Skip to main content
SpringerLink
Log in

Structure and collision-induced dissociation of the protonated cyclo His-Phe dipeptide: mechanistic studies and stereochemical effects

  • Regular Article - Molecular Physics and Chemical Physics
  • Published:
The European Physical Journal D Aims and scope Submit manuscript

Abstract

The role of stereochemical factors on the structure and the fragmentation paths of the protonated cyclic dipeptide cyclo histidine–phenylalanine is studied under ion traps conditions by combining tandem mass spectrometry, laser spectroscopy, quantum chemical calculations and chemical dynamics simulations. Vibrational spectroscopy obtained by Infrared Multiple Photon Dissociation (IRMPD) reveals a small difference between the two diastereomers, c-\(\hbox {LLH}^{+}\) and c-\(\hbox {LDH}^{+}\), arising mainly from ancillary CH...\(\uppi \) interactions. In contrast, there is a strong influence of the residues chirality on the collision-induced dissociation (CID) processes. Chemical dynamics simulations rationalize this effect and evidence that proton mobility takes place, allowing isomerization to intermediate cyclic structures that are different for c-\(\hbox {LLH}^{+}\) and c-\(\hbox {LDH}^{+}\), resulting in different barriers to proton mobility. This effect is related to the protonation of the imidazole ring. It contrasts with the minute stereochemical effects observed for other cyclic dipeptides in which the proton is borne by an amide CO.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2
Fig. 3
Fig. 4
Fig. 5
Fig. 6
Fig. 7
Fig. 8
Fig. 9

Similar content being viewed by others

Data Availability Statement

This manuscript has data included as electronic supplementary material. [Authors’ comment: The online version of this article contains supplementary material, which is available to authorized users.]

References

  1. T.J. Ward, K.D. Ward, Chiral separations: a review of current topics and trends. Anal. Chem. 84(2), 626–635 (2012)

    Article  Google Scholar 

  2. A.K. Shukla, J.H. Futrell, Tandem mass spectrometry: dissociation of ions by collisional activation. J. Mass Spectrom. 35(9), 1069–1090 (2000)

    Article  ADS  Google Scholar 

  3. J. M. Wells, S. A. McLuckey, Collision-induced dissociation (CID) of peptides and proteins. In Biological Mass Spectrometry, ed. by Burlingame, A. L., 402, pp. 148-185 (2005)

  4. G. Tsaprailis, H. Nair, A. Somogyi, V.H. Wysocki, W.Q. Zhong, J.H. Futrell, S.G. Summerfield, S.J. Gaskell, Influence of secondary structure on the fragmentation of protonated peptides. J. Am. Chem. Soc. 121(22), 5142–5154 (1999)

    Article  Google Scholar 

  5. R.A. Zubarev, Reactions of polypeptide ions with electrons in the gas phase. Mass Spectrom. Rev. 22(1), 57–77 (2003)

    Article  ADS  Google Scholar 

  6. B. Paizs, S. Suhai, Fragmentation pathways of protonated peptides. Mass Spectrom. Rev. 24(4), 508–548 (2005)

    Article  ADS  Google Scholar 

  7. R. Sudha, M.F. Jarrold, Left-handed and ambidextrous helices in the gas phase. J. Phys. Chem. B 109(23), 11777–11780 (2005)

    Article  Google Scholar 

  8. V. Domalain, V. Tognetti, M. Hubert-Roux, C.M. Lange, L. Joubert, J. Baudoux, J. Rouden, C. Afonso, Role of cationization and multimers formation for diastereomers differentiation by ion mobility-mass spectrometry. J. Am. Soc. Mass Spectrom. 24(9), 1437–1445 (2013)

    Article  ADS  Google Scholar 

  9. V.H. Wysocki, G. Tsaprailis, L.L. Smith, L.A. Breci, Special feature: Commentary - Mobile and localized protons: a framework for understanding peptide dissociation. J. Mass Spectrom. 35(12), 1399–1406 (2000)

    Article  ADS  Google Scholar 

  10. G. Frison, G. van der Rest, F. Turecek, T. Besson, J. Lemaire, P. Maitre, J. Chamot-Rooke, Structure of electron-capture dissociation fragments from charge-tagged peptides probed by tunable infrared multiple photon dissociation. J. Am. Chem. Soc. 130(45), 14916 (2008)

