Hydrogen-bonded Network Structure Research Articles

Novel supramolecular isomerism in coordination polymer synthesis from unsymmetrical bridging ligands: solvent influence on the ligand placement orientation and final network structure.

The assembly of Co(NCS)(2) with 1-methyl-1'-(3-pyridyl)-2-(4-pyridyl)ethene (L(1)) exhibits a novel supramolecular isomerism of [Co(L(1))(2)(NCS)(2)](infinity) caused by different placement orientation of L(1) around metal centers. The reaction in MeOH/H(2)O and EtOH/H(2)O resulted in a double chain structure of 1, and that in EtOH/CH(3)NO(2) led to an open framework structure of 2. The reaction in MeOH/CH(3)NO(2) solvent system concomitantly afforded 1 and 2. The assemblies of 1-(3-pyridyl)-2-(4-pyrimidyl)ethene (L(2)) with Co(NCS)(2) created the water-coordinated complexes of Co(L(2))(2)(H(2)O)(2)(NCS)(2) (3 and 4), an MeOH coordinated complex of Co(L(2))(2)(H(2)O)(2)(NCS)(2) (5), and an open framework coordination polymer of [Co(L(1))(2)(NCS)(2)](infinity) (6) depending on the reaction solvent system. From these observations, it is suggested that in the formation of 1, the solvent-coordinated intermediate species would be generated first and its trans coordination configuration should define the placement orientation of L(1) in the resulting polymer of 1. On the other hand, it is presumed that the solvent-coordinated intermediate would not be produced during the formation of 2 due to the weaker coordination ability of EtOH and CH(3)NO(2) molecules. The open framework coordination polymers of 2 and 6 are converted in the solid state into the isomeric coordination polymer of 1 and hydrogen bonded network structure of 3, respectively.

2-(4-Pyridyl)-1H-benzimidazole trihydrate

The benz­imidazole and pyridyl portions of the mol­ecule of the title compound, C12H9N3·3H2O are essentially co-planar; the three N atoms interact with the water mol­ecules, forming a three-dimensional hydrogen-bonded network structure.

Infrared spectroscopic evidence for protonated water clusters forming nanoscale cages.

Size-dependent development of the hydrogen bond network structure in large sized clusters of protonated water, H+(H2O)n (n = 4 to 27), was probed by infrared spectroscopy of OH stretches. Spectral changes with cluster size demonstrate that the chain structures at small sizes (n less, similar 10) develop into two-dimensional net structures (approximately 10 < n < 21), and then into nanometer-scaled cages (n >/= 21).

3-Carboxyphenoxyacetic acid monohydrate

The asymmetric unit of the title compound, C9H10O6·H2O, consists of one 3-carboxy­phenoxy­acetic acid (3-CPOAH2) and one water mol­ecule. The intermolecular interactions link symmetry-related mol­ecules into hydrogen-bonded dimers. A supramolecular hydrogen-bonding network structure is formed via further intermolecular hydrogen bonds involving the water mol­ecule.

Phenacyltriphenylphosphonium picrate: intra-and interionic C—H...O interactions

The crystal structure of the title compound, (benzoyl­methyl)­tri­phenyl­phospho­nium 2,4,6-tri­nitro­phenolate, C26H22OP+·C6H2N3O7−, consists of phospho­nium cations and picrate anions stabilized by intra- and interionic C—H⋯O interactions, leading to an extended hydrogen-bonded network structure.

Raman spectroscopic study on the structure of water in aqueous solution of zwitterionic surfactants

The structure and hydrogen bonding of water in aqueous solutions of various surfactants were analyzed using the contours of the OH stretching in the polarized Raman spectra. From the relative intensity of the collective band ( C value) corresponding to a long-range coupling of the OH stretching in the aqueous surfactant solutions, the number of hydrogen bonds disrupted due to the presence of one surfactant molecule ( N corr value) was evaluated. The N corr value for decylsulfobetaine was slightly negative, whereas those for ordinary ionic surfactants such as sodium dodecylsulfate and dodecyltrimethylammonium chloride were large positive values. Furthermore, the N corr for carboxybetaine surfactant was a small positive value. These results suggest that zwitterionic surfactants do not disturb the hydrogen-bonded network structure of water significantly, probably due to the counteraction of the electrostriction effect by the proximity between the anionic and cationic groups.

Model Compounds Study on the Network Structure of Polybenzoxazines

The FT-IR and 1H NMR spectra of model dimers, having different molecular sizes and pKa, are investigated in order to understand the differences in the hydrogen-bonded network structures of polybenzoxazines. The correlation between the −OH···N intramolecular hydrogen-bonding interaction and benzoxazine functional groups in the asymmetric dimers is investigated by 1H NMR spectra. While the FT-IR spectra of the model dimers indicate that the nature of hydrogen bonding is closely related to the basicity of the amine constituent, the spectra of the corresponding polymers suggest the existence of different hydrogen-bonding interactions. The existence of phenolic linkage formation and the stability of the Mannich base structure during polymerization are investigated by a dimerization reaction. It is demonstrated that benzoxazines based upon extremely bulky amines do not develop desirable properties due to the extensive degradation process.

