Siwei Bi

Theoretical Investigation on the Isomerization Reaction of 4-Phenyl-hexa-1,5-enyne Catalyzed by Homogeneous Au Catalysts

By carrying out density functional theory calculations, we have performed a detailed mechanism study for the cycloisomerization reaction of 4-phenyl-hexa-1,5-enyne catalyzed by homogeneous gold to better understand the observed different catalytic activity of several catalysts, including (PPh(3))AuBF(4), (PPh(3))AuCl, AuCl(3), and AuCl. In all situations, the reaction is found to involve two major steps: the initial nucleophilic addition of the alkynyl onto the alkene group and the subsequent 1,2-H migration. It is found that the potential energy surface profiles of systems are very different when different catalysts are used. For (PMe(3))AuBF(4)- and (PMe(3))AuCl-mediated systems, the nucleophilic addition is the rate-determining step, and the calculated free energy barriers are 15.2 and 41.9 kcal/mol, respectively. In contrast, for AuCl(3)- and AuCl-mediated systems, the reactions are controlled by the dissociations of catalysts from the product-like intermediates, and the calculated dissociation energies are 18.1 and 21.7 kcal/mol, respectively, which are larger than both the corresponding free energy barriers of the nucleophilic addition and the H-migration processes (8.5 and 7.3 kcal/mol for the AuCl(3)-mediated reaction, and 16.9 and 11.3 kcal/mol for the AuCl-mediated reaction). These results can rationalize the early experimental observations that the reactant conversion rates are 100, 0, and 50% when using (PPh(3))AuBF(4), (PPh(3))AuCl, and AuCl(3) as catalysts, respectively. The present study indicates that both the ligand and counterion of homogeneous Au catalysts importantly influence their catalytic activities, whereas the oxidation state of Au is not a crucial factor controlling the reactivity.

Theoretical study on the magneto-structural correlation in imidazolate-bridged Cu(II) binuclear complexes

A theoretical study on the magneto-structural correlation in binuclear Cu(II) complexes bridged by the imidazolate anion has been performed using the broken-symmetry approach with the framework of density functional theory (DFT). The calculated results show that the variational trends of the magnetic coupling constant J with geometrical parameters are different for two models. The magnetic coupling constant J mainly depends on the Cu–N–C(im) bond angle ϕ and is insensitive to the variation of the Cu–N(im) distance and the dihedral angle α between the bridged imidazolate ring and copper coordination planes. The dependence of J on the angle ϕ in the two models shows that the J values are equal when the Cu–N–C(im) angle ϕ≈128°.

Advances in theoretical study on transition-metal-catalyzed C−H activation

Transition-metal-catalyzed C–H activation represents one of most attractive research fields in modern organic chemistry while theoretical studies have become a popular and effective tool for elucidating mechanism nowadays. The recent achievements in the cross field of the two orientations are reviewed in this article. The first part introduced the advances in theoretical study on transition-metal-catalyzed C–H activation. The elegant work reported mainly in and after 2013, classified according to the mechanisms of C–H activation, were covered. The second part provided an analysis on the distribution of quantum-chemical methods, solvation models and basis sets in the collected theoretical studies.

Hydrothermal–thermal conversion synthesis of hierarchical porous MgO microrods as efficient adsorbents for lead(II) and chromium(VI) removal

High crystallinity magnesium oxide (MgO) microrods with hierarchical porous structure (ranging from micropores to mesopores and macropores) and well-defined rod-like morphology have been successfully synthesized via a flux NaCl and surfactant nonyl phenol polyoxyethylene ether (NP-9) directed thermal decomposition of the hydrothermally derived magnesium oxalate dihydrate (MgC2O4·2H2O) microrods. The successive and synergistic effect of NaCl and NP-9 assisted the thermal conversion and promoted the final formation of the well-defined porous MgO microrods with a specific surface area of 50.2 m2 g−1 and well preserved rod-like morphology of the MgC2O4·2H2O precursor. The as-obtained porous MgO microrods were employed as efficient adsorbents for removal of heavy metal ions such as Pb(II) and Cr(VI) from aqueous solutions, and the removal efficiency of Pb(II) (original concentration: 50.0 mg L−1) and Cr(VI) (original concentration: 1.0 mg L−1) was up to 99.5% and 55.6%, respectively. Such well-defined MgO microrods with hierarchical porous structure can also serve as promising candidates for catalyst supports and even as a catalyst themselves in addition to their present waste water treatment applications in various fields.

Insights into the mechanism of the reaction between tetrachloro-p- benzoquinone and hydrogen peroxide and their implications in the catalytic role of water molecules in producing the hydroxyl radial

Detailed mechanisms for the formation of hydroxyl or alkoxyl radicals in the reactions between tetrachloro-p-benzoquinone (TCBQ) and organic hydroperoxides are crucial for better understanding the potential carcinogenicity of polyhalogenated quinones. Herein, the mechanism of the reaction between TCBQ and H2O2 has been systematically investigated at the B3LYP/6-311++G** level of theory in the presence of different numbers of water molecules. We report that the whole reaction can easily take place with the assistance of explicit water molecules. Namely, an initial intermediate is formed first. After that, a nucleophilic attack of H2O2 onto TCBQ occurs, which results in the formation of a second intermediate that contains an OOH group. Subsequently, this second intermediate decomposes homolytically through cleavage of the O-O bond to produce a hydroxyl radical. Energy analyses suggest that the nucleophilic attack is the rate-determining step in the whole reaction. The participation of explicit water molecules promotes the reaction significantly, which can be used to explain the experimental phenomena. In addition, the effects of F, Br, and CH3 substituents on this reaction have also been studied.

