H. L. Carrell

Metal Ion Roles and the Movement of Hydrogen during Reaction Catalyzed by D-Xylose Isomerase: A Joint X-Ray and Neutron Diffraction Study

Conversion of aldo to keto sugars by the metalloenzyme D-xylose isomerase (XI) is a multistep reaction that involves hydrogen transfer. We have determined the structure of this enzyme by neutron diffraction in order to locate H atoms (or their isotope D). Two studies are presented, one of XI containing cadmium and cyclic D-glucose (before sugar ring opening has occurred), and the other containing nickel and linear D-glucose (after ring opening has occurred but before isomerization). Previously we reported the neutron structures of ligand-free enzyme and enzyme with bound product. The data show that His54 is doubly protonated on the ring N in all four structures. Lys289 is neutral before ring opening and gains a proton after this; the catalytic metal-bound water is deprotonated to hydroxyl during isomerization and O5 is deprotonated. These results lead to new suggestions as to how changes might take place over the course of the reaction.

Structure of a dinucleoside phosphate--drug complex as model for nucleic acid--drug interaction.

The crystal structure of a 3 : 2 complex of the frameshift mutagen proflavine with the dinucleoside phosphate cytidylyl-3′5′-guanosine has been determined. The complex has one drug molecule intercalated between Watson–Crick base pairs of the nucleotide duplex. The other two proflavine molecules are bound to the exterior of the miniature double helix. The orientation of the base pairs in this miniature double helix has aspects similar to that found in RNA 11.

Fluorocitrate Inhibition of Aconitase: Relative Configuration of Inhibitory Isomer by X-ray Crystallography

The fluorocitrate isomer that is a strong inhibitor and inactivator of aconitase has been shown by x-ray crystallographic studies on the rubidium ammonium salt to have the configurations (1R : 2R) or (1S : 2S) 1-fluoro-2-hydroxy-1,2,3-propanetricarboxylic acid. A possible mechanism for the action of fluorocitrate is proposed which involves the 1R : 2R isomer suggested from biochemical data.

Hydrogen location in stages of an enzyme-catalyzed reaction: time-of-flight neutron structure of D-xylose isomerase with bound D-xylulose

The time-of-flight neutron Laue technique has been used to determine the location of hydrogen atoms in the enzyme d-xylose isomerase (XI). The neutron structure of crystalline XI with bound product, d-xylulose, shows, unexpectedly, that O5 of d-xylulose is not protonated but is hydrogen-bonded to doubly protonated His54. Also, Lys289, which is neutral in native XI, is protonated (positively charged), while the catalytic water in native XI has become activated to a hydroxyl anion which is in the proximity of C1 and C2, the molecular site of isomerization of xylose. These findings impact our understanding of the reaction mechanism.

X-Ray crystal analysis of the substrates of aconitase: XI. Manganous citrate decahydrate

Abstract The crystal structure of hydrated manganese citrate, [Mn(H2O)6] [Mn C6H5O7(H2O)]22H2O has been determined. The crystals are monoclinic, space group P21/n cell dimensions a = 20.575 ± 0.005, b = 6.755 ± 0.002, c = 9.230 ± 0.002 A, β = 96.74 ± 0.01°. The structure is isomorphous with that of the magnesium salt for which the structure has been determined4. There are two [Mn(H2O)6]2+ ions, four [Mn C6H5O7(H2O)] ions and four water molecules per unit cell. Each citrate ion forms a tridentate chelate to one manganese ion. A correlation of Mn2+ ⋯ H distances for manganese citrate, found in this crystallographic study, was made with those determined by NMR studies in solutions in the absence and presence of the enzyme aconitase, and indicated that the assumption that citrate chelates to enzyme-bound manganese ion fits all the available data.

Solid-state supramoecular assembly via C–H ⋯ O hydrogen bonds: crystal structures of the complexes of 1,3,5-trinitrobenzene with dibenzylideneacetone and 2,5-dibenzylidenecyclopentanone

Dibenzylidene ketones are shown to form stoicheometric complexes with 1,3,5-trinitrobenzene wherein the molecular components are held together with C–H ⋯ O hydrogen bonds.

Hexagonal supramolecular networks in the crystal structure of the 1:1 molecular complex trimethylisocyanurate–1,3,5-trinitrobenzene

Trimethylisocyanurate 2 and 1,3,5-trinitrobenzene 3 form a hexagonal C–H ⋯ O mediated 1:1 complex wherein distinct molecular layers are formed, the molecular symmetry of the components being retained in the crystal.

C-H,O Hydrogen bonded multi-point recognition in molecular assemblies of dibenzylidene ketones and 1,3,5-trinitrobenzenes

Dibenzylideneacetone1a, 2,5-dibenzylidenecyclopentanone 1b, 2,6-dibenzylidenecyclohexanone 1c and 2,5-dibenzylidenecyclopent-3-enone 1d form crystalline stoichiometric complexes with 1,3,5-trinitrobenzene 2a, picryl chloride 2b and picric acid 2c. The structures of these complexes are mediated by multi-point C–HO hydrogen bonds. Some of these patterns of molecular recognition also contain stronger O–HO hydrogen bonds. The C–HO hydrogen bonds within these multi-point supramolecular synthons are generally shorter and more linear than the other C–HO hydrogen bonds found in these complexes.

C-H···O hydrogen bonds in molecular complexes of 1,3,5-trinitrobenzene with some N-heterocycles

The crystal structures of the molecular complexes of sym-trinitrobenzene (TNB) with acridine, 1,10-phenanthroline and phenazine are discussed. In all three cases, the structures are held together by C–H⋯O and π⋯π interactions, and TNB forms hydrogen bonded dimers and tapes that are not found in its native crystal structure. Acridine and 1,10-phenanthroline yield 1 ∶ 1 complexes that have very similar structures. The related molecule phenazine, however, gives a different 2 ∶ 3 complex in which guest exchange, as seen in other recently reported examples, is not observed. A case is made for the reporting of such ‘low yield’ supramolecular reactions because they still provide valuable information about the packing characteristics of organic molecules.

Evidence for the characterisation of the C–H···π interaction as a weak hydrogen bond: toluene and chlorobenzene solvates of 2,3,7,8-tetraphenyl-1,9,10-anthyridine

The crystal structures of the toluene and chlorobenzene solvates of 2,3,7,8-tetraphenyl-1,9,10-anthyridine are nearly identical save for differences in the mode of solvent inclusion; these differences have an important bearing on the nature of the C–H···π interactions in these structures.