Chains Of Hydrogen-bonded Water Molecules Research Articles

Mixed Molecular and Dissociative Water Adsorption on Hydroxylated TiO2(110): An Infrared Spectroscopy and Ab Initio Molecular Dynamics Study

We have investigated the structure and dynamics of water (D2O) adsorbed on TiO2(110) for coverages between 0 and 1 monolayer (ML) with infrared reflection absorption spectroscopy and ab initio molecular dynamics (AIMD) simulations. For D2O coverages as low as 0.4 ML on a hydroxylated surface, IR spectra typical of hydrogen-bonded chains of water molecules are observed. However, for D2O coverages ≥0.3 ML, a sharp, high-frequency peak is also observed in the p-polarized spectra that is red-shifted relative to the bridging hydroxyl peak. This new peak is not observed for water adsorbed on an oxidized surface. Based on the AIMD simulations and comparisons with previous IR spectra for TiO2 nanoparticles, the new peak is assigned to terminal hydroxyl groups produced by dissociative adsorption of some of the water on TiO2(110). The simulations indicate that water dissociation is related to the presence of defect electrons in the system, but not due to direct interactions between adsorbed water and bridging hydroxyls.

Crystalline Forms of Trazodone Dihydrates.

In this study, treatment of anhydrous trazodone powder with ammonium carbamate in warm water crystallised two new polymorphs or dihydrates of trazodone after 5 h, whose structures were determined by X-ray single crystal diffraction. Each dihydrate contains infinite zigzag hydrogen-bonded chains of water molecules, which are stabilised by the N4 acceptor atom of the piperazine ring and the pendant carbonyl O1 atom of the triazole ring, as well as other water molecules. The strong dipole moment expected for the O1 atom makes it a good hydrogen bond acceptor for stabilising the chains of water molecules. Each molecule of trazodone has a similar conformation in both hydrates, except for the propyl chains, which adopt different conformations: anti-gauche in the β hydrate (triazole N-C-C-C and C-C-C-piperazine N) and anti-anti in the γ hydrate. Both piperazine rings adopt chair conformations, and the exocyclic N-C bonds are in equatorial orientations. The Hirshfeld surfaces and two-dimensional fingerprint plots for the polymorphs were calculated using CrystalExplorer17, which indicated contacts significantly shorter than the sum of the van der Waals radii in the vicinity of the piperazine N4 and triazole O1 atoms corresponding to the strong hydrogen bonds accepted by these atoms.

Formation of a Stable Bridge between Two Disjoint Nanotubes with Single-File Chains of Water.

It was recently demonstrated that stable water bridges can form between two relatively large disjoint nanochannels, such as carbon nanotubes (CNTs), under an applied pressure drop. Such bridges are relevant to fabrication of nanostructured materials, drug delivery, water desalination devices, hydrogen fuel cells, dip-pen nanolithography, and several other applications. If the nanotubes are small enough, however, then one has only single-file hydrogen-bonded chains of water molecules. The distribution of water in such nanotubes manifests unusual physical properties that are attributed to the low number of hydrogen bonds (HBs) formed in the channel since, on average, each water molecule in a single-file chain forms only 1.7 HBs, almost half of the value for bulk water. Using extensive molecular dynamics simulations, we demonstrate that stable bridges can form even between two small disjoint CNTs that contain single-file chains of water. The structure, stability, and properties of such bridges and their dependence on the applied pressure drop and the length of the gap between the two CNTs are studied in detail, as is the distribution of the HBs. We demonstrate, in particular, that the efficiency of flow through the bridge is at maximum at a specific pressure difference.

N,N'-Bis(pyridin-3-ylmeth-yl)ethanedi-amide monohydrate: crystal structure, Hirshfeld surface analysis and computational study.

