Glutathione radical: Intramolecular H abstraction by the thiyl radical

2001 ◽  
Vol 79 (4) ◽  
pp. 405-417 ◽  
Author(s):  
A Rauk ◽  
D A Armstrong ◽  
J Berges
Keyword(s):  
Free Energy ◽  
Gas Phase ◽  
Hydrogen Transfer ◽  
Single Point ◽  
Continuum Models ◽  
Thiyl Radical ◽  
Free Energies ◽  
Model Compounds ◽  
Activation Free Energy ◽  
Transition Structures

Ab initio computations (B3LYP/6-31G(D)) were used to predict transition structures and energies of activation for intramolecular H atom transfer to a thiyl radical (RS.) from the α-C—H bonds of glutathione (1) and from the model compounds, N-formylcysteinylglycine (2) and N-(2-thioethanyl)-γ-glutamine (3). For each compound, transition structures were located by in vacuo calculations on the neutral non-zwitterionic system. Thermodynamic functions derived at the same level and single point calculations at the B3LYP/6-311+G(3df,2p) level, were used to derive free energies of activation (ΔG[Formula: see text]) and reaction (ΔG°). For abstraction of the α-C—H (Gly) by the thiyl radical in the gas phase, ΔG[Formula: see text] = 134 kJ mol–1 if the amide link to Gly is in the more stable (Z)-configuration, and ΔG[Formula: see text] = 52 kJ mol–1 if it is in the less stable (E)-configuration. The isomerization of the amide group requires about 95 kJ mol–1. Previous studies had indicated that for intramolecular reaction of the thiyl radical at α-C—H (Cys), ΔG[Formula: see text] = 110 kJ mol–1. The lowest energy pathway for intramolecular H-transfer to the thiyl radical is from α-C—H (Gln), ΔG[Formula: see text] = 37–42 kJ mol–1, and corresponds rather well with experimental results in solution (ΔG[Formula: see text] = 43 kJ mol–1). The calculated free energy change for the equilibrium between thiyl and α-C forms of the glutathione radical is ΔG° = –54 kJ mol–1. The value estimated from experimental data is ΔG° = –37 kJ mol–1. The agreement between the energies from theory in the gas phase and experiment in solution suggests that the free energies of solvation of reactant thiyl radical, transition structures for H abstraction, and the product α-C-centred radical, are very similar. The effects of solution were estimated by two continuum models (SCIPCM and COSMO). The SCIPCM model yields results very similar to the gas phase, predicting a modest lowering of the activation free energy. The results from the COSMO method were inconclusive as to whether a rate enhancement or decrease could be expected.Key words: glutathione, thiyl radical, α-C-radical, hydrogen transfer.

Thermodynamic studies in solution. Part IV. Solvent effect on the solvolysis of tert-butyl chloride. A new treatment of the experimental data

1979 ◽  
Vol 57 (5) ◽  
pp. 500-502 ◽  
Author(s):  
Joaquim Jose Moura Ramos ◽  
Jacques Reisse ◽  
M. H. Abraham
Keyword(s):  
Free Energy ◽  
Solvent Effect ◽  
Free Energies ◽  
Butyl Chloride ◽  
Activation Free Energy ◽  
Tert Butyl ◽  
New Treatment ◽  
The One ◽  
Activated Complex ◽  
Tert Butyl Chloride

A new treatment of the solvent effect on the solvolysis of tert-butyl chloride is proposed. This treatment is based on activation free energy measurements and on transfer free energy measurements of the reactant (R) on the one hand and of a model (M) of the activated complex (AC) on the other hand. Solute–solvent interaction free energies for the reactant, the activated complex and the model compound are estimated. This estimation involves the calculation of the free energy of cavity formation of these various solutes (R, AC, and M) in all the solvents. These cavity terms, which are a function of the cohesive properties of the solvent and of the surface of the cavity do not reflect the electronic structure of the solute whereas the interaction free energy term does. The method we propose can be described as a new 'experimental' approach for the study of the charge separation in an activated complex.

