Intermolecular interactions and unexpected isostructurality in the crystal structures of the dichlorobenzaldehyde isomers

2011 ◽  
Vol 67 (5) ◽  
pp. 437-445 ◽  
Author(s):  
Katarzyna A. Solanko ◽  
Andrew D. Bond
Keyword(s):  
Crystal Structures ◽  
Intermolecular Interaction ◽  
Intermolecular Interactions ◽  
Crystallographic Axis ◽  
Stacking Interactions ◽  
Interaction Energies ◽  
Asymmetric Unit ◽  
Consistent Feature ◽  
Whole Molecule Disorder

The crystal structures of the six dichlorobenzaldehyde isomers, four of them newly determined, are analyzed in terms of the geometry and energies of their intermolecular interactions, quantified using the semi-classical density sums (SCDS-PIXEL) method. A consistent feature in all six structures is molecular stacks propagating along a short crystallographic axis of ca 3.8 Å. The stacks have a closely comparable geometry in each isomer, but the interaction energies between stacked molecules are variable on account of the differing relative positions of the Cl substituents. In the majority of the isomers the stacking interactions are the most stabilizing in the structure. Exceptions are the 2,4- and 3,5-isomers, where more stabilizing interactions are made between stacks. In general, the most stabilizing non-stacking intermolecular interactions in the structures are those involving C—H...O contacts. Observed motifs based on Cl...Cl interactions appear to be largely imposed by the constraints of other more stabilizing intermolecular interactions. The isomeric series displays the following noteworthy features: (i) the 2,3- and 2,6-isomers are isostructural despite having different orientations of the Cl and aldehyde functionalities; (ii) the 2,5-isomer exhibits whole-molecule disorder; (iii) the 2,5- and 3,5-isomers have more than one molecule in the crystallographic asymmetric unit (Z′ > 1). These features in particular are considered on the basis of the intermolecular interaction energies.

scholarly journals Crystal structures of (2E)-1-(3-bromothiophen-2-yl)-3-(2-methoxyphenyl)prop-2-en-1-one and (2E)-1-(3-bromothiophen-2-yl)-3-(3,4-dimethoxyphenyl)prop-2-en-1-one

2015 ◽  
Vol 71 (8) ◽  
pp. 965-971 ◽  
Author(s):  
Vasant S. Naik ◽  
Venkataraya Shettigar ◽  
Tyler S. Berglin ◽  
Jillian S. Coburn ◽  
Jerry P. Jasinski ◽  
...  
Keyword(s):  
Hydrogen Bonds ◽  
Crystal Structures ◽  
Intermolecular Interactions ◽  
Intramolecular Interaction ◽  
Intramolecular Interactions ◽  
Inversion Symmetry ◽  
Stacking Interactions ◽  
Asymmetric Unit ◽  
Space Group ◽  
Independent Molecules

In the molecules of the title compounds, (2E)-1-(3-bromo-thiophen-2-yl)-3-(2-methoxyphenyl)prop-2-en-1-one, C14H11BrO2S, (I), which crystallizes in the space groupP-1 with four independent molecules in the asymmetric unit (Z′ = 8), and (2E)-1-(3-bromothiophen-2-yl)-3-(3,4-dimethoxyphenyl)prop-2-en-1-one, C15H13BrO3S, (II), which crystallizes withZ′ = 8 in the space groupI2/a, the non-H atoms are nearly coplanar. The molecules of (I) pack with inversion symmetry stacked diagonally along thea-axis direction. Weak C—H...Br intramolecular interactions in each of the four molecules in the asymmetric unit are observed. In (II), weak C—H...O, bifurcated three-center intermolecular interactions forming dimers along with weak C—H...π and π–π stacking interactions are observed, linking the molecules into sheets along [001]. A weak C—H...Br intramolecular interaction is also present. There are no classical hydrogen bonds present in either structure.

scholarly journals Different N—H...π interactions in two indole derivatives

2016 ◽  
Vol 72 (5) ◽  
pp. 699-703 ◽  
Author(s):  
Jamie R. Kerr ◽  
Laurent Trembleau ◽  
John M. D. Storey ◽  
James L. Wardell ◽  
William T. A. Harrison
Keyword(s):  
Hydrogen Bonds ◽  
Crystal Structures ◽  
Intermolecular Interaction ◽  
Aromatic Ring ◽  
Stacking Interactions ◽  
Indole Derivatives ◽  
Asymmetric Unit ◽  
Π Interactions ◽  
Π Stacking

