Cai-Yun Geng

Large Equatorial Ligand Effects on C-H Bond Activation by Nonheme Iron(IV)-oxo Complexes

In this article, we present density functional theory (DFT) calculations on the iron(IV)-oxo catalyzed methane C-H activation reactions for complexes in which the Fe(IV)═O core is surrounded by five negatively charged ligands. We found that it follows a hybrid pathway that mixes features of the classical σ- and π-pathways in quintet surfaces. These calculations show that the Fe-O-H arrangement in this hybrid pathway is bent in sharp contrast to the collinear character as observed for the classical quintet σ-pathways before. The calculations have also shown that it is the equatorial ligands that play key roles in tuning the reactivity of Fe(IV)═O complexes. The strong π-donating equatorial ligands employed in the current study cause a weak π(FeO) bond and thereby shift the electronic accepting orbitals (EAO) from the vertically orientated O pz orbital to the horizontally orientated O px. In addition, all the equatorial ligands are small in size and would therefore be expected have small steric effects upon substrate horizontal approaching. Therefore, for the small and strong π-donating equatorial ligands, the collinear Fe-O-H arrangement is not the best choice for the quintet reactivity. This study adds new element to iron(IV)-oxo catalyzed C-H bond activation reactions.

Benchmark Study on Methanol C–H and O–H Bond Activation by Bare [FeIVO]2+

We present a high-level computational study on methanol C-H and O-H bond cleavages by bare [Fe(IV)O](2+), as well as benchmarks of various density functional theory (DFT) methods. We considered direct and concerted hydrogen transfer (DHT and CHT) pathways, respectively. The potential energy surfaces were constructed at the CCSD(T)/def2-TZVPP//B3LYP/def2-TZVP level of theory. Mechanistically, (1) the C-H bond cleavage is dominant and the O-H activation only plays minor role on the PESs; (2) the DHT from methyl should be the most practical channel; and (3) electronic structure analysis demonstrates the proton and electron transfer coupling behavior along the reaction coordinates. The solvent effect is evident and plays distinct roles in regulating the two bond activations in different mechanisms during the catalysis. The effect of optimizing the geometries using different density functionals was also studied, showing that it is not meaningful to discuss which DFT method could give the accurate prediction of the geometries, especially for transition structures. Furthermore, the gold-standard CCSD(T) method was used to benchmark 19 different density functionals with different Hartree-Fock exchange fractions. The results revealed that (i) the structural factor plays a minor role in the single point energy (SPE) calculations; (ii) reaction energy prediction is quite challenging for DFT methods; (iii) the mean absolute deviations (MADs) reflect the problematic description of the DFs when dealing with metal oxidation state change, giving a strong correlation on the HF exchange in the DFs. Knowledge from this study should be of great value for computational chemistry, especially for the de novo design of transition metal catalysts.

A Barrier-Free Atomic Radical-Molecule Reaction: F + Propene

The possible reaction mechanism of atomic radical F with propene is investigated theoretically by a detailed potential energy surface (PES) calculation at the UMP2/6-311++G(d,p) and CCSD(T)/cc-pVTZ (single-point) levels using ab initio quantum chemistry methods and transition-state theory. Various possible reaction paths including addition-isomerization-elimination reactions and direct H-atom abstraction reactions are considered. Among them, the most feasible pathway should be the atomic radical F ((2)F) attacking on the C [Formula: see text] C double bond in propene (CH3CH [Formula: see text] CH2) to form a weakly bound complex I1 with no barrier, followed by atomic radical F addition to the C [Formula: see text] C double bond to form the low-lying intermediate isomer 3 barrierlessly. Starting from intermediate isomer 3, the most competitive reaction pathway is the dissociation of the C2-C3 single bond via transition state TS3-P5, leading to the product P5, CH3 + CHF [Formula: see text] CH2. However, in the direct H-atom abstraction reactions, the atomic radical F picking up the b-allylic hydrogen of propene barrierlessly is the most feasible pathway from thermodynamic consideration. The other reaction pathways on the doublet PES are less competitive because of thermodynamical or kinetic factors. No addition-elimination mechanism exists on the potential energy surface. Because the intermediates and transition states involved in the major pathways are all lower than the reactants in energy, the title reaction is expected to be rapid. Furthermore, on the basis of the analysis of the kinetics of all channels through which the addition and abstraction reactions proceed, we expect that the competitive power of reaction channels may vary with experimental conditions for the title reaction. The present study may be helpful for probing the mechanisms of the title reaction and understanding the halogen chemistry.

