Publications by authors named "Sungyul Lee"

49 Publications

Inter- and Intra-Molecular Organocatalysis of S2 Fluorination by Crown Ether: Kinetics and Quantum Chemical Analysis.

Molecules 2021 May 15;26(10). Epub 2021 May 15.

Department of Chemistry, Inha University, 100 Inha-ro, Nam-gu, Incheon 402-751, Korea.

We present the intra- and inter-molecular organocatalysis of S2 fluorination using CsF by crown ether to estimate the efficacy of the promoter and to elucidate the reaction mechanism. The yields of intramolecular S2 fluorination of the veratrole substrates are measured to be very small (<1% in 12 h) in the absence of crown ether promoters, whereas the S2 fluorination of the substrate possessing a crown ether unit proceeds to near completion (~99%) in 12 h. We also studied the efficacy of intermolecular rate acceleration by an independent promoter 18-crown-6 for comparison. We find that the fluorinating yield of a veratrole substrate (leaving group = -OMs) in the presence of 18-crown-6 follows the almost identical kinetic course as that of intramolecular S2 fluorination, indicating the mechanistic similarity of intra- and inter-molecular organocatalysis of the crown ether for S2 fluorination. The calculated relative Gibbs free energies of activation for these reactions, in which the crown ether units act as Lewis base promoters for S2 fluorination, are in excellent agreement with the experimentally measured yields of fluorination. The role of the metal salt CsF is briefly discussed in terms of whether it reacts as a contact ion pair or as a "free" nucleophile F.
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http://dx.doi.org/10.3390/molecules26102947DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8156096PMC
May 2021

The SARS-CoV-2 RNA interactome.

Mol Cell 2021 Apr 27. Epub 2021 Apr 27.

Center for RNA Research, Institute for Basic Science, Seoul, Republic of Korea; School of Biological Sciences, Seoul National University, Seoul, Republic of Korea. Electronic address:

SARS-CoV-2 is an RNA virus whose success as a pathogen relies on its abilities to repurpose host RNA-binding proteins (RBPs) and to evade antiviral RBPs. To uncover the SARS-CoV-2 RNA interactome, we here develop a robust ribonucleoprotein (RNP) capture protocol and identify 109 host factors that directly bind to SARS-CoV-2 RNAs. Applying RNP capture on another coronavirus, HCoV-OC43, revealed evolutionarily conserved interactions between coronaviral RNAs and host proteins. Transcriptome analyses and knockdown experiments delineated 17 antiviral RBPs, including ZC3HAV1, TRIM25, PARP12, and SHFL, and 8 proviral RBPs, such as EIF3D and CSDE1, which are responsible for co-opting multiple steps of the mRNA life cycle. This also led to the identification of LARP1, a downstream target of the mTOR signaling pathway, as an antiviral host factor that interacts with the SARS-CoV-2 RNAs. Overall, this study provides a comprehensive list of RBPs regulating coronaviral replication and opens new avenues for therapeutic interventions.
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http://dx.doi.org/10.1016/j.molcel.2021.04.022DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8075806PMC
April 2021

Noncovalent Complexes of Cyclodextrin with Small Organic Molecules: Applications and Insights into Host-Guest Interactions in the Gas Phase and Condensed Phase.

Molecules 2020 Sep 4;25(18). Epub 2020 Sep 4.

Department of Chemistry, Sogang University, Seoul 04107, Korea.

Cyclodextrins (CDs) have drawn a lot of attention from the scientific communities as a model system for host-guest chemistry and also due to its variety of applications in the pharmaceutical, cosmetic, food, textile, separation science, and essential oil industries. The formation of the inclusion complexes enables these applications in the condensed phases, which have been confirmed by nuclear magnetic resonance (NMR) spectroscopy, X-ray crystallography, and other methodologies. The advent of soft ionization techniques that can transfer the solution-phase noncovalent complexes to the gas phase has allowed for extensive examination of these complexes and provides valuable insight into the principles governing the formation of gaseous noncovalent complexes. As for the CDs' host-guest chemistry in the gas phase, there has been a controversial issue as to whether noncovalent complexes are inclusion conformers reflecting the solution-phase structure of the complex or not. In this review, the basic principles governing CD's host-guest complex formation will be described. Applications and structures of CDs in the condensed phases will also be presented. More importantly, the experimental and theoretical evidence supporting the two opposing views for the CD-guest structures in the gas phase will be intensively reviewed. These include data obtained via mass spectrometry, ion mobility measurements, infrared multiphoton dissociation (IRMPD) spectroscopy, and density functional theory (DFT) calculations.
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http://dx.doi.org/10.3390/molecules25184048DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7571109PMC
September 2020

Harnessing Ionic Interactions and Hydrogen Bonding for Nucleophilic Fluorination.

Molecules 2020 Feb 7;25(3). Epub 2020 Feb 7.

