Biphotonic Ionization of DNA: From Model Studies to Cell

Oxidation reactions triggered by low‐intensity UV photons represent a minor contribution with respect to the overwhelming pyrimidine base dimerization in both isolated and cellular DNA. The situation is totally different when DNA is exposed to high‐intensity UVC radiation under conditions where biphotonic ionization of the four main purine and pyrimidine bases becomes predominant at the expense of singlet excitation processes. The present review article provides a critical survey of the main chemical reactions of the base radical cations thus generated by one‐electron oxidation of nucleic acids in model systems and cells. These include oxidation of the bases with the predominant formation of 8‐oxo‐7,8‐dihydroguanine as the result of preferential hole transfer to guanine bases that act as sinks in isolated and cellular DNA. In addition to hydration, other nucleophilic addition reactions involving the guanine radical cation give rise to intra‐ and interstrand cross‐links together with DNA–protein cross‐links. Information is provided on the utilization of high‐intensity UV laser pulses as molecular biology tools for studying DNA conformational features, nucleic acid–protein interactions and nucleic acid reactivity through DNA–protein cross‐links and DNA footprinting experiments.     

Formation and Fragmentation of Protonated Molecules after Ionization of Amino Acid and Lactic Acid Clusters by Collision with Ions in the Gas Phase

Collisions between O³⁺ ions and neutral clusters of amino acids (alanine, valine and glycine) as well as lactic acid are performed in the gas phase, in order to investigate the effect of ionizing radiation on these biologically relevant molecular systems. All monomers and dimers are found to be predominantly protonated, and ab initio quantum–chemical calculations on model systems indicate that for amino acids, this is due to proton transfer within the clusters after ionization. For lactic acid, which has a lower proton affinity than amino acids, a significant non‐negligible amount of the radical cation monomer is observed. New fragment‐ion channels observed from clusters, as opposed to isolated molecules, are assigned to the statistical dissociation of protonated molecules formed upon ionization of the clusters. These new dissociation channels exhibit strong delayed fragmentation on the microsecond time scale, especially after multiple ionization.     

Hole transfer energetics in structurally distorted DNA: the nucleosome core particle

The dynamics of long-range hole transport (HT) through DNA are critically dependent on the relative energies of guanine radical cation states. Electrostatic contacts with protein fragments and changes in the secondary structure of the DNA helix are expected to directly influence the stability of a guanine radical cation. This expectation is especially relevant when considering DNA HT in the eukaryotic nucleus, where DNA is condensed into nucleosome core particles (NCPs), the fundamental building blocks of chromatin. Using quantum-chemical calculations, we consider how the electrostatic interactions between the DNA nucleobases and the surrounding protein and water atoms and the structural changes in DNA arising from compaction into a NCP affect the energetics of hole transfer between guanine sites. We find that structural distortions of DNA can have dramatic consequences for the stability of a guanine radical cation, and therefore, these effects must be taken into account during the modeling of in vivo DNA HT and in the interpretation of experimental findings. When the electrostatic potential arising from the water and basic histone proteins is included we find that DNA-histone contacts, particularly between arginine residues and the DNA minor groove, destabilize the hole state on specific guanine residues. Therefore, contacts between the DNA nucleobases and basic amino acids have the potential to perturb the sites of preferred hole stability in DNA.     

The dehydroalanine effect in the fragmentation of ions derived from polypeptides

The fragmentation of peptides and proteins upon collision‐induced dissociation (CID) is highly dependent on sequence and ion type (e.g. protonated, deprotonated, sodiated, odd electron, etc.). Some amino acids, for example aspartic acid and proline, have been found to enhance certain cleavages along the backbone. Here, we show that peptides and proteins containing dehydroalanine, a non‐proteinogenic amino acid with an unsaturated side‐chain, undergo enhanced cleavage of the N—Cα bond of the dehydroalanine residue to generate c‐ and z‐ions. Because these fragment ion types are not commonly observed upon activation of positively charged even‐electron species, they can be used to identify dehydroalanine residues and localize them within the peptide or protein chain. While dehydroalanine can be generated in solution, it can also be generated in the gas phase upon CID of various species. Oxidized S‐alkyl cysteine residues generate dehydroalanine upon activation via highly efficient loss of the alkyl sulfenic acid. Asymmetric cleavage of disulfide bonds upon collisional activation of systems with limited proton mobility also generates dehydroalanine. Furthermore, we show that gas‐phase ion/ion reactions can be used to facilitate the generation of dehydroalanine residues via, for example, oxidation of S‐alkyl cysteine residues and conversion of multiply‐protonated peptides to radical cations. In the latter case, loss of radical side‐chains to generate dehydroalanine from some amino acids gives rise to the possibility for residue‐specific backbone cleavage of polypeptide ions. Copyright © 2016 John Wiley & Sons, Ltd.     

