Takeshi Yanai

Bio: Takeshi Yanai is an academic researcher from Nagoya University. The author has contributed to research in topics: Density matrix renormalization group & Complete active space. The author has an hindex of 42, co-authored 97 publications receiving 17609 citations. Previous affiliations of Takeshi Yanai include National Institutes of Natural Sciences, Japan & Oak Ridge National Laboratory.

A new hybrid exchange–correlation functional using the Coulomb-attenuating method (CAM-B3LYP)

Abstract: A new hybrid exchange–correlation functional named CAM-B3LYP is proposed. It combines the hybrid qualities of B3LYP and the long-range correction presented by Tawada et al. [J. Chem. Phys., in press]. We demonstrate that CAM-B3LYP yields atomization energies of similar quality to those from B3LYP, while also performing well for charge transfer excitations in a dipeptide model, which B3LYP underestimates enormously. The CAM-B3LYP functional comprises of 0.19 Hartree–Fock (HF) plus 0.81 Becke 1988 (B88) exchange interaction at short-range, and 0.65 HF plus 0.35 B88 at long-range. The intermediate region is smoothly described through the standard error function with parameter 0.33.

A long-range correction scheme for generalized-gradient-approximation exchange functionals

Abstract: We propose a new long-range correction scheme that combines generalized-gradient-approximation (GGA) exchange functionals in density-functional theory (DFT) with the ab initio Hartree–Fock exchange integral by using the standard error function. To develop this scheme, we suggest a new technique that constructs an approximate first-order density matrix that corresponds to a GGA exchange functional. The calculated results of the long-range correction scheme are found to support a previous argument that the lack of the long-range interactions in conventional exchange functionals may be responsible for the underestimation of 4s−3d interconfigurational energies of the first-row transition metals and for the overestimation of the longitudinal polarizabilities of π-conjugated polyenes in DFT calculations.

A long-range-corrected time-dependent density functional theory

Abstract: We apply the long-range correction (LC) scheme for exchange functionals of density functional theory to time-dependent density functional theory (TDDFT) and examine its efficiency in dealing with the serious problems of TDDFT, i.e., the underestimations of Rydberg excitation energies, oscillator strengths, and charge-transfer excitation energies. By calculating vertical excitation energies of typical molecules, it was found that LC-TDDFT gives accurate excitation energies, within an error of 0.5 eV, and reasonable oscillator strengths, while TDDFT employing a pure functional provides 1.5 eV lower excitation energies and two orders of magnitude lower oscillator strengths for the Rydberg excitations. It was also found that LC-TDDFT clearly reproduces the correct asymptotic behavior of the charge-transfer excitation energy of ethylene-tetrafluoroethylene dimer for the long intramolecular distance, unlike a conventional far-nucleus asymptotic correction scheme. It is, therefore, presumed that poor TDDFT results for pure functionals may be due to their lack of a long-range orbital-orbital interaction.

Orbital optimization in the density matrix renormalization group, with applications to polyenes and β-carotene

Abstract: In previous work we have shown that the density matrix renormalization group (DMRG) enables near-exact calculations in active spaces much larger than are possible with traditional complete active space algorithms. Here, we implement orbital optimization with the DMRG to further allow the self-consistent improvement of the active orbitals, as is done in the complete active space self-consistent field (CASSCF) method. We use our resulting DMRG-CASSCF method to study the low-lying excited states of the all-trans polyenes up to C_(24)H_(26) as well as β-carotene, correlating with near-exact accuracy the optimized complete π-valence space with up to 24 active electrons and orbitals, and analyze our results in the light of the recent discovery from resonance Raman experiments of new optically dark states in the spectrum.

A pentanuclear iron catalyst designed for water oxidation

Abstract: Although the oxidation of water is efficiently catalysed by the oxygen-evolving complex in photosystem II (refs 1 and 2), it remains one of the main bottlenecks when aiming for synthetic chemical fuel production powered by sunlight or electricity. Consequently, the development of active and stable water oxidation catalysts is crucial, with heterogeneous systems considered more suitable for practical use and their homogeneous counterparts more suitable for targeted, molecular-level design guided by mechanistic understanding. Research into the mechanism of water oxidation has resulted in a range of synthetic molecular catalysts, yet there remains much interest in systems that use abundant, inexpensive and environmentally benign metals such as iron (the most abundant transition metal in the Earth's crust and found in natural and synthetic oxidation catalysts). Water oxidation catalysts based on mononuclear iron complexes have been explored, but they often deactivate rapidly and exhibit relatively low activities. Here we report a pentanuclear iron complex that efficiently and robustly catalyses water oxidation with a turnover frequency of 1,900 per second, which is about three orders of magnitude larger than that of other iron-based catalysts. Electrochemical analysis confirms the redox flexibility of the system, characterized by six different oxidation states between Fe(II)5 and Fe(III)5; the Fe(III)5 state is active for oxidizing water. Quantum chemistry calculations indicate that the presence of adjacent active sites facilitates O-O bond formation with a reaction barrier of less than ten kilocalories per mole. Although the need for a high overpotential and the inability to operate in water-rich solutions limit the practicality of the present system, our findings clearly indicate that efficient water oxidation catalysts based on iron complexes can be created by ensuring that the system has redox flexibility and contains adjacent water-activation sites.

