Intermolecular hydrogen bonds: Comparison of associates in crystals and liquids

The density and sound velocity were measured within wide ranges of temperature for a number of liquids (water, formamide, diols, aliphatic alcohols, cellosolves, ketones), in which various types of H-associate can exist. The temperature dependences of the adiabatic and molar adiabatic compressibility, density, and molar volume are analyzed. The values of the molar adiabatic compressibility permit one to evaluate the dimensionality of H-associates existing in liquids; the values of adiabatic compressibility do not offer this possibility. The terms responsible for the similarity and difference between H-associates in crystals and liquids are discussed.     

Charge‐Transfer Solids Using Nucleobases: Supramolecular Architectures Composed of Cytosine and [Ni(dmit)2] Assembled by Multiple Hydrogen Bonds and Heteroatomic Contacts

Protonated species of the nucleobase cytosine (C), namely the monoprotonated CH⁺ and the hemiprotonated CHC⁺, were used to obtain four charge‐transfer complexes of [Ni(dmit)₂] (dmit: 1,3‐dithiole‐2‐thione‐4,5‐dithiolate). Diffusion methods afforded two semiconducting [Ni(dmit)₂]^? salts; (CH)[Ni(dmit)₂](CH₃CN) ( 1 ) and (CHC)[Ni(dmit)₂] ( 2 ). In salt 1 , the [Ni(dmit)₂]^? ions with a S=1/2 spin construct a uniform one‐dimensional array along the molecular long axis, and the significant intermolecular interaction along the face‐to‐face direction results in a spin‐singlet ground state. In contrast, salt 2 exhibits the Mott insulating behavior associated with uniform 1D arrays of [Ni(dmit)₂]^?, which assemble a two‐dimensional layer that is sandwiched between the layers of hydrogen‐bonded CHC⁺ ribbons. Multiple hydrogen bonds between CHC⁺ and [Ni(dmit)₂]^? seem to result in the absence of structural phase transition down to 0.5 K. Electrooxidation of [Ni(dmit)₂]^? afforded the polymorphs of the [Ni(dmit)₂]^0.5? salts, (CHC⁺)[{Ni(dmit)₂}^0.5?]₂ ( 3 and 4 ), which are the first mixed‐valence salts of nucleobase cations with metal complex anions. Similar to 2 , salt 3 contains CHC⁺ ribbons that are sandwiched between the 2D [Ni(dmit)₂]^0.5? layers. In the layer, the [Ni(dmit)₂]^0.5? ions form dimers with a S=1/2 spin and the narrow electronic bandwidth causes a semiconducting behavior. In salt 4 , the CHC⁺ units form an unprecedented corrugated 2D sheet, which is sandwiched between the 2D [Ni(dmit)₂]^0.5? layers that involve ring‐over‐atom and spanning overlaps. In contrast to 3 , salt 4 exhibits metallic behavior down to 1.8 K, associated with a wide bandwidth and a 2D Fermi surface. The ability of hydrogen‐bonded CHC⁺ sheets as a template for the anion radical arrangements is demonstrated.     

A new method for quick predicting the strength of intermolecular hydrogen bonds

A new method is proposed to quick predict the strength of intermolecular hydrogen bonds. The method is employed to produce the hydrogen-bonding potential energy curves of twenty-nine hydrogen-bonded dimers. The calculation results show that the hydrogen-bonding potential energy curves obtained from this method are in good agreement with those obtained from MP2/6-31+G** calculations by including the BSSE correction, which demonstrate that the method proposed in this work can be used to calculate the hydrogen-bonding interactions in peptides. Supported by the National Natural Science Foundation of China (Grants Nos. 20573049 and 20633050) and the research fund of the Educational Department of Liaoning Province (2004C019, 20060469)     

Controlling the conformation of arylamides: computational studies of intramolecular hydrogen bonds between amides and ethers or thioethers

The role of an ortho-alkylthioether group in controlling the conformation around the ring-N bonds of meta-connected arylamide oligomers is studied. Density functional theory (DFT) geometries of model compounds, including acetanilide, an ether acetanilide, and a thioether acetanilide, and their corresponding diamides, show that for either monoamide or diamide the alkyl side chain of the thioether should be perpendicular to the aryl plane, whereas for the ether monoamide, the alkyl side chain is in the aryl plane. DFT ring-N torsional potentials and constrained geometries of the model compounds demonstrate that carbonyl-S repulsion leads to a high torsional barrier and that intramolecular N-H...S and C-H...O hydrogen bonds and ring-amide conjugation lead to N-H having a preferred orientation in the benzene plane pointing towards S. The N-H bond lengthens and the ortho-ring C-H bond shortens in a regular pattern in the approach to the preferred orientation. Calculated IR frequencies for the N-H stretch show a clear red shift between model compounds without and with the thioether side chain.     

