Water Hexamer Research Articles

Implementation of Dynamical Nucleation Theory Effective Fragment Potentials Method for Modeling Aerosol Chemistry

In this work, the dynamical nucleation theory (DNT) model using the ab initio based effective fragment potential (EFP) is implemented for evaluating the evaporation rate constant and molecular properties of molecular clusters. Predicting the nucleation rates of aerosol particles in different chemical environments is a key step toward understanding the dynamics of complex aerosol chemistry. Therefore, molecular scale models of nanoclusters are required to understand the macroscopic nucleation process. On the basis of variational transition state theory, DNT provides an efficient approach to predict nucleation kinetics. While most DNT Monte Carlo simulations use analytic potentials to model critical sized clusters, or use ab initio potentials to model very small clusters, the DNTEFP Monte Carlo method presented here can treat up to critical sized clusters using the effective fragment potential (EFP), a rigorous nonempirical intermolecular model potential based on ab initio electronic structure theory calculations, improvable in a systematic manner. The DNTEFP method is applied to study the evaporation rates, energetics, and structure factors of multicomponent clusters containing water and isoprene. The most probable topology of the transition state characterizing the evaporation of one water molecule from a water hexamer at 243 K is predicted to be a conformer that contains six hydrogen bonds, with a topology that corresponds to two water molecules stacked on top of a quadrangular (H(2)O)(4) cluster. For the water hexamer in the presence of isoprene, an increase in the cluster size and a 3-fold increase in the evaporation rate are predicted relative to the reaction in which one water molecule evaporates from a water hexamer cluster.

Tapes of water hexamer clusters in the interlayer space of a 2D MOF: Structural, spectroscopic and computational insight of the confined water

The synthesis, crystal structure and characterization of [Er 2(C 4H 4O 4) 3(H 2O) 4]·6H 2O, with particular emphasis on the structural details and the vibrational behavior of the highly organized sub-net of water are reported. X-ray structural analysis reveals that the hybrid framework, which can be classified as belonging to the I 0O 2 type, acts as a host of an infinite tape of six-membered water rings with distorted chair conformation. The water network extends between the hybrid layers helping the close packing and the stabilization of the structure through H-bond interactions, with further development of the supramolecular tridimensional structure. The self-assembly of the hydration water molecules is conditioned by the hybrid host, forcing them to adopt a less stable conformation when compared with hexagonal ice. The vibrational spectra of partially and completely dehydrated samples as well as of partially isotopic diluted ones have been obtained and analyzed. In order to guide the assignment of the vibrational spectra a theoretical calculation was performed at the B3LYP/6-31G ∗∗ level for a model consisting of three water clusters.

Discrete Octamer Water Cluster and 1D T5(2) Water Tape Trapped in Two Luminescent Zn(II)/1,2-Bis(imidazol-1′-yl)ethane/Dicarboxylate Hosts: From 2D (4,4) Net to 3D 5-Fold Interpenetrated Diamond Network

Two new mixed-ligand Zn(II) coordination polymers, namely, [Zn(bime)(glu)·4H2O]n (1) and [Zn(bime)(sub)·3H2O]n (2) (bime = 1,2-bis(imidazol-1′-yl)ethane, H2glu = glutaric acid, H2sub = suberic acid), have been synthesized and structurally characterized. Complex 1 exhibits a wavy two-dimensional (2D) sheet with (4,4) topology. Complex 2 is a three-dimensional (3D) framework with 5-fold interpenetrated diamond topology. Of particular interest, a discrete octamer water cluster comprised of a chairlike hexamer water cluster with two extra water molecules dangling on two diagonally vertices of the chair was observed in the grid of the 2D sheet of 1. In 2, a 1D infinite T5(2) water tape constructed from edge-sharing pentamer water clusters accommodates in the channels of the 3D network. The results suggest that the dicarboxylates play crucial roles in the formation of the different host structures as well as different guest water aggregations. Additionally, the thermal stabilities and photoluminescence spectra of them were discussed.

