To explore the closing mechanism of the substrate pocket,we perform a 16,000 ps molecular dynamics simulation separately on the ligand-free and actinonin-bound peptide deformylase from Leptospira interrogans.Our results show that the CD-loop, hydrophilic inhibitor and hydrophobic cluster are necessary for the formation of semi-open conformation,and Tyr71 plays an important role in mediating the movements of CD-loop.The average MD structure of the actinonin-bound LiPDF complex approaches to the crystal structure.These are consistent with experiment very well.
Reaction resonance or Feshbach resonance in polyatomic reaction is one of the most fascinating phenomena in chemical reaction dynamics. The HO+CH4→HO+CH3 reaction is one of the pivotal polyato-mic reactions concerned with both the experimental and theoretical scientists. Reaction probabilities and other dynamic properties of this system were calculated with quantum scattering theory method, but a simple QH(v)+HO(j)→Q+H2O(m,n) reaction model was used, in which only three degrees of freedom and the rotating of OH were considered while making CH3 as a pseudo atom. In this paper, by an ab initio method, partial potential energy surface(PPES) was constructed and all the 15 internal degrees-freedom were given. Feshbach resonance mechanism of this reaction can be obtained by the dynamic Eyring Lake on the PPES and the lifetime of the reactive resonance-state can be estimated using the gap of the vibrational energy levels of transient collision complex in the critical transition-state region. Above interesting dynamic properties would not be given by simple pseudo atomic reaction model.
Based on the vibrational potential curves coupled with the minimum energy reaction path, the partial potential energy surface of the reaction I＋HI→IH＋I was constructed at the QCISD（T）//MP4SDQ level with pseudo potential method. And the formation mechanism of the scattering resonance states of this reaction was well interpreted with the partial potential energy surface. The scattering resonance states of this reaction should belong to Feshbach resonance because of the coupling of the vibrational mode and the translational mode. With the one-dimensional square potential well model, the resonance width and lifetime of the I＋HI（v=0）→IH（v＇=0）＋I state-to-state reaction were calculated, which preferably explained the high-resolved threshold photodetachment spectroscopy of the IHI- anion performed by Neumark et al..
