Collect. Czech. Chem. Commun.
2008, 73, 1261-1270
https://doi.org/10.1135/cccc20081261
Quantum Chemical Benchmark Energy and Geometry Database for Molecular Clusters and Complex Molecular Systems (www.begdb.com): A Users Manual and Examples
Jan Řezáča, Petr Jurečkab, Kevin E. Rileya, Jiří Černýa, Haydee Valdesa, Kristýna Pluháčkováa, Karel Berkaa, Tomáš Řezáča, Michal Pitoňáka, Jiří Vondrášeka and Pavel Hobzaa,b,*
a Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, v.v.i. and Center for Biomolecules and Complex Systems, 166 10 Prague 6, Czech Republic
b Department of Physical Chemistry, Palacký University, třída Svobody 26, 771 46 Olomouc, Czech Republic
References
1. P., Šponer J., Černý J., Hobza P.: Phys. Chem. Chem. Phys. 2006, 8, 1985.
<https://doi.org/10.1039/b600027d>
2. K. E., Hobza P.: J. Phys. Chem. A 2007, 111, 8257.
<https://doi.org/10.1021/jp073358r>
3. K. E., Hobza P.: J. Chem. Theory Comput. 2008, 4, 232.
<https://doi.org/10.1021/ct700216w>
4. H., Spiwok V., Řezáč J., Řeha D., Abo-Riziq A. G., de Vries M. S., Hobza P.: Chem. Eur. J. 2008, 14, 4886.
<https://doi.org/10.1002/chem.200800085>
5. H., Pluháčková K., Pitoňák M., Řezáč J., Hobza P.: Phys. Chem. Chem. Phys. 2008, 10, 2747.
<https://doi.org/10.1039/b719294k>
6. D., Valdes H., Vondrášek J., Hobza P., Abu-Riziq A., Crews B., de Vries M. S.: Chem. Eur. J. 2005, 11, 6803.
<https://doi.org/10.1002/chem.200500465>
7. P., Černý J., Hobza P., Salahub D. R.: J. Comput. Chem. 2007, 28, 555.
<https://doi.org/10.1002/jcc.20570>
8. T., Thiel W.: Phys. Chem. Chem. Phys. 2008, 10, 2159.
<https://doi.org/10.1039/b718795e>
9a. Y., Vela A., Salahub D. R.: Theor. Chem. Acc. 2007, 118, 693.
<https://doi.org/10.1007/s00214-007-0347-x>
9b. Y., Salahub D. R.: Chem. Phys. Lett. 2007, 436, 394.
<https://doi.org/10.1016/j.cplett.2007.01.074>
10. K. E., Vondrasek J., Hobza P.: Phys. Chem. Chem. Phys. 2007, 9, 5555.
<https://doi.org/10.1039/b708089a>
11a. J. G., Platts J. A.: Phys. Chem. Chem. Phys. 2008, 10, 2785.
<https://doi.org/10.1039/b718691f>
11b. J. G., Platts J. A.: J. Chem. Theory Comput. 2007, 3, 80.
<https://doi.org/10.1021/ct6002737>
12a. J. P., Sharma R., Vincent M. A., Hillier I. H., Morgado C. A.: Phys. Chem. Chem. Phys. 2008, 10, 128.
<https://doi.org/10.1039/b711498b>
12b. C. A., McNamara J. P., Hillier I. H., Burton N. A.: J. Chem. Theory Comput. 2007, 3, 1656.
<https://doi.org/10.1021/ct700072a>
12c. J. P., Hillier I. H.: Phys. Chem. Chem. Phys. 2007, 9, 2362.
<https://doi.org/10.1039/b701890h>
13a. Y., Truhlar D. G.: Theor. Chem. Acc. 2008, 120, 215.
<https://doi.org/10.1007/s00214-007-0310-x>
13b. Y., Truhlar D. G.: J. Phys. Chem. C 2008, 112, 4061.
<https://doi.org/10.1021/jp710918f>
13c. Y., Truhlar D. G.: Acc. Chem. Res. 2008, 41, 157.
<https://doi.org/10.1021/ar700111a>
13d. Y., Truhlar D. G.: J. Chem. Theory Comput. 2007, 3, 289.
