Xray Induced Fragmentation of Protonated Cystine (original) (raw)
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A detailed experimental and theoretical investigation of the dynamics leading to fragmentation of doubly ionized molecular thiophene is presented. Dissociation of double-ionized molecules was induced by S 2p core photoionization and the ionic fragments were detected in coincidence with Auger electrons from the core-hole decay. Rich molecular dynamics was observed in electron-ion-ion coincidence maps exhibiting ring breaks accompanied by hydrogen losses and/or migration. The probabilities of various dissociation channels were seen to be very sensitive to the internal energy of the molecule. Theoretical simulations were performed by using the semiempirical self-consistent charge-density-functional tight-binding method. By running thousands of these simulations, the initial conditions encountered in the experiment were properly taken into account, including the systematic dependencies on the internal (thermal) energy. This systematic approach, not affordable with first-principle methods, provides a good overall description of the complex molecular dynamics observed in the experiment and shows good promise for applicability to larger molecules or clusters, thus opening the door to systematic investigations of complex dynamical processes occurring in radiation damage.
UV Photofragmentation Dynamics of Protonated Cystine: Disulfide Bond Rupture
The Journal of Physical Chemistry Letters, 2014
Disulfide bonds (S−S) play a central role in stabilizing the native structure of proteins against denaturation. Experimentally, identification of these linkages in peptide and protein structure characterization remains challenging. UV photodissociation (UVPD) can be a valuable tool in identifying disulfide linkages. Here, the S−S bond acts as a UV chromophore and absorption of one UV photon corresponds to a σ−σ* transition. We have investigated the photodissociation dynamics of protonated cystine, which is a dimer of two cysteines linked by a disulfide bridge, at 263 nm (4.7 eV) using a multicoincidence technique in which fragments coming from the same fragmentation event are detected. Two types of bond cleavages are observed corresponding to the disulfide (S−S) and adjacent C− S bond ruptures. We show that the S−S cleavage leads to three different fragment ions via three different fragmentation mechanisms. The UVPD results are compared to collision-induced dissociation (CID) and electron-induced dissociation (EID) studies.
Soft-x-ray fragmentation studies of molecular ions
Journal of Physics B: Atomic, Molecular and Optical Physics, 2010
Imaging of photofragments from molecular ions after irradiation by soft X-ray photons has been realized at the ion beam infrastructure TIFF set up at the FLASH facility. Photodissociation of the two-electron system HeH + at 38.7 eV revealed the electronic excitations and the charge-state ratios for the products of this process, reflecting the non-adiabatic dissociation dynamics through multiple avoided crossings among the HeH + Rydberg potential curves. Dissociative ionization of the protonated water molecules H 3 O + and H 5 O + 2 at 90 eV revealed the main fragmentation pathways after the production of valence vacancies in these ionic species, which include a strong three-body channnel with a neutral fragment (OH + H + + H +) in H 3 O + photolysis and a significant two-body fragmentation channel (H 3 O + + H 2 O +) in H 5 O + 2 photolysis. The measurements yield absolute cross sections and fragment angular distributions. Increased precision and sensitivity of the technique was realized in recent developments, creating a tool for exploring X-ray excited molecular states under highly controlled target conditions challenging detailed theoretical understanding.
Dissociation Pathways in the Cysteine Dication after Site-Selective Core Ionization
The Journal of Physical Chemistry B, 2014
A photoelectron-ion-ion coincidence experiment has been carried out on the amino acid molecule cysteine after core-ionization of the O 1s, N 1s, C 1s, and S 2p orbitals. A number of different dissociation channels have been identified. Some of them show strong site-selective dependence that can be attributed to a combination of nuclear motion in the core-ionized state and Auger processes that populate different final electronic states in the dication.
