Mechanisms of alkane CH-activation: The 5/6 effect, single-factor compensation effect, strongest reactant and earliest transition state. A puzzle of Shilov reaction

2017 ◽  
Vol 426 ◽  
pp. 465-473 ◽  
Author(s):  
Elisey S. Rudakov
Keyword(s):  
Transition State ◽  
Compensation Effect ◽  
Single Factor ◽  
Ch Activation

Computational Strategies to Probe CH Activation in Dioxo-Dicopper Complexes

2018 ◽  
Author(s):  
Zhenzhuo Lan ◽  
Shaama Mallikarjun Sharada
Keyword(s):  
Transition State ◽  
Density Functional ◽  
Heterogeneous Catalysts ◽  
Decomposition Analysis ◽  
Energy Decomposition Analysis ◽  
Ch Activation ◽  
Transition State Stabilization ◽  
Highly Sensitive ◽  
One Step ◽  
The One

Our work addresses the long-standing question of the preferred mechanism of CH activation in dioxodicopper complexes, with implications for [Cu2O2]2+ -containing enzymes as well as homogeneous and heterogeneous catalysts, which are capable of performing selective oxidation. Using density functional theory (DFT), we show that the two proposed mechanisms, one-step oxo-insertion and two-step radical recombination, have very distinct and measurable responses to changes in the electrophilicity of N-donors in the catalyst. Using energy decomposition analysis, we calculate the electronic interactions that contribute to transition state stabilization, and the effect of N-donors on these interactions. The analysis shows that oxo-insertion, by virtue of possessing a late and charged transition state, is highly sensitive to N-donor electrophilicity and barriers decrease with more electron-withdrawing N-donors. On the other hand, the radical pathway possesses an early transition state and is therefore relatively insensitive to N-donor variations. One possible strategy, going forward, is the design and execution of complementary experiments to deduce the mechanism based on the presence or absence of N-donor dependence. We adopt an alternative approach where DFT results are contrasted with prior experiments via Hammett relationships. The remarkable agreement between experimental and calculated trends for oxo-insertion with imidazole N-donor catalysts presents compelling evidence in favor of the one-step pathway for CH activation.

Computational Strategies to Probe CH Activation in Dioxo-Dicopper Complexes

2018 ◽  
Author(s):  
Zhenzhuo Lan ◽  
Shaama Mallikarjun Sharada
Keyword(s):  
Transition State ◽  
Density Functional ◽  
Heterogeneous Catalysts ◽  
Decomposition Analysis ◽  
Energy Decomposition Analysis ◽  
Ch Activation ◽  
Transition State Stabilization ◽  
Highly Sensitive ◽  
One Step ◽  
The One

Our work addresses the long-standing question of the preferred mechanism of CH activation in dioxodicopper complexes, with implications for [Cu2O2]2+ -containing enzymes as well as homogeneous and heterogeneous catalysts, which are capable of performing selective oxidation. Using density functional theory (DFT), we show that the two proposed mechanisms, one-step oxo-insertion and two-step radical recombination, have very distinct and measurable responses to changes in the electrophilicity of N-donors in the catalyst. Using energy decomposition analysis, we calculate the electronic interactions that contribute to transition state stabilization, and the effect of N-donors on these interactions. The analysis shows that oxo-insertion, by virtue of possessing a late and charged transition state, is highly sensitive to N-donor electrophilicity and barriers decrease with more electron-withdrawing N-donors. On the other hand, the radical pathway possesses an early transition state and is therefore relatively insensitive to N-donor variations. One possible strategy, going forward, is the design and execution of complementary experiments to deduce the mechanism based on the presence or absence of N-donor dependence. We adopt an alternative approach where DFT results are contrasted with prior experiments via Hammett relationships. The remarkable agreement between experimental and calculated trends for oxo-insertion with imidazole N-donor catalysts presents compelling evidence in favor of the one-step pathway for CH activation.

Memapsin 2, a drug target for Alzheimer's disease

2003 ◽  
Vol 70 ◽  
pp. 213-220 ◽  
Author(s):  
Gerald Koelsch ◽  
Robert T. Turner ◽  
Lin Hong ◽  
Arun K. Ghosh ◽  
Jordan Tang
Keyword(s):  
Crystal Structure ◽  
Alzheimer’S Disease ◽  
Alzheimer's Disease ◽  
Transition State ◽  
Amyloid Precursor Protein ◽  
Therapeutic Target ◽  
Drug Target ◽  
Aspartic Protease ◽  
Precursor Protein ◽  
Memapsin 2

Mempasin 2, a ϐ-secretase, is the membrane-anchored aspartic protease that initiates the cleavage of amyloid precursor protein leading to the production of ϐ-amyloid and the onset of Alzheimer's disease. Thus memapsin 2 is a major therapeutic target for the development of inhibitor drugs for the disease. Many biochemical tools, such as the specificity and crystal structure, have been established and have led to the design of potent and relatively small transition-state inhibitors. Although developing a clinically viable mempasin 2 inhibitor remains challenging, progress to date renders hope that memapsin 2 inhibitors may ultimately be useful for therapeutic reduction of ϐ-amyloid.