Synthesis, Structure, Thermal and Fluorescent Properties of a Novel Mn(II) Coordination Polymer and its Hexacyclic Water Ring

A novel Imazethapyr-bridged complex [Mn(Ima)2] (H2O)2 (1) [Imazethapyr (Ima)=5-ethyl-2-(5-isopropyl-5-methyl-4-oxo-4,5-dihydro-1H-imidazol-2-yl) nicotinic acid, has been synthesized and structurally characterized by X-ray diffraction method, infrared spectra, elemental analysis and thermal analysis. The title polymer contains a monocyclic hexamer water cluster, and the cluster plays an important role in stabilizing the complex. The fluorescence of the complex 1 in the solid state was investigated via FL55 spectrophotometer and it indicated a fluorescent behavior at room temperature. A novel Imazethapyr-bridged complex [Mn(Ima)2] (H2O)2 [Imazethapyr (Ima) = 5-ethyl-2-(5-isopropyl-5-methyl-4-oxo-4,5-dihydro -1H-imidazol-2-yl) nicotinic acid, has been synthesized and structurally characterized by X-ray diffraction method, infrared spectra, elemental analysis and thermal analysis. The title polymer contains a monocyclic hexamer water cluster, and the cluster plays an important role in stabilizing the complex.

Metal–organic framework (MOF) of [Co(II)(1,4-benzenedicarboxylate)2 (pyridine)2(water)2]: Coexistence of water cyclic hexamers through carboxylate oxygens

A metal–organic framework of [Co(II)(1,4-benzenedicarboxylate)2(pyridine)2(water)2] has been synthesized and characterized by IR spectra, TGA and single crystal X-ray diffraction analysis. Discrete cyclic hexameric water clusters through carboxylate oxygens and pyridine molecules are trapped inside a two-dimensional coordination channel. Discrete cyclic hexameric water clusters and pyridine molecules are trapped inside a two-dimensional coordination polymer. Thermal analysis shows that the oxygen atom of water is strongly incorporated as a part of this cluster. ► A Co(II) coordinated polymer, has been synthesized under hydrothermal condition. ► The 3D supramolecular structure is formed by π–π interaction and H O H hydrogen bondings. ► The water cluster plays important role to make 3D supramolecular. ► Thermal analysis shows that the oxygen atom of water is strongly incorporated as a part of this cluster.

Standard hydrogen electrode and potential of zero charge in density functional calculations

Methods to explicitly account for half-cell electrode potentials have recently appeared within the framework of density functional theory. The potential of the electrode relative to the standard hydrogen electrode is typically determined by subtracting the experimental value of the absolute standard hydrogen electrode potential (ASHEP) from the calculated work function. Although conceptually correct, this procedure introduces two sources of errors: (i) the experimental estimate of the ASHEP varies from 4.28 to 4.85 V and, as has been previously shown and is reconfirmed here, (ii) the calculated work function strongly depends on the structure of the water film covering the metal surface. In this paper, we first identify the most accurate experimental reference for the ASHEP by revisiting up-to-date literature, and validate the choice of electron reference level in single-electrode density functional setups. By analyzing a dozen different water structures, built up from water hexamers, in their uncharged [potential of zero charge (PZC)] states on Pt(111), we then determine three different criteria (no net dipole, no charge transfer, and high water flexibility) that a water structure should possess in order for its computed ASHEP to closely match the experimental benchmark. We capture and quantify these three effects by calculating trends in the ASHEP and PZC on eight close-packed transition metals, considering the four most simple and representative water models. Finally, it is also demonstrated how the work function changes with exchange-correlation functional.

