Complex formation during SID and its effect on proton mobility

Journal of Physical Chemistry Letters

Volumn 4, Issue 22, 2013, Pages 3935-3939

  Ijaz, Waleed ^a   Gregg, Zackary ^a   Barnes, George L ^a  

^a SIENA COLLEGE   (United States)

Author keywords

direct dynamics; mobile proton model; molecular dynamics; octaglycine; peptide fragmentation; self assembled monolayer

Indexed keywords

ATOMISTIC SIMULATIONS; DIRECT DYNAMICS; EQUILIBRIUM THERMODYNAMICS; MOBILE PROTON MODELS; OCTAGLYCINE; PEPTIDE FRAGMENTATION; PROTONATED PEPTIDES; SURFACE-INDUCED DISSOCIATION;

COMPLEXATION; DISSOCIATION; MOLECULAR DYNAMICS; PEPTIDES; SELF ASSEMBLED MONOLAYERS;

PROTONS;

EID: 84888332575     PISSN: None     EISSN: 19487185     Source Type: Journal    
DOI: 10.1021/jz402093q     Document Type: Article

References (35)

1. Dongré, A. R.; Jones, J. L.; Somogyi, A.; Wysocki, V. H. Influence of Peptide Composition, Gas-Phase Basicity, and Chemical Modification on Fragmentation Efficiency: Evidence for the Mobile Proton Model J. Am. Chem. Soc. 1996, 118, 8365-8374
2. Laskin, J.; Denisov, E.; Futrell, J. H. A Comparative Study of Collision-Induced and Surface-Induced Dissociation. 1. Fragmentation of Protonated Dialanine J. Am. Chem. Soc. 2000, 122, 9703-9714
3. Laskin, J.; Bailey, T. H.; Futrell, J. H. Shattering of Peptide Ions on Self-Assembled Monolayer Surfaces J. Am. Chem. Soc. 2003, 125, 1625-1632
4. Laskin, J.; Futrell, J. H. Energy Transfer in Collisions of Peptide Ions with Surfaces J. Chem. Phys. 2003, 119, 3413-3420
5. Miller, S. A.; Lou, H.; Pachuta, S. J.; Cooks, R. G. Soft-Landing of Polyatomic Ions at Fluorinated Self-Assembled Monolayer Surfaces Science 1997, 275, 1447-1450
6. Ouyang, Z.; Takáts, Z.; Blake, T. A.; Gologan, B.; Guymon, A. J.; Wiseman, J. M.; Oliver, J. C.; Davisson, V. J.; Cooks, R. G. Preparing Protein Microarrays by Soft-Landing of Mass-Selected Ions Science 2003, 301, 1351-1354
7. Laskin, J. Energetics and Dynamics of Fragmentation of Protonated Leucine Enkephalin from Time- and Energy-Resolved Surface-Induced Dissociation Studies J. Phys. Chem. A 2006, 110, 8554-8562
8. Wysocki, V. H.; Tsaprailis, G.; Smith, L. L.; Breci, L. A. Mobile and Localized Protons: A Framework for Understanding Peptide Dissociation J. Mass Spectrom. 2000, 35, 1399-1406
9. Wysocki, V. H.; Cheng, G.; Zhang, Q.; Hermann, K. A.; Beardsley, R. L.; Hilderbrand, A. E. In Principles of Mass Spectrometry Applied to Biomolecules; Laskin, J.; Lifshitz, C., Eds.; John Wiley and Sons: Hoboken, NJ, 2006; Chapter VIII, pp 279-300.
10. Boyd, R.; Somogyi, A. The Mobile Proton Hypothesis in Fragmentation of Protonated Peptides: A Perspective J. Am. Soc. Mass Spectrom. 2010, 21, 1275-1278
11. Paizs, B.; Suhai, S. Fragmentation Pathways of Protonated Peptides Mass Spectrom. Rev. 2005, 24, 508-548
12. Paizs, B.; Csonka, I. P.; Lendvay, G.; Suhai, S. Proton Mobility in Protonated Glycylglycine and N -Formylglycylglycinamide: A Combined Quantum Chemical and RKKM Study Rapid Commun. Mass Spectrom. 2001, 15, 637-650
13. Humphrey, W.; Dalke, A.; Schulten, K. VMD-Visual Molecular Dynamics J. Mol. Graphics 1996, 14, 33-38
14. Papayannopoulos, I. A. The Interpretation of Collision-Induced Dissociation Tandem Mass Spectra of Peptides Mass Spectrom. Rev. 1995, 14, 49-73
15. Bowen, R. D. Ion-Neutral Complexes Acc. Chem. Res. 1991, 24, 364-371
16. Morton, T. H. Ion-Molecule Complexes in Unimolecular Fragmentations of Gaseous Cations. Alkyl Phenyl Ether Molecular Ions J. Am. Chem. Soc. 1980, 102, 1596-1602
