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Masato KOBAYASHI

Lecturer, Quantum Chemistry Laboratory, Department of Chemistry,
Faculty of Science, Hokkaido University

Hokkaido University School of Science Kita 10, Nishi 8, Kita-ku, Sapporo 
060-0810 Japan

Kobayashi 

 

Profile

Mar. 2003 B. S., Waseda University
Mar. 2004 M. S., Waseda University
Mar. 2007 Ph.D. (Science), Waseda University (Prof. H. Nakai)
Apr. 2006 JSPS Fellow DC2 (up to Mar. 2007)
Apr. 2007 JSPS Fellow PD (up to Mar. 2008)
Oct. 2007 Visiting Scholar, Eötvös Loránd University in Hungary (up
to Dec. 2007) (Prof. P.R. Surján)
Apr. 2008 Visiting Lecturer, Faculty of Science and Engineering,
Waseda University (up to Mar. 2012)
Apr. 2008 Research Fellow, Institute for Molecular Science (up to
Mar. 2012)
Apr. 2012 Assistant Professor, Waseda Institute for Advanced Study,
Waseda University (up to Feb. 2014)
Mar. 2014 Assistant Professor, Faculty of Science, Hokkaido University (up to Jun. 2017)
Apr. 2014 Project Assistant Professor, Elements Strategy Initiative for Catalysts and Batteries (ESICB), Kyoto University (up to Jul. 2017)
Dec. 2015 PRESTO Researcher, Japan Science and Technology Agency (up to Mar. 2019)
Jul. 2017 Lecturer, Faculty of Science, Hokkaido University
Aug. 2018 Project Lecturer, Elements Strategy Initiative for Catalysts and Batteries (ESICB), Kyoto University
Apr. 2019 Concurrent Lecturer, WPI-ICReDD, Hokkaido University

 

Publications

2019

R9. “Essence of Hartree-Fock(-Roothaan) method” (Japanese)
M. Kobayashi, Frontier 1 (2), 5-20 (2019).
R8. “Machine Learning Applied to Yield or Activation Factor Prediction for Catalytic Reactions” (Japanese)
M. Kobayashi, Chemistry and Chemical Industry 72 (5), 422 (2019).
R7. “Analysis and Prediction for Metal Nanocluster Catalyst Systems Using High-Throughput Quantum Chemical Calculation Techniques and Informatics” (Japanese)
M. Kobayashi, Ensemble 21 (1), 22-28 (2019).
50. “Combined Automated Reaction Pathway Searches and Sparse Modeling Analysis for Catalytic Properties of Lowest Energy Twins of Cu13
T. Iwasa, T. Sato, M. Takagi, M. Gao, A. Lyalin, M. Kobayashi, K.-i. Shimizu, S. Maeda, and T. Taketsugu, J. Phys. Chem. A 123 (1), 210-217 (2019).
49. “Dispersion Interaction and Crystal Packing Realize the Ultralong C–C Single Bond: A Theoretical Study on Dispirobis(10-methylacridan) Derivatives”
Y. Kuroda, M. Kobayashi, and T. Taketsugu, Chem. Lett. 48 (2), 137-139 (2019).
B3. “Large Scale Quantum Chemical Calculation”
K. Ishimura and M. Kobayashi, in “The Art of High Performance Computing for Computational Science, Vol. 2”, Ed. by M. Geshi (Springer), 159-201 (2019).

2018

48. Automated Error Control in Divide-and-Conquer Self-Consistent Field Calculations
M. Kobayashi, T. Fujimori, and T. Taketsugu, J. Comput. Chem. 38, 909-916 (2018) [featured as a cover article].
47. All-Electron Relativistic Computations on the Low-Lying Electronic States, Bond Length, and Vibrational Frequency of CeF Diatomic Molecule with Spin-Orbit Coupling Effects
Y. Kondo, M. Kobayashi, T. Akama, T. Noro, and T. Taketsugu, J. Comput. Chem. 38, 964-972 (2018).
R6. “Application of Informatics Techniques to Quantum Chemical Calculations of Catalyst and Surface Adsorption Systems” (Japanese)
M. Kobayashi, Chemical Industry 69, 27-32 (2018).

