Daisuke Yokogawa

New generation of the reference interaction site model self-consistent field method : Introduction of spatial electron density distribution to the solvation theory

The authors propose the new generation of the reference interaction site model self-consistent field (RISM-SCF) method for the solvation effect on the electronic structure of a solute molecule, in which the procedure proposed by Gill et al. [J. Chem. Phys. 96, 7178 (1992)] is adopted. Main improvements are the introduction of spatial electron density distribution and the removal of the grid dependency that is inherent in the original RISM-SCF. The procedure also provides very stable determination of the effective charges even if a buried atom exists in the target molecule and eventually extends the applicability of the RISM-SCF. To demonstrate the superiority of our method, sample calculations for H2O, C2H5OH, and HLi in aqueous solution are presented.

A Strap Strategy for Construction of an Excited‐State Intramolecular Proton Transfer (ESIPT) System with Dual Fluorescence

An amine-embedded flexible alkyl strap has been incorporated into an emissive boryl-substituted dithienylpyrrole skeleton as a new entity of excited-state intramolecular proton transfer (ESIPT) chromophores. The π-electron system shows a dual emission, which covers a wide range of the visible region depending on the solvent polarity. The incorporation of the aminoalkyl strap as well as the terminal boryl groups efficiently stabilize the zwitterionic excited-state species resulting from the ESIPT even in an aqueous medium.

A Theoretical Analysis of a Diels-Alder Reaction in Ionic Liquids

The Diels-Alder reaction of cyclopentadinene (CP) with methyl acrylate (MA) in room-temperature ionic liquids (RTILs) is theoretically examined. In the present study, quantum molecular orbital theory is combined with a multicomponent reference interaction site model (RISM). Because RISM is free from statistical error, it is possible to overcome the serious difficulty in the description of the strong Coulombic interaction in RTILs. We focused on the origin of the relatively moderate solvation effects of RTILs and the mechanism of endo-exo selectivity.

Analytical energy gradient for reference interaction site model self-consistent field explicitly including spatial electron density distribution

Analytical energy gradient formula was derived for reference interaction site model self-consistent field explicitly including spatial electron density distribution (RISM-SCF-SEDD). RISM-SCF-SEDD is a combination method of ab initio electronic structure theory and statistical mechanics for molecular liquids [D. Yokogawa et al., J. Chem. Phys. 126, 244504 (2007)]. As shown previously, RISM-SCF-SEDD is numerically stable and has expanded the applicability of the solvation theory. The energy gradient is an indispensable tool to compute molecular geometry and its implementation further extends the capability of RISM-SCF-SEDD. The present method was applied to chemical systems in aqueous solution; hydration structure and geometry of phosphate anion PO(4) (3-) and tautomerization between 2-pyridone and 2-hydroxypyridine. Compared to available experimental data, the present method correctly reproduced the geometries and relative energies of solvated molecules with microscopic solvent distribution. It is clearly shown that highly sophisticated quantum chemical calculation such as coupled cluster with single and double and perturbative triple excitations coupled with solvation effect is a powerful tool to accurately evaluate molecular properties.

A highly parallelizable integral equation theory for three dimensional solvent distribution function: Application to biomolecules

Three dimensional (3D) hydration structure is informative to clarify the functions of hydrated waters around a protein. We develop a new approach to calculate 3D solvation structure with reasonable computational cost. In the present method, the total solvation structure is obtained using conventional one dimensional reference interaction site model (RISM) followed by integrating the 3D fragment data, which are evaluated around each atom (site) of solute. Thanks to this strategy, time-consuming 3D fast Fourier transformation, which is required in 3D-RISM theory, can be avoided and high-parallel performance is achieved. The method is applied to small molecular systems for comparison with 3D-RISM. The obtained results by the present method and by 3D-RISM show good agreement. The hydration structures for a large protein computed by the present method are also consistent with those obtained by x-ray crystallography.