    Article  Google Scholar 

  11. C.M. Adams, F. Kjeldsen, R.A. Zubarev, B.A. Budnik, K.F. Haselmann, Electron capture dissociation distinguishes a single D-amino acid in a protein and probes the tertiary structure. J. Am. Soc. Mass Spectrom. 15(7), 1087–1098 (2004)

    Article  Google Scholar 

  12. A. Zehnacker, Chirality Effects in Gas-Phase Spectroscopy and Photophysics of Molecular and Ionic Complexes: Contribution of Low and Room Temperature Studies. Int. Rev. Phys. Chem. 33(2), 151–207 (2014)

    Article  Google Scholar 

  13. S. Kumar, B. Lucas, J. Fayeton, D. Scuderi, I. Alata, M. Broquier, K. Le Barbu-Debus, V. Lepere, A. Zehnacker, Photofragmentation mechanisms in protonated chiral cinchona alkaloids. Phys. Chem. Chem. Phys. 18(32), 22668–22677 (2016)

    Article  Google Scholar 

  14. D. Scuderi, P. Maitre, F. Rondino, K. Le Barbu-Debus, V. Lepere, A. Zehnacker-Rentien, Chiral recognition in cinchona alkaloid protonated dimers: mass spectrometry and UV photodissociation studies. J. Phys. Chem. A 114(9), 3306–3312 (2010)

    Article  Google Scholar 

  15. A.M. Rijs, J. Oomens, Gas-Phase IR Spectroscopy and Structure of Biological Molecules (Springer, Berlin, 2015)

    Book  Google Scholar 

  16. A. Sediki, L.C. Snoek, M.P. Gaigeot, N-\(\text{ H}^{+}\) vibrational anharmonicities directly revealed from DFT-based molecular dynamics simulations on the Ala(\(_{7})\)H(\(^{+})\) protonated peptide. Int. J. Mass Spectrom. 308(2–3), 281–288 (2011)

    Article  Google Scholar 

  17. N.C. Polfer, Infrared multiple photon dissociation spectroscopy of trapped ions. Chem. Soc. Rev. 40(5), 2211–2221 (2011)

    Article  Google Scholar 

  18. N.C. Polfer, J. Oomens, S. Suhai, B. Paizs, Infrared spectroscopy and theoretical studies on gas-phase protonated leu-enkephalin and its fragments: Direct experimental evidence for the mobile proton. J. Am. Chem. Soc. 129(18), 5887–5897 (2007)

    Article  Google Scholar 

  19. V. Scutelnic, M.A.S. Perez, M. Marianski, S. Warnke, A. Gregor, U. Rothlisberger, M.T. Bowers, C. Baldauf, G. von Helden, T.R. Rizzo, J. Seo, The structure of the protonated serine octamer. J. Am. Chem. Soc. 140(24), 7554–7560 (2018)

    Article  Google Scholar 

  20. B.J. Bythell, P. Maitre, B. Paizs, Cyclization and rearrangement reactions of a(n) fragment ions of protonated peptides. J. Am. Chem. Soc. 132(42), 14766–14779 (2010)

    Article  Google Scholar 

  21. J.C. Poutsma, J. Martens, J. Oomens, P. Maitre, V. Steinmetz, M. Bernier, M.X. Jia, V. Wysocki, Infrared multiple-photon dissociation action spectroscopy of the b(2)(\(+)\) ion from ppg: evidence of third residue affecting b(2)(\(+)\) fragment structure. J. Am. Soc. Mass Spectrom. 28(7), 1482–1488 (2017)

    Article  Google Scholar 

  22. C.F. Correia, P.O. Balaj, D. Scuderi, P. Maitre, G. Ohanessian, Vibrational signatures of protonated, phosphorylated amino acids in the gas phase. J. Am. Chem. Soc. 130(11), 3359–3370 (2008)

    Article  Google Scholar 

  23. P. Maitre, D. Scuderi, D. Corinti, B. Chiavarino, M.E. Crestoni, S. Fornarini, Applications of infrared multiple photon dissociation (IRMPD) to the detection of posttranslational modifications. Chem. Rev. 120(7), 3261–3295 (2020)

