Hydrogen-Bond Structure and Low-Frequency Dynamics of Electrolyte Solutions: Hydration Numbers from ab Initio Water Reorientation Dynamics and Dielectric Relaxation Spectroscopy

We present an atomistic simulation scheme for the determination of the hydration number (h) of aqueous electrolyte solutions based on the calculation of the water dipole reorientation dynamics. In this methodology, the time evolution of an aqueous electrolyte solution generated from ab initio molecular dynamics simulations is used to compute the reorientation time of different water subpopulations. The value of h is determined by considering whether the reorientation time of the water subpopulations is retarded with respect to bulk-like behavior. The application of this computational protocol to magnesium chloride (MgCl₂) solutions at different concentrations (0.6–2.8 mol kg⁻¹) gives h values in excellent agreement with experimental hydration numbers obtained using GHz-to-THz dielectric relaxation spectroscopy. This methodology is attractive because it is based on a well-defined criterion for the definition of hydration number and provides a link with the molecular-level processes responsible for affecting bulk solution behavior. Analysis of the ab initio molecular dynamics trajectories using radial distribution functions, hydrogen bonding statistics, vibrational density of states, water-water hydrogen bonding lifetimes, and water dipole reorientation reveals that MgCl₂ has a considerable influence on the hydrogen bond network compared with bulk water. These effects have been assigned to the specific strong Mg-water interaction rather than the Cl-water interaction.     

应用极化水分子模型研究单分子层受限水的介电性质

受限条件下水的介电性质因测量极具挑战,其在诸多电化学过程与反应输运过程中如何扮演关键角色从未被定量地澄清.本工作利用平衡态分子动力学模拟和受限体系介电性质计算方法,系统性地探索了0.65 nm限域尺寸、5×10⁸ Pa限域压强、不同温度条件下单分子受限冰和受限水的介电性质.详细比较了恒定偶极矩SPC/E水分子模型和可极化的SWM4-NDP水分子模型在描述受限冰、水结构与介电性质上的优劣势,包括统计分析SWM4-NDP模型模拟的单分子层受限水和受限冰的瞬时分子偶极矩概率密度分布,计算每个模拟体系的静态结构因子、静态偶极空间关联函数、静态介电常数、体系偶极时间关联函数和德拜弛豫时间.首次发现了极化水分子模型描述的低维度受限水和受限冰的奇异分子极性变化,并观察到两种模型描述静态结构性质的效果相当, SWM4-NDP模型对于静态介电常数描述的优势会因受限条件的增强而被大幅削减.但在受限水介电极化弛豫动力学性质描述上SWM4-NDP模型明显优于SPC/E模型.我们推断SWM4-NDP模型在探索受限水结构相变动力学以及受限体系离子输运和溶剂化动力学等过程的模拟研究中是比SPC...     

Phase Behavior of Amphiphilic Molecules in the Presence of One Solvent: A Dissipative Particle Dynamics Study

We simulate the phase behavior of amphiphilic molecules in the presence of one solvent by DPD. In general, DPD has successfully captured most of the effects of composition of amphiphilic molecules, solvent selectivity, and solvent amount, on the phase transition behavior obtained by both SCMF calculations and experiments. When a neutral good solvent is added, the solutions undergo a lyotropic transition analogous to the thermotropic transition in the melts. Furthermore, the order‐disorder transition results obtained via DPD are in good agreement with theoretical predictions by including the fluctuation effects, as well as with experiments. In the selective solvents, various transitions from the “normal” phases (i.e., the minority blocks form the minor domains) to even the “inverted” phases (formed by the majority blocks) have been observed by varying solvent selectivity and solvent amount. Since the packing order of the spheres is greatly affected by the finite size of the simulation box, it becomes difficult to examine the most stable packing array of spheres via DPD as has been predicted by SCMF theory. However, DPD reveals a possible spherical order of A15, which has been ignored in current SCMF work but observed in some amphiphilic molecule systems.