The mol-ecular structure of the title bis-pyridyl substituted di-amide hydrate, C14H14N4O2·H2O, features a central C2N2O2 residue (r.m.s. deviation = 0.0205 Å) linked at each end to 3-pyridyl rings through methyl-ene groups. The pyridyl rings lie to the same side of the plane, i.e. have a syn-periplanar relationship, and form dihedral angles of 59.71 (6) and 68.42 (6)° with the central plane. An almost orthogonal relationship between the pyridyl rings is indicated by the dihedral angle between them [87.86 (5)°]. Owing to an anti disposition between the carbonyl-O atoms in the core, two intra-molecular amide-N-H⋯O(carbon-yl) hydrogen bonds are formed, each closing an S(5) loop. Supra-molecular tapes are formed in the crystal via amide-N-H⋯O(carbon-yl) hydrogen bonds and ten-membered {⋯HNC2O}2 synthons. Two symmetry-related tapes are linked by a helical chain of hydrogen-bonded water mol-ecules via water-O-H⋯N(pyrid-yl) hydrogen bonds. The resulting aggregate is parallel to the b-axis direction. Links between these, via methyl-ene-C-H⋯O(water) and methyl-ene-C-H⋯π(pyrid-yl) inter-actions, give rise to a layer parallel to (10); the layers stack without directional inter-actions between them. The analysis of the Hirshfeld surfaces point to the importance of the specified hydrogen-bonding inter-actions, and to the significant influence of the water mol-ecule of crystallization upon the mol-ecular packing. The analysis also indicates the contribution of methyl-ene-C-H⋯O(carbon-yl) and pyridyl-C-H⋯C(carbon-yl) contacts to the stability of the inter-layer region. The calculated inter-action energies are consistent with importance of significant electrostatic attractions in the crystal.

Hydrogen bonding structure of confined water templated by a metal-organic framework with open metal sites

Water in confinement exhibits properties significantly different from bulk water due to frustration in the hydrogen-bond network induced by interactions with the substrate. Here, we combine infrared spectroscopy and many-body molecular dynamics simulations to probe the structure and dynamics of confined water as a function of relative humidity within a metal-organic framework containing cylindrical pores lined with ordered cobalt open coordination sites. Building upon the agreement between experimental and theoretical spectra, we demonstrate that water at low relative humidity binds initially to open metal sites and subsequently forms disconnected one-dimensional chains of hydrogen-bonded water molecules bridging between cobalt atoms. With increasing relative humidity, these water chains nucleate pore filling, and water molecules occupy the entire pore interior before the relative humidity reaches 30%. Systematic analysis of rotational and translational dynamics indicates heterogeneity in this pore-confined water, with water molecules displaying variable mobility as a function of distance from the interface.

C-H···O Hydrogen Bond Anchored Water Bridge in 1,2,4,5-Tetracyanobenzene-Water Clusters.

The hydrogen-bonded chain of water molecules is known to play a very important role in proton/H transfer in chemistry and biology. This kind of water chain mainly starts from a conventional hydrogen bond (HB) donor/acceptor site. Here, we report the experimental evidence of water chain formation on an unconventional C-H HB donor site in 1,2,4,5-tetracyanobenzene (TCNB). Laser-induced fluorescence (LIF) spectra and fluorescence dip IR (FDIR) spectra of 1: n ( n = 1-3) clusters of TCNB with water prepared in a supersonic molecular jet are presented. Quantum chemical calculations of several intuitive conformers of 1: n ( n = 1-3) clusters were performed, and the computed IR spectra were compared with the experimental FDIR spectra in order to get the structural information on the experimentally observed clusters. We find that the first water molecule binds to the C-H moiety of TCNB (1:1 cluster) and the subsequent water molecules form a water chain (1:2 and 1:3 clusters) that constitutes a bridge between the C-H and the proximal -CN moiety of TCNB, forming a cyclic ring structure. NBO calculations show that upon addition of water molecules significant change in the charge distribution takes place, mainly on the atoms which are involved in cyclic ring structure. This redistribution of charges causes a cooperativity effect in the higher water clusters of TCNB.

Crystal structure of a pyrazine-2,3-dicarboxamide ligand and of its silver(I) nitrate complex, a three-dimensional coordination polymer.

