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postgraduate thesis: Dissociation and characterization of cationic radical peptides

TitleDissociation and characterization of cationic radical peptides
Authors
Advisors
Advisor(s):Chu, IK
Issue Date2013
PublisherThe University of Hong Kong (Pokfulam, Hong Kong)
Citation
Xu, M. [许敏洁]. (2013). Dissociation and characterization of cationic radical peptides. (Thesis). University of Hong Kong, Pokfulam, Hong Kong SAR. Retrieved from http://dx.doi.org/10.5353/th_b5185925
AbstractGas phase fragmentations of cationic radical peptides provide important fundamental information that forms the basis for peptide sequencing by using mass spectrometry. Presenting results from low-energy collision-induced dissociation (CID) experiments and theoretical density functional theory (DFT) calculations in conjunction with Rice–Ramsperger–Kassel–Marcus modeling, this thesis describes some of the chemical properties, including the locations of the charge and radical sites that determine the gas-phase chemistry of peptide radical cations. The first Section (3.1) documents the dissociations of two isomeric glycylglycylarginine methyl ester radical cations, [G•GR–OMe]+ and [GG•R–OMe]+, with well-defined initial radical sites at the N-terminal and middle α-carbon atoms, respectively. These two isomers undergo similar fragmentations to form the y2+ ion and protonated allylguanidine; their identical CID spectra suggest that isomerization occurs prior to dissociation. DFT calculations at the B3LYP/6-31++G(d,p) level revealed that the proton is sequestered on the guanidine group of the side chain in the presence of a highly basic arginine residue, thereby decreasing the isomerization barriers among the α-carbon–centered radicals to approximately 36 kcal mol–1 (cf. 45 kcal mol–1 for the non-basic [GGG]•+ analogues) and facilitating the radical migration along the peptide backbone and subsequent dissociation reactions. The second section (3.2) describes an investigation into the specific effect of the N-terminal basic residue on selective Cα–C bond cleavage of aromatic-containing radical cationic peptides. Upon replacing the arginine residue of [R(G)n–2X(G)7–n]•+ by a less-basic lysine residue, forming [K(G)n–2X(G)7–n]•+ (X = Phe or Tyr; n = 2–7) analogues, the selective Cα–C peptide bond cleavage no longer occurs. The dissociations of the prototypical radical cationic tripeptides [RFG]•+ and [KFG]•+ at the second Cα–C peptide bonds of α-radical intermediates proceed with comparable barriers (ca. 33 and 35 kcal mol–1, respectively); the generation of the competitive [b2 – H]•+ fragment from [RFG]•+ (ca. 40 kcal mol–1) is much higher in energy than that from [KFG]•+ (ca. 27 kcal mol–1). Thus, the selective Cα–C bond cleavage product from [KFG]•+ can be overridden by the [b2 – H]•+ species in the absence of a basic N-terminal residue. Section (3.3) further examines the mechanistic roles of various α- andβ-carbon–centered radicals prior to Cα–C bond cleavage, leading to the observation of novel x-type radical fragments. DFT calculations and RRKM modeling of a prototypical π-radical cationic system, [AY]•+, suggested that direct Cα–C bond cleavage leading to the formation of the [x1 + H]•+ species is thermodynamically comparable (ca. 16 kcal mol–1) with, but kinetically at least three-fold more favorable than, the well-characterized competitive formation of [c1 + 2H]+ and [z1 – H]•+ species. This finding agrees well with the experimental yield of the [x1 + H]•+ radical cation being higher than that of the minor [c1 + 2H]+ species.
DegreeDoctor of Philosophy
SubjectPeptides - Analysis
Cations
Dept/ProgramChemistry
Persistent Identifierhttp://hdl.handle.net/10722/197123

 