2017

46. “Enhanced Luminescence of Asymmetrical Seven-Coordinate EuIII Complexes Including LMCT Perturbation”
K. Yanagisawa, Y. Kitagawa, T. Nakanishi, T. Seki, T. Akama, M. Kobayashi, T. Taketsugu, H. Ito, K. Fushimi, and Y. Hasegawa, Eur. J. Inorg. Chem. 2017, 3843-3848 (2017).
B2. HPC Technology for Computational Science 2 (Japanese)
M. Geshi (ed.) (coauthored by M. Kobayashi), Osaka University Press, 2017.

2016

45. Divide-and-Conquer Hartree-Fock-Bogoliubov Method and Its Application to Conjugated Diradical Systems
M. Kobayashi and T. Taketsugu, Chem. Lett. 45, 1268-1270.
44. Three Pillars for Realizing Quantum Mechanical Molecular Dynamics Simulations of Huge Systems: Divide-and-Conquer, Density Functional Tight-Binding, and Massively Parallel Computation
H. Nishizawa, Y. Nishimura, M. Kobayashi, S. Irle, and H. Nakai, J. Comput. Chem. 37, 1983-1992 (2016).
R5. O(N) Electronic Structure Calculation Using Divide-and-Conquer (DC) Method and Its Application to MD Simulations (Japanese)
M. Kobayashi, Ensemble (Mol. Sim. Soc. Jpn.) 18, 90-94 (2016).
43. Spin-Orbit Coupling Effects on Low-Lying Electronic States of PtCN/PtNC and PdCN/PdNC
Y. Ono, Y. Kondo, M. Kobayashi, and T. Taketsugu, Chem. Lett. 45, 478-480 (2016).
41. Coordination Phenomena of Alkali Metal, Alkaline Earth Metal, and Indium Ions with the 1,3,6-Naphthalenetrisulfonate Ion in Protic and Aprotic Solvents
X. Chen, M. Hojo, Z. Chen, and M. Kobayashi, J. Mol. Liq. 214, 369-377 (2016).

2015

B1. An Easy Guide to Quantum Chemistry Calculations, new edition (Japanese)
K. Hirao (supervisor), T. Taketsugu (ed.) (coauthored by M. Kobayashi), Kodansha, 2015.
42. Mechanisms of Ligand Exchange and Ligand Coupling Reactions of Sb and Te Compounds (Japanese)
M. Kobayashi, Y. Kuroda, K.-y. Akiba, and T. Taketsugu, J. Comput. Chem. Jpn. 14, 199-200 (2015).
40. Theoretical Study on the Ligand Coupling Reaction of Hypervalent Pentacoordinate Antimony Compounds
M. Kobayashi, Y. Kuroda, K.-y. Akiba, and T. Taketsugu, Bull. Chem. Soc. Jpn. 88, 1584-1590 (2015).
39. Second-Order Møller-Plesset Perturbation (MP2) Theory at Finite Temperature: Relation with Surján’s Density Matrix MP2 and Its Application to Linear-Scaling Divide-and-Conquer Method
M. Kobayashi and T. Taketsugu, Theor. Chem. Acc. 134, 107 (2015).
38. Seven-Coordinate Luminophores: Brilliant Luminescence of Lanthanide Complexes with C3v Geometrical Structures
K. Yanagisawa, T. Nakanishi, Y. Kitagawa, T. Seki, T. Akama, M. Kobayashi, T. Taketsugu, H. Ito, K. Fushimi, and Y. Hasegawa, Eur. J. Inorg. Chem. 2015, 4769-4774 (2015).

2014

37. Specific Coordination Phenomena of Alkaline Earth Metal Ions with Aromatic Sulfonate Ions in Alcohols and Binary Solvents of Acetonitrile-Alcohols
X. Chen, K. Ayabe, M. Hojo, Z. Chen, and M. Kobayashi, J. Mol. Liq. 199, 445-453 (2014).
36. Gradient of Molecular Hartree-Fock-Bogoliubov Energy with a Linear Combination of Atomic Orbital Quasiparticle Wave Functions
M. Kobayashi, J. Chem. Phys. 140 (8), 084115 (2014).
35. “Theoretical Study on the Ligand Exchange Reactions of Hypervalent Antimony and Tellurium Compounds”
M. Kobayashi and K.-y. Akiba, Organometallics 33 (5), 1218-1226 (2014).
34. Conductometric and UV-Visible Spectroscopic Studies on the Strong Association between Polysulfonic or Dicarboxylic Acids and Their Conjugate Anions in Acetonitrile
M. Hojo, Y. Kondo, K. Zei, K. Okamura, Z. Chen, and M. Kobayashi, Bull. Chem. Soc. Jpn. 87 (1), 98-109 (2014).