    Article  Google Scholar 

  24. M.E. Crestoni, B. Chiavarino, D. Scuderi, A. Di Marzio, S. Fornarini, Discrimination of 4-hydroxyproline diastereomers by vibrational spectroscopy of the gaseous protonated species. J. Phys. Chem. B 116(30), 8771–8779 (2012)

    Article  Google Scholar 

  25. R.C. Dunbar, J.D. Steill, J. Oomens, Conformations and vibrational spectroscopy of metal-ion/polylalanine complexes. Int. J. Mass Spectrom. 297(1–3), 107–115 (2010)

    Article  Google Scholar 

  26. R.C. Dunbar, J.D. Steill, J. Oomens, Chirality-induced conformational preferences in peptide-metal ion binding revealed by IR spectroscopy. J. Am. Chem. Soc. 133(5), 1212–1215 (2011)

    Article  Google Scholar 

  27. V. Lepere, K. Le Barbu-Debus, C. Clavaguéra, D. Scuderi, G. Piani, A.-L. Simon, F. Chirot, L. MacAleese, P. Dugourd, A. Zehnacker, Chirality-dependent structuration of protonated or sodiated polyphenylalanines: IRMPD and ion mobility studies. Phys. Chem. Chem. Phys. 18(3), 1807–17 (2016)

    Article  Google Scholar 

  28. J.S. Brodbelt, Ion activation methods for peptides and proteins. Anal. Chem. 88(1), 30–51 (2016)

    Article  Google Scholar 

  29. C. Bleiholder, S. Osburn, T.D. Williams, S. Suhai, M. Van Stipdonk, A.G. Harrison, B. Paizs, Sequence-scrambling fragmentation pathways of protonated peptides. J. Am. Chem. Soc. 130(52), 17774–17789 (2008)

    Article  Google Scholar 

  30. B.J. Bythell, S. Suhai, A. Somogyi, B. Paizs, Proton-driven amide bond-cleavage pathways of gas-phase peptide ions lacking mobile protons. J. Am. Chem. Soc. 131(39), 14057–14065 (2009)

    Article  Google Scholar 

  31. A.G. Harrison, A.B. Young, C. Bleiholder, S. Suhai, B. Paizs, Scrambling of sequence information in collision-induced dissociation of peptides. J. Am. Chem. Soc. 128(32), 10364–10365 (2006)

    Article  Google Scholar 

  32. I.K. Chu, C.K. Siu, J.K.C. Lau, W.K. Tang, X.Y. Mu, C.K. Lai, X.H. Guo, X. Wang, N. Li, Y. Xia, X.L. Kong, H.B. Oh, V. Ryzhov, F. Turecek, A.C. Hopkinson, K.W.M. Siu, Proposed nomenclature for peptide ion fragmentation. Int. J. Mass Spectrom. 390, 24–27 (2015)

    Article  Google Scholar 

  33. G. Tsaprailis, H. Nair, W. Zhong, K. Kuppannan, J.H. Futrell, V.H. Wysocki, A mechanistic investigation of the enhanced cleavage at histidine in the gas-phase dissociation of protonated peptides. Anal. Chem. 76(7), 2083–2094 (2004)

    Article  Google Scholar 

  34. A.C. Gucinski, J. Chamot-Rooke, E. Nicol, A. Somogyi, V.H. Wysocki, Structural influences on preferential oxazolone versus diketopiperazine b(2)(\(+)\) ion formation for histidine analogue-containing peptides. J. Phys. Chem. A 116(17), 4296–4304 (2012)

    Article  Google Scholar 

  35. Y.Y. Huang, V.H. Wysocki, D.L. Tabb, J.R. Yates, The influence of histidine on cleavage C-terminal to acidic residues in doubly protonated tryptic peptides. Int. J. Mass Spectrom. 219(1), 233–244 (2002)

    Article  Google Scholar 

  36. M. Alauddin, E. Gloaguen, V. Brenner, B. Tardivel, M. Mons, A. Zehnacker-Rentien, V. Declerck, D.J. Aitken, Intrinsic folding proclivities in cyclic -peptide building blocks: Configuration and heteroatom effects analyzed by conformer-selective spectroscopy and quantum chemistry. Chem.-a Eur. J. 21(46), 16479–16493 (2015)

