• Title/Summary/Keyword: Binding energies

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Molecular Nodeling of Complexation of Alkyl Ammonium Ions by p-tert-Butylcalix[4]crown-6-ether

  • Choe, Jong In;Kim, Gwang Ho;Jang, Seok Gyu
    • Bulletin of the Korean Chemical Society
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    • v.21 no.5
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    • pp.465-470
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    • 2000
  • The conformations and energies of p-tert-butylcalix[4] crown-6-ether (1) and its alkyl ammonium complexes have been simulated by AM1 semi-empirical quantum mechanics and molecular mechanics calculations using a variety of forcefields (MM2, MM+, CVFF). We performed molecular dynamics calculations to simulate the behavior of these coplexes primartily focusing on the three representative conformations (cone, partial cone, 1,3-alternate) of host molecule 1. When we performed AM1 semi-empirical and molecular mechanics calculations, the one conformation was generally found to be most stable for all the employed calculation methods. The primary binding site of host 1 for the recognition of alkyl ammonium guests was confirmed to be the central part of the crown moiety. The complexation enthalpy calculations revealed that the alkyl amonium cations having smaller and linear alkyl group showed the better complexation efficiencies when combined with p-tert-butylcalix[4]crown-6-ether, that is in satisfactory agreement with the experimental results.

Cyclic Host Having Double Bonds as Bridging Units

  • Kyung-Soo Paek;Donald J. Cram
    • Bulletin of the Korean Chemical Society
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    • v.10 no.6
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    • pp.568-572
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    • 1989
  • Terphenyl dialdehyde 6 was obtained in 17.4% overall yield through oxidative coupling, methylation, and bisformylation reactions starting from p-cresol, and then coupled intermolecularly using McMurry reaction to give 22-membered macrocylic host 7 in 14.4% yield. In crystal structure host 7 has $C2_v$ symmetry with cis-cis configuration of two double bonds. Four methoxy groups adjacent to double bonds and the other two methoxy groups are directed opposite side, forming a cavity which can nest a guest. The cavity is filled by two inward-turned methyl groups out of four methoxy groups adjacent to double bonds. The kinetically controlled reaction mechanism leading to cis product was proposed. The cation binding properties of 7 were obtained using picrate extraction experiment from $D_2O\; into\; CDCl_3\; at\; 25^{\circ}C$. All the spherical cations (from $Li^+ to NH4^+)$ are complexed with free energies of $7.3{\pm}0.3$ kcal/mol.

The Binding Nature between Chromophore and Apoprotein in the Photoreceptor of Stentor coeruleus Probed by Conformational Analysis

  • Kang, Young-Kee;Chae, Quae
    • Bulletin of the Korean Chemical Society
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    • v.6 no.5
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    • pp.300-303
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    • 1985
  • To understand the nature of the linkage between chromophore and apoprotein in the photoreceptor of Stentor coeruleus, a conformational analysis has been carried out on the dipeptide amides linked to the chromophore hypericin using an empirical potential function. The conformational energies for the dipeptide amides of Glu (OHyp)-X-NHMe, where X = Leu, Phe, Asp, and Tyr, have been calculated to investigate the influence of peptide residues in stabilizing conformers. It was found that the increase of acidity of hypericin upon photoexcitation may be facilitated by the formation of intramolecular hydrogen bonds between hydroxyl groups of hypericin and carbonyl groups of peptide backbone, and that the stabilities of dipeptide amides do not significantly depend on peptide residues directly linked to chromophore.

Molecular modeling of COX-2 inhibitors: 3D-QSAR and docking studies

  • Kim, Hye-Jung;Chae, Chong-Hak;Yoo, Sung-Eun;Yi, Kyu-Yang;Park, Kyung-Lae
    • Proceedings of the PSK Conference
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    • 2003.10b
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    • pp.65.2-65.2
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    • 2003
  • 88 selective COX-2 inhibitors belonging to three chemical classes (triaryl rings, diaryl cycloalkanopyrazoles, and diphenyl hydrazides) were studied using comparative molecular field analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA). Partial least squares analysis produced statistically significant models with q values of 0.84 and 0.79 for CoMFA and CoMSIA, respectively. The key spatial properties were detected by careful analysis of the isocontour maps. The binding energies calculated from flexible docking correlated with inhibitory activities by the least-squares fit method. (omitted)

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Energy separation and carrier-phonon scattering in CdZnTe/ZnTe quantum dots on Si substrate

