Highly Efficient Charge Transfer in Peptide Cations in the Gas Phase: Threshold Effects and Mechanism

Recent advances in experimental techniques to probe fast excited-state dynamics in biological molecules in the gas phase: dynamics in nucleotides, amino acids and beyond

In many chemical reactions, an activation barrier must be overcome before a chemical transformation can occur. As such, understanding the behaviour of molecules in energetically excited states is critical to understanding the chemical changes that these molecules undergo. Among the most prominent reactions for mankind to understand are chemical changes that occur in our own biological molecules. A notable example is the focus towards understanding the interaction of DNA with ultraviolet radiation and the subsequent chemical changes. However, the interaction of radiation with large biological structures is highly complex, and thus the photochemistry of these systems as a whole is poorly understood. Studying the gas-phase spectroscopy and ultrafast dynamics of the building blocks of these more complex biomolecules offers the tantalizing prospect of providing a scientifically intuitive bottom-up approach, beginning with the study of the subunits of large polymeric biomolecules and monitoring the evolution in photochemistry as the complexity of the molecules is increased. While highly attractive, one of the main challenges of this approach is in transferring large, and in many cases, thermally labile molecules into vacuum. This review discusses the recent advances in cutting-edge experimental methodologies, emerging as excellent candidates for progressing this bottom-up approach.

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.

Single-photon laser-enabled auger spectroscopy for measuring attosecond electron-hole dynamics

We propose and simulate a new type of attosecond time-resolved spectroscopy of electron-hole dynamics, applicable particularly to ultrafast hole migration. Attosecond ionization in the inner-valence region is followed by a vacuum ultraviolet probe inducing single-photon laser-enabled Auger decay, a one-photon-two-electron transition filling the inner-valence vacancy. The double ionization probability as a function of the attosecond pump-vacuum ultraviolet probe delay captures efficiently the ultrafast inner-valence hole dynamics. Detailed ab initio calculations are presented for inner-valence hole migration in glycine.

Observation of Ultrafast Charge Migration in an Amino Acid

We present the first direct measurement of ultrafast charge migration in a biomolecular building block - the amino acid phenylalanine. Using an extreme ultraviolet pulse of 1.5 fs duration to ionize molecules isolated in the gas phase, the location of the resulting hole was probed by a 6 fs visible/near-infrared pulse. By measuring the yield of a doubly charged ion as a function of the delay between the two pulses, the positive hole was observed to migrate to one end of the cation within 30 fs. This process is likely to originate from even faster coherent charge oscillations in the molecule being dephased by bond stretching which eventually localizes the final position of the charge. This demonstration offers a clear template for observing and controlling this phenomenon in the future.

Photodissociation pathways and lifetimes of protonated peptides and their dimers

Photodissociation lifetimes and fragment channels of gas-phase, protonated YA(n) (n = 1,2) peptides and their dimers were measured with 266 nm photons. The protonated monomers were found to have a fast dissociation channel with an exponential lifetime of ~200 ns while the protonated dimers show an additional slow dissociation component with a lifetime of ~2 μs. Laser power dependence measurements enabled us to ascribe the fast channel in the monomer and the slow channel in the dimer to a one-photon process, whereas the fast dimer channel is from a two-photon process. The slow (1 photon) dissociation channel in the dimer was found to result in cleavage of the H-bonds after energy transfer through these H-bonds. In general, the dissociation of these protonated peptides is non-prompt and the decay time was found to increase with the size of the peptides. Quantum RRKM calculations of the microcanonical rate constants also confirmed a statistical nature of the photodissociation processes in the dipeptide monomers and dimers. The classical RRKM expression gives a rate constant as an analytical function of the number of active vibrational modes in the system, estimated separately on the basis of the equipartition theorem. It demonstrates encouraging results in predicting fragmentation lifetimes of protonated peptides. Finally, we present the first experimental evidence for a photo-induced conversion of tyrosine-containing peptides into monocyclic aromatic hydrocarbon along with a formamide molecule both found in space.

