Enhanced sampling methods have been applied to handle chemical reactions rarely observed in limited-scale molecular dynamics simulations. Some of these methods intentionally put the system in a nonequilibrium state. We focus on free energy calculation methods based on the fluctuation theorem to directly estimate free energy from simulations of nonequilibrium systems. In this paper, we derive Jarzynski's equality and Bennett acceptance ratio method, and present their illustrative applications to free energy calculation.

The author's code for VASP POSCAR handling is updated with new methods developed in 2024. Size "1/N"supercells can be obtained to find identical or smaller size unit cells that may belong to a Bravais lattice with a lower degree of freedom if deviations from rigid requirements for each Bravais lattice are allowed. Sortable number "message digests" of the configuration of different species on a (sub)lattice can be derived, which is useful for eliminating identical configurations in exhaustive combinatorial searches of species distributions. A molecule containing a given atom can be extracted from, for example, a molecular crystal supercell with many molecules.

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.