Katsunori Segawa

Bio: Katsunori Segawa is an academic researcher from University of Tsukuba. The author has contributed to research in topics: Radical & Fragment molecular orbital. The author has an hindex of 9, co-authored 15 publications receiving 337 citations.

Parallelized integral-direct CIS(D) calculations with multilayer fragment molecular orbital scheme

Abstract: We have developed a parallelized integral-direct code of the perturbative doubles correction for configuration interaction with singles, proposed as CIS(D) by Head-Gordon et al. (Chem Phys Lett 219:21, 1994). The CIS(D) method provides the energy corrections both of the relaxation and differential correlation for the respective CIS excited states. The implementation of CIS(D) is based on our original algorithm for the second-order Moller–Plesset perturbation (MP2) calculations (Mochizuki et al. in Theor Chem Acc 112:442, 2004). There is no need to communicate bulky intermediate data among worker processes of the parallelized execution. This CIS(D) code is then incorporated into a developer version of ABINIT-MP program, in order to improve the overestimation in excitation energies calculated by the CIS method in conjunction with the multilayer fragment molecular orbital scheme (MLFMO-CIS) (Mochizuki et al. in Chem Phys Lett 406:283, 2005). The MLFMO-CIS(D) method is first used in evaluating the lowest n\(\pi^{*}\) excitation energy of the hydrated formaldehyde. The photoactive yellow protein (PYP) is the second target of MLFMO-CIS(D) calculation. Through these applications, it is shown that the CIS(D) correction improves the CIS results favorably.

Time-Resolved Absorption Studies on the Photochromic Process of 2H-Benzopyrans in the Picosecond to Submillisecond Time Domain

Abstract: Picosecond to submillisecond photochromic reactions of 2,4-diphenyl-2H-benzopyran and 2,2,4-triphenyl-2H-benzopyran have been investigated by time-resolved absorption spectroscopy. The C−O bond cleavage of the benzopyrans (closed forms) occurs via the first excited singlet state within 2 ps to produce vibrationally excited open forms in the ground electronic state. In the subnanosecond to submillisecond time domain, several decay components with almost the same spectral profiles are observed. These components are assigned to respective stereoisomers with respect to two double bonds and one single bond of the open enone forms. From the pump-laser power dependencies of the yields of the open forms, it is suggested that the photocleavage gives at first only the open forms revertible to the closed form by a single-bond rotation, and that the photoexcitation of the first generated open forms gives rise to other open forms which need a double-bond rotation for reversion to the closed form. The photochromic reac...

Behavior of Naphthoyloxyl and Methoxynaphthoyloxyl Radicals Generated from the Photocleavage of Dinaphthoyl Peroxides and 1-(Naphthoyloxy)-2-pyridones.

Abstract: 1-Naphthoyloxyl and 2-naphthoyloxyl radicals were generated from photocleavage of dinaphthoyl peroxides and 1-(naphthoyloxy)-2-pyridones in acetonitrile. The difference in product distribution between the precursors is ascribed to the contribution of the two-bond cleavage in the peroxide decomposition in the singlet state. A series of methoxynaphthoyloxyl radicals were also generated from the corresponding (methoxynaphthoyloxy)pyridones and their behavior was compared with that of unsubstituted naphthoyloxyl radicals. The introduction of a methoxy group in the naphthalene ring stabilizes the naphthoyloxyl radicals to prevent their decarboxylation completely and reduces remarkably their reactivities in the addition to olefins and hydrogen-atom abstraction. The structure of the naphthoyloxyl radicals was discussed on the basis of their absorption spectra and MO calculations.

Fragmentation methods: a route to accurate calculations on large systems.

