Hydrogen-bonded Water Chains Research Articles

Supramolecular Network via Hydrogen Bonding and π–π Stacking in 4,4′-Bipyridin-1-ium Perchlorate Dihydrate

The crystal structure of 4,4′-bipyridin-1-ium perchlorate dihydrate, [C10H9N2](ClO4) · 2H2O, is determined by room temperature X-ray diffraction. The compound crystallizes in the triclinic space group P-1 with a = 8.122(3) A, b = 9.726(3) A, c = 17.648(6) A, α = 78.181(4)°, β = 82.797(5)°, γ = 67.439(4)°, Z = 2, V = 1258.4(7) A3. In the compound, monoprotonated 4,4′-bipyridin-1-ium cations are self-assembled into supramolecular chains along the a-axis through N–H···N hydrogen bonds in a head-to-tail fashion. The chains are stacked via π–π stacking interactions to create two-dimensional sheets. The interlayer space is occupied by the hydrogen-bonded water chains that are linked to the organic sheets via C–H···O interactions and the perchlorate anions that are linked to the water chains and the organic sheets via O–H···O and C–H···O hydrogen bonds, respectively, thus generating a three-dimensional supramolecular architecture. Supramolecular Network via Hydrogen Bonding and π–π Stacking in 4,4′-Bipyridin-1-ium perchlorate dihydrate Jian-Yong Zhang, Ai-Ling Cheng and En-Qing Gao* Monoprotonated 4,4′-bipyridin-1-ium cations are self-assembled into supramolecular chains along the a-axis through N–H···N hydrogen bonds, and these chains are stacked via π–π stacking and hydrogen bond interactions involving water molecules and perchlorate anions.

Exploration on Regulating Factors for Proton Transfer along Hydrogen‐Bonded Water Chains

Proton transfer along a single-file hydrogen-bonded water chain is elucidated with a special emphasis on the investigation of chain length, side water, and solvent effects, as well as the temperature and pressure dependences. The number of water molecules in the chain varies from one to nine. The proton can be transported to the acceptor fragment through the single-file hydrogen-bonded water wire which contains at most five water molecules. If the number of water molecule is more than five, the proton is trapped by the chain in the hydroxyl-centered H(7)O(3) (+) state. The farthest water molecule involved in the formation of H(7)O(3) (+) is the fifth one away from the donor fragment. These phenomena reappear in the molecular dynamics simulations. The energy of the system is reduced along with the proton conduction. The proton transfer mechanism can be altered by excess proton. The augmentation of the solvent dielectric constant weakens the stability of the system, but favors the proton transfer. NMR spin-spin coupling constants can be used as a criterion in judging whether the proton is transferred or not. The enhancement of temperature increases the thermal motion of the molecule, augments the internal energy of the system, and favors the proton transfer. The lengthening of the water wire increases the entropy of the system, concomitantly, the temperature dependence of the Gibbs free energy increases. The most favorable condition for the proton transfer along the H-bonded water wire is the four-water contained chain with side water attached near to the acceptor fragment in polar solvent under higher temperature.

Electrochemical Concerted Proton and Electron Transfers. Further Insights in the Reduction Mechanism of Superoxide Ion in the Presence of Water and Other Weak Acids

Deciphering of the role of water (or other weak acids) in the reduction of superoxide is based on three observations: (i) very large peak potential shifts (and hence a large increase of the apparent standard rate constant) associated with the reaction O2•----H2O + e- → -O2H---OH- upon addition of water (or methanol, or 2-propanol) to the acetonitrile solution; (ii) increase of the hydrogen/deuterium isotope effect with water concentration; (iii) the fact that the positive shift of the peak potential (or equivalently the increase of the standard reduction rate constant) is larger with methanol than with water. Mere invocation of specific solvation by water (or the other weak acids) of the reduction products cannot explain these facts. They instead reveal that short hydrogen-bonded water chains, involving approximately three water molecules, are involved in the concerted proton−electron transfer process, thus providing a preliminary picture of the mechanisms operating in pure water or other H-bonding and H...

