Hydrogen-bonded Network Structure Research Articles

Isomorphous free-base, Ni(ii)- and Cu(ii)-5,10,15,20-tetra(4-hydroxyphenyl)porphyrin nitrobenzene hexasolvates with tetragonal 3D hydrogen-bonded network structures

The crystal structures of 5,10,15,20-tetra(4-hydroxyphenyl)-21,23H-porphyrin nitrobenzene hexasolvate (1), 5,10,15,20-tetra(4-hydroxyphenyl)porphyrinatonickel(ii) and -copper(ii)nitrobenzene hexasolvates (2and3) are described.

Picosecond Pulse Radiolysis Study of Dynamics of Solvation of Electron and Fluorenone Anion in Primary Alcohols

We have studied the dynamics of solvation of electron injected directly into primary alcohols as well as that of fluorenone anion using pulse radiolysis technique with the time resolution of about 15 ps. Unlike in the previous reports, we observe nonexponential dynamics of both electron and anion solvation. While the ultrafast component, τ1 (<15 ps) representing the inertial time scale of the dynamics is faster than the time resolution of the spectrometer, the slower component, τ2, has been assigned to the translational motion leading to structural changes of the hydrogen bonding network of the solvent in the inner solvation cell or alcohol cluster. τ2 agrees well with the electron solvation times reported by the earlier authors. τ3 is associated with the restructuring of the hydrogen bond network structure of the solvent in the region outside the solvation cell. Nonexponential solvation dynamics of the fluorenone anion has been described well by a two-component process. The most important observation in this work is that the lifetime of the shorter component, τ1, determined in four alcoholic solvents, is much longer than the electron solvation time in the corresponding solvents determined in this work or anion solvation time reported earlier. The lifetime of this component is nearly comparable with the average dipolar solvation time but shorter than the longitudinal relaxation time of the solvent. In the case of anion, τ1 has been assigned to the restructuring of the first solvation shell by breakage of solvent hydrogen bonds of the fluorenone molecule and formation of hydrogen bonds with the anion. In this case, too, the longer component, τ2, with the lifetime of a few nanoseconds, has been assigned to reorganization of hydrogen bonds in the solvent hydrogen bond network structure.

Experimental and Computational Studies on the 1:1 Complex of Anthranilic Acid with P-Toluenesulfonic Acid

The proton-transfer compound (3) was synthesized in good yields by the reaction of anthranilic acid with p-toluenesulfonic acid. It was characterized by elemental analysis, infrared spectroscopy, and X-ray single-crystal determination. The crystal structure analysis of 2-carboxyanilinium p-toulenesulfonate (3) has revealed a one-dimensional hydrogen-bonded network structure, involving the tosylate anion, the carboxyl group, and the ammonium group. The H(N)···O distances range from 1.97 to 2.23 Å. The molecular geometry and vibrational frequencies of 3 were calculated using the ab-initio method (HF) with the 6–31G(d) and 6–31+G(d,p) basis sets. The computed results indicate that the optimized geometry reproduces the crystal structure well, and the assignments of fundamental vibrations also agree well with the theoretical frequencies. The intermolecular proton transfer process between the ionic (3) and nonionic (4) structures was also investigated with the theoretical computations. The nonionic form (4) is energetically more stable than the ionic form (3) and TS(3→4) by 9.76 and 7.01 kcal/mol, respectively, including the zero-point vibrational energy correction at the HF/6–31+G(d,p) level. In addition, the atomic charges, the molecular electrostatic potentials, the nucleus-independent chemical shifts, and the frontier molecular orbitals of 3 were carried out at the HF/6–31+G(d,p) level of theory. Supplementary materials are available for this article. Go to the publisher's online edition of Phosphorus, Sulfer, and Silicon and the Related Elements for the following free supplemental files: Additional figures and tables

Pressure Effect on the Reorientational Correlation Time of Water in Formamide–Water Mixtures at 25 °C

Abstract NMR spin–lattice relaxation times (T1) for nucleus D of D2O in deuterated formamide (FA-d3)–D2O mixtures were measured up to 80 mol % of FA-d3 at 25 °C under pressure up to 196.1 MPa. To discuss the pressure effect on the dynamic behavior of water molecules in the mixtures, the reorientational correlation times (τc) of D2O molecules were estimated from the quadrupole coupling equation. τc monotonously increased with increasing FA-d3 content at all pressures studied. However, τc apparently decreased with increasing pressure until 20 mol % of FA-d3, while over 40 mol % of FA-d3 the pressure coefficient of τc (∂τc/∂P) became positive and larger with increasing FA-d3 content. A negative pressure coefficient would indicate the existence of three-dimensional hydrogen-bonded network structure of water, and a positive one would be ascribed to the strengthening of dipole interactions and hydrogen bonds between FA-d3 and D2O by compression. In order to investigate the pressure effect on the reorientational dynamics of water molecules in detail, we performed molecular dynamics (MD) simulations paying attention to the pressure effect on hydrogen-bonding and dipole interactions.

