Computational study of mutarotation in erythrose and threose

For the first time the mutarotation mechanism of furanose rings has been investigated, with and without solvent. The transformations from open-chain furanose to d-erythrose and d-threose have been studied at B3LYP/6-311++G(d,p) and G3MP2B3 levels, in vacuum and in solution through continuum solvation models. We studied the catalytic influence of one, two or three water molecules, as well as simplified models of carbohydrates, that is, methanol and 1,2-ethanediol. Water molecules significantly reduce the energy barrier of the hemiacetal formation occurring between the open-chain and furanose configurations. The energy barrier is optimally reduced by two water molecules. Methanol yields a smaller transition state barrier than the one obtained with a single water molecule. In contrast, 1,2-ethanediol does not provide a lower transition state compared to the barrier in the presence of two water molecules.     

Selective monoacetylation of diol compounds by Aspergillus niger lipase

Summary The primary monoesters of diol compounds were formed exclusively in the reaction with vinyl acetate and Aspergillus niger lipase for 24~72 h. Various diol compounds which included 1,3-butanediol, 1,4-butanediol, 1,5-hexanediol, 1-phenyl-1,2-ethanediol, 1-phenyl-1,3-propanediol, 2, 3, or 4-hydroxybenzyl alcohol, methyl 2, 3-O-acetyl-D-glycopyranosides and phenyl 1-thio--D-xylopyranoside have been examined and showed nearly 100% regioselectivity.     

Tuning the morphology of cellulose acetate gels by manipulating the mechanism of phase separation

The effect of dihydric alcohol (nonsolvent) addition on the rheological and microstructural behavior of cellulose acetate (CA) in a ternary CA, N,N-dimethylacetamide (DMA), nonsolvent system was investigated. Increasing the dihydric alcohol concentration led to enhanced steady shear viscosity and dynamic viscoelastic properties that were dependent on CA concentration. Changing the dihydric alcohol from 1,2-ethanediol to 1,4-butanediol and 1,6-hexanediol increased the moduli and decreased the concentration of nonsolvent at which the sol-gel transition occurred. At 10 wt % CA concentration the modulus and gel morphology of the 1,2-ethanediol and 1,4-butanediol systems were quite similar and distinctly different from that of 1,6-hexanediol. In the former, the gel morphologies were more heterogeneous, evident of more extensive coarsening, and likely obtained via nucleation and growth and spinoidal decomposition of off-critical mixtures. The latter exhibited more uniform dense network morphology, indicative of a spinoidal decomposition of near-critical mixtures. The gels were fractal in nature and exhibited different fractal dimensions in-line with the observed differences in microstructure; D ～ 1.87 ± 0.02 (1,2-ethanediol and 1,4-butanediol) and D ～ 1.97 ± 0.02 (1,6-hexanediol). However, at 15 wt % CA content, the gels exhibited more similar viscoelastic behavior and gel microstructures; D ～ 1.97 ± 0.02 for all three dihydric alcohol systems.     

Structure analysis of montmorillonite intercalated with rhodamine B: modeling and experiment

The intercalation process and the structure of montmorillonite intercalated with [rhodamine B]+ cations have been investigated using molecular modeling (molecular mechanics and molecular dynamics simulations), X-ray powder diffraction and IR spectroscopy. The structure of the intercalate depends strongly on the concentration of rhodamine B in the intercalation solution. The presence of two phases in the intercalated structure was revealed by modeling and X-ray powder diffraction: (i) phase with basal spacing 18 A and with bilayer arrangement of guests and (ii) phase with average basal spacing 23 A and with monolayer arrangement of guests. In both phases the monomeric and dimeric arrangement can coexist in the interlayer space. Three types of dimers in the interlayer structure have been found by modeling: (i) H-dimer (head-to-head arrangement) present in the 18 A phase, (ii) sandwich type of the head-to-tail arrangement (present in the 23 A phase) and (iii) J-dimer (head-to-tail arrangement) present in the 23 A phase. Figure Montmorillonite intercalated with rhodamine B cations. On the left: phase 18 A, bilayer dimeric arrangement of guests (H-dimers). On the right: phase 23 A, monolayer arrangement of guests prepared using intercalation solution with a low concentration of rhodamine B     

