A·I and A·G polynucleotide pairing. Controlling effect of amino-group hydrogen bonds to solvent water

Biochemistry ◽  
1977 ◽  
Vol 16 (21) ◽  
pp. 4637-4646 ◽  
Author(s):  
F. B. Howard ◽  
Masao Hattori ◽  
Joe Frazier ◽  
H. Todd Miles
Keyword(s):  
Hydrogen Bonds ◽  
Amino Group ◽  
Solvent Water ◽  
Controlling Effect

The effect of partial methylation of the glycine amino group on crystal structure inN,N-dimethylglycine and its hemihydrate

2012 ◽  
Vol 68 (8) ◽  
pp. o283-o287 ◽  
Author(s):  
Vasily S. Minkov ◽  
Elena V. Boldyreva
Keyword(s):  
Crystal Structure ◽  
Hydrogen Bonds ◽  
Water Molecules ◽  
Amino Group ◽  
Asymmetric Unit ◽  
Partial Methylation ◽  
Space Groups ◽  
Carboxylate Groups ◽  
Anhydrous Compound ◽  
Additional Hydrogen

N,N-Dimethylglycine, C4H9NO2, and its hemihydrate, C4H9NO2·0.5H2O, are discussed in order to follow the effect of the methylation of the glycine amino group (and thus its ability to form several hydrogen bonds) on crystal structure, in particular on the possibility of the formation of hydrogen-bonded `head-to-tail' chains, which are typical for the crystal structures of amino acids and essential for considering amino acid crystals as mimics of peptide chains. Both compounds crystallize in centrosymmetric space groups (PbcaandC2/c, respectively) and have twoN,N-dimethylglycine zwitterions in the asymmetric unit. In the anhydrous compound, there are no head-to-tail chains but the zwitterions formR44(20) ring motifs, which are not bonded to each other by any hydrogen bonds. In contrast, in the crystal structure ofN,N-dimethylglycinium hemihydrate, the zwitterions are linked to each other by N—H...O hydrogen bonds into infiniteC22(10) head-to-tail chains, while the water molecules outside the chains provide additional hydrogen bonds to the carboxylate groups.

scholarly journals (2,2′-Bipyridine-κ2 N,N′)(pyridine-2,6-dicarboxylato-κ2 N,O)palladium(II) monohydrate

IUCrData ◽  
2019 ◽  
Vol 4 (12) ◽  
Author(s):  
Kwang Ha
Keyword(s):  
Hydrogen Bonds ◽  
Water Molecule ◽  
Title Compound ◽  
Coordination Geometry ◽  
Intermolecular Hydrogen Bonds ◽  
Complex Molecules ◽  
Solvent Water Molecule ◽  
Solvent Water ◽  
Square Planar ◽  
Bipyridine Ligand

In the title compound, [Pd(C7H3NO4)(C10H8N2)]·H2O, the PdII cation is four-coordinated in a distorted square-planar coordination geometry defined by the two N atoms of the 2,2′-bipyridine ligand, one O atom and one N atom from the pyridine-2,6-dicarboxylate anion. The complex and solvent water molecule are linked by intermolecular hydrogen bonds. In the crystal, the complex molecules are stacked in columns along the a axis.

scholarly journals Crystal structure and Hirshfeld surface analysis of 2,4-diamino-6-phenyl-1,3,5-triazin-1-ium 4-methylbenzenesulfonate

2018 ◽  
Vol 74 (8) ◽  
pp. 1159-1162
Author(s):  
Ramalingam Sangeetha ◽  
Kasthuri Balasubramani ◽  
Kaliyaperumal Thanigaimani ◽  
Savaridasson Jose Kavitha
Keyword(s):  
Crystal Structure ◽  
Hydrogen Bonds ◽  
Intermolecular Interactions ◽  
Hirshfeld Surface ◽  
Amino Group ◽  
Asymmetric Unit ◽  
Graph Set ◽  
Molecular Salt ◽  
Sulfonate Anion ◽  
Hydrogen Bonded

