Synthesis and crystal packing of perylene-derivatives with extreme sterically demanding pentaphenylbenzene bay-substituents

2021 ◽  
Author(s):  
Carolin Dusold ◽  
Corinna Weiss ◽  
Frank Hampel ◽  
Andreas Hirsch
Keyword(s):  
Crystal Packing ◽  
X Ray ◽  
X Ray Crystallography ◽  
Sterically Demanding ◽  
Perylene Derivatives

Extremely flexible PDI-PPBs: perylenes with a varying number of PPBs and different peri-moieties were synthesized. The isolated regioisomers exhibit remarkably different properties. X-ray crystallography reveals sufficient suppression of aggregation.

scholarly journals A hybrid approach reveals the allosteric regulation of GTP cyclohydrolase I

2020 ◽  
Vol 117 (50) ◽  
pp. 31838-31849
Author(s):  
Rebecca Ebenhoch ◽  
Simone Prinz ◽  
Susann Kaltwasser ◽  
Deryck J. Mills ◽  
Robert Meinecke ◽  
...  
Keyword(s):  
Crystal Packing ◽  
Substrate Binding ◽  
Regulatory Protein ◽  
Allosteric Regulation ◽  
Hybrid Approach ◽  
Site Directed Mutagenesis ◽  
Gtp Cyclohydrolase I ◽  
Gtp Cyclohydrolase ◽  
X Ray ◽  
X Ray Crystallography

Guanosine triphosphate (GTP) cyclohydrolase I (GCH1) catalyzes the conversion of GTP to dihydroneopterin triphosphate (H2NTP), the initiating step in the biosynthesis of tetrahydrobiopterin (BH4). Besides other roles, BH4 functions as cofactor in neurotransmitter biosynthesis. The BH4 biosynthetic pathway and GCH1 have been identified as promising targets to treat pain disorders in patients. The function of mammalian GCH1s is regulated by a metabolic sensing mechanism involving a regulator protein, GCH1 feedback regulatory protein (GFRP). GFRP binds to GCH1 to form inhibited or activated complexes dependent on availability of cofactor ligands, BH4 and phenylalanine, respectively. We determined high-resolution structures of human GCH1−GFRP complexes by cryoelectron microscopy (cryo-EM). Cryo-EM revealed structural flexibility of specific and relevant surface lining loops, which previously was not detected by X-ray crystallography due to crystal packing effects. Further, we studied allosteric regulation of isolated GCH1 by X-ray crystallography. Using the combined structural information, we are able to obtain a comprehensive picture of the mechanism of allosteric regulation. Local rearrangements in the allosteric pocket upon BH4 binding result in drastic changes in the quaternary structure of the enzyme, leading to a more compact, tense form of the inhibited protein, and translocate to the active site, leading to an open, more flexible structure of its surroundings. Inhibition of the enzymatic activity is not a result of hindrance of substrate binding, but rather a consequence of accelerated substrate binding kinetics as shown by saturation transfer difference NMR (STD-NMR) and site-directed mutagenesis. We propose a dissociation rate controlled mechanism of allosteric, noncompetitive inhibition.

Substituent position effect on the crystal structures of N-phenyl-2-phthalimidoethanesulfonamide derivatives

2018 ◽  
Vol 74 (1) ◽  
pp. 31-36
Author(s):  
Resul Sevinçek ◽  
Duygu Barut Celepci ◽  
Serap Köktaş Koca ◽  
Özlem Akgül ◽  
Muittin Aygün
Keyword(s):  
Hydrogen Bonds ◽  
Crystal Packing ◽  
Biological Activities ◽  
Position Effect ◽  
Intermolecular Hydrogen Bond ◽  
X Ray ◽  
Space Groups ◽  
X Ray Crystallography ◽  
Hydrogen Bond Interactions ◽  
The Impact

In order to determine the impact of different substituents and their positions on intermolecular interactions and ultimately on the crystal packing, unsubstituted N-phenyl-2-phthalimidoethanesulfonamide, C16H14N2O4S, (I), and the N-(4-nitrophenyl)-, C16H13N3O6S, (II), N-(4-methoxyphenyl)-, C16H16N3O6S, (III), and N-(2-ethylphenyl)-, as the monohydrate, C18H18N2O4S·H2O, (IV), derivatives have been characterized by single-crystal X-ray crystallography. Sulfonamides (I) and (II) have triclinic crystal systems, while (III) and (IV) are monoclinic. Although the molecules differ from each other only with respect to small substituents and their positions, they crystallized in different space groups as a result of differing intra- and intermolecular hydrogen-bond interactions. The structures of (I), (II) and (III) are stabilized by intermolecular N—H...O and C—H...O hydrogen bonds, while that of (IV) is stabilized by intermolecular O—H...O and C—H...O hydrogen bonds. All four structures are of interest with respect to their biological activities and have been studied as part of a program to develop anticonvulsant drugs for the treatment of epilepsy.

