Three-center Hydrogen Research Articles

Hydrogen bonding: Part 25. The nature of the hydrogen bond in hydroxytropenylium chloride (tropone hydrochloride)

Hydroxytropenylium iodide and bromide contain normal electrostatic OH⋯X − hydrogen bonds. Hydroxytropenylium chloride, however, contains a hydrogen bond intermediate between the normal electrostatic type and the very strong covalent type, similar to the hydrogen bonds found in choline fluoride or the Type I C ∞v hydrogen dihalide ions. Infrared comparisons with compounds previously studied demonstrate that the hydroxytropenylium ion is a stronger hydrogen bond donor than either choline cation or protonated betaine cation, and suggest that hydroxytropenylium fluoride, if it can be prepared, should contain a three-center covalent hydrogen bond.

The crystal structure of the C-nucleoside, 1,3-Dimethyl-8-β-D-ribofuranosylxanthine monohydrate

1,3-Dimethyl-8-β-Dribofuranosylxanthine monohydrate, C12H16N4O6·H2O, is monoclonic, P21, with two molecules in a unit cell having a = 8.186(1), b = 19.222(3), c = 4.7655(8) Å, β = 103.79(1)°, V = 728.2 Å, and Dx = 1.506 g·cm-3.The structure was solved by the direct methods, using MoKα radiation and refined with anisotropic temperature-factors. The final agreement factors were R = 0.061, Rw = 0.042 for 2254 structure amplitudes having |Fo| > 2 σ(Fo). The ribose ring has the C-2’;-exo-C-3’;-endo (2T3) conformation with pseudorotation parameters P = -3.2, τm = 39.9°, and a gauche-gauche conformation around the ribose C-4’;-C-5’; bond. The β-link conformation is anti, with 0-4’;-C1’;-C-8-N-9 = -162.6°. The pyrimidine and imidazole rings are planar, making an interplanar angle of 1.0(1)°. The molecular conformation is stabilized by an unsymmetrical, three-center hydrogen bond from N-7-H to O-5’;-H as the major component and to O-4’;Has the minor component. The hydrogen bonding includes a cooperative cycle involving the HN-C-C=O moiety, two hydroxyl groups, and a water molecule.

Binding of Hoechst 33258 to the minor groove of B-DNA

An X-ray crystallographic structure analysis has been carried out on the complex between the antibiotic and DNA fluorochrome Hoechst 33258 and a synthetic B-DNA dodecamer of sequence C-G-C-G-A-A-T-T-C-G-C-G. The drug molecule, which can be schematized as: phenol-benzimidazole-benzimidazole-piperazine, sits within the minor groove in the A-T-T-C region of the DNA double helix, displacing the spine of hydration that is found in drugfree DNA. The NH groups of the benzimidazoles make bridging three-center hydrogen bonds between adenine N-3 and thymine O-2 atoms on the edges of base-pairs, in a manner both mimicking the spine of hydration and calling to mind the binding of the auti-tumor drug netropsin. Two conformers of Hoechst are seen in roughly equal populations, related by 180 ° rotation about the central benzimidazole-benzimidazole bond: one form in which the piperazine ring extends out from the surface of the double helix, and another in which it is buried deep within the minor groove. Steric clash between the drug and DNA dictates that the phenol-benzimidazole-benzimidazole portion of Hoechst 33258 binds only to A · T regions of DNA, whereas the piperazine ring demands the wider groove characteristic of G · C regions. Hence, the piperazine ring suggests a possible G · C-reading element for synthetic DNA sequence-reading drug analogs.

Three-center hydrogen bonds C-F...H(N)...O=C in crystal structures of O2NCF2CONHCH2Ph and O2NCF2conhnhtol

1. Using the x-ray diffraction method, we have determined the crystal and molecular structure of N-benzyldifluoronitroacetamide and 1-difluoronitroacetyl-2-p-tolylhydrazine. 2. In the investigated compounds, we have observed three-center hydrogen bonds, C-F... H(N)...O=C.

Disubstituted norbornadiene ? -complexes. Communication 1. Synthesis and some chemical properties of 2,3-disubstituted norbornadiene complexes of rhodium

1. We have obtained a series of new π complexes of rhodium with 2,3-dicarboalkoxy- and 2,3-dicarboxynorbornadiene ligand, for which we have found mild conditions for selective hydrolysis and esterification of one of the ester or acid groups. 2. Using the IR and PMR spectroscopy method, we have studied the structure of the 2,3-disubstituted norbornadiene complexes in the solid state and in dilute solutions. Depending on the structure and the phase state, the carboxylic acids of this series form intramolecular, intermolecular, and possibly three-center hydrogen bonds. 3. We have studied the reaction of protonation of (2,3-dicarboalkoxynorbornadiene)-cyclopentadienylrhodium complexes with the acids HPF6 or HBF4· Et2O, as a result of which we have obtained stable cationic products of composition 1:1 with a strong hydrogen bond of the O...H...O type.

