CURRENT RESEARCH INTERESTS AND PUBLICATION IN 2000-2006

The principle theme of research of the Morokuma group is theoretical/computational studies of chemical reactions and electronic structure of molecular systems of all sorts, from elementary reaction dynamics of small gas phase molecules through catalyses to reactions of nanosystems and biomolecular systems. Major tools of research used in our studies are ab initio and density functional molecular orbital methods as well as our own hybrid method, ONIOM, supplemented with classical and quantum molecular dynamics and statistical theories of chemical reactions.

Research Area 1. Mechanisms and Dynamics of Simple Gas Phase Elementary and Photochemical Reactions

Potential energy surfaces for elementary reactions, including photodissociation and ion-molecule reactions, of small gas phase molecules are studied in connection to upper atmosphere (ionosphere, space-shuttle reentry) and lower atmosphere (air pollution) chemistry as well as combustion reactions. In these reactions, a special attention is paid to non-adiabatic processes involving transition between potential energy surfaces. We are also in multi-university teams developing iodine chemical laser systems, and are performing theoretical computations on elementary chemical reactions involved in chemical laser systems.

  Profile of the PESs for charge transfer reaction:
  O+ (4S) + C2H2 (1Sg+) → O (1D) + C2H2+ (2Pu). (Reference: Paper #465)

441.  L. Kaledin, and K. Morokuma, An ab initio direct-trajectory study of the photodissociation of ClOOCl, J. Chem. Phys., 113, 5750-5762 (2000).

442.  W. Eisfeld and K. Morokuma, A detailed study on the symmetry breaking and its effect on the potential surface of NO₃, J. Chem. Phys., 113 , 5587-5597 (2000).

443.  S. Irle and K. Morokuma, A molecular orbita l study on H and H₂ elimination pathways from methane, ethane and propane, J. Chem. Phys., 113, 6139-6148 (2000).

447.  A. Kaledin, S. Skokov, J. M. Bowman and K. Morokuma^, Theoretical stud y of the photoelectron spectroscopy of the IHBr and IDBr anions, J. Chem. Phys. , 113, 9479-9487 (2000).

452.  A. L. Kaledin, J. Seong and K. Morokuma, Predominance of Non-equilibrium Dynamics in the Photodissociation of Ketene in the Triplet State, J. Phys. Chem. A, 105, 2731-2737 (2001).

453.  S. Irle and K. Morokuma, Ab initio investigation of the potential energy profile s of gas phase CH₄ + O₂⁺ (²P_g) reaction system, J. Chem. Phys., 114, 6119-6127 (2001).

460.  J. M. Bowman, S. Irle, K. Morokuma, and A. Wodtke, Dipole moments of highly vibrationally excited HCN: theoretical prediction of an experimental diagnostic for delocalized states. J. Chem. Phys., 114, 7923-7934 (2001).

461.  W. Eisfeld and K. Morokuma, Ab initio investigation of the vertical and adiabatic excitation spectra of NO₃, J. Chem. Phys., 114, 9430-9440 (200 1).

463.  S. Re and K. Morokuma, An ONIOM Study of Chemical Reactions in Micro-solvation Cluster: (H₂O)_nCH₃Cl + OH^–( H₂O)_m (n+m=1,2), J. Phys. Chem. A, 105, 7185-7197 (2001).

465.  K. Fukuzawa, T. Matsushita, K. Morokuma, D. J. Levandier, Y. Chiu, R. A. Dressler, E. Murad, A. Midey, S. Williams, and A. A. Viggiano, An ab initio and experimental study of vibrational effect s in low energy O⁺ + C₂H₂ charge-transfer coll isions, J. Chem. Phys., 115, 3184-3194 (2001). 

481.  G. S. Tschumper, M. C. Heaven and K. Morokuma, An ab initio Excursion on the Lowest 18 E lectronic Surfaces o f the NCl + NCl System: Some Insight into the Long-Range Self-Quenching Pathways of the First Excite d State of NCl, J. P hys. Chem. A, 106, 8453-8460 (2002).

