Methods
Hybrid QM/MM methods:
SICTWO: ONIOM(QM:MM) implementation in SICTWO supports for the AMOEBA polarizable model, the Liam Dang's polarizable model, AMBER, CHARMM, MM2, MM3, OPLS-AA, MMFF force fields, and user defined forcefields. Visit SICTWO home for more information.
Publications from SICTWO:
[3] W. M. C. Sameera, B. Senevirathne, S. Andersson, F. Maseras, G. Nyman, “ONIOM(QM:AMOEBA09) study on binding energies and binding preference of OH, HCO, and CH3 radicals on hexagonal ice (Ih)”. J. Phy. Chem. C, 2017, 121, 15223-15232.
[2] D. Sharma, W. M. C Sameera, S. Andersson, G. Nyman, M. J. Paterson, "Computational study of the interactions between benzene and crystalline ice Ih: Ground and excited states ", ChemPhysChem, 2016, 17, 4079-4089.
[1] I. Rivilla, W. M. C. Sameera, E. Alvarez, M. M. Díaz-Requejo, F. Maseras, P. J. Pérez. “Catalytic cross-coupling of diazo compounds with coinage metal-based catalysts: an experimental and theoretical study”, Dalton Trans, 2013, 42, 4132-4138. [Front cover page picture in the themed collection: Mechanistic Organometallic Chemistry]
Reaction path search methods:
Publications from the the artificial force induced reaction (AFIR) method:
[8] A. Sharma, W. M. C. Sameera, M. Jin, Masayoshi, L. Adak, C. Chiemi, T. Iwamoto, M. Kato, M. Nakamura, K. Morokuma, "DFT and AFIR Study on the Mechanism and the Origin of Enantioselectivity in Iron-Catalyzed Cross-Coupling Reactions". (Submitted) J. Am. Chem. Soc.
[7] BOOK CHAPTER: R. Ramozzi, W. M. C. Sameera, K. Morokuma, "Predicting reaction pathways from reactants", Applied Theoretical Chemistry, World scientific publishing.
Book title: Applied theoretical organic chemistry, Ed. Dean J. Tantillo (ISBN: 978-1-78634-408-3)
[6] M. Isegawa, W. M. C. Sameera, A. K. Sharma, T. Kitanosono, M. Kato, S. Kobayashi, K. Morokuma, "Copper-catalyzed Enantioselective Boron Conjugate Addition: DFT and AFIR Study on Different Selectivities of Cu(I) and Cu(II) Catalysts", ACS Catal. 2017, 7, 5370-5380.
[5] M.-C. Yang, A. K. Sharma, W. M. C. Sameera, K. Morokuma, M.-D. Su, "A Theoretical study on the addition reactions of L4M(M = Rh, Ir) and L2M(M = Pd, Pt) to Li+@C60", (In press). DOI: 10.1021/acs.jpca.7b01086
[4] REVIEW: W. M. C. Sameera, A. K. Sharma, S. Maeda, K. Morokuma, "Artificial force induced reaction method for systematic determination of complex reaction mechanisms", Chem. Rec., 16, 2016, 2349-2363.
[3] Y. Takeda, A. Kuroda, W. M. C. Sameera, K. Morokuma, S. Minakata, "Palladium-catalyzed regioselective ring-opening borylation of 2-arylaziridines with bis(pinacolato)diboron: experimental and computational studies", Chem. Sci. 2016, 7, 6141-6152. open access
[2] REVIEW: W. M. C. Sameera, S. Maeda, K. Morokuma, "Computational catalysis using the artificial force induced reaction (AFIR) method", Acc. Chem. Res. 2016, 49, 763-773. open access
[1] W. M. C. Sameera, M. Hatanaka, T. Kitanosono, S. Kobayashi, K. Morokuma. "The Mechanism of Iron(II)-catalyzed Asymmetric Mukaiyama Aldol Reaction in Aqueous Media: Density Functional Theory and Artificial Force-Induced Reaction Study", J. Am. Chem. Soc.2015, 137, 11085-11094. open access
Hybrid QM/MM methods:
SICTWO: ONIOM(QM:MM) implementation in SICTWO supports for the AMOEBA polarizable model, the Liam Dang's polarizable model, AMBER, CHARMM, MM2, MM3, OPLS-AA, MMFF force fields, and user defined forcefields. Visit SICTWO home for more information.
