Structures and IR spectra of the gramicidin s peptide: Pushing the quest for low-energy conformations

Journal of Physical Chemistry B

Volumn 116, Issue 1, 2012, Pages 483-490

  Joshi, Kaustubh ^a   Semrouni, David ^a   Ohanessian, Gilles ^a   Clavaguéra, Carine ^a  

^a LABORATOIRE HÉTÉROÉLÉMENTS ET COORDINATION   (France)

Author keywords

[No Author keywords available]

Indexed keywords

COMPUTATIONAL CHEMISTRY; EXPERIMENTS; MOLECULAR DYNAMICS; QUANTUM CHEMISTRY;

COMPUTATIONAL STRATEGY; DENSITY FUNCTIONAL THEORY CALCULATIONS; DENSITY FUNCTIONALS; ENERGY SURFACE; FORCE FIELDS; FUNCTIONALS; GASPHASE; GRAMICIDIN S; IR SPECTRUM; LOW ENERGY STRUCTURES; LOW TEMPERATURES; LOW-ENERGY CONFORMATIONS; MOLECULAR MODELING STUDIES; PROTONATED; REPLICA-EXCHANGE MOLECULAR DYNAMICS SIMULATIONS; STABLE STRUCTURES;

DENSITY FUNCTIONAL THEORY;

EID: 84855849839     PISSN: 15206106     EISSN: 15205207     Source Type: Journal    
DOI: 10.1021/jp207102v     Document Type: Article

References (42)

