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Sang Tae Park

Publications and source records attributed to Sang Tae Park.

11 recordsLinked to original sources

Ultrafast electron diffraction: excited state structures and chemistries of aromatic carbonyls.

The photophysics and photochemistry of molecules with complex electronic structures, such as aromatic carbonyls, involve dark structures of radiationless processes. With ultrafast electron diffraction (UED) of isolated molecular beams it is possible to determine these transient structures, and in this contribution we examine the nature of structural dynamics in two systems, benzaldehyde and acetophenone. Both molecules are seen to undergo a bifurcation upon excitation (S(2)). Following femtosecond conversion to S(1), the bifurcation leads to the formation of molecular dissociation products, benzene and carbon monoxide for benzaldehyde, and benzoyl and methyl radicals for acetophenone, as well as intersystem crossing to the triplet state in both cases. The structure of the triplet state was determined to be "quinoidlike" of pipi(*) character with the excitation being localized in the phenyl ring. For the chemical channels, the product structures were also determined. The difference in photochemistry between the two species is discussed with respect to the change in large amplitude motion caused by the added methyl group in acetophenone. This discussion is also expanded to compare these results with the prototypical aliphatic carbonyl compounds, acetaldehyde and acetone. From these studies of structural dynamics, experimental and theoretical, we provide a landscape picture for, and the structures involved in, the radiationless pathways which determine the fate of molecules following excitation. For completeness, the UED methodology and the theoretical framework for structure determination are described in this full account of an earlier communication [J. S. Feenstra et al., J. Chem. Phys. 123, 221104 (2005)].

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Molecular cloning of the DNA gyrase genes from Methylovorus sp. strain SS1 and the mechanism of intrinsic quinolone resistance in methylotrophic bacteria.

The genes encoding the DNA gyrase A (GyrA) and B subunits (GyrB) of Methylovorus sp. strain SS1 were cloned and sequenced. gyrA and gyrB coded for proteins of 846 and 799 amino acids with calculated molecular weights of 94,328 and 88,714, respectively, and complemented Escherichia coli gyrA and gyrB temperature sensitive (ts) mutants. To analyze the role of type II topoisomerases in the intrinsic quinolone resistance of methylotrophic bacteria, the sequences of the quinolone resistance-determining regions (QRDRs) in the A subunit of DNA gyrase and the C subunit (ParC) of topoisomerase IV (Topo IV) of Methylovorus sp. strain SS1, Methylobacterium extorquens AM1 NCIB 9133, Methylobacillus sp, strain SK1 DSM 8269, and Methylophilus methylotrophus NCIB 10515 were determined. The deduced amino acid sequences of the QRDRs of the ParCs in the four methylotrophic bacteria were identical to that of E. coli ParC. The sequences of the QRDR in GyrA were also identical to those in E. coli GyrA except for the amino acids at positions 83, 87, or 95. The Ser83 to Thr substitution in Methylovorus sp. strain SS1, and the Ser83 to Leu and Asp87 to Asn substitutions in the three other methylotrophs, agreed well with the minimal inhibitory concentrations of quinolones in the four bacteria, suggesting that these residues play a role in the intrinsic susceptibility of methylotrophic bacteria to quinolones.

Amino Acid Sequence↗

Excited state molecular structures and reactions directly determined by ultrafast electron diffraction.

In this communication, we report on the use of ultrafast electron diffraction to determine structural dynamics of excited states and reaction products of isolated aromatic carbonyls, acetophenone and benzaldehyde. For a 266 nm excitation, a bifurcation of pathways is structurally resolved, one leading to the formation of the triplet state (quinoid structure) and another to chemical products: for benzaldehyde the products are benzene and carbon monoxide (hydrogen migration and bond rupture) while those for acetophenone are the benzoyl and methyl radicals (bond rupture). The refined structures are compared with those predicted by theory. These dark structures and their radiationless transitions define the reduced energy landscape for complex reactions.

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Ultrafast electron diffraction: dynamical structures on complex energy landscapes.

