Experimental and theoretical electron density study of estrone

The electron density and the electrostatic potential (ESP) distributions of estrone have been determined using X-ray diffraction analysis and compared with theoretical calculations in the solid and gas phases. X-ray diffraction measurements are performed with a Rigaku Rapid rotating anode diffractometer at 20 K. The electron density in the estrone crystal has been described with the multipole model, which allowed extensive topological analysis and calculation of the ESP. From DFT calculations in the solid state a theoretical X-ray diffraction data set has been produced and treated in the same way as the experimental data. Two sets of single molecule DFT calculations were performed: (a) An electron density distribution was obtained via a single-point calculation with a large basis set at the experimental geometry and subsequently analyzed according to the quantum theory of atoms in molecules (AIM) to obtain the bond and most atomic properties, and (b) another electron density distribution was obtained with a smaller basis set, but at a geometry optimized using the same basis set for the analysis of atomic energies. An interesting locally stabilizing hydrogen-hydrogen bond path linking H(1) and H(11B) is found which represents the first characterization of such bonding in a steroid molecule. AIM delocalization indices were shown to be well correlated to the experimental electron density at the bond critical points through an exponential relationship. The aromaticity of ring A, chemical bonding, the O(1)...O(2) distance necessary for estrogenic activity, and the electrostatic potential features are also discussed.     

Experimental and theoretical electron density study of a highly twisted polycyclic aromatic hydrocarbon: 4-methyl-[4]helicene

Helicenes are molecules of considerable interest in view of their aromaticity which persists despite a marked departure from planarity and because of the extreme potency of some of their metabolites as tumor and mutation promoters. In this study, the electron density of 4-methyl-[4]helicene (or 4-methylbenzo[c]phenanthrene) is studied topologically with an emphasis on the fjord region since this region is where metabolic activation is initiated. The molecule consists of four fused aromatic rings that assume a twisted geometry. This geometry brings two hydrogen atoms into close proximity in the fjord region of the molecule accompanied by the appearance of an intramolecular C-Hdelta+...delta+H-C bond path (an interaction termed hydrogen-hydrogen or H- H bonding to distinguish it from dihydrogen bonding from which it is qualitatively distinct). In addition to the intramolecular H-H interaction, a number of intermolecular interactions are shown to be involved in the packing of this molecule in the crystalline state. The effect of the nonplanarity of the molecule on the local aromaticity of each ring is also discussed.     

The localized electrons detector as an ab initio representation of molecular structures

The local single particle momentum is proposed as a localized‐electrons detector (LED) that provides a direct three‐dimensional representation of bonding interactions in molecules. It is given exclusively in terms of the electron density and its gradient. We show that the graphical representation of bonding interactions given by LED is consistent with the local curvatures of the electron density as given by the eigenvalues of the Hessian matrix, according to a local symmetry classification of the critical points here introduced. LED consistently complements the topological analysis of the electron density given by the quantum theory of atoms in molecules, by providing a graphical representation of the symmetry of the bonding interactions in molecular systems. © 2010 Wiley Periodicals, Inc. Int J Quantum Chem 110:2418–2425, 2010     

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.     

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.     

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.     

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.     

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.     

Extended weak bonding interactions in DNA: pi-stacking (base-base), base-backbone, and backbone-backbone interactions

We report on several weak interactions in nucleic acids, which, collectively, can make a nonnegligible contribution to the structure and stability of these molecules. Fragments of DNA were obtained from previously determined accurate experimental geometries and their electron density distributions calculated using density functional theory (DFT). The electron densities were analyzed topologically according to the quantum theory of atoms in molecules (AIM). A web of closed-shell bonding interactions is shown to connect neighboring base pairs in base-pair duplexes and in dinuleotide steps. This bonding underlies the well-known pi-stacking interaction between adjacent nucleic acid bases and is characterized topologically for the first time. Two less widely appreciated modes of weak closed-shell interactions in nucleic acids are also described: (i) interactions between atoms in the bases and atoms belonging to the backbone (base-backbone) and (ii) interactions among atoms within the backbone itself (backbone-backbone). These interactions include hydrogen bonding, dihydrogen bonding, hydrogen-hydrogen bonding, and several other weak closed-shell X-Y interactions (X, Y = O, N, C). While each individual interaction is very weak and typically accompanied by perhaps 0.5-3 kcal/mol, the sum total of these interactions is postulated to play a role in stabilizing the structure of nucleic acids. The Watson-and-Crick hydrogen bonding is also characterized in detail at the experimental geometries as a prelude to the discussion of the modes of interactions listed in the title.     

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.