scholarly journals Invariom-model refinement and Hirshfeld surface analysis of well-ordered solvent-free dibenzo-21-crown-7

2017 ◽  
Vol 73 (9) ◽  
pp. 654-659 ◽  
Author(s):  
Dennis Wiedemann ◽  
Julia Kohl
Keyword(s):  
Crystal Structure ◽  
Interaction Energy ◽  
Surface Analysis ◽  
Crown Ethers ◽  
Three Dimensional ◽  
Crystal Structure Analysis ◽  
Hirshfeld Surface ◽  
Solvent Free ◽  
Hirshfeld Surface Analysis ◽  
Dimensional Structure

Crown ethers and their supramolecular derivatives are well-known chelators and scavengers for a variety of cations, most notably heavier alkali and alkaline-earth ions. Although they are widely used in synthetic chemistry, available crystal structures of uncoordinated and solvent-free crown ethers regularly suffer from disorder. In this study, we present the X-ray crystal structure analysis of well-ordered solvent-free crystals of dibenzo-21-crown-7 (systematic name: dibenzo[b,k]-1,4,7,10,13,16,19-heptaoxacycloheneicosa-2,11-diene, C22H28O7). Because of the quality of the crystal and diffraction data, we have chosen invarioms, in addition to standard independent spherical atoms, for modelling and briefly discuss the different refinement results. The electrostatic potential, which is directly deducible from the invariom model, and the Hirshfeld surface are analysed and complemented with interaction-energy computations to characterize intermolecular contacts. The boat-like molecules stack along the a axis and are arranged as dimers of chains, which assemble as rows to form a three-dimensional structure. Dispersive C—H...H—C and C—H...π interactions dominate, but nonclassical hydrogen bonds are present and reflect the overall rather weak electrostatic influence. A fingerprint plot of the Hirshfeld surface summarizes and visualizes the intermolecular interactions. The insight gained into the crystal structure of dibenzo-21-crown-7 not only demonstrates the power of invariom refinement, Hirshfeld surface analysis and interaction-energy computation, but also hints at favourable conditions for crystallizing solvent-free crown ethers.

scholarly journals Crystal structure and Hirshfeld surface analysis of 2-amino-3-hydroxypyridin-1-ium 6-methyl-2,2,4-trioxo-2H,4H-1,2,3-oxathiazin-3-ide

2020 ◽  
Vol 76 (4) ◽  
pp. 572-575
Author(s):  
Sevgi Kansiz ◽  
Md. Serajul Haque Faizi ◽  
Tansu Merve Aydin ◽  
Necmi Dege ◽  
Hasan Icbudak ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Surface Analysis ◽  
Crystal Packing ◽  
Three Dimensional ◽  
Hirshfeld Surface ◽  
Hirshfeld Surface Analysis ◽  
Dimensional Structure ◽  
Asymmetric Unit ◽  
Compound C ◽  
Anions And Cations

The asymmetric unit of the title compound, C5H7N2O+·C4H4NO4S−, contains one cation and one anion. The 6-methyl-2,2,4-trioxo-2H,4H-1,2,3-oxathiazin-3-ide anion adopts an envelope conformation with the S atom as the flap. In the crystal, the anions and cations are held together by N—H...O, N—H...N, O—H...O and C—H...O hydrogen bonds, thus forming a three-dimensional structure. The Hirshfeld surface analysis and fingerprint plots reveal that the crystal packing is dominated by O...H/H...O (43.1%) and H...H (24.2%) contacts.

scholarly journals Crystal structure and Hirshfeld surface analysis of (E)-4-{[2-(4-hydroxybenzoyl)hydrazin-1-ylidene]methyl}pyridin-1-ium nitrate

2018 ◽  
Vol 74 (3) ◽  
pp. 323-327
Author(s):  
Mir Abolfazl Naziri ◽  
Ertan Şahin ◽  
Tuncer Hökelek
Keyword(s):  
Crystal Structure ◽  
Hydrogen Bonds ◽  
Surface Analysis ◽  
Crystal Packing ◽  
Three Dimensional ◽  
Hirshfeld Surface ◽  
Hirshfeld Surface Analysis ◽  
Dimensional Structure ◽  
Nitrate Anion ◽  
Base Salt

