The search for formal electrostatic effects on molecular conformation and crystal packing: crystal structure of 2,2′′-disubstituted (HversusPPh2) 1,1′-(1,2-phenylene)bis(3-methyl-1H-imidazol-3-ium) bis(trifluoromethanesulfonate)

2016 ◽  
Vol 72 (3) ◽  
pp. 198-202
Author(s):  
Carine Duhayon ◽  
Yves Canac ◽  
Laurent Dubrulle ◽  
Carine Maaliki ◽  
Remi Chauvin
Keyword(s):  
Crystal Structure ◽  
Electrostatic Interactions ◽  
Molecular Conformation ◽  
Crystal Packing ◽  
Relative Orientation ◽  
Electron Delocalization ◽  
Electrostatic Effects ◽  
Conformational Freedom ◽  
The Stability ◽  
Bond Character

Electrostatic interactions between localized integral charges make the stability and structure of highly charged small and rigid organics intriguing. Can σ/π-electron delocalization compensate reduced conformational freedom by lowering the repulsion between identical charges? The crystal structure of the title salt, C14H16N42+·2CF3SO3−, (2), is described and compared with that of the 2,2′′-bis(diphenylphosphanyl) derivative, (4). The conformations of the dications and their interactions with neighbouring trifluoromethanesulfonate anions are first analyzed from the standpoint of formal electrostatic effects. Neither cation exhibits any geometrical strain induced by the intrinsic repulsion between the positive charges. In contrast, the relative orientation of the imidazolium rings [i.e. antifor (2) andsynfor (4)] is controlled by different configurations of the interactions with the closest trifluoromethanesulfonate anions. The long-range arrangement is also found to be specific: beyond the formal electrostatic packing, C—H...O and C—H...F contacts have no definite `hydrogen-bond' character but allow the delineation of layers, which are either pleated or flat in the packing of (2) or (4), respectively.

scholarly journals Insight from energy surfaces: structure prediction by lattice energy exploration

2014 ◽  
Vol 70 (a1) ◽  
pp. C28-C28
Author(s):  
Graeme Day
Keyword(s):  
Crystal Structure ◽  
Structure Prediction ◽  
Crystal Packing ◽  
Lattice Energy ◽  
Organic Crystals ◽  
Crystal Structure Prediction ◽  
Stability Order ◽  
The Stability ◽  
Solid Form ◽  
Energy Surfaces

A long-standing challenge for the application of computational chemistry in the field of crystallography is the prediction of crystal packing, given no more than the chemical bonding of the molecules being crystallised. Recent years have seen significant progress towards reliable crystal structure prediction methods, even for traditionally challenging systems involving flexible molecules and multi-component solids [1]. These methods are based on global searches of the lattice energy surface: a search is performed to locate all possible packing arrangements, and these structures are ranked by their calculated energy [2]. One aim of this lecture is to provide an overview of advances in methods for crystal structure prediction, focussing on molecular organic crystals, and highlighting strategies that are being explored to extend the reach of these methods to more complex systems. A second aim is to discuss the range applications of crystal structure prediction calculations, which have traditionally included solid form screening, particularly of pharmaceutically active molecules, and structure determination. As energy models become more reliable at correctly ranking the stability order of putative structures, and the timescale required for structure searching decreases, crystal structure prediction has the potential for the discovery of novel molecular materials with targeted properties. Prospects for computer-guided discovery of materials will be discussed.

Structure–property relationships of molecular shape and orientation with compression and expansion of xylitol

2021 ◽  
Vol 77 (2) ◽  
Author(s):  
Fatemeh Safari ◽  
Andrzej Katrusiak
Keyword(s):  
Crystal Structure ◽  
Molecular Conformation ◽  
Orthorhombic Phase ◽  
Molecular Shape ◽  
Structure Property ◽  
Uniform Compression ◽  
Structure Property Relationships ◽  
Compression And Expansion ◽  
Strain Relationship ◽  
The Stability

