Water Molecules In Hydration Shell Research Articles

Monte Carlo simulation study of the structure of calcium and potassium chlorides ternary solutions

ABSTRACT Monte Carlo simulations were conducted on pure water and aqueous calciumand potassium chloride ternary solutions at different salts concentrations. To assess the local order within the solutions, the Monte Carlo simulations utilised the Madrid-2019 force field, usingtheTIP4P/2005 water model and scaled charges. The results demonstrate that as the salt concentrations increase, there is a notable decrease in the contribution of the structured tetrahedral arrangement of water molecules, favouring an unstructured configuration instead. The use of the nearest neighbour approach, provided unambiguous information regarding the radial and orientation characteristics of the unstructured configuration of water. Structures of the solvation shells around ions are also studied. The Monte Carlo simulations indicate that as the salt concentration increases, the hydration number around the cation decreases. This effect is likely due to the occasional substitution of some water molecules in the first hydration shell by chlorine ions.

Designing Reaction Coordinate for Ion-Induced Pore-Assisted Mechanism of Halide Ions Permeation through Lipid Bilayer by Umbrella Sampling.

Ion permeation mechanism through lipid membranes helps to understand cellular processes. We propose new reaction coordinates that allow ions to permeate according to their water affinity and interaction with the hydrophilic layer. Simulations were done for three different halides (F-, Cl-, and I-) in two different lipid bilayers, 1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC) and 1,2-dinervonoyl-sn-glycero-3-phosphocholine (DNPC). It is found that the involvement of the water molecules decreases the free energy barrier. The ions were found to follow different pathways for permeation. Formation of proper pores required a collaboration effort of the hydration shell water molecules and the hydrophilic lipid layer, which was favored in the case of Cl- ions. The optimum charge density and good water affinity of Cl- with respect to F- and I- ions helped to form the pore. The effect was prominently seen in the case of DNPC membrane because of its higher hydrophobic thickness. The umbrella sampling results were compared with other methods such as the Markov state model (MSM) and well-tempered metadynamics (WT-metaD).

Water molecule ordering on the surface of an intrinsically disordered protein

The dynamics and local structure of the hydration water on surfaces of folded proteins have been extensively investigated. However, our knowledge of the hydration of intrinsically disordered proteins (IDPs) is more limited. Here, we compare the local structure of water molecules hydrating a globular protein, lysozyme, and the intrinsically disordered N-terminal of c-Src kinase (SH4UD) using molecular dynamics simulation. The radial distributions from the protein surface of the first and the second hydration shells are similar for the folded protein and the IDP. However, water molecules in the first hydration shell of both the folded protein and the IDP are perturbed from the bulk. This perturbation involves a loss of tetrahedrality, which is, however, significantly more marked for the folded protein than the IDP. This difference arises from an increase in the first hydration shell of the IDP of the fraction of hydration water molecules interacting with oxygen. The water ordering is independent of the compactness of the IDP. In contrast, the lifetimes of water molecules in the first hydration shell increase with IDP compactness, indicating a significant impact of IDP configuration on water surface pocket kinetics, which here is linked to differential pocket volumes and polarities.

Model-Dependent Solvation of the K-18 Domain of the Intrinsically Disordered Protein Tau.

A known imbalance between intra-protein and protein-water interactions in many empirical force fields results in collapsed conformational ensembles of intrinsically disordered proteins in explicit solvent simulations that disagree with experiments. Multiple strategies have been introduced in the literature to modify protein-water interactions, which improve agreement between experiments and simulations. In this work, we combine simulations with standard and modified force fields with a spatially resolved analysis of solvation free energy contributions and compare the consequences of each strategy. We find that enhanced Lennard-Jones (LJ) interactions between protein atoms and water oxygens primarily improve the solvation of nonpolar functional groups of the protein. In contrast, modified electrostatics in the water model or strengthened LJ interactions between the protein and water hydrogens mainly affect the hydration of polar functional groups. Modified electrostatics further impact the average orientation of water molecules in the hydration shell. As a result, protein-water interactions with the first hydration layers are strengthened, while interactions with water molecules in higher hydration shells are weakened. Hence, distinct strategies to balance intra-protein and protein-water interactions in simulations have qualitatively different effects on protein solvation. These differences are not necessarily captured by comparisons to experiments that report on global parameters describing protein conformational ensembles, e.g., the radius of gyration, but will influence the tendency of a protein to form aggregates or phase-separated droplets.

