Side-chain fragmentation of alkylated cysteine residues in electron capture dissociation mass spectrometry

The recent development of novel fragmentation processes based on either electron capture directly or transfer from an anion show great potential for solving problems in proteomics that are intractable by the more widely employed thermal-based fragmentation processes such as collision induced dissociation. The dominant fragmentation occurring upon electron capture dissociation of peptides is cleavage of N-C alpha bonds in the peptide backbone to form c and z* ions. In the case of disulfide-linked peptides, it has also been shown that electron capture on one of the cystine sulfur atoms is favored, resulting in cleavage of the disulfide bond. In this study, we report that electron capture on the sulfur of alkylated cysteine residues is also a dominant process, causing cysteine side-chain loss from z* ions.     

Redox behaviour of cysteine in the presence of ammonium trioxovanadate(V)

The interaction of ammonium trioxovanadate(V) with cysteine in aqueous solution was studied by cyclic voltammetry and absorption spectroscopy techniques. In the absence of cysteine, the cyclic voltammogram (CV) of ammonium trioxovanadate(V) solution in 0.1 M phosphate buffer (pH 7) gave two peaks at -0.130 V (reversible) and -0.400 V (irreversible). These peaks (-0.130 V, -0.400 V) can be attributed to V(V)/V(IV) and V(IV)/V(III) redox processes, respectively. In the presence of cysteine at low scan rate (40 mV/s), the peak at -0.780 V, which is assigned to the irreversible reduction of free cystine, was observed. In addition, the reduction peak of the disulfidic anion S(2)(2-) was seen at -0.650 V. Under aerobic conditions, the peaks of the disulfidic anion S(2)(2-) and free cystine are well separated. From electronic spectra of ammonium trioxovanadate(V) and cysteine mixtures, LMCT transition associated with V(V)-cyteine complex was obtained at 743 nm. The stoichiometry (ML(2)) and stability constant (log beta(1:2)=6.67) of V(V)-cysteine complex were determined by means of mole ratio method.     

Negative ions of ethylene sulfite

The formation of negative ions in molecular beams of ethylene sulfite (ES, alternately called glycol sulfite or ethylene glycol, C(2)H(4)SO(3)) molecules has been studied using both Rydberg electron transfer (RET) and free electron attachment methods. RET experiments with jet-cooled ES show an unexpected broad profile of anion formation as a function of the effective quantum number (n(*)) of the excited rubidium atoms, with peaks at n(max)(*) approximately 13.5 and 16.8. The peak at n(max)(*) approximately 16.8 corresponds to an expected dipole-bound anion with an electron binding energy of 8.5 meV. It is speculated that the peak at n(max)(*) approximately 13.5 derives from the formation of a distorted C(2)H(4)SO(3)(-) ion. We suggest that quasifree electron attachment promotes the breaking of one ring bond giving a long-lived acyclic anion and term this process incomplete dissociative electron attachment. Theoretical calculations of plausible ionic structures are presented and discussed. Electron beam studies of ES reveal the presence of multiple dissociative attachment channels, with the dominant fragment, SO(2)(-), peaking at 1.3 eV and much weaker signals due to SO(3)(-), SO(-), and (ES-H)(-) peaking at 1.5, 1.7, and 0.9 eV, respectively. All of these products appear to originate from a broad temporary negative ion resonance centered at approximately 1.4 eV.     

Temporary anion states and dissociative electron attachment in diphenyl disulfide

The temporary anion states of gas-phase diphenyl disulfide are characterized by means of electron transmission (ET) and dissociative electron attachment (DEA) spectroscopies. The measured energies of vertical electron attachment are compared to the virtual orbital energies of the neutral state molecule supplied by MP2 and B3LYP calculations with the 6-31G basis set. The calculated energies, scaled with empirical equations, reproduce satisfactorily the attachment energies measured in the ET spectrum. The first anion state of diphenyl disulfide is stable, thus escaping detection in ETS. The vertical and adiabatic electron affinities, evaluated with B3LYP/6-31+G calculations as the energy difference between the neutral and anion states, are predicted to be 0.37 and 1.38 eV, respectively. The anion current displayed in the DEA spectrum has a sharp and intense peak at zero energy, essentially due to the C6H5S- negative fragment. In agreement, according to the calculations, the localization properties of the first anion state are strongly S-S antibonding, and the energetic requirement for its dissociation along the S-S bond is fulfilled even at zero energy.     

