scholarly journals π–π Noncovalent Interaction Involving 1,2,4- and 1,3,4-Oxadiazole Systems: The Combined Experimental, Theoretical, and Database Study

Molecules ◽  
2021 ◽  
Vol 26 (18) ◽  
pp. 5672
Author(s):  
Sergey V. Baykov ◽  
Alexander S. Mikherdov ◽  
Alexander S. Novikov ◽  
Kirill K. Geyl ◽  
Marina V. Tarasenko ◽  
...  
Keyword(s):  
Crystal Structures ◽  
13C Nmr Spectroscopy ◽  
Data Bank ◽  
Noncovalent Interaction ◽  
X Ray Diffraction ◽  
1H And 13C Nmr ◽  
Nci Analysis ◽  
Equilibrium Structures ◽  
Structural Database ◽  
Anti Hiv

A series of N-pyridyl ureas bearing 1,2,4- (1a, 2a, and 3a) and 1,3,4-oxadiazole moiety (1b, 2b, 3b) was prepared and characterized by HRMS, 1H and 13C NMR spectroscopy, as well as X-ray diffraction. The inspection of the crystal structures of (1–3)a,b and the Hirshfeld surface analysis made possible the recognition of the (oxadiazole)···(pyridine) and (oxadiazole)···(oxadiazole) interactions. The presence of these interactions was confirmed theoretically by DFT calculations, including NCI analysis for experimentally determined crystal structures as well as QTAIM analysis for optimized equilibrium structures. The preformed database survey allowed the verification of additional examples of relevant (oxadiazole)···π interactions both in Cambridge Structural Database and in Protein Data Bank, including the cocrystal of commercial anti-HIV drug Raltegravir.

scholarly journals Conformation-dependent restraints for polynucleotides: the sugar moiety

2019 ◽  
Vol 48 (2) ◽  
pp. 962-973
Author(s):  
Marcin Kowiel ◽  
Dariusz Brzezinski ◽  
Miroslaw Gilski ◽  
Mariusz Jaskolski
Keyword(s):  
Nucleic Acids ◽  
Crystal Structures ◽  
Protein Data Bank ◽  
Data Bank ◽  
Experimental Methods ◽  
Side Chain ◽  
Torsion Angles ◽  
Sugar Moiety ◽  
Structural Database ◽  
Different Parts

Abstract Stereochemical restraints are commonly used to aid the refinement of macromolecular structures obtained by experimental methods at lower resolution. The standard restraint library for nucleic acids has not been updated for over two decades and needs revision. In this paper, geometrical restraints for nucleic acids sugars are derived using information from high-resolution crystal structures in the Cambridge Structural Database. In contrast to the existing restraints, this work shows that different parts of the sugar moiety form groups of covalent geometry dependent on various chemical and conformational factors, such as the type of ribose or the attached nucleobase, and ring puckering or rotamers of the glycosidic (χ) or side-chain (γ) torsion angles. Moreover, the geometry of the glycosidic link and the endocyclic ribose bond angles are functionally dependent on χ and sugar pucker amplitude (τm), respectively. The proposed restraints have been positively validated against data from the Nucleic Acid Database, compared with an ultrahigh-resolution Z-DNA structure in the Protein Data Bank, and tested by re-refining hundreds of crystal structures in the Protein Data Bank. The conformation-dependent sugar restraints presented in this work are publicly available in REFMAC, PHENIX and SHELXL format through a dedicated RestraintLib web server with an API function.

Synthesis, Characterization, and Catalytic Activity of a Series of Aluminium–Amidate Complexes

2015 ◽  
Vol 68 (3) ◽  
pp. 357 ◽  
Author(s):  
Kevin P. Yeagle ◽  
Darryl Hester ◽  
Nicholas A. Piro ◽  
William G. Dougherty ◽  
W. Scott Kassel ◽  
...  
Keyword(s):  
Catalytic Activity ◽  
Nmr Spectroscopy ◽  
Diffraction Analysis ◽  
13C Nmr ◽  
13C Nmr Spectroscopy ◽  
X Ray Diffraction ◽  
Metathesis Reaction ◽  
Chloride Complexes ◽  
1H And 13C Nmr ◽  
X Ray

