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ABSTRACT: Given that half-metals are promising futuristic materials for spintronics, organic materials showing half-metal character are highly desirable for spintronic devices, not only owing to their weak spin-orbit and hyperfine interactions, but also their light and flexible properties. We predict that a two-dimensional organic 2,4,6-tri-(1,3,5-triazinyl)methyl radical polymer has half-metallic properties as well as a spontaneous magnetic ordering at ambient temperature. The quantum transmission is studied based on the nonequilibrium Green function theory coupled with density functional theory. The half-metallic property in the triazine-based polymer depends mainly on the nature of the p-band in contrast to of conventional half metals in which the nature of the d-band is more important.
Chemistry 10/2010; 16(40):12141-6. · 5.93 Impact Factor
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ABSTRACT: Protonated and deprotonated adipic acids (PAA: HOOC-(CH(2))(4)--COOH(2) (+) and DAA: HOOC-(CH(2))(4)-COO(-)) have a charged hydrogen bond under the influence of steric constraint due to the molecular skeleton of a circular ring. Despite the similarity between PAA and DAA, it is surprising that the lowest energy structure of PAA is predicted to have (H(2)O...H...OH(2))(+) Zundel-like symmetric hydrogen bonding, whereas that of DAA has H(3)O(+) Eigen-like asymmetric hydrogen bonding. The energy profiles show that direct proton transfer between mirror image structures is unfavorable. Instead, the chiral transformation is possible by subsequent backbone twistings through stepwise proton transfer along multistep intermediate structures, which are Zundel-like ions for PAA and Eigen-like ions for DAA. This type of chiral transformation by multistep intramolecular proton transfers is unprecedented. Several prominent OH...O short hydrogen-bond stretching peaks are predicted in the range of 1000-1700 cm(-1) in the Car-Parrinello molecular dynamics (CPMD) simulations, which show distinctive signatures different from ordinary hydrogen-bond peaks. The O-H-O stretching peaks in the range of 1800-2700 cm(-1) become insignificant above around 150 K and are almost washed out at about 300 K.
Chemistry 09/2010; 16(34):10373-9. · 5.93 Impact Factor
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ABSTRACT: Short Strong Hydrogen Bonds (SSHBs) play an important role in many fields of physics, chemistry and biology. Since it is known that SSHBs exist in many biological systems, the role of hydrogen bonding motifs has been particularly interesting in enzyme catalysis, bio-metabolism, protein folding and proton transport phenomena. To explore the characteristic features of neutral, anionic and cationic hydrogen bonds, we have carried out theoretical studies of diverse homogeneous and heterogeneous hydrogen bonded dimers including water, peroxides, alcohols, ethers, aldehydes, ketones, carboxylic acids, anhydrides, and nitriles. Geometry optimization and harmonic frequency calculations are performed at the levels of Density Functional Theory (DFT) and Møller-Plesset second order perturbation (MP2) theory. First principles Car-Parrinello molecular dynamics (CPMD) simulations are performed to obtain IR spectra derived from velocity- and dipole-autocorrelation functions. We find that the hydrogen bond energy is roughly inversely proportional to the fourth power of the r(O/N-H) distance. Namely, the polarization of the proton accepting O/N atom by the proton-donating H atom reflects most of the binding energy in these diverse cation/anion/neutral hydrogen bonds. The present study gives deeper insight into the nature of hydrogen-bonded dimers including SSHBs.
Physical Chemistry Chemical Physics 06/2010; 12(23):6278-87. · 3.57 Impact Factor
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ABSTRACT: The intermolecular interaction driven structural change is vital to molecular architecturing. In the Cambridge Structural Database (CSD), we find that the preference for geometrical conformations of electron-deficient π systems is different from those of electron-rich π systems. Indeed, ab initio calculations find that electron-deficient π ring systems should involve different structures and energetics, consistent with the CSD search, due to the electric multipole moments and the decrease in the spatial extent of π-electron density.
06/2010;
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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 Møller-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), pi-H interaction (benzene-water), cation-water, anion-water, pi-cation interaction (cation-benzene), and pi-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 (CBS(B)). Another CBS limit (CBS(C)) 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 CBS(C) are found to be robust because of their consistency. However, for small N (in particular, for N = 2, 3), CBS(N)(B) is found to be slightly better for water-water interactions and cation-water and cation-benzene interactions, whereas CBS(N)(C) 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-pi interactions, but not for cationic complexes.
