Sungyul Lee

Dynamic paths between neutral alanine–water and zwitterionic alanine–water clusters: single, double and triple proton transfer

Abstract Computations are presented for the alanine–(H 2 O) n ( n =1–3) and its zwitterion–(H 2 O) n clusters. We find that at least two water molecules need to bind to alanine to give stable alanine zwitterion–water cluster. Structures of the conformers are predicted, and their relative energies are compared. Detailed analysis is presented on the dynamic (proton transfer) pathways between the neutral alanine–(H 2 O) n and the zwitterionic alanine–(H 2 O) n ( n =2, 3) clusters, including the structures of the transition states. A variety of proton transfer pathways are predicted between alanine–(H 2 O) n and the zwitterion–(H 2 O) n clusters, depending on their structures: direct proton transfer, concerted double and triple proton transfer mechanism.

Density functional study of polycarbon sulfides CnS (n = 2−9)

Abstract Density functional theory calculations are presented for linear polycarbon sulfides C n S ( n = 2−9). Good agreements are obtained between the computed properties of the ground state of these molecules and experimental observations. The BLYP/6–311G ∗ or BLYP/6–311 + G ∗ methods give stretching frequencies for C 3 S that are in better agreement than corerlated ab initio methods. Calculated results are also presented for larger clusters C n S ( n ⩾ 4), for which only fragmentary information is available. The alternating pattern of the ν 1 frequency is related to the variations in the strength of the active bonds with respect to the cluster size.

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

The use of transition metals as unsaturated C C bond activators toward nucleophilic attack continues to grow exponentially for efficient and atom-economic organic transformations. The majority of nucleophilic additions proceed through the outer-sphere mechanism, that is, anti addition to the metal-coordinated C C multiple bond complexes. However, few alternative inner-sphere mechanisms have been proposed, in which the coordination of the nucleophile to the metal is followed by insertion of a C C multiple bond into the M Nu bond, such as the Ir, Ln, Pd, and Au-catalyzed hydrofunctionalization reactions. While the detailed variation of the inner-sphere mechanism highly depends on the electronic and redox character of transition metals, more importantly, these reactions are distinguished by syn-stereochemical pathways from the outer-sphere mechanism. While intensive stereochemical investigations into various kinds of gold(I) catalysis suggested the anti-addition mechanism, our specific interest began from the significant enantioselectivity in the gold(I)-catalyzed transformations of allenes. Despite a number of reports on transition metal catalyzed addition of heteroatom nucleophiles to allenes, the asymmetric variants are reported exclusively with the gold catalyst. This fact stimulates ideas for the perfect role of a gold catalyst in the challenging control of stereoselectivities, especially when substituted allenes are used as substrates. Enantioselective gold(I) catalysis is not restricted to classic p-activation processes. The efficient gold catalyst has been selected as the form of chiral bis ACHTUNGTRENNUNG(gold)-phosphine complexes, which could lead to formation of aurophilic Au Au interactions. Another intriguing phenomenon is the pronounced counterion effect that points to the importance of nonbonding interactions between the auxiliary (AuX) group and the reactive gold center. Herein we report a new type of the counterion-directed syn-addition pathway in gold-catalyzed hydroamination reactions. In parallel, we have found that the nonbonding interaction between the nucleophile and gold in the pre-reaction complex is the origin of the enantioselectivity of complex allene substrates. To obtain insight into the possible origins of enantioselectivity in the gold-catalyzed hydroamination reactions, we have carried out both experiments and quantum chemical studies, employing the density functional theory method B3LYP with the 6-31G basis set and the effective core potential for Au (Hay–Wadt VDZ), as implemented in the Gaussian 09 set program. Stationary structures are confirmed by ascertaining that all the harmonic frequencies are real. The structure of the transition state is obtained by verifying that one and only one of the harmonic frequencies is imaginary, and also by carrying out the intrinsic reaction coordinate (IRC) analysis along the reaction pathway. Zero point energies (ZPE) are taken into account, and default criteria are used for all optimizations. Based on the previous observations in the gold-catalyzed enantioselective hydroamination (Scheme 1), the enantioselectivity was concluded to be strongly affected by the remaining counterion coordinated to gold, and the para-nitrobenzoate (OPNB) counterion proved to be an ideal one to transfer the chiral information of the 2,2’-bis(diphenylphosphino)-1,1’-binaphthyl (binap) ligand to the relatively distant reaction center. Furthermore, this counterion effect in goldcatalyzed hydroamination was developed and applied by using a chiral 2,2’-dihydroxy-1,1’-binaphthyl (binol)-derived phosphate anion, thus rendering the chiral counterion-mediated transition metal catalysis powerful. To check the role of the counterion in the catalytically active species, we [a] J. H. Kim, S.-W. Park, S. R. Park, Prof. S. Lee, Prof. E. J. Kang Department of Applied Chemistry Kyung Hee University Yongin-si, Gyeonggi-do, 446-701 (Korea) Fax: (+82) 31-202-7337 E-mail : sylee@khu.ac.kr ejkang24@khu.ac.kr [] These authors contributed equally to this work. Supporting information for this article is available on the WWW under http://dx.doi.org/10.1002/asia.201100135.

Microsolvation of Lysine by Water: Computational Study of Stabilized Zwitterion

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.

Arginine Zwitterion is More Stable than the Canonical Form when Solvated by a Water Molecule

We present calculations for the Arg-H2O system and predict that the zwitterionic Arg is thermodynamically more stable than the canonical form in the gas phase under the influence of a single water molecule because of the strongly basic guanidine side chain. Canonical conformers of Arg-H2O are found to isomerize to the zwitterionic forms via a small barrier (approximately 6 kcal/mol).

