• Title/Summary/Keyword: Ring-ring stacking interaction

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Intramolecular Ring-Ring Stacking Interartions between 8-Methoxypsoralen and Adenine Induced by Polymethylene Bridges.

  • Yu, Dong Jin;Hyeon, Seung Hak;Sim, Sang Cheol
    • Bulletin of the Korean Chemical Society
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    • v.22 no.6
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    • pp.575-580
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    • 2001
  • Intramolecular ring-ring interactions in the model compounds, $8-methoxypsoralen-CH_2O(CH_2)n-adenine(MOPCH_2OCnAd$, n=2, 3, 5, and 6) in which 5' position of 8-methoxypsoralne (8-MOP) is linked by different polymethylene bridges to N9 of adenine, have been investigated by hypochromism measurements. Efficient ring-ring stacking interactions have been observed in $MOPCH_2CO2Ad$ (7) from the percent hypochromism(%H) and fluorescence spectra of the models and a reference molecule. The 8-methoxyposralen-adenine systems have shown stronger ring-ring stacking interaction than the psoralen-adenine system.

Synthesis and Photophysical Properties of Bispsoralen Derivatives Linked by a Bisamide-polymethylene Chain

  • Yoo, Dong-Jin
    • Bulletin of the Korean Chemical Society
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    • v.28 no.10
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    • pp.1715-1719
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    • 2007
  • New bispsoralen derivatives 5-10, 8-MOP-NHCO(CH2)nCONH-8-MOP (BPSBA-Cn, n = 0, 1, 2, 3, 4 and 5) in which 5 position of an 8-methoxypsoralen (8-MOP) is linked by various lengths of bisamide polymethylene chain to 5 position of the other 8-MOP, have been synthesized by the amidation of 5-amino-8-methoxypsoralen (12) with α,ω-alkanoyl dichloride. Photophysical properties of their derivatives including π?π stacking interaction between the two aromatic moieties were investigated by UV absorption and fluorescence emission spectra. Efficient ring-ring stacking interactions have been observed in BPSBA-C4 (9) from the percent hypochromism (%H) of the models.

Theoretical Study on The Interaction Between Benzo(a)pyrene and Cytochrome P-450 (Benzo(a)pyrene 과 Cytochrome P-450의 대한 상호작용에 대한 이론적 연구)

  • 도성탁
    • Biomedical Science Letters
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    • v.1 no.1
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    • pp.89-94
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    • 1995
  • Considering the planar structure and nonpolar properity of benzo(a)pyrene(B(a)p) and the planar heme part of cytochrome P-450, stacking interaction is probable. MO calculation on B(a)P and heme part of cytochrome P-450 were carried out to dertermine probable stacking interaction models. In this case, orbital interaction is most important. Accordingly, the stacking positions have high eigen vector in frontier orbital and boning type between two molecules. In this way, five probate models were selected and examined by MN2 and MO method. The most probable .stacking interaction model which is the 4, 5, 6 positions of B(a)P overlap carbon atom and pyrrole ring of ring of heme group was determined.

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Theoretical Mechanism Studies on the Enantioselectivity of aza-MBH-type Reaction of Nitroalkene to N-tosylimine Catalyzed by Thiourea-tertiary Amine

  • Lu, Nan;Wang, Huatian;Wang, Yangping
    • Bulletin of the Korean Chemical Society
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    • v.34 no.12
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    • pp.3591-3596
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    • 2013
  • The enantioselective aza-Morita Baylis Hillman reaction of nitroalkene and N-tosylimine catalyzed by thiourea-tertiary amine has been investigated using density functional theory. Enantioselectivity is dominated by the cooperative effect of non-covalent and weak covalent interactions imposed by different units of catalyst. As Lewis base, the tertiary amine unit activates nitroalkene via weak covalent bond. The weak covalent interaction orients the reaction in a major path with smaller variations of this bond. The aromatic ring unit activates N-tosylimine via ${\pi}-{\pi}$ stacking. The non-covalent interaction selects the major path with smaller changes of the efficient packing areas. Thiourea unit donates more compact H-bonded network for species of the major path. The calculated ee value in xylene solution phase (97.6%) is much higher than that in N,N-Dimethylformamide (27.2%). Our conclusion is also supported by NBO analysis.