Factors Governing the Three-Dimensional Hydrogen-Bond Network Structure of Poly(m-phenylene isophthalamide) and a Series of Its Model Compounds. 3. Energy Terms Indispensable to the Crystal Structure Prediction

To clarify the factors that govern the complicated three-dimensional hydrogen-bond network structure of poly(m-phenylene isophthalamide) and its model compounds, the packing energy calculations were performed with computer simulation software (Polymorph Predictor) and the important energy terms were extracted successfully. The crystal structures were predicted with and without the various types of interaction terms being taken into consideration and were compared with the X-ray-analyzed structures. Initially, the conformation analysis was made for a single molecule. However, the structure with the lowest energy did not always correspond to the actually observed structure. This finding suggested the importance of intermolecular, as well as intramolecular, interactions. By performing the lattice-energy calculations with and without various types of intermolecular interactions being taken into consideration, and by comparing the results with the observed structures, it has been found that the van der Waals interaction was a primarily important factor in the prediction of the molecular packing structures; however, the electrostatic (and hydrogen-bond) interaction could not be ignored at all. In other words, a good and sensitive balance between these interaction terms was quite important for obtaining a successful reproduction of the observed molecular packing structures of the model compounds.

Flash extraction of pectin from orange albedo by steam injection.

Pectin was acid extracted from orange albedo by steam injection heating under pressure. Extraction times ranged from 2 to 6 min at a pressure of about 15 psi. Solubilized pectin was characterized by HPSEC with online light scattering and viscosity detection. Molar mass (M), radius of gyration (R(g)), and intrinsic viscosity ([eta]) all decreased with increasing extraction time when heating temperature was 120 degrees C. At heating times of 3 min, M(w) ranged from 4.9 to 4.5 x 10(5), R(gz) was about 44 nm, and [eta](w) ranged from 8.4 to 7.9 dL/g. Chromatography revealed that solubilized pectin distributions were bimodal in nature at 3 min extraction time and trimodal when the extraction time was 6 min. Scaling law exponents obtained for the highest molar mass fractions were consistent with a very compact spherical structure. For the intermediate fraction, scaling law exponents were consistent with a less compact spherical structure comparable to a random coil. In the case of the low molar mass fractions, scaling law exponents were consistent with a structure more asymmetric in shape. These results are consistent with earlier results which indicated that pectin distributions were mixtures of two or more of the following due to disaggregation during extraction: spherical aggregates, hydrogen bonded network structures, and partially or fully disaggregated components of network structures which could include branched structures, rods, segmented rods, and kinked rods.

Hydrogen-bond-assisted control of H versus J aggregation mode of porphyrins stacks in an organogel system.

To obtain insights into a correlation relationship between the structure and the aggregation mode in an organogel system, we synthesized gelators 2a-4a bearing a porphyrin moiety as a one-dimensional aggregation unit and amide groups as peripheral hydrogen-bonding sites. Gelators 3a and 3b bearing the amide groups at the 4-position of the meso-phenyl groups are classified as versatile gelators, gelating 10 and 14 solvents, respectively, among 23 solvents tested herein. In contrast, gelators 2a and 4a bearing the amide groups at the 3,5-positions and 3-position, respectively, are classified as poor gelators. Examination by spectroscopic methods (UV-vis, ATR-FTIR, XRD, etc.) revealed that in the organogel phase porphyrins in 3a adopt the H aggregation mode whereas those in 2a and 4a adopt the J aggregation mode. X-ray analysis of the single crystals established that in fact 3b features a columnar stack of porphyrin moieties that can be classified as the H-aggregate, whereas 2a results in a two-dimensional a-b plane, in which porphyrin moieties are arranged in the J-aggregate. Very interestingly, the difference in the H versus J aggregation mode is well-reflected by the difference in the macroscopic aggregate morphology observed by SEM: 3a + cyclohexane gel results in a one-dimensionally aggregated fibrillar structure, whereas 2a + cyclohexane gel results in a two-dimensional sheetlike structure. These findings indicate that the H versus J aggregation mode of porphyrin stacks can be controlled by the peripheral hydrogen-bonding interactions and the microscopic hydrogen-bonding network structure is well-reflected by the macroscopic SEM-observed structure.

Hydrogen-bonded superstructures of a small host molecule and lanthanide aquo ions.

