Three-dimensional Hydrogen-bonded Network Research Articles

Thermal-induced transformation of glutamic acid to pyroglutamic acid and self-cocrystallization: a charge-density analysis.

Thermal-induced transformation of glutamic acid to pyroglutamic acid is well known. However, confusion remains over the exact temperature at which this happens. Moreover, no diffraction data are available to support the transition. In this article, we make a systematic investigation involving thermal analysis, hot-stage microscopy and single-crystal X-ray diffraction to study a one-pot thermal transition of glutamic acid to pyroglutamic acid and subsequent self-cocrystallization between the product (hydrated pyroglutamic acid) and the unreacted precursor (glutamic acid). The melt upon cooling gave a robust cocrystal, namely, glutamic acid-pyroglutamic acid-water (1/1/1), C5H7NO3·C5H9NO4·H2O, whose structure has been elucidated from single-crystal X-ray diffraction data collected at room temperature. A three-dimensional network of strong hydrogen bonds has been found. A Hirshfeld surface analysis was carried out to make a quantitative estimation of the intermolecular interactions. In order to gain insight into the strength and stability of the cocrystal, the transferability principle was utilized to make a topological analysis and to study the electron-density-derived properties. The transferred model has been found to be superior to the classical independent atom model (IAM). The experimental results have been compared with results from a multipolar refinement carried out using theoretical structure factors generated from density functional theory (DFT) calculations. Very strong classical hydrogen bonds drive the cocrystallization and lend stability to the resulting cocrystal. Important conclusions have been drawn about this transition.

Vibrational mode analysis of hydrogen-bonded organic frameworks (HOFs): synchrotron infrared studies.

Hydrogen-bonded organic frameworks (HOFs) are a promising class of porous crystalline materials for gas sorption and gas separation technologies that can be constructed under mild synthetic conditions. In forming three-dimensional networks of flexible hydrogen bonds between donor/acceptor subunits, these materials have displayed high stability at elevated temperature and under vacuum. Although the structural properties of HOFs are commonly characterized by diffraction techniques, new complimentary methods to elucidate phase behaviour and host-guest interactions at the molecular level are sought, particularly those that can be applied under changing physical conditions or solvent environment. To this end, this study has applied synchrotron far-IR and mid-IR spectroscopy to probe the properties of two known and one new HOF system assembled from tetrahedral amidinium and carboxylate building blocks. All three frameworks produce feature-rich and resolved infrared profiles from 30 to 4000 cm-1 that provide information on hydrogen-bonded water solvent networks and the HOF channel topography via lattice and torsional bands. Comparison of experimental peaks to frequencies and atomic displacements (eigenvectors) predicted by high-level periodic DFT calculations have allowed for the assignment of vibrational modes associated with the aforementioned physicochemical properties. Now compiled, the specific vibrational modes identified as common to charge-assisted hydrogen-bonding motifs, as well as low frequency lattice and torsional bands attributed to HOF pore morphology and water-of-hydration networks, can act as diagnostic features in future spectroscopic investigations of HOF properties, such as those toward the design and tuning of host-guest properties for targeted applications.

Triazine based eccentric Piedfort units towards a single source hydrogen bonded network.

Herein we report a hydrogen-bonded three-dimensional network originating from a single source precursor, sym-triisopropylaminotriazine, that is both a donor and an acceptor of hydrogen bonds. The C3h symmetric design allowed the formation of intermolecular hydrogen bonds leading to helices in all three directions. The eccentric Piedfort units present in the framework with a distance of 8.15 Å between the two triazine rings allowed the CHCl3 guest to be parked.

Engineered design of a new HOF by simultaneous monitoring of reaction environment conductivity

The self-assembled Hydrogen−bonded organic frameworks (HOFs) formed by H-bonding between organic linkers were introduced as an exciting type of polymeric porous materials. Here, for the first time, we used sequential conductometry for online monitoring of the self-assembly process as a simple and effective way to find the optimal synthesis ratio of a new HOF. The pentagonal 1,2,4-triazole and the square molecule squaric acid were selected as synthons with different shapes. The obtained structure, [H4C2N3+][HC4O4-] (HOF-1), was revealed by single-crystal X-ray diffraction and further characterized by IR, solid-state UV, and thermogravimetric analysis (TGA). Crystal structure determination shows that HOF-1 crystallizes in monoclinic Cc space group with three-dimensional supramolecular hydrogen-bonded networks via intermolecular O－H⋯O, N－H⋯O, and C－H⋯O interactions. Based on the Electrochemical Impedance Spectroscopy (EIS) results, resistance characteristics of the material after crystallization are significantly reduced, and the dispersion effect is small, indicating that the compound has better uniformity and conductivity after crystallization. By calculation, the electrical conductivity of HOF-1 is excellent at about 10-6 ​S/cm and can be used as a potential proton conductive material.