Montmorillonite and Beidellite Intercalated with Tetramethylammonium Cations

Molecular mechanics simulations, combined with X-ray powder diffraction and infrared spectroscopy, have been used in structure analysis of montmorillonite and beidellite intercalated with tetramethylammonium cations. A complex structure analysis provided us with the detailed structure model, including characterization of the disorder, the total sublimation energy and a charge distribution in the structure of intercalates. The calculated basal spacings (14.36 Å for TMA-montmorillonite and 14.12 Å for TMA-beidellite) are in good agreement with the experimental values (14.31 Å for TMA-montmorillonite and 14.147 Å for TMA-beidellite). Both intercalated structures exhibit positional and orientational disorder in the arrangement of TMA cations, and consequently disorder in layer-stacking. In the present work we analyse the effect of octahedral and tetrahedral substitutions in a 2:1 silicate layer on the arrangement of tetramethylammonium (TMA) cations in the interlayer space of montmorillonite and beidellite. The most significant difference between TMA-montmorillonite and TMA-beidellite is in the charge distribution on the TMA cations and silicate layer. The TMA-beidellite structure is highly polarized, the total charge on one TMA cation is +0.167 e^–, while the total charge on the TMA cation in montmorillonite is +0.050 e^–.     

Immunochemical evidence for the difference between coenzyme-B12-dependent diol dehydratase and glycerol dehydratase.

Klebsiella pneumoniae ATCC 25955 (formerly named Aerobacter aerogenes PZH 572, Warsaw), which is known to produce coenzyme-B12-dependent glycerol dehydratase when grown anaerobically in a glycerol medium, formed coenzyme-B12-dependent diol dehydratase in a 1,2-propanediol-containing medium. Both the diol dehydratase and the glycerol dehydratase produced by the organism catalyzed the conversion of glycerol, 1,2-propanediol and 1,2-ethanediol to the corresponding aldehydes and underwent concomitant inactivation during the catalysis of glycerol dehydration, as does the diol dehydratase of K. pneumoniae (A. aerogenes) ATCC 8724. However, the two enzymes were distinguishable from each other by the monovalent-cation-selectivity pattern and by substrate specificity; that is, glycerol dehydratase preferred glycerol to 1,2-propanediol as a substrate, whereas diol dehydratase preferred 1,2-propanediol to glycerol, as judged from initial velocity studies. Ouchterlony double-diffusion analysis and immunochemical titration with rabbit antiserum against diol dehydratase of K. pneumoniae ATCC 8724 established clearly that the diol dehydratase of K. pneumoniae ATCC 25955 is immunologically similar to that of K. pneumoniae ATCC 8724, while the glycerol dehydratase of the former is different from the diol dehydratase of both strains. Both the enzymes were found to be distributed in several bacteria of the family Enterobacteriaceae.     

