Showing papers by "Kwang S. Kim published in 2004"

Fluorescent GTP-sensing in aqueous solution of physiological pH

Abstract: A new water-soluble imidazolium anthracene derivative not only differentiates two structurally similar compounds GTP and ATP but also acts as potential fluorescent chemosensors (as a quencher and an enhancer, respectively) for GTP and ATP in 100% aqueous solution (pH = 7.4, 10 mM HEPES).

Theoretical Investigations of Anion−π Interactions: The Role of Anions and the Nature of π Systems

Abstract: The nature of the anion−π interaction has been investigated by carrying out high level ab initio calculations of the complexes of halide (F-, Cl-, and Br-), linear organic (CN-, NC-), and trigonal planar organic (NO3- and CO32-) anions with different kinds of π systems, viz. olefinic (tetrafluoroethene), aromatic (hexafluorobenzene), and heteroaromatic (1,3,5-triazine). In an effort to comprehend the underlying basis of this interaction, we have also carried out a rigorous decomposition of the interaction energies using the symmetry adapted perturbational theory (SAPT) method. Contrary to our expectations, the results indicate that the magnitudes of total interation energies of anion−π and cation−π interactions are similar. In contrast to cation−π interactions, anion−π interactions are, however, marked by substantial contributions from dispersion energies. As in the case of cation−π interactions, the role of anions also have a marked influence on the nature and magnitude of the anion−π interaction with in...

Highly effective fluorescent sensor for H2PO4(

Abstract: A new anthracene dimer connected by two imidazolium moieties has been systematically designed and synthesized as a fluorescent chemosensor for selective binding of H2PO4- over other anions, which have been examined using fluorescence and 1H NMR and rationalized with ab initio study.

Insights into the Structures, Energetics, and Vibrations of Monovalent Cation-(Water)1-6 Clusters †

Abstract: This study details the interactions prevailing in aqueous clusters of monovalent alkali metal, ammonium, and hydronium cations. The calculations involve a detailed evaluation of the structures, thermodynamic energies, andIR spectra of several plausible conformers of M + .(H 2 O) 1 - 6 (M = Li, Na, K, Rb, Cs, NH 4 , H 3 O) clusters at the second-order Miller-Plesset (MP2) and density functional levels of theory. A detailed decomposition of the interaction energies has been carried out for complexes involving one or two water molecules using symmetry adapted perturbation theory. Some of the salient insights on the structures include the emergence of the second solvent shell even before the realization of the maximal coordination number of the cation. This effect was more pronounced in clusters involving the larger cations. The quantitative estimates of various components of the interaction energy indicate the predominance of electrostatic energies in the binding of these cations to water molecules. Interestingly, for all the hydrated alkali metal cation complexes, the contribution of electrostatic energy is almost the same as the total attractive interaction energy, whereas the sum of the induction and dispersion energies are almost canceled out by exchange-repulsion energy. However, the contribution of dispersion energies slowly starts increasing as the size of the cation increases and is quite substantial in case of the Cs + complexes. In the organic cations, the dispersion energies become significant, though not comparable to the electrostatic energies. In addition to the evaluation of the harmonic frequencies of -OH stretching mode of all the structures, the anharmonic frequencies were evaluated for the smaller clusters. As the size of the cation and the size of the water cluster increases, the red shifts associated with the -OH stretching mode progressively become larger for the alkali metal cation containing complexes. For the organic cation (NH 4 +, H 3 O + ) containing complexes, an opposite trend is observed. Compared to the isolated water monomer, the ratio of the infrared intensities of the asymmetric and symmetric -OH stretching modes is very small. However, this ratio progressively becomes larger as the size of the cation increases.