Easy crystallization distinguishes xylitol from other sugars, which usually condense into a syrup from aqueous solution. Although two polymorphs, i.e. metastable monoclinic and high-density orthorhombic, have been reported for xylitol, only the latter is in practical use. Under high pressure, the same orthorhombic phase has been obtained by both isothermal and isochoric recrystallization. The stability of the orthorhombic xylitol phase to 5.0 GPa has been correlated with a uniform compression of all hydrogen bonds and some flexibility of the molecular conformation, which cushion the pressure-induced local strains. The anisotropic compressibility of xylitol and its thermal expansion are consistent with the rule of inverse effects of pressure and temperature. This inverse strain relationship has been correlated with the dimensions and orientation of xylitol molecules in the crystal structure.

scholarly journals Crystal structure of 2-benzamido-N-(2,2-diethoxyethyl)benzamide

2015 ◽  
Vol 71 (3) ◽  
pp. o214-o215
Author(s):  
Abdelaaziz Ouahrouch ◽  
Moha Taourirte ◽  
Hassan B. Lazrek ◽  
Joachim W. Engels ◽  
Michael Bolte
Keyword(s):  
Crystal Structure ◽  
Hydrogen Bond ◽  
Dihedral Angle ◽  
Title Compound ◽  
Molecular Conformation ◽  
Crystal Packing ◽  
Aromatic Rings ◽  
Peptide Bonds ◽  
Axis Direction ◽  
Compound C

In the title compound, C20H24N2O4, both peptide bonds adopt atransconfiguration with respect to the —N—H and —C=O groups. The dihedral angle between the aromatic rings is 53.58 (4)°. The molecular conformation is stabilized by an intramolecular N—H...O hydrogen bond. The crystal packing is characterized by zigzag chains of N—H...O hydrogen-bonded molecules running along theb-axis direction.

scholarly journals Crystal structure and Hirshfeld surface analysis of (E)-3-(2-chlorophenyl)-1-(2,5-dichlorothiophen-3-yl)prop-2-en-1-one

2019 ◽  
Vol 75 (2) ◽  
pp. 124-128
Author(s):  
T. N. Sanjeeva Murthy ◽  
Zeliha Atioğlu ◽  
Mehmet Akkurt ◽  
M. K. Veeraiah ◽  
Ching Kheng Quah ◽  
...  
Keyword(s):  
Molecular Structure ◽  
Crystal Structure ◽  
Surface Analysis ◽  
Title Compound ◽  
Molecular Conformation ◽  
Crystal Packing ◽  
Hirshfeld Surface ◽  
Face To Face ◽  
Compound C ◽  
Benzene Rings

The molecular structure of the title compound, C13H7Cl3OS, consists of a 2,5- dichlorothiophene ring and a 2-chlorophenyl ring linked via a prop-2-en-1-one spacer. The dihedral angle between the 2,5-dichlorothiophene and 2-chlorophenyl rings is 9.69 (12)°. The molecule has an E configuration about the C=C bond and the carbonyl group is syn with respect to the C=C bond. The molecular conformation is stabilized by two intramolecular C—H...Cl contacts and one intramolecular C—H...O contact, forming S(5)S(5)S(6) ring motifs. In the crystal, the molecules are linked along the a-axis direction through van der Waals forces and along the b axis by face-to-face π-stacking between the thiophene rings and between the benzene rings of neighbouring molecules, forming corrugated sheets lying parallel to the bc plane. The intermolecular interactions in the crystal packing were further analysed using Hirshfield surface analysis, which indicates that the most significant contacts are Cl...H/ H...Cl (28.6%), followed by C...H/H...C (11.9%), C...C (11.1%), H...H (11.0%), Cl...Cl (8.1%), O...H/H...O (8.0%) and S...H/H...S (6.6%).