<https://doi.org/10.1021/ct6002719>
13e. Y., Truhlar D. G.: J. Chem. Phys. 2006, 125, 194101.
<https://doi.org/10.1063/1.2370993>
14. T., Guerra C. F., Swart M., Bickelhaupt F. M.: Chem. Phys. Lett. 2006, 426, 415.
<https://doi.org/10.1016/j.cplett.2006.06.057>
15a. S., Antony J., Schwabe T., Muck-Lichtenfeld C.: Org. Biomol. Chem. 2007, 5, 741.
<https://doi.org/10.1039/b615319b>
15b. J., Grimme S.: Phys. Chem. Chem. Phys. 2006, 8, 5287.
<https://doi.org/10.1039/b612585a>
16. C., Vincent M. A., Hillier I. H., Shan X.: Phys. Chem. Chem. Phys. 2007, 9, 448.
<https://doi.org/10.1039/b615263e>
17. J. M., Cavallo L.: J. Phys. Chem. B 2007, 111, 13124.
<https://doi.org/10.1021/jp072317s>
18a. C., Grimme S.: Mol. Phys. 2007, 105, 2793.
<https://doi.org/10.1080/00268970701635543>
18b. T., Grimme S.: Phys. Chem. Chem. Phys. 2007, 9, 3397.
<https://doi.org/10.1039/b704725h>
19. E., Leininger T., Manby F. R., Mitrushchenkov A., Werner H. J., Stoll H.: Phys. Chem. Chem. Phys. 2008, 10, 3353.
<https://doi.org/10.1039/b804672g>
20. T., DiStasio R. A., Lochan R. C., Chai J. D., Head-Gordon M.: J. Phys. Chem. A 2008, 112, 2702.
<https://doi.org/10.1021/jp710439w>
21. V. R., Thonhauser T., Langreth D. C.: J. Chem. Phys. 2008, 128, 204102.
<https://doi.org/10.1063/1.2924133>
22. T., Tsuneda T., Hirao K.: J. Chem. Phys. 2007, 126, 234114.
<https://doi.org/10.1063/1.2747243>
23. J., Grimme S.: Phys. Chem. Chem. Phys. 2006, 8, 5287.
<https://doi.org/10.1039/b612585a>
24. J. G., Platts J. A.: J. Chem. Theory Comput. 2007, 3, 80.
<https://doi.org/10.1021/ct6002737>
25. R. A., Head-Gordon M.: Mol. Phys. 2007, 105, 1073.
<https://doi.org/10.1080/00268970701283781>
26. T., Hohenstein E. G., Sherrill C. D.: J. Chem. Phys. 2008, 128, 124111.
<https://doi.org/10.1063/1.2883974>
27. O., Werner H. J.: Phys. Chem. Chem. Phys. 2008, 10, 3400.
<https://doi.org/10.1039/b804334e>
28. M., Luchow A., Grimme S.: J. Phys. Chem. A 2008, 112, 2104.
<https://doi.org/10.1021/jp077592t>
29a. A., Jansen G., Schutz M.: J. Am. Chem. Soc. 2006, 128, 11730.
<https://doi.org/10.1021/ja0633363>
29b. R., Jurečka P., Hobza P.: J. Chem. Phys. 2007, 127, 075104.
<https://doi.org/10.1063/1.2759207>
30a. M., Bludský O., Nachtigall P.: ChemPhysChem 2008, 9, 1702.
<https://doi.org/10.1002/cphc.200800274>
30b. O., Rubeš M., Soldán P., Nachtigall P.: J. Chem. Phys. 2008, 128, 114102.
<https://doi.org/10.1063/1.2890968>
31a. I. C., Rothlisberger U.: Phys. Chem. Chem. Phys. 2008, 10, 2730.
<https://doi.org/10.1039/b718594d>
31b. I. C., von Lilienfeld O. A., Coutinho-Neto M. D., Tavernelli I., Rothlisberger U.: J. Phys. Chem. B 2007, 111, 14346.
