The dynamics of water in nanoporous silica studied by dielectric spectroscopy

Broad-band dielectric spectroscopy is used to investigate the dynamics of hydration water on the surface of the cylindrical pores of a nanostructured silica material (MCM-41, with pore diameter of 3.2 nm) at various hydrations, in the temperature range 250-150 K. We focus our attention on orientational relaxations that shift from 0.5 MHz at 250 K to less than 1 Hz at 150 K. The measurements distinguish the relaxation of the hydroxyl groups at the surface of silica from the orientational dynamics of hydration water which strongly depends on the degree of hydration. Although it is significantly faster than the dynamics of water in ice, the orientational relaxation of non-freezing water has an activation energy comparable to that in ice when the hydration layer is complete and approximately two-molecule thick.     

Connection between Adam-Gibbs theory and spatially heterogeneous dynamics

We investigate the spatially heterogeneous dynamics in the extended simple point charge model of water using molecular dynamics simulations. We relate the average mass n* of mobile particle clusters to the diffusion constant and the configurational entropy. Hence, n* can be interpreted as the mass of the "cooperatively rearranging regions" that form the basis of the Adam-Gibbs theory of the dynamics of supercooled liquids. We also examine the time and temperature dependence of these transient clusters.     

Orientation restraints in molecular dynamics simulations using time and ensemble averaging

In this article we present methodology for simulating protein dynamics while imposing restraints derived from NMR measurements on partially ordered molecules. Such measurements may include residual dipolar couplings and chemical-shift anisotropies. We define a restraint potential for use in molecular dynamics and energy minimization. The presented potential is consistent with the simultaneously optimized molecular order tensor. Restraining can be performed with time and ensemble averaging. We performed a large number of molecular dynamics simulations of the histidine containing phosphocarrier protein with restraints on backbone N-H vector orientations derived from residual dipolar couplings. From these simulations it is evident that the use of time- or ensemble-averaged restraints is essential to leave the fluctuations of the restrained vectors unaffected. Without averaging the fluctuations of the restrained vectors are reduced significantly. This also has the effect of decreasing the apparent molecular order-parameter tensor.     

Water in contact with extended hydrophobic surfaces: direct evidence of weak dewetting

X-ray reflectivity measurements reveal a significant dewetting of a large hydrophobic paraffin surface floating on water. The dewetting phenomenon extends less than 15 A into the bulk water phase and results in an integrated density deficit of about one water molecule per 25-30 A(2) of water in contact with the paraffin surface. The results are supported by molecular dynamics simulations and related to the hydrophobic effect.     

Fast anomalous diffusion of small hydrophobic species in water

Using Car-Parrinello molecular dynamics a structural diffusion mechanism for the simplest hydrophobic species in water, an H atom, is proposed. The hydrophobic solvation cavity is a highly dynamical aggregate that actually drives, by its own hydrogen-bond fluctuations, the diffusion of the enclosed solute. This makes possible an anomalously fast diffusion that falls only short of that of "Grotthuss structural diffusion" of H+ in water. Here, the picture of a static, i.e., "iceberglike," clathrate cage is a misleading concept. The uncovered scenario is similar to the "dynamical hole mechanism" found in a very different context, that is, large molecules moving in hot polymeric melts.     

相干振动动力学和高分辨非线性光谱学：空气/二甲亚砜液体界面的比较

研究了空气/二甲亚砜界面C?H伸缩振动的自由诱导衰减的相干振动动力学和亚波数高分辨宽带和频振动光谱．对于特定分子体系,频率域光谱测量和时间域动力学测量原则上应获得相同的信息．但对具有耦合或者重叠在一起的若干振动模式的分子体系,通过时域或者频域测量以获取光谱和动力学信息细节均非易事．对于振动光谱并非过于复杂的空气/二甲亚砜界面,基于亚波数高分辨宽带和频振动光谱的频域测量较超快时域测量更有益于获取界面结构和相干动力学定量信     

Residue-specific NH exchange rates studied by NMR diffusion experiments

We present a novel approach to the investigation of rapid (>2s(-1)) NH exchange rates in proteins, based on residue-specific diffusion measurements. (1)H, (15)N-DOSY-HSQC spectra are recorded in order to observe resolved amide proton signals for most residues of the protein. Human ubiquitin was used to demonstrate the proposed method. Exchange rates are derived directly from the decay data of the diffusion experiment by applying a model deduced from the assumption of a two-site exchange with water and the "pure" diffusion coefficients of water and protein. The "pure" diffusion coefficient of the protein is determined in an experiment with selective excitation of the amide protons in order to suppress the influence of magnetization transfer from water to amide protons on the decay data. For rapidly exchanging residues a comparison of our results with the exchange rates obtained in a MEXICO experiment showed good agreement. Molecular dynamics (MD) and quantum mechanical calculations were performed to find molecular parameters correlating with the exchangeability of the NH protons. The RMS fluctuations of the amide protons, obtained from the MD simulations, together with the NH coupling constants provide a bilinear model which shows a good correlation with the experimental NH exchange rates.     