Energy Transduction: Proton Transfer Through the Respiratory Complexes

A series of metalloprotein complexes embedded in a mitochondrial or bacterial membrane utilize electron transfer reactions to pump protons across the membrane and create an electrochemical potential (DeltamuH+). Current understanding of the principles of electron-driven proton transfer is discussed, mainly with respect to the wealth of knowledge available from studies of cytochrome c oxidase. Structural, experimental, and theoretical evidence supports the model of long-distance proton transfer via hydrogen-bonded water chains in proteins as well as the basic concept that proton uptake and release in a redox-driven pump are driven by charge changes at the membrane-embedded centers. Key elements in the pumping mechanism may include bound water, carboxylates, and the heme propionates, arginines, and associated water above the hemes. There is evidence for an important role of subunit III and proton backflow, but the number and nature of gating mechanisms remain elusive, as does the mechanism of physiological control of efficiency.

Tetrahedral structure or chains for liquid water.

It has been suggested, based on x-ray absorption spectroscopy (XAS) experiments on liquid water [Wernet, Ph., et al. (2004) Science 304, 995-999], that a condensed-phase water molecule's asymmetric electron density results in only two hydrogen bonds per water molecule on average. The larger implication of the XAS interpretation is that the conventional view of liquid water being a tetrahedrally coordinated random network is now replaced by a structural organization that instead strongly favors hydrogen-bonded water chains or large rings embedded in a weakly hydrogen-bonded disordered network. This work reports that the asymmetry of the hydrogen density exhibited in the XAS experiments agrees with reported x-ray scattering structure factors and intensities for Q > 6.5 A(-1). However, the assumption that the asymmetry in the hydrogen electron density does not fluctuate and is persistent in all local molecular liquid water environments is inconsistent with longer-ranged tetrahedral network signatures present in experimental x-ray scattering intensity and structure factor data for Q < 6.5 A(-1).

Water Chain Formation and Possible Proton Pumping Routes inRhodobacter sphaeroidesCytochromecOxidase: A Molecular Dynamics Comparison of the Wild Type and R481K Mutant

Cytochrome c oxidase (CcO) converts the energy from redox and oxygen chemistry to support proton translocation and create a transmembrane DeltamuH(+) used for ATP production. Molecular dynamics (MD) simulations were carried out to probe for the formation water chains capable of participating in proton translocation. Attention was focused on the region between and above the a and a(3) hemes where well-defined water chains have not been identified in crystallographic studies. An arginine (R481) (Rhodobacter sphaeroides numbering), positioned between the D-propionates of the hemes, had been mutated in vivo to lysine and showed to have altered activity consistent with an altered proton conductance [Qian, J., Mills, D. A., Geren, L., Wang, K. F., Hoganson, C. W., Schmidt, B., Hiser, C., Babcock, G. T., Durham, B., Millett, F., and Ferguson-Miller, S. (2004) Role of the conserved arginine pair in proton and electron transfer in cytochrome c oxidase, Biochemistry 43, 5748-5756; also see the accompanying paper by Mills et al.]. This mutant was created in silico, and the MD results for the mutant and wild type were compared to explore the effects on the formation of hydrogen-bonded water chains by this mutation. The simulations reveal the presence of hydrogen-bonded water chains that lead from E286 through the region above the hemes to the Mg(2+), and from E286 to the heme a(3) D-propionate and the binuclear center. The R481K mutant does not form as many, or as extensive, water chains as wild-type CcO, due to a new conformation of residues in a large loop between helices III and IV in subunit I, indicating a reduction in the level of water chain formation in the mutant. This loop appears to play a role in controlling the formation of hydrogen-bonded water chains above the hemes. The results suggest a possible gating mechanism for proton movement that includes key residues W172 and Y175 on the loop and F282 on helix VI.

A New Conformation of a Water Hexamer Chain and its Reversible Formation/Removal in the Host Channel by Gas–Solid Reaction

A new type of cyclic water hexamer chain was found to occupy the host channel of a supramolecule, formulated as [Zn(bdc)en·3(H2O)] n (1) [H2bdc=1,3-benzenedicarboxylic acid; en=ethylenediamine] and characterized by X-ray crystallography. As each water molecule was only involved in hydrogen bonding, facile removal of the lattice water was anticipated. The hydrogen-bonded water chain was completely removed by heating 1 at 96°C, forming the dehydrated solid [Zn(bdc)en] n (2). Interestingly, complex 1 can be regenerated in water vapor by a gas–solid reaction.