Length effects in VUV photofragmentation of protonated peptides

We have studied photoionization of protonated synthetic peptides YG(n)F (n = 0, 1, 3, 5, 10). Photon energies ranging from 8 to 30 eV were used. For YG(n)F peptides up to n = 5 small fragment ions related to the sidechains of the aromatic terminal amino acids Y and F dominate the fragmentation patterns. The associated yields scale with total photoabsorption cross section, demonstrating efficient hole migration towards the terminal amino acids upon photoionization of the peptide backbone. For n = 10 the side-chain loss channel is quenched and a series of large dications appear.

Effects of charge location on the absorptions and lifetimes of protonated tyrosine peptides in vacuo

Nearby charges affect the electronic energy levels of chromophores, with the extent of the effect being determined by the magnitude of the charge and degree of charge-chromophore separation. The molecular configuration dictates the charge-chromophore distance. Hence, in this study, we aim to assess how the location of the charge influences the absorption of a set of model protonated and diprotonated peptide ions, and whether spectral differences are large enough to be identified. The studied ions were the dipeptide YK, the tripeptide KYK (Y = tyrosine; K = lysine) and their complexes with 18-crown-6-ether (CE). The CE targets the ammonium group by forming internal ionic hydrogen bonds and limits the folding of the peptide. In the tripeptide, the distance between the chromophore and the backbone ammonium is enlarged relative to that in the dipeptide. Experiments were performed in an electrostatic ion storage ring using a tunable laser system, and action spectra based on lifetime measurements were obtained in the range from 210 to 310 nm. The spectra are all quite similar though there seems to be some changes in the absorption band between 210 and 250 nm, while in the lower energy band all ions had a maximum absorption at ~275 nm. Lifetimes after photoexcitation were found to shorten upon protonation and lengthen upon CE complexation, in accordance with the increased number of degrees of freedom and an increase in activation energies for dissociation as the mobile proton model is no longer operative.

Visible and ultraviolet spectroscopy of gas phase protein ions

Optical spectroscopy has contributed enormously to our knowledge of the structure and dynamics of atoms and molecules and is now emerging as a cornerstone of the gas phase methods available for investigating biomolecular ions. This article focuses on the UV and visible spectroscopy of peptide and protein ions stored in ion traps, with emphasis placed on recent results obtained on protein polyanions, by electron photodetachment experiments. We show that among a large number of possible de-excitation pathways, the relaxation of biomolecular polyanions is mainly achieved by electron emission following photo-excitation in electronically excited states. Electron photodetachment is a fast process that occurs prior to relaxation on vibrational degrees of freedom. Electron photodetachment yield can then be used to record gas phase action spectra for systems as large as entire proteins, without the limitation of system size that would arise from energy redistribution on numerous modes and prevent fragmentation after the absorption of a photon. The optical activity of proteins in the near UV is directly related to the electronic structure and optical absorption of aromatic amino acids (Trp, Phe and Tyr). UV spectra for peptides and proteins containing neutral, deprotonated and radical aromatic amino acids were recorded. They displayed strong bathochromic shifts. In particular, the results outline the privileged role played by open shell ions in molecular spectroscopy which, in the case of biomolecules, is directly related to their reactivity and biological functions. The optical shifts observed are sufficient to provide unambiguous fingerprints of the electronic structure of chromophores without the requirement of theoretical calculations. They constitute benchmarks for calculating the absorption spectra of chromophores embedded in entire proteins and could be used in the future to study biochemical processes in the gas phase involving charge transfer in aromatic amino acids, such as in the mediation of electron transfer or redox reactions. We then addressed the important question of the sensitivity of protein optical spectra to the intrinsic properties of protein ions, including conformation, charge state, etc., and to environmental factors. We report optical spectra for different charge states of insulin, for ubiquitin starting from native and denaturated solutions, and for apo-myoglobin protein. All these spectra are compared critically to spectra recorded in solution, in order to assess solvent effects. We also report the spectra of peptides complexed with metal cations and show that complexation gives rise to new optical transitions related to charge transfer types of excitation. The perspectives of this work include integrative approaches where UV-Vis spectroscopy could, for example, be combined with ion mobility spectrometry and high level calculations for protein structural characterization. It could also be used in spectroscopy to probe biological processes in the gas phase, with different light sources including VUV radiation (to probe different types of excitations) and ultra short pulses with time and phase modulation (to probe and control the dynamics of de-excitation or charge transfer events), and with the derivatization of proteins with chromophores to modulate their optical properties. We also envision that photo-excitation will play an important role in the future to produce intermediates with new chemical and reactive properties. Another promising route is to conduct activated electron photodetachment dissociation experiments.

