Mechanistic Study of the Deamination Reaction of Guanine: A Computational Study

2011 ◽  
Vol 115 (10) ◽  
pp. 2065-2076 ◽  
Author(s):  
Kabir M. Uddin ◽  
Mansour H. Almatarneh ◽  
Dawn M. Shaw ◽  
Raymond A. Poirier
Keyword(s):  
Computational Study ◽  
Mechanistic Study ◽  
Deamination Reaction

Nitrenium ions and trivalent boron ligands as analogues of N-heterocyclic carbenes in olefin metathesis: a computational study

2015 ◽  
Vol 44 (46) ◽  
pp. 20021-20026 ◽  
Author(s):  
A. Pazio ◽  
K. Woźniak ◽  
K. Grela ◽  
B. Trzaskowski
Keyword(s):  
Olefin Metathesis ◽  
Computational Study ◽  
Heterocyclic Carbenes ◽  
Mechanistic Study ◽  
Nitrenium Ions ◽  
Nitrenium Ion ◽  
Metathesis Catalysts

A DFT mechanistic study reveals that nitrenium ion-modified Hoveyda-like complexes are good candidates for latent metathesis catalysts, while boron-modified systems are candidates for very fast metathesis catalysts.

Effect of soya phosphatidylcholine and possible underlying mechanism on ischemia/reperfusion injury in isolated perfused rat heart: an experimental and computational study

2022 ◽  
pp. 1-7
Author(s):  
Anita A. Mehta ◽  
Purav Patel ◽  
Vandana R. Thakur ◽  
Jayesh V. Beladiya
Keyword(s):  
Ischemia Reperfusion Injury ◽  
Computational Study ◽  
Ischemia Reperfusion ◽  
Underlying Mechanism ◽  
Left Ventricular ◽  
Global Ischemia ◽  
Mechanistic Study ◽  
Cardiac Damage ◽  
Nitric Oxide Synthase Inhibitor ◽  
Triton X

This study was designed to assess the effect of soya phosphatidylcholine (SPC) against ischemia/reperfusion (I/R) injury and the possible underlying mechanism using experimental and computational studies. I/R injury was induced by global ischemia for 30 min followed by reperfusion for 120 min. The perfusion of the SPC was performed for 10 min before inducing global ischemia. In the mechanistic study, the involvement of specific cellular pathways was identified using various inhibitors such as ATP-dependent potassium channel (KATP) inhibitor (glibenclamide), protein kinase C (PKC) inhibitor (chelerythrine), non-selective nitric oxide synthase inhibitor (L-NAME), and endothelium remover (Triton X-100). The computational study of various ligands was performed on toll-like receptor 4 (TLR4) protein using AutoDock version 4.0. SPC (100 μM) significantly decreased the levels of cardiac damage markers and %infarction compared with the vehicle control (VC). Furthermore, cardiodynamics (indices of left ventricular contraction (dp/dtmax), indices of left ventricular relaxation (dp/dtmin), coronary flow, and antioxidant enzyme levels were significantly improved as compared with VC. This protective effect was attenuated by glibenclamide, chelerythrine, and Triton X-100, but it was not attenuated by L-NAME. The computational study showed a significant bonding affinity of SPC to the TLR4-MD2 complex. Thus, SPC reduced myocardial I/R injury in isolated perfused rat hearts, which might be governed by the KATP channel, PKC, endothelium response, and TLR4-MyD88 signaling pathway.

scholarly journals Computational mechanistic study of the unimolecular dissociation of ethyl hydroperoxide and its bimolecular reactions with atmospheric species

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Mansour H. Almatarneh ◽  
Asmaa Alnajajrah ◽  
Mohammednoor Altarawneh ◽  
Yuming Zhao ◽  
Mohammad A. Halim
Keyword(s):  
Activation Energy ◽  
Density Functional ◽  
Computational Study ◽  
Basis Sets ◽  
Mechanistic Study ◽  
Intrinsic Reaction Coordinate ◽  
Unimolecular Dissociation ◽  
Phase Reaction ◽  
Atmospheric Species ◽  
Solvation Models