Peptide cation-radicals. A computational study of the competition between peptide N-Calpha bond cleavage and loss of the side chain in the [GlyPhe-NH2 + 2H]+. cation-radical

Cation‐radicals and dications corresponding to hydrogen atom adducts to N‐terminus‐protonated N_α‐glycylphenylalanine amide (Gly‐Phe‐NH₂) are studied by combined density functional theory and Møller‐Plesset perturbational computations (B3‐MP2) as models for electron‐capture dissociation of peptide bonds and elimination of side‐chain groups in gas‐phase peptide ions. Several structures are identified as local energy minima including isomeric aminoketyl cation‐radicals, and hydrogen‐bonded ion‐radicals, and ylid‐cation‐radical complexes. The hydrogen‐bonded complexes are substantially more stable than the classical aminoketyl structures. Dissociations of the peptide N? C_α bonds in aminoketyl cation‐radicals are 18–47 kJ mol^?1 exothermic and require low activation energies to produce ion‐radical complexes as stable intermediates. Loss of the side‐chain benzyl group is calculated to be 44 kJ mol^?1 endothermic and requires 68 kJ mol^?1 activation energy. Rice‐Ramsperger‐Kassel‐Marcus (RRKM) and transition‐state theory (TST) calculations of unimolecular rate constants predict fast preferential N? C_α bond cleavage resulting in isomerization to ion‐molecule complexes, while dissociation of the C_α? CH₂C₆H₅ bond is much slower. Because of the very low activation energies, the peptide bond dissociations are predicted to be fast in peptide cation‐radicals that have thermal (298 K) energies and thus behave ergodically. Copyright © 2003 John Wiley & Sons, Ltd.     

Solvent Migration in Microhydrated Aromatic Aggregates: Ionization‐Induced Site Switching in the 4‐Aminobenzonitrile–Water Cluster

The dependence of the preferred microhydration sites of 4‐aminobenzonitrile (4ABN) on electronic excitation and ionization is determined through IR spectroscopy of its clusters with water (W) in a supersonic expansion and through quantum chemical calculations. IR spectra of neutral 4ABN and two isomers of its hydrogen‐bonded (H‐bonded) 4ABN–W complexes are obtained in the ground and first excited singlet states (S₀, S₁) through IR depletion spectroscopy associated with resonance‐enhanced multiphoton ionization. Spectral analysis reveals that electronic excitation does not change the H‐bonding motif of each isomer, that is, H₂O binding either to the CN or the NH site of 4ABN, denoted as 4ABN–W(CN) and 4ABN–W(NH), respectively. The IR spectra of 4ABN⁺–W in the doublet cation ground electronic state (D₀) are measured by generating them either in an electron ionization source (EI‐IR) or through resonant multiphoton ionization (REMPI‐IR). The EI‐IR spectrum shows only transitions of the most stable isomer of the cation, which is assigned to 4ABN⁺–W(NH). The REMPI‐IR spectrum obtained through isomer‐selective resonant photoionization of 4ABN–W(NH) is essentially the same as the EI‐IR spectrum. The REMPI‐IR spectrum obtained by ionizing 4ABN–W(CN) is also similar to that of the 4ABN⁺–W(NH) isomer, but differs from that calculated for 4ABN⁺–W(CN), indicating that the H₂O ligand migrates from the CN to the NH site upon ionization with a yield of 100 %. The mechanism of this CN→NH site‐switching reaction is discussed in the light of the calculated potential energy surface and the role of intracluster vibrational energy redistribution.     

Specific fragmentation of the K‐shell excited/ionized pyridine derivatives studied by electron impact: 2‐, 3‐ and 4‐methylpyridine

Fragmentation of the pyridine ring upon K‐shell excitation/ionization has been studied with gaseous 2‐, 3‐ and 4‐methylpyridine by the electron‐impact method. Ab initio molecular orbital (MO) calculations were also carried out to explore electronic states correlating with specific fragments. Some specific fragmentation channels were identified from the ionic fragments enhanced characteristically at the N 1s edge. Yields of the C₂HN⁺ and C₅H₅⁺/C₅H₆⁺ ions show that the fission of the N? C2 and C4? C5/C5? C6 bonds of the ring is likely to occur after the N 1s excitation and ionization. Ab initio MO calculations for the 2‐methylpyridine molecule indicate that the dissociation channels to produce these ions are only accessible through the excited states of the parent molecular dication, which can be formed by Auger decays after the N 1s ionization. Fragment ions via hydrogen rearrangement are produced as well, but the rearrangement is not a phenomenon specific to the K‐shell excitation/ionization. Copyright © 2010 John Wiley & Sons, Ltd.     

