Dynamical changes in hydration water accompanying lysozyme thermal denaturation

We study the dynamics of the first hydration shell of lysozyme to determine the role of hydration water that accompanies lysozyme thermal denaturation. We use nuclear magnetic resonance spectroscopy to investigate both the translational and rotational contributions. Data on proton self-diffusion and reorentational correlation time indicate that the kinetics of the lysozyme folding/unfolding process is controlled by the dynamics of the water molecules in the first hydration shell. When the hydration water dynamics change, because of the weakening of the hydrogen bond network, the three-dimensional structure of the lysozyme is lost and denaturation is triggered. Our data indicates that at temperatures above approximately 315 K, water behaves as a simple liquid and is no longer a good solvent.     

Ab initio molecular dynamics study of aqueous formaldehyde and methanediol

The solvation shell of aqueous formaldehyde has been studied by ab initio molecular dynamics. Two different DFT approaches using BLYP and PBE functionals were explored. The results show only a slightly different mobility in the solvation shells and allow characterization of the hydrogen bonded structure with a H₂C?=?O··HOH hydrogen bond lifetime of ca. 3 ps. Formaldehyde hydrolysis was studied by following the reverse process, methanediol decomposition, by Blue Moon constrained MD showing that four water molecules are directly involved in the reaction and assisted by the whole hydration shell. The total energy of the aqueous methanediol to formaldehyde inter-conversion process is calculated with a barrier height of ca. 95?kJ?mol^?1 while the corresponding free energy barrier is only ΔG^??=?46?kJ?mol^?1 at 300?K.     

Self-diffusion coefficients and orientational correlation times in aqueous NaCl solutions: Complementarity with structural investigations

The dynamical properties of pure water and aqueous NaCl solutions over a wide range of salt concentrations (0-6 m) at ambient conditions are characterized by molecular dynamics (MD) simulations. MD simulations are performed with a flexible SPC water model as a solvent, while the ions are treated as charged Lennard-Jones particles. In this paper, attention has been focused on the self-diffusion coefficients (D_i) of ions and water molecules and on orientational correlation time of water molecules. It is found that the self-diffusion coefficients decrease with ion concentration. Moreover, the self diffusion coefficients of sodium and chloride at higher salt concentrations are very comparable which may be due to the formation of clusters of these ions. The deduced rotational dynamics speeds up as the salt concentration increases. Some complementarities between dynamical properties and structural ones, recently obtained, are carried out.     

Molecular dynamics and quantum chemical approaches in the study of the hydration of protonated cyclohexyldiamines

Explicit hydration of the neutral and charged cyclohexylamine and of the cyclohexyldiamine isomers in their mono- or diprotonated forms is investigated through classical molecular dynamics (MD) simulations in aqueous solutions combined with DFT calculations in amine–water complexes. The MD studies performed in the monoamines reveal that the structure of the hydration shell around the neutral amino group (NH₂) is quite distinct from that around the charged one (NH₃⁺). On average, the number of water molecules surrounding the two groups is calculated to be ～2 and 3–4, respectively. The variation of the hydration structure prompted by the groups’ proximity is discussed based on the data found for the mono- and diprotonated diamines. To have a more detailed picture of the water molecules’ arrangement around the amino groups and of the amine–water hydrogen bonds, geometry optimisations in hydrates with up to six water molecules are carried out at the B3LYP/aug-cc-pVDZ level. Complexation energies are also computed. The main findings emerging from these calculations are found to be very helpful to rationalise the mutual influence of the amino groups and therefore to better elucidate the MD findings. The complementary nature of the two research methods is emphasised as an excellent tool in order to closely examine the hydration of polyamines, as exemplified for the cyclohexyldiamines.     

Ratiometric detection of Raman hydration shell spectra

The micro‐structure of hydration shell of solute in water is significant for understanding the properties of aqueous solutions. However the spectra of hydration shell are difficult to be obtained. Herein, a novel Raman ratio spectra, which is obtained through dividing the Raman spectra of aqueous solutions from the spectrum of water, was applied to deduce the spectra of hydration shell of organic (acetone‐D6) and inorganic compounds (NaNO₃, NaSCN, NaClO₄, Na₂SO₄, NaCl) in water. Those spectra of the hydration shell were employed to study the micro‐structures of the first hydration shells of anions, the number of water molecules in the first hydration shell of free anions and acetone‐D6, and the aggregation behavior of ions in the concentrated aqueous NaNO₃. The number of water molecules in the hydration shell was supported by our molecular dynamic simulations. The Raman ratio spectra can be widely employed to obtain the spectra of the first hydration shell, and it is helpful to understand the micro‐structure of aqueous solutions. Copyright © 2016 John Wiley & Sons, Ltd.     

