Showing papers by "Kwang S. Kim published in 2008"

Prediction of very large values of magnetoresistance in a graphene nanoribbon device.

Abstract: On the basis of first-principles computer simulations, theorists have predicted that zigzag graphene nanoribbons should display magnetoresistance values that are thousands of times higher than previously reported experimental values, and also should be able to generate highly spin-polarized currents.

Complete basis set limit of Ab initio binding energies and geometrical parameters for various typical types of complexes.

Abstract: Using basis-set extrapolation schemes for a given data set, we evaluated the binding energies and geometries at the complete basis set (CBS) limit at the levels of the second order Moller–Plesset perturbation theory (MP2) and the coupled cluster theory with singles, doubles, and perturbative triples excitations [CCSD(T)]. The systems include the hydrogen bonding (water dimer), aromatic interaction (benzene dimer), π–H interaction (benzene–water), cation–water, anion–water, π–cation interaction (cation–benzene), and π–anion interaction (anion–triazine). One extrapolation method is to exploit both BSSE-corrected and BSSE-uncorrected binding energies for the aug-cc-pVNZ (N = 2, 3, 4, …) basis set in consideration that both binding energies give the same CBS limit (CBSB). Another CBS limit (CBSC) is to use the commonly known extrapolation approach to exploit that the electron correlation energy is proportional to N−3. Since both methods are complementary, they are useful for estimating the errors and trend of the asymptotic values. There is no significant difference between both methods. Overall, the values of CBSC are found to be robust because of their consistency. However, for small N (in particular, for N = 2, 3), CBS is found to be slightly better for water–water interactions and cation–water and cation–benzene interactions, whereas CBS is found to be more reliable for bezene–water and anion–water interactions. We also note that the MP2 CBS limit value based on N = 2 and 3 combined with the difference between CCSD(T) and MP2 at N = 2 would be exploited to obtain a CCSD(T)/CBS value for aromatic–aromatic interactions and anion–π interactions, but not for cationic complexes. © 2007 Wiley Periodicals, Inc. J Comput Chem, 2008

Anthracene Derivatives Bearing Thiourea and Glucopyranosyl Groups for the Highly Selective Chiral Recognition of Amino Acids : Opposite Chiral Selectivities from Similar Binding Units

Abstract: Two new anthracene thiourea derivatives, 1 and 2, were investigated as fluorescent chemosensors for the chiral recognition of the two enantiomers of alpha-amino carboxylates. Especially, host 2 displayed K(L)/K(D) values as high as 10.4 with t-Boc alanine. Furthermore, the D/L selectivity of hosts 1 and 2 is opposite, even though both hosts bear the same glucopyranosyl units. These intriguing opposite D/L binding affinities by 1 and 2 were obtained without/with H-pi interaction between anthrancene moiety and the methyl groups, which were explained by extensive high-level theoretical investigations taking into account the dispersion energy as well as the 2D-NMR chemical shifts.

Cyameluric Acid as Anion-π Type Receptor for ClO4− and NO3−: π-Stacked and Edge-to-Face Structures

Abstract: Based on the binding energies at high levels of ab initio theory including coupled cluster theory at the complete basis limit, we show that cyameluric acid (C6N7O3H3) is a potent receptor for ClO4(-) and NO3(-) anions through the anion-π interactions. In contrast, cyanuric acid (C3N3O3H3) binds Cl(-), NO3(-), and ClO4(-) with the hydrogen bonding type structures, while their anion-π type structures show slightly weaker binding. Consequently, the cyameluric acid having the C3h symmetric C6N7 nucleus with electron withdrawing oxygen atoms is a novel anion-π type receptor for trigonal-planar and tetrahedral anions. The structures of the cyameluric acid interacting with Cl(-) and ClO4(-) are considered as the π stacking type. For the cyameluric acid interacting with NO3(-), the π(edge) type complex is only slightly more favored over the π(stack) type in the gas phase, but the π(stack) type is likely to be as stable as the π(edge) type in the solvent phase.

Carbon nanotube, graphene, nanowire, and molecule-based electron and spin transport phenomena using the nonequilibrium Green's function method at the level of first principles theory.

Abstract: Based on density functional theory, we have developed a program code to investigate the electron transport characteristics for a variety of nanometer scaled devices in the presence of an external bias voltage. We employed basis sets comprised of linear combinations of numerical type atomic orbitals, particularly focusing on k-point sampling for the realistic modeling of the bulk electrode. The scheme coupled with the matrix version of the nonequilibrium Green's function method enables calculation of the transmission coefficients at a given energy and voltage in a self-consistent manner as well as the corresponding current-voltage (I-V) characteristics. This scheme has advantages because it is applicable to large systems, easily transportable to different types of quantum chemistry packages, and extendable to time-dependent phenomena or inelastic scatterings. It has been applied to diverse types of practical electronic devices such as carbon nanotubes, graphene nanoribbons, metallic nanowires, and molecular electronic devices. The quantum conductance phenomena for systems involving quantum point contacts and I-V curves for a single molecule in contact with metal electrodes using the k-point sampling method are described.

