Skip to main content
Log in

Knowledge discovery through chemical space networks: the case of organic electronics

  • Original Paper
  • Published:
Journal of Molecular Modeling Aims and scope Submit manuscript

Abstract

Modern materials discovery and design studies often rely on the computational screening of large databases. Complementing experimental databases, virtual databases are thereby increasingly established through the first-principles calculation of computationally inexpensive, but for a given application, decisive microscopic quantities of the system. These so-called descriptors are calculated for vast numbers of candidate materials. In general, the sheer volume of datapoints generated in such studies precludes an in depth human analysis. To this end, smart visualization techniques, based e.g., on so-called chemical space networks (CSN), have been developed to extract general design rules connecting structural modifications to changes in the target functionality. In this work, we generate and visualize the CSN of possible crystalline organic semiconductors based on an in-house database of > 64,000 molecular crystals that we extracted from the exhaustive Cambridge Structural Database and for which we computed prominent charge-mobility descriptors. Our CSN thereby links clusters of molecular crystals based on the chemical similarity of the scaffolds of their molecular building blocks and thus groups communities of similar molecules. Including each cluster’s median descriptor values, the CSN visualization not only reproduces known trends of good organic semiconductors but also allows us to extract general design rules for organic molecular scaffolds. Finally, the local environment of each scaffold in our visualization shows how thoroughly its local chemical space has already been explored synthetically. Of special interest here are those clusters with promising descriptor values, yet with little or no connections in the sampled chemical space, as these offer the most room for scaffold optimization.

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

Access this article

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Fig. 1
Fig. 2
Fig. 3
Fig. 4

Similar content being viewed by others

References

  1. Gómez-Bombarelli R, Aguilera-Iparraguirre J, Hirzel TD, Duvenaud D, Maclaurin D, Blood-Forsythe MA, Chae HS, Einzinger M, Ha D-G, Wu T, Markopoulos G, Jeon S, Kang H, Miyazaki H, Numata M, Kim S, Huang W, Hong SI, Baldo M, Adams RP, Aspuru-Guzik A (2016) vol 15

  2. Agrawal A, Choudhary A (2016) APL Mater 4:053208

    Article  Google Scholar 

  3. Lo Y-C, Senese S, Li C-M, Hu Q, Huang Y, Damoiseaux R, Torres JZ (2015) PLoS Comput Biol 11:1

    Article  Google Scholar 

  4. Ferguson A, Hachmann J (2018) Mol Syst Des Eng 3:429

    Article  CAS  Google Scholar 

  5. Isayev O, Fourches D, Muratov EN, Oses C, Rasch K, Tropsha A, Curtarolo S (2015) Chem Mater 27:735

    Article  CAS  Google Scholar 

  6. Olivares-Amaya R, Amador-Bedolla C, Hachmann J, Atahan-Evrenk S, Sanchez-Carrera RS, Vogt L, Aspuru-Guzik A (2011) Energy Environ Sci 4:4849

