Sakaki: Molecular Theory for Science and Technology Group

Professor Sakaki leads the Molecular Theory for Science and Technology (MTST) group (http://www.moleng.kyoto-u.ac.jp/~moleng_02/) within the Department of Molecular Engineering in the University of Kyoto Graduate School of Engineering, as well as serving as Director of the FIFC. In addition to Professor Sakaki, the MTST group consists of one associate professor (Hirofumi Sato), one assistant professor (Yoshihide Nakao), nine PhD students, eight MS students, and four undergraduate students. The focus of the group is on theories of chemical reactions and solvent systems, quantum chemical design of novel reactions, chemical bonding and molecular properties, and statistical mechanics of chemical processes. Sakaki performs theoretical studies of reaction mechanisms mediated by organometallic catalysts (Ray et al. 2007; Ochi et al. 2007). His research is primarily supported by MEXT (Ministry of Education, Culture, Sports, Science, and Technology). The techniques used include CASPT2 (Complete Active Space with Second-order Perturbation Theory); the codes used are Gaussian and GAMESS-US. The primary computing resources are a PC cluster in Sakaki’s group and the Altics cluster at the Institute for Molecular Science in Okazaki. The shared memory model of the IMS Altics cluster means that the codes used by Sakaki and co-workers scale well on this machine.

Shigehiko Hayashi is an associate professor in the Theoretical Chemistry Group (TCG) (http://kuchem.kyoto-u.ac.jp/riron/indexe.html), headed by Shigeki Kato, within the Department of Chemistry in the Faculty of Sciences at Kyoto University. In addition to Professor Kato and Dr. Hayashi, this group consists of one assistant professor (Takeshi Yamamoto), one research fellow (Atsushi Yamashiro), twelve PhD students, six MS students, and five undergraduate researchers. Hayashi provided an overview of the TCG research, which could be summarized as chemical reactions in various environments (Hayashi and Kato 1998; Higashi, Hayashi, and Kato 2007; Yamamoto and Kato 2007)—in the gas phase, where the main tool is quantum dynamics; in solution, where the main tools are integral equation methods and MD; and for proteins, where the main tools are hybrid QM/MM and MD.

Masahiro Ehara is an associate professor in the research group of Hiroshi Nakatsuji (http://www.sbchem.kyoto-u.ac.jp/nakatsuji-lab/english/index.htm) in the Department of Synthetic Chemistry and Biological Chemistry within the Graduate School of Engineering. Nakatsuji is also affiliated with the FIFC. In the 1970s, Nakatsuji and Hirao developed the symmetry adapted cluster (SAC) method (Nakatsuji and Hirao 1977; Hirao and Nakatsuji 1978a and b) for the ground states of closed and open-shell electronic structures that was subsequently generalized to the SAC-CI (SAC-configuration interaction) method for excited states by Nakatsuji (1978, 1979a and b). Much of the work in the Nakatsuji group involves further development of the SAC-CI method, including using gradients of the SAC-CI energies (yielding forces) to study dynamics involving ground and excited states, and the application of these methods to increasingly complex systems. The original SAC-CI codes were in-house codes, but they are now available in Gaussian. A guide to the use of SAC-CI is available at the Nakatsuji group website, http://www.sbchem.kyoto-u.ac.jp/nakatsuji-lab/sacci.html. Ehara focused on the application of SAC-CI to photofunctional materials—specifically, an artificial fluorescent probe used as a biological chemosensor with emphasis on the photoinduced electron transfer (PET) mechanism, and organic light-emitting diodes (OLEDs) with emphasis on excited-state dynamics and conformational effects. Ehara demonstrated the superiority of SAC-CI as a methodology for the study of these complex systems.

Kyoto University has a long history in theoretical chemistry and computational quantum chemistry, including the Nobel-prize-winning work of Kenichi Fukui. This tradition is alive and well at Kyoto University, as was demonstrated by the presentations to the WTEC delegation. The work presented was all first-class. Researchers rely on a combination of in-house and external (e.g., IMS) computational resources to accomplish their work. There is clearly a trend towards nanoscience and biological applications in all of the work presented. The WTEC team’s hosts were generally upbeat about the current state of funding in Japan for computational research such as theirs.

Dapprich, S., I. Komaromi, K.S. Byun, K. Morokuma, and M.J. Frisch. 1999. A new ONIOM implementation in Gaussian98. Part I. The calculation of energies, gradients, vibrational frequencies and electric field derivatives. Journal of Molecular Structure-Theochem 462:1-21.