 

2013

33. “Novel Approach to Excited-State Calculations of Large Molecules Based on Divide-and-Conquer Method: Application to Photoactive Yellow Protein”
T. Yoshikawa, M. Kobayashi, A. Fujii, and H. Nakai, J. Phys. Chem. B 117 (18), 5565-5573 (2013).
32. “An Effective Energy Gradient Expression for Divide-and-Conquer Second-Order Møller-Plesset Perturbation Theory”
M. Kobayashi and H. Nakai, J. Chem. Phys. 138 (4), 044102 (2013).
30. “Divide-and-Conquer Electronic-Structure Study on the Mechanism of the West Nile Virus NS3 Protease Inhibitor”
P. Saparpakorn, M. Kobayashi, and H. Nakai, Bull. Chem. Soc. Jpn. 86 (1), 67-74 (2013).
29. “Divide-and-Conquer-Based Quantum Chemical Study for Interaction between HIV-1 Reverse Transcriptase and MK-4965 Inhibitor”
P. Saparpakorn, M. Kobayashi, S. Hannongbua, and H. Nakai, Int. J. Quantum Chem. 113 (4), 510-517 (2013).
28. “Divide-and-Conquer-Based Symmetry Adapted Cluster Method: Synergistic Effect of Subsystem Fragmentation and Configuration Selection”
T. Yoshikawa, M. Kobayashi, and H. Nakai, Int. J. Quantum Chem. 113 (3), 218-223 (2013).
26. “Accelerating Convergence in the Antisymmetric Product of Strongly Orthogonal Geminals Method”
M. Tarumi, M. Kobayashi, and H. Nakai, Int. J. Quantum Chem. 113 (3), 239-244 (2013).

 

2012

P3. “Development of Divide-and-Conquer Quantum Chemical Code for Biomolecules and Nano Materials”
M. Kobayashi, P. Saparpakorn, and H. Nakai, 31st Annual Conference of Japan Society for Simulation Technology, 330-333 (2012).
R4. “How Does It Become Possible to Treat Delocalized and/or Open-Shell Systems in Fragmentation-Based Linear-Scaling Electronic Structure Calculation? The Case of the Divide-and-Conquer Method”
M. Kobayashi and H. Nakai, Phys. Chem. Chem. Phys. 14, 7629-7639 (2012).
31. “Generalized Møller–Plesset Multiconfiguration Perturbation Theory Applied to an Open-Shell Antisymmetric Product of Strongly Orthogonal Geminals Reference Wave Function”
M. Tarumi, M. Kobayashi, and H. Nakai, J. Chem. Theory Comput. 8 (11), 4330-4335 (2012).
27. “Dynamic Hyperpolarizability Calculations of Large Systems: The Linear-Scaling Divide-and-Conquer Approach”
M. Kobayashi, T. Touma, and H. Nakai, J. Chem. Phys. 136 (8), 084108 (2012).

 