In the title molecular salt, C9H10N5 +·C7H7O3S−, the asymmetric unit consists of a 2,4-diamino-6-phenyl-1,3,5-triazin-1-ium cation and a 4-methylbenzenesulfonate anion. The cation is protonated at the N atom lying between the amine and phenyl substituents. The protonated N and amino-group N atoms are involved in hydrogen bonding with the sulfonate O atoms through a pair of intermolecular N—H...O hydrogen bonds, giving rise to a hydrogen-bonded cyclic motif with R 2 2(8) graph-set notation. The inversion-related molecules are further linked by four N—H...O intermolecular interactions to produce a complementary DDAA (D = donor, A = acceptor) hydrogen-bonded array, forming R 2 2(8), R 4 2(8) and R 2 2(8) ring motifs. The centrosymmetrically paired cations form R 2 2(8) ring motifs through base-pairing via N—H...N hydrogen bonds. In addition, another R 3 3(10) motif is formed between centrosymetrically paired cations and a sulfonate anion via N—H...O hydrogen bonds. The crystal structure also features weak S=O...π and π–π interactions. Hirshfeld surface and fingerprint plots were employed in order to further study the intermolecular interactions.

Hydrogen-bonding patterns in the cocrystal 2,4-diamino-6-phenyl-1,3,5-triazine–sorbic acid (1/1)

2007 ◽  
Vol 63 (11) ◽  
pp. o4450-o4451 ◽  
Author(s):  
Kaliyaperumal Thanigaimani ◽  
Packianathan Thomas Muthiah ◽  
Daniel E. Lynch
Keyword(s):  
Hydrogen Bonding ◽  
Hydrogen Bonds ◽  
Sorbic Acid ◽  
Carboxyl Group ◽  
Amino Group ◽  
Acid Molecule ◽  
Asymmetric Unit ◽  
Graph Set ◽  
Bonding Patterns

In the title cocrystal, C9H9N5·C6H8O2, the asymmetric unit contains one 2,4-diamino-6-phenyl-1,3,5-triazine molecule and a sorbic acid molecule. The triazine molecules are base-paired [with a graph set of R 2 2(8)] on either side via N—H...N hydrogen bonds, forming a supramolecular ribbon along the c axis. Each triazine molecule interacts with the carboxyl group of a sorbic acid molecule via N—H...O and O—H...N hydrogen bonds, generating R 2 2(8) motifs. The supramolecular ribbons are interlinked by N—H...O hydrogen bonds involving the 2-amino group of the triazine molecules and the carboxyl O atom of the sorbic acid molecule.

Synthesis, spectroscopic (FT–IR and UV–Vis), crystallographic and theoretical studies, and a molecular docking simulation of an imatinib-like template

2019 ◽  
Vol 75 (12) ◽  
pp. 1681-1689
Author(s):  
Rodolfo Moreno-Fuquen ◽  
Kevin Arango-Daraviña ◽  
Esteban Garcia ◽  
Juan-C. Tenorio ◽  
Javier Ellena
Keyword(s):  
Crystal Growth ◽  
Hydrogen Bonds ◽  
Docking Simulation ◽  
Myelogenous Leukemia ◽  
Amino Group ◽  
Protein Residues ◽  
Function Analyzer ◽  
Stretching Vibration ◽  
Donor Acceptor ◽  
Ft Ir

The aim of the present study was to report the crystal structure and spectroscopic, electronic, supramolecular and electrostatic properties of a new polymorph of 4-(pyridin-2-yl)pyrimidin-2-amine (C9H8N4). The compound was synthesized under microwave irradiation. The single-crystal X-ray structure analysis revealed an angle of 13.36 (8)° between the planes of the rings, as well as molecules linked by Nsp 2—H...N hydrogen bonds forming dimers along the crystal. The material was analyzed by FT–IR vibrational spectroscopy, while a computational approach was used to elucidate the vibrational frequency couplings. The existence of Nsp 2—H...N hydrogen bonds in the crystal was confirmed spectroscopically by the IR peaks from the N—H stretching vibration shifting to lower wavenumbers in the solid state relative to those in the gas phase. The supramolecular studies confirmed the formation of centrosymmetric R 2 2(8) rings, which correspond to the formation of dimers that stack parallel to the b direction. Other weak C—H...π interactions, essential for crystal growth, were found. The UV–Vis spectroscopic analysis showed a donor–acceptor process, where the amino group acts as a donor and the pyridine and pyrimidine rings act as acceptors. The reactive sites of the molecule were identified and their quantitative values were defined using the electrostatic potential model proposed in the multifunctional wave function analyzer multiwfn. The calculated interaction energies between pairs of molecules were used to visualize the electrostatic terms as the leading factors against the dispersion factors in the crystal-growth process. The docking results showed that the amino group of the pyrimidine moiety was simultaneously anchored by hydrogen-bonding interactions with the Asp427 and His407 protein residues. This compound could be key for the realization of a series of syntheses of molecules that could be used as possible inhibitors of chronic myelogenous leukemia.

