Water Hexamer Research Articles

Data sampling scheme for reproducing energies along reaction coordinates in high-dimensional neural network potentials.

We propose a data sampling scheme for high-dimensional neural network potentials that can predict energies along the reaction pathway calculated using the hybrid density functional theory. We observed that a data sampling scheme that combined partial geometry optimization of intermediate structures with random displacement of atoms successfully predicted the energies along the reaction path with respect to five chemical reactions: Claisen rearrangement, Diels-Alder reaction, [1,5]-sigmatropic hydrogen shift, concerted hydrogen transfer in the water hexamer, and Cornforth rearrangement.

Water Vapor Single-Gas Selectivity via Flexibility of Three Potential Materials for Autonomous Indoor Humidity Control

Two new isostructural porous supramolecular materials {[Cu2(amp)4Cl][M(C2O4)3]·6H2O}n (amp = 2-aminomethylpyridine), designated as II and III for M = Cr(III) and M = Fe(III) respectively, have been synthesized by a self-assembly process of two ionic complexes [Cu2(amp)4Cl]3+ and [M(C2O4)3]3–, M = Fe(III) and Cr(III). They build heterometallic hydrogen-bonded-, oxalato- and chlorido-bridged zigzag chains with interchain hydrogen bonds and π–π interactions. This results in supramolecular potentially porous architectures exhibiting large channels filled with hexameric water clusters. Their activated phases, II′ and III′, can readsorb the water molecules to regenerate the initial materials which are stable for many water adsorption and desorption cycles like that of their homologous catena-{[(Co(amp)3][Cr(C2O4)3]·6H2O} (I′). The three materials I′, II′, and III′ exhibit water adsorption and desorption isotherms having a sigmoidal shape and resulting in the combination of a type I(b) profile followed by an S-s...

Tetranuclear MnII/ZnII and Novel Azido‐Bridged Chair‐Shaped Heptanuclear CdII Compounds: The Effect of Metal Ion and Coordination Mode of the Azide Group on the Structure of the Products

We report two tetranuclear compounds [MnL(N3)]4 (1), [Zn4L4(N3)2][Zn(N3)4]·3H2O (2) and a novel heptanuclear cluster [Cd7L6(N3)6](NO3)1.33(N3)0.66·12H2O (3) where L is a hydrazone Schiff base ligand based on pyridine. The ligand acts as a negatively charged tetradentate N3O‐donor ligand and coordinates to the metal centers in the enolic form in 1–3. However, in compound 2, the ligand coordinated to the ZnII ion in the two different coordination modes. Metal centers in 1 and 2, bridged by the organic ligand form tetranuclear metal organic complexes and the N3– anion acts as terminal ligand. In compound 3, N3– acts as bridging ligand to the cadmium(II) centers, and form a rare heptanuclear cluster with an interesting chair conformation. The latter compound is a novel azido‐bridged chair‐shaped heptanuclear CdII cluster that guides the formation of a water hexamer in the solid state. It acts as a robust binding block in the recognition of nitrate. The ability of the water hexamer to bind anions has been analyzed using DFT calculations and several computational tools.

Hexagonal Monolayer Ice without Shared Edges.

When adsorbed on solids, water molecules are usually arranged into a honeycomb hydrogen-bond network. Here we report the discovery of a novel monolayer ice built exclusively from water hexamers but without shared edges, distinct from all conventional ice phases. Water grown on graphite crystalizes into a robust monolayer ice after annealing, attaining an exceedingly high density of 0.134 Å^{-2}. Unlike chemisorbed ice on metal surfaces, the ice monolayer can translate and rotate on graphite terraces and grow across steps, confirming its two-dimensional nature. First-principles calculations identify the monolayer ice structure as a robust self-assembly of closely packed water hexamers without edge sharing, whose stability is maintained by maximizing the number of intralayer hydrogen bonds on inert surfaces.

Isostructural series of [{Al(H2O)6}{Ln(pda)3}].10H2O: Synthesis, structure and photoluminescence

A new series of six isostructural molecular solids of the composition [{Al(H2O)6}{Ln(pda)3}].10H2O where Ln = Sm, Eu, Gd, Tb, Dy and Yb have been synthesized and structurally characterised. All the solids are built of three major building blocks: the lanthanide dipicolinate anion, {Ln(pda)3}3−, the counter cation, {Al(H2O)6}3+ and a hexameric water cluster in chair form. The cations and the anions supramolecularly aggregate forming a 2D H-bonded sheet; the sheets are further stabilised through hexameric water clusters in chair form and water molecules. The crystals containing Sm, Eu, Tb and Dy showed characteristic emission of lanthanide ions.