Article

1999 ◽  
Vol 77 (5-6) ◽  
pp. 934-942
Author(s):  
J Peter Guthrie
Keyword(s):  
Carbon Dioxide ◽  
Free Energy ◽  
Equilibrium Constants ◽  
Marcus Theory ◽  
Energy Of Activation ◽  
Free Energies ◽  
Orbital Theory ◽  
Activation Free Energy ◽  
Free Energy Of Activation ◽  
Rms Error

Rate constants for hydration of carbon dioxide and ketene can be calculated by applying No Barrier Theory, which needs only equilibrium constants and distortion energies, the latter calculated using molecular orbital theory. The calculated free energies of activation are in satisfactory agreement with experiment: the rms error in free energy of activation is 2.38 kcal/mol. These compounds can also be described using Marcus Theory or Multidimensional Marcus Theory using the transferable intrinsic barrier appropriate to simple carbonyl compounds; in this case the rms error in free energy of activation is 2.19 kcal/mol. The two methods agree on preferred mechanistic path except for uncatalyzed hydration of ketene where Multidimensional Marcus Theory leads to a lower activation free energy for addition to the C=O, while No Barrier Theory leads to a lower free energy of activation for addition to the C=CH2. A rate constant for hydroxide ion catalyzed hydration of ketene can be calculated and is in accord with preliminary experimental results.Key words: ketene, carbon dioxide, hydration, Marcus Theory, No Barrier Theory.

Studies on the iodide–triiodide equilibrium

1977 ◽  
Vol 55 (5) ◽  
pp. 792-797 ◽  
Author(s):  
Robert L. Benoit ◽  
Michael F. Wilson ◽  
Sing-Yeung Lam
Keyword(s):  
Free Energy ◽  
Solvent Effect ◽  
Gas Phase ◽  
Formation Enthalpy ◽  
Aprotic Solvents ◽  
Free Energies ◽  
Potentiometric Measurements ◽  
Cast Doubt ◽  
Transfer Parameters ◽  
The Enthalpy Of Formation

The solvent effect on the iodide–triiodide equilibrium has been investigated by means of calorimetric and potentiometric measurements. The aprotic solvents studied were nitromethane, nitrobenzene, sulfolane, acetonitrile, propylene carbonate, acetophenone, dimethylformamide, dimethylsulfoxide, and o-dichlorobenzene. The resulting enthalpy and free energy changes imply that the variations of the enthalpies and free energies of transfer of the iodide and triiodide ions probably are small and that there is an important non-coulombic contribution to these transfer parameters. Values were obtained for the enthalpy of formation of two solid triiodides, which together with values for other triiodides, cast doubt on reported calculated lattice enthalpies of triiodides and formation enthalpy of I3− ion in the gas phase. This latter formation enthalpy is found to be, from our solution data, more negative than −22 kcal mol−1.

scholarly journals Sorption Hysteresis on Soils and Sediments: Obtaining Characteristic Free Energies Using "Single-Point Desorption Isotherms"

2020 ◽  
Author(s):  
Mikhail Borisover
Keyword(s):  
Free Energy ◽  
Liquid Phase ◽  
Single Point ◽  
Solute Concentration ◽  
Metastable States ◽  
Environmental Literature ◽  
Free Energies ◽  
Novel Approach ◽  
Soils And Sediments ◽  
Desorption Isotherms

<p>Sorption-desorption hysteresis (SDH) may control distributions of chemicals between diverse environmental phases, including soils and sediments. Formation of metastable states caused by pore deformation or inelastic swelling of a sorbent and their persistence during desorption were considered in the literature as one reason for "true" SDH. Such metastable states persisting during desorption lead to the lack of closure of sorption-desorption loop at non-zero sorbate concentrations, which is often observed in soil and environmental literature. Also, SDH was often characterized using single-point desorption isotherms (DIs) combining sorbed states reached during single desorption steps started from different points along a sorption isotherm (SI). The objective of this contribution is to demonstrate how the single-point DIs could be used to characterize SDH in liquid phase sorption experiments in terms of Gibbs free energy. This free energy is accumulated in some non-relaxed sorbed states belonging to DI as compared with the states of the same composition (sorbed concentration) belonging to SI. Using the literature data on SIs and single-point DIs of some polycyclic aromatic hydrocarbons and pesticides on soils and sediments, it is shown how these extra free energies could be obtained and how they could change in the selected sorbate-sorbent systems. When the extent of SDH decreases with increasing solute concentration, these additional free energies decline. They may remain constant or even increase, suggesting in the latter case that a larger work is needed to perturb a sorbent structure at higher sorbed concentrations. This paper proposes a novel approach for quantifying and understanding liquid phase SDH in the cases when a thermodynamic justification is sought, and, therefore, it advances the ability to predict the fate and activity of multiple chemicals in typical soil/sediment environments. </p><p><br></p>