We describe the syntheses and crystal structures of two indole derivatives, namely 6-isopropyl-3-(2-nitro-1-phenylethyl)-1H-indole, C19H20N2O2, (I), and 2-(4-methoxyphenyl)-3-(2-nitro-1-phenylethyl)-1H-indole, C23H20N2O3, (II); the latter crystallizes with two molecules (AandB) with similar conformations (r.m.s. overlay fit = 0.139 Å) in the asymmetric unit. Despite the presence of O atoms as potential acceptors for classical hydrogen bonds, the dominant intermolecular interaction in each crystal is an N—H...π bond, which generates chains in (I) andA+AandB+Binversion dimers in (II). A different aromatic ring acts as the acceptor in each case. The packing is consolidated by C—H...π interactions in each case but aromatic π–π stacking interactions are absent.

Crystal structures and Hirshfeld surface analyses of halogen substituted azine derivatives, 1,4-bis(halophenyl)-2,3-diazabuta-1,3-dienes

2018 ◽  
Vol 233 (2) ◽  
pp. 135-143
Author(s):  
Nathasha R. de L Correira ◽  
Thais C.M. Noguiera ◽  
Alessandra C. Pinheiro ◽  
Marcus V.N. de Souza ◽  
Ligia R. Gomes ◽  
...  
Keyword(s):  
Crystal Structures ◽  
Intermolecular Interactions ◽  
Hirshfeld Surface ◽  
Stacking Interactions ◽  
Asymmetric Unit ◽  
Π Interactions ◽  
Cutoff Values ◽  
Π Stacking ◽  
Hirshfeld Analysis ◽  
Intermolecular Contacts

AbstractThe crystal structures and Hirshfeld surface analyses are reported, from data collected at 100 K, of six 1,4-bis(X,Y-phenyl)-2,3-diazabuta-1,3-dienes (1–6), namely (1: X, Y=H, 4-Cl;2: X, Y=3,4-Cl2;3: X, Y=2,4-Cl2;4: X, Y=H, 2-Br, H;5: X, Y=H, 3-Br;6: X, Y=H, 4-Br. The six halogen derivatives crystallise in themonoclinicgroupP21/c. In each case, the asymmetric unit is one half of the molecule, with the molecules lying across inversion centres, midway between the N–N bonds, with the central C–C=N–N=C–C fragments having all transoid conformations. Each of the six molecules deviates a little from overall planarity. The π···π stacking interactions are the most important intermolecular interactions in each of the six compounds. In the cases of3and4, the π···π stacks are augmented by additional C–X···π (X=Cl or Br) interactions, while in4, the π···π stacks are linked by weak Br···Br interactions, and in3, weak Cl···Cl contacts are considered to be also involved in cementing the supra molecular arrangements. The short separations of the layers within the stacks and the extent of the overlaps of the π systems point to significant strengths of the π···π interactions. Comparisons with published structures of related chloro and fluoro compounds indicated similar results: related iodo derivatives, IC6H4CH=N–N=CHC6H4I do not possess as strong π···π interactions. The Hirshfeld analysis indicated further intermolecular contacts which fell outside the normal PLATON cutoff values.

scholarly journals Intermolecular interaction energies in transition metal coordination compounds

CrystEngComm ◽  
2015 ◽  
Vol 17 (48) ◽  
pp. 9300-9310 ◽  
Author(s):  
Andrew G. P. Maloney ◽  
Peter A. Wood ◽  
Simon Parsons
Keyword(s):  
Transition Metal ◽  
Transition Metals ◽  
Crystal Structures ◽  
Intermolecular Interaction ◽  
Coordination Compounds ◽  
Metal Coordination ◽  
Interaction Energies

The PIXEL method has been parameterised and validated for transition metals, extending its applicability from ~40% to ~85% of all published crystal structures.

