OH Reorientation Research Articles

Investigating the Hydroxyl Reorientation in Hydroxyapatite Using Machine Learning Potentials

The chain or network of hydroxyl groups (OH–) is crucial in determining the structure and function of materials, especially in hydroxyapatite (HAP), a mineral essential for human bones. HAP exhibits a linear arrangement of OH– along the c-axis, which determines its phase transition, dielectric, and piezoelectric properties. However, the mechanism underlying OH– reorientation with temperature remains elusive using traditional experimental and theoretical methods. To address this, we developed a machine learning atomistic potential for HAP using an active learning algorithm, which achieved density functional theory-level accuracy in describing OH– of HAP. The machine learning molecular dynamics simulations revealed that the reorientation of OH– in HAP with temperature occurs through ″flip-flop″ motion, rather than proton transfer. This process starts at about 473 K and accelerates with increasing temperature, consistent with the experimentally observed transformation from the monoclinic to hexagonal phase. At 973 K and above, the rapid “flip-flop” reorientation process leads to an undetermined orientation of OH– along the c-axis. These findings highlight the potential of machine learning-accelerated molecular dynamics simulations in unraveling the microscopic mechanisms underlying the hydrogen bond network in complex multicomponent materials at the atomic level.

On water reorientation dynamics in cation hydration shells

The effects of ions on liquid water’s structural, dynamical, and thermodynamical properties have key implications for a wide range of biological and technological processes. Based on simulations and analytic modeling, we have recently developed a framework that rationalizes the effects of solutes and interfaces on water reorientation dynamics. However, this picture still misses some contributions of the cations to the experimentally measured slowdown or acceleration of water dynamics. All-atom classical simulations also face some limitations in quantitatively reproducing water structural and dynamical features in ionic aqueous solutions. Here, we show that a scaled-charge approach can successfully reproduce experimental trends and that ab initio descriptions are not required. We show that a picture where the cation would lock a water molecule dipole and lead to partial OH reorientation is both incorrect for some ions, and largely exaggerated for others. We demonstrate that a combination of two effects on the hydrogen-bond (H-bond) exchange dynamics explains the ambient temperature acceleration of water reorientation next to a cesium cation, and the retardation next to lithium and magnesium cations. First, ions create a local excluded volume, which hinders the approach of possible new H-bond partners, leading to a retarding contribution. However, they also perturb the local water structure, reducing the energetic cost of elongating the initial H-bond. For magnesium and lithium cations, the excluded volume effect dominates, which leads to an overall retardation of the H-bond exchange. For the cesium cation, at room temperature, this latter contribution overcomes the excluded volume effect, leading to an acceleration; moreover, the strong temperature dependence observed in the experiments, going from a large acceleration close to freezing to a retardation close to boiling, is understood by the key enthalpic effect of the elongation contribution. Overall, our framework now provides a comprehensive understanding of cations’ and anions’ effects on water reorientation dynamics.

Examining the Role of Different Molecular Interactions on Activation Energies and Activation Volumes in Liquid Water.

There are a large number of force fields available to model water in molecular dynamics simulations, which each have their own strengths and weaknesses in describing the behavior of the liquid. One particular weakness in many of these models is their description of dynamics away from ambient conditions, where their ability to reproduce measurements is mixed. To investigate this issue, we use the recently developed fluctuation theory for dynamics to directly evaluate measures of the local temperature and pressure dependence: the activation energy and the activation volume. We examine these activation parameters for hydrogen-bond jump exchange times, OH reorientation times, and diffusion coefficients calculated from the SPC/E, SPC/Fw, TIP3P-PME, TIP3P-PME/Fw, OPC3, TIP4P/2005, TIP4P/Ew, E3B2, and E3B3 water models. Activation energy decompositions available through the fluctuation theory approach provide mechanistic insight into the origins of different temperature dependences between the various models, as well as the influence of three-body effects and flexibility.

Stability, Elastic Properties, and the Li Transport Mechanism of the Protonated and Fluorinated Antiperovskite Lithium Conductors.