Quantitative Crystal Structure Analysis of (E)-1-[(2-Chloro-1,3-thiazol-5-yl)methyl]-3-methyl-2-nitroguanidine

2014 ◽  
Vol 2014 ◽  
pp. 1-8 ◽  
Author(s):  
Dhananjay Dey ◽  
Chetan S. Shripanavar ◽  
Kaushik Banerjee ◽  
Deepak Chopra
Keyword(s):  
Crystal Structure ◽  
Intermolecular Interactions ◽  
Molecular Conformation ◽  
Crystal Packing ◽  
Lattice Energy ◽  
Crystal Structure Analysis ◽  
Hirshfeld Surface ◽  
Biologically Active ◽  
Molecular Formula ◽  
Periodic Calculations

The crystal structure of a biologically active (E)-1-[(2-chloro-1,3-thiazol-5-yl)methyl)]-3-methyl-2-nitroguanidine with molecular formula C6H8N5O2ClS has been investigated based on the molecular conformation and the supramolecular packing in terms of intermolecular interactions involving N–H⋯O, N–H⋯N, and C–H⋯O–N (nitro group), C–H⋯N (thiazol) hydrogen bonds, offset π–π stacking, C–H⋯π and N(–NO2)⋯C=N intermolecular interactions. Furthermore, a short C–Cl⋯O–N contact is also present which contributes towards the crystal packing. The lattice energy of the title compound has been calculated using the PIXEL approach (the Coulomb-London-Pauli (CLP) model) and compared with periodic calculations performed using CRYSTAL09. In addition, Hirshfeld surface analysis and fingerprint plots provide a platform for the evaluation of the contribution of different intermolecular interactions towards the packing behaviour.

N-(5-Chloro-3-methyl-1-phenylpyrazol-4-ylcarbonyl)-N′-(4-methylphenyl)thiourea

2007 ◽  
Vol 63 (11) ◽  
pp. o4287-o4287 ◽  
Author(s):  
Hai-Tang Du ◽  
Ming Lu ◽  
Wei-Yi Zhou ◽  
Li-Li Sun
Keyword(s):  
Crystal Structure ◽  
Hydrogen Bonds ◽  
Title Compound ◽  
Molecular Conformation ◽  
Crystal Packing ◽  
Pyrazole Ring ◽  
Dihedral Angles ◽  
Compound C

The crystal structure of the title compound, C19H17ClN4OS, has been determined in order to elucidate the molecular conformation. The pyrazole ring makes dihedral angles of 74.3 (3)° and 2.9 (3)° with the phenyl and tolyl rings, respectively; these two six-membered rings are twisted by 71.6 (3)° with respect to each other. The crystal packing of the title compound is stabilized by intramolcular N—H...O and intermolcular N—H...S hydrogen bonds.

scholarly journals Crystal structure of (E)-2-(tert-butylamino)-4-(tert-butylimino)naphthalen-1(4H)-one

2018 ◽  
Vol 74 (7) ◽  
pp. 973-976 ◽  
Author(s):  
Guy Lamoureux ◽  
Mónica Alvarado-Rojas ◽  
Leslie W. Pineda
Keyword(s):  
Crystal Structure ◽  
Hydrogen Bond ◽  
Carbonyl Group ◽  
Title Compound ◽  
Tautomeric Form ◽  
Molecular Conformation ◽  
Crystal Packing ◽  
Van Der Waals Interactions ◽  
Compound C ◽  
Intramolecular Hydrogen

The title compound, C18H24N2O, is the first example of a naphthoquinone imine derivative isolated in the 4-imine/2-amine tautomeric form having bulky alkyl substituents at the N atoms. The molecular conformation is stabilized by an intramolecular hydrogen bond between the amine and a carbonyl group and by London attraction between the two tert-butyl groups. Only van der Waals interactions were identified in the crystal packing.

scholarly journals Crystal structure and Hirshfeld surface analysis of 4-(4-methylbenzyl)-6-phenylpyridazin-3(2H)-one

2019 ◽  
Vol 75 (9) ◽  
pp. 1352-1356 ◽  
Author(s):  
Said Daoui ◽  
Emine Berrin Cinar ◽  
Fouad El Kalai ◽  
Rafik Saddik ◽  
Khalid Karrouchi ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Dihedral Angle ◽  
Surface Analysis ◽  
Molecular Conformation ◽  
Crystal Packing ◽  
Hirshfeld Surface ◽  
Hirshfeld Surface Analysis ◽  
Two Dimensional ◽  
Pyridazine Ring ◽  
Ring Motif

