• Title, Summary, Keyword: Molecular interactions

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Relationship between Infrared Peak Maximum Position and Molecular Interactions

  • Ryu, Soo-Ryeon;Noda, Isao;Jung, Young-Mee
    • Bulletin of the Korean Chemical Society
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    • v.32 no.11
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    • pp.4011-4015
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    • 2011
  • We explored the interpretation of the well-accepted correlation between the apparent peak maximum position shift and extent of molecular interactions, like hydrogen bonding and dipole-dipole interactions, based on the overlapped multiple band model. The simulation of two overlapped Lorentzian bands was carried out to interpret how the maximum position of a composite peak relates to the relative contributions of two species representing the different levels of molecular interactions, i.e., free (or very weekly bound) vs. strongly bound. To demonstrate the validity of our interpretation of the origin of the peak position shift, the temperaturedependent IR spectra of ethylene glycol were also analyzed. It was found through the analysis of simulated and experimental spectra that the apparent peak shift in certain case can be safely interpreted as the measure of the strength of hydrogen bonding. The result of this study gives a new insight to interpret molecular interactions probed by vibrational spectroscopy.

Molecular Dynamics Simulation Studies of the Effects of the Protonation State of Chitosan in Interactions with Bacterial Membranes (키토산의 양성자화가 세균막과의 상호작용에 미치는 효과 연구)

  • Truong, Gia Khuong;Yi, Myunggi
    • Korean Journal of Fisheries and Aquatic Sciences
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    • v.49 no.6
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    • pp.815-822
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    • 2016
  • The cationic biopolymer chitosan has several applications in medicine. Chitosan is the deacetylated derivative of chitin, the second most abundant naturally occurring polymer. Recent studies have investigated the relationship between chitosan and antibacterial activity. However, the molecular interactions and mechanisms have not been detailed. This study used molecular dynamics simulations to study interactions between chitosan and anionic bacterial membranes (POPE-POPG) and electrically neutral non-bacterial membranes (POPC). We calculated the free energy using umbrella sampling to compare the interactions between membranes and chitosan in different protonation states. Fully protonated chitosan interacted most strongly with the bacterial membranes, but weakly with non-bacterial membranes. These results suggest that electrostatic interactions are the main mechanism of the antibacterial activity of chitosan, and they provide insights into the design of novel antibacterial and antimicrobial agents.

Two-dimensional Supramolecular Structures by Hydrogen and Halogen Interactions

  • Yoon, Jong-Keon;Kim, Ho-Won;Chung, Kyung-Hoon;Kahng, Se-Jong
    • Proceedings of the Korean Vacuum Society Conference
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    • pp.354-354
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    • 2010
  • Supramolecualr ordering has been actively studied due to it's possible applications to the fabrication processes of nano-electronic devices. Van der Waals interaction and hydrogen bonding are frequently studied mechanisms for various molecular structures based on non-uniform charge distributions. Halogen atoms in molecules can have electrostatic interactions with similar strength. Big halogen atoms have strong non-uniform charge distributions. To study molecular orderings formed by hydrogen and halogen interactions, we chose a molecular system containing oxygen, hydrogen, and bromine atoms, a bromo-quinone. A two-dimensional molecular network was studied on Au(111) using a low-temperature scanning tunneling microscope. Bromo-quinone molecules form self-assembled square grids having windmill structures. Their molecular orderings, chiral structures, and defects are explained in terms of hydrogen and halogen interactions.

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The Influence of Dielectric Constant on Ionic and Non-polar Interactions

  • Hwang, Kae-Jung;Nam, Ky-Youb;Kim, Jung-Sup;Cho, Kwang-Hwi;Kong, Seong-Gon;No, Kyoung-Tai
    • Bulletin of the Korean Chemical Society
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    • v.24 no.1
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    • pp.55-59
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    • 2003
  • This work is focused on analyzing ion-pair interactions and showing the effect of solvent induced inter-atomic attractions in various dielectric environments. To estimate the stability of ion-pairs, SCI-PCM ab initio MO calculations were carried out. We show that the solvent-induced attraction or ‘cavitation' energy of the ion-pair interactions in solution that arises mainly from the stabilization of the water molecules by the generation of an electrostatic field. In fact, even the strong electrostatic interaction characteristic of ion-pair interactions in the gas phase cannot overcome the destabilization or reorganization of the water molecules around solute cavities that arise from cancellation of the electrostatic field. The solvent environment, possibly supplemented by some specific solvent molecules, may help place the solute molecule in a cavity whose surroundings are characterized by an infinite polarizable dielectric medium. This behavior suggests that hydrophobic residues at a protein surface could easily contact the side chains of other nearby residues through the solvent environment, instead of by direct intra-molecular interactions.

