Hydrogen bonding interactions between <Emphasis Type="Italic">N</Emphasis>,<Emphasis Type="Italic">N</Emphasis>-dimethylformamide and cysteine: DFT studies of structures,properties, and topologies

The hydrogen bonding interactions between cysteine and N,N-dimethylformamide (DMF) were studied at the extended hybrid functional DFT-X3LYP/6-311++G(d,p) level regarding their geometries, energies, vibrational frequencies, and topological features of the electron density. The quantum theory of atoms in molecules (QTAIM) and natural bond orbital (NBO) analyses were employed to elucidate the interaction characteristics in the complexes. The results show that two intermolecular hydrogen bonds (H-bonds) are formed in one complex except few complexes with one intermolecular H-bond. The H-bonds involving O atom of DMF as H-bond acceptor usually are red-shifting H-bonds, while the blue-shifting H-bond usually involve methyl of DMF or methenyl of cysteine moiety as H-bond donors. Both hydrogen bonding interaction and structural deformation play important roles in the relative stabilities of the complexes. Due to the π-bond cooperativity, the strongest H-bond is formed between hydroxyl of cysteine moiety and O atom of DMF, however, the serious deformation counteract the hydrogen bonding interaction to a great extent. The complex involves a stronger hydrogen bonding interaction as well as the smaller deformation is the most stable one. The electron density (ρ_b) as well as its Laplacian (∇²ρ_b) at the H-bond critical point predicted by QTAIM is strongly correlated with the H-bond structural parameter (δR _H···Y) and the second-perturbation energies E(2) in the NBO scheme.     

Glycosidic linkage,N‐acetyl side‐chain,and other structural properties of methyl 2‐acetamido‐2‐deoxy‐β‐d‐glucopyranosyl‐(1→4)‐β‐d‐mannopyranoside monohydrate and related compounds

The crystal structure of methyl 2‐acetamido‐2‐deoxy‐β‐d ‐glycopyranosyl‐(1→4)‐β‐d ‐mannopyranoside monohydrate, C₁₅H₂₇NO₁₁·H₂O, was determined and its structural properties compared to those in a set of mono‐ and disaccharides bearing N‐acetyl side‐chains in βGlcNAc aldohexopyranosyl rings. Valence bond angles and torsion angles in these side chains are relatively uniform, but C—N (amide) and C—O (carbonyl) bond lengths depend on the state of hydrogen bonding to the carbonyl O atom and N—H hydrogen. Relative to N‐acetyl side chains devoid of hydrogen bonding, those in which the carbonyl O atom serves as a hydrogen‐bond acceptor display elongated C—O and shortened C—N bonds. This behavior is reproduced by density functional theory (DFT) calculations, indicating that the relative contributions of amide resonance forms to experimental C—N and C—O bond lengths depend on the solvation state, leading to expectations that activation barriers to amide cis–trans isomerization will depend on the polarity of the environment. DFT calculations also revealed useful predictive information on the dependencies of inter‐residue hydrogen bonding and some bond angles in or proximal to β‐(1→4) O‐glycosidic linkages on linkage torsion angles ? and ψ. Hypersurfaces correlating ? and ψ with the linkage C—O—C bond angle and total energy are sufficiently similar to render the former a proxy of the latter.     

Density and temperature effect on hydrogen-bonded clusters in water - MD simulation study

Molecular dynamics NVE simulations have been performed for five thermodynamic states of water including ambient, sub-and supercritical conditions. Clustering of molecules via hydrogen bonding interaction has been studied with respect to the increasing temperature and decreasing density to examine the relationship between the extent of hydrogen bonding and macroscopic properties. Calculations confirmed decrease of the average number of H-bonds per molecule and of cluster-size with increasing temperature and decreasing density. In the sub-and supercritical region studied, linear correlations between several physical quantities (density, viscosity, static dielectric constant) and the total engagement of molecules in clusters of size k > 4, P _k>4, have been found. In that region there was a linear relationship between P _k>4 and the average number of H-bonds per water molecule. The structural heterogeneity resulting from hydrogen bonding interactions in low-density supercritical water has been also discussed.      