Bases, solvates and salts: new benzimidazole- and pyridine-scaffolded ligands

2020 ◽  
Vol 76 (4) ◽  
pp. 367-374
Author(s):  
Aleksandra Bocian ◽  
Adam Gorczyński ◽  
Dawid Marcinkowski ◽  
Grzegorz Dutkiewicz ◽  
Violetta Patroniak ◽  
...  
Keyword(s):  
Schiff Base ◽  
Hydrogen Bonds ◽  
Crystal Structures ◽  
Intermolecular Interactions ◽  
Stabilization Energy ◽  
Interaction Energies ◽  
Free Base ◽  
Schiff Base Ligands ◽  
Π Interactions ◽  
Charged Ligands

The intermolecular interactions in the structures of a series of Schiff base ligands have been thoroughly studied. These ligands can be obtained in different forms, namely, as the free base 2-[(2E)-2-(1H-imidazol-4-ylmethylidene)-1-methylhydrazinyl]pyridine, C10H11N5, 1, the hydrates 2-[(2E)-2-(1H-imidazol-2-ylmethylidene)-1-methylhydrazinyl]-1H-benzimidazole monohydrate, C12H12N6·H2O, 2, and 2-{(2E)-1-methyl-2-[(1-methyl-1H-imidazol-2-yl)methylidene]hydrazinyl}-1H-benzimidazole 1.25-hydrate, C13H14N6·1.25H2O, 3, the monocationic hydrate 5-{(1E)-[2-(1H-1,3-benzodiazol-2-yl)-2-methylhydrazinylidene]methyl}-1H-imidazol-3-ium trifluoromethanesulfonate monohydrate, C12H13N6 +·CF3O3S−·H2O, 5, and the dicationic 2-{(2E)-1-methyl-2-[(1H-imidazol-3-ium-2-yl)methylidene]hydrazinyl}pyridinium bis(trifluoromethanesulfonate), C10H13N5 2+·2CF3O3S−, 6. The connection between the forms and the preferred intermolecular interactions is described and further studied by means of the calculation of the interaction energies between the neutral and charged components of the crystal structures. These studies show that, in general, the most important contribution to the stabilization energy of the crystal is provided by π–π interactions, especially between charged ligands, while the details of the crystal architecture are influenced by directional interactions, especially relatively strong hydrogen bonds. In one of the structures, a very interesting example of the nontypical F...O interaction was found and its length, 2.859 (2) Å, is one of the shortest ever reported.

Crystal structures and Hirshfeld surface analyses of a des-A-B-aromatic steroidal compound, and two of its derivatives, having a trans-2,3,4,5-tetrahydro-3a-methyl-7-methoxybenz[e]indane skeleton – structural comparisons with reported tetrahydrobenz[e]indene derivatives

2019 ◽  
Vol 74 (9) ◽  
pp. 649-663
Author(s):  
Ligia R. Gomes ◽  
John N. Low ◽  
Alan B. Turner ◽  
Alexander W. Nowicki ◽  
Thomas C. Baddeley ◽  
...  
Keyword(s):  
Hydrogen Bonds ◽  
Crystal Structures ◽  
Intermolecular Interactions ◽  
Hirshfeld Surface ◽  
Dimensional Structure ◽  
Monoclinic Space Group ◽  
Asymmetric Unit ◽  
Space Group ◽  
Π Interactions ◽  
Independent Molecules

AbstractThe crystal structures and Hirshfeld surface analyses of the des-A-B-aromatic steroid derivative, (3a,9b)-1,2,3a,4,5,9b-hexahydro-7-methoxy-3a-methyl-3H-benz[e]-inden-3-one (or 5-methoxy-des-A-estra-5,7,9-triene-17-one) 1, its acetohydrazide derivative, 2, and its hydrazone derivative, 3, are reported. All three compounds crystallize in chiral space groups: compounds 1 and 2 in the orthorhombic space group P212121 each with one molecule in the asymmetric unit, and compound 3 in the monoclinic space group P21 with two similar but independent molecules, Mol A and Mol B, in the asymmetric unit. Both the five-membered and six-membered non-aromatic rings in all three compounds have envelope or near envelope shapes. In compounds 2 and 3 the N=N units have (E)-arrangements. The intermolecular interactions in crystals of compound 1 are C–H · · · O hydrogen bonds and C–H · · · π interactions, in compound 2 N–H · · · O and C–H · · · O hydrogen bonds and C–H · · · π interactions are present, while in compound 3 there are just C–H · · · π interactions. An important substructure in 1 is a sheet of molecules, composed of ${\rm{R}}_6^6(44)$ rings, formed from C–H · · · O(methoxy) and C–H · · · O(carbonyl) hydrogen bonds, the molecules of which form columns linked via the B and D rings, i.e. in a head-to-tail fashion. Compound 2 is an acylhydrazonyl compound, in which the two independent molecules are linked into asymmetric dimers via strong classical N–H · · · O hydrogen bonds, with the formation of ${\rm{R}}_2^2(8)$ rings. In both 1 and 2, further intermolecular interactions result in 3-dimensional structures, while compound 3 has a 1-dimensional structure arising from C–H · · · O interactions generating spiral chains. The results have been compared with existing data.

