David E. Zacharias

Metal ion coordination in cobalt formate dihydrate

The structure of cobalt formate dihydrate, Co(HCO2)2 · 2H2O, was determined using single-crystal X-ray diffraction data. The crystals are monoclinic, space groupP21/c, with unit-cell dimensionsa=8.680(2),b=7.160(2),c=9.272(2) Å,β=97.43(2)°,V=571.4(3) Å3Z=4.Robs=0.038 for 1282 unique reflections withI>3σ(I). The crystal structure is found to be isomorphous with those of other divalent metal formates. This structure is interesting crystallographically because the Patterson map is homometric with respect to the positions of the heavy atoms. The asymmetric unit consists of two independent cobalt atoms on special positions, two formate ions (HCOO−), and two water molecules. The two cobalt atoms are each coordinated to six oxygen atoms in an octahedral arrangement. One of the cobalt octahedra contains only oxygen atoms from six formate ions. The second cobalt ion is surrounded by four water molecules and an oxygen atom from each of two formate ions. The two different octahedra are bridged by one of the formate ions and by hydrogen bonds. This network extends in a three-dimensional polymeric manner throughout the crystal structure. Each of the four oxygen atoms in the two independent formate ions forms a hydrogen bond to water and is coordinated to a metal ion. It is found that the metal ions lie in the plane of the formate carboxyl group to which they are coordinated, while molecules to which the formate ion is hydrogen bonded lie more out of this plane.

A new type of organocobalt complex with a buckled equatorial ligand

Abstract Weakening of the CoC bond in coenzyme B 12 has been attributed to steric influences, especially to flexing or folding of the equatorial corrin ring. With this in mind we have synthesized four new cobalt complexes with unusual steric properties as model compounds: Co((DO)(DOH)bn)Cl 2 ( I ), where (DO)- (DOH)bn is the equatorial ligand N 2 ,N 2 ′ -butanediylbis (2,3-butanedione 2-imine 3-oxime), and organocobalt complexes [LCo((DO)(DOH)bn)R] + , where R = methyl, ethyl ( II ), or methylpropyl and L = OH 2 . The NMR spectra and crystal structures of Co((DO)- (DOH)bn)Cl 2 ( I ) and [OH 2 Co((DO)(DOH)bn)CH 2 - CH 3 ]ClO 4 ( II ) are reported. The respective crystal systems, space groups, lattice constants and final R factors for these two compounds are as follows: I orthorhombic, P 2 1 2 1 2 1 , a = 14.017(2), b = 29.014(4), c = 8.005(2) A, Z = 8, R = 0.061, R w = 0.076; II monoclinic, C 2/ c , a = 21.820(3), b = 7.386(2), c = 25.652(4) A, β = 101.22(1)°, Z = 8, R = 0.077, R w = 0.075. These are the first cobalt complexes reported with the (DO)- (DOH)bn equatorial ligand; in both I and II the equatorial nitrogen donor atoms form a planar array around the Co atom, in contrast to the non-planar coordination geometry in [Cu((DO)(DOH)bn)]- (ClO 4 ). The (DO)(DOH)bn ligand folds toward the two central carbon atoms of the four-carbon bridge in both complexes. In complex II the equatorial ligand folds toward the water ligand at an angle of 6.0°; it is also folded (3.8, 12.0°) in both independent molecules of I , where the two axial Cl − ligands are identical. The new ethylcobalt complex ( II ) is similar to coenzyme B 12 in that there is an equatorial ligand with a ‘built-in’ fold, and in the steric adjustments produced by the folded equatorial ligand. The CoC and CO bonds are lengthened to 2.012(6) and 2.119(3) A and the CoCC bond angle of the alkyl ligand is widened to 119.3(5)°.

