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.

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 CpTi(III)Cl leading to a Ti(IV)-bound β-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.

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

The macrocycle effect of [2]rotaxane on the highly -stereoselective cyclization reaction of -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 -lactam within [2]rotaxane initiates with deprotonation of a -benzyl group of the interlocked fumaramide substrate by CsOH, followed by the -selective C-C bond formation and protonation by one amide functional group of the macrocycle. Our distortion/interaction analysis further shows that the uncommon -stereoselective cyclization forming β-lactam within the rotaxane may be attributed to a higher distortion energy (mainly from the distortion of the twisted fumaramide conformation enforced by the rotaxane).

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.

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.

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.

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.

Breaking Conventional Site Selectivity in C-H Bond Activation: Selective sp versus sp 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(sp)-H bond is less reactive than an aromatic C(sp)-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(sp)-H (δ to the Si atom) with exclusive site selectivity over typically more reactive δ-C(sp)-H bonds. A variety of tertiary hydrosilanes undergo δ-C(sp)-H silylation to form 5-membered silolanes, including chiral silolanes, which can undergo further oxidation to produce enantiopure β-aryl-substituted 1,4-diols.

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(SiMe) using (PPh)CoCl 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 PPh ligand, (b) concerted oxidative addition (OA) of the C-I bond, (c) transmetalation, (d) (optional) dissociation of the second PPh ligand, (e) C-N bond-forming reductive elimination (RE), and (f) ligand exchange to regenerate the active species.

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(sp )-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,β-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.

Multiscale Quantum Refinement Approaches for Metalloproteins.

Biomolecules with metal ion(s) (e.g., metalloproteins) play many important biological roles.

β-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 β-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.

Enantioselective Hydrogenation of Tetrasubstituted α,β-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,β-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,β-unsaturated carboxylic acids is rarely reported.

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(sp)-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--diarylsubstituted α,β-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.

Water as a Direct Proton Source for Asymmetric Hydroarylation Catalyzed by a Rh(I)-Diene: Access to Nonproteinogenic β/γ/δ-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 β-, γ-, and δ-amino esters with excellent enantioselectivities (up to 98% ee) under exceptionally mild conditions.

Ru-Catalyzed Geminal Hydroboration of Silyl Alkynes via a New -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 -(H,B) addition to an alkyne triple bond. With the superior [CpRu(MeCN)]PF 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.

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.

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 - and -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.

Colorimetric Calcium Probe with Comparison to an Ion-Selective Optode.

Design strategies for small molecular probes lay the foundation of numerous synthetic chemosensors. A water-soluble colorimetric calcium molecular probe inspired by the ionophore-based ion-selective optode is presented here with a tunable detection range (around micromolar at pH 7). The binding of Ca resulted in the deprotonation of the probe and thus a significant spectral change, mimicking the ion-exchange process in ion-selective optodes.

Enantioselective Rhodium-Catalyzed Cycloisomerization of 1,6-Allenynes to access 5/6-Fused Bicycle[4.3.0]nonadienes.

Transition-metal-catalyzed cycloisomerization of 1,n-allenynes represents a powerful synthetic tool to rapidly assemble complex polycyclic skeletons from simple linear substrates. Nevertheless, there are no reports of the asymmetric version of these reactions. Moreover, most of these reactions proceed through a 6-endo-dig cyclization pathway, which preferentially delivers the distal product (via 5/5 rhodacyclic intermediate) rather than the proximal one (via 6/5 rhodacyclic intermediate).

Asymmetric Total Synthesis of Cerorubenic Acid-III.

The first asymmetric total synthesis of the highly strained compound cerorubenic acid-III is reported. A type II intramolecular [5 + 2] cycloaddition allowed efficient and diastereoselective construction of the synthetically challenging bicyclo[4.4.

Novel Molecular Doping Mechanism for n-Doping of SnO via Triphenylphosphine Oxide and Its Effect on Perovskite Solar Cells.

Molecular doping of inorganic semiconductors is a rising topic in the field of organic/inorganic hybrid electronics. However, it is difficult to find dopant molecules which simultaneously exhibit strong reducibility and stability in ambient atmosphere, which are needed for n-type doping of oxide semiconductors. Herein, successful n-type doping of SnO is demonstrated by a simple, air-robust, and cost-effective triphenylphosphine oxide molecule.

Kinetic Resolution of Alkylidene Norcamphors via a Ligand-Controlled Umpolung-Type 1,3-Dipolar Cycloaddition.

Development of a general catalytic and highly efficient method utilizing readily available precursors for the regio- and stereoselective construction of bioactive natural-product-inspired spiro architectures remains a formidable challenge in chemical research. Transition metal-catalyzed asymmetric 1,3-dipolar cycloaddition of azomethine ylides produces numerous N-heterocycles, but reaction control with the regioselectivity opposite to the conventional fashion has rarely been demonstrated. Herein, we report a unique ligand-controlled Cu(I)-catalyzed umpolung-type 1,3-dipolar cycloaddition of azomethine ylide to realize efficient kinetic resolution of racemic alkylidene norcamphors with the concomitant construction of previously inaccessible spiro N-heterocycles with high levels of regio- and stereoselectivity.