1,177 results on '"Alkane stereochemistry"'
Search Results
2. Palladium-Catalyzed Formal (3 + 2) Cycloaddition Reactions of 2-Nitro-1,3-enynes with Vinylaziridines, -epoxides, and -cyclopropanes
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Andrew J. Tague, Christopher Richardson, Melanie A. Drew, Stephen G. Pyne, and Christopher J. T. Hyland
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010405 organic chemistry ,Chemistry ,Organic Chemistry ,Diastereomer ,chemistry.chemical_element ,010402 general chemistry ,01 natural sciences ,Biochemistry ,Medicinal chemistry ,Cycloaddition ,0104 chemical sciences ,Catalysis ,Elimination reaction ,Alkane stereochemistry ,Nitro ,Physical and Theoretical Chemistry ,Single crystal ,Palladium - Abstract
A two-step Pd-catalyzed (3 + 2) cycloaddition/HNO2 elimination reaction sequence has been developed to give novel cyclic 1,3-dien-5-yne systems from Pd-stabilized zwitterionic 1,3-dipoles and 2-nitro-1,3-enyne substrates. The process is highly atom-efficient and tolerates the reaction of 2-vinyloxirane, 1-tosyl-2-vinylaziridine, and diethyl 2-vinylcyclopropane-1,1-dicarboxylate derived 1,3-dipoles with a variety of 2-nitro-1,3-enyne substrates. The stereochemistry of the intermediate (3 + 2) cycloadducts was determined by single crystal X-ray analysis. Furthermore, a selective kinetic elimination of the cycloadduct with an antiperiplanar relationship between the NO2 group and the participating hydrogen was demonstrated, allowing for efficient isolation of a single diastereoisomer of the cycloadduct.
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- 2021
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3. A rotational spectroscopic and ab initio study of cis- and trans-(−)-carveol: further insights into conformational dynamics in monoterpenes and monoterpenoids
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Raiden Speelman, Arsh Hazrah, Wolfgang Jäger, and Mohamad Al-Jabiri
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Quantitative Biology::Biomolecules ,Materials science ,010304 chemical physics ,Hydrogen bond ,Ab initio ,General Physics and Astronomy ,010402 general chemistry ,01 natural sciences ,Transition state ,0104 chemical sciences ,Crystallography ,Atomic orbital ,0103 physical sciences ,Alkane stereochemistry ,Physical and Theoretical Chemistry ,Conformational isomerism ,Cis–trans isomerism ,Natural bond orbital - Abstract
Broadband rotational spectra of cis- and trans-(−)-carveol were recorded using a chirped pulse Fourier transform microwave spectrometer in the 2–6 GHz region. To aid in spectroscopic assignments a theoretical conformational search was carried out using a combination of a two dimensional potential energy scan, scanning over the isopropenyl and hydroxyl groups torsional angles, and the Conformer–Rotamer Ensemble Sampling Tool. The theoretical results yielded a total of 23 conformers for the trans- and 19 for the cis-conformer. Utilizing these results, a total of five conformers could be assigned in the spectra, two for trans- and three for cis-(−)-carveol. In both conformers of trans-carveol, the isopropenyl group is in an equatorial position and adopts the gauche− conformation in one and the the antiperiplanar conformation in the other, with the hydroxyl group in the axial position and adopting the antiperiplanar conformation in both. For cis-carveol the analogous conformers were found but with the hydroxyl in a equatorial position, in addition to an axial isopropenyl conformer. To interpret the experimental intensity patterns and examine conformational cooling effects, transition states were identified using the Synchronous Transit Quasi-Newton method. We found that most of the higher energy conformers cool out to the five experimentally observed ones and the others are too high in energy to be sufficiently populated in the molecular expansion for an experimental observation. To investigate the interesting preference for the axial position of the isopropenyl group in cis-(−)-carveol, which has not been seen before in monoterpenoids, non-covalent interactions and quantum theory of atoms-in-molecules analyses were carried out. These analyses reveal a hydrogen bonding interaction between the hydroxyl group and the isopropenyl π-system. A natural bond orbital analysis of the hydrogen bond allowed us to decompose the interaction into its constituent natural bond orbitals, and to quantify its strength. Although relatively weak, the hydrogen bond tips the balance towards the axial position of the isopropenyl group.
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- 2021
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4. SYNTHESIS, CRYSTAL STRUCTURE, AND DFT STUDIES OF ETHYL 4-HYDROXY-2-(4-METHOXYPHENYL)-5-OXO- 1-PHENYL-2,5-DIHYDRO-1H-PYRROLE-3-CARBOXYLATE
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Hamideh Ahankar, Ali Ramazani, H. Saeidian, Katarzyna Ślepokura, and Tadeusz Lis
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Chemical shift ,Crystal structure ,Medicinal chemistry ,Inorganic Chemistry ,chemistry.chemical_compound ,chemistry ,Alkane stereochemistry ,Materials Chemistry ,Molecule ,Carboxylate ,Physical and Theoretical Chemistry ,Single crystal ,Derivative (chemistry) ,Pyrrole - Abstract
An efficient method for the synthesis of a new highly substituted pyrrolidinone derivative is developed via a three-component one-pot reaction of aniline, diethyl acetylenedicarboxylate, and 4-anisaldehyde. The structure of ethyl 4-hydroxy-2-(4-methoxyphenyl)-5-oxo-1-phenyl-2,5-dihydro-1H-pyrrole-3-carboxylate is confirmed by FTIR, 1H and 13C NMR spectroscopy. Unambiguous evidence for the structure of the synthesized product is obtained from the single crystal X-ray analysis. The comparison of both its molecular structure and intermolecular interactions with the previously known analogous compounds reveals that the mutual syn- or antiperiplanar orientation of ester C=O and pyrrolinone-bound OH is related to the type of molecular dimers formed in the solid state. The geometrical structure, the HOMO–LUMO analysis (electrophilicity index), 1H and 13C chemical shifts of the desired product are also calculated by DFT at the B3LYP level with the 6-31++G(d,p) basis set. The calculated chemical shifts are in compliance with the experimental data.
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- 2021
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5. Molecular Dynamics Simulation of the Conformational Preferences of Pseudouridine Derivatives: Improving the Distribution in the Glycosidic Torsion Space
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Joanna Sarzynska, Ansuman Lahiri, and Nivedita Dutta
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chemistry.chemical_classification ,Physics ,010304 chemical physics ,General Chemical Engineering ,Carbohydrates ,Molecular Conformation ,Torsion (mechanics) ,Thermodynamics ,Glycosidic bond ,General Chemistry ,Molecular Dynamics Simulation ,Library and Information Sciences ,01 natural sciences ,Pseudouridine ,0104 chemical sciences ,Computer Science Applications ,010404 medicinal & biomolecular chemistry ,chemistry.chemical_compound ,Molecular dynamics ,chemistry ,0103 physical sciences ,Alkane stereochemistry ,Glycosides ,Isomerization - Abstract
There are only four derivatives of pseudouridine (Ψ) that are known to occur naturally in RNA as post-transcriptional modifications. We have studied the conformational consequences of pseudouridylation and further modifications using replica exchange molecular dynamics simulations at the nucleoside level, and the simulated conformational preferences were compared with the available experimental (NMR) data. We found that the existing AMBER FF99-derived parameters for these nucleosides did not reproduce the observed experimental features and while the recommended bsc0 correction could be combined with these parameters leading to an improvement in the description of sugar pucker distributions, the χOL3 correction could not be applied to these nucleosides as such because of base isomerization. On the other hand, the revised χ torsion parameters (χIDRP) for Ψ developed earlier by us (Deb, I., J. Comput. Chem., 2016, 37, 1576-1588) in combination with the AMBER provided parameters and the revised γ torsion parameters generated conformational distributions, which generally were in better agreement with the experimental data. A significant shift of the distribution of base orientation toward the syn conformation was observed with our revised parameter sets compared to the large excess of anti conformation predicted by the FF99 parameters. Overall, our observations indicated that our revised set of parameters (χIDRP) for Ψ were also able to generate conformational distributions for all of the derivatives of Ψ in better agreement with the experimental data.
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- 2020
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6. Synthesis and crystal structure of 1,1′-bis{[4-(pyridin-2-yl)-1,2,3-triazol-1-yl]methyl}ferrocene, and its complexation with CuI
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Frank R. Fronczek, Aaron P. Naquin, Connor P. Brochon, and Uttam R. Pokharel
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crystal structure ,Crystal structure ,010402 general chemistry ,01 natural sciences ,Medicinal chemistry ,Research Communications ,lcsh:Chemistry ,Crystal ,chemistry.chemical_compound ,Reaction sequence ,disubstituted ferrocene ,Alkane stereochemistry ,General Materials Science ,1,1′-bis(pyridyltriazoylmethyl)ferrocene ,010405 organic chemistry ,Chemistry ,Ligand ,General Chemistry ,Condensed Matter Physics ,0104 chemical sciences ,tetradentate ligand ,lcsh:QD1-999 ,Ferrocene ,copper(I) complex ,Yield (chemistry) ,Click chemistry ,1,1′-bis(pyridyltriazoylmethyl)ferrocene ,click reaction ,tetradentate ligand - Abstract
The ferrocene-bridged compound 1,1′-bis(pyridyltriazoylmethyl)ferrocene acquires an anti conformation in its solid state but forms a discrete tetranuclear [2 + 2] complex with [Cu(CH3CN)4](PF6) in solution., The title compound, [Fe(C13H11N4)2], was synthesized starting from 1,1′-ferrocenedicarboxylic acid in a three-step reaction sequence. The dicarboxylic acid was reduced to 1,1′-ferrocenedimethanol using LiAlH4 and subsequently converted to 1,1′-bis(azidomethyl)ferrocene in the presence of NaN3. The diazide was treated with 2-ethynylpyridine under ‘click’ conditions to give the title compound in 75% yield. The FeII center lies on an inversion center in the crystal. The two pyridyltriazole wings are oriented in an anti conformation and positioned exo from the FeII center. In the solid state, the molecules interact by C—H⋯N, C—H⋯π, and π–π interactions. The complexation of the ligand with [Cu(CH3CN)4](PF6) gives a tetranuclear dimeric complex.
