Crystallization of Arthrobacter sp. strain 1C N-(1-D-carboxyethyl)-L-norvaline dehydrogenase and its complex with NAD+

The novel NAD+-linked opine dehydrogenase from a soil isolate Arthrobacter sp. strain 1C belongs to an enzyme superfamily whose members exhibit quite diverse substrate specificites. Crystals of this opine dehydrogenase, obtained in the presence or absence of co-factor and substrates, have been shown to diffract to beyond 1.8 ? resolution. X-ray precession photographs have established that the crystals belong to space group P21212, with cell parameters a = 104.9, b = 80.0, c = 45.5 ? and a single subunit in the asymmetric unit. The elucidation of the three-dimensional structure of this enzyme will provide a structural framework for this novel class of dehydrogenases to enable a comparison to be made with other enzyme families and also as the basis for mutagenesis experiments directed towards the production of natural and synthetic opine-type compounds containing two chiral centres.     

Comparison of localization and delocalization indices obtained with Hartree-Fock and conventional correlated methods: effect of Coulomb correlation

Atomic populations and localization [lambda(A)] and delocalization [delta(A,B)] indices (LIs and DIs) are calculated for a large set of molecules at the Hartree-Fock (HF), MP2, MP4(SDQ), CISD, and QCISD levels with the 6-311++G(2d,2p) basis set. The HF method and the conventional correlation methods [MP2, MP4(SDQ), CISD, and QCISD] yield distinct sets of LIs and DIs. Yet, within the four conventional correlation methods the differences in atomic populations and LIs and DIs are small. Relative to HF, the conventional correlation methods [MP2, MP4(SDQ), CISD, QCISD] yield virtually the same LIs and DIs for molecules with large charge separations while LIs and DIs that differ significantly from the HF values--the LIs are increased and DIs decreased--are obtained for bonds with no or small charge separations. Such is the case in the archetypal homopolar molecules HC(triple bond)CH, H2C=CH2, CH3-CH3, and "protonated cyclopropane" C(3)H(7) (+), in which case the bonding may be atypical. Relative to HF, the typical effect of the conventional correlation methods is to decrease the DI between atoms.     

Environmental UV‐A and UV‐B Threshold Doses for Apoptosis and Necrosis in Humans Fibroblasts¶

Apoptosis involves a highly organized and programmed series of events aimed at maintaining genomic stability by eliminating defective host cells. The purpose of this study was to determine the threshold doses and environmental UV‐A and UV‐B exposure times necessary to produce apoptosis and necrosis in the normal cells of a human fibroblast cell line. Enviromental UV‐A and UV‐B doses were measured over a 6 year period with a four‐channel UV radiometer. The fibroblasts were irradiated once using an Oriel UV Solar Simulator with six doses of environmentally‐based UV. Doses corresponded to 0,11,19,23 and 45 min of average environmental UV‐A and UV‐B radiation at solar noon in Puerto Rico. The Annexin‐V binding method was used to differentiate between normal fibroblasts and apoptotic or necrotic fibroblasts. The threshold dose from apoptosis to necrosis was found between 24–28 kJ/m², which corresponded to 19 and 23 min of environmental UV‐A and UV‐B exposure. This study provides the first data that specify the environmental threshold doses of UV‐A and UV‐B at which human fibroblasts undergo apoptosis and necrosis. These results may provide valuable dose‐response thresholds for apoptosis and necrosis for future mechanistic studies and baseline data for skin cancer prevention programs.     

