Anti-Markovnikov Intermolecular Hydroamination of Alkenes and Alkynes: A Mechanistic View.

Hydroamination, the addition of an N-H bond across a C-C multiple bond, is a reaction with a great synthetic potential. Important advances have been made in the last decades concerning catalysis of these reactions. However, controlling the regioselectivity in the amine addition toward the formation of anti-Markovnikov products (addition to the less substituted carbon) still remains a challenge, particularly in intermolecular hydroaminations of alkenes and alkynes. The goal of this review is to collect the systems in which intermolecular hydroamination of terminal alkynes and alkenes with anti-Markovnikov regioselectivity has been achieved. The focus will be placed on the mechanistic aspects of such reactions, to discern the step at which regioselectivity is decided and to unravel the factors that favor the anti-Markovnikov regioselectivity. In addition to the processes entailing direct addition of the amine to the C-C multiple bond, alternative pathways, involving several reactions to accomplish anti-Markovnikov regioselectivity (formal hydroamination processes), will also be discussed in this review. The catalysts gathered embrace most of the metal groups of the Periodic Table. Finally, a section discussing radical-mediated and metal-free approaches, as well as heterogeneous catalyzed processes, is also included.

Rationalization of a Streptavidin Based Enantioselective Artificial Suzukiase: An Integrative Computational Approach.

An Artificial Metalloenzyme (ArM) built employing the streptavidin-biotin technology has been used for the enantioselective synthesis of binaphthyls by means of asymmetric Suzuki-Miyaura cross-coupling reactions. Despite its success, it remains a challenge to understand how the length of the biotin cofactors or the introduction of mutations to streptavidin leads the preferential synthesis of one atropisomer over the other. In this study, we apply an integrated computational modeling approach, including DFT calculations, protein-ligand dockings and molecular dynamics to rationalize the impact of mutations and length of the biotion cofactor on the enantioselectivities of the biaryl product. The results unravel that the enantiomeric differences found experimentally can be rationalized by the disposition of the first intermediate, coming from the oxidative addition step, and the entrance of the second substrate. The work also showcases the difficulties facing to control the enantioselection when engineering ArM to catalyze enantioselective Suzuki-Miyaura couplings and how the combination of DFT calculations, molecular dockings and MD simulations can be used to rationalize artificial metalloenzymes.

Carboranylphosphines: B9-Substituted Derivatives with Enhanced Reactivity for the Anchoring to Dendrimers.

Several ortho-carboranes bearing a phenoxy or a phenylamino group in the B9 position were prepared employing various protection and deprotection strategies. Following established protocols, dendritic compounds were synthesized from a hexachlorocyclotriphosphazene or thiophosphoryl chloride core, and possible anchoring options for the B9-substituted ortho-carboranes were investigated experimentally and theoretically (DFT). Furthermore, 1- or 1,2-phosphanyl-substituted carborane derivatives were obtained. The resulting diethyl-, diisopropyl-, di-tert-butyl-, diphenyl- or diethoxyphosphines bearing a tunable ortho-carborane moiety are intriguing ligands for future applications in homogeneous catalysis or the medicinal sector.

Carboranylphosphines: B9-Substituted Derivatives with Enhanced Reactivity for Anchoring to Dendrimers.

Invited for the cover of this issue are the groups and colleagues of Anne-Marie Caminade at the CNRS and University of Toulouse, Evamarie Hey-Hawkins at Leipzig University, and Agustí Lledós from the Autonomous University of Barcelona. The image depicts birds crowned by a carborane competing for access to food, to illustrate the steric hindrance encountered when grafting carboranes to dendrimers (artwork by Dr. Christoph Selg). Read the full text of the article at 10.1002/chem.202303867.

Tripodal BODIPY-Tagged and Functional Molecular Probes: Synthesis, Computational Investigations and Explorations by Multiphoton Fluorescence Lifetime Imaging Microscopy.

A range of novel BODIPY derivatives with a tripodal aromatic core was synthesized and characterized spectroscopically. These new fluorophores showed promising features as probes for in vitro assays in live cells and offer strategic routes for further functionalization towards hybrid nanomaterials. Incorporation of biotin tags facilitated proof-of-concept access to targeted bioconjugates as molecular probes. Computational explorations using DFT and TD-DFT calculations identified the most stable tripodal linker conformations and predicted their absorption and emission behavior. The uptake and speciation of these molecules in living prostate cancer cells was imaged by single- and two-photon excitation techniques coupled with two-photon fluorescence lifetime imaging (2P FLIM).

Dithienylethene-Based Photoswitchable Phosphines for the Palladium-Catalyzed Stille Coupling Reaction.

