Structural characterization and theoretical calculations of the monohydrate of the 1:2 cocrystal salt formed from acriflavine and 3,5-dinitrobenzoic acid

2021 ◽  
Vol 77 (2) ◽  
pp. 116-122
Author(s):  
Maria Marczak ◽  
Kinga Biereg ◽  
Beata Zadykowicz ◽  
Artur Sikorski
Keyword(s):  
Hydrogen Bonds ◽  
Water Molecule ◽  
Intermolecular Interactions ◽  
Structural Characterization ◽  
Theoretical Calculations ◽  
Lattice Energy ◽  
Monoclinic Space Group ◽  
X Ray Diffraction ◽  
Porous Organic Framework ◽  
Organic Framework

The synthesis and structural characterization of the monohydrated 1:2 cocrystal salt of acriflavine with 3,5-dinitrobenzoic acid [systematic name: 3,6-diamino-10-methylacridin-10-ium 3,5-dinitrobenzoate–3,5-dinitrobenzoic acid–water (1/1/1), C14H14N3 +·C7H3N2O6 −·C7H4N2O6·H2O] are reported. Single-crystal X-ray diffraction measurements show that the title solvated monohydrate salt crystalizes in the monoclinic space group P21 with one acriflavine cation, a 3,5-dinitrobenzoate anion, a 3,5-dinitrobenzoic acid molecule and a water molecule in the asymmetric unit. The neutral and anionic forms of 3,5-dinitrobenzoic acid are linked via O—H...O hydrogen bonds to form a monoanionic dimer. Neighbouring monoanionic dimers of 3,5-dinitrobenzoic acid are linked by nitro–nitro N—O...N and nitro–acid N—O...π intermolecular interactions to produce a porous organic framework. The acriflavine cations are linked with carboxylic acid molecules directly via amine–carboxy N—H...O, amine–nitro N—H...O and acriflavine–carboxy C—H...O hydrogen bonds, and carboxy–acriflavine C—O...π, nitro–acriflavine N—O...π and acriflavine–nitro π–π interactions, or through the water molecule by amino–water N—H...O and water–carboxy O—H...O hydrogen bonds, and are located in the voids of the porous organic framework. The intermolecular interactions were studied using the CrystalExplorer program to provide information about the interaction energies and the dispersion, electrostatic, polarization and repulsion contributions to the lattice energy.

scholarly journals Crystal Structure, Spectroscopy, SEM Analysis, and Computational Studies of N-(1,3-Dioxoisoindolin-2yl)benzamide

2015 ◽  
Vol 2015 ◽  
pp. 1-6
Author(s):  
Hakan Bülbül ◽  
Yavuz Köysal ◽  
Necmi Dege ◽  
Sümeyye Gümüş ◽  
Erbil Ağar
Keyword(s):  
Crystal Structure ◽  
Ir Spectroscopy ◽  
Hydrogen Bonds ◽  
Theoretical Calculations ◽  
Sem Analysis ◽  
Monoclinic Space Group ◽  
Computational Studies ◽  
X Ray Diffraction ◽  
Ethanolic Solution ◽  
X Ray

The compound N-(1,3-dioxoisoindolin-2yl)benzamide, C15H10N2O3, was prepared by the heating of an ethanolic solution of 2-hydroxy-1H-isoindole-1,3(2H)-dione and 4-chloroaniline. The product was characterised using a combination of IR spectroscopy, SEM, and single crystal X-ray diffraction techniques. In addition to the experimental analysis, theoretical calculations were used to investigate the crystal structure in order to compare experimental and theoretical values. The X-ray diffraction analysis shows that the compound crystallises in the monoclinic space group P21/c with the geometric parameters of a=13.5324(11) Å, b=9.8982(8) Å, c=9.7080(8) Å, and β=95.425(6)°. The crystal structure is held together by a network of N-H⋯O hydrogen bonds involving the carboxamide group.

scholarly journals Structure of (E)-N-((5-Nitrothiophen-2-YL)Methylene)-3-(Trifluoromethyl)Aniline

