Search

Abstract Water dynamics inside hydrophobic confinement, such as carbon nanotubes (CNTs), has garnered significant attention, focusing on water diffusion. However, a crucial aspect remains unexplored - the influence of confinement size on water ordering and intrinsic hydrogen bond dynamics. To address this gap, we conducted extensive molecular dynamics simulations to investigate local ordering and intrinsic hydrogen bond dynamics of water molecules within CNTs of various sizes (length:20 nm, diameters: 1.0 nm to 5.0 nm) over a wide range of temperatures (260K, 280K, 300K, and 320K). A striking observation emerged: in smaller CNTs, water molecules adopt an icy structure near tube walls while maintaining liquid state towards the center. Notably, water behavior within a 2.0 nm CNT stands out as an anomaly, distinct from other CNT sizes considered in this study. This anomaly was explained through the formation of water layers inside CNTs. The hydrogen bond correlation function of water within CNTs decayed more slowly than bulk water, with an increasing rate as CNT diameter increased. In smaller CNTs, water molecules hold onto their hydrogen bond longer than larger ones. Interestingly, in larger CNTs, the innermost layer’s hydrogen bond lasts a shorter time compared to the other layers, and this changes with temperature.

Genetically encoded fluorescent biosensors (GEFBs) proved to be reliable tracers for many metabolites and cellular processes. In the simplest case, a fluorescent protein (FP) is genetically fused to a sensing protein which undergoes a conformational change upon ligand binding. This drives a rearrangement in the chromophore environment and changes the spectral properties of the FP. Structural determinants of successful biosensors are revealed only in hindsight when the crystal structures of both ligand‐bound and ligand‐free forms are available. This makes the development of new biosensors for desired analytes a long trial‐and‐error process. In the current study, we conducted μs‐long all atom molecular dynamics (MD) simulations of a maltose biosensor in both the apo (dark) and holo (bright) forms. We performed detailed hydrogen bond occupancy analyses to shed light on the mechanism of ligand induced conformational change in the sensor protein and its allosteric effect on the chromophore environment. We find that two strong indicators for distinguishing bright and dark states of biosensors are due to substantial changes in hydrogen bond dynamics in the system and solvent accessibility of the chromophore. [ABSTRACT FROM AUTHOR]

Water dynamics inside hydrophobic confinement, such as carbon nanotubes (CNTs), has garnered significant attention, focusing on water diffusion. However, a crucial aspect remains unexplored - the influence of confinement size on water ordering and intrinsic hydrogen bond dynamics. To address this gap, we conducted extensive molecular dynamics simulations to investigate local ordering and intrinsic hydrogen bond dynamics of water molecules within CNTs of various sizes (length:20 nm, diameters: 1.0 nm to 5.0 nm) over a wide range of temperatures (260K, 280K, 300K, and 320K). A striking observation emerged: in smaller CNTs, water molecules adopt an icy structure near tube walls while maintaining liquid state towards the center. Notably, water behavior within a 2.0 nm CNT stands out as an anomaly, distinct from other CNT sizes considered in this study. This anomaly was explained through the formation of water layers inside CNTs. The hydrogen bond correlation function of water within CNTs decayed more slowly than bulk water, with an increasing rate as CNT diameter increased. In smaller CNTs, water molecules hold onto their hydrogen bond longer than larger ones. Interestingly, in larger CNTs, the innermost layer's hydrogen bond lasts a shorter time compared to the other layers, and this changes with temperature. [ABSTRACT FROM AUTHOR]

Water dynamics in nanochannels are altered by confinement, particularly in small carbon nanotubes (CNTs). However, the mechanisms behind these effects remain unclear. To address these issues, we carried out extensive molecular dynamics (MD) simulations to investigate the structure and dynamics of water inside CNTs of different sizes (length of 20 nm and diameters vary from 0.8 nm to 5.0 nm) at different temperatures (from 200 K to 420 K). The radial density profile of water inside CNTs shows a single peak near the CNT walls for small nanotubes. For CNTs with larger sizes, water molecules are arranged into coaxial tubular sheets, the number of which increases with the CNT size. Subdiffusive behavior is observed for ultranarrow CNTs with diameters of 0.8 nm and 1 nm. As the size of CNTs increases, Fickian diffusion becomes evident. The hydrogen bond correlation function of water inside CNT decays slower than in bulk water, and the decay rate decreases as we increase the diameter of the CNTs. In large CNTs, the hydrogen bond lifetime of the innermost layer is shorter than the other layers and depends on temperature. Additional analysis of our results reveals that water molecules along the CNT axis show a non-Arrhenius to Arrhenius diffusion crossover. In general, the diffusion transition temperature is higher than that of bulk water, but it depends on the size of the CNT. [ABSTRACT FROM AUTHOR]

The Green Fluorescent Protein (GFP) is a widely studied chemical system both for its large amount of applications and the complexity of the excited state proton transfer responsible of the change in the protonation state of the chromophore. A detailed investigation on the structure of the chromophore environment and the influence of chromophore form (either neutral or anionic) on it is of crucial importance to understand how these factors could potentially influence the protein function. In this study, we perform a detailed computational investigation based on the analysis of ab-initio molecular dynamics simulations, to disentangle the main structural quantities determining the fine balance in the chromophore environment. We found that specific hydrogen bonds interactions directly involving the chromophore (or not), are correlated to quantities, such as the volume of the cavity in which the chromophore is embedded and that it is importantly affected by the chromophore protonation state. The cross-correlation analysis performed on some of these hydrogen bonds and the cavity volume, demonstrates a direct correlation among them and we also identified the ones specifically involved in this correlation. We also found that specific interactions among residues far in the space are correlated, demonstrating the complexity of the chromophore environment and that many structural quantities have to be taken into account to properly describe and understand the main factors tuning the active site of the protein. From an overall evaluation of the results obtained in this work, it is shown that the residues which a priori are perceived to be spectators play instead an important role in both influencing the chromophore environment (cavity volume) and its dynamics (cross-correlations among spatially distant residues).