Ultrastructure of Compatible and Incompatible Interactions of Pumpkin Stems Infected with Phytophthora capsici

  • Lee, Byung-Kook;Hong, Jeum-Kyu;Hwang, Byung-Kook
    • The Plant Pathology Journal
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    • v.17 no.1
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    • pp.29-35
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    • 2001
  • Early infection process of Phytophthora capsici in pumpkin stems was similar in the compatible and incompatible interactions 24 h after inoculation. Intercellularly growing hyphae penetrated host parenchyma cells by growing hyphae penetrated host parenchyma cells by forming haustoria. An extrahaustorial matrix was found around the haustoria in both compatible and incompatible interactions. No wall appositions were observed at the infection sites in the parenchyma cells. In the compatible interaction, infecting hyphae grew well in the intercellular spaces between xylem vessels in stem tissues. Degraded host cell wall, plasmolysis of plasma membrane, and degenerated chloroplasts were pathological features of pumpkin stem tissues in both compatible and incompatible interactions. A characteristic host response in the resistant pumkin cultivar Danmatmaetdol was rapid cytoplasmic movement of host cells toward the oomycete haustoria.

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RNA-Protein Interactions and Protein-Protein Interactions during Regulation of Eukaryotic Gene Expression

  • Varani, Luca;Ramos, Andres;Cole, Pual T.;Neuhaus, David;Varani, Gabriele
    • Journal of the Korean Magnetic Resonance Society
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    • v.2 no.2
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    • pp.152-157
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    • 1998
  • The diversity of RNA functions ranges from storage and propagation of genetic information to enzymatic activity during RNA processing and protein synthesis. This diversity of functions requires an equally diverse arrays of structures, and, very often, the formation of functional RNA-protein complexes. Recognition of specific RNA signals by RNA-binding proteins is central to all aspects of post-transcriptional regulation of gene expression. We will describe how NMR is being used to understand at the atomic level how these important biological processes occur.

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Hydrogen-bonded Molecular Network of Anthraquinone on Au(111)

  • Kim, Ji-Yeon;Yoon, Jong-Keon;Park, Ji-Hun;Kim, Ho-Won;Kahng, Se-Jong
    • Proceedings of the Korean Vacuum Society Conference
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    • pp.107-107
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    • 2011
  • Supramolecular structures of anthraquinone molecules on a metallic surface are studied using scanning tunneling microscope (STM) under ultrahigh-vacuum conditions. When we deposited anthraquinone molecules on Au(111) substrate, the molecules formed three different phases (Chevron type, tetragon type and disordered type) on the surface. Based on our STM measurements, we proposed models for the observed molecular structures. Chevrons are consisted of several molecular chains, which make well-ordered two-dimensional islands by some weak interrow interactions and we could observe tetragon structures which make array of (111) metallic surface. each molecular rows in the chevrons are stabilized by two parallel O-H hydrogen bonds and disordered structures are observed 1-dimensional phase with hydrogen bond. First-principles calculations based on density functional theory are performed to reproduce the proposed models. Distances and energy gains for each intermolecular bond are estimated. In this presentation, we explain possible origins of these molecular structures in terms of hydrogen bonds, Van der Waals interactions and molecule-substrate interactions.

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Two-dimensional Supramolecular Ordering via Hydrogen and Halogen Bondings

  • Yoon, Jong-Keon;Kim, Ho-Won;Jeon, Jeong-Heum;Kahng, Se-Jong
    • Proceedings of the Korean Vacuum Society Conference
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    • pp.11-11
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    • 2010
  • Supramolecualr ordering has been actively studied due to it's possible applications to the fabrication processes of nano-electronic devices. Van der Waals interaction and hydrogen bonding are frequently studied mechanisms for various molecular structures based on non-uniform charge distributions. Halogen atoms in molecules can have electrostatic interactions with similar strength. Big halogen atoms have strong non-uniform charge distributions. To study molecular orderings formed by hydrogen and halogen interactions, we chose a molecular system containing oxygen, hydrogen, and bromine atoms, a bromo-quinone. A two-dimensional molecular network was studied on Au(111) using a low-temperature scanning tunneling microscope. Bromo-quinonemolecules form self-assembled square grids having windmill structures. Their molecular orderings, chiral structures, and defects are explained in terms of hydrogen and halogen interactions.

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Darapladib Binds to Lipoprotein-Associated Phospholipase A2 with Meaningful Interactions

  • Do, Kyoung-Rok;Kim, Chul;Chang, Byungha;An, Seong Soo A.;Shin, Jae-Min;Yea, Sang-Jun;Song, Mi-Young;No, Kyoung Tai;Lee, Jee-Young
    • Bulletin of the Korean Chemical Society
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    • v.35 no.1
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    • pp.250-252
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    • 2014
  • Lipoprotein-associated phospholipase A2 (Lp-$PLA_2$) is a crucial enzyme in atherosclerosis as a potential drug target. The most remarkable Lp-$PLA_2$ inhibitory drug is Darapladib. We determined the binding pose of Darapladib to Lp-$PLA_2$ through docking study. Darapladib formed two hydrogen bonding interactions with the side chain of Tyr160 and Gln352 and several pi-pi interactions with aromatic and aliphatic hydrophobic residues of Lp-$PLA_2$. It is known that the dietylpropan-amine moiety of Darapladib has influence on the improvement of its oral bioavailability and we supposed this in our docking results.