The title ligand, C18H16N6O2·2H2O (L1) [N2,N3-bis-(pyridin-4-ylmeth-yl)pyrazine-2,3-dicarboxamide], crystallized as a dihydrate. The mol-ecule is U-shaped with the carboxamide groups being cis to one another, making a dihedral angle of 81.6 (5)°. The terminal pyridine rings are inclined to one another by 58.5 (4)°. There is an intra-molecular N-H⋯Npyrazine hydrogen bond present, forming an S(5) ring motif. In the crystal, adjacent mol-ecules are linked by N-H⋯Ocarboxamide hydrogen bonds, forming a chain along [001]. A chain of hydrogen-bonded water mol-ecules is linked to the chain of (L1) mol-ecules by O-H⋯N hydrogen bonds, forming columns propagating along the c axis. The columns are linked by C-H⋯O and C-H⋯N hydrogen bonds, forming a three-dimensional supra-molecular structure. The reaction of ligand (L1) with silver(I) nitrate led to the formation of a new three-dimensional coordination polymer, {[Ag(C18H16N6O2)]NO3} n , poly[[[μ4-N2,N3-bis-(pyridin-4-ylmeth-yl)pyrazine-2,3-dicarboxamide]-silver(I)] nitrate] (I). The asymmetric unit is composed of half of one silver ion, located on a twofold rotation axis, half a ligand mol-ecule and half a positionally disordered nitrate anion located about a twofold rotation axis. The full mol-ecule of the ligand is generated by twofold rotational symmetry, with this twofold axis bis-ecting the Car-Car bonds of the pyrazine ring and the Ag-Ag bond. The carboxamide groups are now trans to one another, making a dihedral angle of 65.8 (4)°. The two terminal pyridine rings are inclined to one another by 6.6 (3)°. Two ligands wrap around an Ag-Ag bond of 3.1638 (11) Å, forming a figure-of-eight-shaped complex mol-ecule. Each silver ion is coordinated by two pyridine N atoms and by two carboxamide O atoms of neighbouring mol-ecules, hence forming a three-dimensional framework. The nitrate anion is linked to the framework by N-H⋯O and C-H⋯O hydrogen bonds.

Hydrogen-Stuffed, Quartz-like Water Ice.

Through use of in situ Raman spectroscopy and single-crystal/powder X-ray diffraction, we resolve the "C0" phase structure discovered recently in the H2 + H2O system. This phase forms at ∼400 MPa and 280 K with the nominal composition (H2O)2H2 and three formula units per unit cell. The hexagonal structure is chiral, consisting of interpenetrating spiral chains of hydrogen-bonded water molecules and rotationally disordered H2 molecules, and shows topological similarities with the mineral quartz. Like other clathrate hydrates and forms of ice, the protons of H2O molecules within C0 are disordered. The large zeolite-like channels accommodate significant amounts of hydrogen (5.3% by weight) in a unique hydrogen-bonded lattice, which might be applicable to the thermodynamic conditions found on icy planetary bodies.

Ultrafast proton transport in sub-1-nm diameter carbon nanotube porins.

Proton transport plays an important role in many biological processes due to the ability of protons to rapidly translocate along chains of hydrogen-bonded water molecules. Molecular dynamics simulations have predicted that confinement in hydrophobic nanochannels should enhance the rate of proton transport. Here, we show that 0.8-nm-diameter carbon nanotube porins, which promote the formation of one-dimensional water wires, can support proton transport rates exceeding those of bulk water by an order of magnitude. The transport rates in these narrow nanotube pores also exceed those of biological channels and Nafion. With larger 1.5-nm-diameter nanotube porins, proton transport rates comparable to bulk water are observed. We also show that the proton conductance of these channels can be modulated by the presence of Ca(2+) ions. Our results illustrate the potential of small-diameter carbon nanotube porins as a proton conductor material and suggest that strong spatial confinement is a key factor in enabling efficient proton transport.

Ultra-Fast Proton Transport in Sub-1-nm Diameter Carbon Nanotube Porins

Proton transport plays a key role in many biological processes due to the proton's ability to rapidly translocate along the chains of hydrogen-bonded water molecules. Molecular dynamics simulations have predicted that confinement in hydrophobic nanochannels should enhance the rate of proton transport. We demonstrate that 0.8 nm diameter carbon nanotube porins, which promote formation of true one- dimensional water wires, support proton transport with rates exceeding those in bulk water by an order of magnitude. Proton transport rates in these narrow CNT pores also exceed those of biological channels and Nafion. Surprisingly, the larger 1.5 nm diameter nanotube porins still showed proton transport rates comparable to bulk water. This work establishes small diameter CNT porins as a promising membrane proton conductor material and points to strong spatial confinement as a key factor in enabling efficient proton transport.

