conformational search software, low energy conformers, conformation analysis
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Original Papers | Proceedings and Research Reports | Computer Programs

Original Papers
A list of publications on the conformational space search methodologies and algorithms used in CONFLEX is given below. Other related works are referenced in these papers.

  • Osamu Niyomura, Tetsuo Iwasawa, Naoki Sawada, Makoto Tokunaga,Yasushi Obora, and Yasushi Tsuji, Catalysis Research Center and Division of Chemistry, Graduate School of Science, Hokkaido University, CREST, Japan Science and Technology Corporation (JST), Sapporo 001-0021, Japan, A Bowl-Shaped Phosphine as a Ligand in Rhodium-Catalyzed Hydrosilylation: Rate Enhancement by a Mono(phosphine) Rhodium Species, Organometallics, 2005, 24, 3468-3475
     
  • Tetsuaki Fujihara, Yasushi Obora, Makoto Tokunaga, Hiromichi Sato and Yasushi Tsuji, Dendrimer N-heterocyclic carbene complexes with rhodium(I) at the core. Received (in Cambridge, UK) 17th May 2005, Accepted 27th July 2005. First published as an Advance Article on the web 19th August 2005, Chem. Commun., 2005, 4526–4528. This journal is The Royal Society of Chemistry 2005.
     
  • B. S. Balaji, Yasushi Obora, Daisuke Ohara, Shigehiro Koide, and Yasushi Tsuji, Catalysis Research Center and Division of Chemistry, Graduate School of Science, Hokkaido University, Sapporo 060-0811, Japan, Dendrimer-Phosphine Complexes with Platinum(0) at the Core, Organometallics, 2001, 20, 5342-5350
     
  • Osamu Niyomura, Makoto Tokunaga, Yasushi Obora, Tetsuo Iwasawa, and Yasushi Tsuji, Rate Enhancement with a Bowl-Shaped Phosphane in the Rhodium-Catalyzed Hydrosilylation of Ketones, Angew. Chem. Int., Ed. 2003, 42, No. 11
     
  • Tetsutaro Hattori, Yuhi Shimazumi, Hitoshi Goto, Osamu Yamabe, Naoya Morohashi,Wataru Kawai, Sotaro Miyano, Synthesis, Resolution, and Absolute Stereochemistry of (-)-Blestriarene C, J. Org. Chem., in press.
     
  • M. Ozawa, H. Goto, M. Kusunoki, E. Osawa, Continuously Growing Spiral Carbon Nanoparticles as the Intermediates in the Formation of Fullerenes and Nanoonions, J. Phys. Chem., 2002, 106, 7135-7138.
     
  • M. Suchy, P. Kutschy, K. Monde, H. Goto, N. Harada, M. Takasugi, M. Dzurilla, E. Balentova, Synthesis, Absolute Configuration and Enantiomeric Enrichment of a Cruciferous Oxindole Phytoalexin, (S)-(-)-Spirobrassinin, and Its Oxazoline Analog, J. Org. Chem., 2001, 66, 3940-3947.
     
  • Z. Slanina, X. Zhao, N. Kurita, H. Gotoh, F. Uhlik, J. M. Rudzinski, K. H. Lee, L. Adamowicz, Computing the Relative Gas-phase Populations of C60 and C70: Beyond the Traditional ‡™H0f,298 Scale, J. Molecular Graphics and Modeling, 2001, 19, 216-221.
     
  • R. W. J. Zijlstra, Wolter F. Jager, B. Lange, P. T. Duijnen, B. L. Feringa, H. Goto, A. Saito, N. Koumura, N. Harada, Chemistry of Unique Chiral Olefins. Part 4. Theoretical Studies of the Racemization Mechanism of trans- and cis-1,1',2,2',3,3',4,4'-Octahydro-4,4'-biphenanthrylidenes, J. Org. Chem., 1999, 64, 1667-1674.
     
  • T. Hattri, K. Sakurai, N. Koike, S. Miyano, H. Goto, F. Ishiya, N. Harada,
    Is the CD Exciton Chirality Method Applicable to Chiral 1,1'-Biphenanthryl Compounds?, J. Am. Chem. Soc., 1998, 120, 1719-1723.
     
  • H. Goto, A frontier mode-following method for mapping saddle-points of conformational interconversion in flexible molecules starting from the energy minimum, Chem. Phys. Lett., 1998, 292, 254-258.
     
  • H. Goto, N. Harada, J. Crassous, F. Diederich, Absolute configuration of chiral fullerenes and covalent derivatives from their calculated circular dichroism spectra, J. Chem. Soc. Perkin Trans. 2, 1998, 1719-1723.
     
