Isomerization versus Fragmentation of Glycine Radical Cation in Gas Phase

Intermolecular hydrogen bonding behavior of amino acid radical cations

Amino acid and peptide radicals are of broad interest due to their roles in biochemical oxidative damage, pathogenesis and protein radical catalysis, among others. Using density functional theory (DFT) calculations at the ωB97X-D/def2-QZVPPD//ωB97X-D/def2-TZVPP level of theory, we systematically investigated the hydrogen bonding between water and fourteen α-amino acids (Ala, Asn, Cys, Gln, Gly, His, Met, Phe, Pro, Sel, Ser, Thr, Trp, and Tyr) in both neutral and radical cation forms. For all amino acids surveyed, stronger hydrogen-bonding interactions with water were observed upon single-electron oxidation, with the greatest increases in hydrogen-bonding strength occurring in Gly, Ala and His. We demonstrate that the side chain has a significant impact on the most favorable hydrogen-bonding modes experienced by amino acid radical cations. Our computations also explored the fragmentation of amino acid radical cations through the loss of a COOH radical facilitated by hydrogen bonding. The most favorable pathways provided stabilization of the resulting cationic fragments through hydrogen bonding, resulting in more favorable thermodynamics for the fragmentation process. These results indicate that non-covalent interactions with the environment have a profound impact on the structure and chemical fate of oxidized amino acids.

Ultrafast Hydrogen Migration in Photoionized Glycine

Hydrogen migration in the glycine cation has been investigated using a combination of a short train of attosecond extreme ultraviolet pulses with few-optical-cycle near-infrared pulses. The yield of the photofragments produced has been measured as a function of pump-probe delay. These time-dependent measurements reveal the presence of a hydrogen migration process occurring in 48 fs. Previous mass spectrometric experiments and theoretical calculations have allowed us to identify the conformations and cation states involved in the process induced by the broad band extreme ultraviolet radiation.

Insights into the dissociative ionization of glycine by PEPICO experiments

The fragmentation of glycine (NH₂CH₂COOH) has been studied by photoelectron–photoion coincidence, PEPICO, experiments at 60 eV photon energy.

Influence of the Side Chain in the Structure and Fragmentation of Amino Acids Radical Cations

The conformational properties of ionized amino acids (Gly, Ala, Ser, Cys, Asp, Gln, Phe, Tyr, and His) have been theoretically analyzed using the hybrid B3LYP and the hybrid-meta MPWB1K functionals as well as with the post-Hartree Fock CCSD(T) level of theory. As a general trend, ionization is mainly localized at the -NH2 group, which becomes more planar and acidic, the intramolecular hydrogen bond in which -NH2 acts as proton donor being strengthened upon ionization. For this reason, the so-called conformer IV(+) becomes the most stable for nonaromatic amino acid radical cations. Aromatic amino acids do not follow this trend because ionization takes place mainly at the side chain. For these amino acids for which ionization of the side chain prevails over the -NH2 group, structures III(+) and II(+) become competitive. The Cα-X fragmentations of the ionized systems have also been studied. Among the different decompositions considered, the one that leads to the loss of COOH(•) is the most favorable one. Nevertheless, for aromatic amino acids fragmentations leading to R(•) or R(+) start being competitive. In fact, for His and Tyr, results indicate that the fragmentation leading to R(+) is the most favorable process.

N-Acetylglycine Cation Tautomerization Enabled by the Peptide Bond

We present a combined experimental and theoretical study of the ionization of N-acetylglycine molecules by 48 keV O(6+) ions. We focus on the single ionization channel of this interaction. In addition to the prompt fragmentation of the N-acetylglycine cation, we also observe the formation of metastable parent ions with lifetimes in the microsecond range. On the basis of density functional theory calculations, we assign these metastable ions to the diol tautomer of N-acetylglycine. In comparison with the simple amino acids, the tautomerization rate is higher because of the presence of the peptide bond. The study of a simple biologically relevant molecule containing a peptide bond allows us to demonstrate how increasing the complexity of the structure influences the behavior of the ionized molecule.