Dialane anion: three-center two-electron or two-center one-electron bonded

Dialane anions can be formed via a single three-center two-electron (3c-2e) or two-center one-electron (2c-1e) bond. The 2c-1e bonded anion Al(2)H(6)(-)(D(3)(d)) and the 3c-2e bonded anion Al(2)H(6)(-)(C(s)) have significant thermodynamic stabilities with respect to the neutral Al(2)H(6)(D(2)(h)) and correspond to 0.22 and 0.32 eV of the adiabatic electron affinities, respectively. In particular, the 2c-1e bond plays an essential role in stabilizing the Al(2)H(6)(-)(D(3)(d)) anion.     

Empty-level structure and reactive species produced by dissociative electron attachment to tert-butyl peroxybenzoate

The energy and nature of the gas-phase temporary anion states of tert-butylperoxybenzoate in the 0-6 eV energy range are determined for the first time by means of electron transmission spectroscopy (ETS) and appropriate theoretical calculations. The first anion state, associated with electron capture into a delocalized π* MO with mainly ring and carbonyl character, is found to lie close to zero energy, i.e., sizably more stable (about 2 eV) than the ground (σ*) anion state of saturated peroxides. Dissociative decay channels of the unstable parent molecular anions are detected with dissociative attachment spectroscopy (DEAS), as a function of the incident electron energy, in the 0-14 eV energy range. A large DEA cross-section, with maxima at zero energy, 0.7 and 1.3 eV, is found for production of the (m/e = 121) PhCOO(-) anion fragment, together with the corresponding tert-butoxy neutral radical, following cleavage of the O-O bond. Although with much smaller intensities, a variety of other negative currents are observed and assigned to the corresponding anion fragments with the support of density functional theory calculations.     

Low energy (0-10 eV) electron driven reactions in the halogenated organic acids CCl3COOH, CClF2COOH, and CF3CHNH2COOH (trifluoroalanine)

Negative ion formation following resonant electron attachment to the three title molecules is studied by means of a beam experiment with mass spectrometric detection of the anions. All three molecules exhibit a pronounced resonance in the energy range around 1 eV which decomposes by the loss of a neutral hydrogen atom thereby generating the closed shell anion (M-H)(-) (or RCOO(-)), a reaction which is also a common feature in the non-substituted organic acids. The two chlorine containing molecules CCl(3)COOH and CClF(2)COOH exhibit an additional strong and narrow resonance at very low energy (close to 0 eV) which decomposes by the cleavage of the C-Cl bond with the excess charge finally localised on either of the two fragments Cl(-) and (M-Cl)(-). This reaction is by two to three orders of magnitude more effective than hydrogen loss. Apart from these direct bond cleavages (C-Cl, O-H) resonant attachment of subexcitation electrons trigger additional remarkably complex unimolecular decompositions leading, e.g., to the formation of the bihalide ions ClHCl(-) and ClHF(-) from CCl(3)COOH and CClF(2)COOH, respectively, or the loss of a neutral CF(2) unit from trifluoroalanine thereby generating the fluoroglycine radical anion. These reactions require substantial rearrangement in the transitory negative ion, i.e., the cleavage of different bonds and formation of new bonds. F(-) from both chlorodifluoroacetic acid and trifluoroalanine is formed at comparatively low intensity (more than three orders of magnitude less than Cl(-) from the chlorine containing molecules) and predominantly within a broad resonant feature around 7-8 eV characterised as core excited resonance.     