The aluminium complexes {[κ2-N,O-(t-BuNCOPh)]AlMe2}2 (2), [κ2-N,O-(t-BuNCOPh)]2AlMe (3), and [κ2-N,O-(t-BuNCOPh)]3Al (4) were prepared through the protonolysis reaction between trimethylaluminium and one, two, or three equivalents, respectively, of N-tert-butylbenzamide. Complex 2 was also prepared via a salt metathesis reaction between K(t-BuNCOPh) and dimethylaluminium chloride. Complexes 2–4 were characterized using 1H and 13C NMR spectroscopy. Single-crystal X-ray diffraction analysis of the complexes corroborated ligand : metal stoichiometries and revealed that all the amidate ligands coordinate to the aluminium ion in a κ2 fashion. The Al–amidate complexes 2–4 were viable catalyst precursors for the Meerwein–Ponndorf–Verley–Oppenauer reduction–oxidation manifold, successfully interconverting several classes of carbonyl and alcohol substrates.

scholarly journals Synthesis of mono and bis-substituted asymmetrical compounds, (1-(pyridin-2-yl)ethylidene)carbonohydrazide and 1-(2'-hydroxybenzylidene)-5-(1'-pyridylethylidene)carbonohydrazone: Structural characterization and antioxidant activity study

2020 ◽  
Vol 11 (4) ◽  
pp. 285-290
Author(s):  
Thierno Moussa Seck ◽  
Fatou Dieng Faye ◽  
Aissatou Alioune Gaye ◽  
Ibrahima Elhadji Thiam ◽  
Ousmane Diouf ◽  
...  
Keyword(s):  
Nitrogen Atom ◽  
Crystal Packing ◽  
Condensation Reaction ◽  
13C Nmr Spectroscopy ◽  
Azomethine Nitrogen ◽  
Monoclinic Space Group ◽  
X Ray Diffraction ◽  
1H And 13C Nmr ◽  
Azomethine Nitrogen Atom ◽  
Cell Parameters

Carbonohydrazide was used for synthetizing a new dissymmetrical bis-substituted Schiff base 1-(2'-hydroxybenzylidene)-5-(1'-pyridylethylidene)carbonohydrazone (2). A mono substituted compound (1-(pyridin-2-yl)ethylidene)carbonohydrazide (1) was firstly prepared by condensation reaction of carbonohydrazide and 2-acetylpyridine in 1:1 ratio. Secondly, compound 2 was obtained by condensation reaction of compound 1 and salicylaldehyde in 1:1 ratio. The prepared compounds were characterized by elemental analysis, infrared and 1H and 13C NMR spectroscopy techniques, and the structure of compound 2 was determined by single-crystal X-ray diffraction study. The compound 2 (C15H15N5O2) crystallises in the monoclinic space group P21/c with the following unit cell parameters: a = 8.3683(3) Å, b = 13.9986(4) Å, c = 12.1610(4) Å, β = 97.512(3)°, V = 1412.37(8) Å3, Z = 4, T = 100(2) K, μ(MoKα) = 0.098 mm-1, Dcalc = 1.398 g/cm3, 6057 reflections measured (5.708° ≤ 2Θ ≤ 54.962°), 6057 unique (Rsigma = 0.0395) which were used in all calculations. The final R1 was 0.0474 (I > 2σ(I)) and wR2 was 0.1971 (all data). The oxygen atom O1 and the azomethine nitrogen atom N5 adopt cis-configuration relative to the C8-N4 bond, while O1 adopts trans-configuration with the azomethine nitrogen atom N2 relative to C8-N3 bond. The crystal packing of compound 2 is stabilized by intramolecular O(phenol)–H···N(carbohydrazide) and intermolecular N (carbohydrazide)–H···O (carbo-hydrazide) hydrogen bonds which form layers parallel to [010] axis. Additional C–H···O hydrogen bond consolidate the structure. The carbonohydrazide moiety C=N–N–C(O)–N–N=C fragment and the phenyl ring are almost coplanar; with an angle of 1.73(1)° between their means plans. The dihedral angle between the mean planes of the phenyl and the pyridine rings is 22.267(2)°.

X-ray diffraction and packing analysis on vintage crystals: Wilhelm Koerner's nitrobenzene derivatives from the School of Agricultural Sciences in Milano

2004 ◽  
Vol 60 (5) ◽  
pp. 609-620 ◽  
Author(s):  
Francesco Demartin ◽  
Giuseppe Filippini ◽  
Angelo Gavezzotti ◽  
Silvia Rizzato
Keyword(s):  
Crystal Structures ◽  
Molecular Structures ◽  
X Ray Diffraction ◽  
Factors Affecting ◽  
Correct Assignment ◽  
Molecular Electron ◽  
Structural Database ◽  
Potential Methods ◽  
The University ◽  
Crystal Packings