Structural and Kinetic Characterization of Active-Site Histidine as a Proton Shuttle in Catalysis by Human Carbonic Anhydrase II,

In the catalysis of the hydration of carbon dioxide and dehydration of bicarbonate by human carbonic anhydrase II (HCA II), a histidine residue (His64) shuttles protons between the zinc-bound solvent molecule and the bulk solution. To evaluate the effect of the position of the shuttle histidine and pH on proton shuttling, we have examined the catalysis and crystal structures of wild-type HCA II and two double mutants: H64A/N62H and H64A/N67H HCA II. His62 and His67 both have their side chains extending into the active-site cavity with distances from the zinc approximately equivalent to that of His64. Crystal structures were determined at pH 5.1-10.0, and the catalysis of the exchange of (18)O between CO(2) and water was assessed by mass spectrometry. Efficient proton shuttle exceeding a rate of 10(5) s(-)(1) was observed for histidine at positions 64 and 67; in contrast, relatively inefficient proton transfer at a rate near 10(3) s(-)(1) was observed for His62. The observation, in the crystal structures, of a completed hydrogen-bonded water chain between the histidine shuttle residue and the zinc-bound solvent does not appear to be required for efficient proton transfer. The data suggest that the number of intervening water molecules between the donor and acceptor supporting efficient proton transfer in HCA II is important, and furthermore suggest that a water bridge consisting of two intervening water molecules is consistent with efficient proton transfer.

A molecular dynamics study of water chain formation in the proton-conducting K channel of cytochrome c oxidase

The formation of water chains in cytochrome c oxidase (CcO) is studied by molecular dynamics (MD). Focus is on water chains in the K channel that can supply a proton to the binuclear center (the heme a 3 Fe/Cu B region), the site of O 2 reduction. By assessing the presence of chains of any length on a short time scale (0.1 ps), a view of the kinds of chains and their persistence is obtained. Chains from the entry of the channel on the inner membrane to Thr359 ( Rhodobacter sphaeroides numbering) are often present but are blocked at that point until a rotation of the Thr359 side chain occurs, permitting formation of chains from Thr359 towards the binuclear center. No continuous hydrogen-bonded water chains are found connecting Thr359 and the binuclear center. Instead, waters hydrogen bond from Thr359 to the hydroxyl of the heme a 3 farnesyl and then continue to the binuclear center via Tyr288, which has been identified as a source of a proton for O 2 reduction. Three hydrogen-bonded waters are found to be present in the binuclear center after a sufficiently long simulation time. One is ligated to the Cu B and could be associated with a water (or hydroxyl) identified in the crystal structure as the fourth ligand of Cu B. The water hydrogen-bonded to the hydroxyl of Tyr288 is extremely persistent and well positioned to participate in O 2 reduction. The third water is located where O 2 is often suggested to reside in mechanistic studies of O 2 reduction.

A temperature-dependent Hartree approach for excess proton transport in hydrogen-bonded chains

We develop a temperature-dependent Hartree (TeDH) approach to solving the N-dimensional Schrödinger equation, based on the time-dependent Hartree (TDH) approximation. The goal is to describe the dynamics of protonated hydrogen-bonded water chains in condensed phases, where the medium fluctuations drive the proton transfer. An adiabatic simulation method (ASM) that couples the TeDH wavefunction to classical molecular dynamics (MD) propagation is used to obtain the real-time dynamics of the quantum protons that interact with the nuclear degrees of freedom. Iteration of the TeDH-ASM provides a trajectory from which the quantum dynamics of the protonated chains can be obtained. The method is applied to proton transfer in cytochrome c oxidase (CcO), which has a glutamate residue whose carboxylate may become protonated, as part of the mechanism of proton translocation. By using MD, we find that this glutamate can be hydrogen bonded to two water molecules in a cyclic structure. Application of the TeDH-ASM shows that a proton can transfer from one of the hydrogen-bonded waters to protonate this glutamate.