Froese, R.D.J., and K. Morokuma. 1999. Accurate calculations of bond-breaking energies in C-60 using the three-layered ONIOM method. Chemical Physics Letters 305:419-424.

Hayashi, S., and S. Kato. 1998. Solvent effect on intramolecular long-range electron-transfer reactions between porphyrin and benzoquinone in an acetonitrile solution: Molecular dynamics calculations of reaction rate constants. Journal of Physical Chemistry A 102:3333-3342.

Higashi, M., S. Hayashi, and S. Kato. 2007. Transition state determination of enzyme reaction on free energy surface: Application to chorismate mutase. Chemical Physics Letters 437:293-297.

Hirao, K., and H. Nakatsuji. 1978a. Cluster expansion of wavefunction — Open-shell orbital theory including electron correlation. Journal of Chemical Physics 69:4548-4563.

———. 1978b. Cluster expansion of wavefunction — Structure of closed-shell orbital theory. Journal of Chemical Physics 69:4535-4547.

Irle, S., G.S. Zheng, M. Elstner, and K. Morokuma. 2003. Formation of fullerene molecules from carbon nanotubes: A quantum chemical molecular dynamics study. Nano Letters 3:465-470.

Irle, S., Z. Wang, G.S. Zheng, K. Morokuma, and M. Kusunoki. 2006. Theory and experiment agree: Single-walled carbon nanotube caps grow catalyst-free with chirality preference on a SiC surface. Journal of Chemical Physics 125.

Morokuma, K. 2002. New challenges in quantum chemistry: quests for accurate calculations for large molecular systems. Philosophical Transactions of the Royal Society of London Series a-Mathematical Physical and Engineering Sciences 360:1149-1164.

Nakatsuji, H. 1978. Cluster expansion of wavefunction — Excited-states. Chemical Physics Letters 59:362-364.

Nakatsuji, H. 1979a. Cluster expansion of the wavefunction — Calculation of electron correlations in ground and excited-states by SAC and SAC Ci theories. Chemical Physics Letters 67:334-342.

———. 1979b. Cluster expansion of the wavefunction — Electron correlations in ground and excited-states by SAC (Symmetry-Adapted-Cluster) and SAC Ci theories. Chemical Physics Letters 67:329-333.

Nakatsuji, H. and K. Hirao. 1997. Cluster expansion of wavefunction — Pseudo-orbital theory applied to spin correlation. Chemical Physics Letters 47:569-571.

Ochi, N., Y. Nakao, H. Sato, and S. Sakaki. 2007. Theoretical study of C-H and N-H sigma-bond activation reactions by titinium(IV)-imido complex. Good understanding based on orbital interaction and theoretical proposal for N-H sigma-bond activation of ammonia. Journal of the American Chemical Society 129: 8615-8624.

Ray, M., Y. Nakao, H. Sato, and S. Sakaki. 2007. Theoretical study of tungsten eta(3)-Silaallyl/eta(3)-Vinylsilyl and vinyl silylene complexes: Interesting bonding nature and relative stability. Organometallics 26:4413-4423.

Svensson, M., S. Humbel, R.D.J. Froese, T. Matsubara, S. Sieber, and K. Morokuma. 1996. ONIOM: A multilayered integrated MO+MM method for geometry optimizations and single point energy predictions. A test for Diels-Alder reactions and Pt(P(t-Bu)(3))(2)+H-2 oxidative addition. Journal of Physical Chemistry 100:19357-19363.

Wang, Z., S. Irle, G. Zheng, M. Kusunoki, and K. Morokuma. 2007. Carbon nanotubes grow on the C face of SiC (000(1)over-bar) during sublimation decomposition: Quantum chemical molecular dynamics simulations. Journal of Physical Chemistry C 111:12960-12972.

Westmoreland, P.R., P.A. Kollman, A.M. Chaka, P.T. Cummings, K. Morokuma, M. Neurock, E.B. Stechel, and P. Vashishta 2002. Applying molecular and materials modeling. Dordrecht, Holland: Kluwer Academic Publishers.

Yamamoto, T., and S. Kato. 2007. Ab initio calculation of proton-coupled electron transfer rates using the external-potential representation: A ubiquinol complex in solution. Journal of Chemical Physics 126.

Zheng, G.S., S. Irle, and K. Morokuma. 2005. Towards formation of buckminsterfullerene C-60 in quantum chemical molecular dynamics. Journal of Chemical Physics 122.