The structure of 2Zn pig insulin crystals at 1.5 A resolution

The paper describes the arrangement of the atoms within rhombohedral crystals of 2Zn pig insulin as seen in electron density maps calculated from X-ray data extending to 1.5 A (1 A = 10(-10) m = 10(-1) nm) at room temperature and refined to R = 0.153. The unit cell contains 2 zinc ions, 6 insulin molecules and about 3 x 283 water molecules. The atoms in the protein molecules appear well defined, 7 of the 102 side chains in the asymmetric unit have been assigned alternative disordered positions. The electron density over the water molecules has been interpreted in terms of 349 sites, 217 weighted 1.0, 126 weighted 0.5, 5 at 0.33 and 1 at 0.25 giving ca. 282 molecules. The positions and contacts of all the residues belonging to the two A and B chains of the asymmetric unit are shown first and then details of their arrangement in the two insulin molecules, 1 and 2, which are different. The formation from these molecules of a compact dimer and the further aggregation of three dimers to form a hexamer around two zinc ions, follows. It appears that in the packing of the hexamers in the crystal there are conflicting influences; too-close contacts between histidine B5 residues in neighbouring hexamers are probably responsible for movements of atoms at the beginning of the A chain of one of the two molecules of the dimer that initiate movements in other parts, particularly near the end of the B chain. At every stage of the building of the protein structure, residues to chains of definite conformation, molecules, dimers, hexamers and crystals, we can trace the effect of the packing of like groups to like, aliphatic groups together, aromatic groups together, hydrogen-bonded structures, positive and negative ions. Between the protein molecules, the water is distributed in cavities and channels that are continuous throughout the crystals. More than half the water molecules appear directly hydrogen bonded to protein atoms. These are generally in contact with other water molecules in chains and rings of increasing disorder, corresponding with their movement through the crystals. Within the established crystal structure we survey next the distribution of hydrogen bonds within the protein molecules and between water and protein and water and water; all but eight of the active atoms in the protein form at least one hydrogen bond.(ABSTRACT TRUNCATED AT 400 WORDS)     

The role of stacking interactions in the mechanisms of binding of the glycine site of NMDA-receptor with antagonists and 3-hydroxykynurenine

Ab initio quantum chemical calculations of benzene dimer, benzene dimer with 5,7 clorination of one aromatic ring, 3-hydroxykynurenine, and kunurenic acid molecules situated above Phe484 aromatic ring of receptor binding site fragment were carried out in order to investigate the role of stacking interaction in the binding of agonists and antagonists with the glycine site of the NMDA receptor NR1 subunit. All calculations were done with the help of GAMESS 6.4 software with 6-31G** atomic gaussian basal functions with complete optimization of geometry and taking into account the electron correlation up to the second-order Moller-Plesset perturbation theory. It was shown that the parallel dislodged conformations of the benzene dimer is energetically most advantageous. Successive substitution of chlorine atoms for the protons of one aromatic ring in 7 and 5 positions leads to an increase in stacking-interaction energy and a mutual displacement of aromatic rings. In the case of kunurenic acid and its derivatives, which are NMDA receptor antagonists, the increase in the energy of stacking interactions leads to the strengthening of inhibition of the ion channel, whereas the 3-hydroxykynurenine molecule is neither agonist, nor antagonist for the glycine site of the NMDA receptor due to the sterical constraints.     

Packing analysis of crystalline myosin subfragment-1. Implications for the size and shape of the myosin head

Crystals of myosin subfragment-1 have been examined by X-ray diffraction and electron microscopy to determine how the molecules pack in the unit cell and to gain preliminary information on the size and shape of the myosin head. Subfragment-1 crystallizes in space group P212121. Analysis of the X-ray diffraction photographs shows that there are eight molecules in the unit cell with two in the asymmetric unit related by a non-crystallographic or local 2-fold axis. It also indicates that in projection down the a axis, two molecules of myosin subfragment-1 lie almost directly on top of one another except for a translation of about 9 A along c. Small crystals were fixed and embedded in the presence of tannic acid, and thin sections were cut perpendicular to each of the three crystallographic axes. Image analysis of micrographs recorded from these sections confirm the packing arrangement deduced from X-ray diffraction, and give the approximate size and shape of the molecule in the crystal lattice. They show that the molecule is at least 160 A long with a maximum thickness of about 60 A, and that it has marked curvature in the unit cell.     

Stereospecific dihydroxylation of the styrene vinyl group by purified naphthalene dioxygenase from Pseudomonas sp. strain NCIB 9816-4.

Naphthalene dioxygenase (NDO) from Pseudomonas sp. strain NCIB 9816-4 adds both atoms of the dioxygen molecule to styrene to form (R)-l-phenyl-1,2-ethanediol. Product formation is tightly coupled to dioxygen consumption and NADH oxidation. NDO oxidizes styrene-d8 at almost the same initial rate as styrene. The results indicate that dioxygen activation by NDO is different from that by cytochrome P-450 and other monooxygenases, which oxidize styrene to styrene 1,2-oxide.     