Monodisperse water clusters grown on the semimetallic Bi(111) surface

All forms of water are essential for life and a wide range of scientific and technological processes. When adsorbed on metal surfaces, water usually forms a variety of clusters with a broad size distribution. Here we report the monodisperse water clusters formed on the semimetallic Bi(111) surface. High-resolution scanning tunneling microscopy images combined with density functional theory calculations demonstrate that the monodisperse clusters are built exclusively from hexagonal arrangement of six water molecules with slight buckling. All the water hexamers are oriented at the same direction and reveal the identical motif: three-lobed protrusions at high bias and a trigonal hole at low bias. The monodispersity of cyclic water clusters can be rationalized by the fact that hydrogen bonding is the dominant interaction responsible for water cluster stability on Bi(111). The water hexamer is the most favorable because of the maximum strength of H bonds. The decrease of H bonds (the presence of double acceptors) makes it difficult for water molecules to form a smaller (larger) cluster.

Origin of Many-Body Vibrational Frequency Shifts in Water Clusters.

We have demonstrated the application of many-body expansions to calculations of the anharmonic, local-mode, OH-stretching vibrational frequencies of water clusters. We focused on five low-lying isomers of the water hexamer and the DD*(20,1) isomer of (H2O)21. Our approach provides accurate OH-stretching vibrational frequencies when treating one- and two-body interactions with the CCSD(T)-F12 level of theory and the three- and four-body interactions with the DF-MP2-F12 level. Additionally, we have investigated the physical origin of the large contribution that two- and three-body interactions make to the shifts of vibrational frequencies using symmetry-adapted perturbation theory (SAPT). We conclude that while two-body vibrational frequency shifts can be correlated linearly with electrostatic energies, all strongly shifted three-body interactions can be correlated to the induction energy with a single regression coefficient of approximately 70 cm-1 (kcal·mol-1)-1.

Fermi resonance in OH-stretch vibrational spectroscopy of liquid water and the water hexamer.

Vibrational spectroscopy of water contains a wealth of information about the structure and dynamics of this fascinating substance. Theoretical modeling of fundamental vibrational transitions in condensed water has proven difficult, and in many circumstances, one cannot reach even qualitative agreement with experiment. Due to the ability of water to form hydrogen bonds of various strengths, the OH stretching band spans several hundreds of wave numbers in the spectra, overlapping with the first overtone of the HOH bending band and triggering a resonance between these two vibrations. This effect, known as Fermi resonance, has been traditionally ignored in theoretical condensed-phase simulations due to the additional computational burden and its deemed low importance. Depending on a particular molecular environment, the Fermi resonance manifests itself from small spectral features in the spectra of liquid water to pronounced distinct peaks in the spectra of ice and water clusters. The goal of this work is to illustrate the effects of including the Fermi resonance coupling between the bending overtone and stretching fundamental vibrations in the mixed quantum-classical formalism developed by Skinner and co-workers on the IR and Raman spectra of liquid water and the water hexamer. We show that by adding the Fermi resonance coupling, we are able to reproduce the location of the peak and a shoulder on the red side of the IR spectrum as well as the bimodal structure of the polarized Raman spectrum of liquid water at 300 K. Very good agreement between theory and experiment is achieved for the IR spectra of the water hexamer as well. We suggest that the Fermi resonance should not be ignored if intricate features of spectra are of interest. In spite of these promising results obtained in the region of a spectrum where Fermi resonance is important, further development of spectroscopic maps is needed to improve agreement with the experiment outside of the frequency range affected by the Fermi resonance.

Identifying Few-Molecule Water Clusters with High Precision on Au(111) Surface.

Revealing the nature of a hydrogen-bond network in water structures is one of the imperative objectives of science. With the use of a low-temperature scanning tunneling microscope, water clusters on a Au(111) surface were directly imaged with molecular resolution by a functionalized tip. The internal structures of the water clusters as well as the geometry variations with the increase of size were identified. In contrast to a buckled water hexamer predicted by previous theoretical calculations, our results present deterministic evidence for a flat configuration of water hexamers on Au(111), corroborated by density functional theory calculations with properly implemented van der Waals corrections. The consistency between the experimental observations and improved theoretical calculations not only renders the internal structures of absorbed water clusters unambiguously, but also directly manifests the crucial role of van der Waals interactions in constructing water-solid interfaces.