Structure and properties of poly(2,5-dimethylterephthalamides)

Six methyl-substituted wholly aromatic polyamides were synthesized from the reaction of 2,5-dimethylterephthaloyl chloride with p-phenylenediamine, its 2,5-dimethyl and 2-methyl derivatives, m-phenylenediamine, or its 2-methyl and 4-methyl derivatives by solution polycondensation at low temperature. The x-ray diffraction diagrams of the polyamides obtained exhibit crystal patterns. Density values range from 1.26 to 1.37 g/cm³. NMR spectra determined in concentrated H₂SO₄ solution are reported. Poly(2,5-dimethylterephthalamides) have lower thermal stability than the corresponding polyterephthalamides. The increase in solubility of polyamide by the introduction of the 2,5-dimethylterephthaloyl linkage is accompanied by a decrease in thermal stability. The effect of methyl substituents on thermal properties and solubility is discussed in terms of the packing of polymeric molecules and the extent of hydrogen bonding of the amide groups.     

Comparative study on the nonadditivity of methyl group in lithium bonding and hydrogen bonding

Quantum chemical calculations at the second‐order Moeller–Plesset (MP2) level with 6‐311++G(d,p) basis set have been performed on the lithium‐bonded and hydrogen‐bonded systems. The interaction energy, binding distance, bond length, and stretch frequency in these systems have been analyzed to study the nonadditivity of methyl group in the lithium bonding and hydrogen bonding. In the complexes involving with NH₃, the introduction of one methyl group into NH₃ molecule results in an increase of the strength of lithium bonding and hydrogen bonding. The insertion of two methyl groups into NH₃ molecule also leads to an increase of the hydrogen bonding strength but a decrease of the lithium bonding strength relative to that of the first methyl group. The addition of three methyl groups into NH₃ molecule causes the strongest hydrogen bonding and the weakest lithium bonding. Although the presence of methyl group has a different influence on the lithium bonding and hydrogen bonding, a negative nonadditivity of methyl group is found in both interactions. The effect of methyl group on the lithium bonding and hydrogen bonding has also been investigated with the natural bond orbital and atoms in molecule analyses. © 2008 Wiley Periodicals, Inc. Int J Quantum Chem, 2009     

Planarity of heteroaryldithiocarbazic acid derivatives showing tuberculostatic activity: structure–activity relationships

The search for new tuberculostatics is an important issue due to the increasing resistance of Mycobacterium tuberculosis to existing agents and the resulting spread of the pathogen. Heteroaryldithiocarbazic acid derivatives have shown potential tuberculostatic activity and investigations of the structural aspects of these compounds are thus of interest. Three new examples have been synthesized. The structure of methyl 2‐[amino(pyridin‐3‐yl)methylidene]hydrazinecarbodithioate, C₈H₁₀N₄S₂, at 293 K has monoclinic (P2₁/n) symmetry. It is of interest with respect to antibacterial properties. The structure displays N—H…N and N—H…S hydrogen bonding. The structure of N′‐(pyrrolidine‐1‐carbonothioyl)picolinohydrazonamide, C₁₁H₁₅N₅S, at 100 K has monoclinic (P2₁/n) symmetry and is also of interest with respect to antibacterial properties. The structure displays N—H…S hydrogen bonding. The structure of (Z)‐methyl 2‐[amino(pyridin‐2‐yl)methylidene]‐1‐methylhydrazinecarbodithioate, C₉H₁₃N₄S₂, has triclinic (P) symmetry. The structure displays N—H…S hydrogen bonding.     

Detection of halogen bond formation by correlation of proton solvent shifts. 1. Haloforms in n-electron donor solvents

The solvent shifts of haloformic protons, (Cl₃CH, Br₃CH, I₃CH), have been measured in 24 n-electron donor solvents consisting of halogenated hydrocarbons, esters, ketones, ethers and amines. Deviations of Δ_Br and Δ₁ from linear dependence with Δ_Cl are indicative of the presence of halogen bond formation competitive with hydrogen bonding interactions. Bromoform interacts predominantly by hydrogen bonding, halogen bonding being detected to a small extent in chlorinated hydrocarbons and amines. Iodoform shows halogen bonding interactions which increase in relative importance to hydrogen bonding with solvent basicity. Halogen bonding is predominant for solutions of iodoform in amines.     