Reactivity of DNA guanyl radicals with phenolate anions

Guanine bases are the most easily oxidized sites in DNA. Electron-deficient guanine species are major intermediates produced in DNA by the direct effect of ionizing radiation (ionization of the DNA itself) because of preferential hole migration within DNA to guanine bases. By using thiocyanate ions to modify the indirect effect (ionization of the solvent), we are able to produce these single-electron-oxidized guanine radical species in dilute aqueous solutions of plasmid DNA where the direct effect is negligible. The guanyl radical species produce stable modified guanine products. They can be detected in the plasmid by converting them to strand breaks after incubation with a DNA repair enzyme. If a phenol is present during irradiation, the yield of modified guanines is decreased. The mechanism is reduction of the guanine radical species by the phenol. It is possible to derive a rate constant for the reaction of the phenol with the guanyl radical. The pH dependence shows that phenolate anions are more reactive than their conjugate acids, although the difference for guanyl radicals is smaller than with other single-electron-oxidizing agents. At physiological pH values, the reduction of a guanyl radical entails the transfer of a proton in addition to the electron. The relatively small dependence of the rate constant on the driving force implies that the electron cannot be transferred before the proton. These results emphasize the potential importance of acidic tyrosine residues and the intimate involvement of protons in DNA repair.     

DFT performance for the hole transfer parameters in DNA π stacks

Recently, we showed that unoccupied Kohn‐Sham (KS) orbitals stemming from DFT calculations of a neutral system can be used to derive accurate estimates of the free energy and electronic couplings for excess electron transfer in DNA (Félix and Voityuk, J Phys Chem A 2008, 112, 9043). In this article, we consider the propagation of radical cation states (hole transfer) through DNA π‐stacks and compare the performance of different exchange‐correlation functionals to estimate the hole transfer (HT) parameters. Two different approaches are used: (1) calculations that use occupied KS orbitals of neutral π stacks of nucleobases, and (2) the time‐dependent DFT method which is applied to the radical cation states of these stacks. Comparison of the calculated parameters with the reference data suggests that the best results are provided by the KS scheme with hybrid functionals (B3LYP, PBE0, and BH&HLYP). The TD DFT approach gives significantly less accurate values of the HT parameters. In agreement with high‐level ab initio results, the KS scheme predicts that the hole in π stacks is confined to a single nucleobase; in contrast, the spin‐unrestricted DFT method considerably overestimates the hole delocalization in the radical cations. © 2009 Wiley Periodicals, Inc. Int J Quantum Chem, 2011     

Quantum-Chemical Estimation of the Stability and Reactivity of Diphosphonium Salts

For a series of diphosphonium salts containing two positively charged covalently bonded phosphorus atoms, X_{/sub> n} Y_3-n P⁺P⁺X _n Y_3-n (X = alkyl substituent, Y = amino group, n = 0-3), the stability, reactivity, and P-P bond strength were evaluated by various physicochemical methods. The P-P bond energy is appreciably influenced by both steric factors and donor properties of the substituents. The calculations confirmed that transformations of diphosphonium salts can involve cleavage of both P-P and P-N (or P-C) bonds.     

A Carbon Nanohorn?Porphyrin Supramolecular Assembly for Photoinduced Electron‐Transfer Processes

A supramolecular assembly of zinc porphyrin? carbon nanohorns ( CNH s) was constructed in a polar solvent. An ammonium cation was covalently connected to the CNH through a spacer (sp) ( CNH ‐sp‐NH₃⁺) and bound to a crown ether linked to a zinc porphyrin (Crown? ZnP). Nanohybrids CNH ‐sp‐NH₃⁺;Crown? ZnP and CNH ‐sp‐NH₃⁺ were characterized by several techniques, such as high‐resolution transmission electron microscopy, thermogravimetric analysis, X‐ray photoelectron spectroscopy, and Raman spectroscopy. The photoinduced electron‐transfer processes of the nanohybrids have been confirmed by using time‐resolved absorption and fluorescence measurements by combining the steady‐state spectral data. Fluorescence quenching of the ZnP unit by CNH ‐sp‐NH₃⁺ has been observed, therefore, photoinduced charge separation through the excited singlet state of the ZnP unit is suggested for the hybrid material, CNH ‐sp‐NH₃⁺;Crown? ZnP. As transient absorption spectral experiments reveal the formation of the radical cation of the ZnP unit, electron generation is suggested as a counterpart of the charge‐separation on the CNH s; such an electron on the CNH s is further confirmed by migrating to the hexylviologen dication (HV²⁺). Accumulation of the electron captured from HV^.+ is observed as electron pooling in solution in the presence of a hole‐shifting reagent. Photovoltaic performance with moderate efficiency is confirmed for CNH‐ sp‐NH₃⁺;Crown? ZnP deposited onto nanostructured SnO₂ films.     

