Evidence for O-H.cntdot..cntdot..cntdot.C and N-H.cntdot..cntdot..cntdot.C hydrogen bonding in crystalline alkynes, alkenes, and aromatics

Attempts have been made to understand the nature and significance of hydrogen bonds of the type X-H-C (X = 0, N) . These unusual interactions have been discussed recently. Crystallographic studies on 17a-ethynylandrosta- 2,4-dieno[2,3-d]dihydroxazol1-7 8-01 (donazole) provide direct evidence of such an 0-H.0-C interaction. Ab initio computations, IR spectroscopy, and database studies show that these hydrogen bonds, while uncommon, are energetically and structurally significant.

Analysis of Hydrogen Bonding and Stability of Protein Secondary Structures in Molecular Dynamics Simulation

Molecular Dynamics (MD) simulations provide an atomic level account of the molecular motions and have proven to be immensely useful in the investigation of the dynamical structure of proteins. Once an MD trajectory is obtained, specific interactions at the molecular level can be directly studied by setting up appropriate combinations of distance and angle monitors. However, if a study of the dynamical behavior of secondary structures in proteins becomes important, this approach can become unwieldy. We present herein a method to study the dynamical stability of secondary structures in proteins, based on a relatively simple analysis of backbone hydrogen bonds. The method was developed for studying the thermal unfolding of beta-lactamases, but can be extended to other systems and adapted to study relevant properties.

Molecular self-assembly of cadmium-triazolate complexes via hydrogen bonding: Synthesis, structures and photoluminescent properties

Two new cadmium coordination polymers namely Cd(HAmTrz-COO)(4)(NH4+)(2)] 1; and Cd(HAmTrz)(2)I-2](n) 2; (HAmTrz-COOH = 3-amino-1,2,4-triazole-5-carboxylic acid), have been prepared based on HAmTrz-COOH as ligand. The crystal structures of 1 and 2 have been determined by single-crystal X-ray diffraction technique. In coordination-complex 1 four triazole ligands coordinate via N1 nitrogen leading to a tetrahedral geometry around cadmium ion, while in 2 the ligand prefers to coordinate to the metal in a bidentate bridging mode. The structures of both the coordination polymers can be envisaged as 3D hydrogen bonded networks. Thermogravimetric analysis shows that 2 is more stable than 1 owing to different coordination numbers of cadmium atoms. Photoluminescence properties of both the compounds have been investigated in the solid state. (C) 2011 Elsevier B.V. All rights reserved.

Crystal packing and melting temperatures of small oxalate esters: the role of C-H center dot center dot center dot O hydrogen bonding

The simple dialkyl oxalates are generally liquids at room temperature except for dimethyl and di-tert-butyl oxalate which melt at 327 and 343 K. The crystal structures of diethyl, di-iso-propyl, di-n-butyl, di-tert-butyl and methyl ethyl oxalates were determined. The liquid esters were crystallized using the cryocrystallization technique. A comparison of the intermolecular interactions and packing features in these crystal structures was carried out. The crystal structure of dimethyl oxalate was redetermined at various temperatures. The other compounds were also studied at several temperatures in order to assess the attractive nature of the hydrogen bonds therein. A number of moderate to well defined C-H center dot center dot center dot O interactions account for the higher melting points of the two solid esters. Additionally, a diminished entropic contribution Delta S(m) in di-tert-butyl oxalate possibly increases the melting point of this compound further.

Intra-molecular hydrogen bonding with organic fluorine in the solution state: Deriving evidence by a two dimensional NMR experiment

The direct evidence for the existence of intra-molecular C-F center dot center dot center dot H-N hydrogen bond in organofluorine molecules, in the liquid state, is derived using NMR spectroscopy by the detection of long range interactions among fluorine, nitrogen and hydrogen atoms. The present study reports the determination of the relative signs and magnitudes of through space and through bond couplings to draw unambiguous evidence on the existence of weak molecular interactions involving organic fluorine. It is a simple, easy to implement, N-15 natural abundant two dimensional heteronuclear N-15-H-1 double quantum-single quantum correlation experiment. The existence of intra-molecular hydrogen bond is conclusively established in the investigated molecules. (C) 2011 Elsevier B.V. All rights reserved.

Homo- or Heterosynthon? A Crystallographic Study on a Series of New Cocrystals Derived from Pyrazinecarboxamide and Various Carboxylic Acids Equipped with Additional Hydrogen Bonding Sites

Four new cocrystals of a well studied active pharmaceutical ingredient (API), namely, pyrazinecarboxamide (PZA), with various monocarboxylic acids equipped with additional hydrogen bonding sites such as vanillic acid (VA), gallic acid (GA), 1-hydroxy-2-naphthoic acid (1HNA), and indole-2-carboxylic acid (I2CA) have been successfully prepared and characterized by FTIR, H-1 NMR, differential scanning calorimetry (DSC), and single crystal and powder X-ray diffraction (SXRD and PXRD, respectively) techniques. In the majority of the cases, preferential occurrence amide amide and acid acid homosynthons has been observed. Since the heterosynthon is energetically preferred to homosynthon, such unusual occurrence of homosynthon in these cocrystals is intriguing.