scholarly journals Crystal Packing and Supramolecular Motifs in Four Phenoxyalkanoic Acid Herbicides—Low-Temperature Redeterminations

2011 ◽  
Vol 2011 ◽  
pp. 1-5 ◽  
Author(s):  
Lesław Sieroń ◽  
Joanna Kobyłecka ◽  
Anna Turek
Keyword(s):  
Low Temperature ◽  
Propionic Acid ◽  
Crystal Packing ◽  
Dichlorophenoxyacetic Acid ◽  
X Ray ◽  
Π Interactions ◽  
X Ray Crystallography ◽  
Supramolecular Motifs ◽  
2,4 Dichlorophenoxyacetic Acid ◽  
Acid Herbicides

A low-temperature redetermination by X-ray crystallography of four phenoxyalkanoic acid herbicides, 4-chloro-2-methylphenoxyacetic acid (MCPA), rac-2-(4-chloro-2-methylphenoxy)propionic acid (MCPP), 2,4-dichlorophenoxyacetic acid (2,4-D), and 2,4-dichlorophenoxybutyric acid (2,4-DB), allowed the supramolecular structures of these compounds to be precisely described in terms of C⋯O/C–H⋯π interactions. The geometric parameters of the redetermined structures agree with those previously reported, but with improved precision.

Crystal packing and theoretical analysis of halogen- and hydrogen-bonded hydrazones from pharmaceuticals. Evidence of type I and II halogen bonds in extended chains of dichloromethane

2018 ◽  
Vol 74 (6) ◽  
pp. 618-627 ◽  
Author(s):  
Gilles Berger ◽  
Jalal Soubhye ◽  
René Wintjens ◽  
Koen Robeyns ◽  
Franck Meyer
Keyword(s):  
Crystal Packing ◽  
Interaction Strength ◽  
Supramolecular Assembly ◽  
Coupled Cluster ◽  
Type I ◽  
Energy Decomposition ◽  
Halogen Bonds ◽  
Linear Arrangement ◽  
X Ray ◽  
X Ray Crystallography

The supramolecular assembly of halogenated and hydroxyl hydrazones derived from two well known pharmaceuticals, isoniazid (IsX, where X = I, Br, OH) and hydralazine (HyX, where X = I, Br, OH), was studied by X-ray crystallography and theoretical methods. Crystal packing of IsI and HyI shows weak I...N and I...π halogen bonds, whereas the hydrogen bonds are dominant in the brominated scaffolds IsBr and HyBr. Although the calculated I...N interaction strength appears almost three times weaker than the O—H...N contacts in the isoniazid-based hydrazones, the higher directionality of the halogen bonds induces a linear and planar architecture of self-complementary tectons, observed only with the help of a bridging water molecule in the case of IsOH. Finally, the X-ray structure of HyOH is characterized by an unexpected linear arrangement of clathrated dichloromethane molecules bound through type I and II halogen bonds. This rare phenomenon, observed in less than ten structures, was studied by coupled cluster-based energy decomposition.

scholarly journals Structural characterization and Hirshfeld surface analysis of a CoII complex with imidazo[1,2-a]pyridine

2018 ◽  
Vol 74 (5) ◽  
pp. 600-606 ◽  
Author(s):  
Saikat Kumar Seth
Keyword(s):  
Surface Analysis ◽  
Crystal Packing ◽  
Building Blocks ◽  
Hirshfeld Surface ◽  
Title Complex ◽  
Hirshfeld Surface Analysis ◽  
X Ray ◽  
X Ray Crystallography ◽  
Π Stacking ◽  
Coii Complex

A new mononuclear tetrahedral CoII complex, dichloridobis(imidazo[1,2-a]pyridine-κN 1)cobalt(II), [CoCl2(C7H6N2)2], has been synthesized using a bioactive imidazopyridine ligand. X-ray crystallography reveals that the solid-state structure of the title complex exhibits both C—H...Cl and π–π stacking interactions in building supramolecular assemblies. Indeed, the molecules are linked by C—H...Cl interactions into a two-dimensional framework, with finite zero-dimensional dimeric units as building blocks, whereas π–π stacking plays a crucial role in building a supramolecular layered network. An exhaustive investigation of the diverse intermolecular interactions via Hirshfeld surface analysis enables contributions to the crystal packing of the title complex to be quantified. The fingerprint plots associated with the Hirshfeld surface clearly display each significant interaction involved in the structure, by quantifying them in an effective visual manner.

