Search results for "molecular-dynamics"
showing 10 items of 33 documents
Crystal Chemistry of CdIn2S4, MgIn2S4, and MnIn2S4 Thiospinels under High Pressure
2012
We report X-ray diffraction measurements in CdIn2S4, MgIn2S4, and MnIn2S4 thiospinels at room temperature and high pressures. The pressure dependences of the structural parameters have been determined and compared to those from theoretical calculations. It is found that the three thiospinels have similar bulk moduli (B-0) between 75 and 80 GPa (B-0' similar to 3). The degree of inversion of these thiospinels has also been determined. The three thiospinels undergo a phase transition toward a defect LiTiO2-type structure above 9.5, 8.3, and 6.8 GPa in CdIn2S4, MgIn2S4, and MnIn2S4, respectively. Interestingly, the low- and high-pressure phases belong to the same symmetry group (Fd-3m), the tr…
Structural and vibrational study of pseudocubic CdIn2Se4 under compression
2014
We report a comprehensive experimental and theoretical study of the structural and vibrational properties of a-CdIn2Se4 under compression. Angle-dispersive synchrotron X-ray diffraction and Raman spectroscopy evidence that this ordered-vacancy compound with pseudocubic structure undergoes a phase transition (7 GPa) toward a disordered rocksalt structure as observed in many other ordered-vacancy compounds. The equation of state and the pressure dependence of the Raman-active modes of this semiconductor have been determined and compared both to ab initio total energy and lattice dynamics calculations and to related compounds. Interestingly, on decreasing pressure, at similar to 2 GPa, CdIn2Se…
Water-Hydrophobic Zeolite Systems
2012
Water intrusion-extrusion in hydrophobic microporous AFI, IFR, MTW and TON pure silica zeolites (zeosils) has been investigated through molecular dynamics (MD) simulations. It was found that intruded water volumes correlate with the free volume of the zeosil unit cells. Calculated adsorption isotherms allowed us to estimate the amounts of water intruded, and deviations from experiments (lower experimental with respect to calculated intrusion pressures) have been;explained in terms of connectivity defects in the synthesized materials. Water phase transitions in defectless zeosils occur in a narrow range at high pressure. On the basis of a simple model, we derived a thermodynamic equation tha…
Myoglobin embedded in saccharide amorphous matrices: water-dependent domains evidenced by small angle X-ray scattering
2010
We report Small Angle X-ray Scattering (SAXS) measurements performed on samples of carboxy-myoglobin (MbCO) embedded in low-water trehalose glasses. Results showed that, in such samples, "low-protein" trehalose-water domains are present, surrounded by a protein-trehalose-water background; such finding is supported by Infrared Spectroscopy (FTIR) measurements. These domains, which do not appear in the absence of the protein and in analogous sucrose systems, preferentially incorporate the incoming water at the onset of rehydration, and disappear following large hydration. This observation suggests that, in organisms under anhydrobiosis, analogous domains could play a buffering role against th…
Observing myoglobin proteinquake with an X-ray free-electron laser
2015
The events following the photodissociation of the bond be- tween myoglobin and its ligand have been extensively studied with a variety of experimental, theoretical and computational methods [1]. The results of these investigations have been rationalized in terms of a model that implies a protein quake- like motion [2], i.e. the propagation of the strain released upon photoexcitation through the protein similar to the prop- agation of acoustic waves during an earthquake. The exper- imental investigations performed so far have been based on spectroscopic measurements or did not have sufficient time- resolution to measure the timescale of such “proteinquake”. We have obtained direct experiment…
Lattice Dynamics Study of HgGa2Se4 at High Pressures
2013
We report on Raman scattering measurements in mercury digallium selenide (HgGa2Se4) up to 25 GPa. We also performed, for the low-pressure defect-chalcopyrite structure, lattice-dynamics ab initio calculations at high pressures which agree with experiments. Measurements evidence that the semiconductor HgGa2Se4 exhibits a pressure-induced phase transition above 19 GPa to a previously undetected structure. This transition is followed by a transformation to a Raman-inactive phase above 23.4 GPa. On downstroke from 25 GPa until 2.5 GPa, a broad Raman spectrum was observed, which has been attributed to a fourth phase, and whose pressure dependence was followed during a second upstroke. Candidate …
Elastic neutron scattering of dry and rehydrated trehalose coated carboxy-myoglobin
2008
We report here a comparison between the hydrogen atoms mean square displacements measured by elastic neutron scattering on trehalose coated carboxy-myoglobin, at ILL on the backscattering spectrometers IN13 and IN16. An inconsistency is observed when comparing the mean square displacements measured on the two spectrometer, on samples of identical composition, since they resulted of larger amplitude on IN13 (either in condition of drought or after overnight rehydration under 75% D2O atmosphere), notwithstanding the lower time window accessible on this instrument with respect to IN16. Such inconsistency disappears when the data obtained on this last spectrometer are analyzed in two separate r…
Anomalous surface diffusion of protons on lipid membranes.
2014
AbstractThe cellular energy machinery depends on the presence and properties of protons at or in the vicinity of lipid membranes. To asses the energetics and mobility of a proton near a membrane, we simulated an excess proton near a solvated DMPC bilayer at 323 K, using a recently developed method to include the Grotthuss proton shuttling mechanism in classical molecular dynamics simulations. We obtained a proton surface affinity of −13.0 ± 0.5 kJ mol−1. The proton interacted strongly with both lipid headgroup and linker carbonyl oxygens. Furthermore, the surface diffusion of the proton was anomalous, with a subdiffusive regime over the first few nanoseconds, followed by a superdiffusive re…
NMR structure of a non-conjugatable, ADP-ribosylation associated, ubiquitin-like domain from Tetrahymena thermophila polyubiquitin locus.
2019
Abstract Background Ubiquitin-like domains (UbLs), in addition to being post-translationally conjugated to the target through the E1-E2-E3 enzymatic cascade, can be translated as a part of the protein they ought to regulate. As integral UbLs coexist with the rest of the protein, their structural properties can differ from canonical ubiquitin, depending on the protein context and how they interact with it. In this work, we investigate T.th-ubl5, a UbL present in a polyubiquitin locus of Tetrahymena thermophila, which is integral to an ADP-ribosyl transferase protein. Only one other co-occurrence of these two domains within the same protein has been reported. Methods NMR, multiple sequence al…
Pressure-Driven Isostructural Phase Transition in InNbO4: In Situ Experimental and Theoretical Investigations
2017
[EN] The high-pressure behavior of technologically important visible-light photocatalytic semiconductor In.NbO4, adopting a monoclinic wolframite-type structure at ambient conditions, was investigated using synchrotron-based X-ray diffraction, Raman spectroscopic measurements, and first-principles calculations. The experimental results indicate the occurrence of a pressure-induced isostructural phase transition in the studied compound beyond 10.8 GPa. The large volume collapse associated with the phase transition and the coexistence of two phases observed over a wide range of pressure shows the nature of transition to be first-order. There is an increase in the oxygen anion coordination num…