Lithium-rich antiperovskites (APs) have attracted significant research attention due to their ionic conductivity above 1 mS cm-1 at room temperature. However, recent experimental reports suggest that proton-free lithium-rich APs, such as Li3OCl, may not be synthesized using conventional methods. While Li2OHCl has a lower conductivity of about 0.1 mS cm-1 at 100 °C, its partially fluorinated counterpart, Li2(OH)0.9F0.1Cl, is a significantly better ionic conductor. In this article, using density functional theory simulations, we show that it is easier to synthesize Li2OHCl and two of its fluorinated variants, i.e., Li2(OH)0.9F0.1Cl and Li2OHF0.1Cl0.9, than Li3OCl. The transport properties and electrochemical windows of Li2OHCl and the fluorinated variants are also studied. The ab initio molecular dynamics simulations suggest that the greater conductivity of Li2(OH)0.9F0.1Cl is due to structural distortion of the lattice and correspondingly faster OH reorientation dynamics. Partially fluorinating the Cl site to obtain Li2OHF0.1Cl0.9 leads to an even greater ionic conductivity without impacting the electrochemical window and synthesizability of the materials. This study motivates further research on the correlation between local structure distortion, OH dynamics, and increased Li mobility. Furthermore, it introduces Li2OHF0.1Cl0.9 as a novel Li conductor.

Activation energies and the extended jump model: How temperature affects reorientation and hydrogen-bond exchange dynamics in water.

Hydrogen-bond exchanges drive many dynamical processes in water and aqueous solutions. The extended jump model (EJM) provides a quantitative description of OH reorientation in water based on contributions from hydrogen-bond exchanges, or jumps, and the "frame" reorientation of intact hydrogen-bond pairs. Here, we show that the activation energies of OH reorientation in bulk water can be calculated accurately from the EJM and that the model provides a consistent picture of hydrogen-bond exchanges based on molecular interactions. Specifically, we use the recently developed fluctuation theory for dynamics to calculate activation energies, from simulations at a single temperature, of the hydrogen-bond jumps and the frame reorientation, including their decompositions into contributions from different interactions. These are shown to be in accord, when interpreted using the EJM, with the corresponding activation energies obtained directly for OH reorientation. Thus, the present results demonstrate that the EJM can be used to describe the temperature dependence of reorientational dynamics and the underlying mechanistic details.

Removing the barrier to the calculation of activation energies: Diffusion coefficients and reorientation times in liquid water.

General approaches for directly calculating the temperature dependence of dynamical quantities from simulations at a single temperature are presented. The method is demonstrated for self-diffusion and OH reorientation in liquid water. For quantities which possess an activation energy, e.g., the diffusion coefficient and the reorientation time, the results from the direct calculation are in excellent agreement with those obtained from an Arrhenius plot. However, additional information is obtained, including the decomposition of the contributions to the activation energy. These results are discussed along with prospects for additional applications of the direct approach.

Reorientation of Isomeric Butanols: The Multiple Effects of Steric Bulk Arrangement on Hydrogen-Bond Dynamics.

Molecular dynamics simulations are used to investigate OH reorientation in the four isomeric butanols in their bulk liquid state to examine the influence of the arrangement of the steric bulk on the alcohol reorientational and hydrogen-bond (H-bond) dynamics. The results are interpreted within the extended jump model in which the OH reorientation is decomposed into contributions due to "jumps" between H-bond partners and "frame" reorientation of the intact H-bonded pair. Reorientation is fastest in iso-butanol and slowest in tert-butanol, while sec- and n-butanol have similar reorientation times. This latter result is a fortuitous cancellation between the jump and frame reorientation in the two alcohols. The extended jump model is shown to provide a quantitative description of the OH reorientation times. A detailed analysis of the jump times shows that a combination of entropic, enthalpic, and dynamical factors, including transition state recrossing effects, all play a role. A simple model based on the liquid structure is proposed to estimate the energetic and entropic contributions to the jump time. This represents the groundwork for a predictive model of OH reorientation in alcohols, but additional studies are required to better understand the frame reorientation and transition state recrossing effects.

Origins of the non-exponential reorientation dynamics of nanoconfined water.

