Mechanistic study on the Cp*iridium-catalyzed N-alkylation of amines with alcohols

The mechanism of the addition of indazole (Ind)—a bifunctional aromatic N,NH-nucleophile—to cyclohexyl isocyanide coordinated to the palladium(II) center in the model complex cis-[PdCl2(CNMe)(CNCy)] (1) to give the corresponding aminocarbene ligand was investigated in detail by theoretical (DFT) methods. The most plausible mechanism of this reaction is that of the associative type involving nucleophilic attack of Ind by its unprotonated N atom at the isocyanide carbon atom followed by the stepwise proton transfer from the nucleophile molecule to the isocyanide N atom via deprotonation/protonation steps. Two reaction channels based on two tautomeric forms of indazole were found. The channel leading to the experimentally isolated aminocarbene product is based on the less stable tautomeric form. Another channel based on the more stable tautomer of Ind is slightly kinetically more favorable but it is endergonic. Thus, the regioselectivity of this reaction is thermodynamically rather than kinetically driven. The bonding situation in key species was analyzed.

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Mechanistic study of CO oxidation by N 2 O over Ag 7 Au 6 cluster investigated by DFT methods

Applied Catalysis A General ◽

10.1016/j.apcata.2017.03.025 ◽

2017 ◽

Vol 538 ◽

pp. 99-106 ◽

Cited By ~ 11

Author(s):

Yutthana Wongnongwa ◽

Supawadee Namuangruk ◽

Nawee Kungwan ◽

Siriporn Jungsuttiwong

Keyword(s):

Co Oxidation ◽

Mechanistic Study ◽

Dft Methods

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A Mechanistic Study on the Tautomerism of H-Phosphonates, H-Phosphinates and Secondary Phosphine Oxides

Molecules ◽

10.3390/molecules24213859 ◽

2019 ◽

Vol 24 (21) ◽

pp. 3859 ◽

Cited By ~ 6

Author(s):

Daniella Vincze ◽

Péter Ábrányi-Balogh ◽

Péter Bagi ◽

György Keglevich

Keyword(s):

Molecular Descriptors ◽

Substituent Effects ◽

Building Blocks ◽

Mechanistic Study ◽

Secondary Phosphine ◽

Phosphine Oxides ◽

Dft Methods ◽

Implicit Solvents ◽

Different Levels ◽

P Ligands

H-phosphonates, H-phosphinates and secondary phosphine oxides may be preligands, and are important building blocks in the synthesis of pharmaceuticals, pesticides, and P-ligands. The prototropic tautomerism influenced by substituent effects plays an important role in the reactivity of these species. The main goal of our research was to study the tautomerism of the >P(O)H reagents by means of computational investigations applying several DFT methods at different levels. We focused on the effect of implicit solvents, and on explaining the observed trends with physical chemical molecular descriptors. In addition, multiple reaction pathways incorporating three P-molecules were elucidated for the mechanism of the interconversion.

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Mechanistic study of proliferation induced by Angelica sinensis in gastric epithelial cells

Gastroenterology ◽

10.1016/s0016-5085(01)80716-2 ◽

2001 ◽

Vol 120 (5) ◽

pp. A145-A145

Author(s):

C CHO ◽

Y YE ◽

E LIU ◽

V SHIN ◽

N SHAM

Keyword(s):

Epithelial Cells ◽

Mechanistic Study ◽

Angelica Sinensis ◽

Gastric Epithelial Cells

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Mechanistic study on the cardioprotective and chemosensitizing effects of a novel danshensu derivative

Planta Medica ◽

10.1055/s-0034-1394728 ◽

2014 ◽

Vol 80 (16) ◽

Author(s):

L Wang ◽

L Shan ◽

G Cui ◽

Y Chen ◽

J li ◽

...

