The early life of a peptide cation-radical. Ground and excited-state trajectories of electron-based peptide dissociations during the first 330 femtoseconds

Journal of the American Society for Mass Spectrometry

Volumn 23, Issue 3, 2012, Pages 446-459

  Moss, Christopher L ^a   Liang, Wenkel ^a   Li, Xiaosong ^a   Tureček, František ^a  

^a UNIVERSITY OF WASHINGTON   (United States)

Author keywords

Ehrenfest quantum dynamics; Electron transfer dissociation; Peptide ions

Indexed keywords

BOND DISSOCIATION; BRANCHING RATIO; CARBOXYL GROUPS; CATION-RADICALS; CCSD; DENSITY FUNCTIONALS; DISSOCIATION CHANNELS; EARLY LIFE; EHRENFEST DYNAMICS; ELECTRON ATTACHMENT; ELECTRON CAPTURE; ELECTRON TRANSFER DISSOCIATION; EXCITED ELECTRONIC STATE; EXCITED-STATE DYNAMICS; FEMTOSECONDS; GROUND ELECTRONIC STATE; HYDROGEN ATOMS; MODEL SYSTEM; N-TERMINALS; PEPTIDE IONS; QUANTUM DYNAMICS; REACTION COURSE; REACTION PATHWAYS; REACTION PROGRESS; SHORT TIME SCALE; STATIONARY POINTS; TIME-RESOLVED; VIBRATIONAL ENERGIES;

AMMONIA; DYNAMICS; ELECTRONIC STATES; ELECTRONS; EXCITED STATES; HYDROGEN; MASS SPECTROMETRY; PEPTIDES; QUANTUM THEORY;

PHOTODISSOCIATION;

ALANINE; AMINOKETONE; AMMONIA; ARGININE; GUANIDINE; HYDROGEN; PEPTIDE; CATION; FREE RADICAL;

AMINO TERMINAL SEQUENCE; ARTICLE; ATOM; CALCULATION; CHEMICAL BOND; CHEMICAL REACTION; CHEMICAL REACTION KINETICS; DENSITY FUNCTIONAL THEORY; DISSOCIATION; DYNAMICS; EHRENFEST DYNAMICS; ELECTRON TRANSPORT; EXCITED STATE TRAJECTORY; GROUND STATE TRAJECTORY; ISOMERIZATION; MASS SPECTROMETRY; PEPTIDE CATION RADICAL DISSOCIATION; PHYSICAL PARAMETERS; SURFACE CHARGE; TIME; VIBRATION; CHEMISTRY; ISOMERISM; THERMODYNAMICS;

ARGININE; CATIONS; FREE RADICALS; GUANIDINE; ISOMERISM; MASS SPECTROMETRY; PEPTIDES; THERMODYNAMICS;

EID: 84860556033     PISSN: 10440305     EISSN: 18791123     Source Type: Journal    
DOI: 10.1007/s13361-011-0283-9     Document Type: Article

References (62)

