Skip to main content
SpringerLink
Log in
Book cover

Advances in the Theory of Quantum Systems in Chemistry and Physics pp 433–460Cite as

Theoretical Studies on Metal-Containing Artificial DNA Bases

  • Chapter
  • First Online:

  • 1387 Accesses

Part of the book series: Progress in Theoretical Chemistry and Physics ((PTCP,volume 22))

Abstract

We have studied three topics about (i) the structural stabilities and electronic structures of metal-ion containing artificial DNA bases and (ii) conductivity of them. Before proceeding to the main topics, we have shown that a van der Waals corrected density functional method gives the stacking interaction, which agrees well with the reference value obtained by accurate methods in both cases for stacking two bases and two base pairs. We also investigated an origin of structural stability and electronic properties of several metal ion containing artificial DNA bases including chalcogen-substituted compounds. We estimated current-voltage characteristics of stacking natural and metal-containing artificial DNA bases by the scattering theory based on the non-equilibrium Green’s function method. We found that the current-voltage characteristics dramatically change by capturing metal ion in the artificial DNA bases.

This is a preview of subscription content, log in via an institution.

Chapter
USD   29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD   169.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD   219.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD   219.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Learn about institutional subscriptions

References

  1. Jurečka P, Hobza P (2004) J Am Chem Soc 125:15608

    Article  Google Scholar 

  2. Šponer J, Jurečka P, Hobza P (2004) J Am Chem Soc 126:10142

    Article  Google Scholar 

  3. Braun E, Eichen Y, Sivan U, Ben-Yoseph G (1998) Nature 391:775

    Article  CAS  Google Scholar 

  4. Porath D, Berzryadin A, de Vries S, Dekker C (2000) Nature 403:635

    Article  CAS  Google Scholar 

  5. Fink H-W, Schönenberger C (1999) Nature 398:407

    Article  CAS  Google Scholar 

  6. Yu Kasumov A, Kociak M, Gueron S, Reulet B, Volkov VT, Klinov DV, Bouchiat H (2001) Science 291:280

    Google Scholar 

  7. Giese B, Spichty M (2000) ChemPhysChem 1:195

    Article  CAS  Google Scholar 

  8. Giese, B.; Wessely, S. Chem. Commun. 2001, 2108.

    Google Scholar 

  9. Zilberberg, I.L.; Avdeev G.M.; Zhidomirov, G.M. J. Mol. Struct. (Theochem) 1997, 418, 73.

    Google Scholar 

  10. Hush NS, Schamberger J, Bacskay GB (2005) Coord Chem Rev 249:299

    Article  CAS  Google Scholar 

  11. Lee JS, Latimer LJP, Reid RS (1993) Biochem Cell Biol 71:162

    Article  CAS  Google Scholar 

  12. Abrescia NGA, Malinina L, Fernandez LG, Huynh-Dinh T, Neidle S, Subirana JA (1999) Nucl Acids Res 27:1593

    Article  CAS  Google Scholar 

  13. Baeyens KJ, DeBondt H, Pardi A, Holbrook SR (1996) Proc Natl Acad Sci 93:12851

    Article  CAS  Google Scholar 

  14. Kankia BI (2000) Nucl Acids Res 28:911

    Article  CAS  Google Scholar 

  15. Robinson H, Gao Y, Sabusgvill R, Joachimiak A, Wang AHJ (2000) Nucl Acids Res 28:1760

    Article  CAS  Google Scholar 

  16. Miyake Y, Togashi H, Tashiro M, Yamaguchi H, Oda S, Kudo M, Tanaka Y, Kondo Y, Sawa R, Fujimoto T, Machinami T, Ono A (2006) J Am Chem Soc 128:2172

    Article  CAS  Google Scholar 

  17. Iikura H, Tsuneda T, Yanai T, Hirao K (2001) J Chem Phys 115:3540

    Article  CAS  Google Scholar 

  18. Andersson Y, Langreth DC, Lundqvist BI (1996) Phys Rev Lett 76:102

    Article  CAS  Google Scholar 

  19. Kamiya M, Tsuneda T, Hirao K (2002) J Chem Phys 117:6010

    Article  CAS  Google Scholar 

  20. Matsui T, Sato T, Shigeta Y, Hirao K (2009) Chem Phys Lett 478:238

    Article  CAS  Google Scholar 

  21. Matsui T, Miyachi H, Sato T, Shigeta Y, Hirao K (2008) J Phys Chem B 112:16960

    Article  CAS  Google Scholar 

  22. Matsui T, Miyachi H, Nakanishi Y, Shigeta Y, Sato T, Kitagawa Y, Okumura M, Hirao K (2009) J Phys Chem B 113:12790

    Article  CAS  Google Scholar 

  23. Nakanishi Y, Matsui T, Shigeta Y, Kitagawa Y, Saito T, Kataoka Y, Kawakami T, Okumura M, Yamaguchi K (2010) Int J Quantum Chem 110:2221