Intramolecular hydrogen bonds in crystals of thiophosphorylbenzopyrane derivatives – X-ray and FT-IR studies

The crystal structures of two new benzopyrane derivatives are analyzed and compared with previous X-ray investigations on related compounds. A particular attention is focused on intramolecular interactions. For the chromone derivatives (1 and 3) only one kind of interaction is possible, i.e., N–HO, whereas for the coumarine derivatives (2 and 4) two types of intramolecular hydrogen bonding are observed – N–HO and O–HN. Two types of H-bond for coumarine derivatives are the result of the existence of two tautomeric forms – enamine and iminoenol. Combined spectroscopic, NMR and IR measurements confirm such tautomeric equilibrium in solution. The influence of the additional intermolecular hydrogen bonds on the stabilization of tautomeric forms in crystals is also discussed here.     

Steric control over hydrogen bonding in crystalline organic solids: a structural study of N,N'-dialkylthioureas

Hydrogen bonding in crystalline N,N'-dialkylthioureas was examined with the help of single-crystal X-ray diffraction, DFT calculations, and Cambridge Structural Database (CSD) analysis. A CSD survey indicated that unlike the related urea derivatives, which persistently self-assemble into one-dimensional hydrogen-bonded chains, the analogous thioureas can form two different hydrogen-bonding motifs in the solid state: chains, structurally similar with those found in ureas, and dimers, that further associate into hydrogen-bonded layers. The formation of one motif or another can be manipulated by the bulkiness of the organic substituents on the thiourea group, which provides a clear example of steric control over the hydrogen bonding arrangement in crystalline organic solids.     

fac-Acetato-bis(pyrazole) complexes: A systematic study on intra- and intermolecular hydrogen bonds

Acetato-bis(pyrazole) complexes [Mo(η³-methallyl)(O₂CMe)(CO)₂(pz^∗H)₂], (methallyl = CH₂C(CH₃)CH₂) and fac-[M(O₂CMe)(CO)₃(pz^∗H)₂], (pz^∗H = pyrazole or 3,5-dimethylpyrazole, dmpzH; M = Mn, Re) are obtained from [Mo(η³-methallyl)Cl(CO)₂(NCMe)₂] or fac-[MBr(CO)₃(NCMe)₂] [M = Mn (synthesized in situ), Re], 2 equiv. of pyrazole, and 1 equiv. of sodium acetate for Mo complexes, or silver acetate for Mn or Re complexes. The chlorido-complexes [Mo(η³-methallyl)Cl(CO)₂L₂] (L = pzH, dmpzH), obtained from the same starting material by substitution of MeCN by pzH or dmpzH, are also described. The crystal structures of the fac-acetato-bis(dimethylpyrazole) complexes present the same pattern of intramolecular hydrogen bonds between the acetate and the dimetylpyrazole ligands, whereas the crystal structures of the fac-acetato-bis(pyrazole) complexes show different hydrogen bonds patterns, with intermolecular interactions. NMR data indicate that these interactions are not maintained in solution.     

Structural rationalisation of co-crystals formed between trithiocyanuric acid and molecules containing hydrogen bonding functionality

Crystallisation of trithiocyanuric acid (TTCA) from various organic solvents that have hydrogen bonding capability (acetone, 2-butanone, dimethylformamide, dimethyl sulfoxide, methanol and acetonitrile) leads to the formation of co-crystals in which the solvent molecules are incorporated together with TTCA in the crystal structure. Structure determination by single-crystal X-ray diffraction reveals that these co-crystals can be classified into different groups depending upon the topological arrangement of the TTCA molecules in the crystal structure. Thus, three different types of single-tape arrangements of TTCA molecules and one type of double-tape arrangement of TTCA molecules are identified. In all co-crystals, hydrogen-bonding interactions are formed through the involvement of N-H bonds of TTCA molecules in these tapes and the other molecule in the co-crystal. Detailed rationalisation of the structural properties of these co-crystals is presented.     

