Reorientation Of Water Molecules Research Articles

Exploring the Heterogeneous Dynamical Environment at the Interface of Aβ42 Peptide in Aqueous Ionic Liquid Solution.

In this study, we have investigated the heterogeneous dynamical environment around an ensemble of full-length amyloid-β (Aβ42) peptide monomers in binary aqueous solution containing the ionic liquid (IL) 1-butyl-3-methylimidazolium tetrafluoroborate [BMIM][BF4] as a co-solvent. Atomistic molecular dynamics (MD) simulations have been employed with the aim of understanding the effect of the IL on the distribution of water molecules and IL components around distinct segments of the peptide. As compared to pure aqueous medium, locally heterogeneous restricted water motions at the interface have been spotted in the presence of the IL. Our calculations revealed faster diffusion of water molecules hydrating hydrophilic segments (N-term and turn) as opposed to that around hydrophobic segments (hp1, hp2, and C-term). The extent of non-uniform restriction on the center-of-mass motions as well as the reorientation of water molecules and IL ions have been similarly affected in the binary IL-water solution. The effects of IL on the formation of hydrogen bond networks have been evident from the longer hydrogen bond relaxation time scales of peptide-water, with only a small fraction of peptide-anion hydrogen bonds contributing to the structural relaxation. Due to the size and shape factors, the increasingly sluggish dynamics of the IL components in the solvation shell can be attributed to a longer time scale for the onset of maximum dynamic heterogeneity. Interestingly, the water molecules around the polar segments of the peptide take longer to attain dynamic heterogeneity, which intensifies in the presence of IL. These calculations clearly suggest that electrostatic interaction plays a crucial role in water-mediated peptide-IL interaction, thereby shielding the surface from hydrophobic collapse and preventing possible further growth of the monomers into fibrils at higher peptide concentrations.

Comprehensive Approach to the Interpretation of the Electrical Properties of Film-Forming Molecules.

This paper presents a general protocol for the interpretation of the electric surface potential of Langmuir monolayers based on a three-layer capacitor model. The measured values were correlated with the results from DFT molecular dynamics simulations, and, as a result, the local dielectric permittivities and dipole-moment components of molecules organized in the monolayer were obtained. The main advantage of the developed approach is applicability to amphiphiles of any type; irrespective of the structure of the polar head as well as the molecular organization and inclination in the surface film. The developed methodology was successively applied to an atypical surface-active compound, perfluorodecyldecane, and its derivatives containing the hydroxyl, thiol, and carboxyl moiety. The following contributions to the apparent dipole moments connected with the reorientation of water molecules and local dielectric permittivities in the vicinity of polar and apolar molecule parts, respectively, were determined: μw/εw = −0.85 D, εp = 5.00, and εa = 1.80. Moreover, the investigated perfluorodecyldecane derivatives were comprehensively characterized in terms of their surface activity, film rheology, and effective surface dissociation equilibria. The proposed methodology may be crucial for the process of the design and the preliminary characterization of molecules for sensor and material science applications.

Comparative analysis of hydration layer reorientation dynamics of antifreeze protein and protein cytochrome P450

Antifreeze proteins (AFPs) inhibit ice re-crystallization by a mechanism remaining largely elusive. Dynamics of AFPs’ hydration water and its involvement in the antifreeze activity have not been identified conclusively. We herein, by simulation and theory, examined the water reorientation dynamics in the first hydration layer of an AFP from the spruce budworm, Choristoneura fumiferana, compared with a protein cytochrome P450 (CYP). The increase of potential acceptor water molecules around donor water molecules leads to the acceleration of hydrogen bond exchange between water molecules. Therefore, the jump reorientation of water molecules around the AFP active region is accelerated. Due to the mutual coupling and excitation of hydrogen bond exchange, with the acceleration of hydrogen bond exchange, the rearrangement of the hydrogen bond network and the frame reorientation of water are accelerated. Therefore, the water reorientation dynamics of AFP is faster than that of CYP. The results of this study provide a new physical image of antifreeze protein and a new understanding of the antifreeze mechanism of antifreeze proteins.

Ionic Transport in Electrostatic Janus Membranes. An Explicit Solvent Molecular Dynamic Simulation.