Despite containing only relatively small molecular components, the structure of [Eu(H(2)O)(9)](1.5)(CTV)(6)(CH(3)CN)(5.5)(H(2)O)(7.5)[Co(C(2)B(9)H(11))(2)](4.5) (C(191)H(337.5)B(81)Co(4.5)Eu(1.5)N(5.5)O(57), a = 54.590(2) A, b = 37.5788(17) A, c = 31.8067(14) A, beta = 116.573(2) degrees, monoclinic, C2/c, Z = 8) is of an unusually large size and level of complexity, with an intricate hydrogen-bonding network formed between lanthanide aquo ions, water, and the small host molecule cyclotriveratrylene (=CTV). The 3D hydrogen-bonded network structure that results is unique and too complicated to apply the usual topological analysis. Instead a simplified model using structural subunits is described.

First principle calculations of benzotriazole adsorption onto clean Cu(1 1 1)

The adsorption of benzotriazole (BTAH or C6N3H5) on a Cu(111) surface is investigated by using first principle density functional theory calculations (VASP). It is found that BTAH can be physisorbed (<0.1 eV) or weakly chemisorbed (∼0.43 eV) onto Cu(111), and the chemical bond is formed through nitrogen sp2 lone pairs. The weak chemisorption can be stabilized by reaction with neighboring protonphilic radicals, like OH−. Furthermore, the geometries and associated energies of intermolecular hydrogen bonds between adsorbates on Cu(111) are also calculated. A model of the first layer of BTAH/BTA− on Cu(111) surface is developed based on a hydrogen bond network structure.

Two-Dimensional Hydrogen Bond Networks Supported by CH/π Interaction Leading to a Molecular Packing Appropriate for Topochemical Polymerization of 1,3-Diene Monomers

Strong and weak hydrogen bonds, as intermolecular interactions, are used for the construction of designer crystals with organic small molecules as the building blocks. We report here crystal engineering for the synthetic plan of the topochemical polymerization using the ammonium derivatives of 1,3-diene mono- and dicarboxylic acids on the basis of intermolecular interactions such as NH/O and CH/π interactions. The isomerism of hydrogen bond network structures obstructs the prediction of crystal structure and reactivity, although topochemical polymerization requires that monomer molecules stack in a column with a stacking distance of 5 A in the crystals. The structures of hydrogen bond networks are roughly classified into a two-dimensional type appropriate for topochemical polymerization, and the others consisting of two-dimensional sheets or one-dimensional ladders not for polymerization. We conclude that the CH/π interaction of naphthylmethyl and benzyl substituents promises to give polymerizable lamella...

Factors Governing the 3-Dimensional Hydrogen-Bond Network Structure of Poly(m-phenylene isophthalamide) and a Series of Its Model Compounds (2) Computer Simulation of Crystal Structures of Aromatic Amide Compounds and Comparison with X-ray Analyzed Structures

Crystal structures have been predicted by using a software Polymorph Predictor and compared with those analyzed by X-ray method for a series of low-molecular-weight aromatic amide compounds as models of poly(m-phenylene isophthalamide) and poly(p-phenylene terephthalamide). For most of the compounds investigated here, the predicted crystal structure of the lowest or the next lowest packing energy has been found to be in good agreement with the X-ray analyzed structure. However, the energy difference was not very large between these energetically most plausible structures and the other less stable candidates, indicating a difficulty of unique prediction of 3D molecular packing structure and a possibility of existence of various types of crystal modification.

Synthesis and crystal structure of nickel complex of N, N-bis(benzimidazol-2-yl-methyl)amine

A new nickel(II) complex, [NiL 2]Cl 2 (L= N, N-bis(benzimidazol-2-yl-methyl)amine), was synthesized and its crystal structure was determined. According to X-ray crystallographic studies, each nickel(II) ion was six-coordinated with six nitrogen atoms of two L ligands. The complex crystallizes in triclinic system, space group P 1 ̄ , a=9.764(3) A ̊ , b=11.032(3) A ̊ , c=16.402(5) A ̊ , α=80.529(6)°, β=79.180(7)°, γ=74.232(6)°, and Z=2. The title complex forms two-dimensional hydrogen bond network structures between the chlorine atoms and the nitrogens of L. The IR and UV spectroscopy were measured. The absorption bands of d–d electron transition are assigned, the values of Dq and B were calculated according to the electronic spectrum of the complex.

