Bulk Water Molecules Research Articles

Propensity of hydroxide and hydronium ions for the air-water and graphene-water interfaces from abinitio and force field simulations.

Understanding acids and bases at interfaces is relevant for a range of applications from environmental chemistry to energy storage. We present combined abinitio and force-field molecular dynamics simulations of hydrochloric acid and sodium hydroxide highly concentrated electrolytes at the interface with air and graphene. In agreement with surface tension measurements at the air-water interface, we find that HCl presents an ionic surface excess, while NaOH displays an ionic surface depletion, for both interfaces. We further show that graphene becomes less hydrophilic as the water ions concentration increases, with a transition to being hydrophobic for highly basic solutions. For HCl, we observe that hydronium adsorbs to both interfaces and orients strongly toward the water phase, due to the hydrogen bonding behavior of hydronium ions, which donate three hydrogen bonds to bulk water molecules when adsorbed at the interface. For NaOH, we observe density peaks of strongly oriented hydroxide ions at the interface with air and graphene. To extrapolate our results from concentrated electrolytes to dilute solutions, we perform single ion-pair abinitio simulations, as well as develop force-field parameters for ions and graphene that reproduce the density profiles at high concentrations. We find the behavior of hydronium ions to be rather independent of concentration. For NaOH electrolytes, the force-field simulations of dilute NaOH solutions suggest no hydroxide adsorption but some adsorption at high concentrations. For both interfaces, we predict that the surface potential is positive for HCl and close to neutral for NaOH.

D1-Tyr246 and D2-Tyr244 in photosystem II: Insights into bicarbonate binding and electron transfer from QA•− to QB

In photosystem II (PSII), D1-Tyr246 and D2-Tyr244 are symmetrically located at the binding site of the bicarbonate ligand of the non-heme Fe complex. Here, we investigated the role of the symmetrically arranged tyrosine pair, D1-Tyr246 and D2-Tyr244, in the function of PSII, by generating four chloroplast mutants of PSII from Chlamydomonas reinhardtii: D1-Y246F, D1-Y246T, D2-Y244F, and D2-Y244T. The mutants exhibited altered photoautotrophic growth, reduced PSII protein accumulation, and impaired O2-evolving activity. Flash-induced fluorescence yield decay kinetics indicated a significant slowdown in electron transfer from QA•− to QB in all mutants. Bicarbonate reconstitution resulted in enhanced O2-evolving activity, suggesting destabilization of bicarbonate binding in the mutants. Structural analyses based on a quantum mechanical/molecular mechanical approach identified the existence of a water channel that leads to incorporation of bulk water molecules and destabilization of the bicarbonate binding site. The water intake channels, crucial for bicarbonate stability, exhibited distinct paths in the mutants. These findings shed light on the essential role of the tyrosine pair in maintaining bicarbonate stability and facilitating efficient electron transfer in native PSII.

Femtosecond Terahertz Pulse Propagation Measurements and Simulations of Dewetting Kinetics in Real Time.

We report a terahertz time-domain study of dewetting kinetics on two time scales: femtoseconds and in real time (on the order of minutes). We recorded full electric field terahertz time domain signals with femtosecond time resolution during dewetting of water in cellulose. The femtosecond time-domain signals were analyzed with respect to the amplitude and signal emission times and how these two quantities changed over the course of dewetting kinetics. The femtosecond time-domain signals were modeled by a combination of finite-difference time-domain electromagnetic simulations of linear terahertz pulse propagation and an effective medium description of the dielectric permittivity. A logistic regression mechanism was incorporated into the electrodynamics simulations to account for the observed kinetics. In addition, analysis of the area-normalized, real-time time-dependent terahertz spectra was used to identify broad regions in the terahertz spectral range that correlated with the kinetic process. Real-time two-dimensional terahertz correlation maps were used to identify the pure rotational spectrum of water vapor, thus characterizing the evaporation part of the dewetting kinetics problem. We conclude with a kinetic model that accounts for our observations through a microscopic mechanism involving the interconversion among bulk water, water clusters, and individual water molecules in the gas phase. Overall, the approach presented here illustrates an application of femtosecond time-resolved experiments in the terahertz spectral range to the study of kinetic processes.

