A Computational Mechanistic Analysis of Iridium-Catalyzed C(sp3)–H Borylation Reveals a One-Stone–Two-Birds Strategy to Enhance Catalytic Activity

The Difference in Ir-Catalyzed C(sp2)-H and C(sp3)-H Bond Activation Assisted by a Directing Group: Cyclometalation via Cis- or Trans-Chelation?

Iridium-catalyzed C-H borylation of aromatic and aliphatic hydrocarbons assisted by a directing group was theoretically investigated. Density functional theory (DFT) calculations revealed both Ir-catalyzed C(sp2)-H and C(sp3)-H borylations via an IrIII/IrV catalytic cycle, where the tetra-coordinated (C, N)IrIII(Bpin)2 complex with two vacant sites is an active species. Dramatically, the orientation of cyclometalation for C(sp2)-H bond activation assisted by a directing group is different from the C(sp3)-H one. The activation energy (ΔG°‡ = 28.5 kcal mol-1) of the C(sp2)-H bond via trans-chelation to form cyclometalation is lower than that (41.4 kcal mol-1) via cis-chelation. In contrast, the ΔG°‡ (26.6 kcal mol-1) of the C(sp3)-H bond via cis-chelation to form cyclometalation is lower than that (34.3 kcal mol-1) via trans-chelation. In addition, the rate-determining step of Ir-catalyzed C(sp2)-H borylation is oxidative addition of the C(sp2)-H bond, while that of C(sp3)-H analogues is hydride migration. Such differences arise from not only the differences in the steric hindrance of the C(sp2) and secondary C(sp3) atoms but also the differences in the trans effect and steric effect of the two vacant sites of active species. These findings were expected to facilitate further studies on the design and synthesis of innovative ligands for Ir-catalyzed C-H borylation.

A-Frame-Templated High-Coordinate Platinum(IV) cis-Bis(boryl) Complexes

The addition of Et2O·BF3 or Me2S·BCl3 to the BNBN-cumulene-bridged Pt(II) A-frame complexes [(μ-1,1-BNBN(TMS)2)(μ-dmpm)2Pt2X2] (TMS = SiMe3, dmpm = CH2(PMe2)2, X = Br 1Br, I 1I) resulted in the oxidative addition of one B-F or B-Cl bond, respectively, to the internal BN bond of the bridging, iminoborane-like B-N≡B-N moiety, and coordination of one Pt(II) center to the resulting adjacent BF2 (complex 2Br-F) or BCl2 (complexes 2Br-Cl and 2I-Cl) moiety, respectively. X-ray crystallographic and multinuclear NMR-spectroscopic data show that the Pt→BF2 interaction in 2Br-F is very weak and merely electrostatic, while the Pt→BCl2 interaction in 2Br-Cl and 2I-Cl is a stronger donor-acceptor bond. In contrast, the reaction of Me2S·BBr3 with 1Br yielded a ca. 3:2 mixture of the analogous B-Br addition product to the iminoborane, 2Br-Br, and the product of a subsequent oxidative addition of one B-Br bond of the chelating BBr2 moiety to the adjacent platinum center, the mixed-valence boranediyl-bridged, Pt(II)-Pt(IV)-bromoboryl complex 3-Br5. The analogous reactions of Me2S·BI3 with 1Br and Me2S·BBr3 with 1I yielded complex product mixtures of Pt(II)-Pt(II)-borane (2Br-I and 2I-Br, respectively) and Pt(II)-Pt(IV)-boryl complexes (3-BrnI5-n, n = 1-3) analogous to 2X-Y and 3-Br5, respectively, the proportion of the latter increasing with the proportion of iodide in the precursor mixture. Both multinuclear NMR-spectroscopic and X-ray crystallographic data show evidence of complex and extensive inter- and intramolecular bromide-iodide exchanges between the soft, iodide-affine platinum centers and the harder, more bromide-affine boron centers. A clue to the mechanism of these halide exchanges is provided by the reactions of BBr2Ar (Ar = 2,4,6-Me3C6H2 (Mes), 2,3,5,6-Me4C6H (Dur)) with 1Br, which yielded the cationic Pt(II)-Pt(II)-borenium analogues of 2Br-Br, the complexes 4Br-Ar, generated by the sterics-induced displacement of the bromide substituent from the chelating Pt→BBrAr moiety, and displaying a rare metal→borenium donor-acceptor bond.

