Comparison of AM1 and density functional theory generated transition state structures and activation energies for cyanoalkenes addition to cyclopentadiene

A novel mechanism of oxygen reaction on a metal surface beyond the present charge transfer or hybridization mechanism, spin-orientation dependence via a coupling mechanism due to the finite spin moment of O2 at the transition state, is obtained using a combination of spin density functional theory (SDFT) and constrained DFT.

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

10.26434/chemrxiv.8864204.v1 ◽

2019 ◽

Cited By ~ 3

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>

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Are boat transition states likely to occur in Cope rearrangements? A DFT study of the biogenesis of germacranes

Beilstein Journal of Organic Chemistry ◽

10.3762/bjoc.13.192 ◽

2017 ◽

Vol 13 ◽

pp. 1969-1976 ◽

Cited By ~ 1

Author(s):

José Enrique Barquera-Lozada ◽

Gabriel Cuevas

Keyword(s):

Density Functional Theory ◽

Transition State ◽

Density Functional ◽

Chair Conformation ◽

High Energy ◽

Functional Theory ◽

Sigmatropic Rearrangements ◽

The Density Functional Theory ◽

Reaction Proceeds ◽

Cope Rearrangements

It has been proposed that elemanes are biogenetically formed from germacranes by Cope sigmatropic rearrangements. Normally, this reaction proceeds through a transition state with a chair conformation. However, the transformation of schkuhriolide (germacrane) into elemanschkuhriolide (elemane) may occur through a boat transition state due to the final configuration of the elemanschkuhriolide, but this transition state is questionable due to its high energy. The possible mechanisms of this transformation were studied in the density functional theory frame. The mechanistic differences between the transformation of (Z,E)-germacranes and (E,E)-germacranes were also studied. We found that (Z,E)-germacranolides are significantly more stable than (E,E)-germacranolides and elemanolides. In the specific case of schkuhriolide, even when the boat transition state is not energetically favored, a previous hemiacetalization lowers enough the energetic barrier to allow the formation of a very stable elemanolide that is even more stable than its (Z,E)-germacrane.

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Large-Scale Density Functional Theory Transition State Searching in Enzymes

The Journal of Physical Chemistry Letters ◽

10.1021/jz5018703 ◽

2014 ◽

Vol 5 (21) ◽

pp. 3614-3619 ◽

Cited By ~ 37

Author(s):

Greg Lever ◽

Daniel J. Cole ◽

Richard Lonsdale ◽

Kara E. Ranaghan ◽

David J. Wales ◽

...

Keyword(s):

Density Functional Theory ◽

Transition State ◽

Density Functional ◽

Large Scale ◽

Functional Theory

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Substituent effects in the decarboxylation reactions of coordinated arylcarboxylates in dinuclear copper complexes, [(napy)Cu2(O2CC6H4X)]+

European Journal of Mass Spectrometry ◽

10.1177/1469066717729067 ◽

2017 ◽

Vol 23 (6) ◽

pp. 351-358 ◽

Cited By ~ 5

Author(s):

Qiuyan Jin ◽

Jiaye Li ◽

Alireza Ariafard ◽

Allan J Canty ◽

Richard AJ O’Hair

Keyword(s):

Density Functional Theory ◽

Transition State ◽

Density Functional ◽

Copper Complexes ◽

Substituent Effects ◽

Density Functional Theory Calculations ◽

Molecular Formula ◽

Binuclear Complexes ◽

Aryl Group ◽

Functional Theory

A combination of gas-phase ion trap mass spectrometry experiments and density functional theory (DFT) calculations have been used to examine the role of substituents on the decarboxylation of 25 different coordinated aromatic carboxylates in binuclear complexes, [(napy)Cu2(O2CC6H4X)]+, where napy is the ligand 1,8-naphthyridine (molecular formula, C8H6N2) and X = H and the ortho ( o), meta ( m) and para ( p) isomers of F, Br, CN, NO2, CF3, OAc, Me and MeO. Two competing unimolecular reaction pathways were found: decarboxylation to give the organometallic cation [(napy)Cu2(C6H4X)]+ or loss of the neutral copper benzoate to yield [(napy)Cu]+. The substituents on the aryl group influence the branching ratios of these product channels, but decarboxylation is always the dominant pathway. Density functional theory calculations reveal that decarboxylation proceeds via two transition states. The first enables a change in the coordination mode of the coordinated benzoate in [(napy)Cu2(O2CC6H4X)]+ from the thermodynamically favoured O, O-bridged form to the O-bound form, which is the reactive conformation for the second transition state which involves extrusion of CO2 with concomitant formation of the CO2 coordinated organometallic cation, [(napy)Cu2(C6H4X)(CO2)]+, which then loses CO2 in the final step to yield [(napy)Cu2(C6H4X)]+. In all cases the barrier is highest for the second transition state. The o-substituted benzoates show a lower activation energy than the m-substituted ones, while the p-substituted ones have the highest energy, which is consistent with the experimentally determined normalised collision energy required to induce fragmentation of [(napy)Cu2(O2CC6H4X)]+.

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Unveiling the Different Reactivity of Bent and Linear Three-Atom-Components Participating in [3 + 2] Cycloaddition Reactions

Organics ◽

10.3390/org2030014 ◽

2021 ◽

Vol 2 (3) ◽

pp. 274-286

Author(s):

Mar Ríos-Gutiérrez ◽

Luis R. Domingo ◽

Fatemeh Ghodsi

Keyword(s):

Density Functional Theory ◽

Transition State ◽

Electron Density ◽

Density Functional ◽

Geometrical Parameters ◽

Single Bond ◽

Conceptual Density Functional Theory ◽

Functional Theory ◽

Molecular Electron ◽

Molecular Electron Density Theory

The reactivity of a series of pairs of bent and linear three-atom-component (B-TACs and L-TACs) participating in [3 + 2] cycloaddition (32CA) reactions towards ethylene and electrophilic dicyanoethylene (DCE) have been studied within the Molecular Electron Density Theory. While the pseudodiradical structure of B-TACs changes to that of pseudoradical or carbenoid L-TACs upon dehydrogenation, zwitterionic B-TACs remain unchanged. Conceptual Density Functional Theory (CDFT) indices characterize five of the nine TACs as strong nucleophiles participating in polar reactions towards electrophilic ethylenes. The activation energies of the 32CA reactions with electrophilic DCE range from 0.5 to 22.0 kcal·mol−1, being between 4.3 and 9.1 kcal·mol−1 lower than those with ethylene. In general, B-TACs are more reactive than their L-TAC counterparts. A change in the regioselectivity is found in these polar 32CA reactions; in general, while B-TACs are meta regioselective, L-TACs are ortho regioselective. The geometrical parameters of the transition state structures suggest that the formation of the single bond involving the most electrophilic carbon of DCE is more advanced. A change in the asynchronicity in the reactions involving B-TACs and L-TACs is also found.

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

10.26434/chemrxiv.8864204.v5 ◽

2019 ◽

Cited By ~ 12

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>

Download Full-text