Hydrogen-bonded Water Chains Research Articles

Noncovalent Interactions in Hydrated Nitrosonium Ion Clusters Mediated by Hydrogen-Bonded Water Networks.

As important species in the D region of the ionosphere, hydrated nitrosonium ion clusters [NO+(H2O)n] are also archetypal and concise models to illustrate effects of different solvent shells. We have investigated noncovalent interactions in NO+(H2O)3 and NO+(H2O)4 isomers with high levels of ab initio and symmetry-adapted perturbation theory (SAPT) methods. On the basis of our computations, the exchange energies become much more repulsive, whereas the induction energies are significantly more attractive for the noncovalent interactions of NO+ with hydrogen-bonded water chains. Combined with analyses of the electron densities for the NO+(H2O)3 and NO+(H2O)4 isomers, we propose that the counteracting effect of the exchange and induction energies could be deemed as an index for the tendency to form the HO-NO covalent bond. Moreover, we have also found that the third-order induction terms are very important to evaluate reasonable charge transfer energies with the SAPT computations.

Action at a distance: organic cation induced long range organization of interfacial water enhances hydrogen evolution and oxidation kinetics.

Engineering efficient electrode-electrolyte interfaces for the hydrogen evolution and oxidation reactions (HOR/HER) is central to the growing hydrogen economy. Existing descriptors for HOR/HER catalysts focused on species that could directly impact the immediate micro-environment of surface-mediated reactions, such as the binding energies of adsorbates. In this work, we demonstrate that bulky organic cations, such as tetrapropyl ammonium, are able to induce a long-range structure of interfacial water molecules and enhance the HOR/HER kinetics even though they are located outside the outer Helmholtz plane. Through a combination of electrokinetic analysis, molecular dynamics and in situ spectroscopic investigations, we propose that the structure-making ability of bulky hydrophobic cations promotes the formation of hydrogen-bonded water chains connecting the electrode surface to the bulk electrolyte. In alkaline electrolytes, the HOR/HER involve the activation of interfacial water by donating or abstracting protons. The structural diffusion mechanism of protons in aqueous electrolytes enables water molecules and cations located at a distance from the electrode to influence surface-mediated reactions. The findings reported in this work highlight the prospect of leveraging the nonlocal mechanism to enhance electrocatalytic performance.

Interplay between local protein interactions and water bridging of a proton antenna carboxylate cluster

Proteins that bind protons at cell membrane interfaces often expose to the bulk clusters of carboxylate and histidine sidechains that capture protons transiently and, in proton transporters, deliver protons to an internal site. The protonation-coupled dynamics of bulk-exposed carboxylate clusters, also known as proton antennas, is poorly described. An essential open question is how water-mediated bridges between sidechains of the cluster respond to protonation change and facilitate transient proton storage. To address this question, here I studied the protonation-coupled dynamics at the proton-binding antenna of PsbO, a small extrinsinc subunit of the photosystem II complex, with atomistic molecular dynamics simulations and systematic graph-based analyses of dynamic protein and protein-water hydrogen-bond networks. The protonation of specific carboxylate groups is found to impact the dynamics of their local protein-water hydrogen-bond clusters. Regardless of the protonation state considered for PsbO, carboxylate pairs that can sample direct hydrogen bonding, or bridge via short hydrogen-bonded water chains, anchor to nearby basic or polar protein sidechains. As a result, carboxylic sidechains of the hypothesized antenna cluster are part of dynamic hydrogen bond networks that may rearrange rapidly when the protonation changes.

Conformational Motions and Water Networks at the α/β Interface in E. coli Ribonucleotide Reductase.

Ribonucleotide reductases (RNRs) catalyze the conversion of all four ribonucleotides to deoxyribonucleotides and are essential for DNA synthesis in all organisms. The active form of E. coli Ia RNR is composed of two homodimers that form the active α2β2 complex. Catalysis is initiated by long-range radical translocation over a ∼32 Å proton-coupled electron transfer (PCET) pathway involving Y356β and Y731α at the interface. Resolving the PCET pathway at the α/β interface has been a long-standing challenge due to the lack of structural data. Herein, molecular dynamics simulations based on a recently solved cryogenic-electron microscopy structure of an active α2β2 complex are performed to examine the structure and fluctuations of interfacial water, as well as the hydrogen-bonding interactions and conformational motions of interfacial residues along the PCET pathway. Our free energy simulations reveal that Y731 is able to sample both a flipped-out conformation, where it points toward the interface to facilitate interfacial PCET with Y356, and a stacked conformation with Y730 to enable collinear PCET with this residue. Y356 and Y731 exhibit hydrogen-bonding interactions with interfacial water molecules and, in some conformations, share a bridging water molecule, suggesting that the primary proton acceptor for PCET from Y356 and from Y731 is interfacial water. The conformational flexibility of Y731 and the hydrogen-bonding interactions of both Y731 and Y356 with interfacial water and hydrogen-bonded water chains appear critical for effective radical translocation along the PCET pathway. These simulations are consistent with biochemical and spectroscopic data and provide previously unattainable atomic-level insights into the fundamental mechanism of RNR.