Observation of a Hydrogen-Bonded 3D Structure of Crystalline Glycerol

Abstract The crystal structure analysis of glycerol was revisited and the hydrogen atoms of three hydroxy groups were observed. A hydrogen-bonded 3D network structure of glycerol was created by the formation of a wave-like sheet structure and its assembly through hydrogen bonding.

Micro-Raman observation on the H2PO4− association structures in a supersaturated droplet of potassium dihydrogen phosphate (KH2PO4)

The efflorescence of an individual KH(2)PO(4) droplet on Teflon substrate was investigated by micro-Raman spectroscopy. With the decrease of relative humidity (RH) from 98.0% to 73.0%, the KH(2)PO(4) droplet lost water gradually and entered into supersaturated state, which was reflected by the area ratio between the water stretching band to the sum of ν(s)-PO(2) and ν(s)-P(OH)(2) bands of the H(2)PO(4)(-) (A(H(2)O)/(A((ν(s)-PO(2))+A(ν(s)-P(OH)(2))))). In 1.0 mol l(-1) KH(2)PO(4) solution, the ν(s)-P(OH)(2) and ν(s)-PO(2) bands appeared at 877 and 1077 cm(-1). In the KH(2)PO(4) droplet, the two bands shifted to 894 and 1039 cm(-1) at 98.0% RH, to 899 and 1031 cm(-1) at 89.6% RH, and then to 904 and 997 cm(-1) at 73.0% RH. Moreover, the aggregation process between the H(2)PO(4)(-) ions was observed from the spectral characteristic of the ν(s)-P(OH)(2) band in the concentration process, including the transitions of the H(2)PO(4)(-) ions from monomer in bulk solutions (0.5-1.0 mol l(-1)) to possible dimers at 98.0% RH and then further to oligomers in the droplet with the RH decrease, which were indicated by the blueshift of the ν(s)-P(OH)(2) band and its full width at half-height as a function of the RH. When the RH reached at 72.0%, the anhydrous crystal was obtained. A strong peak appeared at 928 cm(-1), implying that the four oxygen atoms of the H(2)PO(4 (-) were all hydrogen bonding through the bridge hydrogen atoms to get the extensive hydrogen-bonded network structure of the H(2)PO(4)(-) association, leading to the symmetric increase of the H(2)PO(4)(-) ion from C(2v) in dilute solution to quasi-T(d) in the anhydrous crystal.

Comment on “The structure and formation of hydrogen-bonded molecular networks on Au(111) surfaces revealed by scanning tunnelling and torsional-tapping atomic force microscopy” by V. V. Korolkov, N. Mullin, S. Allen, C. J. Roberts, J. K. Hobbs and S. J. B. Tendler, Phys. Chem. Chem. Phys., 2012, 14, 15909

Comment on “The structure and formation of hydrogen-bonded molecular networks on Au(111) surfaces revealed by scanning tunnelling and torsional-tapping atomic force microscopy” by V. V. Korolkov, N. Mullin, S. Allen, C. J. Roberts, J. K. Hobbs and S. J. B. Tendler, Phys. Chem. Chem. Phys., 2012, 14, 15909

Reply to the ‘Comment on “The structure and formation of hydrogen-bonded molecular networks on Au(111) surfaces revealed by scanning tunnelling and torsional-tapping atomic force microscopy”’ by I. Cebula, M. T. Räisänen, R. Madueno, B. Karamzadeh and M. Buck, Phys. Chem. Chem. Phys., 2013, 15, DOI: 10.1039/c3cp50754h

Reply to the ‘Comment on “The structure and formation of hydrogen-bonded molecular networks on Au(111) surfaces revealed by scanning tunnelling and torsional-tapping atomic force microscopy”’ by I. Cebula, M. T. Räisänen, R. Madueno, B. Karamzadeh and M. Buck, Phys. Chem. Chem. Phys., 2013, 15, DOI: 10.1039/c3cp50754h

Novel Structural and Dynamical Features of Water Permeation through an Aquaporin Crystallized at Sub-Angstrom Resolution