     

The Solvent‐Dependent Shift of the Amide I Band of a Fully Solvated Peptide as a Local Probe for the Solvent Composition in the Peptide/Solvent Interface

We determine the shift and line shape of the amide I band of a model AK peptide from molecular dynamics (MD) simulations of the peptide dissolved in methanol/water mixtures with varying composition. The IR spectra are determined from a transition dipole coupling exciton model. A simplified empirical model Hamiltonian is employed, which takes into account both the effect of hydrogen bonding and the intramolecular vibrational coupling. We consider a single isolated AK peptide in a mostly helical conformation, while the solvent is represented by 2600 methanol or water molecules, simulated for a pressure of 1 bar and a temperature of 300 K. Over the course of the simulations, minor reversible conformational changes at the termini are observed, which are found to only slightly affect the calculated spectral properties. Over the entire composition range, which varies from pure water to the pure methanol solvent, a monotonous shift towards higher frequency of the IR amide I band of about 8 wavenumbers is observed. This shift towards higher frequency is comparable to the shift found in preliminary experimental data also presented here on the amide I′ band. The shift is found to be caused by two counter‐compensating effects. An intramolecular red shift of about 1.2 wavenumbers occurs, due to stronger intramolecular hydrogen bonding in a methanol‐rich environment. Dominating, however, is the intermolecular solvent‐dependent shift towards higher frequency of about 10 wavenumbers, which is attributed to the less effective hydrogen‐bond‐donor capabilities of methanol compared to water. The importance of the solvent contribution to the IR shift, as well as the significantly different hydrogen formation capabilities of water and methanol, makes the amide I band sensitive to composition changes in the local environment close to the peptide/solvent interface. This allows, in principle, an experimental determination of the composition of the solvent in close proximity to the peptide surface. For the AK peptide case, we observe at low methanol concentrations a significantly enhanced methanol concentration at the peptide/solvent interface, supposedly promoted by the partially hydrophobic character of the AK peptide’s solvent‐accessible surface.     

Fast Water Relaxation through One‐Dimensional Channels by Rapid Energy Transfer

Water in carbon nanotubes is surrounded by hydrophobic carbon surfaces and shows anomalous structural and fast transport properties. However, the dynamics of water in hydrophobic nanospaces is only phenomenologically understood. In this study, water dynamics in hydrophobic carbon nanotubes is evaluated based on water relaxation using nuclear magnetic resonance spectroscopy and molecular dynamics simulations. Extremely fast relaxation (0.001 s) of water confined in carbon nanotubes of 1 nm in diameter on average is observed; the relaxation times of water confined in carbon nanotubes with an average diameter of 2 nm (0.40 s) is similar to that of bulk water (0.44 s). The extremely fast relaxation time of water confined in carbon nanotubes with an average diameter of 1 nm is a result of frequent energy transfer between water and carbon surfaces. Water relaxation in carbon nanotubes of average diameter 2 nm is slow because of the limited number of collisions between water molecules. The dynamics of interfacial water can therefore be controlled by varying the size of the hydrophobic nanospace.     

Molecular Dynamics Study on Properties of Hydration Layers above Polymer Antifouling Membranes

Zwitterionic polymers as crucial antifouling materials exhibit excellent antifouling performance due to their strong hydration ability. The structure–property relationship at the molecular level still remains to be elucidated. In this work, the surface hydration ability of three antifouling polymer membranes grafting on polysiloxane membranes Poly(sulfobetaine methacrylate) (T4-SB), poly(3-(methacryloyloxy)propane-1-sulfonate) (T4-SP), and poly(2-(dimethylamino)ethyl methacrylate) (T4-DM) was investigated. An orderly packed, and tightly bound surface hydration layer above T4-SP and T4-SB antifouling membranes was found by means of analyzing the dipole orientation distribution, diffusion coefficient, and average residence time. To further understand the surface hydration ability of three antifouling membranes, the surface structure, density profile, roughness, and area percentage of hydrophilic surface combining electrostatic potential, RDFs, SDFs, and noncovalent interactions of three polymers’ monomers were studied. It was concluded that the broadest distribution of electrostatic potential on the surface and the nature of anionic SO3- groups led to the following antifouling order of T4-SB > T4-SP > T4-DM. We hope that this work will gain some insight for the rational design and optimization of ecofriendly antifouling materials.     

