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.

scholarly journals The CryoEM Method MicroED as a Powerful Tool for Small Molecule Structure Determination

2018 ◽  
Author(s):  
Christopher G. Jones ◽  
Michael W. Martynowycz ◽  
Johan Hattne ◽  
Tyler J. Fulton ◽  
Brian M. Stoltz ◽  
...  
Keyword(s):  
Organic Chemistry ◽  
Organic Molecules ◽  
Spectroscopic Techniques ◽  
Small Organic Molecules ◽  
X Ray ◽  
X Ray Crystallography ◽  
Minimal Sample ◽  
The Many ◽  
Almost All

<p>In the many scientific endeavors that are driven by organic chemistry, unambiguous identification of small molecules is of paramount importance. Over the past 50 years, NMR and other powerful spectroscopic techniques have been developed to address this challenge. While almost all of these techniques rely on inference of connectivity, the unambiguous determination of a small molecule’s structure requires X-ray and/or neutron diffraction studies. In practice, however, x-ray crystallography is rarely applied in routine organic chemistry due to intrinsic limitations of both the analytes and the technique. Here we report the use of the CryoEM method MicroED to provide routine and unambiguous structural determination of small organic molecules. From simple powders, with minimal sample preparation, we could collect high quality MicroED data from nanocrystals (~100x100x100 nm, ~10<sup>–15</sup>g) resulting in atomic resolution (<1 Å) crystal structures in minutes.</p>

scholarly journals The CryoEM Method MicroED as a Powerful Tool for Small Molecule Structure Determination

2018 ◽  
Author(s):  
Christopher G. Jones ◽  
Michael W. Martynowycz ◽  
Johan Hattne ◽  
Tyler J. Fulton ◽  
Brian M. Stoltz ◽  
...  
Keyword(s):  
Organic Chemistry ◽  
Organic Molecules ◽  
Spectroscopic Techniques ◽  
Small Organic Molecules ◽  
X Ray ◽  
X Ray Crystallography ◽  
Minimal Sample ◽  
The Many ◽  
Almost All

<p>In the many scientific endeavors that are driven by organic chemistry, unambiguous identification of small molecules is of paramount importance. Over the past 50 years, NMR and other powerful spectroscopic techniques have been developed to address this challenge. While almost all of these techniques rely on inference of connectivity, the unambiguous determination of a small molecule’s structure requires X-ray and/or neutron diffraction studies. In practice, however, x-ray crystallography is rarely applied in routine organic chemistry due to intrinsic limitations of both the analytes and the technique. Here we report the use of the CryoEM method MicroED to provide routine and unambiguous structural determination of small organic molecules. From simple powders, with minimal sample preparation, we could collect high quality MicroED data from nanocrystals (~100x100x100 nm, ~10<sup>–15</sup>g) resulting in atomic resolution (<1 Å) crystal structures in minutes.</p>

scholarly journals Structural Characterization of Heterodinuclear ZnII-LnIII Complexes (Ln = Pr, Nd) with a Ring-Contracted H2valdien-Derived Schiff Base Ligand

2021 ◽  
Author(s):  
Shabana Noor ◽  
Richard Goddard ◽  
Fehmeeda Khatoon ◽  
Sarvendra Kumar ◽  
Rüdiger W. Seidel
Keyword(s):  
Molecular Structure ◽  
Schiff Base ◽  
Structural Characterization ◽  
Schiff Base Ligand ◽  
Crystal And Molecular Structure ◽  
X Ray ◽  
X Ray Crystallography ◽  
Imidazoline Ring

AbstractSynthesis and structural characterization of two heterodinuclear ZnII-LnIII complexes with the formula [ZnLn(HL)(µ-OAc)(NO3)2(H2O)x(MeOH)1-x]NO3 · n H2O · n MeOH [Ln = Pr (1), Nd (2)] and the crystal and molecular structure of [ZnNd(HL)(µ-OAc)(NO3)2(H2O)] [ZnNd(HL)(OAc)(NO3)2(H2O)](NO3)2 · n H2O · n MeOH (3) are reported. The asymmetrical compartmental ligand (E)-2-(1-(2-((2-hydroxy-3-methoxybenzylidene)amino)-ethyl)imidazolidin-2-yl)-6-methoxyphenol (H2L) is formed from N1,N3-bis(3-methoxysalicylidene)diethylenetriamine (H2valdien) through intramolecular aminal formation, resulting in a peripheral imidazoline ring. The structures of 1–3 were revealed by X-ray crystallography. The smaller ZnII ion occupies the inner N2O2 compartment of the ligand, whereas the larger and more oxophilic LnIII ions are found in the outer O2O2’ site. Graphic Abstract Synthesis and structural characterization of two heterodinuclear ZnII-LnIII complexes (Ln = Pr, Nd) bearing an asymmetrical compartmental ligand formed in situ from N1,N3-bis(3-methoxysalicylidene)diethylenetriamine (H2valdien) through intramolecular aminal formation are reported.

