Hydrogen bond

About: Hydrogen bond is a research topic. Over the lifetime, 57701 publications have been published within this topic receiving 1306326 citations.

Infrared studies of hydrogen bonding interaction between kaolinite surfaces and intercalated potassium acetate, hydrazine, formamide, and urea

Abstract: Expansion of kaolinite by intercalation of urea, formamide, hydrazine, and potassium acetate permits infrared studies of deuterium exchange and hydrogen bonding interaction of CO and NH2 groups with the internal mineral surfaces. Intercalation of kaolinite with potassium acetate increases the d001 spacing from 7.13 A. to 11.6 A., and the 3695 cm.−1 absorption band is shifted to 3600 cm.−1 owing to weak hydrogen bonding between the acetate anion and the OH groups. Intercalation of hydrazine within the kaolinite structure increases the ν(NH2) stretching frequency from 3338 cm.−1 for the liquid to 3365 cm.−1 for the intercalated molecules. The asymmetric and symmetric ν(NH2) stretching frequencies of liquid formamide are shifted from 3420 and 3340 cm.−1 to 3500 and 3380 cm.−1, respectively, in the formamide-kaolinite complex. In the urea-kaolinite complex, the asymmetric and symmetric ν(NH2) stretching frequencies at 3500 and 3380 cm.−1 correspond to NH2 groups interacting with the oxygens located on the basal tetrahedral layer; bands at 3520 and 3415 cm.−1 are assigned to similar NH2 groups involved in weak hydrogen bonding with the inner-surface OH.

Theoretical studies of hydrogen bonding in liquid water and dilute aqueous solutions

Abstract: Monte Carlo computer simulations of liquid water and dilute aqueous solutions are analyzed in terms of the nature and extent of intermolecular hydrogen bonding. A geometric definition of the hydrogen bond is used. Calculations on liquid water at 25 °C, 37 °C, and 50 °C, were carried out based on the quantum mechanical MCY potential of Matsuoka, Clementi, and Yoshimine and at 10 °C based on the empirical ST2 potential. The effect of a dissolved solute on aqueous hydrogen bonding was studied for dilute aqueous solutions of Li+, Na+, K+, F−, Cl−, and CH4. The nature of the hydrogen bonding was characterized with quasicomponent distribution functions defined as a function of the intermolecular coordinates relevant to hydrogen bonding. The extent of the hydrogen bonding is described using a network analysis approach developed by Geiger, Stillinger, and Rahman. The results on the quasicomponent distribution functions show that the average hydrogen bond angle deviates with 10 °–25 ° from a linear form, quite ind...

Thermal effects on the optical properties of single crystals and solution‐cast films of urethane substituted polydiacetylenes

Abstract: The optical properties of single crystals and solution‐cast films of two polydiacetylenes, poly3BCMU and poly4BCMU where the substituent group is– (CH2)3.4OCONHCH4COOC4H9, are characterized. Visible absorption and reflection spectra for the polymer crystals are typical of those observed for other urethane substituted polydiacetylenes. The optical properties of the polymer films are controlled primarily by intramolecular hydrogen bonding between the N–H and C=O of the urethane functionalities on adjacent substituent groups. Hydrogen bonding stabilizes the planar, fully conjugated conformation of the individual polymer chains in the films. Increased temperature causes a disruption of the hydrogen bond network and a destabilization of the planar polymer conformation. Dramatic color changes result because of the sensitivity of the optical properties to backbone conformation.

First−Second Shell Interactions in Metal Binding Sites in Proteins: A PDB Survey and DFT/CDM Calculations

Abstract: The role of the second shell in the process of metal binding and selectivity in metalloproteins has been elucidated by combining Protein Data Bank (PDB) surveys of Mg, Mn, Ca, and Zn binding sites with density functional theory/continuum dielectric methods (DFT/CDM). Peptide backbone groups were found to be the most common second-shell ligand in Mg, Mn, Ca, and Zn binding sites, followed (in decreasing order) by Asp/Glu, Lys/Arg, Asn/Gln, and Ser/Thr side chains. Aromatic oxygen- or nitrogen-containing side chains (Tyr, His, and Trp) and sulfur-containing side chains (Cys and Met) are seldom found in the second coordination layer. The backbone and Asn/Gln side chain are ubiquitous in the metal second coordination layer as their carbonyl oxygen and amide hydrogen can act as a hydrogen-bond acceptor and donor, respectively, and can therefore partner practically every first-shell ligand. The second most common outer-shell ligand, Asp/Glu, predominantly hydrogen bonds to a metal-bound water or Zn-bound histidine and polarizes the H-O or H-N bond. In certain cases, a second-shell Asp/Glu could affect the protonation state of the metal ligand. It could also energetically stabilize a positively charged metal complex more than a neutral ligand such as the backbone and Asn/Gln side chain. As for the first shell, the second shell is predicted to contribute to the metal selectivity of the binding site by discriminating between metal cations of different ionic radii and coordination geometries. The first-shell-second-shell interaction energies decay rapidly with increasing solvent exposure of the metal binding site. They are less favorable but are of the same order of magnitude as compared to the respective metal-first-shell interaction energies. Altogether, the results indicate that the structure and properties of the second shell are dictated by those of the first layer. The outer shell is apparently designed to stabilize/protect the inner-shell and complement/enhance its properties.

Large Angular Jump Mechanism Observed for Hydrogen Bond Exchange in Aqueous Perchlorate Solution

Abstract: The mechanism for hydrogen bond (H-bond) switching in solution has remained subject to debate despite extensive experimental and theoretical studies. We have applied polarization-selective multidimensional vibrational spectroscopy to investigate the H-bond exchange mechanism in aqueous NaClO4 solution. The results show that a water molecule shifts its donated H-bonds between water and perchlorate acceptors by means of large, prompt angular rotation. Using a jump-exchange kinetic model, we extracted an average jump angle of 49 +/- 4 degrees, in qualitative agreement with the jump angle observed in molecular dynamics simulations of the same aqueous NaClO4 solution.