The dynamics of water are dramatically modified upon confinement in nanoscale hydrophilic silica pores. In particular, the OH reorientation dynamics of the interfacial water are non-exponential and dramatically slowed relative to the bulk liquid. A detailed analysis of molecular dynamics simulations is carried out to elucidate the microscopic origins of this behavior. The results are analyzed in the context of the extended jump model for water that describes the reorientation as a combination of hydrogen-bond exchanges, or jumps, and rotation of intact hydrogen bonds, with the former representing the dominant contribution. Within this model, the roles of surface and dynamical heterogeneities are considered by spatially resolving the hydrogen-bond jump dynamics into individual sites on the silica pore surface. For each site the dynamics is nearly mono-exponential, indicating that dynamical heterogeneity is at most a minor influence, while the distribution of these individual site jump times is broad. The non-exponential dynamics can also not be attributed to enthalpic contributions to the barriers to hydrogen-bond exchanges. Two entropic effects related to the surface roughness are found to explain the retarded and diverse dynamics: those associated with the approach of a new hydrogen-bond acceptor and with the breaking of the initial hydrogen-bond.

Reorientation dynamics of nanoconfined water: Power-law decay, hydrogen-bond jumps, and test of a two-state model

The reorientation dynamics of water confined within nanoscale, hydrophilic silica pores are investigated using molecular dynamics simulations. The effect of surface hydrogen-bonding and electrostatic interactions are examined by comparing with both a silica pore with no charges (representing hydrophobic confinement) and bulk water. The OH reorientation in water is found to slow significantly in hydrophilic confinement compared to bulk water, and is well-described by a power-law decay extending beyond one nanosecond. In contrast, the dynamics of water in the hydrophobic pore are more modestly affected. A two-state model, commonly used to interpret confined liquid properties, is tested by analysis of the position-dependence of the water dynamics. While the two-state model provides a good fit of the orientational decay, our molecular-level analysis evidences that it relies on an over-simplified picture of water dynamics. In contrast with the two-state model assumptions, the interface dynamics is markedly heterogeneous, especially in the hydrophilic pore and there is no single interfacial state with a common dynamics.

On the Reorientation and Hydrogen-Bond Dynamics of Alcohols

The mechanism of the OH bond reorientation in liquid methanol and ethanol is examined. It is found that the extended jump model, recently developed for water, describes the OH reorientation in these liquids. The slower reorientational dynamics in these alcohols compared to water can be explained by two key factors. The alkyl groups on the alcohol molecules exclude potential partners for hydrogen bonding exchanges, an effect that grows with the size of the alkyl chain. This increases the importance of the reorientation of intact hydrogen bonds, which also slows with increasing size of the alcohol and becomes the dominant reorientation pathway.

The reorientation mechanism of hydroxide ions in water: A molecular dynamics study

Classical molecular dynamics simulations with a polarizable force field indicate two major structural motifs for the aqueous bulk solvation of OH −: a four- and a five-coordinated solvent hydrogen bond donor to OH − in addition to a weak solvent hydrogen bond acceptor by OH −. A two-step mechanism for the reorientation of OH − in water is proposed: first, the reorientation of OH − is initiated by the coupled translation with the water molecules in its first solvation shell; second, the OH − relaxes to the minimum energy configuration. The first step is the rate-limiting one for this mechanism.

Do more strongly hydrogen-bonded water molecules reorient more slowly ?

We study how water OH reorientation dynamics’ short and long-time contributions depend on the hydrogen(H)-bond strength. The initial librational reorientation occurs within a cone. We show quantitatively that the stronger the H-bond, the smaller the cone angle and librational reorientation amplitude. The long-time decay is independent of the initial OH ⋯ O H-bond strength, as explained by our recently proposed molecular jump mechanism for the water reorientation mechanism: in the vast majority of (transient) H-bond breaking events, a new H-bond partner is unavailable and the reorientation is unsuccessful; successful reorientation requires this availability, which is independent of the H-bond strength.

Atomistic Simulation Study of the Order/Disorder (Monoclinic to Hexagonal) Phase Transition of Hydroxyapatite.

The transformation of the low-temperature (monoclinic, P21/b) to the high-temperature (hexagonal, P63/m) modification of hydroxyapatiteCa5[(OH)(PO4)3]is investigated by means of molecular dynamics simulations. In the monoclinic phase the orientation of the hydroxide ions is strictly ordered. Above the critical temperature of about 200 °C orientational changes of the hydroxide ions are observed. In the course of each reorientation event a hydroxide ion passes through the surrounding calcium triangle. From an Arrhenius fit the related activation energy is calculated. In the high-temperature phase the hydroxide ions are statistically disordered. Out of the two possible concepts for the formation and structure of hexagonal hydroxyapatite, our simulations clearly identify the disordering of hydroxide ions orientation to occur in a nonconcerted manner, i.e., collective reorientation of OH- ion rows is not observed.

