Showing papers by "Kwang S. Kim published in 2005"

Theory and applications of computational chemistry : the first forty years

Abstract: Computing Technologies, Theories, and Algorithms. The Making of 40 Years and More of Theoretical and Computational. A Dynamical, Time-Dependent View of Molecular Theory. Computation of Non-covalent Binding. Electrodynamics in Computational Chemistry. Variational Transition State. Attempting to Simulate Large Molecular Systems. The Beginnings of Coupled Cluster Theory: An Eyewitness Account. Controlling Quantum Phenomena with Photonic Reagents. First-Principles Calculations of Anharmonic Vibrational Spectroscopy of Large Molecules. Finding Minima, Transition States, and Following Reaction Pathways on Ab Initio Potential Energy Surfaces. Progress in the Quantum Description of Vibrational Motion of Polyatomic Molecules. Toward Accurate Computations in Photobiology. The Nature of the Chemical Bond in the Light of an Energy Decomposition Analysis. Superoperator Many-body Theory of Molecular Currents: Non-equilibrium Green Functions in Real Time. Role of Computational Chemistry in the Theory of Unimolecular Reaction Rates. Molecular Dynamics: An Account of its Evolution. Equations of Motion (EOM) Methods for Computing Electron Affinities and Ionization Potentials. Multireference Coupled Cluster Method Based on the Brillouin-Wigner Perturbation Theory. Electronic Structure: The Momentum Perspective. Recent Advances in ab initio, DFT, and Relativistic Electronic Structure Theory . Semiempirical Quantum-Chemical Methods in Computational Chemistry. Size-consistent State-specific Multi-reference Methods: A Survey of Some Recent Developments. The Valence Bond Diagram Approach - A Paradigm for Chemical Reactivity. Development of Approximate Exchange-Correlation Functionals. Multiconfigurational Quantum Chemistry. Concepts of Perturbation, Orbital interaction, Orbital Mixing and Orbital Occupation. G2, G3 and Associated Quantum Chemical Models for Accurate Theoretical Thermochemistry. Factors that Affect Conductance at the Molecular Level. The CH O Hydrogen Bond. A Historical Account. Ab Initio and DFT Calculations on the Cope Rearrangement, a Reaction with a Chameleonic Transition State. High-Temperature Quantum Chemical Molecular Dynamics Simulations of Carbon Nanostructure Self-Assembly Processes. Computational Chemistry of Isomeric Fullerenes and Endofullerenes. On the importance of Many-Body Forces in Clusters and Condensed Phase. Clusters to Functional Molecules, Nanomaterials, and Molecular Devices: Theoretical Exploration. Monte Carlo Simulations of the Finite Temperature Properties of (H2O)6. Computational Quantum Chemistry on Polymer Chains: Aspects of the Last Half Century. Forty Years of Ab Initio Calculations on Intermolecular. Applied Density Functional Theory and the deMon Codes 1964 to 2004. SAC-CI Method Applied to Molecular Spectroscopy. Forty Years of Fenske-Hall Molecular Orbital Theory. Advances in Electronic Structure Theory: GAMESS a Decade Later. How and Why Coupled-Cluster Theory Became the Preeminent Method in Ab initio Quantum Chemistry.

Substituent effects on the edge-to-face aromatic interactions.

Abstract: The edge-to-face interactions for either axially or facially substituted benzenes are investigated by using ab initio calculations. The predicted maximum energy difference between substituted and unsubstituted systems is ∼0.7 kcal/mol (∼1.2 kcal/mol if substituents are on both axially and facially substituted positions). In the case of axially substituted aromatic systems, the electron density at the para position is an important stabilizing factor, and thus the stabilization/destabilization by substitution is highly correlated to the electrostatic energy. This results in its subsequent correlation with the polarization and charge transfer. Thus, the stabilization/destabilization by substitution is represented by the sum of electrostatic energy and induction energy. On the other hand, the facially substituted aromatic system depends on not only the electron-donating ability responsible for the electrostatic energy but also the dispersion interaction and exchange repulsion. Although the dispersion energy i...

Quasi-Continuous Growth of Ultralong Carbon Nanotube Arrays

Abstract: We report the growth of ultralong (>10 cm) multi-walled and single-walled carbon nanotubes such that the length is limited by the size of the furnace rather than by the termination of growth The disturbance of microscale laminar flows results in disordered or shorter growth of carbon nanotubes By downsizing reaction pipes, reaction gas flows are stabilized with low Reynolds numbers In this way, the catalyst nanoparticles at the end of growing carbon nanotubes can travel a longer distance to grow ultralong nanotubes

Size control of semimetal bismuth nanoparticles and the UV-visible and IR absorption spectra.