483.  W. Eisfeld and K. Morokuma, Theoretical study of the photoelectron spectrum of NO3 and t he excited states of NO3+. Part I: Electronic spectrum, J. Chem. Phys., 117, 4361 (2002).

#43. P. Zhang and K. Morokuma, Ab initio molecular orbit al study of the weak C²A'←X²A' transition of the vinyl radical, Chem. Phys. Lett., in press.

Research Area 2. Development and Applications of Hybrid Method: ONIOM (Our own N-layered Integrated molecular Orbital and molecular Mechanics)

In the last several years we have proposed the theory and developed codes for th e hybrid method, ONIOM, for accurate calculations of large molecular systems. A large molecular system is divided into onion-like layers and a most accurate and computationally most demanding method is used for the layer where reactions are taking place or physical properties are measured, and a progressively less accu rate method is used for each outer layer. The code has been implemented in a mos t popular electronic structure package, Gaussian, and is being used by many peop le throughout the world. We are involved in further extension of the ONIOM metho d and applications to varieties of problems.

  Four Possible Schemes for Incorporation of an ONIOM Molecule into the
  Polarizable Continuum Model. (Reference: #462)

435.  P. B. Karadakov and K. Morokuma, ONIOM as an Efficient Tool for calculating NMR Chemical Shielding Constants in Large Molecules, Chem. Phys. Lett., 317, 589-59 (2000).

445.  T. Vreven and K. Morokuma, On the Application of the IMOMO (Integrated Molecular Orbital + Molecular Orbital) Method, J. Comp. Chem., 21, 1419-1432 (2000).

462.  T. Vreven, B. Mennucci, C. O. da Silva, K. Morokuma, and J. Tomasi, The ONIOM-PCM method: Combining the hybrid molecular orbital method and the polarizable continuum model for solvation. Application to the geometry and properties of a merocyanine in solution, J. Chem. Phys., 115, 62-72 (2001).

477.  T. Kerdcharoen and K. Morokuma, ONIOM-XS: An Extension of ONIOM Method for Molecular Simulation in Condensed Phase, Chem. Phys. Lett, 355, 257-262 (2002).

478.  T. Vreven and K. Morokuma, The Prediction of the Dissociation Energy of Hexaphenylethane Using the ONIOM(MO:MO:MO) Method. J. Phys. Chem. A, 101, 6167 (2002).

479.  K. Morokuma, New Challenges in Quantum Chemistry -- Quests for Accurate Calculations for Large Molecular Systems, Phil. Trans. R. Soc. Lond. A, 360, 1149 (2002).

482.  G. S. Tschumper and K. Morokuma, Gauging the Applicability of ONIOM(MO:MO) Methods to We ak Chemical Interact ions in Large Systems: Hydrogen Bonding in Alcohol Dimers, J. Mol. Str. (Theochem), 592, 137-147. ( 2002).

#30. T. Vreven, K. Morokuma, Ö. arkas, H. B. Schlegel and M . J. Frisch, Geometry Optimization with Combined Methods. I. Micro-Iterations and Constraints, J. Co mp. Chem., in press.

#55. G. A. Rickard, P. B. Karadakov, G. A. Webb and K. Morokuma , Calculation of NMR Chemical Shifts in Carbohydrates with ONIOM:A Study of the Conformers of ß ;-D-Glucopyranose, J. Phys. Chem. A, in press.

Research Area 3. Structure, Interactions and Reactions of Nanomaterials

We have been studying the structure, energies, properties, reactivities and electronic structure of nanomaterials, using the ONIOM and other electronic structure methods. For instance, we have studies the mechanism and feasibility of inserting metal atom into C60 after opening it by organic addition reaction. Reactions and interactions of fullerene other species, such as C and Si atoms and metal a toms, are also being studied. Molecular dynamics studies of the mechanism of fullerene formation are also in progress.

