Structures of the crystalline supramolecular associates of imidazole with 1,1′-binaphthyl-8,8′-dicarboxylic acid and 2,2′-dihydroxy-1,1′-binaphthyl. Spatial similarity of the acid associate crystal packing to the active site of a serine protease

Abstract

Crystal structure analysis of the imidazole associates with 1,1′-binaphthyl-8,8′-dicarboxylic acid (1), [1a, triclinic, P1, a = 7.569(4), b = 8.393(2), c = 8.634(1) Å, α = 93.21(2), β = 106.88(3), γ = 105.17(3)°, D_c = 1.36 g/cm³, Z = 1, R = 0.045 for 1031 data] and with 2,2′-dihydroxy-1,1′-binaphthyl (2), [2a, tetragonal P4₁2₁2, a = 8.519(1), c = 29.821(2), D_c = 1.30 g/cm³, Z = 4, R = 0.051 for 1236 reflections] revealed 1:1 and 1:2 stoichiometry, respectively. Spontaneous resolution occur during crystallization in both compound crystals. 1a is a salt-like associate with hydrogen bonds between the carboxylate and imidazolium ion pairs while the neutral 2a has also well defined hydrogen bonds between host and guest molecules. In a modeling experiment corresponding Brookhaven Protein Data Bank atomic coordinates from the active site of the bacterial serine protease enzyme Subtilisin BPN were fitted to the crystal packing of the small molecule associate 1a crystal. The relative displacement of the ion pair components and a symmetry related carboxyl function in 1a has fair steric resemblance to similar moieties in the active site of Subtilisin (Δ_ave = 0.24 Å for 9 fitted atoms). The agreement in the results of two fully independent and totally different (i.e. a native protein active site and an artificial small molecule associate) crystal structure determinations underlines the assumed conceptual similarity of crystals (“giant supramolecules”) to protein sequences optimized through evolution.     

A macrocyclic ligand incorporating both a 2,2′-bipyridyl and a 2,9-diphenyl 1,10-phenanthroline fragment: Reciprocal control of one site by complexation of the other site to a transition metal.

A coordinating system containing two different complexing sites has been synthesised. Binding of ruthenium(II) to the octahedral-preferred part allows complexation of copper(I) at the tetrahedral site.     

Chiroptical properties and new derivatives of cyclopalladated 6-ferrocenyl-2,2′-bipyridine. Molecular structure of a tert-butyl isocyanide derivative

Optically active cyclopalladated 6-ferrocenyl-2,2′-bipyridine has been studied by circular dichroism and luminescent spectroscopy; a replacement of the chloride ion at palladium with the rhodanide ion and tert-butyl isocyanide molecule has been carried out; molecular structure of the product in the latter case has been determined by X-ray diffraction analysis.     

Studies of the atomization mechanism in a graphite furnace—I. The contents of the gaseous impurities in the furnace and their variations

Using theoretical calculations of the partial pressures of gaseous impurities in the atmosphere in a GFA as a basis, the authors arrived at conclusions which are at variance with those of L'vov and frech and their co-workers. Accordingly, the partial pressure of free oxygen (p_o) in a GFA originates predominantly from the thermal decomposition of the oxides of the analyte and impurities in the matrix during atomization when the temperature is higher than 1000°C; then, p_o depends on the nature of the sample. The total amount of oxygen in a GFA depends on the initial amount of it in the argon gas and the amount released from the sample when the temperature is lower than 1000°C.The variation of the partial pressure of CO is for the first time characterized as follows: the content of CO, which is mainly dependent on the sample and the total amounts of gaseous impurities in the argon purge gas, does not vary markedly with the temperature and other factors during the whole process of atomization. The gaseous impurities exist mainly in the form of CO.     

Molecular Interactions of Macrocycles with Dipeptides in Aqueous Solutions. Partial Molar Volumes and Heat Capacities of Transfer of a Chiral 18-Crown-6 and of a Calix[4]resorcinarene Derivative from Water to Aqueous Dipeptide Solutions at 25°C

Densities and specific heat capacities of ternary aqueous systems containing a dipeptide (alanyl-alanine, alanyl-glutamic acid, alanyl-serine or L-seryl-L-leucine) and a macrocycle (D--manno-naphtho-18-crown-6-ether or 2,8,14,20-tetrakis[-methyl (aminoformyl)]-4,6,10,12,16,18,22,24-octahydroxycalix[4]arene) were determined at 25°C by flow densimetry and flow calorimetry. The partial molar volume and heat capacity of transfer of a macrocycle from water to the dipeptide solution was determined as a function of the dipeptide concentration. Positive values for transfer volumes and transfer heat capacities are observed with all the solutions studied. With the crown ether, except for alanyl-glutamic acid where a 1:1 complex is clearly evidenced due to specific interactions of the side-chain functional group of the peptide with the crown ether, no stoichiometric complexes are confirmed and the partial molar quantities of transfer increase with the hydrophobic character of the dipeptide. Partial quantities of transfer are smaller with the calixarene than with the crown ether and stoichiometric complexes [calixarene]/[dipeptide] from 2:1 to 1:4 are evidenced, depending on the nature and the concentration of the dipeptide.     