Abstract: We introduced a simple chemical method to synthesize semimetal bismuth nanoparticles in N,N-dimethylformamide (DMF) by reducing Bi3+ with sodium borohydride (NaBH4) in the presence of poly(vinylpyrroldone) (PVP) at room temperature. The size and dispersibility of Bi nanoparticles can be easily controlled by changing the synthetic conditions such as the molar ratio of PVP to BiCl3 and the concentration of BiCl3. The UV−visible absorption spectra of Bi nanoparticles of different diameters are systematically studied. The surface plasmon peaks broaden with the increasing molar ratio of PVP to BiCl3 as the size of bismuth nanoparticles decreases. Infrared (IR) spectra of the complexes with different molar ratios of PVP/BiCl3 show a strong interaction between the carboxyl oxygen (CO) of PVP and Bi3+ ion and a weak interaction between the carboxyl oxygen (CO) of PVP and the Bi atom in nanoparticles. This indicates that PVP serves as an effective capping ligand, which prevents the nanoparticles from aggregation.

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

Abstract: Electron-bound water clusters [e−(H2O)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 (H2O)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.

Extracting subnanometer single shells from ultralong multiwalled carbon nanotubes.

Abstract: We report a simple but powerful method for engineering multi-walled carbon nanotubes (MWNTs) by using manipulation by an atomic-force microscope. The successive shell-by-shell extraction process of ultralong MWNTs allows the exposure of the innermost single-walled carbon nanotubes (SWNTs), which have diameters as small as ≈0.4 nm. The inner-shell extraction process changes the electrical characteristics of the MWNTs. Whereas the outer hollowed-out nanotubes show either metallic or semiconducting character, the innermost SWNTs of small diameter exhibit predominantly metallic transport properties.

Theoretical Investigation of Normal to Strong Hydrogen Bonds

Abstract: We review our theoretical work done on a variety of different chemical systems, which show different H-bonding characteristics. The systems include water clusters, its interactions with polar molecules and π-systems, organic nanotubes, enzymes, and ionophores/receptors. Special features of normal, short, short strong, and π-type H-bonding interactions in these systems are discussed in terms of structures, interaction energies, and spectra.

Role of molecular orbitals of the benzene in electronic nanodevices.

Abstract: 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.

Phenol vs Water Molecule Interacting with Various Molecules: σ-type, π-type, and χ-type Hydrogen Bonds, Interaction Energies, and Their Energy Components

Abstract: The nature of interactions of phenol with various molecules (Y = HF, HCl, H2O, H2S, NH3, PH3, MeOH, MeSH) is investigated using ab initio calculations. The optimized geometrical parameters and spectra for the global energy minima of the complexes match the available experimental data. The contribution of attractive (electrostatic, inductive, dispersive) and repulsive (exchange) components to the binding energy is analyzed. HF favors σO-type H-bonding, while H2O, NH3, and MeOH favor σH-type H-bonding, where σO-/σH-type is the case when a H-bond forms between the phenolic O/H atom and its interacting molecule. On the other hand, HCl, H2S, and PH3 favor π-type H-bonding, which are slightly favored over σO-, σH-, σH-type bonding, respectively. MeSH favors χH-type bonding, which has characteristics of both π and σH. The origin of these conformational preferences depending on the type of molecules is elucidated. Finally, phenol−Y complexes are compared with water−Y complexes. In the water−Y complexes where σO/σ...

Hydrated copper and gold monovalent cations: Ab initio study.

Abstract: To understand the hydration phenomena of noble transition metals, we investigated the structures, hydration energies, electronic properties, and spectra of the Cu+(H3O)1–6 and Au+(H2O)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+(H2O)n (which have the coordination numbers of 3–4) as well as the hydrated alkali metal ions (which have the coordination numbers of ∼6). For the possible identification of their interesting hydration structures, we predict their IR spectra for the OH stretch modes.