Department of Applied Chemistry, Kyung Hee University, Gyeonggi 17104, Korea.

We review recent works for nucleophilic fluorination of organic compounds in which the Coulombic interactions between ionic species and/or hydrogen bonding affect the outcome of the reaction. S2 fluorination of aliphatic compounds promoted by ionic liquids is first discussed, focusing on the mechanistic features for reaction using alkali metal fluorides. The influence of the interplay of ionic liquid cation, anion, nucleophile and counter-cation is treated in detail. The role of ionic liquid as bifunctional (both electrophilic and nucleophilic) activator is envisaged. We also review the SAr fluorination of diaryliodonium salts from the same perspective. Nucleophilic fluorination of guanidine-containing of diaryliodonium salts, which are capable of forming hydrogen bonds with the nucleophile, is exemplified as an excellent case where ionic interactions and hydrogen bonding significantly affect the efficiency of reaction. The origin of experimental observation for the strong dependence of fluorination yields on the positions of -Boc protection is understood in terms of the location of the nucleophile with respect to the reaction center, being either close to far from it. Recent advances in the synthesis of [F]F-dopa are also cited in relation to SAr fluorination of diaryliodonium salts. Discussions are made with a focus on tailor-making promoters and solvent engineering based on ionic interactions and hydrogen bonding.
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http://dx.doi.org/10.3390/molecules25030721DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7037423PMC
February 2020

PUMILIO hyperactivity drives premature aging of -deficient mice.

Elife 2019 02 8;8. Epub 2019 Feb 8.

Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, United States.

Although numerous long noncoding RNAs (lncRNAs) have been identified, our understanding of their roles in mammalian physiology remains limited. Here, we investigated the physiologic function of the conserved lncRNA in vivo. Deletion of in mice results in genomic instability and mitochondrial dysfunction, leading to a dramatic multi-system degenerative phenotype resembling premature aging. Loss of tissue homeostasis in -deficient animals is attributable to augmented activity of PUMILIO proteins, which act as post-transcriptional repressors of target mRNAs to which they bind. is the preferred RNA target of PUMILIO2 (PUM2) in mouse tissues and, upon loss of , PUM2 hyperactively represses key genes required for mitosis and mitochondrial function. Accordingly, enforced expression fully phenocopies deletion, resulting in rapid-onset aging-associated phenotypes. These findings provide new insights and open new lines of investigation into the roles of noncoding RNAs and RNA binding proteins in normal physiology and aging.
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http://dx.doi.org/10.7554/eLife.42650DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6407921PMC
February 2019

Chiral differentiation of d- and l-isoleucine using permethylated β-cyclodextrin: infrared multiple photon dissociation spectroscopy, ion-mobility mass spectrometry, and DFT calculations.

Phys Chem Chem Phys 2018 Dec;20(48):30428-30436

Department of Applied Chemistry, Kyung Hee University, Gyeonggi 17104, Republic of Korea.

Chiral differentiation of protonated isoleucine (Ile) using permethylated β-cyclodextrin (perCD) in the gas-phase was studied using infrared multiple photon dissociation (IRMPD) spectroscopy, ion-mobility, and density functional theory (DFT) calculations. The gaseous protonated non-covalent complexes of perCD and d-Ile or l-Ile produced by electrospray ionization were interrogated by laser pulses in the wavenumber region of 2650 to 3800 cm-1. The IRMPD spectra showed remarkably different IR spectral features for the d-Ile or l-Ile and perCD non-covalent complexes. However, drift-tube ion-mobility experiments provided only a small difference in their collision cross-sections, and thus a limited separation of the d- and l-Ile complexes. DFT calculations revealed that the chiral distinction of the d- and l-complexes by IRMPD spectroscopy resulted from local interactions of the protonated Ile with perCD. Furthermore, the theoretical results showed that the IR absorption spectra of higher energy conformers (by ∼13.7 kcal mol-1) matched best with the experimentally observed IRMPD spectra. These conformers are speculated to be formed from kinetic-trapping of the solution-phase conformers. This study demonstrated that IRMPD spectroscopy provides an excellent platform for differentiating the subtle chiral difference of a small amino acid in a cyclodextrin-complexation environment; however, drift-tube ion-mobility did not have sufficient resolution to distinguish the chiral difference.
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http://dx.doi.org/10.1039/c8cp05617jDOI Listing
December 2018

Chiral differentiation of d- and l-alanine by permethylated β-cyclodextrin: IRMPD spectroscopy and DFT methods.

Phys Chem Chem Phys 2017 Jun;19(22):14729-14737

Department of Applied Chemistry, Kyung Hee University, Gyeonggi 446-701, Republic of Korea.