Aquaporins are ubiquitous trans-membrane channels that maintain water homeostasis of the cell by facilitating selective diffusion of water across the membrane while preventing proton diffusion. The selectivity has been suggested to be achieved by two conserved regions located along the pore: the dual asparagine, proline, alanine (NPA) aquaporin signature motif, and the aromatic/arginine (ar/R) selectivity filter. Recently, our collaborators have crystallized a yeast aquaporin at sub-angstrom resolution, the highest resolution achieved to date for a membrane protein. The structure reveals a great deal of novel information on the structure of hydrogen-bonded network of water and protein side chains. In order to complement the experimental results by determining the dynamics and energetics of water diffusion along the channel, we performed molecular dynamics simulations of this impressively high quality crystal structure. The results show disruption of the water chain in both NPA and ar/R regions in this aquaporin, due to characteristic hydrogen-bonding patterns that dictate specific orientations to water molecules. The motion of water molecules is highly correlated on either side of the NPA region. On the other hand, the correlation is reduced at the NPA region, attesting yet another possible mechanism for this region to contribute to a barrier against proton transport. Besides, the NPA region appears as a barrier region with low occupancy for water, a feature not seen in other aquaporins. The correlated motion of adjacent water molecules along with their binary co-occupancies in the ar/R selectivity filter show that water molecules move in pairs in this region. Specific hydrogen-bonding patterns in the ar/R region may also play a role in exclusion of hydronium and/or hydroxide ions. These simulations have helped elucidate the dynamical basis of many intricate features revealed by this new structure.

Different behavior of water in confined solutions of high and low solute concentrations

Water-glycerol solutions confined in 21 Å pores of the silica matrix MCM-41 C10 have been studied using differential scanning calorimetry (DSC) and broadband dielectric spectroscopy (BDS). The results suggest a micro-phase separation caused by the confinement. Likely the water molecules coordinate to the hydroxyl surface groups of the pores, leaving most of the glycerol molecules in the centre of the pores. This makes the dynamics of glycerol almost concentration independent up to water concentrations of about 85 wt%. However, at higher water concentrations no substantial clustering of glycerol molecules should occur and the glass transition related dynamics exhibit an anomalous behaviour. Instead of a common plasticization effect of water, as for the corresponding bulk solutions (when no ice is formed), it is evident that water acts as an anti-plasticizer in the confinement at high water concentrations. We propose that the increased water concentration slows down the glass transition related dynamics in the deeply supercooled regime due to that a rigid hydrogen bonded network structure of water molecules is formed at low temperatures and low glycerol concentrations. This is in contrast to the situation in a homogenously mixed bulk solution of a high solute concentration where the water molecules will be less hydrogen bonded, and therefore are typically more mobile than the surrounding solute molecules. An almost complete hydrogen bonded network of water molecules may, even in confinements, be sufficiently rigid to slow down the relaxation of embedded solute molecules. It can also be expressed the other way around, i.e. small amounts of glycerol act as a plasticizer for water, due to its breaking up of the nearly tetrahedral network structure. From the here observed concentration dependent behaviour of the deeply supercooled bulk and confined solutions it seems, furthermore, evident that the Tg value of bulk water cannot be estimated from extrapolations of aqueous solutions.

A theoretical study of molecular conformations and gelation ability of N,N′-dipyridyl urea compounds in ethanol solution: DFT calculations and MD simulations

The molecular conformations and gelation ability of N,N′-bis(4-pyridyl) urea (1) and N,N′-bis(2-pyridyl) urea (3) in ethanol solution were studied through density functional theory (DFT) calculations and molecular dynamics (MD) simulations. DFT calculations demonstrated that compound 1 adopts an energetically more favorable ZZ conformation (1a), which is polarized significantly from the gas phase to ethanol solution. Moreover, the hydrogen-bond donors and acceptors such as carbonyl group, amidogen, and pyridine nitrogen atoms are exposed to molecular lateral sides of compound 1, which is conducive to form fascinating hydrogen bond network structures in multiple directions between gelator molecules and gelling solvents. The intramolecular hydrogen-bonded ZE isomer (3d) is beneficial to the conformational stability, but weakens the gelation property of compound 3 due to steric hindrance. The dimerisation effect further reduces its gelling ability with ethanol molecules. The microscopic solvation structures, including short-range solute–solvent intermolecular interactions were also illustrated through MD simulations from the viewpoint of radial distribution functions, angle probability distribution, three-dimensional spatial distribution functions, and especially solvent coordination number. It demonstrated that the averaged solvent coordination number decreased from 4.56 for compound 1 to 3.08 for compound 3. The dimerisation effect of compound 3 in ethanol solution further reduced the solvent coordination number to 1.32. It is remarkable that by going from 4-pyridyl (1) to 2-pyridyl (3) urea-based derivatives, the gelation ability disappears, in good agreement with experimental phenomena.

