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ISSN 0253-2964(Print)
ISSN 1229-5949(Online)
Volume 33, Number 3
BKCSDE 33(3)
March 20, 2012
Festschrift for Professor Kook Joe Shin |
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A Tribute to Professor Kook Joe Shin by Mino Yang and Hyojoon Kim
Kook-Joe Shin Retiring
Kook Joe Shin, An Excellent Scientist, Teacher, and Administer
Autobiography
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763 |
Unusual Non-magnetic Metallic State in Narrow Silicon Carbon Nanoribbons by Electron or Hole Doping
Ping Lou*, Jin Yong Lee*
Keywords: Magnetic, Silicon carbon nanoribbon, Electron doping, Hole doping, Band structure
Online date: February 24, 2012
DOI: https://doi.org/10.5012/bkcs.2012.33.3.763
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770 |
Conformational Sampling of Flexible Ligand-binding Protein Loops
Gyu Rie Lee, Woong-Hee Shin, Hahnbeom Park, Seokmin Shin, Chaok Seok*
Keywords: Loop modeling, Ligand binding, Conformational change, Conformational sampling
Online date: February 24, 2012
DOI: https://doi.org/10.5012/bkcs.2012.33.3.770
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775 |
Adsorption Mechanisms of NH3 on Chlorinated Si(100)-2 × 1 Surface
Hee Soon Lee, Cheol Ho Choi*
Keywords: SIMOMM, Mechanism, Ammonia, Silicon surface, Ab initio
Online date: February 23, 2012
DOI: https://doi.org/10.5012/bkcs.2012.33.3.775
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779 |
Eigenfunctions for Liouville Operators, Classical Collision Operators, and Collision Bracket Integrals in Kinetic Theory Made Amenable to Computer Simulations
Byung Chan Eu
Keywords: Liouville operator, Eigenfuntions, Classical scattering, Collision bracket integrals, Transport coefficients
Online date: February 29, 2012
DOI: https://doi.org/10.5012/bkcs.2012.33.3.779
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790 |
Isotachophoretically Assisted On-Line Complexation of Trace Metal Ions in a Highly Saline Matrix for Capillary Electrophoresis
Jihye Kim, Kihwan Choi, Sunyoung Cho, Asif Riaz, Doo Soo Chung*
Keywords: Transient isotachophoresis, Salt, Trace metals, Cadmium, 4-(2-Thiazolylazo) resorcinol
Online date: February 27, 2012
DOI: https://doi.org/10.5012/bkcs.2012.33.3.790
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795 |
Effects of Energetic Disorder and Mobility Anisotropy on Geminate Electron-hole Recombination in the Presence of a Donor-acceptor Heterojunction
Mariusz Wojcik,* Przemyslaw Michalak, M. Tachiya*
Keywords: Organic solar cells, Photogeneration, Charge carriers, Simulation
Online date: February 29, 2012
DOI: https://doi.org/10.5012/bkcs.2012.33.3.795
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803 |
Two-Component Spin-orbit Effective Core Potential Calculations with an All-electron Relativistic Program DIRAC
Young Choon Park, Ivan S. Lim, Yoon Sup Lee*
Keywords: Two-component method, Relativistic effective core potentials, Spin-orbit interaction, Hydrogen Halide, Hydrogen bihalide
Online date: February 24, 2012
DOI: https://doi.org/10.5012/bkcs.2012.33.3.803
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809 |
Study of the Resonance Structures of the Preionizing Spectrum of Molecular Hydrogen by Phase-shifted Multichannel Quantum Defect Theory
Chun-Woo Lee
Keywords: Phase-shifted MQDT, Overlapping resonances, Preionization of H2, Interlopers
Online date: March 06, 2012
DOI: https://doi.org/10.5012/bkcs.2012.33.3.809
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818 |
Langer Modification in WKB Quantization for Translationally Shape Invariant Potentials
Hosung Sun
Keywords: WKB quantization, Langer modification, Shape invariant potentials
Online date: March 07, 2012
DOI: https://doi.org/10.5012/bkcs.2012.33.3.818
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825 |