Highly Sheared Anti-Parallel Dipolar Carbonyl···Carbonyl Interaction in the Crystal Packing of Strapped Crown-3-Pyromellitimide

2012 ◽  
Vol 65 (10) ◽  
pp. 1384 ◽  
Author(s):  
Ethan Nam Wei Howe ◽  
Mohan Bhadbhade ◽  
Pall Thordarson
Keyword(s):  
Molecular Structure ◽  
Torsion Angle ◽  
Organic Molecules ◽  
Crystal Packing ◽  
Dipolar Interactions ◽  
High Dilution ◽  
Small Organic Molecules ◽  
X Ray ◽  
X Ray Crystallography ◽  
Structural Architecture

Non-covalent dipolar interactions between pairs of carbonyls have been demonstrated to play a significant role in the crystal packing and formation of supramolecular structural architecture of small organic molecules. Under high dilution, the strapped crown-3-pyromellitimide 4 and macrocyclic crown-6-bispyromellitimide 5 were synthesised in concert and demonstrated selective molecular recognition towards Na+ and K+, respectively. The molecular structure of strapped crown-3-pyromellitimide 4 was solved using X-ray crystallography and an unusual highly sheared anti-parallel dipolar carbonyl···carbonyl interaction was observed in the crystal packing. The intermolecular interaction has a torsion angle of 44.1°, and deviates from the three idealised motifs reported in literature. This finding further highlights the importance and versatility of dipolar carbonyl···carbonyl interaction in the crystal packing of organic molecules.

Preparations, X-ray crystal structures, and spectral studies of seleninyl bis(trifluoromethanesulfonate) and seleninyl bis(acetate)

1988 ◽  
Vol 66 (9) ◽  
pp. 2367-2374 ◽  
Author(s):  
Ramesh Kapoor ◽  
Poonam Wadhawan ◽  
Pratibha Kapoor ◽  
Jeffery F. Sawyer
Keyword(s):  
Crystal Packing ◽  
Spectral Studies ◽  
Monoclinic Space Group ◽  
Coordination Geometry ◽  
Orthorhombic Space Group ◽  
Space Group ◽  
X Ray ◽  
X Ray Crystallography ◽  
Intermolecular Contacts ◽  
Ir And Raman

The compounds seleninyl bis(trifluoromethanesulphonate) (1) and seleninyl bis(acetate) (2) have been prepared and characterized by elemental analysis, ir and Raman spectroscopy, and X-ray crystallography. Crystals of 1 are monoclinic, space group P21/n with a = 12.735(1) Å, b = 5.163(4) Å, c = 16.133(2) Å, β = 96.426(8)°, U = 1054 Å3, Dx = 2.48 g cm−3 for Z = 4, R = 0.038 for 1745 observed reflections with I > 2.5σ(I). Those of 2 are orthorhombic, space group Pcab with a = 6,845(3) Å, b = 8.992(2) Å, c = 23.560(9) Å, U = 1450 Å3Dx = 1.95 g cm−3 for Z = 8, R = 0.074 for 1073 observed reflections with I > 3.0σ(I). The primary geometry of the Se atom in SeO(O3SCF3)2 is AX3E with a Se=O distance of 1.571(3) Å and Se—O bond lengths to the CF3SO3 ligands of 1.902(3) and 1.922(3) Å. Completing the overall coordination geometry of the Se atom are 2 intramolecular and 4 intermolecular Se … O contacts which are less than van der Waals limits. The overall coordination geometry is somewhat irregular since the two triflate anions are significantly differently arranged with respect to the SeO3E tetrahedron. The crystal packing consists of layers of interacting molecules. In 2 there is some disorder. However, the major arrangement of the molecule has Se=O and Se—O(1), Se—O(3) distances to the acetate ligands of lengths 1.575(9), 1.847(7), and 1.831(8) Å respectively. The overall geometry of the Se atom in this compound is completed by two intramolecular secondary Se … O contacts involving the second O atoms of both acetates and two intermolecular contacts involving the seleninyl oxygen atom and atom O(2) of an acetate group in two different symmetry related molecules. Overall, the crystal packing consists of essentially centrosymmetric dimeric units linked together through Se=O—Se bridges. A 1:2 adduct of 1 with pyridine has also been prepared and characterised.