Collisional dynamics of Ca1D + HBr reactions: evidence for transition-state motions

1999 ◽  
Vol 97 (8) ◽  
pp. 967-976 ◽  
Author(s):  
M. Garay Salazar, J. M. Orea Rocha, A.
Keyword(s):  
Transition State ◽  
Collisional Dynamics

Reactions of an Aluminium(I) Reagent with 1,2-, 1,3- and 1,5-Dienes: Dearomatisation, Reversibility, and a Pericyclic Mechanism

2019 ◽  
Author(s):  
Clare Bakewell ◽  
Martí Garçon ◽  
Richard Y Kong ◽  
Louisa O'Hare ◽  
Andrew J. P. White ◽  
...  
Keyword(s):  
Reaction Mechanism ◽  
Dft Calculations ◽  
Transition State ◽  
Reaction Pathways ◽  
Aromatic Rings ◽  
Aromatic Character ◽  
Pericyclic Reaction

The reactions of an aluminium(I) reagent with a series of 1,2-, 1,3- and 1,5-dienes are reported. In the case of 1,3-dienes the reaction occurs by a pericyclic reaction mechanism, specifically a cheletropic cycloaddition, to form aluminocyclopentene containing products. This mechanism has been interrogated by stereochemical experiments and DFT calculations. The stereochemical experiments show that the (4+1) cycloaddition follows a suprafacial topology, while calculations support a concerted albeit asynchronous pathway in which the transition state demonstrates aromatic character. Remarkably, the substrate scope of the (4+1) cycloaddition includes dienes that are either in part, or entirely, contained within aromatic rings. In these cases, reactions occur with dearomatisation of the substrate and can be reversible. In the case of 1,2- or 1,5-dienes complementary reactivity is observed; the orthogonal nature of the C=C π-bonds (1,2-diene) and the homoconjugated system (1,5-diene) both disfavour a (4+1) cycloaddition. Rather, reaction pathways are determined by an initial (2+1) cycloaddition to form an aluminocyclopropane intermediate which can in turn undergo insertion of a further C=C π-bond leading to complex organometallic products that incorporate fused hydrocarbon rings.

Active Learning Accelerates Ab Initio Molecular Dynamics on Pericyclic Reactive Energy Surfaces

2020 ◽  
Author(s):  
Shi Jun Ang ◽  
Wujie Wang ◽  
Daniel Schwalbe-Koda ◽  
Simon Axelrod ◽  
Rafael Gomez-Bombarelli
Keyword(s):  
Molecular Dynamics ◽  
Potential Energy ◽  
Transition State ◽  
Potential Energy Surface ◽  
Ab Initio ◽  
Energy Surface ◽  
Computational Cost ◽  
Reactive Trajectories ◽  
Dynamics Simulations ◽  
Energy Surfaces

<div>Modeling dynamical effects in chemical reactions, such as post-transition state bifurcation, requires <i>ab initio</i> molecular dynamics simulations due to the breakdown of simpler static models like transition state theory. However, these simulations tend to be restricted to lower-accuracy electronic structure methods and scarce sampling because of their high computational cost. Here, we report the use of statistical learning to accelerate reactive molecular dynamics simulations by combining high-throughput ab initio calculations, graph-convolution interatomic potentials and active learning. This pipeline was demonstrated on an ambimodal trispericyclic reaction involving 8,8-dicyanoheptafulvene and 6,6-dimethylfulvene. With a dataset size of approximately</div><div>31,000 M062X/def2-SVP quantum mechanical calculations, the computational cost of exploring the reactive potential energy surface was reduced by an order of magnitude. Thousands of virtually costless picosecond-long reactive trajectories suggest that post-transition state bifurcation plays a minor role for the reaction in vacuum. Furthermore, a transfer-learning strategy effectively upgraded the potential energy surface to higher</div><div>levels of theory ((SMD-)M06-2X/def2-TZVPD in vacuum and three other solvents, as well as the more accurate DLPNO-DSD-PBEP86 D3BJ/def2-TZVPD) using about 10% additional calculations for each surface. Since the larger basis set and the dynamic correlation capture intramolecular non-covalent interactions more accurately, they uncover longer lifetimes for the charge-separated intermediate on the more accurate potential energy surfaces. The character of the intermediate switches from entropic to thermodynamic upon including implicit solvation effects, with lifetimes increasing with solvent polarity. Analysis of 2,000 reactive trajectories on the chloroform PES shows a qualitative agreement with the experimentally-reported periselectivity for this reaction. This overall approach is broadly applicable and opens a door to the study of dynamical effects in larger, previously-intractable reactive systems.</div>

An Alternate Energy-Conserved Pathway for the Morita-Baylis-Hillman (MBH) Reaction

2020 ◽  
Author(s):  
Veejendra Yadav
Keyword(s):  
Proton Transfer ◽  
Transition State ◽  
Lower Energy ◽  
Aldol Reaction ◽  
Membered Ring ◽  
Ammonium Ion ◽  
Alternate Energy ◽  
Ring Transition State ◽  
Mbh Reaction

An new overall lower energy pathway for the amine-catalysed Morita-Baylis-Hillman reaction is proposed from computations at the M06-2X/6-311++G(d,p) level. The pathway involves proton-transfer from the ammonium ion to the alkoxide formed from the aldol reaction through a seven-membered ring transition state (TS) structure followed by highly exothermic Hofmann<i> </i>elimination through a five-membered ring TS structure to form the product and also release the catalyst to carry on with the process all over again.

An Alternate Energy-Conserved Pathway for the Morita-Baylis-Hillman (MBH) Reaction

2020 ◽  
Author(s):  
Veejendra Yadav
Keyword(s):  
Proton Transfer ◽  
Transition State ◽  
Lower Energy ◽  
Aldol Reaction ◽  
Membered Ring ◽  
Ammonium Ion ◽  
Alternate Energy ◽  
Ring Transition State ◽  
Mbh Reaction

An new overall lower energy pathway for the amine-catalysed Morita-Baylis-Hillman reaction is proposed from computations at the M06-2X/6-311++G(d,p) level. The pathway involves proton-transfer from the ammonium ion to the alkoxide formed from the aldol reaction through a seven-membered ring transition state (TS) structure followed by highly exothermic Hofmann<i> </i>elimination through a five-membered ring TS structure to form the product and also release the catalyst to carry on with the process all over again.

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