Ab Initio Free Energy Calculations at Multiple Electronic Structure Levels Made Affordable: An Effective Combination of Perturbation Theory and Machine Learning

2020 ◽  
Author(s):  
Tomas Bucko ◽  
Monika Gešvandtnerová ◽  
Dario Rocca
Keyword(s):  
Machine Learning ◽  
Free Energy ◽  
Perturbation Theory ◽  
Ab Initio ◽  
Single Point ◽  
Free Energy Calculations ◽  
Thermodynamic Quantities ◽  
Free Energies ◽  
Energy Calculations ◽  
Ab Initio Theory

<div>While free energies are fundamental thermodynamic quantities to characterize chemical reactions, their calculation based on ab initio theory is usually limited by the high computational cost. This is particularly true if multiple levels of theory have to be tested to establish their relative accuracy, if highly expensive quantum mechanical approximations are of interest, and also if several different temperatures have to be considered. We present an ab initio approach that effectively couples perturbation theory and machine learning to make ab initio free energy calculations more affordable. Starting from results based on a certain production ab initio theory, perturbation theory is applied to obtain free energies. The large number of single point calculations required by a brute force application of this approach are here significantly decreased by applying machine learning techniques. Importantly, the </div><div>training of the machine learning model requires only a small amount of data and does not need to be </div><div>performed again when the temperature is decreased.</div><div>The accuracy and efficiency of this method is demonstrated by computing the free energy of activation of the </div><div>proton exchange reaction in the zeolite chabazite. Starting from an ab initio calculation based on a semilocal</div><div>approximation of density functional theory, free energies based on significantly </div><div>more expensive non-local van der Waals and hybrid functionals are obtained with only a few tens</div><div>of additional single point calculations. In this way this work paves the route to</div><div>quick free energy calculations using different levels of theory or approximations that would be</div><div>too computationally expensive to be directly employed in molecular dynamics or Monte Carlo simulations.</div>

Are thermodynamic cycles necessary for continuum solvent calculation of pKas and reduction potentials?

2015 ◽  
Vol 17 (4) ◽  
pp. 2859-2868 ◽  
Author(s):  
Junming Ho
Keyword(s):  
Free Energy ◽  
Gas Phase ◽  
Thermodynamic Cycle ◽  
Free Energies ◽  
Thermodynamic Cycles ◽  
Reduction Potentials ◽  
Reaction Free Energy

Continuum solvent calculations of pKas and reduction potentials usually entail the use of a thermodynamic cycle to express the reaction free energy in terms of gas phase energies and free energies of solvation.

scholarly journals Ab initio calculations of free energy of activation at multiple electronic structure levels made affordable: An effective combination of perturbation theory and machine learning

2020 ◽  
Author(s):  
Tomas Bucko ◽  
Monika Gešvandtnerová ◽  
Dario Rocca
Keyword(s):  
Machine Learning ◽  
Free Energy ◽  
Perturbation Theory ◽  
Ab Initio ◽  
Single Point ◽  
Free Energy Calculations ◽  
Free Energies ◽  
Energy Calculations ◽  
Free Energy Of Activation ◽  
Ab Initio Theory

<div>While free energies are fundamental thermodynamic quantities to characterize chemical reactions, their calculation based on ab initio theory is usually limited by the high computational cost. This is particularly true if multiple levels of theory have to be tested to establish their relative accuracy, if highly expensive quantum mechanical approximations are of interest, and also if several different temperatures have to be considered. We present an ab initio approach that effectively couples perturbation theory and machine learning to make ab initio free energy calculations more affordable. Starting from results based on a certain production ab initio theory, perturbation theory is applied to obtain free energies. The large number of single point calculations required by a brute force application of this approach are here significantly decreased by applying machine learning techniques. Importantly, the training of the machine learning model requires only a small amount of data and does not need to be performed again when the temperature is decreased. The accuracy and efficiency of this method is demonstrated by computing the free energy of activation of the proton exchange reaction in the zeolite chabazite. Starting from an ab initio calculation based on a semilocal approximation of density functional theory, free energies based on significantly more expensive non-local van der Waals and hybrid functionals are obtained with only a few tens of additional single point calculations. In this way this work paves the route to quick free energy calculations using different levels of theory or approximations that would be too computationally expensive to be directly employed in molecular dynamics or Monte Carlo simulations.</div>

scholarly journals Ab initio calculations of free energy of activation at multiple electronic structure levels made affordable: An effective combination of perturbation theory and machine learning