The gaseous chiral differentiation of alanine by permethylated β-cyclodextrin was studied using IRMPD spectroscopy and density functional theory calculations. The protonated non-covalent complexes of permethylated β-cyclodextrin and d- or l-alanine were mass-selected and investigated by IR laser pulses in the wavelength region of 2650-3800 cm. The remarkably different features of the IRMPD spectra for d- and l-alanine are described, and their origin is elucidated by quantum chemical calculations. We show that the differentiation of the experimentally observed spectral features is the result of different local interactions of d- and l-alanine with permethylated β-cyclodextrin. We also assign the extremely high-frequency (>3700 cm) bands in the observed spectra to the stretch motions of completely isolated alanine -OH groups.
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http://dx.doi.org/10.1039/c7cp01085kDOI Listing
June 2017

Hydrogen-bond promoted nucleophilic fluorination: concept, mechanism and applications in positron emission tomography.

Chem Soc Rev 2016 08;45(17):4638-50

Department of Chemistry, Sungkyunkwan University, 2066, Seobu-ro, Jangan-gu, Suwon-si, Gyeonggi-do 440-746, Korea.

Due to the tremendous interest in carbon-fluorine bond-forming reactions, research efforts in this area have been dedicated to the development of facile processes to synthesize small fluorine-containing organic molecules. Among others, PET (Positron Emission Tomography) is one of the most important applications of fluorine chemistry. Recognizing the specific requirements of PET processes, some groups have focused on fluorination reactions using alkali metal fluorides, particularly through SN2-type reactions. However, a common "misconception" about the role of protic solvents and hydrogen bonding interactions in this class of reactions has hampered the employment of these excellent promoters. Herein, we would like to review recent discoveries in this context, showing straightforward nucleophilic fluorination reactions using alkali metal fluorides promoted by protic solvents. Simultaneous dual activation of reacting partners by intermolecular hydrogen bonding and the enhancement of the "effective fluoride nucleophilicity", which is Nature's biocatalytic approach with the fluorinase enzyme, are the key to this unprecedentedly successful nucleophilic fluorination.
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http://dx.doi.org/10.1039/c6cs00286bDOI Listing
August 2016

Stereo-epitaxial growth of single-crystal Ni nanowires and nanoplates from aligned seed crystals.

Nanoscale 2016 May 29;8(19):10291-7. Epub 2016 Apr 29.

Department of Chemistry, KAIST, Daejeon 34141, Korea.

Epitaxially grown anisotropic Ni nanostructures are promising building blocks for the development of miniaturized and stereo-integrated data storage kits because they can store multiple magnetic domain walls (DWs). Here, we report stereo-epitaxially grown single-crystalline Ni nanowires (NWs) and nanoplates, and their magnetic properties. Vertical and inclined Ni NWs were grown at the center and edge regions of c-cut sapphire substrates, respectively. Vertical Ni nanoplates were grown on r-cut sapphire substrates. The morphology and growth direction of Ni nanostructures can be steered by seed crystals. Cubic Ni seeds grow into vertical Ni NWs, tetrahedral Ni seeds grow into inclined Ni NWs, and triangular Ni seeds grow into vertical Ni nanoplates. The shapes of the Ni seeds are determined by the interfacial energy between the bottom plane of the seeds and the substrates. The as-synthesized Ni NWs and nanoplates have blocking temperature values greater than 300 K at 500 Oe, verifying that these Ni nanostructures can form large magnetic DWs with high magnetic anisotropy properties. We anticipate that epitaxially grown Ni NWs and nanoplates will be used in various types of 3-dimensional magnetic devices.
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http://dx.doi.org/10.1039/c5nr08080kDOI Listing
May 2016

Bis-tert-Alcohol-Functionalized Crown-6-Calix[4]arene: An Organic Promoter for Nucleophilic Fluorination.

Chemistry 2016 Mar 16;22(13):4515-20. Epub 2016 Feb 16.

Department of Chemistry, Inha University, 100 Inha-ro, Nam-gu, Incheon, 402-751, Korea), Fax: (+82) 32-867-5604.

A bis-tert-alcohol-functionalized crown-6-calix[4]arene (BACCA) was designed and prepared as a multifunctional organic promoter for nucleophilic fluorinations with CsF. By formation of a CsF/BACCA complex, BACCA could release a significantly active and selective fluoride source for SN2 fluorination reactions. The origin of the promoting effects of BACCA was studied by quantum chemical methods. The role of BACCA was revealed to be separation of the metal fluoride to a large distance (>8 Å), thereby producing an essentially "free" F(-). The synergistic actions of the crown-6-calix[4]arene subunit (whose O atoms coordinate the counter-cation Cs(+)) and the terminal tert-alcohol OH groups (forming controlled hydrogen bonds with F(-)) of BACCA led to tremendous efficiency in SN2 fluorination of base-sensitive substrates.
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http://dx.doi.org/10.1002/chem.201504602DOI Listing
March 2016

Noncoding RNA NORAD Regulates Genomic Stability by Sequestering PUMILIO Proteins.

