Accelerating reliable multiscale quantum refinement of protein-drug systems enabled by machine learning.

Biomacromolecule structures are essential for drug development and biocatalysis. Quantum refinement (QR) methods, which employ reliable quantum mechanics (QM) methods in crystallographic refinement, showed promise in improving the structural quality or even correcting the structure of biomacromolecules. However, vast computational costs and complex quantum mechanics/molecular mechanics (QM/MM) setups limit QR applications. Here we incorporate robust machine learning potentials (MLPs) in multiscale ONIOM(QM:MM) schemes to describe the core parts (e.g., drugs/inhibitors), replacing the expensive QM method. Additionally, two levels of MLPs are combined for the first time to overcome MLP limitations. Our unique MLPs+ONIOM-based QR methods achieve QM-level accuracy with significantly higher efficiency. Furthermore, our refinements provide computational evidence for the existence of bonded and nonbonded forms of the Food and Drug Administration (FDA)-approved drug nirmatrelvir in one SARS-CoV-2 main protease structure. This study highlights that powerful MLPs accelerate QRs for reliable protein-drug complexes, promote broader QR applications and provide more atomistic insights into drug development.

A Synergistic Bimetallic Ti/Co-Catalyzed Isomerization of Epoxides to Allylic Alcohols Enabled by Two-State Reactivity.

Isomerization of epoxides into versatile allylic alcohols is an atom-economical synthetic method to afford vicinal bifunctional groups. Comprehensive density functional theory (DFT) calculations were carried out to elucidate the complex mechanism of a bimetallic Ti/Co-catalyzed selective isomerization of epoxides to allyl alcohols by examining several possible pathways. Our results suggest a possible mechanism involving (1) radical-type epoxide ring opening catalyzed by Cp2Ti(III)Cl leading to a Ti(IV)-bound ß-alkyl radical, (2) hydrogen-atom transfer (HAT) catalyzed by the Co(II) catalyst to form the Ti(IV)-enolate and Co(III)-H intermediate, (3) protonation to give the alcohols, and (4) proton abstraction to form the Co(I) species followed by electron transfer to regenerate the active Co(II) and Ti(III) species. Moreover, bimetallic catalysis and two-state reactivity enable the key rate-determining HAT step. Furthermore, a subtle balance between dispersion-driven bimetallic processes and entropy-driven monometallic processes determines the most favorable pathway, among which the monometallic process is energetically more favorable in all steps except the vital hydrogen-atom transfer step. Our study should provide an in-depth mechanistic understanding of bimetallic catalysis.

Electron-rich benzofulvenes as effective dipolarophiles in copper(i)-catalyzed asymmetric 1,3-dipolar cycloaddition of azomethine ylides.

A series of benzofulvenes without any electron-withdrawing substituents were employed as 2π-type dipolarophiles for the first time to participate in Cu(i)-catalyzed asymmetric 1,3-dipolar cycloaddition (1,3-DC) reactions of azomethine ylides. An intrinsic non-benzenoid aromatic characteristic from benzofulvenes serves as a key driving force for activation of the electron-rich benzofulvenes. Utilizing the current methodology, a wide range of multi-substituted chiral spiro-pyrrolidine derivatives containing two contiguous all-carbon quaternary centers were formed in good yield with exclusive chemo-/regioselectivity and high to excellent stereoselectivity. Computational mechanistic studies elucidate the origin of the stereochemical outcome and the chemoselectivity, in which the thermostability of these cycloaddition products is the major factor.

A Computational Study on the Reaction Mechanism of Stereocontrolled Synthesis of ß-Lactam within [2]Rotaxane.

The macrocycle effect of [2]rotaxane on the highly trans-stereoselective cyclization reaction of N-benzylfumaramide was extensively investigated by various computational methods, including DFT and high-level DLPNO-CCSD(T) methods. Our computational results suggest that the most favorable mechanism of the CsOH-promoted cyclization of the fumaramide into trans-ß-lactam within [2]rotaxane initiates with deprotonation of a N-benzyl group of the interlocked fumaramide substrate by CsOH, followed by the trans-selective C-C bond formation and protonation by one amide functional group of the macrocycle. Our distortion/interaction analysis further shows that the uncommon trans-stereoselective cyclization forming ß-lactam within the rotaxane may be attributed to a higher distortion energy (mainly from the distortion of the twisted cis-fumaramide conformation enforced by the rotaxane). Our systematic study should give deeper mechanistic insight into the reaction mechanism influenced by a supramolecular host.