[Display omitted] • Asymmetric model is more hydrated and ticker compared to the symetric. • The models differ in structural and statistics characteristics of H-Bonds. • Membranes rich in F-residues exhibit varying levels of organizations. In this work, we conducted a study on peptide membranes formed by the amino acid sequences EF 4 E and KF 4 K with the aim of obtaining energetic and structural results for asymmetric and symmetric membrane nanostructures. The results show that the lifetime of hydrogen bonds (HBs) for peptides in the symmetric membrane is ∼12 % higher than that observed for the asymmetric structure, providing greater rigidity to the former. These findings are consistent with those obtained for Coulomb and van der Waals interaction energies and demonstrate that the Symmetric model exhibits better stability compared to the Asymmetric model. The average thickness of the membranes is ∼1.72 ± 0.06 nm and ∼2.27 ± 0.02 nm for the asymmetric and symmetric models, respectively. Our results show that the symmetric model stands out due to greater structural organization and consequently a less hydrated appearance in the membrane region, which could be crucial for applications. From an electrical perspective, both membranes display clear differences, underscoring the influence of peptide arrangement on the membrane structure. [ABSTRACT FROM AUTHOR]

The structural and dynamical properties of water confined in nanoporous silica with a pore diameter of 2.7 nm were investigated by performing large-scale molecular dynamics simulations using the reactive force field. The radial distribution function and diffusion coefficient of water were calculated, and the values at the centre of the pore agreed well with experimental values for real water. In addition, the pore was divided into thin coaxial layers, and the average number of hydrogen bonds, hydrogen bond lifetime and hydrogen bond strength were calculated as a function of the radial distance from the pore central axis. The analysis showed that hydrogen bonds involving silanol (Si–OH) have a longer lifetime, although the average number of hydrogen bonds per atom does not change from that at the pore centre. The longer lifetime, as well as smaller diffusion coefficient, of these hydrogen bonds is attributed to their greater strength. [ABSTRACT FROM AUTHOR]

Using Molecular Dynamics simulations, we investigate the effect of alternating (AC) electric field on static and dynamic properties of water. The central question we address is how hydrogen bonds respond to perpetual field-induced dipole reorientations. We assess structural perturbations of water network and changes of hydrogen bond dynamics in a range of alternating electric field strengths and frequencies using a non-polarisable water model, SPC/E, and two distinct polarisable models: SWM4-NDP and BK3. We confirm that AC field causes only moderate structural perturbations. Dynamic properties, including the rates of bond breaking, switching of hydrogen-bonding partners, and diffusion, accelerate with the strength of AC fields. All models reveal a nonmonotonic frequency dependence with fastest dynamics at frequencies around 200 GHz where the period of the field oscillation is commensurate with the average time it takes a typical proton to switch from one acceptor to another. Higher frequencies result in smaller amplitudes of angle oscillations and in reduced probability to complete the switch to another acceptor before the field reversal restores the original configuration. As frequency increases, these effects gradually weaken the influence of the field on the kinetics of hydrogen bonding and the associated rates of translational and rotational diffusion in water. [ABSTRACT FROM AUTHOR]

We present a combined quantum chemical and molecular dynamics study of cyclic and noncyclic water n‐mers ([(H2O]n, n= 2–6) at four different temperatures and showcase that the dynamics of small water clusters can reproduce the known properties of bulk water reasonably well. We investigate the making and breaking of the water clusters by computing the hydrogen bond strengths, average lifetimes, and relative stabilities, which are important to understand the complex solution dynamics. We compare the behavior of water clusters in the gas phase and in the solution phase as well as the variation in the properties as a function of cluster size and highlight the notably more interesting cluster dynamics of the water trimer when compared to the other water clusters. © 2019 Wiley Periodicals, Inc. The paper focusses on the making and breaking of hydrogen bonds in small water clusters through an analysis of the hydrogen bond correlation functions computed from the molecular trajectories and the hydrogen bond strength based on interaction coordinates derived from the cartesian force constant matrix. The water cluster dynamics reproduces the known bulk water properties reasonably well. [ABSTRACT FROM AUTHOR]

Graphical abstract Highlights • Self-diffusion (D w) and D OH coefficients comparable up to 470 K. • Above 470 K D OH by 30% lower due to enhanced complexation of OH with H 2 O. • Continuous lifetime ∼10−14 s calculated for both H-donor and H-acceptor bond. • Intermittent lifetime 4 ps (373 K) drops to 1 ps (673 K) exceeding translational time. • Conclusions on OH aq translational dynamics depend on model potential used. Abstract MD simulations using flexible models were performed to show how velocity autocorrelation functions, diffusion (D OH) and self-diffusion (D w) coefficients, continuous and intermittent lifetimes of H-donor and H-acceptor bonds depend on: i) transformations in the hydrogen-bond network (HBN) of water below the critical point, and ii) decreasing density at the supercritical isotherm (∼670 K). Contrary to simulations neglecting short-range hydrogen-oxygen interactions, we show that complexation of OH aq with H 2 O is enhanced by breakage of the continuous HBN, resulting in the increase of OH aq hydrodynamic radius and the D OH values smaller than D w by 30%. Difference between D OH and D w increases to 65% at 670 K below the critical density. It is explained by enhanced aggregation of water molecules around OH aq , earlier recognized as the self-trapping mechanism. Except near-ambient conditions, the intermittent lifetime of H-bonds is longer than the translational time, indicating that OH aq is complexed with water and moves as a molecular aggregate. [ABSTRACT FROM AUTHOR]