Highly reversible Zn anode by guiding uniform Zn deposition through LiF protective layer

Deep-seated issues such as ineluctable dendrite deposition and parasitic reaction of Zn anode pose a major obstacle to the commercialization of aqueous zinc ion batteries (AZIBs). Herein, we proposed LiF as a solid-electrolyte interphase for highly reversible Zn anode. Combining experimental analyses and theoretical simulation calculations, the electronegative fluorine atoms could provide uniform zincophilic nucleation sites to regulate Zn deposition behavior. Additionally, a ZnF2 layer with outstanding Zn2+ conductive can be formed insitu thus further shielding bulk water molecules and expediting the Zn2+ transfer kinetics. Therefore, the LiF@Zn symmetric cells manifest long-cycling stability with 650 h at 1.0 mA/cm2 and 1.0 mAh/cm2 and 1000 h at 2.0 mA/cm2 and 1.0 mAh/cm2. Meanwhile, the rate performance of Zn//MnO2 and Zn//NH4V4O10 full cells are also enhanced by the LiF coating. This work provides a horizon for the design of artificial protective layer and promotes the large-scale practical development of AZIBs.

Nuclear quantum effects on the vibrational dynamics of the water-air interface.

We have applied path-integral molecular dynamics simulations to investigate the impact of nuclear quantum effects on the vibrational dynamics of water molecules at the water-air interface. The instantaneous fluctuations in the frequencies of the O-H stretch modes are calculated using the wavelet method of time series analysis, while the time scales of vibrational spectral diffusion are determined from frequency-time correlation functions and joint probability distributions. We find that the inclusion of nuclear quantum effects leads not only to a redshift in the vibrational frequency distribution by about 120 cm-1 for both the bulk and interfacial water molecules but also to an acceleration of the vibrational dynamics at the water-air interface by as much as 35%. In addition, a blueshift of about 45 cm-1 is seen in the vibrational frequency distribution of interfacial water molecules compared to that of the bulk. Furthermore, the dynamics of water molecules beyond the topmost molecular layer was found to be rather similar to that of bulk water.

The Signature of Fluctuations of the Hydrogen Bond Network Formed by Water Molecules in the Interfacial Layer of Anionic Lipids

As the water molecules found at the interface of lipid bilayers exhibit distinct structural and reorientation dynamics compared to water molecules found in bulk, the fluctuations in their hydrogen bond (HB) network are expected to be different from those generated by the bulk water molecules. The research presented here aims to gain an insight into temperature-dependent fluctuations of a HB network of water molecules found in an interfacial layer of multilamellar liposomes (MLVs) composed of anionic 1,2-dimyristoyl-sn-glycero-3-phospho-L-serine (DMPS) lipids. Besides suspending DMPS lipids in phosphate buffer saline (PBS) of different pH values (6.0, 7.4, and 8.0), the changes in HB network fluctuations were altered by the incorporation of a non-polar flavonoid molecule myricetin (MCE) within the hydrocarbon chain region. By performing a multivariate analysis on the water combination band observed in temperature-dependent FTIR spectra, the results of which were further mathematically analyzed, the temperature-dependent fluctuations of interfacial water molecules were captured; the latter were the greatest for DMPS in PBS with a pH value of 7.4 and in general were greater for DMPS multibilayers in the absence of MCE. The presence of MCE made DMPS lipids more separated, allowing deeper penetration of water molecules towards the non-polar region and their restricted motion that resulted in decreased fluctuations. The experimentally observed results were supported by MD simulations of DMPS (+MCE) lipid bilayers.

Water-air interface revisited by means of path-integral ab initio molecular dynamics.

Although nuclear quantum effects (NQEs) have been considered on bulk liquid water, the impact of these latter on the air-water interface has not yet been reported. Herein, by performing and comparing ab initio molecular dynamics (AIMD) and path integral AIMD (PI-AIMD) simulations, we reveal the impact of NQEs on structural, dynamical and electronic properties as well as IR spectra of the air-water interface at room temperature. NQEs, being able to describe a more accurate proton delocalization in H-bonded system than AIMD, reveal a different structural arrangement and dynamical behaviour of both bulk and interfacial water molecules in comparison to AIMD results. A more de-structured and de-bound water arrangement and coordination are identified when the quantum nature of nuclei are considered for both bulk and interfacial water molecules. Structural properties, such as inter-/intra-molecular bond lengths, coordination numbers and H-bonding angles of bulk and interfacial water molecules here calculated, are affected by NQEs mitigating the overstructured description given by AIMD. Further evidences of an AIMD overstructured description of bulk water are in the computed IR spectra, where an increased absorption peak intensity and an increased strength of the hydrogen-bond network are alleviated by NQEs. In addition, NQEs show a valuable impact on the electronic structure of the air-water interface, reducing the total valence bandwidth and the electronic energy band-gap when passing from bulk to interfacial water. This work proves how NQEs significantly affect properties and features of the air-water interface, that are essential to accurately describe H-bonded interfacial systems.

