• Title/Summary/Keyword: H-bonding

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Kinetic Study on Aminolysis of Phenyl 2-Pyridyl Carbonate in Acetonitrile: Effect of Intramolecular H-bonding Interaction on Reactivity and Reaction Mechanism

  • Song, Ji-Hyun;Lee, Jae-In;Um, Ik-Hwan
    • Bulletin of the Korean Chemical Society
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    • v.35 no.7
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    • pp.2081-2085
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    • 2014

  • Second-order rate constants ($k_N$) have been measured spectrophotometrically for the reactions of phenyl 2- pyridyl carbonate (6) with a series of cyclic secondary amines in MeCN at $25.0{\pm}0.1^{\circ}C$. The Br${\o}$nsted-type plot for the reaction of 6 is linear with ${\beta}_{nuc}$ = 0.54, which is typical for reactions reported previously to proceed through a concerted mechanism. Substrate 6 is over $10^3$ times more reactive than 2-pyridyl benzoate (5), although the reactions of 6 and 5 proceed through the same mechanism. A combination of steric hindrance, inductive effect and resonance contribution is responsible for the kinetic results. The reactions of 6 and 5 proceed through a cyclic transition state (TS) in which H-bonding interactions increase the nucleofugality of the leaving group (i.e., 2-pyridiniumoxide). The enhanced nucleofugality forces the reactions of 6 and 5 to proceed through a concerted mechanism. In contrast, the corresponding reaction of 4-nitrophenyl 2-pyridyl carbonate (7) proceeds through a stepwise mechanism with quantitative liberation of 4-nitrophenoxide ion as the leaving group, indicating that replacement of the 4-nitrophenoxy group in 7 by the PhO group in 6 changes the reaction mechanism (i.e., from a stepwise mechanism to a concerted pathway) as well as the leaving group (i.e., from 4-nitrophenoxide to 2-pyridiniumoxide). The strong electron-withdrawing ability of the 4-nitrophenoxy group in 7 inhibits formation of a H-bonded cyclic TS. The presence or absence of a H-bonded cyclic TS governs the reaction mechanism (i.e., a concerted or stepwise mechanism) as well as the leaving group (i.e., 2-pyridiniumoxide or 4-nitrophenoxide).

  • https://doi.org/10.5012/bkcs.2014.35.7.2081 인용 PDF KSCI KPUBS HTML

Evidence for a Common Molecular Basis for Sequence Recognition of N3-Guanine and N3-Adenine DNA Adducts Involving the Covalent Bonding Reaction of (+)-CC-1065

  • Park, Hyun-Ju
    • Archives of Pharmacal Research
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    • v.25 no.1
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    • pp.11-24
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    • 2002

  • The antitumor antibiotic (+)-CC-1065 can alkylate N3 of guanine in certain sequences. A previous high-field $^1H$ NMR study on the$(+)-CC-1065d[GCGCAATTG*CGC]_2$ adduct ($^*$ indicates the drug alkylation site) showed that drag modification on N3 of guanine results in protonation of the cross-strand cytosine [Park, H-J.; Hurley, L. H. J. Am. Chem. Soc.1997, 119,629]. In this contribution we describe a further analysis of the NMR data sets together with restrained molecular dynamics. This study provides not only a solution structure of the (+)-CC-1065(N3- guanine) DNA duplex adduct but also new insight into the molecular basis for the sequence- specific interaction between (+)-CC-1065 and N3-guanine in the DNA duplex. On the basis of NOESY data, we propose that the narrow minor groove at the 7T8T step and conformational kinks at the junctions of 16C17A and 18A19T are both related to DNA bending in the drugDNA adduct. Analysis of the one-dimensional $^1H$ NMR (in $H_2O$) data and rMD trajectories strongly suggests that hydrogen bonding linkages between the 8-OH group of the (+)-CC-1065 A-sub-unit and the 9G10C phosphate via a water molecule are present. All the phenomena observed here in the (+)-CC-1065(N3-guanine) adduct at 5'$-AATTG^*$are reminiscent of those obtained from the studies on the (+)-CC-1065(N3-adenine) adduct at $5'-AGTTA^*$, suggesting that (+)-CC-1065 takes advantage of the conformational flexibility of the 5'-TPu step to entrap the bent structure required for the covalent bonding reaction. This study reveals a common molecular basis for (+)-CC-1065 alkylation at both $5'-TTG^*$ and $5'-TTA^*$, which involves a trapping out of sequence-dependent DNA conformational flexibility as well as sequence-dependent general acid and general base catalysis by duplex DNA.

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The study of SiON thin film for optical properties. (SiON 박막의 광학적 특성에 대한 연구)

  • Kim, D.H.;Im, K.J.;Kim, K.H.;Kim, H.S.;Sung, M.Y.
    • Proceedings of the Korean Institute of Electrical and Electronic Material Engineers Conference
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    • 2001.11b
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    • pp.247-250
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    • 2001

  • We studied optical properties of SiON thin-film in the applications of optical waveguide. SiON thin-film was grown in $300^{\circ}C$ by PECVD(plasma enhanced chemical vapor deposition) system. The change of SiON thin-film composition and refractive Index was studied as a function of varying $NH_3$ gas flow rate. As $NH_3$ gas flow rate was increased, Quantity of N and refractive index were increased at the same time. By the results, we could form the SiON thin-film to use of a waveguide with refractive index of 1.6. We analyzed the conditions of the thin-film with FTIR(fourier transform infrared) and OES (optical emission spectroscopy). N-H bonding($3390cm^{-1}$ ) can be removed by thermal annealing. And we could observe the SiH bonding state and quantity by OES analysis in $SiH_4$

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