Face-to-Face Structures Formed by 3D Hydrogen-Bonded Networks of Tris(4-carboxyphenyl)cyclotriguaiacylene

A novel tris(4-carboxyphenyl)cyclotriguaiacylene 2 was synthesized by hydrolysis of a novel tris[(4-(methoxycarbonyl)phenyl]cyclotriguaiacylene. The structure was determined by 1H NMR, 13C NMR and mass spectroscopic techniques. The crystal structure of 2 was shown by X-ray crystallography to have a face-to-face structure of a pair of molecules of 2. The structure was constructed from 3D hydrogen-bonded network structure. .

High Pressure Kinetics Studies of Water Solidification in Dynamic-DAC

The phase diagram of water is both unusual and complex, exhibiting a wide range of polymorphs including proton-ordered or disordered forms. In addition, a variety of stable and metastable forms are observed. The richness of H2O phases attests the versatility of hydrogen bonded network structures that include kinetically stable amorphous ices. In addition, natural gas hydrates are observed upon cooling and/or pressurization. The structures of gas hydrates are quite different from ices, yet guest molecules are enclathrated inside hydrogen bonded water cages. Hence, the presence of small impurity molecules can affect strongly the behaviours of hydrogen bonding and alter the phase diagram and phase boundaries of H2O. In this paper, we report the effect of methane impurity on solidification and melting of H2O under dynamic loading conditions. The presence of impurity mainly affects the growth rate of metastable ice VII, slowing down from 1.4 m/s in pure H2O to 0.26 m/s in impure H2O, neither the occurrence of metastable ice VII nor the melting of ice VI.

Two Tetrachlorocobaltate(II) Salts With Substituted Benzyl Triphenylphosphonium: Syntheses, Crystal Structures, Weak Interactions, and Magnetic Properties

Two new tetrachlorocobaltate(II) salts, [BzTPP]2[CoCl4]·H2O (1) and [4NO2BzTPP]2[CoCl4]·H2O (2) ([BzTPP]+ = 1-benzyl- triphenylphosphonium; [4NO2BzTPP]+ = 1-(4′-nitrobenzyl)tri- phenylphosphonium), have been prepared and characterized by elemental analysis, IR, MS, single-crystal X-ray diffraction, and magnetic susceptibility. Both 1 and 2 crystallize in the monoclinic space group P21/c. The [CoCl4]2− anion exhibits a distorted tetrahedral coordination geometry. The C-H···Cl, C-H···O, and C-H···π hydrogen bonds in 1 and 2 give rise to a 3D hydrogen-bonded network structure. Magnetic susceptibility measurements in the temperature range 2–300 K show that both 1 and 2 exhibit an antiferromagnetic coupling behavior.

Investigation of structural evolution of hydrogen-bond networks of water clusters at 1 and 300 K

Computer simulation of water clusters (H2O)n, Na+(H2O)n and K+(H2O)n (n ≤ 8) at temperatures of 1 and 300 K was carried out using the Monte Carlo method. All the types of the hydrogen-bond network structures at equilibrium configurations of the water clusters and, among them, the most probable ones at temperatures of 1 and 300 K, were detected. The analysis of the most probable types of hydrogen-bond networks at equilibrium configurations of water clusters revealed that clusters with n water molecules inherit the configuration of clusters with n − 1 water molecules with an accuracy of one hydrogen bond.

Size-Dependent Metamorphosis of Electron Binding Motif in Cluster Anions of Primary Amide Molecules

Electron binding motifs in cluster anions of primary amides, (acetamide)(n)(-) and (propionamide)(n)(-), were studied with photoelectron spectroscopy. For both the amides, two band series due to distinct isomeric species in the multipole-bound states were found in the low electron binding energy region (<~0.4 eV) of the photoelectron spectra at the excitation wavelength of 1064 nm. In the case of acetamide, the isomer of higher band peak energies is predominant for 6≤ n ≤ 8, but it vanishes completely for n ≥ 9 to be replaced with the lower energy isomer. The same spectral behavior was seen for propionamide exhibiting an exception at n = 7. The isomers appearing in the lower and higher energy sides were attributed to the straight and folded forms of ladder-like hydrogen bond network structures, respectively, on the basis of density functional calculations. In the folded forms, the excess electron is held in the space between two terminal amide molecules of the ladder-like networks. Referring to calculations of potential energy curves with respect to the folding coordinate of the ladder-like networks, it is inferred that the major isomer alternation between n = 8 and 9 originates from an increase of stiffness of the molecular ladders depending on the cluster sizes. In photoelectron spectra at the 355 nm excitation, the valence anion state having a band peak around 2.5 eV was observed to emerge with threshold sizes of n = 13 and 9 for acetamide and propionamide, respectively. Static and dynamical effects of alkyl groups on the electron binding motifs are discussed in comparison with the previous study on formamide cluster anions.