Theoretical Study of the Two-Dimensional Vibrational Sum Frequency Generation Spectroscopy of the Air-Water Interface at Varying Temperature and Its Connections to the Interfacial Structure and Dynamics.

We performed a theoretical study of the temperature variation of two-dimensional vibrational sum frequency generation (2D-VSFG) spectra of the OH stretch modes at air-water interfaces in the mid-IR region. The calculations are performed at four different temperatures from 250 to 325 K by using a combination of techniques involving response function formalism of nonlinear spectroscopy, electronic structure calculations, and molecular dynamics simulations. Also, the calculations are performed for isotopically dilute solutions so that the intra- and intermolecular coupling between the vibrational modes of interest can be ignored. We have established the connections of temperature variation of various frequency- and time-dependent features of the calculated spectra to the changes in the underlying structure and dynamics of the interfaces. The results reveal that interfacial water is dynamically more heterogeneous than bulk water, with three dominant dynamical processes exhibiting their corresponding time-dependent features in the 2D-VSFG spectrum. These are the spectral diffusion of hydrogen-bonded OH groups at the interface, conversion of an initially hydrogen-bonded OH group to a dangling OH which is a stable state for surface water, unlike the bulk water, and the third one, which involves the conversion of an initially free or dangling OH group to its hydrogen-bonded state at the interface. The temporal appearance of the cross peaks corresponding to interconversion of the hydrogen-bonded state to the dangling state or vice versa of an interfacial OH group is found to take place at a slower rate than the dynamics of spectral diffusion of hydrogen-bonded molecules at the interface, which, in turn, is slower than the corresponding spectral diffusion of bulk water molecules. The temperature variation of these dynamic processes can be linked to the decay of appropriate hydrogen-bond and non-hydrogen-bond time correlation functions of interfacial water molecules for the different air-water systems studied in this work.

Raman Spectrum of the Li2SO4-MgSO4-H2O System: Excess Spectrum and Hydration Shell Spectrum.

Lithium, as a green energy metal used to promote world development, is an important raw material for lithium-ion, lithium-air, and lithium-sulfur batteries. It is challenging to directly extract lithium resources from brine with a high Mg/Li mass ratio. The microstructure study of salt solutions provides an important theoretical basis for the separation of lithium and magnesium. The changes in the hydrogen bond network structure and ion association of the Li2SO4 aqueous solution and Li2SO4-MgSO4-H2O mixed aqueous solution were studied by Raman spectroscopy. The SO42- fully symmetric stretching vibration peak at 940~1020 cm-1 and the O-H stretching vibration peak at 2800~3800 cm-1 of the Li2SO4 aqueous solution at room temperature were studied by Raman spectroscopy and excess spectroscopy. According to the peak of the O-H stretching vibration spectrum, with an increase in the mass fraction of the Li2SO4 solution, the proportion of DAA-type and DDAA-type hydrogen bonds at low wavenumbers decreases gradually, while the proportion of DA-type hydrogen bonds at 3300 cm-1 increases. When the mass fraction is greater than 6.00%, this proportion increases sharply. Although the spectra of hydrated water molecules and bulk water molecules are different, the spectra of the two water molecules seriously overlap. The spectrum of the anion hydration shell in a solution can be extracted via spectrum division. By analyzing the spectra of these hydration shells, the interaction between the solute and water molecules, the structure of the hydration shell and the number of water molecules are obtained. For the same ionic strength solution, different cationic salts have different hydration numbers of anions, indicating that there is a strong interaction between ions in a strong electrolytic solution, which will lead to ion aggregation and the formation of ion pairs. When the concentration of salt solution increases, the hydration number decreases rapidly, indicating that the degree of ion aggregation increases with increasing concentration.

