For all the isomers of conjugated polyenes C2nH2n+2 (n = 1∼6) total π-electron energy Eπ, topological index Z, mean length of conjugation L were calculated, and their correlations were analyzed to get their genealogy. These Eπ values can be estimated fairly well from Z, moderately from L, and roughly from the number of tertiary carbon atoms. The Eπ change caused by the attachment of one C=C— unit to a given polyene can be classified into elongation, outer branching, inner branching, and horn growing, by the site of the attached C atom. The genealogy of conjugated acyclic polyenes can thus be understood and interpreted even by chemistry beginners. By extending this analysis one can obtain mathematical proof and its limitation of the "organic electron theory."
Network structure of sodium silicate glasses was investigated by molecular dynamics simulation. The simulations were performed that determined using the first-principles calculation. Variation of SiO4 units and bond angles for alkali content were consistent with experimental results. It was also suggested that sodium ion and calcium ion give different effect to glass structure each other.
The structures of iron(III) complexes with biodegradative chelating agent, methylglycinediacetic acid [H3(mgda)], were computationally predicted based on the DFT method. The structures of dinuclear iron(III) complexes, [Fe2O(mgda)2(CO3)]4– and [Fe2O(mgda)2(H2O)4]2–, were predicted, and the structures were thought to be similar to those of related dinuclear iron(III) complexes with nitrilotriacetate (nta3–), [Fe2O(nta)2(CO3)]4– and [Fe2O(nta)2(H2O)4]2–, respectively. The mgda complex, [Fe2O(mgda)2(H2O)4]2–, is thought to interact with hydrogen peroxide like the nta complex [Fe2O(nta)2(H2O)4]2–.
The carbon number dependences of the chemical stabilities the several kinds of carbon nanotubes (CNTs) with unique Clar formula were examined by means of reduced HOMO-LUMO gap. It was found that the distributions of reduced HOMO-LUMO gaps of CNTs are divided into two regions with a border line of reduced HOMO-LUMO gap = about 3.0 and that the dependences on the tube length have distinct characters in the two regions. The difference in the dependences on the tube length is characterized by the existence of the 4n-conjugated circuit and by the existence of the fully-benzenoid structure. It was also indicated that the existence of the fully-benzenoid structure generates chemical instability in CNTs.
A high external quantum efficiency observed for organic light-emitting diodes using PTZ-BZP (PTZ: 10-hexyl-phenothiazin, and BZP:4-phenyl-2,1,3-benzothiadiazole) is attributed to fluorescence from S1 via reverse intersystem crossing from the T3 or T2 state under electrical excitation. The radiative and non-radiative transitions from these higher triplet states to the lower triplet states are suppressed because of their small overlap densities. In this study, a principle to design such an electronic structure is proposed.
In chemical structure elucidation, symmetric structures sometimes need careful handling. In the course of the development of a system for NMR-based structure elucidation, we have developed a method for processing chemical structures with high symmetry by applying an efficient algorithm for graph inference. In the present letter, we describe the outline of the algorithm by taking bibenzyl as an example. The method has been implemented to CAST/CNMR, a system for NMR-based structure/chemical shift prediction.
We developed an AR molecular graphics application for chemical education at secondary level. Flash which can execute on all platforms is used as a programming language for software development for smartphone, which the possession rate of which in junior and senior high school students is high. By developing and mounting the AR function, students can examine molecular graphics in 3D or when they look at a marker printed in a text or a handout just to read. To develop the web interface for making molecular data, the teacher can use molecular graphics in 3D easily when necessary.
Theoretical and computational studies on the mechanisms of ligand exchange reaction (LER) and ligand coupling reaction (LCR) of hypervalent pentacoordinate Sb and tetracoordinate Te compounds were carried out. Contrary to the previous suggestion from experimentalists, the lone pair electrons of Te do not participate in LER. Also, LER of R5Sb proceeds via a similar mechanism to that of R4Te. As for the LCR of R5Sb, the apical-equatorial coupling mechanism was suggested.
Power is the most important resource on the next-generation supercomputers, and they will be operated under power constraint. Therefore, there is a need to maximize performance of HPC application under power constraint. To do such optimization, we've developed and reported a method to improve performance by power allocation for each processor, which is called the variation-aware power budgeting. In this study, we carried out large-scale performance evaluation of a proposed method for two mini-applications related to molecular science, Modylas-mini and NTChem-mini. As a result, our method can improve their performance under power constraint up to 1.99 times speedup compared to conventional power constraint.
We have applied time-dependent density functional theory (TDDFT) in real-time and real-space to 11-cis retinal to investigate the optical absorption. As the exchange-correlation functional, we use the usual LDA and B88, which is the simplest GGA to describe the correct asymptotic behavior. The calculated result of B88 is closer to that of experiment, compared to that of LDA. Our results indicate that, if the functional to express the correct asymptotic form is selected, more accurate results can be obtained. In our TDDFT calculation, the peak position is confirmed by the maximum entropy method, which is applied to the spectrum analysis to find the peak related to the optical absorption effectively.
The ionization energies of single, double, and triple core-hole (SCH, DCH, and TCH) states were calculated for three isomers of aminophenol with the framework of density functional theory. Our calculated single core-hole ionization potentials were consistent with experiment and the previous theoretical values. Core-ionization energies via complex processes were also estimated. The difference of relaxation energy of two-site DCH (tsDCH) states can be visualized using Wagner plots. We found that the electron density of π orbitals on benzene ring are relaxed to core-vacancy sites at N,O tsDCH state.
We have studied the first excited state of o-hydoroxybenzaldehyde with TD DFT calculations. We have attempted systematic calculations to select a proper functional to describe the correlation between the absorption and emission spectra and the Hammett's σ values. The results with XAB95 functional are considered to be near the experimental results of the emission spectra.
Molecular dynamics simulation of 4-n-alkyl-4'-cyanobiphenyl series (nCB) using the full-atom model was carried out. We used a force field that was fitting the dihedral angle parameter and the LJ parameters of the AMBER Force Field against nCB. The dihedral angle parameter is set to reference the quantum chemical calculation, and the LJ parameters were fitted to reproduce the experimental data. By using the modified force field, experimental data such as isotropic-nematic phase transition temperature and density were reproduced.
The geometric structures of the phenoxenium cation which is a cation intermediate of 2-azaspiro ring compounds (2-azaspiro[4.5]decane) from N-methoxy-N-prenylbenzamide are studied by means of the Hamiltonian algorithm with ab intio molecular orbital calculations at HF/3-21G level. The geometries are further refined with MP2/6-311G** level. We tried four substituted compounds with the methyl group. Among them only one compound with two methyl groups gives a ring-closure intermediate, which agrees well with the experimental results.
Mechanistic studies for linear cross-dimerization between 2,3-dimethylbuta-1,3-diene and para-substituted styrenes by a Ru(0) complex, Ru(η6-naphthalene) (η4–1,5-COD), were performed computationally. The COD ligand is actually not a simple spectator ligand, it engages to assist the hydrogen migration steps. The computational studies verified the oxidative coupling step to govern the overall reaction as a rate-determining step. The reaction rate was found to be correlated well with the electronegativity of styrenes.