Radical Migration Research Articles

ChemInform Abstract: Radical Migration—Addition of N‐tert‐Butanesulfinyl Imines with Organozinc Reagents.

AbstractThe reaction of tert‐butanesulfinyl iminoacetate (Ia) with benzyl zinc bromides results in unusual formation of migration—addition products without any catalyst.

Peroxidase-Type Reactions Suggest a Heterolytic/Nucleophilic O–O Joining Mechanism in the Heme-Dependent Chlorite Dismutase

Heme-containing chlorite dismutases (Clds) catalyze a highly unusual O-O bond-forming reaction. The O-O cleaving reactions of hydrogen peroxide and peracetic acid (PAA) with the Cld from Dechloromonas aromatica (DaCld) were studied to better understand the Cl-O cleavage of the natural substrate and subsequent O-O bond formation. While reactions with H2O2 result in slow destruction of the heme, at acidic pH heterolytic cleavage of the O-O bond of PAA cleanly yields the ferryl porphyrin cation radical (compound I). At alkaline pH, the reaction proceeds more rapidly, and the first observed intermediate is a ferryl heme. Freeze-quench EPR confirmed that the latter has an uncoupled protein-based radical, indicating that compound I is the first intermediate formed at all pH values and that radical migration is faster at alkaline pH. These results suggest by analogy that two-electron Cl-O bond cleavage to yield a ferryl-porphyrin cation radical is the most likely initial step in O-O bond formation from chlorite.

Fragmentation of Neutral Amino Acids and Small Peptides by Intense, Femtosecond Laser Pulses

High power femtosecond laser pulses have unique properties that could lead to their application as ionization or activation sources in mass spectrometry. By concentrating many photons into pulse lengths approaching the timescales associated with atomic motion, very strong electric field strengths are generated, which can efficiently ionize and fragment molecules without the need for resonant absorption. However, the complex interaction between these pulses and biomolecular species is not well understood. To address this issue, we have studied the interaction of intense, femtosecond pulses with a number of amino acids and small peptides. Unlike previous studies, we have used neutral forms of these molecular targets, which allowed us to investigate dissociation of radical cations without the spectra being complicated by the action of mobile protons. We found fragmentation was dominated by fast, radical-initiated dissociation close to the charge site generated by the initial ionization or from subsequent ultrafast migration of this charge. Fragments with lower yields, which are useful for structural determinations, were also observed and attributed to radical migration caused by hydrogen atom transfer within the molecule.

Structure and Reactivity of the Glutathione Radical Cation: Radical Rearrangement from the Cysteine Sulfur to the Glutamic Acid α-Carbon Atom.

A gas-phase radical rearrangement through intramolecular hydrogen-atom transfer (HAT) was studied in the glutathione radical cation, [γ-ECG]+. , which was generated by a homolytic cleavage of the protonated S-nitrosoglutathione. Ion-molecule reactions suggested that the radical migrates from the original sulfur position to one of the α-carbon atoms. Experiments on the radical cations of dipeptides derived from the glutathione sequence, [γ-EC]+. and [CG]+. , pointed to the glutamic acid α-carbon atom as the most likely site of the radical migration. Infrared multiple-photon dissociation (IRMPD) spectroscopy was employed to generate complementary information. IRMPD of [γ-ECG]+. in the approximately 1000-1800 cm-1 region was inconclusive owing to the relatively broad, overlapping absorption bands. However, the IRMPD spectrum of [γ-EC]+. in this region was consistent with the radical migrating from the sulfur to the α-carbon atom of glutamic acid. IRMPD in the 2800-3700 cm-1 region performed on [γ-ECG]+. is consistent with a mixture of both the original sulfur-based radical and the resulting glutamic acid α-carbon-based species. Comparisons are made with previously published condensed and gas-phase studies on intramolecular HAT in glutathione.

