1H and13C nuclear magnetic relaxation and local dynamics of lysozyme and synthetic polypeptides

The combined analysis of¹H and¹³C NMR relaxation data in solid lysozyme and some typical homopolypeptides was carried out by using “model-free” approach. Three types of relaxation transitions (γ’, γ and β) were revealed in the temperature range investigated. The microdynamical parameters of these motions were determined. From the comparison of these parameters with those of selected synthetic polymers it follows that the molecular motions in proteins and synthetic polymers are of the same nature. All these motions show pronounced anisotropic character. In the investigated temperature range no molecular motions corresponding to α-relaxation (liquid-like) transition were revealed. The hydration effects on parameters of the motions in proteins were considered. The most pronounced effect takes place for β-transition. The effect of Brownian rotation of protein molecule in solution on measured correlation function of local motions was also discussed.     

Infrared absorption spectrum of a small-polaron system

Characteristic features and the temperature dependence of the small-polaron absorption spectrum are discussed using a recently published model. The physical interpretation of formal results is introduced, in particular a connection of small-polaron states with oscillator coherent states is emphasized. The continuous change of absorption curves with temperature is illustrated by numerical calculations.     

On the liquid-vapour-like critical point in the model of the rare earth iron garnet

The transition between two canted phases in YbIG atH 100 is examined in the framework of the model with one saturated Fe-sublattice and six sublattices of mutually independent Yb ions. In particular, the equations determining the continuous transition point and the coexistence line of these canted phases are derived. The existence of a zero frequency mode in this second order transition point is clear from this analysis, too. The analogy with the classical theory of the liquid-vapour-like phase transition, as well as the limits of the mean field approach are discussed.     

Heat capacity and heat content of BiNb<Subscript>5</Subscript>O<Subscript>14</Subscript>

The heat capacity and the heat content of bismuth niobate BiNb₅O₁₄ were measured by the relaxation time method, DSC and drop method, respectively. The temperature dependence of heat capacity in the form C _pm=455.84+0.06016T–7.7342·10⁶/T ² (J K^–1 mol^–1) was derived by the least squares method from the experimental data. Furthermore, the standard molar entropy at 298.15 K S _m=397.17 J K^–1 mol^–1 was derived from the low temperature heat capacity measurement.     

Experimental and Theoretical Evidence of Spin-Orbit Heavy Atom on the Light Atom 1H NMR Chemical Shifts Induced through H⋅⋅⋅I− Hydrogen Bond

Spin-orbit (SO) heavy-atom on the light-atom (SO-HALA) effect is the largest relativistic effect caused by a heavy atom on its light-atom neighbors, leading, for example, to unexpected NMR chemical shifts of ¹H, ¹³C, and ¹⁵N nuclei. In this study, a combined experimental and theoretical evidence for the SO-HALA effect transmitted through hydrogen bond is presented. Solid-state NMR data for a series of 4-dimethylaminopyridine salts containing I⁻, Br⁻ and Cl⁻ counter ions were obtained experimentally and by theoretical calculations. A comparison of the experimental chemical shifts with those calculated by a standard DFT methodology without the SO contribution to the chemical shifts revealed a remarkable error of the calculated proton chemical shift of a hydrogen atom that is in close contact with the iodide anion. The addition of the relativistic SO correction in the calculations significantly improves overall agreement with the experiment and confirms the propagation of the SO-HALA effect through hydrogen bonds.     

129Xe NMR chemical shift in Xe@C60 calculated at experimental conditions: Essential role of the relativity,dynamics, and explicit solvent

The isotropic ¹²⁹Xe nuclear magnetic resonance (NMR) chemical shift (CS) in Xe@C₆₀ dissolved in liquid benzene was calculated by piecewise approximation to faithfully simulate the experimental conditions and to evaluate the role of different physical factors influencing the ¹²⁹Xe NMR CS. The ¹²⁹Xe shielding constant was obtained by averaging the ¹²⁹Xe nuclear magnetic shieldings calculated for snapshots obtained from the molecular dynamics trajectory of the Xe@C₆₀ system embedded in a periodic box of benzene molecules. Relativistic corrections were added at the Breit–Pauli perturbation theory (BPPT) level, included the solvent, and were dynamically averaged. It is demonstrated that the contribution of internal dynamics of the Xe@C₆₀ system represents about 8% of the total nonrelativistic NMR CS, whereas the effects of dynamical solvent add another 8%. The dynamically averaged relativistic effects contribute by 9% to the total calculated ¹²⁹Xe NMR CS. The final theoretical value of 172.7 ppm corresponds well to the experimental ¹²⁹Xe CS of 179.2 ppm and lies within the estimated errors of the model. The presented computational protocol serves as a prototype for calculations of ¹²⁹Xe NMR parameters in different Xe atom guest–host systems. © 2013 Wiley Periodicals, Inc.     