Carrier Gas Assisted Solvent Vapor Treatment for Surface Nanostructuring of Molecular Thin Films
Hyejin Gong, Jinhyun Kim, Sanggyu Yim*
Keywords: Solvent treatment, Suface nanostructuring, Molecular thin film, CuPc
Online date: February 29, 2012
DOI: https://doi.org/10.5012/bkcs.2012.33.3.825
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828 |
Comparative Study of Implicit and Explicit Solvation Models for Probing Tryptophan Side Chain Packing in Proteins
Changwon Yang, Youngshang Pak*
Keywords: Replica exchange molecular dynamics simulation, Implicit solvation model, Tryptophan side chain packing, Protein folding
Online date: February 23, 2012
DOI: https://doi.org/10.5012/bkcs.2012.33.3.828
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833 |
Characterization of Thermal Degradation of Polytrimethylene Terephthalate by MALDI-TOF Mass Spectrometry
Sungwoo Jang, Eun Kyung Yang, Sung Il Jin, Young Dal Cho, Eun Kyung Choe, Chan Ryang Park*
Keywords: MALDI-TOF MS, PTT, Thermal degradation, β-CH hydrogen transfer, End group
Online date: March 05, 2012
DOI: https://doi.org/10.5012/bkcs.2012.33.3.833
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839 |
Single Crystalline NbO2 Nanowire Synthesis by Chemical Vapor Transport Method
Sunghun Lee, Hana Yoon, Ilsun Yoon, Bongsoo Kim*
Keywords: NbO2, Nanowires, Single crystal, Vapor transport, Raman spectrum
Online date: February 24, 2012
DOI: https://doi.org/10.5012/bkcs.2012.33.3.839
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843 |
Kinetics and Mechanism of the Anilinolysis of Dibutyl Chlorothiophosphate in Acetonitrile
Md. Ehtesham Ul Hoque, Hai Whang Lee*
Keywords: Thiophosphoryl transfer reaction, Anilinolysis, Dibutyl chlorothiophosphate, Deuterium kinetic isotope effect
Online date: March 05, 2012
DOI: https://doi.org/10.5012/bkcs.2012.33.3.843
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Supporting Information | Full Text: PDF
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848 |
Computational Study on Oligomer Formation of Fibril-forming peptide of α-Synuclein
SeongByeong Park, Jeseong Yoon, Soonmin Jang, Kyunghee Lee, Seokmin Shin*
Keywords: α-Synuclein, Replica-exchange molecular dynamics (REMD), Fibril formation, Antiparallel β- sheet
Online date: March 05, 2012
DOI: https://doi.org/10.5012/bkcs.2012.33.3.848
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855 |
MS-HEMs: An On-line Management System for High-Energy Molecules at ADD and BMDRC in Korea
Sung Kwang Lee, Soo Gyeong Cho, Jae Sung Park, Kwang Yeon Kim, Kyoung Tae No
Keywords: Management system, High-energy molecules (HEMs), Chemical search, Molecular descriptor, Impact sensitivity
Online date: February 29, 2012
DOI: https://doi.org/10.5012/bkcs.2012.33.3.855
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862 |
Calculation of the Absolute Rate of Human Cu/Zn Superoxide Dismutases from Atomic-Level Molecular Dynamics Simulations
Jinuk Lee,* Woojin Lee, Hwangseo Park, Sangyoub Lee*
Keywords: Reaction rates, Molecular dynamics simulations, Superoxide dismutase
Online date: February 24, 2012
DOI: https://doi.org/10.5012/bkcs.2012.33.3.862
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869 |
Pharmacophore Modeling and Molecular Dynamics Simulation to Find the Potent Leads for Aurora Kinase B
Sugunadevi Sakkiah, Sundarapandian Thangapandian, Yongseong Kim, Keun Woo Lee*
Keywords: Aurora kinase, Pharmacophore, Molecular dynamics, Homology modeling, Molecular docking
Online date: February 29, 2012
DOI: https://doi.org/10.5012/bkcs.2012.33.3.869
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881 |
Very Efficient Nucleophilic Aromatic Fluorination Reaction in Molten Salts: A Mechanistic Study
Sung-Woo Jang, Sung-Woo Park, Byoung Se Lee, Dae Yoon Chi,* Choong Eui Song,* Sungyul Lee*
Keywords: Mechanism, SNAr, Molten salt