Дырочная проводимость в неоднородных фрагментах ДНК

The characteristics of cation radical (hole) migration in heterogeneous DNA were investigated on the basis of Kubo formula, in which correlation functions were obtained from solutions of systems of Bogoliubov hierarchy. The cutting of Bogoliubov hierarchy was carried out by excepting correlations of the third and higher order. The obtained system of non-linear differential equations was investigated both analytically and numerically. The environment polarization, caused by interaction of holes with base pairs vibrations, was shown to play the key role in transport processes. The energy of the interaction can ten-fold exceed vibration energy. The transfer rate between adjacent DNA bases in one-dimensional case was shown to be almost independent of the nature and behavior of more distant pairs. The charge probability amplitude oscillates in the picosecond timescale. Nonetheless, the rates of hole transfer, obtained by averaging over these oscillations, turned out to be very close to the experimental data. The calculated dependence of the hole transfer rate between two guanine bases on the number of intervening adenine bases was also in good agreement with the experimental data. Besides, the temperature dependence of the transfer rate was investigated. Hopping mechanism was shown to make the main contribution to the hole transport process at 300 K.

Exploring Radical Migration Pathways in Peptides with Positional Isomers, Deuterium Labeling, and Molecular Dynamics Simulations

One of the keys for understanding radical directed dissociation in peptides is a detailed knowledge of the factors that mediate radical migration. Peptide radicals can be created by a variety of means; however, in most circumstances, the originally created radicals must migrate to alternate locations in order to facilitate fragmentation such as backbone cleavage or side chain loss. The kinetics of radical migration are examined herein by comparing results from ortho-, meta-, and para-benzoyl radical positional isomers for several peptides. Isomers of a constrained cyclic peptide generated by several orthogonal radical initiators are also probed as a function of charge state. Cumulatively, the results suggest that small changes in radical position can significantly impact radical migration, and overall structural flexibility of the peptide is also an important controlling factor. A particularly interesting pathway for the peptide RGYALG that is sensitive to ortho versus meta or para substitution was fully mapped out by a suite of deuterium labeled peptides. This data was then used to optimize parameters in molecular dynamics-based simulations, which were subsequently used to obtain further insight into the structural underpinnings that most strongly influence the kinetics of radical migration.

A Density Functional Theory Study of Secondary Reactions in n‐Butyl Acrylate Free Radical Polymerization

AbstractIn this work, secondary reactions involved in the free radical polymerization of butyl acrylate are investigated using quantum chemistry. First, various backbiting reactions are studied by adopting a simplified molecular model suitable for treating long polymer chains. The predicted reaction kinetics suggest the possibility of a radical migration along the poly(butyl acrylate) (PBA) chain as a consequence of subsequent j:j + 4 hydrogen abstractions, which are characterized by a low activation energy. Moreover, branching propagation and β‐scission reactions originating from mid‐chain radicals are investigated using a complete PBA model composed of five monomer units. The reaction kinetics involving short‐branch radicals are also examined, and a novel backbiting step leading to the formation of short branches is proposed. magnified image

Termination of Surface Radicals and Kinetic Analysis of Surface‐Initiated RAFT Polymerization on Flat Surfaces

Abstractsi‐RAFT polymerization is widely used for surface modification. However, how the surface radicals terminate requires further elucidation. A kinetic model is developed for si‐RAFT via the R group approach. The model describes the molecular weight of grafted polymers as well as polymer layer thickness and various chain concentrations. It is shown that surface/surface radical termination plays an important role. The termination is facilitated by the migration of surface radicals through “hopping” and “rolling” mechanisms. “Hopping” occurs through activation/deactivation cycles between surface and solution chains, dependent on the RAFT concentration in solution. “Rolling” occurs through transfers between surface/surface chains, dependent on the grafting density at surface. magnified image

Macromonomers from AGET Activation of Poly(n-butyl acrylate) Precursors: Radical Transfer Pathways and Midchain Radical Migration

Macromonomers are synthesized from AGET activation of poly(n-butyl acrylate), P(nBuA), synthesized via ATRP. Reactivation of the polymer chains is achieved at 140 °C using Sn(EH)2 as reducing agent. Under such conditions, P(nBuA) macroradicals undergo fast chain transfer reactions forming midchain radicals, MCR, followed by β-scission reactions leading to unsaturated macromonomers. Furthermore, intermolecular transfer-to-polymer reactions lead to considerable amounts of hydrogen-terminated products. Soft ionization mass spectrometry of product samples reveals that under very dilute conditions the macromonomer formation is predominant over the hydrogen transfer reaction of the macroradicals, and macromonomers with overall 80% end-group purity can be achieved, which is, however, accompanied by a reduction in molecular weight from 2100 to 1300 g mol–1 and an increase in polydispersity from 1.33 to roughly 1.5. Furthermore, we demonstrate not only that macromonomers under these reaction conditions are formed ...