Dissociation chemistry of hydrogen halides in water

Abstract: To understand the mechanism of aqueous acid dissociation, which plays a fundamental role in aqueous chemistry, the ionic dissociation of HX acids (X=F, Cl, Br, and I) in water clusters up to hexamer is examined using density functional theory and Moller–Plesset second-order perturbation methods (MP2). Further accurate analysis based on the coupled clusters theory with singles and doubles excitations agrees with the MP2 results. The equilibrium structures, binding energies, electronic properties, stretching frequencies, and rotational constants of HX(H2O)n and X−(H3O)+(H2O)n−1 are calculated. The dissociated structures of HF and HCl can be formed for n⩾4, while those of HBr and HI can be formed for n⩾3. Among these, the dissociated structures of HX (X=Cl, Br, and I) are more stable than the undissociated ones for n⩾4, while such cases for HF would require much more than six water molecules, in agreement with previous reports. The IR spectra of stable clusters including anharmonic frequencies are predicted to facilitate IR experimental studies. Undissociated systems have X–H stretching modes which are highly redshifted by hydration. Dissociated hydrogen halides show three characteristic OH stretching modes of hydronium moiety, which are redshifted from the OH stretching modes of water molecules.

Nature of one-dimensional short hydrogen bonding: bond distances, bond energies, and solvent effects.

Abstract: On the basis of recently synthesized calix[4]hydroquinone (CHQ) nanotubes which were self-assembled with infinitely long one-dimensional (1-D) short hydrogen bonds (SHB), we have investigated the nature of 1-D SHB using first-principles calculations for all the systems including the solvent water. The H-bonds relay (i.e., contiguous H-bonds) effect in CHQs shortens the H...O bond distances significantly (by more than 0.2 A) and increases the bond dissociation energy to a large extent (by more than approximately 4 kcal/mol) due to the highly enhanced polarization effect along the H-bond relay chain. The H-bonds relay effect shows a large increase in the chemical shift associated with the SHB. The average binding energies for the infinite 1-D H-bond arrays of dioles and dions increase by approximately 4 and approximately 9 kcal/mol per H-bond, respectively. The solvent effect (due to nonbridging water molecules) has been studied by explicitly adding water molecules in the CHQ tube crystals. This effect is found to be small with slight weakening of the SHB strength; the H...O bond distance increases only by 0.02 A, and the average binding energy decreases by approximately 1 kcal/mol per H-bond. All these results based on the first-principles calculations are the first detailed analysis of energy gain by SHB and energy loss by solvent effect, based on a partitioning scheme of the interaction energy components. These reliable results elucidate not only the self-assembly phenomena based on the H-bond relay but also the solvent effect on the SHB strength.

Aging behavior of oxygen plasma-treated polypropylene with different crystallinities

Abstract: Oxygen plasma-treated quenched and annealed polypropylene (PP) films with different crystallinities were investigated to characterize the surface rearrangement behavior during aging using contact-angle measurements and X-ray photoelectron spectroscopy. Optimum plasma conditions were examined by varying the power, time and pressure. Less crystalline quenched PP showed a larger increase in water contact angle and a larger decrease of oxygen atomic concentration during aging than the more crystalline annealed PP, since the oxygen species, such as hydroxyl groups, introduced by oxygen plasma treatment, oriented towards or diffused faster into the bulk with lower crystallinity. The degree of crosslinking on the surface was enhanced after plasma treatment and, in addition to increased crystallinity, the crosslinked structure induced by plasma treatment restricted chain mobility and lowered the aging rate of the PP surface.

Structures, energetics, and spectra of hydrated hydroxide anion clusters.

Abstract: The structures, energetics, electronic properties, and spectra of hydrated hydroxide anions are studied using density functional and high level ab initio calculations. The overall structures and binding energies are similar to the hydrated anion clusters, in particular, to the hydrated fluoride anion clusters except for the tetrahydrated clusters and hexahydrated clusters. In tetrahydrated system, tricoordinated structures and tetracoordinated structures are compatible, while in pentahydrated systems and hexahydrated systems, tetracoordinated structures are stable. The hexahydrated system is similar in structure to the hydrated chloride cluster. The thermodynamic quantities (enthalpies and free energies) of the clusters are in good agreement with the experimental values. The electronic properties induced by hydration are similar to hydrated chloride anions. The charge-transfer-to-solvent energies of these hydrated-hydroxide anions are discussed, and the predicted ir spectra are used to explain the experimental data in terms of the cluster structures. The low-energy barriers between the conformations along potential energy surfaces are reported.