Journal of Computational Chemistry 07/2008; 29(8):1208-21. · 4.58 Impact Factor
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Journal of Computational Chemistry. 01/2008; 29:1208-1221.
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ABSTRACT: Cation-pi and the corresponding anion-pi interactions have in general been investigated as binary complexes despite their association with counterions. However, a recent study of the ammonia channel highlights the important but overlooked role of anions in cation-pi interactions. In an effort to examine the structural and energetic consequences of the presence of counterions, we have carried out detailed ab initio calculations on some model cation-pi-anion ternary complexes and evaluated the nonpair potential terms, three-body contributions, and attractive and repulsive energy components of the interaction energy. The presence of the anion in the vicinity of the pi system leads to a large redistribution of electron density and hence leads to an inductive stabilization. The resulting electronic and geometrical changes have important consequences in both chemical and biological systems. Compared to cation-pi-anion ternary complexes, the magnitude of the cation-pi interaction in pi-cation-anion ternary complexes is markedly lower because of charge transfer from the anion to the cation.
The Journal of Physical Chemistry A 09/2007; 111(32):7980-6. · 2.95 Impact Factor
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ABSTRACT: In this account, we highlight the theoretical investigations of various cluster systems comprising of water clusters, -containing clusters, and metallic clusters. We illustrate how these investigations help us understand and design struc-tures and properties of nanowires, novel functional ionophores/receptors, and nanomaterials. Many of these theoretically predicted systems have been experimentally realized and some of the predicted structures/properties are left for the future which of course could be promising challenges for experimentalists.
Bulletin of the Chemical Society of Japan 08/2007; 80(8):1437-1450. · 1.44 Impact Factor
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ABSTRACT: Interactions involving aromatic rings are important in molecular/biomolecular assembly and engineering. As a consequence, there have been a number of investigations on dimers involving benzene or other substituted pi systems. In this Feature Article, we examine the relevance of the magnitudes of their attractive and repulsive interaction energy components in governing the geometries of several pi-pi systems. The geometries and the associated binding energies were evaluated at the complete basis set (CBS) limit of coupled cluster theory with singles, doubles, and perturbative triples excitations [CCSD(T)] using a least biased scheme for the given data set. The results for the benzene dimer indicate that the floppy T-shaped structure (center-to-center distance: 4.96 A, with an axial benzene off-centered above the facial benzene) is isoenergetic in zero-point-energy (ZPE) corrected binding energy (D0) to the displaced-stacked structure (vertical interplanar distance: 3.54 A). However, the T-shaped structure is likely to be slightly more stable (D0 approximately equal to 2.4-2.5 kcal/mol) if quadruple excitations are included in the coupled cluster calculations. The presence of substituents on the aromatic ring, irrespective of their electron withdrawing or donating nature, leads to an increase in the binding energy, and the displaced-stacked conformations are more stabilized than the T-shaped conformers. This explains the wide prevalence of displaced stacked structures in organic crystals. Despite that the dispersion energy is dominating, the substituent as well as the conformational effects are correlated to the electrostatic interaction. This electrostatic origin implies that the substituent effect would be reduced in polar solution, but important in apolar media, in particular, for assembling processes.
The Journal of Physical Chemistry A 06/2007; 111(18):3446-57. · 2.95 Impact Factor
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ABSTRACT: The two dimensional (2D) to three dimensional (3D) transition for the protonated water cluster has been controversial, in particular, for H(+)(H(2)O)(7). For H(+)(H(2)O)(7) the 3D structure is predicted to be lower in energy than the 2D structure at most levels of theory without zero-point energy (ZPE) correction. On the other hand, with ZPE correction it is predicted to be either 2D or 3D depending on the calculational levels. Although the ZPE correction favors the 3D structure at the level of coupled cluster theory with singles, doubles, and perturbative triples excitations [CCSD(T)] using the aug-cc-pVDZ basis set, the result based on the anharmonic zero-point vibrational energy correction favors the 2D structure. Therefore, the authors investigated the energies based on the complete basis set limit scheme (which we devised in an unbiased way) at the resolution of the identity approximation Moller-Plesset second order perturbation theory and CCSD(T) levels, and found that the 2D structure has the lowest energy for H(+)(H(2)O)(7) [though nearly isoenergetic to the 3D structure for D(+)(D(2)O)(7)]. This structure has the Zundel-type configuration, but it shows the quantum probabilistic distribution including some of the Eigen-type configuration. The vibrational spectra of MP2/aug-cc-pVDZ calculations and Car-Parrinello molecular dynamics simulations, taking into account the thermal and dynamic effects, show that the 2D Zundel-type form is in good agreement with experiments.