Asymmetric Synthesis of Vicinal Tetrasubstituted Diamines via Reductive Coupling of Ketimines Templated by Chiral Diborons.

We herein describe the chiral diboron-templated asymmetric homocoupling of aryl alkyl ketimines, providing for the first time a series of chiral vicinal tetrasubstituted diamines with excellent ee values and good to high yields. The powerful and efficient diboron-participated [3,3]-sigmatropic rearrangement is successfully demonstrated by the homocoupling of a variety of ketimines thanks to the rational design and engineering of chiral diborons. Systematic DFT studies suggest that two chiral diborons adopt different conformational assembling strategies to couple the diboron template with ketimine substrates in their tight concerted transition states to ensure the excellent enantioselectivities. The synthetic value of chiral vicinal tetrasubstituted diamines is demonstrated by the asymmetric α-bromination of aliphatic aldehydes by employing a chiral vicinal tetrasubstituted diamine-based organocatalyst.

Quantum Tunneling in Reactions Modulated by External Electric Fields: Reactivity and Selectivity.

Quantum tunneling and external electric fields (EEFs) can promote some reactions. However, the synergetic effect of an EEF on a tunneling-involving reaction and its temperature-dependence is not very clear. In this study, we extensively investigated how EEFs affect three reactions that involve hydrogen- or (ground- and excited-state) carbon-tunneling using reliable DFT, DLPNO-CCSD(T1), and variational transition-state theory methods. Our study revealed that oriented EEFs can significantly reduce the barrier and corresponding barrier width (and vice versa) through more electrostatic stabilization in transition states. These EEF effects enhance the nontunneling and tunneling-involving rates. Such EEF effects also decrease the crossover temperatures and quantum tunneling contribution, albeit with lower and thinner barriers. Moreover, EEFs can modulate and switch on/off the tunneling-driven 1,2-H migration of hydroxycarbenes under cryogenic conditions. Furthermore, our study predicts for the first time that EEF/tunneling synergy can control the chemo- or site-selectivity of one molecule bearing two similar/same reactive sites.

Breaking Conventional Site Selectivity in C-H Bond Activation: Selective sp3 versus sp2 Silylation by a Pincer-Based Pocket.

A deeply ingrained assumption in the conventional understanding and practice of organometallic chemistry is that an unactivated aliphatic C(sp3)-H bond is less reactive than an aromatic C(sp2)-H bond within the same molecule given that they are at positions unbiasedly accessible for activation. Herein, we demonstrate that a pincer-ligated iridium complex catalyzes intramolecular dehydrogenative silylation of the unactivated δ-C(sp3)-H (δ to the Si atom) with exclusive site selectivity over typically more reactive ortho δ-C(sp2)-H bonds. A variety of tertiary hydrosilanes undergo δ-C(sp3)-H silylation to form 5-membered silolanes, including chiral silolanes, which can undergo further oxidation to produce enantiopure ß-aryl-substituted 1,4-diols. Combined computational and experimental studies reveal that the silylation occurs via the Si-H addition to a 14-electron Ir(I) fragment to give an Ir(III) silyl hydride complex, which then activates the C(sp3)-H bond to form a 7-coordinate, 18-electron Ir(V) dihydride silyl intermediate, followed by sequential reductive elimination of H2 and silolane. The unprecedented site selectivity is governed by the distortion energy difference between the rate-determining δ-C(sp3)-H and δ-C(sp2)-H activation, although the activation at sp2 sites is much more favorable than sp3 sites by the interaction energy.

A Mechanistic Study of the Cobalt(I)-Catalyzed Amination of Aryl Halides: Effects of Metal and Ligand.

Transition-metal-catalyzed amination of aryl halides is a useful approach for the synthesis of medicinal compounds, organic functional materials, and agrochemical compounds. A systematic DFT study has been performed to investigate the mechanism of the Co(I)-catalyzed amination of aryl halides by LiN(SiMe3)2 using (PPh3)3CoCl as the precatalyst. Our computational results suggest that the most favorable dissociative concerted C-I activation pathway in a triplet state consists of (a) dissociation of one PPh3 ligand, (b) concerted oxidative addition (OA) of the C-I bond, (c) transmetalation, (d) (optional) dissociation of the second PPh3 ligand, (e) C-N bond-forming reductive elimination (RE), and (f) ligand exchange to regenerate the active species. Comparatively, the associative concerted OA, radical, SH2/SN2, single electron transfer (SET), and σ-bond metathesis pathways should be less favorable due to their higher barriers or unfavorable reaction free energies. The effects of different metals (Rh and Ir) as centers in the catalyst were further examined and found to require higher reaction barriers, due to unfavorable dissociation of their stronger M-PPh3 bonds. These results highlight an advantage of the earth-abundant Co catalysts for the dissociative pathway(s). Overall, our study offers deeper mechanistic insights for the transition-metal-catalyzed amination and guides the design for efficient Co-based catalysts.