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- 2020
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7. Synthesis and Evaluation of FICA Derivatives as Chiral Derivatizing Agents
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Hiroyuki Teramae, Tomoyo Kamei, Tamiko Takahashi, and Jyunichi Koyanagi
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Magnetic Resonance Spectroscopy ,Proton Magnetic Resonance Spectroscopy ,Carboxylic Acids ,Substituent ,Fluorine-19 NMR ,010402 general chemistry ,01 natural sciences ,Medicinal chemistry ,chemistry.chemical_compound ,symbols.namesake ,Drug Discovery ,Alkane stereochemistry ,Chiral derivatizing agent ,Benzene ,Conformational isomerism ,Density Functional Theory ,010405 organic chemistry ,Diastereomer ,Esters ,Stereoisomerism ,Fluorine ,General Chemistry ,General Medicine ,0104 chemical sciences ,Gibbs free energy ,chemistry ,symbols - Abstract
1-Fluoroindan-1-carboxyic acid (FICA) derivatives containing a monosubstituted benzene ring (1b-e) were synthesized as their methyl esters and their potential as chiral derivatizing agents (CDAs) were assessed by both 19F- and 1H-NMR spectroscopy. Introduction of a substituent at the 4-position in the benzene ring caused a 1.2-2 fold increase in ΔδF values when compared with that of FICA. This increase was investigated using a correlation model for 19F-NMR and by the order of the stability of the synperiplanar (sp) and antiperiplanar (ap) conformers of the (R,S) and (S,S) diastereomers from the Gibbs' free energy at 298.15 K.
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- 2020
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8. Bent Bond/Antiperiplanar Hypothesis: Modulating the Reactivity and the Selectivity in the Glycosylation of Bicyclic Pyranoside Models
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Jean-François Parent, Pierre Deslongchamps, and Ghislain Deslongchamps
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animal structures ,Glycosylation ,Bicyclic molecule ,010405 organic chemistry ,Stereochemistry ,Organic Chemistry ,macromolecular substances ,010402 general chemistry ,01 natural sciences ,Bent bond ,0104 chemical sciences ,carbohydrates (lipids) ,chemistry.chemical_compound ,chemistry ,Alkane stereochemistry ,lipids (amino acids, peptides, and proteins) ,Reactivity (chemistry) ,Selectivity - Abstract
Glycosylation reactions were performed on a series of bicyclic C2-substituted pyranoside models to isolate and analyze factors that control the glycosylation stereoselectivities observed in carbohy...
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- 2020
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9. Applying the Bent Bond/Antiperiplanar Hypothesis to the Stereoselective Glycosylation of Bicyclic Furanosides
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Xavier Bertrand, Ghislain Deslongchamps, Jean-François Parent, and Pierre Deslongchamps
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Glycosylation ,Bicyclic molecule ,010405 organic chemistry ,Stereochemistry ,Chemistry ,Organic Chemistry ,010402 general chemistry ,01 natural sciences ,Bent bond ,0104 chemical sciences ,carbohydrates (lipids) ,chemistry.chemical_compound ,Nucleophile ,Alkane stereochemistry ,lipids (amino acids, peptides, and proteins) ,Stereoselectivity - Abstract
The glycosylation stereoselectivities for a series of bicyclic furanoside models have been carried out in the presence of weak nucleophiles. These results were analyzed through the bent bond/antiperiplanar hypothesis (BBAH) orbital model to test its validity. According to the BBAH, incoming nucleophiles displace one of the two bent bonds of bicyclic oxocarbenium ion intermediates in an antiperiplanar fashion. The glycosylation stereoselectivity is then governed by the displacement of the weaker bent bond as determined by the presence of electron-withdrawing or -donating substituents at C
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- 2019
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10. Nature and origin of γ-gauche effect in sulfoxides: A density functional theory and information-theoretic approach study
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Bin Wang, Dongbo Zhao, Chunying Rong, Donghai Yu, and Shubin Liu
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Physics ,Gauche effect ,General Physics and Astronomy ,Charge density ,02 engineering and technology ,Dihedral angle ,010402 general chemistry ,021001 nanoscience & nanotechnology ,Hyperconjugation ,01 natural sciences ,0104 chemical sciences ,Chemical physics ,Alkane stereochemistry ,Single bond ,Density functional theory ,Physical and Theoretical Chemistry ,0210 nano-technology ,Conformational isomerism - Abstract
Bulky vicinal groups around a single bond usually prefer to be in the opposite (anti) conformation but when extra interactions come into play, more stable could be the gauche conformer, where the neighboring groups embrace a dihedral angle around 60°. This is called the gauche effect. The γ-gauche effect historically features the upfield shift of 13C NMR spectra when a carbon atom and its nonprotonic γ-substituent are in a gauche arrangement. In this work, using sulfoxides as illustrative examples, we show that the nature of the γ-gauche effect is the same as that of the gauche effect, i.e., the gauche conformation is more stable than the anti conformation. To unveil the origin of this effect, we employ two total energy partition schemes in density functional theory and four quantities from the information-theoretic approach. Our results unambiguously show that the γ-gauche effect is of the stereoelectronic origin with a multifaceted nature. Its origin can be understood from a few different perspectives including energetic contributions, dipole moment, charge distribution, hyperconjugation, and information theory. Substantially different from other stereoelectronic effects such as anomeric and generalized anomeric effects, this effect has its unique features as demonstrated from our results in the present work. Having successfully established the link of the γ-gauche with other gauche effects and unveiled its multi-faceted origin, this study should shed new light towards the comprehensive understanding about this important effect of conformational stability in sulfoxides and other systems alike.
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- 2019
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11. Steric and electronic evaluations of P(o-tol)R 2, where R is phenyl or cyclohexyl: crystal structures of SeP(o-tol)R 2
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Wade L. Davis and Alfred Muller
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Steric effects ,Substituent ,Crystal structure ,Condensed Matter Physics ,Inorganic Chemistry ,Bond length ,chemistry.chemical_compound ,Crystallography ,chemistry ,Alkane stereochemistry ,Materials Chemistry ,Density functional theory ,Physical and Theoretical Chemistry ,Conformational isomerism ,Monoclinic crystal system - Abstract
The crystal structures of SeP(o-tol)R 2, where o-tol is ortho-tolyl (2-methylphenyl) and R is Ph (phenyl), namely (2-methylphenyl)diphenylphosphane selenide, C19H17PSe, or Cy (cyclohexyl), namely dicyclohexyl(2-methylphenyl)phosphane selenide, C19H29PSe, were determined to aid in the evaluation of the steric and electronic behaviour of these analogous phosphane compounds. The compounds crystallized in similar monoclinic crystal systems, but are differentiated in their unit cells by a doubling of the number of independent molecules for R = Cy (Z′ = 2) and the choice of glide plane by convention. The preferred orientation for the o-tolyl substituent obtained from the X-ray structural analysis is gauche for R = Ph and anti for R = Cy (using the Se—P—C ipso —C ortho torsion angles as reference). Density functional theory (DFT) calculations showed both conformations to be equally probable and indicate that the preferred solid-state conformer is probably due to the minimization of repulsion energies, resulting in a packing arrangement primarily featuring weak C—H...Se interactions and additional C—H...π interactions in the R = Ph structure. A detailed electronic and steric analysis was conducted on both phosphanes using Se—P bond lengths, multinuclear NMR 1 J Se–P coupling constants, theoretical topological evaluation and crystallographic and solid-angle calculations, and compared to selected literature examples. The results indicate that the use of the o-tolyl substituent increases both the electron-donating capability and the steric size, but is also dependent on whether the o-tolyl group adopts a gauche or anti conformation. The single-crystal geometrical data are unable to detect electronic differences between these two structures due to the somewhat large displacement parameters observed for the Se atom in the R = Cy structure.
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- 2019
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12. Solid State Structure and Intermolecular Interactions of two N-Benzylidenephenylethylamines
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Sebastian Chaves, Adrián Pérez-Redondo, and Rodolfo Quevedo
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Crystallography ,Chemistry ,Hydrogen bond ,Alkane stereochemistry ,Intermolecular force ,Moiety ,Molecule ,Aromaticity ,General Chemistry ,Crystal structure ,Condensed Matter Physics ,Ring (chemistry) - Abstract
This article describes single crystal X-ray diffraction studies of two Schiff bases containing hydroxyl groups in aromatic rings: N-(4-hydroxybenzylidene)phenylethylamine (1) and N-(4-hydroxy-3-methoxybenzylidene)tyramine (2). Molecules of compound 1, with just one phenolic OH group, adopted an anti conformation, and were associated in zigzag chains with O–H···N hydrogen bonds between the azomethine fragment and the hydroxyl group. However, a gauche conformation was preferred by compound 2, which contained two hydroxyl groups in aromatic rings. Molecules of 2 were arranged in a three-dimensional array through O–H···N and O–H···O hydrogen bonding interactions. The results highlighted the importance of OH positions in the aromatic ring for the structural behaviour of the Schiff bases derived from phenylethylamines. Molecules of Schiff bases containing the moiety ArCH=N–CH2CH2Ar with one or two hydroxyl groups in the para position in the aromatic rings are associated in zigzag chains in the solid state through O–H···N hydrogen bonding interactions.
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- 2019
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13. The rotameric (R*,S*)- and (R*,R*)-biaryl-3,3′-diphthalides of polyphenylene series
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V. A. Kraikin, Sergey N. Salazkin, T. A. Yangirov, A. A. Fatykhov, Leonard M. Khalilov, E. S. Meshcheryakova, E. A. Sedova, and Sergey P. Ivanov
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010405 organic chemistry ,Chemical shift ,Chemical structure ,Organic Chemistry ,Diastereomer ,010402 general chemistry ,01 natural sciences ,Biochemistry ,0104 chemical sciences ,Phthalide ,chemistry.chemical_compound ,Crystallography ,chemistry ,Drug Discovery ,Halogen ,Alkane stereochemistry ,Solubility ,Conformational isomerism - Abstract
A wide range of diastereomeric pairs of biaryl-3,3′-diphthalides with aromatic (heteroaromatic) substituents of polyphenylene series (including halogen substituted) was synthesized. All of them were separated and characterized by the methods of X-ray analysis, HPLC, IR-, 1H and 13C NMR spectroscopy. It was determined that solubility, tendency to adsorption and related to it retention times, chemical shifts of equivalent hydrogen and carbon atoms of biaryl-3,3′-diphthalides diastereoisomers are determined firstly by the stereo-electronic effects of two adjacent strongly polar phthalide groups. It was shown that both in crystalline phase and in solution all the diphthalides, regardless of the chemical structure of their substituents, are existing as stable rotamers with cis or synperiplanar (chiral forms) and trans or antiperiplanar (meso-forms) conformation.