Probing acid-amide intermolecular hydrogen bonding by NMR spectroscopy and DFT calculations

Benzene carboxylic acids and Benzamide act as their self-complement in molecular recognition to form inter-molecular hydrogen bonded dimers between amide and carboxylic acid groups, which have been investigated by H-1, C-13 and N-15 NMR spectroscopy. Extensive NMR studies using diffusion ordered spectroscopy (DOSY), variable temperature 1D, 2D NMR, established the formation of heterodimers of benzamide with benzoic acid, salicylic acid and phenyl acetic acid in deuterated chloroform solution. Association constants for the complex formation in the solution state have been determined. The results are ascertained by X-ray diffraction in the solid state. Intermolecular interactions in solution and in solid state were found to be similar. The structural parameters obtained by X-ray diffraction studies are compared with those obtained by DFT calculations. (C) 2012 Elsevier B.V. All rights reserved.

Intermolecular charge transfer and vibrational analysis of hydrogen bonding in acetazolamide

In the present work the structural and spectral characteristics of acetazolamide have been studied by methods of infrared, Raman spectroscopy and quantum chemistry. Electrostatic potential surface, optimized geometry, harmonic vibrational frequencies, infrared intensities and activities of Raman scattering were calculated by density functional theory (DFT) employing B3LYP with complete relaxation in the potential energy surface using 6-311++G(d,p) basis set. Based on these results, we have discussed the correlation between the vibrational modes and the structure of the dimers of acetazolamide. The calculated vibrational spectra of three dimers of acetazolamide have been compared with observed spectra, and the assignment of observed bands was carried out using potential energy distribution. The observed spectra agree well with the values computed from the OFT. A comparison of observed and calculated vibrational spectra clearly shows the effect of hydrogen bonding. The frequency shifts observed for the different dimers are in accord with the hydrogen bonding in acetazolamide. Natural bond orbital (NBO) analyses reflect the charge transfer interaction in the individual hydrogen bond units and the stability of different dimers of acetazolamide. (C) 2012 Elsevier B.V. All rights reserved.

Critical investigation on hydrogen bonding by Fourier transform infrared spectroscopy in hydrogenated amorphous silicon thin films

Fourier Transform Infrared (FTIR) spectroscopic analysis has been carried out on the hydrogenated amorphous silicon (a-Si:H) thin films deposited by DC, pulsed DC (PDC) and RF sputtering process to get insight regarding the total hydrogen concentration (C-H) in the films, configuration of hydrogen bonding, density of the films (decided by the vacancy and void incorporation) and the microstructure factor (R*) which varies with the type of sputtering carried out at the same processing conditions. The hydrogen incorporation is found to be more in RF sputter deposited films as compared to PDC and DC sputter deposited films. All the films were broadly divided into two regions namely vacancy dominated and void dominated regions. At low hydrogen dilutions the films are vacancy dominated and at high hydrogen dilutions they are void dominated. This demarcation is at C-H = 23 at.% H for RF, C-H = 18 at.% H for PDC and C-H = 14 at.% H for DC sputter deposited films. The microstructure structure factor R* is found to be as low as 0.029 for DC sputter deposited films at low C-H. For a given C-H, DC sputter deposited films have low R* as compared to PDC and RF sputter deposited films. Signature of dihydride incorporation is found to be more in DC sputter deposited films at low C-H.

ENDOR studies of hydrogen bonding of the AsO44- centre in x-ray irradiated KH2AsO4

We here report what we believe to be an important method for studying hydrogen bonding in systems containing a paramagnetic centre. The technique of electron-nuclear double resonance ( ENDOR) has been applied to study the hydrogen-bond network around the AsO44-. centre in X-ray irradiated KH2AsO4. ENDOR transitions from several sets of hydrogen nuclei surrounding the centre were observed at 4.2 degrees K and the spectra for two sets of neighbouring nuclei are identified. The angular dependences for these spectra are fitted with a spin-Hamiltonian to obtain the isotropic and anisotropic magnetic hyperfine constants. The results are discussed in terms of the available spectroscopic and crystallographic data on KH2AsO4 and the order-disorder model of ferroelectrictricity in this class of crystals.