Molecular simulation of partially denatured β-lactoglobulin

The unfolding of β-lactoglobulin (β-lac) upon heating was comprehensively studied through molecular dynamics computer simulations. A β-lac molecule in the aqueous solution was firstly heated at 500 K for unfolding and then annealed at 300 K to collect stable conformations. There were five meta-stable conformations observed based on the Free Energy Landscape (FEL). The β-lac molecule was found to exhibit an open and extended conformation on heating followed by limited refolding upon cooling. The cysteine residues –SH121 and S–S66-160 in the most open conformation were located at the opposite ends of the β-lac molecule. This would favour the intermolecular –SH/S–S interchange reactions that are known to occur in β-lac as part of the inter-molecular aggregation process. Furthermore, the unfolding of the β-lac increased the hydrogen bond forming capacity between water molecules and the protein and between water molecules themselves. The interactions and the properties of the water molecules in the protein hydration shell also indicated that the hydration shell was stabilized by protein unfolding. However, it was found that the unfolding of β-lac increased diffusion of hydration water molecules, including those in the first hydration shell that interact more strongly with the protein. This may partly explain why unfolded proteins are more likely to aggregate even though there were more hydration water molecules protecting them. Such results provided more detailed information on the structure-functionality relationship of β-lac based on both the protein molecule and its hydration shell. This provides insight into how we can control the processing of proteins for desirable functional properties such as thickening and gelation, which are modified through protein-water interactions.

An Affordable Topography-Based Protocol for Assigning a Residue's Character on a Hydropathy (PARCH) Scale.

The hydropathy of proteins or quantitative assessment of protein-water interactions has been a topic of interest for decades. Most hydropathy scales use a residue-based or atom-based approach to assign fixed numerical values to the 20 amino acids and categorize them as hydrophilic, hydroneutral, or hydrophobic. These scales overlook the protein's nanoscale topography, such as bumps, crevices, cavities, clefts, pockets, and channels, in calculating the hydropathy of the residues. Some recent studies have included protein topography in determining hydrophobic patches on protein surfaces, but these methods do not provide a hydropathy scale. To overcome the limitations in the existing methods, we have developed a Protocol for Assigning a Residue's Character on the Hydropathy (PARCH) scale that adopts a holistic approach to assigning the hydropathy of a residue. The parch scale evaluates the collective response of the water molecules in the protein's first hydration shell to increasing temperatures. We performed the parch analysis of a set of well-studied proteins that include the following─enzymes, immune proteins, and integral membrane proteins, as well as fungal and virus capsid proteins. Since the parch scale evaluates every residue based on its location, a residue may have very different parch values inside a crevice versus a surface bump. Thus, a residue can have a range of parch values (or hydropathies) dictated by the local geometry. The parch scale calculations are computationally inexpensive and can compare hydropathies of different proteins. The parch analysis can affordably and reliably aid in designing nanostructured surfaces, identifying hydrophilic and hydrophobic patches, and drug discovery.