The crystal structure of the 1:1 inclusion complex of beta-cyclodextrin with squaric acid.

The crystal and molecular structure of the 1:1 inclusion complex of beta-cyclodextrin (cyclomaltoheptaose) with squaric acid (3,4-dihydroxycyclobutene-1,2-dione) was determined by X-ray diffraction. The complex crystallizes in the monoclinic P2(1) space group and belongs to the monomeric cage-type, characterized by a herringbone-like packing motif. Co-crystallized water molecules are present on seven sites, of which six are fully occupied. The guest molecule is placed inside the beta-cyclodextrin cavity, perpendicular to the plane defined by the glycosidic O-4n atoms, and held in place by direct and water-mediated hydrogen bonds mainly involving symmetry-related beta-cyclodextrin molecules. The accommodation of the planar guest molecule into the beta-cyclodextrin cavity determines a significant distortion of the latter from the sevenfold symmetry.     

Molecular Mechanics Simulations in Structure Analysis of Intercalate VOPO4·2CH3CH2OH

Molecular mechanics simulations using Cerius² combined with X-ray diffraction and supported with vibrational spectroscopy have been used to investigate the layered structure of vanadyl phosphate VOPO₄ intercalated with ethanol. This intercalated structure exhibits certain degree of disorder, which affects the diffraction diagram and obstructs the conventional structure analysis based on diffraction methods only. Present structure analysis is focused to the crystal packing in the interlayer space and layer stacking in the intercalate. The bilayer arrangement of ethanol molecules in the interlayer has been found, giving the basal spacing d = 13.21 Å, experimental d-value obtained from X-ray diffraction is 13.17 Å. One half from the total number of CH₃CH₂OH molecules is anchored with their oxygens to VOPO₄ layers to complete vanadium octahedra and their orientation is not very strictly defined. The second half of ethanoles is linked with hydrogen bridges to the anchored etahanoles and sometimes also to the layer oxygens. Positions and orientations of these unachored ethanoles with respect to VOPO₄ layers exhibit certain degree of disorder, resulting in the disorder in layer stacking. Molecular mechanics simulations revealed the character of this displacement disorder in layer stacking and enabled to determine the components of the displacement vector.     

Conformations and interactions of excited stales. I. Model compounds for polymers

From observations on model compounds having two or more benzene rings and structures analogous to high polymers of interest (polystyrene and aromatic polypeptides), we conclude that interactions of pairs of benzene rings sufficiently strong to cause observable excimer emission requires that these rings be separated by no more than 2–3 A. and that they be in an approximately parallel-stacked, face-to-face arrangement. If a molecule does not have such a configuration of its aromatic rings in its ground-state conformation, strong excimer emission can still occur provided there is a conformation with the appropriate ring configuration which can be attained within the radiative lifetime of the excited state.     

Synthesis, crystal structure and magnetic properties of the first structurally characterized 1,2-dithiocroconato-containing Cu(II) complex, [Cu(bpca)(H2O)]2[Cu(1,2-dtcr)2]·2H2O

