Why Is the Suzuki−Miyaura Cross-Coupling of sp3 Carbons in α-Bromo Sulfoxide Systems Fast and Stereoselective? A DFT Study on the Mechanism

C-C Bond Formation Reaction Catalyzed by a Lithium Atom: Benzene-to-Biphenyl Coupling

Transition-metal-catalyzed carbon-carbon (C-C) bond formation is an important reaction in pharmaceutical and organic chemistry. However, the reaction process is composed of multiple steps and is expensive owing to the presence of transition metals. This study proposes a lithium-catalyzed C-C coupling reaction of two benzene molecules (Bz) to form a biphenyl molecule, which is a transition-metal-free reaction, based on ab initio and direct ab initio molecular dynamics (AIMD) calculations. The static ab initio calculations indicate that the reaction of two Bz molecules with Li^- ions (reactant state, RC) can form a stable sandwiched complex (precomplex), where the Li^- ion is sandwiched by two Bz molecules. The complex formation reaction can be expressed as 2Bz + Li ^- → Bz(Li ^-)Bz, where the C-C distance between the Bz rings is 2.449 Å. This complex moves to the transition state (TS) via the structural deformation of Bz(Li^-)Bz, where the C-C distance is shortened to 2.118 Å. The barrier height was calculated to be -9.9 kcal/mol (relative to RC) at the MP2/6-311++G(d,p) level. After TS, the C(sp³)-C(sp³) single bond was completely formed between the Bz rings (the C-C bond distance was 1.635 Å) (late complex). After the dissociation of H₂ from the late complex, a biphenyl molecule was formed: the C(sp²)-C(sp²) bond. The calculations suggest that the C-C bond coupling of Bz occurred spontaneously from 2Bz + Li^-, and biphenyl molecules were directly formed without an activation barrier. Direct AIMD calculations show that the C-C coupling reaction also takes place under electron attachment to Li(Bz)₂: Li(Bz)₂ + e^- → [Li^-(Bz)₂]_ver → precomplex → TS → late complex, where [Li^-(Bz)₂]_ver is the vertical electron capture species of Li(Bz)₂. Namely, the C-C coupling reaction spontaneously occurred in Li(Bz)₂ owing to electron attachment. Similar C-C coupling reactions were also observed for halogen-substituted benzene molecules (Bz-X, X = F and Cl). Furthermore, this study discusses the mechanism of C-C bond formation in electron capture based on the theoretical results.

Mechanistic Aspects of the Palladium-Catalyzed Suzuki-Miyaura Cross-Coupling Reaction

The story of C-C bond formation includes several reactions, and surely Suzuki-Miyaura is among the most outstanding ones. Herein, a brief historical overview of insights regarding the reaction mechanism is provided. In particular, the formation of the catalytically active species is probably the main concern, thus the preactivation is in competition with, or even assumes the role of the rate determining step (rds) of the overall reaction. Computational chemistry is key in identifying the rds and thus leading to milder conditions on an experimental level by means of predictive catalysis.

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.

Compatibility Score for Rational Electrophile Selection in Pd/NBE Cooperative Catalysis

A mechanistically guided approach is developed to predict electrophile compatibility in the palladium/norbornene (Pd/NBE) cooperative catalysis for the ipso/ortho difunctionalization of aryl halides. A key challenge in these reactions is to identify orthogonal electrophile and aryl hali de starting materials that react selectively with different transition metal complexes in separate oxidative addition events in the catalytic cycle. We performed detailed experimental and computational mechanistic studies to identify the catalytically active Pd(II) intermediate and the substrate-dependent mechanisms in reactions with various types of carbon and nitrogen electrophiles. We introduced the concept of electrophile compatibility score (ECS) to rationally select electrophiles based on the orthogonal reactivity of electrophile and aryl halide towards the Pd(0) and Pd(II) complexes. This approach was applied to predict electrophile compatibility in the Pd/NBE cooperative catalysis with a variety of electrophilic coupling partners used in alkylation, arylation, amination, and acylation reactions.

