Lai-Cai Li

Semi-empirical quantum chemical study on structure–activity relationship in monocyclic-β-lactam antibiotics

Abstract β-Lactam antibiotics have been highly emphasized in theoretical research and practical synthesis for a long time. They have been the main drugs used in the clinical treatment of bacterial diseases. In this paper, PM3 semi-empirical quantum chemical method has been employed to optimize the molecular geometry, and quantitative structure–activity relationship in 23 kinds of monocyclic-β-lactam antibiotics systematically. Moreover, the structure–activity model of monocyclic-β-lactam antibiotics was studied.

Theoretical study on the ring‐opening isomerization reaction mechanism of the ring isomers of N8H8

Ring‐opening isomerization from ring‐shaped isomers to chain‐shaped isomers of N8H8 has been studied by a density function B3LYP method at 6‐311++G** level. 20 ring‐shaped isomers have been found to be able to transform into chain‐shaped isomers, with 20 possible transition states got by ring‐opening structure optimization. Furthermore, the ring‐openings have been found in the longer NN single bond by analyzing the length change of NN bond of ring‐shaped isomers in ring‐opening processes. In addition, with the activation energies in ring‐opening processes, the differences of the activation energies in isomerization between the isomers have been found according to the classification of rings. The activation energies in ring‐opening isomerization of six‐membered ring‐shaped isomers are higher than that of the four‐membered ring‐shaped isomers. It indicates that six‐membered ring‐shaped isomers difficult in ring‐opening in the isomerization are the steadiest ring‐shaped isomers of N8H8 while four‐membered ring‐shaped isomers easy in ring‐opening are the most unstable.

THEORETICAL STUDIES ON THE REACTION MECHANISM OF HNCS WITH CH2CH RADICAL

The reaction mechanisms of HNCS with CH2CH radical have been investigated by density functional theory (DFT). The geometries and harmonic frequencies of the reactants, intermediates, transition states and products have been calculated at the B3LYP/6-311++G(d,p) level. The results show that the reaction is very complicated. Nine possible reaction pathways were identified. The results show that the most feasible reaction channel is the hydrogen-transfer pathway CH2CH + HNCS → IMA1 → TSA1 → CH2CHH + NCS. The pathway VIC C-S addition channel (CH2CH + HNCS → TSD5 → IMD4 → TSD9 → CH2CHS + CNH) can also occur easily. Ethene and radical NCS is the main product of the studied reaction, and product P8 (CH2CHS and CNH) may also be observed. Compared with our previous study on the reaction HNCS + CH2CH, the present reaction is easier to proceed.

Investigating the mechanism of the selective hydrogenation reaction of cinnamaldehyde catalyzed by Ptn clusters.

AbstractCinnamaldehyde (CAL) belongs to the group of aromatic α,β-unsaturated aldehydes; the selective hydrogenation of CAL plays an important role in the fine chemical and pharmaceutical industries. Using Ptn clusters as catalytic models, we studied the selective hydrogenation reaction mechanism for CAL catalyzed by Ptn (n = 6, 10, 14, 18) clusters by means of B3LYP in density functional theory at the 6-31+ G(d) level (the LanL2DZ extra basis set was used for the Pt atom). The rationality of the transition state was proved by vibration frequency analysis and intrinsic reaction coordinate computation. Moreover, atoms in molecules theory and nature bond orbital theory were applied to discuss the interaction among orbitals and the bonding characteristics. The results indicate that three kinds of products, namely 3-phenylpropyl aldehyde, 3-phenyl allyl alcohol and cinnamyl alcohol, are produced in the selective hydrogenation reaction catalyzed by Ptn clusters; each pathway possesses two reaction channels. Ptn clusters are more likely to catalyze the activation and hydrogenation of the C = O bond in CAL molecules, eventually producing cinnamic alcohol, which proves that Ptn clusters have a strong reaction selectivity to catalyze CAL. The reaction selectivity of the catalyzer cluster is closely related to the size of the Ptn cluster, with Pt14 clusters having the greatest reaction selectivity. Graphical AbstractThe reaction mechanism for the selective hydrogenation reaction ofcinnamaldehyde catalyzed by Ptn clusters was studied by densityfunctional theory. The reactionselectivity of cluster catalyzer was concluded to be closely related to the size of Ptn clusters, with Pt14 clusters having the greatest reaction selectivity

Investigation on the photodriven catalytic coupling reaction mechanism of p-aminothiophenol on the silver cluster

The catalytic coupling reaction mechanism for the transformation from p-aminothiophenol (PATP) to 4,4′-dimercaptoazobenzene (4,4′-DMAB) on silver cluster was studied by the density functional theory. All the reactants, intermediates, transition states and products were optimized with B3LYP method at 6-311+G (d, p) basis set (the LanL2DZ basis set was used for Ag atom). Transition states and intermediates have been confirmed by the corresponding vibration analysis and intrinsic reactions coordinate (IRC). In addition, nature bond orbital (NBO) and atoms in molecules (AIM) theories have been used to analyze orbital interactions and bond natures. Consistent with the conclusions reported in the literature, the core of obtaining the production of azobenzene according to the coupling reaction of PATP absorbed on Ag5 clusters is the elimination of two H atoms. Meanwhile, we find that the effect of illumination in that reaction matters a lot. We also found in PATP molecular that the synergistic catalytic effect of S end absorbed on the catalyzer draws dramatically evident under no illumination conditions, while it draws less obvious under light. According to the papers conclusion, PATP absorbed on the surface of Ag5 tends to generate azobenzene easily.