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- 2019
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14. Structural, thermal and topological characterization of coordination networks containing flexible aminocarboxylate ligands with a central biphenylene scaffold
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Patrick Scilabra, Andrea Delledonne, Claudia Carraro, Davide Balestri, Paolo Pelagatti, Paolo Pio Mazzeo, Lucia Carlucci, and Alessia Bacchi
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Ligand ,Supramolecular chemistry ,02 engineering and technology ,General Chemistry ,Biphenylene ,010402 general chemistry ,021001 nanoscience & nanotechnology ,Condensed Matter Physics ,Topology ,01 natural sciences ,0104 chemical sciences ,chemistry.chemical_compound ,chemistry ,Transition metal ,Alkane stereochemistry ,Molecule ,General Materials Science ,Amine gas treating ,0210 nano-technology ,Stoichiometry - Abstract
Herein, four different coordination networks were isolated and structurally characterized by combining two aminocarboxylate ligands, 4,4′-[biphenyl-4,4′-diylbis(azanediyl)]dibenzoic acid and 5,5′-[biphenyl-4,4′-diylbis(azanediyl)]diisophthalic acid (H2L1 and H4L2, respectively), with different transition metals (Zn(II), Zr(IV) and Cd(II)) under solvothermal conditions. The reaction between H2L1 and Zn(NO3)2·6H2O led to two different coordination networks. In PUMflex1-Zn, which has the formula {[Zn4O(L1)3(DMF)2](DMF)5}n·(DMF)x, the ligand always displays a syn conformation (with respect to the central biphenylene scaffold), whereas in the polymorph PUMflex1.1-Zn, one of the three ligands composing the asymmetric unit adopts an anti conformation. Although the two supramolecular isomers have equivalent stoichiometry and dimensionality, they show different topologies and entanglement types: parallel polycatenation of the 63-hcb and 2-fold interpenetration of the 44-sql layers, respectively. In the case of PUMflex1-Zr, with the formula {[Zr6O4(OH)8(L1)4(H2O)2]n·(DMF)x, H2L1 exclusively adopts the syn conformation, forming 1D-chains of rugby-ball shaped aggregates (topological type 2,8C1) interconnected through H-bonds with water molecules. In contrast, H4L2 behaves as a dianionic ligand in PUMflex2-Cd, with the formula [Cd(κ2-COO)2(DMF)3(DMF)]n, forming 1D zig-zag chains connected through the N–H⋯OC(OH) H-bonds to provide planar layers of sql topology. In all cases, the ability of the amine functions to interact with the H-bond active guests is structurally highlighted by the recurrent N–H⋯ODMF interaction modelled in the X-ray structures.
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- 2019
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15. Graphical Transition Moment Decomposition and Conceptual Density Functional Theory Approaches to Study the Fundamental and Lower-Level Overtone Absorption Intensities of Some OH Stretching Vibrations
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Satoshi Yabushita, Shunki Furudate, Yuto Kugaya, and Masafumi Tsuyuki
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Quantitative Biology::Biomolecules ,Electron density ,010304 chemical physics ,Chemistry ,Atoms in molecules ,Transition dipole moment ,010402 general chemistry ,01 natural sciences ,Molecular physics ,0104 chemical sciences ,Dipole ,0103 physical sciences ,Alkane stereochemistry ,Molecule ,Density functional theory ,Physical and Theoretical Chemistry ,Conformational isomerism - Abstract
The investigation of electron density migrations caused by molecular structure changes is of central importance in various fields of chemistry. To address this topic in general and to study absorption intensities of vibrations, we analyze sensitive dipole moment functions (DMFs) of a molecule by combining the linear response function of conceptual DFT and bond dipoles separated by the quantum theory of atoms in molecules with a graphical transition moment decomposition scheme. The fundamental intensities of OH stretching vibrations depend strongly on the substituents but only weakly on the molecular conformations. Interestingly, in some alcohols, completely opposite trends have been observed for the lower-level overtone intensities: a weak substituent dependence but a stronger conformation dependence. It is well known that the formation of a hydrogen-bonded complex increases the OH stretching fundamental intensity, but less well known is the decrease in their overtone intensities. To investigate these characteristics comprehensively, we calculated their intensities (Δv = 1, 2, and 3) for conformers of ethanol and trifluoroethanol (TFE) and hydrogen-bonded phenol (PhOH) systems via the DFT method in the local mode model for the OH stretching coordinate ΔR. Their first and second derivatives of the electron density with respect to ΔR were calculated and interpreted using their bond moments. For ethanol and TFE, the OH, CC, and CH bond moments were found to make an important contribution to the molecular DMF derivatives parallel to the OH bond. The OH bond contributes only to the first derivative of DMF, and its conformational dependence is determined by the magnitude of the charge polarization of each structure. The electron density derivatives in the CC bond region were largely maintained during the internal rotation; thus, their conformation-dependent contributions were expressed by a geometrical factor of the CC bond direction. The CH bond at the antiperiplanar position of the OH bond was found to make a remarkably large contribution to the second derivative of DMF in the gauche conformer. The importance of electron density migration on substituents was also identified in the hydrogen-bonded phenol, in which the π-electron density change on the aromatic ring was clearly shown. This migration creates the DMF derivatives both perpendicular and parallel to the OH bond and strongly affects the absorption intensities. In all the cases, some bond moments on the substituents contribute to the first and second DMF derivatives in a structure-dependent manner, thus explaining their stereoelectronic effects.
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- 2021
16. Conformational analysis of two new organotin(IV) structures completed with a CSD survey
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Azam As'habi, Sudarshan Acharya, Mehrdad Pourayoubi, Anahid Saneei, Marek Nečas, Michal Dušek, Abdul Ajees Abdul Salam, Monika Kučeráková, and Fahimeh Sabbaghi
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010405 organic chemistry ,Chemistry ,Supramolecular chemistry ,Center (category theory) ,Crystal structure ,010402 general chemistry ,Condensed Matter Physics ,01 natural sciences ,0104 chemical sciences ,Inorganic Chemistry ,Crystallography ,Octahedron ,Atom ,Alkane stereochemistry ,Materials Chemistry ,Physical and Theoretical Chemistry - Abstract
The conformational flexibilities are studied in two new organotin(IV) complexes, namely,trans-dichloridodimethylbis[N,N′,N′′-tris(2-chlorobenzyl)phosphoric triamide]tin(IV), [Sn(CH3)2(C21H21Cl3N3OP)2Cl2] or Sn(CH3)2Cl2{OP[NHCH2C6H4(2-Cl)]3}2, (I), and bis(dipropylammonium) tetrachloridodimethylstannate(IV), [(CH3CH2CH2)2NH2]2[Sn(CH3)2Cl4], (II), and their analogous structures from the Cambridge Structural Database (CSD). The conformations are considered based on the N—P=O—Sn torsion angles for (I) and the C—C—C—N, C—C—N—C, C—N—C—C and N—C—C—C torsion angles for the two symmetry-independent [CH3CH2CH2NH2CH2CH2CH3]+cations in (II), and the ±ac±sp±ac (ac = anticlinal and sp = synperiplanar) and ±ap±ap±ap±ap (ap = antiperiplanar) conformations are observed, respectively. In both structures, the four atoms in the corners of the square-planar segment of the octahedral shape around the Sn atom participate in normal hydrogen-bonding interactions as acceptors, which include two O and two Cl atoms for (I), and four Cl atoms for (II). However, the phosphoric triamide ligands block the environment around the Sn atom and limit the hydrogen-bond pattern to form a supramolecular ribbon assembly, while in the presence of small organic cations in (II), a two-dimensional hydrogen-bonded architecture is achieved. The weak interactions π–π, C—H...π and C—Cl...π in (I), and C—H...Cl in (II) do not change the dimensionality of the hydrogen-bond pattern. The 62 CSD structures analogous to (I),i.e.with an SnOPN3segment (including 83 entries) fall into four categories of conformations based on the N—P=O—Sn torsion angles. The 132 [(CH3CH2CH2)2NH2]+cations from 85 CSD structures are classified into seven groups based on the torsion angles noted for (II). Most of the CSD structures adopt the same associated conformations noted for (I) and (II). 15 [Sn(CH3)2Cl4]2−anions extracted from the CSD are compared with the structure of (II).
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- 2020
17. 2-(2,4-Di-nitro-phen-yl)-1-(pyridin-4-yl)ethanol monohydrate
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Zhichao Wu and Houshi Huang
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crystal structure ,Crystallography ,010405 organic chemistry ,Chemistry ,Hydrogen bond ,Aromaticity ,Crystal structure ,Dihedral angle ,010403 inorganic & nuclear chemistry ,dihedral angle ,01 natural sciences ,0104 chemical sciences ,Crystal ,Chain (algebraic topology) ,QD901-999 ,hydrogen bonds ,Alkane stereochemistry ,Nitro ,layered structure - Abstract
In the title compound, C13H11N3O5·H2O, the dihedral angle between the aromatic rings is 9.60 (7)° and the chain linking the rings has an anti conformation with a torsion angle of −178.28 (12)°. In the crystal, the components are linked by O—H...O and O—H...N hydrogen bonds, generating (010) sheets.
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- 2020
18. Bent Bond/Antiperiplanar Hypothesis and the Chemical Reactivity of Annulenes
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Pierre Deslongchamps and Ghislain Deslongchamps
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010405 organic chemistry ,Organic Chemistry ,Annulene ,010402 general chemistry ,01 natural sciences ,Bent bond ,0104 chemical sciences ,Cyclooctatetraene ,chemistry.chemical_compound ,chemistry ,Computational chemistry ,Alkane stereochemistry ,Cyclobutadiene ,Reactivity (chemistry) ,Benzene - Abstract
The properties and stereochemical reactivity of cyclobutadiene, benzene, cyclooctatetraene, and the [10]- to [14]annulenes can be uniformly rationalized through the bent bond/antiperiplanar hypothesis (BBAH). This new orbital model considers electronic delocalization between pyramidal diradical resonance structures and associated bent bonds, as it applies to aromatic, nonaromatic, and antiaromatic molecules.
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- 2020
19. Probing the Structural and Electronic Effects on the Origin of π-Facial Stereoselectivity in 1-Methylphosphole 1-Oxide Cycloadditions and Cyclodimerization
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Surjit Bhai, Bishwajit Ganguly, and Kalyanashis Jana
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010405 organic chemistry ,General Chemical Engineering ,Phosphole ,General Chemistry ,010402 general chemistry ,01 natural sciences ,Article ,Transition state ,0104 chemical sciences ,Adduct ,lcsh:Chemistry ,chemistry.chemical_compound ,lcsh:QD1-999 ,chemistry ,Computational chemistry ,Alkane stereochemistry ,Electronic effect ,Stereoselectivity ,Natural bond orbital ,Methyl group - Abstract
We have examined the π-facial stereoselectivity in the Diels–Alder reactions of phosphole oxides computationally. The experimentally observed syn-cycloadditions have been rationalized with the Cieplak model and distortion–interaction model. The natural bond orbital analysis suggests that the hyperconjugative interactions are energetically preferred between the antiperiplanar methyl group present in the −P=O unit and the developing incipient (−C–C−) bond in syn-adducts in accordance with the Cieplak model. The distortion–interaction analysis carried out for syn and anti transition states of Diels–Alder reactions of 1-substituted phosphole 1-oxide with different dienophiles reveals that the syn selectivity is favored by distortions and interaction energies compared with the anti selectivity. The formation of a syn adduct is also stabilized by the πCC–σ*PO orbital interaction, and the repulsive n−π interaction destabilizes the anti adduct that leads to the 7.0 kcal/mol thermodynamic preference for the former adduct. Furthermore, the distortion–interaction model rationalizes the formation of stereospecific products in these Diels–Alder reactions, which however is not explicable with the much-debated Cieplak model.
