Solution structure and thermolysis of Cobeta-5'-deoxyadenosylimidazolylcobamide, a coenzyme B12 analogue with an imidazole axial nucleoside

The solution structure of Cobeta-5'-deoxyadenosylimidazolylcobamide, Ado(Im)Cbl, the coenzyme B(12) analogue in which the axial 5,6-dimethylbenzimidazole (Bzm) ligand is replaced by imidazole, has been determined by NMR-restrained molecular modeling. A two-state model, in which a conformation with the adenosyl moiety over the southern quadrant of the corrin and a conformation with the adenosyl ligand over the eastern quadrant of the corrin are both populated at room temperature, was required by the nOe data. A rotation profile and molecular dynamics simulations suggest that the eastern conformation is the more stable, in contrast to AdoCbl itself in which the southern conformation is preferred. Consensus structures of the two conformers show that the axial Co-N bond is slightly shorter and the corrin ring is less folded in Ado(Im)Cbl than in AdoCbl. A study of the thermolysis of Ado(Im)Cbl in aqueous solution (50-125 degrees C) revealed competing homolytic and heterolytic pathways as for AdoCbl but with heterolysis being 9-fold faster and homolysis being 3-fold slower at 100 degrees C than for AdoCbl. Determination of the pK(a)'s for the Ado(Im)Cbl base-on/base-off reaction and for the detached imidazole ribonucleoside as a function of temperature permitted correction of the homolysis and heterolysis rate constants for the temperature-dependent presence of the base-off species of Ado(Im)Cbl. Activation analysis of the resulting rate constants for the base-on species show that the entropy of activation for Ado(Im)Cbl homolysis (13.7 +/- 0.9 cal mol(-1) K(-1)) is identical with that of AdoCbl (13.5 +/- 0.7 cal mol(-1) K(-1)) but that the enthalpy of activation (34.8 kcal mol(-1)) is 1.0 +/- 0.4 kcal mol(-1) larger. The opposite effect is seen for heterolysis, where the enthalpies of activation are identical but the entropy of activation is 5 +/- 1 cal mol(-1) K(-1) less negative for Ado(Im)Cbl. Extrapolation to 37 degrees C provides a rate constant for Ado(Im)Cbl homolysis of 2.1 x 10(-9) s(-1), 4.3-fold smaller than for AdoCbl. Combined with earlier results for the enzyme-induced homolysis of Ado(Im)Cbl by the ribonucleoside triphosphate reductase from Lactobacillus leichmannii, the catalytic efficiency of the enzyme for homolysis of Ado(Im)Cbl at 37 degrees C can be calculated to be 4.0 x 10(8), 3.8-fold, or 0.8 kcal mol(-1), smaller than for AdoCbl. Thus, the bulky Bzm ligand makes at best a <1 kcal mol(-1) contribution to the enzymatic activation of coenzyme B(12).     

A molecular mechanics force field for the cobalt corrinoids

A force field for the cobalt (III) corrinoids (derivatives of vitamin B₁₂) for use with a modified version of the molecular mechanics program 2(87) has been developed empirically around 19 cobalt corrinoid crystal structures. Bond lengths, bond angles and torsional angles are reproduced with r.m.s. differences of 0.01 Å, 2.4 °, and 4.2 °, respectively, within the standard deviation of the mean of these parameters found in the solid state. The axial ligand occupying the lower coordination site in the cobalamins, 5,6-dimethylbenzimidazole, is shown to have very limited rotational freedom and is constrained by the downward-pointing b and d propionamide side chains of the corrin ring. Strain-energy profiles for rotation of the side chains of the corrin ring show the existence of several local energy minima and this explains the observed variability in the orientations of these side chains in the solid state. The known change in conformation which occurs in the C ring when the e side chain is epimerized from the lower to the upper face of the corrin ring in cyano-13-epicobalamin is correctly predicted, provided the starting conformation of the C ring is unbiased. A study of cyano-8-epicobalamin indicates that an analogous conformational change does not occur in the B ring and the epimerized d side chain assumes an equatorial orientation relative to the corrin ring. Parameters for the Co---C bond in alkylcobalamins were developed and the structure of methyl- and adenosylcobalamin are accurately reproduced. An examination of the strain energy consequences of rotation of the adenosyl ligand about the Co---C bond identifies a number of low-energy conformations at least two of which, in which adenosyl lies over the “southern” and “eastern” portions of the corrin ring, respectively, have been previously deduced from NMR observations. Coordinated neopentyl in neopentylcobalamin is much more hindered to rotation about the Co---C bond and the lowest conformation finds two γ(C) atoms straddling the upwardly projecting C46 methyl group of the corrin.     

Hydrogen‐bonding controls the solid‐state and enantiomeric comformations of the amino alcohol ligand 2‐[(2‐hydroxyethyl)amino]cyclohexanol

The crystal structure of the title compound, C₈H₁₇NO₂, consists of (R,R) and (S,S) enantiomeric pairs packed in adjacent double layers which are characterized by centrosymmetric hydrogen‐bonded dimers, generated via N—H...O and O—H...O interactions, respectively. Intermolecular interactions, related to acceptor and donor molecule chirality, link the achiral double layers into tubular columns, which consist of a staggered hydrophilic inner core surrounded by a hydrophobic cycloalkyl outer surface and extend in the [011] direction.     

