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https://www.readbyqxmd.com/read/28210717/the-molecular-mechanism-of-the-ligand-exchange-reaction-of-an-antibody-against-a-glutathione-coated-gold-cluster
#1
Víctor Rojas-Cervellera, Lluís Raich, Jaakko Akola, Carme Rovira
The labeling of proteins with heavy atom clusters is of paramount importance in biomedical research, but its detailed molecular mechanism remains unknown. Here we uncover it for the particular case of the anti-influenza N9 neuraminidase NC10 antibody against a glutathione-coated gold cluster by means of ab initio QM/MM calculations. We show that the labeling reaction follows an associative double SN2-like reaction mechanism, involving a proton transfer, with low activation barriers only if one of the two distinct peptide/peptidic ligands (the one that occupies the side position) is substituted...
February 17, 2017: Nanoscale
https://www.readbyqxmd.com/read/28195472/synthesis-of-polysubstituted-2-aminoimidazoles-via-alkene-diamination-of-guanidine-with-conjugated-%C3%AE-bromoalkenones
#2
Sankar K Guchhait, Neha Hura, Archana P Shah
A step-economical access to polysubstituted aminoimidazoles has been accomplished via alkene vicinal C-N bonds formation of 2-bromo-2-alkenones with guanidine avoiding its NH-protection/derivatization prerequisite for electronic modulation. The approach has excellent substrate scope, is amenable to diverse guanidine-containing substrates, and introduces distinctive substitutions/functionalities into aminoimidazole core. It is also applicable to preparation of fused-imidazoles. The reaction involves a tandem pathway of aza-Michael addition, SN2, and a unique redox-neutral process, as evident by spectroscopic study and control experiments...
February 20, 2017: Journal of Organic Chemistry
https://www.readbyqxmd.com/read/28186779/gas-phase-ion-molecule-reactions-of-copper-hydride-anions-cuh2-and-cu2h3
#3
Athanasios Zavras, Hossein Ghari, Alireza Ariafard, Allan J Canty, Richard A J O'Hair
Gas-phase reactivity of the copper hydride anions [CuH2](-) and [Cu2H3](-) toward a range of neutral reagents has been examined via multistage mass spectrometry experiments in a linear ion trap mass spectrometer in conjunction with isotope labeling studies and Density Functional Theory (DFT) calculations. [CuH2](-) is more reactive than [Cu2H3](-), consistent with DFT calculations, which show it has a higher energy HOMO. Experimentally, [CuH2](-) was found to react with CS2 via hydride transfer to give thioformate (HCS2(-)) in competition with the formation of the organometallic [CuCS2](-) ion via liberation of hydrogen; CO2 via insertion to produce [HCuO2CH](-); methyl iodide and allyl iodide to give I(-) and [CuHI](-); and 2,2,2-trifluoroethanol and 1-butanethiol via protonation to give hydrogen and the product anions [CuH(OCH2CF3)](-) and [CuH(SBu)](-)...
February 10, 2017: Inorganic Chemistry
https://www.readbyqxmd.com/read/28184399/access-to-thiopyrano-2-3-b-indole-via-tertiary-amine-catalyzed-formal-3-3-annulations-of-%C3%AE-acetoxy-allenoates-with-indoline-2-thiones
#4
Chunjie Ni, Yuwen Zhang, Yading Hou, Xiaofeng Tong
DABCO-catalyzed formal (3+3) annulations of β'-acetoxy allenoates with indoline-2-thiones are described, which provide facile access to thiopyrano[2,3-b]indole under mild reaction conditions. The reaction might proceed via the SN2'-SN2'-type process between β'-acetoxy allenoate and indole-2-thiolate with the assistance of the DABCO catalyst and K2CO3 additive, followed by intramolecular Friedel-Crafts reaction at the 3-position of indole and central carbon of allene.
February 10, 2017: Chemical Communications: Chem Comm
https://www.readbyqxmd.com/read/28128849/automated-first-principles-mapping-for-phase-change-materials
#5
Marc Esser, Stefan Maintz, Richard Dronskowski
Plotting materials on bi-coordinate maps according to physically meaningful descriptors has a successful tradition in computational solid-state science spanning more than four decades. Equipped with new ab initio techniques introduced in this work, we generate an improved version of the treasure map for phase-change materials (PCMs) as introduced previously by Lencer et al. which, other than before, charts all industrially used PCMs correctly. Furthermore, we suggest seven new PCM candidates, namely SiSb4 Te7 , Si2 Sb2 Te5 , SiAs2 Te4 , PbAs2 Te4 , SiSb2 Te4 , Sn2 As2 Te5 , and PbAs4 Te7 , to be used as synthetic targets...