Molecular dynamics study of collective water vibrations in a DNA hydration shell

The structure of DNA double helix is stabilized by water molecules and metal counterions that form the ion-hydration shell around the macromolecule. Understanding the role of the ion-hydration shell in the physical mechanisms of the biological functioning of DNA requires detailed studies of its structure and dynamics at the atomistic level. In the present work, the study of collective vibrations of water molecules around the DNA double helix was performed within the framework of classical all-atom molecular dynamics methods. Calculating the vibrational density of states, the vibrations of water molecules in the low-frequency spectra ranged from [Formula: see text]30 to [Formula: see text]300 [Formula: see text] were analyzed for the case of different regions of the DNA double helix (minor groove, major groove, and phosphate groups). The analysis revealed significant differences in the collective vibrations behavior of water molecules in the DNA hydration shell, compared to the vibrations of bulk water. All low-frequency modes of the DNA ion-hydration shell are shifted by about 15-20 [Formula: see text] towards higher frequencies, which is more significant for water molecules in the minor groove region of the double helix. The interactions of water molecules with the atoms of themacromolecule induce intensity decrease of the mode of hydrogen-bond symmetrical stretching near 150 [Formula: see text], leading to the disappearance of this mode in the DNA spectra. The obtained results can provide an interpretation of the experimental data for DNA low-frequency spectra and may be important for the understanding of the processes of indirect protein-nucleic recognition.

Thermal tuning of protein hydration in a hyperthermophilic enzyme.

Water at the protein surface is an active biological molecule that plays a critical role in many functional processes. Using NMR-restrained MD simulations, we here addressed how protein hydration is tuned at high biological temperatures by analysing homologous acylphosphatase enzymes (AcP) possessing similar structure and dynamics under very different thermal conditions. We found that the hyperthermophilic Sso AcP at 80°C interacts with a lower number of structured waters in the first hydration shell than its human homologous mt AcP at 37°C. Overall, the structural and dynamical properties of waters at the surface of the two enzymes resulted similar in the first hydration shell, including solvent molecules residing in the active site. By contrast the dynamical content of water molecules in the second hydration shell was found to diverge, with higher mobility observed in Sso AcP at 80°C. Taken together the results delineate the subtle differences in the hydration properties of mt AcP and Sso AcP, and indicate that the concept of corresponding states with equivalent dynamics in homologous mesophilic and hyperthermophylic proteins should be extended to the first hydration shell.

Dielectric Relaxation of Ion-pairs, Micelles and Hydration in Aqueous Hexyltrimethylammonium Bromide Solutions

Through dielectric measurements of aqueous n-hexyltrimethylammonium bromide solutions, the structure and dynamics of ion-pairs, micelles, and water are investigated as functions of concentration and temperature. The frequency range of the study was ∼ 0.2 ≤ν/GHz ≤ 89, and the concentrations were changed from 0.0448 to 0.8476 mol.dm−3 at 298.15 K. The effects of temperature (278.15 ≤ T/K ≤ 338.15) on two selected solutions with concentrations above and below the critical micelle concentration were examined. A summation of three Debye processes fits the complex permittivity data of solutions with concentrations below the critical micelle concentration. To fit the spectra above the critical micelle concentration, a summation of five Debye processes is needed. Below the critical micelle concentration, solutes relax due to the tumbling motion of solvent-shared ion pairs. The two micelle relaxation processes that have been seen are the result of free and bound counter ions tangentially and radially diffusing around the charged micelles. Maxwell-Wagner relaxation is equivalent to the high frequency micelle relaxation process. Both the solvent and micelle dispersion provide acceptable volume fractions. Hexyltrimethylammonium behaves like higher n-alkyltrimethylammonium micelles in the context of micelle relaxation. Before critical micelle concentration, the cations, anions, and ion pairs strongly hydrate a total of ∼18 ± 4 non-rotational water molecules. Beyond the critical micelle concentration, there are an additional ∼ 5 ± 2 non-rotational water molecules in addition to ∼ 15 ± 3 slower-moving water molecules in the hydrophobic hydration shell.

Extended X-ray absorption fine structure spectroscopy measurements and ab initio molecular dynamics simulations reveal the hydration structure of the radium(II) ion

SummaryRadium is refocused from the viewpoint of an environmental pollutant and cancer therapy using alpha particles, where it mainly exists as a hydrated ion. We investigated the radium hydration structure and the dynamics of water molecules by extended X-ray absorption fine structure (EXAFS) spectroscopy and ab initio molecular dynamics (AIMD) simulation. The EXAFS experiment showed that the coordination number and average distance between radium ion and the oxygen atoms in the first hydration shell are 9.2 ± 1.9 and 2.87 ± 0.06 Å, respectively. They are consistent with those obtained from the AIMD simulations, 8.4 and 2.88 Å. The AIMD simulations also revealed that the water molecules in the first hydration shell of radium are less structured and more mobile than those of barium, which is an analogous element of radium. Our results indicate that radium can be more labile than barium in terms of interactions with water.

