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Xu Liu, Chenyang Zhao, Li Yang, Jiaxu Zhang, Rui Sun
Central atoms have a significant influence on the reaction kinetics and dynamics of nucleophilic substitution (SN2). Herein, atomistic dynamics of a prototype SN2@N reaction F(-) + NH2Cl is uncovered employing direct dynamics simulations that show strikingly distinct features from those determined for a SN2@C congener F(-) + CH3Cl. Indirect scattering is found to prevail, which proceeds predominantly through a hydrogen-bonded F(-)-HNHCl complex in the reactant entrance channel. This unexpected finding of a pronounced contribution of indirect reaction dynamics, even at a high collision energy, is in strong contrast to a general evolution from indirect to direct dynamics with enhanced energy that characterizes SN2@C...
August 17, 2017: Physical Chemistry Chemical Physics: PCCP
Yellaiah Tangella, Kesari Lakshmi Manasa, V Laxma Nayak, Manda Sathish, B Sridhar, Abdullah Alarifi, Narayana Nagesh, Ahmed Kamal
An operationally facile and high yielding one-pot, three-component protocol has been developed for the preparation of selectively trans-2,3-dihydrofuro[3,2-c]coumarins and trans-1,2-dihydrobenzo[h]furo[3,2-c]quinolinones. This protocol proceeds through a domino Knoevenagel condensation, a Michael addition followed by intramolecular SN2 cyclisation. All the synthesized compounds have been evaluated for their in vitro cytotoxic activity against selected human cancer cell lines. Interestingly, most of the compounds have exhibited considerable cytotoxicity with IC50 values <10 μM in all the tested cell lines...
August 16, 2017: Organic & Biomolecular Chemistry
Gregory C Fu
Classical methods for achieving nucleophilic substitutions of alkyl electrophiles (SN1 and SN2) have limited scope and are not generally amenable to enantioselective variants that employ readily available racemic electrophiles. Radical-based pathways catalyzed by chiral transition-metal complexes provide an attractive approach to addressing these limitations.
July 26, 2017: ACS Central Science
Justin A Pals, Elizabeth D Wagner, Michael J Plewa, Menghang Xia, Matias S Attene-Ramos
Haloacetamides (HAMs) are cytotoxic, genotoxic, and mutagenic byproducts of drinking water disinfection. They are soft electrophilic compounds that form covalent bonds with the free thiol/thiolate in cysteine residues through an SN2 reaction mechanism. Toxicity of the monohalogenated HAMs (iodoacetamide, IAM; bromoacetamide, BAM; or chloroacetamide, CAM) varied depending on the halogen substituent. The aim of this research was to investigate how the halogen atom affects the reactivity and toxicological properties of HAMs, measured as induction of oxidative/electrophilic stress response and genotoxicity...
August 2017: Journal of Environmental Sciences (China)
Valeria Zanichelli, Giulio Ragazzon, Guido Orlandini, Margherita Venturi, Alberto Credi, Serena Silvi, Arturo Arduini, Andrea Secchi
A substrate can modify its chemical features, including a change of its reactivity, as a consequence of non-covalent interactions upon inclusion within a molecular host. Since the rise of supramolecular chemistry, this phenomenon has stimulated the ingenuity of scientists to emulate the function of enzymes by designing supramolecular systems in which the energetics and selectivity of reactions can be manipulated through programmed host-guest interactions and/or steric confinement. In this paper we investigate how the engulfment of a positively charged pyridinium-based guest inside the π-rich cavity of a tris-(N-phenylureido)calix[6]arene host affects its reactivity towards a SN2 reaction...
August 16, 2017: Organic & Biomolecular Chemistry
Patrick Chaquin, Franck Fuster
The derivative of a canonical molecular orbital (MO) energy (or dynamical orbital forces (DOF)) with respect to a bond length provides a reliable index of the bonding/antibonding character of this MO on this bond. The DOF of selected MOs as a function of the reaction coordinate has been computed for a panel of model reactions mechanisms: 2 + 4 (diels-Alder) cycloaddition, 2+2 cycloaddition, nucleophilic substitution SN2, nucleophilic addition on carbonyl and [1,2] hydrogen transposition. The results highlights the nature of the main MO reorganization, and at what stage of the RC they occur...
July 26, 2017: Chemphyschem: a European Journal of Chemical Physics and Physical Chemistry
Jian-Bo Wang, Adriana Ilie, Shuguang Yuan, Manfred T Reetz
The possibility of a double Walden inversion mechanism of the fluoracetate dehalogenase FAcD (RPA1163) has been studied by subjecting rac-2-fluoro-2-phenyl acetic acid to the defluorination process. This stereochemical probe led to inversion of configuration in a kinetic resolution with an extremely high selectivity factor (E > 500), showing that the classical mechanism involving SN2 reaction by Asp110 pertains. The high preference for the (S)-substrate is of synthetic value. Wide substrate scope of RPA1163 in such hydrolytic kinetic resolutions can be expected because the reaction of the even more sterically demanding rac-2-fluoro-2-benzyl acetic acid proceeded similarly...