From Nongelating to Gelating: Synthesis and Structural Self‐Assembling Property Relationships of a Homologous Series of Oligo(amide–triazole)s

A homologous series of oligo(amide–triazole)s (OAT) [ OAT‐CO₂H‐2 n and OAT‐COPrg‐(2 n +1) ] with an increasing number of primary amide (CONH) and triazole hydrogen‐bonding functionalities was prepared by an iterative synthetic procedure. It was found that their self‐assembly and thermoreversible gelation strength had a strong correlation to the number of hydrogen‐bonding moieties in the oligomers. There also existed a threshold value of the number of CONH units, above which all the oligomers became organogelators. Hence, oligomers with ≤4 CONH units are devoid of intermolecular hydrogen bonding and also non‐organogelating, whereas those that contain >4 CONH units show intermolecular association and organogelating properties. For the organogelators, the T_gel value increases monotonically with increasing number of CONH units. On the basis of FTIR measurements, both the CONH and triazole C? H groups were involved in the hydrogen‐bonding process. A mixed xerogel that consisted of a 1:1 weight ratio of two oligomers of different lengths ( OAT‐CO₂H‐6 and OAT‐CO₂H‐12 ) was found to show microphase segregation according to differential scanning calorimetry, thus indicating that oligomers that bear a different number of hydrogen‐bonding units exhibited self‐sorting to maximize the extent of intermolecular hydrogen bonding in the xerogel state.     

Statistical theory for hydrogen bonding fluid system of AaDd type (I): The geometrical phase transition

The influence of hydrogen bonds on the physical and chemical properties of hydrogen bonding fluid system of A _a D _d type is investigated from two viewpoints by the principle of statistical mechanics. In detail, we proposed two new ways that can be used to obtain the equilibrium size distribution of the hydrogen bonding clusters, and derived the analytical expression of a relationship between the hydrogen bonding free energy and hydrogen bonding degree. For the nonlinear hydrogen bonding systems, it is shown that the sol-gel phase transition can take place under proper conditions, which is further proven to be a kind of geometrical phase transition rather than a thermodynamic one. Moreover, several problems associated with the geometrical phase transition and liquid-solid phase transition in nonlinear hydrogen bonding systems are discussed.     

Crystal packing in the structures of diethanolamine derivatives

Four distinct hydrogen‐bonding topologies were observed in the structures of six diethanolamine ligands. These compounds are (1R*,2R*)‐2‐[(2‐hydroxyethyl)(methyl)amino]‐1,2‐diphenylethanol, C₁₇H₂₁NO₂, (I), 1‐[(2S)‐2‐(hydroxydiphenylmethyl)pyrrolidin‐1‐yl]‐2‐methylpropan‐2‐ol, C₂₁H₂₇NO₂, (II), 2‐[(2‐hydroxyethyl)(methyl)amino]‐1,1‐diphenylethanol, C₁₇H₂₁NO₂, (III), 1‐{(2‐hydroxy‐2‐methylpropyl)[(1S)‐1‐phenylethyl]amino}‐2‐methylpropan‐2‐ol, C₁₆H₂₇NO₂, (IV), 1‐{[(2R)‐2‐hydroxy‐2‐phenylethyl][(1S)‐1‐phenylethyl]amino}‐2‐methylpropan‐2‐ol, C₂₀H₂₇NO₂, (V), and (1R*,2S*)‐2‐[(2‐hydroxyethyl)(methyl)amino]‐1,2‐diphenylethanol, C₁₇H₂₁NO₂, (VI). In each compound, all `active' hydroxy H atoms are engaged in hydrogen bonding, but the N atoms are not involved in intermolecular hydrogen bonding. In the structures of (I), (II) and (IV)–(VI), molecules are linked into chains by intermolecular O—H...O interactions. These chains are organized in such a way as to hide the hydrophilic groups inside, and so the outer surfaces of the chains are hydrophobic. The structure of (VI) contains two distinct non‐equivalent systems of intermolecular O—H...O hydrogen bonds formed by disordered hydroxy H atoms.     