Temperature dependence of amorphous magnesium carbonate structure studied by PDF and XAFS analyses

Mineral trapping through the precipitation of carbonate minerals is a potential approach to reduce CO2 accumulation in the atmosphere. The temperature dependence of amorphous magnesium carbonate (AMC), a precursor of crystalline magnesium carbonate hydrates, was investigated using synchrotron X-ray scattering experiments with atomic pair distribution function (PDF) and X-ray absorption fine structure analysis. PDF analysis revealed that there were no substantial structural differences among the AMC samples synthesized at 20, 60, and 80 °C. In addition, the medium-range order of all three AMC samples was very similar to that of hydromagnesite. Stirring in aqueous solution at room temperature caused the AMC sample to hydrate immediately and form a three-dimensional hydrogen-bonding network. Consequently, it crystallized with the long-range structural order of nesquehonite. The Mg K-edge X-ray absorption near-edge structure spectrum of AMC prepared at 20 °C was very similar to that of nesquehonite, implying that the electronic structure and coordination geometry of Mg atoms in AMC synthesized at 20 °C are highly similar to those in nesquehonite. Therefore, the short-range order (coordination environment) around the Mg atoms was slightly modified with temperature, but the medium-range order of AMC remained unchanged between 20 and 80 °C.

Drastic Modulation of Molecular Packing and Intrinsic Dissolution Rates by Meniscus-Guided Coating of Extremely Confined Pharmaceutical Thin Films.

Nanosizing has emerged as one of the most effective formulation strategies for enhancement of dissolution properties of active pharmaceutical ingredients (APIs). In addition to enhancing the specific area of the dissolving solids, nanosizing can also capture and stabilize the metastable form of the API, which can further enhance the solubility by drastic modulation of surface energies. Herein, we employ meniscus-guided coating to fabricate nanothin films of three APIs that show anticancer properties and are poorly soluble:10-HCPT, SN-38, and amonafide. By modulating the coating speed, we systematically deposited the APIs in films ranging from ∼200 nm thickness to extreme confinement of ∼10 nm (<10 molecular layers). In all three APIs, we observe a general order-to-disorder transition with semicrystalline (10-HCPT and amonafide) or amorphous (SN-38) form of API solids trapped in thin films when the thickness decreases below a critical value of ∼25-30 nm. The existence of a critical thickness highlights the importance of nanoconfinement in tuning molecular packing. In the case of 10-HCPT, we demonstrate that the disordered form of the API occurs largely due to lack of incorporation of water molecules in thinner films below the critical thickness, thereby disrupting the three-dimensional hydrogen-bonded network held by water molecules. We further developed a dissolution model that predicts variation of the intrinsic dissolution rate (IDR) with API film thickness, which also closely matched with experimental results. We achieved drastic improvement in the IDR of ∼240% in 10-HCPT by decreasing film thickness alone. Further leveraging the order-to-disorder transition led to 2570% modulation of the IDR for amonafide. Our work demonstrates, for the first time, opportunities to largely modulate API dissolution by precisely controlling the dimensionality of thin films.

Polymeric coordination complex of lithium(I) with aqua and cyanurate ligands.

