scholarly journals A computational study of the phosphoryl transfer reaction between ATP and Dha in aqueous solution

2015 ◽  
Vol 13 (40) ◽  
pp. 10179-10190 ◽  
Author(s):  
I. Bordes ◽  
J. J. Ruiz-Pernía ◽  
R. Castillo ◽  
V. Moliner
Keyword(s):  
Aqueous Solution ◽  
Reaction Mechanism ◽  
Transfer Reaction ◽  
Computational Study ◽  
Transfer Reactions ◽  
Phosphoryl Transfer

Phosphoryl transfer reactions are ubiquitous in biology. The reaction mechanism of the phosphorylation of dihydroxyacetone by ATP in aqueous solution has been studied by means of QM/MM simulations in the present paper.

scholarly journals Reaction Mechanism of an Intramolecular Oxime Transfer Reaction: A Computational Study

2014 ◽  
Vol 79 (5) ◽  
pp. 2006-2014 ◽  
Author(s):  
Jani Moilanen ◽  
Antti Neuvonen ◽  
Petri Pihko
Keyword(s):  
Reaction Mechanism ◽  
Transfer Reaction ◽  
Computational Study

scholarly journals A computational study on the reaction mechanism of neutral phenol with formaldehyde in aqueous solution

2016 ◽  
Vol 41 (2) ◽  
pp. 144-152 ◽  
Author(s):  
Ming Cao ◽  
Taohong Li ◽  
Zhigang Wu ◽  
Jiankun Liang ◽  
Xiaoguang Xie ◽  
...  
Keyword(s):  
Aqueous Solution ◽  
Reaction Mechanism ◽  
Computational Study

scholarly journals How a Second Mg2+ Ion Affects the Phosphoryl Transfer Mechanism in a Protein Kinase: A Computational Study

2020 ◽  
Author(s):  
Rodrigo Recabarren ◽  
Kirill Zinovjev ◽  
Iñaki Tuñón ◽  
Jans Alzate-Morales
Keyword(s):  
Free Energy ◽  
Quantum Mechanics ◽  
Active Site ◽  
Transfer Reaction ◽  
Computational Study ◽  
Free Energy Calculations ◽  
Phosphoryl Transfer ◽  
Activation Free Energy ◽  
Lower Activation ◽  
Kinase A

<div>In this contribution, the phosphoryl transfer reaction in CDK2 has been studied in detail considering the presence of an additional Mg2+ ion in the active site. For this purpose, QM/MM (quantum mechanics/molecular mechanics) free energy calculations with the adaptive string method were performed, which showed that indeed the system containing two Mg2+ ions exhibits a lower activation free energy, corroborating the experimental observations.</div>

scholarly journals How a Second Mg2+ Ion Affects the Phosphoryl Transfer Mechanism in a Protein Kinase: A Computational Study

2020 ◽  
Author(s):  
Rodrigo Recabarren ◽  
Kirill Zinovjev ◽  
Iñaki Tuñón ◽  
Jans Alzate-Morales
Keyword(s):  
Free Energy ◽  
Quantum Mechanics ◽  
Active Site ◽  
Transfer Reaction ◽  
Computational Study ◽  
Free Energy Calculations ◽  
Phosphoryl Transfer ◽  
Activation Free Energy ◽  
Lower Activation ◽  
Kinase A

<div>In this contribution, the phosphoryl transfer reaction in CDK2 has been studied in detail considering the presence of an additional Mg2+ ion in the active site. For this purpose, QM/MM (quantum mechanics/molecular mechanics) free energy calculations with the adaptive string method were performed, which showed that indeed the system containing two Mg2+ ions exhibits a lower activation free energy, corroborating the experimental observations.</div>

2-Deoxyribose Radicals in the Gas Phase and Aqueous Solution. Transient Intermediates of Hydrogen Atom Abstraction from 2-Deoxyribofuranose

2005 ◽  
Vol 70 (11) ◽  
pp. 1769-1786 ◽  
Author(s):  
Luc A. Vannier ◽  
Chunxiang Yao ◽  
František Tureček
Keyword(s):  
Aqueous Solution ◽  
Hydrogen Atom ◽  
Gas Phase ◽  
Computational Study ◽  
Hydrogen Atom Abstraction ◽  
Oh Radical ◽  
Free Energies ◽  
Intramolecular Hydrogen ◽  
Solvation Free Energies ◽  
Transient Intermediates

A computational study at correlated levels of theory is reported to address the structures and energetics of transient radicals produced by hydrogen atom abstraction from C-1, C-2, C-3, C-4, C-5, O-1, O-3, and O-5 positions in 2-deoxyribofuranose in the gas phase and in aqueous solution. In general, the carbon-centered radicals are found to be thermodynamically and kinetically more stable than the oxygen-centered ones. The most stable gas-phase radical, 2-deoxyribofuranos-5-yl (5), is produced by H-atom abstraction from C-5 and stabilized by an intramolecular hydrogen bond between the O-5 hydroxy group and O-1. The order of radical stabilities is altered in aqueous solution due to different solvation free energies. These prefer conformers that lack intramolecular hydrogen bonds and expose O-H bonds to the solvent. Carbon-centered deoxyribose radicals can undergo competitive dissociations by loss of H atoms, OH radical, or by ring cleavages that all require threshold dissociation or transition state energies >100 kJ mol-1. This points to largely non-specific dissociations of 2-deoxyribose radicals when produced by exothermic hydrogen atom abstraction from the saccharide molecule. Oxygen-centered 2-deoxyribose radicals show only marginal thermodynamic and kinetic stability and are expected to readily fragment upon formation.