A TD‐DFT Study on the Effect of Intermolecular Hydrogen Bonding on the Photophysical Properties of N‐Methyl‐1,8‐naphthalimide

The effect of intermolecular hydrogen bonding on the photophysical properties of N‐methyl‐1,8‐naphthalimide ( 2 ) has been investigated by time‐dependent density functional theory (TD‐DFT) method. The UV and IR spectra of 2 monomer and its hydrogen‐bonded complexes formed with 2,2,2‐trifluoroethanol (TFE) 2 +TFE and 2 +2TFE have been calculated, which confirm the presence of intermolecular hydrogen bonding interactions between the carbonyl groups of the aromatic imide and the hydroxyl group of the polyfluorinated alcohol. The absorption and fluorescence intensities going from 2 monomer via hydrogen‐bonded complex 2 +TFE to 2 +2TFE were found to be gradually enhanced with the wavelength gradually red‐shifted. The enhancements of the fluorescence intensities from 2 monomer to hydrogen‐bonded complexes 2 +TFE and 2 +2TFE were attributed to the decrease of the intersystem crossing (ISC) efficiency from the first excited singlet state S₁ ¹(ππ*) to the second excited triplet state T₂ ³(nπ*), whose energy was increased relative to its ground state due to the intermolecular hydrogen bonding interactions.     

The effect of hydrogen bonding on the physical and mechanical properties of rigid‐rod polymers

The idea of competing effects between intramolecular and intermolecular hydrogen bonding was investigated. Results indicate that the formation of one type of hydrogen bond does not preclude the formation of the other. The strength of the intermolecular association was measured by ab initio calculations for several polymer systems, including methyl pendant poly(p‐phenylene benzobisimidazole) and poly‐{2,6‐diimidazo[4,5‐b:4′5′‐e]pyridinylene‐1,4(2,5‐dihydroxy)phenylene} (PIPD). Fibers with strong intermolecular association have high compressive strength and torsional modulus. The influence of intermolecular hydrogen bonding on torsional modulus is discussed in light of the transverse texture present in poly(p‐phenylene terephthalamide) and some other high‐performance fibers. Enhanced intermolecular interaction not only influences the aforementioned properties but also results in higher fiber density. © 2000 John Wiley & Sons, Inc. J Polym Sci B: Polym Phys 38: 3053–3061, 2000     

Spectroscopic and Computational Insight into the Intermolecular Interactions between Zwitter‐Type Ionic Liquids and Water Molecules

Geometric and conformational changes of zwitter‐type ionic liquids (ZILs) due to hydrogen‐bonding interactions with water molecules are investigated by density functional theory (DFT), two‐dimensional IR correlation spectroscopy (2D IR COS), and pulsed‐gradient spin‐echo NMR (PGSE NMR). Simulation results indicate that molecular structures in the optimized states are strongly influenced by hydrogen bonding of water molecules with the sulfonate group or imidazolium and pyrrolidinium rings of 3‐(1‐methyl‐3‐imidazolio)propanesulfonate ( 1 ) and 3‐(1‐methyl‐1‐pyrrolidinio)propanesulfonate ( 2 ), respectively. Concentration‐dependent 2D IR COS reveals kinetic conformational changes of the two ZIL–H₂O systems attributable to intermolecular interactions, as well as the interactions of sulfonate groups and imidazolium or pyrrolidinium rings with water molecules. The dramatic changes in the ¹H self‐diffusion coefficients elucidate the formation of proton‐conduction pathways consisting of ZIL networks. In ZIL domains, protons are transferred by a Grotthuss‐type mechanism through formation, breaking, and restructuring of bonds between ZILs and H₂O, leading to an energetically favorable state. The simulation and experimental investigations delineated herein provide a perspective to understanding the interactions with water from an academic point of view as well as to designing ILs with desired properties from the viewpoint of applications.     