The polymeric title complex, poly[hexa-μ-aqua-diaquatetra-μ-cyanurato-tetralithium] [Li4(C3H2N3O3)4(H2O)7] n , synthesized at room temperature from an aqueous solution of lithium hydroxide and cyanuric chloride, crystallizes in the triclinic space group P . There are two distinct Li+ cations in the asymmetric unit, one of which, Li1, has distorted trigonal-bipyramidal geometry and is coordinated via oxygen to two cyanurate anions occupying equatorial positions, and three water mol-ecules, two in the axial positions and the third in an equatorial position. One of the axial water ligands and the equatorial water ligand are involved in bridging to a crystallographically equivalent Li1 cation. A centre of inversion lies between the two Li1 cations and the Li1⋯Li1 distance is 3.037 (5) Å. The remaining axial water ligand bridges to the second Li cation, Li2, which is disordered over two crystallographic sites with approximately equal occupancy, and has an Li1⋯Li2 distance of 3.438 (7) Å. The terminal Li2 cation is coordinated to three water mol-ecules and an oxygen atom from a cyanuric anion and has a distorted tetra-hedral geometry. A three-dimensional network of inter-molecular hydrogen bonds involving N-H⋯O, O-H⋯O and O-H⋯N inter-actions serves to hold the structure together. The title compound was further characterized using IR and UV-vis spectroscopy and TG-DTA analysis.

Thermodynamics of cavity formation in different solvents: Enthalpy, entropy, and the solvophobic effects

For a long time thermodynamics of cavity formation in non-aqueous solvents remained virtually unexplored. We evaluated the entropic and enthalpic contributions into the Gibbs free energy of cavity formation in 22 structurally different organic solvents and water at 298 K. The calculations were carried out using 50–100 ns long molecular dynamics trajectories of solvents and Widom test particle insertion method with up to 1011 insertions per trajectory. It is shown that protic solvents with three-dimensional hydrogen bond networks, namely water, formamide, glycerol, ethylene glycol, propylene glycol, and diethylene glycol, behave differently from other considered solvents. They are characterized with lower values of the entropy of cavity formation than other considered solvents, which also leads to the higher Gibbs free energies. Water has a particularly low entropy as well as the lowest enthalpy of cavity formation at room temperature. We point out the similar tendencies observed for the thermodynamic functions of the cavities and solvation of real molecules in the considered solvents using entropy vs enthalpy and Gibbs free energy vs enthalpy plots. The cavity term governs the difference in solvation properties of protic hydrogen-bonded and aprotic solvents giving rise to the hydrophobic and more general solvophobic effects.

Protonation sites and hydrogen bonding in mono-hydrobromide salts of two N,4-diheteroaryl 2-aminothiazoles

The synthesis and structural characterization of N-(6-methoxypyridin-3-yl)-4-(pyridin-2-yl)thiazol-2-amine mono-hydrobromide monohydrate (3) and N-(6-methoxypyridin-3-yl)-4-(pyrazin-2-yl)thiazol-2-amine mono-hydrobromide 0.35 methanol solvate (4) are reported. The crystal structures of 3 (monoclinic, space group P21/n, Z = 4) and 4 (monoclinic, space group, C2/c, Z = 8) feature N,4-diheteroaryl 2-aminothiazoles showing similar molecular conformations but different sites of protonation and thus distinctly different intermolecular hydrogen bonding patterns. In 3, Namine–H⋯Br−, N+pyridine–H⋯Owater, and Owater–H⋯Br− hydrogen bonds link protonated N-(6-methoxypyridin-3-yl)-4-(pyridin-2-yl)thiazol-2-amine and water molecules and bromide anions into a three-dimensional hydrogen-bonded network, whereas intermolecular N+methoxypyridine–H⋯Npyrazine hydrogen bonds result in hydrogen-bonded zigzag chains of protonated N-(6-methoxypyridin-3-yl)-4-(pyrazin-2-yl)thiazol-2-amine molecules in 4.

Threefold helical assembly via hy-droxy hydrogen bonds: the 2:1 co-crystal of bi-cyclo-[3.3.0]octane-endo-3,endo-7-diol and bi-cyclo-[3.3.0]octane-endo-3,exo-7-diol.