Irregular structure of the hydrated Ag+ in aqueous solution and its Dynamics: An insight from perturbation theory hybrid forces molecular dynamics simulation

The structural and dynamical properties of hydrated Ag+ in a water solution were investigated theoretically using hybrid forces molecular dynamics simulation. The quantum mechanical region was treated using the resolution of identity MP2 (RI-MP2) level of a theory enabling the description of the properties of the hydration shell accurately.In contrast to the previously reported linear configuration, the first hydration shell had an irregular shape, with an average coordination number of 5.5. The Ag+–O distance in the first hydration shell was 2.59 Å. The mean residence time of water molecules in the first hydration shell was 0.89 ps, indicating that Ag+ acted as a structure-breaking agent.

Ion Hydration under Nanoscale Confinement: Dimensionality and Scale Effects

How ions are hydrated in nanoconfined spaces is crucial for understanding many natural phenomena and practical applications, such as biological functionalities and energy conversion devices. In real systems, nanoconfinement shows structural diversity, but the influence of dimensionality and scale on ion hydration remains considerably unrevealed. Here, we study ion hydration under various confinements by systematic molecular dynamics simulations. In a given dimension, the structure and dynamics of water molecules in the first hydration shell are altered to a degree inversely correlated with the confinement scale, as long as there is no central bulk-like region. Further comparison of ion hydration among different dimensional systems shows that this scale effect becomes more pronounced in systems with lower dimensionality, due to a more significant water layering effect and lower probability for ions to stay away from confining surfaces. These findings provide a qualitatively new understanding of ion transport in biological channels and are instrumental for the design of functional nanofluidic devices.

Confinement induces stable calcium carbonate formation in silica nanopores.

Scalable efforts to remove anthropogenic CO2via the formation of durable carbonates require us to harness siliceous nanoporous geologic materials for carbon storage. While calcium carbonate formation has been extensively reported in bulk fluids, there is a limited understanding of the influence of nanoconfined fluids on the formation of specific stable and metastable polymorphs of calcium carbonates in siliceous materials that are abundant in subsurface environments. To address this challenge, silica nanochannels with diameters of 3.7 nm are architected and the formation of specific calcium carbonate phases is investigated using X-ray diffraction (XRD), and molecular dynamics (MD) simulations. The formation of stable calcium carbonate (or calcite) is noted in silica nanochannels. The presence of fewer water molecules in the first hydration shell of calcium ions in confinement compared to in bulk fluids contributes to stable calcium carbonate formation. These studies show that nanoporous siliceous environments favor the formation of stable calcium carbonate formation.

Bridging Structure, Dynamics, and Thermodynamics: An Example Study on Aqueous Potassium Halides.

Aqueous salt systems are ubiquitous in all areas of life. The ions in these solutions impose important structural and dynamic perturbations to water. In this study, we employ a combined neutron scattering, nuclear magnetic resonance, and computational modeling approach to deconstruct ion-specific perturbations to water structure and dynamics and shed light on the molecular origins of bulk thermodynamic properties of the solutions. Our approach uses the atomistic scale resolution offered to us by neutron scattering and computational modeling to investigate how the properties of particular short-ranged microenvironments within aqueous systems can be related to bulk properties of the system. We find that by considering only the water molecules in the first hydration shell of the ions that the enthalpy of hydration can be determined. We also quantify the range over which ions perturb water structure by calculating the average enthalpic interaction between a central halide anion and the surrounding water molecules as a function of distance and find that the favorable anion-water enthalpic interactions only extend to ∼4 Å. We further validate this by showing that ions induce structure in their solvating water molecules by examining the distribution of dipole angles in the first hydration shell of the ions but that this perturbation does not extend into the bulk water. We then use these structural findings to justify mathematical models that allow us to examine perturbations to rotational and diffusive dynamics in the first hydration shell around the potassium halide ions from NMR measurements. This shows that as one moves down the halide series from fluorine to iodine, and ionic charge density is therefore reduced, that the enthalpy of hydration becomes less negative. The first hydration shell also becomes less well structured, and rotational and diffusive motions of the hydrating water molecules are increased. This reduction in structure and increase in dynamics are likely the origin of the previously observed increased entropy of hydration as one moves down the halide series. These results also suggest that simple monovalent potassium halide ions induce mostly local perturbations to water structure and dynamics.