Simulation and visualization of attosecond stimulated x-ray Raman spectroscopy signals in trans-N-methylacetamide at the nitrogen and oxygen K-edges

The stimulated Raman component of the pump-probe spectrum of trans-N-methylacetamide obtained in response to two soft x-ray pulses is calculated by treating the core excitations at the Hartree-Fock static-exchange level. The signal reveals the dynamics of valence-electron wave packets prepared and detected in the vicinity of a selected atom (either nitrogen or oxygen). The evolving electronic charge density as well as electronic coherence of the doorway and the window created by the two pulses are visualized using a time-dependent basis set of natural orbitals, which reveals that the wave packets consist of several entangled valence particle-hole pairs.

Autoionization mediated by electron transfer

Electron-electron coincidence spectra of Ar-Kr clusters after photoionization have been measured. An electron with the kinetic energy range from 0 to approximately 1 eV is found in coincidence with the Ar 3s cluster photoelectron. The low kinetic energy electron can be attributed to an Ar + Kr+ + Kr+ final state which forms after electron transfer mediated decay. This autoionization mechanism results from a concerted transition involving three different atoms in a van der Waals cluster; it was predicted theoretically, but hitherto not observed.

Formation of peptide radical ions through dissociative electron transfer in ternary metal-ligand-peptide complexes

The formation and fragmentation of odd-electron ions of peptides and proteins is of interest to applications in biological mass spectrometry. Gas-phase redox chemistry occurring during collision-induced dissociation of ternary metal-ligand-peptide complexes enables the formation of a variety of peptide radicals, including the canonical radical cations, M(+•), radical dications, [M+H](2+•), radical anions, [M-2H](-•) and phosphorylated radical cations. In addition, odd-electron peptide ions with well-defined initial location of the radical site are produced through side-chain losses from the radical ions. Subsequent fragmentation of these species provides information regarding the role of charge and location of the radical site on the competition between radical-induced and proton-driven fragmentation of odd-electron peptide ions. This account summarizes current understanding of the factors that control the efficiency of the intramolecular electron transfer (ET) in ternary metal-ligand-peptide complexes resulting in formation of odd-electron peptide ions. Specifically, we discuss the effect of the metal center, the ligand and the peptide structure on the competition between the ET, proton transfer (PT) and loss of neutral peptide and neutral peptide fragments from the complex. Fundamental studies of the structures, stabilities and the energetics and dynamics of fragmentation of these complexes are also important for detailed molecular-level understanding of photosynthesis and respiration in biological systems.

Electron delocalization and charge transfer in polypeptide chains

In this work, the electron structure and charge-transfer mechanism in polypeptide chains are investigated according to natural bond orbitals (NBO) analysis at the level of B3LYP/6-311++G**. The results indicate that the delocalization of electrons between neighboring peptide subgroups can occur in two opposite directions, and the delocalization effect in the direction from the carboxyl end to the amino end has an obvious advantage. As a result of a strong hyperconjugative interaction, the lowest unoccupied NBO of the peptide subgroup, pi*C-O, has significant delocalization to neighboring subgroups, and the energies of these NBOs decrease from the carboxyl end to the amino end. The formation of intramolecular O...H-N type hydrogen bonds also helps to delocalize the electron from the carboxyl end to the amino end. Thus, the electron will flow to the amino end. The superexchange mechanism is suggested in the electron-transfer process.

Probing Ultrafast Purely Electronic Charge Migration in Small Peptides

A pump–probe experiment that can examine a pure charge migration on a time scale short compared to the onset of nuclear motion is discussed. The mass spectrometric studies of Schlag et al. suggest that short peptide terminated by an aromatic amino acid are particularly suitable test compounds. The pump pulse needs to ionize the molecule on a time scale short compared to the period of the electronic motion, typically sub-fs. However, ionization occurs preferentially when the electrical field of the light is maximal so that the duration of the pulse envelope can be somewhat longer. Detection by photoelectron spectrometry of the peptide cation, to produce a dication, is shown to be able to probe the electronic rearrangement.