Characteristic features of intra- and intermolecular interactions in crystals of pyrrole-2-carbaldehyde isonicotinoylhydrazone and its hydrate

Pyrrole-2-carbaldehyde isonicotinoylhydrazone (1) and its hydrate [1·H₂O] (2) were studied by single-crystal X-ray diffraction analysis. The introduction of the pyrrole substituent into N"-substituted isonicotinic hydrazide (INH) causes the intramolecular redistribution of the electron density compared to those in INHs studied earlier, which increases the basicity of the hydrazone nitrogen atom (N") involved in intermolecular hydrogen bonding. This effect has not been observed in the structures of N"-substituted INHs and benzhydrazides studied previously. Intermolecular hydrogen bonds play a decisive role in the formation of the crystal structures of 1 and 2.     

Direct evaluation of individual hydrogen bond energy in situ in intra- and intermolecular multiple hydrogen bonds system

The results of evaluating the individual hydrogen bond (H-bond) strength are expected to be helpful for the rational design of new strategies for molecular recognition or supramolecular assemblies. Unfortunately, there is few obvious and unambiguous means of evaluating the energy of a single H-bond within a multiple H-bonds system. We present a local analytic model, ABEEMσπ H-bond energy (HBE) model based on ab initio calculations (MP2) as benchmark, to directly and rapidly evaluate the individual HBE in situ in inter- and intramolecular multiple H-bonds system. This model describes the HBE as the sum of electrostatic and van der Waals (vdW) interactions which all depend upon the geometry and environment, and the ambient environment of H-bond in the model is accounted fairly. Thus, it can fairly consider the cooperative effect and secondary effect. The application range of ABEEMσπ HBE model is rather wide. This work has discussed the individual H-bond in DNA base pair and protein peptide dimers. The results indicate that the interactions among donor H atom, acceptor atom as well as those atoms connected to them with 1,2 or 1,3 relationships are all important for evaluating the HBE, although the interaction between the donor H atom and the acceptor atom is large. Furthermore, our model quantitatively indicates the polarization ability of N, O, and S in a new style, and gives the percentage of the polarization effect in HBE, which can not be given by fixed partial charge force field.     

Triple hydrogen bonds direct crystal engineering of metal-assembled complexes: the effect of a novel organic-inorganic module on supramolecular structure

Novel triply hydrogen bonded suprastructures based on [M(tdpd)2(L)2]2- (H2tdpd=1,4,5,6-tetrahydro-5,6-dioxo-2,3-pyrazinedicarbonitrile, L=solvent) and melamine-analogous cations have been synthesized and characterized. The use of anions containing two AAA sets from [M(tdpd)2(L)2]2- together with cations containing one DDD set (A=hydrogen-bond acceptor, D=hydrogen-bond donor) leads to the formation of complementary triply hydrogen bonded modules in the solid state. In all cases, the building module is further extended via additional hydrogen-bonding interactions to produce a tape, and tapes are assembled into sheets. These results show that a hydrogen-bonded module consisting of different kinds of building blocks, one of which is a metal complex that includes hydrogen-bond acceptor sites and the other is a hydrogen-bond donor molecule, will be attractive for constructing metal-containing supramolecular systems by the self-assembly technique.     

Thermally bandwidth-controllable reflective liquid crystal film from rupture and self-assembly of hydrogen bonds

A cholesteric liquid crystal (Ch-LC) composite containing a hydrogen bond (H-bond) chiral dopant (HCD) was prepared and filled into a planar treated cell. When the cell was heated, the selective reflection of the cell exhibited an unusual red shift. One of the reasonable mechanisms was that the H-bonds of HCD ruptured when the temperature was high, and the HCD split into two new chiral dopants (CDs), which made the whole helical twisting power (HTP) value in the composite changed a lot, thus the pitch length of the composite changed. On the basis of this mechanism, when the composite was polymerised at the temperature of H-bonds of HCD ruptured, the bandwidth of the obtained film can be tuned form wider to narrower reversibly by the rupture and self-assembly of H-bonds chiral molecules as the temperature changed, respectively.     

Asymmetry induction by cooperative intermolecular hydrogen bonds in surface-anchored layers of achiral molecules.