An inorganic-organic protective anode interface towards high‐performance Al-air battery

Aqueous aluminium-air batteries (AABs) are promising candidates for next-generation energy storage devices owing to their high theoretical voltage and theoretical capacity of 2.98 Ah g−1 with additional advantages of aluminium (Al) being abundant, cost-effective, and recyclable. Despite striking advantages, practical application of Al-air batteries is hindered by undesirable self-corrosion and passivation of Al surface, as well as severe hydrogen evolution reaction (HER), thereby reducing anodic efficiency and battery capacity. To address these issues, herein, a dual protective coating comprising LDH-PVA-acetal as an inorganic-organic hybrid material has been developed. This coating forms a stable film over the Al substrate and synergistically suppresses self-corrosion and HER by blocking bulk water molecules from direct contact with the Al anode along with slow diffused release of hydroxide ions. The battery assembled utilizing LDH-PVA-acetal/Al as anode demonstrates an outstanding capacity of 2577 mAh g−1 and 2698 mAh g−1 with 86.4% and 90.5% anodic utilization @30 mA cm−2 and 50 mA cm−2. A waste beverage can coated with LDH-PVA-acetal showed practical applicability towards waste to wealth, thus, demonstrating potential application towards corrosion inhibition in alkaline media for other metals as well.

Structure and ion transport in super-concentrated water-in-salt electrolytes: Insights from molecular dynamics simulations

Water-in-salt electrolyte (WISE) systems hold promise as materials for high performance, more reliable and affordable, energy storage devices including batteries and supercapacitors. However, the structure and ion dynamics in these systems is significantly different from those of aqueous electrolytes and are poorly understood. Here, we present molecular dynamics investigation of water-in-salt electrolyte materials having pure as well as eutectic mixtures of Li-NTF2, and Li-MM3411 salts at several concentrations. We find the existence of small water clusters such as dimers and trimers even at extremely high salt concentrations, but not pockets of bulk water molecules. We find that the water molecules are bound to the cation as well as anion at extremely high salt concentrations. It is found that Li ions display a variety of solvation environments in super concentrated electrolyte solutions depending on the salt and its concentration in water. Our simulation results suggests that ion transport follows a solvent-assisted Li-ion diffusion mechanism whereby Li ion diffuses along with the water molecules, with the Li-ions hopping from one anion site to the other. The cation transport number in WISE systems can be regulated by adding small amount of another salt; for example, the transference of WISE materials Li-NTF2 salt can be improved by adding small amount Li-MM3411 salt. Further, we show that there exists an optimal salt concentration in water, at which high apparent transference number for Li+ as well as high ionic conductivity can be achieved. These observations will provide a guidance for the design of new electrolyte systems and interphases with consequences for accelerating the development of batteries and supercapacitors with enhanced energy density and cycling stability.

Water hydration of polyethylene glycol dimethyl ether.

In this work, GHz and THz complex dielectric spectra of a polyethylene glycol dimethyl ether (2000 g/mol) aqueous solution were studied. The reorientation relaxation of water in this kind of macro-amphiphilic molecule solution can be well described by three Debye models, including under-coordinated water, bulk-like water [water molecules in a tetrahedral hydrogen bond network (bulk water) and bulk water molecules affected by hydrophobic groups], and slow hydrating water (water molecules donating hydrogen bonds to hydrophilic ether groups). The reorientation relaxation timescales of bulk-like water and slow hydration water both show increases with concentration from 9.8 to 26.7ps and from 46.9 to 100.1ps, respectively. By estimating the ratios of the dipole moment of slow hydration water to the dipole moment of bulk-like water, we calculated the experimental Kirkwood factors of bulk-like and slow hydrating water. The experimental Kirkwood factor of bulk-like water increased from 3.17 to 3.44 with concentrations, while the experimental Kirkwood factor of slow hydrating water roughly remained constant at 4.13 from concentrations of 15%-60%. The estimated water molecule numbers of three water components around monomers also confirm our sorting for water components.

Anisotropy and Hybrid Heterosurface-Modulated Two-Dimensional Hydrogen Bond Network of Water