Keyword(s):

Mechanistic Study

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Oxidation of Some Unsaturated Acids by Imidazolium Dichromate: A Kinetics and Mechanistic Study

Journal of Chemical Biological and Physical Sciences ◽

10.24214/jcbps.a.7.3.61425 ◽

2017 ◽

Vol 7 (3) ◽

Keyword(s):

Mechanistic Study

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Performance of Electronic Structure Methods for the Description of Hückel-Möbius Interconversions in Extended π-Systems

10.26434/chemrxiv.10564115 ◽

2019 ◽

Author(s):

Tatiana Woller ◽

Ambar Banerjee ◽

Nitai Sylvetsky ◽

Xavier Deraet ◽

Frank De Proft ◽

...

Keyword(s):

Electronic Structure ◽

Basis Set ◽

Dft Methods ◽

Molecular Switching ◽

Wide Range ◽

Electronic Structure Methods ◽

Explicitly Correlated ◽

Relative Errors ◽

The Stability ◽

Basis Set Expansion

Expanded porphyrins provide a versatile route to molecular switching devices due to their ability to shift between several π-conjugation topologies encoding distinct properties. Taking into account its size and huge conformational flexibility, DFT remains the workhorse for modeling such extended macrocycles. Nevertheless, the stability of Hückel and Möbius conformers depends on a complex interplay of different factors, such as hydrogen bonding, p···p stacking, steric effects, ring strain and electron delocalization. As a consequence, the selection of an exchange-correlation functional for describing the energy profile of topological switches is very difficult. For these reasons, we have examined the performance of a variety of wavefunction methods and density functionals for describing the thermochemistry and kinetics of topology interconversions across a wide range of macrocycles. Especially for hexa- and heptaphyrins, the Möbius structures have a pronouncedly stronger degree of static correlation than the Hückel and figure-eight structures, and as a result the relative energies of singly-twisted structures are a challenging test for electronic structure methods. Comparison of limited orbital space full CI calculations with CCSD(T) calculations within the same active spaces shows that post-CCSD(T) correlation contributions to relative energies are very minor. At the same time, relative energies are weakly sensitive to further basis set expansion, as proven by the minor energy differences between MP2/cc-pVDZ and explicitly correlated MP2-F12/cc-pVDZ-F12 calculations. Hence, our CCSD(T) reference values are reasonably well-converged in both 1-particle and n-particle spaces. While conventional MP2 and MP3 yield very poor results, SCS-MP2 and particularly SOS-MP2 and SCS-MP3 agree to better than 1 kcal mol-1 with the CCSD(T) relative energies. Regarding DFT methods, only M06-2X provides relative errors close to chemical accuracy with a RMSD of 1.2 kcal mol-1. While the original DSD-PBEP86 double hybrid performs fairly poorly for these extended p-systems, the errors drop down to 2 kcal mol-1 for the revised revDSD-PBEP86-NL, again showing that same-spin MP2-like correlation has a detrimental impact on performance like the SOS-MP2 results.

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Accurate and Transferable Multitask Prediction of Chemical Properties with an Atoms-in-Molecule Neural Network

10.26434/chemrxiv.7151435.v2 ◽

2018 ◽

Author(s):

Roman Zubatyuk ◽

Justin S. Smith ◽

Jerzy Leszczynski ◽

Olexandr Isayev

Keyword(s):

Neural Network ◽

Molecular System ◽

Computational Cost ◽

Chemical Properties ◽

The State ◽

Molecular Properties ◽

Training Data ◽

Dft Methods ◽

Benchmark Datasets ◽

Quantum Phenomena

Atomic and molecular properties could be evaluated from the fundamental Schrodinger’s equation and therefore represent different modalities of the same quantum phenomena. Here we present AIMNet, a modular and chemically inspired deep neural network potential. We used AIMNet with multitarget training to learn multiple modalities of the state of the atom in a molecular system. The resulting model shows on several benchmark datasets the state-of-the-art accuracy, comparable to the results of orders of magnitude more expensive DFT methods. It can simultaneously predict several atomic and molecular properties without an increase in computational cost. With AIMNet we show a new dimension of transferability: the ability to learn new targets utilizing multimodal information from previous training. The model can learn implicit solvation energy (like SMD) utilizing only a fraction of original training data, and archive MAD error of 1.1 kcal/mol compared to experimental solvation free energies in MNSol database.

