Hydrogen bonding patterns in salts of derivatives of aminopyrimidine and thiobarbituric acid

2015 ◽  
Vol 71 (2) ◽  
pp. 144-152 ◽  
Author(s):  
Sundaramoorthy Gomathi ◽  
Jeyaraman Selvaraj Nirmalram ◽  
Packianathan Thomas Muthiah
Keyword(s):  
Hydrogen Bonds ◽  
Thiobarbituric Acid ◽  
Water Molecules ◽  
X Ray Diffraction ◽  
Compound I ◽  
Base Pairs ◽  
X Ray ◽  
Acid And Base ◽  
Derivatives Of ◽  
Primary Interaction

Three salts, namely 2-amino-4,6-dimethylpyrimidin-1-ium thiobarbiturate trihydrate (I), 2-amino-4,6-dimethoxypyrimidin-1-ium thiobarbiturate dihydrate (II) and 2,4-diamino-5-(3′,4′,5′-trimethoxybenzyl)pyrimidin-1-ium thiobarbiturate (III), were synthesized and characterized by IR and X-ray diffraction techniques. The primary interaction between the acid and base happensviaN—H...O hydrogen bonds in (II) and (III), andviawater-mediated N—H...OWand OW—HW...S in (I). The water molecules present in compound (I) form a (H2O)12water clusterviawater–water interactions. In all three compounds (I)–(III), thiobarbiturate anions form self-complementary pairs with a robustR22(8) motifviaa pair of N—H...O/N—H...S hydrogen bonds. They mimic the nucleobase base pairs by utilizing the same groups (thymine/uracil uses N3—H and C4=O8 groups during the formation of Watson–Crick and Hoogsteen base pairs with adenine). Compound (I) forms a water-mediated base pair through N—H...OWhydrogen bonds and forms anR42(12) motif. The formation of N—H...S hydrogen bonds, water-mediated base pairs and water–water interactions in these crystal systems offers scope for these systems to be considered as a model in the study of hydration of nucleobases and water-mediated nucleobase base pairs in macromolecules.

Structural Study of a new Compound Based on Acid 1,4-Cyclohexanedicarboxylic (1,4-CDC)

2010 ◽  
Vol 6 (1) ◽  
pp. 891-896
Author(s):  
Manel Halouani ◽  
M. Dammak ◽  
N. Audebrand ◽  
L. Ktari
Keyword(s):  
Aqueous Solution ◽  
Water Molecules ◽  
Carboxyl Group ◽  
X Ray Diffraction ◽  
Compound I ◽  
Unit Cell Parameters ◽  
Monoclinic System ◽  
X Ray ◽  
Cell Parameters ◽  
Cyclohexanedicarboxylic Acid

One nickel 1,4-cyclohexanedicarboxylate coordination polymers, Ni2 [(O10C6H4)(COO)2].2H2O  (I), was hydrothermally synthesized from an aqueous solution of Ni (NO3)2.6H2O, (1,4-CDC) (1,4-CDC = 1,4-cyclohexanedicarboxylic acid) and tetramethylammonium nitrate. Compound (I) crystallizes in the monoclinic system with the C2/m space group. The unit cell parameters are a = 20.1160 (16) Å, b = 9.9387 (10) Å, c = 6.3672 (6) Å, β = 97.007 (3) (°), V= 1263.5 (2) (Å3) and Dx= 1.751g/cm3. The refinement converged into R= 0.036 and RW = 0.092. The structure, determined by single crystal X-ray diffraction, consists of two nickel atoms Ni (1) and Ni (2). Lots of ways of which is surrounded by six oxygen atoms, a carboxyl group and two water molecules.