Publications from SICTWO:
[3] W. M. C. Sameera, B. Senevirathne, S. Andersson, F. Maseras, G. Nyman, “ONIOM(QM:AMOEBA09) study on binding energies and binding preference of OH, HCO, and CH3 radicals on hexagonal ice (Ih)”. J. Phy. Chem. C, 2017, 121, 15223-15232.
[2] D. Sharma, W. M. C Sameera, S. Andersson, G. Nyman, M. J. Paterson, "Computational study of the interactions between benzene and crystalline ice Ih: Ground and excited states ", ChemPhysChem, 2016, 17, 4079-4089.
[1] I. Rivilla, W. M. C. Sameera, E. Alvarez, M. M. Díaz-Requejo, F. Maseras, P. J. Pérez. “Catalytic cross-coupling of diazo compounds with coinage metal-based catalysts: an experimental and theoretical study”, Dalton Trans, 2013, 42, 4132-4138. [Front cover page picture in the themed collection: Mechanistic Organometallic Chemistry]
Reaction path search methods:
Publications from the the artificial force induced reaction (AFIR) method:
[8] A. Sharma, W. M. C. Sameera, M. Jin, Masayoshi, L. Adak, C. Chiemi, T. Iwamoto, M. Kato, M. Nakamura, K. Morokuma, "DFT and AFIR Study on the Mechanism and the Origin of Enantioselectivity in Iron-Catalyzed Cross-Coupling Reactions". (Submitted) J. Am. Chem. Soc.
[7] BOOK CHAPTER: R. Ramozzi, W. M. C. Sameera, K. Morokuma, "Predicting reaction pathways from reactants", Applied Theoretical Chemistry, World scientific publishing.
Book title: Applied theoretical organic chemistry, Ed. Dean J. Tantillo (ISBN: 978-1-78634-408-3)
[6] M. Isegawa, W. M. C. Sameera, A. K. Sharma, T. Kitanosono, M. Kato, S. Kobayashi, K. Morokuma, "Copper-catalyzed Enantioselective Boron Conjugate Addition: DFT and AFIR Study on Different Selectivities of Cu(I) and Cu(II) Catalysts", ACS Catal. 2017, 7, 5370-5380.
[5] M.-C. Yang, A. K. Sharma, W. M. C. Sameera, K. Morokuma, M.-D. Su, "A Theoretical study on the addition reactions of L4M(M = Rh, Ir) and L2M(M = Pd, Pt) to Li+@C60", (In press). DOI: 10.1021/acs.jpca.7b01086
[4] REVIEW: W. M. C. Sameera, A. K. Sharma, S. Maeda, K. Morokuma, "Artificial force induced reaction method for systematic determination of complex reaction mechanisms", Chem. Rec., 16, 2016, 2349-2363.
[3] Y. Takeda, A. Kuroda, W. M. C. Sameera, K. Morokuma, S. Minakata, "Palladium-catalyzed regioselective ring-opening borylation of 2-arylaziridines with bis(pinacolato)diboron: experimental and computational studies", Chem. Sci. 2016, 7, 6141-6152. open access
[2] REVIEW: W. M. C. Sameera, S. Maeda, K. Morokuma, "Computational catalysis using the artificial force induced reaction (AFIR) method", Acc. Chem. Res. 2016, 49, 763-773. open access
[1] W. M. C. Sameera, M. Hatanaka, T. Kitanosono, S. Kobayashi, K. Morokuma. "The Mechanism of Iron(II)-catalyzed Asymmetric Mukaiyama Aldol Reaction in Aqueous Media: Density Functional Theory and Artificial Force-Induced Reaction Study", J. Am. Chem. Soc.2015, 137, 11085-11094. open access