Effect of Residual Water and Microwave Heating on the Half‐Life of the Reagents and Reactive Intermediates in Peptide Synthesis

Precise microwave heating has changed the way many small molecules are being synthesized and, currently, the field of solid‐phase peptide synthesis is undergoing dramatic changes owing to the use of microwave heating. To fully reap the benefits of precise microwave heating for the formation of amide bonds in peptide synthesis, it is important to understand the kinetics of formation and break‐down of activated esters and their N‐acylation of the nascent peptide chain at elevated temperatures. Herein, we present systematic studies of, first, the rate of formation of activated esters by NMR spectroscopy and, second, their N‐acylation during peptide synthesis. A study of the amount of residual water in the solvents revealed a significant effect on electrophilic reagents and intermediates. This observation was expanded into a general study of microwave heating in peptide synthesis.     

Influence of an Unnatural Amino Acid Side Chain on the Conformational Dynamics of Peptides

In this work, a non‐natural amino acid, H‐propargylglycine‐OH (Pra), is chosen to examine the side‐chain effect on the backbone conformation of small peptides. The conformations of two synthesized Pra‐containing tripeptides, Ac‐Pra‐Pra‐NH₂ (PPTP) and Ac‐Pra‐Ala‐NH₂ (PATP), are examined by infrared (IR) spectroscopy in combination with molecular dynamics (MD) simulations and quantum chemical computations. By analyzing the joint distributions of backbone torsional angles, several significant conformations can be identified for the two tripeptides solvated in D₂O. At room temperature, 44 % of PPTP exists in the α‐α conformation and 33 % of PATP exists in the α‐polyproline‐II conformation. Larger structural inhomogeneity is seen in both cases by MD simulations at elevated temperatures. Thus even a small side chain, such as the propargyl group can significantly alter the peptide backbone conformations. The results suggest that there is no overwhelming conformational propensity of the Pra residue in short peptides. IR spectra simulated in the amide‐I region using two different methods, reasonably reproduce the experimental IR spectra and their temperature dependence.     

铁电共聚物VDF／TrFE的低温低频介电松弛

在低温低频下用介电松弛方法研究了液氮淬火，熔融慢冷和热处理结晶铁电共聚物ＶＤＦ（７３）／ＴｒＦＥ（２７）的分子运动特征，随结晶度升高，居里点温度降低，铁电－顺电相变区的介电常数增大。室温以下共聚物的频率谱由低频和高频两部分组成。低频部由非晶工区被冻结分子链段的微布朗运动贡献。高频部则由晶区和非晶区分子链段较小尺度的局域运动产生。由两个Ｃｏｌｅ－Ｃｏｌｅ函数对频率谱进行分峰拟合并根据ＷＬＦ方程和Ａｒ     

壳聚糖微球悬浊液的介电谱研究:弛豫机制的解释和内部信息的获得

结合DLVO理论和壳聚糖微球的特点, 提出了适合实验数据的电动力学模型, 并分析了浓厚分散系的界面极化弛豫的微观机制. 进而测量了不同粒径壳聚糖微球悬浊液的介电谱, 发现在10～100 MHz频率范围内均出现明显的介电弛豫现象. 利用上述模型合理解释了该弛豫现象以及微球粒径对界面极化弛豫的影响, 结果也证明了我们提出的模型的适当性. 此外, 利用Hanai方法, 通过介电参数准确计算出了各悬浊液的内部信息, 并且分析了这些实时信息的合理性. 研究结果从实验和理论两方面展示了介电谱方法在即时获取壳聚糖内部信息上的独到优势.     

Origin of the Director Tilt in the Lyotropic Smectic C* Analog Phase: Hydration Interactions and Solvent Variations

The origin and long‐range correlation of the director tilt in the recently discovered phase, which is the lyotropic analog of the thermotropic smectic C* (SmC*) liquid crystalline phase, are investigated. Polarized micro‐Raman spectroscopy reveals that the director tilt in the phase originates from a tilting of the aromatic 2‐phenylpyrimidine cores of the surfactant molecules. Optical measurements of the tilt angle show that its magnitude decreases with increasing solvent concentration, suggesting that the long‐range inter‐lamellar correlation of the tilt directions is reduced at increasing thickness of the solvent layers. The phase diagrams with four different solvents (water, formamide, N‐methylformamide, N,N‐dimethylformamide) are investigated, showing that the phase is only formed with those solvents that exhibit a dense network of hydrogen bonds. This observation suggests that these hydrogen bond networks play an essential role in the long‐range correlation of the director tilt between adjacent surfactant layers. To verify this assumption, mixtures with deuterated solvents are investigated, showing that the tilt angle in the phase is indeed reduced by this modification of the solvent′s hydrogen bond network.     