Nanoscale Dynamics and Transport in Highly Ordered Low-Dimensional Water.

Highly ordered and highly cooperative water with properties of both solid and liquid states has been observed by means of neutron scattering in hydrophobic one-dimensional channels with van der Waals diameter of 0.78 nm. We have found that in the initial stages of adsorption water molecules occupy niches close to pore walls, followed later by the filling of the central pore area. Intensified by confinement, intermolecular water interactions lead to the formation of well-ordered hydrogen-bonded water chains and to the onset of cooperative vibrations. On the other hand, the same intermolecular interactions lead to two relaxation processes, the faster of which is the spontaneous position exchange between two water molecules placed 3.2-4 Å from each other. Self-diffusion in an axial pore direction is the result of those spontaneous random exchanges and is substantially slower than the self-diffusion in bulk water.

Using Graphs of Dynamic Hydrogen-Bond Networks To Dissect Conformational Coupling in a Protein Motor.

DExD/H-box proteins are soluble enzymes that couple binding and hydrolysis of adenosine triphosphate (ATP) with reactions involving RNA metabolism or bind and push newly synthesized proteins across bacterial cell membranes. Knowledge of the reaction mechanism of these enzymes could help the development of new therapeutics. In order to explore the mechanism of long-distance conformational coupling in SecA, the DEAD-box motor of the Sec protein secretion in bacteria, we implemented algorithms that provide simplified graph representations of the protein's dynamic hydrogen-bond networks. We find that mutations near the nucleotide-binding site or changes of the nucleotide-binding state of SecA associate with altered dynamics at the preprotein binding domain and identify extended networks of hydrogen bonds that connect the active site of SecA to the region where SecA binds newly synthesized secretory proteins. Water molecules participate in hydrogen-bonded water chains that bridge functional domains of SecA and could contribute to long-distance conformational coupling.

Dynamic Water Hydrogen-Bond Networks at the Interface of a Lipid Membrane Containing Palmitoyl-Oleoyl Phosphatidylglycerol.

Lipid membrane interfaces are complex environments that host essential cellular processes such as binding of proteins or drug molecules. A key open question is how water molecules at the interface of membranes with anionic lipids participate in protein binding. To address this question, we studied the dynamics of water hydrogen bonding at the interface of membranes composed of phosphatidylcholine and phosphatidylglycerol, and implemented an algorithm to identify hydrogen-bonded networks at the interface of a lipid membrane, and to characterize their dynamics and linear connections. We find that the membrane interface is characterized by a rich network of hydrogen-bonded water chains that bridge lipid headgroups, some of which form transient lipid clusters. Water-mediated bridges between with lipid phosphate groups are dynamic, with residence lifetimes on the order of picoseconds. These clusters of water/lipid headgroup hydrogen bonds could provide a platform for the binding of proteins or of drug molecules with cationic groups.

Dissociation of Trifluoroacetic Acid in Amorphous Solid Water: Charge-Delocalized Hydroniums and Zundel Continuum Absorption

We studied the ionic dissociation of trifluoroacetic acid (TFA) in D2O amorphous solid water (ASW) using reflection absorption infrared spectroscopy, low-energy sputtering, and H/D isotopic exchange experiment. TFA readily dissociated to hydronium and counterions in ASW at 60 K, which indicates a significant increase in the acidity as compared with that in aqueous solution at room temperature. The acid dissociation produced a Zundel continuum band in the 1000–3000 cm–1 region and an accompanying lowered intensity of the O–D stretching band of D2O. The reduced intensity of D2O was several times larger than that expected for 1:1 stoichiometric proton transfer from TFA to water. Excess protons released from the acid migrated through as many as 20 water layers in ASW. These observations indicate that excess protons are highly mobile and dynamically delocalized in the hydrogen-bonded water chain. Such characteristics of excess protons may be responsible for the appearance of the Zundel continuum absorption.

Rectified Proton Grotthuss Conduction Across a Long Water-Wire in the Test Nanotube of the Polytheonamide B Channel.

