scholarly journals Crystal structure of 4-(dimethylamino)pyridin-1-ium-2,5-dichloro-3,6-dioxocyclohexa-1,4-diene-1,4-bis(olate) 4-dimethylaminopyridine (2:1) water undeca-solvate

2020 ◽  
Vol 11 (3) ◽  
pp. 255-260
Author(s):  
Alebel Nibret Belay ◽  
Johan Andries Venter ◽  
Orbett Teboho Alexander
Keyword(s):  
Title Compound ◽  
Water Clusters ◽  
Crystal Packing ◽  
Proton Donor ◽  
Proton Acceptor ◽  
Strong Hydrogen Bond ◽  
X Ray Diffraction ◽  
Chloranilic Acid ◽  
Triclinic Crystal System ◽  
Hydrogen Bond Interactions

The structure of the title compound, 4-(dimethylamino)pyridin-1-ium-2,5-dichloro-3,6-dioxocyclohexa-1,4-diene-1,4-bis(olate) 4-dimethylaminopyridine water undeca-solvate, C57H87Cl5N12O21, obtained from interaction between chloranilic acid (caH2), and dimethyl aminopyridine (DMAP) has been determined by single crystal X-ray diffraction. The title compound, (DMAPH)5(ca)2.5·(DMAP)·11H2O, crystallized in the triclinic crystal system with space group, P  (no. 2), a = 13.3824(15) Å, b = 13.4515(17) Å, c = 19.048(2) Å, α = 86.014(4)°, β = 88.821(4)°, γ = 86.367(4)°, V = 3413.3(7) Å3, Z = 2, T = 100(2) K, μ(MoKα) = 0.294 mm-1, Dcalc = 1.414 g/cm3, 59413 reflections measured (3.76° ≤ 2Θ ≤ 56°), 16405 unique (Rint = 0.0517, Rsigma = 0.0589) which were used in all calculations. The final R1 was 0.0460 (I ≥ 2σ(I)) and wR2 was 0.1271 (all data). Using supramolecular chemistry principles, proton donors (chloranilic acid) and acceptor (DMAP) were combined to generate a multicomponent hydrogen-bonded system. Due to the presence of protonated bases (DMAPH+), the dominant interactions are the N+-H···O hydrogen bonds, whereas the negative charges of an acceptor from the chloranilate dianion (ca2-) are delocalized. Additionally, three sets of water clusters in the title compound were identified, namely a cyclic pentamer, a linear, and an acute-shaped trimer water cluster. It was further observed that strong hydrogen bond interactions occurred between the solvated aqua molecule(s) acting as a proton donor and the neutral DMAP acting as a proton acceptor. The crystal packing is further stabilized by O-H···Cl and C-H···Cl weak halogen interactions. The lattice metric strength is further held by observed π-π stacking interactions (centroid-centroid) with inter centroid distances between sets of the DMAPH rings of 3.624(3), 3.642(4), 3.739(3), 3.863(3) and 3.898(3) Å, respectively.

scholarly journals Crystal Structure and Computational Study on Methyl-3-Aminothiophene-2-Carboxylate

Crystals ◽  
2020 ◽  
Vol 10 (1) ◽  
pp. 19 ◽  
Author(s):  
Yaping Tao ◽  
Ligang Han ◽  
Andong Sun ◽  
Kexi Sun ◽  
Qian Zhang ◽  
...  
Keyword(s):  
Crystal Packing ◽  
Computational Study ◽  
Three Dimensional ◽  
X Ray Diffraction ◽  
Dispersion Energy ◽  
Monoclinic Crystal ◽  
Hydrogen Bond Interactions ◽  
Calculation Results ◽  
Reduced Density Gradient ◽  
Reduced Density

Methyl-3-aminothiophene-2-carboxylate (matc) is a key intermediate in organic synthesis, medicine, dyes, and pesticides. Single crystal X-ray diffraction analysis reveals that matc crystallizes in the monoclinic crystal system P21/c space group. Three matc molecules in the symmetric unit are crystallographically different and further linked through the N–H⋯O and N–H⋯N hydrogen bond interactions along with weak C–H⋯S and C–H⋯Cg interactions, which is verified by the three-dimensional Hirshfeld surface, two-dimensional fingerprint plot, and reduced density gradient (RDG) analysis. The interaction energies within crystal packing are visualized through dispersion, electrostatic, and total energies using three-dimensional energy-framework analyses. The dispersion energy dominates in crystal packing. To better understand the properties of matc, electrostatic potential (ESP) and frontier molecular orbitals (FMO) were also calculated and discussed. Experimental and calculation results suggested that amino and carboxyl groups can participate in various inter- and intra-interactions.