Anionic water pentamer and hexamer clusters: An extensive study of structures and energetics.

An extensive study of structures and energetics for anionic pentamer and hexamer clusters is performed employing high level ab initio quantum chemical methods, such as the density-fitted orbital-optimized linearized coupled-cluster doubles (DF-OLCCD), coupled-cluster singles and doubles (CCSD), and coupled-cluster singles and doubles with perturbative triples [CCSD(T)] methods. In this study, sixteen anionic pentamer clusters and eighteen anionic hexamer clusters are reported. Relative, binding, and vertical detachment energies (VDE) are presented at the complete basis set limit (CBS), extrapolating energies of aug4-cc-pVTZ and aug4-cc-pVQZ custom basis sets. The largest VDE values obtained at the CCSD(T)/CBS level are 9.9 and 11.2 kcal mol-1 for pentamers and hexamers, respectively, which are in very good agreement with the experimental values of 9.5 and 11.1 kcal mol-1. Our binding energy results, at the CCSD(T)/CBS level, indicate strong bindings in anionic clusters due to hydrogen bond interactions. The average binding energy per water molecules is -5.0 and -5.3 kcal mol-1 for pentamers and hexamers, respectively. Furthermore, our results demonstrate that the DF-OLCCD method approaches to the CCSD(T) quality for anionic clusters. The inexpensive analytic gradients of DF-OLCCD compared to CCSD or CCSD(T) make it very attractive for high-accuracy studies.

Ice-like Cyclic Water Hexamer Trapped within a Halide Encapsulated Hexameric Neutral Receptor Core: First Crystallographic Evidence of a Water Cluster Confined within a Receptor-Anion Capsular Assembly

Over the past few decades, the tren [tris(2-aminoethyl)amine] skeleton has materialized as one of the supreme anion binding building blocks demonstrating a strong interplay among topology, complementarity, cooperativity, and coordination. However, anion recognition by modest tren-based unsubstituted aromatic urea has been underexplored, mainly due to the deficiency of π-acidic or electron-withdrawing aryl terminals. This report establishes an infrequent hexameric neutral receptor-anion-water molecular self-assembly, where a conformationally flexible C3v-symmetric halide (F–/Cl–) encapsulated electron-rich naphthyl group containing N-bridged tripodal urea receptor effectively entraps a chair-shaped ice-like neutral cyclic water hexamer within the hexameric cavity of a neutral receptor-halide host–guest assembly.

Cyclic (H2O)6confined hexameric host–guest assemblies and aerial CO2fixation by electron-rich neutral urea/thiourea scaffolds

Neutral capsular assemblies of electron-rich tris-urea/thiourea receptors are formedviacyclic (H2O)6trapping or atmospheric CO2fixation.

Structural variations in self-assembled coordination complexes of hexamethylenetetramine, zinc(II) and carboxylates (RCOO−, R = –CH3/−C6H5): Encapsulation of the water hexamer in benzoate assembly

Two new zinc(II) complexes [Zn2(ac)3(hmt)2(OH)]·H2O (1) and [{Zn5(Obz)8(H2O)2(μ3-OH)2}(μ2-hmt){Zn2(Obz)4}·6H2O]n (2) have been synthesized using two different carboxylate salts (acetate (ac) for 1 and benzoate (Obz) for 2) and hexamethylenetetramine (hmt). Both the complexes have been structurally characterized by X-ray crystallography. Their identities have also been established by elemental analysis and IR spectral studies. Complex 1 is a dimer in which two zinc atoms contain equivalent four-coordinate tetrahedral environments. On the other hand, complex 2 is a 1D zig-zag coordination polymer containing alternative zinc pentamers and zinc dimers separated by bridging μ2-hmts. The centrosymmetric pentamer unit contains three independent zinc atoms, one being four-coordinate with a tetrahedral environment and other two being six-coordinate with octahedral geometries whereas the centrosymmetric dimer unit contains two five-coordinate Zn atoms with square pyramidal geometries. H-bonding interactions play a key role in stabilizing the observed structures. In complex 1, the water molecule is held within the dimer and in 2, a rare water hexamer is encapsulated in the supramolecular assembly by hydrogen bonds. The DFT calculations reveal that inter- and outer-cluster H-bond stabilization energies of water hexamer are −29.99 and −15.93 kcal/mol respectively. Lower stabilization energy from the ideal hexamer of chair conformer is attributed to the deformation of H-atoms as well as longer hydrogen bonded O⋯O distances. Additionally, the extra stability due to outer-cluster H-bonds is responsible for significant deformation from ideal chair conformer of hexamer cluster.