We report the structure and dynamics of layered water structure near a bilayer heterosurface using classical molecular dynamics simulations and network graph theory. The heterosurfaces of our choice are technologically essential and well-studied hexagonal boron nitride (h-BN) and graphitic carbon nitride (g-C3N4). Starting with the water density distribution profile, we have studied different hydrogen bondings (HBs) associated with distance and angle distributions and correlated them with the HB count, followed by the investigations of dynamic properties. We realize the oddity while corresponding to the tetrahedral order parameter (TOP), HB donor/acceptor count, and HB lifetime. A quantitative gap is observed between the TOP and HB counts, and we perceive another structural factor playing a significant role. We observe a 2D sheetlike arrangement of hydrogen-bonded water molecules, namely, 2D-HB, in the interfacial layer instead of 3D tetrahedral arrangements. 2D-HB qualitatively acts as a key descriptor of the hydrophobicity of the interface. The probability of higher TOP among the interfacial layer water molecules is less for h-BN compared to g-C3N4. However, the per-water HBs for both the heterosurfaces remain indistinguishable, implying the existence of another significant physical factor related to HB. Hence, 2D-HB serves as a deciding factor. In the case of h-BN, water molecules in the first layer form extended 2D sheets compared to the second and bulk, which is not a scenario for g-C3N4. Following the network graph theory, we calculated the temporal evolution of the maximum number of water molecules connected in a single network. The layer 1 water molecules have slower orientational dynamics, higher HB lifetime, and consequently slower translational diffusion than layer 2 and bulk water molecules. The experimental studies suggested that the contact angle of water on h-BN can vary from 61.4 to 85.8°, higher than that of g-C3N4, depending on the surface stacking, support material, and exposure to air, which effectively makes h-BN more hydrophobic compared to g-C3N4. The interfacial water molecules have a smaller HB lifetime and a faster diffusion coefficient than g-C3N4. The HB lifetime of water molecules in bulk is less than that in the interface, irrespective of the surface. A slower reorientation lifetime, that is, 2.69 ps, for g-C3N4 interfacial water molecules is observed versus 2.20 ps for h-BN. Our results agree with the experimental observations and can help to understand the hydrophobicity of other relevant materials.

Crystalline hydrogen bonding of water molecules confined in a metal-organic framework

Hydrogen bonding (H-bonding) of water molecules confined in nanopores is of particular interest because it is expected to exhibit chemical features different from bulk water molecules due to their interaction with the wall lining the pores. Herein, we show a crystalline behavior of H-bonded water molecules residing in the nanocages of a paddlewheel metal-organic framework, providing in situ and ex situ synchrotron single-crystal X-ray diffraction and Raman spectroscopy studies. The crystalline H-bond is demonstrated by proving the vibrational chain connectivity arising between hydrogen bond and paddlewheel Cu−Cu bond in sequentially connected Cu–Cu·····coordinating H2O·····H-bonded H2O and by proving the spatial ordering of H-bonded water molecules at room temperature, where they are anticipated to be disordered. Additionally, we show a substantial distortion of the paddlewheel Cu2+-centers that arises with water coordination simultaneously. Also, we suggest the dynamic coordination bond character of the H-bond of the confined water, by which an H-bond transitions to a coordination-bond at the Cu2+-center instantaneously after dissociating a previously coordinated H2O.

Near Infrared Spectroscopy As an Effective Way of Studying Hydrogen Bonding in a LiCl–H2O–CO2 Ternary Mixture

Abstract The possibility of using near IR spectroscopy to analyze the effect isobaric heating has on hydrogen bonding in an aqueous solution of LiCl in equilibrium with supercritical carbon dioxide (a LiCl–H2O–scCO2 ternary mixture) is demonstrated in a wide range of electrolyte concentrations. It is shown that this approach is highly efficient when studying ion and molecular systems with different types of interparticle interactions. The use of near IR spectroscopy allows distinguishing spectral contributions from hydrogen bonded n-mers of bulk water and water molecules in the solvation shells of ions or in ion–water chains like those formed in solutions with extremely high electrolyte concentrations that do not contain bulk water. It is shown for the studied ternary mixture that raising the concentration of electrolyte completely neutralizes the destructive effect of carbon dioxide on the formation of a hydrogen bonded structure of water. The latter is stabilized under the influence of an ion field, which also substantially weakens the temperature effect.

Employing overhauser dynamic nuclear polarization to inspect extreme instances of hydration water

Protein systems do not live in a vacuum, but participate in dynamic feedback with their surrounding solvent environment. Coating the surface of every macromolecule and assembly, one finds several layers of hydration water. These water molecules, which move typically between 3× and 10× slower than water molecules in bulk water, stabilize the structure and function of macromolecules in ways not yet fully described.

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.