The Mechanism of Proton Exclusion in the Aquaporin-1 Water Channel

Aquaporins are efficient, yet strictly selective water channels. Remarkably, proton permeation is fully blocked, in contrast to most other water-filled pores which are known to conduct protons well. Blocking of protons by aquaporins is essential to maintain the electrochemical gradient across cellular and subcellular membranes. We studied the mechanism of proton exclusion in aquaporin-1 by multiple non-equilibrium molecular dynamics simulations that also allow proton transfer reactions. From the simulations, an effective free energy profile for the proton motion along the channel was determined with a maximum-likelihood approach. The results indicate that the main barrier is not, as had previously been speculated, caused by the interruption of the hydrogen-bonded water chain, but rather by an electrostatic field centered around the fingerprint Asn-Pro-Ala (NPA) motif. Hydrogen bond interruption only forms a secondary barrier located at the ar/R constriction region. The calculated main barrier height of 25–30 kJ mol −1 matches the barrier height for the passage of protons across pure lipid bilayers and, therefore, suffices to prevent major leakage of protons through aquaporins. Conventional molecular dynamics simulations additionally showed that negatively charged hydroxide ions are prevented from being trapped within the NPA region by two adjacent electrostatic barriers of opposite polarity.

Water-chain clusters: Vibronic spectra of 7-hydroxyquinoline⋅(H2O)2

Mass- and isomer-selected S1←S0 resonant two-photon ionization and S1→S0 fluorescence spectra were obtained for the supersonically cooled 7-hydroxyquinoline⋅(H2O)2 cluster. UV/UV-holeburning measurements show that &amp;gt;98% of the spectrum is due to a single “water-chain” cluster isomer, although two different tautomers (7-keto- and 7-hydroxyquinoline), two different rotamers (cis- and trans-hydroxy), and two torsional conformers of the chain are possible. Ab initio calculations of structures and vibrations of five different tautomers/ rotamers/ conformers of this cluster are reported. These predict that the cis-7-hydroxyquinoline⋅(H2O)2 “up/down” water-chain form is the most stable cluster. The experimentally observed S0 and S1 state vibrational frequencies agree well with those calculated for this isomer. We find no evidence for either the trans-rotamer or the keto tautomer clusters. S1←S0 excitation leads to contraction of all three hydrogen-bonds along the hydrogen-bonded water chain, inducing intermolecular stretching vibrations, but no proton transfer.

In Rhodobacter sphaeroides reaction centers, mutation of proline L209 to aromatic residues in the vicinity of a water channel alters the dynamic coupling between electron and proton transfer processes.

The X-ray crystallographic structure of the photosynthetic reaction center from Rhodobacter sphaeroides obtained at high resolution has revealed a number of internal water molecules (Ermler, U., Fritzsch, G., Buchanan, S. K., and Michel, H. (1994) Structure 2, 925-936; Stowell, M. H. B., McPhillips, T. M., Rees, D. C., Soltis, S. M., Abresch, E., and Feher, G. (1997) Science 276, 812-816). Some of them are organized into distinct hydrogen-bonded water chains that connect Q(B) (the terminal quinone electron acceptor of the reaction center) to the aqueous phase. To investigate the role of the water chains in the proton conduction process, proline L209, located immediately adjacent to a water chain, was mutated to the following residues: F, Y, W, E, and T. We have first analyzed the effects of the mutations on the kinetic and thermodynamic properties of the rate constants of the second electron transfer (k(AB)(2)) and of the coupled proton uptake (k(H)+) at the second flash. In all aromatic mutants, k(AB)(2) and k(H)+ are notably and concomitantly decreased compared to the wild-type, while no effect is observed in the other mutants. The temperature dependence of these rates shows activation energy values (DeltaH) similar for the proton and electron-transfer processes in the wild-type and in most of the mutants, except for the L209PW and L209PF mutants. The analysis of the enthalpy factors related to the electron and proton-transfer processes in the L209PF and the L209PW mutants allows to distinguish the respective effects of the mutations for both transfer reactions. It is noteworthy that in the aromatic mutants a substantial increase of the free energies of activation is observed (DeltaG(L209PY) < DeltaG(L209PF) < DeltaG(L209PW)) for both proton and electron-transfer reactions, while in the other mutants, DeltaG is not affected. The salt concentration dependence of k(AB)(2) shows, in the L209PF and L209PW mutants, a higher screening of the protein surface potential experienced by Q(B). Our data suggest that residues F and W in position L209 increase the polarizability of the internal water molecules and polar residues by altering the organization of the hydrogen-bond network. We have also analyzed the rates of the first electron-transfer reaction (k(AB)(1)), in the 100 micros time domain. These kinetics have previously been shown to reflect protein relaxation events possibly including proton uptake events (Tiede, D. M., Vazquez, J., Cordova, J., and Marone, P. M. (1996) Biochemistry 35, 10763-10775). Interestingly, in the L209PF and L209PW mutants, k(AB)(1) is notably decreased in comparison to the wild type and the other mutants, in a similar way as k(AB)(2) and k(H)+. Our data imply that the dynamic organization of this web is tightly coupled to the electron transfer process that is kinetically limited by protonation events and/or conformational rearrangements within the protein.

