Dimensional Network Of Hydrogen Bonds Research Articles

Synthesis, X-ray Single Crystal, Conformational Analysis and Cholinesterase Inhibitory Activity of a New Spiropyrrolidine Scaffold Tethered Benzo[b]Thiophene Analogue

Described herein is a one-pot protocol for the synthesis of a substituted spiropyrrolidine scaffold tethered benzo[b]thiophene analogue from (E)-3-(benzo[b]thiophen-2-yl)-1-(4-fluoro- phenyl)-prop-2-en-1-one. The described protocol has the advantage of the high purity of the cyclized adduct and high chemical yield. To assign the chemical structure, different spectrophotometric tools have been applied, including 1H-NMR, 13C-NMR, FTIR, and the X-ray single crystal technique. The X-ray structure showed that the studied compound exist in two disordered parts with equal partial occupancies. The energies of the two conformers were found to be very similar and not exceed 1 kcal/mol, which justifies their coexistence in the crystal with equal percentage. The molecular packing in the crystal was analyzed using Hirshfeld topology analysis. The packing described as two dimensional hydrogen bond network extended along the ac-plane in both conformers but the intermolecular interactions included in each conformer are not similar. The synthesized spiropyrrolidine scaffold tethered benzo[b]thiophene analogue was examined against cholinesterase inhibitory activity and show moderate activity compared to standard drug galantamine.

Synthesis, Crystal Structure and Characterization of a New Dabcodiium Hexaaquacobalt(II) Bis(Selenate), (C6H14N2)[Co(H2O)6](SeO4)2

The new hybrid material, cobalt selenate templated by 1,4-diazabicyclo[2.2.2]octane (abbreviated dabco), has been synthesised by the slow evaporation method at room temperature. Its crystal structure was investigated using single crystal X-ray diffraction data. It crystallises in the monoclinic system (space group P21/c) with the following unit-cell parameters: a = 12.9169(2) A, b = 11.9101(2) A, c = 12.4951(2) A, β = 108.484(1)°, V = 1823.10(5) A3 and Z = 4. The supramolecular structure of (C6H14N2)[Co(H2O)6](SeO4)2 consists of isolated [Co(H2O)]2+ and (C6H14N2)2+ cations and (SeO4)2− anions linked together by three dimensional hydrogen-bond network. The infrared spectroscopy confirmed the presence of these different entities. The thermal behaviour of the precursor, studied by thermodiffractometry and thermogravimetric analyses, indicates that its decomposition proceeds through three stages giving rise to the cobalt oxide. The supramolecular structure of (C6H14N2)[Co(H2O)6](SeO4)2 consists of isolated [Co(H2O)]2+ and (C6H14N2)2+ cations and (SeO4)2− anions linked together by three dimensional hydrogen-bond network.

Geometric isotope effect on hydrogen-bond structure: A semiquantal analysis

The structural correlation and the geometric isotope effects in hydrogen-bond crystals are studied by the semiquantal time-dependent Hartree (SQTDH) approach recently developed [K. Ando, J. Chem. Phys. 121, 7136 (2004)]. The theory is demonstrated to provide accurate ground state wave functions for both weak and strong hydrogen bonds via a simple potential minimization procedure in an extended phase space of the variational parameters. It is shown that the asymmetry of the potential energy surface plays a significant role in affecting the correlation between A-H and A\ensuremath{\cdots}B distances in A-H\ensuremath{\cdots}B hydrogen bonds in such a way as to explain the observed variation of experimental data from a variety of compounds. The calculated geometric isotope effect on the A\ensuremath{\cdots}B distance induced by deuteration is $0.02\phantom{\rule{0.3em}{0ex}}\mathrm{\AA{}}$ or less, in agreement with experiments on normal compounds. The origin of the exceptionally large geometric isotope effects observed in some crystals having zero dimensional hydrogen-bond network is discussed on the basis of the present results.

