Molecular Conformation and Intermolecular Interactions in the Crystal Structures of Free-Base 5,15-Diarylporphyrins

2002 ◽  
Vol 2 (1) ◽  
pp. 27-39 ◽  
Author(s):  
Andrew D. Bond ◽  
Neil Feeder ◽  
James E. Redman ◽  
Simon J. Teat ◽  
Jeremy K. M. Sanders
Keyword(s):  
Crystal Structures ◽  
Intermolecular Interactions ◽  
Molecular Conformation ◽  
Free Base

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.

scholarly journals Intermolecular Interactions in Crystal Structures of Imatinib-Containing Compounds

2020 ◽  
Vol 21 (23) ◽  
pp. 8970
Author(s):  
Anna V. Vologzhanina ◽  
Ivan E. Ushakov ◽  
Alexander A. Korlyukov
Keyword(s):  
Crystal Structures ◽  
Intermolecular Interactions ◽  
Tyrosine Kinases ◽  
Density Functional ◽  
Molecular Conformation ◽  
Hydrophobic Interactions ◽  
Density Functional Theory Calculations ◽  
Molecular Surface ◽  
Molecular Conformations ◽  
Receptor Complexes

Imatinib, one of the most used therapeutic agents to treat leukemia, is an inhibitor that specifically blocks the activity of tyrosine kinases. The molecule of imatinib is flexible and contains several functional groups able to take part in H-bonding and hydrophobic interactions. Analysis of molecular conformations for this drug was carried out using density functional theory calculations of rotation potentials along single bonds and by analyzing crystal structures of imatinib-containing compounds taken from the Cambridge Structural Database and the Protein Data Bank. Rotation along the N-C bond in the region of the amide group was found to be the reason for two relatively stable molecular conformations, an extended and a folded one. The role of various types of intermolecular interactions in stabilization of the particular molecular conformation was studied in terms of (i) the likelihood of H-bond formation, and (ii) their contribution to the Voronoi molecular surface. It is shown that experimentally observed hydrogen bonds are in accord with the likelihood of their formation. The number of H-bonds in ligand-receptor complexes surpasses that in imatinib salts due to the large number of donors and acceptors of H-bonding within the binding pocket of tyrosine kinases. Contribution of hydrophilic intermolecular interactions to the Voronoi molecular surface is similar for both conformations, while π...π stacking is more typical for the folded conformation of imatinib.

Crystal structures, intermolecular interactions and fluorescence properties of a series of symmetrical bi-1,3,4-oxadiazole derivatives

2016 ◽  
Vol 4 (20) ◽  
pp. 4451-4458 ◽  
Author(s):  
Fangyi Chen ◽  
Taiji Tian ◽  
Binglian Bai ◽  
Jian Wang ◽  
Haitao Wang ◽  
...  
Keyword(s):  
Crystal Structures ◽  
Intermolecular Interactions ◽  
Substituent Effect ◽  
Driving Force ◽  
Molecular Conformation ◽  
Fluorescence Properties ◽  
Oxadiazole Derivatives

This study discusses the substituent effect on molecular conformation and packing, exploring the driving force for different molecular aggregations.

scholarly journals Crystal structures of three newN-halomethylated quaternary ammonium salts

2015 ◽  
Vol 71 (10) ◽  
pp. 1230-1235
Author(s):  
Carolina Múnera-Orozco ◽  
Rogelio Ocampo-Cardona ◽  
David L. Cedeño ◽  
Rubén A. Toscano ◽  
Luz Amalia Ríos-Vásquez
Keyword(s):  
Crystal Structures ◽  
Intermolecular Interactions ◽  
Quaternary Ammonium ◽  
Quaternary Ammonium Salts ◽  
Ammonium Salts ◽  
Compound I ◽  
Nlo Properties ◽  
Π Interactions

In the crystals of the titleN-halomethylated quaternary ammonium salts, C19H23IN+·I−, (I) [systematic name:N-(4,4-diphenylbut-3-en-1-yl)-N-iodomethyl-N,N-dimethylammonium iodide], C20H25IN+·I−, (II) [systematic name:N-(5,5-diphenylpent-4-en-1-yl)-N-iodomethyl-N,N-dimethylammonium iodide], and C21H27IN+·I−, (III) [systematic name:N-(6,6-diphenylhex-5-en-1-yl)-N-iodomethyl-N,N-dimethylammonium iodide], there are short I...I−interactions of 3.564 (4), 3.506 (1) and 3.557 (1) Å for compounds (I), (II) and (III), respectively. Compound (I) crystallizes in the Sohncke groupP21as an `enantiopure' compound and is therefore a potential material for NLO properties. In the crystal of compound (I), molecules are linked by C—H...I−and C—H...π interactions which, together with the I...I−interactions, lead to the formation of ribbons along [100]. In (II), there are only C—H...I−interactions which, together with the I...I−interactions, lead to the formation of helices along [010]. In (III), apart from the I...I−interactions, there are no significant intermolecular interactions present.

scholarly journals Crystal structures of 2,5-diazido-1,4-phenylene diacetate and 2,5-diazido-1,4-phenylene dibutyrate

2014 ◽  
Vol 70 (7) ◽  
pp. 39-42 ◽  
Author(s):  
Florian Glöcklhofer ◽  
Johannes Fröhlich ◽  
Berthold Stöger ◽  
Matthias Weil
Keyword(s):  
Crystal Structures ◽  
Intermolecular Interactions ◽  
Crystal Symmetry ◽  
Dihedral Angles ◽  
Maximum Deviation ◽  
Inversion Symmetry ◽  
Ester Moiety

The asymmetric units of the title compounds, C10H8N6O4, (I), and C14H16N6O4, (II), each contain half of the respective molecule which is completed by inversion symmetry. The two molecules differ in the ester moiety (acetateversusbutyrate) and the crystal symmetry is different,i.e.triclinic for (I) and monoclinic for (II). The diazidophenylene moieties are essentially planar [maximum deviation of 0.0216 (7) Å for (I) and 0.0330 (14) Å for (II)], and the ester functionalities are almost perpendicular to these planes, making dihedral angles of 79.93 (3)° for (I) and 79.42 (6)° for (II). In the crystals of both (I) and (II), there are no significant intermolecular interactions present.