Synthesis and characterization of cobalt(II)–salicylate complexes derived from N 4-donor ligands: Stabilization of a hexameric water cluster in the lattice host of a cobalt(III)–salicylate complex

The syntheses and structural characterization of four cobalt(II)–salicylate complexes, [(TPA)Co II(HSA)](ClO 4) ( 1), [(isoBPMEN)Co II(HSA)](BPh 4) ( 2), [(TPzA)Co II(HSA)](ClO 4) ( 3) and [(6Me 3TPA)Co II(HSA)](BPh 4) ( 4) [TPA = tris(2-pyridylmethyl)amine, isoBPMEN = N 1, N 1-dimethyl- N 2, N 2-bis(2-pyridylmethyl)ethane-1,2-diamine, TPzA = tris((3,5-dimethyl-1H-pyrazole-1-yl)methyl)amine and 6Me 3TPA = tris(6-methyl-2-pyridylmethyl)amine] are described. While 2, 3 and 4 are unreactive towards dioxygen, 1 reacts slowly with molecular oxygen to a cobalt(III)–salicylate complex, [(TPA)Co III(SA)](ClO 4) ( 1a). Two different crystalline forms, 1a and 1a· 4H 2O were isolated depending upon the condition of oxidation and crystallization. The solid-state structures of cobalt(III)–salicylate unit in both 1a and 1a· 4H 2O show a six-coordinate distorted octahedral coordination geometry at the cobalt(III) center ligated by the tetradentate ligand (TPA) where the dianionic salicylate (SA) binds in a bidentate fashion through one carboxylate and one phenolate oxygen. The hydrated form 1a· 4H 2O reveals a hexameric water cluster formation in the inorganic lattice host. The complex cation and the perchlorate counterion are involved in stabilizing the (H 2O) 6 cluster in a rare ‘pentamer planar+1’ conformation. A one-dimensional water tape consisting of edge-shared water hexamers is observed. The water tape represents a subunit of ice structure.

A discrete water hexamer with a new planar tetrameric water moiety trapped in the crystal host of [Ag(azelate)(4,4′-bipyridine)]·(H2O)3

Abstract The ultrasonic reaction of Ag2O, bipy and H2aze gave rise to a novel Ag(I) mixed-ligand coordination polymer, namely [Ag(aze)(bipy)]·(H2O)3 (1) (bipy = 4,4′-bipyridine, H2aze = azelaic acid). In 1, Ag(I) ions are linked by bipy and aze ligands to form a single two-dimensional (2D) undulated net with a (6,3) topology, incorporating Ag6(bipy)4(aze)2 windows of 22.58 × 11.06 A based on Ag⋯Ag distances. A pair of identical 2D single nets are interconnected via π⋯π stacking and unsupported Ag⋯Ag interactions to generate a 2D double-layered net. A discrete water hexamer composed of a new planar tetrameric water ring and two pendent water molecules is perpendicularly located in each hydrophilic cavity of the 2D bilayer and acts as a ‘glue’ to assemble adjacent 2D double-layered nets into a three-dimensional (3D) structure.

Different water clusters dependent on long-chain dicarboxylates in two Ag(I) coordination polymers: Synthesis, structure and thermal stability

Two mixed-ligand Ag(I) coordination polymers (CPs), [Ag 2(bipy) 2(sub)·5H 2O] n ( 1), [Ag 2(bipy) 2(aze)·3H 2O] n ( 2), (bipy = 4,4′-bipyridine, H 2sub = suberic acid, H 2aze = azelaic acid) have been synthesized and structurally characterized by elemental analysis, infrared (IR) spectroscopy, powder X-ray diffraction (PXRD), thermogravimetric (TG) analysis, and single crystal X-ray diffraction. Both 1 and 2 are two-dimensional (2D) sheets based on infinite [Ag(bipy)] n double chain incorporating Ag⋯Ag interactions. Interestingly, two different water clusters are encapsulated in the voids between the sheets of 1 and 2. For 1, one water decamer (H 2O) 10 based on a cyclic water tetramer was hydrogen-bonded with the host 2D sheet. While, one water hexamer (H 2O) 6 also based on a cyclic water tetramer was observed in 2. Comparing the experimental results, it is comprehensible that the dicarboxylates play a crucial role in the formation of the different water clusters. Moreover, the thermal stabilities of them were also discussed.

