Ju-Beom Song

Theoretical study of the reactions of Ar++H2 and Ar++HD using the trajectory surface hopping method

Trajectory surface hopping calculations have been carried out for collisions of Ar++H2 and Ar++HD on three low-lying potential energy surfaces projected from the original six in the Kuntz and Roach diatomics in molecules surface for this system. The location and probability of hops between surfaces were determined using the new algorithm developed by Parlant and Gislason. In addition to the reactive channel and total charge transfer to H2+ and HD+, dissociative channels to, for example, Ar++H+H, and Ar+H++H have been studied. Particular attention was paid to the dissociative charge transfer isotope effect for the processes Ar++HD→Ar+H++D, or Ar+H+D+; near threshold the D+ product is favored over H+ which we attribute to preferential dissociation of excited ArD+ products. This is the first theoretical study of these dissociation processes.

Theoretical study of the reactions of Ar++HX(v=0) and Ar+HX+(v) (X=H and D) at E=0.1 eV using the trajectory surface hopping method

Trajectory surface hopping calculations have been carried out for collisions of Ar++H2 (v=0), Ar++HD (v=0), H2+(v)+Ar, and HD+(v)+Ar, where v=0, 1, and 2 on the Kuntz–Roach diatomics-in-molecules potential surfaces at a relative energy of 0.1 eV. The importance of the mutual “capture” of the two particles on the attractive ground potential energy surface is shown clearly. The fact that capture does not occur on every collision is attributed to an effect of the vibrational phase of the H2 or HD molecule. This vibrational phase effect can explain the drop in the experimental rate constant seen at very low temperatures in the Ar++H2 system. For H2+(v=2)+Ar and HD+(v=2)+Ar we also find that many trajectories hop to the first excited potential surface as the particles approach. Since these trajectories cannot reach small separations, this further reduces the reactive cross section for v=2 and higher levels. The ground potential energy surface has a fairly deep well, particularly when the Ar–H–H angle is near 9...

Application of the pairwise energy model to various isotopic variations of the H + H2 reaction

Abstract The pairwise energy model (PEM) assumes that the cross section QR for the reaction A + BC → AB + C, where B and C are isotopes of hydrogen, depends only on the pairwise relative energy Es between A and B. In this paper the PEM is applied to eight isotopic variations of the H + H2 reaction. We show that the model works well at high energy but breaks down at low energies because QR is sensitive not only to Es but also to the ratio τ vib τ coll , where τvib is the vibrational period of BC, and τcoll is the collision time. In addition, at low energy reactions of HD show the effect of rotational reorientation of the HD by the incoming atom A; this favors the AD product at the expense of AH. We also consider a modified version of the PEM when the cross section is factored as QR = Qhit PR. Here Qhit is the cross section for A hitting BC, and PR is the probability for forming AB once A hits BC. We find that Qhit is a function of the relative energy E rather than Es, but PR is primarily a function of Es. Even though the PEM breaks down at low collision energy it provides a useful framework for understanding the inter- and intra-molecular isotope effects in these reactions.

Comparison of classical and quantal calculations for the reaction O+H2(υ=0, J)→OH(υ′, J′)+H near threshold

State‐to‐state reaction probabilities have been calculated for the reaction O+H2(υ=0,J) →OH(υ′,J′)+H near threshold using the quasiclassical trajectory technique. In most cases the total classical angular momentum J of the system was held equal to zero. The procedure for ‘‘quantizing’’ the product vibrational energy is somewhat ambiguous, and two procedures were used. The results were compared with the quantal calculations of Chatfield et al. on the same system for J=0. Both the classical and quantal calculations give very state‐specific product distributions. The agreement between the classical and quantal calculations is reasonably good, particularly for the classical procedure which conserves the total product internal energy during the quantization procedure. The agreement is worst for J=0. For the case J=14 we have also carried out a calculation for all J values (i.e., all impact parameters and initial orientations) of the product density distribution P(Evib′,Erot′) and compared it with the comparabl...

Theoretical study of collision-induced dissociation cross-sections for the reactions X+H2(X=O(3P), Cl, and F)

Abstract The collision-induced dissociation (CID) cross-sections for the reactions X+H2 (X is O ( 3 P ) , F, and Cl) have been calculated using the QCT method. The goal of this work is to understand the trends of the CID cross-sections. The CID cross-sections are different at any given relative collision energy for the three systems. This result is due to the differences of the potential energy surfaces and the sizes of the incoming atom for the three systems. However, the ratios of the CID cross-sections to the total cross-sections (reaction plus CID cross-sections) are the same at a given relative collision energy for the three systems. We conclude that this is due to the fact that at high collision energies the internal energy distributions of the products for the three systems are the same on the scale of the dissociation energy of the products at given relative collision energy. This theory should be useful for experiments using a mass spectrometer.

In silico analysis of putative drug and vaccine targets of the metabolic pathways of Actinobacillus pleuropneumoniae using a subtractive/comparative genomics approach

Actinobacillus pleuropneumoniae is a Gram-negative bacterium that resides in the respiratory tract of pigs and causes porcine respiratory disease complex, which leads to significant losses in the pig industry worldwide. The incidence of drug resistance in this bacterium is increasing; thus, identifying new protein/gene targets for drug and vaccine development is critical. In this study, we used an in silico approach, utilizing several databases including the Kyoto Encyclopedia of Genes and Genomes (KEGG), the Database of Essential Genes (DEG), DrugBank, and Swiss-Prot to identify non-homologous essential genes and prioritize these proteins for their druggability. The results showed 20 metabolic pathways that were unique and contained 273 non-homologous proteins, of which 122 were essential. Of the 122 essential proteins, there were 95 cytoplasmic proteins and 11 transmembrane proteins, which are potentially suitable for drug and vaccine targets, respectively. Among these, 25 had at least one hit in DrugBank, and three had similarity to metabolic proteins from Mycoplasma hyopneumoniae, another pathogen causing porcine respiratory disease complex; thus, they could serve as common therapeutic targets. In conclusion, we identified glyoxylate and dicarboxylate pathways as potential targets for antimicrobial therapy and tetra-acyldisaccharide 4′-kinase and 3-deoxy-D-manno-octulosonic-acid transferase as vaccine candidates against A. pleuropneumoniae.

Biofilm formation and determination of minimum biofilm eradication concentration of antibiotics in Mycoplasma hyopneumoniae

The study was aimed to investigate biofilm forming ability of Mycoplasma hyopneumoniae and to determine the minimum biofilm eradication concentrations of antibiotics. Biofilm forming ability of six strains of M. hyopneumoniae was examined using crystal violet staining on coverslips. The results demonstrated an apparent line of biofilm growth in 3 of the strains isolated from swine with confirmed cases of enzootic pneumonia. BacLight bacterial viability assay revealed that the majority of the cells were viable after 336 hr of incubation. Moreover, M. hyopneumoniae persists in the biofilm after being exposed to 10 fold higher concentration of antibiotics than the minimum inhibitory concentrations in planktonic cells. To the best of our knowledge, this is the first report of biofilm formation in M. hyopneumoniae. However, comprehensive studies on the mechanisms of biofilm formation are needed to combat swine enzootic pneumonia caused by resistant M. hyopneumoniae.