Rearrangement Of Hydrogen Bond Network Research Articles

Highly Efficient, Recyclable Microplastic Adsorption Enabled by Chitin Hydrogen Bond Network Rearrangement

Highly Efficient, Recyclable Microplastic Adsorption Enabled by Chitin Hydrogen Bond Network Rearrangement

Effect of cations (Na+, Co2+, Fe3+) contamination in Nafion membrane: A molecular simulations study

The cation contamination is an important reason for the degradation of performance and durability of Nafion membrane, but the contamination mechanism for cations with different valence in Nafion membranes at different water content was not revealed at the microscale. In this study, the molecular dynamics simulations are performed to study the effect of the contamination of cations with various valence (Na+, Co2+, Fe3+) on the Nafion membrane at different water content. The mechanism for the degradation of the membrane performance in the presence of cations has been clarified. Moreover, it is found that cations with high valence have more serious negative impact on the connectivity of water clusters and the rearrangement of hydrogen bond network. This study provides a fundamental and comprehensive insight into the mechanism of the cation contamination in Nafion membrane, which is useful for the design of high durable ion exchange membranes.

Understanding the Multifaceted Mechanism of Compound I Formation in Unspecific Peroxygenases through Multiscale Simulations.

Unspecific peroxygenases (UPOs) can selectively oxyfunctionalize unactivated hydrocarbons by using peroxides under mild conditions. They circumvent the oxygen dilemma faced by cytochrome P450s and exhibit greater stability than the latter. As such, they hold great potential for industrial applications. A thorough understanding of their catalysis is needed to improve their catalytic performance. However, it remains elusive how UPOs effectively convert peroxide to Compound I (CpdI), the principal oxidizing intermediate in the catalytic cycle. Previous computational studies of this process primarily focused on heme peroxidases and P450s, which have significant differences in the active site from UPOs. Additionally, the roles of peroxide unbinding in the kinetics of CpdI formation, which is essential for interpreting existing experiments, have been understudied. Moreover, there has been a lack of free energy characterizations with explicit sampling of protein and hydration dynamics, which is critical for understanding the thermodynamics of the proton transport (PT) events involved in CpdI formation. To bridge these gaps, we employed multiscale simulations to comprehensively characterize the CpdI formation in wild-type UPO from Agrocybe aegerita (AaeUPO). Extensive free energy and potential energy calculations were performed in a quantum mechanics/molecular mechanics setting. Our results indicate that substrate-binding dehydrates the active site, impeding the PT from H2O2 to a nearby catalytic base (Glu196). Furthermore, the PT is coupled with considerable hydrogen bond network rearrangements near the active site, facilitating subsequent O-O bond cleavage. Finally, large unbinding free energy barriers kinetically stabilize H2O2 at the active site. These findings reveal a delicate balance among PT, hydration dynamics, hydrogen bond rearrangement, and cosubstrate unbinding, which collectively enable efficient CpdI formation. Our simulation results are consistent with kinetic measurements and offer new insights into the CpdI formation mechanism at atomic-level details, which can potentially aid the design of next-generation biocatalysts for sustainable chemical transformations of feedstocks.

Sequential flipping: the donor-acceptor exchange mechanism in water trimers.

The donor-acceptor exchange (DAE) is a significant hydrogen bond network rearrangement (HBNR) mechanism because it can lead to the change of the hydrogen bond direction. In this work, we report a new DAE mechanism found in water trimers that is realized by sequential flipping (SF) of all molecules rather than the well-known proton transfer (PT) process. Meanwhile, the SF process has a much smaller potential barrier (0.262 eV) than the previously predicted collective rotation process (about 1.7 eV), implying that the SF process is the main flipping process that can lead to DAE. Importantly, high-precision ab initio calculations show that SF-DAE can make the water ring to show a clear chiral difference from PT-DAE, which brings the prospect of distinguishing the two confusing processes based on circular dichroism spectra. The reaction rate analysis including quantum tunneling indicates an obvious temperature-dependent competitive relationship between the SF and PT processes; specifically, the SF process dominates above 65 K, while the PT process dominates below 65 K. Therefore, in most cases, the contribution for DAE mainly comes from the flipping process, rather than the PT process as previously thought. Our work enriches the understanding of the DAE mechanism in water trimers and provides a piece of the jigsaw that has been sought for the HBNR mechanism.

Water Diffusion Proceeds via a Hydrogen-Bond Jump Exchange Mechanism.