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- 2018
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20. Characterization of 11-mercaptoundecanoic and 3-mercaptopropionic acids adsorbed on silver by surface-enhanced Raman scattering
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Gustavo F. S. Andrade, Flávia C. Marques, Gabriela P. Oliveira, Rodrigo M. S. Justo, Raïssa A.R. Teixeira, and Tatiana B. V. Neves
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chemistry.chemical_classification ,02 engineering and technology ,010402 general chemistry ,021001 nanoscience & nanotechnology ,01 natural sciences ,Silver nanoparticle ,0104 chemical sciences ,Solvent ,chemistry.chemical_compound ,symbols.namesake ,Adsorption ,chemistry ,Alkane stereochemistry ,Polymer chemistry ,Thiol ,symbols ,Moiety ,Carboxylate ,0210 nano-technology ,Spectroscopy ,Raman scattering - Abstract
Functionalized n-alkanethiols such as 11-mercaptoundecanoic (MUA) and 3-mercaptopropionic (MPA) acids are likely to adsorb in silver nanoparticles (AgNPs) solely through the thiol group (-SH) or also involving the carboxylate group (−COO−) in their structures. The relative tendency is closely related to pH conditions, solvent or the surface potential of the metallic nanoparticles. The SERS effect (Surface Enhancement Raman Scattering) was used for improving the understanding of MUA and MPA group interaction as well as the orientation of these organic compounds adsorbed on AgNPs and the influence of Cu(II) in solution. When analyzing the MPA SERS spectrum, it was verified that the thiol moiety was preferred to adsorb on the AgNPs surface in the thiolate form, presenting both anti and gauche conformations in both acidic and basic media. MUA SERS spectrum however, indicated that solely an anti conformation for the thiol moiety adsorbed on the AgNPs surface in both acidic and basic media. Adding Cu2+ ion resulted in coordination to the carboxyl or carboxylate moieties was confirmed by the downshift of the band assigned to OCO stretching. The presence of Cu(II) increased the tendency of gauche conformation for MPA; the coordination of MUA to Cu(II) resulted in a more upright conformation of the carboxylic/carboxylate moieties in both acidic and basic media, respectively.
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- 2018
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21. Sterically Crowded Trianglimines-Synthesis, Structure, Solid-State Self-Assembly, and Unexpected Chiroptical Properties
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Natalia Prusinowska, Mateusz Bardziński, Agnieszka Janiak, Paweł Skowronek, and Marcin Kwit
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Steric effects ,Circular dichroism ,010405 organic chemistry ,Aryl ,Organic Chemistry ,Imine ,Substituent ,General Chemistry ,010402 general chemistry ,Ring (chemistry) ,01 natural sciences ,Biochemistry ,0104 chemical sciences ,chemistry.chemical_compound ,Crystallography ,chemistry ,Alkane stereochemistry ,Self-assembly - Abstract
The chiral, triangular-shape hexaimine macrocycles (trianglimines), bearing bulky alkynyl or aryl substituents were synthesized and studied by means of experimental and theoretical methods. The macrocyclization reactions are driven by the extraordinary stability of the trianglimine ring and provided products with high yields. Electrostatic repulsion between imine nitrogen atoms and the substituents forced an anti conformation of the aromatic linkers. Although the DFT-optimized structure of 7 is D3 symmetrical, in the crystal, the macrocycle adopts a bowl-like molecular shape. The macrocycle self-assembles into tail-to-tail dimers by mutual interdigitation of aromatic moieties. In contrast, macrocycle 8 adopts a rigid pillararene-like conformation. The nature of the substituent significantly affects the electronic properties of the linker. As a result, unexpectedly high exciton Cotton effects are observed in the electronic circular dichroism (ECD) spectra. The origin of these effects was subject of an in-depth study.
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- 2018
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22. A comparative study of the coordination of saccharinate, thiosaccharinate and benzisothiozolinate ligands to cyclometalated [Pd(Me2NCH2C6H4-κN,C)(μ-Cl)]2: Molecular structures of [Pd(Me2NCH2C6H4-κN,C)(µ-X)]2 (X = sac, bit and tsac) and [Pd(Me2NCH2C6H4-κN,C)Cl(ampyH-κN)] (ampyH = 2-amino-3-methylpyridine)
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Graeme Hogarth, Christoph Wagner, Sucharita Basak-Modi, Wisam J. Hameed, Ahmed S. M. Al-Janabi, and Subhi A. Al-Jibori
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Local conformation ,010405 organic chemistry ,Ligand ,Sodium ,3-Methylpyridine ,chemistry.chemical_element ,Halide ,010402 general chemistry ,01 natural sciences ,0104 chemical sciences ,Inorganic Chemistry ,chemistry.chemical_compound ,Crystallography ,chemistry ,Alkane stereochemistry ,Materials Chemistry ,Chelation ,Physical and Theoretical Chemistry ,Palladium - Abstract
Reactions of [Pd(Me2NCH2C6H4-κ2N,C)(μ-Cl)]2 with two equivalents of sodium saccharinate (Nasac), thiosaccharin (Htsac) or sodium benzisothiozolinate (Nabit) results in the stepwise substitution of the bridging halides to form sequentially [Pd2(Me2NCH2C6H4-κ2N,C)2(μ-Cl)(μ-X)] (X = sac, tsac) and [Pd(Me2NCH2C6H4-κ2N,C)(μ-X)]2 (X = sac, tsac, bit). The molecular structures of all three disubstituted complexes are reported. In each the two metalated ligands bind in a chelate manner adopting a relative anti conformation, while the new ligands bridge the two palladium atoms adopting a relative cis conformation. The local conformation about each palladium differs with small ligand changes. Thus in the sac and bit complexes all nitrogens lie trans to one another, in the tsac complex they are cis. Conformational changes also lead to large differences in the non-bonded Pd…Pd distance which range over 0.5 A. Treatment of [Pd(Me2NCH2C6H4-κ2N,C)(μ-Cl)]2 with two equivalents of 2-amino-3-methylpyridine (ampyH) in the presence of NEt3 affords mononuclear [PdCl(Me2NCH2C6H4-κ2N,C)(ampyH-κ1N)] as a result of “bridge-splitting”, the ampyH ligand binding through the pyridyl-nitrogen and lying approximately perpendicular to the PdCClN2 plane as shown by a crystallographic study.
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- 2018
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23. Exploring structural and conformational behaviour of cyclophanes incorporating imidazole-2-thiones
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Ahmed Hassoon Mageed, Brian W. Skelton, Murray V. Baker, and Alexandre N. Sobolev
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010405 organic chemistry ,Organic Chemistry ,Solid-state ,Nuclear magnetic resonance spectroscopy ,010402 general chemistry ,01 natural sciences ,Biochemistry ,0104 chemical sciences ,chemistry.chemical_compound ,Crystallography ,Cone conformation ,chemistry ,Drug Discovery ,Alkane stereochemistry ,Imidazole ,Xylylene ,Cyclophane - Abstract
New cyclophanes containing two imidazole-2-thione moieties linked by two xylylene groups have been synthesized by the reaction of imidazolium-linked cyclophanes with sulfur in the presence of K2CO3. The conformational behaviour of the new cyclophanes was explored by NMR spectroscopy and X-ray diffraction studies. In cyclophanes containing o-xylylene or 2,4,6-trimethyl-m-xylylene linking groups, the imidazole-2-thione groups were mutually syn in both the solid state and in solution, the cyclophanes adopting a conformation reminiscent of the cone conformation of calix[4]arenes. Cyclophanes containing p-xylylene or m-xylylene linking groups exhibited two conformations in solution, one in which the imidazole-2-thione groups are mutually syn, the other in which they are mutually anti, and these conformations did not interconvert on the NMR timescale. Both conformations co-crystallised in the m-xylylene linked cyclophane, while for the p-xylylene-linked cyclophane the anti conformation crystallised separately.
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- 2018
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24. Bent Bonds (τ) and the Antiperiplanar Hypothesis—The Chemistry of Cyclooctatetraene and Other C8H8 Isomers
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Ghislain Deslongchamps and Pierre Deslongchamps
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010405 organic chemistry ,Diradical ,Organic Chemistry ,Bent molecular geometry ,010402 general chemistry ,01 natural sciences ,Bent bond ,3. Good health ,0104 chemical sciences ,Cyclooctatetraene ,chemistry.chemical_compound ,Crystallography ,chemistry ,Alkane stereochemistry ,Physics::Atomic and Molecular Clusters ,Singlet state ,Physics::Chemical Physics - Abstract
The bent bond/antiperiplanar hypothesis (BBAH) has been applied to the thermal rearrangements of cyclooctatetraene and related C8H8 isomers. This novel orbital model shows that pyramidal singlet diradical intermediates produced from thermal vibrational states of C8H8 isomers account for their chemical reactivity.
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- 2018
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25. Adenosine hypodiphosphate ester, an analogue of ADP: analysis of the adenine–hypodiphosphate interaction mode in hypodiphosphate nucleotides and adenine salts
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Marta Otręba, Daria Budzikur, Katarzyna Ślepokura, and Łukasz Górecki
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Stereochemistry ,Sodium ,Molecular Conformation ,chemistry.chemical_element ,Crystal structure ,Crystallography, X-Ray ,010402 general chemistry ,01 natural sciences ,Inorganic Chemistry ,chemistry.chemical_compound ,Ribose ,Alkane stereochemistry ,Materials Chemistry ,medicine ,Nucleotide ,Physical and Theoretical Chemistry ,chemistry.chemical_classification ,010405 organic chemistry ,Adenine ,Hydrogen Bonding ,Condensed Matter Physics ,Adenosine ,0104 chemical sciences ,Adenosine Diphosphate ,Adenosine diphosphate ,chemistry ,Salts ,Nucleoside ,medicine.drug - Abstract
Adenosine diphosphate (ADP) plays a crucial role in cell biochemistry, especially in metabolic pathways and energy storage. ADP itself, as well as many of its analogues, such as adenosine hypodiphosphate (AhDP), has been studied extensively, in particular in terms of enzymatic activity. However, structural studies in the solid state, especially for AhDP, are still missing. An analogue of ADP, i.e. adenosine hypodiphosphate ester, has been synthesized and characterized in the crystalline form as two hydrated sodium salts of 2′:3′-isopropylideneadenosine 5′-hypodiphosphate (H3AhDP, C13H19N5O9P2 for the neutral form), namely pentasodium tetrakis(2′:3′-isopropylideneadenosine 5′-hypodiphosphate) tetracosahydrate, 5Na+·3C13H18N5O9P2 −·C13H17N5O9P2 2−·24H2O or Na5(H2AhDP)3(HAhDP)·24H2O, (I), and sodium tetrakis(2′:3′-isopropylideneadenosine 5′-hypodiphosphate) pentadecahydrate, Na+·C13H20N5O9P2 +·2C13H18N5O9P2 −·C13H19N5O9P2·15H2O or Na(H4AhDP)(H3AhDP)(H2AhDP)2·15H2O, (II). Crystal structure analyses of (I) and (II) reveal two nucleoside hypodiphosphate ions in the asymmetric units with different ionization states of the hypodiphosphate unit and adenine base. For all AhDP nucleotides, the same anti conformation about the N-glycosidic bond and similar puckering of the ribose ring have been found. AhDP geometry and interactions have been compared to ADP nucleotides deposited in the Cambridge Structural Database. The adenine–hypodiphosphate interactions, identified as defining nucleotide self-assembly, have been analysed in model systems, i.e. the adenine (Ade) salts of hypodiphosphoric acid, namely bis(adeninium) hypodiphosphate dihydrate, 2C5H6N5 +·H2P2O6 2−·2H2O or (AdeH)2(H2P2O6)·2H2O, (III), and bis(adeninium) hypodiphosphate, 2C5H6N5 +·H2P2O6 2− or (AdeH)2(H2P2O6), (IV).