A hydrogen-bonded water-chain in a nanotube is highly proton conductive, and examining the proton flux under electric fields is crucial to understanding the one-dimensional Grotthuss conduction. Here, we exploited a nanotube-forming natural product, the peptide polytheonamide B (pTB), to examine proton conduction mechanisms at a single-molecule level. The pTB nanotube has a length of ∼40 Å that spans the membrane and a uniform inner diameter of 4 Å that holds a single-file water-chain. Single-channel proton currents were measured using planar lipid bilayers in various proton concentrations and membrane potentials (±400 mV). We found, surprisingly, that the current-voltage curves were asymmetric with symmetric proton concentrations in both solutions across the membrane (rectification). The proton flux from the C-terminal to the N-terminal end was 1.6 times higher than that from the opposite. At lower proton concentrations, the degree of rectification was attenuated, but with the addition of a pH-buffer (dichloroacetate) that supplies protons near the entrance, the rectification emerged. These results indicate that the permeation processes inside the pore generate the rectification, which is masked at low concentrations by the diffusion-limited access of protons to the pore entrance. The permeation processes were characterized by a discrete-state Markov model, in which hops of a proton followed by water-chain turnovers were implemented. The optimized model revealed that the water-chain turnover exhibited unusual voltage dependence, and the distinct voltage-dependencies of the forward and backward transition rates yielded the rectification. The pTB nanotube serves as a rectified proton conductor, and the design principles can be exploited for proton-conducting materials.

Water Structure and Dynamics in Homochiral [Zn(l-L)(X)] Metal–Organic Frameworks

The structural, thermodynamic, and dynamical properties of water adsorbed in two homochiral metal–organic frameworks (MOFs) with general formula [Zn(l-L)(X)], X = Cl and Br, and L = 3-methyl-2-(pyridin-4-ylmethylamino)butanoic acid, are investigated through molecular dynamics simulations. Water molecules establish distinct hydrogen-bonding patterns within the pores of the two MOFs, which directly correlate with the strength of the underlying framework–water interactions. In particular, at low loading, the Zn–Cl groups of [Zn(l-L)(Cl)] effectively provide a templating scaffold for the formation of one-dimensional hydrogen-bonded water chains that propagate along the MOF channels following the helicity of the framework. In contrast, the relatively weaker framework–water interactions in [Zn(l-L)(Br)] lead to less ordered water distributions inside the pores. The simulation results are in agreement with the available experimental data and provide molecular-level insights into specific hydrogen-bonding motifs ...

Transport Properties of Carbon Nanotube Porins in Lipid Vesicles

Cells differ in their individual permeabilities depending on what lipids and proteins are present in the membrane and by regulating the number of channel proteins present in their system. The maintenance and regulation of ion gradients, specifically the electrochemical proton gradient, ΔμH+, across biological membranes has been established as a necessary intermediate in biological energy transduction that is crucial for proper cellular function. In recent years, artificial membrane channels have attracted much attention due to the key role of proton channels in performing a number of specific functions in different cells. Carbon nanotube (CNT) structures are similar to biological channels (e.g. aquaporins) with their smooth, narrow (ca. 1.5 nm), hydrophobic inner pores. The hydrophobic walls of the CNT facilitate the formation of 1D hydrogen bonded water chains and results in weak interactions with water molecules that enable nearly frictionless water transport. CNTs can provide a functional mimic of biological channels, and to that end we have created shortened CNT porins and investigated osmotically-driven transport of protons, ions and uncharged species through these pores. This presentation will discuss measurements of transport efficiency and transport selectivity in these biomimetic membrane channels and compare them with properties of biological ion channels.

3P223 チャネル内の水の水素結合鎖を介するプロトン透過の整流性(生体膜・人工膜 : 興奮・チャネル,ポスター,第52回日本生物物理学会年会(2014年度))

3P223 チャネル内の水の水素結合鎖を介するプロトン透過の整流性(生体膜・人工膜 : 興奮・チャネル,ポスター,第52回日本生物物理学会年会(2014年度))

Calculating Excited States of Molecular Aggregates by the Renormalized Excitonic Method

In this paper, we apply the recently developed ab initio renormalized excitonic method (REM) to the excitation energy calculations of various molecular aggregates, through the extension of REM to the time-dependent density functional theory (TDDFT). Tested molecular aggregate systems include one-dimensional hydrogen-bonded water chains, ring crystals with π-π stacking or van der Waals interactions, two dimensional benzene aggregates and the general aqueous systems with polar and nonpolar solutes. The basis set factor as well as the effect of the exchange-correlation functionals are also investigated. The results indicate that the REM-TDDFT method with suitable basis set and exchange-correlation functionals can give good descriptions of excitation energies and excitation area for lowest electronic excitations in the molecular aggregate systems with economic computational costs. It is shown that the deviations of REM-TDDFT excitation energies from those by standard TDDFT are much less than 0.1 eV and the computational time can be reduced by one order.

