One-dimensional Hydrogen-bonding Network Research Articles

Slow Magnetic Relaxation in Cobalt(II) Complexes with One-Dimensional Hydrogen-Bonded Networks

Two new cobalt(II) complexes with an unsymmetrical bidentate ligand, 2-(1,4,5,6-tetrahydropyrimidin-2-yl)-6-methoxyphenol (H2mthp), were synthesized and crystallographically characterized. Tetra- and hexa-coordinate mononuclear complexes were selectively obtained by adjusting the stoichiometry of the base. The coordination geometry of hexa-coordinated complex was severely distorted from an ideal octahedron, due to the NO5 coordination environment from the mixed coordination of one Hmthp− and two H2mthp ligands. Both complexes formed one-dimensional chain networks by hydrogen-bond and N-H···π interactions. Single-molecule magnet behavior was observed for the tetrahedral complex under zero magnetic field. The relatively short Co···Co distances induced non-zero intermolecular magnetic coupling, which split the ground ±Ms levels to suppress quantum-tunneling of magnetization. In the octahedral complex, by contrast, the distance was not short enough to induce the coupling. As a consequence, single-molecule magnetic behavior was observed for the octahedral complex only in the presence of an external static field.

The phase stability of terephthalic acid under high pressure

Terephthalic acid has been investigated by Raman spectroscopy up to 15 GPa. According to ab initio calculations, it can be speculated that both of π-π stacking interactions between molecules and the symmetry of hydrogen bonds are enhanced with gradually increasing pressure. Furthermore, we use the Hirshfeld surface to map the π-π stacking interaction in the TPA molecule at high pressure. The Raman spectra and ab initio calculation results indicate that the phase stability of TPA is related to the one-dimensional hydrogen bond network and inter-chain aromatic π-π stacking interaction.

Synthesis, X-ray structure and topology (AIM and Hirshfeld) analyses of the new square planar [Ag(pyridine-2-aldoxime)2]ClO4 complex; A comparative study with its nitrato analogue

The new homoleptic square planar complex [AgL2]ClO4·H2O; 1, where L is pyridine-2-aldoxime, is synthesized and characterized using elemental analysis, FTIR and NMR spectra as well as X-ray single crystal structure analysis. The ligand (L) acts as a bidentate ligand via the pyridine and oxime N-atoms while the perchlorate anion is not coordinated to the silver atom. The crystal structure of 1 is characterized by one-dimensional infinite hydrogen bond network with backbone build up by hydrogen bridge interactions between the water molecules, the OH groups of the aldoxime and the perchlorate anions. The structure of 1 is optimized using eight DFT methods. The B97D/def2-TZVP and PBEPBE/def2-TZVP are the best to predict the AgN/AgO distances and the coordination geometry around Ag(I) ion, respectively. Atoms in molecules (AIM) and Hirshfeld topology analyses were used to describe the AgN/AgO bonding nature and the possible intermolecular interactions, respectively, in comparison with the nitrato analogue [AgL(NO3)]; 2. The O⋯H, H⋯H, C⋯C and H⋯C are the most common intermolecular interactions occurred in both complexes. Only complex 2 showed significant Ag⋯O (2.720–2.731 Å) intermolecular interactions. AIM and NBO analyses explained that the ClO4− anion is weakly interacting with Ag(I) in 1 while the NO3− is coordinated via one of its O-atoms in 2.

Crystal structure of 1,2-bis-[(1H-imidazol-2-yl)methylidene]hydrazine and its one-dimensional hydrogen-bonding network.

In the title compound, C8H8N6, two imidazolyl groups are separated by a zigzag -CH=N-N=CH- linkage. An inversion center is located at the mid-point of the N-N single bond and the complete molecule is generated by symmetry. In the crystal, each mol-ecule forms four N-H⋯N hydrogen bonds with two neighbouring mol-ecules to constitute a one-dimensional ladder-like structure propagating along the a-axis direction.

Synthesis and structural characterization of zinc(II) and cobalt(II) complexes based on multidentate hydrazone ligands

Two multidentate Schiff base ligands containing a hydrazone unit have been synthesized and investigated for zinc(II) and cobalt(II) coordination chemistry. The reactions of the 4-pyridyl derived hydrazone ligand HL1 with zinc(II) or cobalt(II) salts gave three mononuclear complexes that were structurally characterized by X-ray diffraction analysis. The results revealed that the ligand could adopt different coordination modes when various counter anions were employed. While in the case that zinc dichloride was used as a metal salt a neutral mononuclear mono-ligand complex was formed, the deprotonation of hydrazone occurred when zinc(II) or cobalt(II) nitrate were present and two new isostructural mononuclear bis-ligand complexes were isolated. Modification of the hydrazone ligand with oxygen donors was found to have a significant impact on the ligand reactivity, and a similar reaction of H2L2 with cobalt(II) nitrate gave a protonated product of H2L2 without the incorporation of cobalt(II), which features a one-dimensional hydrogen-bonded network in the solid state.