2011

P2. “Linear-Scaling Electronic Structure Calculation Program Based on Divide-and-Conquer Method”
H. Nakai and M. Kobayashi, Proc. Comput. Sci. 4, 1145-1150 (2011).
R3. Divide-and-Conquer Quantum Chemical Calculation Method for Nano-Science (Japanese)
M. Kobayashi and H. Nakai, Bull. Nano Sci. Tech. 9 (2), 85-89 (2011).
R2. Divide-and-Conquer Approaches to Quantum Chemistry: Theory and Implementation
M. Kobayashi and H. Nakai, in Linear-Scaling Techniques in Computational Chemistry and Physics: Methods and Applications, Ed. by M.G. Papadopoulos, R. Zalesny, P.G. Mezey, and J. Leszczynski (2011, Springer), pp.97-127.
25. “Linear-Scaling Divide-and-Conquer Second-Order Møller-Plesset Perturbation Calculation for Open-Shell Systems: Implementation and Application”
T. Yoshikawa, M. Kobayashi, and H. Nakai, Theor. Chem. Acc. 130 (2-3), 411-417 (2011).
24. “Finite-Field Evaluation of Static (Hyper)polarizabilities Based on the Linear-Scaling Divide-and-Conquer Method”
T. Touma, M. Kobayashi, and H. Nakai, Theor. Chem. Acc. 130 (4-6), 701-709 (2011).
23. “Two-Level Hierarchical Parallelization of Second-Order Møller-Plesset Perturbation Calculations in Divide-and-Conquer Method”
M. Katouda, M. Kobayashi, H. Nakai, and S. Nagase, J. Comput. Chem. 32 (13), 2756-2764 (2011).
22. “Reconsidering an Analytical Gradient Expression within a Divide-and-Conquer Self-Consistent Field Approach: Exact Formula and Its Approximate Treatment”
M. Kobayashi, T. Kunisada, T. Akama, D. Sakura, and H. Nakai, J. Chem. Phys. 134 (3), 034105 (2011).

 

2010

21. “Divide-and-Conquer Self-Consistent Field Calculation for Open-Shell Systems: Implementation and Application”
M. Kobayashi, T. Yoshikawa, and H. Nakai, Chem. Phys. Lett. 500 (1-3), 172-177 (2010).
20. “Generalized Møller-Plesset Partitioning in Multiconfiguration Perturbation Theory”
M. Kobayashi, Á. Szabados, H. Nakai, and P. R. Surján, J. Chem. Theory Comput. 6 (7), 2024-2033 (2010).
19. “Time-Dependent Hartree-Fock Frequency-Dependent Polarizability Calculation Applied to Divide-and-Conquer Electronic Structure Method”
T. Touma, M. Kobayashi, and H. Nakai, Chem. Phys. Lett. 485 (1-3), 247-252 (2010).
18. “Observation by UV-Visible and NMR Spectroscopy and Theoretical Confirmation of 4-Isopropyltropolonate Ion, 4-Isopropyltropolone (Hinokitiol), and Protonated 4-Isopropyltropolone in Acetonitrile”
M. Hojo, T. Ueda, M. Ike, K. Okamura, T. Sugiyama, M. Kobayashi, and H. Nakai, J. Chem. Eng. Data 55 (5), 1986-1989 (2010).

2009

R1. Electronic Structure Calculations of Giant Molecules Expand the Field of Chemistry (Japanese)
M. Kobayashi and H. Nakai, Kagaku (Chemistry) 64 (1), 12-16 (2009).
17. “Divide-and-Conquer-Based Linear-Scaling Approach for Traditional and Renormalized Coupled Cluster Methods with Single, Double, and Noniterative Triple Excitations”
M. Kobayashi and H. Nakai, J. Chem. Phys. 131 (11), 114108 (2009).
16. “Electronic Temperature in Divide-and-Conquer Electronic Structure Calculation Revisited: Assessment and Improvement of Self-Consistent Field Convergence”
T. Akama, M. Kobayashi, and H. Nakai, Int. J. Quantum Chem. 109 (12), 2706-2713 (2009).
15. “Dual-Level Hierarchical Scheme for Linear-Scaling Divide-and-Conquer Correlation Theory”
M. Kobayashi and H. Nakai, Int. J. Quantum Chem. 109 (10), 2227-2237 (2009).
14. Implementation of Divide-and-Conquer (DC) Electronic Structure Code to GAMESS Program Package (Japanese)
M. Kobayashi, T. Akama, H. Nakai, J. Comput. Chem. Jpn. 8 (1), 1-12 (2009).
12. “UV-Visble, 1H and 13C NMR Spectroscopic Studies on the Interaction between Protons or Alkaline Earth Metal Ions and the Benzoate Ion in Acetonitrile”
M. Hojo, T. Ueda, M. Ike, M. Kobayashi, and H. Nakai, J. Mol. Liq. 145 (3), 152-157 (2009).