Structural insights into two inorganic-organic hybrids based on chiral amino acids and polyoxomolybdates

A new chiral inorganic-organic hybrid with the formula (L-His)2(H7CoMo6O24)·6H2O (1), based on natural amino acid and Anderson type polyoxomolybdate was synthesized through mild condition. The chiral l-histidine molecules induced chirality to the whole structure through various types of strong and unconventional hydrogen bond (HB) interactions (CH⋯O, NH⋯O and CH···π interactions), as well as bifurcated hydrogen bonds (BHBs) between l-histidine amino acid, hexamer water cluster molecules, and H7CoMo6O24·xH2O. Following, important non-covalent CH⋯O interactions is investigated in another chiral inorganic-organic hybrid structure, (L-Pro)3(PMo12O40).4.5H2O (2), in detail. The CH⋯O hydrogen bonds lead to a chiral network similar to the DNA strands affording a promising candidate to bio-inorganic studies.

Hydrogen bonding characterization in water and small molecules.

The prototypical hydrogen bond in water dimer and hydrogen bonds in the protonated water dimer, in other small molecules, in water cyclic clusters, and in ice, covering a wide range of bond strengths, are theoretically investigated by first-principles calculations based on density functional theory, considering not only a standard generalized gradient approximation functional but also, for the water dimer, hybrid and van der Waals corrected functionals. We compute structural, energetic, and electrostatic (induced molecular dipole moments) properties. In particular, hydrogen bonds are characterized in terms of differential electron density distributions and profiles, and of the shifts of the centres of maximally localized Wannier functions. The information from the latter quantities can be conveyed to a single geometric bonding parameter that appears to be correlated with the Mayer bond order parameter and can be taken as an estimate of the covalent contribution to the hydrogen bond. By considering the water trimer, the cyclic water hexamer, and the hexagonal phase of ice, we also elucidate the importance of cooperative/anticooperative effects in hydrogen-bonding formation.

Spectral characterization, crystal structures and biological activities of iminodiacetate ternary complexes

The ternary complexes with stoichiometry [M(imda)(bipy)]·6H2O (M = Cu) and [M(imda)(bipy)(H2O)]·4H2O (M = Ni, Co and Mn) where H2imda = iminodiacetic acid and bipy = 2,2′-bipyridine, are prepared and characterized to exploit as novel antimicrobial agents and SOD mimics. The chemical structures were elucidated by IR, FAB-Mass, 1H, 13C NMR, EPR and spectral techniques. Single crystal X-ray and spectral studies of the complexes (1) and (2) have confirmed a square pyramidal geometry around Cu(II) ion while a saturated six coordinate (distorted octahedral) geometry around the Ni(II), Co(II) and Mn(II) ions due to the additional coordination from water. A supramolecular network is formed by extensive H-bonding in complex (1). The supramolecular assembly in complex (1) is additionally consolidated via the existence of unusual cyclic hexameric water clusters. The antimicrobial activities for the present complexes have been examined against Escherichia coli (K-12), Bacillus subtilis (MTC-121), Staphylococcus aureus (IOASA-22), Salmonella typhymurium (MTCC-98), Candida albicans, Aspergillus fumigatus and Penicillium marneffei. The superoxide dismutase (SOD) activity of the Cu(II) complex (1) is also assessed employing nitrobluetetrazolium (NBT) assay.

Monitoring Water Clusters "Melt" Through Vibrational Spectroscopy.

Characterizing structural and phase transformations of water at the molecular level is key to understanding a variety of multiphase processes ranging from ice nucleation in the atmosphere to hydration of biomolecules and wetting of solid surfaces. In this study, state-of-the-art quantum simulations with a many-body water potential energy surface, which exhibits chemical and spectroscopic accuracy, are carried out to monitor the microscopic melting of the water hexamer through the analysis of vibrational spectra and appropriate structural order parameters as a function of temperature. The water hexamer is specifically chosen as a case study due to the central role of this cluster in the molecular-level understanding of hydrogen bonding in water. Besides being in agreement with the experimental data available for selected isomers at very low temperature, the present results provide quantitative insights into the interplay between energetic, entropic, and nuclear quantum effects on the evolution of water clusters from "solid-like" to "liquid-like" structures. This study thus demonstrates that computer simulations can now bridge the gap between measurements currently possible for individual isomers at very low temperature and observations of isomer mixtures at ambient conditions.