Generation of Zwitterionic Water Channels: Biszwitterionic Imidazolium Carboxylates as Hydrogen-Bonding Acceptors

Organic crystals containing several types of water channels are generated by clipping water molecules with biszwitterionic imidazolium carboxylates as hydrogen-bonding acceptors. The types of water channels to be generated depend on the size and the shape of the aromatic spacers tethered with two imidazolium carboxylates moieties. Clusters of water tetramers and dimers were obtained from imidazolium carboxylates with phenylene (1) and naphthalene (2) linkers, respectively. The latter showed pseudopolymorphism, affording layers of water hexamers. Imidazolium carboxylate possessing biphenylene linker (3) afforded channels of discrete water tetramers.

Investigation of h -BN/Rh(111) Nanomesh Interacting with Water and Atomic Hydrogen.

Recent STM experiments show that by exposing h-BN/Rh(111) nanomesh to water or atomic hydrogen interesting phenomena can be observed. We investigated by Density Functional Theory (DFT) the structure of bare nanomesh as well as in the presence of water clusters and atomic hydrogen. Our simulations allow the correct interpretation of the observed modifications of the STM topography under different tested conditions. For example, we could determine that the frequently observed three protrusions within the pore appearing in STM images obtained after dosing small amounts of water, are most likely determined by water hexamers. We also could confirm that the flattening of the h-BN overlayer after dosing atomic hydrogen is determined by the intercalation of the latter between BN and metal, which prevents the effective binding between N and Rh.

A Discrete Spirocyclic (H2O)9 Cluster and 1D Novel Water Chain with Tetrameric and Octameric Clusters in Cationic Hosts

Two mixed-ligand Ag(I) coordination polymers (CPs), [Ag2(bpp)2(suc)·12H2O]n (1) and [Ag2(bpe)2(suc)·9H2O]n (2) (where bpp = 1,3-bis(4-pyridyl)propane, bpe = 1,3-bis(4-pyridyl)ethane, and H2suc = succinic acid), have been synthesized and structurally characterized. Both structures consist of cationic layers with Ag···π interacted chains of alternating metal and bis(pyridyl) ligands. The noncoordinated succinate (suc2−) in 1 or 2 serves as an anionic template driving surrounding water molecules to aggregate into an ordered 2D water-suc anionic layer. The interlamellar anions and cationic layers are stacked through weak electrostatic interaction and hydrogen bonds. One novel 1D water chain constructed from alternating water tetramer with uudd configuration and rare octamer exists in the anionic layer of 1. Each octameric water cluster consists of a pair of fused hexameric water clusters, and each water hexamer assumes a rare bag-shaped conformation. A discrete spirocyclic nonameric water cluster featuring two vertex-sharing pentamers, which shows a similar structure to organic hydrocarbon spiro[4.4] nonane, was observed in 2. All water clusters have not been structurally documented so far and illustrate new modes of supramolecular association of water molecules. What is more important is that the present observations demonstrate that the spacer length of N-donor ligands has a significant influence on the final formation of water aggregates.

Infrared photodissociation spectroscopy of H+(H2O)6·Mm (M = Ne, Ar, Kr, Xe, H2, N2, and CH4): messenger-dependent balance between H3O+ and H5O2+ core isomers

Although messenger mediated spectroscopy is a widely-used technique to study gas phase ionic species, effects of messengers themselves are not necessarily clear. In this study, we report infrared photodissociation spectroscopy of H(+)(H(2)O)(6)·M(m) (M = Ne, Ar, Kr, Xe, H(2), N(2), and CH(4)) in the OH stretch region to investigate messenger(M)-dependent cluster structures of the H(+)(H(2)O)(6) moiety. The H(+)(H(2)O)(6), the protonated water hexamer, is the smallest system in which both the H(3)O(+) (Eigen) and H(5)O(2)(+) (Zundel) hydrated proton motifs coexist. All the spectra show narrower band widths reflecting reduced internal energy (lower vibrational temperature) in comparison with bare H(+)(H(2)O)(6). The Xe-, CH(4)-, and N(2)-mediated spectra show additional band features due to the relatively strong perturbation of the messenger. The observed band patterns in the Ar-, Kr-, Xe-, N(2)-, and CH(4)-mediated spectra are attributed mainly to the "Zundel" type isomer, which is more stable. On the other hand, the Ne- and H(2)-mediated spectra are accounted for by a mixture of the "Eigen" and "Zundel" types, like that of bare H(+)(H(2)O)(6). These results suggest that a messenger sometimes imposes unexpected isomer-selectivity even though it has been thought to be inert. Plausible origins of the isomer-selectivity are also discussed.