Zheng, G.S., Z. Wang, S. Irle, and K. Morokuma. 2007. Quantum chemical molecular dynamics study of “Shrinking” of Hot Giant fullerenes. Journal of Nanoscience and Nanotechnology 7:1662-1669.

Dr. Takao Usami, General Manager of Polymer Lab and Board Member, MCRC (location: Yokkaichi); Email: 3700460@cc.m-kagaku.co.jp

Dr. Shinichiro Nakamura, Mitsubishi Chemical Research Fellow and Technology Platform Leader, Fundamental Technology Division, MCRC
(location: Yokohama); Email: shindon@rsi.co.jp

Akio Horiguchi, Production Technology Laboratory and General Manager of Yokkaichi Laboratory, MCRC

Dr. Takeshi Ishikawa, Senior Researcher, Polymer Laboratory, MCRC

Jun Endo, Senior Research Associate, Polymer Laboratory, MCRC

Dr. Tomohisa Nakamura, Group Manager, Planning and Coordination Office, MCRC (location: Yokohama); Email: 2203789@cc.m-kagaku.co.jp

Dr. Yuan Chen, Senior Research Associate, Polymer Laboratory, MCRC
(location: Yokkaichi); Email: 8909684@cc.m-kagaku.co.jp

BACKGROUND

Mitsubishi Chemical Corporation (MCC, http://www.m-kagaku.co.jp/index_en.htm) is one of three subsidiaries of Mitsubishi Chemical Holdings Company (MCHC, http://www.mitsubishichem-hd.co.jp/english/index.html), created in 2005. MCC has ten domestic manufacturing plants (at Kurosaki, Yokkaichi, Naoetsu, Mizushima, Sakaide, Kashima/Tobu Zone, Kashima/Hasaki Zone, Tsukuba, Matsuyama, and Odawara); two central research centers (at Yokohama and Tsukuba); plus three additional plant-based research activities (at the Kurosaki, Yokkaichi, and Mizushima locations); and it has major overseas subsidiaries and offices in the United States, Europe, Hong Kong, Singapore, Thailand, and China. MCHC had annual sales of ¥26 trillion in 2006, of which 47% were in petrochemicals, 20% in performance products, 15% in functional products, and 12% in health care.

The Mitsubishi Chemical Group Science and Technology Research Center (MCRC) is the corporate research center for MCC. It has approximately 3000 R&D staff, with its main location (comprising approximately 1100 R&D staff) at the Yokohama Research Center, the location of the WTEC visit. The majority of the research conducted by MCRC (~90%) is focused on healthcare and performance materials businesses. Researchers from the polymer research group, located in Yokkaichi, also participated in the WTEC visit (see location information in hosts section above). MCRC has established a number of strategic partnerships with academic institutions, both within Japan and in other countries (specifically, at MIT and UC-Santa Barbara in the United States, Dalian University of Technology in China, and Imperial College in the U.K.)

R&D ACTIVITIES

The MCRC research activities presented to the WTEC visitors were focused in areas of interest for the WTEC panelists—specifically, SBES activities.

The first presentation, by Akio Horiguchi, focused on the use of SBES tools to design, construct, and operate the optimum process. In particular, MCRC uses largely commercial computational fluid dynamics (CFD), finite-element method (FEM), and process modeling and simulation (PMS) codes individually and in combination to design and optimize chemical processes and plants. Process design relied extensively in the past on experimental methods (particularly bench-scale and pilot-plant-scale methods) for verification, but as simulation methods have become more sophisticated, there is less reliance on experiment. MCRC primarily uses commercial software (90%) such as Aspen Tech and gPROMS for process-level modeling and STAR CD and FLUENT for CFD. Examples were given of MCRC researchers coupling software packages to obtain more detailed and reliable models/simulations—for example, modeling a multitube reactor by combining CFD with gPROMS (via in-house Fortran code) to couple flow and reaction. Most of the calculations are performed on a 100-core blade server. MCRC researchers perform sensitivity analysis by performing as many as 100 runs with parametric variation in design variables and other disturbances (such as feedstock purity and temperature). Since five years ago, MCC management has become comfortable with relying on the predictions of simulation studies for the design and optimization of chemical processes. Challenges for this group are the cost of software licenses, availability of sufficient computational resources, and the difficulty of linking software packages that were not designed for interoperability.