Quantum chemical study on influence of intermolecular hydrogen bonding on the geometry, the atomic charges and the vibrational dynamics of 2,6-dichlorobenzonitrile

FT-IR (4000-400 cm(-1)) and FT-Raman (4000-200 cm(-1)) spectral measurements on solid 2,6-dichlorobenzonitrile (2,6-DCBN) have been done. The molecular geometry, harmonic vibrational frequencies and bonding features in the ground state have been calculated by density functional theory at the B3LYP/6-311++G (d,p) level. A comparison between the calculated and the experimental results covering the molecular structure has been made. The assignments of the fundamental vibrational modes have been done on the basis of the potential energy distribution (PED). To investigate the influence of intermolecular hydrogen bonding on the geometry, the charge distribution and the vibrational spectrum of 2,6-DCBN; calculations have been done for the monomer as well as the tetramer. The intermolecular interaction energies corrected for basis set superposition error (BSSE) have been calculated using counterpoise method. Based on these results, the correlations between the vibrational modes and the structure of the tetramer have been discussed. Molecular electrostatic potential (MEP) contour map has been plotted in order to predict how different geometries could interact. The Natural Bond Orbital (NBO) analysis has been done for the chemical interpretation of hyperconjugative interactions and electron density transfer between occupied (bonding or lone pair) orbitals to unoccupied (antibonding or Rydberg) orbitals. UV spectrum was measured in methanol solution. The energies and oscillator strengths were calculated by Time Dependent Density Functional Theory (TD-DFT) and matched to the experimental findings. TD-DFT method has also been used for theoretically studying the hydrogen bonding dynamics by monitoring the spectral shifts of some characteristic vibrational modes involved in the formation of hydrogen bonds in the ground and the first excited state. The C-13 nuclear magnetic resonance (NMR) chemical shifts of the molecule were calculated by the Gauge independent atomic orbital (GIAO) method and compared with experimental results. Standard thermodynamic functions have been obtained and changes in thermodynamic properties on going from monomer to tetramer have been presented. (C) 2013 Elsevier B.V. All rights reserved.

Explosives Sensing by Using Electron-Rich Supramolecular Polymers: Role of Intermolecular Hydrogen Bonding in Significant Enhancement of Sensitivity

We demonstrate here that supramolecular interactions enhance the sensitivity towards detection of electron-deficient nitro-aromatic compounds (NACs) over discrete analogues. NACs are the most commonly used explosive ingredients and are common constituents of many unexploded landmines used during World WarII. In this study, we have synthesised a series of pyrene-based polycarboxylic acids along with their corresponding discrete esters. Due to the electron richness and the fluorescent behaviour of the pyrene moiety, all the compounds act as sensors for electron-deficient NACs through a fluorescence quenching mechanism. A Stern-Volmer quenching constant determination revealed that the carboxylic acids are more sensitive than the corresponding esters towards NACs in solution. The high sensitivity of the acids was attributed to supramolecular polymer formation through hydrogen bonding in the case of the acids, and the enhancement mechanism is based on an exciton energy migration upon excitation along the hydrogen-bond backbone. The presence of intermolecular hydrogen bonding in the acids in solution was established by solvent-dependent fluorescence studies and dynamic light scattering (DLS) experiments. In addition, the importance of intermolecular hydrogen bonds in solid-state sensing was further explored by scanning tunnelling microscopy (STM) experiments at the liquid-solid interface, in which structures of self-assembled monolayer of the acids and the corresponding esters were compared. The sensitivity tests revealed that these supramolecular sensors can even detect picric acid and trinitrotoluene in solution at levels as low as parts per trillion (ppt), which is much below the recommended permissible level of these constituents in drinking water.

Hydrogen bonding, halogen bonding and lithium bonding: an atoms in molecules and natural bond orbital perspective towards conservation of total bond order, inter- and intra-molecular bonding

One hundred complexes have been investigated exhibiting D-X center dot center dot center dot A interactions, where X = H, Cl or Li and DX is the `X bond' donor and A is the acceptor. The optimized structures of all these complexes have been used to propose a generalized `Legon-Millen rule' for the angular geometry in all these interactions. A detailed Atoms in Molecules (AIM) theoretical analysis confirms an important conclusion, known in the literature: there is a strong correlation between the electron density at the X center dot center dot center dot A bond critical point (BCP) and the interaction energy for all these interactions. In addition, we show that extrapolation of the fitted line leads to the ionic bond for Li-bonding (electrostatic) while for hydrogen and chlorine bonding, it leads to the covalent bond. Further, we observe a strong correlation between the change in electron density at the D-X BCP and that at the X center dot center dot center dot A BCP, suggesting conservation of the bond order. The correlation found between penetration and electron density at BCP can be very useful for crystal structure analysis, which relies on arbitrary van der Waals radii for estimating penetration. Various criteria proposed for shared-and closed-shell interactions based on electron density topology have been tested for H/Cl/Li bonded complexes. Finally, using the natural bond orbital (NBO) analysis it is shown that the D-X bond weakens upon X bond formation, whether it is ionic (DLi) or covalent (DH/DCl) and the respective indices such as ionicity or covalent bond order decrease. Clearly, one can think of conservation of bond order that includes ionic and covalent contributions to both D-X and X center dot center dot center dot A bonds, for not only X = H/Cl/Li investigated here but also any atom involved in intermolecular bonding.