  • Man, Min-Tan;Lee, Hong-Seok
    • Proceedings of the Korean Vacuum Society Conference
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    • 2015.08a
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    • pp.191.2-191.2
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    • 2015
  • Details of carrier dynamics in self-assembled quantum dots (QDs) with a particular attention to nonradiative processes are not only interesting for fundamental physics, but it is also relevant to performance of optoelectronic devices and the exploitation of nanocrystals in practical applications. In general, the possible processes in such systems can be considered as radiative relaxation, carrier transfer between dots of different dimensions, Auger nonradiactive scattering, thermal escape from the dot, and trapping in surface and/or defects states. Authors of recent studies have proposed a mechanism for the carrier dynamics of time-resolved photoluminescence CdTe (a type II-VI QDs) systems. This mechanism involves the activation of phonons mediated by electron-phonon interactions. Confinement of both electrons and holes is strongly dependent on the thermal escape process, which can include multi-longitudinal optical phonon absorption resulting from carriers trapped in QD surface defects. Furthermore, the discrete quantized energies in the QD density of states (1S, 2S, 1P, etc.) arise mainly from ${\delta}$-functions in the QDs, which are related to different orbitals. Multiple discrete transitions between well separated energy states may play a critical role in carrier dynamics at low temperature when the thermal escape processes is not available. The decay time in QD structures slightly increases with temperature due to the redistribution of the QDs into discrete levels. Among II-VI QDs, wide-gap CdZnTe QD structures characterized by large excitonic binding energies are of great interest because of their potential use in optoelectronic devices that operate in the green spectral range. Furthermore, CdZnTe layers have emerged as excellent candidates for possible fabrication of ferroelectric non-volatile flash memory. In this study, we investigated the optical properties of CdZnTe/ZnTe QDs on Si substrate grown using molecular beam epitaxy. Time-resolved and temperature-dependent PL measurements were carried out in order to investigate the temperature-dependent carrier dynamics and the activation energy of CdZnTe/ZnTe QDs on Si substrate.

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Microstructure and Mechanical Properties of (Ti,Al)N Films Deposited by Ion Beam Sputtering (이온빔 스퍼터링에 의해 제조된 (Ti,Al)N 박막의 미세구조 및 기계적 특성)

  • Oh, Y.G.;Baeg, C.H.;Hong, J.W.;Wey, M.Y.;Kang, H.J.
    • Journal of the Korean Society for Heat Treatment
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    • v.16 no.6
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    • pp.329-334
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    • 2003
  • Microstructure and mechanical properties of $(Ti_{1-x}Alx)N$ films, Produced by the the Ion Beam Sputtering(IBS) method, were studied by changing the Ti, Al contents. The compositions of films determined by RBS were $(Ti_{0.75}Al_{0.25})N$, $(Ti_{0.61}Al_{0.39})N$ and $(Ti_{0.5}Al_{0.5})N$, and XPS binding energies of Ti2P, A12p and N1s shifted to higher energies than those of pure Ti, Al and N, which indicated that nitrides were formed. XRD results indicated that the NaCl structure for $$x{\leq_-}0.39$$ changed into amorphous structure at x=0.5. For films with $$x{\leq_-}0.39$$, the lattice parameter decreased in proportion to the Al content. Nanoindentation hardness value were above HV=3300 at Al content up to x=0.39. However, the hardness of films with x=0.5 abruptly decreased to HV=1800, and this lower hardness values were attributed to different crystal structure. Critical load(Lc) in scratch test showed 23N at x=0.25, 22N at x=0.39 and 22N at x=0.5, which indicated that films with different Al contents showed similar adhesion behavior.

Density Functional Theory Study of Separated Adsorption of O2 and CO on Pt@X(X = Pd, Ru, Rh, Au, or Ag) Bimetallic Nanoparticles (Pt 기반 이원계 나노입자의 산소 및 일산화탄소 흡착 특성에 대한 전자밀도함수이론 연구)

  • An, Hyesung;Ha, Hyunwoo;Yoo, Mi;Choi, Hyuck;Kim, Hyun You
    • Korean Journal of Materials Research
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    • v.28 no.6
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    • pp.365-369
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    • 2018
  • We perform density functional theory calculations to study the CO and $O_2$ adsorption chemistry of Pt@X core@shell bimetallic nanoparticles (X = Pd, Rh, Ru, Au, or Ag). To prevent CO-poisoning of Pt nanoparticles, we introduce a Pt@X core-shell nanoparticle model that is composed of exposed surface sites of Pt and facets of X alloying element. We find that Pt@Pd, Pt@Rh, Pt@Ru, and Pt@Ag nanoparticles spatially bind CO and $O_2$, separately, on Pt and X, respectively. Particularly, Pt@Ag nanoparticles show the most well-balanced CO and $O_2$ binding energy values, which are required for facile CO oxidation. On the other hand, the $O_2$ binding energies of Pt@Pd, Pt@Ru, and Pt@Rh nanoparticles are too strong to catalyze further CO oxidation because of the strong oxygen affinity of Pd, Ru, and Rh. The Au shell of Pt@Au nanoparticles preferentially bond CO rather than $O_2$. From a catalysis design perspective, we believe that Pt@Ag is a better-performing Pt-based CO-tolerant CO oxidation catalyst.