    Article  Google Scholar 

  37. A. Mahjoub, A. Chakraborty, V. Lepere, K. Le Barbu-Debus, N. Guchhait, A. Zehnacker, Chirality-dependent hydrogen bond direction in jet-cooled (S)-1,2,3,4-tetrahydro-3-isoquinoline methanol (THIQM): IR-ion dip vibrational spectroscopy of the neutral and the ion. Phys. Chem. Chem. Phys. 11(25), 5160–5169 (2009)

    Article  Google Scholar 

  38. A. Bouchet, J. Klyne, G. Piani, O. Dopfer, A. Zehnacker, Diastereo-specific conformational properties of neutral, protonated and radical cation forms of (1R,2S)-cis and (1R,2R)-trans amino-indanol by gas phase spectroscopy. Phys. Chem. Chem. Phys. 17, 25809–25821 (2015)

    Article  Google Scholar 

  39. C. Prasad, Bioactive cyclic dipeptides. Peptides 16(1), 151–164 (1995)

    Article  Google Scholar 

  40. I. Bellezza, M.J. Peirce, A. Minelli, Cyclic dipeptides: from bugs to brain. Trends Molecular Med. 20(10), 551–558 (2014)

    Article  Google Scholar 

  41. A. Pérez-Mellor, I. Alata, V. Lepere, R. Spezia, A. Zehnacker-Rentien, Stereospecific collision-induced dissociation and vibrational spectroscopy of protonated Cyclo (Tyr-Pro). Int. J. Mass spectrom. 465, 116590 (2021)

  42. A. Perez-Mellor, I. Alata, V. Lepere, A. Zehnacker, Conformational study of the jet-cooled diketopiperazine peptide cyclo Tyrosyl-Prolyl. J. Phys. Chem. B 123(28), 6023–6033 (2019)

    Article  Google Scholar 

  43. A. Pérez Mellor, A. Zehnacker, Chirality effects in jet-cooled cyclic dipeptides, in Physical chemistry of cold gas-phase functional molecules and clusters, ed. by T. Ebata, M. Fujii (Springer, Singapore, 2019), pp. 63–87

    Chapter  Google Scholar 

  44. A. Perez-Mellor, I. Alata, V. Lepere, A. Zehnacker, Chirality effects in the structures of jet-cooled bichromophoric dipeptides. J. Mol. Spectrosc. 349, 71–84 (2018)

    Article  ADS  Google Scholar 

  45. F. BenNasr, A. Perez-Mellor, I. Alata, V. Lepere, N.E. Jaidane, A. Zehnacker, Stereochemistry-dependent hydrogen bonds stabilise stacked conformations in jet-cooled cyclic dipeptides: (LD) vs. (LL) cyclo tyrosine-tyrosine. Faraday Discuss. 212, 399–419 (2018)

    Article  ADS  Google Scholar 

  46. I. Alata, A. Perez-Mellor, F. Ben Nasr, D. Scuderi, V. Steinmetz, F. Gobert, N.E. Jaidane, A. Zehnacker-Rentien, Does the residues chirality modify the conformation of a cyclo-dipeptide? vibrational spectroscopy of protonated cyclo-diphenylalanine in the gas phase. J. Phys. Chem. A 121(38), 7130–7138 (2017)

    Article  Google Scholar 

  47. S. Wiedemann, A. Metsala, D. Nolting, R. Weinkauf, The dipeptide cyclic(glycyltryptophanyl) in the gas phase: A concerted action of density functional calculations, S-0-S-1 two-photon ionization, spectral UV/UV hole burning and laser photoelectron spectroscopy. Phys. Chem. Chem. Phys. 6(10), 2641–2649 (2004)

    Article  Google Scholar 

  48. A.G. Abo-Riziq, B. Crews, J.E. Bushnell, M.P. Callahan, M.S. De Vries, Conformational analysis of cyclo( Phe-Ser) by UV-UV and IR-UV double resonance spectroscopy and ab initio calculations. Mol. Phys. 103(11–12), 1491–1495 (2005)

    Article  ADS  Google Scholar 

  49. D. Wang, K. Gulyuz, C.N. Stedwell, N.C. Polfer, Diagnostic NH and OH vibrations for oxazolone and diketopiperazine structures: b(2) from protonated triglycine. J. Am. Soc. Mass Spectrom. 22(7), 1197–1203 (2011)