scholarly journals A computational study for the reaction mechanism of metal-free cyanomethylation of aryl alkynoates with acetonitrile

RSC Advances ◽  
2021 ◽  
Vol 11 (30) ◽  
pp. 18246-18251
Author(s):  
Selçuk Eşsiz
Keyword(s):  
Density Functional Theory ◽  
Reaction Mechanism ◽  
Density Functional ◽  
Computational Study ◽  
Coupled Cluster ◽  
Functional Theory ◽  
Metal Free ◽  
Coupled Cluster Methods ◽  
High Level ◽  
Cluster Methods

A computational study of metal-free cyanomethylation and cyclization of aryl alkynoates with acetonitrile is carried out employing density functional theory and high-level coupled-cluster methods, such as [CCSD(T)].

Nonclassical oxygen atom transfer reactions of an eight-coordinate dioxomolybdenum(vi) complex

2021 ◽  
Author(s):  
Leila G. Ranis ◽  
Jacqueline Gianino ◽  
Justin M. Hoffman ◽  
Seth N. Brown
Keyword(s):  
Oxygen Atom ◽  
Transfer Reaction ◽  
Transfer Reactions ◽  
Atom Transfer ◽  
Oxygen Atom Transfer ◽  
Oxygen Atom Transfer Reactions ◽  
Atom Transfer Reactions ◽  
Oxygen Atoms

Eight-coordinate MoO2(DOPOQ)2 can donate two oxygen atoms to substrates such as phosphines in a four-electron nonclassical oxygen atom transfer reaction.

scholarly journals Electron transfer studies of a conventional redox probe in human sweat and saliva bio-mimicking conditions

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
P. Krishnaveni ◽  
V. Ganesh
Keyword(s):  
Electron Transfer ◽  
Crystalline Phase ◽  
Liquid Crystalline ◽  
Transfer Reaction ◽  
Electron Transfer Reaction ◽  
Redox Couple ◽  
Liquid Crystalline Phase ◽  
Transfer Reactions ◽  
Redox Probe ◽  
Human Sweat

AbstractModern day hospital treatments aim at developing electrochemical biosensors for early diagnosis of diseases using unconventional human bio-fluids like sweat and saliva by monitoring the electron transfer reactions of target analytes. Such kinds of health care diagnostics primarily avoid the usage of human blood and urine samples. In this context, here we have investigated the electron transfer reaction of a well-known and commonly used redox probe namely, potassium ferro/ferri cyanide by employing artificially simulated bio-mimics of human sweat and saliva as unconventional electrolytes. Typically, electron transfer characteristics of the redox couple, [Fe(CN)6]3−/4− are investigated using electrochemical techniques like cyclic voltammetry and electrochemical impedance spectroscopy. Many different kinetic parameters are determined and compared with the conventional system. In addition, such electron transfer reactions have also been studied using a lyotropic liquid crystalline phase comprising of Triton X-100 and water in which the aqueous phase is replaced with either human sweat or saliva bio-mimics. From these studies, we find out the electron transfer reaction of [Fe(CN)6]3−/4− redox couple is completely diffusion controlled on both Au and Pt disc shaped electrodes in presence of sweat and saliva bio-mimic solutions. Moreover, the reaction is partially blocked by the presence of lyotropic liquid crystalline phase consisting of sweat and saliva bio-mimics indicating the predominant charge transfer controlled process for the redox probe. However, the rate constant values associated with the electron transfer reaction are drastically reduced in presence of liquid crystalline phase. These studies are essentially carried out to assess the effect of sweat and saliva on the electrochemistry of Fe2+/3+ redox couple.

Structure and activity of phosphoglycerate mutase

1981 ◽  
Vol 293 (1063) ◽  
pp. 121-130 ◽  
Keyword(s):  
Active Site ◽  
Transfer Reaction ◽  
Chemical Kinetic ◽  
Phosphoglycerate Mutase ◽  
Phosphoryl Transfer ◽  
X Ray ◽  
Histidine Residues ◽  
Ping Pong ◽  
Available Information ◽  
Structure And Activity

The structure of yeast phosphoglycerate mutase determined by X-ray crystallographic and amino acid sequence studies has been interpreted in terms of the chemical, kinetic and mechanistic observations made on this enzyme. There are two histidine residues at the active site, with imidazole groups almost parallel to each other and approximately 0.4 nm apart, positioned close to the 2 and 3 positions of the substrate. The simplest interpretation of the available information suggests that a ping-pong type mechanism operates in which at least one of these histidine residues participates in the phosphoryl transfer reaction. The flexible C-terminal region also plays an important role in the enzymic reaction.

Sign in / Sign up

Export Citation Format

Share Document