Cell 2016 Jan 24;164(1-2):69-80. Epub 2015 Dec 24.

Department of Molecular Biology, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390-9148, USA; Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390-9148, USA; Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390-9148, USA; Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390-9148, USA. Electronic address:

Long noncoding RNAs (lncRNAs) have emerged as regulators of diverse biological processes. Here, we describe the initial functional analysis of a poorly characterized human lncRNA (LINC00657) that is induced after DNA damage, which we termed "noncoding RNA activated by DNA damage", or NORAD. NORAD is highly conserved and abundant, with expression levels of approximately 500-1,000 copies per cell. Remarkably, inactivation of NORAD triggers dramatic aneuploidy in previously karyotypically stable cell lines. NORAD maintains genomic stability by sequestering PUMILIO proteins, which repress the stability and translation of mRNAs to which they bind. In the absence of NORAD, PUMILIO proteins drive chromosomal instability by hyperactively repressing mitotic, DNA repair, and DNA replication factors. These findings introduce a mechanism that regulates the activity of a deeply conserved and highly dosage-sensitive family of RNA binding proteins and reveal unanticipated roles for a lncRNA and PUMILIO proteins in the maintenance of genomic stability.
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http://dx.doi.org/10.1016/j.cell.2015.12.017DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4715682PMC
January 2016

Genome-wide annotation of microRNA primary transcript structures reveals novel regulatory mechanisms.

Genome Res 2015 Sep;25(9):1401-9

Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA; Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA; Simmons Cancer Center, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA.

Precise regulation of microRNA (miRNA) expression is critical for diverse physiologic and pathophysiologic processes. Nevertheless, elucidation of the mechanisms through which miRNA expression is regulated has been greatly hindered by the incomplete annotation of primary miRNA (pri-miRNA) transcripts. While a subset of miRNAs are hosted in protein-coding genes, the majority of pri-miRNAs are transcribed as poorly characterized noncoding RNAs that are 10's to 100's of kilobases in length and low in abundance due to efficient processing by the endoribonuclease DROSHA, which initiates miRNA biogenesis. Accordingly, these transcripts are poorly represented in existing RNA-seq data sets and exhibit limited and inaccurate annotation in current transcriptome assemblies. To overcome these challenges, we developed an experimental and computational approach that allows genome-wide detection and mapping of pri-miRNA structures. Deep RNA-seq in cells expressing dominant-negative DROSHA resulted in much greater coverage of pri-miRNA transcripts compared with standard RNA-seq. A computational pipeline was developed that produces highly accurate pri-miRNA assemblies, as confirmed by extensive validation. This approach was applied to a panel of human and mouse cell lines, providing pri-miRNA transcript structures for 1291/1871 human and 888/1181 mouse miRNAs, including 594 human and 425 mouse miRNAs that fall outside protein-coding genes. These new assemblies uncovered unanticipated features and new potential regulatory mechanisms, including links between pri-miRNAs and distant protein-coding genes, alternative pri-miRNA splicing, and transcripts carrying subsets of miRNAs encoded by polycistronic clusters. These results dramatically expand our understanding of the organization of miRNA-encoding genes and provide a valuable resource for the study of mammalian miRNA regulation.
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http://dx.doi.org/10.1101/gr.193607.115DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4561498PMC
September 2015

Infrared multiple photon dissociation spectroscopy and density functional theory (DFT) studies of protonated permethylated β-cyclodextrin-water non-covalent complexes.

Phys Chem Chem Phys 2014 May;16(18):8376-83

Department of Applied Chemistry, Kyung Hee University, Gyeonggi 446-701, Korea.

We present infrared multiple photon dissociation (IRMPD) spectroscopy and quantum chemical calculation results for the protonated permethylated β-cyclodextrin (CD)-water non-covalent complex, the simplest β-CD non-covalent complex, in the gas-phase. The IRMPD spectrum in the region 2700-3750 cm(-1) consisted of three strong peaks at 3096, 3315, and 3490 cm(-1). These spectral features in the experimental IRMPD spectrum were compared with a large set of infrared absorption spectra predicted using density functional theory (DFT) calculations for the protonated β-CD-water complex. Complex III (see ), in which the water molecule (at the primary rim) and the proton (at the secondary rim) were separated, was found to suitably reflect the main spectral characteristics found in the experimental IRMPD spectrum. The absence of the homodromic hydrogen bond ring, due to replacement of hydroxyl groups with methoxy groups in permethylated β-CD, rendered the primary rim open compared with the unmodified β-CD 'one-gate-closed' lowest energy conformer. This study demonstrates that IRMPD studies combined with DFT theoretical calculations can be a good method for studying molecular interactions of large host-guest pairs.
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http://dx.doi.org/10.1039/c3cp54841dDOI Listing
May 2014

Truncated tetrahedron seed crystals initiating stereoaligned growth of FeSi nanowires.

