Showing papers by "Kwang S. Kim published in 2000"

Structures, energies, vibrational spectra, and electronic properties of water monomer to decamer

Abstract: The correlation of various properties of water clusters (H2O)n=1–10 to the cluster size has been investigated using extensive ab initio calculations. Since the transition from two dimensional (2-D) (from the dimer to pentamer) to 3-D structures (for clusters larger than the hexamer) is reflected in the hexamer region, the hexamer can exist in a number of isoenergetic conformers. The wide-ranging zero-point vibrational effects of the water clusters having dangling H atoms on the conformational stability by the O–H flapping or proton tunneling through a small barrier (∼0.5 kcal/mol) between two different orientations of each dangling H atom are not large (∼0.1) kcal/mol). Large dipole moments (>2.5 D) are found in the dimer and decamer, and significant dipole moments (∼2 D) are observed in the monomer, hexamer, and nonamer. The polarization per unit monomer rapidly increases with an increasing size of the cluster. However, this increase tapers down beyond the tetramer. The O–H vibrational frequencies serve as sensitive indicators of the status of proton donation (“d”) and acceptance (“a”) (i.e., the structural signature of H-bond type) for each water monomer in the cluster. In general, the magnitudes of the O–H frequencies (ν) for each cluster can be arranged in the following order: ν3da (single donor–single acceptor) ≅ν3daa (single donor–double acceptor) >ν3dda (double donor–single acceptor) >ν1dda>ν1da> (or ≅) ν1daa. The increase in the cluster size has a pronounced effect on the decrease of the lower frequencies. However, there are small changes in the higher frequencies (ν3da and ν3daa). The intensities of ν1daa and ν1da are very high, since the increased atomic charges can be correlated to the enhanced H-bond relay effect. On the other hand, the intensities of the ν1dda modes are diminished by more than half. Most of the above data have been compared to the available experimental data. Keeping in view the recent experimental reports of the HOH bending modes, we have also analyzed these modes, which show the following trend: ν2dda>ν2daa≅ν2da. The present study therefore would be useful in the assignments of the experimental O–H stretching and HOH bending modes.

Comparative ab initio study of the structures, energetics and spectra of X−⋅(H2O)n=1–4 [X=F, Cl, Br, I] clusters

Abstract: X−⋅(H2O)n=1–4 [X=F, Cl, Br, I] have been studied using high level ab initio calculations. This extensive work compares the structures of the different halide water clusters and has found that the predicted minimum energy geometries for different cluster are accompanied by several other structures close to these global minima. Hence the most highly populated structures can change depending on temperature due to the entropy effect. As the potential surfaces are flat, the wide-ranging zero point vibrational effects are important at 0 K, and not only a number of low-lying energy conformers but also large amplitude motions can be important in determining structures, energies, and spectra at finite temperatures. The binding energies, ionization potentials, charge-transfer-to-solvent (CTTS) energies, and the O–H stretching frequencies are reported, and compared with the experimental data available. A distinctive difference between F−⋅(H2O)n and X−⋅(H2O)n (X=Cl, Br, I) is noted, as the former tends to favor inter...

Charge transfer to solvent (CTTS) energies of small X−(H2O)n=1–4 (X=F, Cl, Br, I) clusters: Ab initio study

Abstract: Charge transfer to solvent (CTTS) energies of small halide–water clusters, X−(H2O)n=1–4 (X=F, Cl, Br, I) have been studied using first-order configuration interaction as well as time dependent discrete Fourier transform density functional methods The only available experimental data are the recently reported CTTS energies for I−(H2O)n=1–4 clusters by Johnson and co-workers [D Serxner, C E H Dessent, and M A Johnson, J Chem Phys 105, 7231 (1996)] These results are in good agreement with our predicted values The calculated CTTS energies indicate that there is regularity in the change of CTTS energies with respect to the change of halide anion as well as the cluster size Our investigations have shown that this observed trend of CTTS energies of X−(H2O)n clusters could be quantitatively explained by the ionization potential of the halide anions and the binding energies of the respective clusters

Catalytic role of enzymes: short strong H-bond-induced partial proton shuttles and charge redistributions