Electron transfers in proteins: investigations with a modified through-bond coupling model

By integrating the merits of previous models, a modified through-bond coupling (MTBC) model is proposed in this work and shows obvious improvement compared with previous models. With the MTBC model, the dominant electron coupling pathways in the polypeptide chains were identified, where the N-H bonds were found to be essential to the electron couplings. The local structures of peptides and proteins were finely characterized by the electron couplings and decay factors since they are structure sensitive. The neighboring carbonyl O-O distances are qualitatively correlated with the decay factors, and the deviations from the transconfigurations will weaken the coupling interactions. When the two amino acids being studied are not close in sequence, the couplings through hydrogen bonds are probably the main pathway because the electron transfers in this way save many steps, albeit the decay factor is less than that of per bond, consistent with the classical electron-tunneling model developed by Beratan [Science 252, 1285 (1991)]. It was found that the MTBC model can be effectively extended to study the electron transfers in complex biological systems with the combination of the fragment approach, which takes into account the contributions of key hydrogen bonds.

Radical cations of amino acids and peptides: structures and stabilities

Amino acid and peptide radical cations, M*+, are formed by oxidative dissociations of [Cu(auxiliary ligand)(M)]*2+ and [Metal(III)(salen)(M)]+ complexes. The most easily formed radicals contain either an aromatic or basic amino acid residue. Aromatic amino acids have low ionization energies, are easily oxidized and delocalize the charge and spin over the ring systems; basic amino acids facilitate formation of alpha-radicals that have captodative structures in which the charge and spin are formally separated, although feeding back some of the charge onto the amide or carboxyl group adjacent to the radical center through hydrogen bonding enriches the electron-withdrawing properties and is highly stabilizing. DFT calculations located five isomers of His*+ with an alpha-radical with a captodative structure at the global minimum in a deep potential well. An IRMPD spectrum confirmed that this isomer is the experimentally observed "long-lived" isomer. When both charge and spin are on the peptide backbone, as in [GGG]*+, captodative structures have the lowest energies; the barriers to interconversion between the three isomeric alpha-radicals of [GGG]*+ are high as the charge impedes migration of a hydrogen atom. Dissociation of [GGG]*+ is charge-driven. In peptide radical cations containing a basic amino acid residue the charge is sequestered on the side chain and the radical center, either on the backbone or on another side chain, initiates the fragmentation.

Kinetics for tautomerizations and dissociations of triglycine radical cations

Fragmentations of tautomers of the alpha-centered radical triglycine radical cation, [GGG(*)](+), [GG(*)G](+), and [G(*)GG](+), are charge-driven, giving b-type ions; these are processes that are facilitated by a mobile proton, as in the fragmentation of protonated triglycine (Rodriquez, C. F. et al. J. Am. Chem. Soc. 2001, 123, 3006-3012). By contrast, radical centers are less mobile. Two mechanisms have been examined theoretically utilizing density functional theory and Rice-Ramsperger-Kassel-Marcus modeling: (1) a direct hydrogen-atom migration between two alpha-carbons, and (2) a two-step proton migration involving canonical [GGG](*+) as an intermediate. Predictions employing the latter mechanism are in good agreement with results of recent CID experiments (Chu, I. K. et al. J. Am. Chem. Soc. 2008, 130, 7862-7872).

Distal charge transport in peptides

Biological systems often transport charges and reactive processes over substantial distances. Traditional models of chemical kinetics generally do not describe such extreme distal processes. In this Review, an atomistic model for a distal transport of information, which was specifically developed for peptides, is considered. Chemical reactivity is taken as the result of distal effects based on two-step bifunctional kinetics involving unique, very rapid motional properties of peptides in the subpicosecond regime. The bifunctional model suggests highly efficient transport of charge and reactivity in an isolated peptide over a substantial distance; conversely, a very low efficiency in a water environment was found. The model suggests ultrafast transport of charge and reactivity over substantial molecular distances in a peptide environment. Many such domains can be active in a protein.

Gas-Phase Spectroscopy of Biomolecular Building Blocks

Gas-phase spectroscopy lends itself ideally to the study of isolated molecules and provides important data for comparison with theory. In recent years, we have seen enormous progress in the study of biomolecular building blocks in the gas phase. The motivation for such work is threefold: (a) It is important to distinguish between intrinsic molecular properties and properties that result from the biological environment. (b) Gas-phase spectroscopy of clusters provides insights into fundamental interactions and into microsolvation. (c) Gas-phase data support quantum-chemical calculations. This review focuses on the current status of (poly)amino acids and DNA bases. Recent results help elucidate structure and hydrogen-bonded interactions, as well as showcase a successful interplay between theory and experiment.