Solvent-Driven Structural Changes in Anion−π Complexes

Abstract: Among the π interactions, the anion-π interaction has been a novel type of interaction. In the cases of halide-π complexes, which are the most typical examples of the anion-π interaction, the theoretically predicted and experimentally observed structures in the gas phase are quite different from the most frequently observed crystal structures. We here investigate the structural changes in complexation of the F(-)/Cl(-) ion with triazine (TAz) as the number of water/acetonitrile molecules increases from 1 to 4. Both the covalent bonding type for F(-)-TAz and the hydrogen-bonding type for Cl(-)-TAz, which are the lowest-energy structures in the gas phase, change to the solvent-mediated anion-π-type or displaced anion-π-type complexes. This study explains why the (displaced) anion-π-type complexes with some flexible orientations are most common in many crystal structures.

Understanding structures and electronic/spintronic properties of single molecules, nanowires, nanotubes, and nanoribbons towards the design of nanodevices

Abstract: Theoretical understanding of metal nanowires and molecular devices is described towards the design of novel nanodevices. We focus our attention on structures, electronic, and spintronic properties of low dimensional metallic/molecular nanostructures based mostly on our recent works. The discussion includes (i) electric field induced molecular orbital control towards molecular electronic and spintronic devices, (ii) conductances of carbon nanotubes and graphene nanoribbons, (iii) low dimensional structures and properties, focusing on the stability, quantum conductance, and magnetic features of metallic nanowires, and (iv) metalvs. carbon nanotube/graphene electrodes for negative differential resistance in molecular electronics.

Photoexcitation and photoionization dynamics of water photolysis.

Abstract: Despite the importance of water photolysis in atmospheric chemistry, its mechanism is not well understood. Two different mechanisms for water photolysis have been proposed. The first mechanism is driven by water photoexcitation, followed by the reaction of the active hydrogen radical with water clusters. The second mechanism is governed by the ionization process. Both photoexcited and photoionized mechanisms are complementary, which is elucidated by using excited-state ab initio molecular dynamics simulations based on complete active space self-consistent field approach and unrestricted Moller-Plesset second-order perturbation theory based Born-Oppenheimer molecular dynamics simulations.

Large-scale polyol synthesis of single-crystal bismuth nanowires and the role of NaOH in the synthesis process.

Abstract: A modified polyol process is introduced for the production of single-crystal bismuth (Bi) nanowires with uniform diameters along each wire in relatively high yield. The appropriate amount of NaOH in the solution reacts with Bi(3+) to form water-soluble complexing ions BiO(2)(-). The tiny Bi nanoparticles formed at the initial stage could serve as seeds for the subsequent growth of Bi nanostructures in the refluxing process with the aid of PVP. We find that the amount of NaOH determines the reduction rate of BiO(2)(-), which influences the morphologies of the synthesized Bi nanostructures. High reduction rates result in nanowires and nanoparticles, while low reduction rates result in nanoplates.

Charge-transfer-to-solvent-driven dissolution dynamics of I- (H2O)2-5 upon excitation: excited-state ab initio molecular dynamics simulations

Abstract: In contrast to the extensive theoretical investigation of the solvation phenomena, the dissolution phenomena have hardly been investigated theoretically. Upon the excitation of hydrated halides, which are important substances in atmospheric chemistry, an excess electron transfers from the anionic precursor (halide anion) to the solvent and is stabilized by the water cluster. This results in the dissociation of hydrated halides into halide radicals and electron-water clusters. Here we demonstrate the charge-transfer-to-solvent (CTTS)-driven femtosecond-scale dissolution dynamics for I-(H2O)n=2-5 clusters using excited state (ES) ab initio molecular dynamics (AIMD) simulations employing the complete-active-space self-consistent-field (CASSCF) method. This study shows that after the iodine radical is released from I-(H2O)n=2-5, a simple population decay is observed for small clusters (2

Undissociated versus dissociated structures for water clusters and ammonia-water clusters: (H2O)n and NH3(H2O)n-1 (n = 5, 8, 9, 21). Theoretical study.