1. Hakånsson, K., Klassen, J.S.: Electrospray and MALDI Mass Spectrometry, 2nd edn, pp. 571-630. Wiley, New York (2010)
2. Syka, J.E.P., Coon, J.J., Schroeder, M.J., Shabanowitz, J., Hunt, D.F.: Peptide and protein sequence analysis by electron transfer dissociation mass spectrometry. Proc. Natl. Acad. Sci. U. S. A. 101, 9528-9533 (2004)
3. Zubarev, R.A., Kelleher, N.L., McLafferty, F.W.: Electron capture dissociation of multiply charged protein cations. A nonergodic process. J. Am. Chem. Soc. 120, 3265-3266 (1998)
4. Zubarev, R.A.: Reactions of polypeptide ions with electrons in the gas phase. Mass Spectrom. Rev. 22, 57-77 (2003)
5. Savitski, M.M., Kjeldsen, F., Nielsen, M.L., Zubarev, R.A.: Complementary sequence preferences of electron-capture dissociation and vibrational excitation in fragmentation of polypeptide polycations. Angew. Chem. Int. Ed. Engl. 45, 5301-5306 (2006)
6. Van der Rest, G., Hui, R., Frison, G., Chamot-Rooke, J.: Dissociation channel dependence on peptide size observed in electron capture dissociation of tryptic peptides. J. Am. Soc. Mass Spectrom. 22, 1631-1644 (2011)
7. Fung, Y.M.E., Chan, T.W.D.: Experimental and theoretical investigations of the loss of amino acid side chains in electron capture dissociation of model peptides. J. Am. Soc. Mass Spectrom. 16, 1523-1535 (2005)
8. Cooper, H.J.: Investigation of the presence of b ions in electron capture dissociation mass spectra. J. Am. Soc. Mass Spectrom. 16, 1932-1940 (2005)
9. Lin, C., Cournoyer, J.J., O'Connor, P.B.: Use of a double resonance electron capture dissociation experiment to probe fragment intermediate lifetimes. J. Am. Soc. Mass Spectrom. 17, 1605-1615 (2006)
10. O'Connor, P.B., Lin, C., Cournoyer, J.J., Pittman, J.L., Belyayev, M., Budnik, B.A.: Long-lived electron capture dissociation product ions experience radical migration via hydrogen abstraction. J. Am. Soc. Mass Spectrom. 17, 576-585 (2006)
11. Jensen, C.S., Holm, A.I.S., Zettergren, H., Overgaard, J.B., Hvelplund, P., Nielsen, S.B.: On the charge partitioning between c and z fragments formed after electroncapture induced dissociation of charge-tagged lys-lys and ala-lys dipeptide cations. J. Am. Soc. Mass Spectrom. 20, 1881-1889 (2009)
12. Vorobyev, A., Ben Hamidane, H., Tsybin, Y.O.: Electron capture dissociation product ion abundances at the X amino acid in RAAAA-XAAAAK peptides correlate with amino acid polarity and radical stability. J. Am. Soc. Mass Spectrom. 20, 2273-2283 (2009)
13. Ben Hamidane, H., He, H., Tsybin, O.Y., Emmett, M.R., Hendrickson, C.L., Marshall, A.G., Tsybin, Y.O.: Periodic sequence distribution of product ion abundances in electron capture dissociation of amphipathic peptides and proteins. J. Am. Soc. Mass Spectrom. 20, 1182-1192 (2009)
14. Crizer, D.M., McLuckey, S.S.: Electron transfer dissociation of amide nitrogen methylated polypeptide cations. J. Am. Soc. Mass Spectrom. 20, 1349-1354 (2009)
15. Chan, W.Y.K., Chan, T.W.D.: Natural structural motifs that suppress peptide ion fragmentation after electron capture. J. Am. Soc. Mass Spectrom. 21, 1235-1244 (2010)
16. Jensen, C.S., Wyer, J.A., Nielsen, S.B.: Electron capture induced dissociation of dipeptide dications: Where does the charge go? Phys. Chem. Chem. Phys. 12, 12961-12963 (2010)
