Hydrogen bond

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

Proton Transfer and Structure-Specific Fluorescence in Hydrogen Bond-Rich Protein Structures

Abstract: Protein structures which form fibrils have recently been shown to absorb light at energies in the near UV range and to exhibit a structure-specific fluorescence in the visible range even in the absence of aromatic amino acids. However, the molecular origin of this phenomenon has so far remained elusive. Here, we combine ab initio molecular dynamics simulations and fluorescence spectroscopy to demonstrate that these intrinsically fluorescent protein fibrils are permissive to proton transfer across hydrogen bonds which can lower electron excitation energies and thereby decrease the likelihood of energy dissipation associated with conventional hydrogen bonds. The importance of proton transfer on the intrinsic fluorescence observed in protein fibrils is signified by large reductions in the fluorescence intensity upon either fully protonating, or deprotonating, the fibrils at pH = 0 or 14, respectively. Thus, our results point to the existence of a structure-specific fluorophore that does not require the presence of aromatic residues or multiple bond conjugation that characterize conventional fluorescent systems. The phenomenon may have a wide range of implications in biological systems and in the design of self-assembled functional materials.

UV Resonance Raman Determination of Molecular Mechanism of Poly(N-isopropylacrylamide) Volume Phase Transition

Abstract: Poly(N-isopropylacrylamide) (PNIPAM) is the premier example of a macromolecule that undergoes a hydrophobic collapse when heated above its lower critical solution temperature (LCST). Here we utilize dynamic light scattering, H-NMR, and steady-state and time-resolved UVRR measurements to determine the molecular mechanism of PNIPAM's hydrophobic collapse. Our steady-state results indicate that in the collapsed state the amide bonds of PNIPAM do not engage in interamide hydrogen bonding, but are hydrogen bonded to water molecules. At low temperatures, the amide bonds of PNIPAM are predominantly fully water hydrogen bonded, whereas, in the collapsed state one of the two normal CO hydrogen bonds is lost. The NH-water hydrogen bonding, however, remains unperturbed by the PNIPAM collapse. Our kinetic results indicate a monoexponential collapse with tau approximately 360 (+/-85) ns. The collapse rate indicates a persistence length of n approximately 10. At lengths shorter than the persistence length the polymer acts as an elastic rod, whereas at lengths longer than the persistence length the polymer backbone conformation forms a random coil. On the basis of these results, we propose the following mechanism for the PNIPAM volume phase transition. At low temperatures PNIPAM adopts an extended, water-exposed conformation that is stabilized by favorable NIPAM-water solvation shell interactions which stabilize large clusters of water molecules. As the temperature increases an increasing entropic penalty occurs for the water molecules situated at the surface of the hydrophobic isopropyl groups. A cooperative transition occurs where hydrophobic collapse minimizes the exposed hydrophobic surface area. The polymer structural change forces the amide carbonyl and N-H to invaginate and the water clusters cease to be stabilized and are expelled. In this compact state, PNIPAM forms small hydrophobic nanopockets where the (i, i + 3) isopropyl groups make hydrophobic contacts. A persistent length of n approximately 10 suggests a cooperative collapse where hydrophobic interactions between adjacent hydrophobic pockets stabilize the collapsed PNIPAM.

Nuclear magnetic resonance of hydrogen bonded clusters between F− and (HF)n: Experiment and theory

