Inverse molecular design in a tight-binding framework

Journal of Chemical Physics

Volumn 129, Issue 4, 2008, Pages

  Xiao, Dequan ^a   Yang, Weitao ^a   Beratan, David N ^a,b  

^a DUKE UNIVERSITY   (United States)

^b DUKE UNIVERSITY SCHOOL OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

AROMATIC COMPOUNDS; ARSENIC COMPOUNDS; BINDING ENERGY; CHEMICAL COMPOUNDS; CHLORINE COMPOUNDS; ERROR ANALYSIS; MATERIALS PROPERTIES; OPTIMIZATION; SULFUR COMPOUNDS; TERBIUM ALLOYS;

ATOMIC POTENTIALS; CHEMICAL LIBRARIES; CHEMICAL SPECIES; CONTINUOUS OPTIMIZATION; FIRST HYPERPOLARIZABILITIES; HYPERPOLARIZABILITIES; LINEAR COMBINATION; LUMO ENERGY; MOLECULAR CANDIDATES; MOLECULAR DESIGNS; MOLECULAR SPECIES; OPTIMAL PROPERTIES; OPTIMAL STRUCTURES; OPTIMIZE TRANSITION; SYNTHETIC METHODS; TIGHT-BINDING; TIGHT-BINDING APPROACH;

STRUCTURAL OPTIMIZATION;

ALGORITHM; ARTICLE; DRUG DESIGN;

ALGORITHMS; DRUG DESIGN;

EID: 49149112707     PISSN: 00219606     EISSN: None     Source Type: Journal    
DOI: 10.1063/1.2955756     Document Type: Article

References (30)