Raman spectroscopy study for the systems (LiCl-H2O and LiCl-MgCl2-H2O): Excess spectra and hydration shell spectra

The micro-structure of hydration shell of solute in water is significant for understanding the properties of aqueous solutions. Raman spectroscopy has been employed for studying the hydration shell structure of the solute for decades, however, Raman imaging data is still seriously overlapped, making it challenging to obtain information on the spectrum of hydrated water molecules. In this paper, Raman spectroscopy was employed to study the O-H vibration peaks of LiCl aqueous solution and LiCl-MgCl2-H2O mixed aqueous solution. The changes of stretching vibration peak of 2800 ∼ 3800 cm-1O-H and hydrogen bond network structure in aqueous solution were analyzed at room temperature and ion association. With the increase of magnesium salt ratio, the damage of solute to the bulk water gradually decreases in the mixed solution, which indicated that LiCl has a more significant influence on the bulk water molecules. It is mainly due to the intense hydration of Li+, which can not only affect the water molecules in the first hydration shell but also affect the water molecules in the second hydration shell. The number of water molecules in the first hydration shell were obtained by extracting the spectra of different solute first hydration shells from the solution spectra. Those spectra of the hydration shell were employed to study the micro-structures of the first hydration shells of anions, and the aggregation behavior of ions in the the mixed solution.

Novel molecular insight into the discrepant distributions for ionic surfactants in light oil/water and heavy oil/water systems

Surfactant exhibits great displacement efficiency for the light oil (aliphatic and aromatic hydrocarbons) reservoir, whereas the heavy components (resins and asphaltenes) in crude oil could seriously affect the interfacial activity of surfactants. Then two simulation systems (light oil/water and heavy oil/water systems) were established and the distribution behaviors of the anionic surfactant sodium dodecyl sulfate (SDS) in above two systems were investigated by molecular dynamics (MD) simulation. The simulation results revealed that some SDS molecules could stay in the heavy oil phase but not in the light oil phase. The potential of mean force (PMF) of two systems were calculated to further probe the Gibbs free energy change in the movement process of SDS molecules form water phase to oil phase. The interaction mechanisms of water/surfactant/oil in the movement process were illustrated by the corresponding system configurations and reduced density gradient (RDG) method. The water molecules in hydration shell could be pulled into heavy oil phase coupled with SDS molecules and connect with SDS and asphaltene molecules to fabricate the SDS-Water-Asphaltenes (S-W-A) ternary structure via hydrogen bonds. Furthermore, the interaction energy calculation directly demonstrated the formation of S-W-A structure should be responsible for the discrepant distributions of surfactants in light oil/water and heavy oil/water systems.

Stability of Two-Dimensional Ionic Clusters at Solid-Liquid Interfaces.

The stability of two-dimensional clusters (2DCs) at the interface between ionic crystals and their solutions was investigated by molecular dynamics simulations. We found that 2DCs show a remarkable feature of odd-even alternation in stability. In NaCl and NaBr systems, the clusters containing an odd number of ions are more stable than those with an even number of ions, while in KCl systems, it is the other way round. Accordingly, the stability of water molecules in the first hydration shell of 2DCs also shows an odd-even alternation, which is consistent with the associated 2DCs. The odd-even alternation is discussed based on a competition mechanism between two factors: the Coulomb repulsion in charged 2DCs and the interaction between charges and water dipoles. Our discussion indicates that this odd-even alternation should be a universal feature in similar systems and would be important for understanding the nucleation and crystallization of solutions on ionic crystal surfaces.