Rhodium(I) Carbene-Promoted Enantioselective C-H Functionalization of Simple Unprotected Indoles, Pyrroles and Heteroanalogues: New Mechanistic Insights.

A rhodium(I)-diene catalyzed highly enantioselective C(sp2 )-H functionalization of simple unprotected indoles, pyrroles, and their common analogues such as furans, thiophenes, and benzofurans with arylvinyldiazoesters has been developed for the first time. This transformation features unusual site-selectivity exclusively at the vinyl terminus of arylvinylcarbene and enables a reliable and rapid synthetic protocol to access a distinctive class of diarylmethine-bearing α,ß-unsaturated esters containing a one or two heteroarene-attached tertiary carbon stereocenter in high yields and excellent enantioselectivities under mild reaction conditions. Mechanistic studies and DFT calculations suggest that, compared to the aniline substrate, the more electron-rich indole substrate lowers the C-C addition barrier and alters the rate-determining step to the reductive elimination, leading to different isotope effect.

New Insights and Predictions into Complex Homogeneous Reactions Enabled by Computational Chemistry in Synergy with Experiments: Isotopes and Mechanisms.

Homogeneous catalysis and biocatalysis have been widely applied in synthetic, medicinal, and energy chemistry as well as synthetic biology. Driven by developments of new computational chemistry methods and better computer hardware, computational chemistry has become an essentially indispensable mechanistic "instrument" to help understand structures and decipher reaction mechanisms in catalysis. In addition, synergy between computational and experimental chemistry deepens our mechanistic understanding, which further promotes the rational design of new catalysts. In this Account, we summarize new or deeper mechanistic insights (including isotope, dispersion, and dynamical effects) into several complex homogeneous reactions from our systematic computational studies along with subsequent experimental studies by different groups. Apart from uncovering new mechanisms in some reactions, a few computational predictions (such as excited-state heavy-atom tunneling, steric-controlled enantioswitching, and a new geminal addition mechanism) based on our mechanistic insights were further verified by ensuing experiments.The Zimmerman group developed a photoinduced triplet di-π-methane rearrangement to form cyclopropane derivatives. Recently, our computational study predicted the first excited-state heavy-atom (carbon) quantum tunneling in one triplet di-π-methane rearrangement, in which the reaction rates and 12C/13C kinetic isotope effects (KIEs) can be enhanced by quantum tunneling at low temperatures. This unprecedented excited-state heavy-atom tunneling in a photoinduced reaction has recently been verified by an experimental 12C/13C KIE study by the Singleton group. Such combined computational and experimental studies should open up opportunities to discover more rare excited-state heavy-atom tunneling in other photoinduced reactions. In addition, we found unexpectedly large secondary KIE values in the five-coordinate Fe(III)-catalyzed hetero-Diels-Alder pathway, even with substantial C-C bond formation, due to the non-negligible equilibrium isotope effect (EIE) derived from altered metal coordination. Therefore, these KIE values cannot reliably reflect transition-state structures for the five-coordinate metal pathway. Furthermore, our density functional theory (DFT) quasi-classical molecular dynamics (MD) simulations demonstrated that the coordination mode and/or spin state of the iron metal as well as an electric field can affect the dynamics of this reaction (e.g., the dynamically stepwise process, the entrance/exit reaction channels).Moreover, we unveiled a new reaction mechanism to account for the uncommon Ru(II)-catalyzed geminal-addition semihydrogenation and hydroboration of silyl alkynes. Our proposed key gem-Ru(II)-carbene intermediates derived from double migrations on the same alkyne carbon were verified by crossover experiments. Additionally, our DFT MD simulations suggested that the first hydrogen migration transition-state structures may directly and quickly form the key gem-Ru-carbene structures, thereby "bypassing" the second migration step. Furthermore, our extensive study revealed the origin of the enantioselectivity of the Cu(I)-catalyzed 1,3-dipolar cycloaddition of azomethine ylides with ß-substituted alkenyl bicyclic heteroarenes enabled by dual coordination of both substrates. Such mechanistic insights promoted our computational predictions of the enantioselectivity reversal for the corresponding monocyclic heteroarene substrates and the regiospecific addition to the less reactive internal C═C bond of one diene substrate. These predictions were proven by our experimental collaborators. Finally, our mechanistic insights into a few other reactions are also presented. Overall, we hope that these interactive computational and experimental studies enrich our mechanistic understanding and aid in reaction development.