Aggregation Behavior of Monomeric Surfactants and a Gemini Cationic Surfactant by NMR and Computer Simulation Data

Aggregation of decyltrimethylammonium bromide and cetyltrimethylammonium bromide (CTAB) in D₂O has been studied. Spin–lattice relaxation time and self-diffusion coefficient of surfactant molecules were measured at concentrations below and above surfactant critical micelle concentration. The aggregation properties of conventional surfactant, CTAB, examined by nuclear magnetic resonance (NMR) and molecular dynamic (MD) simulation, were compared with the properties of double-tail analog, N,N,N′,N′-tetramethyl-N,N′dihexadecyl-1,4-butan di-ammonium di-bromide (BCTA). Both NMR and computer simulation methods suggest that micellization is a stepwise process and the pre-micellar aggregates take place in a solution at concentration below critical micelle concentration. According to MD simulation Gemini surfactant, BCTA, forms worm-like micelles, whereas CTAB, which may be considered as its “monomer”, forms only elongated micelles.     

Properties of Hydrated Alkali Metals Aimed at the Ion Channel Selectivity

The hydration structure properties of different alkali metal ions with eight water molecules and potassium ions with different numbers of water molecules are studied using the mixed density functional theory, B3LYP, with 6-3110 basis set. The hydration structures are obtained from structure optimization and the optimum numbers of water molecules in the innermost hydration shell for the alkali metal ions are found. Some useful information about the ion channel selectivity is presented.     

Determination of the lifetime of an ion-molecular hydrogen bond from vibrational spectroscopy data

The mutual influence of the orientational relaxation of polyatomic anions of different types of symmetry in aqueous solutions and the rupture of H bonds is examined. It is demonstrated that the experimentally measured correlation times of the dipole moment and Raman polarizability tensor of linear anions can be interpreted as the time of the interaction of the anion with water molecules. The reorientation of perchlorate ion in water is accompanied by the rupture of the ion-molecular bond, being associated with the reorientation of the hydration shell. The reorientation of sulfite, nitrate, and carbonate ions does not result in the rupture of the ion-molecular bond, and hence, the orientational relaxation of these anions can be considered as a lower limit of its lifetime.     

Dynamic crossover in hydration water of curing cement paste: the effect of superplasticizer

The influence of a new comb-shaped polycarboxylate-based superplasticizer (CSSP) on the hydration kinetics and transport properties of aged cement pastes has been investigated by high-resolution quasi-elastic neutron scattering (QENS) and low temperature differential scanning calorimetry (LT-DSC). A new method of analysis of QENS spectra is proposed. By applying the refined method we were able to access to four independent physical parameters including the self-diffusion coefficient of the hydration water confined in the cement paste. Mean squared displacement (MSD) of the hydrogen atom for mobile water molecules displays a dynamic crossover temperature in agreement with DSC data. The experimental results indicate that CSSP polymer added into cement paste moderates the hydration process and decreases the dynamic crossover temperature of the hydration water.     

从常温常压到超临界乙醇的分子动力学模拟

采用分子动力学方法系统地研究了从常温常压到超临界状态乙醇的热力学性质、结构性质和动力学性质.模拟发现随着温度的升高,体系焓值增大,乙醇分子间的氢键作用减弱,自扩散系数增大;随着压强的增大,乙醇分子间的氢键作用增强,自扩散系数减小;乙醇自扩散系数在液相区随温度变化不明显,在气相区随压强增大很快减小,超临界区乙醇的自扩散系数比液相区大十几倍.温度和压强对乙醇自扩散系数的影响可通过密度来体现.与常温常压相比,超临界条件下的乙醇体系因密度涨落存在分子聚集现象,且在低密度区域更显著;乙醇分子间的氢键作用明显减弱,结     

Coarse nonlinear dynamics and metastability of filling-emptying transitions: water in carbon nanotubes

Using a coarse-grained molecular dynamics (CMD) approach we study the apparent nonlinear dynamics of water molecules filling or emptying carbon nanotubes as a function of system parameters. Different levels of the pore hydrophobicity give rise to tubes that are empty, water-filled, or fluctuate between these two long-lived metastable states. The corresponding coarse-grained free-energy surfaces and their hysteretic parameter dependence are explored by linking MD to continuum fixed point and bifurcation algorithms. The results are validated through equilibrium MD simulations.     

应用分子动力学模拟和拉曼光谱对钙、镁、氯离子 水化现象的研究

应用分子动力学方法,模拟了298 K下,密度为1.0 g/cm~3的水溶液中Ca²⁺,Mg²⁺,Cl~-的水化现象,得到了相应离子周围水分子的微观分布情况.发现在钙离子周围,水分子以其氧离子去靠近中心离子;而在氯离子周围,水分子则以其中的一个氢原子去靠近中心离子.通过分析三种离子的径向分布函数、配位数曲线、水化数、水化半径,发现Ca²⁺的水化数和水化半径均大于Mg²⁺,即Ca²⁺的水合能力比Mg²⁺强.与以往研究结果相比,本文计算所得的自扩散系数更接近实验所得结果.为了使模型更好的代表真实水溶液体系,本文还应用分子动力学和拉曼光谱法研究了不同浓度的CaCl₂水溶液.分子动力学研究发现随着浓度的升高,CaCl₂溶液中Ca²⁺,Cl~-的配位数分别呈降低趋势.同时,随着浓度的升高,Ca²⁺,Cl~-的自扩散系数也呈现降低的趋势.作者推断这是由于浓度的升高,加剧了离子的微观反...     