A convenient synthesis of a 2,7-difunctional tetra(alkoxy)triphenylene involving 4,4′-diacetoxy-3,3′-dialkoxybiphenyl as a key precursor and its conversion to extended hybrid mesogenic compounds

A new rational pathway to 2,7-difunctionalised-β-hexa-substituted triphenylenes is presented, requiring less protection/deprotection and purification steps than more conventional synthetic procedures in the framework of the ‘biphenyl route’. Main improvements are deprotection via alkaline hydrolysis of an ester in ethanol/water medium instead of using toxic and pyrophoric reagents like lithium diphenylphosphide, and the use of easily prepared brominated precursors instead of iodinated reagents for biphenyl synthesis. 4,4′-Diacetoxy-3,3′-bis(hexyloxy)biphenyl has been synthesised under this scheme, and characterised by proton nuclear magnetic resonance (¹H NMR) spectrometry, elemental analysis and single-crystal crystallography. It crystallises in the P-1 space group, and exhibits a layered structure built-up through dipolar, C–H … π and C–H … O=C non-covalent interactions. This compound has been oxidatively coupled with 1,2-bis(hexyloxy)benzene to yield 2,7-dihydroxy-3,6,10,11-tetrakis(hexyloxy)triphenylene, a non-mesogen key precursor for the synthesis of the corresponding liquid-crystalline 2,7-difunctional triphenylenes. Indeed, a reactive 2,7-difunctional mesogen was prepared and used to produce new triphenylene-siloxane hybrid monomeric, trimeric and polymeric mesogens. All of them exhibited columnar hexagonal (Col_h) mesophases.     

Determination of activity coefficients using a flow EMF method. 1. HCl in methanol-water mixtures at 25, 35 and 45°C

A method to determine activity coefficients of electrolytes in mixed solvent is described which makes use of ion-selective electrode(s) (ISE) and in which a concentrated electrolyte solution is continuously added. Activity coefficients for HCl in methanol-water mixtures containing 0, 10, 20, 30, 50, 70, and 90 weight percent methanol at 25, 35 and 45°C were calculated using the Pitzer equation, and the electromotive force (emf) data of the cell: The experimental results agree well with literature values indicating that the proposed method is procise and reliable.     

Synthetic polymers and biomembranes. How do they interact? Atomistic molecular dynamics simulation study of PEO in contact with a DMPC lipid bilayer

The understanding of interactions of poly(ethylene glycol) (PEG) or poly(ethylene oxide) (PEO) with biological interfaces has important technological application in industry and in medicine. In this paper, structural and dynamical properties of PEO at the dimyristoylphospatidylcholine (DMPC) bilayer/water interface have been investigated by molecular dynamics (MD) and steered molecular dynamics (SMD) simulations. The structural properties of a PEO chain in bulk water, at the water/vacuum interface, and in the presence of the membrane were compared with available experimental data. The presence of a barrier for the PEO penetration into the DMPC bilayer has been found. A qualitative estimation of the barrier provided a value equal to approximately 19 kJ/mol, that is, 7 times the value of kT at 310 K.     

Numerical investigation of the elastic scattering of hydrogen (isotopes) and helium at graphite (0001) surfaces at beam energies of 1 to 4 eV using a split-step Fourier method

We report simulations of the elastic scattering of atomic hydrogen isotopes and helium beams from graphite (0001) surfaces in an energy range of 1–4 eV. To this aim, we numerically solve a time-dependent Schrödinger equation using a split-step Fourier method. The hydrogen- and helium-graphite potentials are derived from density functional theory calculations using a cluster model for the graphite surface. We observe that the elastic interaction of tritium and helium with graphite differs fundamentally. Whereas the wave packets in the helium beam are directed to the centers of the aromatic cycles constituting the hexagonal graphite lattice, they are directed toward the rings in case of the hydrogen beams. These observations emphasize the importance of swift chemical sputtering for the chemical erosion of graphite and provide a fundamental justification of the graphite peeling mechanism observed in molecular dynamics studies. Our investigations imply that wave packet studies, complementary to classical atomistic molecular dynamics simulations open another angle to the microscopic view on the physics underlying the sputtering of graphite exposed to hot plasma.     

Separation of the primary and secondary kinetic isotope effects at a reactive center using starting material reactivities. Application to the FeCl3-Catalyzed oxidation of CH bonds with tert-butyl hydroperoxide

A method is reported for the determination of both the primary and secondary kinetic isotope effects at a reactive center based on staring material reactivities. This allows the determination of the separate KIEs in reactions for which neither product analysis nor absolute rate measurements are applicable. The methodology is applied to the FeCl₃-catalyzed oxidation of ethylbenzene with tert-butyl hydroperoxide, which exhibits both a primary isotope effect and a substantial secondary isotope effect.     