Solvation Dynamics of a Single Water Molecule Probed by Infrared Spectra—Theory Meets Experiment

The dynamics and energetics of water at interfaces or in biological systems plays a fundamental role in all solvation and biological phenomena in aqueous solution. In particular, the migration of water molecules is the first step that controls the overall process in the time domain. Experimentally, the dynamics of individual water molecules is nearly impossible to follow in solution, because signals from molecules in heterogeneous environments overlap. Although molecular dynamics simulations do not have this restriction, there is a lack of experimental data to validate the calculated dynamics. Here, we demonstrate a new strategy, in which the calculated dynamics are verified by measured time‐resolved infrared spectra. The coexistence of fast and slow migrations of water molecules around a CONH peptide linkage is revealed for a model system representative of a hydrate peptide.     

The Structural and Dynamical Properties of the Hydration of SNase Based on a Molecular Dynamics Simulation

The dynamics of protein–water fluctuations are of biological significance. Molecular dynamics simulations were performed in order to explore the hydration dynamics of staphylococcal nuclease (SNase) at different temperatures and mutation levels. A dynamical transition in hydration water (at ~210 K) can trigger larger-amplitude fluctuations of protein. The protein–water hydrogen bonds lost about 40% in the total change from 150 K to 210 K, while the Mean Square Displacement increased by little. The protein was activated when the hydration water in local had a comparable trend in making hydrogen bonds with protein– and other waters. The mutations changed the local chemical properties and the hydration exhibited a biphasic distribution, with two time scales. Hydrogen bonding relaxation governed the local protein fluctuations on the picosecond time scale, with the fastest time (24.9 ps) at the hydrophobic site and slowest time (40.4 ps) in the charged environment. The protein dynamic was related to the water’s translational diffusion via the relaxation of the protein–water’s H-bonding. The structural and dynamical properties of protein–water at the molecular level are fundamental to the physiological and functional mechanisms of SNase.     

Intrinsic Contributions of 2′-Hydroxyl to the Hydration of Nucleosides at the Monomeric Level

Although many reports have revealed structural differences between DNA and RNA at the polymeric level, there are no comparative studies with 2′-deoxyribonucleoside and ribonucleoside to explore the role of the 2′-OH group at the monomeric level under the same conditions. Inspired by this, herein, the intrinsic contributions of the 2′-OH group in the nucleoside have been systematically investigated by directly solving the single-crystal structures of 2′-deoxy-2-aminoadenosine ( 1 ), 2-aminoadenosine ( 2 ), and 2-aminoarabinofuranosyladenine ( 3 ) in water. The 2′-OH group not only influenced the conformation and base-pair pattern of the single-nucleoside molecule, but also played a fundamental role in the entire supramolecular structure. Interestingly, compound 1 , which did not contain the 2′-OH group, displayed strong hydration, whereas 2 and 3 (with the 2′-OH group in the opposite direction) exhibited no hydration, which was completely different from that observed in nucleic acids. Meanwhile, compound 1 trapped water molecules to form unique trihydrol moieties, which further served as the backbone to construct the simplest double-chain DNA-like structures. To this end, to investigate the effect of the biological environment on these unique structures, the solvent was changed from water to phosphate-buffered saline (PBS). Surprisingly, such a subtle adjustment led to entirely different superstructures, consisting of 2D lamellar structures in water and 3D porous structures in PBS. These large morphological differences could be attributed to delicate ion hydration, which was also confirmed through variable-temperature X-ray analysis, SEM, and intermolecular interaction energy calculations. In summary, this study comprehensively investigated the intrinsic contributions of 2′-hydroxyl to the hydration of nucleosides at the monomeric level; this is helpful to further understand the differences in DNA/RNA and the impact of their surrounding environment.     