Janus, or two-sided, charged membranes offer promise as ionic current rectifiers. In such systems, pores consisting of two regions of opposite charge can be used to generate a current from a gradient in salinity. The efficiency of nanoscale Janus pores increases dramatically as their diameter becomes smaller. However, little is known about the underlying transport processes, particularly under experimentally accessible conditions. In this work, we examine the molecular basis for rectification in Janus nanopores using an applied electric field. Molecular simulations with explicit water and ions are used to examine the structure and dynamics of all molecular species in aqueous electrolyte solutions. For several macroscopic observables, the results of such simulations are consistent with experimental observations on asymmetric membranes. Our analysis reveals a number of previously unknown features, including a pronounced local reorientation of water molecules in the pores, and a segregation of ionic species that had not been anticipated by previously reported continuum analyses of Janus pores. Using these insights, a model is proposed for ionic current rectification in which electric leakage at the pore entrance controls net transport.

Ultrafast dynamics of proflavine bound to poly (methacrylic acid) in aqueous solution

The excited-state dynamics of fluorescent probes attached to polymer segments under un-entangled conditions unveil the internal dynamics and interior polarity of both synthetic and natural polymers. Synthetic polyelectrolytes have been considered as a simple model system to circumvent the structural and dynamic complexity of bio-macromolecules on interaction with solvent molecules in the vicinity. In this study, femtosecond dynamics of proflavine cation, a molecular probe with well-established excited state dynamics have been explored by steady-state and time-resolved fluorescence to uncover structural dynamics of polymethacrylic acid at the sub-picosecond to the picosecond time domain. The femtosecond fluorescence transients display a bi-exponential decay. The shorter decay time of 1–5 ps represents the reorientation of the water molecules during the excited state of the fluorophore. The increase in the lifetime of this component from 1.0 ps to 5.0 ps on increasing the pH of the solution from 2.0 to 5.0 is ascribed to the reorientation of water molecules due to the compact and hydrophobic nature of the macromolecule. The second decay component of proflavine bound to PMAA increases from 70 ps to 180 ps on increasing the pH of the solution from 2.5 to 5.0. The hydrophobic part of the polyelectrolyte present under acidic conditions restricts the solvent reorganization during the solvation of the covalently bound dye molecule and the stretched linear chains of the polyelectrolyte do not influence the solvation and the observed decay time is identical to that of free dye in aqueous solution.

Exploring Intra- and Intermolecular Interactions in Selected N-Oxides-The Role of Hydrogen Bonds.

Intra- and intermolecular interactions have been explored in selected N-oxide derivatives: 2-(N,N-dimethylamino-N-oxymethyl)-4,6-dimethylphenyl (1) and 5,5’-dibromo-3-diethylaminomethyl-2,2’-biphenol N-oxide (2). Both compounds possess intramolecular hydrogen bonding, which is classified as moderate in 1 and strong in 2, and resonance-assisted in both cases. Density Functional Theory (DFT) in its classical formulation as well as Time-Dependent extension (TD-DFT) were employed to study proton transfer phenomena. The simulations were performed in the gas phase and with implicit and explicit solvation models. The obtained structures of the studied N-oxides were compared with experimental data available. The proton reaction path was investigated using scan with an optimization method, and water molecule reorientation in the monohydrate of 1 was found upon the proton scan progress. It was found that spontaneous proton transfer phenomenon cannot occur in the electronic ground state of the compound 1. An opposite situation was noticed for the compound 2. The changes of nucleophilicity and electrophilicity upon the bridged proton migration were analyzed on the basis of Fukui functions in the case of 1. The interaction energy decomposition of dimers and microsolvation models was investigated using Symmetry-Adapted Perturbation Theory (SAPT). The simulations were performed in both phases to introduce polar environment influence on the interaction energies. The SAPT study showed rather minor role of induction in the formation of homodimers. However, it is worth noticing that the same induction term is responsible for the preference of water molecules’ interaction with N-oxide hydrogen bond acceptor atoms in the microsolvation study. The Natural Bond Orbital (NBO) analysis was performed for the complexes with water to investigate the charge flow upon the polar environment introduction. Finally, the TD-DFT was applied for isolated molecules as well as for microsolvation models showing that the presence of solvent affects excited states, especially when the N-oxide acceptor atom is microsolvated.