Energy selective excision of CN- following electron attachment to hexafluoroacetone azine ((CF3)2C=N-N=C(CF3)2)

Low energy electron attachment (DEA) to hexafluoroacetone azine (HFAA) leads to a remarkable energy selective excision of CN(-) within a pronounced resonance located at 1.35 eV. The underlying dissociative electron attachment (DEA) reaction involves multiple bond cleavages and rearrangement within the neutral products. A series of further fragment ions (F(-), CF(3)(-), (CF(3))(2)C(-) and (CF(3))(2)CN(-)) are observed from resonant features above 2 eV and only (CF(3))(2)CN(-) is additionally formed within a narrow resonance below 1 eV. In contrast to CN(-) all the remaining fragment ions can be formed by simple bond cleavages with (CF(3))(2)CN(-) being the result of a symmetric decomposition of the target molecule by cleavage of the (N-N) bond with the excess charge localised on either of the identical fragments. Our ab initio calculations predict an adiabatic electron affinity of HFAA close to 2 eV with the geometry of the relaxed anion considerably distorted with respect to that of the neutral molecule.     

A contribution to the voltammetric study of cystine and cysteine at Pt electrodes in 0.5 M H2SO4

Both cysteine and cystine adsorb at the Pt electrode according the Frumkin—Temkin isotherm with the heterogeneity factor f = 51 for cysteine and 21 for cystine. Both the adsorbed cysteine and cystine give in a solution without any dissolved cystine or cysteine almost identical first cyclic voltammetric curves. Each substance dissolved in the electrolyte gives two oxidation peaks which differ when the oxidation is carried out at a “reduced” or an “oxidized” Pt electrode. On the basis of the dependence of the height and potential of the peaks on polarization rate and concentration (in the case of oxidation of dissolved substances) and of coulometric measurements the following conclusions have been made concerning the kinetics and mechanism:(i) Neither cysteine nor cystine change their oxidation state on adsorption at the electrode.(ii) The final oxidation product of both adsorbed cysteine and cystine may be the cysteic acid.(iii) For cysteine there are two adsorbed species, one strongly adsorbed, the other one weakly adsorbed.(iv) The oxidation of dissolved cysteine takes place via the weakly adsorbed species, the surface concentration of which is influenced by the coverage of the strongly adsorbed species. This process is described by an electrode reaction rate equation.(v) In the overall oxidation of cysteine one electron is transferred while the detailed mechanism requires an oxidation by splitting-off two electrons with a subsequent ion—substrate dimerization reaction.     

Remote bond breaking by interacting temporary anion states

The cross section for bond breaking at the site of a dissociative temporary negative ion state through the dissociative electron attachment process can be considerably enhanced by the presence of a second longer-lived temporary negative ion state elsewhere in the molecule, even one quite remote from the first. In a series of chloroalkenes possessing both C-Cl and C==C bonds separated by various distances, we show that the cross sections are determined by the lifetime of the lower anion state created by the mixing of the anion states of these two moieties, with the wave function's coefficients giving the probability that the electron is located at the dissociative site. Furthermore, the lifetime of the composite anion state can be expressed in terms of these same coefficients and the lifetimes of the unmixed resonances. We also discuss how these results may give insight into the means by which strand breaks are induced in DNA by the attachment of slow electrons.     

Photoelectron spectroscopy and theoretical studies of UF5(-) and UF6(-)

The UF(5)(-) and UF(6)(-) anions are produced using electrospray ionization and investigated by photoelectron spectroscopy and relativistic quantum chemistry. An extensive vibrational progression is observed in the spectra of UF(5)(-), indicating significant geometry changes between the anion and neutral ground state. Franck-Condon factor simulations of the observed vibrational progression yield an adiabatic electron detachment energy of 3.82 ± 0.05 eV for UF(5)(-). Relativistic quantum calculations using density functional and ab initio theories are performed on UF(5)(-) and UF(6)(-) and their neutrals. The ground states of UF(5)(-) and UF(5) are found to have C(4v) symmetry, but with a large U-F bond length change. The ground state of UF(5)(-) is a triplet state ((3)B(2)) with the two 5f electrons occupying a 5f(z3)-based 8a(1) highest occupied molecular orbital (HOMO) and the 5f(xyz)-based 2b(2) HOMO-1 orbital. The detachment cross section from the 5f(xyz) orbital is observed to be extremely small and the detachment transition from the 2b(2) orbital is more than ten times weaker than that from the 8a(1) orbital at the photon energies available. The UF(6)(-) anion is found to be octahedral, similar to neutral UF(6) with the extra electron occupying the 5f(xyz)-based a(2u) orbital. Surprisingly, no photoelectron spectrum could be observed for UF(6)(-) due to the extremely low detachment cross section from the 5f(xyz)-based HOMO of UF(6)(-).     