August 16, 2017: Journal of the American Chemical Society
Yong-Tao Ma, Xinyou Ma, Anyang Li, Hua Guo, Li Yang, Jiaxu Zhang, William L Hase
Direct dynamics simulations were performed to study the SN2 double inversion mechanism SN2-DI, with retention of configuration, for the F(-) + CH3I reaction. Previous simulations identified a transition state (TS) structure, i.e. TS0, for the SN2-DI mechanism, including a reaction path. However, intrinsic reaction coordinate (IRC) calculations from TS0 show it is a proton transfer (PT) TS connected to the F(-)HCH2I SN2 pre-reaction complex and the FHCH2I(-) proton transfer post-reaction complex. Inclusion of TS0 in the SN2-DI mechanism would thus involve non-IRC atomistic dynamics...
July 20, 2017: Physical Chemistry Chemical Physics: PCCP
Sérgio M Marques, Zuzana Dunajova, Zbynek Prokop, Radka Chaloupkova, Jan Brezovsky, Jiri Damborsky
The anthropogenic toxic compound 1,2,3-trichloropropane is poorly degradable by natural enzymes. We have previously constructed the haloalkane dehalogenase DhaA31 by focused directed evolution ( Pavlova, M. et al. Nat. Chem. Biol. 2009 , 5 , 727 - 733 ), which is 32 times more active than the wild-type enzyme and is currently the most active variant known against that substrate. Recent evidence has shown that the structural basis responsible for the higher activity of DhaA31 was poorly understood. Here we have undertaken a comprehensive computational study of the main steps involved in the biocatalytic hydrolysis of 1,2,3-trichloropropane to decipher the structural basis for such enhancements...
July 28, 2017: Journal of Chemical Information and Modeling
István Szabó, Gábor Czakó
Benchmark stationary-point structures, vibrational frequencies, and classical/adiabatic relative energies (kcal/mol) are reported for the Cl(-) + CH3I reaction along the back-side attack (ΔETS = -5.48/-5.54) inversion, front-side attack (ΔETS = 36.73/35.89) and double-inversion (ΔETS = 46.97/42.55) retention SN2 pathways, the proton-transfer channel, and the hydride-substitution reaction path. The structures and frequencies are obtained by the frozen-core CCSD(T), CCSD(T)-F12a, and CCSD(T)-F12b methods with the aug-cc-pVnZ [n = D, T, and Q for structures and n = D and T for frequencies] basis sets and all-electron CCSD(T) with aug-cc-pwCVnZ [n = D and T for structures and n = D for frequencies]...
July 24, 2017: Journal of Physical Chemistry. A
Yongsheng Zhao, Nana Li, Cong Xu, Yan Li, Hongyu Zhu, Pinwen Zhu, Xin Wang, Wenge Yang
La2 Sn2 O7 is a transparent conducting oxide (TCO) material and shows a strong near-infrared fluorescent at ambient pressure and room temperature. By in situ high-pressure research, pressure-induced visible photoluminescence (PL) above 2 GPa near 2 eV is observed. The emergence of unusual visible PL behavior is associated with the seriously trigonal lattice distortion of the SnO6 octehedra, under which the Sn-O1-Sn exchange angle θ is decreased below 22.1 GPa, thus enhancing the PL quantum yield leading to Sn (3) P1 → (1) S0 photons transition...
July 10, 2017: Advanced Materials
Borja López-Pérez, Miguel A Maestro, Antonio Mouriño
Herein, we describe a versatile and efficient total synthesis of 1α,25-dihydroxyvitamin D3 (calcitriol). The synthetic strategy relies on an unprecedented Si-assisted SN2'-syn displacement of carbamates by cuprates to set the challenging pivotal quaternary methyl group at the fused-ring junction of the CD-trans-hydrindane core. Other key transformations involve the catalytic asymmetric reduction of an α,β,γ,δ-unsaturated ester with CuH to generate the natural steroidal configuration at C20 and a Pauson-Khand cyclization to form the CD-ring skeleton...
July 18, 2017: Chemical Communications: Chem Comm
Wen Zhang, Chun Pong Tam, Travis Walton, Albert C Fahrenbach, Gabriel Birrane, Jack W Szostak
The nonenzymatic copying of RNA templates with imidazole-activated nucleotides is a well-studied model for the emergence of RNA self-replication during the origin of life. We have recently discovered that this reaction can proceed through the formation of an imidazolium-bridged dinucleotide intermediate that reacts rapidly with the primer. To gain insight into the relationship between the structure of this intermediate and its reactivity, we cocrystallized an RNA primer-template complex with a close analog of the intermediate, the triphosphate-bridged guanosine dinucleotide GpppG, and solved a high-resolution X-ray structure of the complex...