Water-oriented magnetic anisotropy transition

Water reorientation is essential in a wide range of chemical and biological processes. However, the effects of such reorientation through rotation around the metal–oxygen bond on the chemical and physical properties of the resulting complex are usually ignored. Most studies focus on the donor property of water as a recognized σ donor-type ligand rather than a participant in the π interaction. Although a theoretical approach to study water-rotation effects on the functionality of a complex has recently been conducted, it has not been experimentally demonstrated. In this study, we determine that the magnetic anisotropy of a Co(II) complex can be effectively controlled by the slight rotation of coordinating water ligands, which is achieved by a two-step structural phase transition. When the water molecule is rotated by 21.2 ± 0.2° around the Co–O bond, the directional magnetic susceptibility of the single crystal changes by approximately 30% along the a-axis due to the rotation of the magnetic anisotropy axis through the modification of the π interaction between cobalt(II) and the water ligand. The theoretical calculations further support the hypothesis that the reorientation of water molecules is a key factor contributing to the magnetic anisotropy transition of this complex.

Unravelling hydrogen adsorption kinetics on Ir(111) electrode in acid solutions by impedance spectroscopy

The kinetics for hydrogen (H) adsorption on Ir(111) electrode has been studied in both HClO4 and H2SO4 solutions by impedance spectroscopy. In HClO4, the adsorption rate for H adsorption on Ir(111) increases from 1.74×10−8 mol·cm−2·s−1 to 3.47×10−7 mol·cm−2·s−1 with the decrease of the applied potential from 0.2 V to 0.1 V (vs. RHE), which is ca. one to two orders of magnitude slower than that on Pt(111) under otherwise identical condition. This is explained by the stronger binding of water to Ir(111), which needs a higher barrier to reorient during the under potential deposition of H from hydronium within the hydrogen bonded water network. In H2SO4, the adsorption potential is ca. 200 mV negatively shifted, accompanied by a decrease of adsorption rate by up to one order of magnitude, which is explained by the hindrance of the strongly adsorbed sulfate/bisulfate on Ir(111). Our results demonstrate that under electrochemical environment, H adsorption is strongly affected by the accompanying displacement and reorientation of water molecules that initially stay close to the electrode surface.

Electrical Properties of Membrane Phospholipids in Langmuir Monolayers.

Experimental surface pressure () and electric surface potential () isotherms were measured for membrane lipids, including the following phosphatidylcholines (PCs)—1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC); 1,2-distearoyl-sn-glycero-3-phosphocholine (DSPC); 1,2-diarachidoyl-sn-glycero-3-phosphocholine (DAPC); and 1,2-dioleoyl-sn-glycero-3-phosphocholine (DOPC). In addition, other phospholipids, such as phosphatidylethanolamines (represented by 1,2-dipalmitoyl-sn-glycero-3-phosphoethanolamine (DPPE)) and sphingolipids (represented by N-(hexadecanoyl)-sphing-4-enine-1-phosphocholine (SM)) were also studied. The experimental apparent dipole moments () of the abovementioned lipids were determined using the Helmholtz equation. The particular contributions to the apparent dipole moments of the investigated molecules connected with their polar () and apolar parts () were theoretically calculated for geometrically optimized systems. Using a three-layer capacitor model, introducing the group’s apparent dipole moments (calculated herein) and adopting values from other papers to account for the reorientation of water molecules (), as well as the for the local dielectric permittivity in the vicinity of the polar () and apolar () groups, the apparent dipole moments of the investigated molecules were calculated (). Since the comparison of the two values (experimental and calculated) resulted in large discrepancies, we developed a new methodology that correlates the results from density functional theory (DFT) molecular modeling with experimentally determined values using multiple linear regression. From the fitted model, the following contributions to the apparent dipole moments were determined: ; and ). Local dielectric permittivity in the vicinity of apolar groups () is much lower compared to that in the vicinity of polar moieties (), which is in line with the tendency observed by other authors studying simple molecules with small polar groups. A much higher value for the contributions from the reorientation of water molecules () has been interpreted as resulting from bulky and strongly hydrated polar groups of phospholipids.

Magnesium Contact Ions Stabilize the Tertiary Structure of Transfer RNA: Electrostatics Mapped by Two-Dimensional Infrared Spectra and Theoretical Simulations.