Binary salt of a palladium(II) complex with (phosphonomethyl)phosphonic (medronic) acid comprising `handbell-like' [Pd{μ-CH2(PO3)2}]3units

2012 ◽  
Vol 68 (9) ◽  
pp. m242-m245 ◽  
Author(s):  
Artem A. Babaryk ◽  
Alexandra N. Kozachkova ◽  
Natalia V. Tsaryk ◽  
Anatolij V. Dudko ◽  
Vasily I. Pekhnyo
Keyword(s):  
Hydrogen Bonds ◽  
Title Compound ◽  
Three Dimensional ◽  
Water Molecules ◽  
Dense Network ◽  
Asymmetric Unit ◽  
Neutral Complex ◽  
Solvent Water ◽  
Network Of Hydrogen Bonds ◽  
Successive Alternation

The asymmetric unit of the title compound, dipotassium bis[hexaaquanickel(II)] tris(μ2-methylenediphosphonato)tripalladium(II) hexahydrate, K2[Ni(H2O)6]2[Pd3{CH2(PO3)2}3]·6H2O, consists of half a {[Pd{CH2(PO3)2}]3}6−anion [one Pd atom (4e) and a methylene C atom (4e) occupy positions on a twofold axis] in a rare `handbell-like' arrangement, with K+and [Ni(H2O)6]2+cations to form the neutral complex, completed by three solvent water molecules. The {[Pd{CH2(PO3)2}]3}6−units exhibit close Pd...Pd separations of 3.0469 (4) Å and are packedviaintermolecular C—H...Pd hydrogen bonds. The [KO9] and [NiO6] units are assembled into sheets coplanar with (011) and stacked along the [100] direction. Within these sheets there are [K4Ni4O8] and [K2Ni2O4] loops. Successive alternation of the sheets and [Pd{CH2(PO3)2}]3units parallel to [001] produces the three-dimensional packing, which is also supported by a dense network of hydrogen bonds involving the solvent water molecules.

scholarly journals 2-Amino-6-methylpyridinium 2,2,2-trichloroacetate

2014 ◽  
Vol 70 (4) ◽  
pp. o391-o392 ◽  
Author(s):  
K. Syed Suresh Babu ◽  
G. Peramaiyan ◽  
M. NizamMohideen ◽  
R. Mohan
Keyword(s):  
Hydrogen Bonds ◽  
Amino Group ◽  
Asymmetric Unit ◽  
Molecular Salt ◽  
Ring Motif ◽  
Hydrogen Bonded

In the asymmetric unit of the title molecular salt, C6H9N2+·C2Cl3O2−, there are two independent 2-amino-6-methylpyridinium cations and two independent trichloroacetate anions. The pyridine N atom of the 2-amino-6-methylpyridine molecule is protonated and the geometries of these cations reveal amine–imine tautomerism. Both protonated 2-amino-6-methylpyridinium cations are essentially planar [maximum deviations = 0.026 (2) and 0.012 (2) Å]. In the crystal, the protonated N atom and the 2-amino group of the cation are hydrogen bonded to the carboxylate O atoms of the anionviaa pair of N—H...O hydrogen bonds, forming anR22(8) ring motif. These motifs are connectedviaN—H...O and C—H...O hydrogen bonds to form slabs parallel to (101).