Interpretation of NMR data on proteins by molecular dynamics simulations

The stability and the internal mobility of the recently determined solution structure of the activation domain of porcine procarboxypeptidase B (ADB; Vendrell J., Billeter M., Wider G., Avilés F.X., Wüthrich K.: EMBO J.10, 11–15 (1991)) was studied by unrestrained molecular dynamics. A 66 residue long polypeptide corresponding to the structurally well-defined fragment of ADB was immersed in a water bath and carefully equilibrated. A trajectory of 90 ps was then recorded at room temperature, using no constraints deduced from NMR distance measurements. The averages of the inverse third power of the proton-proton distances, for which NMR distance measurements are available, were calculated and converted to time averages of the distances. Comparison of these time averaged distances with the corresponding distance constraints used in the determination of the solution structure show that the dynamic structure described by the molecular dynamics trajectory is consistent with the NMR data for the polypeptide backbone and for most side chains. In the course of the 90 ps trajectory, the ß-sheet of ADB remains intact and well-defined. The last helix of the protein domain is also stable, but moves with respect to the rest of the protein, while the first helix shows increased instability. The structural fluctuations of the side chain do in general not exceed those observed among the 20 conformers describing the solution structure.     

The influence of polarity in binary solvent mixtures on the conformation of bis-triazinyl-pyridine in solution

We report a combined computational and experimental study to investigate the influence of the solvent on the electronic and molecular structure of the bis-triazinyl-pyridine (BTP) ligand. Experimental measurements and quantum-chemical calculations using geometries from molecular dynamics simulations in different solvent methanol/water mixtures reveal a change in the UV/vis absorption spectra for the investigated BTP compound. This change is investigated further using nuclear magnetic resonance (NMR) techniques, both experimental and computational, to gain insight to ligand conformation. Comparison of experimental and computational results enables the analysis of relevant BTP conformers, which cannot be accessed using experimental measurements alone. Based on this approach, we conclude that the BTP ligands change conformation with decreasing solvent polarity to maximise the lipophilic accessible surface – a concept which is transferrable to various classes of compounds.     

Modelling of mutual diffusion for associated electrolytes solution: ZnSO4 and MgSO4 aqueous solutions

We study mutual diffusion of associated electrolyte in water. A theory based on the Smoluchowski equation and on the mean spherical approximation is proposed. It is found to be valid up to molar concentrations. The values of the association constant obtained for ZnSO₄ and MgSO₄ aqueous solutions are consistent with further methods of measurements. Thanks to the elimination of fast variables method, the theory can be generalised to any association in solution. Comparison with molecular dynamics and Brownian dynamics simulations in the case of MgSO₄ indicates that the pair is a global association phenomenon since it corresponds to several association phenomena (contact ion pair and solvent separated ion pair).     

Dynamical properties and the proton transfer mechanism in the wetting water layer on Pt(1 1 1)

We have investigated the structural properties and the dynamics in the ()R16.1° (RT39) wetting layer on Pt(1 1 1) found in recent experiments, by ab initio molecular dynamics simulations. The RT39 bilayer is found to consist of 20% water molecules in the first flat layer, and 66% in the second layer, and a small fraction extending further away. Two-dimensional pair correlation functions are obtained, and calculated vibration spectra are in agreement with experiment. A small fraction of water in this RT39 bilayer dissociates due to both the lateral compression and the substrate effect. Most interestingly, surface mediated proton transfer mechanism in water layers at surface, which differs from the counterparts in bulk water, is discovered.     

Effect of iron doping on the hydrophobicity of titanium dioxide film: experiment and simulation

In this study, we carried out experiments and molecular dynamics simulations to identify the effect of Fe doping on the hydrophobicity of a titanium dioxide film. TiO₂ and Fe-doped TiO₂ films were fabricated in situ by atomic layer deposition without annealing. X-ray diffraction (XRD) and X-ray photoelectron spectroscopy (XPS) were used to characterise the crystal structure and elemental composition. Iron doping resulted in the TiO₂ becoming more hydrophobic at a macroscopic level, as estimated by atomic force microscopy observations and static contact angle measurements. Furthermore, the effect of iron doping on the structure and kinetics of water molecules on the exterior of TiO₂ were studied by molecular dynamics simulations. On the basis of the XPS results, the Fe-TiO₂ surface matrix has a Ti:Fe ratio of 36:5. In addition, the density distribution of oxygen and hydrogen atoms indicate that interfacial water molecules enter the Fe-TiO₂ film more easily and hydrogen atoms in the water molecules are oriented upward at the interface. The self-diffusion coefficients indicate that iron doping makes the TiO₂ more hydrophobic, which is consistent with the macroscopic test results.     

