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Yoon, Jeseong,Jang, Soonmin,Lee, Kyunghee,Shin, Seokmin Adenine Press 2009 Journal of biomolecular structure & dynamics Vol.27 No.3
<P>We performed molecular dynamics simulations for various oligomers with different beta-sheet conformations consisting of alpha-Synuclein 71-82 residues using an all atom force field and explicit water model. Tetramers of antiparallel beta-sheet are shown to be stable, whereas parallel sheets are highly unstable due to the repulsive interactions between bulky and polar side chains as well as the weaker backbone hydrogen bonds. We also investigated the stabilities of double antiparallel beta-sheets stacked with asymmetric and symmetric geometries. Our results show that this 12 amino acid residue peptide can form stable beta-sheet conformers at 320K and higher temperatures. The backbone hydrogen bonds in beta-sheet and the steric packing between hydrophobic side chains between beta-sheets are shown to give conformational stabilities.</P>
Interfacial interactions and dispersion relations in carbon–aluminium nanocomposite systems
Lee, Woong,Jang, Soonmin,Kim, Min Jun,Myoung, Jae-Min IOP Pub 2008 Nanotechnology Vol.19 No.28
<P>The interactions between a graphene sheet and an aluminium (111) layer in carbon–aluminium nanocomposite systems were investigated for various interfacial configurations using an <I>ab initio</I> simulation based on density functional theory. Dispersion relations and electron density distributions obtained for various interface registries suggest that the bond strength of the graphene/Al nanocomposite interface can be controlled by the introduction of compressive in-plane strain and/or by the removal of some atomic rows along specific crystallographic directions in the Al(111) layer. Such changes in the interfacial strength accompanied the evolution of C–Al interaction from weak secondary type to partially covalent type with successive removal of Al atom rows until the state of an ‘effectively isolated’ Al atom is reached. The application of the present simulation results to the selection of suitable material processing was also addressed.</P>
Abnormal adsorption behavior of dimethyl disulfide on gold surfaces
Noh, Jaegeun,Jang, Soonmin,Lee, Donghyung,Shin, Seokmin,Ko, Young Joon,Ito, Eisuke,Joo, Sang-Woo Elsevier 2007 CURRENT APPLIED PHYSICS Vol.7 No.6
<P><B>Abstract</B></P><P>Adsorption of dimethyl disulfide (DMDS) on gold colloidal nanoparticle surfaces has been examined to check its binding mechanism. Differently from previous results, DMDS molecules adsorbed on the gold surface at high concentration showed the S–S stretching band at ∼500cm<SUP>−1</SUP> in surface-enhanced Raman scattering (SERS) spectra, which indicates the presence of intact adsorption of DMDS molecules. However, it was found that the S–S bond of disulfides was easily cleaved on the gold surface at low concentration. These behaviors were not observed for diethyl disulfide (DEDS) or diphenyl disulfide (DPDS). Our results indicate that DMDS molecules with the shortest alkyl chains on the gold surface can be inserted into self-assembled monolayers (SAMs) without the S–S bond cleavage during self-assembly due to insufficient lateral van der Waals interaction and the low adsorption activity of disulfides, whereas DEDS with longer alkyl chains or DPDS with the weak disulfide bond dissociation energy would not. These unusual DMDS adsorption behaviors were examined by scanning tunneling microscopy (STM) and X-ray photoelectron spectroscopy (XPS). We also compared the bonding dissociation energy of the S–S bonds of various disulfides by means of a density functional theory (DFT) calculation.</P>
The contribution of polar C–H hydrogen bonds to anion binding
Choi, Yusun,Kim, Taehoon,Jang, Soonmin,Kang, Jongmin The Royal Society of Chemistry 2016 NEW JOURNAL OF CHEMISTRY Vol.40 No.1
<P>The contribution of C-H hydrogen bonds is one of the key factors to consider in anion binding receptor design. To investigate the participation of C-H hydrogen bonds through C-H polarization in an anion binding event, we have designed and synthesized three new anion receptors (receptors 1, 2 and 3). Essentially, the only difference between these receptors is the relative magnitude of the C-H(H-a) polarization. These receptors utilize two amide N-H, two aromatic C-H(H-a), anthracene 9-C-H and possibly two methyl groups as hydrogen bonding moieties. From the titrations and DFT calculations, we found that the anion binding abilities of these receptors mainly depend on the magnitude of the polarization of C-H(H-a) and receptors 1 and 2 are selective for H2PO4-.</P>
Simulated Q-annealing: conformational search with an effective potential.