The Journal of Chemical Physics 01/2007; 125(23):234305. · 3.33 Impact Factor
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ABSTRACT: To understand the self-assembly process of the transition metal (TM) nanoclusters and nanowires self-synthesized by hydroquinone (HQ) and calix[4]hydroquinone (CHQ) by electrochemical redox processes, we have investigated the binding sites of HQ for the transition-metal cations TM(n+)=Ag(+), Au(+), Pd(2+), Pt(2+), and Hg(2+) and those of quinone (Q) for the reduced neutral metals TM(0), using ab initio calculations. For comparison, TM(0)-HQ and TM(n+)-Q interactions, as well as the cases for Na(+) and Cu(+) (which do not take part in self-synthesis by CHQ) are also included. In general, TM-ligand coordination is controlled by symmetry constraints imposed on the respective orbital interactions. Calculations predict that, due to synergetic interactions, silver and gold are very efficient metals for one-dimensional (1D) nanowire formation in the self-assembly process, platinum and mercury favor both nanowire/nanorod and thin film formation, while palladium favors two-dimensional (2D) thin film formation.
Chemistry 07/2006; 12(18):4885-92. · 5.93 Impact Factor
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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 approximately 0.7 kcal/mol (approximately 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 is the most dominating interaction in both axial and facial substitutions, it is almost canceled by the exchange repulsion in the axial substitution, whereas in the facial substitution, together with the exchange repulsion it augments the electrostatic energy. The systems with electron-accepting substituents (NO2, CN, Br, Cl, F) favor the axial substituent conformation, while those with electron-donating substituents (NH2, CH3, OH) favor the facial substituent conformation. The interactions for the T-shape complex systems of an aromatic ring with other counterpart such as H2, H2O, HCl, and HF are also studied.
Journal of the American Chemical Society 04/2005; 127(12):4530-7. · 9.91 Impact Factor
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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.
The Journal of Chemical Physics 02/2005; 122(6):064314-064314-10. · 3.33 Impact Factor
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ABSTRACT: Owing to the utility of redox phenomena of silver in many chemical systems, it is important to understand the coordination chemistry of Ag+ ion and hence the hydration structure. The lowest-energy conformations of Ag+(H2O)1–6 are sensitive to the calculation method employed. The coordination number (Nc) of Ag+(H2O)n is predicted to be 2 for n = 2–6 at the density functional theory level, while the Nc for n = 3–5 is 3, and that for n = 6 is 4 at the second-order Møller–Plesset perturbation level. Further accurate analysis based on coupled-cluster singles and doubles theory with perturbative corrections for triple excitations agrees with the MP2 results except that Nc of 4 is also as competitive as Nc of 3 for n = 5. To identify the correct Nc, it would be useful to facilitate the IR experimental characterization. We thus provide the OH spectra for various possible structures. It is interesting to note that the hydration chemistry of Ag+ ion is somewhat different from that of alkali metal ions. © 2003 American Institute of Physics.
