What Makes a Good (Computed) Energy Profile?

Remote Functionalization by Pd-Catalyzed Isomerization of Alkynyl Alcohols

In recent years, progress has been made in the development of catalytic methods that allow remote functionalizations based on alkene isomerization. In contrast, protocols based on alkyne isomerization are comparatively rare. Herein, we report a general Pd-catalyzed long-range isomerization of alkynyl alcohols. Starting from aryl-, heteroaryl-, or alkyl-substituted precursors, the optimized system provides access preferentially to the thermodynamically more stable α,β-unsaturated aldehydes and is compatible with potentially sensitive functional groups. We showed that the migration of both π-components of the carbon-carbon triple bond can be sustained over several methylene units. Computational investigations served to shed light on the key elementary steps responsible for the reactivity and selectivity. These include an unorthodox phosphine-assisted deprotonation rather than a more conventional β-hydride elimination in the final tautomerization event.

PyConSolv: A Python Package for Conformer Generation of (Metal-Containing) Systems in Explicit Solvent

We introduce PyConSolv, a freely available Python package that automates the generation of conformers of metal- and nonmetal-containing complexes in explicit solvent, through classical molecular dynamics simulations. Using a streamlined workflow and interfacing with widely used computational chemistry software, PyConSolv is an all-in-one tool for the generation of conformers in any solvent. Input requirements are minimal; only the geometry of the structure and the desired solvent in xyz (XMOL) format are needed. The package can also account for charged systems, by including arbitrary counterions in the simulation. A bonded model parametrization is performed automatically, utilizing AmberTools, ORCA, and Multiwfn software packages. PyConSolv provides a selection of preparametrized solvents and counterions for use in classical molecular dynamics simulations. We show the applicability of our package on a number of (transition-metal-containing) systems. The software is provided open source and free of charge.

Mesomeric Acceleration Counters Slow Initiation of Ruthenium–CAAC Catalysts for Olefin Metathesis (CAAC = Cyclic (Alkyl)(Amino) Carbene)

Ruthenium catalysts bearing cyclic (alkyl)(amino)carbene (CAAC) ligands can attain very high productivities in olefin metathesis, owing to their resistance to unimolecular decomposition. Because the propagating methylidene species RuCl₂(CAAC)(=CH₂) is extremely susceptible to bimolecular decomposition, however, turnover numbers in the metathesis of terminal olefins are highly sensitive to catalyst concentration, and hence loadings. Understanding how, why, and how rapidly the CAAC complexes partition between the precatalyst and the active species is thus critical. Examined in a dual experimental-computational study are the rates and basis of initiation for phosphine-free catalysts containing the leading CAAC ligand C1 ^Ph , in which a CMePh group α to the carbene carbon helps retard degradation. The Hoveyda-class complex HC1 ^Ph (RuCl₂(L)(=CHAr), where L = C1 ^Ph , Ar = C₆H₃-2-O ⁱ Pr-5-R; R = H) is compared with its nitro-Grela analogue (nG-C1 ^Ph ; R = NO₂) and the classic Hoveyda catalyst HII (L = H₂IMes; R = H). t-Butyl vinyl ether (tBuVE) was employed as substrate, to probe the reactivity of these catalysts toward olefins of realistic bulk. Initiation is ca. 100× slower for HC1 ^Ph than HII in C₆D₆, or 44× slower in CDCl₃. The rate-limiting step for the CAAC catalyst is cycloaddition; for HII, it is tBuVE binding. Initiation is 10-13× faster for nG-C1 ^Ph than HC1 ^Ph in either solvent. DFT analysis reveals that this rate acceleration originates in an overlooked role of the nitro group. Rather than weakening the Ru-ether bond, as widely presumed, the NO₂ group accelerates the ensuing, rate-limiting cycloaddition step. Faster reaction is caused by long-range mesomeric effects that modulate key bond orders and Ru-ligand distances, and thereby reduce the trans effect between the carbene and the trans-bound alkene in the transition state for cycloaddition. Mesomeric acceleration may plausibly be introduced via any of the ligands present, and hence offers a powerful, tunable control element for catalyst design.