Spectroscopic Observation of Conformation-Dependent Charge Distribution in a Molecular Cation

A prototypical case of a molecular radical cation is reported whose electrostatic charge distribution is determined entirely and uniquely by its conformational structures. Experimental observation of charge distribution in a molecular ion was for the first time demonstrated to be feasible by optical spectroscopy in the case of L-phenylalanine cation by utilizing the fact that its photodissociation propensity is entirely determined by the electronic character of its charge distribution. The cationic charge was explicitly shown to be localized in a single site or two different sites depending on the molecular conformation.

The time scale for electronic reorganization upon sudden ionization of the water and water-methanol hydrogen bonded dimers and of the weakly bound NO dimer

When the valence molecular orbital is localized sudden ionization can cause the nascent hole to move rapidly even before any relaxation of the geometry occurs. Hydrogen bonded clusters offer suitable test systems where the hole is initially localized on one moiety. Computational studies are reported for the water dimer and water-methanol bimer. The local ionization potential of water is different in the methanol-water and water-methanol conformers and this difference is very clearly reflected in the dynamics of charge migration. For the NO dimer the results are that its structure is symmetric so that the two NO molecules are equivalent and do not exhibit the required localization. The role of symmetry is also evident in the charge propagation for holes created in different orbitals. Localization of the initial hole distribution even if absent in the bare molecule can still be induced by the intense electric field of a sudden photoionization. This effect is computationally studied for the NO dimer in the presence of a static electric field.

Charge Transfer Study through the Determination of the Ionization Energies of Tetrapeptides X3-Tyr, X = Gly, Ala, or Leu. Influence of the Inclusion of One Glycine in Alanine and Leucine Containing Peptides

The energies of the fundamental and several excited states of tetrapeptide radical cations were determined at the outer valence Green's function (OVGF) level, at three geometries corresponding to the lowest energy conformations: two for the neutral and one for the cation. The conformations were optimized at the density functional theory level within the B3LYP framework. It was found that, from a purely energetic point of view, a charge initially created on the tyrosine chromophore could migrate without any geometrical change and without further activation once the excited electronic state of the ionized chromophore was formed. This migration could reach the NH(2) terminus for the neutral conformations but should stop at the adjacent peptide link for the cation conformation. These results stress the probable influence of the electronic coupling between the states rather than the existence of a barrier on the charge pathway to explain the difference between the peptides in the charge-transfer process leading to the loss of an iminium [NH(2)=CHR](+) cation. The dissociation energy of the asymptote related to the formation of this NH(2) terminus iminium cation was calculated for few species and it appears that the excess energy available for dissociation is significant when starting from the lowest energy conformations of the neutral or the cation, provided that the charge transfer is effective. It was also found that the amino acids did not conserve their energetic properties and their zero order energy levels turned to a complete new energetic scheme corresponding to the conformation of the peptide.

Demonstration of a new biosensing concept for immunodiagnostic applications based on change in surface conductance of antibodies after biomolecular interactions

We report an important observation that the surface conductivity of antibody layer immobilized on polylysine-coated glass substrate decreases upon the formation of complex with their specific antigens. This change in conductivity has been observed for both monoclonal and polyclonal antibodies. The conductance of monoclonal mouse IgG immobilized on polylysine-coated glass substrate changed from 1.02x10(-8) ohm(-1) to 1.41x10(-11) ohm(-1) at 10 V when complex is formed due to the specific biomolecular interactions with rabbit anti-mouse IgG F(ab')(2). Similar behavior was observed when the same set up was tested in two clinical assays: (1) anti-Leishmania antigen polyclonal antibodies taken from Kala Azar positive patient serum interacting with Leishmania promastigote antigen, and (2) anti-p21 polyclonal antibodies interacting with p21 antigen. The proposed concept can represent a new immunodiagnostic technique and may have wide ranging applications in biosensors and nanobiotechnology too.