    Article  ADS  Google Scholar 

  50. S. Zou, J. Oomens, N.C. Polfer, Competition between diketopiperazine and oxazolone formation in water loss products from protonated ArgGly and GlyArg. Int. J. Mass Spectrom. 316, 12–17 (2012)

    Article  Google Scholar 

  51. M.C. Bernier, J. Chamot-Rooke, V.H. Wysocki, R vs. S fluoroproline ring substitution: trans/cis effects on the formation of b(2) ions in gas-phase peptide fragmentation. Phys. Chem. Chem. Phys. 18(3), 2202–2209 (2016)

    Article  Google Scholar 

  52. B.R. Perkins, J. Chamot-Rooke, S.H. Yoon, A.C. Gucinski, A. Somogyi, V.H. Wysocki, Evidence of diketopiperazine and oxazolone structures for HA b(2)(\(^{+})\) Ion. J. Am. Chem. Soc. 131(48), 17528–17529 (2009)

    Article  Google Scholar 

  53. J. Cautereels, J. Giribaldi, C. Enjalbal, F. Blockhuys, Quantum chemical mass spectrometry: Ab initio study of b(2)-ion formation mechanisms for the singly protonated Gln-His-Ser tripeptide. Rapid Commun. Mass Spectrom. 34(12) (2020)

  54. P.Y.I. Shek, J.K.-C. Lau, J. Zhao, J. Grzetic, U.H. Verkerk, J. Oomens, A.C. Hopkinson, K.W.M. Siu, Fragmentations of protonated cyclic-glycylglycine and cyclic-alanylalanine. Int. J. Mass Spectrom. 316, 199–205 (2012)

    Article  Google Scholar 

  55. A.M. Somer, V. Macaluso, G.L. Barnes, L. Yang, S. Pratihar, K. Song, W.L. Hase, R. Spezia, Role of chemical dynamics simulations in mass spectrometry studies of collision-induced dissociation and collisions of biological ions with organic surfaces. J. Am. Soc. Mass Spectrom. 31(1), 2–24 (2020)

    Article  Google Scholar 

  56. S.O. Meroueh, Y.F. Wang, W.L. Hase, Direct dynamics simulations of collision- and surface-induced dissociation of N-protonated glycine. Shattering fragmentation. J. Phys. Chem. A 106(42), 9983–9992 (2002)

    Article  Google Scholar 

  57. R. Spezia, J. Martens, J. Oomens, K. Song, Collision-induced dissociation pathways of protonated Gly(2)NH(2) and Gly(3)NH(2) in the short time-scale limit by chemical dynamics and ion spectroscopy. Int. J. Mass Spectrom. 388, 40–52 (2015)

    Article  Google Scholar 

  58. D. Ortiz, P. Martin-Gago, A. Riera, K. Song, J.Y. Salpin, R. Spezia, Gas-phase collision induced dissociation mechanisms of peptides: Theoretical and experimental study of N-formylalanylamide fragmentation. Int. J. Mass Spectrom. 335, 33–44 (2013)

    Article  Google Scholar 

  59. V. Macaluso, D. Scuderi, M.E. Crestoni, S. Fornarini, D. Corinti, E. Dalloz, E. Martinez-Nunez, W.L. Hase, R. Spezia, L-cysteine modified by S-Sulfation: Consequence on fragmentation processes elucidated by tandem mass spectrometry and chemical dynamics simulations. J. Phys. Chem. A 123(17), 3685–3696 (2019)

    Article  Google Scholar 

  60. A. Pérez Mellor, Spezia, R. Determination of kinetic properties in unimolecular dissociation of complex systems from graph-theory based analysis of an ensemble of reactive trajectories. Manuscrpt in preparation

  61. P. Maitre, S. Le Caer, A. Simon, W. Jones, J. Lemaire, H. Mestdagh, M. Heninger, G. Mauclaire, P. Boissel, R. Prazeres, F. Glotin, J.M. Ortega, Ultrasensitive first coupling of FTICR and FEL. Nucl. Instrum. Methods, Sect. A 507, 541–546 (2003)