A novel dinuclear bismuth(III) coordination compound: bis(μ-pyridine-2,6-dicarboxylato)-κ4O2,N,O6:O6′;κ4O2:O2′,N,O6-bis[(azido-κN)(1,10-phenanthroline-κ2N,N′)bismuth(III)] tetrahydrate

2014 ◽  
Vol 70 (6) ◽  
pp. 562-565 ◽  
Author(s):  
Wei Zhang ◽  
Yu-Quan Feng
Keyword(s):  
Molecular Structure ◽  
Hydrogen Bonds ◽  
Coordination Compound ◽  
Photoelectron Spectroscopy ◽  
Three Dimensional ◽  
Water Molecules ◽  
Stacking Interactions ◽  
Coordination Geometry ◽  
X Ray Diffraction ◽  
X Ray

A novel dinuclear bismuth(III) coordination compound, [Bi2(C7H3NO4)2(N3)2(C12H8N2)2]·4H2O, has been synthesized by an ionothermal method and characterized by elemental analysis, energy-dispersive X-ray spectroscopy, IR, X-ray photoelectron spectroscopy and single-crystal X-ray diffraction. The molecular structure consists of one centrosymmetric dinuclear neutral fragment and four water molecules. Within the dinuclear fragment, each BiIIIcentre is seven-coordinated by three O atoms and four N atoms. The coordination geometry of each BiIIIatom is distorted pentagonal–bipyramidal (BiO3N4), with one azide N atom and one bridging carboxylate O atom located in axial positions. The carboxylate O atoms and water molecules are assembledviaO—H...O hydrogen bonds, resulting in the formation of a three-dimensional supramolecular structure. Two types of π–π stacking interactions are found, with centroid-to-centroid distances of 3.461 (4) and 3.641 (4) Å.

Supramolecular architectures in two 1:1 cocrystals of 5-fluorouracil with 5-bromothiophene-2-carboxylic acid and thiophene-2-carboxylic acid

2017 ◽  
Vol 73 (6) ◽  
pp. 481-485 ◽  
Author(s):  
Marimuthu Mohana ◽  
Packianathan Thomas Muthiah ◽  
Colin D. McMillen
Keyword(s):  
Solid State ◽  
Carboxylic Acid ◽  
Hydrogen Bonds ◽  
Crystal Structures ◽  
X Ray Diffraction ◽  
Base Pairs ◽  
X Ray ◽  
Supramolecular Architectures ◽  
Acid Acid ◽  
Carboxylic Acid Dimer

In solid-state engineering, cocrystallization is a strategy actively pursued for pharmaceuticals. Two 1:1 cocrystals of 5-fluorouracil (5FU; systematic name: 5-fluoro-1,3-dihydropyrimidine-2,4-dione), namely 5-fluorouracil–5-bromothiophene-2-carboxylic acid (1/1), C5H3BrO2S·C4H3FN2O2, (I), and 5-fluorouracil–thiophene-2-carboxylic acid (1/1), C4H3FN2O2·C5H4O2S, (II), have been synthesized and characterized by single-crystal X-ray diffraction studies. In both cocrystals, carboxylic acid molecules are linked through an acid–acid R 2 2(8) homosynthon (O—H...O) to form a carboxylic acid dimer and 5FU molecules are connected through two types of base pairs [homosynthon, R 2 2(8) motif] via a pair of N—H...O hydrogen bonds. The crystal structures are further stabilized by C—H...O interactions in (II) and C—Br...O interactions in (I). In both crystal structures, π–π stacking and C—F...π interactions are also observed.

scholarly journals Crystal structure of the DNA sequence d(CGTGAATTCACG)2with DAPI

2017 ◽  
Vol 73 (9) ◽  
pp. 500-504 ◽  
Author(s):  
Hristina I. Sbirkova-Dimitrova ◽  
Boris Shivachev
Keyword(s):  
Crystal Structure ◽  
Crystal Packing ◽  
Minor Groove ◽  
Van Der Waals Interactions ◽  
Water Molecules ◽  
X Ray Diffraction ◽  
Base Pairs ◽  
X Ray ◽  
Dna Molecule ◽  
Dna Fragment