The asymmetric unit of the title aroyl hydrazone Schiff base salt, C13H12N3O2+·N O3−, consists of one molecular cation in the keto tautomeric form, adopting anEconfiguration with respect to the azomethine bond, and one nitrate anion. The two units are linkedviaan N—H...O hydrogen bond. The molecule overall is non-planar, with the pyridinium and benzene rings being inclined to each other by 4.21 (4)°. In the crystal, cations and anions are linkedviaintermolecular O—H...O and bifurcated N—H...O hydrogen bonds, forming a two-dimensional network parallel to (101). These networks are further linked by C—H...O hydrogen bonds, forming slabs parallel to (101). The slabs are linked by offset π–π interactions, involving the benzene and pyridinium rings of adjacent slabs [intercentroid distance = 3.610 (2) Å], forming a three-dimensional structure. The Hirshfeld surface analysis of the crystal structure indicates that the most important contributions for the crystal packing are from H...O/O...H (45.1%), H...H (19.3%), H...C/C...H (14.5%), H...N/N...H (7.9%) and C...C (6.0%) interactions.

scholarly journals Synthesis, crystal structure and Hirshfeld surface analysis of 2-chloro-3-[(E)-(2-phenylhydrazinylidene)methyl]quinoline

2019 ◽  
Vol 75 (7) ◽  
pp. 964-968
Author(s):  
Soufiane Akhramez ◽  
Abderrafia Hafid ◽  
Mostafa Khouili ◽  
Mohamed Saadi ◽  
Lahcen El Ammari ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Surface Analysis ◽  
Phenyl Ring ◽  
Crystal Packing ◽  
Condensation Reaction ◽  
Three Dimensional ◽  
Ring System ◽  
Hirshfeld Surface ◽  
Hirshfeld Surface Analysis ◽  
Dimensional Structure

A new quinoline-based hydrazone, C16H12ClN3, was synthesized by a condensation reaction of 2-chloro-3-formylquinoline with phenylhydrazine. The quinoline ring system is essentially planar (r.m.s. deviation = 0.012 Å), and forms a dihedral angle of 8.46 (10)° with the phenyl ring. The molecule adopts anEconfiguration with respect to the central C=N bond. In the crystal, molecules are linked by a C—H...π-phenyl interaction, forming zigzag chains propagating along the [10\overline{3}] direction. The N—H hydrogen atom does not participate in hydrogen bonding but is directed towards the phenyl ring of an adjacent molecule, so linking the chainsviaweak N—H...π interactions to form of a three-dimensional structure. The Hirshfeld surface analysis of the crystal structure indicates that the most important contributions to the crystal packing are from H...H (35.5%), C...H/H...C (33.7%), Cl...H/H...Cl (12.3%), N...H/H...N (9.5%) contacts.

scholarly journals An Unexpected Trinuclear Cobalt(II) Complex Based on a Half-Salamo-Like Ligand: Synthesis, Crystal Structure, Hirshfeld Surface Analysis, Antimicrobial and Fluorescent Properties

Crystals ◽  
2019 ◽  
Vol 9 (8) ◽  
pp. 408 ◽  
Author(s):  
Ruo-Yan Li ◽  
Xiao-Xin An ◽  
Juan-Li Wu ◽  
You-Peng Zhang ◽  
Wen-Kui Dong
Keyword(s):  
Crystal Structure ◽  
Surface Analysis ◽  
Three Dimensional ◽  
Antimicrobial Activities ◽  
Hirshfeld Surface ◽  
Hirshfeld Surface Analysis ◽  
Fluorescent Properties ◽  
X Ray ◽  
X Ray Crystallography ◽  
Elemental Analyses

An unexpected trinuclear Co(II) complex, [Co3(L2)2(μ-OAc)2(CH3OH)2]·2CH3OH (H2L2 = 4,4′-dibromo-2,2′-[ethylenedioxybis(nitrilomethylidyne)]diphenol) constructed from a half-Salamo-based ligand (HL1 = 2-[O-(1-ethyloxyamide)]oxime-4-bromophenol) and Co(OAc)2·4H2O, has been synthesized and characterized by elemental analyses, infrared spectra (IR), UV-Vis spectra, X-ray crystallography and Hirshfeld surface analysis. The Co(II) complex contains three Co(II) atoms, two completely deprotonated (L2)2− units, two bridged acetate molecules, two coordinated methanol molecules and two crystalline methanol molecules, and finally, a three-dimensional supramolecular structure with infinite extension was formed. Interestingly, during the formation of the Co(II) complex, the ligand changed from half-Salamo-like to a symmetrical single Salamo-like ligand due to the bonding interactions of the molecules. In addition, the antimicrobial activities of HL1 and its Co(II) complex were also investigated.

scholarly journals A cinnamaldehyde Schiff base ofS-(4-methylbenzyl) dithiocarbazate: crystal structure, Hirshfeld surface analysis and computational study

2017 ◽  
Vol 73 (4) ◽  
pp. 543-549 ◽  
Author(s):  
Enis Nadia Md Yusof ◽  
Mohamed I. M. Tahir ◽  
Thahira B. S. A. Ravoof ◽  
Sang Loon Tan ◽  
Edward R. T. Tiekink
Keyword(s):  
Crystal Structure ◽  
Hydrogen Bonds ◽  
Surface Analysis ◽  
Mirror Symmetry ◽  
Computational Study ◽  
Three Dimensional ◽  
Hirshfeld Surface ◽  
Hirshfeld Surface Analysis ◽  
Hydrogen Atoms ◽  
Benzyl Substituent