Effect of absolute laser phase on reaction paths in laser-induced chemical reactions

Potential surfaces, dipole moments, and polarizabilities are calculated by ab initio methods [unrestricted MP2(full)/6-311++G(2d,2p)] along the reaction paths of the F+CH4 and Cl+CH4 reaction systems. It is found that in general dipole moments and polarizabilities exhibit peaks near the transition state. In the case of X=F these peaks are on the products side and in the case of X=Cl they are on the reactants side indicating an early transition state in the case of fluorine and a late transition state in the case of chlorine. An analysis of the geometric changes along the reaction paths reveals a one-to-one correspondence between the peaks in the electric properties and peaks in the rate of change of certain internal geometric coordinates along the reaction path. Interaction with short infrared intense laser fields pulses leads to the possibility of interferences between the dipole and polarizability laser-molecule interactions as a function of laser phase. The larger dipole moment in the Cl+CH4 reaction can lead to the creation of deep wells (instead of energy barriers) and new strongly bound states in the transition state region. This suggests possible coherent control of the reaction path as a function of the absolute phase of the incident field, by significant modification of the potential surfaces along the reaction path and, in particular, in the transition state region.     

Hydrogen–hydrogen bonding in biphenyl revisited

The evidence for the stabilizing nature of the H–H bonding in planar biphenyl is succinctly reviewed. The stabilizing nature of the H–H bonding is revealed through a comparison of the atomic energy of every atom in planar biphenyl with the same atom in the twisted equilibrium structure. It is shown that the barrier to rotation via the planar transition state is the net resultant of a stabilisation of the four ortho-hydrogen atoms (by 8 kcal/mol each), a stabilisation of the two para-carbon atoms (by 3 kcal/mol each) and by the dominant destabilisation of the two carbon atoms joining the two rings—the two junction carbon atoms—(by 22 kcal/mol each). The energetic stabilisation of the four ortho-hydrogen atoms is further shown to be in large proportion due to the formation of the hydrogen–hydrogen interatomic surface. Furthermore, neither the “bond order” between the two junction carbon atoms nor the total electron delocalisation between the two rings exhibit a significant change in going from the planar to the twisted equilibrium geometry. These findings are in contrast with the classical view of a balance between “steric non-bonded repulsion” and better electron delocalisation as a function of the twist dihedral angle. Similar conclusions have been recently reached by Pacios and Gómez through a study of the electrostatic potential at the position of the hydrogen nuclei. We dedicate this article to Professor TM Krygowski on the occasion of his 70th birthday wishing him a long and productive life.     

Twisted amides: X-ray crystallographic and theoretical study of two acylated glycolurils with aromatic substituents

X-ray crystallography and theoretical analysis were applied to explore the molecular basis for the efficient and selective Claisen-like condensations of diacylglycolurils. The crystal structures of 1-acetyl-6-benzoyl-3,4,7,8-tetramethylglycoluril (4b), and of 1-(3′-oxo-3′-phenylpropionyl)-3,4,7,8-tetramethylglycoluril (5b), the product of base-promoted intramolecular condensation of 4b, were obtained by X-ray diffraction. The acetyl (Ac) group in 4b is essentially coplanar with the attached tetrahydroimidazolone ring of the glycoluril core (τ=7°), while the benzoyl (Bz) group is twisted by τ=45° relative to a plane through the ring to which it is bonded. Product 5b contains a flat amide (τ=7°). Ab initio energy optimizations of the experimental structures for 4b and 5b give optimized geometries which are not dramatically altered, suggesting that crystal packing effects are small. An atoms-in-molecules study of the delocalization of the Fermi hole reveals that electrons in the Bz C=O group of 4b are delocalized into the phenyl ring as well as into the urea moiety of the glycoluril core. This effect stabilizes the Bz over the Ac carbonyl group, and accounts for selective twisting of the Bz group. The Laplacian of the electron density reveals a non-bonded valence shell charge concentration at O of the Ac group, corresponding to a lone-pair region, aligned with a charge depletion in the valence shell of the Bz C=O carbon [(C15–O16C18)=113°]. The angle of approach [(O16C18=O19)] is 100°, equal to the angle for ideal nucleophilic attack on a carbonyl group. Oxygen atom O16 is thus poised to attack C18; only the O16C18 distance (3.248 Å) seems to prevent reaction. These results suggest that the same distance restraint may prevent O-acylation in the enolate intermediate 6b derived from4b. By contrast, the transition state for C-acylation, leading from 6b towards product 5b requires a different geometry, which may explain the observed selectivity for C-acylation in this enolate. The results show that, as 4b is converted to 5b, amide torsional strain is relieved, which may account for the high reactivity of 4b and the efficiency and irreversibility of this condensation process. This study provides a starting point for quantitative correlation of substrate structure in diacylglycolurils with kinetic data for the rearrangement reaction.     

