Structural and Computational Analysis of Organic Fluorine-Mediated Interactions in Controlling the Crystal Packing of Tetrafluorinated Secondary Amides in the Presence of Weak C–H···O═C Hydrogen Bonds

2022 ◽  
Author(s):  
Labhini Singla ◽  
Hare Ram Yadav ◽  
Angshuman R. Choudhury
Keyword(s):  
Hydrogen Bonds ◽  
Computational Analysis ◽  
Crystal Packing ◽  
Organic Fluorine ◽  
Secondary Amides

Quantitative characterization of new supramolecular synthons involving fluorine atoms in the crystal structures of di- and tetrafluorinated benzamides

2017 ◽  
Vol 73 (5) ◽  
pp. 805-819 ◽  
Author(s):  
Pradip Kumar Mondal ◽  
Hare Ram Yadav ◽  
Angshuman Roy Choudhury ◽  
Deepak Chopra
Keyword(s):  
Solid State ◽  
Hydrogen Bonds ◽  
Crystal Packing ◽  
Topological Analysis ◽  
Quantitative Characterization ◽  
Supramolecular Synthons ◽  
Molecular Scaffold ◽  
Substituted Benzamides ◽  
Organic Fluorine

Strong hydrogen bonds play a significant role in crystal packing. In particular, the involvement of interactions involving fluorine in controlling the crystal packing requires appropriate attention, especially in the presence of other strong hydrogen bonds. In the present study, a detailed quantitative assessment has been performed of the nature, energetics and topological properties derived from the electron density in model compounds based on fluorinated benzamides (a total of 46 fluorine-substituted benzamides containing multiple fluorine atoms) in the solid state. The primary motivation in the design of such molecules is to enhance the acidity of the interacting H atoms in the presence of an increasing number of F atoms on the molecular scaffold, resulting in increased propensity towards the formation of intermolecular interactions involving organic fluorine. This exercise has resulted in the identification of new and frequently occurring supramolecular synthons involving F atoms in the packing of molecules in the solid state. The energetics associated with short and directional intermolecular Csp2—H...F—Csp2interactions with significantly high electrostatic contributions is noteworthy, and the topological analysis reveals the bonding character of these ubiquitous interactions in crystal packing in addition to the presence of Csp2—F...F—Csp2contacts.

scholarly journals 3-(Adamantan-1-yl)-4-benzyl-1H-1,2,4-triazole-5(4H)-thione

2014 ◽  
Vol 70 (7) ◽  
pp. o766-o767 ◽  
Author(s):  
Fatmah A. M. Al-Omary ◽  
Hazem A. Ghabbour ◽  
Ali A. El-Emam ◽  
C. S. Chidan Kumar ◽  
Hoong-Kun Fun
Keyword(s):  
Hydrogen Bonds ◽  
Dihedral Angle ◽  
Title Compound ◽  
Crystal Packing ◽  
Triazole Ring ◽  
Axis Direction ◽  
Π Interactions ◽  
Compound C ◽  
Supramolecular Chains

The title compound, C19H23N3S, is a functionalized triazoline-3-thione derivative. The benzyl ring is almost normal to the planar 1,2,4-triazole ring (r.m.s. deviation = 0.007 Å) with a dihedral angle of 86.90 (7)°. In the crystal, molecules are linked by pairs of N—H...S hydrogen bonds, forming inversion dimers that encloseR22(8) loops. The crystal packing is further stabilized by weak C—H...π interactions that link adjacent dimeric units into supramolecular chains extending along thea-axis direction.

scholarly journals N′-(3-Hydroxybenzylidene)-4-methylbenzohydrazide

2012 ◽  
Vol 68 (6) ◽  
pp. o1816-o1816
Author(s):  
Ji-Lai Liu ◽  
Ming-Hui Sun ◽  
Jing-Jun Ma
Keyword(s):  
Hydrogen Bonds ◽  
Dihedral Angle ◽  
Title Compound ◽  
Crystal Packing ◽  
Aromatic Rings ◽  
Π Interactions ◽  
Compound C ◽  
Centroid Distance ◽  
Benzene Rings

The title compound, C15H14N2O2, was obtained from the reaction of 3-hydroxybenzaldhyde and 4-methylbenzohydrazide in methanol. In the molecule, the benzene rings form a dihedral angle of 2.9 (3)°. In the crystal, N—H...O and O—H...O hydrogen bonds link the molecules into layers parallel to (101). The crystal packing also exhibits π–π interactions between the aromatic rings [centroid–centroid distance = 3.686 (4) Å].

scholarly journals Tetrahydroberberine, a pharmacologically active naturally occurring alkaloid

2015 ◽  
Vol 71 (4) ◽  
pp. 262-265 ◽  
Author(s):  
Subramanya Pingali ◽  
James P. Donahue ◽  
Florastina Payton-Stewart
Keyword(s):  
Hydrogen Bonds ◽  
Crystal Packing ◽  
Racemic Mixture ◽  
Inversion Center ◽  
Intermolecular Hydrogen Bonds ◽  
Naturally Occurring ◽  
Pharmacologically Active

Tetrahydroberberine (systematic name: 9,10-dimethoxy-5,8,13,13a-tetrahydro-6H-benzo[g][1,3]benzodioxolo[5,6-a]quinolizine), C20H21NO4, a widely distributed naturally occurring alkaloid, has been crystallized as a racemic mixture about an inversion center. A bent conformation of the molecule is observed, with an angle of 24.72 (5)° between the arene rings at the two ends of the reduced quinolizinium core. The intermolecular hydrogen bonds that play an apparent role in crystal packing are 1,3-benzodioxole –CH2...OCH3and –OCH3...OCH3interactions between neighboring molecules.