The M06 suite of density functionals for main group thermochemistry, thermochemical kinetics, noncovalent interactions, excited states, and transition elements: two new functionals and systematic testing of four M06-class functionals and 12 other functionals

Abstract: We present two new hybrid meta exchange- correlation functionals, called M06 and M06-2X. The M06 functional is parametrized including both transition metals and nonmetals, whereas the M06-2X functional is a high-nonlocality functional with double the amount of nonlocal exchange (2X), and it is parametrized only for nonmetals.The functionals, along with the previously published M06-L local functional and the M06-HF full-Hartree–Fock functionals, constitute the M06 suite of complementary functionals. We assess these four functionals by comparing their performance to that of 12 other functionals and Hartree–Fock theory for 403 energetic data in 29 diverse databases, including ten databases for thermochemistry, four databases for kinetics, eight databases for noncovalent interactions, three databases for transition metal bonding, one database for metal atom excitation energies, and three databases for molecular excitation energies. We also illustrate the performance of these 17 methods for three databases containing 40 bond lengths and for databases containing 38 vibrational frequencies and 15 vibrational zero point energies. We recommend the M06-2X functional for applications involving main-group thermochemistry, kinetics, noncovalent interactions, and electronic excitation energies to valence and Rydberg states. We recommend the M06 functional for application in organometallic and inorganometallic chemistry and for noncovalent interactions.

疟原虫var基因转换速率变化导致抗原变异[英]／Paul H, Robert P, Christodoulou Z, et al//Proc Natl Acad Sci U S A

Abstract: 抗原变异可使得多种致病微生物易于逃避宿主免疫应答。表达在感染红细胞表面的恶性疟原虫红细胞表面蛋白1（PfPMP1）与感染红细胞、内皮细胞、树突状细胞以及胎盘的单个或多个受体作用，在黏附及免疫逃避中起关键的作用。每个单倍体基因组var基因家族编码约60种成员，通过启动转录不同的var基因变异体为抗原变异提供了分子基础。

Hybrid functionals based on a screened Coulomb potential

Abstract: Hybrid density functionals are very successful in describing a wide range of molecular properties accurately. In large molecules and solids, however, calculating the exact (Hartree–Fock) exchange is computationally expensive, especially for systems with metallic characteristics. In the present work, we develop a new hybrid density functional based on a screened Coulomb potential for the exchange interaction which circumvents this bottleneck. The results obtained for structural and thermodynamic properties of molecules are comparable in quality to the most widely used hybrid functionals. In addition, we present results of periodic boundary condition calculations for both semiconducting and metallic single wall carbon nanotubes. Using a screened Coulomb potential for Hartree–Fock exchange enables fast and accurate hybrid calculations, even of usually difficult metallic systems. The high accuracy of the new screened Coulomb potential hybrid, combined with its computational advantages, makes it widely applicable to large molecules and periodic systems.

A new hybrid exchange–correlation functional using the Coulomb-attenuating method (CAM-B3LYP)

Abstract: A new hybrid exchange–correlation functional named CAM-B3LYP is proposed. It combines the hybrid qualities of B3LYP and the long-range correction presented by Tawada et al. [J. Chem. Phys., in press]. We demonstrate that CAM-B3LYP yields atomization energies of similar quality to those from B3LYP, while also performing well for charge transfer excitations in a dipeptide model, which B3LYP underestimates enormously. The CAM-B3LYP functional comprises of 0.19 Hartree–Fock (HF) plus 0.81 Becke 1988 (B88) exchange interaction at short-range, and 0.65 HF plus 0.35 B88 at long-range. The intermediate region is smoothly described through the standard error function with parameter 0.33.

Long-range corrected hybrid density functionals with damped atom–atom dispersion corrections

Abstract: We report re-optimization of a recently proposed long-range corrected (LC) hybrid density functional [J.-D. Chai and M. Head-Gordon, J. Chem. Phys., 2008, 128, 084106] to include empirical atom–atom dispersion corrections. The resulting functional, ωB97X-D yields satisfactory accuracy for thermochemistry, kinetics, and non-covalent interactions. Tests show that for non-covalent systems, ωB97X-D shows slight improvement over other empirical dispersion-corrected density functionals, while for covalent systems and kinetics it performs noticeably better. Relative to our previous functionals, such as ωB97X, the new functional is significantly superior for non-bonded interactions, and very similar in performance for bonded interactions.