PH-Dependent Ag(i) coordination architectures constructed from 4-cyanopyridine and phthalic acid: from discrete structure to 2D sheet

Four mixed-ligand Ag(I) coordination complexes (CCs), namely, [Ag(cnpy)2(Hpta)] (1), [Ag2(cnpy)2(Hpta)2] (2), [Ag4(cnpy)2(pta)2(H2O)]n (3) and [Ag2(inta)2(pta)·3H2O]n (4), (cnpy = 4–cyanopyridine, H2pta = phthalic acid, inta = isonicotinamide) have been synthesized through a one-pot ultrasonic reaction of silver(I) oxide, cnpy and H2pta under different pH values and structurally characterized. Complexes 1 and 2 formed at lower pH values (5.0 for 1 and 6.9 for 2) exhibit zero-dimensional (0D) mononuclear and tetranuclear motifs, respectively. Reaction at pH = 8.8 leads to a two-dimensional (2D) structure of 3 in which completely deprotonated H2pta shows two kinds of coordination modes: μ5-η1:η1:η1:η3 and μ6-η1:η1:η1:η3. A further increase of the pH value to 9.4 results in the in situhydrolysis of cnpy and produces complex 4 as a one-dimensional (1D) chain structure. Of particular interest, a well-resolved chair-like centrosymmetric hexamer water cluster, (H2O)6, which is stabilized by 1D chains through six dangling hydrogen bonds, exists in 4. Comparing the experimental results, it is comprehensible that the pH value plays a crucial role in the formation of the resulting structures. Additionally, results about IR spectra, thermogravimetric curves and photoluminescence spectra were discussed.

Conformers and hydrogen bonds in cytidine 5′-diphosphocholine sodium single crystals grown from a mixture of ethanol and water

The molecular structure of cytidine 5′-diphosphocholine sodium (CDPC) grown from a mixture of ethanol and water was determined by X-ray diffraction (XRD). CDPC was found to have an orthorhombic structure with confirmed lattice parameters of a = 6.978 Å, b = 12.406 Å and c = 29.326 Å. This nucleotide coenzyme was highly folded and net-like. Each crystallographic unit consisted of one sodium atom, one pyrophosphate group, one cytosine group, one coordinated water molecule, one pentose molecule, and three lattice water molecules. The interspaces of neighboring CDPC molecules were filled with water molecules and methyl groups. Although the coordinated water was connected to sodium atoms, the lattice water molecules formed chair-shaped water hexamers. The hydrogen bonds which played an important role in maintaining the structure included O H···O, N H···O and C H···O and ranged in length from 2.682 (17) to 3.349 (17) Å. Fourier transform infrared spectroscopy (FTIR) showed a broad absorption in the 400–2000 cm −1 region characteristic of short hydrogen bonds. So for industrial crystallization, methods which could eliminate the influence of hydrogen bonds should be taken, and it would be beneficial for the process of crystallization.