Refinement of the crystal structure of 5,7,12,14-tetrahydro[2,3-b]-quinolinoacridine (γ-form), C20H12N2O2, at 223 Κ

Article Refinement of the crystal structure of 5,7,12,14-tetrahydro[2,3-b]-quinolinoacridine (γ-form), C20H12N2O2, at 223 Κ was published on December 1, 2002 in the journal Zeitschrift für Kristallographie - New Crystal Structures (volume 217, issue 1).

Synthesis, characterization and X-ray structures of the new dinucleating ligand 2,8-dimethyl-1,4,5,6,7,10,11,12-octahydroimidazo[4,5-h] imidazo[4,5-c][1,6]diazecine-5,11-diethanoic acid and its Cu(II) complex; an alternating chain of Cu(II) ions, coupled both intramolecularly and intermolecularly

The design and synthesis of a new, rigid dinucleating ligand 2,8-dimethyl-1,4,5,6,7,10,11,12-octahydroimidazo[4,5-h] imidazo[4,5-c][1,6]diazecine-5,11-diethanoic acid (H2glymeim) is reported together with its molecular and crystal structure. The rigid ligand structure is confirmed by the structure and magnetic properties of its bis Cu(II) complex, [Cu2(C16H22N6O6)(H2O)4](ClO4)2(H2O)2, (Cu2glymeim). Crystals of free glymeim are composed of units of C16H22N6O4 and eight water molecules linked by a two dimensional network of hydrogen bonds. Six of them contribute to a one-dimensional network that links the organic molecules. The 1,6-diazecine ring shows a chair conformation, with expected angles and bond distance values. A stretched conformation of the glycine residue is observed in the free ligand. When this residue is coordinated, it produces significant stress over the diazecine ring caused by the closure of the glycine residue around the metal ion. The copper complex has a dinuclear structure with a square pyramidal environment around both metal ions. The apical position in the two pyramids point to opposite directions in the molecule and they are related by an inversion center. The pyramidal bases of both copper atoms are in the same plane. The intramolecular metal–metal distance in the complex is 7.445(3) Å. However, the shortest distance is of intermolecular nature, with a value of 5.378(2) Å. The crystal structure of the complex consists of a chain of dinuclear units, with an alternating chain arrangement. Low temperature magnetic susceptibility and EPR are in agreement with an antiferromagnetic dinuclear behavior in solution and like a linear chain uniformly spaced, with J=−8.54 cm−1 and α=1. The magnetic behavior of this compound can be explained as the result of an intramolecular magnetic exchange (long distance), and a superexchange path through the hydrogen bond network between adjacent dinuclear molecules.

The Hydrogen Bond Networks in Nicinquinium Salts

Abstract Crystals of nicinquinium chloride and bromide incorporate water molecules due to the im­ balance of hydrogen bond donors and acceptors. The resulting intermolecular hydrogen bond system indicates a better proton accepting ability of chloride ions than bromide ions. The chlo­ ride anions accept four hydrogen bonds in an almost tetrahedral arrangement whereas only two are formed with the bromide anions. As a consequence in the crystal structure of the chloride a three dimensional network of hydrogen bonds is formed, while in that of the bromide only chains of hydrogen bonded species exist. Both cations retain the absolute configuration of all asymmetric carbon atoms as compared with the absolute configuration of the parent cinchonine.

Crystal structure of a hydrated N-glycoprotein linkage region model and its analogue: Hydrogen bonding and π– π stacking driven molecular assembly

X-Ray diffraction analysis of a hydrated N-glycoprotein linkage region model, N 1-(2-acetamido-2-deoxy- β- d-glucopyranosyl)acetamide ( 1) and its N 1-benzamido analogue 2 reveals very interesting molecular architecture involving seven hydrogen bonds in both compounds and further stabilization of packing in 2 due to π– π stacking. The crystal structure has a two dimensional network of hydrogen bonds formed by infinite chains running along the b-axis and homodromic cycles, intersecting at the water oxygens.