Electron attachment to dye-sensitized solar cell components: cyanoacetic acid

The energies of electron attachment associated with temporary occupation of the lower-lying virtual orbitals of cyanoacetic acid (CAA), proposed as a possible component of dye-sensitized solar cells, and its derivative methyl cyanoacetate (MCA) are measured in the gas phase with electron transmission spectroscopy (ETS). The corresponding orbital energies of the neutral molecule, supplied by B3LYP/6-31G(d) calculations and scaled using an empirically calibrated linear equation, are compared with the experimental vertical attachment energies (VAEs). The vertical and adiabatic electron affinities are also evaluated at the B3LYP/6-31+G(d) level as the anion/neutral total energy difference. Dissociative electron attachment spectroscopy (DEAS) is used to measure the total anion current as a function of the incident electron energy in the 0-4 eV energy range, and the negative fragments generated through the dissociative decay channels of the molecular anion are detected with a mass filter. In both compounds only two intense fragment anion currents are observed, that due to loss of a hydrogen atom from the molecular anion ([M - H](-)) and that due to formation of CN(-). In CAA the former signal displays a very sharp feature at 0.68 eV, assigned to a vibrational Feshbach resonance arising from coupling between a dipole bound anion state and a temporary σ* anion state.     

Fluorescent sensing of anions with acridinedione based neutral PET chemosensor

Newly synthesised fluorescent chemosensor ADDTU contains the thiourea receptor connected to the acridinedione (ADD) fluorophore via a covalent bond, giving rise to a fluorophore-receptor motif. In this fluorescent chemosensor, the anion recognition takes place at the receptor site which result in the concomitant changes in the photophysical properties of a ADD fluorophore by modulation of photoinduced electron transfer (PET) process. The binding ability of these sensor with the anions F(-), Cl(-), Br(-), I(-), HSO(4)(-), ClO(4)(-), AcO(-), H(2)PO(4)(-) and BF(4)(-) (as their tetrabutylammounium salts) in acetonitrile were investigated using UV-vis, steady state and time-resolved emission techniques. ADDTU system allows for the selective fluorescent sensing of AcO(-), H(2)PO(4)(-) and F(-) over other anions in acetonitrile.     

Structures and energetics of hydrated oxygen anion clusters

Hydration of the atomic oxygen radical anion is studied with computational electronic structure methods, considering (O(-))(H(2)O)(n) clusters and related proton-transferred (OH(-))(OH)(H(2)O)(n)(-)(1) clusters having n = 1-5. A total of 67 distinct local-minimum structures having various interesting hydrogen bonding motifs are obtained and analyzed. On the basis of the most stable form of each type, (O(-))(H(2)O)(n)) clusters are energetically favored, although for n > or = 3, there is considerable overlap in energy between other members of the (O(-))(H(2)O)(n) family and various members of the (OH(-))(OH)(H(2)O)(n)(-)(1) family. In the lower-energy (O(-))(H(2)O)(n) clusters, the hydrogen bonding arrangement about the oxygen anion center tends to be planar, leaving the oxygen anion p-like orbital containing the unpaired electron uninvolved in hydrogen bonding with any water molecule. In (OH(-))(OH)(H(2)O)(n)(-)(1) clusters, on the other hand, nonplanar arrangements are the rule about the anionic oxygen center that accepts hydrogen bonds. No instances are found of OH(-) acting as a hydrogen bond donor. Those OH bonds that form hydrogen bonds to an anionic O(-) or OH(-) center are significantly stretched from their equilibrium value in isolated water or hydroxyl. A quantitative inverse correlation is established for all hydrogen bonds between the amount of the OH bond stretch and the distance to the other oxygen involved in the hydrogen bond.     

