The academic-free program DCDFTBMD has been released for performing large-scale quantum chemical calculations based on divide-and-conquer density functional tight-binding (DC-DFTB) method. The DC-DFTB method achieves low computational cost with linear complexity and its massively parallel implementation enables efficient geometry optimization, vibrational frequency analysis, and molecular dynamics simulations. The present article describes DCDFTBMD in terms of download and installation details, structure of input and output, and available features together with associated keywords and options.

We systematically investigate the molecular and electronic structures of the group-IV (C, Si, Ge) nano-systems such as nanoribbons (NRBs), nanorings (NRGs) and nanotubes (NTBs). The present calculation reveals that C nano-system has a planar structure whereas Si and Ge ones have a non-planar structure. Focusing on the electron correlation, we further investigate the planarity/non-planarity of these nano-systems, and study the energetics of the singlet-triplet (ST) crossover in the ground state. We then extend our study to the infinite NRB and NTB systems and find that these nano-systems have the ground-state spin singlet.

The new visualization technique of canonical molecule orbitals (MOs) was developed with the cloud-like model. The random position points according with MO distribution were generated by the rejection method. Quasi-isosurface indication was proposed and succeeded in representation of internal structure containing inclusion-type isosurface. Because this method also displays a wide range of MO values simultaneously, MO distribution can be observed with little loss of information. This method is useful for analyses in the complicated protein MOs.

This paper proposes the use of regular expressions for chemical structure search. As regular expressions dramatically improve the convenience of string search, a regular expression extension for SMILES can improve the convenience of chemical structure search．The regular expression extension for SMILES is obtained from the existing SMILES notation by adding the curly brackets “{” and “}” for range specifications, the vertical bar “|” for enumerations of choices, the asterisk “*” for repetitions of 0 or more times, and the plus“+” for repetitions of 1 or more times. Software for chemical structure search using the extended SMILES was implemented and released.

Principal component analysis (PCA) which is one of the dimensionality reduction techniques is adapted to find the common or major factors from sampling big data. In order to be clear the trigger motion of phase transition/change, PCA performed the MD sampling coordinates of crystal structure around phase transition temperature. In this paper, we especially focus on the α − β transition using the PCA analysis to the MD trajectories. The first principal component of PCA can be approximated as a mixed motion of the rotational mode of one SiO₃-OSiO₃ bond and the bending mode of Si-O-Si angle. The result indicated that the PCA can show the trigger motion of phase transition/change as found in previous studies. We could suggest that the PCA is useful tool to understand the importance information of phase transfer/change of crystal structure.

This paper proposes a substructure search method for finding an element of a set of chemical structures represented by a SMILES string with regular expression extension. It is known that substructure search is an NP-hard problem in general. However, by taking advantage of a graph-theoretical characterization of chemical compounds, the proposed method runs fast enough. Software for substructure search using the proposed method was implemented and released.

To investigate the effects of adsorbed H₂O on the surface structure of forsterite glass, we performed molecular dynamics calculations. The results show that the amplitudes of the thermal vibrations of atoms in forsterite surface decrease with H₂O adsorption. Furthermore, it was found that MgO_xH_y units exist in the interface of forsterite glass and grown amorphous ice. The observed decrease in the amplitudes of thermal vibrations is attributed to formation of covalent bonds between Mg and oxygen in H₂O. The interface structure of forsterite glass with amorphous ice has important implications for chemical evolution in interstellar spaces.

To investigate the self-diffusion mechanisms of atoms in forsterite in supercooled liquid state, we performed molecular dynamics calculations. The results show that the atoms migrate with jumps from a stable site to an adjacent site. From analyses of the stress auto-correlation function (SACF) and mean square displacement (MSD), we determined the viscosity and self-diffusion coefficients. Furthermore, it was found that the jumping probabilities of Mg and Si, which are located at positions with high Si densities, are higher than the averaged probability, because of a structural distortion of surrounding SiO₄ units with strong Si–O bonds. The mechanisms of self-diffusion are important to understand the phase transition dynamics of natural forsterite in proto-planetary disks and interstellar molecular clouds.

For indigo and its isomers epindolidione and indirubin, potential energy profiles of the excited-state intramolecular proton transfer (ESIPT) and subsequent nonradiative deactivation via conical intersection (CI) are calculated using the TDDFT and MS-CASPT2 methods. Both methods predict that indigo and indirubin exhibit a lower energy barrier for ESIPT compared to epindolidione. In addition, energy of S₁/S₀ CI relative to the minimum after the ESIPT has been found to be the highest for epindolidione. These findings suggest that nonradiative deactivation is more efficient in indigo and indirubin than in epindolidione, which is consistent with the experimental observation that fluorescence is quenched only in the former.