    ADS  Google Scholar 

  62. R. Prazeres, F. Glotin, C. Insa, D.A. Jaroszynski, J.M. Ortega, Two-colour operation of a Free-Electron Laser and applications in the mid-infrared. Eur. Phys. J. D 3(1), 87–93 (1998)

    Article  ADS  Google Scholar 

  63. J.M. Bakker, T. Besson, J. Lemaire, D. Scuderi, P. Maitre, Gas-phase structure of a pi-allyl-palladium complex: Efficient infrared Spectroscopy in a 7 T Fourier transform mass spectrometer. J. Phys. Chem. A 111(51), 13415–13424 (2007)

    Article  Google Scholar 

  64. R.A. Marta, R.H. Wu, K.R. Eldridge, J.K. Martens, T.B. McMahon, The sodium cation-bound dimer of theophylline: IRMPD spectroscopy of a highly symmetric electrostatically bound species. Int. J. Mass Spectrom. 297(1–3), 76–84 (2010)

    Article  Google Scholar 

  65. A.D. Becke, Density-functional exchange-energy approximation with correct asymptotic-behavior. Phys. Rev. A 38(6), 3098–3100 (1988)

    Article  ADS  Google Scholar 

  66. M.D. Halls, J. Velkovski, H.B. Schlegel, Harmonic frequency scaling factors for Hartree-Fock, S-VWN, B-LYP, B3-LYP, B3-PW91 and MP2 with the Sadlej pVTZ electric property basis set. Theoret. Chem. Acc. 105, 413 (2001)

    Article  Google Scholar 

  67. M.J. Frisch, J.A. Pople, J.S. Binkley, Self-consistent molecular-orbital methods. 25. Supplementary functions for gaussian-basis sets. J. Chem. Phys. 80(7), 3265–3269 (1984)

    Article  ADS  Google Scholar 

  68. L. Goerigk, S. Grimme, A thorough benchmark of density functional methods for general main group thermochemistry, kinetics, and noncovalent interactions. Phys. Chem. Chem. Phys. 13(14), 6670–6688 (2011)

    Article  Google Scholar 

  69. S. Grimme, J. Antony, S. Ehrlich, H. Krieg, A consistent and accurate ab initio parametrization of density functional dispersion correction (DFT-D) for the 94 elements H-Pu. J. Chem. Phys. 132(15), 154104 (2010)

    Article  ADS  Google Scholar 

  70. N. Mohan, K.P. Vijayalakshmi, N. Koga, C.H. Suresh, Comparison of Aromatic NH \(\ldots \pi \), OH \(\ldots \pi \), and CH \(\ldots \pi \) Interactions of Alanine Using MP2, CCSD, and DFT Methods. J. Comput. Chem. 31(16), 2874–2882 (2010)

    Google Scholar 

  71. A. Perez-Mellor, A. Zehnacker, Vibrational circular dichroism of a 2,5-diketopiperazine (DKP) peptide: Evidence for dimer formation in cyclo LL or LD diphenylalanine in the solid state. Chirality 29(2), 89–96 (2017)

    Article  Google Scholar 

  72. E. Gloaguen, M. Mons, Isolated Neutral Peptides. In Gas-Phase Ir Spectroscopy and Structure of Biological Molecules, ed by Rijs, A. M., Oomens, J., Vol. 364, pp. 225-270 (2015)

  73. R.J. Plowright, E. Gloaguen, M. Mons, Compact folding of isolated four-residue neutral peptide chains: H-bonding patterns and entropy effects. ChemPhysChem 12(10), 1889–1899 (2011)

