Ji-Lai Li

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.

Mechanism of benzene hydroxylation by high-valent bare Fe(IV)=O2+: explicit electronic structure analysis.

The conversion of benzene to phenol by high-valent bare FeO(2+) was comprehensively explored using a density functional theory method. The conductor-like screen model (COSMO) was used to mimic the role of solvent effect with acetonitrile chosen as the solvent. Two radical mechanisms and one oxygen insertion mechanism were tested for this conversion. The first radical mechanism can also be named as the concerted mechanism in which the hydrogen-atom abstraction process is accomplished via a four-centered transition state. The second radical mechanism is initiated by a direct hydrogen-atom abstraction with a collinear C-H-O transition structure. It is actually the same as the well-accepted rebound mechanism for the C-H bond activation by heme and nonheme iron-oxo catalysts. The third is an oxygen insertion mechanism which is essentially an aromatic electrophilic attack leading to an arenium σ-complex intermediate. The formation of a precomplex with an η(4) coordinate environment in the first radical mechanism is energetically more favorable. However, the relatively lower activation energy barrier of the oxygen insertion mechanism compared to the radical ones makes it highly competitive if the Fe=O(2+) collides with benzene in the proper orientation. The detailed potential energy surfaces also indicate that the second radical mechanism, i.e., the benzene C-H bond activation through the rebound mechanism, is less favorable. This thorough theoretical study, especially the electronic structure analysis, may offer very important clues for understanding and studying C-H bond activation by iron-based catalysts and enzymatic reactions in protein active pockets.

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.