PMID-sentid Pub_year Sent_text comp_official_name comp_offsetprotein_name organism prot_offset 31246023-0 2019 QM/MM Calculations for the Cl- + CH3Cl SN2 Reaction in Water Using CM5 Charges and Density Functional Theory. Water 55-60 solute carrier family 38 member 5 Homo sapiens 39-42 35582984-0 2022 Investigating the competing E2 and SN2 mechanisms for the microsolvated HO-(H2O)n=0-4 + CH3CH2X (X = Cl, Br, I) reactions. Water 76-79 solute carrier family 38 member 5 Homo sapiens 35-38 35582984-1 2022 We characterized the anti-E2, syn-E2, inv-SN2, and ret-SN2 reaction channels for the reaction of microsolvated HO-(H2O)n anions with CH3CH2X (X = Cl, Br, I), using the CCSD(T)/PP/t//MP2/ECP/d level method, to understand how a solvent influences the competing E2 and SN2 reactions. Water 115-118 solute carrier family 38 member 5 Homo sapiens 42-45 7287710-7 1981 These findings lead to a view that the proton-catalyzed nucleophilic displacement of O2- from MbO2 by an entering water molecule, or SN2 mechanism with proton assistance, is the basis for most of the autoxidation reaction under normal conditions. Water 114-119 solute carrier family 38 member 5 Homo sapiens 133-136 26185965-0 1991 Activation to the transition state: reactant and solvent energy flow for a model SN2 reaction in water. Water 97-102 solute carrier family 38 member 5 Homo sapiens 81-84 35582984-1 2022 We characterized the anti-E2, syn-E2, inv-SN2, and ret-SN2 reaction channels for the reaction of microsolvated HO-(H2O)n anions with CH3CH2X (X = Cl, Br, I), using the CCSD(T)/PP/t//MP2/ECP/d level method, to understand how a solvent influences the competing E2 and SN2 reactions. Water 115-118 solute carrier family 38 member 5 Homo sapiens 55-58 35582984-1 2022 We characterized the anti-E2, syn-E2, inv-SN2, and ret-SN2 reaction channels for the reaction of microsolvated HO-(H2O)n anions with CH3CH2X (X = Cl, Br, I), using the CCSD(T)/PP/t//MP2/ECP/d level method, to understand how a solvent influences the competing E2 and SN2 reactions. Water 115-118 solute carrier family 38 member 5 Homo sapiens 266-269 35582984-7 2022 In terms of E2/SN2 competition, the barrier difference, , first increases then decreases as the number of explicit water molecules increases, under both microsolvation and bulk solvation conditions, but the inv-SN2 pathway is always favored over the anti-E2 pathway. Water 115-120 solute carrier family 38 member 5 Homo sapiens 15-18 35582984-7 2022 In terms of E2/SN2 competition, the barrier difference, , first increases then decreases as the number of explicit water molecules increases, under both microsolvation and bulk solvation conditions, but the inv-SN2 pathway is always favored over the anti-E2 pathway. Water 115-120 solute carrier family 38 member 5 Homo sapiens 211-214 35384955-3 2022 The limiting stage is the stage of cyclization involving the intramolecular attack by the amino group of the precyclic intermediate on the carbon atom bound to the hydroxyl group with the simultaneous release of a water molecule according to the SN2 mechanism. Water 214-219 solute carrier family 38 member 5 Homo sapiens 246-249 35274635-8 2022 The method is here applied to six SN2 reactions in water at 295.15 K, which differ in the nucleophile and the leaving group. Water 51-56 solute carrier family 38 member 5 Homo sapiens 34-37 33418478-0 2021 Europium(III) complex fluorescent sensor for dual channel recognition of Sn2+ and Cu2+ ions in water. Water 95-100 solute carrier family 38 member 5 Homo sapiens 73-76 33502190-8 2021 We also examined the effect of replacing water with methanol on the ease of the SN2 reaction, finding that the replacement resulted in a higher activation barrier for the generation of BrO-. Water 41-46 solute carrier family 38 member 5 Homo sapiens 80-83 32668925-1 2020 We study the prototypical SN2 reaction Cl- + CH3Cl CH3Cl + Cl- in water using quantum mechanics/molecular mechanics (QM/MM) computer simulations with transition path sampling and inertial likelihood maximization. Water 68-73 solute carrier family 38 member 5 Homo sapiens 26-29 31246023-1 2019 The prototypical SN2 reaction of chloride ion with methyl chloride has been reinvestigated in aqueous solution using QM/MM methodology featuring MO6-2X/6-31+G(d) calculations with the TIP4P water model, and partial charges were computed with the CM5 method. Water 190-195 solute carrier family 38 member 5 Homo sapiens 17-20 30676756-3 2019 The simulations consistently predict that the most dominant mechanism is the proton-assisted SN2 process, where the protonation of the hydroxyl group by water and the C-O bond breaking and formation occur in a single step. Water 153-158 solute carrier family 38 member 5 Homo