2020 ◽  
Author(s):  
Tomas Bucko ◽  
Monika Gešvandtnerová ◽  
Dario Rocca
Keyword(s):  
Machine Learning ◽  
Free Energy ◽  
Perturbation Theory ◽  
Ab Initio ◽  
Single Point ◽  
Free Energy Calculations ◽  
Free Energies ◽  
Energy Calculations ◽  
Free Energy Of Activation ◽  
Ab Initio Theory

<div>While free energies are fundamental thermodynamic quantities to characterize chemical reactions, their calculation based on ab initio theory is usually limited by the high computational cost. This is particularly true if multiple levels of theory have to be tested to establish their relative accuracy, if highly expensive quantum mechanical approximations are of interest, and also if several different temperatures have to be considered. We present an ab initio approach that effectively couples perturbation theory and machine learning to make ab initio free energy calculations more affordable. Starting from results based on a certain production ab initio theory, perturbation theory is applied to obtain free energies. The large number of single point calculations required by a brute force application of this approach are here significantly decreased by applying machine learning techniques. Importantly, the training of the machine learning model requires only a small amount of data and does not need to be performed again when the temperature is decreased. The accuracy and efficiency of this method is demonstrated by computing the free energy of activation of the proton exchange reaction in the zeolite chabazite. Starting from an ab initio calculation based on a semilocal approximation of density functional theory, free energies based on significantly more expensive non-local van der Waals and hybrid functionals are obtained with only a few tens of additional single point calculations. In this way this work paves the route to quick free energy calculations using different levels of theory or approximations that would be too computationally expensive to be directly employed in molecular dynamics or Monte Carlo simulations.</div>

scholarly journals Sorption Hysteresis on Soils and Sediments: Obtaining Characteristic Free Energies Using "Single-Point Desorption Isotherms"

2020 ◽  
Author(s):  
Mikhail Borisover
Keyword(s):  
Free Energy ◽  
Liquid Phase ◽  
Single Point ◽  
Solute Concentration ◽  
Metastable States ◽  
Environmental Literature ◽  
Free Energies ◽  
Novel Approach ◽  
Soils And Sediments ◽  
Desorption Isotherms

<p>Sorption-desorption hysteresis (SDH) may control distributions of chemicals between diverse environmental phases, including soils and sediments. Formation of metastable states caused by pore deformation or inelastic swelling of a sorbent and their persistence during desorption were considered in the literature as one reason for "true" SDH. Such metastable states persisting during desorption lead to the lack of closure of sorption-desorption loop at non-zero sorbate concentrations, which is often observed in soil and environmental literature. Also, SDH was often characterized using single-point desorption isotherms (DIs) combining sorbed states reached during single desorption steps started from different points along a sorption isotherm (SI). The objective of this contribution is to demonstrate how the single-point DIs could be used to characterize SDH in liquid phase sorption experiments in terms of Gibbs free energy. This free energy is accumulated in some non-relaxed sorbed states belonging to DI as compared with the states of the same composition (sorbed concentration) belonging to SI. Using the literature data on SIs and single-point DIs of some polycyclic aromatic hydrocarbons and pesticides on soils and sediments, it is shown how these extra free energies could be obtained and how they could change in the selected sorbate-sorbent systems. When the extent of SDH decreases with increasing solute concentration, these additional free energies decline. They may remain constant or even increase, suggesting in the latter case that a larger work is needed to perturb a sorbent structure at higher sorbed concentrations. This paper proposes a novel approach for quantifying and understanding liquid phase SDH in the cases when a thermodynamic justification is sought, and, therefore, it advances the ability to predict the fate and activity of multiple chemicals in typical soil/sediment environments. </p><p><br></p>

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