2014 ◽  
Vol 70 (a1) ◽  
pp. C997-C997
Author(s):  
Özlem Deveci ◽  
Sümeyye Gümüş ◽  
Erbil Agˇar
Keyword(s):  
Molecular Structure ◽  
Hydrogen Bonds ◽  
Title Compound ◽  
Density Functional ◽  
Theoretical Calculations ◽  
Molecular Geometry ◽  
Basis Set ◽  
Monoclinic Space Group ◽  
X Ray Diffraction ◽  
X Ray

The Schiff base compound, C12H7N2O2F3S, has been synthesized and characterized by IR, UV-Vis, 1H-NMR, 13C-NMR and single-crystal X-ray diffraction (XRD) and elemental analysis. The compound, an Ortep-3 [1] view of which is shown in Fig. 1, crystallizes in the monoclinic space group P-1 with a= 7.5700(11) Å, b= 12.8280(16) Å, c= 13.0170(16) Å, α= 89.295(10)o, β= 88.691(11)o, γ= 82.246(11)o and Z=4 in the unit cell. The molecular structure is stabilized by C-H...O and C-H...F intramolecular hydrogen bonds and molecules are linked through intermolecular C-H...O and C-H...F type hydrogen bonds and C-H...Cg (π-ring) interaction. The molecular geometry from X-ray determination of the title compound in the ground state has been compared using the Hartre-Fock (HF) and density functional theory (DFT/B3LYP) [2] with 6-31G(d) [3] basis set. The results of the optimized molecular structure are exhibited and compared with the experimental X-ray diffraction. To determine conformational flexibility, molecular energy profile of the title compound was obtained by B3LYP with the 6-31G(d) basis set calculations with respect to selected degree of torsional freedom, which was varied from –1800to +1800in steps of 100. In addition, molecular electrostatic potential (MEP) distribution and frontier molecular orbitals (FMOs) properties of the title molecule were investigated by theoretical calculations at the B3LYP/6-31G (d) level. Figure 1. Ortep 3 diagram of the title compound. Displacement ellipsoids are drawn at the 30% probability level and H atoms are shown as small spheres of arbitrary radii.

Influence of the position of the methyl substituent and N-oxide formation on the geometry and intermolecular interactions of 1-(phenoxyethyl)piperidin-4-ol derivatives

2020 ◽  
Vol 76 (1) ◽  
pp. 30-36 ◽  
Author(s):  
Ewa Żesławska ◽  
Justyna Kalinowska-Tłuścik ◽  
Wojciech Nitek ◽  
Henryk Marona ◽  
Anna M. Waszkielewicz
Keyword(s):  
Hydrogen Bonds ◽  
Intermolecular Interactions ◽  
Crystal Packing ◽  
Piperidine Ring ◽  
Monoclinic Space Group ◽  
Asymmetric Unit ◽  
Methyl Substituent ◽  
X Ray Diffraction ◽  
Oxide Formation ◽  
Space Groups

Aminoalkanol derivatives have attracted much interest in the field of medicinal chemistry as part of the search for new anticonvulsant drugs. In order to study the influence of the methyl substituent and N-oxide formation on the geometry of molecules and intermolecular interactions in their crystals, three new examples have been prepared and their crystal structures determined by X-ray diffraction. 1-[(2,6-Dimethylphenoxy)ethyl]piperidin-4-ol, C15H23NO2, 1, and 1-[(2,3-dimethylphenoxy)ethyl]piperidin-4-ol, C15H23NO2, 2, crystallize in the orthorhombic system (space groups P212121 and Pbca, respectively), with one molecule in the asymmetric unit, whereas the N-oxide 1-[(2,3-dimethylphenoxy)ethyl]piperidin-4-ol N-oxide monohydrate, C15H23NO3·H2O, 3, crystallizes in the monoclinic space group P21/c, with one N-oxide molecule and one water molecule in the asymmetric unit. The geometries of the investigated compounds differ significantly with respect to the conformation of the O—C—C linker, the location of the hydroxy group in the piperidine ring and the nature of the intermolecular interactions, which were investigated by Hirshfeld surface and corresponding fingerprint analyses. The crystal packing of 1 and 2 is dominated by a network of O—H...N hydrogen bonds, while in 3, it is dominated by O—H...O hydrogen bonds and results in the formation of chains.