Structure-property relationships of photofunctional diiridium(II) complexes with tetracationic charge and an unsupported Ir-Ir bond.

In contrast to the extensively studied dirhodium(II) complexes and iridium(III) complexes, neutral or dicationic dinuclear iridium(II) complexes with an unsupported ligand are underdeveloped. Here, a series of tetracationic dinuclear iridium(II) complexes, featuring the unsupported Ir(II)-Ir(II) single bond with long bond distances (2.8942(4)-2.9731(4) Å), are synthesized and structurally characterized. Interestingly, compared to the previous unsupported neutral or dicationic diiridium(II) complexes, our DFT and high-level DLPNO-CCSD(T) results found the largest binding energy in these tetracationic complexes even with the long Ir(II)-Ir(II) bond. Our study further reveals that London dispersion interactions enhance the stability cooperatively and significantly to overcome the strong electrostatic repulsion between two half dicationic metal fragments. This class of complexes also exhibit photoluminescence in solution and solid states, which, to our knowledge, represents the first example of this unsupported dinuclear iridium(II) system. In addition, their photoreactivity involving the generation of iridium(II) radical monomer from homolytic cleavage was also explored. The experimental results of photophysical and photochemical behaviours were also correlated with computational studies.

Multiscale Quantum Refinement Approaches for Metalloproteins.

Biomolecules with metal ion(s) (e.g., metalloproteins) play many important biological roles. However, accurate structural determination of metalloproteins, particularly those containing transition metal ion(s), is challenging due to their complicated electronic structure, complex bonding of metal ions, and high number of conformations in biomolecules. Quantum refinement, which was proposed to combine crystallographic data with computational chemistry methods by several groups, can improve the local structures of some proteins. In this study, a quantum refinement method combining several multiscale computational schemes with experimental (X-ray diffraction) information was developed for metalloproteins. Various quantum refinement approaches using different ONIOM (our own N-layered integrated molecular orbital and molecular mechanics) combinations of quantum mechanics (QM), semiempirical (SE), and molecular mechanics (MM) methods were conducted to assess the performance and reliability on the refined local structure in two metalloproteins. The structures for two (Cu- or Zn-containing) metalloproteins were refined by combining two-layer ONIOM2(QM1/QM2) and ONIOM2(QM/MM) and three-layer ONIOM3(QM1/QM2/MM) schemes with experimental data. The accuracy of the quantum-refined metal binding sites was also examined and compared in these multiscale quantum refinement calculations. ONIOM3(QM/SE/MM) schemes were found to give good results with lower computational costs and were proposed to be a good choice for the multiscale computational scheme for quantum refinement calculations of metal binding site(s) in metalloproteins with high efficiency. Additionally, a two-center ONIOM approach was employed to speed up the quantum refinement calculations for the Zn metalloprotein with two remote active sites/ligands. Moreover, a recent quantum-embedding wavefunction-in-density functional theory (WF-in-DFT) method was also adopted as the high-level method in unprecedented ONIOM2(CCSD-in-B3LYP/MM) and ONIOM3(CCSD-in-B3LYP/SE/MM) calculations, which can be regarded as novel pseudo-three- and pseudo-four-layer ONIOM methods, respectively, to refine the key Zn binding site at the coupled-cluster singles and doubles (CCSD) level. These refined results indicate that multiscale quantum refinement schemes can be used to improve the structural accuracy obtained for local metal binding site(s) in metalloproteins with high efficiency.

ß-Substituted Alkenyl Heteroarenes as Dipolarophiles in the Cu(I)-Catalyzed Asymmetric 1,3-Dipolar Cycloaddition of Azomethine Ylides Empowered by a Dual Activation Strategy: Stereoselectivity and Mechanistic Insight.