17. Haag, N., Holm, A.I.S., Johansson, H.A.B., Zettergren, H., Schmidt, H. T., Nielsen, S.B., Hvelplund, P., Cederquist, H.: Electron capture induced dissociation of doubly protonated pentapeptides: Dependence on molecular structure and charge separation. J. Chem. Phys. 134, 035102/1-035102/6 (2011)
18. Moore, B.N., Ly, T., Julian, R.R.: Radical conversion and migration in electron capture dissociation. J. Am. Chem. Soc. 133, 6997-7006 (2011)
19. Zubarev, R.A., Kruger, N.A., Fridriksson, E.K., Lewis, M.A., Horn, D. M., Carpenter, B.K., McLafferty, F.W.: Electron capture dissociation of gaseous multiply-charged proteins is favored at disulfide bonds and other sites of high hydrogen atom affinity. J. Am. Chem. Soc. 121, 2857-2862 (1999)
20. Tureček, F.: N-Cα bond dissociation energies and kinetics in amide and peptide radicals. Is the dissociation a nonergodic process? J. Am. Chem. Soc. 125, 5954-5963 (2003)
21. Chung, T.W., Tureček, F.: Proper and improper aminoketyl radicals in electron-based peptide dissociations. Int. J. Mass Spectrom. 301, 55-61 (2011)
22. Turecek, F., Jones, J.W., Towle, T., Panja, S., Nielsen, S.B., Hvelplund, P., Paizs, B.: Hidden histidine rearrangements upon electron transfer to gas-phase peptide ions. Experimental evidence and theoretical analysis. J. Am. Chem. Soc. 130, 14584-14596 (2008)
23. Patriksson, A., Adams, C., Kjeldsen, F., Raber, J., van der Spoel, D., Zubarev, R.A.: Prediction of NCα bond cleavage frequencies in electron capture dissociation of Trp-cage dications by force-field molecular dynamics simulations. Int. J. Mass Spectrom. 248, 124-130 (2006)
24. Robinson, E.W., Leib, R.D., Williams, E.R.: The role of conformation on electron capture dissociation of ubiquitin. J. Am. Soc. Mass Spectrom. 17, 1469-1479 (2006)
25. Skurski, P., Sobczyk, M., Jakowski, J., Simons, J.: Possible mechanisms for protecting NCα bonds in helical peptides from electroncapture (or transfer) dissociation. Int. J. Mass Spectrom. 265, 197-212 (2007)
26. +• cation radical. J. Mass Spectrom. 38, 1093-1104 (2003)
27. Sobczyk, M., Anusiewicz, I., Berdys-Kochanska, J., Sawicka, A., Skurski, P., Simons, J.: Coulomb-assisted dissociative electron attachment: Application to a model peptide. J. Phys. Chem. A 109, 250-258 (2005)
28. Syrstad, E.A., Tureček, F.: Toward a general mechanism of electroncapture dissociation. J. Am. Soc. Mass Spectrom. 16, 208-224 (2005)
29. Tureček, F., Chen, X., Hao, C.: Where does the electron go? Electron distribution and reactivity of peptide cation-radicals formed by electron transfer in the gas phase. J. Am. Chem. Soc. 130, 8818-8833 (2008)
30. Anusiewicz, I., Berdys-Kochanska, J., Simons, J.: Electron attachment step in electron capture dissociation (ECD) and electron transfer dissociation (ETD). J. Phys. Chem. A 109, 5801-5813 (2005)
31. Simons, J.: Mechanisms for S-S and N-Cα bond cleavage in peptide ECD and ETD mass spectrometry. Chem. Phys. Lett. 484, 81-95 (2010)
32. Simons, J.: Analytical model for rates of electron attachment and intramolecular electron transfer in electron transfer dissociation mass spectrometry. J. Am. Chem. Soc. 132, 7074-7085 (2010)
33. Sobczyk, M., Anusiewicz, I., Berdys-Kochanska, J., Sawicka, A., Skurski, P., Simons, J.: Coulomb-assisted dissociative electron attachment: Application to a model peptide. J. Phys. Chem. A 109, 250-259 (2003)