Abstract The Raman spectra of NaOH water solutions with different concentrations have been successfully obtained at room temperature and normal pressure. The results show that the shift of Raman shifts at different NaOH concentrations is strongly affected by hydrogen bond dynamics. The Raman shifts indicate that the formation of hydrogen bonds exceeds the breaking when the concentration is lower than 4 M, and the hydrogen bond strength is enhanced. When the NaOH concentration is higher than 4 M, the hydrogen bond relaxation dynamics is opposite to that at low concentration. The infrared spectra of NaOH water solutions with different concentrations are also discussed. Highlights • Raman shifts at different NaOH solutions are affected by hydrogen bond dynamics. • The free OH vibration is unaffected by temperature and pressure. • The association structure of the NaOH solution takes place transformation at 4 M·s [ABSTRACT FROM AUTHOR]

The structure and dynamics at the surface of nanoscopic hexadecane droplets immersed in aqueous phase with and without emulsifiers (1-alkanols of varying chain length; pentanol, heptanol, decanol and dodecanol) have been studied using atomistic molecular dynamics simulations. The nature of layering of alcohol molecules on the oil droplet is governed by the hydrophobicity of alkanols. Longer chain alkanols are more likely to penetrate into the oil droplet. The probability of tangential orientation of hexadecane molecules at the interface decreases with decreasing hydrophobic environment around the droplet. The interfacial hexadecane molecules show greater probability to obtain a puckered conformation in binary oil–water system than in ternary oil–water–alkanol systems. Decrease in hydrophobic interaction between hexadecane and water molecules due to the efficient screening of oil surface by longer chain alkanols in ternary oil–water–alkanol systems leads to greater survival probability of water molecules in the oil–water interfacial layer and enhancement in life time of H-bonds formed between alcohol and water molecules. [ABSTRACT FROM AUTHOR]

Amino acids, the building blocks of proteins, are probed in reverse micellar encapsulation processes of biological molecules. To achieve a theoretical picture of the effect of confinement of amino acids on the structure and dynamics of reverse micellar aqueous core, a water/[C 1 C 10 Im][Br] reverse micelles containing variable number of glycine molecules (0 to 8), dispersed in pure nonane has been studied using atomistic molecular dynamics simulations. The size of the central water pool was found to become stable with increase in the number of glycine molecules. Glycine molecules associate together through H-bonding interaction within the aqueous core of the reverse micelles. The radial density profile of glycine molecules from the center of mass of the reverse micellar aqueous core shows the preferential presence of glycine molecules near the center. Confinement in nano-space region stabilizes the H-bonds formed between glycine molecules compared to bulk aqueous solution. Increase in the number of glycine molecules within the reverse micellar aqueous core increases the survival time of H-bonds among glycine molecules as well as among water molecules. Translational and reorientational motion of glycine and water molecules are found to be directly related to the survival probability of intermolecular glycine–glycine and water–water H-bonds suggesting the correlation between the mobility of molecules with the rearrangement of the H-bonding network. [ABSTRACT FROM AUTHOR]

The structure, transport properties and hydrogen bond dynamics of aqueous dopamine solution were calculated via molecular dynamics simulations. The impact of ascorbic acid and uric acid on the structure of water was also investigated. With increasing the concentration of dopamine, the coordination number, tetrahedral order parameter and self-diffusion coefficient decreasing. The coordination number obtained by our simulation is in agreement with the available experimental data. A hydration shell of dopamine and shorter H-bond lifetimes with respect to the water-water system is observed. [ABSTRACT FROM AUTHOR]

[Display omitted] • Alcohol-water mixtures were investigated by TTDS and THz-FTIR spectroscopy. • Correlation between the structure and dynamics of HBond network in alcohol-water binary mixtures. • Alteration of HBond structure of water-network in water-alcohol mixtures was probed. • Change in the dynamics of such mixtures was probed as they change their micro-structures depending on solute composition. • Balance between the local homo-molecular and cross-molecular solvation led to a micro/macro scale self-aggregation. Despite being a simple and widely studied solution, a correlation between the structure and dynamics of the hydrogen bond (HBond) network in alcohol-water binary mixtures remains highly debatable. The present work combined Terahertz time domain spectroscopy (TTDS) and Terahertz-Fourier transform infrared (THz-FTIR) spectroscopy covering a wide frequency window of 0.3–18 THz, which probes most of the intermolecular roto-vibrational modes of water, to extract an extensive idea on such aspect of the binary mixtures. This study demonstrates a unified picture of the solute concentration-dependent HBond network structure and its associated dynamics in alcohol-water binary mixtures considering micro- and macro-scale (for partially water-soluble alcohols) phases present inside the systems. The work extensively took into account both the factors of hydrophobic chain length and macroscopic self-aggregation of alcohols to present a comprehensive view of HBonded intermolecular networks in binary mixtures. We found a balance between the local homo-molecular and cross-molecular solvation which leads to a micro/macro scale self-aggregation for various alcohol-water mixtures. [ABSTRACT FROM AUTHOR]