The catalytic asymmetric 1,3-dipolar cycloaddition reactions of azomethine ylides with various electron-deficient alkenes provide the most straightforward protocol for the preparation of enantioenriched pyrrolidines in organic synthesis. However, the employment of conjugated alkenyl heteroarenes as dipolarophiles in such protocols to afford a class of particularly important molecules in medicinal chemistry is still a great challenge. Herein, we report that various ß-substituted alkenyl heteroarenes, challenging internal alkene substrates without a strong electron-withdrawing substituent, were successfully employed as dipolarophiles for the first time in the Cu(I)-catalyzed asymmetric 1,3-dipolar cycloaddition of azomethine ylides. This reaction furnishes a large array of multistereogenic heterocycles incorporating both the biologically important pyrrolidine and heteroarene skeletons in good yields with exclusive diastereoselectivity and excellent enantioselectivity. Our extensive density functional theory (DFT) calculations proposed a working model to explain the origin of the stereochemical outcome and elucidated uncommon dual activation/coordination of both the dipole and dipolarophile substrates by the metal, in which a sterically bulky, rigid, and monodentate phosphoramidite ligand with triple-homoaxial chirality plays a pivotal role in providing an effective chiral pocket around the metal center, resulting in high enantioselectivity. The additional coordination of the heteroatom in the dipolarophile substrate to Cu is also critical for the exclusive diastereoselectivity and enhanced reactivity. Our calculations also predicted the reverse and high enantioinduction for the corresponding substrates with monocyclic heteroarenes as well as regiospecific cycloaddition to the less reactive internal C═C bond of one related dipolarophile diene substrate. Such unique steric effect-directed enantioswitching and coordination-directed regioselectivity were verified experimentally.

Regiospecific and Enantioselective Arylvinylcarbene Insertion of a C-H Bond of Aniline Derivatives Enabled by a Rh(I)-Diene Catalyst.

Asymmetric insertion of an arylvinylcarbenoid into the C-H bond for direct enantioselective C(sp2)-H functionalization of aniline derivatives catalyzed by a rhodium(I)-diene complex was developed for the first time. The reaction occurred exclusively at the uncommon vinyl terminus site with excellent E selectivity and enantioselectivities, providing various chiral γ,γ-gem-diarylsubstituted α,ß-unsaturated esters with broad functional group compatibility under simple and mild conditions. It provides a rare example of the asymmetric C-H insertion of arenes with selective vinylogous reactivity. Synthesis applications of this protocol were featured by several versatile product transformations. Systematic DFT calculations were also performed to elucidate the reaction mechanism and origin of the uncommon enantio- and regioselectivity of the Rh(I)-catalyzed C(sp2)-H functionalization reaction. The measured and computed inverse deuterium kinetic isotope effect supports the C-C bond-formation step as the rate-determining step. Attractive interactions between the chiral ligand and substrates were also proposed to control the enantioselectivity.

Enantioselective Hydrogenation of Tetrasubstituted α,ß-Unsaturated Carboxylic Acids Enabled by Cobalt(II) Catalysis: Scope and Mechanistic Insights.

Chiral carboxylic acids are important compounds because of their prevalence in pharmaceuticals, natural products and agrochemicals. Asymmetric hydrogenation of α,ß-unsaturated carboxylic acids has been widely recognized as one of the most efficient synthetic approaches to afford such compounds. Although related asymmetric hydrogenation of di- and trisubstituted unsaturated acids with noble metals is well established, asymmetric hydrogenation of challenging tetrasubstituted α,ß-unsaturated carboxylic acids is rarely reported. We demonstrate enantioselective hydrogenation of cyclic and acyclic tetrasubstituted α,ß-unsaturated carboxylic acids via cobalt(II) catalysis. This protocol showed broad substrate scope and gave chiral carboxylic acids in good yields with excellent enantiocontrol (up to 98 % yield and 99 % ee). Combined experimental and computational mechanistic studies support a CoII catalytic cycle involving migratory insertion and σ-bond metathesis processes. DFT calculations reveal that enantioselectivity may originate from the steric effect between the phenyl groups of the ligand and the substrate.

Water as a Direct Proton Source for Asymmetric Hydroarylation Catalyzed by a Rh(I)-Diene: Access to Nonproteinogenic ß2/γ2/δ2-Amino Acid Derivatives.