The structure of 4′,6-diamidine-2-phenylindole (DAPI) bound to the synthetic B-DNA oligonucleotide d(CGTGAATTCACG) has been solved in space groupP212121by single-crystal X-ray diffraction at a resolution of 2.2 Å. The structure is nearly isomorphous to that of the previously reported crystal structure of the oligonucleotide d(CGTGAATTCACG) alone. The adjustments in crystal packing between the native DNA molecule and the DNA–DAPI complex are described. DAPI lies in the narrow minor groove near the centre of the B-DNA fragment, positioned over the A–T base pairs. It is bound to the DNA by hydrogen-bonding and van der Waals interactions. Comparison of the two structures (with and without ligand) shows that DAPI inserts into the minor groove, displacing the ordered spine waters. Indeed, as DAPI is hydrophobic it confers this behaviour on the DNA and thus restricts the presence of water molecules.

Structural and spectroscopic studies of dipotassium 3,3,3′,3′-tetramethylcystinate trihydrate, K2[C10H18N2O4S2]3H2O

1984 ◽  
Vol 62 (6) ◽  
pp. 1127-1133 ◽  
Author(s):  
Romolo Faggiani ◽  
Helen Elaine Howard-Lock ◽  
Colin James Lyne Lock ◽  
Maria Lurdes Martins ◽  
Philip Stuart Smalley
Keyword(s):  
Hydrogen Bonds ◽  
Single Crystal ◽  
Spectroscopic Studies ◽  
The Other ◽  
Ionic Interactions ◽  
Water Molecules ◽  
Torsional Angle ◽  
X Ray Diffraction ◽  
Standard Methods ◽  
X Ray

The compound dipotassium 3,3,3′,3′-tetramethylcystinate trihydrate, K2[C10H18O4N2S2]3H2O, has been prepared and characterized by single crystal X-ray diffraction. Crystals were monoclinic, P21a = 6.160(1), b = 26.473(8), c = 6.193(1) Å, β = 113.94(1)°, with two formula units in the unit cell. Intensities were measured on a Syntex P21, diffractometer with use of MoKα radiation. The structure was solved by standard methods and refined to R1 = 0.0469, R2 = 0.0472 based on 2303 independent observed reflections. The C—S bonds (1.877(6), 1.891(6) Å) are longer than in many similar compounds although the S—S bond (2.040(2) Å) is not. The C—S—S—C torsional angle (108.7(3)°) is larger than normal in dithiol compounds. Other distances and angles are normal. Two types of potassium coordination are present, one a distorted octahedron, the other a distorted trigonal prism. In addition to the ionic interactions, hydrogen bonds involving the water molecules are important in stabilizing the structure.

In-house and synchrotron X-ray diffraction studies of 2-phenyl-1,10-phenanthroline, protonated salts, complexes with gold(III) and copper(II), and an orthometallation product with palladium(II)

2014 ◽  
Vol 70 (3) ◽  
pp. 260-266 ◽  
Author(s):  
Jeanette A. Krause ◽  
Daoli Zhao ◽  
Sayandev Chatterjee ◽  
Roland Falcon ◽  
Kristen Stoltz ◽  
...  
Keyword(s):  
Planar Geometry ◽  
Water Molecules ◽  
X Ray Diffraction ◽  
Compound I ◽  
Complex Iv ◽  
X Ray ◽  
Lattice Water ◽  
Square Planar ◽  
Salt Complex ◽  
Monodentate Complex