Molecular dynamics simulation was conducted to study the structure and dynamics of hydrogen bonds in alcohols (methanol, ethanol, and 1-propanol) confined within graphene nanopores at a constant parallel component of pressure, 101.3 kPa, and at constant temperatures, ranging from 260 to 340 K. The results indicated that, while confined alcohol molecules orient themselves with the hydrophobic methyl groups exposing to the two plates, the polar hydroxyl groups stand away from surface to preserve a hydrogen-bonding with adjacent layer. Contrary to confined water, the average of hydrogen-bond values of confined alcohol molecules is found to be the same as bulk. Decreasing diffusion coefficient, increasing the relaxation time and, accordingly, decreasing hydrogen bond exchange dynamics occur by increasing the size of alkyl group in alcohol molecules in bulk and confined fluids. Our findings in this work indicate that the effect of confining surfaces on the confined fluid increase at lower temperatures compared to the higher temperatures. [ABSTRACT FROM AUTHOR]

The role of water in determining the structure and stability of biomacromolecules has been well studied. In this work, molecular dynamics simulations have been applied to investigate the effect of surface hydrophobicity on the structure and dynamics of water confined between graphene surfaces. In order to evaluate this effect, we apply various attractive/repulsive water–graphene interaction potentials (hydrophobicity). The properties of confined water are studied by applying a purely repulsive interaction potential between water–graphene (modelled as a repulsiver−12potential) and repulsive–attractive forces (modelled as an LJ(12-6) potential). Compared to the case of a purely repulsive graphene–water potential, the inclusion of repulsive–attractive forces leads to formation of sharp peaks for density and the number of hydrogen bonds. Also, it was found that repulsive–attractive graphene–water potential caused slower hydrogen bonds dynamics and restricted the diffusion coefficient of water. Consequently, it was found that hydrogen bond breakage and formation rate with the repulsive r−12potential model, will increase compared to the corresponding water confined with the LJ(12-6) potential. [ABSTRACT FROM PUBLISHER]

Vibrational relaxation of the OH stretching and bending modes of water monomers in acetonitrile is studied by two-color pump–probe experiments in a frequency range from 1400 to 3800 cm −1 . Measurements with resonant infrared excitation reveal vibrational lifetimes of 6.4 ± 1.0 ps of the OH stretching modes and 4.0 ± 0.5 ps of the OH bending mode. After OH stretching excitation, the OH bending mode shows an instantaneous response, a hallmark of the anharmonic coupling of stretching and bending modes, and a delayed population buildup by relaxation of the stretching via the bending mode. The relaxation steps are discussed within the framework of current theoretical pictures of water’s vibrational relaxation. [ABSTRACT FROM AUTHOR]

Radical anions of electron-deficient systems are widely used, but they are easily reoxidized upon exposure to air. Therefore, the stabilization of radical anions under ambient conditions is of great significance, but still remains a scientific challenge. Here, perylene diimide radical anion species is stabilized by an asymmetric anionic low barrier strong hydrogen bond, which is reported firstly. The exchange of a hydrogen atom between one hydrogen atom in nitrogen atom of alkyl amine and the oxygen atom of the carbonyl on perylene diimide radical anion occurs to form such asymmetric anionic type strong hydrogen bond. This bond energy of hydrogen bond is evaluated by the apparent activation energy of thermal decomposition, and it is about 50 kcal/mol. The geometric states in this hydrogen bond depend on external conditions, including solvents and pH value, which will cause the change of their photophysical properties. The hydrogen bond complex shows excellent pH-responsive color switching performance based on the difference in geometric states of this hydrogen bond. To build stable perylene diimide radical anion species using an asymmetric anionic [CO⋯H⋯N]−1 -type strong H-bond. The geometric states of such anionic hydrogen bond depend on the surrounding environment, which then causes changes in their photophysical properties. It shows excellent pH-responsive color switching performance based on the change of surrounding environment. [Display omitted] • There are three highlights in our article. The three highlights are as follows: • Air stable perylene diimide radical anion materials were constructed by using low barrier strong hydrogen bond [CO⋯H⋯N]−1. • The geometric structure of [CO⋯H⋯N]−1 depends on the environment and affects the photophysical properties. • These perylene diimide radical anions can be used as new environmental responsive materials. [ABSTRACT FROM AUTHOR]

Carbon dioxide (CO 2) absorption into aqueous amine solvents is known to be governed by two competing reactions leading to carbamate or bicarbonate formation. Sterically hindered alkanolamines with different degrees of methylation are experimentally known to cause different favorability in forming carbamate or bicarbonate. However, the fundamental mechanisms responsible for the preferential formation of carbamate or bicarbonate still remain unclear. Herein, we present CO 2 absorption behavior with several different sterically hindered amines, especially the effects of methylation and temperature. Our ab initio metadynamics simulations clearly demonstrate that free-energy barriers for the carbamate and bicarbonate formation reactions strongly depend on the degree of steric hindrance of hydrophobic methyl groups. This in turn directly impacts on the kinetic favorability of the two competing reaction pathways. Our analysis shows that various degrees of steric effects cause considerably different temperature-dependent degrees of solvation of the nitrogen atom of hindered amines, which may directly affect CO 2 accessibility to form carbamate. Moreover, the enhanced solvation as a result of increased steric effects particularly at low absorption temperatures lead to kinetically facile protonation of the nitrogen atom of amines, initiating and promoting bicarbonate formation. Our work sheds light on the effects of various degrees of steric hindrance, with different temperature-dependent solvation degrees governing reaction mechanisms and rates during CO 2 capture. • CO 2 absorption rates and mechanisms are governed by temperature-dependent steric effects. • Degree of steric hindrance of hydrophobic methyl groups play a crucial role. • Steric effects directly affect CO 2 accessibility to form carbamate. • Increased steric effects facilitate amine protonation, promoting bicarbonate formation. • Improved understanding provides vital hints on how to design advantaged amines for CO 2 capture. [ABSTRACT FROM AUTHOR]

