We have developed several Scratch-based educational programs for the students in a first-year university chemistry course. Demonstrative programs were made for chemical bonding and chemical thermodynamics. Making of such programs could be easy even for students without coding skills and be valuable for self-education as well.
We investigated the structural units of xNa2O-(1 − x) B2O3 glasses using molecular dynamics (MD) simulation with the interatomic potential provided by first-principles calculations. The results are consistent with experimental trends in interatomic distance, linear thermal expansion coefficient and BO4 units. The amount of 5- to 8-membered rings at x = 0.2 is larger than the other composition range. This suggests that the structural unit constructed by a few rings is related to suppression of thermal expansion.
All isomers for sodium clusters up to Na9 were investigated by graph theory where a vertex and an edge correspond to atom and bond between adjacent atoms, respectively. All isomers, more than 10 million, for Na10 were listed. Structural features for sodium clusters up to Na9 were elucidated by using graph theory. Furthermore, geometrically forbidden graphs were excluded by using molecular mechanics.
Radical copolymerization was theoretically investigated by using correlations between Q-e values and properties of monomers and terminal radical models. As a result, it was found that same e value used for monomers and radicals is reasonable. In addition, it was found that Q value is mainly related in reaction kinetics but not reaction thermodynamics.
Molecular dynamics simulation was performed on the switching behavior of bistable rotaxane having two interaction points on axial components. The switching behavior was reproduced in the case of the rotaxane composed of amine-ester type axial and DB24C8 crown ether ring. In this system, switching was completed in subnano seconds. It is suggested that DB24C8 is more suitable for switching as a ring component than 24C8, which is analog of DB24C8 having no benzene rings.
The crossing of potential energy surfaces plays an important role in photo-decay processes and photochemical reactions. The energies and geometries of the crossing points have been reported for various molecules using quantum chemical calculations. In this research, excitation energy components of uracil are investigated to understand the characteristics of the crossing points. We revealed that the HOMO−LUMO exchange integral becomes approximately zero at the minimum energy conical intersection between S0 and S1 states. Furthermore, it was found that the HOMO−LUMO gap is close to the HOMO−LUMO Coulomb integral at the crossing structures.
The divide-and-conquer (DC) method was extended to time-dependent density functional tight-binding (TDDFTB) theory to enable excited-state calculations of large systems, as denoted by DC-TDDFTB. In this article, the implementation of TDDFTB and DC-TDDFTB methods into our in-house program, DC-DFTB-K, is explained. Dependence of CPU time on system-size for the DC-TDDFTB calculations indicates significant reduction of computational cost by adopting the DC method. Owing to the feature, excited-state calculations for whole photoactive yellow protein (PYP) surrounded by 4684 water molecules could be carried out in order to examine the hydrogen bond between p-coumaric acid and Glu46 in PYP.
The hyaluronan (HA) binding mechanism on CD44 was investigated by using molecular dynamics simulation. The Ordered (O) and partially disordered (PD) structures have been reported for CD44 HA binding domain (HABD). Two binding forms were investigated for the HA binding for O and PD structures in this study. O and PD structures show different HA binding structures, and the HA binding affinity on the PD structure was larger than that on O structure. The mobility of HA molecule on CD44 was high, especially for O structure. High affinity of HA binding on PD structure is suggested to regulate the rate of cell rolling under blood flow.
We propose a scheme based on a kind of self-consistent perturbation theory, where both the one-particle Green's function and the screened Coulomb interaction are determined self-consistently. To describe the screened Coulomb interaction dynamics, we use a functional-integral representation of the free energy. Our main approximation is to replace the exact free energy functional by a variationally chosen quadratic form in the fluctuating field. This procedure leads to the inclusion of electron correlation beyond the GW approximation. As an illustration, the scheme is used to calculate the potential surface of hydrogen fluoride molecule.
Regioselectivity of H2 adsorption on the Ga2O3 surface is investigated using the vibronic coupling density (VCD) as a reactivity index. The cluster model of Ga2O3 surface obtained by Step-by-Step Hydrogen-Terminated (SSHT) approach is employed. The VCD analysis shows that H2 is dissociatively adsorbed as H+ on the Lewis basic O atoms and as H− on the adjacent Ga atoms. The heterolytic dissociation implies that the H− atom bonded to the Ga atom is a reductant responsible for photocatalytic reduction of CO2 to CO.
We have been developing a combination scheme of fragment molecular orbital (FMO) calculations and dissipative particle dynamics (DPD) simulations in order to predict the structure of functional materials. FMO-DPD simulations for polymer electrolyte membrane, lipid membrane, and protein model were conducted using in-house automatic parameter determination software.
The Oakforest-PACS (OFP) system is a many-core type supercomputer with Intel's Knights Landing (KNL) processors. In this paper, we report the performance of fragment molecular orbital (FMO) calculations with the ABINIT-MP program (to which a three-layer parallelization was made recently) on the OFP system. The effect of hyper-threading in KNL is addressed as well.
Ferulic acid is known to have strong antioxidant properties. In the present study, we have investigated the electronic structures of Ferulic acid and its radical extracting the hydrogen atom from its phenolic hydroxyl group. We have discussed the relation of the results with the radical scavenging activity using the DPPH reagent measured by Xuan et al. We have found that the total energies of Ferulic acid derivatives and its radical species made from removing the hydrogen radical from the phenolic hydroxy group have the relation with the IC50 values. The orbital energies of the radical species also have the relation with the IC50 values. The deep learning study with the random forest model suggests that the contribution from α-SOMO and α-LUMO energies is important.
Based on the conformational analysis for an octahedral zinc(II) complex cation, [Zn(dmso)6]2+ (dmso: dimethylsulfoxide), the crystal-to-crystal phase transition behavior of [Co(dmso)6][BPh4]2 and [Zn(dmso)6][BPh4]2 was discussed.
Force field parameters around Au atom that have been lacking in standard parameter set of the MMFF94s were temporarily determined to reproduce the molecular crystal structure of phenyl(phenylisocyanide)gold(I) complex by classical force field calculations. It was confirmed that two polymorphic forms optimized by CONFLEX software with these parameters are in good agreement with the experimental structures. Application of the parameters to other derivatives also gives good results but the Au..Au distances in some crystal structures are longer than those of the experimental. Therefore, further optimization of these parameters will be required.
The purpose of this study is to clarify the regularity of occupancy hidden in the bi-occupied site by Al or Si of mullite crystal．Many mullite models with different atom arrangement were prepared and their stability was examined after performed structural relaxation calculations．The peak intensities of pair correlation function for metal atoms changed with the composition．From the three-view drawings of oxygen vacancy sites，it is suggested that when the oxygen vacancies aligned on the c axis, the crystal structure becomes unstable．
There are two subtypes (α, β) in the estrogen receptor (ER), and ERβ has binding selectivity for phytoestrogens. It is known that only two hydrophobic amino acid residues (Met336Leu and Ile373Met) differ in ligand binding pocket between subtypes. However, the mechanisms of its binding properties and subtype selectivity have not been fully understood. We evaluated the subtype selectivity by comprehensively analyzing the complex of ERβ and ligands based on the fragment molecular orbital (FMO) method. By comparing the interaction between ligand and amino acid residues of ER, it was revealed that both hydrogen bond with Glu305 and CH/π interaction with Phe356 were essential for ligand binding of ERβ, and stable interaction with Met336 and His475 would be related to β selectivity.