Hydrogen bond

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

Enzyme crystal structure in a neat organic solvent

Abstract: The crystal structure of the serine protease subtilisin Carlsberg in anhydrous acetonitrile was determined at 2.3 A resolution. It was found to be essentially identical to the three-dimensional structure of the enzyme in water; the differences observed were smaller than those between two independently determined structures in aqueous solution. The hydrogen bond system of the catalytic triad is intact in acetonitrile. The majority (99 of 119) of enzyme-bound, structural water molecules have such a great affinity to subtilisin that they are not displaced even in anhydrous acetonitrile. Of the 12 enzyme-bound acetonitrile molecules, 4 displace water molecules and 8 bind where no water had been observed before. One-third of all subtilisin-bound acetonitrile molecules reside in the active center, occupying the same region (P1, P2, and P3 binding sites) as the specific protein inhibitor eglin c.

Crystal structures of cytochrome P-450CAM complexed with camphane, thiocamphor, and adamantane: factors controlling P-450 substrate hydroxylation

Abstract: X-ray crystal structures have been determined for complexes of cytochrome P-450CAM with the substrates camphane, adamantane, and thiocamphor. Unlike the natural substrate camphor, which hydrogen bonds to Tyr96 and is metabolized to a single product, camphane, adamantane and thiocamphor do not hydrogen bond to the enzyme and all are hydroxylated at multiple positions. Evidently the lack of a substrate-enzyme hydrogen bond allows substrates greater mobility in the active site, explaining this lower regiospecificity of metabolism as well as the inability of these substrates to displace the distal ligand to the heme iron. Tyr96 is a ligand, via its carbonyl oxygen atom, to a cation that is thought to stabilize the camphor-P-450CAM complex [Poulos, T. L., Finzel, B. C., & Howard, A. J. (1987) J. Mol. Biol. 195, 687-700]. The occupancy and temperature factor of the cationic site are lower and higher, respectively, in the presence of the non-hydrogen-bonding substrates investigated here than in the presence of camphor, underscoring the relationship between cation and substrate binding. Thiocamphor gave the most unexpected orientation in the active site of any of the substrates we have investigated to date. The orientation of thiocamphor is quite different from that of camphor. That is, carbons 5 and 6, at which thiocamphor is primarily hydroxylated [Atkins, W. M., & Sligar, S. G. (1988) J. Biol. Chem. 263, 18842-18849], are positioned near Tyr96 rather than near the heme iron. Therefore, the crystallographically observed thiocamphor-P-450CAM structure may correspond to a nonproductive complex. Disordered solvent has been identified in the active site in the presence of uncoupling substrates that channel reducing equivalents away from substrate hydroxylation toward hydrogen peroxide and/or "excess" water production. A buried solvent molecule has also been identified, which may promote uncoupling by moving from an internal location to the active site in the presence of highly mobile substrates.

Non-conventional bonding between organic molecules. The "halogen bond" in crystalline systems

Abstract: The intermolecular interaction in organic crystals, when close contact between a halogen atom and an oxygen or nitrogen atom is present, is investigated by surveys of existing crystal structure determinations in the Cambridge Structural Database and by theoretical methods. Short halogen–oxygen and–nitrogen contacts are restricted to systems with peculiar electronic and steric properties. Energy well depths for sample systems range from almost nil to about 20 kJ mol−1, considerably less than for hydrogen bonding, with which halogen bonding can hardly compete. The width of the energy wells suggests that some short contacts may correspond to just permissive (i.e. energetically neutral) approach, or even to compressed bonding. The strongest bond is attainable only by aromatic iodine, highly activated by electron-attracting substituents, in molecular complexes with strong and sterically unhindered Lewis bases; only in such special cases is the halogen bond the most relevant cohesive factor in the crystal struc...