A highly enantioselective rhodium-catalyzed intermolecular hydroarylation of α-aminoalkyl acrylates using water as a direct proton source has been realized by employing a chiral bicyclo[3.3.0] diene ligand, allowing efficient access to a broad range of α-aryl-methyl-substituted ß2-, γ2-, and δ2-amino esters with excellent enantioselectivities (up to 98% ee) under exceptionally mild conditions. By utilizing this method, a series of structurally interesting benzo-fused heterocyclic molecules and the corresponding ß2-, γ2-, and δ2-amino acids are facilely constructed.

Ru-Catalyzed Geminal Hydroboration of Silyl Alkynes via a New gem-Addition Mechanism.

While 1,2-addition represents the most common mode of alkyne hydroboration, herein we describe a new 1,1-hydroboration mode. It is the first demonstration of gem-(H,B) addition to an alkyne triple bond. With the superior [CpRu(MeCN)3]PF6 catalyst, a range of silyl alkynes reacted efficiently with HBpin under mild conditions to form various synthetically useful silyl vinyl boronates with complete stereoselectivity and broad functional group compatibility. An extension to germanyl alkynes and the hydrosilylation of alkynyl boronates toward the same type of products were also achieved. Mechanistically, this process features a new pathway featuring gem-(H,B) addition to form the key α-boryl-α-silyl Ru-carbene intermediate followed by silyl migration. It is believed that the orbital interaction between boron and Cß in the coplanar relationship between the boron atom and the ruthenacyclopropene ring preceding boron migration is responsible for the new reactivity. Control experiments and DFT (including molecular dynamics) calculations provided important insights into the mechanism, which excluded the involvement of a metal vinylidene intermediate. This study represents a new step forward not only for alkyne hydroboration but also for other geminal additions of alkynes.

Unusual KIE and dynamics effects in the Fe-catalyzed hetero-Diels-Alder reaction of unactivated aldehydes and dienes.

Hetero-Diels-Alder (HDA) reaction is an important synthetic method for many natural products. An iron(III) catalyst was developed to catalyze the challenging HDA reaction of unactivated aldehydes and dienes with high selectivity. Here we report extensive density-functional theory (DFT) calculations and molecular dynamics simulations that show effects of iron (including its coordinate mode and/or spin state) on the dynamics of this reaction: considerably enhancing dynamically stepwise process, broadening entrance channel and narrowing exit channel from concerted asynchronous transition states. Also, our combined computational and experimental secondary KIE studies reveal unexpectedly large KIE values for the five-coordinate pathway even with considerable C-C bond forming, due to equilibrium isotope effect from the change in the metal coordination. Moreover, steric and electronic effects are computationally shown to dictate the C=O chemoselectivity for an α,ß-unsaturated aldehyde, which is verified experimentally. Our mechanistic study may help design homogeneous, heterogeneous and biological catalysts for this challenging reaction.

Asymmetric synthesis of quaternary α-trifluoromethyl α-amino acids by Ir-catalyzed allylation followed by kinetic resolution.

Facile access to quaternary α-trifluoromethyl α-amino acids has been developed. This sequential reaction involves an Ir-catalyzed asymmetric allylation of α-trifluoromethyl aldimine esters followed by an unprecedented kinetic resolution.

Ru-Catalyzed Migratory Geminal Semihydrogenation of Internal Alkynes to Terminal Olefins.

Semihydrogenation of alkynes to alkenes represents a fundamentally useful transformation. In addition to the well-known cis- and trans-semihydrogenation, herein a geminal semihydrogenation of internal alkynes featuring 1,2-migration is described, which provides new access to the useful terminal vinylsilanes. This process also presents a new mode of reactivity of silyl alkynes. With the proper choice of the cationic [CpRu(MeCN)3]PF6 catalyst and a suitable silyl group, both aryl- and alkyl-substituted silyl alkynes can participate in this highly efficient gem-selective process. Furthermore, dedicated condition optimization also allowed switching of selectivity from gem to trans by using a combination of parameters, including the suitable silyl group, additive, and H2 pressure. A systematic DFT study on the reaction mechanism revealed that the formation of the gem-H2 Ru-carbene might be the key intermediate in both gem- and trans-addition reactions, rather than the Ru-vinylidene intermediate. The DFT results were further supported by carefully designed control experiments. This uncommon gem-addition combined with 1,2-silyl migration in the metal-carbene intermediate should open up a new synthetic avenue for alkyne transformations.