Unusual hydrogen bond patterns contributing to supramolecular assembly: conformational study, Hirshfeld surface analysis and density functional calculations of a new steroid derivative

CrystEngComm ◽  
2014 ◽  
Vol 16 (33) ◽  
pp. 7802-7814 ◽  
Author(s):  
Alberto Ruiz ◽  
Hiram Pérez ◽  
Cercis Morera-Boado ◽  
Luis Almagro ◽  
Cecilia C. P. da Silva ◽  
...  
Keyword(s):  
Hydrogen Bond ◽  
Surface Analysis ◽  
Density Functional Calculations ◽  
Density Functional ◽  
Supramolecular Assembly ◽  
Hirshfeld Surface ◽  
Hirshfeld Surface Analysis ◽  
Conformational Study ◽  
X Ray ◽  
Steroid Derivative

Structural and conformational study of a new steroid derivative using X-ray and density functional calculations.

scholarly journals 4-[(Benzylamino)carbonyl]-1-methylpyridinium halogenide salts: X-ray diffraction study and Hirshfeld surface analysis

2022 ◽  
Vol 78 (2) ◽  
Author(s):  
Svitlana V. Shishkina ◽  
Anna M. Shaposhnik ◽  
Vyacheslav M. Baumer ◽  
Vitalii V. Rudiuk ◽  
Igor A. Levandovskiy
Keyword(s):  
Hydrogen Bond ◽  
Diffraction Study ◽  
Surface Analysis ◽  
Intermolecular Interactions ◽  
Hirshfeld Surface ◽  
Hirshfeld Surface Analysis ◽  
X Ray Diffraction ◽  
Space Group ◽  
X Ray ◽  
Different Types

Two salts of 4-[(benzylamino)carbonyl]-1-methylpyridinium (Am) with chloride (C14H15N2O+·Cl−) and bromide (C14H15N2O+·Br−) anions were studied and compared with the iodide salt. AmCl crystallizes in the centrosymmetric space group P21/n while AmBr and AmI form crystals in the Sohncke space group P212121. Crystals of AmBr are isostructural to those of AmI. The cation and anion are bound by an N–H...Hal hydrogen bond. Hirshfeld surface analysis was used to compare different types of intermolecular interactions in the three structures under study.

scholarly journals (2E)-2-[1-(1,3-Benzodioxol-5-yl)-3-(1H-imidazol-1-yl)propylidene]-N-(2-chlorophenyl)hydrazine carboxamide: Synthesis, X-ray Structure, Hirshfeld Surface Analysis, DFT Calculations, Molecular Docking and Antifungal Profile

Crystals ◽  
2019 ◽  
Vol 9 (2) ◽  
pp. 82 ◽  
Author(s):  
Reem Al-Wabli ◽  
Alwah Al-Ghamdi ◽  
Suchindra Aswathy ◽  
Hazem Ghabbour ◽  
Mohamed Al-Agamy ◽  
...  
Keyword(s):  
Molecular Docking ◽  
Surface Analysis ◽  
Density Functional ◽  
Fungal Infections ◽  
Immune Deficiency Syndrome ◽  
Hirshfeld Surface ◽  
Hirshfeld Surface Analysis ◽  
X Ray ◽  
Title Molecule

Life-threatening fungal infections accounts for a major global health burden especially for individuals suffering from cancer, acquired immune deficiency syndrome (AIDS), or autoimmune diseases. (2E)-2-[1-(1,3-Benzodioxol-5-yl)-3-(1H-imidazol-1-yl)propylidene]-N-(2-chlorophenyl)hydrazinecarboxamide has been synthesized and characterized using various spectroscopic tools to be evaluated as a new antifungal agent. The (E)-configuration of the imine moiety of the title molecule has been unequivocally identified with the aid of single crystal X-ray analysis. The molecular structure of compound 4 was crystallized in the monoclinic, P21/c, a = 8.7780 (6) Å, b = 20.5417 (15) Å, c = 11.0793 (9) Å, β = 100.774 (2)°, V = 1962.5 (3) Å3, and Z = 4. Density functional theory computations have thoroughly explored the electronic characteristics of the title molecule. Moreover, molecular docking studies and Hirshfeld surface analysis were also executed on the title compound 4. The in vitro antifungal potential of the target compound was examined against four different fungal strains.