Structural comparisons of isomeric series of 7-aryl-benzo[h]pyrazolo[3,4-b]quinolines and 11-aryl-benzo[f]pyrazolo[3,4-b]quinolines

2008 ◽  
Vol 64 (1) ◽  
pp. 72-83 ◽  
Author(s):  
Jaime Portilla ◽  
Jairo Quiroga ◽  
Manuel Nogueras ◽  
Jose M. de la Torre ◽  
Justo Cobo ◽  
...  
Keyword(s):  
Crystal Structures ◽  
Intermolecular Interactions ◽  
Oxidation Product ◽  
Recent Literature ◽  
Stacking Interactions ◽  
Aryl Group ◽  
Π Stacking ◽  
Quinoline Series

The structures of three new 7-aryl-benzo[h]pyrazolo[3,4-b]quinolines, 8-methyl-7-(4-chlorophenyl)-10-phenyl-6,10-dihydro-5H-benzo[h]pyrazolo[3,4-b]quinoline, C27H20ClN3, 8-methyl-7-(3-pyridinyl)-10-phenyl-6,10-dihydro-5H-benzo[b]pyrazolo[3,4-b]quinoline, C26H20N4, and 8-methyl-7-(4-pyridinyl)-10-phenyl-10H-benzo[h]pyrazolo[3,4-b]quinoline, C26H18N4, which is an unexpected oxidation product isolated from the attempted synthesis of 8-methyl-7-(4-pyridinyl)-10-phenyl-6,10-dihydro-5H-benzo[h]pyrazolo[3,4-b]quinoline, and those of three new 11-aryl-benzo[f]pyrazolo[3,4-b]quinolines, 11-(4-methylphenyl)-10-methyl-8-phenyl-6,8-dihydro-5H-benzo[f]pyrazolo[3,4-b]quinoline, C28H23N3 (P\bar 1, Z′ = 2), 11-(4-methoxyphenyl)-10-methyl-8-phenyl-6,8-dihydro-5H-benzo[f]pyrazolo[3,4-b]quinoline, C28H23N3O (P21/c, Z′ = 4), and 11-(3,4,5-trimethoxyphenyl)-10-methyl-8-phenyl-6,8-dihydro-5H-benzo[f]pyrazolo[3,4-b]quinoline, C30H27N3O3, are reported. The crystal structures are compared with those of a number of analogues reported in the recent literature; in particular, structural comparisons are drawn within each series as the substituted pendent aryl group is varied, and between several pairs of strictly isomeric 7-aryl-benzo[h]pyrazolo[3,4-b]quinolines and 11-aryl-benzo[f]pyrazolo[3,4-b]quinolines containing the same aryl substituents within each pair. Intermolecular interactions of the C—H...π type are found in the crystal structures of both series, but π...π stacking interactions are found only in the 7-aryl-benzo[h]pyrazolo[3,4-b]quinoline series.

Hydrogen-bonded structures and interaction energies in two forms of the SGLT-2 inhibitor sotagliflozin

2017 ◽  
Vol 73 (9) ◽  
pp. 718-723
Author(s):  
Thomas Gelbrich ◽  
Verena Adamer ◽  
Marijan Stefinovic ◽  
Andrea Thaler ◽  
Ulrich J. Griesser
Keyword(s):  
Intermolecular Interactions ◽  
Crystallographic Axis ◽  
Interaction Energies ◽  
Molecular Conformations ◽  
Oh Groups ◽  
Molecule Interaction ◽  
Hydrogen Bonded