Hydrogen‐Bonding Toughened Hydrogels and Emerging CO2‐Responsive Shape Memory Effect

A double hydrogen bonding (DHB) hydrogel is constructed by copolymerization of 2‐vinyl‐4,6‐diamino‐1,3,5‐triazine (hydrophobic hydrogen bonding monomer) and N,N‐dimethylacrylamide (hydrophilic hydrogen bonding monomer) with polyethylene glycol diacrylates. The DHB hydrogels demonstrate tunable robust mechanical properties by varying the ratio of hydrogen bonding monomer or crosslinker. Importantly, because of synergistic energy dissipating mechanism of strong diaminotriazine (DAT) hydrogen bonding and weak amide hydrogen bonding, the DHB hydrogels exhibit high toughness (up to 2.32 kJ m⁻²), meanwhile maintaining 0.7 MPa tensile strength, 130% elongation at break, and 8.3 MPa compressive strength. Moreover, rehydration can help to recover the mechanical properties of the cyclic loaded–unloaded gels. Attractively, the DHB hydrogels are responsive to CO₂ in water, and demonstrate unprecedented CO₂‐triggered shape memory behavior owing to the reversible destruction and reconstruction of DAT hydrogen bonding upon passing and degassing CO₂ without introducing external acid. The CO₂ triggering mechanism may point out a new approach to fabricate shape memory hydrogels.     

Hydrogen‐bonding patterns of two dihydroxy­lactone derivatives

In the hydrogen‐bonding networks of 8‐hydroxy‐5‐hydroxy­methyl‐3,6‐dioxatricyclo­[6.3.1.0^1.5]dodecan‐2‐one and 5,7‐bis(hydroxy­methyl)‐3,6‐dioxatricyclo­[5.3.1.0^1.5]undecan‐2‐one, both C₁₁H₁₆O₅, layers and double strands, respectively, lead to the formation of chains connected by hydroxy‐to‐hydroxy contacts, where the hydroxy­methyl group, present in both structures, acts as a donor. The secondary structures differ in the hydrogen bonding of these chains via the second hydroxy group, which is involved in hydroxy‐to‐carbonyl and hydroxy‐to‐hydroxy bonds, respectively.     

Theoretical Study of the Interplay between Lithium Bond and Hydrogen Bond in Complexes Involved with HLi and HCN

The lithium‐ and hydrogen‐bonded complex of HLi? NCH? NCH is studied with ab initio calculations. The optimized structure, vibrational frequencies, and binding energy are calculated at the MP2 level with 6‐311++G(2d,2p) basis set. The interplay between lithium bonding and hydrogen bonding in the complex is investigated with these properties. The effect of lithium bonding on the properties of hydrogen bonding is larger than that of hydrogen bonding on the properties of lithium bonding. In the trimer, the binding energies are increased by about 19 % and 61 % for the lithium and hydrogen bonds, respectively. A big cooperative energy (?5.50 kcal mol^?1) is observed in the complex. Both the charge transfer and induction effect due to the electrostatic interaction are responsible for the cooperativity in the trimer. The effect of HCN chain length on the lithium bonding has been considered. The natural bond orbital and atoms in molecules analyses indicate that the electrostatic force plays a main role in the lithium bonding. A many‐body interaction analysis has also been performed for HLi? (NCH)_N (N=2–5) systems.     

Measuring the Relative Hydrogen‐Bonding Strengths of Alcohols in Aprotic Organic Solvents

Voltammetric experiments with 9,10‐anthraquinone and 1,4‐benzoquinone performed under controlled moisture conditions indicate that the hydrogen‐bond strengths of alcohols in aprotic organic solvents can be differentiated by the electrochemical parameter ΔE_p^red=|E_p^red(1)?E_p^red(2)|, which is the potential separation between the two one‐electron reduction processes. This electrochemical parameter is inversely related to the strength of the interactions and can be used to differentiate between primary, secondary, tertiary alcohols, and even diols, as it is sensitive to both their steric and electronic properties. The results are highly reproducible across two solvents with substantially different hydrogen‐bonding properties (CH₃CN and CH₂Cl₂) and are supported by density functional theory calculations. This indicates that the numerous solvent–alcohol interactions are less significant than the quinone–alcohol hydrogen‐bonding interactions. The utility of ΔE_p^red was illustrated by comparisons between 1) 3,3,3‐trifluoro‐n‐propanol and 1,3‐difluoroisopropanol and 2) ethylene glycol and 2,2,2‐trifluoroethanol.     