Crystal and molecular structure of trans-[RhCl(CO)(PtBu2Ph)2]

2018 ◽  
Vol 73 (12) ◽  
pp. 1029-1032
Author(s):  
Peter Mayer ◽  
Hans-Christian Böttcher
Keyword(s):  
Molecular Structure ◽  
Ir Spectroscopy ◽  
Crystal And Molecular Structure ◽  
Title Complex ◽  
High Yield ◽  
X Ray ◽  
Carbonyl Ligands ◽  
Pale Yellow ◽  
X Ray Crystallography ◽  
Type Complex

AbstractTreatment of THF solutions containing the rhodium(II) complex trans-[RhCl2(PtBu2Ph)2] (1) with [Fe2(CO)9] in the same solvent resulted in the formation of the Vaska-type complex trans-[RhCl(CO)(PtBu2Ph)2] (2) in high yield. The title complex 2 was obtained as pale yellow crystals, characterized by NMR and IR spectroscopy, as well as by microanalyses. Additionally, the molecular structure of 2 has been established by X-ray crystallography. As often reported for similar constituted compounds, the chlorido and carbonyl ligands in crystals of 2 are strongly disordered.

Synthesis and molecular structure of tetraphenylarsonium Tetrakis(benzenethiolato)-oxorhenate(V)-Acetonitrile (1/1)

1983 ◽  
Vol 36 (2) ◽  
pp. 253 ◽  
Author(s):  
AC McDonell ◽  
TW Hambley ◽  
MR Snow ◽  
AG Wedd
Keyword(s):  
Molecular Structure ◽  
Crystal And Molecular Structure ◽  
Crystal Data ◽  
Rhenium Atom ◽  
Space Group ◽  
X Ray ◽  
X Ray Crystallography

The salts Ph4As [ReO(SPh)4].MeCN and Ph4As [ReO(SePh)4] have been synthesized and characterized. The crystal and molecular structure of the thiolate compound has been determined by X-ray crystallography which reveals a square-pyramidal arrangement of ligand atoms around the central rhenium atom of the [ReO(SPh)4]- anion. Crystal data: a 9.756(4), b 18.171(3), c 25.684(4) �, space group P212121, Z 4.

Preparation of symmetric dibromides of 1,10-phenanthroline

1997 ◽  
Vol 75 (10) ◽  
pp. 1336-1339 ◽  
Author(s):  
Yutaka Saitoh ◽  
Take-aki Koizumi ◽  
Kohtaro Osakada ◽  
Takakazu Yamamoto
Keyword(s):  
Molecular Structure ◽  
Aqueous Medium ◽  
Good Yield ◽  
X Ray ◽  
X Ray Crystallography

Bromation of 1,10-phenanthroline with Br2 proceeds smoothly in the presence of S2Cl2 and pyridine to give 3,8-dibromo-1,10-phenanthroline in good yield. Bromation of 2,9-dibutoxy-1,10-phenanthroline with Br2, in an aqueous medium gives 5,6-dibromo-2,9-dibutoxy-1,10-phenanthroline selectively. Similar bromination of 4,7-dibutoxy-1,10-phenanthroline with Br2 gives 3,8-dibromo-4,7-dibutoxy-1,10-phenanthroline, which forms a 1:1 adduct with Cu(NO3)2. Molecular structure of the 1:1 adduct has been determined by X-ray crystallography. Keywords: bromination, 1,10-phenanthroline, 3,8-dibromo-1,10-phenanthroline.

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.

Molecular structure and dynamics of C-1-adamantyl substituted N-unsubstituted pyrazoles studied by solid state NMR spectroscopy and X-ray crystallography

1997 ◽  
pp. 1867-1876 ◽  
Author(s):  
Rosa María Claramunt ◽  
María Dolores Santa María ◽  
Isabelle Forfar ◽  
Francisco Aguilar-Parrilla ◽  
María Minguet-Bonvehí ◽  
...  
Keyword(s):  
Molecular Structure ◽  
Solid State ◽  
Nmr Spectroscopy ◽  
Solid State Nmr ◽  
X Ray ◽  
Solid State Nmr Spectroscopy ◽  
X Ray Crystallography ◽  
Structure And Dynamics

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.

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