The title dithiocarbazate ester (I), C18H18N2S2[systematic name: (E)-4-methylbenzyl 2-[(E)-3-phenylallylidene]hydrazinecarbodithioate, comprises an almost planar central CN2S2residue [r.m.s. deviation = 0.0131 Å]. The methylene(tolyl-4) group forms a dihedral angle of 72.25 (4)° with the best plane through the remaining non-hydrogen atoms [r.m.s. deviation = 0.0586 Å] so the molecule approximates mirror symmetry with the 4-tolyl group bisected by the plane. The configuration about both double bonds in the N—N=C—C=C chain isE; the chain has an alltransconformation. In the crystal, eight-membered centrosymmetric thioamide synthons, {...HNCS}2, are formedviaN—H...S(thione) hydrogen bonds. Connections between the dimersviaC—H...π interactions lead to a three-dimensional architecture. A Hirshfeld surface analysis shows that (I) possesses an interaction profile similar to that of a closely related analogue with anS-bound benzyl substituent, (II). Computational chemistry indicates the dimeric species of (II) connectedviaN—H...S hydrogen bonds is about 0.94 kcal mol−1more stable than that in (I).

Intermolecular interactions of proton transfer compounds: synthesis, crystal structure and Hirshfeld surface analysis

2015 ◽  
Vol 71 (4) ◽  
pp. 427-436 ◽  
Author(s):  
Amani Direm ◽  
Angela Altomare ◽  
Anna Moliterni ◽  
Nourredine Benali-Cherif
Keyword(s):  
Crystal Structure ◽  
Proton Transfer ◽  
Surface Analysis ◽  
Three Dimensional ◽  
Hirshfeld Surface ◽  
Hirshfeld Surface Analysis ◽  
X Ray Diffraction ◽  
Hydrogen Bonding Interactions ◽  
Proton Transfer Compounds ◽  
Close Contacts

Three new proton transfer compounds, [2-ammonio-5-methylcarboxybenzene perchlorate (1), (C8H10NO2+·ClO4−), 4-(ammoniomethyl)carboxybenzene nitrate (2), (C8H10NO2+·NO3−), and 4-(ammoniomethyl)carboxybenzene perchlorate (3), (C8H10NO2+·ClO4−)], have been synthesized, their IR modes of vibrations have been assigned and their crystal structures studied by means of single-crystal X-ray diffraction. Their asymmetric units consist of one cation and one anion for both compounds (1) and (2). However, the crystal structure of compound (3) is based on a pair of cations and a pair of anions in its asymmetric unit. The three-dimensional Hirshfeld surface analysis and the two-dimensional fingerprint maps revealed that the three structures are dominated by H...O/O...H and H...H contacts. The strongest hydrogen-bonding interactions are associated with O—H...O and N—H...O constituting the highest fraction of approximately 50%, followed by those of the H...H type contributing 20%. Other close contacts are also present, including weak C...H/H...C contacts (with about 10%).

scholarly journals Crystal structure and Hirshfeld surface analysis of 3,4-dihydro-2H-anthra[1,2-b][1,4]dioxepine-8,13-dione

2020 ◽  
Vol 76 (4) ◽  
pp. 576-580
Author(s):  
Sofia Zazouli ◽  
Mohammed Chigr ◽  
Ahmed Jouaiti ◽  
Nathalie Kyritsakas ◽  
El Mostafa Ketatni
Keyword(s):  
Crystal Structure ◽  
Solid State ◽  
Surface Analysis ◽  
Three Dimensional ◽  
Ring System ◽  
Hirshfeld Surface ◽  
Hirshfeld Surface Analysis ◽  
Supramolecular Network ◽  
Compound C ◽  
The Mean

The title compound, C17H12O4, was synthesized from the dye alizarin. The dihedral angle between the mean plane of the anthraquinone ring system (r.m.s. deviation = 0.039 Å) and the dioxepine ring is 16.29 (8)°. In the crystal, the molecules are linked by C—H...O hydrogen bonds, forming sheets lying parallel to the ab plane. The sheets are connected through π–π and C=O...π interactions to generate a three-dimensional supramolecular network. Hirshfeld surface analysis was used to investigate intermolecular interactions in the solid-state: the most important contributions are from H...H (43.0%), H...O/O...H (27%), H...C/C...H (13.8%) and C...C (12.4%) contacts.