34. Tureček, F., Chung, T.W., Moss, C.L., Wyer, J.A., Ehlerding, A., Holm, A.I.S., Zettergren, H., Nielsen, S.B., Hvelplund, P., Chamot- Rooke, J., Bythell, B., Paizs, B.: The histidine effect. Electron transfer and capture cause different dissociations and rearrangements of histidine peptide cation-radicals. J. Am. Chem. Soc. 132, 10728-10740 (2010)
35. Chamot-Rooke, J., Malosse, C., Frison, G., Tureček, F.: Electron capture in charge- tagged peptides. Evidence for the role of excited electronic states. J. Am. Soc. Mass Spectrom. 18, 2146-2161 (2007)
36. Furche, F., Ahlrichs, A.: Adiabatic time-dependent density functional methods for excited state properties. J. Chem. Phys. 117, 7433-7447 (2002)
37. Li, X., Tully, J.C., Schlegel, H.B., Frisch, M.J.: Ab initio Ehrenfest dynamics. J. Chem. Phys. 123, 084106/1-084106/7 (2005)
38. Isborn, C.M., Li, X., Tully, J.C.: Time-dependent density functional theory Ehrenfest dynamics: Collisions between atomic oxygen and graphite clusters. J. Chem. Phys. 126, 134307/1-134307/7 (2007)
39. Liang, W., Chapman, C.T., Li, X.: Efficient first-principles electronic dynamics. J. Chem. Phys. 134, 184102/1-184102/7 (2011)
40. Bakken, V., Helgaker, T., Uggerud, E.: Models of fragmentations induced by electron attachment to protonated peptides. Eur. J. Mass Spectrom. 10, 625-638 (2004)
41. Panja, S., Nielsen, S.B., Hvelplund, P., Tureček, F.: Inverse hydrogen atom migration in arginine-containing peptide ions upon electron transfer. J. Am. Soc. Mass Spectrom. 19, 1726-1742 (2008)
42. 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., Nakatsuji, H., Caricato, M., Li, X., Hratchian, H.P., Izmaylov, A.F., Bloino, J., Zheng, G., Sonnenberg, J.L., Hada, M., Ehara, M., Toyota, K., Fukuda, R., Hasegawa, J., Ishida, M., Nakajima, T., Honda, Y., Kitao, O., Nakai, H., Vreven, T., Montgomery Jr., J.A., Peralta, J.E., Ogliaro, F., Bearpark, M., Heyd, J.J., Brothers, E., Kudin, K.N., Staroverov, V.N., Kobayashi, R., Normand, J., Raghavachari, K., Rendell, A., Burant, J.C., Iyengar, S.S., Tomasi, J., Cossi, M., Rega, N., Millam, J.M., Klene, M., Knox, J.E., Cross, J.B., Bakken, V., Adamo, C., Jaramillo, J., Gomperts, R., Stratmann, R.E., Yazyev, O., Austin, A.J., Cammi, R., Pomelli, C., Ochterski, J.W., Martin, R.L., Morokuma, K., Zakrzewski, V.G., Voth, G.A., Salvador, P., Dannenberg, J.J., Dapprich, S., Daniels, A.D., Farkas, O., Foresman, J.B., Ortiz, J.V., Cioslowski, J., Fox, D.J.: Gaussian 09, Revision A.02. Gaussian, Inc, Wallingford (2009)
43. Moss, C.L., Chung, T.W., Wyer, J.A., Nielsen, S.B., Hvelplund, P., Tureček, F.: Dipole-guided electron capture causes abnormal dissociations of phosphorylated pentapeptides. J. Am. Soc. Mass Spectrom. 22, 731-751 (2011)
44. Sugita, Y., Okamoto, Y.: Replica-exchange molecular dynamics method for protein folding. Chem. Phys. Lett. 314, 141-151 (1999)
45. Stewart, J.J.P.: Optimization of parameters for semiempirical methods. V. Modification of NDDO approximations and application to 70 elements. J. Mol. Model. 13, 1173-1213 (2007)
46. Becke, A.D.: New mixing of Hartree-Fock and local density-functional theories. J. Chem. Phys. 98, 1372-1377 (1993)
47. Becke, A.D.: Density functional thermochemistry. III. The role of exact exchange. J. Chem. Phys. 98, 5648-5652 (1993)