Efficient Method for Numerical Calculations of Molecular Vibrational Frequencies by Exploiting Sparseness of Hessian Matrix

Molecular vibrational frequency analysis plays an important role in theoretical and computational chemistry. However, in many cases, the analytical frequencies are unavailable, whereas frequency calculations using conventional numerical methods are very expensive. In this work, we propose an efficient method to numerically calculate the frequencies. Our main strategies are to exploit the sparseness of the Hessian matrix and to construct the N-fold two-variable potential energy surfaces to fit the parabola parameters, which are later used for the construction of Hessian matrices. A set of benchmark calculations is performed for typical molecules of different sizes and complexities using the proposed method. The obtained frequencies are compared to those calculated with the analytical methods and conventional numerical methods. It is shown that the results yielded with the new method are in very good agreement with corresponding accurate values (with a maximum error of ∼20 cm-1), while the required computation resource is largely reduced compared to that required by conventional numerical methods. For medium-sized molecules, the calculational scaling is lowered to O(N1.6) (this work) from that of O(N2) (conventional numerical methods). For even larger molecules, more computational savings can be achieved, and the scaling is estimated to be quasilinear with respect to the molecular size.

DFT calculations in solution systems: solvation energy, dispersion energy and entropy

DFT calculations of reaction mechanisms in solution have always been a hot topic, especially for transition-metal-catalyzed reactions. The calculation of solvation energy is performed using either the polarizable continuum model (PCM) or the universal solvation model SMD. The PCM calculation is very sensitive to the choice of atomic radii to form a cavity, where the self-consistent isodensity PCM (SCI-PCM) has been recognized as the best choice and our IDSCRF radii can provide a similar cavity. Moving from a gas-phase case to a solution case, dispersion energy and entropy should be carefully treated. The solvent-solute dispersion is also important in solution systems, and it should be calculated together with the solute dispersion. Only half of the solvent-solute dispersion energy from the PCM calculation belongs to the solute molecules to maintain a thermal equilibrium between a solute molecule and its cavity, similar to the treatment of electrostatic energy. Relative solute dispersion energy should also be shared equally with the newly formed cavity. The entropy change from a gas phase to a liquid phase is quite large, but the modern quantum chemistry programs can only calculate the gas-phase translational entropy based on the idea-gas equation. In this review, we will provide an operable method to calculate the solution translational entropy, which has been coded in our THERMO program.

Identifying molecular structural features by pattern recognition methods

Identification of molecular structural features is a central part of computational chemistry. It would be beneficial if pattern recognition techniques could be incorporated to facilitate the identification. Currently, the quantification of the structural dissimilarity is mainly carried out by root-mean-square-deviation (RMSD) calculations such as in molecular dynamics simulations. However, the RMSD calculation underperforms for large molecules, showing the so-called "curse of dimensionality" problem. Also, it requires consistent ordering of atoms in two comparing structures, which needs nontrivial effort to fulfill. In this work, we propose to take advantage of the point cloud recognition using convex hulls as the basis to recognize molecular structural features. Two advantages of the method can be highlighted. First, the dimension of the input data structure is largely reduced from the number of atoms of molecules to the number of atoms of convex hulls. Therefore, the dimensionality curse problem is avoided, and the atom ordering process is saved. Second, the construction of convex hulls can be used to define new molecular descriptors, such as the contact area of molecular interactions. These new molecular descriptors have different properties from existing ones, therefore they are expected to exhibit different behaviors for certain machine learning studies. Several illustrative applications have been carried out, which provide promising results for structure-activity studies.

Iridium-Catalyzed C(sp3 )-H Borylation Using Silyl-Bipyridine Pincer Ligands

New ligands for the iridium-catalyzed C(sp³ )-H borylation of aliphatic compounds were established. In sharp contrast to 6-methyl-2,2'-bipyridine and 6-isobutyl-2,2'-bipyridine, 2,2'-bipyridine and 1,10-phenanthroline derivatives bearing a hydrosilylmethyl group (which would give a thermally stable NNSi pincer complex) served as suitable ligands for the reaction. Among them, a phenanthroline-based NNSi pincer ligand was shown to be an excellent ligand, and various aliphatic compounds were efficiently converted to the corresponding borylated products using the Ir/NNSi pincer catalyst system. The NNSi pincer ligand showed unique selectivity and enabled the iridium-catalyzed C(sp³ )-H borylation using pinacolborane [H-B(pin)] instead of B₂ (pin)₂ . The formation of an iridium complex bearing a quinoline-based NNSi pincer ligand from [IrCl(cod)]₂ was observed, and the catalytic activity of the complex was demonstrated.

Mechanism and Origins of Enantioselectivity of Cobalt-Catalyzed Intermolecular Hydroarylation/Cyclization of 1,6-Enynes with N-Pyridylindoles

Density functional theory calculations were performed to investigate the cobalt-catalyzed intermolecular hydroarylation/cyclization of 1,6-enynes with N-pyridylindoles. The computations reveal that the reaction begins with the oxidative cyclization of 1,6-enyne to afford the five-membered cobaltacycle, from which the metal-assisted σ-bond metathesis/C-C reductive elimination led to the final hydroarylation/cyclization product. The initial oxidative cyclization constitutes the rate-determining step of the overall reaction. The steric repulsion and π···π interaction were found to play a crucial role in dictating the experimentally observed enantioselectivity.