Rotational Dynamics of Water at the Phospholipid Bilayer Depending on the Head Groups Studied by Molecular Dynamics Simulations

Hydration states are a crucial factor that affect the self-assembly and properties of soft materials and biomolecules. Although previous experiments have revealed that the hydration state strongly depends on the chemical structure of lipid molecules, the mechanisms at the molecular level remain unknown. Classical and density-functional tight-binding (DFTB) molecular dynamics (MD) simulations are employed to determine the mechanisms underlying dissimilar water dynamics between lipid membranes with phosphatidylcholine (PC) and phosphatidylethanolamine (PE) head groups. The classical MD simulation shows that rotational relaxations of water are faster on the PE lipid than on the PC lipid, which is consistent with a previous experimental study using terahertz spectroscopy. Furthermore, DFTB-MD simulation of N(CH3)4+ and NH4+ ions, which correspond to the different head groups in PC and PE, respectively, shows qualitative agreement with the classical MD simulation. Remarkably, the PE lipids and the NH4+ ions break hydrogen bonds between water molecules in the secondary hydration shell. In contrast, the PC lipids and the N(CH3)4+ ions bind water molecules weakly in both the primary and secondary hydration shells and increase hydrogen bonds between water. Our atomistic simulations show that these changes in the hydrogen-bond network of water molecules cause the different rotational relaxation of water molecules between the two lipids.

Effect of the Hydration Shell on the Carbonyl Vibration in the Ala-Leu-Ala-Leu Peptide.

The vibrational spectrum of the Ala-Leu-Ala-Leu peptide in solution, computed from first-principles simulations, shows a prominent band in the amide I region that is assigned to stretching of carbonyl groups. Close inspection reveals combined but slightly different contributions by the three carbonyl groups of the peptide. The shift in their exact vibrational signature is in agreement with the different probabilities of these groups to form hydrogen bonds with the solvent. The central carbonyl group has a hydrogen bond probability intermediate to the other two groups due to interchanges between different hydrogen-bonded states. Analysis of the interaction energies of individual water molecules with that group shows that shifts in its frequency are directly related to the interactions with the water molecules in the first hydration shell. The interaction strength is well correlated with the hydrogen bond distance and hydrogen bond angle, though there is no perfect match, allowing geometrical criteria for hydrogen bonds to be used as long as the sampling is sufficient to consider averages. The hydrogen bond state of a carbonyl group can therefore serve as an indicator of the solvent’s effect on the vibrational frequency.

The effect of electron correlation in unraveling the hydration properties of Sc3+ in aqueous solution: A rigid body quantum mechanics/molecular mechanics simulation study

The structural and dynamical properties of Sc3+ have been studied using quantum mechanics/molecular mechanics (QM/MM) and quantum mechanical charge field (QMCF) MD simulations. The QM region in the QM/MM MD simulation is treated using the resolution-of-identity MP2 level of theory, whereas the Hartree–Fock (HF) level of theory was applied for the QM regions in the QMCF MD simulation. Based on these two approaches, Sc3+ is hydrated by six water molecules in the first hydration shell. The average bond distances of Sc3+ − water are 2.15 and 2.16 Å for the QM/MM and QMCF MD simulations, respectively. No successful ligand exchange events were observed in QM/MM MD, while four successful ligand exchanges occurred in the QMCF MD simulation. These results proved the rigidity of the first hydration shell of Sc3+. In comparison with the other rare earth elements, Sc3+ showed the strongest interaction with water as reflected in the 214.76 and 192.52 N/m force constant values for the QM/MM and QMCF MD simulations, respectively. Electron correlation plays a role in strengthening the interactions between Sc3+ and water molecules in the first hydration shell.