N′-(4-Hydroxy-3-methoxybenzylidene)isonicotinohydrazide monohydrate

2007 ◽  
Vol 63 (3) ◽  
pp. o1119-o1120 ◽  
Author(s):  
Xue-Fang Shi ◽  
Lei He ◽  
Guo-Zhun Ma ◽  
Cui-Cui Yuan
Keyword(s):  
Hydrogen Bonds ◽  
Water Molecule ◽  
Title Compound ◽  
Crystal Packing ◽  
Asymmetric Unit ◽  
Solvent Water Molecule ◽  
Solvent Water ◽  
Compound C

The asymmetric unit of the title compound, C14H13N3O3·H2O, contains one molecule of N′-(4-hydroxy-3-methoxybenzylidene)isonicotinohydrazide and one solvent water molecule. The crystal packing is stabilized by O—H...N and O—H...O hydrogen bonds.

On the differential hydration of various forms of glycine in diluted aqueous solutions: a Monte Carlo study

2012 ◽  
Vol 31 (2) ◽  
pp. 295
Author(s):  
Biljana Bujaroska ◽  
Kiro Stojanoski ◽  
Ljupco Pejov
Keyword(s):  
Monte Carlo ◽  
Hydrogen Bonding ◽  
Hydrogen Bonds ◽  
Water Molecules ◽  
Hydrogen Bonding Interaction ◽  
Liquid Environment ◽  
Zwitterionic Form ◽  
Solvent Water ◽  
Bonding Interaction ◽  
Solvent Molecules

Rigid-body Monte Carlo simulations were carried out to study the differential hydration of zwitterionic and neutral forms of glycine in water. To account for the solute polarization by the rather polar liquid environment, initial geometries were chosen as minima on the MP2/aug-cc-pVTZ potential energy surfaces of neutral and zwitterionic glycine continuously solvated by water, implementing the polarizable continuum model (PCM) within the integral equation formalism (IEFPCM). The dynamically changing hydrogen bonding network between the solute and solvent molecules was analyzed imposing distance, energy and angular distribution-based criteria. It was found that, on average, the zwitterionic form of glycine acts as an acceptor of 4.53 hydrogen bonds, while it plays the role of a proton donor in (on average) 2.73 hydrogen bonds with the solvent water molecules. In particular, we have found out that 2.73 solvent water molecules are involved in hydrogen bonding interaction with the ammonium group, acting as proton-acceptors. This is in excellent agreement with the recent experimental neutron diffraction studies, which have indicated that 3.0 water molecules reside in the vicinity of the NH3+ group of aqueous zwitterionic glycine. Neutral form of aqueous glycine, on the other hand, on average donates protons in 1.63 hydrogen bonds with the solvent water molecules, while at the same time it accepts 2.53 hydrogen bonds from the solvent molecules. The greater charge polarization in the zwitterionic form thus makes it much more exposed to hydrogen bonding interaction in polar medium such as water, which is certainly the main reason of the larger stability of this form of glycine in condensed media.

scholarly journals Crystal structure of (Z)-3-benzyloxy-6-[(2-hydroxyanilino)methylidene]cyclohexa-2,4-dien-1-one

2014 ◽  
Vol 70 (12) ◽  
pp. o1292-o1292 ◽  
Author(s):  
Nadir Ghichi ◽  
Ali Benboudiaf ◽  
Hocine Merazig
Keyword(s):  
Crystal Structure ◽  
Hydrogen Bond ◽  
Hydrogen Bonds ◽  
Three Dimensional ◽  
Maximum Deviation ◽  
Amino Group ◽  
Supramolecular Architecture ◽  
Bond Forming ◽  
Compound C ◽  
Ring Motif

In the title compound, C20H17NO3, the methylidenecyclohexa-2,4-dienone moiety is approximately planar [maximum deviation = 0.0615 (10) Å] and is oriented at diherdral angles of 69.60 (7) and 1.69 (9)° to the phenyl and hydroxybenzene rings, respectively. The amino group links with the carbonyl O atomviaan intramolecular N—H...O hydrogen bond, forming anS(6) ring motif. In the crystal, the molecules are linked by O—H...O hydrogen bonds and weak C—H...O and C—H...π interactions, forming a three-dimensional supramolecular architecture.

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