CNDOL: A fast and reliable method for the calculation of electronic properties of very large systems. Applications to retinal binding pocket in rhodopsin and gas phase porphine

Journal of Chemical Physics

Volumn 127, Issue 14, 2007, Pages

  Montero Cabrera, Luis Alberto ^a   Röhrig, Ute ^b   Padrón Garcia, Juan A ^a   Crespo Otero, Rachel ^a   Montero Alejo, Ana L ^a   Garcia De La Vega, Joś M ^c   Chergui, Majed ^d   Rothlisberger, Ursula ^d  

^a UNIVERSITY OF HAVANA   (Cuba)

^b SWISS INSTITUTE OF BIOINFORMATICS   (Switzerland)

^c UNIVERSIDAD AUTÓNOMA DE MADRID   (Spain)

^d EPFL   (Switzerland)

Author keywords

[No Author keywords available]

Indexed keywords

CHARGE TRANSFER; ELECTRIC EXCITATION; ELECTRONIC PROPERTIES; HAMILTONIANS; MOLECULES; NUMERICAL METHODS;

BINDING POCKET; GAS PHASE PORPHINE; RETINALDEHYDE POLYENE CHAIN; RHODOPSIN;

ORGANIC COMPOUNDS;

POLYENE; PORPHINE; PORPHYRIN; RETINAL; RHODOPSIN; UNCLASSIFIED DRUG;

ARTICLE; BINDING SITE; BIOLOGY; CHEMICAL MODEL; CHEMISTRY; ELECTRONICS; GAS; METHODOLOGY; QUANTUM THEORY; THERMODYNAMICS;

BINDING SITES; COMPUTATIONAL BIOLOGY; ELECTRONICS; GASES; MODELS, CHEMICAL; POLYENES; PORPHYRINS; QUANTUM THEORY; RETINALDEHYDE; RHODOPSIN; THERMODYNAMICS;

EID: 35248864928     PISSN: 00219606     EISSN: None     Source Type: Journal    
DOI: 10.1063/1.2761869     Document Type: Article