scholarly journals Synthesis, characterization and single crystal X-ray analysis of azobenzene-4, 4′-dicarbonyl chloride

2018 ◽  
Vol 6 (2) ◽  
pp. 132-136
Author(s):  
Pramod Kumar Yadav
Keyword(s):  
Molecular Structure ◽  
Single Crystal ◽  
Elemental Analysis ◽  
Title Compound ◽  
Crystal And Molecular Structure ◽  
Molecular Aggregation ◽  
X Ray Diffraction ◽  
Secondary Interaction ◽  
Triclinic Crystal System ◽  
X Ray

The title compound azobenzene-4, 4′-dicarbonyl chloride has been synthesized in distilled dichlomethane and characterized by elemental analysis (C, H, N), IR and NMR (1H & 13C) studies. The crystal and molecular structure was further confirmed using single crystal X-ray diffraction analysis. It was crystallized in triclinic crystal system with space group P-1. The centrosymmetrically related molecules held together via C–H---O secondary interaction result in molecular aggregation of the compound.  Int. J. Appl. Sci. Biotechnol. Vol 6(2): 132-136

scholarly journals Substituent Effect on AIE Mechanism of Two Coumarin Derivatives: Uncommon TICT Fluorescence in Aggregation State

2022 ◽  
Author(s):  
Qiao Li ◽  
Yang Zhao ◽  
Zhigang Niu ◽  
Enju Wang
Keyword(s):  
Intramolecular Charge Transfer ◽  
Knoevenagel Condensation ◽  
Crystal Packing ◽  
Coumarin Derivatives ◽  
Dual Fluorescence ◽  
X Ray Diffraction ◽  
Aggregation State ◽  
X Ray ◽  
Hydrogen Bond Interactions ◽  
Salicylaldehyde Derivatives

Abstract Two coumarin derivatives, 7-diethylamino-3-(4-nitrophenyl)coumarin (DNC) and 7-hydroxy-3-(4-nitrophenyl)coumarin (HNC), were synthesized via Knoevenagel condensation of salicylaldehyde derivatives with 4-nitrophenylacetonitrile and then cyclization reaction. Both of them were characterized by single-crystal X-ray diffraction. The molecules of DNC are stacked via π-π interaction, while the hydrogen bond interactions instead of π-π interaction were observed in the crystal packing of HNC. Both of DNC and HNC showed solvatochromic properties and aggregation-induced emission (AIE) activities, but the AIE characteristics of them were entirely different. HNC exhibited an AIE phenomenon as the result of the restriction of twisted intramolecular charge transfer (TICT), while DNC emited peculiar dual fluorescence which was assigned to the emission based on the inhibition of TICT state formation and the emission from the TICT state respectively.

Structural variety of clofaziminium salts: effect of the counter-ion on clofaziminium conformation and crystal packing

2019 ◽  
Vol 75 (4) ◽  
pp. 674-686 ◽  
Author(s):  
Laurie Bodart ◽  
Nikolay Tumanov ◽  
Johan Wouters
Keyword(s):  
Steric Hindrance ◽  
Terephthalic Acid ◽  
Crystal Packing ◽  
Drug Resistant ◽  
X Ray Diffraction ◽  
Dihydroxybenzoic Acid ◽  
Hydrogen Bond Interactions ◽  
Resistant Tuberculosis ◽  
Counter Ions ◽  
Energy Penalty