    Article  CAS  Google Scholar 

  7. Akimov AV, Prezhdo OV (2015) Chem Rev 115:5797

    Article  CAS  Google Scholar 

  8. Schober C, Reuter K, Oberhofer H (2016) J Phys Chem Lett 7:3973

    Article  CAS  Google Scholar 

  9. Reymond J-L, van Deursen R, Blum LC, Ruddigkeit L (2010) Med Chem Commun 1:30

    Article  CAS  Google Scholar 

  10. Borgatti SP, Mehra A, Brass DJ, Labianca G (2009) Science 323:892

    Article  CAS  Google Scholar 

  11. Barabási A-L, Gulbahce N, Loscalzo J (2010) Nat Rev Gen 12:56 EP

    Article  Google Scholar 

  12. Cotacallapa M, Hase MO (2016) J Phys A 49:065001

    Article  Google Scholar 

  13. Ideker T, Nussinov R (2017) PLOS Comput Biol 13:1

    Article  Google Scholar 

  14. Barabási A, Psfai M (2016) Network science. Cambridge University Press

  15. Hopkins AL (2008) Nat Chem Biol. 4:682 EP

    Article  Google Scholar 

  16. Shelat AA, Guy RK (2007) Nat Chem Biol 3:442

    Article  CAS  Google Scholar 

  17. Kontijevskis A (2017) J Chem Inf Model 57:680

    Article  CAS  Google Scholar 

  18. Sandefur CI, Mincheva M, Schnell S (2013) Mol BioSyst 9:2189

    Article  CAS  Google Scholar 

  19. Simm GN, Reiher M (2017) J Chem Theory Comput 13:6108

    Article  CAS  Google Scholar 

  20. Opassi G, Ges A, Massarotti A (2018) Drug Discov Today 23:565

    Article  CAS  Google Scholar 

  21. Osolodkin DI, Radchenko EV, Orlov AA, Voronkov AE, Palyulin VA, Zefirov NS (2015) Expert Opin Drug Discov 10:959

    Article  Google Scholar 

  22. Gütlein M, Karwath A, Kramer S (2014) J Cheminform 6:41

    Article  Google Scholar 

  23. Gonzlez-Medina M, Medina-Franco JL (2017) J Chem Inf Model 57:1735

    Article  Google Scholar 

  24. Maggiora GM, Bajorath J (2014) J Comput Aided Mol Des 28:795

    Article  CAS  Google Scholar 

  25. Wawer M, Peltason L, Weskamp N, Teckentrup A, Bajorath J (2008) J Med Chem 51:6075

    Article  CAS  Google Scholar 

  26. Minemawari H, Yamada T, Matsui H, Tsutsumi J, Haas S, Chiba R, Kumai R, Hasegawa T (2011) Nature 475:364

    Article  CAS  Google Scholar 

  27. Stavrinidou E, Gabrielsson R, Gomez E, Crispin X, Nilsson O, Simon DT, Berggren M (2015) Sci Adv 1:e1501136

    Article  Google Scholar 

  28. Xu J, Wang S, Wang G-JN, Zhu C, Luo S, Jin L, Gu X, Chen S, Feig VR, To JW et al (2017) Science 355:59

    Article  CAS  Google Scholar 

  29. Nikolka M, Nasrallah I, Rose B, Ravva MK, Broch K, Sadhanala A, Harkin D, Charmet J, Hurhangee M, Brown A et al (2017) Nat Mater 16:356

    Article  CAS  Google Scholar 

  30. Wang C, Dong H, Jiang L, Hu W (2018) Chem Soc Rev 47:422

    Article  CAS  Google Scholar 

  31. Fischer JR, Lessel U, Rarey M (2010) J Chem Inf Model 50:1

    Article  CAS  Google Scholar 

  32. Bian Y, Xie X-QS (2018) AAPS J 20:59

    Article  Google Scholar 

  33. Hall RJ, Murray CW, Verdonk ML (2017) J Med Chem 60:6440

    Article  CAS  Google Scholar 

  34. Misra M, Andrienko D, Baumeier B, Faulon J-L, von Lilienfeld OA (2011) J Chem Theory Comput 7:2549

    Article  CAS  Google Scholar 

  35. Sahu H, Rao W, Troisi A, Ma H (2018) Adv Energy Mater 8:1801032

    Article  Google Scholar 

  36. Sokolov AN, Atahan-Evrenk S, Mondal R, Akkerman HB, Sánchez-Carrera RS, Granados-Focil S, Schrier J, Mannsfeld SCB, Zoombelt AP, Bao Z, Aspuru-Guzik A (2011) Nat Commun, 2

  37. Moral M, Garzón-Ruiz A, Castro M, Canales-Vázquez J, Sancho-García JC (2017) J Phys Chem C 121:28249

    Article  CAS  Google Scholar 

  38. Hutchison GR, Ratner MA, Marks TJ (2005) J Am Chem Soc 127:2339

    Article  CAS  Google Scholar 

  39. Li J, Zhao Y, Tan HS, Guo Y, Di C-A, Yu G, Liu Y, Lin M, Lim SH, Zhou Y, Su H, Ong BS (2012) Sci Rep 2:754 EP

    Article  Google Scholar 

  40. Blouin N, Michaud A, Gendron D, Wakim S, Blair E, Neagu-Plesu R, Belletête M, Durocher G, Tao Y, Leclerc M (2008) J Am Chem Soc 130:732