Effect of the Silyl Substitution on Structure and Vibrational Spectra of Hydrogen-Bonded Networks in Dimers, Cyclic Trimers, and Tetramers

Geometries of the hydrogen bound clusters (ROH)n (n = 1−4, R = H, CH3, and SiH3) are optimized at the B3LYP/DZP+diff level of theory. The reliability of the theoretical method employed for the description of the electronic structure of the hydrogen-bonded network is assesed by a comparison of the predicted geometry parameters and the BSSE corrected association energies with the existing experimental parameters and the higher level theoretical estimates for a water dimer and methanol oligomers. Cyclic structures with S4 symmetry, similar in the hydrogen-bond arrangement to that of the water tetramer, were found as minima at the potential energy surface of methanol and silanol tetramers. The cyclic silanol trimer has the C3h symmetry, in contrast to water and methanol trimers which are characterized by the nonplanar asymmetric structures. The O−O atomic separations decrease and association energies per monomer increase with n and in going from H to SiH3. The silanol tetramer has the highest association energy per monomer among the analyzed systems. This finding is in keeping with the dominance of tetrameric cyclic structures in the experimentally studied crystal structures of silanols. Vibrational frequency shifts with n in the water−methanol−silanol systems are discussed and frequencies for methanol and silanol trimers and tetramers are predicted from the ab initio force fields scaled with factors refined to fit experimental vibrational frequencies of monomers and a water dimer. The main feature of the frequency change with n, along with the lowering of the OH stretch, is the upward shift of the OH bend, which is exceptionally high in silanols.

Hydrogen-Bonded Network Structure of Water in Aqueous Solution of Sulfobetaine Polymers

Poly(N,N-dimethylaminopropyl methacrylamide) (poly(DMAPMA)) was incubated with 1,3-propanesultone and 1,4-butanesultone to afford polymers with various contents of N,N-dimethyl-N-(3-sulfopropyl)-3‘-methacrylamidopropanaminium inner salt residues and N,N-dimethyl-N-(4-sulfobutyl)-3‘-methacrylamidopropanaminium inner salt residues, respectively. The structure and hydrogen bonding of water in an aqueous solution of the sulfobetaine polymers were analyzed using the contours of the O−H stretching in the polarized Raman spectra. With an increase in the content of the sulfobetaine residue, the relative intensity of the collective band (C value) corresponding to a long-range coupling of the O−H stretching in the aqueous polymer solutions became larger and approached the C value of pure water. The number of hydrogen bonds disrupted because of the presence of one monomer residue (N value) for the polymers with a large sulfobetaine content was a small positive value and comparable to those for neutral polymers such as poly(ethylene glycol) and poly(N-vinylpyrrolidone). This is in significant contrast with the largely positive N values for the precursor polymer (poly(DMAPMA)), and ordinary polyelectrolytes such as sodium polyethylenesulfonate, poly-l-lysine hydrobromide, sodium polyacrylate, and poly(acrylic acid). The N value for a small molecular weight zwitterionic compound, 3-aminopropanesulfonic acid, was also slightly positive, which is consistent with the tendency observed for the sulfobetaine polymers. The present results clearly indicate that the zwitterionic polymers do not significantly disturb the hydrogen-bonded network structure of water, probably because of the counteraction of the electrostriction effect by the proximity between the anionic and cationic groups.

A simple model of the hydrophobic effect for molecular simulation of interfacial phenomena

A coarse-grained model for simulation of interfacial phenomena in aqueous systems has been developed. The model captures the hydrophobic effect by only considering the structure and cohesiveness of water. Monte Carlo (MC) simulations of water-oil mixtures show that low concentrations of oil are solvated with little perturbation of the hydrogen bonding network structure of the water, while high concentrations of oil are excluded altogether. Analysis of the water structure in the simulations indicates that the water molecules maintain close to four coordination in the presence of solutes and the distribution of bond angles is not markedly affected by the presence of solutes. MC simulations of an alkane oligomer in water and a poly(ethylene oxide) (PEO) oligomer in water indicate that the chains are quite flexible and also do not perturb the network structure of the water phase.

Factors Governing the Three-Dimensional Hydrogen Bond Network Structure of Poly(m-phenylene isophthalamide) and a Series of Its Model Compounds: (1) Systematic Classification of Structures Analyzed by the X-ray Diffraction Method

Molecular and crystal structures of a series of model compounds of poly(m-phenylene isophthalamide) have been analyzed by the X-ray diffraction method and the various types of 3-D hydrogen bond network structures have been clarified. The twisting angles between benzene and amide groups are in the range of 25−40°, which is common to all of the analyzed model compounds and the parent polymer itself and could be reproduced well by the energy calculation with the nonbonded interatomic interactions between the benzene and amide groups taken into consideration. The molecular conformation, the packing mode of molecules, and the intermolecular hydrogen bond network structure were found to have good correlation with each other and could be classified systematically into several groups. This classification should be important for the energetic interpretation of the formation mechanism of the 3-D hydrogen bond network structure.

Interconvertible Supramolecular Transformations

Interconversion between a 3D hydrogen bonded network structure in [Zn2(Rsala)2(H2O)2]·2H2O, (H2(Rsala) = N-(2-hydroxy-5-R-benzyl)-l-alanine; R = Cl and Me) and a chiral 3D coordination polymeric network [Zn2(Rsala)2] is reported to take place by thermal dehydration and rehydration process.