Free Energy Profiles for H + Conduction along Hydrogen-Bonded Chains of Water Molecules

The molecular mechanism for proton conduction along hydrogen-bonded chains, or “proton wires,” is studied with free energy simulations. The complete transport of a charge along a proton wire requires two complementary processes: 1) translocation of an excess proton (propagation of an ionic defect), and 2) reorientation of the hydrogen-bonded chain (propagation of a bonding defect). The potential of mean force profile for these two steps is computed in model systems comprising a single-file chain of nine dissociable and polarizable water molecules represented by the PM6 model of Stillinger and co-workers. Results of molecular dynamics simulations with umbrella sampling indicate that the unprotonated chain is preferably polarized, and that the inversion of its total dipole moment involves an activation free energy of 8 kcal/mol. In contrast, the rapid translocation of an excess H + across a chain extending between two spherical solvent droplets is an activationless process. These results suggest that the propagation of a bonding defect constitutes a limiting step for the passage of several protons along single-file chains of water molecules, whereas the ionic translocation may be fast enough to occur within the lifetime of transient hydrogen-bonded water chains in biological membranes.

Proton Transfer in the Enzyme Carbonic Anhydrase: An ab Initio Study

Ab initio calculations have been performed to probe possible proton-transfer pathways in carbonic anhydrase. It is found that the proton transfer in the dehydration direction involves an energy barrier of around 8−10 kcal/mol, which agrees well with experiment, while the proton-transfer barrier in the hydration (away from zinc) direction is sensitive to the histidine ligand bonding around the Zn ion. The water ligand dependence of the proton-transfer energy barrier reveals a requirement of certain hydrogen bond formation in the active site. Preliminary studies involving two and three proton transfers through hydrogen-bonded water chains show that the donor−acceptor distance and the water chain motion are crucial to the proton-transfer energetics. On the basis of these results, a picture of the proton-transfer energetics and mechanism is presented and the effect of the His-64 ligand on the process is discussed.

Structure and dynamics of a proton wire: a theoretical study of H+ translocation along the single-file water chain in the gramicidin A channel

The rapid translocation of H+ along a chain of hydrogen-bonded water molecules, or proton wire, is thought to be an important mechanism for proton permeation through transmembrane channels. Computer simulations are used to study the properties of the proton wire formed by the single-file waters in the gramicidin A channel. The model includes the polypeptidic dimer, with 22 water molecules and one excess proton. The dissociation of the water molecules is taken into account by the "polarization model" of Stillinger and co-workers. The importance of quantum effects due to the light mass of the hydrogen nuclei is examined with the use of discretized Feynman path integral molecular dynamics simulations. Results show that the presence of an excess proton in the pore orients the single-file water molecules and affects the geometry of water-water hydrogen bonding interactions. Rather than a well-defined hydronium ion OH3+ in the single-file region, the protonated species is characterized by a strong hydrogen bond resembling that of O2H5+. The quantum dispersion of protons has a small but significant effect on the equilibrium structure of the hydrogen-bonded water chain. During classical trajectories, proton transfer between consecutive water molecules is a very fast spontaneous process that takes place in the subpicosecond time scale. The translocation along extended regions of the chain takes place neither via a totally concerted mechanism in which the donor-acceptor pattern would flip over the entire chain in a single step, nor via a succession of incoherent hops between well-defined intermediates. Rather, proton transfer in the wire is a semicollective process that results from the subtle interplay of rapid hydrogen-bond length fluctuations along the water chain. These rapid structural fluctuations of the protonated single file of waters around an average position and the slow movements of the average position of the excess proton along the channel axis occur on two very different time scales. Ultimately, it is the slow reorganization of hydrogen bonds between single-file water molecules and channel backbone carbonyl groups that, by affecting the connectivity and the dynamics of the single-file water chain, also limits the translocation of the proton across the pore.