      ONIOM(B3LYP/6-31G(Od):B3LYP/STO-3G) optimized geometries of 
      3-layered belt of [12]-cyclacene 3_12 and its doubly oxidized
      forms 3_12_O12 and 3_12_O14. (Reference: #485)

470.  S. Irle, Y. Rubin, and K. Morokuma, An ONIOM Study of Ring Opening and Metal Insertion Reactions with Derivatives of C₆₀: Role of Aromaticity in the Opening Process, J. Phys. Chem. A, 106, 680-688 (2002).

485.  S. Irle, A. Mews, and K. Morokuma, Theoretical study of structures and Raman spectra for models of carbon na notubes in their pristine and oxidized form, J. Phys. Chem. A, 106, 11973-11980 (2002).

Research Area 4. Structure and Reactions of Transition Metal Complexes and Homogeneous Catalyses

We have pioneered in computational studies of mechanisms of reactions of organo-transition metal com plexes and homogenous catalysts. Structures and energies of intermediates and transition states for complicated series of reactions are computationally determined, and the mechanism of the entire cata lytic process is established. Catalyses of our interest include polymerization of olefins, copolymer ization of small molecules, activation of inert C-H and C-C bonds, activation of N2, and oxidation r eactions.

  The overall energy potential profiles of cycloisomerization reactions
  of 4-pentyn-1-ol. (1) endo-cycloisomerization with W(CO)5: bold solid 
  line with labels WN1-WN13. The natures of individual steps and the
  structures of intermediates and TSs are illustrated at the bottom of
  the figure; (2) exo- cycloisomerization with W(CO)5: bold broken line 
  with labels WX1-WX2; (3) endo-cycloisomerization without W(CO)5: thin 
  solid line with labels N1-N6. The natures of individual steps are 
  illustrated at the top of the figure; (4) exo-cycloisomerization 
  without W(CO)5: thin broken line with labels X1-X2. (Reference: #476)

434.  D. V. Khoroshun, D. G. Musaev and K. Morokuma, Does Reaction of Three-coordinate Molybdenum(III) with N₂O Proceed via the Same Mechanism as with N₂? A Theoretical Study, Organometallics, 18,  5653-5660 (1999).

439.  S. Mori, E. Nakamura and K. Morokuma, Mechanism of S_N2 Alkylation Reactions of Lithium Organocuprate Clusters with Alkyl Halides and Epoxides. Solvent effects, Lewis Acid Effects, and Trans-diaxial Epoxide Opening. J. Am. Chem. Soc., 122, 7294-7307 (2000).

440.  H. Basch, D. G. Musaev, K. Morokuma, Can the Binuclear Dinitrogen Complex [P₂N₂]Zr(m-h²-N₂)Zr[P₂N₂] Activate More Than One Hydrogen Molecule? A Theoretical Study, Organometallics, 19, 3393-3403 (2000).

444.  M. Torrent, D. G. Musaev, and K. Morokuma, Theoretical Study of the Mechanism of Oxidative Addition of Allyl-Ammonium and -Iminium Salts to Low-Valent Metal Complexes. Rationalization of Selective C-N and N-H Bond Activation, Organometallics, 19, 4402-4415 (2000).

446.  J. Moc, D. G. Musaev and K. Morokuma, Adsorption of Multiple H₂  Molecules on Pd₃ and Pd₄ Clusters. A Density Functional Study, J. Phys. Chem. A, 104, 11606-11614 (2000).

450.  S. F. Vyboishchikov, D. G. Musaev, R. J. D. Froese, and K. Morokuma, A Density Functional Study of Ethylene Polymerization Catalyzed by Zirconium Non-Cyclopentadienyl Complex, L₂ZrCH₃⁺. Effects of Ligands and Bulky Substituents, Organometallics, 20, 309-323 (2001).

455.  V. P. Ananikov, D. G. Musaev, and K. Morokuma, Catalytic Triple Bond Activation and Vinyl-Vinyl Reductive Coupling by Pt(IV) Complexes. A Density Functional Study, Organometallics, 20, 1652-1667 (2001).