Abstract A detailed computational study of the atmospheric reaction of the simplest Criegee intermediate CH2OO with methane has been performed using the density functional theory (DFT) method and high-level calculations. Solvation models were utilized to address the effect of water molecules on prominent reaction steps and their associated energies. The structures of all proposed mechanisms were optimized using B3LYP functional with several basis sets: 6-31G(d), 6-31G (2df,p), 6-311++G(3df,3pd) and at M06-2X/6-31G(d) and APFD/6-31G(d) levels of theory. Furthermore, all structures were optimized at the B3LYP/6-311++G(3df,3pd) level of theory. The intrinsic reaction coordinate (IRC) analysis was performed for characterizing the transition states on the potential energy surfaces. Fifteen different mechanistic pathways were studied for the reaction of Criegee intermediate with methane. Both thermodynamic functions (ΔH and ΔG), and activation parameters (activation energies Ea, enthalpies of activation ΔHǂ, and Gibbs energies of activation ΔGǂ) were calculated for all pathways investigated. The individual mechanisms for pathways A1, A2, B1, and B2, comprise two key steps: (i) the formation of ethyl hydroperoxide (EHP) accompanying with the hydrogen transfer from the alkanes to the terminal oxygen atom of CIs, and (ii) a following unimolecular dissociation of EHP. Pathways from C1 → H1 involve the bimolecular reaction of EHP with different atmospheric species. The photochemical reaction of methane with EHP (pathway E1) was found to be the most plausible reaction mechanism, exhibiting an overall activation energy of 7 kJ mol−1, which was estimated in vacuum at the B3LYP/6-311++G(3df,3pd) level of theory. All of the reactions were found to be strongly exothermic, expect the case of the sulfur dioxide-involved pathway that is predicted to be endothermic. The solvent effect plays an important role in the reaction of EHP with ammonia (pathway F1). Compared with the gas phase reaction, the overall activation energy for the solution phase reaction is decreased by 162 and 140 kJ mol−1 according to calculations done with the SMD and PCM solvation models, respectively.

Mechanisms for the Deamination Reaction of Cytosine with H2O/OH− and 2H2O/OH−: A Computational Study

2008 ◽  
Vol 48 (4) ◽  
pp. 831-843 ◽  
Author(s):  
Mansour H. Almatarneh ◽  
Christopher G. Flinn ◽  
Raymond A. Poirier
Keyword(s):  
Computational Study ◽  
Deamination Reaction

RADICAL-MOLECULE REACTIONS HCO/HOC + C2H4: A MECHANISTIC STUDY

2005 ◽  
Vol 04 (04) ◽  
pp. 1029-1055 ◽  
Author(s):  
HONG-BIN XIE ◽  
YI-HONG DING ◽  
CHIA-CHUNG SUN
Keyword(s):  
Kinetic Study ◽  
Kinetic Data ◽  
Computational Study ◽  
The Other ◽  
Mechanistic Study ◽  
Potential Importance ◽  
Donation Process ◽  
Combustion Processes ◽  
Extrusion Product ◽  
Orbital Analysis

A detailed computational study is performed on the radical-molecule reactions between HCO/HOC and ethylene ( C 2 H 4) at the Gaussian-3//B3LYP/6-31G(d) level. For the HCO + C 2 H 4 reaction, the most favorable pathway is the direct C -addition forming the intermediate H 2 CCH 2 CHO , followed by a 1,2- H -shift leading to H 3 CCHCHO . Subsequently, there are two highly competitive dissociation pathways for H 3 CCHCHO : one is the formation of the direct H -extrusion product H 2 CCHCHO + H , and the other is the formation of C 2 H 5 + CO via the intermediate H 3 CCH 2 CO . The overall reaction barrier is 14.1 and 14.6 kcal/mol respectively, at the G3B3 level. The quasi-direct H -donation process to produce C 2 H 5 + CO with the barrier 16.5 kcal/mol is less competitive. Thus, only at higher temperatures, the HCO + C 2 H 4 reaction could play a role. In contrast, the HOC + C 2 H 4 reaction just need to overcome a small barrier 2.0 kcal/mol to generate C 2 H 5 + CO via the quasi-direct H -donation mechanism. This is suggestive of the potential importance of the HOC + C 2 H 4 reaction in combustion processes. However, the direct C -addition channel is much less competitive. The present kinetic data and orbital analysis show that the HCO radical has much higher reactivity than HOC , although the latter is more energetic. Till now, no kinetic study on the HOC radical has been reported, the present study can provide useful information on understanding the reactivity and depletion mechanism of the energetic HOC radical.