Homogeneous transition metal catalysis is a constantly developing field in chemical sciences. A growing interest in this area is photoswitchable catalysis, which pursues in situ modulation of catalyst activity through noninvasive light irradiation. Phosphorus ligands are excellent targets to accomplish this goal by introducing photoswitchable moieties; however, only a limited number of examples have been reported so far. In this work, we have developed a series of palladium complexes capable of catalyzing the Stille coupling reaction that contain photoisomerizable phosphine ligands based on dithienylethene switches. Incorporation of electron-withdrawing substituents into these dithienylethene moieties allows variation of the electron density on the phosphorus atom of the ligands upon light irradiation, which in turn leads to a modulation of the catalytic properties of the formed complexes and their activity in a model Stille coupling reaction. These results are supported by theoretical computations, which show that the energy barriers for the rate-determining steps of the catalytic cycle decrease when the photoswitchable phosphine ligands are converted to their closed state.

Cyclometallated Imides as Templates for the H-Bond Directed Iridium-Catalyzed Asymmetric Hydrogenation of N-Methyl, N-Alkyl and N-Aryl Imines.

A combined computational and experimental approach allowed us to develop overall the most selective catalyst for the direct hydrogenation of N-methyl, N-alkyl and N-aryl imines described to date. Iridium catalysts with a cyclometallated cyclic imide group provide selectivity of up to 99 % enantiomeric excess. Computational studies show that the selectivity results from the combined effect of H-bonding of the imide C=O with the substrate iminium ion and a stabilizing π-π interaction with the cyclometallated ligand. The cyclometallated ligand thus exhibits a unique mode of action, serving as a template for the H-bond directed approach of the substrate which results in enhanced selectivity. The catalyst (2) has been synthesized and isolated as a crystalline air-stable solid. X-ray analysis of 2 confirmed the structure of the catalyst and the correct position of the imide C=O groups to engage in an H-bond with the substrate. 19F NMR real-time monitoring showed the hydrogenation of N-methyl imines catalyzed by 2 is very fast, with a TOF of approx. 3500 h-1.

Successes and challenges in multiscale modelling of artificial metalloenzymes: the case study of POP-Rh2 cyclopropanase.

Molecular modelling applications in metalloenzyme design are still scarce due to a series of challenges. On top of that, the simulations of metal-mediated binding and the identification of catalytic competent geometries require both large conformational exploration and simulation of fine electronic properties. Here, we demonstrate how the incorporation of new tools in multiscale strategies, namely substrate diffusion exploration, allows taking a step further. As a showcase, the enantioselective profiles of the most outstanding variants of an artificial Rh2-based cyclopropanase (GSH, HFF and RFY) developed by Lewis and co-workers (Nat. Commun., 2015, 6, 7789 and Nat. Chem., 2018, 10, 318-324) have been rationalized. DFT calculations on the free-cofactor-mediated process identify the carbene insertion and the cyclopropanoid formation as crucial events, the latter being the enantiodetermining step, which displays up to 8 competitive orientations easily altered by the protein environment. The key intermediates of the reaction were docked into the protein scaffold showing that some mutated residues have direct interaction with the cofactor and/or the co-substrate. These interactions take the form of a direct coordination of Rh in GSH and HFF and a strong hydrophobic patch with the carbene moiety in RFY. Posterior molecular dynamics sustain that the cofactor induces global re-arrangements of the protein. Finally, massive exploration of substrate diffusion, based on the GPathFinder approach, defines this event as the origin of the enantioselectivity in GSH and RFY. For HFF, fine molecular dockings suggest that it is likely related to local interactions upon diffusion. This work shows how modelling of long-range mutations on the catalytic profiles of metalloenzymes may be unavoidable and software simulating substrate diffusion should be applied.

Getting Deeper into the Molecular Events of Heme Binding Mechanisms: A Comparative Multi-level Computational Study of HasAsm and HasAyp Hemophores.