Crystal structure of tetra-kis-(μ3-2-{[1,1-bis-(hy-droxy-meth-yl)-2-oxidoeth-yl]imino-meth-yl}-6-meth-oxy-phenolato)tetra-kis-[aqua-copper(II)]: a redetermination at 200 K.

The crystal structure of the tetra-nuclear title compound, [Cu4(C12H15NO5)4(H2O)4], has been previously reported by Back, Oliveira, Canabarro & Iglesias [Z. Anorg. Allg. Chem. (2015), 641, 941-947], based on room-temperature data. In the previously published structure, no standard uncertainties are recorded for the deprotonated hy-droxy-methyl group and water mol-ecule O atoms coordinating to the metal atom indicating that they were not refined; furthermore, the H atoms of some OH groups and water mol-ecules have not been positioned accurately. Since the current structure was determined at a lower temperature, all atoms, including the H atoms of these hy-droxy groups and the water mol-ecule, have been determined more accurately resulting in improved standard uncertainties in the bond lengths and angles. Diffraction data were collected at 200 K, rather than the more usual 100 K, due to apparent disordering at lower temperatures. In addition, it is now possible to report intra- and inter-molecular O-H⋯O inter-actions. In the title complex molecule, which has crystallographic -4 symmetry, the Cu(II) ions are coordinated by the tridentate Schiff base ligands and water mol-ecules, forming a tetra-nuclear Cu4O4 cubane-like core. The Cu(II) ion adopts a CuNO5 elongated octa-hedral environment. The coordination environment of Cu(II) at 200 K displays a small contraction of the Cu-N/O bonds, compared with the room-temperature structure. In the crystal lattice, the neutral clusters are linked by inter-molecular O-H⋯O hydrogen bonds into a one-dimensional hydrogen-bonding network propagating along the b axis.

Enhanced proton-transfer activity in imidazole@MIL-53(Al) systems revealed by molecular-dynamics simulations

Proton-transfer reactions in imidazole molecules confined in the metal-organic framework MIL-53(Al) were studied by means of Born-Oppenheimer molecular-dynamics simulations employing the density-functional tight-binding method. The statistical analysis of the trajectories revealed an essential impact of the framework on the orientation of the molecules in its channels and, thus, on the hydrogen-bond network. The one-dimensional hydrogen-bond network is one reason for faster reorientation dynamics compared to liquid imidazole. A lifetime in the order of 100 fs could be attributed to the proton-transfer transition state, a Zundel-like ion, and the combined imidazole@MIL-53(Al) system exhibited shorter times between hopping events compared to the liquid phase. This goes along with experimental findings of enhanced proton conductivity in this system.

Cocrystals of 6-methyl-2-thiouracil: presence of the acceptor-donor-acceptor/donor-acceptor-donor synthon.