Density functional theory (DFT) based Car–Parrinello molecular dynamics (CPMD) simulations were carried out to investigate the structure and dynamics of aqueous solvation shell of a single formamide (FA) molecule. Vibrational frequency through wavelet analysis and correlation function calculations have been performed to understand the spectral signature of water molecules in the first solvation shell and dynamics of solute–solvent hydrogen bonds, respectively. Structural aspects have been analyzed by calculating various pair correlation functions. FA takes part in more than two hydrogen bonds with water via carbonyl oxygen. Due to the presence of carbonyl group, the solvation through amine group hydrogen atoms is asymmetrical; each hydrogen participates in roughly one hydrogen bond. Carbonyl–water hydrogen bonds are stronger than the water–water hydrogen bonds; amine–water hydrogen bonds are much weaker than other two types of hydrogen bonds. [ABSTRACT FROM AUTHOR]

ABSTRACT The extrinsic proteins of photosystem II of higher plants and green algae PsbO, PsbP, PsbQ, and PsbR are essential for stable oxygen production in the oxygen evolving center. In the available X-ray crystallographic structure of higher plant PsbQ residues S14-Y33 are missing. Building on the backbone NMR assignment of PsbQ, which includes this 'missing link', we report the extended resonance assignment including side chain atoms. Based on nuclear Overhauser effect spectra a high resolution solution structure of PsbQ with a backbone RMSD of 0.81 Å was obtained from torsion angle dynamics. Within the N-terminal residues 1-45 the solution structure deviates significantly from the X-ray crystallographic one, while the four-helix bundle core found previously is confirmed. A short α-helix is observed in the solution structure at the location where a β-strand had been proposed in the earlier crystallographic study. NMR relaxation data and unrestrained molecular dynamics simulations corroborate that the N-terminal region behaves as a flexible tail with a persistent short local helical secondary structure, while no indications of forming a β-strand are found. Proteins 2015; 83:1677-1686. © 2015 The Authors. Proteins: Structure, Function, and Bioinformatics Published by Wiley Periodicals, Inc. [ABSTRACT FROM AUTHOR]

Atomistic molecular dynamics simulations were performed under ambient conditions to explore the conformational features and binding affinities of hexameric glycosaminoglycans (GAGs) with chemokine Interleukin8 (IL8) in an aqueous medium. We tried to understand the role of hydrogen bonds (HBs) involving conserved water in mediating the interactions. The Luzar-Chandler model was adopted to study the kinetics of HB breaking and formation concerning different water-mediated HBs. The conformational flexibilities of bound GAGs are due to the flexible glycosidic linkages than the occasional/rare ring pucker conformation. The free energy landscape constructed with ϕ, and ψ, depicted that different conformational minima associated with the glycosidic linkage flexibility of the GAGs in bound states are separated by energy barriers. The binding affinities of IL8 towards GAGs are favored through the electrostatic and non-polar solvation interactions. 4-different types of conserved water were explored in the solvent-mediated binding of GAGs with IL8. The average lifetime of the IL8-GAG direct HB pairs was ∼ten times less than the IL8-GAG-shared water HBs. This is due to the rapid establishment of HB breaking and reformation kinetics involving water of a shared layer. We find that despite the highly negatively charged surface of GAGs, the IL8 surface populated by non-cationic amino acids could serve as a promising binding site in addition to the cationic surface of the protein., (© 2022 Wiley-VCH GmbH.)

Effects of dispersion interactions on the dynamics of water in bromide ion hydration shells have been studied by first principles simulations using a dispersion corrected density functional. The dynamics of vibrational spectral diffusion and its relations to hydrogen bond dynamics have been investigated for two different ion concentrations. It is found that the vibrational spectral diffusion of water molecules show faster dynamics with inclusion of dispersion interactions for both hydration shell and bulk water. The frequency calculations of hydration shell water reveal a weaker ion–water hydrogen bond than those between two water molecules. In the anionic hydration shell, the frequency of an OD bond is found to decrease with decrease of ion–water hydrogen bond distance. The hole dynamics calculations have been performed for further investigations of vibrational spectral diffusion of the two solutions. The current results are compared with those of recent experiments and other theoretical calculations. [ABSTRACT FROM AUTHOR]

We present insight into the way how vibrational modes of hydration water may be affected by the hydrophilic or hydrophobic nature of protein sites rather than by their curvature. We will illustrate how hydrophobicity promotes a dynamical behaviour similar to that of low density amorphous ice and how it affects the dynamics of the first interacting water molecules. We study the evolution of the hydrogen bond network dynamics as a function of the number of water molecules and explain the origin of the similarities between the dynamics of supercooled and hydration water. Finally we give an insight into the collective dynamics of hydration water and its correlation to the hydrogen bond network around bio-molecules. We discuss hydration dynamics results of our system, as a model of protein, in the context of glassy systems, protein function, folding and stability and protein–protein interfaces, giving a perspective of developments and applications. [ABSTRACT FROM AUTHOR]