ACS Nano 2012 Oct 17;6(10):8652-7. Epub 2012 Sep 17.

Department of Chemistry, KAIST, Daejeon 305-701, Korea.

We have synthesized epitaxially grown freestanding FeSi nanowires (NWs) on an m-Al(2)O(3) substrate by using a catalyst-free chemical vapor transport method. FeSi NW growth is initiated from FeSi nanocrystals, formed on a substrate in a characteristic shape with a specific orientation. Cross-section TEM analysis of seed crystals reveals the crystallographic structure and hidden geometry of the seeds. Close correlation of geometrical shapes and orientations of the observed nanocrystals with those of as-grown NWs indicates that directional growth of NWs is initiated from the epitaxially formed seed crystals. The diameter of NWs can be controlled by adjusting the composition of Si in a Si/C mixture. The epitaxial growth method for FeSi NWs via seed crystals could be employed to heteroepitaxial growth of other compound NWs.
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http://dx.doi.org/10.1021/nn302141wDOI Listing
October 2012

Primary cutaneous sarcomatoid carcinoma.

Indian J Dermatol Venereol Leprol 2012 Sep-Oct;78(5):665

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http://dx.doi.org/10.4103/0378-6323.100536DOI Listing
March 2013

Design of Carbene-Based Organocatalysts for Nitrogen Fixation: Theoretical Study.

J Chem Theory Comput 2012 Jun 4;8(6):1983-8. Epub 2012 May 4.

Center for Superfunctional Materials, Department of Chemistry, Pohang University of Science and Technology, San 31, Hyojadong, Namgu, Pohang 790-784, Korea.

Nitrogen fixation is a great challenge in solving the food supply of mankind. However N2 activation is extremely hard. Up until recently, the investigated catalysts for N2 fixation were based on metallic reducing agents. They are generally not environment friendly. We designed organocatalysts (carbenes) for nitrogen fixation using density functional theory (DFT) and ab initio theory. The reactivity of the carbene catalysts is mainly related to the electrostatic properties of the side chains. We compared the binding affinity to N2 with various carbenes (:CF2, :CCl2, :CBr2, and :CI2). We revealed that the electron donating ability of the central carbene carbon is the most important factor for trapping N2. Among heterocyclic carbenes, the cyclic diphospinocarbenes (PHC) represented a good candidate moiety for an efficient catalyst. We further designed the carbene based catalyst which has two carbene moieties to chelate N2 and investigated the whole catalytic mechanism. The highest energy barrier of the entire catalytic cycle is 28.5 kcal/mol, which is comparable to the previously reported metallic catalysts. This demonstrates the possibility of novel organic catalysts for nitrogen fixation.
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http://dx.doi.org/10.1021/ct300154bDOI Listing
June 2012

Oligoethylene glycols as highly efficient mutifunctional promoters for nucleophilic-substitution reactions.

Chemistry 2012 Mar 16;18(13):3918-24. Epub 2012 Feb 16.

Department of Nuclear Medicine, Cyclotron Research Center, Research Institute of Clinical Medicine, Chonbuk National University Medical School, Jeonju, Jeonbuk 561-712, Korea.

Herein, we report the promising use of n-oligoethylene glycols (oligoEGs) as mutifunctional promoters for nucleophilic-substitution reactions employing alkali metal salts. Among the various oligoEGs tested, pentaethylene glycol (pentaEG) had the most efficient catalytic activity. In particular, when compared with other nucleophiles examined, a fluorine nucleophile generated from CsF was significantly activated by the pentaEG promoter. We also performed various facile nucleophilic-displacement reactions, such as the halogenation, acetoxylation, thioacetoxylation, nitrilation, and azidation of various substrates with potassium halides, acetate, thioacetate, cyanide, and sodium azide, respectively, in the presence of the pentaEG promoter. All of these reactions provided their desired products in excellent yields. Furthermore, the combination of pentaEG and a tert-alcohol medium showed tremendous efficiency in the nucleophilic-displacement reactions (fluorination and methoxylation) of base-sensitive substrates with basic nucleophiles (cesium fluoride and potassium methoxide, respectively). The catalytic role of oligoEGs was examined by quantum-chemical methods. The oxygen atoms in oligoEGs were found to act as Lewis bases on the metal cations to produce the "flexible" nucleophile, whereas the two terminal hydroxy (OH) groups acted as "anchors" to orientate the nucleophile and the substrate into an ideal configuration for the reaction.
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http://dx.doi.org/10.1002/chem.201102455DOI Listing
March 2012

Microsolvation of lysine by water: computational study of stabilized zwitterion.

J Phys Chem B 2011 Aug 28;115(33):10147-53. Epub 2011 Jul 28.

Department of Applied Chemistry, Kyung Hee University, Kyungki 446-701, South Korea.