Discriminating d-Amino Acid-Containing Peptide Epimers by Radical-Directed Dissociation Mass Spectrometry

The presence of a single D-amino acid in a peptide is very difficult to detect. Mass spectrometry-based approaches rely on differences in fragmentation between all L-amino acid-containing peptides and single D-amino acid-containing peptides (which are epimers) for identification. The success of this approach is dependent on the structural sensitivity of the fragmentation method. Recently, experiments have demonstrated that fragmentation initiated by radical chemistry, or radical-directed dissociation (RDD), is particularly sensitive to the structure of the ion being fragmented. Herein, RDD is used to identify the presence of D-serine, D-alanine, or D-aspartic acid in eight biologically relevant peptides. It is demonstrated that chiral disambiguation by RDD is dependent on both the initial radical site and subsequent radical migration. Fortuitously, RDD can be initiated by a variety of different radical precursors which can be associated with the peptide via covalent or noncovalent means, and RDD can be examined in all observable charge states (both positive and negative). This diversity enables numerous initial radical sites and migration pathways to be explored. For all but one of the peptides that were examined, RDD provides significantly better chiral discrimination than CID. Quantitation of peptide epimers by RDD is also described.

Two Tyrosyl Radicals Stabilize High Oxidation States in Cytochrome c Oxidase for Efficient Energy Conservation and Proton Translocation

The reaction of oxidized bovine cytochrome c oxidase (bCcO) with hydrogen peroxide (H(2)O(2)) was studied by electron paramagnetic resonance (EPR) to determine the properties of radical intermediates. Two distinct radicals with widths of 12 and 46 G are directly observed by X-band EPR in the reaction of bCcO with H(2)O(2) at pH 6 and pH 8. High-frequency EPR (D-band) provides assignments to tyrosine for both radicals based on well-resolved g-tensors. The wide radical (46 G) exhibits g-values similar to a radical generated on L-Tyr by UV-irradiation and to tyrosyl radicals identified in many other enzyme systems. In contrast, the g-values of the narrow radical (12 G) deviate from L-Tyr in a trend akin to the radicals on tyrosines with substitutions at the ortho position. X-band EPR demonstrates that the two tyrosyl radicals differ in the orientation of their β-methylene protons. The 12 G wide radical has minimal hyperfine structure and can be fit using parameters unique to the post-translationally modified Y244 in bCcO. The 46 G wide radical has extensive hyperfine structure and can be fit with parameters consistent with Y129. The results are supported by mixed quantum mechanics and molecular mechanics calculations. In addition to providing spectroscopic evidence of a radical formed on the post-translationally modified tyrosine in CcO, this study resolves the much debated controversy of whether the wide radical seen at low pH in the bovine enzyme is a tyrosine or tryptophan. The possible role of radical formation and migration in proton translocation is discussed.

S-to-αC Radical Migration in the Radical Cations of Gly-Cys and Cys-Gly

The radical cations of Cys-Gly and Gly-Cys were studied using ion-molecule reactions (IMR), infrared multiple-photon dissociation (IRMPD) spectroscopy, and density functional theory (DFT) calculations. Homolytic cleavage of the S-NO bond of nitrosylated precursors generated radical cations with the radical site initially located on the sulfur atom. Time-resolved ion-molecule reactions showed that radical site migration via hydrogen atom transfer (HAT) occurred much more quickly in Gly-Cys(•+) than in Cys-Gly(•+). IRMPD and DFT calculations indicated that for Gly-Cys, the radical migrated from the sulfur atom to the α-carbon of glycine, which is lower in energy than the sulfur radical (-53.5kJ/mol). This migration does not occur for Cys-Gly because the glycine α-carbon is higher in energy than the sulfur radical (10.3kJ/mol). DFT calculations showed that the highest energy barriers for rearrangement are 68.2kJ/mol for Gly-Cys and 133.8kJ/mol for Cys-Gly, which is in agreement with both the IMR and IRMPD data and explains the HAT in Gly-Cys.

Carbon‐Centered Radicals Can Transfer Hydrogen Atoms between Amino Acid Side Chains

Radical migration between aliphatic amino acid side chains can occur in solution and intramolecularly in peptides. The kinetic constant of the hydrogen transfer reaction was measured by using competition kinetics, and the half-life as well as the distance that a radical can move within a protein was calculated.