Ions interacting with hydrated RNA play a central role in defining its secondary and tertiary structure. While spatial arrangements of ions, water molecules, and phosphate groups have been inferred from X-ray studies, the role of electrostatic and other noncovalent interactions in stabilizing compact folded RNA structures is not fully understood at the molecular level. Here, we demonstrate that contact ion pairs of magnesium (Mg2+) and phosphate groups embedded in local water shells stabilize the tertiary equilibrium structure of transfer RNA (tRNA). Employing dialyzed tRNAPhe from yeast and tRNA from Escherichia coli, we follow the population of Mg2+ sites close to phosphate groups of the ribose-phosphodiester backbone step by step, combining linear and nonlinear infrared spectroscopy of phosphate vibrations with molecular dynamics simulations and ab initio vibrational frequency calculations. The formation of up to six Mg2+/phosphate contact pairs per tRNA and local field-induced reorientations of water molecules balance the phosphate–phosphate repulsion in nonhelical parts of tRNA, thus stabilizing the folded structure electrostatically. Such geometries display limited sub-picosecond fluctuations in the arrangement of water molecules and ion residence times longer than 1 μs. At higher Mg2+ excess, the number of contact ion pairs per tRNA saturates around 6 and weakly interacting ions prevail. Our results suggest a predominance of contact ion pairs over long-range coupling of the ion atmosphere and the biomolecule in defining and stabilizing the tertiary structure of tRNA.

Effects of Hydrogen Bonding on the Rotational Dynamics of Water-Like Molecules in Liquids: Insights from Molecular Dynamics Simulations

Rotational motion of molecules plays an important role in determining NMR spin relaxation properties of liquids. The textbook theory of NMR spin relaxation predominantly uses the assumption that the reorientational dynamics of molecules is described by a continuous time rotational diffusion random walk with a single rotational diffusion coefficient. Previously we and others have shown that reorientation of water molecules on the timescales of picoseconds is not consistent with the Debye rotational-diffusion model. In particular, multiple timescales of molecular reorientation were observed in liquid water. This was attributed to the hydrogen bonding network in water and the consequent presence of collective rearrangements of the molecular network. In order to better understand the origins of the complex reorientational behaviour of water molecules, we carried out molecular dynamics (MD) simulations of a liquid that has a similar molecular geometry to water but does not form hydrogen bonds: hydrogen sulfide. These simulations were carried out at T=208K and p=1 atm (~5K below the boiling point). Ensemble-averaged Legendre polynomial functions of hydrogen sulfide exhibited a Gaussian decay on the sub-picosecond timescale but, unlike water, did not exhibit oscillatory behaviour. We attribute these differences to hydrogen sulfide’s absence of hydrogen bonding.

Hydrogen order at the surface of ice Ih revealed by vibrational spectroscopy.

Among numerous crystalline phases of ice, the Ih phase is the most stable above 72 K at atmospheric pressure. It is well established that the orientations of water molecules in the bulk of ice Ih are statistical without long-range order. However, the orientational order of water at the surface of ice Ih has been enigmatic. Here we show that the surface of ice Ih at 100 K has hydrogen order with the OH group pointing upward to the air ("H-up" orientation). We applied nonlinear optical spectroscopy and theoretical modeling to the surface of isotopically pure and diluted ice Ih and observed OH stretch vibrational signatures attributed to H-up ordering. Furthermore, we found that this hydrogen order takes place despite a more inhomogeneous microenvironment at the surface than in the bulk. Our results suggest the prominent role of the surface to allow the reorientation of water molecules for hydrogen ordering that is virtually prohibited in the bulk.

Do Molecular Dynamics Force Fields Capture Conformational Dynamics of Alanine in Water?

We examine the ability of six molecular dynamics (MD) force fields (Amber ff14SB, Amber ff99SBnmr1, Amber ff03ws, OPLS-AA/L, OPLS-AA/M, and CHARMM36) to reproduce conformational ensembles of the central alanine in GAG and AAA in a way that is consistent with five (GAG) or six (AAA) J coupling constants and amide I' profiles. MD-derived Ramachandran plots for all six force fields under study differ from those obtained by the Gaussian fit to experimental data in three major ways: (i) the polyproline II (pPII) basin in the Ramachandran plot is too concentrated, (ii) the antiparallel β (aβ) basin is overpopulated, and (iii) the transitional β (βt) basin is underpopulated. Amber ff14SB outperforms the other five MD force fields and yields the highest pPII populations of the central alanine residue in GAG (55%) and AAA (63%), in good agreement with the predictions of the Gaussian model (59 and 76%). The analysis of the hydration layer around the central alanine residue reveals considerable reorientation of water molecules and reduction in both the average number of water molecules and the average number of water-water hydrogen bonds when glycines (in GAG) are replaced by alanines (in AAA), elucidating water-mediated nearest neighbor effects on alanine's conformational dynamics.