Molybdeum Oxide Film Preparation by a Magnetic Null Discharge Sputtering and its Application (자기 중성방전 스퍼터링에 의한 산화몰리브덴 박막의 제작 및 그 응용)

  • Kim, Doo-Hwan;Park, Cha-Soo;Sung, Youl-Moon
    • Journal of the Korean Institute of Illuminating and Electrical Installation Engineers
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    • v.23 no.1
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    • pp.169-175
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    • 2009
  • In this experiment molybdeum oxide($MoO_3$) films were prepared by a magnetic null discharge(MND) sputtering system and fundamental properties by XRD, XPS and SEM analysis were investigated. The initial and mean insulation resistance of the same with $MoO_3$ film were about 1.4[$M{\Omega}$] and 800[$k{\Omega}$] under the condition of applied voltage of 400[V]. The preferred orientation in the films changed from(100) to (210) with substrate temperature. Two XPS peaks of the $MoO_3$ photoelectron were detected at the binding energies of 228.9[eV] and 232.4[eV], while the binding energy of the O1s peak was 532.6[eV]. The substrate temperature and reactivity gives large effects to the structure and growth of the film and system is also very useful for performing the uniform reactive deposition. It can be found from the result of a $MoO_3$ film deposition that the system is very useful for performing the uniform reactive sputtering.

Synthesis of CoTiOx and Its Catalytic Activity in Continuous Wet TCE Oxidation (CoTiOx의 합성 및 연속 습식 TCE 산화반응에서의 촉매활성)

  • Kim, Moon-Hyeon
    • Journal of Environmental Science International
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    • v.16 no.12
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    • pp.1431-1437
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    • 2007
  • Cobalt titanates($CoTiO_x$), such as $CoTiO_3$ and $Co_2TiO_4$, have been synthesized via a solid-state reaction and characterized using X-ray diffraction(XRD) and X-ray photoelectron spectroscopic(XPS) measurement techniques, prior to being used for continuous wet trichloroethylene(TCE) oxidation at $36^{\circ}C$, to support our earlier chemical structure model for Co species in 5 wt% $CoO_x/TiO_2$(fresh) and(spent) catalysts. Each XRD pattern for the synthesized $CoTiO_3$ and $Co_2TiO_4$ was very close to those obtained from the respective standard XRD data files. The two $CoTiO_x$ samples gave Co 2p XPS spectra consisting of very strong main peaks for Co $2p_{3/2}$ and $2p_{1/2}$ with corresponding satellite structures at higher binding energies. The Co $2p_{3/2}$ main structure appeared at 781.3 eV for the $CoTiO_3$, and it was indicated at 781.1 eV with the $Co_2TiO_4$. Not only could these binding energy values be very similar to that exhibited for the 5 wt% $CoO_x/TiO_2$(fresh), but the spin-orbit splitting(${\Delta}E$) had also no noticeable difference between the cobalt titanates and a sample of the fresh catalyst. Neither of all the $CoTiO_x$ samples were active for the wet TCE oxidation, as expected, but a sample of pure $Co_3O_4$ had a good activity for this reaction. The earlier proposed model for the surface $CoO_x$ species existing with the fresh and spent catalysts is very consistent with the XPS characterization and activity measurements for the cobalt titanates.

Reversal of Multidrug Resistance in Mouse Lymphoma Cells by Extracts and Flavonoids from Pistacia integerrima

  • Rauf, Abdur;Uddin, Ghias;Raza, Muslim;Ahmad, Bashir;Jehan, Noor;Siddiqui, Bina S;Molnar, Joseph;Csonka, Akos;Szabo, Diana
    • Asian Pacific Journal of Cancer Prevention
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    • v.17 no.1
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    • pp.51-55
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    • 2016
  • Phytochemical investigation of Pistacia integerrima has highlighted isolation of two known compounds naringenin (1) and dihydrokaempferol (2). A crude extract and these isolated compounds were here evaluated for their effects on reversion of multidrug resistance (MDR) mediated by P-glycoprotein (P-gp). The multidrug resistance P-glycoprotein is a target for chemotherapeutic drugs from cancer cells. In the present study rhodamine-123 exclusion screening test on human mdr1 gene transfected mouse gene transfected L5178 and L5178Y mouse T-cell lymphoma cells showed excellent MDR reversing effects in a dose dependent manner. In-silico molecular docking investigations demonstrated a common binding site for Rhodamine123, and compounds naringenin and dihydrokaempferol. Our results showed that the relative docking energies estimated by docking softwares were in satisfactory correlation with the experimental activities. Preliminary interaction profile of P-gp docked complexes were also analysed in order to understand the nature of binding modes of these compounds. Our computational investigation suggested that the compounds interactions with the hydrophobic pocket of P-gp are mainly related to the inhibitory activity. Moreover this study s a platform for the discovery of novel natural compounds from herbal origin, as inhibitor molecules against the P-glycoprotein for the treatment of cancer.