Arginine (Arg) has long been used to inhibit aggregation of proteins. Despite its frequent use in inhibition of aggregation, the exact mechanism of aggregation and the effect of Arg on the conformation and stability of proteins are still not well understood. In the present study, spectroscopic, calorimetric, and molecular dynamics methods have been used to understand the mechanism of inhibition of aggregation of α-lactalbumin (α-LA) by Arg along with its effect on stability of the protein. It is observed that although Arg inhibits aggregation of α-LA, it also decreases stability of the protein. The results suggest that strong favorable interactions between α-LA and guanidinium group of Arg decrease the stability of the protein. The results also suggest that the guanidinium group preferentially interacts with Gln, Asn and negatively charged residues through hydrogen bonding and electrostatic interactions. [ABSTRACT FROM AUTHOR]

The intermolecular hydrogen bonding dynamics between the functionalized activated carbons (AC) and ethyl mercaptan (ETM) were investigated using DFT and TDDFT methods, respectively. The ground-state and excited-state structures, electronic excitation energies and corresponding oscillation strengths of the low-lying electronically excited states for the functionalized ACs and their hydrogen-bonded complexes I, II, III and IV were calculated. It is demonstrated that the stability trend of forming hydrogen-bonded complexes is I > II and III > IV, which coincides with the results from the interaction energies calculation EHB. Moreover, according to Zhao's rule on the excited hydrogen bonding dynamics, it is found that the hydrogen bonds in the complexes I, II and III are significantly strengthened, with the excitation energy of a related excited state being red shifted, the hydrogen bond interactions can facilitate ETM adsorption onto AC-COOCO, AC-CCC and AC-CO, respectively. The intermolecular hydrogen bond of complex IV in the excited state is noteworthily weakened, in which the excitation energy of a related excited state is blue shifted. Therefore, the hydrogen bond interaction in complex IV is against ETM adsorption onto AC-OH in the excited state. The photoexcitation for complex IV should be controlled during the absorption process. [ABSTRACT FROM AUTHOR]

Highlights: [•] DFT/TDDFT method has been performed to study the ground and excited states. [•] ESIPT was investigated by the characteristic peaks of IR spectra. [•] Hydrogen bonded quasi-aromatic chelating ring becoming smaller facilitates ESIPT. [•] ESIPT of the SA can be attributed to the electronegativity change of O1. [Copyright &y& Elsevier]

The time-dependent density functional theory method was performed to investigate the excited-state hydrogen-bonding dynamics of N-(2-hydroxyethyl)-1,8-naphthalimide (2a) and N-(3-hydroxyethyl)-1,8-naphthalimide (3a) in methanol (meoh) solution. The ground and excited-state geometry optimizations, electronic excitation energies, and corresponding oscillation strengths of the low-lying electronically excited states for the complexes 2a + 2meoh and 3a + 2meoh as well as their monomers 2a and 3a were calculated by density functional theory and time-dependent density functional theory methods, respectively. We demonstrated that the three intermolecular hydrogen bonds of 2a + 2meoh and 3a + 2meoh are strengthened after excitation to the S1 state, and thus induce electronic spectral redshift. Moreover, the electronic excitation energies of the hydrogen-bonded complexes in S1 state are correspondingly decreased compared with those of their corresponding monomer 2a and 3a. In addition, the intramolecular charge transfer of the S1 state for complexes 2a + 2meoh and 3a + 2meoh were theoretically investigated by analysis of molecular orbital. Copyright © 2014 John Wiley & Sons, Ltd. [ABSTRACT FROM AUTHOR]

Highlights: [•] A number of low – frequency modes are sequentially observed in photoexcited HPTS. [•] Evidence of coherent quantum beat in several low – frequency modes with anharmonic coupling. [•] The most transient low – frequency mode is the symmetric ring breathing of HPTS. [•] Excited – state proton transfer occurs nonadiabatically on the 5–200ps timescale. [•] Kinetic isotope effect is 3–4 for the two-stage ESPT components in water. [ABSTRACT FROM AUTHOR]

Abstract: The effects of dispersion interactions on the dynamics of hydrogen bonds and vibrational spectral diffusion in liquid methanol are investigated through first principles simulations with a dispersion corrected density functional. Calculations are done at two different temperatures of 300 and 350K and the results are compared with those of an earlier study where no such dispersion corrections were included. It is found that inclusion of dispersion interactions slightly increases the number of molecules held through non-hydrogen-bonded dispersion interactions in the neighborhood which, in turn, makes the dynamics faster. The inclusion of dispersion corrections gives rise to a faster hydrogen bond dynamics compared to the case when no such dispersion corrections are made. Also, the time scale of vibrational spectral diffusion obtained with the dispersion corrected density functional is found to be in better agreement with experiments. [Copyright &y& Elsevier]

A semiquantal (SQ) molecular dynamics (MD) simulation method using spherical Gaussian wave packets (WPs) is applied to a microscopic analysis of hydrogen-bond (H-bond) exchange dynamics in liquid water. We focus on the molecular jump mechanism of H-bond reorientation dynamics proposed from a classical MD simulation by Laage and Hynes (Science 2006, 311, 832). As a notable quantum effect, broadenings of both the oxygen and hydrogen WPs of jumping water are observed associated with the H-bond switching events. Nonetheless, quantum effects on averaged trajectories of structural parameters measured with respect to the WP centers are rather minor. A 1/ f fluctuation of local H-bond number is observed in both SQ and classical simulations. This is obtained straightforwardly from the real-time trajectories, in contrast with the originally found 1/ f fluctuation (Sasai et al., J. Chem. Phys. 1992, 96, 3045) of the total potential energies collected at quenched inherent structures. The quantum effects are found to accelerate the relaxation of H-bond number fluctuation, which is reflected in the region near the lower bound of the 1/ f behavior in the power spectra. New developments in the implementation of SQMD simulations including all atoms are also described. © 2012 Wiley Periodicals, Inc. [ABSTRACT FROM AUTHOR]