Abstract: Fragmentation Methods: A Route to Accurate Calculations on Large Systems Mark S. Gordon,* Dmitri G. Fedorov, Spencer R. Pruitt, and Lyudmila V. Slipchenko Department of Chemistry and Ames Laboratory, Iowa State University, Ames Iowa 50011, United States Nanosystem Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Umezono, Tsukuba, Ibaraki 305-8568, Japan Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, United States

Extending the Power of Quantum Chemistry to Large Systems with the Fragment Molecular Orbital Method

Abstract: Following the brief review of the modern fragment-based methods and other approaches to perform quantum-mechanical calculations of large systems, the theoretical development of the fragment molecular orbital method (FMO) is covered in detail, with the emphasis on the physical properties, which can be computed with FMO. The FMO-based polarizable continuum model (PCM) for treating the solvent effects in large systems and the pair interaction energy decomposition analysis (PIEDA) are described in some detail, and a range of applications of FMO to biological studies is introduced. The factors determining the relative stability of polypeptide conformers (α-helix, β-turn, and extended form) are elucidated using FMO/PCM and PIEDA, and the interactions in the Trp-cage miniprotein construct (PDB: 1L2Y) are analyzed using PIEDA.

Double-hybrid density functional theory for excited electronic states of molecules

Abstract: Double-hybrid density functionals are based on a mixing of standard generalized gradient approximations (GGAs) for exchange and correlation with Hartree-Fock (HF) exchange and a perturbative second-order correlation part (PT2) that is obtained from the Kohn-Sham (GGA) orbitals and eigenvalues. This virtual orbital-dependent functional (dubbed B2PLYP) contains only two empirical parameters that describe the mixture of HF and GGA exchange (ax) and of the PT2 and GGA correlation (ac), respectively. Extensive testing has recently demonstrated the outstanding accuracy of this approach for various ground state problems in general chemistry applications. The method is extended here without any further empirical adjustments to electronically excited states in the framework of time-dependent density functional theory (TD-DFT) or the closely related Tamm-Dancoff approximation (TDA-DFT). In complete analogy to the ground state treatment, a scaled second-order perturbation correction to configuration interaction with...

CH–π hydrogen bonds in biological macromolecules

Abstract: This is a sequel to the previous Perspective “The CH–π hydrogen bond in chemistry. Conformation, supramolecules, optical resolution and interactions involving carbohydrates”, which featured in a PCCP themed issue on “Weak Hydrogen Bonds – Strong Effects?”: Phys. Chem. Chem. Phys., 2011, 13, 13873–13900. Evidence that weak hydrogen bonds play an enormously important role in chemistry and biochemistry has now accumulated to an extent that the rigid classical concept of hydrogen bonds formulated by Pauling needs to be seriously revised and extended. The concept of a more generalized hydrogen bond definition is indispensable for understanding the folding mechanisms of proteins. The CH–π hydrogen bond, a weak molecular force occurring between a soft acid CH and a soft base π-electron system, among all is one of the most important and plays a functional role in defining the conformation and stability of 3D structures as well as in many molecular recognition events. This concept is also valuable in structure-based drug design efforts. Despite their frequent occurrence in organic molecules and bio-molecules, the importance of CH–π hydrogen bonds is still largely unknown to many chemists and biochemists. Here we present a review that deals with the evidence, nature, characteristics and consequences of the CH–π hydrogen bond in biological macromolecules (proteins, nucleic acids, lipids and polysaccharides). It is hoped that the present Perspective will show the importance of CH–π hydrogen bonds and stimulate interest in the interactions of biological macromolecules, one of the most fascinating fields in bioorganic chemistry. Implication of this concept is enormous and valuable in the scientific community.

Pair interaction energy decomposition analysis

Abstract: The energy decomposition analysis (EDA) by Kitaura and Morokuma was redeveloped in the framework of the fragment molecular orbital method (FMO). The proposed pair interaction energy decomposition analysis (PIEDA) can treat large molecular clusters and the systems in which fragments are connected by covalent bonds, such as proteins. The interaction energy in PIEDA is divided into the same contributions as in EDA: the electrostatic, exchange-repulsion, and charge transfer energies, to which the correlation (dispersion) term was added. The careful comparison to the ab initio EDA interaction energies for water clusters with 2-16 molecules revealed that PIEDA has the error of at most 1.2 kcal/mol (or about 1%). The analysis was applied to (H2O)1024, the alpha helix, beta turn, and beta strand of polyalanine (ALA)10, as well as to the synthetic protein (PDB code 1L2Y) with 20 residues. The comparative aspects of the polypeptide isomer stability are discussed in detail.