The results of seven cocrystallization experiments of the antithyroid drug 6-methyl-2-thiouracil (MTU), C(5)H(6)N(2)OS, with 2,4-diaminopyrimidine, 2,4,6-triaminopyrimidine and 6-amino-3H-isocytosine (viz. 2,6-diamino-3H-pyrimidin-4-one) are reported. MTU features an ADA (A = acceptor and D = donor) hydrogen-bonding site, while the three coformers show complementary DAD hydrogen-bonding sites and therefore should be capable of forming an ADA/DAD N-H...O/N-H...N/N-H...S synthon with MTU. The experiments yielded one cocrystal and six cocrystal solvates, namely 6-methyl-2-thiouracil-2,4-diaminopyrimidine-1-methylpyrrolidin-2-one (1/1/2), C(5)H(6)N(2)OS·C(4)H(6)N(4)·2C(5)H(9)NO, (I), 6-methyl-2-thiouracil-2,4-diaminopyrimidine (1/1), C(5)H(6)N(2)OS·C(4)H(6)N(4), (II), 6-methyl-2-thiouracil-2,4-diaminopyrimidine-N,N-dimethylacetamide (2/1/2), 2C(5)H(6)N(2)OS·C(4)H(6)N(4)·2C(4)H(9)NO, (III), 6-methyl-2-thiouracil-2,4-diaminopyrimidine-N,N-dimethylformamide (2/1/2), C(5)H(6)N(2)OS·0.5C(4)H(6)N(4)·C(3)H(7)NO, (IV), 2,4,6-triaminopyrimidinium 6-methyl-2-thiouracilate-6-methyl-2-thiouracil-N,N-dimethylformamide (1/1/2), C(4)H(8)N(5)(+)·C(5)H(5)N(2)OS(-)·C(5)H(6)N(2)OS·2C(3)H(7)NO, (V), 6-methyl-2-thiouracil-6-amino-3H-isocytosine-N,N-dimethylformamide (1/1/1), C(5)H(6)N(2)OS·C(4)H(6)N(4)O·C(3)H(7)NO, (VI), and 6-methyl-2-thiouracil-6-amino-3H-isocytosine-dimethyl sulfoxide (1/1/1), C(5)H(6)N(2)OS·C(4)H(6)N(4)O·C(2)H(6)OS, (VII). Whereas in cocrystal (I) an R(2)(2)(8) interaction similar to the Watson-Crick adenine/uracil base pair is formed and a two-dimensional hydrogen-bonding network is observed, the cocrystals (II)-(VII) contain the triply hydrogen-bonded ADA/DAD N-H...O/N-H...N/N-H...S synthon and show a one-dimensional hydrogen-bonding network. Although 2,4-diaminopyrimidine possesses only one DAD hydrogen-bonding site, it is, due to orientational disorder, triply connected to two MTU molecules in (III) and (IV).

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

Synthesis and Self‐Assembly of NCN‐Pincer Pd‐Complex‐Bound Norvalines

The NCN-pincer Pd-complex-bound norvalines Boc-D/L-[PdCl(dpb)]Nva-OMe (1) were synthesized in multigram quantities. The molecular structure and absolute configuration of 1 were unequivocally determined by single-crystal X-ray structure analysis. The robustness of 1 under acidic/basic conditions provides a wide range of N-/C-terminus convertibility based on the related synthetic transformations. Installation of a variety of functional groups into the N-/C-terminus of 1 was readily carried out through N-Boc- or C-methyl ester deprotection and subsequent condensations with carboxylic acids, R(1)COOH, or amines, R(2)NH2 , to give the corresponding N-/C-functionalized norvalines R(1)-D/L-[PdCl(dpb)]Nva-R(2) 2-9. The dipeptide bearing two Pd units 10 was successfully synthesized through the condensation of C-free 1 with N-free 1. The robustness of these Pd-bound norvalines was adequately demonstrated by the preservation of the optical purity and Pd unit during the synthetic transformations. The lipophilic Pd-bound norvalines L-2, Boc-L-[PdCl(dpb)]Nva-NH-n-C11H23, and L-4, n-C4H9CO-L-[PdCl(dpb)]Nva-NH-n-C11H23, self-assembled in aromatic solvents to afford supramolecular gels. The assembled structures in a thermodynamically stable single crystal of L-2 and kinetically stable supramolecular aggregates of L-2 were precisely elucidated by cryo-TEM, WAX, SAXS, UV/Vis, IR analyses, and single-crystal X-ray crystallography. An antiparallel β-sheet-type aggregate consisting of an infinite one-dimensional hydrogen-bonding network of amide groups and π-stacking of PdCl(dpb) moieties was observed in the supramolecular gel fiber of L-2, even though discrete dimers are assembled through hydrogen bonding in the thermodynamically stable single crystal of L-2. The disparate DSC profiles of the single crystal and xerogel of L-2 indicate different thermodynamics of the molecular assembly process.

Dibenzyl ferrocene-1,1′-dicarboxylate

In the title compound, [Fe(C13H11O2)2], there are markedly different orientations of the two phenyl­meth­oxy­carbonyl substituents [O—C—C—C torsion angles = 84.5 (3) and 139.6 (2)°]. These orientations are mediated by a number of inter­molecular C—H⋯O inter­actions, which result in a one-dimensional hydrogen-bonded network of mol­ecules.