Abstract: A theoretical study of vibrational spectral diffusion in aqueous NaBr solutions is presented by means of ab initio molecular dynamics simulations and time series analysis. The OD stretch frequencies of deuterated water hydrogen bonded to the bromide ions are found to be higher than those in the bulk which implies a somewhat weaker Br–water hydrogen bonds than those between water molecules. The dependence of OD stretch frequencies of hydration shell water on the length and angle of the associated ion–water hydrogen bonds is also investigated. The dynamics of frequency fluctuations of hydration shell and all water molecules are studied through calculations of hole dynamics and frequency time correlations. The roles of the dynamics of ion–water and water–water hydrogen bonds, escape dynamics of water from ion hydration shells and also that of other non-hydrogen-bonded dynamical modes in influencing the dynamics of vibrational spectral diffusion are discussed. [Copyright &y& Elsevier]

Abstract: Sarcosine is one of the most important protecting osmolytes which is also known to counteract the denaturing effect of urea. We used molecular dynamics simulation methods to investigate the mechanism of protein stabilization and counteraction of urea by sarcosine. We found that sarcosine enhanced the tetrahedral structure of water and strengthened its hydrogen bonding network. We also found that sarcosine did not form clusters unlike glycine. Our results show strong interaction between sarcosine and urea molecules. Addition of sarcosine enhanced the urea–water structure and urea–water lifetime indicated an increase in the solvation of urea. These findings suggest that sarcosine indirectly stabilizes protein by enhancing water–water structure thus decreasing the hydrophobic effect and counteracts the effect of urea by increasing the solvation of urea and directly interacting with it leaving urea less available to interact with protein. [Copyright &y& Elsevier]

In this work, we present the optimized ground state geometrical structures, electronic excitation energies and corresponding oscillation strengths of the low-lying electronically excited states for the isolated Tce-CH3COCOOH and Tce-CH3C(OH)2COOH as well as their corresponding hydrogen-bonded dimers Tce-CH3C0C00H-H20 and Tce-CH3C(0H)2C00H-H20 through time-dependent density functional theory method. It is found that the intermo-lecular hydrogen bonds C=0...H-O are strengthened in the electronically excited states of the hydrogen-bonded dimers Tce-CH3C0C00H-H20 and Tce-CH3C(0H)2C00H-H20, in that the excitation energies of the related excited states for the hydrogen-bonded dimers are decreased compared with those of the corresponding monomers. The calculated results are consistent with the rules that are first demonstrated by Zhao on the excited-state hydrogen bonding dynamics. [ABSTRACT FROM AUTHOR]

The time-dependent density functional theory and the density functional theory are used to investigate the nature of hydrogen bonds formed by the derivative of the coumarin (TFKC) and the water molecules. The ground-state geometry optimizations, electronic excited energies and corresponding oscillation strengths for the TFKC monomer, the hydrogen-bonded TFKC-Water (HBA) dimer, TFKC-Water (HBB) dimer and TFKC-2Water complex are calculated. We find that, upon photoexcitation, the weaker hydrogen bond in the ground state will be affected by the relatively large impact for TFKC in the water. For better understanding the properties of the hydrogen bonds in the excited states, the frontier molecular orbitals of the S0 and S1 states are shown, and we find the obvious electron density transitions form the water molecules to the TFKC monomer. The electron transfer is expected to be the reason the hydrogen bond dynamics happens. [ABSTRACT FROM AUTHOR]

We present an ab initio molecular dynamics study of vibrational spectral diffusion and hydrogen bond dynamics in aqueous solution of acetone at room temperature. It is found that the frequencies of OD bonds in the acetone hydration shell have a higher stretch frequency than those in the bulk water. Also, on average, the frequencies of hydration shell OD modes are found to increase with increase in the acetone-water hydrogen bond distance. The vibrational spectral diffusion of the hydration shell water molecules reveals three time scales: A short-time relaxation (~80fs) corresponding to the dynamics of intact acetone-water hydrogen bonds, a slower relaxation (~1.3ps) corresponding to the lifetime of acetone-water hydrogen bonds and another longer time constant (~12ps) corresponding to the escape dynamics of water from the solute hydration shell. The present first principles results are compared with those of available experiments and classical simulations. [Figure not available: see fulltext.] [ABSTRACT FROM AUTHOR]

Abstract: A theoretical study of the dynamics of water–acetone mixtures is carried out by using the methods of ab initio molecular dynamics for trajectory generation, time series analysis for frequency calculations and time correlation function approach for calculations of various dynamical quantities. It is found that diffusion coefficients and orientational relaxation times of water and acetone molecules change in a nonlinear manner with variation of composition of the mixture. The lifetimes of acetone–water hydrogen bonds are found to be shorter than that of water–water hydrogen bonds and both are found to increase with decrease of water concentration. The vibrational spectral diffusion of OD stretch modes of deuterated water molecules is also investigated for the equimolar mixture of water and acetone and the results are correlated with the dynamics of water–water and water–acetone hydrogen bonds and also of dangling OD modes. [Copyright &y& Elsevier]