January 27, 2017: Journal of Computational Chemistry
https://www.readbyqxmd.com/read/28128567/enantioselective-total-synthesis-of-iso-a82775c-a-proposed-biosynthetic-precursor-of-chloropupukeananin
#6
Takahiro Suzuki, Soichiro Watanabe, Susumu Kobayashi, Keiji Tanino
(+)-Iso-A82775C is a proposed biosynthetic precursor of the chloropupukeananin family and an important intermediate for related natural products. The first enantioselective total synthesis of (+)-iso-A82775C (18 steps, 2.2% overall yield) toward the eventual biomimetic total synthesis of chloropupukeananin is described. The key steps are (1) the enantioselective Diels-Alder reaction of 4-bromo-3-hydroxy-2-pyrone with methyl 2-chloroacrylate using cinchonine as an organocatalyst and (2) the anti-selective Cu-mediated SN2' reaction to afford the axially chiral vinylallene moiety...
January 27, 2017: Organic Letters
https://www.readbyqxmd.com/read/28125809/frequency-of-application-of-amf-naf-sncl2-solution-and-its-potential-in-controlling-human-enamel-erosion-progression-an-in-situ-study
#7
C V da Silva, T M Ramos-Oliveira, T F Mantilla, P M de Freitas
Although several studies have demonstrated the efficacy of AmF/NaF/SnCl2 solution in inhibiting dental erosion progression, measures for further improvement in its effectiveness are paramount. Thus, this in situ study evaluated whether the protective effect promoted by the AmF/NaF/SnCl2 solution would be enhanced by increasing its frequency of use. The study was conducted with 12 volunteers, a 4-phase (5 days each) randomized, crossover model. Extraoral erosive challenges (0.5% citric acid, pH 2.6, 6 × 2 min/day) and rinsing protocol (1 or 2 × 2 min/day) were performed...
January 27, 2017: Caries Research
https://www.readbyqxmd.com/read/28121139/structure-potency-relationships-for-epoxides-in-allergic-contact-dermatitis
#8
David W Roberts, Aynur Aptula, Anne Marie Api
Epoxides are known or proposed to be involved in skin sensitization in various ways. Some are encountered directly, and others have been shown to be formed abiotically and metabolically from various unsaturated chemicals. They can react as SN2 electrophiles. To date no quantitative mechanistic models (QMMs) are known for skin sensitization potency of this subcategory of SN2 electrophiles. Here we have considered the reaction mechanistic chemistry of epoxides and combined published experimental kinetic data (rate constants k for reaction with a cysteine-based peptide) together with calculated hydrophobicity data (logP) to derive a QMM correlating potency in the local lymph node assay (LLNA), expressed as EC3, with a relative alkylation index (RAI, calculated as logk + 0...
February 20, 2017: Chemical Research in Toxicology
https://www.readbyqxmd.com/read/28118543/direct-chemical-dynamics-simulations
#9
Subha Pratihar, Xinyou Ma, Zahra Homayoon, George L Barnes, William L Hase
In a direct dynamics simulation, the technologies of chemical dynamics and electronic structure theory are coupled so that the potential energy, gradient, and Hessian required from the simulation are obtained directly from the electronic structure theory. These simulations are extensively used to (1) interpret experimental results and understand the atomic-level dynamics of chemical reactions; (2) illustrate the ability of classical simulations to correctly interpret and predict chemical dynamics when quantum effects are expected to be unimportant; (3) obtain the correct classical dynamics predicted by an electronic structure theory; (4) determine a deeper understanding of when statistical theories are valid for predicting the mechanisms and rates of chemical reactions; and (5) discover new reaction pathways and chemical dynamics...
February 9, 2017: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/28118013/domino-c-f-bond-activation-of-the-cf3-group-synthesis-of-fluorinated-dibenzo-a-c-7-annulenes-from-2-trifluoromethyl-1-alkenes-and-2-2-diceriobiaryls
#10
Takeshi Fujita, Marina Takazawa, Kazuki Sugiyama, Naoto Suzuki, Junji Ichikawa
The construction of ring-fluorinated seven-membered carbocycles was readily achieved via the domino SN2'-type/SNV reaction between 2-(trifluoromethyl)-1-alkenes and 1,4-carbodianions. The SN2'-type reaction of 2-(trifluoromethyl)-1-alkenes with 2,2'-diceriobiaryls generated the intermediary 1,1-difluoro-1-alkenes bearing a monoceriobiaryl moiety, which in turn underwent intramolecular SNV reaction to afford fluorinated 5H-dibenzo[a,c][7]annulenes.