    Article  CAS  Google Scholar 

  24. Wang C-W, Fu Y, Luo Y (2001) Phys Chem Chem Phys 3:5021

    Google Scholar 

  25. Florian J, Goodman MF, Warshel A (2000) J Phys Chem B 104:10092

    Article  CAS  Google Scholar 

  26. Elstner M, Hobza P, Frauenheim T, Suhai S, Kanxiras E (2001) J Chem Phys 114:5149

    Article  CAS  Google Scholar 

  27. Zhao Y, Truhlar DG (2005) Phys Chem Chem Phys 7:2701

    Article  CAS  Google Scholar 

  28. Antony J, Grimme S (2006) Phys Chem Chem Phys 8:5287

    Article  CAS  Google Scholar 

  29. Becke AD, Johnson ER (2005) J Chem Phys 123:154101

    Article  Google Scholar 

  30. Kamiya M, Tsuneda T, Hirao K (2002) J Phys Chem 117:6010

    Article  CAS  Google Scholar 

  31. Sato T, Tsuneda T, Hirao K (2005) J Phys Chem 123:104307

    Article  Google Scholar 

  32. Sato, T.; Tsuneda, T.; Hirao, K. J. Phys. Chem. 2007, 126, 234114.

    Google Scholar 

  33. Song J-W, Hirosawa T, Tsuneda T, Hirao K (2007) J Chem Phys 126:154105

    Article  Google Scholar 

  34. Jurečka P, Šponer J, Černy J, Hobza P (2006) Phys Chem Chem Phys 8:1985

    Article  Google Scholar 

  35. Boys SF, Bernardi F (1970) Mol Phys 19:553

    Article  CAS  Google Scholar 

  36. Frisch, M. J. et al., Gaussian 03, Revision D.02, Gaussian, Inc., Wallingford CT, USA, 2004

    Google Scholar 

  37. Šponer J, Jurečka P, Marchan I, Luque EJ, Orozco M, Hobza P (2006) Chem Eur J 12:2854

    Article  Google Scholar 

  38. Tanaka K, Shionoya M (1999) J Org Chem 64:5002

    Article  CAS  Google Scholar 

  39. Meggers E, Holland PL, Tolman WB, Romesberg FE, Schultz PG (2000) J Am Chem Soc 122:10714

    Article  CAS  Google Scholar 

  40. Switzer C, Sinha S, Kim PH, Heuberger BD (2005) Angew Chem Int Ed 44:1529

    Article  CAS  Google Scholar 

  41. Tanaka K, Yamada Y, Shionoya M (2002) J Am Chem Soc 124:8802

    Article  CAS  Google Scholar 

  42. Tanaka K, Tengeiji A, Kato T, Toyama N, Shionoya M (2003) Science 299:1212

    Article  CAS  Google Scholar 

  43. Tanaka K, Shionoya M (2006) Chem Lett 35:694

    Article  CAS  Google Scholar 

  44. Tanaka K, Tengeiji A, Kato T, Toyama N, Shiro M, Shionoya M (2002) J Am Chem Soc 124:12494

    Article  CAS  Google Scholar 

  45. Yamaguchi K, Takahara Y, Fueno T (1986) In: Smith VH Jr., Schaefer HF III, Morokuma, K (eds) Applied quantum chemistry. Raidel, Boston, p. 155

    Chapter  Google Scholar 

  46. Yamaguchi K, Okumura M, Maki J, Noro T, Namimoto H, Nakano M, Fueno T, Nakasuji K (1992) Chem Phys Lett 190:353

    Article  CAS  Google Scholar 

  47. Nakanishi Y, Kitagawa Y, Shigeta Y, Saito T, Matsui T, Miyachi H, Kawakami T, Okumura M, Yamaguchi K (2009) Polyhedron 28:1714