Characterization of electron donor sites on Al2O3 surface

Formation of radical anions after adsorption of 1,3,5-trinitrobenzene (TNB) on electron donor sites of fully oxidized Al(2)O(3) samples with different phase compositions is studied by EPR. It is shown that the maximum concentration of the radical anions does not substantially depend on the choice of solvent and reaction temperature, and can be used to measure the total concentration of the donor sites. The donor sites are observed in almost the same concentration about 5 × 10(16) m(-2) on all alumina polymorphs except for α-Al(2)O(3). The formation rate of the TNB radical anions and the activation energy of this process are found to depend on the donor properties of the solvent. The EPR in situ experiments showed that a substantial amount of the adsorbate forming a liquid phase is required for generation of the radical anions. These results prove that the sites measured by the formation of the TNB radical anions are not genuine electron donor sites capable of direct electron transfer to the adsorbed TNB molecules. A model of the observed paramagnetic species based on the obtained experimental data and the results of quantum chemical simulations is suggested. According to this model, a TNB radical anion substitutes a hydroxyl group forming a neutral ion pair with a surface aluminum cation. The suggested mechanism for the formation of such ion pairs involves the migration of simple radicals and does not require long-distance charge separation. It is supposed that the donor site where the process is initiated includes a negatively charged surface hydroxyl group.

Combined Electron Transfer Dissociation–Collision-Induced Dissociation Fragmentation in the Mass Spectrometric Distinction of Leucine, Isoleucine, and Hydroxyproline Residues in Peptide Natural Products

Distinctions between isobaric residues have been a major challenge in mass spectrometric peptide sequencing. Here, we propose a methodology for distinction among isobaric leucine, isoleucine, and hydroxyproline, a commonly found post-translationally modified amino acid with a nominal mass of 113 Da, through a combined electron transfer dissociation-collision-induced dissociation approach. While the absence of c and z(•) ions, corresponding to the Yyy-Xxx (Xxx = Leu, Ile, or Hyp) segment, is indicative of the presence of hydroxyproline, loss of isopropyl (Δm = 43 Da) or ethyl radicals (Δm = 29 Da), through collisional activation of z radical ions, are characteristic of leucine or isoleucine, respectively. Radical migration processes permit distinctions even in cases where the specific z(•) ions, corresponding to the Yyy-Leu or -Ile segments, are absent or of low intensity. This tandem mass spectrometric (MS(n)) method has been successfully implemented in a liquid chromatography-MS(n) platform to determine the identity of 23 different isobaric residues from a mixture of five different peptides. The approach is convenient for distinction of isobaric residues from any crude peptide mixture, typically encountered in natural peptide libraries or proteomic analysis.

Theoretical Study on the Mechanism of NH + HCNO Reaction

DFT B3LYP calculations with the 6-311G(d, p) basis set were carried out to explore the mechanism of the NH (X3Σ-) + HCNO reaction. On the basis of calculated reaction paths, the three reaction channels are predicted to occur via the following reaction steps. The NH radical initially attacks C atom of the HCNO radical, leading to an intermediate HC(NH)NO (a1), followed by formation of a bond between the H atom of NH (X3Σ-) radical and the N atom of HCNO, leading to the formation of product HNO + HCN. In addition to the H atom of NH (X3Σ-) radical migration in the intermediate HC(NH)NO (a1), the H atom migration from C atom to N atom leads to an intermediate HN(H)CNO (b), followed by rupture of H2N－CNO bond, leading to the products NH2 + CNO. The NH radical initially attacks N atom of the HCNO radical, leading to an intermediate HCN(NH)O (a3), followed by formation of the products CH2O + N2, through the intermediates d1, d2, d3, d4, e1, e2 and f. The CCSD(T)/ 6-311G(d,p) energetic results indicated that the total barrier of product 1, product 2 and product 3 is 32.8 kcal/mol, 89.5 kcal/mol, 40.0 kcal/mol, respectively. It is shown that P1(CH2O + N2), P3 (HCN + HNO) are the major product channels with a minor contribution from P2 (NH2 + CNO).

Structure and Reactivity of the N-Acetyl-Cysteine Radical Cation and Anion: Does Radical Migration Occur?