Abstract: To understand the autoionization of pure water and the solvation of ammonia in water, we investigated the undissociated and dissociated (ion-pair) structures of (H2O)n and NH3(H2O)n−1 (n = 5, 8, 9, 21) using density functional theory (DFT) and second order Moller−Plesset perturbation theory (MP2). The stability, thermodynamic properties, and infrared spectra were also studied. The dissociated (ion-pair) form of the clusters tends to favor the solvent-separated ion-pair of H3O+/NH4+ and OH−. As for the NH3(H2O)20 cluster, the undissociated structure has the internal conformation, in contrast to the surface conformation for the (H2O)21 cluster, whereas the dissociated structure of NH3(H2O)20 has the surface conformation. As the cluster size of (H2O)n/NH3(H2O)n−1 increases, the difference in standard free energy between undissociated and dissociated (ion-pair) clusters is asymptotically well corroborated with the experimental free energy change at infinite dilution of H3O+/NH4+ and OH−. The predicted NH and ...

Structures, energetics, vibrational spectra of NH4+ (H2O)(n=4,6) clusters: Ab initio calculations and first principles molecular dynamics simulations.

Abstract: Important structural isomers of NH4+(H2O)n=4,6 have been studied by using density functional theory, Moller–Plesset second order perturbation theory, and coupled-cluster theory with single, double, and perturbative triple excitations [CCSD(T)]. The zero-point energy (ZPE) correction to the complete basis set limit of the CCSD(T) binding energies and free energies is necessary to identify the low energy structures for NH4+(H2O)n=4,6 because otherwise wrong structures could be assigned for the most probable structures. For NH4+(H2O)6, the cage-type structure, which is more stable than the previously reported open structure before the ZPE correction, turns out to be less stable after the ZPE correction. In first principles Car–Parrinello molecular dynamics simulations around 100K, the combined power spectrum of three lowest energy isomers of NH4+(H2O)4 and two lowest energy isomers of NH4+(H2O)6 explains each experimental IR spectrum.

Structure, Stability, Thermodynamic Properties, and Infrared Spectra of the Protonated Water Octamer H+(H2O)8

Abstract: We investigated various two-dimensional (2D) and three-dimensional (3D) structures of H + (H 2 O) 8 , using density functional theory (DFT), Moller-Plesset second-order perturbation theory (MP2), and coupled cluster theory with single, double, and perturbative triple excitations (CCSD(T)). The 3D structure is more stable than the 2D structure at all levels of theory on the Born-Oppenheimer surface. With the zero-point energy (ZPE) correction, the predicted structure varies depending on the level of theory. The DFT employing Becke's three parameters with Lee-Yang-Parr functionals (B3LYP) favors the 2D structure. At the complete basis set (CBS) limit, the MP2 calculation favors the 3D structure by 0.29 kcal/mol, and the CCSD(T) calculation favors the 3D structure by 0.27 kcal/mol. It is thus expected that both 2D and 3D structures are nearly isoenergetic near 0 K. At 100 K, all the calculations show that the 2D structure is much more stable in free binding energy than the 3D structure. The DFT and MP2 vibrational spectra of the 2D structure are consistent with the experimental spectra. First-principles Car-Parrinello molecular dynamics (CPMD) simulations show that the 2D Zundel-type vibrational spectra are in good agreement with the experiment.

Ground state structures and excited state dynamics of pyrrole-water complexes: ab initio excited state molecular dynamics simulations.

Abstract: Structures of the ground state pyrrole-(H2O)n clusters are investigated using ab initio calculations The charge-transfer driven femtosecond scale dynamics are studied with excited state ab initio molecular dynamics simulations employing the complete-active-space self-consistent-field method for pyrrole-(H2O)n clusters Upon the excitation of these clusters, the charge density is located over the farthest water molecule which is repelled by the depleted π-electron cloud of pyrrole ring, resulting in a highly polarized complex For pyrrole-(H2O), the charge transfer is maximized (up to 034au) around ∼100fs and then oscillates For pyrrole-(H2O)2, the initial charge transfer occurs through the space between the pyrrole and the π H-bonded water molecule and then the charge transfer takes place from this water molecule to the σ H-bonded water molecule The total charge transfer from the pyrrole to the water molecules is maximized (up to 053au) around ∼100fs

Photodissociation of Hydrated Hydrogen Iodide Clusters

Abstract: Using high-level ab initio calculations and excited state ab initio molecular dynamics simulations, we show that hydrated iodic acids release hydrogen radicals and/or hydrogen molecules as well as iodine radicals upon excitation. Its photoreaction process involving charge transfer to the solvent takes place in four steps: 1) hydration of the acid, 2) charge transfer to water upon excitation of hydrated acid, 3) detachment of the neutral iodine atom, and 4) detachment of the hydrogen radical. The iodine detachment process from excited hydrated hydro-iodic acids is exothermic and the detachment of hydrogen radicals from hydrated hydronium radicals is spontaneous if the initial kinetic energy of the cluster is high enough to get over the activation barrier of the detachment. The complete release of the radicals can be understood in terms of kinetics. This study shows how the hydrogen and halogen radicals are dissociated and released from their hydrated acids. Simple experiments corroborate our predicted mechanism for the release of hydrogen molecules from iodic acid in water by ultraviolet light.