We have developed the divide-and-conquer (DC) based self-consistent-field (SCF) method with finite-temperature (FT) scheme including the electronic entropy contribution, as denoted by FT-DC-SCF. This could approximately involve the static correlation effect appearing in bond-breaking systems, diradicals, and conjugated polymers, within small additional computational costs. This letter reports the energy errors for the conventional and FT-type DC-SCF calculations of polyethylene and polyacetylene. Furthermore, the singlet-triplet separation in polyacene is examined by adopting the conventional and FT-type DC-SCF methods. The numerical data confirm the effectiveness and accuracy of the FT-DC-SCF method.

The activated carbon synthesized from rice husks has high hydrogen storage on 77K. It is inferred that activated carbon has a lot of defect on the surface compared with graphene. However, the actual structure and hydrogen storage mechanism have unknown by experiments. The purpose of this study is to clarify the hydrogen storage mechanism for multilayered graphene. The sp² hybrid system carbon structure that introduced a defect was prepared and set a hydrogen molecule between the layers. MOPAC PM7 involving the dispersion term for semiempirical MO was used for calculating heat of formation. From the potential curve between graphene layer where hydrogen was inserted, it is suggested that when a defect made on the edge, the structure becomes more stable.

Regioselectivity in the Rh-catalyzed coupling reaction of 3-phenylthiophene with styrene was investigated by quantum chemistry calculations. The coupling reaction experimentally reported that styrene is selectively coupled to the phenyl group of the phenylthiophene. Results of the reaction path search and the natural bond orbital analysis indicate that the coupling position is determined by the preference of the styrene insertion into the 5-membered rhodacycle intermediate, which is produced by the double C–H bond cleavage of 3-phenylthiophene in presence of the Rh-catalyst.

We have studied photovoltaic mechanisms of an organic solar cell using phthalocyanine for a p-type semiconductor and fullerene C₆₀ for an n-type semiconductor in quantum chemistry simulation. This study examines computation of the electronic state of the phthalocyanine–fullerene C₆₀ bimolecular system in the ground state by the DFT method using long-range corrected hybrid functional CAM-B3LYP. Some double bonds in unimolecular phthalocyanine become semi-double bonds in the bimolecular system. Furthermore, some carbon atoms in a fullerene molecule are negatively charged in the bimolecular system. These results suggest the generation of positive holes and conduction electrons in the bimolecular system. Investigation of reports about simulation in an excited state and the actual measurement of electric conductivity has revealed that these positive holes and conduction electrons in the ground state facilitate the migration of positive holes and conduction electrons generated in a photoactive layer by light irradiation.

Antifreezing nature of an antifreezing proteins (AFPs) from Rhagium inquisitor, RiAFP, was assessed by means of molecular dynamics (MD) simulations of RiAFP adsorbing ice surface in water below melting temperature to investigate how RiAFP affects the way of ice growth. We found that the ice growth toward the horizontal direction is accelerated, while that toward the vertical direction is suppressed due to the RiAFP binding on the nascent ice surface. We also showed that a mutant of RiAFP, where all Thr are replaced by Gly, resulted in loss of antifreezing effects due to weaker binding to the ice surface though the structure of the mutant is stable in aqueous solution at the room temperature.

As a new method for discrimination analysis applicable to data containing a large number of variables such as spectra, FDOD (Fisher's Discriminant Orthogonal Decomposition) was developed by incorporating regularization and orthogonal decomposition into ordinary FDA (Fisher's Discriminant Analysis). Here, FDOD was applied to distinguish infrared absorption (IR) spectra of rayon and modal. Since rayon and modal are very similar recycled fibers, their IR spectra cannot be discriminated by score plots based on principle component analysis (PCA). By using FDOD, their discrimination with a correct answer rate of 94% has been achieved.

Machine learning for predicting properties of molecules and designing molecules with desired properties requires suitable numerical representation of molecular structure. In this study we propose to represent a molecular graph as a high dimensional feature vector by counting the number of substructures of a molecule, and report conditions that these vectors should satisfy. The vectors are expanded by the lattice basis extracted from the feature vectors of a large molecular dataset. In addition, an efficient algorithm to reconstruct molecular structures from the feature vector is presented. The latent space provides a continuous and concise representation of molecular graphs, and the representation allows smooth interpolation between two molecules. The proposed method has wide application to studies of quantitative structure activity relationships and machine learning of molecules.

Conformational analysis of the reactant, product, and complex of the polymer and macrocyclic catalyst (PdMC) was carried out in order to investigate the reaction mechanism of the intramolecular cyclization reaction of the polymer chain having a Rotaxane structure. Focusing on the N-C distance of the intramolecular cyclization reaction coordinate, a group of stable conformers with short N-C distances for the reaction was found. By forming a complex with PdMC, the conformations of the reactant with a short N-C distance were stabilized and the intramolecular cyclization reaction was promoted.

Natural rubber is an excellent material in elasticity and abrasion resistance. However, the detailed structure and the reason for excellent physical properties of natural rubber are still unclear. We aimed to conduct a conformational search and structural analysis using computational chemistry and to elucidate the biosynthetic process of natural rubber. From the calculation results, as long as the catalyst (enzyme) required for each stage of the biosynthesis process exists, it turned out that the biosynthesis of natural rubber proceeded spontaneously.