Electrostatic Interaction Between Oligopeptides and Phosphate Residues by Determination of Absolute Raman Intensities

  • Kye-Taek Lim
    • Bulletin of the Korean Chemical Society
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    • v.12 no.3
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    • pp.286-289
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    • 1991
  • The changed isotropic absolute Raman intensities of the phosphate residue in the complexes of positive charge oligopeptides, lys-lys, arg-arg, lys-aromat-lys, negative charge diethyl phosphoric acid (DEP) and polyriboadenylic acid{poly(rA)} were reported and discussed. Our measurements showed that the absolute intensities of phosphate stretch vibration in complexes were different according to the reaction partners. Due to the partial electrical charge and molecular structure of oligopeptides for the complex formation lysine can interact more strongly than arginine when the reaction partners have short chain and no steric hindrance. Owing to these reasons the intensity of phosphate stretching vibration is very sensitive according to the circumstance of reaction. From our results we could suggest that we can discriminate any one of the the lysine and arginine in the complicated biological molecule during interaction between nucleotides and proteins. The activity of reaction of two basical oligopeptides is not quite similar for complex formation in aqueous solution. The activity of dipeptides depends upon the structure of molecule and environment for complex formation. Aromatic ring contributes to electrostatic interaction in complexes. The amount of the absolute intensity for pure stacking interaction is smaller than electrostatic interaction in macromolecular complexes.

Crystal Structure of Rattus norvegicus Visfatin/PBEF/Nampt in Complex with an FK866-Based Inhibitor

  • Kang, Gil Bu;Bae, Man-Ho;Kim, Mun-Kyoung;Im, Isak;Kim, Yong-Chul;Eom, Soo Hyun
    • Molecules and Cells
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    • v.27 no.6
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    • pp.667-671
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    • 2009
  • Visfatin (Nampt/PBEF) plays a pivotal role in the salvage pathway for $NAD^+$ biosynthesis. Its potent inhibitor, FK866, causes cellular $NAD^+$ levels to decline, thereby inducing apoptosis in tumor cells. In an effort to improve the solubility and binding interactions of FK866, we designed and synthesized IS001, in which a ribose group is attached to the FK866 pyridyl ring. Here, we report the crystal structure of rat visfatin in complex with IS001. Like FK866, IS001 is positioned at the dimer interface, and all of the residues that interact with IS001 are involved in hydrophobic or ${\pi}-{\pi}$-stacking interactions. However, we were unable to detect any strong interactions between the added ribose ring of IS001 and visfatin, which implies that a bulkier modifying group is necessary for a tight interaction. This study provides additional structure-based information needed to optimize the design of visfatin inhibitors.

Interaction of Cu(II)-meso-tetrakis(n-N-methylpyridiniumyl)porphyrin (n = 2,3,4) with Native and Synthetic Polynucleotides Probed by Polarized Spectroscopy

  • Lee, Mi-Jin;Lee, Gil-Jun;Lee, Dong-Jin;Kim, Seog-K.;Kim, Jong-Moon
    • Bulletin of the Korean Chemical Society
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    • v.26 no.11
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    • pp.1728-1734
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    • 2005
  • The interactions of Cu(II)-meso-Tetrakis(n-N-methylpyridiniumyl)porphyrin (n = 2,3,4), respectively referred to as o-, m- and p-CuTMPyP, and DNA, poly$[d(A-T)_2]$ and poly$[d(G-C)_2]$ were investigated by circular and linear dichroism (CD and LD). In the o-CuTMPyP case, in which the rotation of the pyridinium ring is prevented, the shape of the CD spectrum when associated to DNA and poly$[d(A-T)_2]$ resembles and is characterized by a positive band at a low drug to DNA concentration ratio (R ratio) and is bisignate at a high R ratio. The former CD spectrum shape has been attributed to porphyrin that is bound monomerically outside of DNA while the latter can be attributed to those that are stacked. When o-CuTMPyP is bound to poly$[d(G-C)_2]$, the excitonic CD appeared at a relatively high R ratio. In contrast, a characteristic negative CD band in the Soret region was apparent for both m- and p-CuTMPyP when bound to DNA and poly$[d(G-C)_2]$ at the low R ratios, indicating that the porphyrin molecule intercalates. However, the DNA is bent near the intercalation site and the plane of the porphyrin molecule tilts relative to the DNA helix axis, as judged by the magnitude of the reduced LD. Various stacking patterns were identified by the shape of the CD spectrum for m- and p-CuTMPyP when bound to poly$[d(A-T)_2]$. Three species for the former complex and two for the latter complex were found which may reflect the extent of the stacking.