Supramolecular Synthons and Hydrates in Stabilization of Multicomponent Crystals of Nicotinamide and Isonicotinamide with N-Containing Aromatic Dicarboxylic Acids

Multicomponent crystals (either cocrystal or salt) of nicotinamide (nicotinic acid amide) and isonicotinamide with various nitrogen heterocycle-containing aromatic dicarboxylic acids, namely, 3,5-pyrazole dicarboxylic acid (pzdca), dipicolinic acid (dpa), and quinolinic acid (qna), have been synthesized and characterized by single-crystal diffraction and thermal studies. The nicotinamide (nic) and isonicotinamide (isonic) cocrystals with 3,5-pyrazole dicarboxylic acid (1 and 2, respectively) possess four different heteromeric supramolecular synthons in each cocrystal, which is rare. The nicotinamide dipicolinic acid cocrystal, 3, showed formation of water-bridged assembly, whereas isonicotinamide-dipicolinic acid cocrystal, 4, led to a six-component assembly through the isolated solvent water molecules occupying the interstitial positions. The salt formed from quinolinic acid with nicotinamide 5 has a hydrogen-bonded 1D water chain in its crystal lattice, whereas quinolinic acid with isonicotinamide resul...

Dielectric Properties of Water Chains Incorporated in Porous Coordination Polymer Crystal [Cu(C6H4NO2)2

Abstract The dielectric constant (ε) of “water chains” incorporated in the channel of porous coordination polymer crystal [Cu(C6H4NO2)2] was small at low temperatures (ε ≈ 10) but became as large as 250 at 370 K. These dielectric behaviors were consistent with the results of molecular dynamics simulation and indicated that a melting of hydrogen-bonded water chains occurred above 300 K.

Enhancement of Proton Conductance by Mutations of the Selectivity Filter of Aquaporin-1

Prevention of cation permeation in wild-type aquaporin-1 (AQP1) is believed to be associated with the Asn-Pro-Ala (NPA) region and the aromatic/arginine selectivity filter (SF) domain. Previous work has suggested that the NPA region helps to impede proton permeation due to the protein backbone collective macrodipoles that create an environment favoring a directionally discontinuous channel hydrogen-bonded water chain and a large electrostatic barrier. The SF domain contributes to the proton permeation barrier by a spatial restriction mechanism and direct electrostatic interactions. To further explore these various effects, the free-energy barriers and the maximum cation conductance for the permeation of various cations through the AQP1-R195V and AQP1-R195S mutants are predicted computationally. The cations studied included the hydrated excess proton that utilizes the Grotthuss shuttling mechanism, a model “classical” charge localized hydronium cation that exhibits no Grotthuss shuttling, and a sodium cation. The hydrated excess proton was simulated using a specialized multi-state molecular dynamics method including a proper physical treatment of the proton shuttling and charge defect delocalization. Both AQP1 mutants exhibit a surprising cooperative effect leading to a reduction in the free-energy barrier for proton permeation around the NPA region due to altered water configurations in the SF region, with AQP1-R195S having a higher conductance than AQP1-R195V. The theoretical predictions are experimentally confirmed in wild-type AQP1 and the mutants expressed in Xenopus oocytes. The combined results suggest that the SF domain is a specialized structure that has evolved to impede proton permeation in aquaporins.

Poly[[μ2-aqua-tetraaquadi-μ3-malonato-nickel(II)strontium(II)] dihydrate

The unit-cell parameters for the title mixed-metal coordination polymer, {[NiSr(C3H2O4)2(H2O)5]·2H2O}n, which is isostructural with its Co-containing analogue, were reported previously [Gil de Muro et al. (1999 ▶). Eur. J. Inorg. Chem. pp. 935–943]; the full crystal structure including a description of the hydrogen bonding is reported here. The Sr2+ ion is bonded to five O atoms from three different malonate dianions and four water mol­ecules, displaying a distorted tricapped trigonal–prismatic coordination geometry. Two malonate dianions, two water mol­ecules and one Ni2+ ion build up a dianionic [Ni(C3H2O4)2(H2O)2]2− unit incorporating a slightly distorted NiO6 octa­hedron, which coordinates to three nearby Sr2+ ions. This arrangement creates a metal-organic framework having a 20-membered ring with four Ni and six Sr atoms lying in the bc plane. The coordinated and uncoordinated water mol­ecules are responsible for the formation of two D5 hydrogen-bonded water chains within the 20-membered ring and they are linked into an R4 water cluster via two bifurcated O—H⋯(O,O) links.