sapiens 93-96 27940912-2 2016 Accumulated evidence suggests that the reaction path of PKMT-catalyzed methylation consists of the formation of a cofactor(cosubstrate)-PKMT-substrate complex, lysine deprotonation through dynamic water channels, and a nucleophilic substitution (SN2) transition state for transmethylation. Water 197-202 solute carrier family 38 member 5 Homo sapiens 246-249 30444620-1 2018 The potential energy profiles of F/OH-induced nucleophilic substitution (SN2) and proton-transfer (PT) channels evolving with solvation for reactions of F-(H2O) n=1-2 + CH3I were characterized using B3LYP/ECP/d method. Water 156-159 solute carrier family 38 member 5 Homo sapiens 73-76 30444620-8 2018 The water delivering process from fluorine to iodine side as illustrated on PES is barely observed, and instead, the reaction tends to dehydrate before passing through the SN2 barrier and proceeds with the less hydrated pathway in order to weaken the steric effect. Water 4-9 solute carrier family 38 member 5 Homo sapiens 172-175 30157632-5 2018 Our results show that the native enzyme limits the access of water molecules to the active site, enhancing the interaction between the reactants and providing a more favorable electrostatic environment to assist the SN2 methyl transfer reaction. Water 61-66 solute carrier family 38 member 5 Homo sapiens 216-219 29306291-0 2018 Dynamic exit-channel pathways of the microsolvated HOO-(H2O) + CH3Cl SN2 reaction: Reaction mechanisms at the atomic level from direct chemical dynamics simulations. Water 56-59 solute carrier family 38 member 5 Homo sapiens 69-72 29306291-1 2018 Microsolvated bimolecular nucleophilic substitution (SN2) reaction of monohydrated hydrogen peroxide anion [HOO-(H2O)] with methyl chloride (CH3Cl) has been investigated with direct chemical dynamics simulations at the M06-2X/6-31+G(d,p) level of theory. Water 113-116 solute carrier family 38 member 5 Homo sapiens 53-56 29306291-9 2018 Compared with the HOO- + CH3Cl SN2 reaction, indirect dynamic reaction mechanisms are enhanced by microsolvation for the HOO-(H2O) + CH3Cl SN2 reaction. Water 126-129 solute carrier family 38 member 5 Homo sapiens 31-34 29306291-9 2018 Compared with the HOO- + CH3Cl SN2 reaction, indirect dynamic reaction mechanisms are enhanced by microsolvation for the HOO-(H2O) + CH3Cl SN2 reaction. Water 126-129 solute carrier family 38 member 5 Homo sapiens 139-142 29306291-10 2018 On the basis of our simulations, further crossed molecular beam imaging experiments are highly suggested for the SN2 reactions of HOO- + CH3Cl and HOO-(H2O) + CH3Cl. Water 152-155 solute carrier family 38 member 5 Homo sapiens 113-116 28394615-1 2017 Influences of solvent molecules on SN2 reaction dynamics of microsolvated F-(H2O)n with CH3I, for n = 0-3, are uncovered by direct chemical dynamics simulations. Water 77-80 solute carrier family 38 member 5 Homo sapiens 35-38 25837687-1 2015 In a kinetic experiment on the SN2 reaction of sodium p-nitrophenoxide with iodomethane in acetone-water mixed solvent, Humeres et al. Water 99-104 solute carrier family 38 member 5 Homo sapiens 31-34 27126610-0 2016 Electronic Structure Theory Study of the Microsolvated F(-)(H2O) + CH3I SN2 Reaction. Water 60-63 solute carrier family 38 member 5 Homo sapiens 72-75 27126610-3 2016 The water molecule remains on the fluorine side until the reactive system goes to the SN2 saddle point. Water 4-9 solute carrier family 38 member 5 Homo sapiens 86-89 26178088-6 2015 The applicability of this approach is demonstrated for the embedded many-body expansion of binding energies of water hexamers and calculation of reaction barriers of SN2 substitution of fluorine by chlorine in alpha-fluoroalkanes. Water 111-116 solute carrier family 38 member 5 Homo sapiens 166-169 26133429-3 2015 The SN2 reaction dominates at all reactant collision energies, but at higher collision energies proton transfer to form CH2I(-), and to a lesser extent CH2I(-) (H2O), becomes important. Water 161-164 solute carrier family 38 member 5 Homo sapiens 4-7 26133429-7 2015 Overall, the simulation results for the OH(-)(H2O) + CH3I SN2 reaction are in good agreement with experiment with respect to reaction rate constant, product branching ratio, etc. Water 46-50 solute carrier family 38 member 5 Homo sapiens 58-61 26133429-10 2015 The SN2 reaction is dominated by events in which H2O leaves the reactive system as CH3OH is formed or before CH3OH formation. Water 49-52 solute carrier family 38 member 5 Homo sapiens 4-7 26609818-1 2009 Kinetic isotope effects (KIEs) on the two alternative reactions, SN2 and E2, between hypochlorite anion and ethyl chloride in water have been studied theoretically using B3LYP and M06-2X