Atomistic Simulation Study of the Order/Disorder (Monoclinic to Hexagonal) Phase Transition of Hydroxyapatite

The transformation of the low-temperature (monoclinic, P21/b) to the high-temperature (hexagonal, P63/m) modification of hydroxyapatiteCa5[(OH)(PO4)3]is investigated by means of molecular dynamics simulations. In the monoclinic phase the orientation of the hydroxide ions is strictly ordered. Above the critical temperature of about 200 °C orientational changes of the hydroxide ions are observed. In the course of each reorientation event a hydroxide ion passes through the surrounding calcium triangle. From an Arrhenius fit the related activation energy is calculated. In the high-temperature phase the hydroxide ions are statistically disordered. Out of the two possible concepts for the formation and structure of hexagonal hydroxyapatite, our simulations clearly identify the disordering of hydroxide ions orientation to occur in a nonconcerted manner, i.e., collective reorientation of OH- ion rows is not observed.

A solid state NMR and molecular orbital study of hydroxylammonium chloride

Deuterium and nitrogen-15 NMR spectroscopy has been used to measure the 2H quadrupolar coupling and 15N chemical shift tensors in solid hydroxylammonium chloride, NH3OH+Cl-, (HAC). In addition, the NH3 and OH dynamics have been investigated by variable temperature 2H line shapes and T1 measurements. The Arrhenius activation energy for NH3 rotation is 22.5 ± 1.8 kJ/mol with a pre-exponential factor of 8 ± 3 × 1012 s-1 from line shapes and 21.3 ± 2 kJ/mol with an infinite temperature correlation time, τinf,, of 5.0 ± 0.4 × 10-14 s from the T1 analysis. The latter value corresponds to a pre-exponential factor of 6.7 ± 0.5 × 1012 s-1, if a three-site exchange is assumed. There was no evidence for OH reorientation up to 405 K, indicating a rather strong OH···Cl hydrogen bond. Previously reported inconsistencies between crystal structure and molecular orbital derived N-O bond lengths are cleared up by performing geometry optimizations with large basis sets and taking electron correlation into account. The internal rotational potential for the isolated HA cation is calculated to be 5.8 kJ/mol at the MP2/6-31G** level, with the trans geometry preferred. Calculations that employ the neutron diffraction geometry and include the Cl- anions that surround the HA+ cation yield an upper limit for the activation energy for NH3 group rotation of 62 kJ/mol. Analysis of the deuterium spectrum and T1 data yield nuclear quadrupolar coupling constants of 160 ± 5 kHz and 194 ± 5 kHz (η = 0.50 ± 0.05) for the ND3 and OD deuterons, respectively. Density functional calculations of the deuterium and nitrogen-14 nuclear quadrupolar coupling constants at the B3LYP level show that it is necessary to include the influence of the surrounding chloride anions. We have also shown that it is possible to obtain accurate proton chemical shifts from the deuterium MAS spectrum of solid HAC-d4.Key words: solid state NMR, molecular dynamics, nitrogen 15 chemical shift anisotropy.

Hepatitis C viral (HCV) infection and liver transplantation (LT) — relation of outcome to posttransplant steroid use: [formula omitted] — Depts of Digestive Surgery, Virology∗, Intensive Care∗∗ — Univ. Hospital St-Luc — Catholic Univ. of Louvain — Brussels — Belgium