Different salts of the 2-phenyl-1,10-phenanthrolin-1-ium cation, (pnpH)+, are obtained by reacting 2-phenyl-1,10-phenanthroline (pnp), C18H12N2, (I), with a variety of anions, such as hexafluoridophosphate, C18H13N2+·PF6−, (II), trifluoromethanesulfonate, C18H13N2+·CF3SO3−, (III), tetrachloridoaurate, (C18H13N2)[AuCl4], (IV), and bromide (as the dihydrate), C18H13N2+·Br−·2H2O, (V). Compound (I) crystallizes withZ′ = 2, with both independent molecules adopting a coplanar conformation. In (II)–(IV), a hydrogen bond exists between the cation and anion, while one of the lattice water molecules serves as a hydrogen-bonded bridge between the cation and anion in (V). Reaction of (I) with HAuCl4gives the salt complex (IV); however, reaction with KAuCl4produces the monodentate complex trichlorido(2-phenyl-1,10-phenanthroline-κN10)gold(III), [AuCl3(C18H12N2)], (VI). Dichlorido(2-phenyl-1,10-phenanthroline-κ2N,N′)copper(II), [CuCl2(C18H12N2)], (VII), results from the reaction of CuCl2·2H2O and (I), in which the CuIIcenter adopts a tetrahedrally distorted square-planar geometry. The pendent phenyl ring twists to a bisecting position relative to the phenanthroline plane. The square-planar PdIIcomplex, bromido[2-(phenanthrolin-2-yl)phenyl-κ3C1,N,N′]palladium(II), [PdBr(C18H11N2)], (VIII), is obtained from the reaction of (I) with [PdCl2(cycloocta-1,5-diene)], followed by addition of bromine. A coplanar geometry for the pendent ring is adopted as a result of the tridentate bonding motif.

scholarly journals Synthesis and Structure of Methylsulfanyl Derivatives of Nickel Bis(Dicarbollide)

Molecules ◽  
2019 ◽  
Vol 24 (24) ◽  
pp. 4449 ◽  
Author(s):  
Sergey A. Anufriev ◽  
Kyrill Yu. Suponitsky ◽  
Oleg A. Filippov ◽  
Igor B. Sivaev
Keyword(s):  
Hydrogen Bonds ◽  
Single Crystal ◽  
Quantum Chemical Calculations ◽  
Quantum Chemical ◽  
X Ray Diffraction ◽  
Gauche Conformation ◽  
X Ray ◽  
Derivatives Of ◽  
Transoid Conformation

Symmetrically and unsymmetrically substituted methylsulfanyl derivatives of nickel(III) bis(dicarbollide) (Bu4N)[8,8′-(MeS)2-3,3′-Ni(1,2-C2B9H10)2], (Bu4N)[4,4′-(MeS)2-3,3′-Ni(1,2-C2B9H10)2], and (Bu4N)[4,7′-(MeS)2-3,3′-Ni(1,2-C2B9H10)2] were synthesized, starting from [Ni(acac)2]3 and the corresponding methylsulfanyl derivatives of nido-carborane (Bu4N)[10-MeS-7,8-C2B9H11] and (Bu4N)[10-MeS-7,8-C2B9H11]. Structures of the synthesized metallacarboranes were studied by single-crystal X-ray diffraction and quantum chemical calculations. The symmetrically substituted 8,8′-isomer adopts transoid conformation stabilized by two pairs of intramolecular C–H···S hydrogen bonds between the dicarbollide ligands. The unsymmetrically substituted 4,7′-isomer adopts gauche conformation, which is stabilized by two nonequivalent C–H···S hydrogen bonds and one short chalcogen B–H···S bond (2.53 Å, −1.4 kcal/mol). The gauche conformation was found to be also preferred for the 4,7′-isomer.

scholarly journals An infinite two-dimensional hybrid water–chloride network in a 4′-(furan-2-yl)-2,2′:6′,2′′-terpyridine nickel(II) matrix

2017 ◽  
Vol 73 (6) ◽  
pp. 871-875 ◽  
Author(s):  
Wei-Wei Fu ◽  
Ya-Qian Li ◽  
Yang Liu ◽  
Man-Sheng Chen ◽  
Wei Li ◽  
...  
Keyword(s):  
Hydrogen Bonds ◽  
Chloride Ions ◽  
Water Molecules ◽  
Two Dimensional ◽  
X Ray Diffraction ◽  
Coordination Environment ◽  
X Ray ◽  
Solvent Water ◽  
Distorted Octahedral ◽  
Shaped Pattern