Ab Initio Molecular Dynamics Simulations of an Excited State of X-(H2O)3 (X = Cl, I) Complex

Abstract: Upon excitation of Cl(-)(H(2)O)(3) and I(-)(H(2)O)(3) clusters, the electron transfers from the anionic precursor to the solvent, and then the excess electron is stabilized by polar solvent molecules. This process has been investigated using ab initio molecular dynamics (AIMD) simulations of excited states of Cl(-)(H(2)O)(3) and I(-)(H(2)O)(3) clusters. The AIMD simulation results of Cl(-)(H(2)O)(3) and I(-)(H(2)O)(3) are compared, and they are found to be similar. Because the role of the halogen atom in the photoexcitation mechanism is controversial, we also carried out AIMD simulations for the ground-state bare excess electron -- water trimer [e(-)(H(2)O)(3)] at 300 K, the results of which are similar to those for the excited state of X(-)(H(2)O)(3) with zero kinetic energy at the initial excitation. This indicates that the rearrangement of the complex is closely related to that of e(-)(H(2)O)(3), whereas the role of the halide anion is not as important.

Dissolution nature of the lithium hydroxide by water molecules.

Abstract: The structures, stabilities, thermodynamic quantities, dissociation energies, infrared spectra, and electronic properties of LiOH hydrated by up to seven water molecules are investigated by using the density-functional theory and the Moller-Plesset second-order perturbation theory (MP2). Further accurate analysis based on the coupled-cluster theory with singles, doubles, and perturbative triples excitations agrees with the MP2 results. The Li–OH stretch mode significantly shifts with the increase of water molecules, and it eventually disappears upon dissociation. It is revealed that seven water molecules are needed for the stable dissociation of LiOH (as a completely dissociated conformation), in contrast to the cases of RbOH and CsOH which require four and three water molecules, respectively.

Theoretical insights into the mechanism of acetylcholinesterase‐catalyzed acylation of acetylcholine

Abstract: Acylation of acetylcholine (ACh) catalyzed by acetylcholinesterase (AChE) has been studied using high-level theoretical calculations on a model system that mimics the reaction center of the enzyme, and compared with uncatalyzed acylation reaction. The geometries of all the intermediates and transition states, activation energies, and solvent effects have been calculated. The calculations predict simultaneous formation of two short-strong hydrogen bonds (SSHB) in the rate-determining transition state structures [the first SSHB involves the hydrogen atom of Ser-200 (Hs) and another involves the hydrogen atom of His-440 (Hh)]. In the intermediate states, the H-bond corresponding to Hh involves SSHB, whereas the one corresponding to Hs does not. © 2005 Wiley Periodicals, Inc. J Comput Chem 26: 606–611, 2005

Why the hydration energy of Au+ is larger for the second water molecule than the first one: skewed orbitals overlap.

Abstract: Using molecular-orbital analysis, we have elucidated the quantum-chemical origin of the intriguing phenomena in sequential hydration energies of the gold cation, which is known to be the most conspicuous among all transition metals. The hydration energy of Au+ with the second water molecule is found to be much larger than that with the first water molecule. Owing to the large relativistic effect of gold (i.e., significant lowering of the 6s orbital energy and significant raising of the 5d orbital energy), the highest occupied molecular orbital of the hydrated gold cation has a large portion of the 6s orbital. As the electron density of the 6s orbital populates in a large outer spherical shell far off the gold nucleus, the p orbitals (or sp hybridized lone-pair orbitals) of the water molecules are able to overlap with the outer part of the 6s orbital in the dihydrated gold cation, resulting in the unusual skewed overlap of p-6s-p orbitals (not the atom-to-atom bond overlap). No previous molecular-orbital analysis has reported this peculiar skewed orbitals overlap. Since this skewed orbitals overlap is saturated with two water molecules, this property is responsible for the low coordination number of the gold ion.

Genetic transformation ofAjuga multiflora bunge withAgrobacterium rhizogenes and 20-hydroxyecdysone production in hairy roots

Abstract: An efficient transformation system forAjuga multiflora Bunge was established by usingAgrobacterium rhizogenes strain A4. After inoculation with the bacteria, we obtained a number of hairy-root clones from micro-calli of the explant petioles. One fast-growing line showed the highest production of 20-hydroxyecdysone (20-HE). PCR amplification of rooting locus (rol) genes revealed that the left hand-transferred DNA of the root-inducing plasmid was inserted into the genome of our transformedAjuga hairy roots. This integration was further confirmed by DNA-DNA hybridization. The 20-HE content in hairy roots was 10 times higher than that measured in the wild type.

Anomalous behavior of mercury in one dimension: Density-functional calculations

Abstract: We have investigated the effect of reduction of dimensionality on Zn, Cd, and Hg. Our results show that Hg stands out with uncommon properties in one dimension s1Dd. The overall trend has been reported for systems of group 8-12 elements all of which continue to be metallic in 1D too, with the exception of Hg: the interatomic distance scohesive energy per bondd shows significant drop srised for all other systems at low dimensions. Hg linear chains settle for a larger interatomic distance, compared to the bulk or two-dimensional state, resulting in vanishing of the s-p band overlap robbing Hg of metallic property in 1D. Relativistic effects are shown to play a crucial role in this change of property.