Water structure in [Phe4 Val6] antamanide X 12H2O crystallized from dioxane.

Crystals of [Phe4 Val6] antamanide (cyclic [ValProProPhePhe]2) grown from dioxane/H2O, with space group P21212 and cell parameters a = 15.099(4), b = 22.008(5) and c = 11.024(3) A, are almost identical to crystals grown from H2O/acetone, the structure of which was determined a number of years ago. Per peptide molecule there are the equivalent of 12 water molecules occupying 16 sites in both crystals; however, in the new investigation a number of water molecules present at one-half occupancy have been found in different positions than in the earlier analysis. The interpretation of the hydrogen bonding between peptide/water and between water/water is much more satisfactory. Pentagonal water assemblies are present in the solvent channel. There is a distinct indication of the occurrence of a bifurcated bond between two water molecules, as well as the presence of three-center hydrogen bonds joining three water molecules. This may be the first experimental example of a bifurcated bond between two water molecules.

A new environment for water. The first authenticated example of water molecules engaged in twin, three-center hydrogen bonds. The crystal and molecular structure of the dimethyltin dichloride complex [(Me2SnCl2.H2O)2.18-crown-6

H 2 O coordonnee a Sn, engage des liaisons hydrogene avec l'ether crown. Ainsi chaque molecule d'eau est pentacoordine. Cristallisation dans le groupe C2/m

Three-center (bifurcated) hydrogen bonding in the crystal structures of amino acids

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTThree-center (bifurcated) hydrogen bonding in the crystal structures of amino acidsG. A. Jeffrey and J. MitraCite this: J. Am. Chem. Soc. 1984, 106, 19, 5546–5553Publication Date (Print):September 1, 1984Publication History Published online1 May 2002Published inissue 1 September 1984https://doi.org/10.1021/ja00331a025RIGHTS & PERMISSIONSArticle Views289Altmetric-Citations74LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InReddit PDF (682 KB) Get e-Alerts Get e-Alerts

A survey of hydrogen bond geometries in the crystal structures of amino acids

An analysis of the geometries of the hydrogen bonds observed by neutron diffraction in thirt-two crystal structures of amino acids shows the following results. Of the 168 hydrogen bonds in the data set, 64 involve the zwitterion groups  ▪ and  C O 2. Another 18 are from ▪ to sulphate or carbonyl oxygens. The majority, 46, of these ▪H … O bonds are three-centered (bifurcated). Nine are four-centered (trifurcated). The geometry in which the three-centered hydrogen bond involves both oxygens of the same carboxylate group is not especially favoured. When it does occur, one hydrogen bond is generally shorter and the other longer, than when the bonding involves oxygens on different carboxylate groups. The shortest hydrogen bonds are the OH … O C , from a carboxylic acid hydroxyl to a carboxylate oxygen, and NH … O C when the nitrogen is the ring atom in histidine or proline. Carboxylate groups, on average, accept six hydrogen bonds, with no examples of less than four bonds. The reason for the large number of three-centered ▪H … O C bonds is therefore a proton deficiency arising from the disparity between the tripled donor property of the ▪ groups and the sextuple, on average, acceptor property of the carboxylate groups. There is good geometrical evidence for the existence of H … O and H … Cl − hydrogen bonds, especially involving the hydrogen atoms on α-atoms.

A Shock Tube Study of the Decomposition Mechanism of Chloroform in the Presence of Deuterium or Methane

Abstract Chloroform was pyrolyzed in the absence and in the presence of one of three additives—D2, CH4, and CD4, over the temperature range of 1000–1200 K in a single-pulse shock tube. The main products of the decomposition of chloroform by itself were tetrachloroethylene and hydrogen chloride. On the other hand, tetrachloroethylene, trichloroethylene, dichloromethane, and hydrogen chloride were the major products in the presence of D2, while in the chloroform–methane systems they were tetrachloroethylene, trichloroethylene, 1,1-dichloroethylene, vinyl chloride, ethane, and hydrogen chloride. From the deuterium distribution of the products, as determined by mass spectrometry, it is found that the hydrogen atoms of trichloroethylene and 1,1-dichloroethylene mainly came from chloroform and methane respectively, while the hydrogen atoms of vinyl chloride came from both chloroform and methane. The change in the product distribution resulting from the addition of deuterium or methane and the hydrogen isotopic distribution suggest that the mechanism is composed of Cl atom elimination in the initiation step and successive reactions involving “hot” molecule reactions. The hydrogen isotopic distribution of vinyl chloride may indicate that the three-centered hydrogen elimination (αα) process competes with the four-centered (αβ) process in the decomposition of “hot” 1,1-dichloroethane.