Two Dimensional Ice Adsorbed on Mica Surface

First principles molecular dynamics simulations have been performed on water adsorption at the surface of muscovite mica. At monolayer coverage we found water to condense into a fully connected two dimensional hydrogen bond network, which we denote as 2D ice. The structure is stable up to 300 K and it is proposed as a candidate for the solidlike structure recently detected in scanning polarization force microscopy on the hydrated muscovite surface at room temperature [Hu et al., Science 268, 267 (1995)].

Crystal structure of 2-debenzoyl, 2-acetoxy paclitaxel (Taxol): conformation of the paclitaxel side-chain.

Crystals of the C2-acetate analog of paclitaxel, grown from a mixture of isopropyl alcohol and methanol, belong to the space group P2(1) with a = 9.058(3), b = 18.306(5), c = 15.043(1) Angstrum, beta = 97.09(1) degrees, Z = 2, V = 2475.1(9)Angstrum3, Dcalc = 1.269 gcm-3 and mu = 0.75 cm-1. The structure was determined by direct methods and refined to R(F) = 0.054 and wR(F) = 0.057 for 605 variables and 3496 observed reflections. The paclitaxel side chain possesses a conformation similar to that observed in the crystal structure of docetaxel (Taxotere). A three dimensional network of hydrogen bonds is formed through solvent molecules and stabilizes the crystal lattice.

Structure of ethylenediammonium dihydrogentetraoxophosphate(V) pentahydrogenbis[tetraoxophosphate(V)

C2HIoN2+.HsP208.H2POg, M,= 354-09, monoclinic, C2/c, a= 13.034 (10), b=7.923 (7), c = 13.225 (10)/~, fl= 107.43 (5) ° , V= 1303 (4) A 3, Z = 4, D x = 1.805 Mg m -3, 2(Ag Ka) = 0.5608 ,/k, =0.278mm ~, F(000)=736, T=293K, final R= 0.024 for 1883 unique reflexions. The main feature of this structure is the existence of (HsP2Os) clusters resulting from the association of two PO4 tetrahedra related by centrosymmetry and linked by two statistical hydrogen bonds. These new groups are themselves interconnected with (H2PO4)- units through a three- dimensional network of hydrogen bonds. The C 2 H~0 N2+ groups are isolated inside this anionic arrangement.

Crystal and molecular structure of (E)-5-(2-bromovinyl-2'-deoxyuridine).

(E)-5-(2-bromovinyl-2'-deoxyuridine) crystallizes in the space group P2(1) with a = 12.976(1), b = 4.800(1), c = 20.385(2) A, beta = 96.88(1) degrees, Z = (two molecules a and b in the asymmetric unit). The structure has been determined by the use of 2400 diffractometer reflexions and refined by least-squares to R of 0.053. Conformational features of both molecules a and b resemble those of thymidine. The ribofuranose rings assume the rare C(3')-exo form observed also in thymidine. Similarly, the torsion angles around the glycosidic bonds (mean = 40(1) and 56(1) degrees fall in the anti range. In each molecule the best plane of the 2-bromovinyl moiety is bent out of the least-squares plane of the pyrimidine base by 6 degrees, so that the positively charged C(8)-H(8) group can donate an intramolecular hydrogen bond to 0(4) atom. Eight strong and weak intermolecular hydrogen bridges are built up between the symmetry independent and related molecules forming a complicated three dimensional hydrogen bond network.

Molecular conformation of L-DOPA

The structure of L-DOPA, a biological precursor of melanins has been determined by a new systematic analysis of the Patterson function. Its molecular conformation is different from that so far reported for any aromatic aminoacid, peptide or related compound. Its crystal structure is characterized by a three dimensional network of hydrogen bonds in which all the oxygens, the nitrogen and all the hydrogens of the NH 3 and OH groups participate.