An Easy-to-Use Three-Dimensional Molecular Visualization and Analysis Program: POSMOL

Abstract: Molecular visualization software has the common objective of manipulation and interpretation of data from numerical simulations. They visualize many complicated molecular structures with personal computer and workstation, to help analyze a large quantity of data produced by various computational methods. However, users are often discouraged from using these tools for visualization and analysis due to the difficult and complicated user interface. In this regard, we have developed an easy-to-use three-dimensional molecular visualization and analysis program named POSMOL. This has been developed on the Microsoft Windows platform for the easy and convenient user environment, as a compact program which reads outputs from various computational chemistry software without editing or changing data. The program animates vibration modes which are needed for locating minima and transition states in computational chemistry, draws two and three dimensional (2D and 3D) views of molecular orbitals (including their atomic orbital components and these partial sums) together with molecular systems, measur es various geometrical parameters, and edits molecules and molecular structures.

Antimony nanowires self-assembled from Sb nanoparticles

Abstract: For the first time, we introduced a simple method of synthesizing segregated thin antimony nanowires based on the principle that nanoparticles can spontaneously self-assemble into crystalline nanowires (∼20 nm) in the absence of any rigid templates at room temperature. By collecting electron energy loss spectra from individual Sb nanowires with different diameters, we investigated the effect of nanowire diameter on plasmon excitations in Sb nanowires. As the diameter of Sb nanowire decreases, we find that the peak energy of surface plasmon shifts toward the lower energy.

Atomic structure and energetics of adsorbed water on the NaCl(001) surface

Abstract: We have studied the structure and energetics of adsorbed water on the NaCl(001) surface using density-functional calculations within the generalized gradient approximation. We predict a new adsorption structure for the $c(4\ifmmode\times\else\texttimes\fi{}2)$ water bilayer which is energetically favored over the previous puckered hexagonal $c(4\ifmmode\times\else\texttimes\fi{}2)$ structure. Our calculations show that the $1\ifmmode\times\else\texttimes\fi{}1$ monolayer structure (wherein every water molecule binds to each surface cation) is metastable, thereby suggesting that the $1\ifmmode\times\else\texttimes\fi{}1$ structure would be transformed to the more stable $c(4\ifmmode\times\else\texttimes\fi{}2)$ structure which has an increased H-bond interactions between water molecules.

Aqua dissociation nature of cesium hydroxide.

Abstract: To understand the mechanism of aqueous base dissociation chemistry, the ionic dissociation of cesium–hydroxide in water clusters is examined using density functional theory and ab initio calculations. In this study, we report hydrated structures, stabilities, thermodynamic quantities, dissociation energies, infrared spectra, and electronic properties of CsOH⋅(H2O)n=0–4. With the addition of water molecules, the Cs–OH bond lengthened significantly from 2.46 A for n=1 to 3.08 A for n=4, which causes redshift in Cs–O stretching frequency. It is found that three water molecules are needed for the dissociation of Cs–OH, in contrast to the case of strong acid dissociation which requires at least four water molecules. However, the dissociation for n=3 could be considered as incomplete because a very weak CS…OH stretch mode is still present, while that for n=4 is complete since the Cs…OH mode no longer exists. This study can be related with hydration chemistry of cations and anions, and extended into the intra- and intercharge-transfer phenomena.

Insights into the structures, energetics, and vibrations of aqua-rubidium(I) complexes: ab initio study.