Many biological systems obtain their activity by the inclusion of metalloporphyrins into one or several binding pockets. However, decoding the molecular mechanism under which these compounds bind to their receptors is something that has not been widely explored and is a field with open questions. In the present work, we apply computational techniques to unravel and compare the mechanisms of two heme-binding systems, concretely the HasA hemophores from Gram negative bacteria Serratiamarcescens (HasAsm) and Yersinia pestis (HasAyp). Despite the high sequence identity between both systems, the comparison between the X-ray structures of their apo and holo forms suggests different heme-binding mechanisms. HasAyp has extremely similar structures for heme-free and heme-bound forms, while HasAsm presents a very large displacement of a loop that ultimately leads to an additional coordination to the metal with respect to HasAyp. We combined Gaussian accelerated molecular dynamics simulations (GaMDs) in explicit solvent and protein-ligand docking optimized for metalloligands. GaMDs were first carried out on heme-free forms of both hemophores. Then, protein-ligand dockings of the heme were performed on cluster representatives of these simulations and the best poses were then subjected to a new series of GaMDs. A series of analyses reveal the following: (1) HasAyp has a conformational landscape extremely similar between heme-bound and unbound states with no to limited impact on the binding of the cofactor, (2) HasAsm presents as a slightly broader conformational landscape in its apo state but can only visit conformations similar to the X-ray of the holo form when the heme has been bound. Such behavior results from a complex cascade of changes in interactions that spread from the heme-binding pocket to the flexible loop previously mentioned. This study sheds light on the diversity of molecular mechanisms of heme-binding and discusses the weight between the pre-organization of the receptor as well as the induced motions resulting in association.

Molecular Modeling for Artificial Metalloenzyme Design and Optimization.

Artificial metalloenzymes (ArMs) are obtained by inserting homogeneous catalysts into biological scaffolds and are among the most promising strategies in the quest for new-to-nature biocatalysts. The quality of their design strongly depends on how three partners interact: the biological host, the "artificial cofactor," and the substrate. However, structural characterization of functional artificial metalloenzymes by X-ray or NMR is often partial, elusive, or absent. How the cofactor binds to the protein, how the receptor reorganizes upon the binding of the cofactor and the substrate, and which are the binding mode(s) of the substrate for the reaction to proceed are key questions that are frequently unresolved yet crucial for ArM design. Such questions may eventually be solved by molecular modeling but require a step change beyond the current state-of-the-art methodologies.Here, we summarize our efforts in the study of ArMs, presenting both the development of computational strategies and their application. We first focus on our integrative computational framework that incorporates a variety of methods such as protein-ligand docking, classical molecular dynamics (MD), and pure quantum mechanical (QM) methods, which, when properly combined, are able to depict questions that range from host-cofactor binding predictions to simulations of entire catalytic mechanisms. We also pay particular attention to the protein-ligand docking strategies that we have developed to accurately predict the binding of transition metal-containing molecules to proteins. While this aspect is fundamental to many bioinorganic fields beyond ArMs, it has been disregarded from the molecular modeling landscape until very recently.Next we describe how to apply this computational framework to particular ArMs including systems previously characterized experimentally as well as others where computation served to guide the design. We start with the prediction of the interactions between homogeneous catalysts and biological hosts. Protein-ligand docking is pivotal at that stage, but it needs to be combined with QM/MM or MD approaches when the binding of the cofactor implies significant conformational changes of the protein or involve changes of the electronic state of the metal.Then, we summarize molecular modeling studies aimed at identifying cofactor-substrate arrangements inside the ArM active pocket that are consistent with its reactivity. These calculations stand on "Theozyme"-like dockings, MD-refined or not, which provide molecular rationale of the catalytic profiles of the artificial systems.In the third section, we present case studies to decode the entire catalytic mechanism of two ArMs: (1) an iridium based asymmetric transfer hydrogenase obtained by insertion of Noyori's catalyst into streptavidin and (2) a metallohydrolase achieved by including a receptor. Transition states, second coordination sphere effects, as well as motions of the cofactors are identified as drivers of the enantiomeric profiles.Finally, we report computer-aided designs of ArMs to guide experiments toward chemical and mutational changes that improve their activity and/or enantioselective profiles and expand toward future directions.

Computational Analysis on the Pd-Catalyzed C-N Coupling of Ammonia with Aryl Bromides Using a Chelate Phosphine Ligand.

The Buchwald-Hartwig amination of arylhalides with the Pd-Josiphos complex is a very useful process for the generation of primary amines using ammonia as a reactant. Density-functional theory (DFT) calculations are carried out to examine the reaction mechanism for this process. Although the general mechanism for the C-N cross-coupling reaction is known, there are still some open questions regarding the effect of a chelate phosphine ligand and the role of the base in the process. Reaction pathways involving the release of one of the arms of the phosphine ligand are compared with those where the chelate phosphine remains fully coordinated. Conformational analysis for the complex with the open chelate phosphine is required to properly evaluate the proposed pathways. The role played by the added base (t-BuO-) as a possible ligand or just as a base was also evaluated. The understanding of all of these aspects allowed us to propose a complete reaction mechanism for the Pd-catalyzed C-N coupling of arylhalides with ammonia using the chelate Josiphos ligand.