Dissociations of copper(II)-containing complexes of aromatic amino acids: radical cations of tryptophan, tyrosine, and phenylalanine

The dissociations of two types of copper(II)-containing complexes of tryptophan (Trp), tyrosine (Tyr), or phenylalanine (Phe) are described. The first type is the bis-amino acid complex, [Cu(II)(M)(2)].(2+), where M = Trp, Tyr, or Phe; the second [Cu(II)(4Cl-tpy)(M)].(2+), where 4Cl-tpy is the tridendate ligand 4'-chloro-2,2':6',2''-terpyridine. Dissociations of the Cu(ii) bis-amino acid complexes produce abundant radical cation of the amino acid, M.(+), and/or its secondary products. By contrast, dissociations of the 4Cl-tpy-bearing ternary complexes give abundant M.(+) only for Trp. Density functional theory (DFT) calculations show that for Tyr and Phe, amino-acid displacement reactions by H(2)O and CH(3)OH (giving [Cu(II)(4Cl-tpy)(H(2)O)].(2+) and [Cu(II)(4Cl-tpy)(CH(3)OH)].(2+)) are energetically more favorable than dissociative electron transfer (giving M.(+) and [Cu(I)(4Cl-tpy)](+)). The fragmentation pathway common to all these [Cu(II)(4Cl-tpy)(M)].(2+) ions is the loss of NH(3). DFT calculations show that the loss of NH(3) proceeds via a "phenonium-type" intermediate. Dissociative electron transfer in [Cu(II)(4Cl-tpy)(M-NH(3))].(2+) results in [M-NH(3)].(+). The [Phe-NH(3)] (+) ion dissociates facilely by eliminating CO(2) and giving a metastable phenonium-type ion that rearranges readily into the styrene radical cation.

Radical-cationic gaseous amino acids: a theoretical study

Three major forms of gaseous radical-cationic amino acids (RCAAs), keto (COOH), enolic (C(OH)OH), and zwitterionic (COO(-)), as well as their tautomers, are examined for aliphatic Ala(.+), Pro(.+), and Ser(.+), sulfur-containing Cys(.+), aromatic Trp(.+), Tyr(.+), and Phe(.+), and basic His(.+). The hybrid B3LYP exchange-correlation functional with various basis sets along with the highly correlated CCSD(T) method is used. For all RCAAs considered, the main stabilizing factor is spin delocalization; for His(.+), protonation of the basic side chain is equally important. Minor stabilizing factors are hydrogen bonding and 3e-2c interactions. An efficient spin delocalization along the N-C(alpha)-C(O-)O moiety occurs upon H-transfer from C(alpha) to the carboxylic group to yield the captodative enolic form, which is the lowest-energy isomer for Ala(.+), Pro(.+), Ser(.+), Cys(.+), Tyr(.+), and Phe(.+). This H-transfer occurs in a single step as a 1,3-shift through the sigma-system. For His(.+), the lowest-energy isomer is formed upon H-transfer from C(alpha) to the basic side chain, which results in a keto form, with spin delocalized along the N-C(alpha)-C=O fragment. Trp(.+) is the only RCAA that favors spin delocalization over an aromatic system given the low ionization energy of indole. The lowest-energy isomer of Trp(.+) is a keto form, with no H-transfer.

Effects of ionization on N-glycylglycine peptide: Influence of intramolecular hydrogen bonds

The ionization effects on 28 conformations of N-glycylglycine are analyzed by means of the hybrid B3LYP and the hybrid meta-MPWB1K density functionals and by single-point calculations at the CCSD(T) level of theory. The most favorable process observed corresponds to the ionization of the only neutral conformation that presents a OH...NH2 intramolecular hydrogen bond, which leads to CO2 elimination after a spontaneous proton transfer from -COOH to NH2. The remaining neutral structures evolve to 20 different conformations of N-glycylglycine radical cation, which lie about 25-40 kcal/mol higher than the decarboxylated [NH3CH2CONHCH2]+*...[CO2] complex. Structural changes induced by ionization depend on the intramolecular hydrogen bonds of the initial conformation, since they determine the nature of the electron hole formed. In most cases, ionization takes place at the terminal -NH2 and -CO of the amide bond, which produces a strengthening of the peptide bond and the formation of new -NH2...OC(amide) and -NH2...OCOH hydrogen bonds. However, if -NH2 and -CO(amide) simultaneously act as proton acceptor in the neutral conformation, ionization is mainly localized at the carboxylic group, which produces a strengthening of the -COOH...OC(amide) bond. Both functionals lead to similar trends and compare well with CCSD(T) results except for a few cases for which B3LYP provides a too delocalized picture of the electron hole and consequently leads to artificial geometry reorganization.