Online date: February 23, 2012
DOI: https://doi.org/10.5012/bkcs.2012.33.3.881
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885 |
Dynamics of Resonant Energy Transfer in OH Vibrations of Liquid Water
Mino Yang
Keywords: Water, Master equation, Energy transfer, OH stretching, Förster
Online date: February 23, 2012
DOI: https://doi.org/10.5012/bkcs.2012.33.3.885
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893 |
Molecular Dynamics Simulation Study on the Carbon Nanotube Interacting with a Polymer
Leton C. Saha, Shabeer A. Mian, Joonkyung Jang*
Keywords: Carbon nanotube, Polymer, Molecular dynamics simulation, Deformation, Binding energy
Online date: February 23, 2012
DOI: https://doi.org/10.5012/bkcs.2012.33.3.893
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897 |
Force-induced Unbinding Dynamics in a Multidimensional Free Energy Landscape
Changbong Hyeon
Keywords: Force dynamics, Kramers equation, Multidimensional surface, Hydrodynamic coupling
Online date: March 06, 2012
DOI: https://doi.org/10.5012/bkcs.2012.33.3.897
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901 |
Effect of Pore Geometry on Gas Adsorption: Grand Canonical Monte Carlo Simulation Studies
Eonji Lee, Rakwoo Chang,* Ji-Hyung Han, Taek Dong Chung
Keywords: Pore geometry, Gas adsorption, Grand canonical Monte Carlo simulation
Online date: February 23, 2012
DOI: https://doi.org/10.5012/bkcs.2012.33.3.901
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906 |
Poly(ethylenimine)-Stabilized Hollow Gold-Silver Bimetallic Nanoparticles: Fabrication and Catalytic Application
Kuan Soo Shin,* Ji Hoon Kim, In Hyun Kim, Kwan Kim*
Keywords: Au-Ag, Hollow nanoparticles, Poly(ethylenimine), Catalyst, 4-Nitrophenol
Online date: February 24, 2012
DOI: https://doi.org/10.5012/bkcs.2012.33.3.906
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911 |
Potential of Mean Force Calculations for Ion Selectivity in a Cyclic Peptide Nanotube
Kyu-Min Choi, Chan Ho Kwon, Hong Lae Kim, Hyonseok Hwang*
Keywords: Cyclic peptide nanotube, Ion selectivity, Molecular dynamics simulation, Potential of mean force, Umbrella sampling
Online date: March 05, 2012
DOI: https://doi.org/10.5012/bkcs.2012.33.3.911
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917 |
Conformational Preferences of Glycerol in the Gas Phase and in Water
Keunhong Jeong, Byung Jin Byun, Young Kee Kang*
Keywords: Glycerol, Conformations, Hydrogen bonds, Density functional calculations, Solvation effects
Online date: February 29, 2012
DOI: https://doi.org/10.5012/bkcs.2012.33.3.917
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Supporting Information | Full Text: PDF
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925 |
Role of Diffusion in the Kinetics of Reversible Enzyme-catalyzed Reactions
Attila Szabo, Huan-Xiang Zhou*
Keywords: Diffusion-influenced reaction, Enzyme-catalyzed reaction, Michaelis-Menten kinetics
Online date: March 06, 2012
DOI: https://doi.org/10.5012/bkcs.2012.33.3.925
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929 |
Phase Transition of Confined Gold Nanoparticles: Replica Exchange Molecular Dynamics Study
Hyunsik Kim, Feng-Yin Li, Soonmin Jang*
Keywords: Gold nanoparticle, Molecular dynamics simulation, Confinement
Online date: February 24, 2012
DOI: https://doi.org/10.5012/bkcs.2012.33.3.929
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933 |
Behavior of Poisson Bracket Mapping Equation in Studying Excitation Energy Transfer Dynamics of Cryptophyte Phycocyanin 645 Complex
Weon-Gyu Lee, Aaron Kelly, Young Min Rhee*
Keywords: Semiclassical method, Quantum classical dynamics, Excited state, Excitation energy transfer, Photosynthesis
Online date: March 05, 2012
DOI: https://doi.org/10.5012/bkcs.2012.33.3.933
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941 |