The self-diffusion of water molecules plays a key part in a broad range of essential processes in biochemistry, medical imaging, material science, and engineering. However, its molecular mechanism and the role played by the water hydrogen-bond network rearrangements are not known. Here we combine molecular dynamics simulations and analytic modeling to determine the molecular mechanism of water diffusion. We establish a quantitative connection between the water diffusion coefficient and hydrogen-bond jump exchanges, and identify the features that determine the underlying energetic barrier. We thus provide a unified framework to understand the coupling between translational, rotational, and hydrogen-bond dynamics in liquid water. It explains why these different dynamics do not necessarily exhibit identical temperature dependences although they all result from the same hydrogen-bond exchange events. The consequences for the understanding of water diffusion in supercooled conditions and for water transport in complex aqueous systems, including ionic, biological, and confined solutions, are discussed.

Collective Effect of Transformation of a Hydrogen Bond Network at the Initial State of Growth of Methane Hydrate

The molecular dynamics study of the rearrangement of the dynamic hydrogen bond network of liquid water to the crystal hydrogen bond network of methane hydrate in the process of their formation and growth is conducted. To reveal the nature of nucleation, the time dependences of the degree of “crystallinity” of the nearest environment of all water molecules, the rate of ordering of the hydrogen bond network, and the relation of these parameters to the rate of growth of methane hydrate are studied. The effect of the presence of sea salt ions and hydrate seed on these parameters is analyzed. Systems with a completely mixed gas, i.e., with the minimum induction time, are fabricated, and it is shown that gas hydrates can be nucleated simultaneously in the entire volume of the solution, which in turn indicates the collective formation of hydrates from liquid solution.

Dynamical Behavior of Water; Fluctuation, Reactions and Phase Transitions

Abstract Water dynamical and thermodynamical properties in molecular scale were theoretically investigated in a wide range of temperatures to clarify the physical origin of anomalous water properties. It was found in water that there exist intermittent and collective motions that arise from hydrogen bond network rearrangement. These intermittent motions become more distinctive with temperature decrease and diminish at the glass transition. In a deeply supercooled region, water dynamics shows that a new (“the third”) branch exists in its relaxation and in this branch special defects, H2O1, play a critical role. These defects make water glass transition temperature remarkably low. The intermittent collective motions have significant effects on water phase transitions and chemical reactions. The detailed dynamical mechanisms of the water freezing and the ice melting processes were analyzed. It was found how the embryos of nuclei for these processes are created and grow. The fast proton transfer mechanism in ice was also investigated to find its physical origin. Due to a strong geometrical constraint in ice, the excess proton is not trapped in a deep energy minimum and makes a facile transfer on the small energy barrier surface. As for the auto-dissociation process of water molecules, non-monotonic temperature dependence was theoretically clarified in a wide range of temperatures from ambient to supercritical region. On water roles in biomolecular functions, ion/proton transports and concomitant molecular relaxations were examined in ion-channel, photoactive yellow protein and reaction center.

Effect of an electric field on dewetting transition of nitrogen-water system

We investigate the influence of an external electric field on the dewetting behavior of nitrogen-water systems between two hydrophobic plates using molecular dynamics simulations. It is found that the critical distance of dewetting increases obviously with the electric field strength, indicating that the effective range of hydrophobic attraction is extended. The mechanism behind this interesting phenomenon is related to the rearrangement of hydrogen bond networks between water molecules induced by the external electric field. Changes in the hydrogen bond networks and in the dipole orientation of the water molecules result in the redistribution of the neutral nitrogen molecules, especially in the region close to the hydrophobic plates. Our findings may be helpful for understanding the effects of the electric field on the long-range hydrophobic interactions.

Preparation and Characterization of Films Based on Disintegrated Bacterial Cellulose and Montmorillonite

The food packaging materials from natural polymers including polysaccharides offer an ecologically important alternative to commonly used synthetic, non-biodegradable counterparts. The purpose of this work was to modify of bacterial cellulose (BC) leading to the improvement of its functional properties in terms of use as a food packaging material. Effects of disintegration of BC and addition of montmorillonite (MMT) on its water barrier, mechanical and thermal properties were investigated. Disintegration of BC increased its water vapour permeability (WVP) and thermal stability, but decreased its tensile strength (σ). These changes were closely related to the rearrangement of hydrogen-bond network in the BC structure, resulting in a partial conversion from the Iα to Iβ allomorph. The addition of 2% of MMT did not affect WVP and σ of the disintegrated BC (bBC), while the plasticization of the modified bBC generally decreased WVP, and did not increase σ. The improvement in water barrier properties of bBC modified by adding 2% of MMT in the presence of glycerol was caused by the formation of hydrogen bonds between the components of the composite. The results presented show the potential usefulness of BC modified by disintegration and adding 2% of MMT and 10–15% of glycerol as a food packaging material.