Benzamide-DNA interactions: Deductions from binding, enzyme kinetics and from X-ray structural analysis of a 9-ethyladenine-benzamide adduct

The interaction of benzamide with the isolated components of calf thymus poly(ADP-ribose) polymerase and with liver nuclei has been investigated. A benzamide-agarose affinity gel matrix was prepared by coupling o-aminobenzoic acid with Affi-Gel 10, followed by amidation. The benzamide-agarose matrix bound the DNA that is coenzymic with poly(ADP-ribose) polymerase; the matrix, however, did not bind the purified poly(ADP-ribose) polymerase protein. A highly radioactive derivative of benzamide, the 125I-labelled adduct of o-aminobenzamide and the Bolton-Hunter reagent, was prepared and its binding to liver nuclear DNA, calf thymus DNA and specific coenzymic DNA of poly(ADP-ribose) polymerase was compared. The binding of labelled benzamide to coenzymic DNA was several-fold higher than its binding to unfractionated calf thymus DNA. A DNA-related enzyme inhibitory site of benzamide was demonstrated in a reconstructed poly(ADP-ribose) polymerase system, made up from purified enzyme protein and varying concentrations of a synthetic octadeoxynucleotide that serves as coenzyme. As a model for benzamide binding to DNA, a crystalline complex of 9-ethyladenine and benzamide was prepared and its X-ray crystallographic structure was determined; this indicated a specific hydrogen bond between an amide hydrogen atom and N-3 of adenine. The benzamide also formed a hydrogen bond to another benzamide molecule. The aromatic ring of benzamide does not intercalate between ethyladenine molecules, but lies nearly perpendicular to the planes of stacking ethyladenine molecules in a manner reminiscent of the binding of ethidium bromide to polynucleotides. Thus we have identified DNA as a site of binding of benzamide; this binding is critically dependent on the nature of the DNA and is high for coenzymic DNA that is isolated with the purified enzyme as a tightly associated species. A possible model for such binding has been suggested from the structural analysis of a benzamide-ethyladenine complex.

The geometry of the thioester group and its implications for the chemistry of acyl coenzyme a

Abstract The ground-state geometry of the thioester group has been investigated in an attempt to understand the reactivity of acyl CoAs. The structure of ethyl thiol- d -ribonate tetraacetate has been determined from X-ray diffraction data, and bond lengths, interbond angles, and torsion angles are presented for the two independent molecules in the asymmetric unit of the crystal. In crystals of this compound the ethyl groups are found to be disordered. An analysis of the published data on bond lengths and interbond angles for thioesters, esters, and alkyl aryl/vinyl monosulfides (R 1 SR 2 , R 1  C ( sp 3 ), R 2  C ( sp 2 )) and ethers (R 1 OR 2 ) was made using the Cambridge Crystallographic Data File. This survey, together with the results from our studies, shows that in thioesters the acyl CS bond (marked ∗) is not significantly shorter than a single C ( sp 2 )S bond in alkyl aryl/vinyl monosulfides. This is in contrast to the well-known conjugation in the corresponding bond in esters where we find that the acyl  CO bond is shorter than a single C ( sp 2 )O bond in alkyl aryl/vinyl ethers by 0.076(6) A. Thus there is much more resonance in O-esters than in thioesters. These findings support recent suggestions that the carbonyl group in acyl CoAs is ketone-like. Therefore thioesters (with little or no double bond character in the CS bond) have a higher free energy of hydrolysis than do O-esters (with appreciable double bond character in the CO bond).

Structure refinement and molecular packing of p-chloro-trans-cinnamic acid and β-(p-chlorophenyl)propionic acid

The crystal structures of p-chloro-trans-cinnamic acid (I) and β-(p-chlorophenyl) propionic acid (II) have been determined from X-ray diffractometer data. Both molecules are approximately planar and the crystal packing is similar when viewed down the b axis. Crystals of both compouns are monoclinic, space group P21/a, with Z= 4 in a unit cell of dimensions; for (I): a= 32·813(9), b= 3·890(1), c= 6·538(1)A, β= 95·94(2)°: and for (II): a= 30·024(6), b= 5·071(1), c= 5·728(1)A, β= 98·70(1)°. The structures were refined by full-matrix least-squares to R0·059 [(I), 1160 observed reflections] and 0·052 [(II), 1372 observed reflections]. The cinnamic acid crystallizes in the β-form with head-to-head packing so that the ethylenic bonds lie near each other, thus explaining why a photo-dimerization to a β-truxinic acid can occur. There is disorder of the carboxy hydrogen atom in (I) but it is localized in (II).