Ion-Pair Charge Transfer Photochemistry in Rhenium(I) Borate Salts

The photophysics and photochemistry of the salt [(bpy)Re(CO)(3)(py)(+)][BzBPh(3)(-)] (ReBo, where bpy = 2,2'-bipyridine, py = pyridine, Bz = C(6)H(5)CH(2) and Ph = C(6)H(5)) has been investigated in THF and CH(3)CN solutions. UV-visible absorption and steady-state emission spectroscopy indicates that in THF ReBo exists primairly as an ion-pair. A weak absorption band is observed for the salt in THF solution that is assigned to an optical ion-pair charge transfer transition. Stern-Volmer emission quenching studies indicate that BzBPh(3)(-) quenches the luminescent dpi (Re) --> pi (bpy) metal-to-ligand charge transfer excited state of the (bpy)Re(CO)(3)(py)(+) chromophore. The quenching is attributed to electron transfer from the benzylborate anion to the photoexcited Re(I) complex, (bpy(-)(*))Re(II)(CO)(3)(py)(+) + BzBPh(3)(-) --> (bpy(-)(*))Re(I)(CO)(3)(py) + BzBPh(3)(*). Laser flash photolysis studies reveal that electron transfer quenching leads to irreversible reduction of the Re(I) cation to (bpy(-)(*))Re(I)(CO)(3)(py). Photoinduced electron transfer is irreversible owing to rapid C-B bond fragmentation in the benzylboranyl radical, PhCH(2)BPh(3)(*) --> PhCH(2)(*) + BPh(3)(*). Quantitative laser flash photolysis experiments show that the quantum efficiency for production of the reduced complex (bpy(-)(*))Re(I)(CO)(3)(py) is unity, suggesting that C-B bond fragmentation in the benzylboranyl radical occurs more rapidly than return electron transfer within the geminate radical pair that is formed by photoinduced electron transfer.     

Kinetics and mechanism of the [Ru(III)(edta)(H2O)](-)-mediated oxidation of cysteine by H2O2

The kinetics and mechanism of the [Ru(III)(edta)(H(2)O)](-)-mediated oxidation of cysteine (RSH) by hydrogen peroxide (edta(4-) = ethylenediaminetetraacetate), were studied in detail as a function of both the hydrogen peroxide and cysteine concentrations at pH 5.1 and room temperature. The kinetic traces reveal clear evidence for a catalytic process in which hydrogen peroxide reacts directly with cysteine coordinated to the Ru(III)(edta) complex in the form of [Ru(III)(edta)SR](2-). A parallel process in which [Ru(III)(edta)(H(2)O)](-) first reacts with H(2)O(2) to produce [Ru(V)(edta)O](-) and subsequently oxidizes cysteine, is orders of magnitude slower than the [Ru(III)(edta)(H(2)O)](-)-mediated oxidation in which cysteine rapidly coordinates to [Ru(III)(edta)(H(2)O)](-) prior to the reaction with H(2)O(2). HPLC product analyses revealed the formation of cystine (RSSR) as major product along with cysteine sulfinic acid (RSO(2)H) in the reaction system, and established the catalytic role of [Ru(III)(edta)(H(2)O)](-). Simulations were performed to account for the rather complex kinetic traces in terms of the suggested reaction mechanism. The results of the simulations support the proposed reaction mechanism that involves the oxidation of coordinated cysteine to cysteine sulfenic acid (RSOH), which subsequently rapidly reacts with H(2)O(2) and RSH to form RSO(2)H and RSSR, respectively.     

Stepwise charge separation and charge recombination in ferrocene-meso,meso-linked porphyrin dimer-fullerene triad