Endoplasmic reticulum stress modulates nicotine-induced extracellular matrix degradation in human periodontal ligament cells.

BACKGROUND AND OBJECTIVE Tobacco smoking is considered to be one of the major risk factors for periodontitis. For example, about half the risk of periodontitis can be attributable to smoking in the USA. It is evident that smokers have greater bone loss, greater attachment loss and deeper periodontal pockets than nonsmoking patients. It has recently been reported that endoplasmic reticulum (ER) stress markers are upregulated in periodontitis patients; however, the direct effects of nicotine on ER stress in regard to extracellular matrix (ECM) degradation are unclear. The purpose of this study was to examine the effects of nicotine on cytotoxicity and expression of ER stress markers, selected ECM molecules and MMPs, and to identify the underlying mechanisms in human periodontal ligament cells. We also examined whether ER stress was responsible for the nicotine-induced cytotoxicity and ECM degradation. MATERIAL AND METHODS Cytotoxicity and cell death were measured by 3-[4,5-dimethylthiazol-2-yl]-2,5 diphenyltetrazolium bromide assay and flow cytometric annexin V and propidium iodide staining. The mRNA and protein expressions of MMPs and ER markers were examined by RT-PCR and western blot analysis. RESULTS Treatment with nicotine reduced cell viability and increased the proportion of annexin V-negative, propidium iodide-positive cells, an indication of cell death. Nicotine induced ER stress, as evidenced by survival molecules, such as phosphorylated protein kinase-like ER-resident kinase, phosphorylated eukaryotic initiation factor-2α and glucose-regulated protein-78, and apoptotic molecules, such as CAAT/enhancer binding protein homologous protein (CHOP). Nicotine treatment led to the downregulation of ECM molecules, including collagen type I, elastin and fibronectin, and upregulation of MMPs (MMP-1, MMP-2, MMP-8 and MMP-9). Inhibition of ER stress by salubrinal and transfection of CHOP small interfering RNA attenuated the nicotine-induced cell death, ECM degradation and production of MMPs. Salubrinal and CHOP small interfering RNA inhibited the effects of nicotine on the activation of Akt, JNK and nuclear factor-κB. CONCLUSION These results indicate that nicotine-induced cell death is mediated by the ER stress pathway, involving ECM degradation by MMPs, in human periodontal ligament cells.

Structures and Electronic Spectra of CdSe−Cys Complexes: Density Functional Theory Study of a Simple Peptide-Coated Nanocluster

We present density functional theory (DFT) structures and time-dependent DFT electronic excitation energies of several small CdSe nanoclusters with the composition Cd(n)Se(n) (n = 3, 6, 10, 13). We examine the effects on the geometries and excitation spectra of the nanoclusters induced by two chemical changes: peptide-binding and ligand passivation. We use cysteine (Cys) and cysteine-cysteine dipeptide (Cys-Cys) as model peptides and hydrogen atoms as surface-bound solvent ligands (or stabilizing agents). By comparing the results calculated for bare, hydrogen-passivated (Cd(n)Se(n)H(2n)), as well as the corresponding Cys- and Cys-Cys- bound clusters (Cd(n)Se(n)-, Cd(n)Se(n)H(2n), -Cys, -Cys-Cys), we find that peptide-binding blue shifts the electronic excitations of bare nanoclusters, but red shifts those of hydrogen-passivated nanoclusters. The carboxyl oxygen and the sulfur atom tend to form a four-centered ring with adjacent two Cd atoms when the CdSe cluster forms covalent bonds with Cys or Cys-Cys. Further, this type of bonds may be distinguishable by significant red shifts of the excitation energies.

Multichannel quantum theory for propagation of second order transition amplitudes

We study the Green’s function representation of second order transition amplitudes for the transition from an initial to a final quantum state that occurs because both are weakly coupled to a manifold of intermediate states. These processes apply to Raman scattering, two‐photon absorption, fluoresecence from dissociating molecules, electron stimulated desorption, etc., and the transition amplitudes are called generalized Raman amplitudes. The generalized Raman transition amplitudes are expressed in terms of matrix elements of a multichannel Green’s function whose determination requires the simultaneous generation of the regular and irregular solutions of the multichannel Schrodinger equation for the intermediate state manifold. However, the numerical propagation of the generalized Raman transition amplitudes through classically forbidden regions requires, in effect, the simultaneous propagation (in the same direction) of both the regular and irregular solutions of the intermediate manifold Schrodinger equ...

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

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.

On the stability of glycine-water clusters with excess electron: Implications for photoelectron spectroscopy

Calculations are presented for the glycine-(H(2)O)(n) (-) (n=0-2) anionic clusters with excess electron, with the glycine core in the canonical or zwitterion form. A variety of conformers are predicted, and their relative energy is examined to estimate thermodynamic stability. The dynamic (proton transfer) pathways between the anionic clusters with the canonical and the zwitterion glycine core are examined. Small barrier heights for isomerization from the zwitterion glycine-(H(2)O)(2) (-) anion to those with canonical glycine core suggest that the former conformers may be kinetically unstable and unfavorable for detection of neutral glycine zwitterion-(H(2)O)(n) (n=1,2) clusters by photodetachment, in accordance with the photoelectron spectroscopic experiments by Bowen and co-workers [Xu et al., J. Chem. Phys. 119, 10696 (2003)]. The calculated stability of the glycine-(H(2)O)(n) (-) anion clusters with canonical glycine core relative to those with zwitterion core indicates that the observation of the anionic conformers with the canonical glycine core would be much more feasible, as revealed by Johnson and co-workers [Diken et al. J. Chem. Phys. 120, 9902 (2004)].