The mesoscale induction of two-dimensional supramolecular chirality (formation of 2D organic domains with a single handedness) was achieved by self-assembly of 1,2,4-benzenetricarboxylic (trimellitic) acid on a Cu(100) surface at elevated temperatures. The combination of spectroscopic [X-ray photoelectron spectroscopy (XPS) and near-edge X-ray absorption fine structure (NEXAFS)], real-space-probe [scanning tunneling microscopy (STM)], and computational [density functional theory (DFT)] methods allows a comprehensive characterization of the obtained organic adlayers, where details of molecular adsorption geometry, intermolecular coupling, and surface chemical bonding are elucidated. The trimellitic acid species, comprising three functional carboxylic groups, form distinct stable mirror-symmetric hydrogen-bonded domains. The chiral ordering is associated with conformational restriction in the domains: molecules anchor to the substrate with an ortho carboxylate group, providing two para carboxylic acid moieties for collective lateral interweaving through H bonding, which induces a specific tilt of the molecular plane. The ease of molecular symmetry switching in domain formation makes homochiral-signature propagation solely limited by the terrace width. The molecular layer modifies the morphology of the underlying copper substrate and induces mum-sized strictly homochiral terraces.     

Crystal Engineering of Energetic Materials: Co‐crystals of Ethylenedinitramine (EDNA) with Modified Performance and Improved Chemical Stability

In the area of energetic materials, co‐crystallization is emerging as a new technology for modifying or enhancing the properties of existing energetic substances. Ethylenedinitramine (EDNA) is a known energetic material which requires attention partly due to its chemical instability originating with its two highly acidic protons. In order to stabilize EDNA, a co‐crystallization approach targeting the acidic protons using a series of co‐crystallizing agents with suitable hydrogen‐bond acceptors was employed. Fifteen attempted co‐crystallizations resulted in eight successful outcomes and six of these were crystallographically characterized and all showed evidence of hydrogen bonds to the intended protons. Calculated detonation properties and experimental thermal and impact data for the co‐crystals were obtained and compared with those of pure EDNA. The co‐crystal of EDNA and 1,2‐bis(4‐pyridyl)ethylene was recognized as a more thermally stable alternative to EDNA while the co‐crystal of EDNA and pyrazine N,N′‐dioxide showed comparable detonation strengths (and much improved chemical stability) compared with that of EDNA. The co‐crystals EDNA:4,4′‐bipyridine and EDNA:pyrazine N,N′‐dioxide were found to be about 50 % less impact sensitive than EDNA, all of which illustrate how co‐crystallizations can be utilized for successfully modifying specific aspects of energetic materials.     

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.     

Utilization of Evaporation during the Crystallization Process: Self‐Templation of Organic Parallelogrammatic Pipes

Analogues of 4‐dodecyloxy‐2‐trifluoromethylbenzamide ( 12FH2 ) consisting of a hydrophobic alkyl chain, a trifluoromethylated aromatic ring, and a self‐complementary hydrogen‐bonding amido group were synthesized, and the structural effect of each component on the formation of parallelogrammatic pipes was investigated. Differential scanning calorimetry and powder XRD analyses revealed that all‐trans L and gauche‐rich S polymorphic forms appeared for the analogues with more than eight carbon atoms in the alkyl chain, that is, the polymorphism originates in the conformation of the alkyl groups and hydrogen‐bonding patterns of the benzamide group. Also, the trifluoromethyl substituent is crucial in that it provides an appropriate molecular balance between the benzamide and alkyl groups. Scanning electron microscopy and powder XRD analyses of solids obtained by a drying‐mediated assembly process revealed that production of the L polymorph by polymorphic transition from the S polymorph resulted in evolution of a three‐dimensional structure when the alkyl group has more than 12 carbon atoms. Among the series of compounds, 12FH2 and 4‐tetradecyloxy‐2‐trifluoromethylbenzamide ( 14FH2 ) formed parallelogrammatic pipes with micrometer dimensions. An atomic force microscopy study of 12FH2 suggested that a single pipe may be composed of platelike crystallites of L polymorph. From a mercury‐intrusion porosimetry study, it was determined that macroporous materials with average pore diameters of about 40 μm and porosity of about 80 % were obtained. The previously proposed self‐templation mechanism by polymorphic transition from S to L polymorph was further discussed in view of polymorphism and the crystallization rate. An appropriate molecular balance between the benzamide and alkyl groups is necessary to induce a proper polymorphic transition for the development of a three‐dimensional hollow structure in the evaporation process.