NMR and FTIR studies of clustering of water molecules: From low-temperature matrices to nano-structured materials used in innovative medicine

H-bond clustering of water molecules confined in an argon matrix and in nano-structured calcium hydroxyapatites (Ca10(PO4)6(OH)2, CaHA) was studied by means of FTIR and 1H MAS NMR spectroscopy. FTIR spectra of water in matrix were measured from T=9K to 40K stepping by 2K with sequent 2D correlation analysis (2DCOR) carried out in the range of O–H stretching vibrations 3000–3800cm−1. The peaks of monomer, dimer and the H-bond clusters from trimer to hexamer as well as the surface (dangling) modes were resolved. Some peaks in 2DCOR spectra drop out from the water clustering scheme. They were related to the enhancement of vibration–rotation motion due to increasing temperature and volume of the cavities in argon matrix. Water clusters were revealed in nano-CaHAs in FTIR spectra for the first time. Beside the sharp peak at 3570cm−1 of the stretching vibration of O–H− ion in the bulk, the bands of water dimer, tetramer, hexamer and several surface O–H and P–O–H modes were resolved at 2900–3900cm−1. They were assigned comparing with the spectra of water in argon matrix and in hydrophobic solvent (CCl4). The cluster structure and the size depends on the hydration level. Hexamer- or even higher structures were observed only in the samples containing significant amount of adsorbed water. The amount of adsorbed water in the studied nano-CaHAs was probed using the intensity of the broad 1H signal at ca 5.1ppm normalized respect to OH– peak at 0ppm. Two narrow signals observed in 1H MAS NMR spectra at 0.8 and 1.3ppm are originated from the surface structured H2O molecules. The NMR data perfectly correlate with those obtained by FTIR spectroscopy.

Ab initio and density functional theory (DFT) studies on triflic acid with water and protonated water clusters.

The structure, stability and infrared spectral signatures of triflic acid (TA) with water clusters (Wn) and protonated water clusters (TAH+Wn, n = 1 - 6) were computed using DFT and MP2 methods. Our calculations show that a minimum of three water molecules are necessary to stabilize the dissociated zwitterionic form of TA. It can be seen from the results that there is no significant movement of protons in smaller (n = 1 and 2) and linear (n = 1 - 6) types of water clusters. Further, the geometries of TAWn clusters first form a neutral pair (NP) to contact ion pair (CIP), then form a solvent separated ion pair (SSIP) in a water hexamer. These findings reveal that proton transfer may take place through NP to CIP and then CIP to SSIP. The calculated binding energies (BEs) of ion pair clusters is always higher than that of NP clusters (i.e., more stable than the NP). Existing excess proton linear chain clusters transfer a proton to adjacent water molecules via a Grotthuss mechanism, whereas the same isomers in the branched motifs do not conduct protons. Examination of geometrical parameters and infrared frequencies reveals hydronium ion (H3O+ also called Eigen cation) formation in both TAWn and protonated TAWn clusters. The stability of Eigen water clusters is three times higher than that of other non-Eigen water clusters. Our study shows clearly that formation of ion pairs in TAWn and TAH+Wn clusters greatly favors proton transfer to neighboring water molecules and also enhances the stability of these complexes.

Structural, Dynamical, and Electronic Properties of Liquid Water: A Hybrid Functional Study.

We study structural, dynamical, and electronic properties of liquid water through ab initio molecular dynamics (MD) simulations based on a hybrid functional which includes nonlocal van der Waals (vdW) interactions. The water dimer, the water hexamer, and two phases of ice are studied as benchmark cases. The hydrogen-bond energy depends on the balance between Fock exchange and vdW interactions. Moreover, the energetic competition between extended and compact structural motifs is found to be well described by theory provided vdW interactions are accounted for. Applied to the hydrogen-bond network of liquid water, the dispersion interactions favor more compact structural motifs, bring the density closer to the experimental value, and improve the agreement with experimental observables such as radial distribution functions. The description of the self-diffusion coefficient is also found to improve upon the combined consideration of Fock exchange and vdW interactions. The band gap and the band edges are found to agree with experiment within 0.1 eV.