Transmetalation Reactions Triggered by Electron Transfer between Organocopper Complexes.

[Cu(bipy)(C6F5)] reacts with most aryl iodides to form heterobiphenyls by cross-coupling, but when Rf-I is used (Rf = 3,5-dicholoro-2,4,6-trifluorophenyl), homocoupling products are also formed. Kinetic studies suggest that, for the homocoupling reaction, a mechanism based on transmetalation from [Cu(bipy)(C6F5)] to Cu(III) intermediates formed in the oxidative addition step is at work. Density functional theory calculations show that the interaction between these Cu(III) species and the starting Cu(I) complex involves a Cu(I)-Cu(III) electron transfer concerted with the formation of an iodine bridge between the metals and that a fast transmetalation takes place in a dimer in a triplet state between two Cu(II) units.

Dynamic PdII /CuI Multimetallic Assemblies as Molecular Models to Study Metal-Metal Cooperation in Sonogashira Coupling.

Cooperation between two different metals plays a crucial role in many synergistic catalytic reactions, such as the Sonogashira C-C cross-coupling reaction, where an interaction between the Pd and Cu centers is proposed in the transmetalation step. Although several heterobimetallic Pd/Cu complexes were proposed as structural models of the active species in Sonogashira coupling, the detailed understanding of the metal-metal cooperation in transmetalation is still lacking in current systems. In this work, we report a stepwise and systematic approach to building heteromultimetallic Pd/Cu assemblies as a tool to study metal-metal cooperativity. We obtained fully characterized Pd/Cu multimetallic assemblies that show reactivity in alkyne activation, formation of catalytically relevant aryl/acetylide species, and C-C elimination, serving as functional models for Sonogashira reaction intermediates. The combined experimental and DFT studies highlight the importance of ligand-controlled coordination geometry, metal-metal distances and dynamics of the multimetallic assembly for transmetalation step.

Catalytic Regioselective Isomerization of 2,2-Disubstituted Oxetanes to Homoallylic Alcohols.

The selective isomerization of strained heterocyclic compounds is an important tool in organic synthesis. An unprecedented regioselective isomerization of 2,2-disubstituted oxetanes into homoallylic alcohols is described. The use of tris(pentafluorophenyl)borane (B(C6 F5 )3 ), a commercially available Lewis acid was key to obtaining good yields and selectivities since other Lewis acids afforded mixtures of isomers and substantial polymerization. The reaction took place under exceptionally mild reaction conditions and very low catalyst loading (0.5 mol %). DFT calculations disclose the mechanistic features of the isomerization and account for the high selectivity displayed by the B(C6 F5 )3 catalyst. The synthetic applicability of the new reaction is demonstrated by the preparation of γ-chiral alcohols using iridium-catalyzed asymmetric hydrogenation.

GARLEEK: Adding an extra flavor to ONIOM.

The ONIOM method, developed in the group of Keiji Morokuma, is one of the most successful examples of quantum mechanics/molecular mechanics (QM/MM) treatments, and of multilayer methods in general. Its implementation in the Gaussian program package is in particular widely used. This implementation has access to the wide variety of QM methods available in Gaussian, but is limited to only three specific force fields. The current article presents the GARLEEK interface, which expands the availability of molecular mechanics methods to the wide variety of force fields available in MM packages. The focus is in the simple installation and use. Two examples of the performance of the interface with selected systems are provided. GARLEEK is MIT-licensed and freely available at https://github.com/insilichem/garleek. © 2018 Wiley Periodicals, Inc.

σ-Silane Platinum(II) Complexes as Intermediates in C-Si Bond-Coupling Processes.

Platinum complexes [Pt(NHC')(NHC)][BArF ] (in which NHC' denotes a cyclometalated N-heterocyclic carbene ligand, NHC) react with primary silanes RSiH3 to afford the cyclometalated platinum(II) silyl complexes [Pt(NHC-SiHR')(NHC)][BArF ] through a process that involves the formation of C-Si and Pt-Si bonds with concomitant extrusion of H2 . Low-temperature NMR studies indicate that the process proceeds through initial formation of the σ-SiH complexes [Pt(NHC')(NHC)(HSiH2 R)][BArF ], which are stable at temperatures below -10 °C. At higher temperatures, activation of one Si-H bond followed by a C-Si coupling reaction generates an agostic SiH platinum hydride derivative [Pt(H)(NHC'-SiH2 R)(NHC)][BArF ], which undergoes a second Si-H bond activation to afford the final products. Computational modeling of the reaction mechanism indicates that the stereochemistry of the silyl/hydride ligands after the first Si-H bond cleavage dictates the nature of the products, favoring the formation of a C-Si bond over a C-H bond, in contrast to previous results obtained for tertiary silanes. Furthermore, the process involves a trans-to-cis isomerization of the NHC ligand before the second Si-H bond cleavage.