Salts of purine alkaloids caffeine and theobromine with 2,6-dihydroxybenzoic acid as coformer: structural, theoretical, thermal and spectroscopic studies

2021 ◽  
Vol 77 (11) ◽  
Author(s):  
Mateusz Gołdyn ◽  
Anna Komasa ◽  
Mateusz Pawlaczyk ◽  
Aneta Lewandowska ◽  
Elżbieta Bartoszak-Adamska
Keyword(s):  
Hydrogen Bonds ◽  
Water Solubility ◽  
Theoretical Calculations ◽  
Spectroscopic Studies ◽  
X Ray Diffraction ◽  
Dihydroxybenzoic Acid ◽  
Scanning Calorimetry ◽  
X Ray ◽  
Purine Alkaloids ◽  
Vis Spectroscopy

The study of various forms of pharmaceutical substances with specific physicochemical properties suitable for putting them on the market is one of the elements of research in the pharmaceutical industry. A large proportion of active pharmaceutical ingredients (APIs) occur in the salt form. The use of an acidic coformer with a given structure and a suitable pK a value towards purine alkaloids containing a basic imidazole N atom can lead to salt formation. In this work, 2,6-dihydroxybenzoic acid (26DHBA) was used for cocrystallization of theobromine (TBR) and caffeine (CAF). Two novel salts, namely, theobrominium 2,6-dihydroxybenzoate, C7H9N4O2 +·C7H5O4 − (I), and caffeinium 2,6-dihydroxybenzoate, C8H11N4O2 +·C7H5O4 − (II), were synthesized. Both salts were obtained independently by slow evaporation from solution, by neat grinding and also by microwave-assisted slurry cocrystallization. Powder X-ray diffraction measurements proved the formation of the new substances. Single-crystal X-ray diffraction studies confirmed proton transfer between the given alkaloid and 26DHBA, and the formation of N—H...O hydrogen bonds in both I and II. Unlike the caffeine cations in II, the theobromine cations in I are paired by noncovalent N—H...O=C interactions and a cyclic array is observed. As expected, the two hydroxy groups in the 26DHBA anion in both salts are involved in two intramolecular O—H...O hydrogen bonds. C—H...O and π–π interactions further stabilize the crystal structures of both compounds. Steady-state UV–Vis spectroscopy showed changes in the water solubility of xanthines after ionizable complex formation. The obtained salts I and II were also characterized by theoretical calculations, Fourier-transform IR spectroscopy (FT–IR), thermogravimetric analysis (TGA), differential scanning calorimetry (DSC) and elemental analysis.

Silver(I)-Saccharinato Complexes with 2-(Aminomethyl)pyridine and 2-(2-Aminoethyl)pyridine Ligands: [Ag(sac)(ampy)] and [Ag2(sac)2(μ-aepy)2]

2005 ◽  
Vol 60 (9) ◽  
pp. 978-983 ◽  
Author(s):  
Sevim Hamamci ◽  
Veysel T. Yilmaz ◽  
William T. A. Harrison
Keyword(s):  
Thermal Analysis ◽  
Hydrogen Bonds ◽  
Monoclinic Space Group ◽  
Stacking Interactions ◽  
Coordination Geometry ◽  
X Ray Diffraction ◽  
Triclinic Space Group ◽  
Space Group ◽  
X Ray ◽  
Pyridine Ligands

Two new saccharinato-silver(I) (sac) complexes, [Ag(sac)(ampy)] (1), and [Ag2(sac)2(μ-aepy)2] (2), [ampy = 2-(aminomethyl)pyridine, aepy = 2-(2-aminoethyl)pyridine], have been prepared and characterized by elemental analysis, IR spectroscopy, thermal analysis and single crystal X-ray diffraction. Complexes 1 and 2 crystallize in the monoclinic space group P21/c and triclinic space group P1̄, respectively. The silver(I) ions in both complexes 1 and 2 exhibit a distorted T-shaped AgN3 coordination geometry. 1 consists of individual molecules connected into chains by N-H···O hydrogen bonds. There are two crystallographically distinct dimers in the unit cell of 2 and in each dimer, the aepy ligands act as a bridge between two silver(I) centers, resulting in short argentophilic contacts [Ag1···Ag1 = 3.0199(4) Å and Ag2···Ag2 = 2.9894(4) Å ]. Symmetry equivalent dimers of 2 are connected by N-H···O hydrogen bonds into chains, which are further linked by aromatic π(py)···π(py) stacking interactions into sheets.