IR, Raman and single-crystal Raman spectra of laurionite-type Sr(OH)I, Ba(OH)Cl, Ba(OH)Br, Ba(OH)I, Pb(OH)Cl, Pb(OH)Br and Pb(OH)I, and of deuterated specimens and Ba(OH)Cl1−xBrx, solid solutions recorded at 90–520 K are presented and assigned to OH (OD) stretching, librational and translational modes. The main results obtained are (i) unusually large structural H/D isotope effects of Ba(OH)Cl due to Landau-type isostructural reorientation of OH− ions and (ii) the very different nature and strengths of the hydrogen bonds formed. Thus, the strengths of the partly linear (Ba(OH)Cl), partly multifurcated hydrogen bonds range as Pb(OH)I (vOH: 3497 cm−1) > Pb(OH)Br > Pb(OH)Cl > Sr(OH)I (3591 cm−1), as shown by the red-shift of the OH stretches and the blue-shift of the OH librations. In the cases of Ba(OH)Br (3605 cm−1) and Ba(OH)I (3590 cm−1), hydrogen bonding is negligible. The stronger hydrogen bonds formed in the lead compounds are caused by the greater synergetic effect of Pb2+ ions compared to those of Sr2+ and Ba2+.

Laurionite-type M(OH)X (MBa, Pb; XCl, Br, I) and Sr(OH)I. An IR and Raman spectroscopic study

Abstract IR, Raman and single-crystal Raman spectra of laurionite-type Sr(OH)I, Ba(OH)Cl, Ba(OH)Br, Ba(OH)I, Pb(OH)Cl, Pb(OH)Br and Pb(OH)I, and of deuterated specimens and Ba(OH)Cl1−xBrx, solid solutions recorded at 90–520 K are presented and assigned to OH (OD) stretching, librational and translational modes. The main results obtained are (i) unusually large structural H/D isotope effects of Ba(OH)Cl due to Landau-type isostructural reorientation of OH− ions and (ii) the very different nature and strengths of the hydrogen bonds formed. Thus, the strengths of the partly linear (Ba(OH)Cl), partly multifurcated hydrogen bonds range as Pb(OH)I (vOH: 3497 cm−1) > Pb(OH)Br > Pb(OH)Cl > Sr(OH)I (3591 cm−1), as shown by the red-shift of the OH stretches and the blue-shift of the OH librations. In the cases of Ba(OH)Br (3605 cm−1) and Ba(OH)I (3590 cm−1), hydrogen bonding is negligible. The stronger hydrogen bonds formed in the lead compounds are caused by the greater synergetic effect of Pb2+ ions compared to those of Sr2+ and Ba2+.

Solid NaOH and KOH as superionic proton conductors: Conductivity and its isotope effect

Solid potassium and sodium hydroxides in the high temperature phase are confirmed to be protonic conductors. The conduction is intrinsic, due to OH − disproportionation, 2OH −⇌O −2+H 2O. The rate controlling step in proton transfer is its jump rather than OH reorientation. The NaOH conductivity isotope effect is measured by means of NaOHH 2 isotope exchange directly in a conductivity cell; the NaOH conductivity is 10–20% higher than the NaOD one. The diffusivity of hydrogen in NaOH and the isotope exchange rate are also determined. A tentative explanation of the isotope effect taking into account isotope dependence of both the mobility and the concentration of proton defects is given. The mechanism of proton transfer appears to involve approaching two oxygen atoms to each other to form a nonlinear OHO transition complex. The activation energy of the conductivity is possibly temperature dependent because of high thermal expansion coefficient of the solid alkali hydroxides.

Hydrogen dynamics in hydro-sodalite Na8 [AlSiO4]6 (OH)2 by inelastic and quasielastic neutron scattering

The dynamical properties of hydrogen in the sodalite Na8[AlSiO4]6 (OH)2 were investigated by quasielastic and inelastic neutron scattering techniques. The data were analyzed with a jump model for the hydrogen motion (OH reorientation). The characteristic time of the jump process is 2.1 ps at 295 K, the frequency of the local vibration (jump attempt frequency) is 17.4 THz. The detailed analysis shows that the hydrogen environment in the (Na4OH)3+ complex cation has lower than tetrahedral symmetry.

Reaction-rate approach to some low temperature processes in alkali halides

The general reaction-rate theory is applied to some processes in alkali halide crystals that occur by lattice tunneling at low temperature. The theoretical equations used refer to the strong coupling case comprising both adiabatic and nonadiabatic transitions. The thermal ionization of excited F centers is considered from this point of view. The theory reproduces rather well the experimental temperature dependence of the ionization efficiency. Similarly the reorientation of OH − impurity dipoles is treated and a good agreement is again found between theoretical and experimental relaxation rates in several host crystals.