Ion-induced molecular fragmentation: beyond the Coulomb explosion picture
Journal of Physics B: Atomic, Molecular and Optical Physics, 2000
The fragmentation of the CO molecule by O 7+ ion impact is investigated in two different energy regimes by fragment ion momentum spectroscopy. The improved resolution of the present kinetic energy release measurement together with application of a time-dependent wavepacket dynamics method used in conjunction with new high-level computations of a large number of dication potential energy curves enables one to unambiguously assign each line to an excited state of the transient molecular dication produced during the collision. This is the first direct experimental evidence of the limitations of the Coulomb explosion model to reproduce the molecular fragmentation dynamics induced by ion impact. Electron removal due to a capture process is shown to transfer less excitation to the target than direct ionization. At low collision velocity, the three-body interaction between the projectile and the two fragments is also clearly highlighted.
Analytical and Bioanalytical Chemistry, 2008
Characterisation and identification of disulfide bridges is an important aspect of structural elucidation of proteins. Covalent cysteine-cysteine contacts within the protein give rise to stabilisation of the native tertiary structure of the molecules. Bottom-up identification and sequencing of proteins by mass spectrometry most frequently involves reductive cleavage and alkylation of disulfide links followed by enzymatic digestion. However, when using this approach, information on cysteine-cysteine contacts within the protein is lost. Mass spectrometric characterisation of peptides containing intra-chain disulfides is a challenging analytical task, because peptide bonds within the disulfide loop are believed to be resistant to fragmentation. In this contribution we show recent results on the fragmentation of intra and inter-peptide disulfide bonds of proteolytic peptides by nano electrospray ionisation collision-induced dissociation (nanoESI CID). Disulfide bridge-containing peptides obtained from proteolytic digests were submitted to low-energy nanoESI CID using a quadrupole time-of-flight (Q-TOF) instrument as a mass analyser. Fragmentation of the gaseous peptide ions gave rise to a set of b and y-type fragment ions which enabled derivation of the sequence of the amino acids located outside the disulfide loop. Surprisingly, careful examination of the fragment-ion spectra of peptide ions comprising an intramolecular disulfide bridge revealed the presence of low-abundance fragment ions formed by the cleavage of peptide bonds within the disulfide loop. These fragmentations are preceded by proton-induced asymmetric cleavage of the disulfide bridge giving rise to a modified cysteine containing a disulfohydryl substituent and a dehydroalanine residue on the C-S cleavage site.
The ionic complexes formed by electrospray of methanol/water solutions of all the ␣ amino acids (AA) were studied by collisional activation in a triple quadrupole mass spectrometer. The fragmentation common to all protonated AA, except tryptophan, lysine, and arginine, is the well known sequential loss of H 2 O and CO yielding an immonium ion. For GlyH ϩ it is argued that formation of CH 2 NH 2 ϩ involves the most stable N-protonated form from which a proton is transferred to the hydroxy group. For the amino acids bearing a functional group on their side chain, formation of the immonium ion is in competition either with the loss of ammonia from the amino terminus or with the loss of a small molecule from the side chain. Extensive ab initio calculations at the MP2/6-31G* level have been carried out to determine the various fragmentation pathways of SerH ϩ and CysH ϩ. These calculations are further used to validate an empirical determination of thermochemical data based on experimental heats of formation and Benson increments. Such approximate data are used to interpret the fragmentations of protonated Met, Thr, Asn, Asp, Gln, and Glu. They are in agreement with an initial protonation at the N terminus of these amino acids. On the other hand, side chain protonation is expected to occur for His, Trp, Lys, and Arg. With increasing collision energy, proton transfer to less basic sites X (X ϭ SH, SCH 3 , OH, NH 2. . .) can occur. All primary fragmentations start with an elongation of the C-ϩ XH bond. This elongation may be assisted by a cyclisation stabilizing the incoming carbocation. The competitive fragmentations of each protonated amino acid are governed by a combination of enthalpic factors [bond dissociation energies (BDE) of the various C-ϩ XH bonds and the energy of the final states associated with each HX loss] and activation barriers associated with rearrangements.