Abstract: A two-step reaction mechanism (catalyzed alternatively by acid and base) with partial proton shuttles and charge redistributions promoted by short strong H bonds (SSHBs) (playing a dual role as an amphi-acid/base catalyst) is proposed to explain the enormous rate enhancement observed in enzymatic reactions involving carbanion intermediates. The SSHBs in the two-step reactions are found to be responsible for enhancing enzyme–substrate interactions in favor of the transition state structure over that of reactant. The detailed quantum theoretical studies of ketosteroid isomerase provide evidence of assisting roles of SSHB in enzymatic activity. The understanding of the two-step reaction mechanism would be a useful aid in designing novel functional enzymes and abzymes.

Structures and electronic properties of small carbon nanotube tori

Abstract: Fullerenes and nanotubes are promising candidates in the development of nanodevices. Recently, a form of carbon nanotube torus structures has been observed. In this regard, we have investigated the geometries, electronic structures, and energetics of small carbon nanotube tori, using both the tight-binding and semiempirical quantum chemical approaches. It is shown that ${D}_{5d}$ nanotube tori behave like semiconductors, while ${D}_{6h}$ nanotube tori exhibit metal (or metal-like) characteristics similar to bent nanotubes. We show that the ${D}_{5d}$ nanotube tori, which are as stable as the corresponding fullerenes, are energetically more favored than the corresponding nanotubes. In particular, the pentagons of the ${D}_{5d}$ nanotube tori are less deformed than those of bent nanotubes and ${D}_{6h}$ nanotube tori. This indicates that such small nanotube tori could be observed under optimal kinetic-driven conditions and eventually utilized as nanodevices.

Vibrational spectra and electron detachment energy of the anionic water hexamer

Abstract: A number of experimental and theoretical studies have been carried out on the anionic water hexamer in the last decade. However, none of these studies have reported the adiabatic electron detachment energy. The present study employing extensive high-level ab initio calculations report the adiabatic electron detachment energy, which explains the unusual stability of the anionic water hexamer. This stability can be correlated to the unusually intense peak observed in the photoelectron-detachment spectra. It is also shown that our previously predicted pyramid structure reproduces the important characteristics of the experimental O–H vibrational spectra.

Interaction of the water dimer with π-systems: A theoretical investigation of structures, energies, and vibrational frequencies

Abstract: The interaction of the water dimer with both the olefinic and aromatic π systems (ethene, benzene, toluene, fluorobenzene, and p-difluorobenzene) has been investigated using both the supermolecular [second-order Moller–Plesset (MP2)] and perturbational (symmetry adapted perturbation theory) approaches. The geometry optimizations, harmonic vibrational frequencies, and the components of the binding energy were evaluated using fairly large basis sets (6-31+G* and aug-cc-pVDZ). The minimum energy structures obtained at the MP2/6-31+G* and MP2/aug-cc-pVDZ levels of theory indicate that the water dimer exhibits a π-type of interaction with ethene, benzene, and toluene and a σ-type of interaction with both fluorobenzene and p-difluorobenzene. This is demonstrated from the vibrational frequencies which are in good agreement with the experimentally determined numbers. Our calculations indicate that the nature and strength of the interaction of the donor water molecule (water dimer) with the π system has a significant bearing on the total binding energy of the complex. Apart from the interaction of the water dimer with the π system, we also show how this interaction influences the hydrogen bond characteristics of the water dimer by evaluating the hydrogen bond strengths.

Dissociative adsorption of water on the Si(001) surface: A first-principles study

Abstract: The adsorption of water on the Si(001) surface is studied by using density-functional total-energy calculations within the generalized gradient approximation. We find that water can adsorb molecularly on the down atom of the Si dimer, but a dissociative adsorption wherein OH (H) forms a bond to the down (up) atom of the Si dimer is more favored over the molecular adsorption (by 1.8 eV). The decay of the molecular state to the dissociative state occurs via a transition state with the energy barrier of only 0.15 eV. While the interaction between water molecules is repulsive, that between dissociated OH species is attractive by hydrogen bonding.