Dynamics of Water Molecules and Ions in Concentrated Lithium Chloride Solutions Probed with Ultrafast 2D IR Spectroscopy.

Water and ion dynamics in concentrated LiCl solutions were studied using ultrafast 2D IR spectroscopy with the methyl thiocyanate (MeSCN) CN stretch as the vibrational probe. The IR absorption spectrum of MeSCN has two peaks, one peak for water associated with the nitrogen lone pair of MeSCN (W) and the other peak corresponding to Li+ associated with the lone pair (L). To extract the spectral diffusion (structural dynamics) of W and L species, we developed a method that isolates the peak of interest by subtracting the 2D Gaussian proxies of multiple interfering peaks. Center line slope data (normalized frequency-frequency correlation function) for 2D bands from the W and L are fit with triexponential functions. The fastest component (1.1-1.6 ps) is assigned to local hydrogen bond length fluctuations. The intermediate timescale (∼4.0 ps) corresponds to the hydrogen bond network rearrangement. The slowest component decays in ∼40 ps and corresponds to ion pair and ion cluster dynamics. The very similar W and L spectral diffusion indicates that the motions of the water and ions are strongly coupled. Orientational relaxations of the W and L species were extracted using a new method to eliminate the effects of overlapping peaks. The results show that MeSCN bound to water undergoes orientational relaxation significantly faster than MeSCN bound to Li+. The orientational and spectral diffusion results are compared. A Stark coupling model is used to extract the root mean square average electric field caused by the ion clouds along the CN moiety as a function of concentration.

Searching for crystal-ice domains in amorphous ices

We employ classical molecular dynamics simulations to investigate the molecular-level structure of water during the isothermal compression of hexagonal ice (I$h$) and low-density amorphous (LDA) ice at low temperatures. In both cases, the system transforms to high-density amorphous ice (HDA) via a first-order-like phase transition. We employ a sensitive local order metric (LOM) [Martelli et. al., Phys. Rev. B, 97, 064105 (2018)], that can discriminate among different crystalline and non crystalline ice structures and is based on the positions of the oxygen atoms in the first and/or second hydration shell. Our results confirm that LDA and HDA are indeed amorphous, i.e., they lack of polydispersed ice domains. Interestingly, HDA contains a small number of domains that are reminiscent of the unit cell of ice IV, although the hydrogen-bond network (HBN) of these domains differ from the HBN of ice IV. The presence of ice IV-like domains provides some support to the hypothesis that HDA could be the result of a detour on the HBN rearrangement along the I$h$-to-ice IV pressure induced transformation. Both nonequilibrium LDA-to-HDA and I$h$-to-HDA transformations are two-steps processes where a small distortion of the HBN first occurs at low pressures and then, a sudden, extensive re-arrangement of hydrogen bonds at the corresponding transformation pressure follows. Interestingly, the I$h$-to-HDA and LDA-to-HDA transformations occur when LDA and I$h$ have similar local order, as quantified by the site-averaged LOMs. Since I$h$ has a perfect tetrahedral HBN, while LDA does not, it follows that higher pressures are needed to transform I$h$ into HDA than that for the conversion of LDA to HDA. In correspondence with both first-order-like phase transitions, the samples are composed of a large HDA cluster that percolates within the I$h$/LDA samples.

Dynamical Binding Modes Determine Agonistic and Antagonistic Ligand Effects in the Prostate-Specific G-Protein Coupled Receptor (PSGR)

We analysed the ligand-based activation mechanism of the prostate-specific G-protein coupled receptor (PSGR), which is an olfactory receptor that mediates cellular growth in prostate cancer cells. Furthermore, it is an olfactory receptor with a known chemically near identic antagonist/agonist pair, α- and β-ionone. Using a combined theoretical and experimental approach, we propose that this receptor is activated by a ligand-induced rearrangement of a protein-internal hydrogen bond network. Surprisingly, this rearrangement is not induced by interaction of the ligand with the network, but by dynamic van der Waals contacts of the ligand with the involved amino acid side chains, altering their conformations and intraprotein connectivity. Ligand recognition in this GPCR is therefore highly stereo selective, but seemingly lacks any ligand recognition via polar contacts. A putative olfactory receptor-based drug design scheme will have to take this unique mode of protein/ligand action into account.

Hydrogen bond network rearrangement dynamics in water clusters: Effects of intermolecular vibrational excitation on tunneling rates.