Theoretical studies on hydroquinone-benzene clusters.

Abstract: 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 Moller–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.

Theoretical studies on the mechanism of acid-promoted hydrolysis of N-formylaziridine in comparison with formamide.

Abstract: We present an ab initio study of the acid-promoted hydrolysis reaction mechanism of N-formylaziridine in comparison with formamide. Since the rate of amide hydrolysis reactions depends on the formation of the tetrahedral intermediate, we focused our attention mainly on the reactant complex, the tetrahedral intermediate, and the transition state connecting these two stationary points. Geometries were optimized using the density functional theory, and the energetics were refined using ab initio theory including electron correlation. Solvent effects were investigated by using polarizable continuum method calculations. The proton-transfer reaction between the O-protonated and N-protonated amides was investigated. In acidic media, despite that the N-protonated species is more stable than the O-protonated one, it is predicted that both N-protonated and O-protonated pathways compete in the hydrolysis reaction of N-formylaziridine.

Structural Characterization of the Molten Globule State of Apomyoglobin by Limited Proteolysis and HPLC-Mass Spectrometry †

Abstract: A method to characterize the structural conformation of an acidic molten globule apomyoglobin (apoMb) at pH 4.2 was developed using limited proteolysis and HPLC-mass spectrometry (HPLC-MS). Endoproteinase Glu-C, which has a double maximum activity at pH 4.0 and pH 7.8 toward glutamic acid (Glu), was used as a proteolytic enzyme. Using this method enabled us to compare the proteolytic cleavages of native apoMb (at pH 8.0) and molten globule (at pH 4.2) directly. Only the first cleavage event in each molecule was considered as reflecting original structural information since the original structure of the protein can be altered after the fist cleavage. Structural changes of apoMb in various pH conditions were studied here to elucidate the local helicity of molten globule apoMb. Among 13 Glu sites, only Glu83 and Glu85 in the F-helix were cleaved at pH 8.0, which confirms that only helix F is frayed upon removal of heme group. At acidic molten globule state, rapid cleavages at Glu38, Glu52, Glu54, Glu85, and Glu148 were detected, while the remaining eight sites were protected. Glu6 and Glu18 in the A-helix, and Glu105 in the G-helix were protected due to the helicity of the secondary structures. The cleavage at Glu38 and the protection at Glu41 in the C-helix indicate that the first half of the C-helix is frayed and the second half of the C-helix is structured. Cleavage at both Glu52 and Glu54 in the D-helix proves that the D-helix is disordered. The N-terminal end of the E-helix at Glu59 was protected, and the beginning of the F-helix was protected by aid of the pH-induced C-cap of the E-helix. The cleavage at Glu148 in H suggests that the C-terminal end of the H-helix is disordered. The A-helix and the first half of the B-helix were highly stable.

Computing technologies, theories, and algorithms. The making of 40 years and more of theoretical and computational chemistry

Abstract: In their earliest stages, theoretical chemistry and computational chemistry were often distinct, with the latter having its developments and capabilities directly tied to the state of computer technology. This was especially true for the part of computational chemistry with some of the highest computing demands, ab initio electronic structure theory. The point in time where ab initio electronic structure calculations were first beginning to be carried out is roughly 40 years ago, and since that time, all parts of theoretical chemistry have developed links to computation. The evolution in such links and connections has had a powerful impact on science, something of historical, theoretical, and practical interest.

Clusters to functional molecules, nanomaterials, and molecular devices: Theoretical exploration

Abstract: Publisher Summary This chapter discusses how the insights obtained from theoretical investigations of various cluster systems have enabled a researcher to predict structures and properties of novel functional molecular systems. Clusters are self-assembled structures comprised of a number of monomers under the given condition. Apart from aiding the development of novel materials, clusters are very useful for understanding the intrinsic and fundamental nature of molecular recognition and self-assembling phenomena. This is amply illustrated in a number of publications on a wide variety of atomic and molecular clusters, ranging from H-bonded clusters, p-system-containing clusters, and metal clusters. These investigations not only provide pertinent information useful for nanomaterial design but also highlight some of the important similarities and differences in their physical characteristics. These characteristics include structures, magnitudes of both attractive and repulsive interaction energies, vibrational frequencies, and charge redistributions. Additionally, one also obtains an insight into the contributions of cooperative and competitive forces, both of which govern self-assembly and molecular recognition.