scholarly journals Crystal structure, Hirshfeld surface analysis and interaction energy calculation of 1-decyl-2,3-dihydro-1H-benzimidazol-2-one

2021 ◽  
Vol 77 (5) ◽  
pp. 559-563
Author(s):  
Younesse Ait Elmachkouri ◽  
Asmaa Saber ◽  
Ezaddine Irrou ◽  
Bushra Amer ◽  
Joel T. Mague ◽  
...  
Keyword(s):  
Hydrogen Bonds ◽  
Surface Analysis ◽  
Crystal Packing ◽  
Three Dimensional ◽  
Hirshfeld Surface ◽  
Hirshfeld Surface Analysis ◽  
Dimensional Structure ◽  
Energy Calculation ◽  
Model C ◽  
Hydrogen Bond Energies

The title molecule, C17H26N2O, adopts an L-shaped conformation, with the straight n-decyl chain positioned nearly perpendicular to the dihydrobenzimidazole moiety. The dihydrobenzimidazole portion is not quite planar as there is a dihedral angle of 1.20 (6)° between the constituent planes. In the crystal, N—H...O hydrogen bonds form inversion dimers, which are connected into the three-dimensional structure by C—H...O hydrogen bonds and C—H...π(ring) interactions. Hirshfeld surface analysis indicates that the most important contributions for the crystal packing are from H...H (75.9%), H...C/C...H (12.5%) and H...O/O...H (7.0%) interactions. Based on computational chemistry using the CE–B3LYP/6–31 G(d,p) energy model, C—H...O hydrogen bond energies are −74.9 (for N—H...O) and −42.7 (for C—H...O) kJ mol−1.

scholarly journals Crystal structure and Hirshfeld surface analysis of 4-{[(anthracen-9-yl)methyl]amino}benzoic acid dimethylformamide monosolvate

2020 ◽  
Vol 76 (5) ◽  
pp. 728-731
Author(s):  
Adeeba Ahmed ◽  
Aiman Ahmad ◽  
Musheer Ahmad ◽  
Valentina A. Kalibabchuk
Keyword(s):  
Crystal Structure ◽  
Surface Analysis ◽  
Three Dimensional ◽  
Hirshfeld Surface ◽  
Hirshfeld Surface Analysis ◽  
Supramolecular Network ◽  
Compound C ◽  
Hydrogen Bonding Interactions ◽  
The Mean ◽  
Dimethylformamide Solution

The title compound, C22H17NO2·C3H7NO, was synthesized by condensation of an aromatic aldehyde with a secondary amine and subsequent reduction. It was crystallized from a dimethylformamide solution as a monosolvate, C22H17NO2·C3H7NO. The aromatic molecule is non-planar with a dihedral angle between the mean planes of the aniline moiety and the methyl anthracene moiety of 81.36 (8)°. The torsion angle of the Caryl—CH2—NH—Caryl backbone is 175.9 (2)°. The crystal structure exhibits a three-dimensional supramolecular network, resulting from hydrogen-bonding interactions between the carboxylic OH group and the solvent O atom as well as between the amine functionality and the O atom of the carboxylic group and additional C—H...π interactions. Hirshfeld surface analysis was performed to quantify the intermolecular interactions.

scholarly journals Bis{4-methylbenzyl 2-[4-(propan-2-yl)benzylidene]hydrazinecarbodithioato-κ2N2,S}nickel(II): crystal structure and Hirshfeld surface analysis

2017 ◽  
Vol 73 (3) ◽  
pp. 397-402 ◽  
Author(s):  
Enis Nadia Md Yusof ◽  
Thahira B. S. A. Ravoof ◽  
Mohamed I. M. Tahir ◽  
Mukesh M. Jotani ◽  
Edward R. T. Tiekink
Keyword(s):  
Crystal Structure ◽  
Surface Analysis ◽  
Chelate Ring ◽  
Three Dimensional ◽  
Hirshfeld Surface ◽  
Hirshfeld Surface Analysis ◽  
Planar Geometry ◽  
Π Interactions ◽  
Centroid Distance ◽  
Square Planar

The complete molecule of the title hydrazine carbodithioate complex, [Ni(C19H21N2S2)2], is generated by the application of a centre of inversion. The NiIIatom isN,S-chelated by two hydrazinecarbodithioate ligands, which provide atrans-N2S2donor set that defines a distorted square-planar geometry. The conformation of the five-membered chelate ring is an envelope with the NiIIatom being the flap atom. In the crystal,p-tolyl-C—H...π(benzene-iPr),iPr-C—H...π(p-tolyl) and π–π interactions [betweenp-tolyl rings with inter-centroid distance = 3.8051 (12) Å] help to consolidate the three-dimensional architecture. The analysis of the Hirshfeld surface confirms the importance of H-atom contacts in establishing the packing.

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