Direct Benzene Hydroxylation with Dioxygen Induced by Copper Complexes: Uncovering the Active Species by DFT Calculations

The direct oxidation of benzene into phenol using molecular oxygen at very mild temperatures can be promoted in the presence of the copper complex Tp^Br3Cu(NCMe) in the homogeneous phase in the presence of ascorbic acid as the source of protons and electrons. The stoichiometric nature, relative to copper, of this transformation prompted a thorough DFT study in order to understand the reaction pathway. As a result, the dinuclear species Tp^Br3Cu^II(μ-O^•)(μ-OH)Cu^IITp^Br3 is proposed as the relevant structure which is responsible for activating the arene C–H bond leading to phenol formation.

Computational Studies on the Mechanisms for Deaminative Amide Hydrogenation by Homogeneous Bifunctional Catalysts

The deaminative hydrogenation of amides is one of the most convenient pathways for the synthesis of amines and alcohols. The ideal source of reducing equivalents for this reaction is molecular hydrogen, though, in practice, this approach requires high pressures and temperatures, with many catalysts achieving only small turnover numbers and frequencies. Nonetheless, during the last ten years, this field has made major advances towards larger turnovers under milder conditions thanks to the development of bifunctional catalysts. These systems promote the heterolytic cleavage of hydrogen into proton and hydride by combining a basic ligand with an acidic metal centre. The present review focuses on the computational study of the reaction mechanism underlying bifunctional catalysis. This review is structured around the fundamental steps of this mechanism, namely the C=O and C–N hydrogenation of the amide, the C–N protonolysis of the hemiaminal, the C=O hydrogenation of the aldehyde, and the competition between hydrogen activation and catalyst deactivation. In line with the complexity of the mechanism, we also provide a perspective on the use of microkinetic models. Both Noyori- and Milstein-type catalysts are discussed and compared.

Beyond Continuum Solvent Models in Computational Homogeneous Catalysis

In homogeneous catalysis solvent is an inherent part of the catalytic system. As such, it must be considered in the computational modeling. The most common approach to include solvent effects in quantum mechanical calculations is by means of continuum solvent models. When they are properly used, average solvent effects are efficiently captured, mainly those related with solvent polarity. However, neglecting atomistic description of solvent molecules has its limitations, and continuum solvent models all alone cannot be applied to whatever situation. In many cases, inclusion of explicit solvent molecules in the quantum mechanical description of the system is mandatory. The purpose of this article is to highlight through selected examples what are the reasons that urge to go beyond the continuum models to the employment of micro-solvated (cluster-continuum) of fully explicit solvent models, in this way setting the limits of continuum solvent models in computational homogeneous catalysis. These examples showcase that inclusion of solvent molecules in the calculation not only can improve the description of already known mechanisms but can yield new mechanistic views of a reaction. With the aim of systematizing the use of explicit solvent models, after discussing the success and limitations of continuum solvent models, issues related with solvent coordination and solvent dynamics, solvent effects in reactions involving small, charged species, as well as reactions in protic solvents and the role of solvent as reagent itself are successively considered.

Melding of Experiment and Theory Illuminates Mechanisms of Metal-Catalyzed Rearrangements: Computational Approaches and Caveats

This review summarizes approaches and caveats in computational modeling of transition-metal-catalyzed sigmatropic rearrangements involving carbene transfer. We highlight contemporary examples of combined synthetic and theoretical investigations that showcase the synergy achievable by integrating experiment and theory.

1 Introduction

2 Mechanistic Models

3 Theoretical Approaches and Caveats

3.1 Recommended Computational Tools

3.2 Choice of Functional and Basis Set

3.3 Conformations and Ligand-Binding Modes

3.4 Solvation

4 Synergy of Experiment and Theory – Case Studies

4.1 Metal-Bound or Free Ylides?

4.2 Conformations and Ligand-Binding Modes of Paddlewheel Complexes

4.3 No Metal, Just Light

4.4 How To ‘Cope’ with Nonstatistical Dynamic Effects

5 Outlook