Son, Won-joon,Jang, Soonmin,Shin, Seokmin Springer 2012 Journal of molecular modeling Vol.18 No.1
<P>We have tested a version of the generalized simulated annealing algorithm based on molecular dynamics simulations with effective potential suggested by Tsallis statistics. The generalized annealing method, termed 'simulated Q-annealing (SQ),' is applied to the simulations of a synthetic 11-residue peptide segment (1AQG). In SQ, the energy barriers between local minima change as the parameter q is varied and specific degrees of freedom can be selectively heated up and annealed. Conformational dynamics obtained by ordinary simulated annealing (SA) and SQ simulations are compared in order to illustrate the effectiveness of the SQ approach in conformational searching. We show that SQ can navigate the potential energy surface efficiently with a simple annealing protocol and demonstrate that conformations sampled by SQ can represent the funnel-like free energy surface.</P>
Nguyễn Hoàng Ly,Cheolmin Lee,Soonmin Jang,Jung Il Lee,주상우 대한화학회 2020 Bulletin of the Korean Chemical Society Vol.41 No.12
The evaporation of the semivolatile organic compound (SVOC) benzothiazole (BZT) from glass surfaces has been estimated by means of surface-enhanced Raman scattering (SERS) and gas-phase Fourier-transform infrared (FTIR) spectroscopy. The FTIR spectrum in the gas cell indicates the presence of BZT in the air. The density functional theory (DFT) of the vibrational spectra of BZT was tested using the B3LYP/6-311G++(d,p) basis sets with potential energy distribution (PED) analysis. The BZT thin film could be investigated using SERS by dropping a gold nanoparticle (AuNP) solution on glass surfaces. The intensified modes in the SERS spectra suggest the plausible binding modes of BZT via its N11 atom on AuNPs. A decrease in the SERS spectra indicate a substantial evaporation of BZT. The concentration of BZT in the air could be estimated as low as ~0.8% according to the infrared spectra after 24?h.
Duvjir, Ganbat,Choi, Byoung Ki,Jang, Iksu,Ulstrup, Søren,Kang, Soonmin,Thi Ly, Trinh,Kim, Sanghwa,Choi, Young Hwan,Jozwiak, Chris,Bostwick, Aaron,Rotenberg, Eli,Park, Je-Geun,Sankar, Raman,Kim, Ki-Seo American Chemical Society 2018 NANO LETTERS Vol.18 No.9
<P>Emergent phenomena driven by electronic reconstructions in oxide heterostructures have been intensively discussed. However, the role of these phenomena in shaping the electronic properties in van der Waals heterointerfaces has hitherto not been established. By reducing the material thickness and forming a heterointerface, we find two types of charge-ordering transitions in monolayer VSe<SUB>2</SUB> on graphene substrates. Angle-resolved photoemission spectroscopy (ARPES) uncovers that Fermi-surface nesting becomes perfect in ML VSe<SUB>2</SUB>. Renormalization-group analysis confirms that imperfect nesting in three dimensions universally flows into perfect nesting in two dimensions. As a result, the charge-density wave-transition temperature is dramatically enhanced to a value of 350 K compared to the 105 K in bulk VSe<SUB>2</SUB>. More interestingly, ARPES and scanning tunneling microscopy measurements confirm an unexpected metal-insulator transition at 135 K that is driven by lattice distortions. The heterointerface plays an important role in driving this novel metal-insulator transition in the family of monolayer transition-metal dichalcogenides.</P> [FIG OMISSION]</BR>