The second presentation, by Takeshi Ishikawa and Jun Endo, focused on MCRC’s efforts in polymer modeling. The goal of this effort is to be able to relate molecular structure to polymer properties, including rheology, in a methodology that is truly multiscale (i.e., both upscaling from the molecular level to macroscopic properties, and downscaling from desirable/customer-prescribed macroscopic properties to the corresponding chemical architecture). For equilibrium properties (thermodynamics and structure), Jun Endo described MCRC’s effort over a three-year period to develop a capability to relate molecular structure and properties, based on a combination of the molecular self-consistent polymer reference interaction site model (SC-PRISM) and self-consistent field (SCF) theories, utilizing the expertise of David Wu at the Colorado School of Mines and Dilip Gersappe at State University of New York at Stony Brook, respectively. This in-house software is unique to MCRC. The effort to develop this capability was the result of MCRC not obtaining the capability it hoped for from the Octa project (http://octa.jp). Unlike, for example, molecular dynamics simulations, SC-PRISM and SCF methods are not heavily computational. Much of the rheology modeling, reported by Takeshi Ishikawa, is based on the primitive chain network model developed by Yuichi Masubuchi (http://masubuchi.jp/), now at Kyoto University. In collaboration with Kyushu University, MCRC has developed its own CFD/FEM software for polymer process processing, to apply to problems such as twin-screw extrusion and polymer film blowing.

The third and final presentation was given by Shinichiro Nakamura describing activities of the Computational Science Laboratory (CSL) of MCRC. The CSL consists of ~17 members (almost all holding doctorates), and it has in-house computing capabilities consisting of CSL-built clusters of various sizes, the largest containing 800 CPUs. CSL also uses the TSUBAME machine (http://www.gsic.titech.ac.jp) operated by the Global Scientific Information and Computing Center (GSIC) at the Tokyo Institute of Technology. In the latest Top 500 ranking (http://www.top500.org) of computing speeds (based on actual speeds executing the LINPACK benchmark), TSUBAME is ranked 14th overall and first in Asia. Nakamura gave four examples of research accomplishments by the CSL:

10. 
    Design of a robust (nonphotodegrading) dye for use in printing (Kobayashi et al. 2007)
    
11. 
    Design of a high-quantum-yield yttrium oxysulfide phosphor for use in television sets (Mikami and Oshiyama 1998; 1999; and 2000; Mikami et al. 2002)
    
12. 
    Finding an effective additive to improve the performance of Li-ion batteries (Wang, Nakamura, Tasaki, and Balbuena 2002; Wang, Nakamura, Ue, and Balbuena 2001)
    
13. 
    Development of a new methodology for protein NMR (Gao et al. 2007) based on calculating the NMR shift using the fragment molecular orbital (FMO) methodology developed by Kazuo Kitaura for large-scale ab initio calculations.
    

MCRC has a broad portfolio of SBES research, ranging from fundamental efforts publishable in the general scientific and engineering literature, to highly focused proprietary research that directly impacts current and near-future manufacturing activities of MCC and MCHC. Much computing is done in-house with commercial and community-based codes on in-house clusters, although some of the most demanding calculations are performed on external supercomputers. Adapting commercial codes to provide more detailed models through integration of their inputs and outputs is one of the features of the research being performed at MCRC.

Gao, Q., S. Yokojima, T. Kohno, T. Ishida, D.G. Fedorov, K. Kitaura, M. Fujihira, and S. Nakamura. 2007. Ab initio NMR chemical shift calculations on proteins using fragment molecular orbitals with electrostatic environment. Chemical Physics Letters 445:331-339.

Gonze, X., J.M. Beuken, R. Caracas, F. Detraux, M. Fuchs, G.M. Rignanese, L. Sindic, M. Verstraete, G. Zerah, F. Jollet, M. Torrent, A. Roy, M. Mikami, P. Ghosez, J.Y. Raty, and D.C. Allan. 2002. First-principles computation of material properties: The ABINIT software project. Computational Materials Science 25:478-492.

Ishikawa, T. S. Kihara, and K. Funats. 2000. 3-D Numerical simulations of nonisothermal flow in co-rotating twin screw extuders. Polymer Engineering and Science 40:357.

Ishikawa, T., F. Nagano, T. Kajiwara, and K. Funatsu. 2006. Tip-clearance effect on mixing performance of twin screw extruders. International Polymer Processing 11:354.