Glass transition in biomolecules and the liquid-liquid critical point of water

Using molecular dynamics simulations, we investigate the relation between the dynamic transitions of biomolecules (lysozyme and DNA) and the dynamic and thermodynamic properties of hydration water. We find that the dynamic transition of the macromolecules, sometimes called a "protein glass transition," occurs at the temperature of dynamic crossover in the diffusivity of hydration water and also coincides with the maxima of the isobaric specific heat C_{P} and the temperature derivative of the orientational order parameter. We relate these findings to the hypothesis of a liquid-liquid critical point in water. Our simulations are consistent with the possibility that the protein glass transition results from crossing the Widom line, which is defined as the locus of correlation length maxima emanating from the hypothesized second critical point of water.     

自旋弛豫时间测定对固体代谢物分子力学性质的研究

自旋弛豫时间测定是研究固体物质分子动力学性质的有效手段,已广泛应用于植物糖、氨基酸、维生素、肾上腺素以及睾丸激素等多类代谢物分子动力学性质的研究中. 近来上述方法也被用于其他代谢物分子动力学性质与其多晶型相变的关系以及对代谢物结构依赖性的研究. 该文将在介绍自旋弛豫时间及其测定方法的基础上,着重对自旋弛豫时间测定研究植物糖、氨基酸及其衍生物分子动力学性质的应用工作进行讨论.     

Dynamics of water in molecular sieves by dielectric spectroscopy

We present recent dielectric data on the dynamics of water confined in molecular sieves with pore sizes 5 and 10 A. The dielectric measurements in the frequency and temperature ranges 10(-2)-10(6) Hz and 120-300 K show three relaxation processes for both samples. In the case of the 10 A pore the slowest process shows an Arrhenius temperature dependence at low temperatures (<220 K), while at high temperatures the relaxation appears to follow a more Vogel-Fulcher-Tammann (VFT) like behaviour. The relaxation time for this process is 100 s at about 170 K. The second slowest process is at low temperatures very similar to the main process of (bulk-like) water in a fully hydrated clay, but also this process seems to exhibit some kind of dynamical transition, in this case at T approximately 185 K. All the three processes in the 5 A pore exhibit Arrhenius temperature dependence, and two of them are considerably slower than the main relaxation in the hydrated clay. Thus, dynamics of bulk-like water is only observed in the 10 A molecular sieves, and most of the water molecules in both 5 and 10 A pores have considerably slower dielectric relaxation than has been observed for water confined in clay, most likely due to strong interactions with the considerably more hydrophilic inner surfaces of molecular sieves.     

Helical Structure of Nucleation in a Solution of a Chiral Trifluoroacetylated Amino Alcohol

The occurrence of a nanoscale disperse phase in the homochiral solutions of N-trifluoroacetylated α-amino alcohols (TFAAAs) was found experimentally by the observation of the Tyndall effect and dynamic light scattering (DLS) measurements. The nanoscale fraction was observed at concentrations lower than the critical concentration of gelation and string formation (c*). Direct optical microscopy showed that, as a rule, strings with a helical structure resulted from the homogeneous nucleations. Chirooptical measurements revealed some signs of helicity below the concentration threshold (c*). The molecular dynamics simulation of the condensation of a homochiral TFAAA in heptane showed that TFAAA molecular aggregates 2–3 nm in diameter were formed already after 100 ns. These aggregates have some signs of the homogeneous nucleations with a helical structure, and they can be considered as the nuclei of helical strings.     

Nuclear quantum effects in water

A path-integral Car-Parrinello molecular dynamics simulation of liquid water and ice is performed. It is found that the inclusion of nuclear quantum effects systematically improves the agreement of first-principles simulations of liquid water with experiment. In addition, the proton momentum distribution is computed utilizing a recently developed open path-integral molecular dynamics methodology. It is shown that these results are in good agreement with experimental data.     

Discretization errors in molecular dynamics simulations with deterministic and stochastic thermostats

We investigate the influence of numerical discretization errors on computed averages in a molecular dynamics simulation of TIP4P liquid water at 300 K coupled to different deterministic (Nosé–Hoover and Nosé–Poincaré) and stochastic (Langevin) thermostats. We propose a couple of simple practical approaches to estimating such errors and taking them into account when computing the averages. We show that it is possible to obtain accurate measurements of various system quantities using step sizes of up to 70% of the stability threshold of the integrator, which for the system of TIP4P liquid water at 300 K corresponds to the step size of about 7 fs.