January 24, 2017: Organic Letters
https://www.readbyqxmd.com/read/28106144/electronic-and-atomic-structures-of-the-sr3ir4sn13-single-crystal-a-possible-charge-density-wave-material
#11
H-T Wang, M K Srivastava, C-C Wu, S-H Hsieh, Y-F Wang, Y-C Shao, Y-H Liang, C-H Du, J-W Chiou, C-M Cheng, J-L Chen, C-W Pao, J-F Lee, C N Kuo, C S Lue, M-K Wu, W-F Pong
X-ray scattering (XRS), x-ray absorption near-edge structure (XANES) and extended x-ray absorption fine structure (EXAFS) spectroscopic techniques were used to study the electronic and atomic structures of the high-quality Sr3Ir4Sn13 (SIS) single crystal below and above the transition temperature (T(*) ≈ 147 K). The evolution of a series of modulated satellite peaks below the transition temperature in the XRS experiment indicated the formation of a possible charge density wave (CDW) in the (110) plane...
January 20, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28102315/methyl-cytosine-driven-structural-changes-enhance-adduction-kinetics-of-an-exon-7-fragment-of-the-p53-gene
#12
Spundana Malla, Karteek Kadimisetty, You-Jun Fu, Dharamainder Choudhary, John B Schenkman, James F Rusling
Methylation of cytosine (C) at C-phosphate-guanine (CpG) sites enhances reactivity of DNA towards electrophiles. Mutations at CpG sites on the p53 tumor suppressor gene that can result from these adductions are in turn correlated with specific cancers. Here we describe the first restriction-enzyme-assisted LC-MS/MS sequencing study of the influence of methyl cytosines (MeC) on kinetics of p53 gene adduction by model metabolite benzo[a]pyrene-7,8-dihydrodiol-9,10-epoxide (BPDE), using methodology applicable to correlate gene damage sites for drug and pollutant metabolites with mutation sites...
January 19, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28094946/competing-e2-and-sn2-mechanisms-for-the-f-ch3ch2i-reaction
#13
Li Yang, Jiaxu Zhang, Jing Xie, Xinyou Ma, Linyao Zhang, Chenyang Zhao, William L Hase
Anti-E2, syn-E2, inv-, and ret-SN2 reaction channels for the gas-phase reaction of F(-) + CH3CH2I were characterized with a variety of electronic structure calculations. Geometrical analysis confirmed synchronous E2-type transition states for the elimination of the current reaction, instead of nonconcerted processes through E1cb-like and E1-like mechanisms. Importantly, the controversy concerning the reactant complex for anti-E2 and inv-SN2 paths has been clarified in the present work. A positive barrier of +19...
February 9, 2017: Journal of Physical Chemistry. A
https://www.readbyqxmd.com/read/28094460/n-heterocyclic-carbene-catalyzed-intramolecular-nucleophilic-substitution-reaction-enantioselective-construction-of-all-carbon-quaternary-stereocenters
#14
Ming Zhao, Jie Chen, Hui Yang, Ling Zhou
An efficient enantioselective N-heterocyclic carbene (NHC) catalyzed intramolecular SN2' nucleophilic substitution reaction of aldehyde with (E/Z)-trisubstituted allylic bromides has been accomplished. A range of enantioenriched chromanones bearing an all-carbon quaternary stereocenter at the C3 position were prepared with up to 97% yield and 98% ee. The resulting vinyl and carbonyl groups in these products can be transformed to a variety of synthetically important building blocks.
January 17, 2017: Chemistry: a European Journal
https://www.readbyqxmd.com/read/28075601/nitrogen-doped-mesoporous-carbons-as-counter-electrodes-in-quantum-dot-sensitized-solar-cells-with-a-conversion-efficiency-exceeding-12
#15
Shuang Jiao, Jun Du, Zhonglin Du, Donghui Long, Wuyou Jiang, Zhenxiao Pan, Yan Li, Xinhua Zhong
The exploration of catalyst materials for counter electrodes (CEs) in quantum dot sensitized solar cells (QDSCs) that have both high electrocatalytic activity and low charge transfer resistance is always significant yet challenging. In this work, we report the incorporation of nitrogen heteroatoms into carbon lattices leading to nitrogen-doped mesoporous carbon (N-MC) materials with superior catalytic activity when used as CEs in Zn-Cu-In-Se QDSCs. A series of N-MC materials with different nitrogen contents were synthesized by a colloidal silica nanocasting method...