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- 2018
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26. Different molecular conformations in the crystal structures of three 5-nitroimidazolyl derivatives
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William T. A. Harrison, Carlos A. M. Fraga, Samir A. Carvalho, Luis F. B. Osorio, Bruce F. Milne, Solange M. S. V. Wardell, James L. Wardell, and Edson F. da Silva
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crystal structure ,Stacking ,Crystal structure ,Dihedral angle ,010402 general chemistry ,010403 inorganic & nuclear chemistry ,01 natural sciences ,Research Communications ,chemistry.chemical_compound ,Alkane stereochemistry ,General Materials Science ,Isostructural ,Crystallography ,benzoxathiol-2-one ,Chemistry ,Hydrogen bond ,Hirshfeld surface ,Aromaticity ,General Chemistry ,Condensed Matter Physics ,Oxime ,0104 chemical sciences ,QD901-999 ,hydrogen bonds ,benzoxathiol-2-one - Abstract
The title compounds show different conformations in the solid state., The crystal structures of (E)-1-methyl-5-nitro-1H-imidazole-2-carbaldehyde O-benzyloxime, C12H12N4O3, (I), (E)-1-methyl-5-nitro-1H-imidazole-2-carbaldehyde O-(4-fluorobenzyl) oxime, C12H11FN4O3, (II), and (E)-1-methyl-5-nitro-1H-imidazole-2-carbaldehyde O-(4-bromobenzyl) oxime, C12H11BrN4O3, (III), are described. The dihedral angle between the ring systems in (I) is 49.66 (5)° and the linking Nm—C—C=N (m = methylated) bond shows an anti conformation [torsion angle = 175.00 (15)°]. Compounds (II) and (III) are isostructural [dihedral angle between the aromatic rings = 8.31 (5)° in (II) and 5.34 (15)° in (III)] and differ from (I) in showing a near-syn conformation for the Nm—C—C=N linker [torsion angles for (II) and (III) = 17.64 (18) and 8.7 (5)°, respectively], which allows for the occurrence of a short intramolecular C—H⋯N contact. In the crystal of (I), C—H⋯N hydrogen bonds link the molecules into [010] chains, which are cross-linked by very weak C—H⋯O bonds into (100) sheets. Weak aromatic π–π stacking interactions occur between the sheets. The extended structures of (II) and (III) feature several C—H⋯N and C—H⋯O hydrogen bonds, which link the molecules into three-dimensional networks, which are consolidated by aromatic π–π stacking interactions. Conformational energy calculations and Hirshfeld fingerprint analyses for (I), (II) and (III) are presented and discussed.
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- 2018
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27. High-Temperature Isomerization of Benzenoid Polycyclic Aromatic Hydrocarbons. Analysis through the Bent Bond and Antiperiplanar Hypothesis Orbital Model
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Jean-François Parent and Pierre Deslongchamps
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Hydrogen ,010405 organic chemistry ,Chemistry ,Diradical ,Organic Chemistry ,chemistry.chemical_element ,010402 general chemistry ,01 natural sciences ,Bent bond ,3. Good health ,0104 chemical sciences ,Computational chemistry ,Alkane stereochemistry ,Atom ,Singlet state ,Carbon ,Isomerization - Abstract
L. T. Scott has discovered the 1,2-swapping of carbon and hydrogen atoms which is known to take place on benzenoid aromatics (up to ∼1000 °C range). For example, 13C-1-naphthalene is specifically converted to 13C-2-naphthalene, and there is evidence that this occurs through the formation of benzofulvene and a naphthalene–carbene intermediate. Application of the bent bond/antiperiplanar hypothesis leads to the postulate that higher in energy pyramidal singlet diradical intermediates can be used to propose a mechanism that rationalizes various atom rearrangements on benzenoid aromatics and related isomeric compounds.
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- 2018
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28. Conformational polymorphs of a novel TCNQ derivative carrying an acetylene group
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Yuki Iida, Makoto Kataoka, and Tsunehisa Okuno
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0301 basic medicine ,Hydrogen bond ,Stereochemistry ,Organic Chemistry ,Intermolecular force ,Substituent ,010403 inorganic & nuclear chemistry ,01 natural sciences ,0104 chemical sciences ,Analytical Chemistry ,Inorganic Chemistry ,Solvent ,03 medical and health sciences ,Crystallography ,chemistry.chemical_compound ,030104 developmental biology ,Acetylene ,chemistry ,Alkane stereochemistry ,Molecule ,Conformational isomerism ,Spectroscopy - Abstract
TCNQ is one of the most important organic acceptors and lots of its derivatives have been prepared. However the reports on their crystal polymorphs are limited to their complexes, and simple polymorphs of TCNQ derivatives are uncommon. We succeeded in preparation of a novel TCNQ derivative, 2,2'-(2-(prop-2-yn-1-yloxy)cyclohexa-2,5-diene-1,4-diylidene)dimalononitrile, having a propynyloxy group on a substituent. This compound was found to have two crystal polymorphs depending on a solvent for recrystallization. In polymorph I, dimeric hydrogen bonds are formed between acetylenic hydrogens and cyano nitrogens with the molecule in an inversion symmetry. While, in polymorph II, the molecules make intermolecular hydrogen bonds between acetylenic hydrogens and cyano nitrogens with the molecule in 21 symmetry, forming a hydrogen bonded molecular helix along the b axis. Besides patterns of the intermolecular hydrogen bonds, difference was recognized in conformation of propynyloxy group. The molecule has an anti conformation in polymorph I and a gauche conformation in polymorph II. DFT calculation indicates that the anti conformer is less stable than the gauche one. But a solvation model suggests the anti conformer is estimated to be more stable in a toluene solution.
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- 2018
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29. Stereochemistry of Eʹ and Eʹʹ decarboxylative-dehydration reactions and the bent bond / antiperiplanar hypothesis orbital model
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Pierre Deslongchamps
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chemistry.chemical_classification ,Delocalized electron ,Crystallography ,Double bond ,Chemistry ,Organic Chemistry ,Drug Discovery ,Alkane stereochemistry ,medicine ,Dehydration ,medicine.disease ,Biochemistry ,Bent bond - Abstract
The known concerted decarboxylative-dehydration reaction of unsaturated hydroxy-carboxylic acids 1–18 is analyzed through the Bent Bond/Antiperiplanar Hypothesis (BBAH), which considers double bonds as Pauling τ bonds. These reactions produce various mixtures of dienes or trienes having either the E or Z configuration. The relative formation of these mixtures of dienes or trienes can be rationalized through the BBAH model by the analysis of resonance structures leading to the antiperiplanar (APP) or the synperiplanar (SPP) electronic delocalization modes.
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- 2021
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30. Synthesis of Novel N-Acylhydrazones and Their C-N/N-N Bond Conformational Characterization by NMR Spectroscopy
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Noman Javid, Ayesha Roohi, Muhammad Makshoof Athar, Rubina Munir, Muhammad Zaheer, Rahila Huma, and Muhammad Zia-ur-Rehman
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Pharmaceutical Science ,Medicinal chemistry ,Analytical Chemistry ,conformer ,chemistry.chemical_compound ,QD241-441 ,quinoline ,rotamer ,Drug Discovery ,Alkane stereochemistry ,Physical and Theoretical Chemistry ,Conformational isomerism ,stereoisomer ,Organic Chemistry ,Quinoline ,Nuclear magnetic resonance spectroscopy ,Carbon-13 NMR ,NMR ,Solvent ,NMR spectra database ,chemistry ,Chemistry (miscellaneous) ,Proton NMR ,pyrazolo[3,4-b]quinoline ,Molecular Medicine ,acylhydrazone - Abstract
In this article, a synthesis of N’-(benzylidene)-2-(6-methyl-1H-pyrazolo[3,4-b]quinolin-1-yl)acetohydrazides and their structural interpretation by NMR experiments is described in an attempt to explain the duplication of some peaks in their 1H- and 13C-NMR spectra. Twenty new 6-methyl-1H-pyrazolo[3,4-b]quinoline substituted N-acylhydrazones 6(a–t) were synthesized from 2-chloro-6-methylquinoline-3-carbaldehyde (1) in four steps. 2-Chloro-6-methylquinoline-3-carbaldehyde (1) afforded 6-methyl-1H-pyrazolo[3,4-b]quinoline (2), which upon N-alkylation yielded 2-(6-methyl-1H-pyrazolo[3,4-b]quinolin-1-yl)acetate (3). The hydrazinolysis of 3 followed by the condensation of resulting 2-(6-methyl-1H-pyrazolo[3,4-b]quinolin-1-yl)acetohydrazide (4) with aromatic aldehydes gave N-acylhydrazones 6(a–t). Structures of the synthesized compounds were established by readily available techniques such as FT-IR, NMR and mass spectral studies. The stereochemical behavior of 6(a–t) was studied in dimethyl sulfoxide-d6 solvent by means of 1H NMR and 13C NMR techniques at room temperature. NMR spectra revealed the presence of N’-(benzylidene)-2-(6-methyl-1H-pyrazolo[3,4-b]quinolin-1-yl)acetohydrazides as a mixture of two conformers, i.e., E(C=N)(N-N) , synperiplanar and E(C=N)(N-N)antiperiplanar at room temperature in DMSO-d6. The ratio of both conformers was also calculated and E(C=N) (N-N) , syn-periplanar conformer was established to be in higher percentage in equilibrium with the E(C=N) (N-N)anti-periplanar form.
