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Hydrogen-bond Formation (hydrogen-bond + formation)
Selected AbstractsAnion Receptors Containing -NH Binding Sites: Hydrogen-Bond Formation or Neat Proton Transfer?CHEMISTRY - A EUROPEAN JOURNAL, Issue 1 2005Valeria Amendola Dr. Abstract When the amide-containing receptor 1+ is in a solution of dimethyl sulfoxide (DMSO) in the presence of basic anions (CH3COO,, F,, H2PO4,), it undergoes deprotonation of the -NH fragment to give the corresponding zwitterion, which can be isolated as a crystalline solid. In the presence of less basic anions (Cl,, Br,, NO3,), 1+ establishes true hydrogen-bond interactions of decreasing intensity. The less acidic receptor 2+ undergoes neat proton transfer with only the more basic anions CH3COO, and F,, and establishes hydrogen-bond interactions with H2PO4,. An empirical criterion for discerning neutralisation and hydrogen bonding, based on UV/Vis and 1H NMR spectra, is proposed. [source] Ionic Hydrogen Bonds Controlling Two-Dimensional Supramolecular Systems at a Metal SurfaceCHEMISTRY - A EUROPEAN JOURNAL, Issue 14 2007Dietmar Payer Abstract Hydrogen-bond formation between ionic adsorbates on an Ag(111) surface under ultrahigh vacuum was studied by scanning tunneling microscopy/spectroscopy (STM/STS), X-ray photoelectron spectroscopy (XPS), near-edge X-ray absorption fine structure (NEXAFS), and molecular dynamics calculations. The adsorbate, 1,3,5-benzenetricarboxylic acid (trimesic acid, TMA), self-assembles at low temperatures (250,300,K) into the known open honeycomb motif through neutral hydrogen bonds formed between carboxyl groups, whereas annealing at 420,K leads to a densely packed quartet structure consisting of flat-lying molecules with one deprotonated carboxyl group per molecule. The resulting charged carboxylate groups form intermolecular ionic hydrogen bonds with enhanced strength compared to the neutral hydrogen bonds; this represents an alternative supramolecular bonding motif in 2D supramolecular organization. [source] Synthesis of 1,5-Substituted Iminodibenzo[b,f][1,5]diazocine, an Analogue of Tröger's BaseEUROPEAN JOURNAL OF ORGANIC CHEMISTRY, Issue 13 2006Alessandro Leganza Abstract A method for the synthesis of 1,5-disubstituted iminodibenzo[b,f][1,5]diazocines is presented. The synthesis is achieved by the metal-free cyclization of 2-aminophenyl ketimines using the corresponding 2-aminophenyl ketone as the catalyst. The synthesis gives new insight into the mechanism of formation of this class of compounds. The presence of potential sites for hydrogen-bond formation and two aromatic bromine atoms available for functionalization make these targets attractive for further development in supramolecular chemistry. The structure of the complex derived from the iminodibenzo[b,f][1,5]diazocine and PdCl2 was determined by X-ray crystallography. (© Wiley-VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2006) [source] 4,4,-Methylenediphenol,4,4,-bipyridine (2/3): decarboxylation of 5,5,-methylenedisalicylic acid under hydrothermal conditionsACTA CRYSTALLOGRAPHICA SECTION C, Issue 9 2009Zhi-Hui Zhang Reaction of 5,5,-methylenedisalicylic acid (5,5,-H4mdsa) with 4,4,-bipyridine (4,4,-bipy) and manganese(II) acetate under hydrothermal conditions led to the unexpected 2:3 binary cocrystal 4,4,-methylenediphenol,4,4,-bipyridine (2/3), C13H12O2·1.5C10H8N2 or (4,4,-H2dhdp)(4,4,-bipy)1.5, which is formed with a concomitant decarboxylation. The asymmetric unit contains one and a half 4,4,-bipy molecules, one of which straddles a centre of inversion, and one 4,4,-H2dhdp molecule. O,H...N interactions between the hydroxy and pyridyl groups lead to a discrete ribbon motif with an unusual 2:3 stoichiometric ratio of strong hydrogen-bonding donors and acceptors. One of the pyridyl N-atom donors is not involved in hydrogen-bond formation. Additional weak C,H...O interactions between 4,4,-bipy and 4,4,-H2dhdp molecules complete a two-dimensional bilayer supramolecular structure. [source] Two-dimensional hydrogen-bonded networks in 1-(diaminomethylene)thiouron-1-ium nitrate and bis[1-(diaminomethylene)thiouron-1-ium] phosphonate monohydrateACTA CRYSTALLOGRAPHICA SECTION C, Issue 3 2009Jan Janczak Crystals of the title compounds, C2H7N4S+·NO3,, (I), and 2C2H7N4S+·HPO32,·H2O, (II), are built up from 1-(diaminomethylene)thiouron-1-ium cations and nitrate anions in (I), and from phosphonate anions and water molecules in (II). In both crystals, the cations and anions are linked together via N,H...O hydrogen bonds. The 1-(diaminomethylene)thiouron-1-ium cations exhibit a twisted conformation. Both arms of the cations are planar and are turned in opposite directions around the C,N bond involving the central N atom. Hydrogen-bonding interactions join oppositely charged units into layers in the nitrate salt and into double layers in the phosphonate monohydrate salt. In addition, the structures are stabilized by ,,, interactions between the delocalized , bonds of the cations. The significance of this study lies in the illustration of the differences between the supramolecular aggregations in the nitrate and phosphonate salts of a small organic molecule. The different geometries of the counter-ions and their different potential for hydrogen-bond formation results in markedly different hydrogen-bond