THERMODYNAMIC AND PARTICLE-DYNAMIC STUDIES ON SYNTHESIS OF SILICA NANOPARTICLES USING MICROWAVE-INDUCED PLASMA CVD

1. Introduction1.1 Silica nanoparticles and synthesis methods Silica (SiO2) nanoparticles are widely used in industry asan active filler for polymer reinforcement, a rheologicaladditive in fluids, a free flow agent in powders, and anagent for chemical mechanical polishing during IC (inte-grated circuit) fabrication (Sniegowski & de Boer, 2000).Silica powder is also used for producing silicon carbide(Koc & Cattamanchi, 1998) or opaque silica aerosols (Leeet al., 1995). Many methods can …     

Conformational analysis of 18-azacrown-6 and its bonding with late first transition series divalent metals: insight from DFT combined with NPA and QTAIM analyses

Density functional theory calculations, together with quantum theory of atoms in molecules (QTAIM) analyses, have been performed to investigate 18-azacrown-6 complexes of the high-spin late first transition series divalent metal ions in the gas phase and, in some cases, in aqueous solution simulated by a polarizable continuum model. Six intramolecular H-H bonding interactions in the meso-complexes are found to arise from folding of the ligand upon its electrostatic interaction with the metal ions, which are largely absent in the lowest-energy C(2h) conformer of the free ligand. The ligand-to-metal charge transfer obtained from QTAIM analysis, among other things, is found to be an important factor that controls the stability of these complexes. The inter-relationship between the ligand preorganization energy, the zero-point corrected formation energy of the metal complexes, and the H-H bonding pair distances, as well as the dependence of the electron density and the total energy density at the H-H bond critical points on the H-H bonding pair distances, provides a physical basis for understanding and explaining the stabilizing nature of these closed-shell interactions, which are often viewed as steric clashes that lead to complex destabilization.     

The use of poly(L-lactide-co-caprolactone) as a scaffold for adipose stem cells in bone tissue engineering: application in a spinal fusion model

Since the early 1990s, tissue engineering has been heralded as a strategy that may solve problems associated with bone grafting procedures. The original concept of growing bone in the laboratory, however, has proven illusive due to biological, logistic, and regulatory problems. Fat-derived stem cells and synthetic polymers open new, more practicable routes for bone tissue engineering. In this paper, we highlight the potential of poly(L-lactide-co-caprolactone) (PLCL) to serve as a radiolucent scaffold in bone tissue engineering. It appears that PLCL quickly and preferentially binds adipose stem cells (ASCs), which proliferate rapidly and eventually differentiate into the osteogenic phenotype. An in vivo spinal fusion study in a goat model provides a preclinical proof-of-concept for a one-step surgical procedure with ASCs in bone tissue engineering.     

Probing the nature of the Co(III) ion in corrins: the structural and electronic properties of dicyano- and aquacyanocobyrinic acid heptamethyl ester and a stable yellow dicyano- and aquacyanocobyrinic acid heptamethyl ester

A stable yellow derivative of cobyrinic acid heptamethyl ester, (5R,6R)-Coα,Coβ-dicyano-5,6-dihydro-5-hydroxy-heptamethylcob(III)yrinate-c,6-lactone (DCSYCbs), was prepared from dicyanocobyrinic acid heptamethyl ester (DCCbs). The C5 carbon is oxidized and the c side chain cyclized to form a lactone at C6; the 13 atom, 14 π-e(-) delocalized system of corrins is interrupted, giving a triazamethine system with four conjugated double bonds between N22 and N24 and an isolated double bond between N21 and C4. Stable yellow aquacyanocobyrinic acid heptamethyl ester (ACSYCbs) was prepared by driving off HCN with N(2) in a methanol/acetic acid solution. The electronic spectra of DCCbs and DCSYCbs appear similar except that the bands in DCSYCbs are shifted to shorter wavelengths and the γ-band is much less intense. The experimental spectra were adequately modeled using TD-DFT at the PBE1PBE/6-311G(d,p) level of theory. DCSYCbs crystallizes in the space group P2(1)2(1)2(1) (R(1) = 6.08%) with Z = 4, including one methanol solvent molecule and one water molecule per cobester. The addition of a hydroxyl group at C5 causes loss of the double bond between C5 and C6 and elongation of the C5-C6 bond. From a combination of two-dimensional (1)H TOCSY and ROESY NMR spectra and (1)H/(13)C HSQC and HMBC data, the complete (1)H and (13)C NMR assignments of DCSYCbs were possible, except for two of the ester methyl groups and the (13)C resonances of the two axial cyanide ligands. The latter were assigned using relative chemical shifts calculated by GIAO-DFT methods. The (59)Co resonance of DCCbs was observed at 4074 ppm while that of DCSYCbs is shifted downfield to 4298 ppm. Comparison with available (59)Co data of analogous systems suggests that the more π-conjugated corrin of DCCbs interacts more strongly with the metal than the less extensively conjugated macrocycle of DCSYCbs. As the strength of the interaction between Co(III) and an equatorial macrocycle increases, ν(CN) of axially coordinated CN(-) shifts to lower frequency; in DCSYCbs and DCCbs ν(CN) occurs at 2138 and 2123 cm(-1), respectively. Hence the corrin ligand in DCCbs interacts more strongly with the metal than the stable yellow corrin ligand, with its diminished conjugation. The UV-vis spectral data and DFT-calculated MOs are consistent with greater overlap between the corrin and the metal orbitals in DCCbs relative to DCSYCbs, which gives the metal in the former a softer, more covalent character.