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- 2021
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31. Theoretical study on the anomeric effect in α-substituted tetrahydropyrans and piperidines
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Josué M. Silla, Matheus P. Freitas, and Francisco A. Martins
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Models, Molecular ,Steric effects ,Anomer ,Anomeric effect ,Stereochemistry ,Molecular Conformation ,Substituent ,010402 general chemistry ,Hyperconjugation ,01 natural sciences ,Biochemistry ,Analytical Chemistry ,chemistry.chemical_compound ,Piperidines ,Alkane stereochemistry ,Conformational isomerism ,Pyrans ,010405 organic chemistry ,Chemistry ,Organic Chemistry ,Stereoisomerism ,General Medicine ,0104 chemical sciences ,Quantum Theory ,Thermodynamics ,Methyl group - Abstract
Conformational effects, including some controversial examples, have been reported in this work for 2-substituted tetrahydropyrans and piperidines, and for the respective protonated compounds [substituent = F, OH, OCH3, NH2, NHCH3 and N(CH3)2]. Hyperconjugation plays a major role in most cases, either due to endo or exo-anomeric interactions, especially when nitrogen is the electron donor to an antiperiplanar σ* orbital. This interaction also seems to contribute for the Perlin and reverse fluorine Perlin-like effects, which are related to the relative magnitude of 1JC,H and 1JC,F coupling constants, respectively, in axial and equatorial conformers. However, the preference for an equatorial conformation appears when a hydrogen or methyl group of the substituent faces the ring, increasing the steric repulsion, even if concomitant with a hyperconjugative interaction in the axial isomer, such as for the well-known 2-aminotetrahydropyran. Unlike some reports in the literature, the gas phase 2-hydroxypiperidine experiences the herein called reverse anomeric effect, although the highly stabilizing nN → σ*C-O interaction in the axial isomer. Overall, steric effects should be taken into account when deciding for the normal or reverse anomeric effects as determinant factors of the stereochemical control of carbohydrate-like molecules.
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- 2017
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32. Protonation-dependent base flipping in the catalytic triad of a small RNA
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John Z. H. Zhang, Xiaohui Wang, and Zhaoxi Sun
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Quantitative Biology::Biomolecules ,010304 chemical physics ,Base pair ,Guanine ,Stereochemistry ,General Physics and Astronomy ,RNA ,Protonation ,Dihedral angle ,010402 general chemistry ,01 natural sciences ,0104 chemical sciences ,Crystallography ,chemistry.chemical_compound ,Molecular dynamics ,chemistry ,0103 physical sciences ,Alkane stereochemistry ,Catalytic triad ,Physical and Theoretical Chemistry - Abstract
Protonation dependent base flipping in RNA has never been studied theoretically. In this work we studied protonation-dependent behavior of the base flipping in the catalytic triad of a single-stranded RNA which was previously characterized by NMR experiment. Molecular dynamics simulation reveals that the GA mismatch in this region accounts for this behavior. Free energy profiles show that the stable point for flipping dihedral shifts about 35° and the free energy barrier along the flipping pathway is elevated upon protonation. The orientation of Guanine from syn to anti conformation is coupled with protonation-dependent base flipping and G-HA + base pair is formed under acidic condition.
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- 2017
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33. Conformational Landscape and Torsion–Rotation–Vibration Effects in the Two Conformers of Methyl Vinyl Ketone, a Major Oxidation Product of Isoprene
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Olena Zakharenko, Juan Ramón Avilés Moreno, Thérèse R. Huet, Roman A. Motiyenko, Laboratoire de Physique des Lasers, Atomes et Molécules - UMR 8523 (PhLAM), and Université de Lille-Centre National de la Recherche Scientifique (CNRS)
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[PHYS.PHYS.PHYS-AO-PH]Physics [physics]/Physics [physics]/Atmospheric and Oceanic Physics [physics.ao-ph] ,010304 chemical physics ,Infrared spectroscopy ,010402 general chemistry ,Photochemistry ,7. Clean energy ,01 natural sciences ,0104 chemical sciences ,[CHIM.THEO]Chemical Sciences/Theoretical and/or physical chemistry ,chemistry.chemical_compound ,[PHYS.QPHY]Physics [physics]/Quantum Physics [quant-ph] ,chemistry ,13. Climate action ,Excited state ,0103 physical sciences ,Methyl vinyl ketone ,Alkane stereochemistry ,Physical chemistry ,[PHYS.PHYS.PHYS-CHEM-PH]Physics [physics]/Physics [physics]/Chemical Physics [physics.chem-ph] ,Physical and Theoretical Chemistry ,Ground state ,Conformational isomerism ,ComputingMilieux_MISCELLANEOUS ,Isoprene ,Methyl group - Abstract
Methyl vinyl ketone is the second major oxidation product of isoprene, and as such an important volatile organic compound present in the troposphere. In the present study, quantum chemical calculations coupled to high-resolution millimeter-wave spectroscopy have been performed to characterize the ground and first excited vibrational states of the two stable conformers. Equilibrium structures, internal rotation barriers, and relative energies have been calculated at the MP2 and M062X levels of theory. Experimental molecular parameters have been obtained that model the rotational and torsional structures, including splitting patterns due to the internal rotation of the methyl group. For the most stable antiperiplanar (s-trans) conformer, the set of parameters obtained for the ground state should be useful to further model IR spectra up to room temperature. By combining theoretical and experimental data, we obtained a relative energy value of 164 ± 30 cm–1 in the gas phase between the more stable antiperipla...
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- 2017
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34. (α-Diimine)nickel Complexes That Contain Menthyl Substituents: Synthesis, Conformational Behavior, and Olefin Polymerization Catalysis
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Richard F. Jordan and Feng Zhai
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chemistry.chemical_classification ,Ethylene ,010405 organic chemistry ,Stereochemistry ,Organic Chemistry ,Acenaphthene ,010402 general chemistry ,01 natural sciences ,Medicinal chemistry ,0104 chemical sciences ,Catalysis ,Coordination complex ,Inorganic Chemistry ,chemistry.chemical_compound ,chemistry ,Polymerization ,Alkane stereochemistry ,Physical and Theoretical Chemistry ,Conformational isomerism ,Diimine - Abstract
We describe the synthesis and coordination chemistry of the (1R,2S,5R)-menthyl-substituted N,N′-diaryl-α-diimine ligands N,N′-(2-Men-4-Me-Ph)2-BIAN (L1, Men = menthyl, BIAN = bis(imino)acenaphthene) and N,N′-(2-Men-4,6-Me2-Ph)2-BIAN (L2), the conformational properties of these ligands and their metal complexes, and the ethylene and 1-hexene polymerization behavior of the corresponding (α-diimine)Ni complexes. Free ligands L1 and L2 and square-planar (L1)PdCl2 and (L1,2)Ni(acac)+ complexes exhibit a preference for the syn conformation, in which the two menthyl units are located on the same side of the N═CC═N plane, while tetrahedral (L1,2)MX2 (MX2 = ZnCl2, NiBr2) complexes exhibit a preference for the anti conformation, in which the menthyl units are located on opposite sides of the N═CC═N plane. Both the anti and the syn conformers of [(L2)Ni(acac)][B(C6F5)4] can be activated by Et2AlCl to generate highly active ethylene polymerization catalysts (activity (2.5–6.6) × 106 g of PE/((mol of Ni) h) at 15 psi ...
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- 2017
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35. Tethered 1,2-Si-Group Migrations in Radical-Mediated Ring Enlargements of Cyclic Alkoxysilanes: An EPR Spectroscopic and Computational Investigation
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Takeaki Iwamoto, Hiroshi Abe, Ryutaro Kanada, John C. Walton, and Satoshi Shuto
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010405 organic chemistry ,Chemistry ,Radical ,Organic Chemistry ,chemistry.chemical_element ,010402 general chemistry ,Ring (chemistry) ,Photochemistry ,Kinetic energy ,01 natural sciences ,0104 chemical sciences ,law.invention ,law ,Computational chemistry ,Alkane stereochemistry ,Steady state (chemistry) ,Electron paramagnetic resonance ,Ground state ,Carbon - Abstract
5- to 6-member ring enlargements of 3-oxa-2-silacyclopentylmethyl to 4-oxa-3-silacyclohexyl radicals were investigated by EPR spectroscopy and QM computations of model indano-oxasilacyclopentane and oxasilinanyl compounds. Both experimental and computational evidence favored a mechanism via a concerted 1,2-migration of the "tethered" Si-group. Thus, the "forbidden" 1,2-Si-group migration from carbon to carbon becomes allowed when the Si-group is "tethered". The EPR data from 3-oxa-2-silacyclopentylmethyl radicals disclosed ground state conformations having semioccupied p-orbitals close to antiperiplanar with respect to their β-Si-C bonds, but indicated Si-hyperconjugation (β-silicon effect) was insignificant in radicals. Kinetic data was obtained by the steady state EPR method for ring enlargement of indano-3-oxa-2-silacyclopentylmethyl radicals. The scope of the novel rearrangement in terms of other ring types and sizes, as well as the analogous 1,2-migration of "tethered" C-centered groups, was explored computationally.
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- 2017
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36. Selenium carboxylic acids betaine; 3,3′,3″-selenotris(propanoic acid) betaine, Se(CH 2 CH 2 COOH) 2 (CH 2 CH 2 COO)
- Author
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Khalid Doudin and Karl W. Törnroos
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010405 organic chemistry ,Hydrogen bond ,Stereochemistry ,Organic Chemistry ,Crystal structure ,010402 general chemistry ,01 natural sciences ,0104 chemical sciences ,Analytical Chemistry ,Inorganic Chemistry ,Bond length ,Crystallography ,chemistry.chemical_compound ,Molecular geometry ,chemistry ,Intramolecular force ,Alkane stereochemistry ,Molecule ,Carboxylate ,Spectroscopy - Abstract
Attempts to prepare [Se(CH2CH2COOH)3]+Cl− from Se(CH2CH2COOH)2 and H2C=CHCOOH in concentrated hydrochloricacid, for the corresponding sulfonium salt, led exclusively to the Se-betaine,Se(CH2CH2COOH)2(CH2CH2COO). The Se-betaine crystallises in the space group P2l/c with the cell dimensions at 223 K, a = 5.5717(1), b = 24.6358(4), c = 8.4361(1) A, β = 104.762(1)°, V = 1119.74(3) A3, Z = 4, Dcalc = 1.763 Mgm− 3,μ = 3.364 Mm−1. The structure refined to RI = 0.0223 for 2801 reflections with F0 > 4σ(F0). In the crystalline state the molecule is intermolecularly linked to neighbouring molecules by a number of hydrogen bonds; a very strong carboxylic-carboxylate bond with an O⋯O distance of 2.4435(16) A, a medium strong carboxylic-carboxylate bond with an O⋯O distance of 2.6431(16) A and several weak O⋯H(CH2) with O⋯C distances between 3.2 and 3.3 A. In the carboxylicgroup involved in the very strong hydrogen bond the O⋯H bond is antiperiplanar to the C O bond while the OH bond is periplanar to the C=O bond in the second carboxylic group. Based upon the C-O bond lengths and theelongation of the O-H bond involved in the strong hydrogen bond one may describe the compound as strongly linked units of Se(CH2CH2COOH)(CH2CH2COO)2 rather than Se(CH2CH2COOH)2(CH2CH2COO). The selenium atom forms two strong intramolecular 1,5-Se⋯O contacts, with a carboxylate oxygen atom, 2.9385(12) A, and with a carboxylicoxygen atom, 2.8979(11) A. To allow for these contacts the two organic fragments have been forced into the periplanar conformation. The molecule is only slightly asymmetric with regard to the C-Se-C bond angles but is very asymmetric with regard to the torsion angles.