Synthesis of O-α-L-Fucopyranosyl-(1→2)-O-β-D-galactopyranosyl-(1→4)-2-acetamido-2-deoxy-D-glucopyranose. The H-Blood Group Specific Trisaccharide

Abstract

Different reaction conditions were investigated for the preparation of benzyl 2-acetamido-3,6-di-O-benzyl-2-deoxy-β-D-glucopyranoside (5). Compound 5 on reaction with 2,3,4,6-tetra-O-acetyl-α-D-galactopyranosyl bromide afforded the 4-O-substituted 2-acetamido-2-deoxy-β-D-glucopyranosyl derivative which, on O-deacetylation, gave benzyl 2-acetamido-3,6-di-O-benzyl-2-deoxy-4-O-β-D-galactopyranosyl-β-D-glucopyranoside (8). The trimethylsilyl (Me₃Si) derivative of 8, on treatment with pyridineacetic anhydride-acetic acid for 2 days, gave the disaccharide derivative having an O-acetyl group selectively introduced at the primary position and Me₃Si groups at the secondary positions. The latter groups were readily cleaved by treatment with aqueous acetic acid in methanol to afford benzyl 2-acetamido-4-O-(6-O-acetyl-β-D-galactopyranosyl)-3,6-di-O-benzyl-2-deoxy-β-D-glucopyranoside, which on isopropylidenation gave the desired, key intermediate benzyl 2-acetamido-4-O-(6-O-acetyl-3,4-O-isopropylidene-β-D-galactopyranosyl)-3,6-di-O-benzyl-2-deoxy-β-D-glucopyranoside (12). Reaction of 12 with 2,3,4-tri-O-benzyl-α-L-fucopyranosyl bromide under catalysis by bromide ion afforded the trisaccharlde derivative from which the title trisaccharide was obtained by systematic removal of the protective groups. The structures of the final trisaccharide and of various intermediates were established by ¹H and ¹³C NMR spectroscopy.     

Structures,g-tensors,and hyperfine coupling constants of L-α-alanine radicals in radiation dosimetry: An ab initio molecular dynamics simulation study

Alanine is used as a transfer standard dosimeter for gamma ray and electron beam calibration. An important factor affecting its dosimetric response is humidity which can lead to errors in absorbed dose calculations. Ab initio molecular dynamics calculations were performed to determine the environmental effects on the electron paramagnetic resonance (EPR) parameters of L-α-alanine radicals in acidic and alkaline solutions. A new result, not dissimilar to the closed-shell amino acid molecule alanine, is that the non-zwitterionic form of the alanine radical is the stable form in the gas phase while the zwitterionic neutral alanine radical is not a stable structure in the gas phase. Geometric and EPR parameters of radicals in both gas and solution phases are found to be dependent on hydrogen bonding of water molecules with the polar groups and on dynamic solvation. Calculations on the optimized free radicals in the gas phase revealed that for the neutral radical, hydrogen bonding to water molecules drives a decrease in the magnitudes of g-tensor components g _xx and g _yy without affecting neither g _zz component nor the hyperfine coupling constants (HFCCs). The transfer from the gas to solution phase of the alanine radical anion is accompanied with an increase in the spin density on the carboxylic group's oxygen atoms. However, for the neutral radical, this transfer from gas to solution phase is accompanied with the decrease in the spin density on oxygen atoms. Calculated isotropic HFCCs and g-tensor of all radicals are in good agreement with experiment in both acidic and alkaline solutions.     

Beta zeolite supported on silicon carbide for Friedel-Crafts fixed-bed reactions

Beta zeolite supported on silicon carbide, with high thermal conductivity and high mechanical strength, was successfully used as an active and stable catalyst for Friedel-Crafts reactions in a fixed bed configuration.