Preferential binding affinity of ions and their effect on structure and dynamics of water near antimicrobial peptide

Water containing dissolved salts is often found to play important roles in many chemical and biological processes. They affect the stability of the amino acids and proteins by altering the liquid water structure. The formation of a mixture of non-uniform density regions in liquid water; commonly known as Low-density water and High-density water is a well-known fact experimentally; which lends uniqueness to the ubiquitous water. The behavior of these different types of water at the interface and the bulk region of the biomolecules around the hydrophobic and hydrophilic residues under the influence of different alkali metal ions, such as LiCl, NaCl, and KCl is an important unexplored question in understanding of many biomolecular processes. To address this, we carried out MD simulation of antimicrobial peptide (PDB ID: 5Z32) for two different model potentials (CHARMM-SPC/E and AMBER-TIP4P) and performed the structural analysis of water in terms of the radial distribution function, number of hydrogen bonds, orientation, tetrahedral order parameter, voids analysis to analyze the related dynamical properties like preferential binding affinity, diffusion, hydrogen bond dynamics, entropy. The water molecules around the hydrophilic environment are found to be more disruptive containing more broken hydrogen bonds in comparison to the hydrophobic environment. It is also found that the water molecules present near the protein surface are of low density and that near the bulk is of high density. This leads to the higher self-diffusion coefficient of the water molecules and less hydrogen bond lifetime at the bulk. The maximum difference is found for the solutions containing high charge density, Lithium ions. Lithium ions have a strong preferential binding affinity towards protein surface resulting in strong solvation shells containing more tetrahedral-like water structure which has low diffusion, low entropy, and higher hydrogen bond lifetime. The diffusion of the water molecules, however, increases towards the higher solvation shells. Potassium on the other hand has less preference to live on protein surfaces resulting in similar diffusion values in the bulk and interface water molecules.

Bridging the 12-6-4 Model and the Fluctuating Charge Model.

Metal ions play important roles in various biological systems. Molecular dynamics (MD) using classical force field has become a popular research tool to study biological systems at the atomic level. However, meaningful MD simulations require reliable models and parameters. Previously we showed that the 12-6 Lennard-Jones nonbonded model for ions could not reproduce the experimental hydration free energy (HFE) and ion-oxygen distance (IOD) values simultaneously when ion has a charge of +2 or higher. We discussed that this deficiency arises from the overlook of the ion-induced dipole interaction in the 12-6 model, and this term is proportional to 1/r 4 based on theory. Hence, we developed the 12-6-4 model and showed it could solve this deficiency in a physically meaningful way. However, our previous research also found that the 12-6-4 model overestimated the coordination numbers (CNs) for some highly charged metal ions. And we attributed this artifact to that the current 12-6-4 scheme lacks a correction for the interactions among the first solvation shell water molecules. In the present study, we considered the ion-included dipole interaction by using the 12-6 model with adjusting the atomic charges of the first solvation shell water molecules. This strategy not only considers the ion-induced dipole interaction between ion and the first solvation shell water molecules but also well accounts for the increased repulsion among these water molecules compared to the bulk water molecules. We showed this strategy could well reproduce the experimental HFE and IOD values for Mg2+, Zn2+, Al3+, Fe3+, and In3+ and solve the CN overestimation issue of the 12-6-4 model for Fe3+ and In3+. Moreover, our simulation results showed good agreement with previous ab initio MD simulations. In addition, we derived the physical relationship between the C 4 parameter and induced dipole moment, which agreed well with our simulation results. Finally, we discussed the implications of the present work for simulating metalloproteins. Due to the fluctuating charge model uses a similar concept to the 12-6 model with adjusting atomic charges, we believe the present study builds a bridge between the 12-6-4 model and the fluctuating charge model.

Recognition of N6-Methyladenosine by the YTHDC1 YTH Domain Studied by Molecular Dynamics and NMR Spectroscopy: The Role of Hydration.

The YTH domain of YTHDC1 belongs to a class of protein "readers", recognizing the N6-methyladenosine (m6A) chemical modification in mRNA. Static ensemble-averaged structures revealed details of N6-methyl recognition via a conserved aromatic cage. Here, we performed molecular dynamics (MD) simulations along with nuclear magnetic resonance (NMR) and isothermal titration calorimetry (ITC) to examine how dynamics and solvent interactions contribute to the m6A recognition and negative selectivity toward an unmethylated substrate. The structured water molecules surrounding the bound RNA and the methylated substrate's ability to exclude bulk water molecules contribute to the YTH domain's preference for m6A. Intrusions of bulk water deep into the binding pocket disrupt binding of unmethylated adenosine. The YTHDC1's preference for the 5'-Gm6A-3' motif is partially facilitated by a network of water-mediated interactions between the 2-amino group of the guanosine and residues in the m6A binding pocket. The 5'-Im6A-3' (where I is inosine) motif can be recognized too, but disruption of the water network lowers affinity. The D479A mutant also disrupts the water network and destabilizes m6A binding. Our interdisciplinary study of the YTHDC1 protein-RNA complex reveals an unusual physical mechanism by which solvent interactions contribute toward m6A recognition.