Temperature Dependence Of Mean Square Displacement Research Articles

Towards anab initiotheory for the temperature dependence of electric field gradients in solids: Application to hexagonal lattices of Zn and Cd

Based on ab initio band structure calculations we formulate a general theoretical method for description of the temperature dependence of electric field gradient in solids. The method employs a procedure of averaging multipole electron density component (l \neq 0) inside a sphere vibrating with the nucleus at its center. As a result of averaging each Fourier component (K \neq 0) on the sphere is effectively reduced by the square root of the Debye-Waller factor [exp(-W)]. The electric field gradient related to a sum of K-components most frequently decreases with temperature (T), but under certain conditions because of the interplay between terms of opposite signs it can also increase with T. The method is applied to calculations of the temperature evolution of the electric field gradients of pristine zinc and cadmium crystallized in the hexagonal lattice. For calculations within our model of crucial importance is the temperature dependence of mean-square displacements which can be taken from experiment or obtained from the phonon modes in the harmonic approximation. For the case of Zn we have used data obtained from single crystal x-ray diffraction. In addition, for Zn and Cd we have calculated mean-square displacements with the density functional perturbation treatment of the Quantum Espresso package. With the experimental data for displacements in Zn our calculations reproduce the temperature dependence of the electric field gradient very accurately. Within the harmonic approximation of the Quantum Espresso package the decrease of electric field gradients in Zn and Cd with temperature is overestimated. Our calculations indicate that the anharmonic effects are of considerable importance in the temperature dependence of electric field gradients.

Role of Hydration Layer in Dynamical Transition in Proteins: Insights from Translational Self-Diffusivity.

Elucidation of the role of hydration water underpinning dynamical crossover in proteins has proven challenging. Indeed, many contradictory findings in the literature seek to establish either causal or correlative links between water and protein behavior. Here, via molecular dynamics, we compute the temperature dependence of mean-square displacement and translational self-diffusivities for both hen egg white lysozyme and its hydration layer from 190 to 300 K. We find that the protein's mobility increases sharply at ∼230 K, indicating dynamical onset; concerted motion with hydration-water molecules is evident up to ∼285 K, confirming dynamical correlation between them. Exploring underlying mechanisms of such concerted motion, we scrutinize the water-protein hydrogen-bonding network as a function of temperature, noting sharp deviation from linearity of the hydrogen bond number's profile with temperature originating near the protein dynamical transition. Our studies reveal a common temperature profile/dependence of self-diffusivity values of the protein, hydration water, and the bulk solvent, originating from a common dependence on the bulk solvent viscosity, ηS. The key mechanistic role adopted by the protein-water hydrogen bond network in relation to the onset of proteins' dynamical transition is also discussed.

Parameters for temperature dependence of mean-square displacements for B-, Bi- and Tl-containing binary III–V compounds

Mean-square displacements were computed within the harmonic approximation from ab initio force constants for binary B-, Tl- and Bi-containing III-V compounds in sphalerite crystal structures in the temperature range from 0 to 1000 K in steps of 1 K. An Einstein model with a temperature-dependent characteristic frequency was used to model the temperature dependence of the mean-square displacements. A Gaussian was fitted to the temperature dependence of the characteristic frequency and parameters of the Gaussian are given. Phonon dispersion relations and densities of states derived during the computation of the mean-square displacements are also shown.

Effect of conformational states on protein dynamical transition

In order to examine the properties specific to the folded protein, the effect of the conformational states on protein dynamical transition was studied by incoherent elastic neutron scattering for both wild type and a deletion mutant of staphylococcal nuclease. The deletion mutant of SNase which lacks C-terminal 13 residues takes a compact denatured structure, and can be regarded as a model of intrinsic unstructured protein. Incoherent elastic neutron scattering experiments were carried out at various temperature between 10 K and 300 K on IN10 and IN13 installed at ILL. Temperature dependence of mean-square displacements was obtained by the q-dependence of elastic scattering intensity. The measurements were performed on dried and hydrated powder samples. No significant differences were observed between wild type and the mutant for the hydrated samples, while significant differences were observed for the dried samples. A dynamical transition at ∼140 K observed for both dried and hydrated samples. The slopes of the temperature dependence of MSD before transition and after transition are different between wild type and the mutant, indicating the folding induces hardening. The hydration water activates a further transition at ∼240 K. The behavior of the temperature dependence of MSD is indistinguishable for wild type and the mutant, indicating that hydration water dynamics dominate the dynamical properties.

EXAFS Study of Orientational Glasses

The extended X-ray absorption fine structure (EXAFS) study of K1-x(NH4)xI and KBr1-x(NO2)x mixed crystals was performed to elucidate the local structure of their glassy state associated with the reorientational freezing of molecular ions without any long-range order. The magnitude of EXAFS spectra of K1-x(NH4)xI was reduced with increasing ammonium ion concentration, while that of KBr1-x(NO2)x exhibits no anomalous changes with increasing nitrite ion concentration even below the glass transition temperature Tg. The results indicate that the local distortion which breaks the symmetry of fcc lattice is induced by the short-range antiferroelectric order of ammonium ions in K1-x(NH4)xI and the local structure is retained by the short-range ferroelectric order of nitrite ions in KBr1-x(NO2)x. The temperature dependence of mean-square displacement of bromine-potassium pair-distribution in KBr1-x(NO2)x obeys the Debye approximation even below Tg, which conflicts the result of previous X-ray diffraction studies that the mean-square displacement deviates largely from the Debye approximation.