A new complex, namely bis[4′-(furan-2-yl)-2,2′:6′,2′′-terpyridine]nickel(II) dichloride decahydrate, [Ni(C19H13N3O)2]Cl2·10H2O, has been crystallized by solvent evaporation and characterized by single-crystal X-ray diffraction. The coordination environment of the NiIIcation is distorted octahedral with slight deviations from an idealized geometry. The most intriguing structural feature is an infinite two-dimensional hybrid water–chloride network parallel to (011) constructed by O—H...O and O—H...Cl hydrogen bonds involving two independent chloride ions and ten independent solvent water molecules with an L-shaped pattern. One of the furyl rings is disordered with a refined occupancy ratio of 0.786 (13):0.214 (13)

A new organically templated magnesium sulfate: structure, spectroscopic analysis, and thermal behaviour

2014 ◽  
Vol 68 (2) ◽  
Author(s):  
Dhouha Hassan ◽  
Walid Rekik ◽  
Houcine Naïli ◽  
Tahar Mhiri
Keyword(s):  
Thermal Decomposition ◽  
Hydrogen Bonds ◽  
Magnesium Sulfate ◽  
Spectroscopic Analysis ◽  
Water Molecules ◽  
Supramolecular Network ◽  
Slow Evaporation ◽  
X Ray Diffraction ◽  
Monoclinic System ◽  
X Ray

AbstractA new magnesium sulfate templated by 2-methylpiperazine, (C5H14N2)[Mg(H2O)6](SO4)2, was prepared by the slow evaporation method. The obtained crystals were investigated by the Raman and FTIR spectroscopy and crystallographically characterised by single-crystal X-ray diffraction. The compound crystallises in the monoclinic system, space group P21/n. Supramolecular network of this hybrid material consists of Mg2+ cations octahedrally coordinated by six water molecules, sulfate tetrahedra and protonated and disordered diamine linked together by two types of hydrogen bonds: OW—H…O and N—H…O. Dehydration of the title compound takes place in three steps. Thermal decomposition of the anhydrous phase consists in the loss of the organic moiety and one sulfate group leading to the formation of magnesium sulfate.

Synthesis and crystal structures of a 3-acetylated (20S,24S)-ocotillol-type saponin and its C-24 epimer

2017 ◽  
Vol 73 (6) ◽  
pp. 464-469 ◽  
Author(s):  
Juan Liu ◽  
Yang-Rong Xu ◽  
Xing-Si An ◽  
Gui-Ge Hou ◽  
Qing-Guo Meng
Keyword(s):  
Hydrogen Bonds ◽  
Three Dimensional ◽  
Water Molecules ◽  
X Ray Diffraction ◽  
X Ray ◽  
H Nmr ◽  
Dimensional Network ◽  
Crystal Packings ◽  
C Nmr

In order to study the in vivo protective effect on myocardial ischemia, (20S,24R)-epoxydammarane-12β,25-diol, (V), and (20S,24S)-epoxydammarane-12β,25-diol, (VI), were synthesized through a novel synthetic route. Two key intermediates, namely (20S,24R)-3-acetyl-20,24-epoxydammarane-3β,12β,25-triol, (III) [obtained as the hemihydrate, C32H54O5·0.5H2O, (IIIa), and the ethanol hemisolvate, C32H54O5·0.5C2H5OH, (IIIb), with identical conformations but different crystal packings], and (20S,24S)-3-acetyl-20,24-epoxydammarane-3β,12β,25-triol, C32H54O5, (IV), were obtained during the synthesis. The structures were confirmed by 1H NMR, 13C NMR and HRMS analyses, and single-crystal X-ray diffraction. Molecules of (IIIa) are extended into a two-dimensional network constructed with water molecules linked alternately through intermolecular O—H...O hydrogen bonds, which are further stacked into a three-dimensional network. Compound (IIIb) contains two completely asymmetric molecules, which are linked in a disordered manner through intermolecular C—H...O hydrogen bonds. While the crystal stacks in compound (IV) are linked via weak C—H...O hydrogen bonds, the hydrogen-bonded chains extend helically along the crystallographic b axis.

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