July 18, 2017: Proceedings of the National Academy of Sciences of the United States of America
Jie-Ling Xie, Yu-Hua Zhou, Long-Hua Li, Jian-Han Zhang, Jun-Ling Song
Herein, unprecedented NLO-brominated tin hypophosphites, namely [Sn2(H2PO2)3]Br, were discovered via a facile surfactant-induced method, which displayed a moderate powder SHG intensity (3.0 × KDP) in type - I phase matching behavior. This complex has high chemical and thermal stability at room temperature. DFT calculations and SHG coefficient analyses revealed that the alignment of the SHG-active-units SnO3 trigonal pyramids and Br(-) anions in its structure mainly contribute to the macroscopical SHG behaviors...
July 25, 2017: Dalton Transactions: An International Journal of Inorganic Chemistry
Stefan Aichhorn, Raphael Bigler, Eddie L Myers, Varinder K Aggarwal
Coupling reactions between benzylamines and boronic esters have been investigated. ortho-Lithiated benzylamines react with boronic esters and a N-activator to afford ortho-substituted benzylic boronic esters with formal 1,1'-benzylidene insertion into the C-B bond. The reaction occurs by a SN2' elimination and 1,2-metalate rearrangement of the N-activated boronate complex to afford a dearomatized intermediate, which undergoes a Lewis-acid catalyzed 1,3-borotropic shift to afford the boronic ester products in high yield and with excellent enantiospecificity...
July 19, 2017: Journal of the American Chemical Society
Hiroaki Ichio, Hidetoshi Murakami, Yen-Chou Chen, Tamotsu Takahashi, Masamichi Ogasawara
A palladium-catalyzed reaction for preparing various endocyclic allenes was developed. The substrates for the reaction were readily available ω-(pronucleophile-tethered)-3-bromo-1,3-alkadienes, and a palladium-catalyst facilitated their unimolecular SN2'-cyclization in the presence of potassium tert-butoxide to give the corresponding 9- to 16-membered endocyclic allenes in fair yields of up to 67% together with the dimeric 16- to 32-membered endocyclic bis-allenes and other oligomeric/polymeric intermolecular reaction products...
June 30, 2017: Journal of Organic Chemistry
Ernest Salomó, Amparo Prades, Antoni Riera, Xavier Verdaguer
The preparation of shelf-stable crystalline salts of tert-butylmethylphosphinous acid borane 1 is described. X-ray analysis of diisopropylammonium tert-butylmethylphosphinite borane 6 revealed the presence of a cyclic hydrogen-bond network in the solid state which accounts for an increased melting point and stability. Dialkylammonium phosphinite boranes are convenient precursors of the chiral tert-butylmethylphosphine fragment. Compound 6 can be used directly in SN2@P reactions with various nucleophiles to yield valuable P-stereogenic intermediates and ligands...
June 22, 2017: Journal of Organic Chemistry
Warot Chotpatiwetchkul, Kanokthip Boonyarattanakalin, Duangkamol Gleeson, M Paul Gleeson
Dihydropteroate synthase (DHPS) catalyzes the condensation of 6-hydroxymethyl-7,8-dihydropterin pyrophosphate (DHPPP) with p-aminobenzoic acid (pABA) and is a well validated target for anti-malarial and anti-bacterial drugs. However, in recent years its utility as a therapeutic target has diminished considerably due to multiple mutations. As such, considerable structural biology and medicinal chemistry effort has been expended to understand and overcome this issue. To date no detailed computational analysis of the protein mechanism has been made despite the detailed crystal structures and multiple mechanistic proposals being made...
July 5, 2017: Organic & Biomolecular Chemistry
Eduardo Carrascosa, Jennifer Meyer, Jiaxu Zhang, Martin Stei, Tim Michaelsen, William L Hase, Li Yang, Roland Wester
The competition between bimolecular nucleophilic substitution and base-induced elimination is of fundamental importance for the synthesis of pure samples in organic chemistry. Many factors that influence this competition have been identified over the years, but the underlying atomistic dynamics have remained difficult to observe. We present product velocity distributions for a series of reactive collisions of the type X(-) + RY with X and Y denoting the halogen atoms fluorine, chlorine and iodine. By increasing the size of the residue R from methyl to tert-butyl in several steps, we find that the dynamics drastically change from backward to dominant forward scattering of the leaving ion relative to the reactant RY velocity...
June 21, 2017: Nature Communications
Abu Taher, Kyo Chul Lee, Hye Ji Han, Dong Wook Kim
We prepared pyrene-substituted imidazolium-based ionic liquids (PILs) as organic catalysts for the SN2 fluorination using alkali metal fluoride (MF). In this system, the PIL significantly enhanced the reactivity of MF due to the phase-transfer catalytic effect of the imidazolium moiety as well as the metal cation-π (pyrene) interactions. Furthermore, this homogeneous catalyst PIL was easily separated from the reaction mixture using reduced graphene oxide by π-π stacking with the pyrene of PIL.
June 20, 2017: Organic Letters
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