Theoretical studies of hydrogen bond network rearrangement (HBNR) dynamics in liquid water have indicated that librational motions initiate the hydrogen bond breaking/formation processes. We present the results of using a simple time evolution method to extract and compare the tunneling lifetimes for motions that break and reform the hydrogen bond for the water dimer, trimer, and pentamer from the experimentally measured tunneling splittings in the ground and excited intermolecular vibrational states. We find that the specific nature of the intermolecular vibrational excitation does not significantly influence the tunneling lifetime of the dimer, but that only excitations to a librational vibration affect the water trimer and pentamer lifetimes. The specific enhancement of bifurcation tunneling in larger clusters relative to the dimer also indicates that hydrogen bond cooperativity is a vital element of these dynamics.

New representatives of solid acid conductors: CsmHn((HSO4),(H2PO4))m+n

Crystals - superprotonics are extensively studied with the goal of elucidating the influence of the hydrogen subsystem on the physicochemical properties and designing new functional materials. As opposed to other hydrogen-containing compounds, phase transitions in these crystals are accompanied by a hydrogen-bond network rearrangement, resulting in radical changes of their properties, in particular, in the appearance of proton conductivity about 10–1 Ω–1 cm–1. These crystals are unique in the class of proton conductors, since the superprotonic conductivity is related to the structural features of these compounds rather than to the presence of doping additives. The occurrence of high superprotonic conductivity in the Me3H(XO4)2 (Me = K, Rb, Cs, NH4; X = S, Se, P, As) crystals is associated with the formation of a qualitatively new and dynamically disordered hydrogen-bond system [1]. In K9H7(SO4)8·N2O crystals, the only known representative of the Me9H7(XO4)8·xN2O family, the occurrence of high conductivity is associated with the outward diffusion of water molecules, the hydrogen-bond network rearrangement, and the formation of channels for the possible motion of K+ ions [2]. The hydrogen-bond rearrangement and the hindered back diffusion of water to the crystal bulk stabilize the high-temperature crystal structure and ensure its supercooling to low temperatures. The new crystals of Cs3(HSO4)2(H2PO4), Cs4(HSO4)3(H2PO4) and Cs6H(HSO4)3(H2PO4)4 were grown up in the CsHSO4–CsH2PO4-H2O system - enough big, with good optic quality [3]. The thermal and optical properties of crystals as well as their conductivity have been investigated in the temperature range 295 – 445 K. It was observed superprotonic phase transitions at 409, 411 and 365 K correspondingly. The distinction in the properties of Cs3(HSO4)2(H2PO4) and Cs4(HSO4)3(H2PO4) (sp. gr. C2/c at 295 K) is related to differences in nets of hydrogen bonds formed between different-occupied XO4 tetrahedra. Cs6H(HSO4)3(H2PO4)4 srystals (sp. gr. I-43d at 295 K) have the net of hydrogen bonds which is completely different. After cooling the high-temperature superprotonic phase preserves long enough without essential decrease in conductivity. This study was supported by the Russian Foundation for Basic Research (projects 13-03-12216 and 13-02-92693).

Quantum effects of hydrogen nuclei on a structure and a dynamical rearrangement of hydrogen-bond networks

To understand anomalous energetics and dynamics in water, nuclear quantum effects such as zero-point energy and delocalization of wave packets (WPs) representing water hydrogen atoms should be essential. However, since quantum calculations of many-body dynamics are highly complicated in general, none has yet directly viewed the quantum WP dynamics of hydrogen atoms in liquid water. Our semiquantum molecular dynamics simulation for the first time made it possible to observe the hydrogen WP dynamics in liquid water. Here, we demonstrate that the microscopic WP dynamics are closely correlated to and play key roles in the dynamical rearrangements in the hydrogen-bond network (HBN) of liquid water. Especially, the memory loss of the dipolar angle formed by two waters is accelerated with the nuclear quantum effect introduced by the nuclear WP, rationalizing the faster memory decay of the HBN in the quantum liquid water. We found the quantum effects of hydrogen atoms on mesoscopic liquid water behaviors such as intermittent collective motions associated with the rearrangement of HBN and the concomitant fluctuation and relaxation. Our results will provide new physical insights on HBN dynamics in water whose significance is not limited to the pure liquid dynamics but also for understanding chemical and biological reactions in liquid water.