Hydrogen-Bonding-Assisted Self-Doping in Tetrathiafulvalene (TTF) Conductor

The synthesis, characterization, and carrier generation mechanism of self-doping in a tetrathiafulvalene (TTF) conductor, ammonium tetrathiafulvalene-2-carboxylate (TTFCOO(-)NH(4)(+)), are described together with molecular orbital characteristics. Insulating TTFCOOH changes into a hole-doped conductor TTFCOO(-)NH(4)(+) with a conductivity of sigma = 2.0 x 10(-4) S/cm (300 K), upon salt formation with NH(3). A radical species, TTF(*+)COO(-)NH(4)(+), is generated via protonation of the TTF moiety as demonstrated by UV-vis, ESR, and (1)H NMR spectra. The X-ray crystallographic structure of TTFCOO(-)NH(4)(+) reveals supramolecular arrays of TTFCOO(-) moieties with short S...S contact, assisted by the one-dimensional hydrogen-bonding network composed of the ammonium and carboxylate ions. Molecular orbital calculations of cluster models show that the singly occupied molecular orbital (SOMO) of TTF(*+)COO(-)NH(4)(+) in the supramolecular array is not at the highest energy level, which is characterized as a quasi-closed-shell state. The ab initio periodic calculation with a one-dimensional boundary condition reveals that TTF(*+)COO(-)NH(4)(+) behaves as a dopant leading to the semiconducting behavior of the stacked TTF moieties assembled by the hydrogen-bonding network. Namely, TTFCOO(-)NH(4)(+) can be described as a "hydrogen-bonding-assisted self-doped conductor". The contribution of the hydrogen-bonding interaction to the electron conduction is experimentally supported by a large isotope effect in the ac conductivity of TTFCOO(-)NH(4)(+) at low temperature.

Deuterium NMR Study of Molecular Dynamics and Phase Transition in Acetonitrile Crystal

The molecular dynamics and local structure in the alpha and beta phases of CD(3)CN were studied by (2)H NMR spectroscopy. From the (2)H NMR spin-lattice relaxation time (T(1)), the activation energies of the rotation of the CD(3) group about the C(3) axis in both phases were found to be 6.2 and 11 kJ mol(-1), respectively. These activation energy values suggest that the packing between CD(3)CN molecules in the alpha phase is weaker than that in the beta phase. The slow structural change of the crystal due to the alpha-beta phase transition was investigated using the (2)H NMR spectra and T(1). A jump of CH(3)CN between two neighboring sites in the hydrogen-bond network accompanying the molecular reorientation was observed by the (2)H NMR 2D exchange spectra and the stimulated-echo method in the alpha phase. Vacancy diffusion occurred in the one-dimensional hydrogen-bond network in the alpha phase.

Kinetics of Switchable Proton Escape from a Proton-Wire within Green Fluorescence Protein

The emission from the acidic form of the green fluorescence protein (GFP) changes with increasing time and temperature from t-1/2 to t-3/2 asymptotics. It is shown that a model of proton diffusion along a one-dimensional hydrogen-bond network within the protein, with a switch (Thr203) allowing for proton escape, explains the data quantitatively. From a comparison of the model with experiment, we obtain the rate parameters for proton dissociation from the chromophore (showing an inverse temperature effect), the ratio of the proton association constant squared to its diffusion constant (exhibiting no temperature effect), and the time constant for switch opening (with a significant Arrhenius dependence). Thus, proton dissociation has a small negative activation energy (assigned to a complex of the anionic chromophore with H3O+), whereas the switch has a large positive activation energy (assigned to Thr203 side-chain rotation). Proton migration is possibly the outcome of the concerted motion of several protons within GFP.

2,4,6-Tris{[(S)-1-hydroxy-3-methylbutan-2-ylamino]methylene}cyclohexane-1,3,5-trione

The title compound, C24H39N3O6, also known as tris­[(S)-N-salicylidenevalinol], crystallizes with two mol­ecules in the asymmetric unit. These two mol­ecules form a disc-shaped dimeric box and are linked to each other through 11 O—H⋯O hydrogen bonds. These self-assembled dimers are connected by a 12th hydrogen bond to form a one-dimensional hydrogen-bonded network along the b-axis direction.

Solvent water tapes in two hydrates of μ-oxo-bis[bis(2,2′-bipyridine-κ2N,N′)(sulfato-κO)iron(III)

The title compound, [Fe2O(SO4)2(C10H8N2)4], crystallizes as two different hydrates, viz. 11H2O, (I), and 15H2O, (II). The complex is binuclear, in which the two FeIII atoms are coordinated in an octahedral geometry to four N atoms from the two bipyridine ligands, to one O atom from the sulfate ion and to an oxide ion on a twofold axis, which acts as a bridge between the symmetry-related units. The Fe...Fe separation is 3.556 (4) A and the Fe-O-Fe angle is 161.6 (2) degrees in (I); the corresponding values are 3.544 (1) A and 165.8 (2) degrees in (II). In (II), one of the O atoms of the sulfate ion is disordered over two positions. In both compounds, the solvent water molecules form slightly different one-dimensional hydrogen-bonded networks which pass along the c axis of the unit cell. In (I), three solvent water molecules and, in (II), one solvent water molecule, are situated on the twofold axis. In both (I) and (II), the central O atom of the metal complex lies on a twofold axis.