In this contribution, we report studies in ultrafast electron diffraction (UED), with the aim of exploring new directions. The main focus is on the determination of complex structures and their dynamics with spatial and temporal resolutions sufficient to give an atomic-scale picture for the evolution in chemical or biological change. We also provide the theoretical framework for UED, and compare the experimental findings of UED to those predicted by density functional and charge density calculations. Selected applications are given in order to highlight phenomena related to concepts such as bifurcation of trajectories in dynamics, far-from-equilibrium coherent structures, and conformational robustness in biological structures. For the former two cases, we consider chemical systems, and, for the latter, we examine proteins of 200 atoms (angiotensin I) or more.

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The Mycobacterium tuberculosis serine/threonine kinases PknA and PknB: substrate identification and regulation of cell shape.

The Mycobacterium tuberculosis genome contains 11 serine/threonine kinase genes including two, pknA and pknB, that are part of an operon encoding genes involved in cell shape control and cell wall synthesis. Here we demonstrate that pknA and pknB are predominantly expressed during exponential growth, and that overexpression of these kinases slows growth and alters cell morphology. We determined the preferred substrate motifs of PknA and PknB, and identified three in vivo substrates of these kinases: PknB; Wag31, an ortholog of the cell division protein DivIVA; and Rv1422, a conserved protein of unknown function. Expression of different alleles of wag31 in vivo alters cell shape, in a manner dependent on the phosphoacceptor residue in the protein produced. Partial depletion of pknA or pknB results in narrow, elongated cells. These data indicate that signal transduction mediated by these kinases is a novel mechanism for the regulation of cell shape in mycobacteria, one that may be conserved among gram-positive bacteria.

Amino Acid Sequence↗

Dark structures in molecular radiationless transitions determined by ultrafast diffraction.

The intermediate structures formed through radiationless transitions are termed "dark" because their existence is inferred indirectly from radiative transitions. We used ultrafast electron diffraction to directly determine these transient structures on both ground-state and excited-state potential energy surfaces of several aromatic molecules. The resolution in space and time (0.01 angstrom and 1 picosecond) enables differentiation between competing nonradiative pathways of bond breaking, vibronic coupling, and spin transition. For the systems reported here, the results reveal unexpected dynamical behavior. The observed ring opening of the structure depends on molecular substituents. This, together with the parallel bifurcation into physical and chemical channels, redefines structural dynamics of the energy landscape in radiationless processes.

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Direct determination of hydrogen-bonded structures in resonant and tautomeric reactions using ultrafast electron diffraction.

We elucidate the keto-enol tautomeric equilibrium in acetylacetone, the structure of both keto and enol forms, and the nature of the intramolecular O-H...O HB in enolic acetylacetone using our ultrafast electron diffraction apparatus, thereby shedding new light on the nature of the hydrogen bond in resonant tautomeric structures. The enolic structure exhibits some pi-resonance delocalization; however, this delocalization is not strong enough to give a symmetric skeletal geometry. The long O...O distance in the refined structure renders the homonuclear O-H...O hydrogen bond in acetylacetone localized and asymmetric.

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Prevalence of human herpesvirus-6B in Korean hematopoietic stem cell transplantation recipients.

Human herpesvirus-6 (HHV-6) is a major pathogen associated with diseases of recipients of hematopoietic stem cell transplants (HSCT). We have isolated HHV-6 in Korean HSCT recipients and carried out a prospective investigation of its prevalence. We obtained peripheral blood from HSCT recipients who had signs of HHV-6 infection. Cord blood mononuclear cells (CBMC) and Sup-T1 cells were used to culture the HHV-6. Indirect immunofluorescence assays (IFA), and the polymerase chain reaction (PCR) were employed to detect HHV-6. The prevalence of HHV-6 infection in HSCT recipients was calculated on the basis of the PCR results. HHV-6 was isolated from four clinical samples. After culturing the HHV-6 in CBMC, the standard strain and the four clinical isolates were propagated in Sup-T1 cells. The infected cells became grossly enlarged and multinucleate after 7-21 days. The virus was identified primarily on the basis of the morphological changes of the cultured cells, and confirmed by specific IFA with monoclonal antibody to HHV-6. HHV-6 was detected in each sample by PCR with primers specific for the major immediate early gene. Sequencing of the standard strain and PCR products confirmed identification of the HHV-6B variant. By PCR we detected 415 instances of HHV-6 in 3966 samples (14.6% of peripheral blood mononuclear cells and 6.3% of sera), and HHV-6 DNAemia was most frequent from the second to the fourth week after HSCT.