Accumulation and Decay of Macroscopic Correlations in Elementary Reactions Kinetics
Alexander B. Doktorov,* Alexander A. Kipriyanov, Alexey A. Kipriyanov
Keywords: Elementary reaction, Kinetics, Correlations, Smoluchowski, Encounter theory
Online date: March 14, 2012
DOI: https://doi.org/10.5012/bkcs.2012.33.3.941
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953 |
Synthesis of Biologically Active Chalcones and their Anti-inflammatory Effects
Jae-Ho Jeon, Si-Jun Kim, Cheol Gi Kim, Jin-Kyung Kim, Jong-Gab Jun*
Keywords: Chalcones, Claisen-Schmidt condensation, Anti-inflammatory studies, EDDA, NO production
Online date: February 29, 2012
DOI: https://doi.org/10.5012/bkcs.2012.33.3.953
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958 |
The Effect of the Oxygen Scavenging System on the pH of Buffered Sample Solutions: in the Context of Single-molecule Fluorescence Measurements
Sung Eun Kim, Il Buem Lee, Seok-Cheol Hong*
Keywords: Oxygen scavenging system, pH, Single-molecule fluorescence, i-motif, Gloxy
Online date: March 05, 2012
DOI: https://doi.org/10.5012/bkcs.2012.33.3.958
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963 |
Nonclassical Chemical Kinetics for description of Chemical Fluctuation in a Dynamically Heterogeneous Biological System
Yu Rim Lim, Seong Jun Park, Sangyoub Lee, Jaeyoung Sung*
Keywords: Chemical fluctuation, Nonclassical kinetics, Single enzyme kinetics, Reaction event counting
Online date: February 27, 2012
DOI: https://doi.org/10.5012/bkcs.2012.33.3.963
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971 |
Facilitated Protein-DNA Binding: Theory and Monte Carlo Simulation
Kihyun Park,* Taejun Kim, Hyojoon Kim*
Keywords: Diffusion-influenced reaction, Facilitated diffusion, Protein-DNA binding, Dimension reduction, Exact solution
Online date: March 08, 2012
DOI: https://doi.org/10.5012/bkcs.2012.33.3.971
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975 |
Structure and Dynamics of Dilute Two-Dimensional Ring Polymer Solutions
Younghoon Oh, Hyun Woo Cho, Jeongmin Kim, Chang Hyun Park, Bong June Sung*
Keywords: Ring polymer, Molecular dynamics, Two-dimensions, Confinement
Online date: March 05, 2012
DOI: https://doi.org/10.5012/bkcs.2012.33.3.975
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980 |
A Minimalist Model of Single Molecule Spectroscopy in a Dynamic Environment Studied by Metadynamics
Inrok Oh, Eunsang Lee, YounJoon Jung*
Keywords: Single molecule spectroscopy, Lattice model, Dynamic environment, Lineshape, Metadynamics
Online date: March 06, 2012
DOI: https://doi.org/10.5012/bkcs.2012.33.3.980
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987 |
Sequence Coverage Enhancement Using Magnetic Nanoparticles in Matrix-Assisted Laser Desorption/Ionization Mass Spectrometric Protein Analysis
Eunhye Park, Jin-Su Song, Hie-Joon Kim*
Keywords: Matrix-assisted laser desorption/ionization (MALDI), Sequence coverage, Magnetic nanoparticles (MNPs), Phosphoric acid
Online date: March 06, 2012
DOI: https://doi.org/10.5012/bkcs.2012.33.3.987
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993 |
Fluorescence Spectroscopic and Time-Dependent Density-functional Theory Studies of Diphenylsilane
Bong Hyun Boo*, Jae Kwang Lee
Keywords: Diphenylsilane, Fluorescence excitation, Time-dependent density-functional theory, Oscillator strength, Molecular beam
Online date: March 06, 2012
DOI: https://doi.org/10.5012/bkcs.2012.33.3.993
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997 |
Multistep Quantum Master Equation Theory for Response Functions in Four Wave Mixing Electronic Spectroscopy of Multichromophoric Macromolecules
Seogjoo jang
Keywords: Four wave mixing, Response function, Multichromophoric macromolecule
Online date: March 14, 2012
DOI: https://doi.org/10.5012/bkcs.2012.33.3.997