    Article  Google Scholar 

  74. M.J. Frisch, G.W. Trucks, H.B. Schlegel, G.E. Scuseria, M.A. Robb, J.R. Cheeseman, G. Scalmani, V. Barone, B. Mennucci, G.A. Petersson, H. Nakatsuji, M. Caricato, X.J. Li, H.P. Hratchian, A.F. Izmaylov, J. Bloino, G. Zheng, J.L. Sonnenberg, M. Hada, M. Ehara, K. Toyota, R. Fukuda, J. Hasegawa, M. Ishida, T. Nakajima, Y. Honda, O. Kitao, H. Nakai, T. Vreven, J.J.A. Montgomery, J.E.Peralta, F. Ogliaro, M. Bearpark, J.J. Heyd, E. Brothers, K.N. Kudin, V.N. Staroverov, R. Kobayashi, J. Normand, K. Raghavachari, A. Rendell, J.C. Burant, S.S. Iyengar, J. Tomasi, M. Cossi, N. Rega, J.M. Millam, M. Klene, J.E. Knox, J.B. Cross, V. Bakken, C. Adamo, J. Jaramillo, R. Gomperts, R.E. Stratmann, O. Yazyev, A.J. Austin, R. Cammi, C. Pomelli, J.W. Ochterski, R.L. Martin, K. Morokuma, V.G. Zakrzewski, G.A. Voth, P. Salvador, J.J. Dannenberg, S. Dapprich, A.D. Daniels, O. Farkas, J.B. Foresman, J.V. Ortiz, J. Cioslowski, D.J.S. Fox, Gaussian 09, Revision D.01, Gaussian Inc.: Wallingford CT, (2009)

  75. W.L. Hase, D.G. Buckowski, Monte-carlo sampling of a micro-canonical ensemble of classical Harmonic-Oscillators. Chem. Phys. Lett. 74(2), 284–287 (1980)

    Article  ADS  Google Scholar 

  76. W.L. Hase, R.J. Duchovic, X. Hu, A. Komornicki, K.F. Lim, D.-H. Lu, G.H. Peslherbe, K.N. Swamy, S.R. Vande Linde, L. Zhu, A. Varandas, H. Wang, R. Wolf, VENUS96: A general chemical dynamics computer program. QCPE Bull. 16, 43 (1996)

    Google Scholar 

  77. J.J.P. Stewart, L.J. Fiedler, P. Zhang, J. Zheng, I. Rossi, W.-P. Hu, G. C. Lynch, Y.-P. Liu, Y.Y. Chuang, J. Pu, J. Li, C.J. Cramer, P.L. Fast, D.G. Truhlar, MOPAC 5.022mn., Department of Chemistry and Supercomputing Institute, University of Minnesota, Minneapolis: Department of Chemistry and Supercomputing Institute, University of Minnesota, Minneapolis, (2015)

  78. G.B. Rocha, R.O. Freire, A.M. Simas, J.J.P. Stewart, RM1: A reparameterization of AM1 for H, C, N, O, P, S, F, Cl, Br, and I. J. Comput. Chem. 27(10), 1101–1111 (2006)

    Article  Google Scholar 

  79. R. Spezia, A. Martin-Somer, V. Macaluso, Z. Homayoon, S. Pratihar, W.L. Hase, Unimolecular dissociation of peptides: statistical vs. non-statistical fragmentation mechanisms and time scales. Faraday Discuss. 195, 599–618 (2016)

    Article  ADS  Google Scholar 

  80. A. Carra, R. Spezia, In silico tandem mass spectrometer: an analytical and fundamental tool. Chemistry -Methods 1, 123–130 (2021)

    Article  Google Scholar 

  81. A. Martin-Somer, J. Martens, J. Grzetic, W.L. Hase, J. Oomens, R. Spezia, Unimolecular fragmentation of deprotonated diproline Pro(2)-H (-) studied by chemical dynamics simulations and IRMPD spectroscopy. J. Phys. Chem. A 122(10), 2612–2625 (2018)

    Article  Google Scholar 

  82. M. Citir, C.S. Hinton, J. Oomens, J.D. Steill, P.B. Armentrout, Infrared multiple photon dissociation spectroscopy of protonated histidine and 4-phenyl imidazole. Int. J. Mass Spectrom. 330, 6–15 (2012)

    Article  Google Scholar 

  83. K. Hirata, Y. Mori, S.-I. Ishiuchi, M. Fujii, A. Zehnacker, Chiral discrimination between tyrosine and beta-cyclodextrin revealed by cryogenic ion trap infrared spectroscopy. Phys. Chem. Chem. Phys.?: PCCP 22(43), 24887–24894 (2020)

    Article  Google Scholar 

  84. L. Voronina, T.R. Rizzo, Spectroscopic studies of kinetically trapped conformations in the gas phase: the case of triply protonated bradykinin. Phys. Chem. Chem. Phys. 17, 25828–25836 (2015)

