Organic chemistry as a language and the implications of chemical linguistics for structural and retrosynthetic analyses

Angewandte Chemie - International Edition

Volumn 53, Issue 31, 2014, Pages 8108-8112

  Cadeddu, Andrea ^a   Wylie, Elizabeth K ^a   Jurczak, Janusz ^b   Wampler Doty, Matthew ^a   Grzybowski, Bartosz A ^a  

^a Northwestern University   (United States)

^b INSTITUTE OF ORGANIC CHEMISTRY   (Poland)

Author keywords

chemical linguistics; graphs; information technology; retrosynthesis; symmetry

Indexed keywords

COMPUTATIONAL LINGUISTICS; CRYSTAL SYMMETRY; INFORMATION TECHNOLOGY; MOLECULES;

ASYMMETRIC MOLECULES; CORPUS LINGUISTICS; GRAPHS; INFORMATION CONTENTS; MOLECULAR FRAGMENTS; QUANTITATIVE CORRESPONDENCE; RETROSYNTHESIS; RETROSYNTHETIC ANALYSIS;

CHEMICAL ANALYSIS;

EID: 84905364269     PISSN: 14337851     EISSN: 15213773     Source Type: Journal    
DOI: 10.1002/anie.201403708     Document Type: Article

References (23)

1. J. M. Lehn, Supramolecular Chemistry: Concepts and Perspectives, 1 ed., Wiley VCH, Weinheim, 1995.
2. C. D. Manning, H. Schuetze, Foundations of statistical language processing, MIT, Cambridge, 1999
3. K. S. Jones, Thesaurus, Encyclopedia of artificial intelligence, 2nd ed. (Ed.:, S. C. Shapiro,), Wiley, New York, 1992, pp. 1605-1613
4. H. Saggion, T. Poibeau, P. Piskorski, Theory and Applications of Natural Language Processing, Multi-source, Multilingual Information Extraction and Summarization, Springer, Berlin, 2013.
5. G. Zipf, The Psychobiology of Language: An Introduction to Dynamic Philology, MIT, Cambridge, 1935
6. G. Zipf, Human Behavior and the Principle of Last Effort, Addison-Wesley, Cambridge, 1949.
7. While the Zipf law is the most universal characterictic of any natural language, it alone does not describe complexity of languages, relations between grammar and vocabulary, and so on. Zipf's law is also applicable to phenomena outside of linguistics, such as dolphins' sounds, brain waves, and stock markets. For additional literature, see: a) R. Ferrer-i-Cancho, B. McCowan, Entropy 2009, 11, 688-701
8. J. Baixeries, B. Elvevåg, R. Ferrer-i-Cancho, PLoS One 2013, 8, e 53227
9. J. Kwapien, S. Drozdz, Phys. Rep. 2012, 515, 115-226
10. X. Gabaix, Quart. J. Econ. 1999, 3, 739-767.
11. T. McEnery, A. Hardie, Corpus Linguistics: Method, Theory and Practice, Cambridge University Press, Cambridge, 2012
12. N. S. Dash, Corpus Linguistics and Language Technology, Mittal, New Delhi, 2005.
13. E. L. Thorndike, I. Lorge, The Teacher's Word Book of 30 000 Words, Teachers' College, Columbia University, 1944
14. I. S. P. Nation, Vocabulary size, text coverage, and word lists, in Schmitt; McCarthy, Vocabulary: Description, Acquisition and Pedagogy, Cambridge University Press, Cambridge, 1997.
15. We use a modification of a Bag of Words algorithm, based on the Longest Common Substring. BOW algorithms were probably developed by 15th century cryptographers. For a modern mathematical treatment, see:, C. E. Shannon, Bell Syst. Tech. J. 1948, 27, 379-423
16. C. E. Shannon, Bell Syst. Tech. J. 1948, 27, 623-656; for the discussion of largest common substrings, see
17. D. Gusfield, Algorithms on Strings, Trees and Sequences: Computer Science and Computational Biology, Cambridge University Press, Cambridge, 1999.
18. S. Soh, Y. Wei, B. Kowalczyk, C. M. Gothard, B. Baytekin, N. Gothard, B. A. Grzybowski, Chem. Sci. 2012, 3, 1497-1502.
19. M. Kowalik, C. M. Gothard, A. M. Drews, N. A. Gothard, A. Wieckiewicz, P. E. Fuller, B. A. Grzybowski, K. J. M. Bishop, Angew. Chem. 2012, 124, 8052-8056
20. Angew. Chem. Int. Ed. 2012, 51, 7928-7932
21. P. E. Fuller, C. M. Gothard, N. A. Gothard, A. Wieckiewicz, B. A. Grzybowski, Angew. Chem. 2012, 124, 8057-8061
22. Angew. Chem. Int. Ed. 2012, 51, 7933-7937.
23. Disclosure: B. A. G. has a financial interest in Chematica, which is distributed by GSI (Grzybowski Scientific Inventions).