This will be discussed in detail.     

基于分子对接的thanatin与NDM-1分子动力学模拟研究

耐碳青霉烯类抗生素的超级细菌给人类健康带来了严重威胁,其所携带的金属 β-内酰胺酶编码基因是耐药性的主要来源。NDM-1作为其中传播最广、活性最强的 β-内酰胺酶,其抑制剂的研发刻不容缓。具有广谱作用的抗菌肽thanatin对NDM-1展现出了较好的抑制效果,但抑制机理并不清楚。本文使用HPEPDOCK与Rosetta FlexPepDock服务器,将thanatin与NDM-1进行了分子对接,并使用Desmond软件包对对接模型进行了分子动力学模拟。结果表明,thanatin与NDM-1活性中心的Zn2+ 并无直接相互作用,而作为竞争性抑制剂结合于NDM-1的活性口袋,阻止抗生素分子进入活性口袋与Zn2+ 结合,从而抑制NDM-1的水解活性。本文为研发有效的NDM临床抑制剂探索了可行的方法。     

High-temperature FeS-FeS2 solid-state transitions: Reactions of solid mackinawite with gaseous H2S

Phase transitions and reactions of non-oxidized and surface-oxidized mackinawite (FeS) in helium and H₂S gas were investigated by means of X-ray diffraction (XRD), X-ray photoelectron spectroscopy (XPS) and density functional theory (DFT). DFT was used to obtain optimized structures of the iron-sulfur phases mackinawite, hexagonal pyrrhotite, greigite, marcasite and pyrite and to determine the thermochemical properties of reactions of mackinawite with H₂S to these phases. The phase transitions of mackinawite to hexagonal pyrrhotite are endothermic, while reactions to greigite, marcasite and pyrite are exothermic. The experiments show that non-oxidized mackinawite converts into hexagonal pyrrhotite (Fe₉S₁₀ first and then Fe₇S₈) in He and also in H₂S but at a lower temperature. No further reactions can be observed under these conditions. In the case of surface-oxidized mackinawite, the extent of surface oxidation determines the course and the final product of the reaction with H₂S. If the extent of surface oxidation is low, only Fe²⁺ is oxidized to Fe³⁺. Under these conditions mackinawite converts into the mixed-valence thiospinel compound greigite. In case of pronounced surface oxidation all surface Fe centers are oxidized to the Fe³⁺ state and S²⁻ is oxidized to SO₄²⁻. Oxidation of sulfur is a prerequisite for the formation of pyrite.     

Crystal structures and phase behaviour of acetaldehyde-d4: a study by high-resolution neutron powder diffraction and calorimetry

High-resolution neutron powder diffraction is particularly suited for structure solution and refinement of low-melting point organic crystals of moderate complexity. Here we present the ab initio structure solution and refinement of stable-phase and metastable-phase perdeuterated acetaldehyde (m.p.: 151 K). In the stable phase, the molecule crystallises in the space group P2₁/c (no. 14) with a=3.9069(1) Å, b=5.4224(1) Å, c=12.1868(1) Å, β=94.2970(2)° at 5 K, Z=4. In the metastable phase, the molecule crystallises in the space group Pna2₁ (no. 33) with a=5.1973(1) Å, b=6.9791(1) Å, c=6.9712(1) Å at 5 K, Z=4. The metastable to stable phase transition is characterised by heat capacity measurements.