Carbacylamidophosphates: Synthethis and Structure of N,N'-Tetramethyl-NM-benzoylphosphoryltriamide and Dimorpholido-N-benzoylphosphorylamide

2000 ◽  
Vol 55 (6) ◽  
pp. 495-498 ◽  
Author(s):  
Katerina E. Gubina ◽  
Vladimir A. Ovchynnikov ◽  
Vladimir M. Amirkhanov ◽  
Viktor V. Skopenkoa ◽  
Oleg V. Shishkinb
Keyword(s):  
Nmr Spectroscopy ◽  
Hydrogen Bonds ◽  
Monoclinic Space Group ◽  
X Ray Diffraction ◽  
Hydrogen Atoms ◽  
Sodium Salts ◽  
Space Group ◽  
X Ray ◽  
Centrosymmetric Dimers ◽  
Oxygen Atoms

N,N′-Tetramethyl-N"-benzoylphosphoryltriamide (I) and dimorpholido-N-benzoylphosphorylamide (II), and their sodium salts Nal, Nall were synthesized and characterized by means of IR and 1H, 31P NMR spectroscopy. The structures of I, II were determined by X-ray diffraction: I monoclinic, space group P2i/c with a = 10.162(3), b= 11.469(4), c = 12.286(4) Å , β = 94.04°, V = 1428.4(8) A 3, Z = 4, p(calcd) = 1.187 g/cm3; II monoclinic, space group C2/c with a = 15.503(4), b = 10.991(3), c = 22.000(6) Å, β = 106.39°, V = 3596.3(17) Å3, Z = 8, p(calcd.) = 1.253 g/cm3. The refinement of the structures converged at R = 0.0425 for I, and R = 0.068 for II. In both structures the molecules are connected into centrosymmetric dimers via hydrogen bonds formed by the phosphorylic oxygen atoms and hydrogen atoms of amide groups.

Combining CDIF and PDF information in problem solving: Crystal structure of a corrosion deposit, hexaaquairon(II) trifluoromethanesulfonate

1999 ◽  
Vol 14 (3) ◽  
pp. 166-170
Author(s):  
J. A. Kaduk
Keyword(s):  
Crystal Structure ◽  
Problem Solving ◽  
Hydrogen Bonds ◽  
Water Molecule ◽  
Powder Diffraction ◽  
Title Compound ◽  
Monoclinic Space Group ◽  
Crystal Data ◽  
Major Phase ◽  
Corrosion Deposit

The title compound was identified as the major phase in a corrosion deposit by indexing its powder pattern, and locating an isostructural vanadium(II) compound in the NIST Crystal Data Identification File. The identity of the compound was confirmed by a Rietveld refinement. Hexaaquairon(II) trifluoromethanesulfonate crystallizes in the monoclinic space group C2/m, with a=18.6415(14), b=6.9291(5), c=6.5938(5) Å, β=104.742(6)°, V=823.68(10) Å3, and Z=2. The structure consists of alternating layers of octahedral hexaaquairon(II) cations and triflate anions. The cations and anions are linked into layers parallel to the bc plane by hydrogen bonds. Each water molecule donates two protons to sulfonate oxygens, and each sulfonate oxygen acts as an acceptor of two protons. A reference powder diffraction pattern is reported.

scholarly journals A new one-dimensional NiIIcoordination polymer with a two-dimensional supramolecular architecture

2017 ◽  
Vol 73 (2) ◽  
pp. 192-195
Author(s):  
Kai-Long Zhong
Keyword(s):  
Hydrogen Bonds ◽  
Water Molecule ◽  
Two Dimensional ◽  
X Ray Diffraction ◽  
Sulfate Ions ◽  
Sulfate Anion ◽  
One Dimensional ◽  
X Ray ◽  
Distorted Octahedral ◽  
Metal Organic