Clofazimine is a water-insoluble antimycobacterial agent gaining attention as a treatment for multi-drug resistant and extensively drug-resistant tuberculosis. Novel salts of clofazimine are reported with fumaric, succinic, 2,4-dihydroxybenzoic and terephthalic acids and with saccharin. The salt structures were obtained by single-crystal X-ray diffraction. The salts with 2,4-dihydroxybenzoic acid and with saccharin are solvated (methanol and acetonitrile, respectively). The reaction of clofazimine with terephthalic acid led to two salt cocrystals, one solvated and one non-solvated. These new clofaziminium salts are compared with the currently known ones in terms of crystal packing and clofazimine/ium conformation. Clofaziminium hydrogen succinate presents isostructurality with clofaziminium hydrogen malonate, an already described salt. In the structure of clofaziminium terephthalate terephthalic acid salt cocrystal, solvent evaporation leads to packing and hydrogen-bonding modifications. In all the new structures, the clofaziminium conformation is quite well conserved and steric hindrance is observed around the protonated site. Conformational optimization of clofaziminium reveals that this steric-hindrance energy penalty is compensated for by hydrogen-bond interactions with the salt counter-ions.

Hydrogen bonding in the crystal structures of the adducts between 1-phenyl-3,5-dimethylpyrazole with oxalic and perchloric acids

1984 ◽  
Vol 62 (4) ◽  
pp. 725-728 ◽  
Author(s):  
J. Zukerman-Schpector ◽  
E. E. Castellano ◽  
G. Oliva ◽  
A. C. Massabni ◽  
A. Derbli Pinto
Keyword(s):  
Crystal Structures ◽  
Proton Donor ◽  
Proton Acceptor ◽  
Strong Hydrogen Bond ◽  
Full Matrix ◽  
X Ray ◽  
Space Groups ◽  
Cell Dimensions ◽  
R Factors ◽  
Positively Charged

The crystal structures of the title compounds have been determined from diffractometric X-ray data and refined by full-matrix least-squares to final R factors of 0.057 and 0.071 for the oxalic and perchloric adducts respectively.The space groups and cell dimensions are: (oxalic) C2/c, a = 16.516(3), b = 11.685(2), c = 12.587(3) Å, β = 107.11(2)° with Z = 4; (perchloric) Pbca, a = 16.204(3), b = 15.329(6), c = 10.296(3) Å with Z = 8.In both structures the complex is stabilized by a strong hydrogen bond between the N(2) of the 1-phenyl-3,5-dimethylpyrazole (PDMP) group and an oxygen of the acid. In the oxalic adduct the PDMP group is neutral and the N(2) atom acts as a proton acceptor, while in the perchloric complex the PDMP group is positively charged with the N(2) atom acting as a proton donor.

2-[1-(3-Aminophenyl)ethylidene]propanedinitrile

2007 ◽  
Vol 63 (11) ◽  
pp. o4316-o4316
Author(s):  
Qingfang Cheng ◽  
Xingyou Xu ◽  
Changyong Zong ◽  
Huiling Feng
Keyword(s):  
Hydrogen Bond ◽  
Title Compound ◽  
Crystal Packing ◽  
Amino Groups ◽  
Bond Lengths ◽  
Hydrogen Bond Interactions ◽  
Compound C ◽  
Cyano Groups

In the title compound, C11H9N3, all bond lengths and angles are normal. The crystal packing is stabilized by intermolecular N—H...N hydrogen-bond interactions involving the H atoms of the amino groups and N atoms of the cyano groups.

scholarly journals 7-Iodo-5-aza-7-deazaguanine ribonucleoside: crystal structure, physical properties, base-pair stability and functionalization

2020 ◽  
Vol 76 (5) ◽  
pp. 513-523
Author(s):  
Dasharath Kondhare ◽  
Simone Budow-Busse ◽  
Constantin Daniliuc ◽  
Frank Seela
Keyword(s):  
Base Pair ◽  
Crystal Packing ◽  
Donor Site ◽  
Proton Donor ◽  
Proton Acceptor ◽  
Acceptor Site ◽  
Base Pairs ◽  
Purine Base ◽  
Value Differences ◽  
Ribose Moiety