1. Gause, G. F.; Brazhnikova, M. G. Nature 1944, 154, 703-703
2. Llamas-Saiz, A. L.; Grotenbreg, G. M.; Overhand, M.; Van Raaij, M. J. Acta Crystallogr., Sect. D 2007, D63, 401-407
3. Crowfoot Hodgkin, D.; Oughton, B. M. Biochem. J. 1957, 65, 752-756
4. Xu, Y.; Sugár, I. P.; Krishna, N. R. J. Biomol. NMR 1995, 5, 37-48
5. Prenner, E. J.; Lewis, R. N. A. H.; McElhaney, R. N. Biochim. Biophys. Acta Biomembr. 1999, 1462, 201-221
6. Tishchenko, G. N.; Andrianov, V. I.; Vainstein, B. K.; Woolfson, M. M.; Dodson, E. Acta Crystallogr., Sect. D 1997, 53, 151-159
7. Kupser, P.; Pagel, K.; Oomens, J.; Polfer, N.; Koksch, B.; Meijer, G.; von Helden, G. J. Am. Chem. Soc. 2010, 132, 2085-2093
8. Nagornova, N. S; Rizzo, T. R.; Boyarkin, O. V. J. Am. Chem. Soc. 2010, 132, 4040-4041
9. Nagornova, N. S; Guglielmi, M.; Doemer, M.; Tavernelli, I.; Rothlisberger, U.; Rizzo, T. R.; Boyarkin, O. V. Angew. Chem., Int. Ed. 2011, 50, 5383-5386
10. Rasmussen, T. D.; Ren, P.; Ponder, J. W.; Jensen, F. Int. J. Quantum Chem. 2007, 107, 1390-1395
11. Semrouni, D.; Balaj, O. P.; Calvo, F.; Correia, C.; Clavaguera, C.; Ohanessian, G. J. Am. Soc. Mass Spectrom. 2010, 21, 728-738
12. Jacquemin, D.; Perpete, E. A.; Michaux, C.; Frison, G. J. Phys. Chem. B 2011, 115, 3604-3613
13. Ponder, J. W.; Wu, C. J.; Ren, P. Y.; Pande, V. S.; Chodera, J. D.; Schnieders, M. J.; Haque, I.; Mobley, D. L.; Lambrecht, D. S.; DiStasio, R. A. J. Phys. Chem. B 2010, 114, 2549-2564
14. Riley, K. E.; Pitoňák, M.; Jurečka, P.; Hobza, P. Chem. Rev. 2010, 110, 5023-5063
15. Zhao, Y.; Truhlar, D. G. Acc. Chem. Res. 2008, 41, 157-167
16. Zhao, Y.; Truhlar, D. G. Theor. Chem. Acc. 2008, 120, 215-241
17. Schwabe, T.; Grimme, S. Acc. Chem. Res. 2008, 41, 569-579
18. Bouteiller, Y.; Poully, J. C.; Desfrançois, C.; Gregoire, G. J. Phys. Chem. A 2009, 113, 6301-6307
19. Gloaguen, E.; Valdes, H.; Pangliarulo, F.; Pollet, R.; Tardivel, B.; Hobza, P.; Piuzzi, F.; Mons, M. J. Phys. Chem. A 2010, 114, 2973-2982
20. Semrouni, D.; Clavaguera, C.; Dognon, J. P.; Ohanessian, G. Int. J. Mass Spectrom. 2010, 297, 152-161
21. Stearns, J.; Guidi, M.; Boyarkin, O. V; Rizzo, T. R. J. Chem. Phys. 2007, 127, 154322
22. Cappelli, C.; Monti, S.; Scalmani, G.; Barone, V. J. Chem. Theory Comput. 2010, 6, 1660-1669
23. Carbonniere, P; Dargelos, A.; Ciofini, I.; Adamo, C.; Pouchan, C. Phys. Chem. Chem. Phys. 2009, 11, 4375-4384
24. Corral, I.; Lamsabhi, A. M.; Mó, O.; Yáñez, M. Int. J. Quantum Chem. 2011, not supplied.
25. Ponder, J. W. TINKER, Software Tools for Molecular Design, version 5.1, 2010; http://dasher.wustl.edu/tinker/.
26. Ahlrichs, R.; Bär, M.; Häser, M.; Horn, H.; Kölmel, C. Chem. Phys. Lett. 1989, 162, 165-169; for the current version, see http://www.turbomole.com.
27. Frisch, M. J.; Trucks, G. W.; Schlegel, H. B.; Scuseria, G. E.; Robb, M. A.; Cheeseman, J. R.; Scalmani, G.; Barone, V.; Mennucci, B.; Petersson, G. A.; Gaussian 09, revision B.01; Gaussian, Inc.: Wallingford, CT, 2009.
28. Stearns, J.; Boyarkin, O. V; Rizzo, T. R. J. Am. Chem. Soc. 2010, 129, 13820-13821
29. Rizzo, T. R.; Stearns, J. A.; Boyarkin, O. V. Int. Rev. Phys. Chem. 2009, 28, 481-515
30. Stearns, J.; Seaiby, C.; Boyarkin, O. V; Rizzo, T. R. Phys. Chem. Chem. Phys. 2009, 11, 125-132
31. Prell, J. S.; O'Brien, J. T.; Steill, J. D.; Oomens, J.; Williams, E. R. J. Am. Chem. Soc. 2009, 131, 11442-11449
32. Dunbar, R. C.; Steill, J. D.; Oomens, J. J. Am. Chem. Soc. 2011, 133, 9376-9386
33. Dunbar, R. C.; Steill, J. D.; Polfer, N. C.; Oomens, J. J. Phys. Chem. B 2009, 113, 10552-10554
34. Polfer, N. C.; Oomens, J. Mass Spectrom. Rev. 2009, 28, 468-494
35. Polfer, N. C.; Paizs, B.; Snoek, L. C.; Compagnon, I.; Suhai, S.; Meijer, G.; von Helden, G.; Oomens, J. J. Am. Chem. Soc. 2005, 127, 8571-8579
36. Lucas, B.; Gregoire, G.; Lemaire, J.; Maitre, P.; Glotin, F.; Schermann, J. P.; Desfrançois, C. Int. J. Mass Spectrom. 2005, 243, 105-113
37. Gregoire, G.; Gaigeot, M. P.; Marinica, D. C.; Lemaire, J.; Schermann, J. P.; Desfrançois, C. Phys. Chem. Chem. Phys. 2007, 9, 3082-3097
38. Balaj, O. P.; Kapota, C.; Lemaire, J.; Ohanessian, G. Int. J. Mass Spectrom. 2008, 269, 196-209
39. Poully, J. C.; Lecomte, F.; Nieuwjaer, N.; Manil, B.; Schermann, J.-P.; Desfrançois, C.; Calvo, F.; Gregoire, G. Phys. Chem. Chem. Phys. 2010, 12, 3606-3615
40. Poully, J. C.; Lecomte, F.; Nieuwjaer, N.; Manil, B.; Schermann, J.-P.; Desfrançois, C.; Gregoire, G.; Ballivian, R.; Chirot, F.; Lemoine, J.; Calvo, F.; Antoine, R.; Dugourd, P. Int. J. Mass Spectrom. 2010, 297, 28-35
41. Oomens, J.; Polfer, N. C.; Moore, D. T.; Van der Meer, L.; Marshall, A. G.; Eyler, J. T.; Meijer, G.; von Helden, G. Phys. Chem. Chem. Phys. 2005, 7, 1345-1348
42. Fung, Y. M. E.; Besson, T.; Lemaire, J.; Maître, P.; Zubarev, R. A. Angew. Chem., Int. Ed. 2009, 48, 8340-8342