January 13, 2017: Journal of Physical Chemistry Letters
https://www.readbyqxmd.com/read/28075138/control-of-chemo-regio-and-enantioselectivity-in-copper-hydride-reductions-of-morita-baylis-hillman-adducts
#16
Roscoe T H Linstadt, Carl A Peterson, Carina I Jette, Zarko V Boskovic, Bruce H Lipshutz
Nonracemically ligated copper hydride can be used to effect tandem SN2'/1,2-reductions of racemic Morita-Baylis-Hillman (MBH) acetates to access enantioenriched chiral allylic alcohols with defined olefin geometry. MBH esters, including those with β-substitution, can be transformed to stereodefined enoates by taking advantage of a bulky, oligomeric, in situ generated trialkoxysiloxane leaving group. Finally, an atypical conversion of easily arrived at MBH alcohol derivatives to nonracemic allylic alcohols is disclosed...
January 11, 2017: Organic Letters
https://www.readbyqxmd.com/read/28071915/variational-flooding-study-of-a-sn2-reaction
#17
GiovanniMaria Piccini, James J McCarty, Omar Valsson, Michele Parrinello
We have studied the reaction dynamics of a prototypical organic reaction using a variationally optimized truncated bias to accelerate transitions between educt and product reactant states. The asymmetric SN2 nucleophilic substitution reaction of fluoromethane and chloromethane CH3F + Cl(-) ⇌ CH3Cl + F(-) is considered, and many independent biased molecular dynamics simulations have been performed at 600, 900, and 1200 K, collecting several hundred transitions at each temperature. The transition times and relative rate constants have been obtained for both reaction directions...
January 17, 2017: Journal of Physical Chemistry Letters
https://www.readbyqxmd.com/read/28071904/new-insight-into-the-formation-mechanism-of-imidazolium-based-ionic-liquids-from-n-alkyl-imidazoles-and-halogenated-hydrocarbons-a-polar-microenvironment-induced-and-autopromoted-process
#18
Xueli Mu, Nan Jiang, Chengbu Liu, Dongju Zhang
To illustrate the formation mechanism of imidazolium-based ionic liquids (ILs) from N-alkyl imidazoles and halogenated hydrocarbons, density functional theory calculations have been carried out on a representative system, the reaction of N-methyl imidazole with chloroethane to form 1-ethyl-3-methyl imidazolium chloride ([Emim]Cl) IL. The reaction is shown to proceed via an SN2 transition state with a free energy barrier of 34.4 kcal/mol in the gas phase and 27.6 kcal/mol in toluene solvent. The reaction can be remarkably promoted by the presence of ionic products and water molecules...
February 9, 2017: Journal of Physical Chemistry. A
https://www.readbyqxmd.com/read/28051314/mapping-the-reactivity-and-selectivity-of-2-azidofucosyl-donors-for-the-assembly-of-n-acetylfucosamine-containing-bacterial-oligosaccharides
#19
Bas Hagen, Sara Ali, Herman S Overkleeft, Gijsbert A van der Marel, Jeroen D C Codée
The synthesis of complex oligosaccharides is often hindered by a lack of knowledge on the reactivity and selectivity of their constituent building blocks. We investigated the reactivity and selectivity of 2-azidofucosyl (FucN3) donors, valuable synthons in the synthesis of 2-acetamido-2-deoxyfucose (FucNAc) containing oligosaccharides. Six FucN3 donors, bearing benzyl, benzoyl, or tert-butyldimethylsilyl protecting groups at the C3-O and C4-O positions, were synthesized, and their reactivity was assessed in a series of glycosylations using acceptors of varying nucleophilicity and size...
January 10, 2017: Journal of Organic Chemistry
https://www.readbyqxmd.com/read/28045531/activation-strain-analysis-of-sn2-reactions-at-c-n-o-and-f-centers
#20
Jan Kubelka, F Matthias Bickelhaupt
Fundamental principles that determine chemical reactivity and reaction mechanisms are the very foundation of chemistry and many related fields of science. Bimolecular nucleophilic substitutions (SN2) are among the most common and therefore most important reaction types. In this report, we examine the trends in the SN2 reactions with respect to increasing electronegativity of the reaction center by comparing the well-studied backside SN2 Cl(-) + CH3Cl with similar Cl(-) substitutions on the isoelectronic series with the second period elements N, O, and F in place of C...
January 20, 2017: Journal of Physical Chemistry. A
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