Ethylammonium saccharinate

2006 ◽  
Vol 62 (5) ◽  
pp. o1800-o1801
Author(s):  
Zi-Liang Wang ◽  
Lin-Heng Wei ◽  
Ming-Xue Li ◽  
Jing-Ping Wang
Keyword(s):  
Hydrogen Bonds ◽  
Title Compound ◽  
Crystal Packing ◽  
Two Dimensional ◽  
Asymmetric Unit ◽  
Framework Structure ◽  
Compound C

The asymmetric unit of the title compound, C2H8N+·C7H4NO3S−, contains a saccharinate anion and a protonated ethylamine cation. Intermolecular N—H...O hydrogen bonds link these ions into a two-dimensional framework structure. The crystal packing is further stabilized by weak intermolecular C—H...O hydrogen bonds

scholarly journals 4-Acetylpiperazinium picrate

2014 ◽  
Vol 70 (6) ◽  
pp. o717-o718 ◽  
Author(s):  
Channappa N. Kavitha ◽  
Manpreet Kaur ◽  
Jerry P. Jasinski ◽  
Hemmige S. Yathirajan
Keyword(s):  
Hydrogen Bonds ◽  
Benzene Ring ◽  
Intermolecular Interactions ◽  
Crystal Packing ◽  
Chair Conformation ◽  
Centroid Distance ◽  
Sheet Structure ◽  
Benzene Rings ◽  
Π Stacking Interaction ◽  
The Mean

In the title salt, C6H13N2O+·C6H2N3O7−(systematic name: 4-acetylpiperazin-1-ium 2,4,6-trinitrophenolate), the piperazin-1-ium ring has a slightly distorted chair conformation. In the picrate anion, the mean planes of the twoo-NO2andp-NO2groups are twisted with respect to the benzene ring by 15.0 (2), 68.9 (4) and 4.4 (3)°, respectively. In the crystal, N—H...O hydrogen bonds are observed, linking the ions into an infinite chain along [010]. In addition, weak cation–anion C—H...O intermolecular interactions and a weak π–π stacking interaction between the benzene rings of the anions, with an inter-centroid distance of 3.771 (8) Å, help to stabilize the crystal packing, giving an overall sheet structure lying parallel to (100). Disorder was modelled for one of the O atoms in one of theo-NO2groups over two sites with an occupancy ratio of 0.57 (6):0.43 (6).

Undecacarbonyl(pyridine-κN)-tetrahedro-tetrairidium(4Ir—Ir)

2006 ◽  
Vol 62 (4) ◽  
pp. m838-m840 ◽  
Author(s):  
Alvaro J. Pardey ◽  
Manoa A. Moreno ◽  
Matthias Lutz ◽  
Matti Haukka ◽  
Reinaldo Atencio
Keyword(s):  
Hydrogen Bonds ◽  
Title Compound ◽  
Triple Bond ◽  
Crystal Packing ◽  
Pyridine Molecule ◽  
Carbonyl Groups ◽  
Carbonyl Ligands

The title compound, [Ir4(C5H5N)(CO)11], shows a tetrahedral Ir4 core in which each Ir atom is linked to three other Ir atoms and three terminal carbonyl groups, except for one Ir atom, which carries two carbonyl ligands and one N-coordinated pyridine molecule. An intricate set of C—H...π hydrogen bonds stabilizes the crystal packing, where the π-systems are those of the C[triple-bond]O bonds of the carbonyl ligands.

1-Benzoyl-3-(4-chlorophenyl)thiourea

2006 ◽  
Vol 62 (4) ◽  
pp. o1419-o1420 ◽  
Author(s):  
M. Khawar Rauf ◽  
Amin Badshah ◽  
Ulrich Flörke ◽  
Aamer Saeed
Keyword(s):  
Crystal Structure ◽  
Hydrogen Bonds ◽  
Aromatic Ring ◽  
Dihedral Angle ◽  
Title Compound ◽  
Crystal Packing ◽  
Compound C

In the crystal structure of the title compound, C14H11ClN2OS, the dihedral angle between the two aromatic ring planes is 43.93 (6)°. The crystal packing shows dimers formed by intermolecular N—H...S hydrogen bonds which are stacked along [100].

scholarly journals Diaquabis(2,2′-bi-1H-imidazole)manganese(II) benzene-1,4-dicarboxylate

2012 ◽  
Vol 68 (6) ◽  
pp. m829-m829
Author(s):  
Lining Yang ◽  
Yanxiang Zhi ◽  
Jiahui Hei ◽  
Yanqing Miao
Keyword(s):  
Hydrogen Bonds ◽  
Title Compound ◽  
Crystal Packing ◽  
Octahedral Geometry ◽  
Distorted Octahedral Geometry ◽  
Water Molecules ◽  
Asymmetric Unit ◽  
Π Interactions ◽  
Centroid Distance ◽  
Distorted Octahedral

The asymmetric unit of the title compound, [Mn(C6H6N4)2(H2O)2](C8H4O4), contains one-half each of the centrosymmetric cation and anion. The MnII atom is coordinated by four N atoms [Mn—N = 2.2168 (14) and 2.2407 (14) Å] from two 2,2′-biimidazole ligands and two water molecules [Mn—O = 2.2521 (14) Å] in a distorted octahedral geometry. Intermolecular N—H...O and O—H...O hydrogen bonds consolidate the crystal packing, which also exhibits π–π interactions between five-membered rings, with a centroid–centroid distance of 3.409 (2) Å.

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