Internal Hydrogen Bond Formation in a syn-Hydroxyepoxide

The existence of an internal hydrogen bond in a compound representative of a syn diol epoxide (a possible intermediate in chemical carcinogenesis by certain polycyclic aromatic hydrocarbons) has been demonstrated by x-ray crystallographic and nuclear magnetic resonance studies. This internal hydrogen bond was found in 3,4-epoxy-2-methyl-1,2,3,4-tetrahydro-1-naphthol and was shown to persist in dioxane-water solutions containing up to 80 mole percent water. In this structure, the 1-hydroxy and 2-methyl groups are shown to occupy axial positions. In the anti diol epoxide, which has no internal hydrogen bond, analogous groups are equatorial. Crystals of the compound were unstable in the x-ray beam while the data were being collected (even at low temperatures), presumably as a result of decomposition.

Intramolecular Michael-type addition in the solid state

Several substituted 2′-hydroxy-4′,6′-dimethylchalcones undergo a solid state Intramolecular Michaeltype addition reaction to yield the corresponding flavanones, at temperatures significantly below the melting points of the reactants or products. Single crystal X-ray diffraction studies of the reactant and product phases have been carried out and indicate that these solid state reactions most likely proceed in a non-topochemical fashion. A similar conclusion is deduced from X-ray powder diffraction, differential scanning calorimetry and packing energy calculations. Reaction in the defect regions is probably important because considerable relaxation in the molecular conformation of the chalcone is required in the crystal before Intramolecular ring-closure to the flavanone can occur.

Refinement of the crystal structure of orthorhombic dibenz[a,h]-anthracene

The crystal structure of the title compound has been refined from (a) three-dimensional, single-crystal X-ray diffractometer data and (b) three-dimensional photographic data. Crystals are orthorhombic, space group Pcab, with a= 8.263(2), b= 11.466(2), c= 15.238(2)A, Z= 4. Starting with previously reported atomic parameters the structure was refined anisotropically (a) by full-matrix least-squares to R 0.035 (715 unique reflections), and (b) by block-diagonal least-squares to R 0.067 (1 148 unique reflections). Bond-lengths for each refinement are in good agreement with each other and with those predicted by Paulings formula for single-bond-double-bond resonance. The molecule is centrosymmetric and planar.

Probing the Mechanism of Coenzyme B 12 : Synthesis, Crystal Structures, and Molecular Modeling of Coenzyme B 12 Model Compounds

Coenzyme B 12 is an organometallic compound that catalyzes biological rearrangement reactions. Homolytic cleavage of the unusual cobalt-carbon bond in the coenzyme initiates the free-radical reaction. In an attempt to understand the factors that might be important in the mechanism, we synthesized a series of model complexes [LCo{(DO)(DOH)bn}R] + with a folded equatorial ligand and determined the crystal structures. Semi-empirical calculations with these and other model compounds provide evidence for a transelectronic influence; when the Co-N bond is shortened, the Co-C bond lengthens. These results are compared to density functional calculations carried out by others.

Structure of the molecular complex of anthracene with 1,8:4,5-naphthalenetetracarboxylic dianhydride

C14H10.C14H4O6, M(r) = 446.42, monoclinic, P2(1)/a, a = 17.572 (10), b = 7.727 (4), c = 7.398 (4) A, beta = 101.90 (4) degrees, V = 982.9 (9) A3, Z = 2, Dx = 1.508 Mg m-3, lambda (Mo K alpha) = 0.71069 A, mu = 0.100 mm-1, F(000) = 460, T = 293 K, R = 0.050 for 1429 unique reflections with I > 3 sigma (I). The molecules stack with alternating rows of anthracene and dianhydride molecules. The two types of molecule do not lie parallel to each other in these stacks, possibly as a result of interactions between the peripheral H atoms of the anthracene and O atoms of the anhydride.