The diverse mechanisms for the oxidative addition of C-Br bonds to Pd(PR3) and Pd(PR3)2 complexes

The reaction between bromobenzene and palladium(0) complexes leading to a palladium(ii) complex containing bromide and phenyl ligands is studied computationally with DFT methods. Three different mechanisms are considered: concerted, nucleophilic substitution and radical. A systematic analysis is carried out on the effect on each of these mechanisms of a number of variables: the identity of the phosphine (PF₃, PH₃, PMe₃ or PPh₃), the nature of the solvent (vacuum, tetrahydrofuran, dimethylformamide or water) and the number of phosphine ligands (mono- or bis-phosphine). The concerted and nucleophilic substitution mechanisms are competitive in many cases, the identity of the preferred one depending on a combination of factors. Additional calculations with bromomethane, bromoethylene and bromoethane are carried out in selected cases for further clarification.

DFT Investigation of Suzuki-Miyaura Reactions with Aryl Sulfamates Using a Dialkylbiarylphosphine-Ligated Palladium Catalyst

Aryl sulfamates are valuable electrophiles for cross-coupling reactions because they can easily be synthesized from phenols and can act as directing groups for C-H bond functionalization prior to cross-coupling. Recently, it was demonstrated that (1-^tBu-Indenyl)Pd(XPhos)Cl (XPhos = 2-dicyclohexylphosphino-2',4',6'-triisopropylbiphenyl) is a highly active precatalyst for room-temperature Suzuki-Miyaura couplings of a variety of aryl sulfamates. Herein, we report an in-depth computational investigation into the mechanism of Suzuki-Miyaura reactions with aryl sulfamates using an XPhos-ligated palladium catalyst. Particular emphasis is placed on the turnover-limiting oxidative addition of the aryl sulfamate C-O bond, which has not been studied in detail previously. We show that bidentate coordination of the XPhos ligand via an additional interaction between the biaryl ring and palladium plays a key role in lowering the barrier to oxidative addition. This result is supported by NBO and NCI-Plot analysis on the transition states for oxidative addition. After oxidative addition, the catalytic cycle is completed by transmetalation and reductive elimination, which are both calculated to be facile processes. Our computational findings explain a number of experimental results, including why elevated temperatures are required for the coupling of phenyl sulfamates without electron-withdrawing groups and why aryl carbamate electrophiles are not reactive with this catalyst.

Mechanistic Insights into Palladium-Catalyzed Silylation of Aryl Iodides with Hydrosilanes through a DFT Study

The catalytic cycles of palladium-catalyzed silylation of aryl iodides, which are initiated by oxidative addition of hydrosilane or aryl iodide through three different mechanisms characterized by intermediates R₃ Si-Pd^II -H (Cycle A), Ar-Pd^II -I (Cycle B), and Pd^IV (Cycle C), have been explored in detail by hybrid DFT. Calculations suggest that the chemical selectivity and reactivity of the reaction depend on the ligation state of the catalyst and specific reaction conditions, including feeding order of substrates and the presence of base. For less bulky biligated catalyst, Cycle C is energetically favored over Cycle A, through which the silylation process is slightly favored over the reduction process. Interestingly, for bulky monoligated catalyst, Cycle B is energetically more favored over generally accepted Cycle A, in which the silylation channel is slightly disfavored in comparison to that of the reduction channel. Moreover, the inclusion of base in this channel allows the silylated product become dominant. These findings offer a good explanation for the complex experimental observations. Designing a reaction process that allows the oxidative addition of palladium(0) complex to aryl iodide to occur prior to that with hydrosilane is thus suggested to improve the reactivity and chemoselectivity for the silylated product by encouraging the catalytic cycle to proceed through Cycles B (monoligated Pd⁰ catalyst) or C (biligated Pd⁰ catalyst), instead of Cycle A.