The Journal of Chemical Physics 10/2003; 119(15):7725-7736. · 3.33 Impact Factor
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Kwang S Kim,
Seung Bum Suh,
Jong Chan Kim,
Byung Hee Hong, Eun Cheol Lee,
Sunggoo Yun,
P Tarakeshwar,
Jin Yong Lee,
Yukyung Kim,
Hyejae Ihm, [......],
Han Myoung Lee,
Dongwook Kim,
Chunzhi Cui,
Suk Joo Youn,
Hae Yong Chung,
Hyuck Soon Choi,
Chi-Wan Lee,
Seung Joo Cho,
Sukmin Jeong,
Jun-Hyung Cho
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ABSTRACT: Using the computer-aided molecular design approach, we recently reported the synthesis of calix[4]hydroquinone (CHQ) nanotube arrays self-assembled with infinitely long one-dimensional (1-D) short hydrogen bonds (H-bonds) and aromatic-aromatic interactions. Here, we assess various calculation methods employed for both the design of the CHQ nanotubes and the study of their assembly process. Our calculations include ab initio and density functional theories and first principles calculations using ultrasoft pseudopotential plane wave methods. The assembly phenomena predicted prior to the synthesis of the nanotubes and details of the refined structure and electronic properties obtained after the experimental characterization of the nanotube crystal are reported. For better characterization of intriguing 1-D short H-bonds and exemplary displaced pi-pi stacks, the X-ray structures have been further refined with samples grown in different solvent conditions. Since X-ray structures do not contain the positions of H atoms, it is necessary to analyze the system using quantum theoretical calculations. The competition between H-bonding and displaced pi-pi stacking in the assembling process has been clarified. The IR spectroscopic features and NMR chemical shifts of 1-D short H-bonds have been investigated both experimentally and theoretically. The dissection of the two most important interaction components leading to self-assembly processes would help design new functional materials and nanomaterials.
Journal of the American Chemical Society 12/2002; 124(47):14268-79. · 9.91 Impact Factor
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Heon Gon Kim,
Chi-Wan Lee,
Sunggoo Yun,
Byung Hee Hong,
Young-Ok Kim,
Dongwook Kim,
Hyejae Ihm,
Jung Woo Lee, Eun Cheol Lee,
P Tarakeshwar,
Su-Moon Park,
Kwang S Kim
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ABSTRACT: [formula: see text] A new molecular system, 2,11-dithio[4,4]metametaquinocyclophane containing a quinone moiety, was designed and synthesized. As the quinone moiety can readily be converted into an aromatic pi-system (hydroquinone) upon reduction, the nanomechanical molecular cyclophane system exhibits a large flapping motion like a molecular flipper from the electrochemical redox process. The conformational changes upon reduction and oxidation are caused by changes of nonbonding interaction forces (devoid of bond formation/breaking) from the edge-to-face to face-to-face aromatic interactions and vice versa, respectively.
Organic Letters 11/2002; 4(22):3971-4. · 5.86 Impact Factor
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Kwang S. Kim,
Seung Bum Suh,
Jong Chan Kim,
Byung Hee Hong, Eun Cheol Lee,
Sunggoo Yun,
P. Tarakeshwar,
Jin Yong Lee,
Yukyung Kim,
Hyejae Ihm, [......],
Han Myoung Lee,
Dongwook Kim,
Chunzhi Cui,
Suk Joo Youn,
Hae Yong Chung,
Hyuck Soon Choi,
Chi-Wan Lee,
Seung Joo Cho,
Sukmin Jeong,
Jun-Hyung Cho
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ABSTRACT: Using the computer-aided molecular design approach, we recently reported the synthesis of calix[4]hydroquinone (CHQ) nanotube arrays self-assembled with infinitely long one-dimensional (1-D) short hydrogen bonds (H-bonds) and aromatic−aromatic interactions. Here, we assess various calculation methods employed for both the design of the CHQ nanotubes and the study of their assembly process. Our calculations include ab initio and density functional theories and first principles calculations using ultrasoft pseudopotential plane wave methods. The assembly phenomena predicted prior to the synthesis of the nanotubes and details of the refined structure and electronic properties obtained after the experimental characterization of the nanotube crystal are reported. For better characterization of intriguing 1-D short H-bonds and exemplary displaced π−π stacks, the X-ray structures have been further refined with samples grown in different solvent conditions. Since X-ray structures do not contain the positions of H atoms, it is necessary to analyze the system using quantum theoretical calculations. The competition between H-bonding and displaced π−π stacking in the assembling process has been clarified. The IR spectroscopic features and NMR chemical shifts of 1-D short H-bonds have been investigated both experimentally and theoretically. The dissection of the two most important interaction components leading to self-assembly processes would help design new functional materials and nanomaterials.
10/2002;
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ABSTRACT: Using excited-state ab initio molecular dynamics simulations employing the complete-active-space self-consistent-field approach, we study the mechanism of photodissociation in terms of time evolution of structure, kinetic energy, charges and potential energy for the first excited state of hydrogen halides and methyl halides. Although the hydrogen halides and methyl halides are similar in the photodissociation mechanism, their dynamics are slightly different. The presence of the methyl group causes delay in photodissociation as compared to hydrogen halides.