(4R,5R)-Bis(hydroxydimethylmethyl)-2,2-dimethyl-1,3-dioxolane

In the title compound, C11H22O4, certain C—C bond lengths are shorter than expected. As a result of the synthetic precursor being enanti­omerically pure, only the R,R enanti­omer occurs in the structure. There are two molecules in the asymmetric unit. Both intra- and inter­molecular hydrogen bonds are present between the hydroxyl groups, resulting in a one-dimensional hydrogen-bonding network.

Tunable organic clay mimic structures with di(primary ammonium) dicarboxylates

Design of supramolecular architectures as intended is one of the ultimate goals of supramolecular chemistry. To achieve the worthwhile goal, design of crystal structures are a promising approach because X-ray single crystallographic analysis is the only way for precise elucidation of molecular arrangements and intermolecular interactions at a molecular level. One of the approaches to design supramolecular architectures, organic salts is useful tool. The organic salts have the following excellent advantages; i) robust supramolecular synthons are formed with charge-assisted hydrogen bonds, ii) a wide variety of cations or anions are able to be arranged on the clays by just changing combinations of the salts. In previous work, we showed the control of interlayer distance of organic clay mimic structures composed of 1-naphthylmethylammonium carboxylates [1] by just varying the carbon numbers of the n-alkanoate. The clays are formedwith robust two-dimensional hydrogen bondnetwork, and the anions between layers are arranged at invariable intervals. Consequently, the clays have difficulties to control and vary intervals of molecules. Here we show the tunable organic clay mimic structures, which are designed and constructed with tert-amylammonium dicarboxylates [2]. The tunability takes important roles in association with various points: configurations of inclusion spaces, possibilities of topochemical reactions, solid-state physical properties, etc. The resulting structures give us a powerful and useful key to solve the conventional difficulties. To design the 2D motif with a tunable axle, a robust one-dimensional hydrogen bond network and tectons as a link are necessary. For this purpose, we adopted a robust supramolecular synthon composed of primary ammonium carboxylates. Many kinds of crystal structures composed of primary ammonium carboxylates have been analyzed and 287 salts are found in Cambridge Structural Database (CSD) (queried on components that contain at least two molecules, one primary amine and one carboxylic acid, except any other extra acids, bases andmetals). And 173 (60.3%) of them form the specified one-dimensional hydrogen bond network with directionality. The same network formed when several types of dicarboxylic acids, such as terephthalic acid, biphenyl-4,4’-dicarboxylic acid and isophthalic acid, were employed as a tecton. X-ray analysis revealed that most of the organic salts formed the layer structures with interdigitated arrangements of primary ammonium cations. By varying the tecton, intervals of the cations on the layer and polarity of the layer are tunable. This design mentioned above is widely applicable to construct the predictable organic crystals.

Cation-Induced Supramolecular Isomerism in the Hydrogen-Bonded Network of Secondary Ammonium Monocarboxylate Salts: A New Class of Organo Gelator and Their Structures

A series of secondary ammonium monocarboxylate salts have been prepared by reacting variously substituted cinnamic acids and benzoic acids with dibenzylamine. Gelation tests reveal that 19 salts (9 cinnamates and 10 benzoates) are moderate to good gelators of various organic fluids, including commercial fuels such as gasoline and diesel fuel. Structure−property correlation studies based on single-crystal structures of 18 salts indicate that the one-dimensional hydrogen-bonded network is indeed important for gelation. The conformational flexibility of the dibenzyl cation and various intra- and internetwork C−H···π and C−H···O interactions appear to be responsible for the stabilization of the one-dimensional network in these salts. The gel fibrils in the xerogel state for 8 salts also adopt a 1D hydrogen-bonded network, as revealed by detailed X-ray powder diffraction studies, further supporting the importance of the one-dimensional network in the gelation process.

Noncovalent Syntheses of Supramolecular Organo Gelators

Four new organo gelators, namely, dicyclohexylammonium hydrogen cyclobutane-1,1-dicarboxylate (1), dicyclohexylammonium cyclobutane-1,1-dicarboxylate (2), dibenzylammonium hydrogen cyclobutane-1,1-dicarboxylate (3), and dibenzylammonium cyclobutane-1,1-dicarboxylate (4), have been noncovalently synthesized. Single-crystal structures of all the gelators were determined to make an attempt to correlate their structure with their properties (gelation). The results support the conclusion that a one-dimensional hydrogen-bonded network in the crystal structure appears to be one of the prerequisites for gelation behavior.