Computational study on NHC-catalyzed enantioselective and chemoselective fluorination of aliphatic aldehydes

2017 ◽  
Vol 4 (10) ◽  
pp. 1987-1998 ◽  
Author(s):  
Yang Wang ◽  
Yan Qiao ◽  
Donghui Wei ◽  
Mingsheng Tang
Keyword(s):  
Computational Study ◽  
Mechanistic Study ◽  
Aliphatic Aldehydes ◽  
First Time

A mechanistic study on NHC-catalyzed enantioselective and chemoselective fluorination of aliphatic aldehydes has been performed for the first time.

scholarly journals Mechanistic insights on the Pd-catalyzed addition of C–X bonds across alkynes – a combined experimental and computational study

2017 ◽  
Vol 8 (4) ◽  
pp. 2914-2922 ◽  
Author(s):  
Theresa Sperger ◽  
Christine M. Le ◽  
Mark Lautens ◽  
Franziska Schoenebeck
Keyword(s):  
Computational Study ◽  
Aryl Halides ◽  
Mechanistic Study

A mechanistic study of the Pd-catalyzed intramolecular addition of carbamoyl chlorides and aryl halides across alkynes is presented.

scholarly journals Modeling the Alkaline Hydrolysis of Diaryl Sulfate Diesters: A Mechanistic Study

2020 ◽  
Author(s):  
Klaudia Szeler ◽  
Nicholas Williams ◽  
Alvan C. Hengge ◽  
Shina Caroline Lynn Kamerlin
Keyword(s):  
Alkaline Hydrolysis ◽  
Computational Study ◽  
Transition States ◽  
Building Blocks ◽  
Ester Hydrolysis ◽  
Mechanistic Study ◽  
Phosphate Ester ◽  
Sulfate Ester ◽  
The Impact ◽  
Hydrolysis Of

<div> <div> <div> <p>Phosphate and sulfate esters have important roles as biological building blocks and in regulating cellular processes. However, while there has been substantial experimental and computational investigation of the mechanisms and the transition states involved in phosphate ester hydrolysis, there is far less (in particular computational) work on sulfate ester hydrolysis. Here, we report a detailed computational study of the alkaline hydrolysis of diaryl sulfate diesters, using different DFT functionals and both pure implicit solvation as well as mixed implicit/explicit solvation with varying numbers of explicit water molecules. We consider both the impact of how the system is modeled on computed linear free energy relationships (LFER) and the nature of the transition states. Although our calculations consistently underestimate the absolute activation free energies, we obtain good agreement with experimental LFER data when using pure implicit solvent, and excellent agreement with experimental kinetic isotope effects for all models used. Our calculations suggest that the hydrolysis of sulfate diesters proceeds through loose transition states, with minimal bond formation to the nucleophile and with bond cleavage to the leaving group already initiated. Comparison to prior work indicates that these transition states are similar in nature to those of analogous reactions such as the alkaline hydrolysis of neutral arylsulfonate monoesters or charged phosphate diesters and fluorophosphates. Obtaining more detailed insight into the transition states involved assists in understanding the selectivity of enzymes that hydrolyze these reactions; however, this work also highlights the methodological challenges involved in reliably modeling sulfate ester hydrolysis. </p> </div> </div> </div>

Sign in / Sign up

Export Citation Format

Share Document