    Article  Google Scholar 

  85. A. Sen, K. Le Barbu-Debus, D. Scuderi, A. Zehnacker-Rentien, Mass spectrometry study and infrared spectroscopy of the complex between camphor and the two enantiomers of protonated alanine: the role of higher-energy conformers in the enantioselectivity of the dissociation rate constants. Chirality 25(8), 436–443 (2013)

    Article  Google Scholar 

  86. S.M. Bratakos, V.J. Sinanoglou, M.T. Matsoukas, E. Siapi, D.P. Papahatjis, K. Riganakos, P. Zoumpoulakis, Fragmentation patterns of aromatic 2,5-diketopiperazines using liquid chromatography/mass spectrometry. Curr. Anal. Chem. 12(5), 439–449 (2016)

    Article  Google Scholar 

  87. Y.H. Chen, S.E. Liou, C.C. Chen, Two-step mass spectrometric approach for the identification of diketopiperazines in chicken essence. Eur. Food Res. Technol. 218(6), 589–597 (2004)

    Article  Google Scholar 

  88. J. Vandergreef, A.C. Tas, L.M. Nijssen, J. Jetten, M. Hohn, Identification and quantitation of diketopiperazines by liquid-chromatography mass-spectrometry, using a moving belt interface. J. Chromatogr. 394(1), 77–88 (1987)

    Article  Google Scholar 

  89. A. Somogyi, V.H. Wysocki, I. Mayer, The effect of protonation site on bond strengths in simple peptides - application of ab-initio and modified neglect of differential-overlap bond orders and modified neglect of differential-overlap energy partitioning. J. Am. Soc. Mass Spectrom. 5(8), 704–717 (1994)

    Article  Google Scholar 

Download references

Acknowledgements

We thank Dr. J. M. Ortega and the CLIO team for technical assistance and Dr. D. Scuderi for helpful discussion. We thank F. Gobert for experimental help. We acknowledge the use of the computing facility cluster MésoLUM of the LUMAT federation (FR LUMAT 2764). AFPM and RS thank ANR DynBioReact (Grant No. ANR-14-CE06-0029-01) for financial support. The research described here has been supported by the Investissements d’Avenir LabEx PALM contract (ANR-10-LABX-0039-PALM).

Author information

Authors and Affiliations

  1. CNRS, Institut des Sciences Moléculaires d’Orsay, Université Paris-Saclay, 91405, Orsay, France

    Ariel Pérez-Mellor, Katia Le Barbu-Debus, Valeria Lepere, Ivan Alata & Anne Zehnacker

  2. Laboratoire de Chimie Théorique, Sorbonne Université UMR 7616 CNRS, 4, Place Jussieu, 75005, Paris, France

    Ariel Pérez-Mellor & Riccardo Spezia

Authors
  1. Ariel Pérez-Mellor
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Katia Le Barbu-Debus
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Valeria Lepere
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Ivan Alata
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Riccardo Spezia
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Anne Zehnacker
    View author publications

    You can also search for this author in PubMed Google Scholar

Contributions

Ariel Pérez Mellor contributed to quantum chemistry calculations, chemical dynamics simulations, experimental investigation, data curation, and writing—original draft preparation. Ivan Alata was involved in experimental investigation. Katia Le Barbu-Debus contributed to quantum chemistry calculations and writing—reviewing and editing. Valeria Lepere was involved in experimental investigation, data curation, and writing—reviewing and editing. Riccardo Spezia contributed to methodology, chemical dynamics simulations, and writing—reviewing and editing. Anne Zehnacker was involved in conceptualization, quantum chemistry calculations, experimental investigation, and writing—original draft preparation, reviewing and editing.

Corresponding author

Correspondence to Anne Zehnacker.

Supplementary Information

Below is the link to the electronic supplementary material.

Supplementary material 1 (docx 856 KB)

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Pérez-Mellor, A., Le Barbu-Debus, K., Lepere, V. et al. Structure and collision-induced dissociation of the protonated cyclo His-Phe dipeptide: mechanistic studies and stereochemical effects. Eur. Phys. J. D 75, 165 (2021). https://doi.org/10.1140/epjd/s10053-021-00173-w

Download citation

  • Received:

  • Accepted:

  • Published:

  • DOI: https://doi.org/10.1140/epjd/s10053-021-00173-w

Search

Navigation