- Published
- 2017
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37. Acyclic αγα-Tripeptides with Fluorinated- and Nonfluorinated-Furanoid Sugar Framework: Importance of Fluoro Substituent in Reverse-Turn Induced Self-Assembly and Transmembrane Ion-Transport Activity
- Author
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Sopan Valiba Shinde, Dilip D. Dhavale, Amol S. Kotmale, Sachin S. Burade, Rajesh G. Gonnade, Naresh Bhuma, Pattuparambil R. Rajamohanan, Pinaki Talukdar, and Navanath Kumbhar
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010405 organic chemistry ,Stereochemistry ,Hydrogen bond ,Organic Chemistry ,Substituent ,Tripeptide ,010402 general chemistry ,Antiparallel (biochemistry) ,01 natural sciences ,0104 chemical sciences ,Turn (biochemistry) ,chemistry.chemical_compound ,chemistry ,Intramolecular force ,Amide ,Alkane stereochemistry - Abstract
Acyclic αγα-tripeptides derived from fluorinated-furanoid sugar amino acid frameworks act as reverse-turn inducers with a U-shaped conformation, whereas the corresponding nonfluorinated αγα-tripeptides show random peptide conformations. The NMR studies showed the presence of bifurcated weak intramolecular hydrogen bonding (F···HN) and N+···Fδ- charge-dipole attraction compel the amide carbonyl groups to orient antiperiplanar to the C–F bond, thus, demonstrating the role of the fluorine substituent in stabilizing the U-shaped conformation. The NOESY data indicate that the U-shaped tripeptides self-assembly formation is stabilized by the intermolecular hydrogen bonding between C═O···HN with antiparallel orientation. This fact is supported by ESI-MS data, which showed mass peaks up to the pentameric self-assembly, even in the gas phase. The morphological analysis by FE-SEM, on solid samples, showed arrangement of fibers into nanorods. The antiparallel self-assembled pore of the fluorinated tripeptides illust...
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- 2017
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38. An Organic Receptor Isolated in an Unusual Intermediate Conformation: Computation, Crystallography, and Hirshfeld Surface Analysis
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Indravath K. Naik, Ravada Kishore, Rudraditya Sarkar, Samar K. Das, Ramababu Bolligarla, and Vedichi Madhu
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chemistry.chemical_classification ,010405 organic chemistry ,Stereochemistry ,Salt (chemistry) ,Space group ,Triclinic crystal system ,010402 general chemistry ,01 natural sciences ,0104 chemical sciences ,Crystallography ,chemistry.chemical_compound ,chemistry ,Alkane stereochemistry ,Dimethylformamide ,Density functional theory ,Physical and Theoretical Chemistry ,Methylene ,Monoclinic crystal system - Abstract
1,1″-1,4-Phenylene-bis(methylene)bis-4,4′-bipyridinium cation [C28H24N4]2+ (c), an organic receptor that generally crystallizes in its anti conformation, has recently been shown to be isolated in its syn conformation in an ion-paired compound [C28H24N4][Zn(dmit)2]·2DMF (dmit2– = 1,3-dithiole-2-thione-4,5-dithiolate; DMF = dimethylformamide). In this article, we demonstrated that the same receptor [C28H24N4]2+ (c) can also be stabilized in an unusual intermediate conformation (neither syn nor anti) with PF6– anion in compound [C28H24N4](PF6)2·(1,4-dioxane) (1·(1,4-dioxane)). The energetically favored anti conformation has been described in its nitrate salt [C28H24N4](NO3)2·2H2O (2·2H2O). Compounds 1·(1,4-dioxane) and 2·2H2O, crystallizing in triclinic and monoclinic systems with space groups P1 and P21/n, respectively, were additionally characterized by Hirshfeld surface analysis. The density functional theory calculations are performed to understand the internal mechanism of the stability of various conf...
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- 2017
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39. Polymorphism and Isostructurality of the Series of 3-(4,5-Diaryl-4H-1,2,4-triazole-3-yl)propenoic Acid Derivatives
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Renata Paprocka, Katarzyna Jarzembska, Anna Koziol, Beata Modzelewska, Bożena Modzelewska-Banachiewicz, and Liliana Mazur
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Hydrogen bond ,Stereochemistry ,1,2,4-Triazole ,02 engineering and technology ,General Chemistry ,Crystal structure ,Interaction energy ,010402 general chemistry ,021001 nanoscience & nanotechnology ,Condensed Matter Physics ,01 natural sciences ,0104 chemical sciences ,chemistry.chemical_compound ,Polymorphism (materials science) ,chemistry ,Intramolecular force ,Alkane stereochemistry ,Anhydrous ,General Materials Science ,0210 nano-technology - Abstract
Polymorphism of four biologically active 3-(4,5-diaryl-4H-1,2,4-triazole-3-yl)propenoic acid derivatives has been investigated. Traditional solution-based solid-state forms screening revealed three anhydrous forms of 3-[4-phenyl-5-(2-pyridyl)-4H-1,2,4-triazole-3-yl]propenoic acid. Noteworthy, two pairs of concomitant polymorphs were detected for this system. Two other compounds were found to be dimorphic. The molecular and crystal structures of all obtained crystal forms were established by single-crystal X-ray diffraction. The resulting crystal structures were analyzed in terms of molecular conformation, intermolecular interaction patterns, and crystal packing motifs. The experimental studies were supported by extended lattice and interaction energy calculations. It was found that the carboxylic group adopts the anti conformation in all studied forms and is involved in the intramolecular O–H···Ntriazole hydrogen bonding. In consequence, the association modes are dominated by the weak C–H···O, C–H···N hyd...
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- 2017
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40. Planarity of benzoylthiocarbazate tuberculostatics. III. Diesters of 3-(2-hydroxybenzoyl)dithiocarbazic acid
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Małgorzata Szczesio, Katarzyna Gobis, Ida Mazerant, Andrzej Olczak, Marek L. Główka, and Henryk Foks
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Chemistry ,Hydrogen bond ,Biological activity ,Crystal structure ,010402 general chemistry ,010403 inorganic & nuclear chemistry ,Condensed Matter Physics ,Ring (chemistry) ,Hydrazide ,01 natural sciences ,Medicinal chemistry ,Planarity testing ,0104 chemical sciences ,Inorganic Chemistry ,chemistry.chemical_compound ,Alkane stereochemistry ,Materials Chemistry ,Organic chemistry ,Physical and Theoretical Chemistry ,Isopropyl - Abstract
Searches for new tuberculostatic agents are important considering the occurrence of drug-resistant strains ofMycobacterium tuberculosis. The structures of three new potentially tuberculostatic compounds, namely isopropyl methyl (2-hydroxybenzoyl)carbonohydrazonodithioate, C12H16N2O2S2, (Z)-benzyl methyl (2-hydroxybenzoyl)carbonohydrazonodithioate, C16H16N2O2S2, and dibenzyl (2-hydroxybenzoyl)carbonohydrazonodithioate propan-2-ol monosolvate, C22H20N2O2S2·C3H8O, were determined by X-ray diffraction. The mutual orientation of the three main fragments of the compounds, namely an aromatic ring, a dithioester group and a hydrazide group, can influence the biological activity of the compounds. In all three of the structures studied, the C(=O)NH group is in theanticonformation. In addition, the presence of the hydroxy group in theorthoposition of the aromatic ring in all three structures leads to the formation of an intramolecular hydrogen bond stabilizing the planarity of the molecules.
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- 2017
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41. Coordination chemistry of mercury(<scp>ii</scp>) with 2-pyridylnitrones: monomers to polymers
- Author
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Richard J. Puddephatt, Mahmood Azizpoor Fard, and Ava Behnia
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chemistry.chemical_classification ,Denticity ,010405 organic chemistry ,Stereochemistry ,Intermolecular force ,010402 general chemistry ,01 natural sciences ,0104 chemical sciences ,Nitrone ,Coordination complex ,Inorganic Chemistry ,chemistry.chemical_compound ,Crystallography ,Monomer ,chemistry ,Alkane stereochemistry ,Chelation ,Stoichiometry - Abstract
The coordination chemistry of mercury(II) halides, HgX2, X = Cl, Br, I, with N-methyl-α-(2-pyridyl)nitrone, L1, and N-t-butyl-α-(2-pyridyl)nitrone, L2, is reported. The structures of 1 : 1 complexes [HgX2L], X = Cl, L = L1; X = Br, L = L2, 2 : 1 complexes [(HgX2)2L], X = Br or I, L = L1; X = Cl or I, L = L2, and a unique compound [(HgBr2)5(L2)3] have been determined. In the 1 : 1 and 1 : 2 complexes, the ligand L1 adopts the anti conformation, and is either monodentate or bridging, while the ligand L2 adopts the syn conformation and acts as a chelate ligand. In the compound [(HgBr2)5(L2)3] the ligand L2 is present in both syn-chelate and anti-bridging bonding modes. Secondary intermolecular bonding, involving O⋯Hg or X⋯Hg interactions, can lead to association of the molecular compounds to form polymers of several kinds. In solution, the complexes are labile and the crystalline products do not necessarily reflect the reaction stoichiometry.
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- 2017
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42. The conformations of new CF3 and CF3-CHF containing amides derived from carbohydrates: NMR, crystallographic and DFT study
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Ewa Patyk-Kaźmierczak, Tomasz Siodła, Monika Bilska-Markowska, Andrzej Katrusiak, and Henryk Koroniak
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Trifluoromethyl ,010405 organic chemistry ,Stereochemistry ,General Chemistry ,010402 general chemistry ,01 natural sciences ,Catalysis ,0104 chemical sciences ,Crystal ,chemistry.chemical_compound ,Crystallography ,chemistry ,Alkane stereochemistry ,Materials Chemistry ,Molecule - Abstract
A new convenient synthetic procedure for the preparation of tri- and tetrafluoropropanamides derived from sugars has been described. The conformations of fluorinated amides calculated for isolated molecules and those in the crystal state have been compared. In contrast to single α-fluorine substituted amides, which preferred the anti conformation around the F–C–CO bond, for tetrafluorinated amides the additional trifluoromethyl group forces the conformation of the F–C–CO bond to be nearly syn.