The positional change of nitrogen-7 of the RNA constituent guanosine to the bridgehead position-5 leads to the base-modified nucleoside 5-aza-7-deazaguanosine. Contrary to guanosine, this molecule cannot form Hoogsteen base pairs and the Watson–Crick proton donor site N3—H becomes a proton-acceptor site. This causes changes in nucleobase recognition in nucleic acids and has been used to construct stable `all-purine' DNA and DNA with silver-mediated base pairs. The present work reports the single-crystal X-ray structure of 7-iodo-5-aza-7-deazaguanosine, C10H12IN5O5 (1). The iodinated nucleoside shows an anti conformation at the glycosylic bond and an N conformation (O4′-endo) for the ribose moiety, with an antiperiplanar orientation of the 5′-hydroxy group. Crystal packing is controlled by interactions between nucleobase and sugar moieties. The 7-iodo substituent forms a contact to oxygen-2′ of the ribose moiety. Self-pairing of the nucleobases does not take place. A Hirshfeld surface analysis of 1 highlights the contacts of the nucleobase and sugar moiety (O—H...O and N—H...O). The concept of pK-value differences to evaluate base-pair stability was applied to purine–purine base pairing and stable base pairs were predicted for the construction of `all-purine' RNA. Furthermore, the 7-iodo substituent of 1 was functionalized with benzofuran to detect motional constraints by fluorescence spectroscopy.

scholarly journals Synthesis, crystal structure and Hirshfeld surface analysis of 2-(perfluorophenyl)acetamide in comparison with some related compounds

2022 ◽  
Vol 78 (1) ◽  
Author(s):  
Anton P. Novikov ◽  
Alexey A. Bezdomnikov ◽  
Mikhail S. Grigoriev ◽  
Konstantin E. German
Keyword(s):  
Surface Analysis ◽  
Title Compound ◽  
Crystal Packing ◽  
Hirshfeld Surface ◽  
Hirshfeld Surface Analysis ◽  
Double Layers ◽  
X Ray Diffraction ◽  
Compound C ◽  
Hirshfeld Surfaces ◽  
Related Compounds

The molecular and crystal structures of the title compound, C8H4F5NO, were examined by single-crystal X-ray diffraction and Hirshfeld surface analysis. The title compound was synthesized by a new method at the interface of aqueous solutions of LiOH and pentafluorophenylacetonitrile. In the crystal, hydrogen bonds and π–halogen interactions connect the molecules into double layers. Analysis of the Hirshfeld surface showed that the most important contributions to the crystal packing are made by F...F (30.4%), C...F/F...C (22.9%), O...H/H...O (14.9%), H...F/F...H (14.0%) and H...H (10.2%) contacts. The Hirshfeld surfaces of analogues of the title compound were compared and the effect of perfluorination on the crystal packing was shown.

scholarly journals Synthesis and structure of (E)-N-(4-methoxyphenyl)-2-[4-(3-oxo-3-phenylprop-1-en-1-yl)phenoxy]acetamide

2021 ◽  
Vol 77 (2) ◽  
pp. 184-189
Author(s):  
Cong Nguyen Tien ◽  
Trung Vu Quoc ◽  
Dat Nguyen Dang ◽  
Giang Le Duc ◽  
Luc Van Meervelt
Keyword(s):  
Title Compound ◽  
Crystal Packing ◽  
Asymmetric Unit ◽  
X Ray Diffraction ◽  
X Ray ◽  
H Nmr ◽  
Hydrogen Bonding Interactions ◽  
Hirshfeld Analysis ◽  
Phenyl Rings ◽  
C Nmr

The title compound N-(4-methoxyphenyl)-2-[4-(3-oxo-3-phenylprop-1-en-1-yl)phenoxy]acetamide, C24H21NO4, was prepared from reaction of N-(4-methoxyphenyl)-2-chloroacetamide and (E)-3-(4-hydroxyphenyl)-1-phenylprop-2-en-1-one, which was obtained from the reaction of 4-hydroxybenzaldehyde and acetophenone. The structure of the title compound was determined by IR, 1H-NMR, 13C-NMR and HR–MS spectroscopic data and further characterized by single-crystal X-ray diffraction. The asymmetric unit contains four molecules, each displaying an E-configuration of the C=C bond. The dihedral angle between the phenyl rings in each molecule varies between 14.9 (2) and 45.8 (2)°. In the crystal, C—H...O hydrogen-bonding interactions link the molecules into chains running along the [001] direction. In addition, C—H...π interactions further stabilize the crystal packing. A Hirshfeld analysis indicates that the most important contributions to the surface contacts are from H...H (43.6%), C...H/H...C (32.1%) and O...H/H...O (18.1%) interactions.

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