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1009 |
Prediction of a Strong Effect of a Weak Magnetic Field on Diffusion Assisted Reactions in Non Equilibrium Conditions
Alexey A. Kipriyanov (Jr.)*, Peter A. Purtov*
Keywords: Radicals, Magnetic effects, Nonlinear phenomena
Online date: March 05, 2012
DOI: https://doi.org/10.5012/bkcs.2012.33.3.1009
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1015 |
Direct Calculation Method for Excited-state Diffusion-influenced Reversible Reactions with an External Field
Shang Yik Reigh*, Hyojoon Kim*
Keywords: Reversible reaction, External field, Reaction-diffusion systems, Excited state reaction, Anisotropy
Online date: March 08, 2012
DOI: https://doi.org/10.5012/bkcs.2012.33.3.1015
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1020 |
Comparison of Alternate Approaches for Reversible Geminate Recombination
Svetlana S. Khokhlova, Noam Agmon*
Keywords: Diffusion, Feynman-Kac equation, Geminate reaction, Reversibility
Online date: March 08, 2012
DOI: https://doi.org/10.5012/bkcs.2012.33.3.1020
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1029 |
Time-Dependent Density Functional Theory Study on Cyclopentadithiophene- Benzothiadiazole-Based Push-Pull-Type Copolymers for New Design of Donor Materials in Bulk Heterojunction Organic Solar Cells
Jamin Ku, Daekyun Kim, Taekhee Ryu, Eunhwan Jung, Yves Lansac,* Yun Hee Jang*
Keywords: Organic solar cell, Push-pull-type copolymer, Time dependent density functional theory
Online date: March 06, 2012
DOI: https://doi.org/10.5012/bkcs.2012.33.3.1029
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1037 |
Kinetics and Mechanism of the Anilinolysis of (2R,4R,5S)-(+)-2-Chloro-3,4-dimethyl -5-phenyl-1,3,2-oxazaphospholidine 2-Sulfide in Acetonitrile
Hasi Rani Barai, Hai Whang Lee*
Keywords: Phosphoryl transfer reaction, Anilinolysis, (2R,4R,5S)-(+)-2-Chloro-3,4-dimethyl-5-phenyl- 1,3,2-oxazaphospholidine 2-sulfide, Deuterium kinetic isotope effect
Online date: March 05, 2012
DOI: https://doi.org/10.5012/bkcs.2012.33.3.1037
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Supporting Information | Full Text: PDF
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1042 |
Kinetics and Mechanism of the Pyridinolysis of Diethyl Isothiocyanophosphate in Acetonitrile
Keshab Kumar Adhikary, Hai Whang Lee*
Keywords: Phosphoryl transfer reaction, Pyridinolysis, Diethyl isothiocyanophosphate, Discrete biphasic free energy relationship
Online date: March 05, 2012
DOI: https://doi.org/10.5012/bkcs.2012.33.3.1042
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Supporting Information | Full Text: PDF
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1047 |
Kinetics and Mechanism of the Pyridinolysis of (2R,4R,5S)-(+)-2-Chloro-3,4-dimethyl- 5-phenyl-1,3,2-oxazaphospholidine 2-Sulfide in Acetonitrile
Hasi Rani Barai, Hai Whang Lee*
Keywords: Thiophosphoryl transfer reaction, Pyridinolysis, (2R,4R,5S)-(+)-2-Chloro-3,4-dimethyl-5-phenyl- 1,3,2-oxazaphospholidine 2-sulfide, Biphasic concave upward free energy relationship, Isokinetic relationship
Online date: March 05, 2012
DOI: https://doi.org/10.5012/bkcs.2012.33.3.1047
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Supporting Information | Full Text: PDF
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1052 |
Density Functional Theoretical Study on the Carbon–halide Oxidative Additions to a Rh Pincer Complex
Yongseong Kim, Han Young Woo, Yong-Jae Lee, Sungu Hwang*
Keywords: DFT, Oxidative addition, Aryl halides, Alkyl halides, Rh pincer ligand
Online date: February 24, 2012
DOI: https://doi.org/10.5012/bkcs.2012.33.3.1052
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1055 |
Pyridinolysis of Dibutyl Chlorophosphate in Acetonitrile
Md. Ehtesham Ul Hoque, Hai Whang Lee*
Keywords: Phosphoryl transfer reaction, Pyridinolysis, Dibutyl chlorophosphate, Steric effect