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- 2017
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43. The effect of hexyl side chains on molecular conformations, crystal packing, and charge transport of oligothiophenes
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Steven A. Lopez, Kendall N. Houk, Ilhan Yavuz, Sean Parkin, Lei Zhang, Alejandro L. Briseno, Edmund K. Burnett, and Benjamin P. Cherniawski
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chemistry.chemical_classification ,Chemistry ,Stereochemistry ,Dimer ,Substituent ,02 engineering and technology ,General Chemistry ,Crystal structure ,010402 general chemistry ,021001 nanoscience & nanotechnology ,01 natural sciences ,0104 chemical sciences ,chemistry.chemical_compound ,Crystallography ,Monomer ,Alkane stereochemistry ,Materials Chemistry ,Side chain ,Molecule ,0210 nano-technology ,Alkyl - Abstract
We report substituent effects on conformational preferences and hole mobilities of 2,5-bis-(thiophen-2-yl)thieno[3,2-b]thiophenes (BTTT) monomer and dimer, and hexyl derivatives. We employ single-crystal X-ray diffraction, quantum mechanical calculations, and thin-film transistors to explore the difference between monomer, dimer, and effect of hexyl substitution. The hexyl-substituted molecules show marked differences in solid-state packing compared to the unsubstituted analogs. Most notably, the alkylated monomer crystal structure exhibits terminal thiophenes in the syn conformation. In contrast, the unsubstituted monomer adopts the more common anti conformation. The hexyl-substituted dimer, however, features a mixture of syn and anti thiophenes. Gas phase conformations of oligomers rationalize the intrinsic conformational preferences. We use a multimode simulation to compute hole mobilities and find excellent agreement with experiment. Theoretical results support our hypothesis that alkyl side chains cause these small molecules to adopt orientations that enhance hole mobilities by an order of magnitude upon hexyl substitution of the monomer.
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- 2017
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44. Felkin-Anh Model from an Orbital Phase Perspective: Diastereoselectivity in Nucleophilic Addition to 2,3-bis(trifluoromethyl)bicyclo[2.2.1]heptan-7-One
- Author
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Takamori A, Yuji Naruse, and Hibino H
- Subjects
chemistry.chemical_classification ,chemistry.chemical_compound ,Trifluoromethyl ,Nucleophilic addition ,Ketone ,Nucleophile ,chemistry ,Bicyclic molecule ,Stereochemistry ,Alkane stereochemistry ,Electronic effect ,HOMO/LUMO - Abstract
To address the electronic effect in nucleophilic addition, we often use the Felkin-Anh model, in which the most s-electron-withdrawing group (sEWG) at the a-position of the carbonyl should be located anti to the nucleophile approach. The diastereoselectivity is often explained by the antiperiplanar effect of the sEWG. Reetz and Frenking reported that the FMO, the LUMO in the a-substituted ketone, has greater expansion anti the sEWG. Thus, the FMO theory can also apply to this diastereoselectivity. However, there is still no explanation for why the LUMO has greater expansion anti to the sEWG and toward the nucleophile approach with this conformation, as is suggested by the FMO theory. We show here that the phase-continuous cyclic orbital interaction among nNu:--p*C=O-s*C-A/vic-s*CC/gem- controls the diastereoselectivity, which is confirmed with theoretical calculations and the bond model analysis using a conformationally-fixed bicyclic molecule, 2,3-bis(trifluoromethyl)bicyclo[2.2.1]heptan-7-one 1, as a model.
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- 2019
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45. Diastereoselection in Intermolecular Nitrile Oxide Cycloaddition (NOC) Reactions: Confirmation of the 'Anti-Periplanar Effect' through a Simple Synthesis of 2-Deoxy-d-ribose
- Author
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Arun K. Ghosh and Alan P. Kozikowski
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Nitrile ,Chemistry ,Stereochemistry ,Intermolecular force ,Oxide ,General Chemistry ,Biochemistry ,Catalysis ,Cycloaddition ,Article ,chemistry.chemical_compound ,Colloid and Surface Chemistry ,Alkane stereochemistry ,2 deoxy d ribose - Published
- 2019
46. Shape adaptation of quinine in cyclodextrin cavities: NMR studies
- Author
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Michał Nowakowski, Jacek Wójcik, and Andrzej Ejchart
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chemistry.chemical_classification ,Quinine ,Cyclodextrin ,Chemistry ,Quinoline ,General Physics and Astronomy ,02 engineering and technology ,Nuclear magnetic resonance spectroscopy ,010402 general chemistry ,021001 nanoscience & nanotechnology ,01 natural sciences ,0104 chemical sciences ,chemistry.chemical_compound ,Crystallography ,Alkane stereochemistry ,medicine ,Molecule ,Physical and Theoretical Chemistry ,0210 nano-technology ,Conformational isomerism ,medicine.drug ,Quinuclidine - Abstract
Complex formation between quinine and natural cyclodextrins (CD) was studied using NMR spectroscopy. The strongest association was observed for complexes of neutral quinine molecules with βCD. Association constants for monocationic quinine were one order of magnitude smaller, while dicationic quinine did not bind to CDs. The distribution of complexation-induced shifts and ROESY spectra revealed bimodal quinine binding in complexes formed with βCD and γCD. Complex formation resulted in a decrease of the vicinal coupling constant between H2 and H9 protons owing to the rotation about the C2-C9 bond and in consequence in mutual reorientation of two main constituents of quinine: quinoline and quinuclidine. DFT calculations allowed establishing that H2 and H9 protons are antiperiplanar in the prevailing quinine conformer(s) in aqueous solution. Conformers with synclinal H2 and H9 protons participated in quinine complexation with CDs.
- Published
- 2019
47. Bent bond / antiperiplanar hypothesis and antiaromatic, aromatic and nonaromatic molecules
- Author
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Pierre Deslongchamps
- Subjects
chemistry.chemical_classification ,Double bond ,Bicyclic molecule ,010405 organic chemistry ,Organic Chemistry ,010402 general chemistry ,01 natural sciences ,Biochemistry ,Bent bond ,0104 chemical sciences ,Crystallography ,chemistry.chemical_compound ,Delocalized electron ,chemistry ,Drug Discovery ,Alkane stereochemistry ,Heptalene ,Molecule ,Antiaromaticity - Abstract
The stereochemical reactivities of monocyclic unsaturated compounds having 3–5 and 7–8 membered rings and of bicyclic pentalenes and heptalene can be rationalized through the bent bond/antiperiplanar hypothesis (BBAH) orbital model at the molecular level. This new orbital model considers unsaturations as Pauling τ bonds and that electron delocalization with adjacent pyramidal radical structures (derived from resonance structures) must strictly occur in antiperiplanar fashion. The BBAH shows that, contrary to aromatic (4n+2 Huckel) and nonaromatic molecules, antiaromatic molecules (4n Huckel) have adjacent double bonds that cannot conjugate through antiperiplanar electronic delocalization.
- Published
- 2021
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48. The conformation and reactivity of butadiene and the bent bond/antiperiplanar hypothesis orbital model
- Author
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Pierre Deslongchamps
- Subjects
Nucleophilic addition ,010405 organic chemistry ,Organic Chemistry ,Regioselectivity ,010402 general chemistry ,01 natural sciences ,Biochemistry ,Medicinal chemistry ,Bent bond ,0104 chemical sciences ,Sulfone ,chemistry.chemical_compound ,chemistry ,Drug Discovery ,Alkane stereochemistry ,Reactivity (chemistry) ,Isomerization - Abstract
The bent bond/antiperiplanar hypothesis (BBAH) is a useful orbital model explaining the conformational analysis and chemical reactivity of butadiene, the regioselective isomerization of α,β-unsaturated esters to their β,γ-deconjugated isomer, and the stereocontrolled nucleophilic addition of amines to ethyl 2,4-pentadienolate and 1,3-butadienyl sulfone.
- Published
- 2021
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49. The thermal rearrangements of naphthalene and azulene. An analysis through the bent bond and antiperiplanar hypothesis orbital model
- Author
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Pierre Deslongchamps
- Subjects
010405 organic chemistry ,Diradical ,Organic Chemistry ,Azulene ,010402 general chemistry ,Photochemistry ,01 natural sciences ,Biochemistry ,Bent bond ,0104 chemical sciences ,chemistry.chemical_compound ,chemistry ,Drug Discovery ,Thermal ,Alkane stereochemistry ,Singlet state ,Physics::Chemical Physics ,Computer Science::Databases ,Naphthalene - Abstract
The thermal conversion of azulene, naphthalene, norcaradiene, and polycyclic analogues can be rationalized through the Bent Bond/Antiperiplanar Hypothesis (BBAH) orbital model. The BBAH postulates that higher-energy pyramidal singlet diradical intermediates can be used to rationalize molecular rearrangements of these benzenoid aromatics under thermal conditions.
- Published
- 2021
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50. Synthesis, characterization and structures of cadmium(II) and mercury(II) complexes with bis(dipiperidinylphosphino)methylamine dichalcogenides
- Author
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Alexandra M. Z. Slawin, J. Derek Woollins, M. Abderrahmane Sanhoury, M. R. Khaddar, M. T. Ben Dhia, T. Mbarek, University of St Andrews. School of Chemistry, University of St Andrews. EaSTCHEM, and University of St Andrews. Office of the Principal
- Subjects
Mercury complex ,Denticity ,Stereochemistry ,010402 general chemistry ,01 natural sciences ,Inorganic Chemistry ,Metal ,chemistry.chemical_compound ,bis(dichlorophosphino)methylamine ,Alkane stereochemistry ,Materials Chemistry ,QD ,Physical and Theoretical Chemistry ,113Cd ,010405 organic chemistry ,Methylamine ,Ligand ,DAS ,Nuclear magnetic resonance spectroscopy ,QD Chemistry ,31P ,NMR ,0104 chemical sciences ,77Se ,Bond length ,Crystallography ,chemistry ,visual_art ,visual_art.visual_art_medium ,Phosphine ,Cadmium - Abstract
The authors are grateful to the Tunisian Ministry of High Education and Scientific Research for financial support (LR99ES14) of this research. Two new bidentate phosphine dichalcogenide ligands of the type MeN(Pip2PE)2 [(Pip = piperidinyl; E = S ( 1 ) or Se ( 2 )] and their cadmium(II) and mercury(II) chloride complexes MCl2{MeN(Pip2PE)2} [M = Cd; E = S ( 3 ); Se ( 4 ) or M = Hg; L = S ( 5 ); Se ( 6 )] were prepared and characterized by elemental analysis, IR, multinuclear (31P, 77Se and 113Cd) NMR spectroscopy and single crystal X-ray analyses. Ligands 1 and 2 were found to adopt anti conformation structures in the solid state in which both P=E groups are trans to each other. Complexes 3 - 6 are comprised of one ligand coordinated in a bidentate fashion to the metal centre in a distorted tetrahedral arrangement [98.46(3)-121.24(4)°]. The P=S bond lengths of 1.999(15)-2.003(14) Å in the complex ( 3 ) are slightly elongated compared to those in free ligand [1.933(15)-1.950(14) Å]. The results are discussed and compared with closely related analogues. Postprint
- Published
- 2016
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Catalog
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