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A Systematic DFT Study of Two Elementary Steps Involving Hydrogen Peroxide and the Hydroxyl Radical in the Fenton Reaction

10.26434/chemrxiv.6160142 ◽

2018 ◽

Author(s):

Danilo Carmona ◽

David Contreras ◽

Oscar A. Douglas-Gallardo ◽

Stefan Vogt-Geisse ◽

Pablo Jaque ◽

...

Keyword(s):

Hydrogen Peroxide ◽

Hydroxyl Radical ◽

Ab Initio ◽

Fenton Reaction ◽

Basis Set ◽

Basis Sets ◽

Dft Methods ◽

Elementary Steps ◽

Oxygen Oxygen ◽

Complete Basis Set

The Fenton reaction plays a central role in many chemical and biological processes and has various applications as e.g. water remediation. The reaction consists of the iron-catalyzed homolytic cleavage of the oxygen-oxygen bond in the hydrogen peroxide molecule and the reduction of the hydroxyl radical. Here, we study these two elementary steps with high-level ab-initio calculations at the complete basis set limit and address the performance of different DFT methods following a specific classification based on the Jacob´s ladder in combination with various Pople's basis sets. Ab-initio calculations at the complete basis set limit are in agreement to experimental reference data and identified a significant contribution of the electron correlation energy to the bond dissociation energy (BDE) of the oxygen-oxygen bond in hydrogen peroxide and the electron affinity (EA) of the hydroxyl radical. The studied DFT methods were able to reproduce the ab-initio reference values, although no functional was particularly better for both reactions. The inclusion of HF exchange in the DFT functionals lead in most cases to larger deviations, which might be related to the poor description of the two reactions by the HF method. Considering the computational cost, DFT methods provide better BDE and EA values than HF and post--HF methods with an almost MP2 or CCSD level of accuracy. However, no systematic general prediction of the error based on the employed functional could be established and no systematic improvement with increasing the size in the Pople's basis set was found, although for BDE values certain systematic basis set dependence was observed. Moreover, the quality of the hydrogen peroxide, hydroxyl radical and hydroxyl anion structures obtained from these functionals was compared to experimental reference data. In general, bond lengths were well reproduced and the error in the angles were between one and two degrees with some systematic trend with the basis sets. From our results we conclude that DFT methods present a computationally less expensive alternative to describe the two elementary steps of the Fenton reaction. However, choice of approximated functionals and basis sets must be carefully done and the provided benchmark allows a systematic validation of the electronic structure method to be employed

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Mechanistic Study and Development of Catalytic Reactions of Sm(II)

10.26434/chemrxiv.7355069 ◽

2018 ◽

Author(s):

Sandepan Maity ◽

Robert Flowers

Keyword(s):

Molecular Weight ◽

High Molecular Weight ◽

Proton Donor ◽

Catalytic Reactions ◽

Mechanistic Study ◽

Mechanistic Studies ◽

Cyclization Reactions ◽

Mechanistic Approach ◽

Donor Source

Despite the broad utility and application of SmI2in synthesis, the reagent is used in stoichiometric amounts and has a high molecular weight, resulting in a large amount of material being used for reactions requiring one or more equivalents of electrons. We report mechanistic studies on catalytic reactions of Sm(II) employing a terminal magnesium reductant and trimethyl silyl chloride in concert with a non-coordinating proton donor source. Reactions using this approach permitted reductions with as little as 1 mol% Sm. The mechanistic approach enabled catalysis employing HMPA as a ligand, facilitating the development of catalytic Sm(II) 5-exo-trig ketyl olefin cyclization reactions.

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