Biomedical subjects

Kwang S Kim

Publications and source records attributed to Kwang S Kim.

At least 55 records · Page 3Linked to original sources

PubMed2005

Role of molecular orbitals of the benzene in electronic nanodevices.

In an effort to examine the intricacies of electronic nanodevices, we present an atomistic description of the electronic transport properties of an isolated benzene molecule. We have carried out ab initio calculations to understand the modulation of the molecular orbitals (MOs) and their energy spectra under the external electric field, and conducting behavior of the benzene molecule. Our study shows that with an increase in the applied electric field, the energy of the third lowest unoccupied molecular orbital (LUMO) of benzene decreases, while the first and second LUMO energies are not affected. Above a certain threshold of the external electric field, the third LUMO is lowered below the original LUMO and becomes the real LUMO. Since the transport through a molecule is to a large extent mediated by the molecular orbitals, the change in MOs can lead to a dramatic increase in the current passing through the benzene molecule. Thus, in the course of this study, we show that the modulation of the molecular orbitals in the presence of a tuning parameter(s) such as the external electric field can play important roles in the operation of molecular devices. We believe that this understanding would be helpful in the design of electronic nanodevices.

Journal Article↗

PubMed2005

Hydrated copper and gold monovalent cations: Ab initio study.

To understand the hydration phenomena of noble transition metals, we investigated the structures, hydration energies, electronic properties, and spectra of the Cu(+)(H(3)O)(1-6) and Au(+)(H(2)O)(1-6) clusters using ab initio calculations. The coordination numbers of these clusters are found to be only two, which is highly contrasted to those of Ag(+)(H(2)O)(n) (which have the coordination numbers of 3-4) as well as the hydrated alkali metal ions (which have the coordination numbers of approximately 6). For the possible identification of their interesting hydration structures, we predict their IR spectra for the OH stretch modes.

Journal Article↗

PubMed2005

Origin of the magic numbers of water clusters with an excess electron.

Electron-bound water clusters [e(-)(H(2)O)(n)] show very strong peaks in mass spectra for n=2, 6, 7, and (11), which are called magic numbers. The origin of the magic numbers has been an enigma for the last two decades. Although the magic numbers have often been conjectured to arise from the intrinsic properties of electron-bound water clusters, we attributed them not to their intrinsic properties but to the particularly weak stability of the corresponding neutral water clusters (H(2)O)(n=2,6,7, and (11)). As the cluster size increases; this nonsmooth characteristic feature in stability of neutral water clusters is contrasted to the smooth increase in stability of e(-)-water clusters. As the magic number clusters have significant positive adiabatic electron affinities, their abundant distributions in atmosphere could play a significant role in atmospheric thermodynamics.

Journal Article↗

PubMed2005

Theoretical studies on hydroquinone-benzene clusters.

High-level ab initio calculations were carried out to evaluate the interaction between the hydroquinone and benzene molecules. The intermolecular interaction energy was calculated using the Møller-Plesset second-order perturbation theory at the complete basis set limit and also at the coupled cluster theory with single, double, and perturbatively triple excitations. The calculated binding energy is larger than the benzene dimer interaction energy. The T-shaped cluster (T-a) and the parallel conformation (P-a) are calculated to be nearly isoenergetic. Owing to the large energy gain in the attraction by electron correlation, the dispersion interaction is important for the attraction.

Journal Article↗

PubMed2005

PavA of Streptococcus pneumoniae modulates adherence, invasion, and meningeal inflammation.

Pneumococcal adherence and virulence factor A (PavA) is displayed to the cell outer surface of Streptococcus pneumoniae and mediates pneumococcal binding to immobilized fibronectin. PavA, which lacks a typical gram-positive signal sequence and cell surface anchorage motif, is essential for pneumococcal virulence in a mouse infection model of septicemia. In this report the impact of PavA on pneumococcal adhesion to and invasion of eukaryotic cells and on experimental pneumococcal meningitis was investigated. In the experimental mouse meningitis model, the virulence of the pavA knockout mutant of S. pneumoniae D39, which did not show alterations of subcellular structures as indicated by electron microscopic studies, was strongly decreased. Pneumococcal strains deficient in PavA showed substantially reduced adherence to and internalization of epithelial cell lines A549 and HEp-2. Similar results were obtained with human brain-derived microvascular endothelial cells and human umbilical vein-derived endothelial cells. Attachment and internalization of pneumococci were not significantly affected by preincubation or cocultivations of pneumococci with anti-PavA antisera. Pneumococcal adherence was also not significantly affected by the addition of PavA protein. Complementation of the pavA knockout strain with exogenously added PavA polypeptide did not restore adherence of the mutant. These data suggest that PavA affects pneumococcal colonization by modulating expression or function of important virulence determinants of S. pneumoniae.

Adhesins, Bacterial↗

PubMed2004

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

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.

Journal Article↗

PubMed2004

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

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.

Anions↗

PubMed2004

Dissolution of a base (RbOH) by water clusters.

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.