Car-Parrinello molecular dynamics study on the interaction between lignite and water molecules

Water-desorption from lignite surface is an important issue in energy usage, however, corresponding researches are inadequate. Herein, in order to comprehensive understand the process of water-desorption from lignite surface, the interaction between water molecules and carboxyl group of lignite were investigated systematically from 298.15 K to 440 K, by using Car–Parrinello molecular dynamics (CPMD) method. The result indicated that in the key carboxyl group, the hydrogen site (H51) showed stronger adsorption capacity for water molecules than the oxygen site (O23) of the carboxyl group. Based on the statistical result, the water molecules adsorbed at H51 and O23 were considered as removed after 360 K. Vibration analysis was performed to acquire stretching frequencies of carboxyl group before and after water adsorption. The NBO analysis was used to study the reorientation of water molecules in a 0.14 ps trajectory when they replace with each other. The NBO orbitals obtained show that when water molecule is replacing, the two lone pair orbitals of O31 and O32 interact with the σ antibonding orbital of O24H51 bond at the same time. It enhances the formation of new H-bond and facilitates the fracture of old H-bond. This work can not only reveal the mechanism of water desorption from lignite, but also lay valuable foundations for efficient utilization of lignite resource.

Re-orientation of water molecules in response to surface charge at surfactant interfaces.

We present a measurement of molecular orientation of water at charged surfactant aqueous interfaces as a function of surface charge density. The polarization dependent spectral line shapes of the water bend mode were measured by vibrational sum-frequency generation at the positively charged surfactant cetyltrimethylammonium bromide (CTAB)/water interface and negatively charged surfactant sodium dodecyl sulfate/water interface. Orientational analysis using the water bend mode as a vibrational probe, within the electric dipole approximation, reveals structural differences between these surfaces and quantifies how different hydrogen bonded species re-orient around the surfactant head groups as the surface charge density changes. As the concentration of the positively charged surfactant (CTAB) increases, the surface water molecules with free-OH groups reorient their hydrogen away from the bulk water and the C2v axis closer to the surface normal. This suggests that these free-OH molecules are in general located above the positively charged head groups of CTAB, and thus, the charge-dipole interaction pulls their oxygen "down" and pushes hydrogen "up." On the contrary, water molecules with two donor hydrogen bonds re-orient their hydrogen toward the bulk water, likely because most of these molecules are below the CTAB surfactant head groups.

Enhancement of the local asymmetry in the hydrogen bond network of liquid water by an ultrafast electric field pulse

Condensed phase electron decomposition analysis based on density functional theory has recently revealed an asymmetry in the hydrogen-bond network in liquid water, in the sense that a significant population of water molecules are simultaneously donating and accepting one strong hydrogen-bond and another substantially weaker one. Here we investigate this asymmetry, as well as broader structural and energetic features of water’s hydrogen-bond network, following the application of an intense electric field square pulse that invokes the ultrafast reorientation of water molecules. We find that the necessary field-strength required to invoke an ultrafast alignment in a picosecond time window is on the order of 108 Vm−1. The resulting orientational anisotropy imposes an experimentally measurable signature on the structure and dynamics of the hydrogen-bond network, including its asymmetry, which is strongly enhanced. The dependence of the molecular reorientation dynamics on the field-strength can be understood by relating the magnitude of the water dipole–field interaction to the rotational kinetic energy, as well as the hydrogen-bond energy.