The first crystal and molecular structure of a transition metal complex containing 1,2-dithiocroconate (1,2-dtcr, dianion of 1,2-dimercaptocylopent-1-ene-3,4,5-trione), [Cu(bpca)(H₂O)]₂[Cu(1,2-dtcr)₂]·2H₂O (where bpca is the bis(2-pyrdidylcarbonyl)amide anion), has been determined by single crystal X-ray diffraction methods. The compound crystallizesin the monoclinic syste, space group P2₁/c, with a = 11.661(3), b = 20.255(6), c = 8.265(3) Å, ß = 107.26(2)° and Z = 2. The structure is formally built of [Cu(1,2-dtcr)₂]²⁻ and [Cu(bpca)(H₂O)]⁺ ions and water of hydration. The copper atom of the anion is situated at a crystallographic inversion centre, bonded to four sulfur atoms in a planar, approximately square arrangement. In the cation the copper equatorial plane is formed by the three nitrogen atoms of the bpca ligand and a water oxygen atom. In addition there is a very weak axial bond to one of the sulfur atoms of a 1,2-dtcr ligand in the anion. Through these latter weak bonds each anion is connected to, and sandwiched between, two cations, resulting in neutral, trinuclear, centrosymmetric formula units. The triple-decker molecules are arranged in stacks along the crystallographic a-axis creating close contacts between the terminal copper atoms and bpca groups of the neighbouring molecules. This intermolecular interaction is, however, too weak to define the structure as a chain compound. The distance between adjacent copper atoms within the trinuclear unit is 4.189(1) Å, while the shortest intra-stack metal-metal separation between terminal copper atoms is 5.281(1) Å. Variable-temperature magnetic susceptibility measurements in the temperature r.2–140 K reveal that a Curie law is followed; with three non-interacting copper(II) ions in the formula unit.     

The crystal structure of the 1:1 complex of beta-cyclodextrin with trans-cinnamic acid

The crystal structure of the 1:1 complex of beta-cyclodextrin (cyclomaltoheptaose) with trans-cinnamic acid was studied by X-ray diffraction. Two beta-cyclodextrin molecules related by a twofold crystal axis form dimers in the hydrophobic cavity of which, two guest molecules are entirely buried. The complex crystallizes in the monoclinic C2 space group with channel-type molecular packing. The oxygen atoms of the carboxylate group of the trans-cinnamic acid molecule form strong hydrogen bonds with two water molecules lying in the interdimeric space of the hydrophobic channel.     

Interaction between beta-cyclodextrin and 1,10-phenanthroline: uncommon 2:3 inclusion complex in the solid state

The crystallographic structure of the complex formed by beta-cyclodextrin with 1,10-phenanthroline has been studied by X-ray diffraction. The result shows that the complex adopts an uncommon 2:3 stoichiometry in solid state, that is, every complex unit contains three 1,10-phenanthroline molecules and two beta-cyclodextrin molecules, where two 1,10-phenanthroline molecules individually occupy two cyclodextrin cavities, and the third guest molecule is located in the interstitial space between two head-to-head cyclodextrin molecules. The intermolecular hydrogen bonds between the adjacent complex units further link these individual monomers to a channel-type assembly. Furthermore, 1H and 2D NMR spectroscopy has been employed to investigate the inclusion behavior between the host beta-cyclodextrin and guest 1,10-phenanthroline in aqueous solution.     

Interactions between metal ions and carbohydrates. The coordination behavior of neutral erythritol to neodymium ion

A single crystal of a coordinated complex of neutral erythritol (C4H10O4,E) with a neodymium ion, NdE(II), was synthesized and studied using FT-IR and X-ray diffraction analysis. In NdE(II) (NdCl3.2.5C4H10O4.C2H5OH) the Nd3+ coordinates with one chloride ion and eight OH groups from three erythritol molecules. There are two neodymium centers linked by one erythritol molecule with same coordination structure in the molecule. Two erythritol molecules provide 1,3,4-hydroxyl groups to coordinate with a neodymium ion; another erythritol molecule coordinates to two Nd ions via its 1,2-hydroxyl groups and 3,4-hydroxyl groups, respectively. The OH groups of erythritol act as ligand to coordinate to neodymium ions, and OH groups of erythritol form hydrogen bond networks that link chain and layer together to build three-dimensional structures. The ratio of metal to ligand is 1:2.5. The structure of NdE(II) is more complicated than the previously reported NdE(I), which is NdCl3.C4H10O4.6H2O; in NdE(I), Nd3+ is coordinated to four hydroxyl groups from two erythritol molecules, four water molecules and one chloride ion. The results indicate the complexity of metal-sugar interaction.     

Bacteriorhodospin: a trans-membrane pump containing alpha-helix.

