Menghai Lin

Molecular dynamics simulations of the detoxification of paraoxon catalyzed by phosphotriesterase.

Combined QM(PM3)/MM molecular dynamics simulations together with QM(DFT)/MM optimizations for key configurations have been performed to elucidate the enzymatic catalysis mechanism on the detoxification of paraoxon by phosphotriesterase (PTE). In the simulations, the PM3 parameters for the phosphorous atom were reoptimized. The equilibrated configuration of the enzyme/substrate complex showed that paraoxon can strongly bind to the more solvent‐exposed metal ion Znβ, but the free energy profile along the binding path demonstrated that the binding is thermodynamically unfavorable. This explains why the crystal structures of PTE with substrate analogues often exhibit long distances between the phosphoral oxygen and Znβ. The subsequent SN2 reaction plays the key role in the whole process, but controversies exist over the identity of the nucleophilic species, which could be either a hydroxide ion terminally coordinated to Znα or the μ‐hydroxo bridge between the α‐ and β‐metals. Our simulations supported the latter and showed that the rate‐limiting step is the distortion of the bound paraoxon to approach the bridging hydroxide. After this preparation step, the bridging hydroxide ion attacks the phosphorous center and replaces the diethyl phosphate with a low barrier. Thus, a plausible way to engineer PTE with enhanced catalytic activity is to stabilize the deformed paraoxon. Conformational analyses indicate that Trp131 is the closest residue to the phosphoryl oxygen, and mutations to Arg or Gln or even Lys, which can shorten the hydrogen bond distance with the phosphoryl oxygen, could potentially lead to a mutant with enhanced activity for the detoxification of organophosphates.

BLOCK-LOCALIZED WAVEFUNCTION ENERGY DECOMPOSITION (BLW-ED) ANALYSIS OF σ/π INTERACTIONS IN METAL-CARBONYL BONDING

The bonding features in metal-carbonyls including neutral MCO (M = Ni, Pd, Pt) and MCO+ (M+ = Cu+, Ag+, Au+) complexes have been elucidated at the DFT level with relativistic compact effective potentials for transition metals and 6-311+G(d) basis sets for C and O by the block-localized wavefunction (BLW) method. The BLW method can decompose the intermolecular interactions in terms of Heitler–London, polarization, and charge transfer energy contributions. Since the metal–CO bonding involves two synergic interactions, namely the σ-dative bond from the carbon lone electron pair to an empty dσ orbital on the metal, and the π back-donation from filled dπ orbitals to the empty 2π* orbital on CO, the present BLW-ED analyses quantitatively demonstrated that in neutral MCO complexes the π-bonding dominates over the σ-bonding, whereas in cationic MCO+ complexes, the σ-bonding plays a major role. But in both neutral and cationic species, the CO polarization induced by the metals enhances the C–O bond and increases t...

Structure and stability of binary transition-metal clusters (NbCo)n (n⩽5): A relativistic density-functional study

Equilibrium geometries and electronic properties of binary transition-metal clusters, (NbCo)n (n < or = 5), have been investigated by means of the relativistic density-functional approach. The metal-metal bonding and stability aspects of these clusters have been analyzed on the basis of calculations. Present results show that these clusters exhibit rich structural varieties on the potential-energy surfaces. The most stable structures have a compact conformation in relatively high symmetry, in which the Nb atoms prefer to form an inner core and Co atoms are capped to the facets of the core. Such building features in clustering of the Nb/Co system are related to the order of bond strength: Nb-Nb>Nb-Co>Co-Co. As the binary cluster size increases, the Nb-Co bond may become stronger than the Nb-Nb bond in the inner niobium core, which results in a remarkable increment of the Nb-Nb bond length. Amongst these binary transition-metal clusters, the singlet (NbCo)4 in T(d) symmetry has a striking high stability due to the presence of the spherical aromaticity and electronic shell closure. The size dependence of the bond length and stability of the cluster has been explored.

Theoretical Study of Decachlorocorannulene and its Congeners C20X10 and C20Z5

Abstract The electronic structure of C20Cl10 synthesized by arc discharge has been studied using ab initio calculation at MP2/3-21G theory level. Theoretical studies of C20F10 and C20O5, C20S5, C20P5 have been carried out using the same method.

Orbital deletion procedure and its applications

The orbital deletion procedure is introduced, which is suited to quantitatively investigating the electronic delocalization effect in carbocations and boranes. While the routineab initio molecular orbital methods can generate wavefunctions for real systems where all electrons are delocalized, the present orbital deletion procedure can generate wavefunctions for hypothetical reference molecules where electronic delocalization effect is deactivated. The latter wave-function normally corresponds to the most stable resonance structure in terms of the resonance theory. By comparing and analyzing the delocalized and the localized wavefunctions, one can obtain a quantitative and instinct picture to show how electronic delocalization inside a molecule affects the molecular structure, energy as well as other physical properties. Two examples are detailedly discussed. The first is related to the hyperconjugation of alkyl groups in carbocations and a comparison of the order of stability of carbocations is made. The second concerns the Lewis acidity of boron trihalides where the conjugation effect among the doubly-occupied π atomic orbitals on the halide atoms and the vacant π atomic rbital on the boron atom plays a dominant role in determining the relative acceptor properties. The results demonstrate that the orbital deletion procedure can be used to very successfully interpret some traditional chemical intuitions and concepts in a quantitative way.