Reduction of bi-cyclo-[3.3.0]octane-3,7-dione yields a mixture of the endo-3,endo-7-diol and endo-3, exo-7-diol (C8H14O2) isomers (5 and 6). These form (5)2·(6) co-crystals in the monoclinic P21/n space group (with Z = 6, Z' = 1.5) rather than undergoing separation by means of fractional recrystallization or column chromatography. The mol-ecule of 5 occupies a general position, whereas the mol-ecule of 6 is disordered over two orientations across a centre of symmetry with occupancies of 0.463 (2) and 0.037 (2). Individual diol hy-droxy groups associate around a pseudo-threefold screw axis by means of hydrogen bonding. The second hy-droxy group of each diol behaves in a similar manner, generating a three-dimensional hydrogen-bonded network structure. This hydrogen-bond connectivity is identical to that present in three known helical tubuland diol-hydro-quinone co-crystals, and the new crystal structure is even more similar to two homologous aliphatic diol co-crystals.

Molecular Clustering in Formaldehyde-Methanol-Water Mixtures Revealed by High-Intensity, High-q Small-Angle Neutron Scattering.

Methanol-Water (mw) mixtures, with or without a solute, display a nonideal thermodynamic behavior, typically attributed to the structure of the microphase. However, experimental observation of the microphase structures at the molecular length scale has been a challenge. We report the presence of molecular clusters in mw and formaldehyde-methanol-water (fmw) mixtures using small-angle neutron scattering (SANS) experiments and molecular dynamics (MD) simulations. Hydrophobic clusters of methanol in mw and formaldehyde-methanol in fmw mixtures were observed at low methanol compositions (xm ≤ 0.3). A three-dimensional hydrogen-bonded network of water with the solute is observed at xm = 0.5. Linear chains of methanol surrounding the formaldehyde and water molecules were observed at high methanol compositions (xm ≥ 0.7). The calculated size of the molecular clusters (r ≈ 0.5 nm, spherical) from the SANS data and their volume fraction closely matched the MD simulation results.

A silicododecamolybdate/pyridinium-tetrazole hybrid molecular salt as a catalyst for the epoxidation of bio-derived olefins

The hybrid polyoxometalate (POM) salt (Hptz)4[SiMo12O40]∙nH2O (1) (ptz = 5-(2-pyridyl)tetrazole) has been prepared, characterized by X-ray crystallography, and examined as a catalyst for the epoxidation of cis-cyclooctene (Cy) and bio-derived olefins, namely dl-limonene (Lim; a naturally occurring monoterpene found in the rinds of citrus fruits), methyl oleate and methyl linoleate (fatty acid methyl esters (FAMEs) obtained by transesterification of vegetable oils). The crystal structure of 1 consists of α-Keggin-type heteropolyanions, [SiMo12O40]4-, surrounded by space-filling and charge-balancing 2-(tetrazol-5-yl)pyridinium (Hptz+) cations, as well as by a large number of water molecules of crystallization (n = 9). The water molecules mediate an extensive three-dimensional (3D) hydrogen-bonding network involving the inorganic anions and organic cations. For the epoxidation of the model substrate Cy in a nonaqueous system (tert-butylhydroperoxide as oxidant), the catalytic performance of 1 (100% epoxide yield at 24 h, 70 °C) was superior to that of the tetrabutylammonium salt (Bu4N)4[SiMo12O40] (2) (63% epoxide yield at 24 h), illustrating the role of the counterion Hptz+ in enhancing catalytic activity. The hybrid salt 1 was effective for the epoxidation of Lim (69%/85% conversion at 6 h/24 h) and the FAMEs (87–88%/100% conversion at 6 h/24 h), leading to useful bio-based products (epoxides, diepoxides and diol products).

Reorientation-induced relaxation of free OH at the air/water interface revealed by ultrafast heterodyne-detected nonlinear spectroscopy

The uniqueness of water originates from its three-dimensional hydrogen-bond network, but this hydrogen-bond network is suddenly truncated at the interface and non-hydrogen-bonded OH (free OH) appears. Although this free OH is the most characteristic feature of interfacial water, the molecular-level understanding of its dynamic property is still limited due to the technical difficulty. We study ultrafast vibrational relaxation dynamics of the free OH at the air/water interface using time-resolved heterodyne-detected vibrational sum frequency generation (TR-HD-VSFG) spectroscopy. With the use of singular value decomposition (SVD) analysis, the vibrational relaxation (T1) times of the free OH at the neat H2O and isotopically-diluted water interfaces are determined to be 0.87 ± 0.06 ps (neat H2O), 0.84 ± 0.09 ps (H2O/HOD/D2O = 1/2/1), and 0.88 ± 0.16 ps (H2O/HOD/D2O = 1/8/16). The absence of the isotope effect on the T1 time indicates that the main mechanism of the vibrational relaxation of the free OH is reorientation of the topmost water molecules. The determined sub-picosecond T1 time also suggests that the free OH reorients diffusively without the switching of the hydrogen-bond partner by the topmost water molecule.