The crystal structures of six nitrotoluene derivatives, synthesized by Wilhelm Koerner about a century ago and retrieved from a depository at the University of Milano, were determined. The correct assignment of molecular structures is verified. The geometry of the nitro groups and factors affecting the orientation of nitro groups with respect to the benzene ring are discussed, also using an auxiliary set of crystal structures retrieved from the Cambridge Structural Database. The crystal packings have been analyzed, and lattice energies have been calculated by atom–atom potential methods and by the newly proposed Pixel method. This method allows a more complete description of intermolecular potentials in terms of the interaction between molecular electron densities and separate Coulombic, polarization, dispersion and overlap repulsion energies. Lattice vibrations and external entropies were calculated by lattice-dynamical procedures. The results of the Pixel energy calculations allow a reliable, quantitative assessment of the relative importance of stacking interactions and hydrogen bonding in the rationalization of the recognition modes of nitrobenzene derivatives, which is impossible to attain using only qualitative atom– atom geometry concepts.

scholarly journals Synthesis and Characterization of Ammonium Acesulfamate

2014 ◽  
Vol 69 (6) ◽  
pp. 737-741 ◽  
Author(s):  
Gustavo A. Echeverría ◽  
Oscar E. Piro ◽  
Beatriz S. Parajón-Costa ◽  
Enrique J. Baran
Keyword(s):  
Molecular Structure ◽  
Ammonium Carbonate ◽  
Crystal And Molecular Structure ◽  
13C Nmr Spectroscopy ◽  
Synthesis And Characterization ◽  
X Ray Diffraction ◽  
Orthorhombic Space Group ◽  
1H And 13C Nmr ◽  
X Ray

Ammonium acesulfamate, (NH4)C4H4NO4S, was prepared by the reaction of acesulfamic acid and ammonium carbonate in aqueous solution, and characterized by elemental analysis and 1H and 13C NMR spectroscopy. Its crystal and molecular structure was determined by single-crystal X-ray diffraction methods. The substance crystallizes in the orthorhombic space group Pnma with Z = 4 molecules per unit cell. The NH4+ ion generates medium to strong hydrogen bonds with the carbonylic oxygen, the iminic nitrogen and the sulfonyl oxygen atoms of the acesulfamate anion. The FTIR spectrum of the compound was also recorded and is briefly discussed.

scholarly journals Synthesis, Crystal Structure and Bioactivity of Phenazine-1-carboxylic Acylhydrazone Derivatives

Molecules ◽  
2021 ◽  
Vol 26 (17) ◽  
pp. 5320
Author(s):  
Shouting Wu ◽  
Xi Liang ◽  
Fang Luo ◽  
Hua Liu ◽  
Lingyi Shen ◽  
...  
Keyword(s):  
Carboxylic Acid ◽  
Condensation Reaction ◽  
Acid Hydrazide ◽  
13C Nmr Spectroscopy ◽  
X Ray Diffraction ◽  
1H And 13C Nmr ◽  
X Ray ◽  
Thiazolyl Blue Tetrazolium Bromide ◽  
Thiazolyl Blue Tetrazolium

A phenazine-1-carboxylic acid intermediate was synthesized from the reaction of aniline and 2-bromo-3-nitro-benzoic acid. It was then esterified and reacted with hydrazine hydrate to afford phenazine-1-carboxylic hydrazine. Finally, 10 new hydrazone compounds 3a–3j were obtained by the condensation reaction of phenazine-1-carboxylic acid hydrazide and the respective aldehyde-containing compound. The structures were characterized by 1H and 13C NMR spectroscopy, MS and single crystal X-ray diffraction. The antitumor activity of the target compounds in vitro (HeLa and A549) was determined by thiazolyl blue tetrazolium bromide. The results showed that compound (E)-N′-(2-hydroxy-4-(2-(piperidine-1-yl) ethoxy) benzyl) phenazine-1-carbonyl hydrazide 3d exhibited good cytotoxic activity.

scholarly journals Bimetallic Aluminum 5,6-Dihydro-7,7-dimethyl quinolin-8-olates as Pro-Initiators for the ROP of ε-CL; Probing the Nuclearity of the Active Initiator

Polymers ◽  
2018 ◽  
Vol 10 (7) ◽  
pp. 764 ◽  
Author(s):  
Qiurui Zhang ◽  
Wenjuan Zhang ◽  
Gregory Solan ◽  
Tongling Liang ◽  
Wen-Hua Sun
Keyword(s):  
Nmr Spectroscopy ◽  
Good Control ◽  
13C Nmr Spectroscopy ◽  
Molecular Structures ◽  
Linear Polymers ◽  
X Ray Diffraction ◽  
1H And 13C Nmr ◽  
Operational Temperature ◽  
Species Being ◽  
Active Initiator