Online date: March 05, 2012
DOI: https://doi.org/10.5012/bkcs.2012.33.3.1055
Abstract |
Supporting Information | Full Text: PDF
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1059 |
A Structural Model of Glycosylated Neuraminidase Based on Molecular Dynamics Simulations for Virtual Inhibitor Screening Against Influenza Virus
Youngjin Choi, Chanho Kwon, Eunae Cho, In-Cheol Kang, Hyun-Ja Jeong, Sungjun Park, Karpjoo Jeong, Tak Hur, Seunho Jung*
Keywords: Glycosylation, Influenza virus, Neuraminidase, Virtual screening, Molecular dynamics
Online date: February 23, 2012
DOI: https://doi.org/10.5012/bkcs.2012.33.3.1059
Abstract |
Supporting Information | Full Text: PDF
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1063 |
Energy Flow and Bond Dissociation in the Collision between Vibrationally Excited Toluene and HBr
Sang Kwon Lee, Jongbaik Ree*
Keywords: Collision-induced, Intramolecular, Toluene, HBr, Dissociation
Online date: February 27, 2012
DOI: https://doi.org/10.5012/bkcs.2012.33.3.1063
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1067 |
Precise Size-control of Silica Nanoparticles via Alkoxy Exchange Equilibrium of Tetraethyl Orthosilicate (TEOS) in the Mixed Alcohol Solution
Joohyun Lim, Shin-Woo Ha, Jin-Kyu Lee*
Keywords: Silica size, Alkoxy exchange, TEOS, Solvent effect, Nanoparticle
Online date: March 05, 2012
DOI: https://doi.org/10.5012/bkcs.2012.33.3.1067
Abstract |
Supporting Information | Full Text: PDF
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1071 |
Volume-Bloch Operator Approach to Quantum Reactive Scattering on Non-orthogonal Scattering Coordinates
Hyo Weon Jang
Keywords: Quantum reactive scattering, Bloch operator, Galerkin’s method, Multiarrangement scattering
Online date: March 06, 2012
DOI: https://doi.org/10.5012/bkcs.2012.33.3.1071
Abstract |
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1075 |
Amplified Spontaneous Emission of GaN Nanorods
Hyeong Seop Shim, Joo Hee Seo, Noh Soo Han, Seung Min Park, Yuri Sohn, Chinkyo Kim*, Jae Kyu Song*
Keywords: Gallium nitride, Amplified spontaneous emission, Superlinear increase, Wide band gap
Online date: March 06, 2012
DOI: https://doi.org/10.5012/bkcs.2012.33.3.1075
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1078 |
Preferential Evolution of Prussian Blue's Morphology from Cube to Hexapod
Seung-Hyun Lee, Young-Duk Huh*
Keywords: Prussian blue, Morphology evolution, Preferential etching
Online date: February 29, 2012
DOI: https://doi.org/10.5012/bkcs.2012.33.3.1078
Abstract |
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1081 |
Origin for Fluxional Structure of Tetracoordinate PdII Complexes
Ock Keum Kwak, Jeong-Seon Choi, Kyungok Park, Jong Keun Park*
Keywords: Orbital interaction, Geometric configuration, Relative energy, dz2-orbital, Tridentate macrocycles
Online date: March 05, 2012
DOI: https://doi.org/10.5012/bkcs.2012.33.3.1081
Abstract |
Full Text: PDF
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1085 |
Pyridinolysis of Dibutyl Chlorothiophosphate in Acetonitrile
Md. Ehtesham Ul Hoque, Hai Whang Lee*
Keywords: Thiophosphoryl transfer reaction, Pyridinolysis, Dibutyl chlorothiophosphate, Biphasic concave upward free energy relationship
Online date: March 05, 2012
DOI: https://doi.org/10.5012/bkcs.2012.33.3.1085
Abstract |
Supporting Information | Full Text: PDF
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1089 |
Anilinolysis of Diethyl Isothiocyanophosphate in Acetonitrile
Hasi Rani Barai, Keshab Kumar Adhikary, Hai Whang Lee*
Keywords: Phosphoryl transfer reaction, Anilinolysis, Diethyl Isothiocyanophosphate, Discrete biphasic free energy relationship, Deuterium kinetic isotope effect
Online date: March 05, 2012
DOI: https://doi.org/10.5012/bkcs.2012.33.3.1089
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