We present calculations for Lys-(H(2)O)(n) (n = 2, 3) to examine the effects of microsolvating water on the relative stability of the zwitterionic vs canonical forms of Lys. We calculate the structures, energies, and Gibbs free energies of the conformers at the B3LYP/6-311++G(d,p), wB97XD/6-311++G(d,p), and MP2/aug-cc-pvdz levels of theory, finding that three water molecules are required to stabilize the Lys zwitterion. By calculating the barriers of the canonical ↔ zwitterionic pathways of Lys-(H(2)O)(3) conformers, we suggest that both forms of Lys-(H(2)O)(3) may be observed in low temperature gas phase.
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http://dx.doi.org/10.1021/jp202850sDOI Listing
August 2011

Counterion-mediated hydrogen-bonding effects: mechanistic study of gold(I)-catalyzed enantioselective hydroamination of allenes.

Chem Asian J 2011 Aug 6;6(8):1982-6. Epub 2011 Jul 6.

Department of Applied Chemistry, Kyung Hee University, Yongin-si, Gyeonggi-do, 446-701, Korea.

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http://dx.doi.org/10.1002/asia.201100135DOI Listing
August 2011

Unravelling complex spectra of a simple molecule: REMPI study of the 420 nm band system of KRb.

Chemphyschem 2011 Jul 4;12(10):2018-23. Epub 2011 Mar 4.

Department of Chemistry, Mokpo National University, Muan-gun, Jeonnam 534-729, Korea.

Complex spectra of the KRb 420 nm system are analyzed by mass-resolved resonance enhanced two-photon ionization in a cold molecular beam. Vibronic structures of three singlet-singlet (4(1)Π, 7(1)Σ(+), and 5(1)Π←X(1)Σ(+)) transitions were identified for the first time. By comparing with highly accurate ab initio calculations, we assigned the singlet excited electronic states, and determined their electronic term values and vibrational constants. Weak singlet-triplet transitions were observed and identified as the 5(3)Π(0(+))←X(1)Σ(+) transitions by the homogeneous perturbation selection rule.
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http://dx.doi.org/10.1002/cphc.201000989DOI Listing
July 2011

Proton transfer from the inactive gas-phase nicotine structure to the bioactive aqueous-phase structure.

J Am Chem Soc 2010 Dec 8;132(51):18067-77. Epub 2010 Dec 8.

Laboratoire Analyse et Modélisation pour la Biologie et l'Environnement, LAMBE UMR8587 CNRS, Université d'Evry val d'Essonne, boulevard F. Mitterrand, Bat. Maupertuis, 91025 Evry Cedex, France.

The role of water in the structural change of nicotine from its inactive form in the gas phase to its bioactive form in aqueous solution has been investigated by two complementary theoretical approaches, i.e., geometry optimizations and molecular dynamics. Structures of the lowest-energy nicotineH(+)-(H(2)O)(n) complexes protonated either on the pyridine (inactive form) or pyrrolidine (active form) ring have been calculated, as well as the free-energy barriers for the proton-transfer tautomerization between the two cycles. These structures show chains of 2-4 water molecules bridging the two protonation sites. The room-temperature free-energy barrier to tautomerization along the minimum-energy path from the pyridine to the pyrrolidine cycle drops rapidly when the number of water molecules increases from 0 to 4, but still remains rather high (16 kJ/mol with four water molecules), indicating that the proton transfer is a rather difficult and rare event. We compare results obtained through this explicit water molecule approach to those obtained by means of continuum methods. Car-Parrinello molecular dynamics (CPMD) simulations of the proton-transfer process in bulk with explicit water molecules have been conducted at room temperature. No spontaneous proton transfers have been observed during the dynamics, and biased CPMD simulations have therefore been performed in order to measure the free-energy profile of the proton transfer in the aqueous phase and to reveal the proton-transfer mechanism through water bridges. The MD bias involves pulling the proton from the pyridine ring to the surrounding bulk. Dynamics show that this triggers the tautomerization toward the pyrrolidine ring, proceeding without energy barrier. The proton transfer is extremely fast, and protonation of the pyrrolidine ring was achieved within 0.5 ps. CPMD simulations confirmed the pivotal role played by the water molecules that bridge the two protonation sites of nicotine within the bulk of the surrounding water.
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http://dx.doi.org/10.1021/ja103759vDOI Listing
December 2010

SN2 fluorination reactions in ionic liquids: a mechanistic study towards solvent engineering.

Org Biomol Chem 2011 Jan 15;9(2):418-22. Epub 2010 Oct 15.

Department of Applied Chemistry, Kyunghee University, Yongin, Gyeoggi 446-701, Korea.