The probable arrangement of the bacteriorhodopsin molecules in the purple membrane of Halobacterium halobium is in clusters of three, with a 3-fold axis at the centre of each cluster; the axis is at right angles to the plane of the membrane. The proposed arrangement and the results of model calculations together indicate that each protein molecule spans the entire thickness of the membrane. An earlier proposal for the structure had the protein molecules in two layers, and it was symmetric in projection onto the profile-axis. This model is now rejected since it would be difficult to account for the recently discovered function of pumping protons. There remains a discrepancy in that the calculated number of protein molecules in the unit-cell is 3.4 compared to the three expected.The X-ray diffraction patterns from dispersions of the lipids extracted from the red and purple membranes of H. halobium are described.Model calculations are reported, which are based on the bilayer profile calculated for the extracted lipids and on two simple profiles for the protein. The calculations favour a structure for the purple membrane having the lipid molecules in two layers, as in a bilayer, although there may be more of the lipid on one side of the membrane than on the other. Assuming bilayer structure, the diffraction nearest the centre of the oriented pattern suggests that the lipid molecules may be located mainly in a few discrete regions, roughly 20 Å across, between the protein molecules. An uninterrupted monolayer of the lipid on one surface of a sheet of the protein molecules gives poor agreement with the observed profile-diffraction.The X-ray diffraction pattern from the oriented membranes suggested α-helix in the bacteriorhodopsin, and this has been confirmed by recording a 1.5 Å-reflection oriented on the profile-axis. There appear to be at least two segments of α-helix, which are somewhat inclined to one another, and the two may be packed together. Prominent diffraction on the in-plane axis near 10 Å is consistent with the segments lying more or less perpendicular to the plane of the membrane.     

One-dimensional zinc(II) polymers with 4,6-dimethyl-1,2,3-triazolo[4,5-d]pyrimidin-5,7-dionato built by bipyridyl-based ligands acting as spacers both in the first and in the second sphere

Three solids formed by the reaction of the hexaaquazinc(II) salt of 4,6-dimethyl-1,2,3-triazolo[4,5-d]pyrimidin-5,7-diona (Hdmax) and the potentially bridging ligands 1,2-bis(4-pyridyl)ethane (bpe), 1,3-bis(4-pyridyl)propane (bpp) and trans-1,2-bis(4-pyridyl)ethene (bpethe) are described. The crystal structure of those containing bpe and bpethe has been solved by X-ray diffraction turning out to be one-dimensional polymers with zigzag (bpe) or linear (bpethe) disposition of the metal atoms. The triazolopyrimidinato anion is in both cases monodentately coordinated through the N atom furthest from the pyrimidine ring whereas the bipyridyl ligands bridge through their N atoms consecutive metal atoms in the polymer. For the bpethe compound, an additional non-coordinated molecule of the spacer per Zn atom is present, accepting H-bonds from coordinated water molecules and linking in this way the one-dimensional chains into a two-dimensional superstructure. Therefore, bpethe acts as spacer both in the first and second coordination spheres.     

Substrate specificity of coenzyme B12-dependent diol dehydrase: glycerol as both a good substrate and a potent inactivator.

The substrate specificity of adenosylcobalamin-dependent diol dehydrase was further studied in detail using an enzyme preparation that appears homogeneous by ultracentrifugal and gel electrophoretical criteria. Besides 1,2-propanediol and 1,2-ethanediol, glycerol, 1,2- and 2,3-butanediol were found to serve as substrate for the enzyme, whereas 1,3-propanediol was not. Of the substrate analogs tested, glycerol displayed some striking features: it was dehydrated to β-hydroxypropionaldehyde with concomitant inactivation of the enzyme. Although the initial velocity with glycerol was comparable to that with 1,2-propanediol, the dehydration reaction ceased almost completely within 3 min accompanying rapid, irreversible inactivation of the holoenzyme. 1,2- and 2,3-Butanediol were converted to butyraldehyde and methyl ethyl ketone, respectively, at a rate much lower than that with 1,2-propanediol. 2,3-Butanediol is the only compound, other than 1,2-diols, known at present to show a considerable substrate activity.