Resonance Raman spectroscopic studies of 2-(4′-hydroxyphenylazo)-benzoic acid and some substituted analogs—II. Binding to avidin and bovine serum albumin

Resonance Raman spectroscopic studies unequivocally indicate that the absorption band at about 500 nm, observed when 2-(4′hydroxyphenylazo)-benzoic acid (HABA) interacts with either avidin or bovine serum albumin in neutral aqueous solution, originates from the protein-bound hydrazone form of the dye. Spectroscopic comparison of the protein-bound and unbound hydrazone forms enables some of the ligand—protein interactions to be defined. Studies with HABA and some selected analogs in aqueous solution, in buffer-doped dimethyl sulfoxide (d₆), and in the presence of α-cyclodextrin indicate that two important factors responsible for stabilising the hydrazone forms of HABA analogs are the ring substitution pattern, and intramolecular hydrogen bonding. A possible model for the HABA—protein interaction is proposed.     

Concerted and Selective Electrooxidation of Polyethylene-Terephthalate-Derived Alcohol to Glycolic Acid at an Industry-Level Current Density over a Pd−Ni(OH)2 Catalyst

Electro-reforming of Polyethylene-terephthalate-derived (PET-derived) ethylene glycol (EG) into fine chemicals and H₂ is an ideal solution to address severe plastic pollution. Here, we report the electrooxidation of EG to glycolic acid (GA) with a high Faraday efficiency and selectivity (>85 %) even at an industry-level current density (600 mA cm⁻² at 1.15 V vs. RHE) over a Pd−Ni(OH)₂ catalyst. Notably, stable electrolysis over 200 h can be achieved, outperforming all available Pd-based catalysts. Combined experimental and theoretical results reveal that 1) the OH* generation promoted by Ni(OH)₂ plays a critical role in facilitating EG-to-GA oxidation and removing poisonous carbonyl species, thereby achieving high activity and stability; 2) Pd with a downshifted d-band center and the oxophilic Ni can synergistically facilitate the rapid desorption and transfer of GA from the active Pd sites to the inactive Ni sites, avoiding over-oxidation and thus achieving high selectivity.     

Migration of hydrogen from metal to alkene promoted by dioxygen addition. Oxygen atom transfer from a cis-(alkyl)(η2-dioxygen) complex of rhodium to organic and inorganic substrates

The novel cis-(σ-alkyl)(η²-O₂) complexes of rhodium [(THF)(EtOH)Naμ-EtOH₂μ-(CO₂R)CH₂CH(CO₂R)Rh(η²-O₂)(triphos)₂Na(EtOH)(THF)][BPh₄]₂·2EtOH (R = Me,3; Et,4) have been synthesized by reaction of dioxygen with the hydrides (triphos)(RhH(η²-alkene) followed by NaBPh₄ addition (alkene = dimethyl fumarate,1; diethyl fumarate,2) (triphos = MeC(CH₂PPh₂)₃). The structure of4 has been determined by X-ray diffraction. Oxygen atom transfer reactions from the η²-O₂ complexes to various inorganic and organic substrates have been studied.     

Measurements of the(p,ρ,T) relation of methane and carbon dioxide in the temperature range 240 K to 520 K at pressures up to 30 MPa using a new accurate single-sinker densimeter

Comprehensive (p, ρ, T) measurements on pure methane (159 values) and pure carbon dioxide (118 values) have been carried out in the temperature range 240 K to 520 K at pressures up to 30 MPa. The measurements were performed by means of a single-sinker densimeter that is based on Archimedes’ buoyancy principle. The total relative uncertainty of the measurements in the density ρ was estimated to be⩽ |(1.5 to 2) · 10 ^− 4·ρ | for methane and⩽ |(2 to 3) · 10 ^− 4·ρ | for carbon dioxide. The measurements are compared with previous results of other experimentalists and with values calculated from current equations of state. Moreover, previously unpublished results of (p, ρ, T) measurements on carbon dioxide (29 values) and methane (53 values) are listed in the appendix.     

Revising Space Groups from Simulated SHELXfcf Structure Factors. More Examples of Incorrect Space Groups, an Example of a Chemically-Incorrect Structure and the Special Case of Pgl to PRevisions

1 INTRODUCTION Although the incorrect assignment of the space groups of crystal structures has been addressed in a number of reports, instances of crystal structures refined in incorrect symmetry turn up even in the recent literature[1～4]. A simple method of space group revision makes use of the published atomic coordinates and temperature factors to simulate the diffraction intensities; the structure is then 搒olved?in the correct space group from the simulated hkl-F2 data[5] and an O…     

Coordination Polymers. IV. Physicochemical Studies on Chelate Polymers of Cr(III), Mn(II), Fe(II), Co(II), Ni(II), and Cu(II) with a Schiff Base of 4,4′-(4,4′-Biphenylylene Bisazo)di-(salicylaldehyde) with m. Toluidine

Coordination polymers of Cr(III), Mn(II), Fe(II), Co(II), Ni(II), and Cu(II) with a Schiff base derived from 4,4′ - (4,4′ -biphenylylene bisazo) di (salicylaldehyde) and m-toluidine have been prepared. All the polychelates are dark colored and insoluble in common organic solvents. Magnetic susceptibility and electronic and IR spectra of the polychelates have been studied. All the polychelates except Cu(II) show octahedral structures while Cu(II) polychelate is suggested to be a square planar.