Theoretical Study of H+Translocation along a Model Proton Wire

The mechanism of proton translocation along linear hydrogen-bonded water chains is investigated. Classical and discretized Feynman path integral molecular dynamics simulations are performed on protonated linear chains of 4, 5, and 9 water molecules. The dissociable and polarizable water model PM6 of Stillinger and co-workers is used to represent the potential energy surface of the systems. The simulations show that quantum and thermal effects are both important because the height of the barriers opposing proton transfer are strongly coupled to the configuration of the chain, which is, in turn, affected by the presence of an excess proton. For characterization of the quantum effects, the energy levels of the hydrogen nucleus located at the center of a protonated tetrameric water chain are calculated by solving the Schroedinger equation for an ensemble of configurations which were generated with path integral simulations. Analysis shows that the first excitation energies are significantly larger than the thermal energy kBT and that quantum effects are dominated by the zero-point energy of the proton. The quantum correlations between the different proton nuclei are found to be negligibly small, suggesting that an effective one-particle description could be valid. Potential of mean force surfaces for proton motion in relation to the donor−acceptor separation are calculated with classical and path integral simulations for tetrameric and pentameric water chains. The mechanism for long-range proton transfer is illustrated with a simulation of a hydrogen-bonded chain of nine water molecules. During the simulation, cooperative fluctuations which modulate the asymmetry of the chain enable the spontaneous translocation of protons over half of the length of the chain.

A model for passive transport of H + and OH − across lipid membranes

Hydrogen bonded water chains as H + and OH − channels through lipid bilayers have been reexamined. The water concentration in the hydrocarbon layer as inferred from the permeability to water is sufficiently high to yield an adequate concentration of water chains spanning the hydrocarbon layer. The zwitterionic water chain with an H + attached on one side of the hydrocarbon layer and an OH − on the other side is suggested to be the effective H +/OH − channel. It is energetically more stable than the channel with one charge only adsorbed and its permeability to H + and OH − is higher.

A model for passive transport of H + and OH − across lipid membranes

Hydrogen bonded water chains as H + and OH − channels through lipid bilayers have been reexamined. The water concentration in the hydrocarbon layer as inferred from the permeability to water is sufficiently high to yield an adequate concentration of water chains spanning the hydrocarbon layer. The zwitterionic water chain with an H + attached on one side of the hydrocarbon layer and an OH − on the other side is suggested to be the effective H +/OH − channel. It is energetically more stable than the channel with one charge only adsorbed and its permeability to H + and OH − is higher.

Proton/hydroxide conductance through phospholipid bilayer membranes: effects of phytanic acid

Mechanisms of proton/hydroxide conductance ( G H/OH ) were investigated in planar (Mueller-Rudin) bilayer membranes made from decane solutions of phospholipids or phospholipids plus phytanic acid (a 20-carbon, branched chain fatty acid). At neutral pH, membranes made from diphytanoylphosphatidylcholine or bacterial phosphatidylethanolamine had G H/OH values in the range of (2–5) · 10 −9 S · cm −2 , corresponding to H +/OH − ‘net’ permeabilities of about (0.4–1.0) · 10 −5 cm · s −1 . G H/OH was inhibited by serum albumin, phloretin, glycerol and low pH, but was increased by chlorodecane and voltage > 80 mV . Water permeability and G H/OH were not correlated, suggesting that water and H +/OH − cross the membrane by separate pathways. Addition of phytanic acid to the phospholipids caused an increase in G H/OH which was proportional to the first power of the phytanic acid concentration. In membranes containing phytanic acid, G H/OH was inhibited by albumin, phloretin, glycerol and low pH, but was increased by chlorodecane and voltages > 80 mV . The results suggest that phytanic acid acts as a simple (A − type) proton carrier. The qualitative similarities between the behavior of G H/OH in unmodified and phytanic-acid containing membranes suggest that phospholipids may contain weakly acidic contaminants which cause most of G H/OH at pH > 4 . However, there is also a significant background (pH independent) G H/OH which may be due to hydrogen-bonded water chains. The ability of phytanic acid to act as a proton carrier may help to explain the toxicity of phytanic acid in Refsum's disease, a metabolic disorder in which phytanic acid accumulates to high levels in plasma, cells and tissues.