超高压水的分子动力学模拟

 采用平衡分子动力学（EMD）方法,模拟研究了温度范围为243~348 K、压强范围为0.1~400 MPa条件下水的热力学性质、结构和动力学性质,模拟结果与实验值吻合较好。模拟结果表明,随着压强的增大,水分子间的氢键作用增强,扩散系数减小;随着温度的升高,水分子间的氢键作用减弱,有序程度下降,扩散系数增大。但在过冷水中,扩散系数随压强的增大有增加的趋势。     

A molecular dynamics study of uranyl hydration

Molecular dynamics calculations were carried out in order to investigate the hydration structure of uranyl in aqueous solution. The CF1 model of flexible water molecules is used. This model allows one to investigate a hydrolysis reaction for water molecules in the first uranyl hydration shell. Charge redistribution effects on hydrolysis products are also taken into account. We found five ligands in uranyl hydration shell, which is of bipyramidal pentacoordinated structure. The charge redistribution effects resulted in ligands of four water molecules and one hydroxyl, which was found closer to uranium than the other ligands.     

Translational Mobility of Components and Structure of Water–Ethanol Solutions

The concentration dependences of self-diffusion coefficients of water and ethanol molecules in water–ethanol solutions are obtained by the method of nuclear magnetic resonance spectroscopy with the pulse magnetic field gradient. On the basis of the ideas of hydration of ethanol molecules, the obtained dependences are interpreted and assumptions are made about the structural organization of water–ethanol solutions in the region of diluted and concentrated solutions.     

水在不均匀纳米通道内自扩散性质的分子动力学研究

本文用分子动力学(MD)方法模拟了受限水在不均匀润湿性微通道中的自扩散性质.通过考察不均匀润湿通道内水的自扩散行为,发现在微通道中水的扩散性质表现出明显的尺度效应,随着通道高度的增加水的扩散增强.更重要的是,由于通道高度的不同,通道内的不均匀润湿段对水的扩散与均匀通道相比有不同的影响.当通道高度为0.8 nm时,不均匀润湿通道内水的扩散增强;当通道高度为1.0 nm时,不均匀润湿通道内水的扩散减弱;而当通道高度达到1.2 nm时,不均匀润湿通道内水的扩散基本相同.     

Calculation of diffusion coefficient of long chain molecules using molecular dynamics

Molecular dynamics (MD) is a powerful tool for calculating several thermo-physical properties of wide range of materials. In this study, the diffusivities (D) of two widely used long chain molecules MHA and ODT are calculated at various temperatures using MD simulations coupled with Einstein relationship. Four different kinds of forcefields COMPASS, UFF, CVFF and PCFF are employed in the MD simulation and the results are compared. Diffusivity values are evaluated in a humid environment in presence of water molecules.     

The structure,dynamics and solvation mechanisms of ions in water from long time molecular dynamics simulations: a case study of CaCl2 (aq) aqueous solutions

Systematic long time (5–20 ns) molecular dynamics (MD) simulations have been carried out to study the structural and dynamical properties of CaCl₂ aqueous solutions over a wide range of concentrations (≤9.26 m) in this study. Our simulations reveal totally different structural characteristics of those yielded from short time (≤1 ns) MD simulations [A.A. Chialvo and J.M. Simonson, J. Chem. Phys. 119, 8052 (2003); T. Megyes, I. Bako, S. Balint, T. Grosz, and T. Radnai, J. Mol. Liq. 129, 63 (2006)]. An apparent discontinuity was found at 4–5 m of CaCl₂ in various properties including ion–water coordination number and self-diffusion coefficient of ions, which were first noticed by Phutela and Pitzer in their thermodynamic modelling [R.C. Phutela and K.S. Pitzer, J. Sol. Chem. 12, 201 (1983)]. In this study, residence time was first taken into consideration in the study of Ca²⁺–Cl^? ion pairing, and it was found that contact ion pair and solvent-sharing ion pair start to form at the CaCl₂(aq) concentrations of about 4.5 and 4 m, respectively, which may be responsible for the apparent discontinuity. In addition, the residence time of water molecules around Ca²⁺ or Cl^? showed that the hydration structures of Ca²⁺ and Cl^? are flexible with short residence time (<1 ns). It needs to be pointed out that it takes much longer simulation time for the CaCl₂–H₂O system to reach equilibrium than what was assumed in previous studies.     

Protein hydration and location of water molecules in oxidized horse heart cytochrome c by (1)H NMR

The hydration properties of the oxidized form of horse heart cytochrome c have been studied by (1)H NMR spectroscopy. Two-dimensional, homonuclear ePHOGSY-NOESY experiments are used to map water-protein interactions. The detected NOEs reveal interactions between nonexchangeable protein protons and both water protons and labile protein protons which exchange with water protons. Among the many water molecules apparent in the X-ray structure, three have been identified with a residence time longer than 300 ps. One of them is located inside the distal heme cavity, in the deepest part of a hydration pathway extending toward the surface. The identification of hydrophilic regions and detection of three long-lived water molecules settles some ambiguities and provides a better representation of the water-protein interactions in oxidized cytochrome c.