  • Osawa, E., H. Goto, T. Hata and E. Deretey, Cluster conformational analysis of a seco acid used in Woodward's total synthesis of erythromycin A, J. Mol. Struct.(THEOCHEM), 1997, 399, 229-236.
     
  • M. Yoshida, H. Goto, Y. Hirose, X. Zhao and E. Osawa, Prediction of favorable isomeric structures for the C100 to C120 giant fullerenes. An application of the phason line criteria, Electronic J. Theo. Chem., 1996, 1, 163-171.
     
  • M. Yoshida, M. Fujita, H. Goto, and E. Osawa, The phason line: a new criterion for the stability of fullerenes, Electronic J. Theo. Chem., 1996, 1, 151-162.
     
  • H. Nagashima, M. Saito, Y. Kato, H. Goto, E. Osawa, M. Haga, K. Itoh, Electronic structures and redox properties of silylmethylated C60, Tetrahedron, 1996, 52, 5053-5064.
     
  • H. Suginome, T. Kondoh, C. Gogonea, V. Singh, H. Goto, and E. Osawa, Photinduced Molecular Transformations. Part 155. General Synthesis of Macrocyclic Ketones based on a Ring Expansion involving a Selective b-Scission of Alkoxyl Radicals, its Application to a New Synthesis of (+-)-Isocaryophyllene and (+-)-Caryopyllene, and a Conformational Analysis of the Two Sesquiterpenes and the Radical Intermediate in the Synthesis by MM3 Calculations, J. Chem. Soc., Perkin Trans.1, 1995, 69-81.
     
  • T. Hata, H. Goto, E. Osawa, T. Hamada, and O. Yonemitsu,Cluster Conformational Analysis of Woodward’s Erythronolide A Seco-Acids. Part 1. Methodology, Discovery of Reactive Conformers in the Macrolactonization, and the Adverse Effect of Acetonide Protection,Electr. J. Theo. Chem. in press.
     
  • H. Suginome, T. Kondoh, C. Gogonea, V. Singh, H. Goto, and E. Osawa, Photinduced Molecular Transformations. Part 155. General Synthesis of Macrocyclic Ketones based on a Ring Expansion involving a Selective b-Scission of Alkoxyl Radicals, its Application to a New Synthesis of (±)-Isocaryophyllene and (±)-Caryopyllene, and a Conformational Analysis of the Two Sesquiterpenes and the Radical Intermediate in the Synthesis by MM3 Calculations, J. Chem. Soc., Perkin Trans.1, 1995, 69-81.
      
  • H. Goto, Y. Kawashima, M. Kashimura, S. Morimoto, and E. Osawa, Origin of Regioselectivity in O-Methylation of Erythromycin with the Aid of Computational Conformational Space Search, J. Chem. Soc., Perkin Trans. 2, 1993, 1647- 1654.
      
  • H. Goto, Approach to Global Minimum Problem, J. Mol. Struct. (THEOCHEM), 1993, 285, 157-168.
      
  • K. Shimazaki, M. Mori, K. Okada, T. Chuman, S. Kuwahara, T. Kitahara, K. Mori, H. Goto, E. Osawa, K. Sakakibara, and M. Hirota, Combined Molecular Mechanics (MM2) and Molecular Orbital (AM1) Study of Periplanone-A and Analogues. Evaluation of Biological Activity from Electronic Properties and Geometries. Part 2, J. Chem. Soc., Perkin Trans. 2, 1993, 1167-1173.
      
  • H. Goto and E. Osawa, An Efficient Algorithm for Searching Low-energy Conformers of Cyclic and Acyclic Molecules, J. Chem. Soc., Perkin Trans. 2, 1993, 187-198.
      
  • H. Goto and M. Yamato, How Many Conformers Are There for Small n-Alkanes? Consequences of Asymmetric Deformation in GG’ Segment, Tetrahedron, 1993, 49, 387-396.
      
  • H. Goto, A Revised Nomenclature for the Ring Conformation and a Note on Conformational Distance in Cyclododecane, Tetrahedron, 1992, 48, 7131-7144.
       
  • H. Goto, Further Developments in the Algorithm for Generating Cyclic Conformers. Test with Cycloheptadecane, Tetrahedron Lett, 1992, 33, 1343-1346.
      
  • K. Shimazaki, M. Mori, K. Okada, T. Chuman, H. Goto, K. Sakakibara, and M. Hirota, Combined Molecular Mechanics (MM2) and Molecular Orbital (AM1) Study of Periplanone-B and Analogues. Evaluation of Biological Activity from Electronic Properties and Geometries, J. Chem. Soc, Perkin Trans, 2, 1992, 811-818.
      