The structure and reactivity of the N-acetyl-cysteine radical cation and anion were studied using ion-molecule reactions, infrared multi-photon dissociation (IRMPD) spectroscopy, and density functional theory (DFT) calculations. The radical cation was generated by first nitrosylating the thiol of N-acetyl-cysteine followed by the homolytic cleavage of the S-NO bond in the gas phase. IRMPD spectroscopy coupled with DFT calculations revealed that for the radical cation the radical migrates from its initial position on the sulfur atom to the α-carbon position, which is 2.5 kJ mol(-1) lower in energy. The radical migration was confirmed by time-resolved ion-molecule reactions. These results are in contrast with our previous study on cysteine methyl ester radical cation (Osburn et al., Chem. Eur. J. 2011, 17, 873-879) and the study by Sinha et al. for cysteine radical cation (Phys. Chem. Chem. Phys. 2010, 12, 9794-9800) where the radical was found to stay on the sulfur atom as formed. A similar approach allowed us to form a hydrogen-deficient radical anion of N-acetyl-cysteine, (M - 2H)( •- ). IRMPD studies and ion-molecule reactions performed on the radical anion showed that the radical remains on the sulfur, which is the initial and more stable (by 63.6 kJ mol(-1)) position, and does not rearrange.

The amide bond rotation controlled by an unusual C–H···O hydrogen bonding that favors the 1,4-phenyl radical migration

Experimental evidence in support of the presence of a weak C–H···O hydrogen bonding that favors 1,4-phenyl radical migration in a chiral amide is provided.

Proton Transfer Drives Protein Radical Formation in Helicobacter pylori Catalase but Not in Penicillium vitale Catalase

Heme catalases prevent cells from oxidative damage by decomposing hydrogen peroxide into water and molecular oxygen. Here we investigate the factors that give rise to an undesirable side reaction competing with normal catalase activity, the migration of a radical from the heme active site to the protein in the principal reaction intermediate compound I (Cpd I). Recently, it has been proposed that this electron transfer reaction takes place in Cpd I of Helicobacter pylori catalase (HPC), but not in Cpd I of Penicillium vitale catalase (PVC), where the oxidation equivalent remains located on the heme active site. Unraveling the factors determining the different radical locations could help engineer enzymes with enhanced catalase activity for detection or removal of hydrogen peroxide. Using quantum mechanics/molecular mechanics metadynamics simulations, we show that radical migration in HPC is facilitated by the large driving force (-0.65 eV) of the subsequent proton transfer from a histidine residue to the ferryl oxygen atom of reduced Cpd I. The corresponding free energy in PVC is significantly smaller (-0.19 eV) and, as we argue, not sufficiently high to support radical migration. Our results suggest that the energetics of oxoferryl protonation is a key factor regulating radical migration in catalases and possibly also in hydroperoxidases.

Arginine‐Facilitated α‐ and π‐Radical Migrations in Glycylarginyltryptophan Radical Cations

We have used model tripeptides GXW (with X being one of the amino acid residues glycine (G), alanine (A), leucine (L), phenylalanine (F), glutamic acid (E), histidine (H), lysine (K), or arginine (R)) to study the effects of the basicity of the amino acid residue on the radical migrations and dissociations of odd-electron molecular peptide radical cations M(·+) in the gas phase. Low-energy collision-induced dissociation (CID) experiments revealed that the interconvertibility of the isomers [G(·)XW](+) (radical centered on the N-terminal α-carbon atom) and [GXW](·+) (radical centered on the π system of the indolyl ring) generally increased upon increasing the proton affinity of residue X. When X was arginine, the most basic amino acid, the two isomers were fully interconvertible and produced almost identical CID spectra despite the different locations of their initial radical sites. The presence of the very basic arginine residue allowed radical migrations to proceed readily among the [G(·)RW](+) and [GRW](·+) isomers prior to their dissociations. Density functional theory calculations revealed that the energy barriers for isomerizations among the α-carbon-centered radical [G(·)RW](+), the π-centered radical [GRW](·+), and the β-carbon-centered radical [GRW(β)(·)](+) (ca. 32-36 kcal mol(-1)) were comparable with those for their dissociations (ca. 32-34 kcal mol(-1)). The arginine residue in these GRW radical cations tightly sequesters the proton, thereby resulting in minimal changes in the chemical environment during the radical migrations, in contrast to the situation for the analogous GGW system, in which the proton is inefficiently stabilized during the course of radical migration.