In the catalysis of S(N)2 fluorination reactions, the ionic liquid anion plays a key role as a Lewis base by binding to the counterion Cs(+) and thereby reducing the retarding Coulombic influence of Cs(+) on the nucleophile F(-). The reaction rates also depend critically on the structures of ionic liquid cation, for example, n-butyl imidazolium gives no S(N)2 products, whereas n-butylmethyl imidazolium works well. The origin of the observed phenomenal synergetic effects by the ionic liquid [mim-(t)OH][OMs], in which t-butanol is bonded covalently to the cation [mim], is that the t-butanol moiety binds to the leaving group of the substrate, moderating the retarding interactions between the acidic hydrogen and F(-). This work is a significant step toward designing and engineering solvents for promoting specific chemical reactions.
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http://dx.doi.org/10.1039/c0ob00426jDOI Listing
January 2011

The 480 nm system of KRb: 1 3Delta1, 4 1Sigma+, and 5 1Sigma+ states.

J Phys Chem A 2010 Jul;114(29):7742-8

Department of Chemistry, Mokpo National University, Jeonnam 534-729, Korea.

We have investigated the KRb 480 nm system by mass-resolved resonance enhanced two-photon ionization in a cold molecular beam. The 1 (3)Delta(1), 4 (1)Sigma(+), and 5 (1)Sigma(+) <-- X (1)Sigma(+) transitions have been identified. For the 1 (3)Delta(1) and 5 (1)Sigma(+) states, the electronic term values and vibrational constants are determined experimentally for the first time. Potential energy curves of the 4 (1)Sigma(+) and 5 (1)Sigma(+) states undergo multiple avoided crossings with nearby (1)Sigma(+) states in the observed spectral region. For the 4 (1)Sigma(+) state, a vibrational numbering of the experimentally observed levels is suggested. Anomalies in vibronic structures of the 4 (1)Sigma(+) and 5 (1)Sigma(+) states are understood by comparison with high-level ab initio calculations currently available. The avoided crossing energies are also experimentally estimated.
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http://dx.doi.org/10.1021/jp1028799DOI Listing
July 2010

Mode-dependent Fano resonances observed in the predissociation of diazirine in the S1 state.

Angew Chem Int Ed Engl 2010 Feb;49(7):1244-7

Department of Chemistry and KI for Nanocentury, KAIST, Daejeon 301-750, Korea.

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http://dx.doi.org/10.1002/anie.200905619DOI Listing
February 2010

Effects of bioconjugation on the structures and electronic spectra of CdSe: density functional theory study of CdSe-adenine complexes.

J Phys Chem B 2010 Jan;114(1):471-9

Department of Applied Chemistry, Kyung Hee University, 1 Seocheon-dong, Giheung-gu, Yongin-si, Gyeonggi-do 446-701, Republic of Korea.

We present density functional theory (DFT) and time-dependent DFT (TD-DFT) study of the structures and electronic spectra of small CdSe nanocluster-adenine complexes Cd(n)Se(n)-adenine (n = 3, 6, 10, 13). We examine the changes in the geometries and excitation spectra of the nanoclusters induced by DNA base-binding. By comparing the results calculated for the bare (Cd(n)Se(n)), hydrogen-passivated (Cd(n)Se(n)H(2n)), as well as the corresponding adenine (Ade)-bound clusters (Cd(n)Se(n)-Ade, Cd(n)Se(n)H(2n)-Ade, Cd(n)Se(n)H(2n-2)-Ade), we find that binding with Ade slightly blue-shifts (up to 0.18 eV) the electronic excitations of bare nanoclusters but strongly red-shifts (<1.2 eV) those of hydrogen-passivated nanoclusters. Natural bond orbital analysis shows that the LUMO of Cd(n)Se(n)H(2n)-Ade is a pi* orbital located on the purine ring.
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http://dx.doi.org/10.1021/jp907725fDOI Listing
January 2010

Adsorbate-induced absorption redshift in an organic-inorganic cluster conjugate: Electronic effects of surfactants and organic adsorbates on the lowest excited states of a methanethiol-CdSe conjugate.

J Chem Phys 2009 Nov;131(17):174705

Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095-1569, USA.