 

2008

P1. Development of Linear-Scaling Techniques Based on Divide-and-Conquer Method (Japanese)
H. Nakai, M. Kobayashi, and T. Akama, Bull. Soc. Discrete Var. Xα 21 (1,2), 47-54 (2008).
13. “Extension of Linear-Scaling Divide-and-Conquer-Based Correlation Method to Coupled Cluster Theory with Singles and Doubles Excitations”
M. Kobayashi and H. Nakai, J. Chem. Phys. 129 (4), 044103 (2008).
11. “Application of the Sakurai-Sugiura Projection Method to Core-Excited-State Calculation by Time-Dependent Density Functional Theory”
T. Tsuchimochi, M. Kobayashi, A. Nakata, Y. Imamura, and H. Nakai, J. Comput. Chem. 29 (14), 2311-2316 (2008).

 

2007

10. “Is the Divide-and-Conquer Hartree-Fock Method Valid for Calculations of Delocalized Systems?”
T. Akama, A. Fujii, M. Kobayashi, and H. Nakai, Mol. Phys. 105 (19-22), 2799-2804 (2007).
9. “Alternative Linear-Scaling Methodology for the Second-Order Møller-Plesset Perturbation Calculation Based on the Divide-and-Conquer Method”
M. Kobayashi, Y. Imamura, and H. Nakai, J. Chem. Phys. 127 (7), 074103 (2007).
8. “Implementation of Divide-and-Conquer Method Including Hartree-Fock Exchange Interaction”
T. Akama, M. Kobayashi, and H. Nakai, J. Comput. Chem. 28 (12), 2003-2012 (2007).
7. “UV-Visible and 1H or 13C NMR Spectroscopic Studies on the Specific Interaction between Lithium Ions and the Anion from Tropolone or 4-Isopropyltropolone (Hinokitiol) and on the Formation of Protonated Tropolones in Acetonitrile or Other Solvents”
M. Hojo, T. Ueda, T. Inoue, M. Ike, M. Kobayashi, and H. Nakai, J. Phys. Chem. B 111 (7), 1759-1768 (2007).
6. “Hybrid Treatment Combining the Translation- and Rotation-Free Nuclear Orbital Plus Molecular Orbital Theory with Generator Coordinate Method: TRF-NOMO/GCM”
K. Sodeyama, H. Nishizawa, M. Hoshino, M. Kobayashi, and H. Nakai, Chem. Phys. Lett. 433 (4-6), 409-415 (2007).

 

2006

5. “Second-Order Møller-Plesset Perturbation Energy Obtained from Divide-and-Conquer Hartree-Fock Density Matrix”
M. Kobayashi, T. Akama, and H. Nakai, J. Chem. Phys. 125 (20), 204106 (2006).
4. “Implementation of Surján’s Density Matrix Formulae for Calculating Second-Order Møller-Plesset Energy”
M. Kobayashi and H. Nakai, Chem. Phys. Lett. 420 (1-3), 250-255 (2006).

 

2005

3. “Practical Performance Assessment of Accompanying Coordinate Expansion Recurrence Relation Algorithm for Computation of Electron Repulsion Integrals”
M. Katouda, M. Kobayashi, H. Nakai, and S. Nagase, J. Theor. Comput. Chem. 4 (1), 139-149 (2005).

 

2004

2. “New Recurrence Relations for the Rapid Evaluation of Electron Repulsion Integrals Based on the Accompanying Coordinate Expansion Formula”
M. Kobayashi and H. Nakai, J. Chem. Phys. 121 (9), 4050-4058 (2004).
1. “New Algorithm for the Rapid Evaluation of Electron Repulsion Integrals: Elementary Basis Algorithm”
H. Nakai and M. Kobayashi, Chem. Phys. Lett. 388 (1-3), 50-54 (2004).

 

Awards

Sep.2008 Poster Prize, WATOC 2008 (Eighth Triennial Congress of World Association of Theoretical and Computational Chemists), Sydney, Australia.
May 2009 Yoshida Award (Excellent Paper Award), Society of Computer Chemistry, Japan.
May 2011 Fellowships to Young Researchers, The Association for the Progress of New Chemistry.
Jan.2012 Poster Prize, 2nd CMSI Workshop, Sendai.

 

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