1. P. Ertl, J. Chem. Inf. Comput. Sci. 43, 374 (2003).
2. M. M. Hann and T. I. Opera, Curr. Opin. Chem. Biol. 8, 255 (2004).
3. F. Besenbacher, I. Chorkendorff, B. S. Clausen, B. Hammer, A. M. Molenbroek, J. K. Nørskov, and I. Stensgaard, Science 0036-8075 10.1126/science.279.5358.1913 279, 1913 (1998); G. Ceder, Y. M. Chiang, D. R. Sadoway, M. K. Aydinol, Y. I. Jang, and B. Huang, Nature (London) 0028-0836 10.1038/33647 392, 694 (1998); S. V. Dudiy and A. Zunger, Phys. Rev. Lett. 0031-9007 10.1103/PhysRevLett.97.046401 97, 046401 (2006); K. Honkala, A. Hellman, I. N. Remediakis, A. Logadottir, A. Carlsson, S. Dahl, C. H. Christensen, and J. K. Nørskov, Science 0036-8075 10.1126/science.1106435 307, 555 (2005); G. H. Jóannesson, T. Bligaard, A. V. Ruban, H. L. Skriver, K. W. Jacobsen, and J. K. Nøskov, Phys. Rev. Lett. 0031-9007 10.1103/PhysRevLett.88.255506 88, 255506 (2002); O. A. von Lilienfeld and M. E. Tuckerman, J. Chem. Phys. 0021-9606 10.1063/1.2338537 125, 154104 (2006); O. A. von Lilienfeld and M. E. Tuckerman, J. Chem. Theory Comput. 3, 1083 (2007).
4. H. An and P. D. Cook, Chem. Rev. (Washington, D.C.) 0009-2665 10.1021/cr990014r 100, 3311 (2000); J. Ellman, B. Stoddard, and J. Wells, Proc. Natl. Acad. Sci. U.S.A. 0027-8424 10.1073/pnas.94.7.2779 94, 2779 (1997); M. C. Pirrung, Molecular Diversity and Combinatorial Chemistry: Principles and Applications (Elsevier, Oxford, 2004); B. K. Shoichet, Nature (London) 0028-0836 10.1038/nature03197 432, 862 (2004); B. R. Stockwell, Nature (London) 132, 846 (2004); N. K. Terrett, Combinatorial Chemistry, (Oxford University Press, New York, 1998).
5. X.-D. Xiang, X. Sun, G. Briceno, Y. Lou, K.-A. Wang, H. Chang, W. G. Wallace-Freedman, S.-W. Chen, and P. G. Schultz, Science 268, 1738 (1995).
6. A. Franceschetti and A. Zunger, Nature (London) 252, 103 (1999).
7. D. Morgan, G. Ceder, and S. Curtarolo, Meas. Sci. Technol. 16, 196 (2005).
8. G. L. W. Hart, V. Blum, M. J. Walorski, and A. Zunger, Nat. Mater. 4, 391 (2005).
9. G. E. Kellogg and S. F. Semus, in Modern Methods of Drug Discovery, edited by, A. Hillisch, and, R. Hilgenfeld, (Birkhäuser Verlag, Boston, 2003).
10. M. Wang, X. Hu, D. N. Beratan, and W. Yang, J. Am. Chem. Soc. 128, 3228 (2006).
11. C. Kuhn and D. N. Beratan, J. Phys. Chem. 100, 10595 (1996).
12. X. Hu, D. N. Beratan, and W. Yang, J. Chem. Phys., (in press, 2008); S. Keinan, X. Hu, D. N. Beratan, and W. Yang, J. Phys. Chem. A 111, 176 (2007); S. Keinan, W. D. Paquette, J. K. Skoko, D. N. Beratan, W. Yang, S. Shinde, P. A. Johnston, J. S. Law, and P. Wipf, Org. Biomol. Chem. (in press, 2008).
13. O. A. von Lilienfeld, R. D. Lins, and U. Rothlisberger, Phys. Rev. Lett. 95, 153021 (2005).
14. M. d'Avezac and A. Zunger, J. Phys.: Condens. Matter 19, 402201 (2007).
15. A. Franceschetti, S. V. Dudiy, S. V. Barabash, A. Zunger, J. Xu, and M. van Schilfgaarde, Phys. Rev. Lett. 0031-9007 10.1103/PhysRevLett.97.047202 97, 047202 (2006); L.-W. Wang and A. Zunger, J. Chem. Phys. 100, 2394 (1994).
16. V. Marcon, O. A. von Lilienfeld, and D. Andrienko, J. Chem. Phys. 127, 064305 (2007).
17. E. Hückel, Z. Phys. 70, 204 (1931).
18. F. A. Van-Catledge, J. Org. Chem. 45, 4801 (1980).
19. D. Porezag, T. Frauenheim, T. Köhler, G. Seifert, and R. Kaschner, Phys. Rev. B 0163-1829 10.1103/PhysRevB.51.12947 51, 12947 (1995); M. Elstner, D. Porezag, G. Jungnickel, J. Elsner, M. Haugk, T. Frauenheim, S. Suhai, and G. Seifert, Phys. Rev. B 58, 7260 (1998).
20. G. Maerkl and P. Kreitmeier, in Phosphorus-Carbon Heterocyclic Chemistry: The Rise of a New Domain, edited by, F. Mathey, (Elsevier Science, Oxford, 2001).
21. H. A. Kurtz and D. S. Dudis, in Reviews in Computational Chemistry, edited by, K. B. Lipkowitz, and, D. B. Boyd, (Wiley-VCH, New York, 1998), Vol. 12.
22. I. D. L. Albert, T. J. Marks, and M. A. Ratner, J. Am. Chem. Soc. 120, 11174 (1998).
23. See EPAPS Document No. E-JCPSA6-129-618829 for details of the property calculations using the Hückel tight method; optimization details; comparison to sum-over-state calculations; optimized transition moments and energy gaps; optimization result histograms; and normalized statistic histograms of the enumerating chemical spaces. For more information on EPAPS, see http://www.aip.org/pubservs/epaps.html; source code is available on request from the authors.
24. R. W. Boyd, Nonlinear Optics (Academic, New York, 1992); D. R. Kanis, M. A. Ratner, and T. J. Marks, Chem. Rev. (Washington, D.C.) 0009-2665 10.1021/cr00025a007 94, 195 (1994); S. M. Risser, D. N. Beratan, and S. R. Marder, J. Am. Chem. Soc. 115, 7719 (1993).
25. S. S. Rao, Optimization Theory and Application, 2nd ed. (Halsted, New York, 1978).
26. E. F. Archibong and A. J. Thakkar, J. Chem. Phys. 0021-9606 10.1063/1.464537 98, 8324 (1993); M. Blanchard-Desce, J. M. Lehn, M. Barzoukas, I. Ledoux, and J. Zyss, Chem. Phys. 181, 281 (1994).
27. D. N. Beratan, J. N. Onuchic, and J. W. Perry, J. Phys. Chem. 91, 2696 (1987).
28. D. S. Chemla and J. Zyss, Nonlinear Optical Properties of Organic Molecules and Crystals (Academic, Orlando, 1987).
29. S. R. Marder, D. N. Beratan, and L.-T. Cheng, Science 252, 103 (1991).
30. For a diatomic π system, the Hückel Hamiltonian is (Ha Hab Hba Hb) with the eigenstate energies E= (Ha + Hb) 2± 4 H ab 2 + (Ha - Hb)2 2. The energy gap is Egap = 4 H ab 2 + (Ha - Hb)2. Egap decreases as H ab 2 decreases.