Theoretical study on the molecular structures of X-, α-, and β-types of lithium phthalocyanine dimer

We report here the results from theoretical calculations of the potential energy curves, the geometry optimizations, and the electronic structures for three dimers of lithium phthalocyanine (LiPc) by using three types of functional systems: PBE1PBE, B3LYP, and M06. The results were discussed in comparison with those obtained for the dimers of magnesium phthalocyanine (MgPc). The long‐range dispersive interactions were considered in part using these functional systems in the increasing order of PBE1PBE, B3LYP, and M06. The mechanism whereby the dispersive interactions affect the geometric and electronic structures of the LiPc and MgPc dimers is discussed. The calculated results provide insight into the computational methods for both open‐ and closed‐shell metal phthalocyanine (MPc) dimers: Although the PBE1PBE and B3LYP functional systems cannot evaluate a weak dispersion interaction appropriately, the M06 functional can estimate a weak dispersion interaction well in both open‐ and closed‐shell MPc dimers. Basis set superposition error (BSSE) corrections play an important role for the quantitative analysis; however, the calculation results without BSSE corrections may be sufficient for the qualitative discussion on the properties of these dimers such as geometries, stabilities, electronic structures, and so on.

New evaluation of reconstructed spatial distribution function from radial distribution functions

Although three dimensional (3D) solvation structure is much more informative than one dimensional structure, its evaluation is difficult experimentally and theoretically. In our previous Communication [Yokogawa et al., J. Chem. Phys. 123, 211102 (2005)], we proposed a new method to present reconstructed spatial distribution function (RC-SDF) from a set of radial distribution functions (RDFs). In this article, we successfully extended the method more accurately with new basis sets. This new method was applied to two liquid solvation structures, methanol and dimethyl sulfoxide, as examples. Their RC-SDFs evaluated here clearly show that the former solvation structure is well defined while the latter one is broad, which agrees well with the SDFs calculated directly from molecular dynamics simulations. These results indicate that the method can reproduce well these 3D solvation structures in reasonable computational cost.

A Macrocyclic Fluorophore Dimer with Flexible Linkers: Bright Excimer Emission with a Long Fluorescence Lifetime

Bright fluorescent molecules with long fluorescence lifetimes are important for the development of lifetime-based fluorescence imaging techniques. Herein, a molecular design is described for simultaneously attaining long fluorescence lifetime (τ) and high brightness (ΦF ×ɛ) in a system that features macrocyclic dimerization of fluorescent π-conjugated skeletons with flexible linkers. An alkylene-linked macrocyclic dimer of bis(thienylethynyl)anthracene was found to show excimer emission with a long fluorescence lifetime (τ≈19 ns) in solution, while maintaining high brightness. A comparison with various relevant derivatives revealed that the macrocyclic structure and the length of the alkylene chains play crucial roles in attaining these properties. In vitro time-gated imaging experiments were conducted as a proof-of-principle for the superiority of this macrocyclic fluorophore relative to the commercial fluorescent dye Alexa Fluor 488.

A new method to reconstruct three-dimensional spatial distribution function from radial distribution function in solvation structure

Three-dimensional spatial distribution function (SDF) of solvent is a fundamental quantity for analysis of solvation. However, its calculation has been very limited because long computational time is required. We here developed a novel and robust method to construct approximated SDFs of solvent sites from radial distribution functions. In this method, the expansion of SDFs in real solid harmonics around atoms of solute leads to a linear equation, from which SDFs are evaluated with reasonable computational time. This method is applied to the analysis of the solvation structure of liquid water, as an example. The successful results clearly show that this method is very powerful to investigate solvation structure.

An Analysis of 3D Solvation Structure in Biomolecules: Application to Coiled Coil Serine and Bacteriorhodopsin

Three-dimensional (3D) solvation structure around coiled coil serine (Coil-Ser) and inner 3D hydration structure in bacteriorhodopsin (bR) were studied using a recently developed method named multicenter molecular Ornstein-Zernike equation (MC-MOZ) theory. In addition, a procedure for analyzing the 3D solvent distribution was proposed. The method enables us to calculate the coordination number of solvent water as well as the strength of hydrogen bonding between the water molecule and the protein. The results for Coil-Ser and bR showed very good agreement with the experimental observations.