In this paper, we describe the synthesis of a new dihydro-2H-pyridazin-3-one derivative. The molecule, C18H16N2O, is not planar; the benzene and pyridazine rings are twisted with respect to each other, making a dihedral angle of 11.47 (2)°, and the toluene ring is nearly perpendicular to the pyridazine ring, with a dihedral angle of 89.624 (1)°. The molecular conformation is stabilized by weak intramolecular C—H...N contacts. In the crystal, pairs of N—H...O hydrogen bonds link the molecules into inversion dimers with an R 2 2(8) ring motif. The intermolecular interactions were investigated using Hirshfeld surface analysis and two-dimensional (2D) fingerprint plots, revealing that the most important contributions for the crystal packing are from H...H (56.6%), H...C/C...H (22.6%), O...H/H...O (10.0%) and N...C/C...N (3.5%) interactions.

scholarly journals Crystal structure and Hirshfeld surface analysis of (2E)-3-(2,4-dichlorophenyl)-1-(2,5-dichlorothiophen-3-yl)prop-2-en-1-one

2018 ◽  
Vol 74 (9) ◽  
pp. 1201-1205 ◽  
Author(s):  
T. N. Sanjeeva Murthy ◽  
Zeliha Atioğlu ◽  
Mehmet Akkurt ◽  
C. S. Chidan Kumar ◽  
M. K. Veeraiah ◽  
...  
Keyword(s):  
Molecular Structure ◽  
Crystal Structure ◽  
Surface Analysis ◽  
Title Compound ◽  
Molecular Conformation ◽  
Crystal Packing ◽  
Hirshfeld Surface ◽  
Face To Face ◽  
Compound C ◽  
Benzene Rings

The molecular structure of the title compound, C13H6Cl4OS, consists of a 2,5-dichlorothiophene ring and a 2,4-dichlorophenyl ring linked via a prop-2-en-1-one spacer. The dihedral angle between the 2,5-dichlorothiophene ring and the 2,4-dichlorophenyl ring is 12.24 (15)°. The molecule has an E configuration about the C=C bond and the carbonyl group is syn with respect to the C=C bond. The molecular conformation is stabilized by intramolecular C—H...Cl contacts, producing S(6) and S(5) ring motifs. In the crystal, the molecules are linked along the a-axis direction through face-to-face π-stacking between the thiophene rings and the benzene rings of the molecules in zigzag sheets lying parallel to the bc plane along the c axis. The intermolecular interactions in the crystal packing were further analysed using Hirshfield surface analysis, which indicates that the most significant contacts are Cl...H/ H...Cl (20.8%), followed by Cl...Cl (18.7%), C...C (11.9%), Cl...S/S...Cl (10.9%), H...H (10.1%), C...H/H...C (9.3%) and O...H/H...O (7.6%).

scholarly journals Synthesis and Crystal Structure of 1-(4-Nitrobenzyl)-3-allyl-1H-benzo[d]imidazol-2(3H)-one

2013 ◽  
Vol 2013 ◽  
pp. 1-8
Author(s):  
Dounia Belaziz ◽  
Santiago V. Luis ◽  
Youssef Kandri Rodi ◽  
Inés Martí ◽  
Vicente Martí-Centelles
Keyword(s):  
Crystal Structure ◽  
Solid State ◽  
Intermolecular Interactions ◽  
Crystal Packing ◽  
Van Der Waals Interactions ◽  
Monoclinic Space Group ◽  
Synthesis And Crystal Structure ◽  
Cell Parameters ◽  
Computational Calculations ◽  
The Stability

A functionalized benzimidazole, 1-(4-nitrobenzyl)-3-allyl-1H-benzo[d]imidazol-2(3H)-one, has been synthesized, and the crystal structure was determined and analyzed. This compound crystallizes in the monoclinic, space group P21/n (number 14)cwith cell parameters,a=7.12148(8) Å,b=16.12035(17) Å,c=13.04169(17) Å,β=93.3043(11),V=1494.71(3) Å3, andDcalc= 1.375 g/mm3. The solid state geometry is stabilized by intermolecularπ–πinteractions along with the van der Waals interactions which contribute to the stability of the crystal packing. Computational calculations have been used to properly understand the main intermolecular interactions present in the crystal.

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