Density functional theory meta-GGA + U study of water incorporation in the metal-organic framework material Cu-BTC.

Water absorption in the metal-organic framework (MOF) material Cu-BTC, up to a concentration of 3.5 H2O per Cu ion, is studied via density functional theory at the meta-GGA + U level. The stable arrangements of water molecules show chains of hydrogen-bonded water molecules and a tendency to form closed cages at high concentration. Water clusters are stabilized primarily by a combination of water-water hydrogen bonding and Cu-water oxygen interactions. Stability is further enhanced by van der Waals interactions, electric field enhancement of water-water bonding, and hydrogen bonding of water to framework oxygens. We hypothesize that the tendency to form such stable clusters explains the particularly strong affinity of water to Cu-BTC and related MOFs with exposed metal sites.

Water Networks in Fast Proton Transfer during Catalysis by Human Carbonic Anhydrase II

Variants of human carbonic anhydrase II (HCA II) with amino acid replacements at residues in contact with water molecules in the active-site cavity have provided insights into the proton transfer rates in this protein environment. X-ray crystallography and (18)O exchange measured by membrane inlet mass spectrometry have been used to investigate structural and catalytic properties of variants of HCA II containing replacements of Tyr7 with Phe (Y7F) and Asn67 with Gln (N67Q). The rate constants for transfer of a proton from His64 to the zinc-bound hydroxide during catalysis were 4 and 9 μs(-1) for Y7F and Y7F/N67Q, respectively, compared with a value of 0.8 μs(-1) for wild-type HCA II. These higher values observed for Y7F and Y7F/N67Q HCA II could not be explained by differences in the values of the pK(a) of the proton donor (His64) and acceptor (zinc-bound hydroxide) or by the orientation of the side chain of the proton shuttle residue His64. They appeared to be associated with a reduced level of branching in the networks of hydrogen-bonded water molecules between proton shuttle residue His64 and the zinc-bound solvent molecule as observed in crystal structures at 1.5-1.6 Å resolution. Moreover, Y7F/N67Q HCA II is unique among the variants studied in having a direct, hydrogen-bonded chain of water molecules between the zinc-bound solvent and N(ε) of His64. This study provides the clearest example to date of the relevance of ordered water structure to rate constants for proton transfer in catalysis by carbonic anhydrase.

On the role and impact of electromagnetic fields in ecosystems

Role and effects of electromagnetic fiin living organisms and ecosystems are discussed within a nonlinear mechanism of charge transport processes that take place during respiration and photosynthesis, as well as in hydrogen-bonded chains of water molecules. Such mechanism is based on the account of the interaction between charges and induced by the distortions of macromolecules or water chains, which results in the self-trapping of charges in soliton states. It is shown that electrosolitons have some characteristic frequency, with respect to which periodic electromagnetic fi elds have resonant effect on their dynamics and stability. At certain conditions unbiased (with zero mean-value) periodic electromagnetic radiation can cause drift of solitons along molecular chains, and, therefore, affect charge transport processes. Such drift of particles in unbiased fi elds is known as ratchet phenomenon. Similar dynamics can be caused by stochastic fi elds and takes place in water chains present in interfacial water in cells, in coherence domains of water in the atmosphere and oceans. These results can explain the mechanism of impact of the electromagnetic solar activity on metabolism of living organisms and functioning of ecosystems. Moreover, it provides the mechanism for the formation of ecosystems via fi eld-mediated exchange of information between the ecosystem elements and existence of the hierarchy of ecosystems. This study also indicates a possible danger of the electromagnetic smog on ecosystems.