scholarly journals Synthesis, X-ray crystal structure, Hirshfeld surface analysis and DFT studies of (E)-N′-(2-bromobenzylidene)-4-methylbenzohydrazide

2019 ◽  
Vol 75 (2) ◽  
pp. 109-114 ◽  
Author(s):  
Azhagan Ganapathi Anitha ◽  
Chidambaram Arunagiri ◽  
Annamalai Subashini
Keyword(s):  
Surface Analysis ◽  
Density Functional ◽  
Energy Gap ◽  
Hirshfeld Surface ◽  
Basis Set ◽  
Hirshfeld Surface Analysis ◽  
Functional Theory ◽  
X Ray ◽  
Homo Lumo ◽  
Good Support

The title molecule, C15H13BrN2O, displays a trans configuration with respect to the C=N double bond. The dihedral angle between the bromo- and methyl-substituted benzene rings is 16.1 (3)°. In the crystal, molecules are connected by N—H...O and weak C—H...O hydrogen bonds, forming R 2 1(6) ring motifs and generating chains along the a–axis direction. The optimized structure generated theoretically via density functional theory (DFT) using standard B3LYP functional and 6–311 G(d,p) basis-set calculations renders good support to the experimental data. The HOMO–LUMO behaviour was elucidated to determine the energy gap. The intermolecular interactions were quantified and analysed using Hirshfeld surface analysis.

C–H···O and C–H···X (X = Cl/Br) hydrogen bond tuned supramolecular assembly: a combined X-ray powder diffraction and Hirshfeld surface analysis

2014 ◽  
Vol 29 (3) ◽  
pp. 280-288 ◽  
Author(s):  
Dipak K. Hazra ◽  
Soumen Ghosh ◽  
Paramita Chatterjee ◽  
Somnath Ghosh ◽  
Monika Mukherjee ◽  
...  
Keyword(s):  
Surface Analysis ◽  
Powder Diffraction ◽  
Crystal Packing ◽  
Three Dimensional ◽  
Supramolecular Assembly ◽  
Hirshfeld Surface ◽  
Hirshfeld Surface Analysis ◽  
Powder Diffraction Data ◽  
X Ray ◽  
Surface Areas

Crystal structures of N-(2-chlorophenyl) acetamide (1) and phenyl (2-bromomethyl) benzoate (2) have been determined from laboratory X-ray powder diffraction data. In addition to intermolecular N–H···O and C–H···O hydrogen bonds, the crystal packing in (1) and (2) exhibits weak C–H···Cl/Br interactions, which facilitate formation of three-dimensional architectures. Hirshfeld surface analysis of compounds (1), (2), and a few related chloro- and bromo-phenyl derivatives retrieved from the CSD indicates that 83–97% of Hirshfeld surface areas in this class of compounds are due to H···H, H···π, H···O, and H···Cl/Br contacts.

2,4-Diamino-6-phenyl-1,3,5-triazin-1-ium nitrate: intriguing crystal structure with high Z′/Z′′ and hydrogen bond numbers and Hirshfeld surface analysis of intermolecular interactions

CrystEngComm ◽  
2021 ◽  
Author(s):  
Nicoleta Caimac ◽  
Elena Melnic ◽  
Diana Chisca ◽  
Marina S. Fonari
Keyword(s):  
Crystal Structure ◽  
Hydrogen Bond ◽  
Surface Analysis ◽  
Intermolecular Interactions ◽  
Title Compound ◽  
Ionic Species ◽  
Hirshfeld Surface ◽  
Hirshfeld Surface Analysis ◽  
Asymmetric Unit ◽  
Space Group

The title compound crystallises in the triclinic centrosymmetric space group P1̄ with an intriguing high number of crystallographically unique binary salt-like adducts (Z′ = 8) and a total number of ionic species (Z′′ = 16) in the asymmetric unit.