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.

Crystal structures and Hirshfeld surface analysis of four 1,4-bis(methoxyphenyl)-2,3-diazabuta-1,3-dienes: comparisons of the intermolecular interactions in related compounds

2019 ◽  
Vol 234 (1) ◽  
pp. 59-71 ◽  
Author(s):  
Ligia R. Gomes ◽  
John N. Low ◽  
Nathasha R. de L. Correira ◽  
Thais C.M. Noguiera ◽  
Alessandra C. Pinheiro ◽  
...  
Keyword(s):  
Hydrogen Bonds ◽  
Crystal Structures ◽  
Intermolecular Interactions ◽  
Three Dimensional ◽  
Hirshfeld Surface ◽  
Dimensional Structure ◽  
Intermolecular Hydrogen Bonds ◽  
Π Interactions ◽  
Isomeric Compound ◽  
Related Compounds

Abstract The crystal structures of four azines, namely 1-3-bis(4-methoxyphenyl)-2,3-diaza-1,4-butadiene, 1, 1,3-bis(2,3-dimethoxyphenyl)-2,3-diaza-1,4-butadiene, 2, 1,3-bis(2-hydroxy-3-methoxyphenyl)-2,3-diaza-1,4-butadiene, 3, and 1,3-bis(2-hydroxy-4-methoxyphenyl)-2,3-diaza-1,4-butadiene, 4, are reported. Molecules of 3 and 4, and both independent molecules of 2, Mol A and Mol B, possess inversion centers. The central C=N–N=C units in each molecule is planar with an (E,E) conformation. The intermolecular interactions found in the four compounds are C–H···O, C–H–N, C–H---π and π---π interactions. However, there is no consistent set of intermolecular interactions for the four compounds. Compound, 1, has a two-dimensional undulating sheet structure, generated from C–H···O and C–H···N intermolecular hydrogen bonds. The only recognized intermolecular interaction in 2 is a C–H···O hydrogen bond, which results in a zig-zag chain of alternating molecules, Mol A and Mol B. While 3 forms a puckered sheet of molecules, solely via C–H···π interactions, its isomeric compound, 4, has a more elaborate three-dimensional structure generated from a combination of C–H···O hydrogen bonds, C–H···π and π···π interactions. The findings in this study, based on both PLATON and Hirshfeld approaches, for the four representative compounds match well the reported structural findings in the literature of related compounds, which are based solely on geometric parameters.

Molekül- und Kristallstrukturen zweier einkerniger Ruthenium(II)-Komplexe mit dem starken π·Akzeptorliganden 2,2'-Azobis(pyridin) (abpy): [mer-Ru(abpy)3](PF6)2 und Ru(abpy)2Cl2 (ctc-Isomer) / Molecular and Crystal Structures of Two Mononuclear Ruthenium(II) Complexes with the Strongly π Accepting Ligand 2,2'-Azobis(pyridine) (abpy): [mer-Ru(abpy)3](PF6)2 and Ru(abpy)2Cl2 (ctc Isomer)

1995 ◽  
Vol 50 (1) ◽  
pp. 15-22 ◽  
Author(s):  
Jörg Fees ◽  
H.-D. Hausen ◽  
Wolfgang Kaim
Keyword(s):  
Crystal Structure ◽  
Crystal Structures ◽  
Dihedral Angle ◽  
Intermolecular Interactions ◽  
Chelate Compound ◽  
Steric Repulsion ◽  
Structural Reorganization ◽  
Nitrogen Donor ◽  
Molecular And Crystal Structures ◽  
Halide Ligands

Crystal structure analyses of the title complexes have been carried out in order to establish their molecular configurations. The tris(chelate) complex dication in (1)(PF6)2 exhibits a mer configuration of pyridine and azo nitrogen atoms in an approximately octahedral arrangement at the metal. The dichlororuthenium bis(chelate) compound 2 has the halide ligands and the coordinated azo nitrogen centers in an equatorial cis arrangement whereas two pyridyl groups (one of each abpy ligand) occupy the axial positions. The bond distances from the metal to the nitrogen donor centers are systematically smaller for the stronger π accepting azo functions than for the more basic but less π acidic pyridyl groups, a result which differs from that obtained for Mo(0) and Cu(I) complexes of abpy. All Ru—N distances are shorter in the neutral dichloro complex 2. The non-coordinated pyridyl rings of the potentially tetradentate abpy ligands are tilted into approximate s-cis/(NN-trans)/s-trans positions (dihedral angle ω ≈ 145°) as to minimize steric repulsion, however, they do not coordinate to the metal (dRu-N > 327 pm). While there are no significant intermolecular interactions, the observed conformation implies that considerable structural reorganization is necessary for the formation of oligonuclear complexes.

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