Base Sequence↗

Cloning, molecular characterization, and transcriptional analysis of dnaK operon in a methylotrophic bacterium Methylovorus sp. strain SS1 DSM 11726.

Three structural genes that consist of a dnaK operon in a restricted facultative methylotrophic bacterium Methylovorus sp. strain SS1 DSM 11726 were cloned and characterized. The genes were clustered in the transcription order grpE-dnaK-dnaJ. The cloned grpE, dnaK, and dnaJ genes had open-reading frames of 474, 1,926, and 1,116 nucleotides, coding for proteins with calculated molecular masses of 17,390, 69,761, and 41,050, respectively. The overall identities in the deduced amino acid sequences of GrpE, DnaK, and DnaJ with those of the Escherichia coli homologs were 45.2, 74.5, and 61.2%, respectively. Northern blot analyses with grpE-, dnaK-, and dnaJ-specific probes revealed that the three genes are co-transcribed as a 4.0-kb mRNA. A primer extension analysis revealed that the transcription of the dnaK operon started at the nucleotide A that is located 28 bp upstream of the grpE start codon. The transcription start site was preceded by a putative promoter region 15'-CCCCGCTTGAA(13-bp)CCCCAATTT-3'], which is highly homologous to the consensus sequences of the E. coli sigma32-type heat shock promoter. The putative promoter worked under both normal and heat shock conditions in E. coli. The nature of the nucleotide sequence in the second half of the -35 region played a critical role during transcription. The heat shock mRNA was maximally produced at about 10 min after transfer of the Methylovorus sp. strain SS1 from 30 to 42 degrees C. The dnaK operon was also induced by ethanol, hydrogen peroxide, and NaCl shocks. The cloned dnaK operon complemented the E. coli dnaK mutant.

Bacterial Proteins↗

Photodissociation dynamics of various conformers of iodobutane isomer ions prepared selectively by vacuum ultraviolet mass-analyzed threshold ionization.

Various conformers of 1-C(4)H(9)I(+*), 2-C(4)H(9)I(+*), and i-C(4)H(9)I(+*) were prepared selectively by mass-analyzed threshold ionization with coherent vacuum ultraviolet radiation. Conformer-selective photodissociation of these ions was studied in the 560-730 nm spectral region, which corresponds to excitation to the first excited electronic state. Rapid dissociation was observed as manifested by noticeable laser polarization dependence of the product signals. In particular, photodissociation of i-C(4)H(9)I(+*) was found to be conformer specific, occurring without interconversion between conformers. The product's asymptote energies estimated from the experimental data were compared with the reaction enthalpies at 0 K to get information on the structures and states of products. It was found that a simple S(N)2-type mechanism deduced from the previous study of 1-C(3)H(7)I(+*) was compatible with the present observations. Validity of the widely adopted postulate in stereochemistry that different conformations can be gateways to different reactions has been demonstrated in the gas phase.

Journal Article↗

Observation of conformation-specific pathways in the photodissociation of 1-iodopropane ions.

Many molecules can rotate freely around single bonds and thereby interconvert between different conformations, such as gauche and anti 1,2-disubstituted ethane, a classic example of conformational isomerism. Even though rotation occurs rapidly at room temperature, the product selectivity seen in some reactions has been explained by conformation-dependent reaction mechanisms: if reactant molecules differing only in their conformation are located at different positions on the reaction path, they may undergo different reactions. But a direct verification of this effect is difficult, because the energy barrier separating conformational isomers is so low that under ambient conditions reactants with more than one conformation will be present. But by using temperatures low enough to suppress the interconversion between different conformations, gauche-1-iodopropane ions and anti-1-iodopropane ions have been selectively generated. Here we show that the kinetic energy released during the photodissociation of 1-iodopropane ions depends strongly on the conformation of the ions. Thermodynamic arguments and ab initio calculations indicate that this difference in kinetic energy release results from differences in the reaction mechanism, with gauche-1-iodopropane ions forming 2-propyl ions and anti-1-iodopropane ions forming protonated cyclopropane ions. These findings suggest that the well-known concept of conformation selection forms the basis of a simple scheme for reaction control, thus providing in some cases an attractive alternative for more involved schemes that utilize the phase and pulse shape of laser beams to control chemical reactions.

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