First-Principles Molecular Dynamics Analysis of Ligand-Free Suzuki-Miyaura Cross-Coupling in Water Solvent: Oxidative Addition Step

We investigated the oxidative addition of PhX (X = Cl, Br) to a single Pd(0) atom or a PdX^- complex in water using first-principles molecular dynamics simulations, with solvent H₂O molecules explicitly included in the calculation models, to clarify the origin of the extremely high reactivity of a ligand-free Pd catalyst in an aqueous solution for the Suzuki-Miyaura reaction. The free-energy profiles are estimated using blue moon ensemble sampling to include the entropy effect in chemical reactions in a water solvent. The free-energy barrier of the oxidative addition step is quite low for PhBr, whereas the barrier for PhCl is sizable, indicating that the reaction can proceed at room temperature with a high rate for PhBr but a rather low rate for PhCl. We also investigated the effect of the additional halogen anion on the Pd catalyst as a "supporting ligand". The activation barrier of the oxidative addition step is not affected by the supporting halogen ligand, but the final state is significantly destabilized, which should be important for the following transmetalation step. The solvent effect has also been investigated and discussed.

Why different ligands can control stereochemistry selectivity of Ni-catalyzed Suzuki–Miyaura cross-coupling of benzylic carbamates with arylboronic esters: a mechanistic study

Transmetallation is the rate-determining step for the whole catalytic cycle, and oxidative addition controls the stereoselectivity of products.

Computational study on alkenyl/aryl C(sp2)–O homolytic cleavage of carboxylates and carbamates

The alkenyl/aryl C(sp²)–O cleavage and the substituent effect in both carboxylates/carbamates and corresponding Ni complexes were investigated in detail by wB97 method.

Platinum(0)-mediated C–O bond activation of ethers via an SN2 mechanism

DFT calculations demonstrate that Pt(0) bis(phosphine) complexes react with Ar^F–O–Me via an S_N2 mechanism to activate the O–CH₃ bond; experimental support is provided by reaction of Pt(PCy₃)₂ with 2,3,5,6-tetrafluoro-4-allyloxypyridine to form an aryloxide salt of [Pt(η³-allyl)(PCy₃)₂]⁺.

Alkali metal mediated C-C bond coupling reaction

Metal catalyzed carbon-carbon (C-C) bond formation is one of the important reactions in pharmacy and in organic chemistry. In the present study, the electron and hole capture dynamics of a lithium-benzene sandwich complex, expressed by Li(Bz)2, have been investigated by means of direct ab-initio molecular dynamics method. Following the electron capture of Li(Bz)2, the structure of [Li(Bz)2](-) was drastically changed: Bz-Bz parallel form was rapidly fluctuated as a function of time, and a new C-C single bond was formed in the C1-C1' position of Bz-Bz interaction system. In the hole capture, the intermolecular vibration between Bz-Bz rings was only enhanced. The mechanism of C-C bond formation in the electron capture was discussed on the basis of theoretical results.

Computational perspective on Pd-catalyzed C-C cross-coupling reaction mechanisms

Palladium-catalyzed C-C cross-coupling reactions (Suzuki-Miyaura, Negishi, Stille, Sonogashira, etc.) are among the most useful reactions in modern organic synthesis because of their wide scope and selectivity under mild conditions. The many steps involved and the availability of competing pathways with similar energy barriers cause the mechanism to be quite complicated. In addition, the short-lived intermediates are difficult to detect, making it challenging to fully characterize the mechanism of these reactions using purely experimental techniques. Therefore, computational chemistry has proven crucial for elucidating the mechanism and shaping our current understanding of these processes. This mechanistic elucidation provides an opportunity to further expand these reactions to new substrates and to refine the selectivity of these reactions. During the past decade, we have applied computational chemistry, mostly using density functional theory (DFT), to the study of the mechanism of C-C cross-coupling reactions. This Account summarizes the results of our work, as well as significant contributions from others. Apart from a few studies on the general features of the catalytic cycles that have highlighted the existence of manifold competing pathways, most studies have focused on a specific reaction step, leading to the analysis of the oxidative addition, transmetalation, and reductive elimination steps of these processes. In oxidative addition, computational studies have clarified the connection between coordination number and selectivity. For transmetalation, computation has increased the understanding of different issues for the various named reactions: the role of the base in the Suzuki-Miyaura cross-coupling, the factors distinguishing the cyclic and open mechanisms in the Stille reaction, the identity of the active intermediates in the Negishi cross-coupling, and the different mechanistic alternatives in the Sonogashira reaction. We have also studied the closely related direct arylation process and highlighted the role of an external base as proton abstractor. Finally, we have also rationalized the effect of ligand substitution on the reductive elimination process. Computational chemistry has improved our understanding of palladium-catalyzed cross-coupling processes, allowing us to identify the mechanistic complexity of these reactions and, in a few selected cases, to fully clarify their mechanisms. Modern computational tools can deal with systems of the size and complexity involved in cross-coupling and have a continuing role in solving specific problems in this field.