48. Yanai, T., Tew, D.P., Handy, N.C.: A new hybrid exchange-correlation functional using the Coulomb-Attenuating Method (CAM-B3LYP). Chem. Phys. Lett. 393, 51-57 (2004)
49. Zhao, Y., Truhlar, D.G.: The M06 suite of density functionals for main group thermochemistry, thermochemical kinetics, noncovalent interactions, excited states, and transition elements: Two new functionals and systematic testing of four M06-class fucntionals and 12 other functionals. Theo. Chem. Acc. 120, 215-241 (2008)
50. Møller, C., Plesset, M.S.: A note on an approximation treatment for many-electron systems. Phys. Rev. 46, 618-622 (1934)
51. Čížek, J., Paldus, J., Šroubková, L.: Cluster expansion analysis for delocalized systems. Int. J. Quantum Chem. 3, 149-167 (1969)
52. Purvis, G.D., Bartlett, R.J.: A full coupled-cluster singles and doubles model. The inclusion of disconnected triples. J. Chem. Phys. 76, 1910-1918 (1982)
53. Curtiss, L.A., Raghavachari, K., Pople, J.A.: Gaussian-2 theory using reduced møller-plesset orders. J. Chem. Phys. 98, 1293-1298 (1993)
54. Phillips, J.C., Braun, R., Wang, W., Gumbart, J., Tajkhorshid, E., Villa, E., Chipot, C., Skeel, R.D., Kale, L., Schulten, K.: Scalable molecular dynamics with NAMD. J. Comp. Chem. 26, 1781-1802 (2005)
55. MacKerell Jr., A.D., Bashford, D., Bellott, M., Dunbrack Jr., R.L., Evanseck, J.D., Field, M.J., Fischer, S., Gao, J., Guo, H., Ha, S., Joseph-McCarthy, D., Kuchnir, L., Kuczera, K., Lau, F.T.K., Mattos, C., Michnick, S., Ngo, T., Nguyen, D.T., Prodhom, B., Reiher, W.E.I.I. I., Roux, B., Schlenkrich, M., Smith, J.C., Stote, R., Straub, J., Watanabe, M., Wiorkiewicz-Kuczera, J., Yin, D., Karplus, M.: Allatom empirical potential for molecular modeling and dynamics studies of proteins. J. Phys. Chem. B 102, 3586-3616 (1998)
56. Tureček, F.: Temperature effects in mass spectrometry. On the estimation of thermal energies of organic molecules. Org. Mass Spectrom. 26, 1074-1081 (1991)
57. Tureček, F.: Transient intermediates of chemical reactions by neutralization- reionization mass spectrometry. Top. Curr. Chem. 225, 77-129 (2003)
58. Gilson, T.W., van der Rest, G., Chamot-Rooke, J., Kurlancheek, W., Head-Gordon, M., Jacquenin, D., Frison, G.: Ground electronic state of peptide cation-radicals: A delocalized unpaired electron? J. Phys. Chem. Lett. 2, 1426-1431 (2011)
59. Holm, A.I.S., Hvelplund, P., Kadhane, U., Larsen, M.K., Liu, B., Nielsen, S.B., Panja, S., Pedersen, J.M., Skydstrup, T., Stochkel, K., Williams, E.R., Worm, E.S.: On the mechanism of electron-captureinduced dissociation of peptide dications from 15N-labeling and crownether complexation. J. Phys. Chem. A 111, 9641-9643 (2007)
60. Tureček, F., Syrstad, E.A.: Mechanism and energetics of intramolecular hydrogen transfer in amide and peptide radicals and cation-radicals. J. Am. Chem. Soc. 125, 3353-3369 (2003)
61. Moss, C.L., Isborn, C.M., Li, X.: Ehrenfest dynamics with a timedependent density-functional-theory calculation of lifetimes and resonant widths of charge-transfer states of Li+ Near an aluminum cluster surface. Phys. Rev. A 80, 024503/1-024503/4 (2009)
62. Chapman, C.T., Liang, W., Li, X.: Ultrafast coherent electron-hole separation dynamics in a fullerene derivative. J. Phys. Chem. Lett. 2, 1189-1192 (2011)