1,3‐Bis(ethylamino)‐2‐nitrobenzene, 1,3‐bis(n‐octylamino)‐2‐nitrobenzene and 4‐ethylamino‐2‐methyl‐1H‐benzimidazole

1,3‐Bis(ethylamino)‐2‐nitrobenzene, C₁₀H₁₅N₃O₂, (I), and 1,3‐bis(n‐octylamino)‐2‐nitrobenzene, C₂₂H₃₉N₃O₂, (II), are the first structurally characterized 1,3‐bis(n‐alkylamino)‐2‐nitrobenzenes. Both molecules are bisected though the nitro N atom and the 2‐C and 5‐C atoms of the ring by twofold rotation axes. Both display intramolecular N—H...O hydrogen bonds between the amine and nitro groups, but no intermolecular hydrogen bonding. The nearly planar molecules pack into flat layers ca 3.4 Å apart that interact by hydrophobic interactions involving the n‐alkyl groups rather than by π–π interactions between the rings. The intra‐ and intermolecular interactions in these molecules are of interest in understanding the physical properties of polymers made from them. Upon heating in the presence of anhydrous potassium carbonate in dimethylacetamide, (I) and (II) cyclize with formal loss of hydrogen peroxide to form substituted benzimidazoles. Thus, 4‐ethylamino‐2‐methyl‐1H‐benzimidazole, C₁₀H₁₃N₃, (III), was obtained from (I) under these reaction conditions. Compound (III) contains two independent molecules with no imposed internal symmetry. The molecules are linked into chains via N—H...N hydrogen bonds involving the imidazole rings, while the ethylamino groups do not participate in any hydrogen bonding. This is the first reported structure of a benzimidazole derivative with 4‐amino and 2‐alkyl substituents.     

All‐atom Molecular Dynamic Simulations Combined with the Chemical Shifts Study on the Weak Interactions of Ethanol‐water System

All‐atom molecular dynamics (MD) simulation combined with chemical shifts was performed to investigate the interactions over the entire concentration range of the ethanol (EtOH)‐water system. The results of the simulation were adopted to explain the NMR experiments by hydrogen bonding analysis. The strong hydrogen bonds and weak C–H···O contacts coexist in the mixtures through the analysis of the radial distribution functions. And the liquid structures in the whole concentration of EtOH‐water mixtures can be classified into three regions by the statistic analysis of the hydrogen‐bonding network in the MD simulations. Moreover, the chemical shifts of the hydrogen atom are in agreement with the statistical results of the average number hydrogen bonds in the MD simulations. Interestingly, the excess relative extent of η_rel^E calculated by the MD simulations and chemical shifts in the EtOH aqueous solutions shows the largest deviation at x_EtOH≈0.18. The excess properties present good agreement with the excess enthalpy in the concentration dependence.     

trans‐4‐Acetylcyclo­hexane­carboxyl­ic acid and ()‐trans‐2‐acetyl­cyclo­hexane­carboxyl­ic acid: hydrogen‐bonding patterns in two isomeric keto acids

Both title compounds, C₉H₁₄O₃, display carboxyl‐dimer hydrogen‐bonding patterns. The 4‐acetyl isomer adopts a chiral conformation with negligible disordering of the methyl and carboxyl groups and forms centrosymmetric dimers across the b and c edges of the chosen cell [O?O = 2.667 (3) Å and O—H?O = 175°]. Intermolecular C—H?O close contacts were found for both carbonyl groups. In the 2‐acetyl isomer, there is no intramolecular interaction between the carboxyl and acetyl groups and the hydrogen bonding involves centrosymmetric carboxyl dimerization across the ab and ac faces of the chosen cell [O?O = 2.668 (2) Å and O—H?O = 173°]. The carboxyl group is negligibly disordered, but significant rotational disordering was found for the acetyl methyl group. An intermolecular C—H?O close contact was found involving the ketone group.