FMO‐MD Simulations on the Hydration of Formaldehyde in Water Solution with Constraint Dynamics

Full‐quantum mechanical fragment molecular orbital‐based molecular dynamics (FMO‐MD) simulations were applied to the hydration reaction of formaldehyde in water solution under neutral conditions. Two mechanisms, a concerted and a stepwise one, were considered with respect to the nucleophilic addition and the proton transfer. Preliminary molecular orbital calculations by means of polarized continuum model reaction field predicted that the hydration prefers a concerted mechanism. Because the calculated activation barriers were too high for free FMO‐MD simulations to give reactive trajectories spontaneously, a More O’Ferrall–Jencks‐type diagram was constructed from the statistical analysis of the FMO‐MD simulations with constraint dynamics. The diagram showed that the hydration proceeds through a zwitterionic‐like (ZW‐like) structure. The free energy changes along the reaction coordinate calculated by means of the blue moon ensemble for the hydration and the amination of formaldehyde indicated that the hydration proceeds through a concerted process through the ZW‐like structure, whereas the amination goes through a stepwise mechanism with a ZW intermediate. In inspection of the FMO‐MD trajectories, water‐mediated cyclic proton transfers were observed in both reactions on the way from the ZW‐like structure to the product. These proton transfers also have an asynchronous character, in which deprotonation from the nucleophilic oxygen atom (or nitrogen atom for amination) precedes the protonation of the carbonyl oxygen atom. The results showed the strong advantage of the FMO‐MD simulations to obtain detailed information at a molecular level for solution reactions.     

核糖核酸酶Sa表面水和尿素分子的分布和动力学行为的分子动力学模拟

利用分子动力学模拟研究了在不同尿素浓度下,核糖核酸酶Sa(RNase Sa)表面水和尿素分子的分布和动力学行为。 结果表明,尿素分子可与RNase Sa酶形成较强的相互作用,并取代其表面的水分子而富集在蛋白质表面。 尿素分子更倾向与RNase Sa酶的疏水残基作用,与RNase Sa酶主链形成氢键的能力更强。 尿素分子的平动和转动远远慢于水分子的平动和转动。 RNase Sa酶表面水分子的平动和转动随着尿素浓度增加而逐渐变慢,但RNase Sa酶表面尿素分子的动力学并不依赖于尿素浓度变化。 本研究中明晰的RNase Sa酶表面水和尿素分子分布和动力学有助于理解水和尿素分子对蛋白质稳定性的影响。     

Hydrogen Bonding in Liquid Water and in the Hydration Shell of Salts

A near‐IR spectral study on pure water and aqueous salt solutions is used to investigate stoichiometric concentrations of different types of hydrogen‐bonded water species in liquid water and in water comprising the hydration shell of salts. Analysis of the thermodynamics of hydrogen‐bond formation signifies that hydrogen‐bond making and breaking processes are dominated by enthalpy with non‐negligible heat capacity effects, as revealed by the temperature dependence of standard molar enthalpies of hydrogen‐bond formation and from analysis of the linear enthalpy–entropy compensation effects. A generalized method is proposed for the simultaneous calculation of the spectrum of water in the hydration shell and hydration number of solutes. Resolved spectra of water in the hydration shell of different salts clearly differentiate hydrogen bonding of water in the hydration shell around cations and anions. A comparison of resolved liquid water spectra and resolved hydration‐shell spectra of ions highlights that the ordering of absorption frequencies of different kinds of hydrogen‐bonded water species is also preserved in the bound state with significant changes in band position, band width, and band intensity because of the polarization of water molecules in the vicinity of ions.     

Insight into Protein–Polymer Conjugate Relaxation Dynamics: The Importance of Polymer Grafting

The bio and chemical physics of protein–polymer conjugates are related to parameters that characterize each component. With this work, it is intended to feature the dynamical properties of the protein–polymer conjugate myoglobin (Mb)–poly(ethyl ethylene phosphate), in the ps and ns time scales, in order to understand the respective roles of the protein and of the polymer size in the dynamics of the conjugate. Elastic and quasi‐elastic neutron scattering is performed on completely hydrogenated samples with variable number of polymer chains covalently attached to the protein. The role of the polymer length in the protein solvation and internal dynamics is investigated using two conjugates formed by polymers of different molecular weight. It is confirmed that the flexibility of the complex increases with the number of grafted polymer chains and that a sharp dynamical transition appears when either grafting density or polymer molecular weight are high. It is shown that protein size is crucial for the polymer structural organization and interaction on the protein surface and it is established that the glass properties of the polymer change upon conjugation. The results give a better insight of the equivalence of the polymer coating and the role of water on the surface of proteins.