  • S. Tsuzuki, L. Schäfer, H. Goto, E. D. Jemmis, H. Hosoya, K. Siam, K. Tanabe, and E. Osawa, Investigation of Intramolecular Interactions in n-Alkanes. Cooperative Energy Increments Associated with GG and GTG' Sequences, J. Am. Chem. Soc, 1991, 113, 4665-4671.
      
  • N. Nakajima, T. Matsushima, O. Yonemitsu, and H. Goto., Stereoselective Total Synthesis of 16-Membered Macrolide Aglycons, Leuconolides and Maridonolides. Macrocyclic Stereocontrol Based on Conformational Analysis of the 16-Membered Macrolide Ring, Chem. Pharm. Bull, 1991, 39, 2819-2829.
      
  • K. Shimazaki, M. Mori, K. Okada, T. Chuman, H. Goto, E. Osawa, K. Sakakibara, and M. Hirota, Conformational Analysis of Periplanone Analogs by Molecular Mechanics Calculations, J. Chem. Ecol, 1991, 17, 779-788.
      
  • T. Chuman, K. Shimazaki, M. Mori, K. Okada, H. Goto, K. Sakakibara, and M. Hirota, Conformational Analysis of Serricornin: Application of Molecular Mechanics Calculations to Stereochemical Assignment of Serricornin, Sex Pheromone of Cigarette Beetle (Lasioderma serricorne F.), J. Chem. Ecol, 1990, 16, 2877-2888.
      
  • N. Nakajima, K. Uoto, T. Matsushima, O. Yonemitsu, H. Goto, and E. Osawa, Synthesis of 16-Membered Macrolide Aglycones, Carbonolide A, Leuconolides, and Maridonolides, via Carbonolide B Type Compounds by Virtue of Completely Stereoselective Epoxidation and Reduction Based on the Conformational Control of Macrolide Rings with Protecting Groups, J. Org. Chem, 1990, 55, 1129-1132.
     
  • H. Goto, Corner Flapping: A Simple and Fast Algorithm for Exhaustive Generation of Ring Conformations, J. Am. Chem. Soc, 1989, 111, 8950-8951.
      
  • E. Osawa, H. Goto, T. Oishi, Y. Otsuka, and T. Chuman, Application of Molecular Mechanics to Natural Product Chemistry, Pure & Appl. Chem, 1989, 61, 597-600


Proceedings and Research Reports

  • H. Goto , T. Takahashi , Y. Takata , K. Ohta and U. Nagashima, CONFLEX: Conformational Behaviors of Polypeptides as Predicted by a Conformational Space Search, Technical Proceedings of the 2003 Nanotechnology Conference and Trade Show (Nanotech 2003), San Francisco. 2003
     
  • E. Osawa, H. Goto, T. Sugiki, K, Imai, Study of Intermolecular Interactions using Crystal Structure Database as Refference: A Preliminary Report on the Adjustment of van der Waals Constants, Intermolecular Interactions, Gans and Boeyens, Ed., Plenum Press, New York, 1998, 121-134.
     
  • E. Osawa, E. Deretey, and H. Goto, Conformational Analysis of Long Chain Seco-Acids used in Woodward's Total Synthesis of Erythromycin A - Conformational Space Search as the Basis of Molecular Modeling, Fundamental Principles of Molecular Modeling, W. Gans et al., Eds., Plenum Press, New York, 1996, p.189-197.
     
  • E. Osawa, H. Goto and M. Yamato, An Efficient Algorithm for Finding Low-energy Conformations of chain molecules, M. Doyama, T. Suzuki, J. Kihara and R. Yamamoto, Eds., Computer Aided Innovation of New Materials II, Elservier Sci. Publ.: Amsterdam, 1993, p.845-848.
      
  • K. Simazaki, M. Mori, K. Okada, T. Chuman, H. Goto, E. Osawa, K. Sakakibara, M. Hirota, Combined Molecular Mechanics (MM2) and Molecular Orbital (AM1) Study of Periplanones and Their Analogs, M. Doyama, T. Suzuki, J. Kihara and R. Yamamoto, Eds., Computer Aided Innovation of New Materials II, Elservier SCI Publ.: Amsterdam, 1993, p.857-860.
      
  • E. Osawa and H. Goto, Fast Algorithm for Covering Conformational Space by Molecular Mechanics, M. Doyama, T. Suzuki, J. Kihara and R. Yamamoto, Eds., Computer Aided Innovation of New Materials, Elservier SCI Publ.: Amsterdam, 1991, p.411-416.


Computer Programs

  • H. Goto, E. Osawa, CONFLEX 3, JCPE, P40.
     
  • H. Goto, E. Osawa, CONFLEX: Generation of Ring Conformers by Corner Flapping Algorithm, JCPE, P21.
     
  • H. Goto, E. Osawa, CONFLEX: Generation of Ring Conformers by Corner Flapping Algorithm, QCPE, #592


 
 
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