Inner-Sphere Oxygen Activation Promoting Outer-Sphere Nucleophilic Attack on Olefins.

Alkoxylation and hydroxylation reactions of 1,5-cyclooctadiene (cod) in an iridium complex with alcohols and water promoted by the reduction of oxygen to hydrogen peroxide are described. The exo configuration of the OH/OR groups in the products agrees with nucleophilic attack at the external face of the olefin as the key step. The reactions also require the presence of a coordinating protic acid (such as picolinic acid (Hpic)) and involve the participation of a cationic diolefin iridium(III) complex, [Ir(cod)(pic)2 ]+ , which has been isolated. Independently, this cation is also involved in easy alkoxy group exchange reactions, which are very unusual for organic ethers. DFT studies on the mechanism of olefin alkoxylation mediated by oxygen show a low-energy proton-coupled electron-transfer step connecting a superoxide-iridium(II) complex with hydroperoxide-iridium(III) intermediates, rather than peroxide complexes. Accordingly, a more complex reaction, with up to four different products, occurred upon reacting the diolefin-peroxide iridium(III) complex with Hpic. Moreover, such hydroperoxide intermediates are the origin of the regio- and stereoselectivity of the hydroxylation/alkoxylation reactions. If this protocol is applied to the diolefin-rhodium(I) complex [Rh(pic)(cod)], free alkyl ethers ORC8 H11 (R=Me, Et) resulted, and the reaction is enantioselective if a chiral amino acid, such as l-proline, is used instead of Hpic.

Activating a Peroxo Ligand for C-O Bond Formation.

Dioxygen activation for effective C-O bond formation in the coordination sphere of a metal is a long-standing challenge in chemistry for which the design of catalysts for oxygenations is slowed down by the complicated, and sometimes poorly understood, mechanistic panorama. In this context, olefin-peroxide complexes could be valuable models for the study of such reactions. Herein, we showcase the isolation of rare "Ir(cod)(peroxide)" complexes (cod=1,5-cyclooctadiene) from reactions with oxygen, and then the activation of the peroxide ligand for O-O bond cleavage and C-O bond formation by transfer of a hydrogen atom through proton transfer/electron transfer reactions to give 2-iradaoxetane complexes and water. 2,4,6-Trimethylphenol, 1,4-hydroquinone, and 1,4-cyclohexadiene were used as hydrogen atom donors. These reactions can be key steps in the oxy-functionalization of olefins with oxygen, and they constitute a novel mechanistic pathway for iridium, whose full reaction profile is supported by DFT calculations.

Direct Asymmetric Hydrogenation of N-Methyl and N-Alkyl Imines with an Ir(III)H Catalyst.

A novel cationic [IrH(THF)(P,N)(imine)] [BArF] catalyst containing a P-stereogenic MaxPHOX ligand is described for the direct asymmetric hydrogenation of N-methyl and N-alkyl imines. This is the first catalytic system to attain high enantioselectivity (up to 94% ee) in this type of transformation. The labile tetrahydrofuran ligand allows for effective activation and reactivity, even at low temperatures. Density functional theory calculations allowed the rationalization of the stereochemical course of the reaction.

Prediction of the interaction of metallic moieties with proteins: An update for protein-ligand docking techniques.

In this article, we present a new approach to expand the range of application of protein-ligand docking methods in the prediction of the interaction of coordination complexes (i.e., metallodrugs, natural and artificial cofactors, etc.) with proteins. To do so, we assume that, from a pure computational point of view, hydrogen bond functions could be an adequate model for the coordination bonds as both share directionality and polarity aspects. In this model, docking of metalloligands can be performed without using any geometrical constraints or energy restraints. The hard work consists in generating the convenient atom types and scoring functions. To test this approach, we applied our model to 39 high-quality X-ray structures with transition and main group metal complexes bound via a unique coordination bond to a protein. This concept was implemented in the protein-ligand docking program GOLD. The results are in very good agreement with the experimental structures: the percentage for which the RMSD of the simulated pose is smaller than the X-ray spectra resolution is 92.3% and the mean value of RMSD is < 1.0 Å. Such results also show the viability of the method to predict metal complexes-proteins interactions when the X-ray structure is not available. This work could be the first step for novel applicability of docking techniques in medicinal and bioinorganic chemistry and appears generalizable enough to be implemented in most protein-ligand docking programs nowadays available. © 2017 Wiley Periodicals, Inc.