Theoretical study on the mechanism of Ni-catalyzed alkyl-alkyl Suzuki cross-coupling

Ni-catalyzed cross-coupling of unactivated secondary alkyl halides with alkylboranes provides an efficient way to construct alkyl-alkyl bonds. The mechanism of this reaction with the Ni/L1 (L1=trans-N,N'-dimethyl-1,2-cyclohexanediamine) system was examined for the first time by using theoretical calculations. The feasible mechanism was found to involve a Ni(I)-Ni(III) catalytic cycle with three main steps: transmetalation of [Ni(I)(L1)X] (X=Cl, Br) with 9-borabicyclo[3.3.1]nonane (9-BBN)R(1) to produce [Ni(I)(L1)(R(1))], oxidative addition of R(2) X with [Ni(I)(L1)(R(1))] to produce [Ni(III)(L1)(R(1))(R(2))X] through a radical pathway, and C-C reductive elimination to generate the product and [Ni(I)(L1)X]. The transmetalation step is rate-determining for both primary and secondary alkyl bromides. KOiBu decreases the activation barrier of the transmetalation step by forming a potassium alkyl boronate salt with alkyl borane. Tertiary alkyl halides are not reactive because the activation barrier of reductive elimination is too high (+34.7 kcal mol(-1)). On the other hand, the cross-coupling of alkyl chlorides can be catalyzed by Ni/L2 (L2=trans-N,N'-dimethyl-1,2-diphenylethane-1,2-diamine) because the activation barrier of transmetalation with L2 is lower than that with L1. Importantly, the Ni(0)-Ni(II) catalytic cycle is not favored in the present systems because reductive elimination from both singlet and triplet [Ni(II)(L1)(R(1))(R(2))] is very difficult.

Suzuki-Miyaura cross-coupling of aryl carbamates and sulfamates: experimental and computational studies

The first Suzuki-Miyaura cross-coupling reactions of the synthetically versatile aryl O-carbamate and O-sulfamate groups are described. The transformations utilize the inexpensive, bench-stable catalyst NiCl(2)(PCy(3))(2) to furnish biaryls in good to excellent yields. A broad scope for this methodology has been demonstrated. Substrates with electron-donating and electron-withdrawing groups are tolerated, in addition to those that possess ortho substituents. Furthermore, heteroaryl substrates may be employed as coupling partners. A computational study providing the full catalytic cycles for these cross-coupling reactions is described. The oxidative addition with carbamates or sulfamates occurs via a five-centered transition state, resulting in the exclusive cleavage of the aryl C-O bond. Water is found to stabilize the Ni-carbamate catalyst resting state, which thus provides rationalization of the relative decreased rate of coupling of carbamates. Several synthetic applications are presented to showcase the utility of the methodology in the synthesis of polysubstituted aromatic compounds of natural product and bioactive molecule interest.

How reliable are DFT transition structures? Comparison of GGA, hybrid-meta-GGA and meta-GGA functionals

There have been many comparisons of computational methods applied to ground states, but studies of organic reactions usually require calculations on transition states, and these provide a different test of the methods. We present calculations of the geometries of nineteen covalent-bond forming transition states using HF and twelve different functionals, including GGA, hybrid-GGA and hybrid meta-GGA approaches. For the calculation of the TS geometries, the results suggest that B3LYP is only slightly less accurate than newer, computationally more expensive methods, and is less sensitive to choice of integration grid. We conclude that the use of B3LYP and related functionals is still appropriate for many studies of organic reaction mechanisms.