MmHn(XO4)(m+n)/2crystals: structure, phase transitions, hydrogen bonds, conductivity. I. K9H7(SO4)8·H2O crystals – a new representative of the family of solid acid conductors

To reveal the structural conditionality for anomalies in physical properties, including dielectric and optical properties, diffraction studies of K9H7(SO4)8·H2O crystals were performed using synchrotron radiation in the temperature range 293-450 K and determined at 405 K, taking H atoms into account. The results indicate that the occurrence of high conductivity in K9H7(SO4)8·H2O crystals with a temperature increase is associated with the outward diffusion of water molecules, hydrogen-bond network rearrangement and the formation of channels for the possible motion of K(+) ions. A rearranged system of hydrogen bonds consists of permanent bonds and partly of dynamically disordered bonds. Hydrogen-bond rearrangement and the hindered back diffusion of water to the crystal bulk stabilize the high-temperature crystal structure right down to room temperature.

Correlated Dynamical Crossovers of the Hydration Layer of a Single-Stranded DNA Oligomer

Atomistic molecular dynamics (MD) simulations at different temperatures ranging from 160 to 300 K have been carried out to explore the correlated dynamical transitions of a single-stranded DNA (ss-DNA) oligomer with heterogeneous distribution of nucleobases, 5'-CGCGAATTCGCG-3', and that of its hydration water. The calculations reveal a distinct dynamical crossover of the DNA oligomer associated with abrupt changes of motions of its atoms at around 200-220 K. Importantly, it is found from calculated water diffusivities and relaxation times that the hydration water molecules also exhibit a crossover within 210-220 K. This indicates that the dynamical crossover of the DNA strand is coupled with that exhibited by its hydration water. In addition, another crossover point for the surface water molecules has been found around 180-185 K with the water layer exhibiting highly frozen dynamics. The rearrangement of hydrogen bond network that occurs due to population transition from two-coordinated to four-coordinated tetrahedrally arranged water molecules at the interface with lowering of temperature is found to be the microscopic origin of such correlated two-step dynamic crossovers of hydration water. Such modified hydrogen bonding results in transformation of hydration layer water structuring from high density to low density liquid under supercooled conditions.

In silico investigation of PHD-3 specific HIF1-α proline 567 hydroxylation: A new player in the VHL/HIF-1α interaction pathway?

Hypoxia inducible factor 1α (HIF-1α) regulates oxygen homeostasis in the cell through a sensing mechanism involving its hydroxylation and binding to the von Hippel–Lindau (VHL) tumor suppressor. This mechanism is mediated through hydroxylation of HIF-1α proline 564, although in vitro tests have previously shown an alternative hydroxylation at proline 567 by PHD-3. Here, molecular dynamics simulations were used to investigate the structural effect of this alternative hydroxylation. A specific hydrogen bond network rearrangement and improved electrostatic energy for hydroxylated P567 are compatible with an increase in HIF-1α binding affinity. Sequence analysis also confirms P567 to be vastly conserved during evolution, indicating a possible role for this alternative, PHD-3 driven, post translational modification in pVHL–HIF-1α complex formation.

Temperature-induced changes in the single-crystal structure of K9H7(SO4)8 · H2O

Interest in superprotonic crystals of MmHn(XO4)(m + n)/2 is associated with the solution to the fundamental problem of modern condensed matter physics: investigations of structural phase transitions and the stabilization of phases with high proton conductivity with the aim of designing new functional materials. The available data suggest that changes in the physical properties in these crystals can occur through different structural mechanisms. To reveal the structural conditionality for anomalies in the physical properties, the crystals of K9H7(SO4)8 · H2O were studied by X-ray diffraction in the temperature range of 25–463 K, and the crystal structure of the high-temperature phase was determined at 418 K (sp. gr. Pcan). The results of the study indicate that the occurrence of high conductivity in K9H7(SO4)8 · H2O crystals at high temperatures is associated with the diffusion of water of crystallization, the hydrogen-bond network rearrangement, and the motion of K ions. The hydrogen-bond rearrangement and the hindered back diffusion of water to the crystal stabilize the high-temperature phase and ensure its supercooling to low temperatures.

Structural basis for vitamin D receptor agonism by novel non-secosteroidal ligands

Non-secosteroidal ligands for vitamin D receptor (VDR) have been developed for the agonist with non-calcemic profiles. Here, we provide the structural mechanism of VDR agonism by novel non-secosteroidal ligands. All ligands had the similar efficacy, while two had the higher potency. Crystallographic analyses revealed that all ligands interacted with helix H10 and the loop between helices H6 and H7 in a similar manner, but also that the two ligands with higher potency had different interaction modes. This study suggests that distinct ligand potency depend upon differences in the formation and rearrangement of hydrogen-bond networks induced by each ligand.