Energetics and dynamics of proton transfer reactions along short water wires

Proton transfer (pT) reactions in biochemical processes are often mediated by chains of hydrogen-bonded water molecules. We use hybrid density functional calculations to study pT along quasi one-dimensional water arrays that connect an imidazolium-imidazole proton donor-acceptor pair. We characterize the structures of intermediates and transition states, the energetics, and the dynamics of the pT reactions, including vibrational contributions to kinetic isotope effects. In molecular dynamics simulations of pT transition paths, we find that for short water chains with four water molecules, the pT reactions are semi-concerted. The formation of a high-energy hydronium intermediate next to the proton-donating group is avoided by a simultaneous transfer of a proton from the donor to the first water molecule, and from the first water molecule into the water chain. Lowering the dielectric constant of the environment and increasing the water chain length both reduce the barrier for pT. We study the effect of the driving force on the energetics of the pT reaction by changing the proton affinity of the donor and acceptor groups through halogen and methyl substitutions. We find that the barrier of the pT reaction depends linearly on the proton affinity of the donor but is nearly independent of the proton affinity of the acceptor, corresponding to Brønsted slopes of one and zero, respectively.

Single-file water as a one-dimensional Ising model

We show that single-file water in nanopores can be viewed as a one-dimensional (1D) Ising model, and we investigate, on the basis of this, the static dielectric response of a chain of hydrogen-bonded water molecules to an external field. To achieve this, we use a recently developed dipole lattice model that accurately captures the free energetics of nanopore water. In this model, the total energy of the system can be expressed as the sum of the effective interactions of chain ends and orientational defects. Neglecting these interactions, we essentially obtain the 1D Ising model, which allows us to derive analytical expressions for the free energy as a function of the total dipole moment and for the dielectric susceptibility. Our expressions, which agree very well with simulation results, provide the basis for the interpretation of future dielectric spectroscopy experiments on water-filled nanopore membranes.

A novel three-dimensional framework constructed by 2-[(1H-imidazol-1-yl)methyl]-1H-benzimidazole and infinite chains of hydrogen-bonded water molecules

A novel three-dimensional framework of 2-[(1H-imidazol-1-yl)methyl]-1H-benzimidazole dihydrate, C(11)H(10)N(4).2H(2)O or L.2H(2)O, (I), in which L acts as both hydrogen-bond acceptor and donor in the supramolecular construction with water, has been obtained by self-assembly reaction of L with H(2)O. The two independent water molecules are hydrogen bonded alternately with each other to form a one-dimensional infinite zigzag water chain. These water chains are linked by the benzimidazole molecules into a three-dimensional framework, in which each organic molecule is hydrogen bonded by three water molecules. This study shows that the diversity of hydrogen-bonded patterns plays a crucial role in the formation of the three-dimensional framework. More significantly, as water molecules are important in contributing to the conformation, stability, function and dynamics of biomacromolecules, the infinite chains of hydrogen-bonded water molecules seen in (I) may be a useful model for water in other chemical and biological processes.

Three coordination polymers with helical chains based on methylenediisophthalic acid (H4MDIP)

Based on methylenediisophthalic acid (H4MDIP), three novel coordination polymers {[Mn2(MDIP)(bime)(H2O)2]2·2H2O}n (1) [bime = 1,2-ethanediylbis(imidazole)], {[Mn3(HMDIP)2(H2O)4]·4,4′-bipy·3H2O}n (2) [4,4′-bipy = 4,4′-bipyridine], and {[Co5(MDIP)2(H2O)6(μ-OH)2]·7H2O}n (3) have been synthesized and characterized by IR spectra, single-crystal X-ray diffraction analyses and thermal stability studies. The introduction of the bime and 4,4′-bipy ligands into Mn(CH3COO)2·4H2O and H4MDIP system leads to the formation of complexes 1 and 2, and the absence of the second ligand in the Co(NO3)2·6H2O and H4MDIP system leads to shape complex 3. Complex 1 is a 3D architecture with [Mn(–OCO–)]∞ helical chain. Coordination polymer2 is a 2D sheet structure with trinuclear unit, in which two kinds of 21 helical chains ([Mn(IP)]∞ (IP = isophthalic acid) and [Mn(MDIP)]∞) are included. Complex 3 exhibits the 3D porous structure with a pentanuclear cobalt unit in which a 1D shallow helical chain of hydrogen-bonded water molecules is shaped. From the topology point of view, complex 1 exhibits a (4,6)-connected network with the Schläfli symbol (42.63.8)2(44.62.74.84.9), complex 2 displays a (3,6)-connected network with CdI2 topology, and complex 3 displays a (4, 8)-connected network with Schläfli symbol (44.62)2(416.612) which is a decorated scu net.