Peptide electron transfer: more questions than answers

Nature has specifically designed proteins, as opposed to DNA, for electron transfer. There is no doubt about the electron transfer within proteins compared with the uncertain and continuing debate about charge transfer through DNA. However, the exact mechanism of electron transfer within peptide systems has been a source of controversy. Two different mechanisms for electron transfer between a donor and an acceptor, electron hopping and bridge-assisted superexchange, have been proposed, and are supported by experimental evidence and theoretical calculations. Several factors were found to affect the kinetics of this process, including peptide chain length, secondary structure and hydrogen bonding. Electrochemical measurements of surface-supported peptides have contributed significantly to the debate. Here we summarize the current approaches to the study of electron transfer in peptides with a focus on surface measurements and comment on these results in light of the current and often controversial debate on electron transfer mechanisms in peptides.

An electronic time scale in chemistry

Ultrafast, subfemtosecond charge migration in small peptides is discussed on the basis of computational studies and compared with the selective bond dissociation after ionization as observed by Schlag and Weinkauf. The reported relaxation could be probed in real time if the removal of an electron could be achieved on the attosecond time scale. Then the mean field seen by an electron would be changing rapidly enough to initiate the migration. Tyrosine-terminated tetrapeptides have a particularly fast charge migration where in <1 fs the charge arrives at the other end. A femtosecond pulse can be used to observe the somewhat slower relaxation induced by correlation between electrons of different spins. A slower relaxation also is indicated when removing a deeper-lying valence electron. When a chromophoric amino acid is at one end of the peptide, the charge can migrate all along the peptide backbone up to the N end, but site-selective ionization is probably easier to detect for tryptophan than for tyrosine.

Photoinduced processes in protonated tryptamine

The electronic excited state dynamics of protonated tryptamine ions generated by an electrospray source have been studied by means of photoinduced dissociation technique on the femtosecond time scale. The result is that the initially excited state decays very quickly within 250 fs. The photoinduced dissociation channels observed can be sorted in two groups of fragments coming from two competing primary processes on the singlet electronic surface. The first one corresponds to a hydrogen-atom loss channel that creates a tryptamine radical cation. The radical cation subsequently fragments to smaller ions. The second process is internal conversion due to the H-atom recombination on the electronic ground state. Time-dependent density functional theory calculations show that an excited pisigma* state dissociative along the protonated amino N-H stretch crosses both the locally excited pipi* state and the electronic ground state S(0) and thus triggers the photofragmentation reactions. The two processes have equivalent quantum yields, approximately equal to 50% of the fragments coming from the H-atom loss reaction. The two primary reaction paths can clearly be distinguished by their femtosecond pump/probe dynamics recorded on the different fragmentation channels.

Stable Gas-Phase Radical Cations of Dimeric Tryptophan and Tyrosine Derivatives

Stable radical cations of dimeric amino acid derivatives of tryptophan and tyrosine were generated by collision-induced dissociation of [Cu(II)(diethylenetriamine)(amino acid derivative)2]*2+. The yields of the dimer radical cations were dependent on both the auxiliary ligand and the tryptophan or tyrosine derivatives used. Amino acid derivatives with an unmodified carboxylic acid group did not generate dimer radical cations. For the amino acid derivatives Ac-Trp-OMe and Ac-Trp-NH2 (Ac is N-acetyl; OMe and NH2 are the methyl ester and amide modifications of the C-terminal carboxylic group), no auxiliary ligand was required for generating the dimer radical cations. Collision-induced dissociation of the [Cu(II)(amino acid derivative)4]*2+ precursor generated the dimer radical cation [(amino acid derivative)2]*+. Stabilizing interactions, most likely involving hydrogen bonding, between the two amino acid derivatives are proposed to account for observation of the dimer radical cations. Dissociation of these ions yields protonated or radical cationic amino acid derivatives; these observations are consistent with the expectation of proton competition between monomeric units, whose proton affinities were calculated using density functional theory.

