We have been developing the ABINIT-MP program for the fragment molecular orbital (FMO) method. The list of inter-fragment interaction energies (IFIEs) is available from FMO calculations and is useful in analyzing the nature of interactions in a given target system. In this Letter, we summarize the current status of ABINIT-MP and also the machine-learning assisted analyses of IFIE data.
In this article, a new index was developed for predicting the band gap of π-conjugated polymers based on isodesmic reactions between a dimethylated monomer and an oligo-acetylene. The index can be uniquely defined for hetero-cyclic and poly-cyclic monomers. The index correlated well with the calculated band gap of polymers. In addition, it shows that band gap can be controlled by copolymerization using the index based on only monomer information without calculations of polymers.
Recently, simulations with coarse-graining models, such as coarse-grained molecular dynamics (CG-MD) and dissipative particle dynamics (DPD), have attracted practical interest. We have developed a portable code CAMUS for DPD simulations. Performance evaluations of CAMUS (Code for dissipative particle dynAMics simUlationS) have been made by comparison with COGNAC (Coarse-Grained molecular dynamics program by Nagoya Cooperation) as a standard DPD code, in 5,000 − 100,000 particles systems.
Mullite has a complicated crystal structure in which double occupancy of metal atoms and oxygen vacancies take a random arrangement．Various attempts have been made to describe its structure，but it has not yet been fully described．The purpose of this study is to clarify that the random arrangement has regularity. Excluding arbitrariness，the arrangement of metal atoms and oxygen vacancies of mullite crystals of three compositions (1.58Al2O3，1.75Al2O3，1.95Al2O3 for 1SiO2) was randomly generated．Structural relaxation calculations of these models were performed，and their stability was examined．The wide distribution of the heat of formation obtained by the structural relaxation calculation was consistent with the composition．
Organic reactions with fullerene realize functional nanomaterials, although selective functionalization is still challenging because of many equivalent olefins causing various regioisomers. Thus, the improvement of reactivity and regioselectivity of C60 reaction has been realized by structural organic chemistry such as enhancement of strain, introduction of heteroatom, and nucleophilic additoin via single eletron transfer (Figure 1). This paper presents the theoretical clarification for the reactivity and selectivity of these activated reaction conditions.
A simple model of localized electron wave packets, floating and breathing Gaussians with non-orthogonal valence-bond spin-coupling, is demonstrated to produce an accurate high-harmonic generation (HHG) spectrum from an LiH molecule induced by an intense laser pulse. In contrast with the conventional molecular orbital picture in which the Li 2s and H 1s atomic orbitals are strongly mixed in the valence σ bonding orbital, the present calculation indicates that a superposition of independent responses of the electrons reproduces the spectrum in which the contribution of the H 1s electron dominates the characteristic plateau and cut-off of HHG.
We propose a unique strategy based on the dimensionality of anionic electrons for new inorganic electride search. We adopted strontium phosphide as the initiator for the evolutionary search, and our evolutionary calculations combined with experimental synthesis found the Sr5P3 is a new one-dimensional electride.
Since the appearance of bulk heterostructures, organic thin film solar cells have attracted attention as next-generation energy sources. Earlier studies have addressed quantum chemical calculation in an excited state and a ground state of phthalocyanine–fullerene bimolecular systems. Phthalocyanines and fullerenes are well known as materials of organic thin film solar cells. Based on these reports, we have devised a new method of manufacturing organic thin film solar cells and have prepared a device incorporating those features. Nevertheless, the device is so soft that it is considered necessary to strengthen the device by incorporating a fibrous substance. This study investigated the effects on its electronic properties of incorporating molecules like nylon 6 into phthalocyanine using quantum chemical calculation. Results demonstrate partial defects in the electron cloud of phthalocyanine molecules, revealing the occurrence of positive holes. These electron cloud defects result from interaction between nylon dimer molecules and phthalocyanine molecules.
