Kyushu University [Yuriko Aoki (Professor) Faculty of Engineering Sciences, Department of Advanced Materials Science and Engineering]

Highly accurate Order(N) computational method for gigantic systems and material design for nano-bio systems
keyword : Quantum chemistry, electronic states, MO method, gigantic systems, polymers,Elongation method
2004.03.

Current and Past Project

The conventional quantum chemical approach based on the molecular orbital method is difficult to apply to large systems like biopolymers, though it is useful for small molecules. We are developing the Elongation method that makes it possible to obtain the electronic states of large aperiodic polymers, treating only a few units at a time of the total system. This study develops the construction of molecular design integrated system of functional polymers and the relation software by combining the quantum-chemical method for obtaining physical properties with the efficient Elongation method. This software can assist with the molecular design of functional polymers, and drastic cost reduction of material synthesis can be expected.

Academic Activities

Books

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Reports

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Papers

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D. Mashkovtsev, Y. Orimoto, and Y. Aoki, Fast and accurate calculation of UV-Vis spectrum with Modified Local Excitation Approximation, J. Chem. Theory Comput., https://doi.org/10.1021/acs.jctc.3c00266, 19, 5548-5562, 2023.07, The local excitation approximation (LEA), a method for the calculation of electronic excitations localized in a specific region of a molecule, has been modified with new approaches to enhance the accuracy of the original method. The primary concept behind LEA involves isolating the region of interest as a submolecule from the full molecule using a localization method, followed by calculating electronic excitations solely within this submolecule. In this study, we examined approaches that improve the accuracy in describing the region of interest, particularly its molecular orbital energies. Additionally, the localization method was extended with a new projection technique to accelerate calculations. These approaches were studied in time-dependent density functional theory (TDDFT) calculations applied to four testing systems with a chromophore as the region of interest: two basic linear molecules, acrolein surrounded by 24 water molecules, and a model of a green fluorescent protein. For all studied systems, the results of TDDFT calculations combined with LEA exhibited near-zero error when groups of atoms adjacent to the chromophore were explicitly included in the submolecule. This was achieved with at least a quadratic speedup of the calculation time as a function of the submolecule size..

Works, Software and Database

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Presentations

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M. Ivonina, Y. Orimoto, and Y. Aoki, Through-space/Through-bond method for analyzing molecular orbital interactions and its application to DNA mutations (Physical Chemistry Chemical Physics poster award), The 10th edition of the conference of The Asia Pacific Association of Theoretical and Computational Chemists (APATCC-10), 2023.02, [URL], Being able to quantify molecular orbital interactions is helpful for studying properties of molecular systems such as stability, reactivity, chemical bonds pattern, etc. For this purpose, we developed an ab initio approach for analyzing various molecular orbital interactions that occur through space and through bond, the so-called “Through-space/Through-bond” (TS/TB) method.
The proposed approach is based on the idea of extremely increasing the absolute value of exponent for interacting orbitals and, thus, cutting off the corresponding one- and two-electron integrals. Within two rounds of SCF calculation (i.e., one before and one after cutting off integrals) it is possible to estimate the contribution of target interaction into system stability through the difference in the resulting total energies.
In this presentation, we will discuss the concept of TS/TB method and some relevant features: (1) using natural orbitals instead of Gaussian-type orbitals to investigate charge transfer or conjugation effects, (2) taking solvent effect into account via PCM integrals, and (3) including electron correlation via MP2 correction. As an application example, we will demonstrate how TS/TB method was used to evaluate the inter- and intra-molecular interactions (i.e. hydrogen bonds, π-conjugation, stacking) in a DNA fragment that includes O6-methylated guanine lesion, which causes transition mutation G···C→A···T..

Awards

for outstanding research in quantum chemistry

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