Dissociation Kinetics of Peptide Ions

The dissociation of peptide ions has been found to have ultrafast components that in many ways are uniquely different from typical unimolecular kinetics. As such, some peptide reactions provide new channels, which do not conform to statistical models of reaction kinetics. When the dissociation rates are in the 100 fs range, they are in a time scale where statistical methods do not yet apply, although molecules that have not yet dissociated will later in time undergo statistical redistribution of their excess energy, which, however, may not lead to noticeable reactivity within the experimental time frames for large peptides and hence are simply dissipative. This work is meant to reconcile the long time statistical results of Lifshitz et al. (2003) with the work of Schlag et al. (1995/6) that suggests an alternate parallel and much faster time scale for dissociation. It is argued that the two sets of results and interpretations augment one another and in fact open up a most interesting new field of peptide kinetics in addition to the unimolecular behavior, which becomes de facto arrested by the shear size of the molecule being unable to find a transition state on any reasonable time scale.

IR-Spectroscopic Characterization of Acetophenone Complexes with Fe+, Co+, and Ni+ Using Free-Electron-Laser IRMPD

The gas-phase complexes M(+)(acet)(2), where M is Fe, Co, or Ni and acet is acetophenone, were studied spectroscopically by infrared multiple-photon dissociation (IRMPD) supported by density functional (DFT) computations. The FELIX free electron laser was used to give tunable radiation from approximately 500 to 2200 cm(-1). The spectra were interpreted to determine the metal-ion binding sites on the ligands (oxygen (O) or ring (R)) and to see if rearrangement of the ligand(s) to toluene plus CO occurred. For Ni(+), O binding was found to predominate (similar to the previously studied Cr(+) case), with less than approximately 10% of R-bound ligands in the population. For Co(+), a roughly equal mixture of R-bound and O-bound ligands was present; based on the computed thermochemistry, the OR complex was considered likely to predominate. Fe(+) complexes appeared largely O-bound, but with clear evidence for some R-binding. The exceptionally large extent of R binding for Co(+) highlights the special affinity of this metal ion for aromatic ring ligands. In contrast, the predominant O binding for Ni(+) emphasizes the especially high metal-ion affinity of the O site of acetophenone compared with other ligands such as anisole where R binding of Ni(+) predominates. The spectra did not indicate significant intracomplex rearrangement of ligands to toluene plus CO, and in particular for the Co(+) case the absence of a metal-bound C triple bond O stretching peak near 2100 cm(-1) strongly ruled out such a rearrangement.

Electron transfer processes in DNA: mechanisms, biological relevance and applications in DNA analytics

In principle, DNA-mediated charge transfer processes can be categorized as oxidative hole transfer and reductive electron transfer. With respect to the routes of DNA damage most of the past research has been focused on the investigation of oxidative hole transfer or transport. On the other hand, the transport or transfer of excess electrons has a large potential for biomedical applications, mainly for DNA chip technology.

Electrical transport in saturated and conjugated molecular wires

The mechanism for charge transport in dithio molecular wires tethered between two gold electrodes is investigated, using both a steady state and a time-dependent quantum mechanical approach. The interface with the electrodes is modeled by two gold clusters and the electronic structure of the entire Au(n)-S-bridge-S-Au(n) system is computed ab initio at the DFT level and semi-empirically, with the extended Hückel theory. Current vs. applied bias, I-V, curves are computed using a scattering Landauer-type formalism in a steady state picture. The applied source-drain and gate voltages are included at the ab initio level in the electronic Hamiltonian and found to influence strongly the I-V characteristics. The time evolution of a non stationary electronic wave packet initially localized on a gold atom at one end of the extended system shows that charge transfer proceeds sequentially, by a hopping mechanism, to the opposite end. Analysis of the effective one electron Hamiltonian matrix shows that the sulfur atom endows a resistive character to the Au-C-S junctions. The S atoms are however rather well coupled to both the gold and carbon atoms so that typically the super exchange limit for electron transfer is not reached unless the molecular bridge is saturated and the Fermi window function is narrow.

Statistical vs. non-statistical deactivation pathways in the UV photo-fragmentation of protonated tryptophan-leucine dipeptide

The excited state dynamics of protonated tryptophan-leucine ions WLH+, generated in an electrospray source, is investigated by photo-induced fragmentation in the gas phase, using femtosecond laser pulses. Two main features arise from the experiment. Firstly, the initially excited pipi* state decays very quickly with 2 time constants of 1 and 10 ps. Secondly, the transient signals recorded on different fragments are not the same which indicates two competing primary fragmentation processes. One involves a direct dissociation from the excited state that gives evidence for a non-statistical deactivation path. The other is attributed to a statistical decay following internal conversion to the ground electronic surface.