Study of electret effect of rat skin by thermally stimulated discharge analysis

Abstract The thermally stimulated discharge (TSD) spectra of three types of rat skin treated and untreated by negative polypropylene (PP) electret were measured. The natural rat skin shows an excellent electret effect due to the lamellar lipid structure, reticular structure of collagen and protein space structure related hydrogen bond network and non-covalent bond system. Hydration intensifies the skin electret effect. Electret could change the lamellar lipid structure and charge state of skin surface by alteration of dipolar orientation, intermolecular non-covalent action and protein transformation from α helix to β sheet. The regulation of skin electret effect depends on tightly bound water.

4-(4-Aminophenylsulfonyl)aniline–1,3,5-trinitrobenzene (1/2)

The asymmetric unit of the title co-crystalline 1:2 adduct, C12H12N2O2·2C6H3N3O6, contains two independent mol­ecules of bis­(4-amino­phen­yl) sulfone (the drug Dapsone) and four mol­ecules of 1,3,5-trinitro­benzene and is extended into a two-dimensional hydrogen-bonded network structure through amino N—H⋯O hydrogen-bonding associations with nitro O-atom acceptors. In the two independent Dapsone mol­ecules, the inter-ring dihedral anges are 69.6 (3) and 63.63 (9)°. Aromatic π–π inter­actions are also found between one of the Dapsone aromatic rings and a trinitro­benzene ring [minimum ring centroid separation = 3.596 (3) Å]. A 4-amino­phenyl ring moiety of one of the Dapsone mol­ecules and two nitro groups of a trinitro­benzene are disordered in a 50:50 ratio.

The structure and formation of hydrogen-bonded molecular networks on Au(111) surfaces revealed by scanning tunnelling and torsional-tapping atomic force microscopy

A comprehensive scanning probe microscopy study has been carried out to characterise 3,4,9,10-Perylenetetracarboxylic diimide (PTCDI)-melamine hydrogen-bonded networks deposited on Au(111)-surfaces. Both scanning tunnelling and atomic force microscopy were utilized. Such complementary analysis revealed a multilayered structure of the networks on the Au(111)-surface as opposed to a widely reported monolayer structure. Details of the network formation mechanism are presented. We have also demonstrated that despite the apparent network stability in ambient conditions it is unstable in aqueous solutions of pH 4.5 and 7.1.

Origin of strong synergism in weakly perturbed binary solvent system: a case study of primary alcohols and chlorinated methanes.

A strong synergistic solvation was observed for the mixtures of hydrogen bond donating and accepting solvent pairs. The nature of the interactions between two solvent pairs was investigated with different dye molecules viz. coumarin 480, coumarin 153, 4-aminophthalimide, and p-nitroaniline. Coumarin 480 in differenet alcohols-CHCl(3) (alcohols: MeOH, EtOH, BuOH) binary mixture shows a strong synergism, which is explained in the backdrop of solvent-solvent interactions. Fluorescence quenching of C480 by 1,2-phenylenediamine in the binary solvent mixture exhibited the maximum deviation in quenching constant corresponding to ~0.45 mol fraction of MeOH in MeOH-CHCl(3) binary mixture and hence suggested the maximum extent of hydrogen-bonding interactions prevailing at this proportion of mixture. The solvation behavior of MeOH-CHCl(3) mixture shows strong probe dependence with no synergism observed in p-nitroaniline, which is ascribed to its higher ground state dipole moment (8.8 D) relative to C480 (6.3 D). Interestingly, the strong synergistic signature observed through spectrophotometric measurement of C480 in alcohol-CHCl(3) binary mixture is absent when studied by fluorescence measurement. The higher excited state dipole moment of coumarin 480 (13.1 D) is considered to be the driving force for the absence of synergism in the excited state. In such strongly perturbed systems (due to high dipole moment values) the dominant phenomenon is preferential solvation. Analysis of proton NMR of MeOH-CHCl(3) binary solvent mixture indicates the existence of MeOH-CHCl(3) clusters in the stoichiometric ratio of 1:2.15. Refractive index measurement also infers the existence of hydrogen bonded network structure between MeOH and CHCl(3). A modified Bosch solvent exchange model has been used to determine the feasibility of synergistic behavior and polarity parameter of the mixed solvent structure of MeOH-CHCl(3) binary solvent mixture.