Recently, renewable energy is attracting attention globally. In Japan today, there is a shift with growing momentum to photovoltaic power generation from thermal power generation, which has heretofore served as the foundation of electrical power generation. We are studying improvement of the photovoltaic conversion efficiency of bulk heterojunction organic thin film solar cells and are preparing a device that requires detailed elucidation of its electronic properties and its mechanism of power generation. Accordingly, we have conducted quantum chemical calculations using a molecular pair of phthalocyanine and fullerene C60 employed as a specimen. Specifically, we have computed charge densities and electron clouds in the ground state while varying the molecular distance to 12 Å and 24 Å using the density functional method. Results demonstrate quite high negative charge density in C atoms near phthalocyanine in C60 when the distance between the two molecules is decreased to 12 Å, with a positive charge density in C atoms on the opposite side of phthalocyanine in C60. Results suggest that many conduction electrons and positive holes, the so-called carriers, are generated in the phthalocyanine − fullerene C60 bimolecular system when the molecular distance is decreased to 12 Å.
We investigated the C–H bond cleavage of methane on various binary alloys using periodic density functional theory (DFT) calculations for catalyst screening. Cohesive energy, which strongly correlates with activation energy and heat of reaction for the C–H bond cleavage, was computed for 337 alloys in AFLOW database to enable rapid screening.
We computationally design GaN and GaP heteroatom nanostructures of nanoribbons (NRBs), nanorings (NRGs), and nanotubes (NTBs), and study the atomistic and electronic structures theoretically. First-principles calculations demonstrate that GaN finite NRBs have a flat molecular plane whereas GaP NRBs break the flatness of the NRB molecular planes. Although an NRG is produced by rolling an NRB (head to tail), the GaP system produces a specific NRG having a "magic ring numbe" whereas the GaN system can freely change the NRG diameter. A NTB stacked by these NRGs has a potential to be a one-dimensional semiconductor having a band gap of 1.5 ∼3 eV and effective mass ratios 0.3 ∼1.7 eV for an electron and a hole.
To elucidate the temperature effects on the crystal growth of C60 molecules at a molecular level, we performed molecular dynamics calculations for the crystal growth to the substrate and nucleation in gas-phase. We found two crystallization processes: (i) a direct crystal growth of C60 molecules onto the crystal substrate, and (ii) a nucleation in the gas-phase under low temperature conditions.
We carried out electronic structure calculations on molecules having scent, and evaluated their electronic descriptors. Based on the calculated descriptors, a correlation between electronic similarities and scents of the molecules was investigated. Through this analysis, we found that a good correlation exists between these characteristics.
As an electronic structure calculation of the B-type model-DNA, the calculation of (poly-(guanine) poly-(cytosine)) model polymer is performed by means of the ab initio crystal orbital method adapting the screw axis-symmetry which results in great reduction of computational efforts. All sugar backbones and sodium phosphate are included in the calculations. Energy band structures are calculated at the 6-31G level. For a comparison, the calculation without sodium phosphate is also performed. The resultant energy band structure is very different from that of the original one and it should be concluded that the alkali phosphate is necessary to describe the electronic structure of model-DNA.
The substrate specificity and selectivity on the chymotrypsin-type serine protease, neuropsin was investigated by using molecular dynamic simulation. The amino acid residues at l1 and l5, which are located adjacent to the neighboring residues of cleave site Argl3 on both sides, play important roles, and the interactions between these amino residues of peptide and loops D and H of protein regulate the affinity and catalytic activity.
The mechanism of enantioselectivity of the asymmetric aldol reaction catalyzed by Zn (II) complex was discussed based on the transition states (TSs) of the stereo-determining C−C bond formation step. To gather the TSs of the stereo-determining step exhaustively, an automated reaction path search method, called the artificial force induced reaction (AFIR) method, was applied. Though the obtained TSs reproduced the stereoselective ratio, it was difficult to extract the key information for the enantioselectivity. To analyze such TS structures efficiently, the automated clustering of the TSs by using the K−Means++ method, which was one of the unsupervised learning methods, was helpful.
Natural rubber is an excellent material in elasticity and abrasion resistance. However, the detailed structure of natural rubber is still unclear. We aimed to conduct conformational search and structural analysis using computational chemistry and to elucidate the biosynthetic process of natural rubber. From the calculation results, it was found that the structure is likely to have a rounded structure due to the intramolecular and intermolecular interaction that the terminal phosphate group gives to the polyisoprene moiety as a polar group, and both ends are fixed on the particle surface and become stable.
A cluster validity index (CVI) called "simplicity index" (SI) is newly proposed to enhance the accuracy of data clustering in machine learning. This index is derived to emphasize the importance of simplicity in cluster structures. The characteristics ofSI and its advantages over the known methods in the literature are discussed. SI is applied to classification of nucleotide sequences of nitrogen-fixing genes.