    Article  CAS  Google Scholar 

  41. Kunkel C, Schober C, Margraf JT, Reuter K, Oberhofer H (2018) submitted

  42. Allen FH (2002) Acta Crystallogr B 58:380

    Article  Google Scholar 

  43. Oberhofer H, Reuter K, Blumberger J (2017) Chem Rev 117:10319

    Article  CAS  Google Scholar 

  44. Marcus RA (1956) J Chem Phys 24:966

    Article  CAS  Google Scholar 

  45. Marcus RA (1993) Rev Mod Phys 65:599

    Article  CAS  Google Scholar 

  46. Schober C, Reuter K, Oberhofer H (2016) J Chem Phys 144:054103

    Article  Google Scholar 

  47. Nelsen SF, Blackstock SC, Kim Y (1987) J Am Chem Soc 109:677

    Article  CAS  Google Scholar 

  48. Blum V, Gehrke R, Hanke F, Havu P, Havu V, Ren X, Reuter K, Scheffler M (2009) Comp Phys Commun 180:2175

    Article  CAS  Google Scholar 

  49. Zhang IY, Ren X, Rinke P, Blum V, Scheffler M (2013) J Phys 15:123033

    Google Scholar 

  50. Becke AD (1988) Phys Rev A 38:3098

    Article  CAS  Google Scholar 

  51. Lee C, Yang W, Parr RG (1988) Phys Rev B 37:785

    Article  CAS  Google Scholar 

  52. Hu Y, Stumpfe D, Bajorath J (2016) J Med Chem 59:4062

    Article  CAS  Google Scholar 

  53. Bemis GW, Murcko MA (1996) J Med Chem 39:2887

    Article  CAS  Google Scholar 

  54. Wang C, Dong H, Hu W, Liu Y, Zhu D (2012) Chem Rev 112:2208

    Article  CAS  Google Scholar 

  55. Jiang W, Li Y, Wang Z (2013) Chem Soc Rev 42:6113

    Article  CAS  Google Scholar 

  56. Landrum G (2018) RDKit: open-source cheminformatics, http://www.rdkit.org [Online; Accessed 07 Aug 2018]

  57. Python software foundation. Python language reference, version 2.7. available at http://www.python.org

  58. Ertl P (2014) J Chem Inf Model 54:1617

    Article  CAS  Google Scholar 

  59. Rabal O, Amr FI, Oyarzabal J (2015) J Chem Inf Model 55:1

    Article  CAS  Google Scholar 

  60. Vogt M, Stumpfe D, Maggiora GM, Bajorath J (2016) J Comput Aided Mol Des 30:191

    Article  CAS  Google Scholar 

  61. Carhart RE, Smith DH, Venkataraghavan R (1985) J Chem Inf Comput Sci 25:64

    Article  CAS  Google Scholar 

  62. Rogers D, Hahn M (2010) J Chem Inf Model 50:742

    Article  CAS  Google Scholar 

  63. Bastian M, Heymann S, Jacomy M (2009) In: International AAAI conference on weblogs and social media

  64. Jacomy M, Venturini T, Heymann S, Bastian M (2014) PLOS ONE 9:1

    Article  Google Scholar 

  65. ChemAxon (2017) Marvin 17.5.0, http://www.chemaxon.com, [Online; Accessed 07 Aug 2018]

  66. Bokeh Development Team (2018) Bokeh: Python library for interactive visualization

  67. Kunkel C, Schober C, Oberhofer H, Reuter K (2018) A chemical space network for organic electronics, https://mediatum.ub.tum.de/147052, [Online, published 22 Dec 2018]

  68. Webcsd (2019) https://www.ccdc.cam.ac.uk/structures/, [Online, Accessed 14 Jan 2019]

  69. Agrafiotisand DK, Wiener JJM (2010) J Med Chem 53:5002

    Article  Google Scholar 

  70. Varin T, Schuffenhauer A, Ertl P, Renner S (2011) J Chem Inf Model 51:1528

    Article  CAS  Google Scholar 

  71. Shelat AA, Guy RK (2007) Nat Chem Biol 3:442 EP

    Article  Google Scholar 

  72. Lin Y, Li Y, Zhan X (2012) Chem Soc Rev 41:4245

    Article  CAS  Google Scholar 

  73. Kitamura M, Arakawa Y (2008) J Phys Condens Matter 20:184011

    Article  Google Scholar 

  74. de la Vega León A, Bajorath J (2016) Future Med Chem 8:1769

    Article  Google Scholar 

  75. Lin Y, Fan H, Li Y, Zhan X (2012) Adv Mater 24:3087

    Article  CAS  Google Scholar 

  76. Canevet D, Sallé M., Zhang G, Zhang D, Zhu D (2009) Chem Commun, 2245

  77. Mei J, Diao Y, Appleton AL, Fang L, Bao Z (2013) J Am Chem Soc 135:6724

    Article  CAS  Google Scholar 

  78. Reig M, Bagdziunas G, Volyniuk D, Grazulevicius JV, Velasco D (2017) Phys Chem Chem Phys 19:6721

    Article  CAS  Google Scholar 

Download references

Acknowledgements

We acknowledge support from the Solar Technologies Go Hybrid initiative of the State of Bavaria and the Leibniz Supercomputing Centre for high-performance computing time at the SuperMUC facility. We further acknowledge support by Deutsche Forschungsgemeinschaft (DFG) through TUM International Graduate School of Science and Engineering (IGSSE), GSC 81.

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Harald Oberhofer.

Additional information

Publisher’s note

Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

This paper belongs to the Topical Collection Tim Clark 70th Birthday Festschrift

Electronic supplementary material

Below is the link to the electronic supplementary material.

(PDF 707 KB)

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Kunkel, C., Schober, C., Oberhofer, H. et al. Knowledge discovery through chemical space networks: the case of organic electronics. J Mol Model 25, 87 (2019). https://doi.org/10.1007/s00894-019-3950-6

Download citation

  • Received:

  • Accepted:

  • Published:

  • DOI: https://doi.org/10.1007/s00894-019-3950-6

Keywords

Navigation