functionals. Water 126-131 solute carrier family 38 member 5 Homo sapiens 65-68 18795240-2 2009 In previous communications, we have shown that Sn-2 monoglycerides can replace Sn-1,3 regiospecific lipases at the oil-water interface, causing a drastically reduced rate of lipolysis. Water 119-124 solute carrier family 38 member 5 Homo sapiens 47-51 18795240-3 2009 We here demonstrate that even if the lipase is expelled from the interface, it can catalyze esterification of the Sn-2 monoglyceride with fatty acids in both macroscopic oil-water systems and in microemulsions, leading to formation of di- and triglycerides. Water 174-179 solute carrier family 38 member 5 Homo sapiens 114-118 25121958-0 2014 Transition-state structure for the quintessential SN2 reaction of a carbohydrate: reaction of alpha-glucopyranosyl fluoride with azide ion in water. Water 142-147 solute carrier family 38 member 5 Homo sapiens 50-53 23534338-1 2013 We report on the reaction dynamics of the monosolvated SN2 reaction of cold OH(-)(H2O) with CH3I that have been studied using crossed beam ion imaging. Water 82-85 solute carrier family 38 member 5 Homo sapiens 55-58 23534338-2 2013 Two SN2 reaction channels are possible for this reaction: Formation of unsolvated I(-) and of solvated I(-)(H2O) products. Water 108-111 solute carrier family 38 member 5 Homo sapiens 4-7 17029445-0 2006 Direct ab initio molecular dynamics study on a microsolvated SN2 reaction of OH-(H2O) with CH3Cl. Water 81-84 solute carrier family 38 member 5 Homo sapiens 61-64 17266358-2 2007 Adding water to the organic phase, the SN2 yield increases in the cost of decreased reactivity. Water 7-12 solute carrier family 38 member 5 Homo sapiens 39-42 17530724-8 2007 Several mechanistic hypotheses, including the hydrolysis of an allenol ester intermediate and SN2" addition of water, were examined to gain an insight into this transformation. Water 111-116 solute carrier family 38 member 5 Homo sapiens 94-97 17029445-1 2006 Reaction dynamics for a microsolvated SN2 reaction OH-(H2O)+CH3Cl have been investigated by means of the direct ab initio molecular dynamics method. Water 55-59 solute carrier family 38 member 5 Homo sapiens 38-41 12929387-2 2003 Non-steady-state kinetic studies reveal that the SN2 reaction between p-nitrophenoxide ion and methyl iodide in acetonitrile containing water follows a 2-step mechanism involving the formation of a kinetically significant intermediate. Water 136-141 solute carrier family 38 member 5 Homo sapiens 49-52 16851554-0 2005 A coupled reference interaction site model/molecular dynamics study of the potential of mean force curve of the SN2 Cl- + CH3Cl reaction in water. Water 140-145 solute carrier family 38 member 5 Homo sapiens 112-115 12610210-0 2003 Comparison of formation of reactive conformers for the SN2 displacements by CH3CO2- in water and by Asp124-CO2- in a haloalkane dehalogenase. Water 87-92 solute carrier family 38 member 5 Homo sapiens 55-58 12929387-0 2003 Non-steady-state kinetic study of the SN2 reaction between p-nitrophenoxide ion and methyl iodide in aprotic solvents containing water. Water 129-134 solute carrier family 38 member 5 Homo sapiens 38-41 7836427-5 1995 (i) When a single cis-carbon-carbon double bond (delta) is incorporated into a saturated diacylphosphatidylcholine molecule at any position within the central segment of the long sn-2 acyl chain, the resulting monoenoic lipid molecules will, in excess water, exhibit reduced phase transition temperature (Tm) and transition enthalpy (delta H) as they undergo the gel to liquid-crystalline phase transition. Water 252-257 solute carrier family 38 member 5 Homo sapiens 179-183 12602343-2 2002 With the Onsager approach to account for the variation in local dielectric constant, these results are used to determine the effective penetration profile of water into fluid phospholipid membranes, from recent electron paramagnetic resonance (EPR) studies on phospholipids spin-labelled systematically down the sn-2 chain. Water 158-163 solute carrier family 38 member 5 Homo sapiens 312-316 11349907-3 2001 From the mechanistic point of view the reaction is found to be similar to a SN2 mechanism and coupled with water-mediated proton transfer in accordance with the intriguing findings of Bianco and Hynes [R. Bianco, J. T. Hynes. Water 107-112 solute carrier family 38 member 5 Homo sapiens 76-79 10049533-1 1999 The SN2 reaction of Br- with methylnaphthalene-2-sulfonate (MeONs) in water is accelerated by micelles of tetradecyldialkyl amine oxide (alkyl = methyl, n-propyl) and rates increase sharply in HBr due to increased binding of Br- to the protonated amine oxide. Water 70-75 solute carrier family 38 member 5 Homo sapiens 4-7