Excess Electron and Lithium Atom Solvation in Water Clusters at Finite Temperature: An ab Initio Molecular Dynamics Study of the Structural, Spectral, and Dynamical Behavior of (H2O)6− and Li(H2O)6

The roles of hydrogen bonds in the solvation of an excess electron and a lithium atom in water hexamer cluster at 150 K have been studied by means of ab initio molecular dynamics simulations. It is found that the hydrogen bonded structures of (H(2)O)(6)(-) and Li(H(2)O)(6) clusters are very different from each other and they dynamically evolve from one conformer to other along their simulation trajectories. The populations of the single acceptor, double acceptor, and free type water molecules are found to be significantly high unlike that in pure water clusters. Free hydrogens of these type of water molecules primarily capture the unbound electron density in these clusters. It is found that the binding motifs of the free electron evolve with time and the vertical detachment energy of (H(2)O)(6)(-) and vertical ionization energy of Li(H(2)O)(6) also change with time. Assignments of the observed peaks in vibrational power spectra are done, and we found direct correlations between the time-averaged population of water molecules in different hydrogen bonding states and the spectral features. The dynamical aspects of these clusters have also been studied through calculations of time correlations of instantaneous stretch frequencies of OH modes which are obtained from the simulation trajectories through a time series analysis.

Synthesis, structural and theoretical studies of a rare hexameric water cluster held in the lattice of {[Zn(HL)(phen)(H2O)]∙3(H2O)}2 (H3L=trans-aconitic acid)

The reaction of Zn(NO 3 ) 2 ∙3(H 2 O) with trans -aconitic acid (H 3 L), in presence of chelating 1,10-phenanthroline, leads to the formation of a dinuclear unit {[Zn(HL)(phen)(H 2 O)]∙3(H 2 O)} 2 . The lattice water molecules are assembled as a centrosymmetric hexamer. The crystal structure, thermal studies, theoretical calculations, and the factors that stabilize this water hexamer are presented. A new type of binodal network has been constructed by a zinc(II) trans-aconitate dimer and a water hexamer through H-bonds.

Intermolecular Interaction in Water Hexamer

The origin of the intermolecular interaction, especially the many-body interaction, in eight low-lying water hexamer structures (prism, cage, book-1, book-2, cyclic-chair, bag, cyclic-boat-1, and cyclic-boat-2) is unraveled using the localized molecular orbital energy decomposition analysis (LMO-EDA) method at the second-order Møller-Plesset perturbation (MP2) level of theory with a large basis set. It is found that the relative stabilities of these hexamer structures are determined by delicate balances between different types of interaction. According to LMO-EDA, electrostatic and exchange interactions are strictly pairwise additive. Dispersion interaction in these water hexamer structures is almost pairwise additive, with many-body effects varying from -0.13 to +0.05 kcal/mol. Repulsion interaction is roughly pairwise additive, with many-body effects varying from -0.84 to -0.62 kcal/mol. Polarization interaction is not pairwise additive, with many-body effects varying from -13.10 to -8.85 kcal/mol.

Synthesis and Characterization of a Novel Binuclear Cobalt(II) Complex with Discrete Water Clusters (H2O)8

AbstractA new octameric water cluster was observed in the complex Co2(dptc)(bipy)2(H2O)6·4H2O (1) (H4dptc = diphenyl‐3,3′,4,4′‐tetracarboxylic acid; bipy = 2,2′‐bipyridine), which was characterized by single‐crystal X‐ray diffraction, elemental analysis and IR spectroscopy. The centrosymmetric octamer consists of a water hexamer in the chair form and two water molecules and brings to light a novel mode of the cooperative association of water molecules. Those complex units are connected into a 2D infinite layer framework through hydrogen bonding. Consequently, the 2D layers are further aggregated by hydrogen bonding with octameric subunits and π···π stacking interactions to form a 3D supramolecular architecture.

Structural Studies of the Water Hexamer

In this paper we report the geometries and properties of 24 structural isomers located on the MP2/6-311++g** potential energy surface of the water hexamer. At least 15 structural patterns are located within 3 kcal/mol of the most stable conformation, leading to a very complex potential energy surface, several isomers having significant contributions. A quadratic correlation between the distance from the proton to the center of the hydrogen bond with the distance between oxygen atoms for all clusters is reported. MP2/6-311++g** and CCSD(T)/aug-cc-pvdz//MP2/6-311++g** predict different stabilization orderings but are in good agreement for binding energies. Compact structures are energetically favored by electronic energies with zero point energy corrections, while noncompact cyclic structures are preferred when temperature and entropy are accounted for.