Fluorobenzene and p-difluorobenzene microsolvated by methanol: An infrared spectroscopic and ab initio theoretical investigation

Abstract: Laser spectroscopy, i.e., resonant two-photon ionization (R2PI), IR/R2PI ion depletion and hole burning spectroscopy have been applied in an experimental study of heterogenous clusters consisting of fluorobenzene (FB) or p-difluorobenzene (pDFB), respectively, microsolvated by up to three methanol molecules. Their infrared ion depletion spectra were taken in the region of the OH and CH stretches of methanol. In these complexes the methanol molecules form subclusters, which are weakly hydrogen bonded to either the aromatic π-system (πOH) or to the fluorine substituent (σF) and a CH group (σCH). In FB⋅(MeOH)1, pDFB⋅(MeOH)1, pDFB⋅(MeOH)2 and one isomer of FB⋅(MeOH)2 the methanol subunits exclusively exhibit σF and σCH H-bonds. A further isomer of FB⋅(MeOH)2 exhibits a πOH type interaction. For FB⋅(MeOH)3 and pDFB⋅(MeOH)3 (1:3) complexes the methanol subcluster may take on either a chainlike or a ringlike conformation. In the chainlike isomer of FB⋅(MeOH)3 the methanol trimer interacts with the chromophore vi...

Ab initio study of the low-lying electronic states of Ag3−, Ag3, and Ag3+: A coupled-cluster approach

Abstract: The low-lying electronic states of Ag3−(1Σg+,3B2), Ag3(2B2,2A1,2B1,4B2,2Σu+,1 2Σg+,2 2Σg+,2Πu,4Σu+), and Ag3+(1A1,1Σg+,3Σu+,3A1) are studied by ab initio calculations with the Stuttgart effective core potentials and corresponding (8s7p6d)/[6s5p3d] and (8s7p5d3f )/[6s5p3d3f] basis sets. The geometries, vibrational frequencies, and energetic splittings are obtained by the coupled-cluster method including singles and doubles (CCSD) and those including up to the noniterative triples [CCSD(T)] correlation methods with additional frozen core molecular orbitals corresponding to 4s and 4p orbitals. The results for well-studied states (Ag3− 1Σg+;Ag3 2B2,2A1,2Σu+;Ag3+ 1A1) are in good agreement with previous experimental results, and therefore our results for other newly studied states are expected to be reliable. The vertical detachment energies of Ag3− are obtained by the electron excitation equation-of-motion coupled-cluster (EE-EOM-CCSD) method and the average deviation from the experimental results is small wi...

Role of catalytic residues in enzymatic mechanisms of homologous ketosteroid isomerases.

Abstract: Ketosteroid isomerase (KSI) is one of the most proficient enzymes catalyzing an allylic isomerization reaction at a diffusion-controlled rate. In this study of KSI, we have detailed the structures of its active site, the role of various catalytic residues, and have explained the origin of the its fast reactivity by carrying out a detailed investigation of the enzymatic reaction mechanism. This investigation included the X-ray determination of 15 crystal structures of two homologous enzymes in free and complexed states (with inhibitors) and extensive ab initio calculations of the interactions between the active sites and the reaction intermediates. The catalytic residues, through short strong hydrogen bonds, play the role of charge buffer to stabilize the negative charge built up on the intermediates in the course of the reaction. The hydrogen bond distances in the intermediate analogues are found to be about 0.2 A shorter in the product analogues both experimentally and theoretically.

Structures, vibrational frequencies, and infrared spectra of the hexa-hydrated benzene clusters

Abstract: The water hexamer is known to have a number of isoenergetic structures. The first experimental identification of the O–H stretching vibrational spectra of the water hexamer was done in the presence of benzene. It was followed by the identification of the pure water hexamer structure by vibration-rotational tunneling (VRT) spectroscopy. Although both experiments seem to have located only the Cage structure, the structure of the benzene–water hexamer complex is not clearly known, and the effect of benzene in the water hexamer is unclear. In particular, it is not obvious how the energy difference between nearly isoenergetic water hexamer conformers changes in the presence of benzene. Thus, we have compared the benzene complexes with four low-lying isoenergetic water hexamers, Ring, Book, Cage, and Prism structures, using ab initio calculations. We also investigated the effects of the presence of benzene on the structures, harmonic vibrational frequencies, and infrared (IR) intensities for the four low-lying energy conformers. There is little change in the structure of the water hexamer upon its interaction with the benzene molecule. Hence the deformation energies are very small. The dominant contribution to the benzene–water cluster interaction mainly comes from the π–H interactions between benzene and a single water molecule. As a result of this π–H interaction, O–Hπ bond length increases and the corresponding stretching vibrational frequencies are redshifted. The IR spectral features of both (H2O)6 and benzene–(H2O)6 are quite similar. From both the energetics and the comparison of calculated and experimental spectra of the benzene–(H2O)6, the water structure in these complexes is found to have the Cage form. In particular, among the four different Cage structures, only one conformer matches the experimental O–H vibrational frequencies.