Density Functional Theory Study on Interaction between Catechin and Thymine

The interacting patterns and mechanism of the catechin and thymine have been investigated with the density functional theory Beckes three-parameter nonlocal exchange functional and the Lee, Yang, and Parr nonlocal correlation functional (B3LYP) method by 6−31+G* basis set. Thirteen stable structures for the catechin-thymine complexes have been found which form two hydrogen bonds at least. The vibrational frequencies are also studied at the same level to analyze these complexes. The results indicated that catechin interacted with thymine by three different hydrogen bonds as N—H···O, C—H···O, O—H···O and the complexes are mainly stabilized by the hydrogen bonding interactions. Theories of atoms in molecules and natural bond orbital have been adopted to investigate the hydrogen bonds involved in all systems. The interaction energies of all complexes have been corrected for basis set superposition error, which are from −18.15 kJ/mol to −32.99 kJ/mol. The results showed that the hydrogen bonding contribute to the interaction energies dominantly. The corresponding bonds stretching motions in all complexes are red-shifted relative to that of the monomer, which is in agreement with experimental results.

QUANTUM CHEMISTRY STUDY ON THE CLEAVAGE OF METHANOL CATALYZED BY HYDROXYL ZnO

The reaction mechanism of the decomposition of the methanol catalyzed by hydroxyl ZnO has been investigated by density function theory (DFT). The geometries of reactants, intermediates, transition states, and products on both doublet and quartet potential energy surfaces (PESs) have been fully optimized at the B3LYP/6-31G* level. The calculated results show that the reaction is slightly endothermic by 5.3 kJ/mol, which is in good accordance with the previous experiment. The energies and structures of the crossing points (CPs) between two PESs have been determined. The CP appears after the formation of transition states. The two theoretical models chosen to study the reaction mechanism were compared and discussed.

THEORETICAL INVESTIGATION ON THE ACTIVATION OF ETHANE VIA NICKEL ATOM CATALYSIS

The reaction mechanism of the activation of ethane by nickel atom has been investigated by density functional theory (DFT). The geometries and vibration frequencies of reactants, intermediates, transition states and products have been calculated at the B3LYP/6-311 + +G(d, p) level. Two main pathways, C–C bond activation and C–H bond activation, are identified. In former channel, the rate-limiting step is found to be hydrogen-transferring step with a high barrier of 227 kJ · mol-1. In the C–H bond activation pathway, the second hydrogen-transferring step is the rate-determining step of the whole reaction. The barrier of the step is 71 kJ · mol-1. Our results show that the studied reaction would undergo along C–H bond activation pathway to form the products H2 molecule and Ni⋯ethene complex. The present theoretical work indicates that Ni atom is more active than Ni+ cation in activating ethane.

Amino acid adsorption on anatase (101) surface at vacuum and aqueous solution: a density functional study

AbstractThe adsorption of 20 amino acids (AAs) on the (101) surface of anatase titanium dioxide (TiO2) has been investigated under the scheme of density functional theory. Through the analysis of adsorption geometries, amino group and side chains of AAs have been identified as the major side to adsorb on TiO2, while the carboxyl group prefers to stay outside to avoid the repulsion between negatively charged oxygen from TiO2 and AAs. On the surface, two-coordinated oxygen is the major site to stabilize AAs through O–H interactions. The above conclusion does not change when it is in the aqueous solution based on the calculations with AAs surrounded by explicit water molecules. The above knowledge is helpful in predicting how AAs and even peptides adsorb on inorganic materials. Graphical abstractThe adsorption of 20 amino acids (AAs) on the (101) surface of anatase titanium dioxide (TiO2) has been investigated under the scheme of density functional theory.

Confinement of hydrogen and hydroxyl radicals in water cages: a density functional theory study

Density functional theory calculations with D3 empirical dispersion correction reveal that hydrogen and hydroxyl radicals encapsulated in typical water cages found in clathrate hydrates exhibit similar structures and properties in their confined states to those in their corresponding free states, including atomic charges, spin densities, and electronic configurations. Diffusion studies reveal that energy barriers exist for these radicals to approach or exit these water cages. Energy decomposition analyses further reveal that coulombic repulsion between the radical and water cage is responsible for these energy barriers and the inability of these species to react with cage water molecules. This study provides insight into mechanisms for the storage of free radicals, which is normally extremely difficult because of their high reactivities toward many substances.