A new one-dimensional NiIIcoordination polymer of 1,3,5-tris(imidazol-1-ylmethyl)benzene, namelycatena-poly[[aqua(sulfato-κO)hemi(μ-ethane-1,2-diol-κ2O:O′)[μ3-1,3,5-tris(1H-imidazol-1-ylmethyl)benzene-κ3N3,N3′,N3′′]nickel(II)] ethane-1,2-diol monosolvate monohydrate], {[Ni(SO4)(C18H18N6)(C2H6O2)0.5(H2O)]·C2H6O2·H2O}n, was synthesized and characterized by elemental analysis, IR spectroscopy and single-crystal X-ray diffraction. The NiIIcation is coordinated by three N atoms of three different 1,3,5-tris(imidazol-1-ylmethyl)benzene ligands, one O atom of an ethane-1,2-diol molecule, by a sulfate anion and a water molecule, forming a distorted octahedral NiN3O3coordination geometry. The tripodal 1,3,5-tris(imidazol-1-ylmethyl)benzene ligands link the NiIIcations, generating metal–organic chains running along the [100] direction. Adjacent chains are further connected by O—H...O hydrogen bonds, resulting in a two-dimensional supermolecular architecture running parallel to the (001) plane. Another water molecule and a second ethane-1,2-diol molecule are non-coordinating and are linked to the coordinating sulfate ionsviaO—H...O hydrogen bonds.

Notizen: Solid State Structure of N,N-Dibenzylhydroxylamine

1995 ◽  
Vol 50 (4) ◽  
pp. 699-701 ◽  
Author(s):  
Norbert W. Mitzel ◽  
Jürgen Riede ◽  
Klaus Angermaier ◽  
Hubert Schmidbaur
Keyword(s):  
Solid State ◽  
Hydrogen Bonds ◽  
Single Crystal ◽  
Unit Cell ◽  
Monoclinic Space Group ◽  
State Structure ◽  
X Ray Diffraction ◽  
Space Group ◽  
Solid State Structure ◽  
X Ray

The solid-state structure of N,N-dibenzylhydroxylamine (1) has been determined by single crystal X-ray diffraction. The compound crystallizes in the monoclinic space group P 21/n with four formula units in the unit cell. N,N-dibenzylhydroxylamine dimerizes to give N2O2H2 sixmembered rings as a result of the formation of two hydrogen bonds O - H ··· N in the solid state.

Exploring concomitant/conformational dimorphism in a difluoro-substituted phosphoramidate derivative

2019 ◽  
Vol 75 (4) ◽  
pp. 451-461 ◽  
Author(s):  
Avantika Hasija ◽  
Deepak Chopra
Keyword(s):  
Hydrogen Bonds ◽  
Intermolecular Interactions ◽  
Crystallization Process ◽  
X Ray Diffraction ◽  
Scanning Calorimetry ◽  
Dispersion Energy ◽  
Torsion Angles ◽  
X Ray ◽  
Electrostatic Contribution ◽  
Distinguished Contribution

The concomitant occurrence of dimorphs of diphenyl (3,4-difluorophenyl)phosphoramidate, C18H14F2NO3P, was observed via a solution-mediated crystallization process with variation in the symmetry-free molecules (Z′). The existence of two forms, i.e. Form I (block, Z′ = 1) and Form II (needle, Z′ = 2), was characterized by single-crystal X-ray diffraction, differential scanning calorimetry and powder X-ray diffraction. Furthermore, a quantitative analysis of the energetics of the different intermolecular interactions was carried out via the energy decomposition method (PIXEL), which corroborates with inputs from the energy framework and looks at the topology of the various intermolecular interactions present in both forms. The unequivocally distinguished contribution of strong N—H...O hydrogen bonds along with other interactions, such as C—H...O, C—H...F, π–π and C—H...π, mapped on the Hirshfeld surface is depicted by two-dimensional fingerprint plots. Apart from the major electrostatic contribution from N—H...O hydrogen bonds, the crystal structures are stabilized by contributions from the dispersion energy. The closely related melting points and opposite trends in the calculated lattice energies are interesting to investigate with respect to the thermodynamic stability of the observed dimorphs. The significant variation in the torsion angles in both forms helps in classifying them in the category of conformational polymorphs.

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