Thermodynamics of tetramethylurea solutions in ethylene glycol: The evidence of pairwise solvophobic interaction

This paper focuses on the solute – solute interactions in dilute solutions of a typically hydrophobic solute tetramethylurea (TMU) in ethylene glycol (EG) which forms the three-dimensional hydrogen-bond network at the supramolecular level. The results of our experimental efforts based on dilution calorimetry and phase partition techniques are able to make a conclusion that thermodynamics of the TMU – TMU pairwise interaction in EG is to a great extent similar to that occurs in liquid water. All effects, however, are weaker expressed in the non-aqueous medium. In particular, the integrand of the potential of mean force, i.e. the second virial coefficient, between two TMU molecules becomes negative only at elevated temperatures indicating the appearance of a rather weak solvophobic interaction in EG. Since C=O-groups of TMU are well-incorporated into the H-bond network of EG, it is reasonable to assume that the attraction observed should be mainly induced by apolar methyl groups. The correlation between the enthalpy- and volume-related parameters of pairwise interaction provides the additional confirmation of the existence of the solvent-induced solvophobic interaction between TMU molecules in EG.

Hydrogen-bonding patterns in 2,2-bis-(4-methyl-phen-yl)hexa-fluoro-propane pyridinium and ethyl-enedi-ammonium salt crystals.

The crystal structures of two salt crystals of 2,2-bis-(4-methyl-phen-yl)hexa-fluoro-propane (Bmphfp) with amines, namely, dipyridinium 4,4'-(1,1,1,3,3,3-hexa-fluoro-propane-2,2-di-yl)dibenzoate 4,4'-(1,1,1,3,3,3-hexa-fluoro-propane-2,2-di-yl)di-benzoic acid, 2C5H6N+·C17H8F6O4 2-·C17H10F6O4, (1), and a monohydrated ethyl-enedi-ammonium salt ethane-1,2-diaminium 4,4'-(1,1,1,3,3,3-hexa-fluoro-propane-2,2-di-yl)dibenzoate monohydrate, C2H10N2 2+·C17H8F6O4 2-·H2O, (2), are reported. Compounds 1 and 2 crystallize, respectively, in space group P21/c with Z' = 2 and in space group Pbca with Z' = 1. The crystals of compound 1 contain neutral and anionic Bmphfp mol-ecules, and form a one-dimensional hydrogen-bonded chain motif. The crystals of compound 2 contain anionic Bmphfp mol-ecules, which form a complex three-dimensional hydrogen-bonded network with the ethyl-enedi-amine and water mol-ecules.

Structure, Dynamics, and Some Properties of Water

Development of ideas of liquid water structure since the end of the 19th century is briefly reviewed. According to the modern concepts based on experimental data and computer simulation, there is a three-dimensional hydrogen bond network in water. The structural and dynamic inhomogeneity of this network is analyzed in detail.

The first coordination compound of 6-fluoro-nicotinate: the crystal structure of a one-dimensional nickel(II) coordination polymer containing the mixed ligands 6-fluoro-nicotinate and 4,4'-bi-pyridine.

A one-dimensional nickel(II) coordination polymer with the mixed ligands 6-fluoro-nicotinate (6-Fnic) and 4,4'-bi-pyridine (4,4'-bpy), namely, catena-poly[[di-aqua-bis-(6-fluoro-pyridine-3-carboxyl-ato-κO)nickel(II)]-μ-4,4'-bi-pyri-dine-κ2 N:N'] trihydrate], {[Ni(6-Fnic)2(4,4'-bpy)(H2O)2]·3H2O} n , (1), was prepared by the reaction of nickel(II) sulfate hepta-hydrate, 6-fluoro-nicotinic acid (C6H4FNO2) and 4,4'-bi-pyridine (C10H8N2) in a mixture of water and ethanol. The nickel(II) ion in 1 is octa-hedrally coordinated by the O atoms of two water mol-ecules, two O atoms from O-monodentate 6-fluoro-nicotinate ligands and two N atoms from bridging 4,4'-bi-pyridine ligands, forming a trans isomer. The bridging 4,4'-bi-pyridine ligands connect symmetry-related nickel(II) ions into infinite one-dimensional polymeric chains running in the [10] direction. In the extended structure of 1, the polymeric chains and lattice water mol-ecules are connected into a three-dimensional hydrogen-bonded network via strong O-H⋯O and O-H⋯N hydrogen bonds, leading to the formation of distinct hydrogen-bond ring motifs: octa-meric R 8 8(24) and hexa-meric R 8 6(16) loops.