Water in an electric field does not dance alone: The relation between equilibrium structure, time dependent viscosity and molecular motions

Dynamic structuring of water is a key player in a large class of processes underlying biochemical and technological developments today, the latter often involving electric fields. However, the anisotropic coupling between the water structure and the field has not been understood on a molecular level so far. Here we perform extensive molecular dynamics simulations to explore the influence of an externally imposed electric field on liquid water under ambient conditions. Using self-developed analysis tools and rigorous statistical analysis, we unambiguously show that water hydration shells break into subcompartments, which were hitherto not observed due to radial averaging. The shape of subcompartments is sensitive to the field magnitude and affects excitations of the hydrogen bond network including the femtosecond stretching and the sub-picosecond restructuring of hydrogen bonds. Furthermore, by analysing the reorientational dynamics of water molecules, we ascertain the existence of cooperative excitations of small water clusters. Enabled by the interplay between hydrogen bonding, and the coupling of water dipoles to the field, these coordinated motions, occurring on the picosecond time scale, are associated with fluctuations between torque-free states of water dipoles. We show that unlike the coupling between translation and reorientation of water molecules, which takes place on even longer time scales, these coordinated motions are the key for understanding the emergent anisotropy of diffusion and viscosity of water. Particular effort is invested to provide an analysis that allows for future experimental validation.

Aqueous solvation from the water perspective.

The response of water re-solvating a charge-transfer dye (deprotonated Coumarin 343) after photoexcitation has been measured by means of transient THz spectroscopy. Two steps of increasing THz absorption are observed, a first ∼10 ps step on the time scale of Debye relaxation of bulk water and a much slower step on a 3.9 ns time scale, the latter of which reflecting heating of the bulk solution upon electronic relaxation of the dye molecules from the S1 back into the S0 state. As an additional reference experiment, the hydroxyl vibration of water has been excited directly by a short IR pulse, establishing that the THz signal measures an elevated temperature within ∼1 ps. This result shows that the first step upon dye excitation (10 ps) is not limited by the response time of the THz signal; it rather reflects the reorientation of water molecules in the solvation layer. The apparent discrepancy between the relatively slow reorientation time and the general notion that water is among the fastest solvents with a solvation time in the sub-picosecond regime is discussed. Furthermore, non-equilibrium molecular dynamics simulations have been performed, revealing a close-to-quantitative agreement with experiment, which allows one to disentangle the contribution of heating to the overall THz response from that of water orientation.

Red/Green Color Tuning of Visual Rhodopsins: Electrostatic Theory Provides a Quantitative Explanation

We present a structure-based theory of the long-wavelength (red/green) color tuning in visual rhodopsins and its application to the analysis of site-directed mutagenesis experiments. Using a combination of electrostatic and molecular-mechanics methods, we explain the measured mutant-minus-wild-type absorption shifts and conclude that the dominant mechanism of the color tuning in these systems is electrostatic pigment-protein coupling. An important element of our analysis is the independent determination of protonation states of titratable residues in the wild type and the mutant protein as well as the self-consistent reoptimization of hydrogen atom positions, which includes the relaxation of the hydrogen bonding network and the reorientation of water molecules. On the basis of this analysis, we propose a "dipole-orientation rule" according to which both the position and the orientation of a polar group introduced in the protein environment determine the direction of the transition energy shift of the retinal chromophore.

Dielectric relaxations of confined water in porous silica ceramics

In this study, dielectric properties of water confined in porous silica ceramics were investigated. Two porous ceramics were characterized in the frequency range \(10^{-1}~\hbox {to}~10^{7}\) Hz and temperature interval from \(-100\) to \(200^{\circ }\hbox {C}\). While the first sample was a ceramic with opened lateral pores, the second one was a ceramic with sealed lateral pores. In both ceramics, three dielectric processes were identified. The first, which appeared at lower temperatures, was attributed to the reorientation of water molecules in ice-like water cluster structures. The second is the relaxation observed over an intermediate temperature range, associated with the kinetic transition due to water molecule reorientation near a defect. At higher temperatures, the third was relaxation identified as the Maxwell–Wagner–Sillars polarization process due to the trapping of free charge carriers at the interface of the porous media. The first and second dielectric relaxations were analysed to prove the effect of the lateral surface state of the sample on water–inner surfaces of the porous media interaction. These analyses revealed a great similarity in the ice-like structure for both ceramics. However, the lateral surface state of the sample might enhance the dielectric strength of the first relaxation when lateral pores are sealed. Furthermore, it might improve the water–inner surfaces interaction when lateral pores are opened.