Van der Waals isomers and ionic reactivity of the cluster system para-chlorofluorobenzene/methanol

Abstract: This combined experimental and computational study is aimed at elucidating the structure and reactivity of heterogeneous molecular clusters. We report results for the system para-chlorofluorobenzene/methanol (pClFB/MeOH). Particularly, three different van der Waals (vdW) isomers of the neutral (1:1) aggregate (π,σF,σCl) have been assigned by comparison of experimental infrared frequencies in the O–H and C–H stretch regions measured by IR/R2PI depletion spectroscopy with calculated frequencies at MP2/6-31+G(d) and B3LYP/6-31+G(d) level. The isomers are weakly hydrogen-bonded complexes with methanol’s OH group coordinated toward the aromatic π-electron cloud, the fluorine or the chlorine substituent, respectively. This assignment is corroborated by the UV and IR spectra of the corresponding monosubstituted benzene/methanol complexes. After resonant photoionization of pClFB⋅(MeOH)n, for n=1 besides vdW fragmentation, no chemical reactivity was observed for any isomer. The investigation of aggregates with n⩾5 indicated a substitution reaction taking place to produce chloroanisole+, emphasizing the importance of neutral precursor cluster size over cluster structure for intracluster ion–molecule reactions.

Polyenes vs polyynes: Efficient π-frame for nonlinear optical pathways

Abstract: The electronic and vibrational hyperpolarizabilities of polyenes NH2–(HC=CH)n–NO2 and polyynes NH2–(C≡C)n–NO2 have been investigated. As the chain length increases, the first hyperpolarizabilities increase drastically for polyenes, while they increase moderately for polyynes. Furthermore, in polyenes the vibrational first hyperpolarizabilities are almost the same as the electronic first hyperpolarizabilities, while in polyynes the former is much smaller than the latter. An analysis of the electron densities of HOMOs of polyenes and polyynes confirms that the polyene π-frame is more efficient for long pathways of nonlinear optical molecules, while the polyyne π-frame is slightly better for very short pathways. In both polyenes and polyynes, the IR intensities arise mainly from the terminal carbon sites, while the Raman intensities, from the central carbon sites.

Dimer to monomer phase transition in alkali-metal fullerides: magnetic susceptibility changes

Abstract: Ab initio calculations have been employed to investigate the peculiar change in magnetic property (from diamagnetic to paramagnetic) of the dianionic C60-dimer phase in a rapidly cooled AC60 samples ( A: alkali metal). We first note that the triplet state of (C60)-22 which was never considered previously is nearly degenerate with the singlet state, and the transition barrier between the two states is reasonably small. This explains the susceptibility increase with an increase in temperature and the magnetic phase transition in the process of the dimer to monomer phase transition.

Ab initio investigations on the HOSO2+O2→SO3+HO2 reaction

Abstract: HOSO2 radical is the key intermediate for the oxidation SO2 to SO3 by OH radical in the atmosphere. The structural aspects and the energetics of the reaction HOSO2+O2→SO3+HO2 have been studied using Mo/ller–Plesset (MP2) and density functional (DFT) techniques with 6-31G** and triple-ζ, quadruple-ζ, and quintuple-ζ quality basis sets including diffuse basis functions. The detailed theoretical analyses have further revealed that this reaction could proceed through the formation of intermediate complexes and an intramolecular proton transfer like transition state. The energetics of these intermediate reactions has been studied in detail. The use of MP2 methods to study such radical mechanisms had some characteristic symmetry-breaking problem with larger basis sets. This unphysical situation with larger basis set MP2 calculations in this hypervalent system has been explained through the interpretation of the relevant energy surface.