    Article  CAS  Google Scholar 

  48. Nakanishi Y, Kitagawa Y, Shigeta Y, Saito T, Matsui T, Miyachi H, Kawakami T, Okumura M, Yamaguchi K (2009) Polyhedron 28:1945

    Article  CAS  Google Scholar 

  49. Clever GH, Reitmeier SJ, Carell T, Schiemann O (2010) Angew Chem Int Ed 49:4927

    Article  CAS  Google Scholar 

  50. Takezawa Y, Tanaka K, Yori M, Tashiro S, Shiro M, Shionoya M (2008) J Org Chem 73:6092

    Article  CAS  Google Scholar 

  51. Weigend F, Ahlrichs R (2005) Phys Chem Chem Phys 7:3297

    Article  CAS  Google Scholar 

  52. Natsume T, Dedachi K, Tanaka S, Higuchi T, Kurita N (2005) Chem Phys Lett 408:381

    Article  CAS  Google Scholar 

  53. Rak J, Makowska J, Voityuk AA (2006) Chem Phys 325:567

    Article  CAS  Google Scholar 

  54. Sadowska-Sleksiejew A, Rak J, Voityuk AA (2006) Chem Phys Lett 429:546

    Article  Google Scholar 

  55. Mujica V, Kemp M, Ratner MA (1994) J Chem Phys 101:6849

    Article  Google Scholar 

  56. Asai Y (2003) J Phys Chem B 107:4647

    Article  CAS  Google Scholar 

  57. Shimazaki T, Maruyama H, Asai Y, Yamashita K (2005) J Chem Phys 123:164111

    Article  Google Scholar 

  58. Shimazaki T, Xue Y, Ratner MA, Yamashita K (2006) J Chem Phys 126:114708

    Article  Google Scholar 

  59. Reed MA, Zhou C, Muller CJ, Burgin TP, Tour JM (1997) Science 298:252

    Article  Google Scholar 

Download references

Acknowledgments

This research was supported by the Core Research for Evolutional Science and Technology (CREST) Program High “Performance Computing for Multi-Scale and Multi-Physics Phenomena” of the Japan Science and Technology Agency (JST) and Grant-in-Aid for Young Scientists (A) (No. 22685003).

Author information

Authors and Affiliations

  1. Institute of Picobiology, Graduate School of Lifescience, University of Hyogo, Koto 3-2-1, Hyogo, 678-1297, Japan

    Toru Matsui & Yasuteru Shigeta

  2. Core Research for Evolutional Science and Technology, Japan Science and Technology Agency (CREST, JST), Saitama, Japan

    Toru Matsui & Yasuteru Shigeta

  3. Department of Applied Chemistry, School of Engineering, The University of Tokyo, Hongo 7-3-1, Tokyo, 678-1297, Japan

    Hideaki Miyachi

Authors
  1. Toru Matsui
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Hideaki Miyachi
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Yasuteru Shigeta
    View author publications

    You can also search for this author in PubMed Google Scholar

Editor information

Editors and Affiliations

  1. , LASMEA, Clermont University, avenue des Landais 24, Aubiere Cedex, 63177, France

    Philip E. Hoggan

  2. Dept. Quantum Chemistry, Uppsala University, Uppsala, Sweden

    Erkki J. Brändas

  3. Labo. Chimie Physique, CNRS, rue Pierre et Marie Curie 11, Paris, 75005, France

    Jean Maruani

  4. Dept. Chemistry, Michigan State University, Chemistry Building, East Lansing, 48824, Michigan, USA

    Piotr Piecuch

  5. Inst. Matemáticas y Física, Fundamental (IMAFF), CSIC Madrid, C/ Serrano 123, Madrid, 28006, Spain

    Gerardo Delgado-Barrio

Rights and permissions

Reprints and permissions

Copyright information

© 2012 Springer Science+Business Media B.V.

About this chapter

Cite this chapter

Matsui, T., Miyachi, H., Shigeta, Y. (2012). Theoretical Studies on Metal-Containing Artificial DNA Bases. In: Hoggan, P., Brändas, E., Maruani, J., Piecuch, P., Delgado-Barrio, G. (eds) Advances in the Theory of Quantum Systems in Chemistry and Physics. Progress in Theoretical Chemistry and Physics, vol 22. Springer, Dordrecht. https://doi.org/10.1007/978-94-007-2076-3_25

Download citation

Publish with us

Policies and ethics

Search

Navigation