Classical Trajectory Simulations of Photoionization Dynamics of Tryptophan: Intramolecular Energy Flow, Hydrogen-Transfer Processes and Conformational Transitions

One-photon and two-photon ionization dynamics of tryptophan is studied by classical trajectory simulations using the semiempirical parametric method number 3 (PM3) potential surface in "on the fly" calculations. The tryptophan conformer is assumed to be in the vibrational ground state prior to ionization. Initial conditions for the trajectories are weighted according to the Wigner distribution function computed for that state. Vertical ionization in the spirit of the classical Franck-Condon principle is assumed. For the two-photon ionization process the ionization is assumed to go resonantively through the first excited state. Most trajectories are computed, and the analysis is carried out for the first 10 ps. A range of interesting effects are observed. The main findings are as follows: (1) Multiple conformational transitions are observed in most of the trajectories within the ultrafast duration of 10 ps. (2) Hydrogen transfer from the carboxyl group to the amino group and back has been observed. A zwitterion is formed as a transient state. (3) Two new isomers are formed during the dynamics, which have apparently not been previously observed. (4) Fast energy flow between the ring modes and the amino acid backbone is observed for both one- and two-photon ionization. However, the effective vibrational temperatures only approach the same value after 90 ps. The conformation transition dynamics, the proton-transfer processes and the vibrational energy flow are discussed and analyzed.

Different chemical dynamics for different conformers of biological molecules: Photoionization of glycine

Single-photon ionization dynamics of two conformers of glycine is studied by classical trajectory simulations using the semiempirical PM3 potential surface in "on the fly" calculations. Initial conditions for the trajectories are weighted according to the Wigner distribution function computed for the initial vibrational ground state. Vertical ionization in the spirit of the classical Franck-Condon principle is assumed. The dynamics of the two conformers are compared during the first 10 ps. The comparison shows very different dynamical behavior for the two conformers. In particular, the chemical fragmentation pathways differ in part. Also, one of the conformers gives much higher rates of conformational transitions, while the other conformer gives larger chemical fragmentation yields. The example shows significantly different chemical dynamics for two conformers close in energy and separated by a low barrier.

Fragmentation and deformation mechanism of glycine isomers in gas phase: Investigations of charge effect

The structural parameters, relative stability, proton transfer energy barriers of four typical and life related isomers and conformers of different charged (n=0,+/-1,+/-2) glycine species have been investigated using B3LYP, BHLYP, and CCSD(T) methods. Results indicate that those neutral and (+/-1)-charged species are stable. For the (+2)-charged cases, all four triplet-state glycine species and only the singlet-state zwitterionic one are stable. On the other hand, only the singlet-state zwtterionic glycine ((1)GlyZW(-2)) and the corresponding neutral form counterpart ((1)Gly(-2)) are stable for the (-2)-charged cases. Either of the two stable structures holds a proton lying in the position (2-3 A) of being separated from its corresponding parental species. Those unstable divalent glycine species are dissociated into different smaller species spontaneously according to the characters of their different structures and electron spins. The presented fragmentation and deformation mechanisms can effectively predict and satisfactorily explain some experimental phenomena, which had been puzzling the mass spectrometry chemists. Also, the mechanisms should be suitable for any other similar molecule systems. Comparisons of the relative energies of the four (+1)-charged glycine species show that doublet-state glycine III ((2)GlyIII1) is more stable in energy by 12.1 kcal/mol than the (+1)-charged glycine Gly ((2)Gly1). This is consistent with the energy ordering of their corresponding mono-valence metal ion-bound derivatives. In addition, calculations show that an intramolecular proton transfer of (2)Gly(-1) to become its zwitterionic counterpart is preferred due to its least activation energy barrier (5.8 kcal/mol) among four discussed processes.

Gas phase dissociation energies of saturated AHn*+ radical cations and AHn neutrals (A = Li-F, Na-Cl): dehydrogenation, deprotonation, and formation of AHn-2*+ - H2 complexes

The dissociation energies corresponding to the two possible A-H cleavages of A (A = Li-F and Na-Cl) radical cations (loss of a H(+) and loss of a H(.)) have been computed at the CCSD(T)/ 6-311++G(3df,2pd) level of theory and compared to those of their neutral precursors. Removing an electron from AH(n)() decreases dramatically its deprotonation energy, especially for the A molecules (C and ), which become one of the most acidic species of the row, their acid character being only exceeded by FH(.+) and ClH(.+), respectively. However, dehydrogenation energies only decrease for the systems on the left side of the row (up to C and SiH(4)(.+)) for which the electron is removed from a A-H bonding orbital. Nevertheless, the loss of hydrogen is the more favorable cleavage in all cases except FH(.+). Ionization of SiH(4) leads to a Jahn-Teller distorted structure that corresponds to a Si - H(2) complex. Other - eta(2)H(2) complexes in the doublet spin state have also been found to be stable for A = Be, Mg, Al, and P, the hydrogen molecule complexes being more stable than their corresponding radical cations, for Be, Mg, and Al.