Abstract: Liquid state 1 H and 19 F NMR experiments in the temperature range between 110 and 150 K have been performed on mixtures of tetrabutylammonium fluoride with HF dissolved in a 1:2 mixture of CDF 3 and CDF 2 Cl, Under these conditions hydrogen bonded complexes between F and a varying number of HF molecules were observed in the slow proton and hydrogen bond exchange regime. At low HF concentrations the well known hydrogen bifluoride ion [FHF] - is observed, exhibiting a strong symmetric H-bond. At higher HF concentrations the species [F(HF) 2 ] - , [F(HF) 3 ] - are formed and a species to which we assign the structure [F(HF) 4 ] - . The spectra indicate a central fluoride anion which forms multiple hydrogen bonds to HF. With increasing number of HF units the hydrogen bond protons shift towards the terminal fluorine's. The optimized gas-phase geometries of [F(HF) n ] - , n = 1 to 4, calculated using ab initio methods confirm the D xh , C 2v , D 3h and T d symmetries of these ions. For the first time, both one-bond couplings between a hydrogen bond proton and the two heavy atoms of a hydrogen bridge, here 1 J HF and 1 J HF , where | 1 J HF |≥| 1 J HF |, as well as a a two-bond coupling between the heavy atoms, here 2 J FF . have been observed. The analysis of the differential width of various multiplet components gives evidence for the signs of these constants, i.e. 1 J HF and 2 J SF >0, and 1 J HF <0, Ab initio calculations of NMR chemical shifts and the scalar coupling constants using the Density Functional formalism and the Multiconfiguration Complete Active Space method show a reasonable agreement with the experimental parameters and confirm the covalent character of the hydrogen bonds studied.

Spontaneous Resolution Induced by Self-Organization of Chiral Self-Complementary Cobalt(III) Complexes with Achiral Tripod-Type Ligands Containing Three Imidazole Groups

Abstract: The progression from synthetically achiral ligand and metal ion, to isolated chiral metal complex, to homochiral two-dimensional (2D) assembly layer, and finally to conglomerate is presented. The cobalt(III) complexes of achiral tripod-type ligands involving three imidazole groups with the chemical formulas [Co(H3L6)](ClO4)3*H2O (6) and [Co(H3L7)](ClO4)3*0.5H2O (7) were synthesized, where H3L6 = tris[2-(((imidazol-4-yl)methylidene)amino)ethyl]amine and H3L7 = tris[2-(((2-methylimidazol-4-yl)methylidene)amino)ethyl]amine. Each complex induces the chirality of clockwise (C) and anticlockwise (A) enantiomers due to the screw coordination arrangement of the achiral tripod-type ligand around the Co(III) ion. The fully protonated (6, 7), the formally hemi-deprotonated (6', 7'), and the fully deprotonated (6' ', 7' ') complexes were obtained as good quality crystals by adjusting the pH of the solutions. The crystal structures were determined by single-crystal X-ray analyses. There is no intermolecular network structure in the fully protonated complexes (6, 7). The fully deprotonated complexes (6' ', 7' ') form a hydrogen-bonded network structure, in which the C and A enantiomers coexist and are connected through a water molecule. The formally hemi-deprotonated species [Co(H1.5L6 or 7)]1.5+, which functions as a self-complementary chiral building block, generates equal numbers of protonated and deprotonated molecules by an acid-base reaction to form an extended 2D homochiral layer structure consisting of a hexanuclear structure with a trigonal void as a unit. The 2D structure arises from the intermolecular imidazole-imidazolate hydrogen bonds between [Co(H3L6 or 7)]3+ and [Co(L6 or 7)]0, in which adjacent molecules with the same chirality are arrayed in an up-and-down fashion. In the crystal lattices of the perchlorate salts (6', 7'), the perchlorate ions are located in the cavity, and the homochiral layer consisting of C enantiomers and the adjacent layer consisting of A enantiomers are stacked alternately to give an achiral crystal. The chloride salt of the hemi-deprotonated complex [Co(H1.5L6)]Cl1.5*H2O (6a') is found to be a conglomerate, in which the chloride ions are positioned in the intermediate region of the double layer, and layers with the same chirality are well stacked by adopting the up-and-down layer's shape to generate channels, and so form a chiral crystal. The circular dichroism (CD) spectrum of 6a' showed a positive peak and a negative peak at 480 and 350 nm, respectively, and the spectrum of another crystal showed an enantiomeric CD pattern, providing further evidence of spontaneous resolution on crystallization.