Ishikawa, T., T. Amano, S. Kihara, and F. Kazumori. 2002. Flow patterns and mixing mechanisms in the screw mixing element of a co-rotating twin-screw extruder. Polymer Engineering and Science 42:925

Kobayashi, T., M. Shiga, A. Murakami, and S. Nakamura. 2007. Ab initio study of ultrafast photochemical reaction dynamics of phenol blue. Journal of the American Chemical Society 129:6405-6424.

Mikami, M., and A. Oshiyama. 1998. First-principles band-structure calculation of yttrium oxysulfide. Physical Review B 57:8939-8944.

———. 1999. First-principles study of intrinsic defects in yttrium oxysulfide. Physical Review B 60:1707-1715.

———. 2000. First-principles study of yttrium oxysulfide: Bulk and its defects. Journal of Luminescence 87 9:1206-09.

Mikami, M., S. Nakamura, M. Itoh, K. Nakajima, and T. Shishido. 2002. Lattice dynamics and dielectric properties of yttrium oxysulfide. Physical Review B 65:094302-1-4.

Wang, Y.X., S. Nakamura, K. Tasaki, and P.B. Balbuena. 2002. Theoretical studies to understand surface chemistry on carbon anodes for lithium-ion batteries: How does vinylene carbonate play its role as an electrolyte additive? Journal of the American Chemical Society 124:4408-4421.

Wang, Y.X., S. Nakamura, M. Ue, and P.B. Balbuena. 2001. Theoretical studies to understand surface chemistry on carbon anodes for lithium-ion batteries: Reduction mechanisms of ethylene carbonate. Journal of the American Chemical Society 123:11708-11718
Site: Nissan Research Center, Fuel Cell Laboratory

1, Natsushima-cho, Yokosuka-shi

Kanagawa 237-8523, Japan
Date Visited: December 7, 2007
WTEC Attendees: D. Nelson (report author), L. Petzold, T. Arsenlis, C. Cooper
Hosts: Dr. Kazuhiko Shinohara, Senior Manager, Fuel Cell Laboratory
Email: k-shino@mail.nissan.co.jp

Dr. Kev Adjemian, Manager Fuel Cell Laboratory

Dr. Shyam Kocha, Manager Fuel Cell Laboratory

Kazuo Nagashima, Asst. Manager, Fuel Cell Laboratory

Dr. Noboru Yamauchi, Fuel Cell Laboratory

Mitsutaka Abe, Fuel Cell Laboratory

Yuichiro Tabuchi, Fuel Cell Laboratory

Nissan Research Center conducts wide-ranging R&D on vehicle technology. Headquarters of the Research Center are currently in Tokyo but will be moved to Yokohama. This visit focused on the company’s research on fuel cells for vehicular applications. Development is done at the Kanagawa technical center for advanced engineering; Nissan’s testing grounds are mostly in Kanagawa Prefecture

Nissan is pursuing fuel cell vehicles because the company promises to reduce CO₂ emissions and because renewable fuels can be used to produce the necessary hydrogen. The Nissan power train roadmap includes, in the short-term, high-efficiency internal combustion engines (ICE), and in the mid- and long-term, introduction of hybrid electric vehicles (HEV) and early introduction of electric vehicles (EV) and fuel cell vehicles (FCV.)

Nissan FCV Development Status

FCV Research began in 1996, with the first actual FCV in 2001. Initial fuel-cell stacks were procured from suppliers. In 2004 Nissan introduced its own stack as well as a high-pressure in-vehicle H₂ storage tank using carbon fiber and aluminum to achieve 10K psi. The Nissan FC stack reduces size, weight, and cost compared with the supplier’s version. In 2005, the company placed its first FCV on lease. Its cruising range is the same as for a regular car. Subzero temperature startup is not possible. The car uses a Li-ion battery for acceleration augmentation. Nissan and NEC have a joint venture in Li-ion cells.

FCV development issues include performance, cost reduction, durability, and H₂ storage systems. Basic research issues include reaction mechanism, catalyst selection and processing, proton and H₂O transport. Research on new FC materials includes a non-Platinum catalyst and new polymer membranes. Infrastructure issues include H₂ production and distribution. The primary fuel cell target is a polymer electrode membrane, or proton exchange membrane (PEM) type.

Most Nissan research in this area focuses on the membrane-electrode assembly (MEA). Durability improvements include reduced degradation caused by operation modes (start-stop, load cycle, idle) and reduced degradation by environment (temperature, air pollution). A serious problem is that Pt migrates from the electrode into the membrane, degrading cell performance. Cost reduction focuses on reducing the volume of Pt (by a factor of one-tenth), cost reduction by innovative material substitution, and system simplification.