Conformational transition pathway in the allosteric process of calcium‐induced recoverin: Molecular dynamics simulations

Recoverin is an important neuronal calcium sensor (NCS) protein, which have been implicated in a wide range of Ca2+ signaling events in neurons and photoreceptors. To characterize the conformational transition of recoverin from the myristoyl sequestered state to the extrusion state, a series of conventional molecular dynamics (CMD) and targeted molecular dynamics (TMD) simulations were performed. The 36.8 ns long CMD and TMD simulations on recoverin revealed a reliably conformational transition pathway, which can be viewed as a sequential two‐stage process. A very important mechanistic conclusion from the present TMD simulations is that the hydrophobic and hydrophilic interactions modulate the allostery cooperatively in the conformational transition pathway. In the first stage, three salt‐bridges broken between Lys‐84 and Gly‐124, between Lys‐5 and Glu‐103 and between Gly‐16 and Lys‐97 are major components to destabilize the structure of state T and trigger the swivel of the N‐ and C‐terminal domains. In the second stage, the rupture of H‐bond Phe‐56‐O…H(O)‐Thr‐21 leads to the two helices of EF‐1 apart from each other, destabilizing the hydrophobic interactions of the myristoyl group with its environment, whereas the making of H‐bond Leu‐108‐O…H(O)‐Ser‐72 helps the interfacial domain maintain its structural integrity during the course of the myristoyl extrusion. The molecular dynamics simulations results are beneficial to understanding the mechanism of how and why NCS proteins make progress in the photo‐signal transduction processes. Further experimental and theoretical studies are still very desirable.

Theoretical Study of the Reaction Mechanism of HCN+ and CH4 of Relevance to Titan's Ion Chemistry

Titan is the largest satellite of Saturn. In its atmosphere, CH4 is the most abundant neutral after nitrogen. In this paper, the complex doublet potential-energy surface related to the reaction between HCN+ and CH4 is investigated at the B3LYP/6-311G(d,p), CCSD(T)/6-311G++(3df,2pd)(single-point), and QCISD/6-311G(d,p) computational levels. A total of seven products are located on the PES. The initial association of HCN+ with CH4 is found to be a prereaction complex 1 (HCNHCH3(+)) without barrier. Starting from 1, the most feasible pathway is the direct H-abstraction process (the internal C-H bond dissociation) leading to the product P1 (HCNH++CH3). By C-C addition, prereaction complex 1 can form intermediate 2 (HNCHCH3(+)) and then lead to the product P2 (CH3CNH++H). The rate-controlling step of this process is only 25.6 kcal/mol. It makes the Path P2 (1) R --> 1 --> TS1/2 --> 2 --> TS2/P2 --> P2 another possible way for the reaction. P3 (HCNCH3(+) + H), P5 (cNCHCH2(+) + H2), and P6 (NCCH3(+) + H2) are exothermic products, but they have higher barriers (more than 40.0 kcal/mol); P4 (H + HCN + CH3(+)) and P7 (H + H2 + HCCNH+) are endothermic products. They should be discovered under different experimental or interstellar conditions. The present study may be helpful for investigating the analogous ion-molecule reaction in Titans atmosphere.

Theoretical elucidation of the rhodium‐catalyzed [4 + 2] annulation reactions

The reaction mechanism of the Rh‐catalyzed [4 + 2] annulation of 4‐alkynals with isocyanates is unraveled using density functional calculations. The reaction mechanisms of the model system and the real substituted system have been investigated and the results are compared. From our theoretical results based on the model and real substituted system, it is shown that (a) the rate‐determining step is the Rh‐H addition to the alkyne, (b) the formation of the cyclopentenone G and glutarimide K represents a severe competition, and (c) the product selectivity should be controlled by the amount of the isocyanates. In addition, it is demonstrated that there exist steric effects in the real substituted system, but missed in model system. Our calculations also show that although the results obtained on the model system could explain the mechanism in principle, the real substituted system could reflect the mechanism more exactly and make the reaction proceed with regioselectivity.