Free energies and entropies of transfer from methanol to aqueous methanol of the reactants and the transition state in the bimolecular substitution of tetraethyltin by mercuric chloride

1969 ◽  
pp. 930 ◽  
Author(s):  
M. H. Abraham ◽  
G. F. Johnston ◽  
J. F. C. Oliver ◽  
John A. Richards
Keyword(s):  
Transition State ◽  
Mercuric Chloride ◽  
Free Energies ◽  
Aqueous Methanol

scholarly journals Popular Integration Grids Can Result in Large Errors in DFT-Computed Free Energies

2019 ◽  
Author(s):  
Andrea N. Bootsma ◽  
Steven Wheeler
Keyword(s):  
Transition State ◽  
Molecular Orientation ◽  
Density Functional ◽  
Basis Sets ◽  
Free Energies ◽  
Functional Theory ◽  
Metal Free ◽  
Stereoselective Reactions ◽  
Functionalization Reaction ◽  
Transition State Structures

<div>Density functional theory (DFT) has emerged as a powerful tool for analyzing organic and organometallic systems and proved remarkably accurate in computing the small free energy differences that underpin many chemical phenomena (e.g. regio- and stereoselective reactions). We show that the lack of rotational invariance of popular DFT integration grids reveals large uncertainties in computed free energies for isomerizations, torsional barriers, and regio- and stereoselective reactions. The result is that predictions based on DFT-computed free energies for many systems can change qualitatively depending on molecular orientation. For example, for a metal-free propargylation of benzaldehyde, predicted enantioselectivities based on B97-D/def2-TZVP free energies using the popular (75,302) integration grid can vary from 62:38 to 99:1 by simply rotating the transition state structures. Relative free energies for the regiocontrolling transition state structures for an Ir-catalyzed C–H functionalization reaction computed using M06/6-31G(d,p)/LANL2DZ and the same grid can vary by more than 5 kcal mol–1, resulting in predicted regioselectivities that range anywhere from 14:86 to >99:1. Errors of these magnitudes occur for different functionals and basis sets, are widespread among modern applications of DFT, and can be reduced by using much denser integration grids than commonly employed.</div>

Initial state and transition state contributions to solvent effects on activation enthalpies for substitution reactions of tris(1,10-phenanthroline)iron(II) in aqueous methanol

1983 ◽  
Vol 8 (3) ◽  
pp. 148-152 ◽  
Author(s):  
Michael J. Blandamer ◽  
John Burgess ◽  
Timothy Digman ◽  
Philip P. Duce ◽  
John P. McCann ◽  
...  
Keyword(s):  
Transition State ◽  
Solvent Effects ◽  
Aqueous Methanol ◽  
Substitution Reactions ◽  
Initial State

scholarly journals Monitoring the stabilities of a mixture of peptides by mass-spectrometry-based techniques

2019 ◽  
Vol 25 (1) ◽  
pp. 73-81 ◽  
Author(s):  
Daniel R Fuller ◽  
Christopher R Conant ◽  
Tarick J El-Baba ◽  
Zhichao Zhang ◽  
Kameron R Molloy ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Amino Acid ◽  
Transition State ◽  
Elevated Temperatures ◽  
Proteolytic Enzymes ◽  
Side Chain ◽  
Free Energies ◽  
Dissociation Kinetics ◽  
Penultimate Proline ◽  
The Stability