Bioconjugated CdSe quantum dots are promising reagents for bioimaging applications. Experimentally, the binding of a short peptide has been found to redshift the optical absorption of nanoclusters [J. Tsay et al., J. Phys. Chem. B 109, 1669 (2005)]. This study examines this issue by performing density functional theory (DFT) and time-dependent-DFT calculations to study the ground state and low-lying excited states of (CdSe)(6)[SCH(3)](-), a transition metal complex built by binding methanethiolate to a CdSe molecular cluster. Natural bond orbital results show that the redshift is caused by ligand-inorganic cluster orbital interaction. The highest occupied molecular orbital (HOMO) of (CdSe)(6) is dominated by selenium 4p orbitals; in contrast, the HOMO of (CdSe)(6)[SCH(3)](-) is dominated by sulfur 3p orbitals. This difference shows that [SCH(3)](-) binding effectively introduces filled sulfur orbitals above the selenium 4p orbitals of (CdSe)(6). The resulting smaller HOMO-LUMO gap of (CdSe)(6)[SCH(3)](-) indeed leads to redshifts in its excitation energies compared to (CdSe)(6). In contrast, binding of multiple NH(3) destabilizes cadmium 5p orbitals, which contribute significantly to the lowest unoccupied molecular orbital (LUMO) of (CdSe)(6), while leaving the selenium 4p orbitals near the HOMO relatively unaffected. This has the effect of widening the HOMO-LUMO gap of (CdSe)(6)6NH(3) compared to (CdSe)(6). As expected, the excitation energies of the passivated (CdSe)(6)6NH(3) are also blueshifted compared to (CdSe)(6). As far as NH(3) is a faithful representation of a surfactant, the results clearly illustrate the differences between the electronic effects of an alkylthiolate versus those of surfactant molecules. Surface passivation of (CdSe)(6)[SCH(3)](-) is then simulated by coating it with multiple NH(3) molecules. The results suggest that the [SCH(3)](-) adsorption induces a redshift in the excitation energies in a surfactant environment.
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http://dx.doi.org/10.1063/1.3251774DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2787060PMC
November 2009

500 nm system of RbCs: assignments and intensity anomalies.

J Phys Chem A 2009 Nov;113(44):12187-92

Advanced Photonics Research Institute, Gwangju Institute of Science and Technology, Gwangju 500-712, Korea.

We have investigated the RbCs 500 nm system by mass-resolved resonance enhanced two-photon ionization in a cold molecular beam. The 4 3Pi0 v' = 10-39, 4 3Pi1 v' = 14-28, and 6 1Sigma+ v' = 12-28 <-- X 1Sigma+ v'' = 0 transitions have been observed and assigned for the first time. The 4 3Pi0 v' <-- X 1Sigma+ v'' = 0 transitions abnormally show double maxima of the vibronic-band intensity distribution around v' = 22 and 38. The intensities of the transitions to the lower vibrational levels (4 3Pi0 v' = 10-32) are explained well by the direct transitions from the X 1Sigma+ v'' = 0 level following the Franck-Condon principle. The transitions to the higher vibrational levels (4 3Pi0 v' > or = 33) borrow intensities through the interaction with nearby 6 1Sigma+ perturber levels.
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http://dx.doi.org/10.1021/jp904927uDOI Listing
November 2009

Bis-terminal hydroxy polyethers as all-purpose, multifunctional organic promoters: a mechanistic investigation and applications.

Angew Chem Int Ed Engl 2009 ;48(41):7683-6

Department of Chemistry, Sungkyunkwan University, 300 Cheoncheon, Jangan, Suwon, Gyeonggi, Korea.

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http://dx.doi.org/10.1002/anie.200903903DOI Listing
December 2009

Ab initio and DFT studies of the thermal rearrangement of trimethylsilyl(methyl)silylene: remarkable rearrangements of silicon intermediates.

J Comput Chem 2010 Jan;31(1):154-63

Department of Chemistry, Chungnam National University, Daejeon 305-764, Republic of Korea.

A reaction scheme for the rearrangement of trimethylsilyl(methyl)silylene (Me3Si-Si-Me) discovered in a pioneering work of organosilicon chemistry (Wulff et al., J Am Chem Soc 1978, 100, 6236) was studied by the MP2 and DFT methods. We report a thermal reaction scheme for the rearrangement of Me3Si-Si-Me with the structures and energies of various silicon species along the isomerization paths, that can account for the experimentally found product ratio. The experimental product ratio is in good agreement with the theoretical one derived from the Gibbs free energy changes calculated in the present study.
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http://dx.doi.org/10.1002/jcc.21254DOI Listing
January 2010

A mechanistic study of S(N)2 reaction in a diol solvent.

J Phys Chem A 2009 Apr;113(15):3685-9

College of Environmental Science and Applied Chemistry (BK 21), Kyunghee University, Kyungki 446-701, S. Korea.

We present calculations for the mechanism of S(N)2 reactions in ethylene glycol, focusing on the role of two protic functional groups (-OH) in the solvent molecule. We find that some hydroxyl groups act as Lewis base to interact with the cation, whereas others affect the reaction as Lewis acid to the nucleophile. We predict that the nucleophile (F-) reacts as an ion pair rather than as a solvent-separated ion when metal cation (Cs+) is used as a counterion. The overall influence of ethylene glycol manifests itself as the reaction barrier (E(double dagger) = 20.0, G(353K)(double dagger) = 21.5 kcal/mol) that is a bit smaller than that in tert-butyl alcohol, which proved to be a very efficient solvent for S(N)2 reactions [Kim, D. W., et al. J. Am. Chem. Soc. 2006, 128, 16394]. We therefore show that a small protic solvent such as ethylene glycol may be as efficient as a bulky alcohol for S(N)2 reactions.
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http://dx.doi.org/10.1021/jp900576xDOI Listing
April 2009