The orientational dynamics of water at a neutral surfactant reverse micelle interface are measured with ultrafast infrared spectroscopy of the hydroxyl stretch, and the results are compared to orientational relaxation of water interacting with an ionic interface. The comparison provides insights into the influence of a neutral vs. ionic interface on hydrogen bond dynamics. Measurements are made and analyzed for large nonionic surfactant Igepal CO-520reverse micelles (water nanopool with a 9-nm diameter). The results are compared with those from a previous study of reverse micelles of the same size formed with the ionic surfactant Aerosol-OT (AOT). The results demonstrate that the orientational relaxation times for interfacial water molecules in the two types of reverse micelles are very similar (13 ps for Igepal and 18 ps for AOT) and are significantly slower than that of bulk water (2.6 ps). The comparison of water orientational relaxation at neutral and ionic interfaces shows that the presence of an interface plays the dominant role in determining the hydrogen bond dynamics, whereas the chemical nature of the interface plays a secondary role. [ABSTRACT FROM AUTHOR]

The exchange of water hydroxyl hydrogen bonds between anions and water oxygens is observed directly with ultrafast 2D IR vibrational echo chemical exchange spectroscopy (CES). The 00 hydroxyl stretch of dilute HOD in H[sub2]O in concentrated (5.5 M) aqueous solutions of sodium tetrafluoroborate (NaBF[sub4]) displays a spectrum with a broad water-like band (hydroxyl bound to water oxygen) and a resolved, blue shifted band (hydroxyl bound to BF[sup-][sub4]). At short time (200 fs). the 2D IR vibrational echo spectrum has 4 peaks, 2 on the diagonal and 2 off-diagonal. The 2 diagonal peaks are the 0-1 transitions of the water-like band and the hydroxylanion band. Vibrational echo emissions at the 1-2 transition frequencies give rise to 2 off-diagonal peaks. On a picosecond time scale, additional off-diagonal peaks grow in. These new peaks arise from chemical exchange between water hydroxyls bound to anions and hydroxyls bound to water oxygens. The growth of the chemical exchange peaks yields the time dependence of anionwater hydroxyl hydrogen bond switching under thermal equilibrium conditions as T[subaw] = 7 ± 1 ps. Pump-probe measurements of the orientational relaxation rates and vibrational lifetimes are used in the CES data analysis. The pump-probe measurements are shown to have the correct functional form for a system undergoing exchange. [ABSTRACT FROM AUTHOR]

Multidimensional vibrational echo correlation spectroscopy with full phase resolution is used to measure hydrogen bond dynamics in water and methanol. The OD hydroxyl stretches of methanol-OD oligomers in CCl4 and HOD in H2O are studied using the shortest mid-IR pulses (<50 fs, <4 cycles of light) produced to date. The pulses have sufficient spectral bandwidth to span the very broad (>400 cm−1) spectrum of the 0–1 and 1–2 transitions. Hydrogen bond population dynamics are extricated with exceptional detail in MeOD oligomers because the different hydrogen bonded species are spectrally distinct. The experimental results along with detailed calculations indicate the strongest hydrogen bonds are selectively broken through a non-equilibrium relaxation pathway following vibrational relaxation of the hydroxyl stretch. The correlation spectra are also a sensitive probe of the fluctuations in water and provide a stringent test of water models that are widely used in simulations of aqueous systems. The analysis of the 2D band shapes demonstrates that different hydrogen bonded species are subject to distinct (wavelength dependent) ultrafast (∼100 fs) local fluctuations and essentially identical slow (0.4 and ∼2 ps) structural rearrangements. Observation of wavelength dependent dynamics demonstrates that standard theoretical approaches assuming Gaussian fluctuations cannot adequately describe water dynamics. [Copyright &y& Elsevier]

[Display omitted] • Water molecules near the protein surface are of low density in presence of salts. • Hydrophilic residues are found to have more disruptive water structure. • Strong preferential binding affinity of Li+ with protein makes more tetrahedral water. • The entropy of the water molecules is less for Li+ near the protein surface. • Hydrogen bond life time of the water molecules decreases from interface to bulk. 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. [ABSTRACT FROM AUTHOR]

The dynamics of water molecules plays a vital role in understanding water. We combined computer simulation and deep learning to study the dynamics of H-bonds between water molecules. Based on ab initio molecular dynamics simulations and a newly defined directed Hydrogen (H-) bond population operator, we studied a typical dynamic process in bulk water: interchange, in which the H-bond donor reverses roles with the acceptor. By designing a recurrent neural network-based model, we have successfully classified the interchange and breakage processes in water. We have found that the ratio between them is approximately 1 : 4, and it hardly depends on temperatures from 280 to 360 K. This work implies that deep learning has the great potential to help distinguish complex dynamic processes containing H-bonds in other systems., (© 2021 Wiley-VCH GmbH.)

Molecular dynamics (MD) simulation were employed to explore the microwave (MW) non-thermal effects of the supercritical water (SCW) using the SPC and SPC/E potential models. The field dependent radial distribution function, tetrahedral structure, dielectric constant, diffusion coefficient, hydrogen bonding and energy distribution were investigated. A field induced threshold effect is observed, where the dielectric constant noticeably increases with the increase of field intensity. It is noted that the molecular diffusion is nonlinear fluctuation under the microwave field. The non-thermal effect has a major influence on the hydrogen bond network are exhibited. And the relevant mechanism of microwave field-dependence hydrogen bond dynamics is discussed. This work may be expected to provide a new technique for the extraction of herbal medicine and environmental protection on basis of the SCW-MW properties. • The non-thermal effect of microwave in supercritical water was simulated. • Field-induced the tetrahedral structure of water was reconstructed. • The application of microwave field causes the nonlinear diffusion in SCW. • The microwave energy was partly transferred to the intermolecular energy of water. [ABSTRACT FROM AUTHOR]