Understanding the origins of reactivity and selectivity in chemical reactions is not only academically intriguing but also crucial for controlling reactions. Recently, we proposed a novel method to quantitatively evaluate the stereoelectronic state and rationally explain the facial selectivity in nucleophilic reactions of cyclic ketones [1]. This paper introduces previous studies on chemical reactions and stereoelectronic states, as well as our newly developed method, based on the oral presentation delivered at the 2024 Autumn Annual Meeting of the Society of Computational Chemistry Japan [2].

Dimethyl sulfoxide (DMSO), widely used as a cryoprotectant, drug, and oxidant, contains a hydrophilic S=O and hydrophobic CH₃ groups and is fully miscible with water in any ratio. In this study, intermolecular interactions in dilute aqueous DMSO solution were analyzed using effective fragment potential based molecular dynamics (EFP-MD) simulations. The analysis revealed that DMSO induced stable interactions with water molecules not only around its hydrophilic S=O group but also near the CH₃ groups. The interaction lifetimes suggested that the hydrogen bonding network in the first hydration shell is directional.

The global reaction route mapping (GRRM) strategy enables an exhaustive search of static chemical reaction pathways, providing deep insight into chemical reactions. On the other hand, ab initio molecular dynamics (AIMD) simulations explicitly account for the momenta of atoms, revealing the realistic dynamical motion of molecules. In this study, we constructed the reaction path network for the ground-state OCS²⁺ species, which has attracted significant interest from spectroscopists. Recently, a new dissociation mechanism of S⁺via the COS²⁺ isomer has been proposed. By referencing the results of AIMD simulations and focusing on the isomerization process, we emphasize the crucial role of dynamical effects and the concept of dynamically hidden reaction paths.

Alkylation reactions of aromatic nitriles using Grignard reagents produce ketones after hydrolysis. However, this addition reaction is slower than when using reactive organolithium(I) reagents. In the previous paper, we improved the reaction by using zinc(II)ates, which are generated in situ using Grignard reagents and zinc chloride (ZnCl₂). The corresponding ketones and amines were obtained in good yields under mild reaction conditions. In this study, the reaction mechanism was theoretically investigated by using density functional theory (DFT). The reactivity with ZnCl₂ was verified thorough orbital interaction analysis and non-covalent interactions analysis.

Molecular dynamics simulations combined with 3D-RISM theory provided new insights into how mutations influence the distribution of zinc ions in mutant ZIP8. When both Q58 and E221, which function as metal ion recognition filters, were replaced with histidine, the distance between residues 58 and 221 remained nearly unchanged compared to the wild type. However, the distance between the transmembrane domains on the intracellular side exhibited significant changes, suggesting a potential enhancement of zinc transport. This result aligns with experimental findings indicating that the mutation enhances zinc transport ability.

A mixed solution of organic semiconductors Ph-BTBT-Cn with different alkyl chain length (n) forms a high-quality molecular bilayer by suppressing layer-by-layer stacking when the molar fraction of the longer chains (χ_L) is 0.1–0.6. In this study, we performed molecular dynamics simulations to investigate the dynamics of alkyl chains in the mixed bilayer. The order parameters and dihedral angles of the alkyl chains were analyzed as a function of χ_L. The results revealed that increasing χ_L enhances the ordering of the longer alkyl chains, thereby reducing their torsional motion. A stochastic model of the number of free surplus chains explains the molar fraction dependence of film morphology.

Molecular dynamics (MD) simulations, accelerated by a universal neural network potential, were employed to investigate the dynamic behaviors of ten inorganic anions (Br^-, Cl^-, F^-, OH^-_, NO₃^-_, H₂PO₂^-_, H₂PO₃^-_, HPO₄^2-_, CO₃^2- and SO₄^2-) intercalated into NiFe layered double hydroxide at varying hydration levels. Our results show that the lattice parameters along the layered double hydroxide (LDH) layers are minimally affected by the intercalated anions and water content, while the lattice parameter perpendicular to the layers, i.e., the basal spacing, is strongly influenced by the type of anion and hydration level. The basal spacing is closely correlated with the ionic radius and charge of the anions, as well as the amount of water uptake. Mean squared displacement (MSD) analysis reveals distinct behaviors of the anions under different hydration conditions. While some anions, such as NO₃^- and H₂PO₂^-, exhibit noticeable mobility, others remain largely immobilized, primarily due to strong electrostatic interactions with the LDH layers and water molecules. Hydration weakens the interaction between anions and the LDH but also restricts the mobility of anions due to the formation of hydration shells. These findings provide insights into anion dynamics and selectivity in NiFe LDH, which are critical for designing materials for anion removal applications.

Molecular dynamics simulations of hydrogen absorption and diffusion in Pd and AgRh alloy nanoclusters were performed. Parameters for atomic interaction potentials were determined from relativistic quantum chemical calculations. Although Rh is known not to absorb hydrogen in bulk, the Rh-H interaction strength obtained from the calculations was about 80% of that of the Pd-H. Using the parameters obtained, molecular dynamics simulations were performed. Molecular dynamics simulations of AgRh clusters with different Ag:Rh ratio have shown no significant difference in the Rh-Rh distance distribution at the nearest neighbor except for Ag₇₀Rh₃₀. However, at the second nearest neighbor the distance increased as the Ag fraction increased.

Surface-molecule interaction has always been an integral part in the analysis of reactions and surface reactivity in heterogenous catalysis. With the advent of computational resource advancement, the search for the next generation catalysts explores the combination of several metal elements in the multi-elemental nanoparticles (NP). However, with the complexity of the catalysts' surface comes the difficulty of understanding surface-molecule interaction and methods to overcome this should be considered. In our previous study, we used metal-coordination to predict CO adsorption on the ternary alloy combinations. This method describes the adsorption site by the network of metal elements interacting with the site that contributes to the change in its electronic properties. Since this network considers up to the neighbor of the first nearest neighbor of the adsorption site, in this study, we considered to use the dataset of regression coefficient of ternary alloy combinations to predict molecular adsorption on a multi-elemental NP. We tested the method on CO molecular adsorption on the quaternary RuRhIrPt NP and used the regression coefficient obtained from RuRhPt, RhIrPt, RuIrPt and RuRhIr ternary alloy. Results show that the predicted values of CO adsorption energy on the RuRhIrPt NP have comparable values of coefficient of determination (R²) and mean absolute error (MAE) with the prediction of CO adsorption on ternary alloy. Thus, this method could pave the way for predicting molecular adsorption on multi-elemental NP using only the dataset of regression coefficient from ternary alloy combinations and the atomic configurational structure of the multi-elemental NP.

We have recently proposed a highly efficient convergence method for self-consistent (SCF) calculations combining Givens rotation and error back-propagation (EBP) algorithms, referred to as direct Givens rotation (DGR) method [J. Chem. Phys. 162, 014108 (2025)]. The Givens rotation corresponds to unitary transformations that guarantee the orthogonality of molecular orbitals. Complicated gradients constructed through sequential Givens rotations were computed using the EBP technique without deriving explicit forms. This article reviews the proposed DGR method and compares it with conventional methods such as the standard SCF procedure, the second-order SCF method, and the direct inversion in iterative subspace technique for H₂O molecule. The DGR method exhibited a convergence speed comparable to that of the SOSCF method while achieving a lower and more reliable energy.