Architecture and evolution of organic chemistry

Angewandte Chemie - International Edition

Volumn 44, Issue 44, 2005, Pages 7263-7269

  Fialkowski, Marcin ^a   Bishop, Kyle J M ^a   Chubukov, Victor A ^a   Campbell, Christopher J ^a   Grzybowski, Bartosz A ^a  

^a Northwestern University   (United States)

Author keywords

Combinatorial chemistry; Master equations; Networks; Organic reactions; Stochastic modeling

Indexed keywords

CHEMICAL INDUSTRY; INDUSTRIAL ENGINEERING; REACTION KINETICS; STATISTICAL METHODS;

ORGANIC CHEMISTRY; ORGANIC MOLECULES; ORGANIC SYNTHESES; STATISTICAL LAWS;

SYNTHESIS (CHEMICAL);

EID: 27844501228     PISSN: 14337851     EISSN: None     Source Type: Journal    
DOI: 10.1002/anie.200502272     Document Type: Article

References (47)

1. K. C. Nicolaou, E. J. Sorensen, Classics in Total Synthesis: Targets Strategies, Methods, Weinheim, New York, 1996.
2. N. Anand, J. S. Bindra, S. Randanathan, Art in Organic Synthesis, Holden-Day, San Francisco, 1970.
3. E. J. Corey, A. K. Long, S. D. Rubenstein, Science 1985, 228, 408.
4. S. L. Schreiber, Science 2000, 287, 1964.
5. K. C. Nicolaou, D. Vourloumis, N. Winssinger, P. S. Baran, Angew. Chem. 2000, 112, 46;
6. Angew. Chem. Int. Ed. 2000, 39, 44.
7. M. D. Burke, S. L. Schreiber, Angew. Chem. 2004, 116, 48;
8. Angew. Chem. Int. Ed. 2004, 43, 46.
9. E. J. Corey, X.-M. Cheng, The Logic of Chemical Synthesis, Wiley, New York, 1989.
10. M. R. Spaller, M. T. Burger, M. Fardis, P. A. Bartlett, Curr. Opin. Chem. Biol. 1997, 1, 47.
11. C. Lipinski, A. Hopkins, Nature 2004, 432, 855.
12. R. Albert, A. L. Barabasi, Rev. Mod. Phys. 2002, 74, 47.
13. A. L. Barabasi, R. Albert, Science 1999, 286, 509.
14. L. A. N. Amaral, J. M. Ottino, Eur. Phys. J. B 2004, 38, 147.
15. L. A. N. Amaral, A. Scala, M. Barthelemy, H. E. Stanley, Proc. Natl. Acad. Sci. USA 2000, 97, 11 149.
16. C. M. Song, S. Havlin, H. A. Makse, Nature 2005, 433, 392.
17. R. Albert, H. Jeong, A. L. Barabasi, Nature 1999, 401, 130.
18. A. Broder, R. Kumar, F. Maghoul, P. Raghavan, S. Rajagopalan, R. Stata, A. Tomkins, J. Wiener, Comput. Networking 2000, 33, 309.
19. D. Sornette, R. Cont, J. Phys. I 1997, 7, 431.
20. L. Dehaan, R. L. Karandikar, Stock. Process. Their Appl. 1989, 32, 225.
21. MDL Crossfire Beilstein database; we stress that although Beilstein has data on numerous man-made polymers, it is not a comprehensive repository of biological polymers (proteins, DNA).
22. M. Faloutsos, P. Faloutsos, C. Faloutsos, Comput. Commun. Rev. 1999, 29, 251.
23. H. Jeong, B. Tombor, R. Albert, Z. N. Oltval, A. L. Barabasi, Nature 2000, 407, 651.
24. S. Redner, Eur. Phys. J. B 1998, 4, 131.
25. F. Liljeros, C. R. Edling, L. A. N. Amaral, H. E. Stanley, Y. Aberg, Nature 2001, 411, 907.
26. C. G. Screttas, G. A. Heropoulos, THEOCHEM 1994, 309, 149.
27. C. Wandrey, A. Bartkowiak, D. Hunkeler, Langmuir 1999, 15, 4062.
28. J. B. Hendrickson, P. Huang, A. G. Toczko, J. Chem. Inf. Comput. Sci. 1987, 27, 63; we wrote a computer program based on the Hendrickson algorithm, which was used to calculate complexity factors of 1000 randomly chosen organic molecules from the BD. We found that the values of the factors correlated with molecular masses with the correlation coefficient R = 0.72. The executable of the program along with instructions can be downloaded free of charge from our web page (http://www.dysa.northwestern. edu).
29. T. K. Allu, T. I. Oprea, J. Chem. Info. Model 2005, 45, 1237.
30. max corresponds to the distribution maximum.
31. μ) = 1.
32. This is unlike the pure Kesten process, in which the old distribution is discarded after each iteration.
33. The values of the effective multiplicative (a = 0.67) and additive (b = 179.94) coefficients are commensurate with those derived from the stochastic master equation, (Formula Presented).
34. These observations can also be understood in terms of combinatorial considerations and reflect the fact that 1) on one hand, there are relatively few combinations of atoms that give rise to structures of low molecular mass. It can be readily estimated that the possible numbers of molecules of mass m increase roughly exponentially with m. 2) On the other hand, when two large molecules are "stitched" together, there are many possible combinations (orientations) of doing so and achieving a selective, high-yield synthesis is problematic.
35. D. C. Rees, M. Congreve, C. W. Murray, R. Carr, Nat. Rev. Drug Discovery 2004, 3, 660.
36. E. J. Martin, R. E. Critchlow, J. Comb. Chem. 1999, 1, 32.
37. A. K. Ghose, V. N. Viswanadhan, J. J. Wendoloski, J. Comb. Chem. 1999, 1, 55.
38. T. I. Oprea, J. Comput.-Aided Mater. Des. 2000, 14, 251; therein a comparison is made between the mass distributions of the Available Chemical Directory (ADC) and MACCS II Drug Data Report (MDDR) (we note that the ADC is not necessarily representative of "random" substances).
39. J. Xu, J. Stevenson, J. Chem. Inf. Comput. Sci. 2000, 40, 1177.
40. Medical Essential Drug Database http://lsb.sbs.auckland.ac.nz/classic/ medbase.
41. Chemical Prices, Chemical Market Reporter, March 7, 2005 http://www.chemicalmarketreporterrcom.
42. S. Camazine, Behav. Ecol. Sociobiol. 1991, 28, 61.
43. S. Camazine, J.-L. Deneubourg, N. R. Franks, J. Sneyd, G. Theraulaz, E. Bonabeau, Self-Organization in Biological Systems, Princeton University Press, Princeton, 2001.
44. D. J. Watts, S. H. Strogatz, Nature 1998, 393, 440.
45. R. V. Sole, J. M. Montoya, Proc. R. Soc. London Ser. B 2001, 268, 2039.
46. A. Sih, G. Englund, D. Wooster, Trends Ecol. Evol. 1998, 13, 350.
47. Details of an example for combinatorial chemistry, a discussion of the network wiring scheme, and details of the Beilstein Database are given in the Supporting Information.