A meso,meso-linked porphyrin dimer [(ZnP)(2)] as a light-harvesting chromophore has been incorporated into a photosynthetic multistep electron-transfer model for the first time, including ferrocene (Fc), as an electron donor and fullerene (C(60)) as an electron acceptor to construct the ferrocene-meso,meso-linked porphyrin dimer-fullerene system (Fc-(ZnP)(2)-C(60)). Photoirradiation of Fc-(ZnP)(2)-C(60) results in photoinduced electron transfer from the singlet excited state of the porphyrin dimer [(1)(ZnP)(2)] to the C(60) moiety to produce the porphyrin dimer radical cation-C(60) radical anion pair, Fc-(ZnP)(2)(*+)-C(60)(*-). In competition with the back electron transfer from C(60)(*-) to (ZnP)(2)(*+) to the ground state, an electron transfer from Fc to (ZnP)(2)(*+) occurs to give the final charge-separated (CS) state, that is, Fc(+)-(ZnP)(2)-C(60)(*-), which is detected as the transient absorption spectra by the laser flash photolysis. The quantum yield of formation of the final CS state is determined as 0.80 in benzonitrile. The final CS state decays obeying first-order kinetics with a lifetime of 19 micros in benzonitrile at 295 K. The activation energy for the charge recombination (CR) process is determined as 0.15 eV in benzonitrile, which is much larger than the value expected from the direct CR process to the ground state. This value is rather comparable to the energy difference between the initial CS state (Fc-(ZnP)(2)(*+)-C(60)(*-)) and the final CS state (Fc(+)-(ZnP)(2)-C(60)(*-)). This indicates that the back electron transfer to the ground state occurs via the reversed stepwise processes,that is, a rate-limiting electron transfer from (ZnP)(2) to Fc(+) to give the initial CS state (Fc-(ZnP)(2)(*+)-C(60)(*-)), followed by a fast electron transfer from C(60)(*-) to (ZnP)(2)(*+) to regenerate the ground state, Fc-(ZnP)(2)-C(60). This is in sharp contrast with the extremely slow direct CR process of bacteriochlorophyll dimer radical cation-quinone radical anion pair in bacterial reaction centers.     

Cystine and cysteine analysis as the same phenylthiocarbamyl derivatives by HPLC in protein hydrolyzates

Summary A new approach is described, and a novel explanation presented, for the high performance liquid chromatographic analysis of cystine and cysteine as their phenylthiocarbamyl derivatives. PTC cystine and cysteine have been eluted with the same retention times and molar responses, most probably due to electrophilic attack of phenylisothiocyanate on cystine resulting in the scission of the disulfide bond yielding two moles of cysteine. Further, total PTC cystine and cysteine have been measured both in model solutions and in standard protein hydrolyzates (lysozyme, bovine albumin, ribonuclease) with the same linearity as the other ineteen amino acids. The reproducibility of the measurements, at the 250–750 pmole level, proved to be 4.1% (Relative Standard Deviation %) or less.     

Dissociative electron capture of halocarbon caused by the internal electron transfer from water trimer anion

Dissociative electron capture dynamics of halocarbon absorbed on water cluster anion, caused by internal electron transfer from the water trimer anion to the halocarbon, have been investigated by means of the direct density functional theory (DFT)-molecular dynamics (MD) method. The CF(2)Cl(2) molecule and a water trimer anion e(-)(H(2)O)(3) were used as a halocarbon and a trapped electron, respectively. First, the structure of trapped electron state, expressed by e(-)(H(2)O)(3)-CF(2)Cl(2), was fully optimized. The excess electron was trapped by a dipole moment of water trimer. Next, initial geometries were randomly generated around the equilibrium point of the trapped electron state, and then trajectories were run. The direct DFT-MD calculations showed that the spin density distribution of excess electron is gradually changed from the water cluster (trapped electron state) to CF(2)Cl(2) as a function of time. Immediately, the Cl(-) ion was dissociated from CF(2)Cl(2)(-) adsorbed on the water cluster. The reaction was schematically expressed by e(-)(H(2)O)(3)-CF(2)Cl(2)-->[(H(2)O)(3)-->-CF(2)CL(2)](-) --> (H(2O)(3) + CF(2)CL + CI(-) (I) where [(H(2)O)(3)-CF(2)Cl(2)](-) indicates a transient intermediate state in which the excess electron is widely distributed on both the water cluster and CF(2)Cl(2). The mechanism of the electron capture of halocarbon from the trapped electron in water ice was discussed on the basis of the theoretical results. Also, the dynamics feature was compared with those of the direct electron capture reactions of CF(2)Cl(2) and CF(2)Cl(2)-(H(2)O)(3), i.e. e(-) + CF(2)Cl(2), and e(-) + CF(2)Cl(2)-(H(2)O)(3), investigated in our previous paper [Tachikawa and Abe, J. Chem. Phys., 2007, 126, 194310].