Theoretical Study of Microscopic Molecular Structure of Helicenebisquinone Aggregates

Abstract: Molecular level studies of intermolecular interaction forces and microscopic structures are essential to understand molecular aggregates and self-assembly phenomena. Recently, fibrous helicenebisquinone (HBQ) aggregates have been of great interest because of their strongly enhanced nonlinear optical (NLO) properties. The intermolecular interaction force and microscopic structure of HBQ aggregates were proposed to be donor−acceptor interaction and a columnar stack, respectively. However, our present study suggests that the intermolecular interaction force of HBQ aggregates would be the paired hydrogen bonding between quinone moieties, and its molecular structure would be one-dimensional hydrogen bond chain. Though the information from the experiments is somewhat limited, our prediction of molecular level structure is consistent with the experimentally observed macroscopic structure.

Hydrogen-bonded array of NH 2 on the Si(100) surface

Abstract: The atomic and electronic structures of the dissociative adsorption of ammonia on the $\mathrm{Si}(100)\ensuremath{-}(2\ifmmode\times\else\texttimes\fi{}1)$ surface are studied by first-principles calculations. We find that the hydrogen-bonding interactions between the dissociated ${\mathrm{NH}}_{2}$ species favor the ``gauche'' model over the existing models. This strong attractive force can form a one-dimensional hydrogen-bonded array of ${\mathrm{NH}}_{2}$ along the Si dimer row. Our analysis identifies three ${\mathrm{NH}}_{2}$-derived electronic states, composed of one delocalized state along the dimer row and two localized molecular orbitals.

Ab initio study of peroxyacetic nitric anhydride and peroxyacetyl radical: Characteristic infrared band of peroxyacetyl radical

Abstract: The equilibrium geometries, the bond dissociation energies, harmonic vibrational frequencies, and infrared intensities of peroxyacetic nitric anhydride (PAN), peroxyacetyl radical (PA), and NO{sub 2} which are important species in environmental chemistry, have been studied using high level of ab initio calculations. The global minimum energy conformation of the PAN molecule is found to be s-cis-PAN. The predicted enthalpy and entropy changes at 1 atm and 298.15 K for the thermal decomposition of PAN are 25.8 kcal/mol and 42.3 cal/(mol{center_dot} K), respectively. These values are in excellent agreement with the experimental values. A characteristic IR band of PAN appears at 1,232 cm{sup {minus}1}, which is a CH{sub 3} rocking mode coupled with CO and OO stretches. The corresponding band of the PA radical appears at 1,216 cm{sup {minus}1}, about 10 cm{sup {minus}1} lower than that of PAN. Thus, determining the concentrations of PAN based on only this band would not be so reliable. The authors find that the PA radical has a strong IR band at 1,150 cm{sup {minus}1} due to the O-O stretch mode, while the PAN molecule has the corresponding band at 977 cm{sup {minus}1}. Since PAN and the PA radical do not have other IR bands at thismore » region, this characteristic band could be used for identification and measurement of the PA radical and thus for spectroscopic study of thermal decomposition mechanism of PAN.« less

Molecular Structure of p-Cyclohexylaniline. Comparison of Results Obtained by X-ray Diffraction with Gas Phase Laser Experiments and ab Initio Calculations

Abstract: The results of a combined experimental and theoretical investigation of the molecular structure of p-cyclohexylaniline (pCHA) in the electronic ground and the first electronically excited state are reported. The experimental investigations are performed for the crystalline phase by X-ray diffraction for the first time and related to former gas phase results obtained by time-resolved rotational laser spectroscopy. The theoretical results, from new ab initio calculations at the MP2/6-31+G(d) and CIS/6-31+G(d) level of theory for the electronic ground and excited state, respectively, give an adequate description of the rotational constants as obtained by the gas phase experiments. Thus, a detailed comparison of the ab initio structure for the ground state with the X-ray structure is performed in order to ascertain differences in the molecular geometry between the gas and crystalline phase. In particular, the size of the aromatic and cyclohexyl ring, their mutual orientation, and the conformation of the NH2 g...