Abstract: We have carried out ab initio and density functional theory calculations of hydrated rubidium cations. The calculations involve a detailed evaluation of the structures, thermodynamic properties, and IR spectra of several plausible conformers of Rb+(H2O)n=1–8 clusters. An extensive search was made to find out the most stable conformers. Since the water-water interactions are important in hydrated Rb+ complexes, we investigated the vibrational frequency shifts of the OH stretching modes depending on the number of water molecules and the presence/absence of outer-shell water molecules. The predicted harmonic and anharmonic vibrational frequencies of the aqua-Rb+ clusters reflect the H-bonding signature, and would be used in experimental identification of the hydrated structures of Rb+ cation.

p-benzoquinone-benzene clusters as potential nanomechanical devices: a theoretical study.

Abstract: The equilibrium structures and binding energies of the benzene complexes of p-benzoquinones (PBQ) and its negatively charged anionic species (PBQ− and PBQ2−) have been investigated theoretically using second-order Moller-Plesset calculations. While neutral p-benzoquinone-benzene clusters (PBQ-Bz) prefer to have a parallel displaced geometry (P-c), CH⋯π interactions (T-shaped geometries) prevail in the di-anionic PBQ-benzene (PBQ2−-Bz) complexes (T-e2−). Studies on dianionic p-benzoquinone-benzene clusters showed that two nonbonded intermolecular interactions compete in the most stable conformation. One is H-bonding interaction (C–H⋯O type) between carbonyl oxygen of p-benzoquinone and one of the hydrogen atoms of benzene, and the other is a π–H interaction between π-electron cloud of PBQ2− and another hydrogen atom of benzene. Blueshifted H-bonds were observed in T-shaped clusters. The changes in the geometrical preference of PBQ-Bz complex upon addition of electrons would be useful in designing optimized...

HF(H2O)n clusters with an excess electron: ab initio study.

Abstract: The structures of electron-bound and neutral clusters of HF(H2O)n (n=1-3) were optimized at the level of second-order Moller-Plesset perturbation theory (MP2). Then, the energies were studied using the coupled cluster singles, doubles, and perturbative triples correction [CCSD(T)] method. The vertical detachment energies of the electron-bound clusters for n=1-3 are 60, 180, and approximately 300 meV, respectively. In the case of the n=3, two structures are competing energetically. The electron-bound clusters for n=1 and 2 are 1.5 and 1.8 kcal/mol more stable than the neutral, while that for n=3 is 0.6-0.9 kcal/mol less stable. The excess electron is stabilized in the surface-bound state of the dipole oriented structures of the hydrated acid clusters. Vibrational spectra of the electron-bound clusters are discussed.

Dissolution of a base (RbOH) by water clusters.

Abstract: Density functional and ab intio calculations are employed in order to understand the base dissociation of rubidium hydroxide by water molecules. The hydrated structures, stabilities, thermodynamic quantities, dissociation energies, infrared spectra, and electronic properties of RbOH(H2O)(n = 0-5) are investigated. With the successive addition of water molecules to RbOH, the Rb-OH bond lengthens significantly from 2.45 angstroms for n = 0 to 3.06 angstroms for n = 5. It is interesting to note that four water molecules are needed for the stable dissociation of RbOH (as an almost dissociate conformation) and five water molecules are needed for the complete dissociation without any Rb-OH stretch mode, in contrast to the same group base of CsOH which requires only three water molecules for an almost dissociate conformation and four water molecules for the complete dissociation.

Solvent rearrangement for an excited electron of the iodide-water pentamer

Abstract: We have investigated the solvent rearrangement process for the excited electron in the iodide–water pentamer using density functional and ab initio calculations. Upon excitation of the iodide–water pentamer, an electron transfers from the iodide anion to the water cluster, resulting in release of the iodine atom and formation of the anionic water pentamer undergoing rearrangement process toward the most stable conformation. Thus, the transformation pathway is elucidated.