17. Biermann, H. W.; Freeman, W. P.; Morton, T. H. Ion-Molecule Complexes in Decompositions of Gaseous Cations: 130 nm Photolysis of 4-Pyridyl Ethers J. Am. Chem. Soc. 1982, 104, 2307-2308
18. Somogyi, A.; Harrison, A. G.; Paizs, B. Using Gas-Phase Guest-Host Chemistry to Probe the Structures of b Ions of Peptides J. Am. Soc. Mass Spectrom. 2012, 23, 2055-2058
19. Morrison, L.; Somogyi, A.; Wysocki, V. H. The Influence Glutamic Acid in Protonated b3→b2 Formation from VGEIG and Related Analogs Int. J. Mass Spectrom. 2012, 325, 139-149
20. Park, K.; Deb, B.; Song, K.; Hase, W. L. Importance of Shattering Fragmentation in the Surface-Induced Dissociation of Protonated Octaglycine J. Am. Soc. Mass Spectrom. 2009, 20, 939-948
21. Yang, L.; Mazyar, O. A.; Lourderaj, U.; Wang, J.; Rodgers, M. T.; Martinez-Núñez, E.; Addepalli, S. V.; Hase, W. L. Chemical Dynamics Simulations of Energy Transfer in Collisions of Protonated Peptide Ions with a Perfluorinated Alkylthiol Self-Assembled Monolayer Surface J. Phys. Chem. C 2008, 112, 9377-9386
22. Barnes, G. L.; Hase, W. L. Energy Transfer, Unfolding, and Fragmentation Dynamics in Collisions of N-Protonated Octaglycine with an H-SAM Surface J. Am. Chem. Soc. 2009, 131, 17185-17193
23. Bolton, K.; Hase, W. L.; Peslherbe, G. H. In Modern Methods for Multidimensional Dynamics Computations in Chemistry; Thompson, D. L., Ed.; World Scientific: Singapore, 1998; pp 143-189.
24. Sun, L.; Hase, W. L. Born-Oppenheimer Direct Dynamics Classical Trajectory Simulations Rev. Comput. Chem. 2003, 19, 79-146
25. Warshel, A.; Levitt, M. Theoretical Studies of Enzymic Reactions: Dielectric, Electrostatic and Steric Stabilization of the Carbonium Ion in the Reaction of Lysozyme J. Mol. Biol. 1976, 103, 227-249
26. Rocha, G. B.; Freire, R. O.; Simas, A. M.; Stewart, J. J. P. RM1: A Reparameterization of AM1 for H, C, N, O, P, S, F, Cl, Br, and I J. Comput. Chem. 2006, 27, 1101-1111
27. Barnes, G. L.; Young, K.; Yang, L.; Hase, W. L. Fragmentation and Reactivity in Collisions of Protonated Diglycine with Chemically Modified Perfluorinated Alkylthiolate-Self-Assembled Monolayer Surfaces J. Chem. Phys. 2011, 134, 094106
28. Geragotelis, A.; Barnes, G. L. Surface Deposition Resulting from Collisions Between Diglycine and Chemically Modified Alkylthiolate Self-Assembled Monolayer Surfaces J. Phys. Chem. C 2013, 117, 13087-13093
29. + Ion-Surface Scattering J. Chem. Phys. 1997, 106, 10337-10348
30. Song, K.; de Sainte Claire, P.; Hase, W. L.; Hass, K. C. Comparison of Molecular Dynamics and Variational Transition-State-Theory Calculations of the Rate Constant for H-Atom Association with the Diamond {111} Surface Phys. Rev. B 1995, 52, 2949-2958
31. Accary, C.; Barbarat, P.; Hase, W. L.; Hass, K. C. Importance of Energy Transfer and Lattice Properties in Hydrogen-Atom Association with the (111) Surface of Diamond J. Phys. Chem. 1993, 97, 9934-9941
32. Schlier, C.; Seiter, A. High-Order Symplectic Integration: An Assessment Comput. Phys. Commun. 2000, 130, 176-189
33. Hu, X.; Hase, W. L.; Pirraglia, T. Vectorization of the General Monte Carlo Classical Trajectory Program VENUS J. Comput. Chem. 1991, 12, 1014-1024
34. Hase, W. L.; Duchovic, R. J.; Hu, X.; Komornicki, A.; Lim, K. F.; Lu, D. H.; Peslherbe, G. H.; Swamy, K. N.; Vande Linde, S. R.; Varandas, A. VENUS96: A General Chemical Dynamics Computer Program Quant. Chem. Prog. Exch. Bull. 1996, 16, 671
35. Stewart, J. J. P.; Fiedler, L.; Zhang, P.; Zheng, J.; Rossi, I.; Hu, W.-P.; Lynch, G. C.; Liu, Y.-P.; Chuang, Y.-Y.; Pu, J.; MOPAC-Version 5.016mn; University of Minnesota: Minneapolis, MN, 2010.