Kinetics and Mechanism of Proton Transport across Membrane Nanopores

We use computer simulations to study the kinetics and mechanism of proton passage through a narrow-pore carbon-nanotube membrane separating reservoirs of liquid water. Free energy and rate constant calculations show that protons move across the membrane diffusively along single-file chains of hydrogen-bonded water molecules. Proton passage through the membrane is opposed by a high barrier in the effective potential, reflecting the large electrostatic penalty for desolvation and reminiscent of charge exclusion in biological water channels. At neutral pH, we estimate a translocation rate of about 1 proton per hour and tube.

Crystallographic Structures of the M and N Intermediates of Bacteriorhodopsin: Assembly of a Hydrogen-bonded Chain of Water Molecules Between Asp-96 and the Retinal Schiff Base

An M intermediate of wild-type bacteriorhodopsin and an N intermediate of the V49A mutant were accumulated in photostationary states at pH 5.6 and 295 K, and their crystal structures determined to 1.52 Å and 1.62 Å resolution, respectively. They appear to be M 1 and N′ in the sequence, M 1↔M 2↔M′ 2↔N↔N′→O→BR, where M 1, M 2, and M′ 2 contain an unprotonated retinal Schiff base before and after a reorientation switch and after proton release to the extracellular surface, while N and N′ contain a reprotonated Schiff base, before and after reprotonation of Asp96 from the cytoplasmic surface. In M 1, we detect a cluster of three hydrogen-bonded water molecules at Asp96, not present in the BR state. In M 2, whose structure we reported earlier, one of these water molecules intercalates between Asp96 and Thr46. In N′, the cluster is transformed into a single-file hydrogen-bonded chain of four water molecules that connects Asp96 to the Schiff base. We find a network of three water molecules near residue 219 in the crystal structure of the non-illuminated F219L mutant, where the residue replacement creates a cavity. This suggests that the hydration of the cytoplasmic region we observe in N′ might have occurred spontaneously, beginning at an existing water molecule as nucleus, in the cavities from residue rearrangements in the photocycle.

Molecular Mechanism of H + Conduction in the Single-File Water Chain of the Gramicidin Channel

The conduction of protons in the hydrogen-bonded chain of water molecules (or “proton wire”) embedded in the lumen of gramicidin A is studied with molecular dynamics free energy simulations. The process may be described as a “hop-and-turn” or Grotthuss mechanism involving the chemical exchange (hop) of hydrogen nuclei between hydrogen-bonded water molecules arranged in single file in the lumen of the pore, and the subsequent reorganization (turn) of the hydrogen-bonded network. Accordingly, the conduction cycle is modeled by two complementary steps corresponding respectively to the translocation 1) of an ionic defect (H +) and 2) of a bonding defect along the hydrogen-bonded chain of water molecules in the pore interior. The molecular mechanism and the potential of mean force are analyzed for each of these two translocation steps. It is found that the mobility of protons in gramicidin A is essentially determined by the fine structure and the dynamic fluctuations of the hydrogen-bonded network. The translocation of H + is mediated by spontaneous (thermal) fluctuations in the relative positions of oxygen atoms in the wire. In this diffusive mechanism, a shallow free-energy well slightly favors the presence of the excess proton near the middle of the channel. In the absence of H +, the water chain adopts either one of two polarized configurations, each of which corresponds to an oriented donor-acceptor hydrogen-bond pattern along the channel axis. Interconversion between these two conformations is an activated process that occurs through the sequential and directional reorientation of water molecules of the wire. The effect of hydrogen-bonding interactions between channel and water on proton translocation is analyzed from a comparison to the results obtained previously in a study of model nonpolar channels, in which such interactions were missing. Hydrogen-bond donation from water to the backbone carbonyl oxygen atoms lining the pore interior has a dual effect: it provides a coordination of water molecules well suited both to proton hydration and to high proton mobility, and it facilitates the slower reorientation or turn step of the Grotthuss mechanism by stabilizing intermediate configurations of the hydrogen-bonded network in which water molecules are in the process of flipping between their two preferred, polarized states. This mechanism offers a detailed molecular model for the rapid transport of protons in channels, in energy-transducing membrane proteins, and in enzymes.