<https://doi.org/10.1021/jp0750102>
32. T., Jurečka P., Černý J., Řezáč J., Otyepka M., Valdes H., Hobza P.: J. Phys. Chem. A 2007, 111, 5642.
<https://doi.org/10.1021/jp068858j>
33. E. R., McKay D. J. J., DiLabio G. A.: Chem. Phys. Lett. 2007, 435, 201.
<https://doi.org/10.1016/j.cplett.2006.12.080>
34a. V., Biczysko M., Pavone M.: Chem. Phys. 2008, 346, 247.
<https://doi.org/10.1016/j.chemphys.2008.02.036>
34b. P., Czyznikowska Z., Zalesny R., Czelen P.: Phys. Chem. Chem. Phys. 2008, 10, 2665.
<https://doi.org/10.1039/b718635e>
34c. L. R., Durst H. F., Wetmore S. D.: Phys. Chem. Chem. Phys. 2008, 10, 2801.
<https://doi.org/10.1039/b718621e>
34d. J., Palermo N. Y., Murphy R. F., Lovas S.: J. Comput. Chem. 2008, 29, 1344.
<https://doi.org/10.1002/jcc.20898>
34e. O., Budzak S., Medved M., Mach P.: Int. J. Quantum Chem. 2008, 108, 1533.
<https://doi.org/10.1002/qua.21685>
34f. I. C., von Lilienfeld O. A., Coutinho-Neto M. D., Tavernelli I., Rothlisberger U.: J. Phys. Chem. B 2007, 111, 14346.
<https://doi.org/10.1021/jp0750102>
34g. M., Gonzalez L.: J. Comput. Chem. 2007, 28, 2299.
<https://doi.org/10.1002/jcc.20743>
34h. K. M., Sokalski W. A., Leszczynski J.: J. Chem. Phys. 2007, 127.
34i. M., Hobza P.: J. Phys. Chem. A 2007, 111, 5851.
<https://doi.org/10.1021/jp071486+>
34j. W., Kelly R. E. A., Dong M. D., Kantorovich L. N., Besenbacher F.: J. Am. Chem. Soc. 2008, 130, 695.
<https://doi.org/10.1021/ja076832f>
34k. J. P., Sharma R., Vincent M. A., Hillier I. H., Morgado C. A.: Phys. Chem. Chem. Phys. 2008, 10, 128.
<https://doi.org/10.1039/b711498b>
34l. J. P., Chevreau H., Gresh N.: J. Chem. Theory Comput. 2007, 3, 824.
<https://doi.org/10.1021/ct7000182>
35a. T. D., de Boer T., Simons J. P., Snoek L. C.: Phys. Chem. Chem. Phys. 2008, 10, 1443.
<https://doi.org/10.1039/b716666d>
35b. D. F., Siegrist K., Heilweil E. J., Esenturk M.: ChemPhysChem 2007, 8, 2412.
<https://doi.org/10.1002/cphc.200700332>
36a. T., Grimme S.: Phys. Chem. Chem. Phys. 2007, 9, 3397.
<https://doi.org/10.1039/b704725h>
36b. L. F., van Mourik T.: Chem. Phys. Lett. 2007, 442, 42.
<https://doi.org/10.1016/j.cplett.2007.05.072>
36c. K. E., Op’t Holt B. T., Merz K. M.: J. Chem. Theory Comput. 2007, 3, 407.
<https://doi.org/10.1021/ct600185a>
36d. T., Karamertzanis P. G., Price S. L.: J. Phys. Chem. A 2006, 110, 8.
<https://doi.org/10.1021/jp0563181>
37. Jmol: An Open-Source Java Viewer for Chemical Structures in 3D. http://www.jmol.org/.
38. http://www.php.net/.
39. http://www.mysql.com/.
40a. M., Pozerag D., Jungnickel G., Elsner J., Haugk M., Frauenheim T., Suhai S., Seifert G.: Phys. Rev. B 1998, 58, 7260.
<https://doi.org/10.1103/PhysRevB.58.7260>
40b. M., Hobza P., Frauenheim T., Suhai S., Kaxiras E.: J. Chem. Phys. 2001, 114, 5149.
<https://doi.org/10.1063/1.1329889>

