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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, 727-73), 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 11, 2017: Journal of Chemical Information and Modeling
Istvan Szabo, Gabor Czako
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 10, 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 3, 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 3, 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 6, 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
Pedro Ojeda-May, Kwangho Nam
The strategy and implementation of scalable and efficient semiempirical (SE) QM/MM methods in CHARMM are described. The serial version of the code was first profiled to identify routines that required parallelization. Afterward, the code was parallelized and accelerated with three approaches. The first approach was the parallelization of the entire QM/MM routines, including the Fock matrix diagonalization routines, using the CHARMM message passage interface (MPI) machinery. In the second approach, two different self-consistent field (SCF) energy convergence accelerators were implemented using density and Fock matrices as targets for their extrapolations in the SCF procedure...
July 6, 2017: Journal of Chemical Theory and Computation
Brendan Fisher, Romain J Lepage, Jonathan M White, Young Ye, Elizabeth H Krenske, Mark A Rizzacasa
A unprecedented base-induced trimerization of bromovinylsulfone 1 afforded the cyclohexene 6 as a single diastereoisomer. Optimization of this reaction gave the adduct 6 in 49% yield. A mechanistic rationale for the trimerization involving consecutive SN2' additions and [3,3]-rearrangements and a final stereoselective intramolecular conjugate addition is proposed and supported by M06-2X density functional theory calculations.
July 5, 2017: Organic & Biomolecular Chemistry
Sajan Pradhan, Chandan Kumar Shahi, Aditya Bhattacharyya, Navya Chauhan, Manas K Ghorai
Two efficient, modular, step- and pot-economic strategies to access various 5,6,7,12-tetrahydrobenzo[2,3]azepino[4,5-b]indoles and 6,7-dihydro-5H-benzo[5,6][1,4]diazepino[1,7-a]indoles are disclosed that advance via SN2-type regioselective ring opening of enantiopure aziridines with 2-(2-bromophenyl)-1H-indoles at their C3 and indolyl N centers, respectively, followed by Cu-mediated C-N cyclization which furnishes the products in excellent yields with outstanding enantiomeric excesses (up to >99%).
June 14, 2017: Organic Letters
Andreas Gansäuer, Stefan Grimme, Yong-Qiang Zhang, Christina Poppel, Anastasia Panfilova, Fabian Bohle
We describe a novel concept for SN2 reactions at tertiary carbon centers in epoxides without activation of the leaving group. Quantum chemical calculations show why SN2 reactions at tertiary carbon centers are proceeding in these systems. Our reaction allows a flexible synthesis of 1,3-diol building blocks for natural product synthesis with excellent control of relative and absolute configuration.
June 13, 2017: Angewandte Chemie
Rong Zhou, Rongfang Liu, Kai Zhang, Ling Han, Honghui Zhang, Wenchao Gao, Ruifeng Li
A novel P(NMe2)3-mediated formal carbon-halogen bond insertion of isatins into allylic and benzylic bromides/chlorides has been realized, leading to a facile synthesis of 3-halo 3,3'-disubstituted oxindoles. This reaction relies on the unique dual nucleophilic-electrophilic reactivity pattern of the Kukhtin-Ramirez adduct via a cascade SN2-SN2 process. It also represents a rare metal-free approach for carbon-halogen bond insertion. Upon treatment with trifluoroacetic acid, spirooxindole-γ-butyrolactones have been efficiently prepared from the corresponding insertion products...
June 22, 2017: Chemical Communications: Chem Comm
Javier Iglesias-Fernández, Susan M Hancock, Seung Seo Lee, Maola Khan, Jo Kirkpatrick, Neil J Oldham, Katherine McAuley, Anthony Fordham-Skelton, Carme Rovira, Benjamin G Davis
SNi-like mechanisms, which involve front-face leaving group departure and nucleophile approach, have been observed experimentally and computationally in chemical and enzymatic substitution at α-glycosyl electrophiles. Since SNi-like, SN1 and SN2 substitution pathways can be energetically comparable, engineered switching could be feasible. Here, engineering of Sulfolobus solfataricus β-glycosidase, which originally catalyzed double SN2 substitution, changed its mode to SNi-like. Destruction of the first SN2 nucleophile through E387Y mutation created a β-stereoselective catalyst for glycoside synthesis from activated substrates, despite lacking a nucleophile...
June 12, 2017: Nature Chemical Biology
István Szabó, Balázs Olasz, Gábor Czakó
Due to their importance in organic chemistry, the atomistic understanding of bimolecular nucleophilic substitution (SN2) reactions shows exponentially growing interest. In this publication, the effect of front-side complex (FSC) formation is uncovered via quasi-classical trajectory computations combined with a novel analysis method called trajectory orthogonal projection (TOP). For both F(-) + CH3Y [Y = Cl,I] reactions, the lifetime distributions of the F(-)···YCH3 front-side complex revealed weakly trapped nucleophiles (F(-))...
June 14, 2017: Journal of Physical Chemistry Letters
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