scholarly journals Symmetry transitions during gating of the TRPV2 ion channel in lipid membranes

eLife ◽  
2019 ◽  
Vol 8 ◽  
Author(s):  
Lejla Zubcevic ◽  
Allen L Hsu ◽  
Mario J Borgnia ◽  
Seok-Yong Lee
Keyword(s):  
Lipid Membranes ◽  
Transient Receptor Potential ◽  
Crystal Packing ◽  
Receptor Potential ◽  
Temperature Sensing ◽  
Transient Receptor Potential Vanilloid ◽  
X Ray ◽  
X Ray Crystallography ◽  
Transient Receptor ◽  
Lipid Environment

The Transient Receptor Potential Vanilloid 2 (TRPV2) channel is a member of the temperature-sensing thermoTRPV family. Recent advances in cryo-electronmicroscopy (cryo-EM) and X-ray crystallography have provided many important insights into the gating mechanisms of thermoTRPV channels. Interestingly, crystallographic studies of ligand-dependent TRPV2 gating have shown that the TRPV2 channel adopts two-fold symmetric arrangements during the gating cycle. However, it was unclear if crystal packing forces played a role in stabilizing the two-fold symmetric arrangement of the channel. Here, we employ cryo-EM to elucidate the structure of full-length rabbit TRPV2 in complex with the agonist resiniferatoxin (RTx) in nanodiscs and amphipol. We show that RTx induces two-fold symmetric conformations of TRPV2 in both environments. However, the two-fold symmetry is more pronounced in the native-like lipid environment of the nanodiscs. Our data offers insights into a gating pathway in TRPV2 involving symmetry transitions.

scholarly journals Intermolecular Hydrogen and Halogen Bonds in Fluorinated Benzimidazoles

2014 ◽  
Vol 70 (a1) ◽  
pp. C643-C643
Author(s):  
Rosa M Claramunt ◽  
Marta Pérez-Torralba ◽  
M. Ángeles García ◽  
Concepción López ◽  
M. Carmen Torralba ◽  
...  
Keyword(s):  
Hydrogen Bonds ◽  
Crystal Packing ◽  
Weak Interactions ◽  
Bond Distance ◽  
Imidazole Ring ◽  
Halogen Bonds ◽  
Aromatic Rings ◽  
Molecular Plane ◽  
X Ray ◽  
X Ray Crystallography

After hydrogen bonds (HB) the most studied of related weak interactions are the halogen bonds (XB). The competition between these two interactions as well as their interplay to determine the crystal packing of organic derivatives is a subject of interest. Most the studies related to XB concerns the heaviest halogen atoms, I and Br, less Cl and much less F, because the interaction energy decreases in this order. [1,2] We present here our studies on the structure of five tetrafluorinated benzazoles by X-ray crystallography and solid-state NMR, a powerful synergic mixture of techniques. The compounds are 4,5,6,7-tetrafluoro-1H-benzimidazole (1), 4,5,6,7-tetrafluoro-2-(trifluoromethyl)-1H-benzimidazole (2), 4,5,6,7-tetrafluoro-1H-benzimidazole-2(3H)-one (3), 4,5,6,7-tetrafluoro-1-methyl-1H-benzimidazole-2(3H)-one (4), and 4,5,6,7-tetrafluoro-1,3-dimethyl-1H-benzimidazole-2(3H)-one (5). As a common general feature, these compounds are quite planar due to the presence of the two aromatic rings. The existence of the methyl groups as substituent in the nitrogen atoms does not modify the planarity of the molecule. The bond distances and angles are in agreement with the expected ones for this kind of compounds. The presence of the carbonyl group induces some electronic changes in the imidazole ring that is resembled in the lengthening of the C2N3 bond distance and in a higher deviation of C2 atom from the molecular plane. Moreover, all the compounds show one or more interactions by strong linear hydrogen bonds, which lead to the formation of chains that, in some cases, can exhibit additional interactions via pi-pi and/or F···F contacts spreading out the dimensionality of the structure in the crystal. [3] The distribution of the F···F contacts in compounds 1-5 is similar to those of the literature and includes for 4,5,6,7-tetrafluoro-1H-benzimidazole-2(3H)-one (3) one of the shortest F···F distances ever reported [2.596(3) Å]. Two polymorphs of compound 4 are identified.

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