arrangements. [source] The influence of sulfur substituents on the molecular geometry and packing of thio derivatives of N -methylphenobarbitalACTA CRYSTALLOGRAPHICA SECTION C, Issue 2 2009Alicja Janik The room-temperature crystal structures of four new thio derivatives of N -methylphenobarbital [systematic name: 5-ethyl-1-methyl-5-phenylpyrimidine-2,4,6(1H,3H,5H)-trione], C13H14N2O3, are compared with the structure of the parent compound. The sulfur substituents in N -methyl-2-thiophenobarbital [5-ethyl-1-methyl-5-phenyl-2-thioxo-1,2-dihydropyrimidine-4,6(3H,5H)-dione], C13H14N2O2S, N -methyl-4-thiophenobarbital [5-ethyl-1-methyl-5-phenyl-4-thioxo-3,4-dihydropyrimidine-2,6(1H,5H)-dione], C13H14N2O2S, and N -methyl-2,4,6-trithiophenobarbital [5-ethyl-1-methyl-5-phenylpyrimidine-2,4,6(1H,3H,5H)-trithione], C13H14N2S3, preserve the heterocyclic ring puckering observed for N -methylphenobarbital (a half-chair conformation), whereas in N -methyl-2,4-dithiophenobarbital [5-ethyl-1-methyl-5-phenyl-2,4-dithioxo-1,2,3,4-tetrahydropyrimidine-6(5H)-one], C13H14N2OS2, significant flattening of the ring was detected. The number and positions of the sulfur substituents influence the packing and hydrogen-bonding patterns of the derivatives. In the cases of the 2-thio, 4-thio and 2,4,6-trithio derivatives, there is a preference for the formation of a ring motif of the R22(8) type, which is also a characteristic of N -methylphenobarbital, whereas a C(6) chain forms in the 2,4-dithio derivative. The preferences for hydrogen-bond formation, which follow the sequence of acceptor position 4 > 2 > 6, confirm the differences in the nucleophilic properties of the C atoms of the heterocyclic ring and are consistent with the course of N -methylphenobarbital thionation reactions. [source] A structural systematic study of three isomers of difluoro- N -(4-pyridyl)benzamideACTA CRYSTALLOGRAPHICA SECTION C, Issue 9 2008Joyce McMahon The isomers 2,3-, (I), 2,4-, (II), and 2,5-difluoro- N -(4-pyridyl)benzamide, (III), all with formula C12H8F2N2O, all exhibit intramolecular C,H...O=C and N,H...F contacts [both with S(6) motifs]. In (I), intermolecular N,H...O=C interactions form one-dimensional chains along [010] [N...O = 3.0181,(16),Å], with weaker C,H...N interactions linking the chains into sheets parallel to the [001] plane, further linked into pairs via C,H...F contacts about inversion centres; a three-dimensional herring-bone network forms via C,H...,(py) (py is pyridyl) interactions. In (II), weak aromatic C,H...N(py) interactions form one-dimensional zigzag chains along [001]; no other interactions with H...N/O/F < 2.50,Å are present, apart from long N/C,H...O=C and C,H...F contacts. In (III), N,H...N(py) interactions form one-dimensional zigzag chains [as C(6) chains] along [010] augmented by a myriad of weak C,H...,(arene) and O=C...O=C interactions and C,H...O/N/F contacts. Compound (III) is isomorphous with the parent N -(4-pyridyl)benzamide [Noveron, Lah, Del Sesto, Arif, Miller & Stang (2002). J. Am. Chem. Soc.124, 6613,6625] and the three 2/3/4-fluoro- N -(4-pyridyl)benzamides [Donnelly, Gallagher & Lough (2008). Acta Cryst. C64, o335,o340]. The study expands our series of fluoro(pyridyl)benzamides and augments our understanding of the competition between strong hydrogen-bond formation and weaker influences on crystal packing. [source] Structure of the nondiscriminating aspartyl-tRNA synthetase from the crenarchaeon Sulfolobus tokodaii strain 7 reveals the recognition mechanism for two different tRNA anticodonsACTA CRYSTALLOGRAPHICA SECTION D, Issue 10 2007Yoshiteru Sato In protein synthesis, 20 types of aminoacyl-tRNA synthetase (aaRS) are generally required in order to distinguish between the 20 types of amino acid so that each achieves strict recognition of the cognate amino acid and the cognate tRNA. In the crenarchaeon Sulfolobus tokodaii strain 7 (St), however, asparaginyl-tRNA synthetase (AsnRS) is missing. It is believed that AspRS instead produces Asp-tRNAAsn in addition to Asp-tRNAAsp. In order to reveal the recognition mechanism for the two anticodons, GUC for aspartate and GUU for asparagine, the crystal structure of St -AspRS (nondiscriminating type) has been determined at 2.3,Å resolution as the first example of the nondiscriminating type of AspRS from crenarchaea. A structural comparison with structures of discriminating AspRSs indicates that the structures are similar to each other overall and that the catalytic domain is highly conserved as expected. In the N-terminal domain, however, the binding site for the third anticodon nucleotide is modified to accept two pyrimidine bases, C and U, but not purine bases. The C base can bind to form a hydrogen bond to the surrounding main-chain amide group in the discriminating AspRS, while in the nondiscriminating AspRS the corresponding amino-acid residue is replaced by proline, which has no amide H atom for hydrogen-bond formation, thus allowing the U base to be accommodated in this site. In addition, the residues that cover the base plane are missing in the nondiscriminating AspRS. These amino-acid changes make it possible for both C and U to be accepted by the nondiscriminating AspRS. It is speculated that this type of nondiscriminating AspRS has been introduced into Thermus thermophilus through horizontal gene transfer. [source] | ||||||||||