Journal Article↗

PubMed2004

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

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.

Journal Article↗

PubMed2004

Fluorescent GTP-sensing in aqueous solution of physiological pH.

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).

Adenosine Triphosphate↗

PubMed2004

Aqua dissociation nature of cesium hydroxide.

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(H(2)O)(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 em leader OH stretch mode is still present, while that for n=4 is complete since the Cs em leader 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.

Journal Article↗

PubMed2004

Dissociation chemistry of hydrogen halides in water.

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 Møller-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(H(2)O)(n) and X(-)(H(3)O)(+)(H(2)O)(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.

Journal Article↗

PubMed2004

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

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.

Journal Article↗

PubMed2004

Highly effective fluorescent sensor for H2PO4(-).

A new anthracene dimer connected by two imidazolium moieties has been systematically designed and synthesized as a fluorescent chemosensor for selective binding of H(2)PO(4)(-) over other anions, which have been examined using fluorescence and (1)H NMR and rationalized with ab initio study.

Journal Article↗

PubMed2003

Insights into the structure of cyclohexane from femtosecond degenerate four-wave mixing spectroscopy and ab initio calculations.

In this paper, we report the use of femtosecond time-resolved degenerate four-wave mixing rotationally resolved spectroscopy to obtain very accurate structural information on the symmetric top cyclohexane. Apart from highlighting the versatility of this method in determining accurate structures of large and complex molecules without dipole moment, the present study also details the comparison of the experimentally determined rotational constant B(0) with that obtained from high-level ab initio calculations. The theoretical calculations, which were carried out at both the second-order Møller-Plesset (MP2) and coupled-cluster with single, double, and perturbative triple substitutions [CCSD(T)] levels of theory, also take into account vibrational averaging effects. A detailed investigation of the vibrational averaging effects reveals that the corrections emerge from only the six highly symmetric A(1g) modes, a justification of which is provided by an analysis of these modes.

Journal Article↗

PubMed2003

Highly stereospecific epimerization of alpha-amino acids: conducted tour mechanism.

The highly stereospecific and regiospecific recognition of alpha-amino acids exhibited by a novel Co(III) metal complex embodied in the experimental work (Nature 1999, 401, 254) is rationalized from the energetics and structural characteristics with the use of density functional calculations. The steric repulsion between the chiral center of the receptor [Co(III) complex] and alanine has been a cause for the discrimination of complex stabilities. The energies evaluated for all possible alanine binding modes clearly reveal regiospecificity. Our main emphasis is laid on the base-catalyzed epimerization reaction that drives the stereospecific recognition to near completion. The conducted tour mechanism is found to be the most likely candidate. A similar role by the equivalent Zn(II) complex is found.

Amino Acids↗

PubMed2003

New fluorescent photoinduced electron transfer chemosensor for the recognition of H2PO4-.

[structure: see text] The fluorescent chemosensor 1 bearing two imidazolium groups at the 1,8-position of anthracene has been designed for the recognition of anions through the (C-H)(+)- - -X(-) hydrogen bond formation. As unique tweezer-like binding of 1 with anions is predicted by the ab initio calculations, strong anion-binding properties of chemosensor 1 are demonstrated by using fluorescence as well as (1)H NMR.

Journal Article↗

PubMed2003

Inflammatory stress increases receptor for lysophosphatidylcholine in human microvascular endothelial cells.

The atherogenic serum lysophosphatidylcholine (LPC) is known to mediate vascular endothelial responses ranging from upregulation of adhesion molecules and growth factors to secretion of chemokines and superoxide anion. We investigated whether endothelial cells express receptors for LPC, which may account for their actions. Human brain microvascular (HBMEC) and dermal microvascular endothelial cells (HMEC) were prepared for RT-PCR analysis for possible expression of the G protein-coupled receptors, GPR4 and G2A, which are believed to be specific LPC receptors. Results indicated that HBMEC expressed low basal GPR4 mRNA, but stimulation with tumor necrosis factor-alpha (TNF-alpha) (100 U/ml) or H2O2 (50 micromol/l) for 2 h or overnight upregulated expression severalfold. In contrast, HMEC expressed high basal GPR4 mRNA, which was not further increased by either TNF-alpha or H2O2 stimulation. Another LPC receptor, G2A, was not detected in either endothelial cell type. Competition binding studies were made to evaluate specific binding of [3H]LPC to the intact endothelial cell monolayer. Basal specific [3H]LPC binding in HBMEC was approximately eight times lower than in HMEC; however, TNF-alpha or H2O2 stimulation increased [3H]LPC binding on HMBEC but not HMEC. The results indicated that GPR4 expression was consistent with specific [3H]LPC binding. Overall, we report that endothelial cells selectively expressed GPR4, a specific LPC receptor. Furthermore, GPR4 expression by HBMEC, but not HMEC, was increased by inflammatory stresses. We conclude that endogenous GPR4 in endothelial cells may be a potential G protein-coupled receptor by which LPC signals proinflammatory activities.

Cell Cycle Proteins↗