Improvement of Foaming Ability of Surfactant Solutions by Water-Soluble Polymers: Experiment and Molecular Dynamics Simulation.

Aqueous foam is widely used in fire extinguishing and dust suppression technologies. Improving the foaming ability is the key to reducing the added concentration of foaming agents as well as the economic cost. In this work, the effect of a water-soluble polymer (polyvinyl alcohol, PVA) on the foaming ability of anionic surfactant (sodium dodecyl ether sulfate, SDES) was studied by an experiment and molecular dynamics simulation. The experimental results showed that PVA greatly improves the foaming ability of SDES solutions when the surfactant concentration is less than 0.1%, which is attributed to the fact that the polymer can enhance the stability of bubble films and reduce the bubble rupture rate during the foam generation process. The simulation results indicate that PVA can enhance the hydration of surfactant head groups and contribute to the formation of a three-dimensional hydrogen bond network between surfactants, polymers, and water molecules, thus greatly improving the stability of bubble liquid films. The above results suggest that water-soluble polymers can be used to improve the foaming ability of surfactant solutions by enhancing the bubble film stability, which is beneficial as it reduces the added concentration of foaming agents in aqueous foam applications.

Diversifying molecular and topological space via a supramolecular solid-state synthesis: a purely organic mok net sustained by hydrogen bonds.

A three-dimensional hydrogen-bonded network based on a rare mok topology has been constructed using an organic molecule synthesized in the solid state. The molecule is obtained using a supramolecular protecting-group strategy that is applied to a solid-state [2+2] photodimerization. The photodimerization affords a novel head-to-head cyclo-butane product. The cyclo-butane possesses tetrahedrally disposed cis-hydrogen-bond donor (phenolic) and cis-hydrogen-bond acceptor (pyridyl) groups. The product self-assembles in the solid state to form a mok network that exhibits twofold interpenetration. The cyclo-butane adopts different conformations to provide combinations of hydrogen-bond donor and acceptor sites to conform to the structural requirements of the mok net.

Effect of pH on the construction of CdII coordination polymers involving the 1,1'-[1,4-phenylenebis(methylene)]bis(3,5-dicarboxylatopyridinium) ligand.

Changing the pH value of a reaction system can result in polymers with very different compositions and architectures. Two new coordination polymers based on 1,1'-[1,4-phenylenebis(methylene)]bis(3,5-dicarboxylatopyridinium) (L2-), namely catena-poly[[[tetraaquacadmium(II)]-μ2-1,1'-[1,4-phenylenebis(methylene)]bis(3,5-dicarboxylatopyridinium)] 1.66-hydrate], {[Cd(C22H14N2O8)(H2O)4]·1.66H2O}n, (I), and poly[{μ6-1,1'-[1,4-phenylenebis(methylene)]bis(3,5-dicarboxylatopyridinium)}cadmium(II)], [Cd(C22H14N2O8)]n, (II), have been prepared in the presence of NaOH or HNO3 and structurally characterized by single-crystal X-ray diffraction. In polymer (I), each CdII ion is coordinated by two halves of independent L2- ligands, forming a one-dimensional chain structure. In the crystal, these chains are further connected through O-H...O hydrogen bonds, leading to a three-dimensional hydrogen-bonded network. In polymer (II), each hexadentate L2- ligand coordinates to six CdII ions, resulting in a three-dimensional network structure, in which all of the CdII ions and L2- ligands are equivalent, respectively. The IR spectra, thermogravimetric analyses and fluorescence properties of both reported compounds were investigated.