References of "Kim, Kwang S"
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See detailNoncovalent Interactions of DNA Bases with Naphthalene and Graphene
Cho, Yeonchoo; Min, Seung Kyu; Yun, Jeonghun et al

in JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2013), 9(4), 2090-2096

The complexes of a DNA base bound to graphitic systems are studied. Considering naphthalene as the simplest graphitic system, DNA base naphthalene complexes are scrutinized at high levels of ab initio ... [more ▼]

The complexes of a DNA base bound to graphitic systems are studied. Considering naphthalene as the simplest graphitic system, DNA base naphthalene complexes are scrutinized at high levels of ab initio theory including coupled cluster theory with singles, doubles, and perturbative triples excitations [CCSD(T)] at the complete basis set (CBS) limit. The stacked configurations are the most stable, where the CCSD(T)/CBS binding energies of guanine, adenine, thymine, and cytosine are 9.31 8.48, 8.53, 7.30 kcal/mol, respectively. The energy components are investigated using symmetry-adapted perturbation theory based on density functional theory including the dispersion energy. We compared the CCSD(T)/CBS results with several density functional methods applicable to periodic systems. Considering accuracy and availability, the optB86b nonlocal functional and the Tkatchenko-Scheffler functional are used to study the binding energies of nucleobases on graphene. The predicted values are 18-24 kcal/mol, though many-body effects on screening and energy need to be further considered. [less ▲]

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See detailFirst-Principles Modeling of Non-Covalent Interactions in Supramolecular Systems: The Role of Many-Body Effects
Tkatchenko, Alexandre UL; Alfe, Dario; Kim, Kwang S.

in JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2012), 8(11), 4317-4322

Supramolecular host-guest Systems play an important role for a wide range of applications in chemistry and biology. The prediction of the stability of host-guest complexes represents a great challenge to ... [more ▼]

Supramolecular host-guest Systems play an important role for a wide range of applications in chemistry and biology. The prediction of the stability of host-guest complexes represents a great challenge to first-principles calculations Clue to, an interplay of a ride variety of covalent and noncovalent interactions in these systems. In particular van der Waals (vdW) dispersion interactions frequently play a prominent role in determining the structure, stability, and function of supramolecular systems. On the basis of the widely used benchmark case of the buckyball catcher complex (C-60@C60H28), we assess the feasibility of computing the binding energy of supramolecular host-guest complexes from first principles. Large-scale diffusion Monte Carlo (DMC) calculations are carried out to accurately determine the binding energy for the C-60@C60H28 complex (26 +/- 2 kcal/mol). On the basis of the DMC reference, we assess the accuracy of widely used and efficient density-functional theory (DFT) methods with dispersion interactions. The inclusion of vdW dispersion interactions in DFT leads to a large stabilization of the C-60@C60H28 complex. However, DFT methods including pairwise vdW interactions overestimate the stability of this complex by 9-17 kcal/mol compared to the DMC reference and the extrapolated experimental data. A significant part of this overestimation (9 kcal/mol) stems from the lack of dynamical dielectric screening effects in the description of the molecular polarizability in pairwise dispersion energy approaches. The remaining overstabilization. arises from the isotropic treatment of atomic polarizability tensors and the lack of Many-body dispersion interactions. A further; assessment of a different supramolecular system - glycine anhydride interacting with an amide macrocycle - demonstrates that both the dynamical screening and the many-body dispersion energy are complex contributions that are very sensitive to the underlying molecular geometry and type of bonding. We discuss the required improvements in theoretical methods for achieving ``chemical accuracy'' in the first-principles modeling of supramolecular systems. [less ▲]

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