456.  Arakawa, H.; Aresta, M.; Armor, J. N.; Barteau, M. A.; Beckman, E. J.; Bell, A. T.; Bercaw, J. E.; Creutz, C.; Dinjus, E.; Dixon, D. A.; Domen, K.; DuBois, D. L.; Eckert, J.; Fujita, E.; Gibson, D. H.; Goddard, W. A.; Goodman, D. W.; Keller, J.; Kubas, G. J.; Kung, H. H.; Lyons, J. E.; Manzer, L. E.; Marks, T. J.; Morokuma, K.; Nicholas, K. M.; Periana, R.; Que, L.; Rostrup-Nielson, J.; Sachtler, W. M. H.; Schmidt, L. D.; Sen, A.; Somorjai, G. A.; Stair, P. C.; Stults, B. R.; Tumas, W.  Catalysis Research of Relevance to Carbon Management: Progress, Challenges, and Opportunities. Chem. Rev., 101, 953-996 (2001). 

458.  D. V. Khoroshun, D. G. Musaev, T. Vreven and K. Morokuma, Theoretical Study on Bis(imino)pyridyl-Fe(II) Olefin Poly- and Oligomerization Catalysts. Dominance of Different Spin States in Propagation and b-hydride Transfer Pathways, Organometallics, 20, 2007-2026 (2001).

471.  R. K. Szilagyi, D. G. Musaev and K. Morokuma, Hydrogen Scrambling in [(C₅Me₅)Os(dmpm) CH₃H]⁺. A Density Functional and ONIOM Study, Organometallics, 21, 555-564 (2002).

472.  D V. Khoroshun, D. G. Musaev, K. Morokuma, Sigma trans promotion effect in transition metal complexes: a manifestation of the composite nature of binding energy, Mol. Phys., 100, 523-532 (2002).

473.  Z. Liu, M. Torrent and K. Morokuma, A Molecular Orbital Study of Zn(II)-Catalyzed Alternating Copolymerization of Carbon Dioxide with Epoxide, Organometallics, 21, 1056-1071 (2002).

474.  V. P. Ananikov, D. G. Musaev, and K. Morokuma, Vinyl-Vinyl Coupling on Late Transition Metals through C-C Reductive Elimination Mechanism. A Computational Study, J. Am. Chem. Soc., 124, 2839-2852 (2002).

476.  Y. Sheng, D. G. Musaev, K. S. Reddy, F. E. McDonald and K. Morokuma, Computational studies of tungsten-catalyzed endo-selective cycloisomerization of 4-pentyn-1-ol, J. Am. Chem. Soc., 124, 4149-4157 (2002).

480.  H. Basch, D. G. Musaev, and K. Morokuma, The Density Functional Studies of the Electroni c and Geometric Stru ctures of Pt3+, Pt3O+, Pt3O2+ and Pt3CH4+, J. Mol. Str. (Theochem), 586, 35-46 (2002).

484.  D. G. Musaev, H. Basch and K. Morokuma, The N(N Triple Bond Activation by the Transition Metal Complexes, in F. Maseras and A. Lledos, Ed., Computational Modeling of Homogeneous Catalysis, Kluwer (2002), pp. 325-361.

Research Area 5. Structure and Reactions of Biomolecular Systems

Application of quantum chemical and ONIOM methods to structure, spectroscopy and reaction mechanisms of biological systems is another area of our research activities. We have determined the transition state for activation of methane in models of methane monooxygenase, which has attracted attention. We have also determined structures of active sites of some metalloenzymes with explicit considerati on of protein environment, and are working toward understanding enzymatic reaction mechanisms. Theor etical studies of structure and reactions of bacteriorhodopsin are also in progress.

      Superposition of (A) the B3LYP-optimized active-site-only 
      model structure and experimental structures and (B) the
      ONIOM2-optimized >1000 atom model structure and experimental 
      structure of the active site of R2met (Reference: #469)

434.  D. V. Khoroshun, D. G. Musaev and K. Morokuma, Does Reaction of Three-coordinate Molybdenum(III) with N₂O Proceed via the Same Mechanism as with N₂? A Theoretical Study, Organometallics, 18,  5653-5660 (1999).