Molecular dynamics simulations of the coenzyme induced conformational changes of Mycobacterium tuberculosis L-alanine dehydrogenase

Mycobacterium tuberculosis L-alanine dehydrogenase (L-MtAlaDH) catalyzes the NADH-dependent reversible oxidative deamination of L-alanine to pyruvate and ammonia. L-MtAlaDH has been proposed to be a potential target in the treatment of tuberculosis. Based on the crystal structures of this enzyme, molecular dynamics simulations were performed to investigate the conformational changes of L-MtAlaDH induced by coenzyme NADH. The results show that the presence of NADH in the binding domain restricts the motions and conformational distributions of L-MtAlaDH. There are two loops (residues 94-99 and 238-251) playing important roles for the binding of NADH, while another loop (residues 267-293) is responsible for the binding of substrate. The opening/closing and twisting motions of two domains are closely related to the conformational changes of L-MtAlaDH induced by NADH.

Theoretical studies on the electron capture properties of the H2SO4⋯HOO˙ complex and its implications as an alternative source of HOOH

To better understand the potential role of sulfuric acid aerosols in the atmosphere, the electron capture properties of the H(2)SO(4)...HOO˙ complex have been systematically investigated by employing the MP2 and B3LYP methods in combination with the atoms in molecules (AIM) theory, energy decomposition analysis (EDA), and ab initio molecular dynamics. It was found that the electron capture process is a favorable reaction thermodynamically and kinetically. The excess electron can be captured by the HOO˙ fragment initially, and then the proton of the H(2)SO(4) fragment associated with the intermolecular H-bonds is transferred to the HOO˙ fragment without any activation barriers, resulting in the formation of the HOOH species directly. Therefore, the electron capture process of the H(2)SO(4)...HOO˙ complex provides an alternative source of HOOH in the atmosphere. The nature of the coupling interactions in the electron capture products are clarified, and the most stable anionic complex is also determined. Additionally, the influences of the adjacent water molecules on the electron capture properties are investigated, as well as the distinct IR features of the most stable electron capture product.

Coupling Interactions between Sulfurous Acid and the Hydroperoxyl Radical

Radical-molecule complexes associated with the hydroperoxyl radical (HOO) play an important role in atmospheric chemistry. Herein, the nature of the coupling interactions between sulfurous acid (H(2)SO(3)) and the HOO radical is systematically investigated at the B3LYP/6-311++G(3df,3pd) level of theory in combination with the atoms in molecules (AIM) theory, the natural bond orbital (NBO) method, and energy decomposition analyses (EDA). Eight stable stationary points possessing double H-bonding features were located on the H(2)SO(3)...HOO potential energy surface. The largest binding energies of -12.27 and -11.72 kcal mol(-1) are observed for the two most stable complexes, where both of them possess strong double intermolecular H-bonds of partially covalence. Moreover, the characteristics of the IR spectra for the two most stable complexes are discussed to provide some help for their possible experimental identification.

A Ligand-Dissociation-Involved Mechanism in Amide Formation of Monofluoroacylboronates with Hydroxylamines.

Acylborons, as a growing class of boron reagents, were successfully applied to amide ligation and showed potential in chemoselective bioconjugation reactions in recent years. In this manuscript, a density functional theory (DFT) study was performed to investigate the mechanism of the amide formation between monofluoroacylboronates and hydroxylamines. An updated pathway was clarified herein, including water-assisted hemiaminal formation, pyridine ligand dissociation, elimination via a six-membered-ring transition state, and water-assisted tautomerization. The proposed mechanism was further examined by applying it to investigate the activation barriers of other monofluoroacylboronates, and the related calculations well reproduced the experimentally reported relative reactivities. On the basis of these results, we found that the ortho substitution of the pyridine ligand destabilizes the acylboron substrates and the hemiaminal intermediates by steric effects and thus lowers the energy demand of the ligand dissociation and elimination steps. By contrast, the para substitution of the pyridine ligand with an electron-donating group enhances the coordination of the ligand by electronic effects, which is a disadvantage to the ligand dissociation and elimination steps. The ligand bearing a rigid linkage blocks the rotation of the pyridine ligand and makes ligand dissociation difficult.

Strong chemisorption of CO on M@Bn− (M = Co, Ir, Rh, Ru, Ta, Nb, n = 8–10) clusters: an implication for wheel boron clusters as CO gas detectors

In this study, the adsorption behavior of carbon monoxide (CO) gas molecules on anionic M@Bn− (M = Co, Ir, Rh, Ru, Ta, Nb, n = 8–10) clusters has been systematically investigated by employing density functional theory (DFT). It was found that CO adsorption on boron clusters proceeds spontaneously and easily, accompanied with a dramatic structural deformation for the corresponding M@Bn− clusters. Large adsorption energies ranging from −22.82 to −27.38 kcal mol−1 have been observed for CO on boron clusters. The kinetic stabilities of the formed complexes have been verified by ab initio molecular dynamics. The IR spectra and adiabatic detachment energy of the M@Bn− clusters have been discussed before and after CO adsorption. In addition, the adsorption behavior of the other small gas molecules, such as CO2, N2, CH4, H2O, and O2, have also been explored. The potential applications of these wheel boron M@Bn− clusters in the detection of CO gas have been proposed for the first time.