Biomolecular degradation plays a key role in proteostasis. Typically, proteolytic enzymes degrade proteins into smaller peptides by breaking amino acid bonds between specific residues. Cleavage around proline residues is often missed and requires highly specific enzymes for peptide processing due to the cyclic proline side-chain. However, degradation can occur spontaneously (i.e. in the absence of enzymes). In this study, the influence of the first residue on the stability of a series of penultimate proline containing peptides, with the sequence Xaa–Pro–Gly–Gly (where Xaa is any amino acid), is investigated with mass spectrometry techniques. Peptides were incubated as mixtures at various solution temperatures (70℃ to 90℃) and were periodically sampled over the duration of the experiment. At elevated temperatures, we observe dissociation after the Xaa–Pro motif for all sequences, but at different rates. Transition state thermochemistry was obtained by studying the temperature-dependent kinetics and although all peptides show relatively small differences in the transition state free energies (∼95 kJ/mol), there is significant variability in the transition state entropy and enthalpy. This demonstrates that the side-chain of the first amino acid has a significant influence on the stability of the Xaa–Pro sequence. From these data, we demonstrate the ability to simultaneously measure the dissociation kinetics and relative transition state thermochemistries for a mixture of peptides, which vary only in the identity of the N-terminal amino acid.

The Direct Oxidizing Mechanism for the Reaction of Ozone and Phenol: A DFT Study

2012 ◽  
Vol 554-556 ◽  
pp. 1632-1636
Author(s):  
Shuang Kou Chen ◽  
Jian Fang Zhu ◽  
Wen Zhang Huang ◽  
Bai He ◽  
Li Jun Xiang ◽  
...  
Keyword(s):  
Global Optimization ◽  
Transition State ◽  
Calculation Result ◽  
Substitution Reaction ◽  
Single Point ◽  
Vibrational Analysis ◽  
Ortho Position ◽  
Free Energies ◽  
Point Energy ◽  
Exothermic Reactions

Using DFT/6-31+G (d, p) method, the structure of phenol are gained in the global optimization and properties were theoretically studied. The atomic electric charges, activation of reaction and thermodynamics parameters are obtained. The calculation shows that benzene ring in phenol tends to have electrophonic attacking substitution reaction O3 directly and form catechol and hydroquinol. The calculation of thermodynamics properties indicate that two pathways are exothermic reactions, and the Gibbs free energies (ΔG) are always less than zero, two reactions are easily occurred spontaneously. Dynamics calculations show that there is only one transition state in each reaction; through vibrational analysis we confirm the transition state. After corrected single point energy, we find that the reaction activation energies of the two reactions are small (Ea1=4.48kcal/mol and Ea2=2.87kal/mol), indicating that ortho-position and para-position products exist simultaneously, which is in accordance with the thermodynamics calculation result.

scholarly journals Popular Integration Grids Can Result in Large Errors in DFT-Computed Free Energies

2019 ◽  
Author(s):  
Andrea N. Bootsma ◽  
Steven Wheeler
Keyword(s):  
Transition State ◽  
Molecular Orientation ◽  
Density Functional ◽  
Low Frequency ◽  
Basis Sets ◽  
Vibrational Modes ◽  
Free Energies ◽  
Functional Theory ◽  
Stereoselective Reactions ◽  
Transition State Structures

Density functional theory (DFT) has emerged as a powerful tool for analyzing (bio-)organic and organometallic systems and proved remarkably accurate in computing the small free energy differences that underpin many chemical phenomena (e.g. regio- and stereoselective reactions). We show that the lack of rotational invariance of popular DFT integration grids reveals large uncertainties in computed free energies for some isomerizations, torsional barriers, and regio- and stereoselective reactions. The result is that predictions based on DFT-computed free energies for systems with very low-frequency vibrational modes can change qualitatively depending on molecular orientation. For example, for a metal-free propargylation of benzaldehyde, predicted enantioselectivities based on B97-D/def2-TZVP free energies using a popular pruned (75,302) integration grid can vary from 62:38 to 99:1 by simply rotating the transition state structures. Relative free energies for the regiocontrolling transition state structures for an Ir-catalyzed C–H functionalization reaction computed using M06/6-31G(d,p)/LANL2DZ and the same grid can vary by more than 5 kcal/mol, resulting in predicted regioselectivities that range anywhere from 14:86 to >99:1. Errors of these magnitudes occur for different functionals and basis sets, are potentially widespread among modern applications of DFT, and can be reduced by using much denser integration grids than commonly employed.<br>

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