Mechanistic Study on Electrochemical Reduction of Calix[4]quinone in Acetonitrile Containing Water§

Abstract: The mechanism of electrochemical reduction of calix[4]quinones (CQs) is of vital importance, as their reduction products, calix[4]hydroquinones (CQH8s), are known to self-assemble organic nanotubes, which in turn self-assemble novel metal nanostructures by a self-synthetic process of electrochemical reduction of solvated metals. We therefore conducted detailed studies of electrochemical reduction of CQ in rigorously dried acetonitrile (CH3CN) and in CH3CN containing varied amounts of water as well as perchloric acid. CQ undergoes a series of reversible one electron reductions in dry CH3CN leading to anion radicals of each of p-benzoquinone units followed by formation of dianions. However, a series of following chemical-electrochemical reactions with protons takes place after the initial electron transfer in CH3CN containing water. The final product of this series of reactions is identified as CQH8 via an eight electron, eight proton reaction. The intermediate species are identified, and the reaction mecha...

Metastable phase of symmetric dimers on Si(001)

Abstract: The reconstruction of the Si(001) surface is reexamined by using first-principles density-functional calculations. We find that a symmetric dimer structure in which symmetric dimers are alternately displaced up and down along the dimer rows is more favored by 21 meV/dimer than the conventional symmetric dimer structure where all the dimers have an identical height. In this metastable p( 2 × 2) structure, the up and down symmetric dimers accompany the lateral movements of the second-layer atoms: i.e., on the two sides of the dimer the second-layer atoms bonding to the up (down) dimer move equally toward (outward) each other by 0.15 A. With this predicted symmetric dimer structure we discuss the symmetric dimer phase observed in a recent low-temperature scanning tunneling microscopy experiment.

Nested Fermi surfaces, optical peaks, and laser-induced structural transition in Al

Abstract: Electronic structure and optical properties of Al are reexplored by using the highly precise first-principles band method. The spin-orbit interaction, albeit small, plays a critical role in determining the topology of theFermi surface and yields finite gap for interband transitions. The characteristic optical peaks in Al are shown to arise from the massive interband transitions between two parallel bands over the nested area of two Fermi surfaces. The laser-induced structural transition originates from this massive interband transition which causes the lattice softening via the excitation-driven charge transfer from the tetrahedral bonding to the octahedral antibonding sites.

Chapter 5 – Theoretical Approaches to the Design of Functional Nanomaterials

Abstract: This chapter discusses theoretical approaches to the design of functional nanomaterials. A theoretical description of nanomaterials that belongs to the mesoscopic phase is fraught with a number of problems because neither quantum–chemical methods used to investigate the microscopic phase nor solid-state physics methods used to investigate the macroscopic phase can adequately describe all the desired properties. A judicious combination of both these methods apart from providing a detailed insight of the properties of these nanomaterials also aids the de novo design of novel molecular systems and functional materials. Another area of interest is molecular recognition, wherein quantum chemical calculations aid the design of microscopic chemical/biochemical sensors/monitors such as DNA chips. This chapter examines the ways in which an effective combination of diverse theoretical methods ranging from traditional ab initio , density functional, tight binding, Monte Carlo to molecular dynamics simulations, have helped elucidate the nature of intermolecular interactions in a large number of widely disparate molecular complexes (aqueous and metal clusters, biomolecules), and have also aided the design of novel nanomaterials (ionophores, receptors, endo/exohedral fullerenes, fullerides, nanotori, nanotubes, nanowires, and molecular devices).

Local-field enhancement of spontaneous decay in nanosystems: some estimations for dielectric particles

Abstract: Enhancement of the spontaneous decay rate due to local-field effects is estimated for a luminous dipole inside a small dielectric particle. To do this, we make use of an idea on multiplicativity of the local-field factor. Elongated particles are shown to be promising in respect of the local-field enhancement of the spontaneous emission. Computations are carried out within the framework of modern theory of the spontaneous decay of excited atoms in absorbing media for both the virtual-cavity and real-cavity models. Particular emphasis is placed on dielectric/semiconductor particles in the vicinity of the optical phonon frequencies.