Taste Composition and Biological Activities of Cheonggukjang Containing Rubus coreanum

Abstract: This study was performed to investigate the taste composition and biological activities of cheonggukjang containing Rubus coreanum to improve cheonggukjangs’ flavor and consumption. In R. corenum cheonggukjang (RCC), the total content of soluble sugars, including glucose, fructose, maltose, and sucrose, was 1,052.1 mg/100 g. Glutamic acid, phenlylalanine, leucine, cystine, and tyrosine were the major amino acids, and the ratio of sweet to bitter components was higher in RCC than in general cheonggukjang (GC). The 1,1-diphenyl-2-picrylhydrazyl (DPPH) radical scavenging activities of the extracts, in decreasing order, were found to be: ethanol extract > water extract > chloroform extract, at all concentrations. The water extract had the highest SOD-like activity (10.2%) at a concentration of 0.5 mg/mL, whereas the chloroform extract showed the highest SOD-like activity (19.1%) at a concentration of 2 mg/mL. The nitrite scavenging ability was higher at pH 1.2 than at pH 3.0 or 6.0, and had a positive correlation with the extract concentration. The chloroform extract had the highest nitrite scavenging ability (84.6%) at a concentration of 2 mg/mL and pH 2.0.

Designing Ionophores and Molecular Nanotubes Based on Molecular Recognition

Abstract: In this mini-review we briefly describe intermolecular interactions ranging from hydrogen bonding to ionic interactions to aromatic interactions. Manifestation of these interaction forces is in the design and realization of various ionophores with chemo-sensing capability for biologically important cations and anions. We also explain how the understanding of hydrogen bonding and π-interactions has led to the design of self-assembled organic nanotubes. We further discuss the conformational changes between stacked and edge-to-face conformers in benzoquinone-benzene complexes, which are controlled by alternating electrochemical potential. The resulting flapping motion illustrates a promising pathway toward the design of nanomechanical devices.

Ab Initio Study of Different Acid Molecules Interacting with H2O

Abstract: Using the Gaussian-03 for ab initio calculations, we have studied interaction of different acid molecules with a single water molecule. The molecular and supermolecular optimized structures were found with the Becke-3-Lee-Yang-Parr (B3LYP-hybrid potential) calculations of density-functional theory (DFT) methods as well as the Moeller-Plesset second-order perturbation theory, using the basis set of Aug-cc-pVDZ quality and the CRENBL ECP effective core potential for molecules containing heavy iodine atom. Possible isomers of studied acids and supermolecules, consisting of acid molecules coupled with a single water molecule, are shown. Energies, zero-point energies (ZPEs), thermal enthalpies and free energies, as well as the corresponding binding energies for the theoretical methods were calculated. It was found that optimized structures of supermolecular isomers with lowest energies corresponding to the global minimum on the potential energy surfaces can be different for both theories. The simplest structure acids H2S and H2Se, forming acid-water supermolecules, can give clear evidence of disagreement of the two theoretical methods concerning optimization of lowest energy structures, because the B3LYP-DFT method gives the lowest-energy structure for the first supermolecular isomer, but the MP2 method for the second possible isomer. A dramatic difference between potential energy surfaces for both theories applying to the optimized structure finding of the H2SO3-H2O supermolecular isomers was found, because MP2 supermolecular geometries cannot exist for the corresponding B3LYP-DFT ones, for which the frequency characteristics of the supermolecular isomers were also calculated. In general, the binding energies and ZPE ones for the MP2 method are 10-15% larger than those for the B3LYP-DFT method.

Hydrogen detachment of the hydrated hydrohalogen acids upon attaching an excess electron.

Abstract: High level ab initio calculations are employed to investigate the excess electron attachment to the hydrated hydrohalogen acids. The excess electron leads to the dissociation of hydrogen halide acids, which results in the release of a hydrogen radical. Neutral HCl, HBr, and HI are dissociated by tetrahydration. Upon binding an excess electron, these hydrated hydrohalogen acids show that (i) the H–X bond strength weakens with redshifted H–X stretching frequencies, (ii) HX can have a bound-electron state, a dissociated structure, or a zwitter-ionic structure, and (iii) HCl∕HBr is dissociated by tri/mono-hydration, while HI is dissociated even without hydration. This dissociation is in contrast to the case of electron attachment to hydrated hydrogen fluoric acids for which HF is not dissociated by more than ten water molecules.