scholarly journals Crystal structure from X-ray powder diffraction data, DFT-D calculation, Hirshfeld surface analysis, and energy frameworks of (RS)-trichlormethiazide

2022 ◽  
Vol 78 (2) ◽  
Author(s):  
Robert A. Toro ◽  
Analio Dugarte-Dugarte ◽  
Jacco van de Streek ◽  
José Antonio Henao ◽  
José Miguel Delgado ◽  
...  
Keyword(s):  
Hydrogen Bonds ◽  
Surface Analysis ◽  
Powder Diffraction ◽  
Diffraction Data ◽  
Electrostatic Interactions ◽  
Hirshfeld Surface ◽  
Hirshfeld Surface Analysis ◽  
Powder Diffraction Data ◽  
X Ray ◽  
Π Interactions

The structure of racemic (RS)-trichlormethiazide [systematic name: (RS)-6-chloro-3-(dichloromethyl)-1,1-dioxo-3,4-dihydro-2H-1λ6,2,4-benzothiadiazine-7-sulfonamide], C8H8Cl3N3O4S2 (RS-TCMZ), a diuretic drug used in the treatment of oedema and hypertension, was determined from laboratory X-ray powder diffraction data using DASH [David et al. (2006). J. Appl. Cryst. 39, 910–915.], refined by the Rietveld method with TOPAS-Academic [Coelho (2018). J. Appl. Cryst. 51, 210–218], and optimized using DFT-D calculations. The extended structure consists of head-to-tail dimers connected by π–π interactions which, in turn, are connected by C—Cl...π interactions. They form chains propagating along [101], further connected by N—H...O hydrogen bonds to produce layers parallel to the ac plane that stack along the b-axis direction, connected by additional N—H...O hydrogen bonds. The Hirshfeld surface analysis indicates a major contribution of H...O and H...Cl interactions (32.2 and 21.7%, respectively). Energy framework calculations confirm the major contribution of electrostatic interactions (E elec) to the total energy (E tot). A comparison with the structure of S-TCMZ is also presented.

scholarly journals Crystal structure, Hirshfeld surface analysis and interaction energy and DFT studies of 2-(2,3-dihydro-1H-perimidin-2-yl)-6-methoxyphenol

2020 ◽  
Vol 76 (5) ◽  
pp. 605-610
Author(s):  
Ballo Daouda ◽  
Nanou Tiéba Tuo ◽  
Tuncer Hökelek ◽  
Kangah Niameke Jean-Baptiste ◽  
Kodjo Charles Guillaume ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Surface Analysis ◽  
Density Functional ◽  
Energy Gap ◽  
Crystal Packing ◽  
Hirshfeld Surface ◽  
Van Der Waals Interactions ◽  
Hirshfeld Surface Analysis ◽  
Functional Theory ◽  
Compound C

The title compound, C18H16N2O2, consists of perimidine and methoxyphenol units, where the tricyclic perimidine unit contains a naphthalene ring system and a non-planar C4N2 ring adopting an envelope conformation with the NCN group hinged by 47.44 (7)° with respect to the best plane of the other five atoms. In the crystal, O—HPhnl...NPrmdn and N—HPrmdn...OPhnl (Phnl = phenol and Prmdn = perimidine) hydrogen bonds link the molecules into infinite chains along the b-axis direction. Weak C—H...π interactions may further stabilize the crystal structure. The Hirshfeld surface analysis of the crystal structure indicates that the most important contributions for the crystal packing are from H...H (49.0%), H...C/C...H (35.8%) and H...O/O...H (12.0%) interactions. Hydrogen bonding and van der Waals interactions are the dominant interactions in the crystal packing. Computational chemistry indicates that in the crystal, the O—HPhnl...NPrmdn and N—HPrmdn...OPhnl hydrogen-bond energies are 58.4 and 38.0 kJ mol−1, respectively. Density functional theory (DFT) optimized structures at the B3LYP/ 6–311 G(d,p) level are compared with the experimentally determined molecular structure in the solid state. The HOMO–LUMO behaviour was elucidated to determine the energy gap.

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