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55. A.-N. Bondar, S. Suhai, S. Fischer, J. C. Smith, and M. Elstner, J. Struct. Biol. 1047-8477 157, 454 (2007); S. Sekharan, M. Sugihara, and V. Buss, Angew. Chem., Int. Ed. 1433-7851 10.1002/anie.200603306 46, 269 (2007); K. Fujimoto, S. Hayashi, J.-Y. Hasegawa, and H. Nakatsuji, J. Chem. Theory Comput. 1549-9618 3, 605 (2007); M. Wanko, M. Hoffmann, T. Frauenheim, and M. Elstner, J. Comput.-Aided Mol. Des. 0920-654X 10.1007/s10822-006-9069-8 20, 511 (2006); M. Sugihara, J. Hufen, and V. Buss, Biochemistry 0006-2960 45, 801 (2006); C. Silva López, O. Nieto Faza, S. Lopez Est́vez, and A. R. De Lera, J. Comput. Chem. 0192-8651 10.1002/jcc.20305 27, 116 (2006); S. Sekharan, O. Weingart, and V. Buss, Biophys. J. 0006-3495 91, L7 (2006); M. Schreiber, M. Sugihara, T. Okada, and V. Buss, Angew. Chem., Int. Ed. 1433-7851 45, 4274 (2006); S. Schenkl, F. van Mourik, N. Friedman, M. Sheves, R. Schlesinger, S. Haacke, and M. Chergui, Proc. Natl. Acad. Sci. U.S.A. 0027-8424 103, 4101 (2006); R. M. L. Savedra, M. F. S. Pinto, and M. Trsic, J. Chem. Phys. 0021-9606 125, 144901/1 (2006); D. Riccardi, P. Schaefer, Y. Yang, H. Yu, N. Ghosh, X. Prat-Resina, P. Koenig, G. Li, D. Xu, H. Guo, M. Elstner, and Q. Cui, J. Phys. Chem. B 1089-5647 10.1021/jp056361o 110, 6458 (2006); A. M. Losa, I. F. Galvan, M. E. Martin, and M. A. Aguilar, J. Phys. Chem. B 1089-5647 110, 18064 (2006); M. O. Lenz, R. Huber, B. Schmidt, P. Gilch, R. Kalmbach, M. Engelhard, and J. Wachtveitl, Biophys. J. 91, 255 (2006).
56. A.-N. Bondar, S. Suhai, S. Fischer, J. C. Smith, and M. Elstner, J. Struct. Biol. 1047-8477 157, 454 (2007); S. Sekharan, M. Sugihara, and V. Buss, Angew. Chem., Int. Ed. 1433-7851 10.1002/anie.200603306 46, 269 (2007); K. Fujimoto, S. Hayashi, J.-Y. Hasegawa, and H. Nakatsuji, J. Chem. Theory Comput. 1549-9618 3, 605 (2007); M. Wanko, M. Hoffmann, T. Frauenheim, and M. Elstner, J. Comput.-Aided Mol. Des. 0920-654X 10.1007/s10822-006-9069-8 20, 511 (2006); M. Sugihara, J. Hufen, and V. Buss, Biochemistry 0006-2960 45, 801 (2006); C. Silva López, O. Nieto Faza, S. Lopez Est́vez, and A. R. De Lera, J. Comput. Chem. 0192-8651 10.1002/jcc.20305 27, 116 (2006); S. Sekharan, O. Weingart, and V. Buss, Biophys. J. 0006-3495 91, L7 (2006); M. Schreiber, M. Sugihara, T. Okada, and V. Buss, Angew. Chem., Int. Ed. 1433-7851 45, 4274 (2006); S. Schenkl, F. van Mourik, N. Friedman, M. Sheves, R. Schlesinger, S. Haacke, and M. Chergui, Proc. Natl. Acad. Sci. U.S.A. 0027-8424 103, 4101 (2006); R. M. L. Savedra, M. F. S. Pinto, and M. Trsic, J. Chem. Phys. 0021-9606 125, 144901/1 (2006); D. Riccardi, P. Schaefer, Y. Yang, H. Yu, N. Ghosh, X. Prat-Resina, P. Koenig, G. Li, D. Xu, H. Guo, M. Elstner, and Q. Cui, J. Phys. Chem. B 1089-5647 10.1021/jp056361o 110, 6458 (2006); A. M. Losa, I. F. Galvan, M. E. Martin, and M. A. Aguilar, J. Phys. Chem. B 1089-5647 110, 18064 (2006); M. O. Lenz, R. Huber, B. Schmidt, P. Gilch, R. Kalmbach, M. Engelhard, and J. Wachtveitl, Biophys. J. 91, 255 (2006).
57. A.-N. Bondar, S. Suhai, S. Fischer, J. C. Smith, and M. Elstner, J. Struct. Biol. 1047-8477 157, 454 (2007); S. Sekharan, M. Sugihara, and V. Buss, Angew. Chem., Int. Ed. 1433-7851 10.1002/anie.200603306 46, 269 (2007); K. Fujimoto, S. Hayashi, J.-Y. Hasegawa, and H. Nakatsuji, J. Chem. Theory Comput. 1549-9618 3, 605 (2007); M. Wanko, M. Hoffmann, T. Frauenheim, and M. Elstner, J. Comput.-Aided Mol. Des. 0920-654X 10.1007/s10822-006-9069-8 20, 511 (2006); M. Sugihara, J. Hufen, and V. Buss, Biochemistry 0006-2960 45, 801 (2006); C. Silva López, O. Nieto Faza, S. Lopez Est́vez, and A. R. De Lera, J. Comput. Chem. 0192-8651 10.1002/jcc.20305 27, 116 (2006); S. Sekharan, O. Weingart, and V. Buss, Biophys. J. 0006-3495 91, L7 (2006); M. Schreiber, M. Sugihara, T. Okada, and V. Buss, Angew. Chem., Int. Ed. 1433-7851 45, 4274 (2006); S. Schenkl, F. van Mourik, N. Friedman, M. Sheves, R. Schlesinger, S. Haacke, and M. Chergui, Proc. Natl. Acad. Sci. U.S.A. 0027-8424 103, 4101 (2006); R. M. L. Savedra, M. F. S. Pinto, and M. Trsic, J. Chem. Phys. 0021-9606 125, 144901/1 (2006); D. Riccardi, P. Schaefer, Y. Yang, H. Yu, N. Ghosh, X. Prat-Resina, P. Koenig, G. Li, D. Xu, H. Guo, M. Elstner, and Q. Cui, J. Phys. Chem. B 1089-5647 10.1021/jp056361o 110, 6458 (2006); A. M. Losa, I. F. Galvan, M. E. Martin, and M. A. Aguilar, J. Phys. Chem. B 1089-5647 110, 18064 (2006); M. O. Lenz, R. Huber, B. Schmidt, P. Gilch, R. Kalmbach, M. Engelhard, and J. Wachtveitl, Biophys. J. 91, 255 (2006).
58. A.-N. Bondar, S. Suhai, S. Fischer, J. C. Smith, and M. Elstner, J. Struct. Biol. 1047-8477 157, 454 (2007); S. Sekharan, M. Sugihara, and V. Buss, Angew. Chem., Int. Ed. 1433-7851 10.1002/anie.200603306 46, 269 (2007); K. Fujimoto, S. Hayashi, J.-Y. Hasegawa, and H. Nakatsuji, J. Chem. Theory Comput. 1549-9618 3, 605 (2007); M. Wanko, M. Hoffmann, T. Frauenheim, and M. Elstner, J. Comput.-Aided Mol. Des. 0920-654X 10.1007/s10822-006-9069-8 20, 511 (2006); M. Sugihara, J. Hufen, and V. Buss, Biochemistry 0006-2960 45, 801 (2006); C. Silva López, O. Nieto Faza, S. Lopez Est́vez, and A. R. De Lera, J. Comput. Chem. 0192-8651 10.1002/jcc.20305 27, 116 (2006); S. Sekharan, O. Weingart, and V. Buss, Biophys. J. 0006-3495 91, L7 (2006); M. Schreiber, M. Sugihara, T. Okada, and V. Buss, Angew. Chem., Int. Ed. 1433-7851 45, 4274 (2006); S. Schenkl, F. van Mourik, N. Friedman, M. Sheves, R. Schlesinger, S. Haacke, and M. Chergui, Proc. Natl. Acad. Sci. U.S.A. 0027-8424 103, 4101 (2006); R. M. L. Savedra, M. F. S. Pinto, and M. Trsic, J. Chem. Phys. 0021-9606 125, 144901/1 (2006); D. Riccardi, P. Schaefer, Y. Yang, H. Yu, N. Ghosh, X. Prat-Resina, P. Koenig, G. Li, D. Xu, H. Guo, M. Elstner, and Q. Cui, J. Phys. Chem. B 1089-5647 10.1021/jp056361o 110, 6458 (2006); A. M. Losa, I. F. Galvan, M. E. Martin, and M. A. Aguilar, J. Phys. Chem. B 1089-5647 110, 18064 (2006); M. O. Lenz, R. Huber, B. Schmidt, P. Gilch, R. Kalmbach, M. Engelhard, and J. Wachtveitl, Biophys. J. 91, 255 (2006).
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