DC FieldValueLanguage
dc.contributor.advisorChu, IK-
dc.contributor.authorXu, Minjie-
dc.contributor.author许敏洁-
dc.date.accessioned2014-05-07T23:15:28Z-
dc.date.available2014-05-07T23:15:28Z-
dc.date.issued2013-
dc.identifier.citationXu, M. [许敏洁]. (2013). Dissociation and characterization of cationic radical peptides. (Thesis). University of Hong Kong, Pokfulam, Hong Kong SAR. Retrieved from http://dx.doi.org/10.5353/th_b5185925-
dc.identifier.urihttp://hdl.handle.net/10722/197123-
dc.description.abstractGas phase fragmentations of cationic radical peptides provide important fundamental information that forms the basis for peptide sequencing by using mass spectrometry. Presenting results from low-energy collision-induced dissociation (CID) experiments and theoretical density functional theory (DFT) calculations in conjunction with Rice–Ramsperger–Kassel–Marcus modeling, this thesis describes some of the chemical properties, including the locations of the charge and radical sites that determine the gas-phase chemistry of peptide radical cations. The first Section (3.1) documents the dissociations of two isomeric glycylglycylarginine methyl ester radical cations, [G•GR–OMe]+ and [GG•R–OMe]+, with well-defined initial radical sites at the N-terminal and middle α-carbon atoms, respectively. These two isomers undergo similar fragmentations to form the y2+ ion and protonated allylguanidine; their identical CID spectra suggest that isomerization occurs prior to dissociation. DFT calculations at the B3LYP/6-31++G(d,p) level revealed that the proton is sequestered on the guanidine group of the side chain in the presence of a highly basic arginine residue, thereby decreasing the isomerization barriers among the α-carbon–centered radicals to approximately 36 kcal mol–1 (cf. 45 kcal mol–1 for the non-basic [GGG]•+ analogues) and facilitating the radical migration along the peptide backbone and subsequent dissociation reactions. The second section (3.2) describes an investigation into the specific effect of the N-terminal basic residue on selective Cα–C bond cleavage of aromatic-containing radical cationic peptides. Upon replacing the arginine residue of [R(G)n–2X(G)7–n]•+ by a less-basic lysine residue, forming [K(G)n–2X(G)7–n]•+ (X = Phe or Tyr; n = 2–7) analogues, the selective Cα–C peptide bond cleavage no longer occurs. The dissociations of the prototypical radical cationic tripeptides [RFG]•+ and [KFG]•+ at the second Cα–C peptide bonds of α-radical intermediates proceed with comparable barriers (ca. 33 and 35 kcal mol–1, respectively); the generation of the competitive [b2 – H]•+ fragment from [RFG]•+ (ca. 40 kcal mol–1) is much higher in energy than that from [KFG]•+ (ca. 27 kcal mol–1). Thus, the selective Cα–C bond cleavage product from [KFG]•+ can be overridden by the [b2 – H]•+ species in the absence of a basic N-terminal residue. Section (3.3) further examines the mechanistic roles of various α- andβ-carbon–centered radicals prior to Cα–C bond cleavage, leading to the observation of novel x-type radical fragments. DFT calculations and RRKM modeling of a prototypical π-radical cationic system, [AY]•+, suggested that direct Cα–C bond cleavage leading to the formation of the [x1 + H]•+ species is thermodynamically comparable (ca. 16 kcal mol–1) with, but kinetically at least three-fold more favorable than, the well-characterized competitive formation of [c1 + 2H]+ and [z1 – H]•+ species. This finding agrees well with the experimental yield of the [x1 + H]•+ radical cation being higher than that of the minor [c1 + 2H]+ species.-
dc.languageeng-
dc.publisherThe University of Hong Kong (Pokfulam, Hong Kong)-
dc.relation.ispartofHKU Theses Online (HKUTO)-
dc.rightsThe author retains all proprietary rights, (such as patent rights) and the right to use in future works.-
dc.rightsCreative Commons: Attribution 3.0 Hong Kong License-
dc.subject.lcshPeptides - Analysis-
dc.subject.lcshCations-
dc.titleDissociation and characterization of cationic radical peptides-
dc.typePG_Thesis-
dc.identifier.hkulb5185925-
dc.description.thesisnameDoctor of Philosophy-
dc.description.thesislevelDoctoral-
dc.description.thesisdisciplineChemistry-
dc.description.naturepublished_or_final_version-
dc.identifier.doi10.5353/th_b5185925-

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