Nuclear magnetic relaxation and molecular motion in solid lysozyme

Nuclear magnetic relaxation data for both proton and carbon-13 nuclei in solid lysozyme are analysed together to obtain information on local internal motions in protein. For this analysis the “model-free” approach is used. Three types of internal motion appear to determine the observed nuclear relaxation in protein. They may be attributed to local rotations of methyl groups around symmetry axes, the motion of main and side chain atoms like in rigid lattice, and large-amplitude motions of side groups (mainly, methylene groups). Conclusions on hydrated water influence on local dynamics of protein are made.     

The effect of spatial wandering on experimental laser velocimeter measurements of the end-wall vortices in an axial-flow pump

In a high Reynolds number axial-flow pump, laser velocimeter (LV) measurements were made to study the size and structure of the end-wall vortex. The time mean measurements show that the core size of the end-wall vortex increased with decreasing tip clearance, which is contrary to existing theory. Observations of cavitation in the vortex showed that the flow was unsteady. The vortices emanating from the smaller clearances were observed to wander or meander spatially and to develop kinks more than the vortices emanating from the larger tip clearances. This observed unsteadiness has a significant effect on the time mean size and velocity distribution of the vortex as measured with the LV employing the field point measurement technique. In order to obtain an estimate of the true size and velocity distribution, computational experiments were conducted which modelled a periodically wandering vortex and the LV measurement process. The computational and experimental results show good agreement, including a broadened and reduced tangential velocity distribution. In this paper, the end-wall vortex LV measurements are presented, and the method of analyzing the vortex wandering is described.     

Toward calculations of the 129Xe chemical shift in Xe@C60 at experimental conditions: relativity, correlation, and dynamics

We calculate the 129Xe chemical shift in endohedral Xe@C60 with systematic inclusion of the contributing physical effects to model the real experimental conditions. These are relativistic effects, electron correlation, the temperature-dependent dynamics, and solvent effects. The ultimate task is to obtain the right result for the right reason and to develop a physically justified methodological model for calculations and simulations of endohedral Xe fullerenes and other confined Xe systems. We use the smaller Xe...C6H6 model to calibrate density functional theory approaches against accurate correlated wave function methods. Relativistic effects as well as the coupling of relativity and electron correlation are evaluated using the leading-order Breit-Pauli perturbation theory. The dynamic effects are treated in two ways. In the first approximation, quantum dynamics of the Xe atom in a rigid cage takes advantage of the centrosymmetric potential for Xe within the thermally accessible distance range from the center of the cage. This reduces the problem of obtaining the solution of a diatomic rovibrational problem. In the second approach, first-principles classical molecular dynamics on the density functional potential energy hypersurface is used to produce the dynamical trajectory for the whole system, including the dynamic cage. Snapshots from the trajectory are used for calculations of the dynamic contribution to the absorption 129Xe chemical shift. The calculated nonrelativistic Xe shift is found to be highly sensitive to the optimized molecular structure and to the choice of the exchange-correlation functional. Relativistic and dynamic effects are significant and represent each about 10% of the nonrelativistic static shift at the minimum structure. While the role of the Xe dynamics inside of the rigid cage is negligible, the cage dynamics turns out to be responsible for most of the dynamical correction to the 129Xe shift. Solvent effects evaluated with a polarized continuum model are found to be very small.     

From Ecology to Finance (and Back?): A Review on Entropy-Based Null Models for the Analysis of Bipartite Networks

Journal of Statistical Physics - Bipartite networks provide an insightful representation of many systems, ranging from mutualistic networks of species interactions to investment networks in...