437.  R. K. Szilagyi, D. G. Musaev and K. Morokuma, Theoretical Studies of Biological Nitrogen Fixation II. Hydrogen Bonded Networks as Possible Reactant and Product Channels, Theochem, 506, 131-146 (2000).

448.  M. Torrent, D. G. Musaev and K. Morokuma, The Flexibility of Carboxylate Ligands in Methane Monooxygenase and Ribonucleotide Reductase: A Density Functional Study, J. Phys. Chem. B, 105, 322-327 (2001).

451.  R. Szilagyi, D. G. Musaev and K. Morokuma, Theoretical Studies of Biological Nitrogen Fixation. I. Density Functional Modeling of the Mo-site of the FeMo-cofactor, Inorg. Chem., 40, 766-775 (2001).

454.  H. Basch, D. G. Musaev, K. Mogi and K. Morokuma, Theoretical Studies on Mechanism of the Methane ® Methanol Conversion Reaction Catalyzed by Methane Monooxygenase (MMO): The O-side vs N-side Mechanisms J. Phys. Chem. A, 105, 3615-3622 (2001).

457.  M. Torrent, D. Mansour, E. P. Day, and K. Morokuma, Quantum Chemical Study on Oxygen-17 and Nitrogen-14 Nuclear Quadrupole Coupling Parameters of Peptide Bonds in Alpha-Helix and Beta-Sheet Proteins, J. Phys. Chem. A, 105, 4546-4557 (2001).

459.  M. Torrent, D. G. Musaev K. Morokuma, and H. Basch, A Density Functional Study of the Activation of Dioxygen by Methane Monooxygenase and Ribonucleotide Reductase. II. The Water-Assisted Mechanism, J. Phys. Chem. B, 105, 4453-4463 (2001).

466.  H. Basch, D. G. Musaev, and K. Morokuma, A Density Functional Study of the Completion of the Methane Monooxygenase Catalytic Cycle. Methanol Complex to MMOH Resting State, J. Phys. Chem. B, 105, 8452-8460 (2001).

467.  M. Torrent,^. K. Mogi,^. H. Basch, and K. Morokuma, A Density Functional Study of Possible Intermediates of the Reaction of Dioxygen Molecule with Non-heme Iron Complexes. I. N-side versus O-side Mechanism with Water-Free Model, J. Phys. Chem. B, 105, 8616-8628 (2001).

468.  M. Torrent, D. G. Musaev, H. Basch and K. Morokuma, Computational Studies of Reaction Mechanisms of Methane Monooxygenase and Ribonucleotide Reductase, J. Comp. Chem., 23, 59-76 (2002).

469.  M. Torrent, T. Vreven, D. G. Musaev, K. Morokuma, Ö. Farkas and H. B. Schlegel, Effects of the Protein Environment on the Structure and Energetics of Active Sites of Metalloenzymes. ONIOM Study of Methane Monooxygenase and Ribonucleotide Reductase. J. Am. Chem. Soc. 124, 192-193 (2002).

475.  D. G. Musaev, H. Basch and K. Morokuma, Theoretical Study of the Mechanism of Alkane Hydroxylation and Ethylene Epoxidation Reactions Catalyzed by Diiron Bis-oxo Complexes. The Effect of Substrate Molecules, J. Am. Chem. Soc., 124, 4135-4148 (2002).

#31. T. Vreven and K. Morokuma, Investigation of the S0 – › S1 Excitation in Bacteriorhodopsin with the ONIOM(MO:MM) Hybrid Method, Theo. Chem. Acc., in press.

#46. D. V. Khoroshun, K. Warncke, S.-C. Ke, D. G. Musaev and K . Morokuma, Int ernal degrees of freedom, structural motifs, and conformational energetics of 5'-deoxyadenosyl radic al: Implications for function in adenosylcobalamin-dependent enzymes. A computational study. J. Am. Chem. Soc., in press.