Rhodium Indenyl NHC and Fluorenyl-Tethered NHC Half-Sandwich Complexes: Synthesis, Structures and Applications in the Catalytic C-H Borylation of Arenes and Alkanes

Indenyl (Ind) rhodium N-heterocyclic carbene (NHC) complexes [Rh(η5 -Ind)(NHC)(L)] were synthesised for 1,3-bis(2,6-diisopropylphenyl)-4,5-dihydroimidazol-2-ylidene (SIPr) with L=C2 H4 (1), CO (2 a) and cyclooctene (COE; 3), for 1,3-bis(2,4,6-trimethylphenyl)-4,5-dihydroimidazol-2-ylidene (SIMes) with L=CO (2 b) and COE (4), and 1,3-bis(2,4,6-trimethylphenyl)imidazol-2-ylidene (IMes) with L=CO (2 c) and COE (5). Reaction of SIPr with [Rh(Cp*)(C2 H4 )2 ] did not give the desired SIPr complex, thus demonstrating the "indenyl effect" in the synthesis of 1. Oxidative addition of HSi(OEt)3 to 3 proceeded under mild conditions to give the Rh silyl hydride complex [Rh(Ind){Si(OEt)3 }(H)(SIPr)] (6) with loss of COE. Tethered-fluorenyl NHC rhodium complexes [Rh{(η5 -C13 H8 )C2 H4 N(C)C2 Hx NR}(L)] (x=4, R=Dipp, L=C2 H4 : 11; L=COE: 12; L=CO: 13; R=Mes, L=COE: 14; L=CO: 15; x=2, R=Me, L=COE: 16; L=CO: 17) were synthesised in low yields (5-31 %) in comparison to good yields for the monodentate complexes (49-79 %). Compounds 3 and 1, which contain labile alkene ligands, were successful catalysts for the catalytic borylation of benzene with B2 pin2 (Bpin=pinacolboronate, 97 and 93 % PhBpin respectively with 5 mol % catalyst, 24 h, 80 °C), with SIPr giving a more active catalyst than SIMes or IMes. Fluorenyl-tethered NHC complexes were much less active as borylation catalysts, and the carbonyl complexes were inactive. The borylation of toluene, biphenyl, anisole and diphenyl ether proceeded to give meta substitutions as the major product, with smaller amounts of para substitution and almost no ortho product. The borylation of octane and decane with B2 pin2 at 120 and 140 °C, respectively, was monitored by 11 B NMR spectroscopy, which showed high conversions into octyl and decylBpin over 4-7 days, thus demonstrating catalysed sp3 C-H borylation with new piano stool rhodium indenyl complexes. Irradiation of the monodentate complexes with 400 or 420 nm light confirmed the ready dissociation of C2 H4 and COE ligands, whereas CO complexes were inert. Evidence for C-H bond activation in the alkyl groups of the NHC ligands was obtained.

Cyclometallated complexes as catalysts for C-H activation and functionalization

The development of novel catalysts for C-H activation reactions with increased reactivity and improved selectivities has been attracting significant interest over the last two decades. More recently, promising results have been developed using tridentate pincer ligands, which form a stable C-M bond. Furthermore, based on mechanistic studies, the unique catalytic role of some metallacyclic intermediate species has been revealed. These experimental observations have subsequently translated into the rational design of advanced C-H activation catalysts in both Ru- and Ir-based systems. Recent breakthroughs in the field of C-H activation catalysed by metallacyclic intermediates are thus discussed.

Molecular structure recognition by blob detection

Molecular structure recognition is fundamental in computational chemistry. The most common approach is to calculate the root mean square deviation (RMSD) between two sets of molecular coordinates. However, this method does not perform well for large molecules. In this work, a new method is proposed for structure comparison. Blob detection is used for recognizing structural features. Fragmentation of molecules is proposed as the pre-treatment. Mapping between blobs and atoms is developed as the post-treatment. A set of key parameters important for blob detections are determined. The dissimilarity is quantified by calculating the Euclidean metric of the blob vectors. The overall algorithm is found to be accurate to distinguish structural dissimilarity. The method has potential to be combined with other pattern recognition techniques for new chemistry discoveries.

Molecular structure recognition is fundamental in computational chemistry.

Theoretical Design of a Catalyst with Both High Activity and Selectivity in C-H Borylation

Improving both the activity and selectivity of the C-H borylation reaction is currently a hot research topic but also a challenge. In this regard, we suggest a multistrategy combining directing group, coordination unsaturated metal center, and cationic character. Based on Reek's catalyst, we designed a new unsaturated cationic catalyst (1) featuring a directing group for C-H borylation. The calculated free energy barrier of C-H activation is only 7.2 kcal/mol, indicating that the cationic catalyst has higher activity than the original neutral catalyst in this process. Moreover, the comparison suggests that the ortho-C-H borylation pathway is more favorable than the meta and para pathways. The catalyst deconstructions are further performed and prove that the ortho-selectivity is attributed to hydrogen-bonding interactions between the directing group and the substrate, although the ortho site is sterically and electronically unfavorable.