Mechanisms of proton conduction and gating in influenza M2 proton channels from solid-state NMR.

The M2 protein of influenza viruses forms an acid-activated tetrameric proton channel. We used solid-state nuclear magnetic resonance spectroscopy to determine the structure and functional dynamics of the pH-sensing and proton-selective histidine-37 in M2 bound to a cholesterol-containing virus-envelope-mimetic membrane so as to better understand the proton conduction mechanism. In the high-pH closed state, the four histidines form an edge-face π-stacked structure, preventing the formation of a hydrogen-bonded water chain to conduct protons. In the low-pH conducting state, the imidazoliums hydrogen-bond extensively with water and undergo microsecond ring reorientations with an energy barrier greater than 59 kilojoules per mole. This barrier is consistent with the temperature dependence of proton conductivity, suggesting that histidine-37 dynamically shuttles protons into the virion. We propose a proton conduction mechanism in which ring-flip-assisted imidazole deprotonation is the rate-limiting step.

Effect of N-donor auxiliary ligands on the engineering of crystalline architectures of a series of lead(ii) complexes with 5-amino-2,4,6-triiodoisophthalic acid

The aqueous medium reactions of lead(II) nitrate with H2ATIBDC as a main ligand and bipy or biim as an auxiliary ligand lead to the two fascinating coordination polymers: [Pb(ATIBDC)(bipy)(H2O)]·3H2O (1) and [Pb(ATIBDC)(biim)]·H2O (2) [bipy = 2,2′-bipyridine, biim = 2,2′-biimidazole, and H2ATIBDC = 5-amino-2,4,6-triiodoisophthalic acid]. The interesting chiral three-dimensional (3D) network [Pb(ATIBDC)] (3) is obtained in the absence of any auxiliary ligands. Complex 1 is a one-dimensional (1D) helical chain, which further arrays into a 3D supramolecular metal–organic framework (MOF) with a 1D channel through the hydrogen-bonding and strong offset π⋯π stacking interactions. Furthermore, a 1D hydrogen-bonded helical water chain was found in 1. Interestingly, complex 1 exhibits reversible adsorption/desorption to water molecules. Framework 1 falls within the category of “recoverable collapsing” and “guest-induced re-formation” frameworks. Complex 2 features a fascinating 3D MOF. It displays a novel four-connected 4668-SOD (sodalite) zeotype network structure with 1D nanotubular channels. Complex 3 crystallizes in the chiral space group P31 and possesses a 3D honeycomb-like structure built up from a 1D Pb(II)-carboxylate-bridged helical chain with a 31 helix and ATIBDC2− ligand. The coordination modes of the ATIBDC2− ligand and crystalline architectures of the complexes are greatly dependent on the auxiliary ligands. The thermal stability and solid state fluorescent properties have been studied. Adsorption/desorption properties reveal that 2 may be used as an adsorbent material for some guest molecules. The study broadens the still very limited use of H2ATIBDC as a spacer and lead(II) ion for crystal engineering of MOFs with channels and cavities. These compounds represent the first examples of lead(II) complexes with H2ATIBDC.

A dry ligand-binding cavity in a solvated protein

Ligands usually bind to proteins by displacing water from the binding site. The affinity and kinetics of binding therefore depend on the hydration characteristics of the site. Here, we show that the extreme case of a completely dehydrated free binding site is realized for the large nonpolar binding cavity in bovine beta-lactoglobulin. Because spatially delocalized water molecules may escape detection by x-ray diffraction, we use water (17)O and (2)H magnetic relaxation dispersion (MRD), (13)C NMR spectroscopy, molecular dynamics simulations, and free energy calculations to establish the absence of water from the binding cavity. Whereas carbon nanotubes of the same diameter are filled by a hydrogen-bonded water chain, the MRD data show that the binding pore in the apo protein is either empty or contains water molecules with subnanosecond residence times. However, the latter possibility is ruled out by the computed hydration free energies, so we conclude that the 315 A(3) binding pore is completely empty. The apo protein is thus poised for efficient binding of fatty acids and other nonpolar ligands. The qualitatively different hydration of the beta-lactoglobulin pore and carbon nanotubes is caused by subtle differences in water-wall interactions and water entropy.