The sotagliflozin molecule exhibits two fundamentally different molecular conformations in form 1 {systematic name: (2S,3R,4R,5S,6R)-2-[4-chloro-3-(4-ethoxybenzyl)phenyl]-6-(methylsulfanyl)tetrahydro-2H-pyran-3,4,5-triol, C21H25ClO5S, (I)} and the monohydrate [C21H25ClO5S·H2O, (II)]. Both crystals display hydrogen-bonded layers formed by intermolecular interactions which involve the three –OH groups of the xyloside fragment of the molecule. The layer architectures of (I) and (II) contain a non-hydrogen-bonded molecule–molecule interaction along the short crystallographic axis (a axis) whose total PIXEL energy exceeds that of each hydrogen-bonded molecule–molecule pair. The hydrogen-bonded layer of (I) has the topology of the 4-connected sql net and that formed by the water and sotagliflozin molecules of (II) has the topology of a 3,7-connected net.

scholarly journals Expected and unexpected products of reactions of 2-hydrazinylbenzothiazole with 3-nitrobenzenesulfonyl chloride in different solvents

2018 ◽  
Vol 74 (5) ◽  
pp. 673-677 ◽  
Author(s):  
Alexandra Morscher ◽  
Marcus V. N. de Souza ◽  
James L. Wardell ◽  
William T. A. Harrison
Keyword(s):  
Hydrogen Bonds ◽  
Crystal Structures ◽  
Ion Pairs ◽  
Stacking Interactions ◽  
Asymmetric Unit ◽  
Π Interactions ◽  
Π Stacking ◽  
Unexpected Reaction

The syntheses and crystal structures of 2-[2-(propan-2-ylidene)hydrazinyl]-1,3-benzothiazol-3-ium 3-nitrobenzenesulfonate (C10H12N2S+·C6H4NO5S−), (I), 2-[2-(3-nitrobenzenesulfonyl)hydrazinyl]-1,3-benzothiazole (C13H10N4O4S2), (II) and 2-[2-(3-nitrobenzenesulfonyl)hydrazinyl]-1,3-benzothiazol-3-ium 3-nitrobenzenesulfonate (C13H11N4O4S2 +·C6H4NO5S−), (III) are reported. Salt (I) arose from an unexpected reaction of 2-hydrazinylbenzothiazole with the acetone solvent in the presence of 3-nitrobenzenesulfonyl chloride, whereas (II) and (III) were recovered from the equivalent reaction carried out in methanol. The crystal of (I) features ion pairs linked by pairs of N—H...Os (s = sulfonate) hydrogen bonds; adjacent cations interact by way of short π–π stacking interactions between the thiazole rings [centroid–centroid separation = 3.4274 (18) Å]. In (II), which crystallizes with two neutral molecules in the asymmetric unit, the molecules are linked by N—H...N and N—H...On (n = nitro) hydrogen bonds to generate [\overline{1}1\overline{1}] chains, which are cross-linked by C—H...O and π–π stacking interactions. The crystal of (III) features centrosymmetric tetramers (two cations and two anions) linked by cooperative N—H...O hydrogen bonds; C—H...O and π–π interactions occur between tetramers.

X·F (X=C, N, O and S) Noncovalent Weak Intermolecular Interactions

2014 ◽  
Vol 881-883 ◽  
pp. 192-195
Author(s):  
Yan Zhi Liu ◽  
Huian Tang
Keyword(s):  
Intermolecular Interaction ◽  
Electron Density ◽  
Intermolecular Interactions ◽  
Topological Analysis ◽  
Interaction Energies ◽  
Weak Intermolecular Interaction ◽  
Weak Intermolecular Interactions ◽  
The Stability ◽  
Bsse Correction ◽  
Computational Level

A number of X···F (X=C, N, O and S) noncovalent weak intermolecular interaction systems of CH3-F···XO2 (X=C, N, O and S) has been investigated at B3LYP/6-311++G(d, p) computational level. A topological analysis of the electron density for the X···F (X=C, N, O and S) noncovalent weak bonds was performed using Baders theory of atom-in-molecules (AIM). The interaction content of the F···X in H3CF···CO2 complex would mainly represent more π property than others. The interaction energies data without (ΔE) and with (ΔEcp) BSSE correction showed that the stability of the four complexes of the H3CF···DB2 system increases in the order of H3CF···O3 < H3CF···NO2 < H3CF···CO2 < H3CF···SO2.

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