Six examples of aluminum 5,6-dihydro-7,7-dimethylquinolin-8-olates, [{2-R1-7,7-Me2-8-R2C9H6N-8-O}AlR32]2 (R1 = R2 = H, R3 = Me C1; R1 = R2 = H, R3 = Et C2; R1 = R2 = H, R3 = i-Bu C3; R1 = Cl, R2 = H, R3 = Me C4; R1 = H, R2 = R3 = Me C5; R1 = Cl, R2 = R3 = Me C6), have been prepared by treating the corresponding pro-ligand (L1–L4) with either AlMe3, AlEt3 or Al(i-Bu)3. All complexes have been characterized by 1H and 13C NMR spectroscopy and in the case of C1 and C4 by single crystal X-ray diffraction; dimeric species are a feature of their molecular structures. In the presence of PhCH2OH (BnOH), C1–C6 displayed good control and efficiency for the ROP of ε-CL with almost 100% conversion achievable in 10 min at 90 °C; the chloro-substituted C4 and C6 notably exhibited the lowest activity of the series. However, in the absence of BnOH, C1 showed only low activity with 15% conversion achieved in 30 min forming a linear polymer capped with either a methyl or a L1 group. By contrast, when one or more equivalents of BnOH was employed in combination with C1, the resulting catalyst was not only more active but gave linear polymers capped with BnO end-groups. By using 1H and 27Al NMR spectroscopy to monitor solutions of C1, C1/BnOH and C1/BnOH/10 ε-CL over a range of temperatures, some support for a monomeric species being the active initiator at the operational temperature is presented.

scholarly journals Synthesis, structural and conformational study of selected N-substituted phthalimides

2005 ◽  
Vol 3 (4) ◽  
pp. 683-704 ◽  
Author(s):  
Isabel Iriepa ◽  
F. Javier Villasante ◽  
Enrique Gálvez ◽  
Antonio Herrera ◽  
Angel Sánchez ◽  
...  
Keyword(s):  
Double Resonance ◽  
13C Nmr Spectroscopy ◽  
Two Dimensional ◽  
X Ray Diffraction ◽  
1H And 13C Nmr ◽  
Conformational Studies ◽  
One Dimensional ◽  
X Ray ◽  
Nmr Techniques ◽  
New Compounds

AbstractThis paper synthesizes N-substituted phthalimides derived from nitrogen heterocycles as potential 5-HT4 ligands by using the Mitsunobu reaction. Conformational studies of some of the new compounds have been conducted using 1H and 13C-NMR spectroscopy. Proton and carbon resonances were achieved through the application of one-dimensional selective NOE, two-dimensional NMR techniques-homonuclear COSY-45, NOESY and heteronuclear 1H-13C HMQC correlated spectroscopy- and double resonance experiments. The crystal structure of compound 1 was determined by X-ray diffraction.

An Improved Synthesis of 3,6-Dihydro-as-indacene

Synthesis ◽  
2020 ◽  
Author(s):  
Marcelo Preite ◽  
Elies Molins ◽  
Ivonne Chávez ◽  
Mungalimane K. Amshumali ◽  
Cesar Morales-Verdejo ◽  
...  
Keyword(s):  
Ammonium Hydroxide ◽  
13C Nmr Spectroscopy ◽  
X Ray Diffraction ◽  
1H And 13C Nmr ◽  
Intramolecular Cycloaddition ◽  
X Ray ◽  
Full Characterization ◽  
Mannich Condensation ◽  
Acidic Conditions

AbstractThis contribution describes an updated synthetic route to 3,6-dihydro-as-indacene along with full characterization of all inter­mediates. The title compound is prepared by Mannich condensation of 2-methylfuran with formaldehyde and dimethylamine hydrochloride, quaternization of the resulting amine with methyl iodide, and conversion into the ammonium hydroxide salt by treatment with silver oxide in water. Subsequent Hoffmann elimination and [6,6]-cycloaddition through pyrolysis produces a furanocyclophane, which after photooxidation, intramolecular cycloaddition, and dehydration with sodium carbonate affords 2,3,6,7-tetrahydro-1,8-dione-as-indacene. Reduction of this diketone gives a mixture of alcohols, which after dehydration under slightly basic or acidic conditions produces 3,6-dihydro-as-indacene. The structure is confirmed by X-ray diffraction, and all intermediates are characterized by means of 1H and 13C NMR spectroscopy.

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