Stereospecific control of peptide gas‐phase ion chemistry with cis and trans cyclo ornithine residues

We report non‐chiral amino acid residues cis‐ and trans‐1,4‐diaminocyclohexane‐1‐carboxylic acid (cyclo‐ornithine, cO) that exhibit unprecedented stereospecific control of backbone dissociations of singly charged peptide cations and hydrogen‐rich cation radicals produced by electron‐transfer dissociation. Upon collision‐induced dissociation (CID) in the slow heating regime, peptide cations containing trans‐cO residues undergo facile backbone cleavages of amide bonds C‐terminal to trans‐cO. By contrast, peptides with cis‐cO residues undergo dissociations at several amide bonds along the peptide ion backbone. Diastereoisomeric cO‐containing peptides thus provide remarkably distinct tandem mass spectra. The stereospecific effect in CID of the trans‐cO residue is explained by syn‐facially directed proton transfer from the 4‐ammonium group at cO to the C‐terminal amide followed by neighboring group participation in the cleavage of the CO―NH bond, analogous to the aspartic acid and ornithine effects. Backbone dissociations of diastereoisomeric cO‐containing peptide ions generate distinct [b_n]⁺‐type fragment ions that were characterized by CID‐MS³ spectra. Stereospecific control is also reported for electron‐transfer dissociation of cis‐ and trans‐cO containing doubly charged peptide ions. The stereospecific effect upon electron transfer is related to the different conformations of doubly charged peptide ions that affect the electron attachment sites and ensuing N―C_α bond dissociations.     

Combining UV photodissociation action spectroscopy with electron transfer dissociation for structure analysis of gas‐phase peptide cation‐radicals

We report the first example of using ultraviolet (UV) photodissociation action spectroscopy for the investigation of gas‐phase peptide cation‐radicals produced by electron transfer dissociation. z ‐Type fragment ions ^●Gly‐Gly‐Lys⁺, coordinated to 18‐crown‐6‐ether (CE), are generated, selected by mass and photodissociated in the 200–400 nm region. The UVPD action spectra indicate the presence of valence‐bond isomers differing in the position of the C_α radical defect, (α‐Gly)‐Gly‐Lys⁺(CE), Gly‐(α‐Gly)‐Lys⁺(CE) and Gly‐Gly‐(α‐Lys⁺)(CE). The isomers are readily distinguishable by UV absorption spectra obtained by time‐dependent density functional theory (TD‐DFT) calculations. In contrast, conformational isomers of these radical types are calculated to have similar UV spectra. UV photodissociation action spectroscopy represents a new tool for the investigation of transient intermediates of ion‐electron reactions. Specifically, z ‐type cation radicals are shown to undergo spontaneous hydrogen atom migrations upon electron transfer dissociation. Copyright © 2015 John Wiley & Sons, Ltd.     

Synthesis of Diazacrown Ethers with Chromophores and Their Photoinduced Charge‐Separation with Methyl Viologen

Two 4,13‐diaza‐18‐crown‐6 ethers with either two pyrenyl or two carbazolyl groups were synthesized. The two crown ethers can form complexes with methyl viologen in methanol solution. Photoirradiation of the complexes resulted in the electron transfer from the excited states of the chromophores to methyl viologen as demonstrated by the quenching of the chromophore fluorescence and the detection of the absorption spectrum of the generated viologen radical cation. The back electron transfer in these systems was inhibited by the electrostatic repulsion between the positively charged viologen radical cation and the generated chromophore radical cation. Long‐lived charge separation states (up to tens of min) were observed.     

Theoretical and experimental investigations on the reactions of positively charged phenyl radicals with aromatic amino acids

The chemical behavior of positively charged phenyl radicals 3-dehydro-N-phenylpyridinium (a), N-(3-dehydro-5-chlorophenyl)pyridinium (b), and N-(3-dehydrophenyl)pyridinium (c) toward L-tyrosine, phenylalanine, and tryptophan was investigated in the gas phase both theoretically by performing molecular orbital calculations and experimentally by using FT/ICR mass spectrometry. All radicals react with phenylalanine and tryptophan nearly at the collision rate. The overall reactivity of the radicals toward tyrosine follows the order a > b > c, which is consistent with the electron affinity (EA) ordering of the radicals. The higher the electrophilicity (or EA) of the radical, the greater the reactivity. As expected, all radicals abstract a hydrogen atom from all of the amino acids. However, the most electrophilic radical a was also found to react with these amino acids via NH2 abstraction. A new reaction observed between radicals a-c and aromatic amino acids is the addition of the radical to the aromatic ring of the amino acid followed by Calpha-Cbeta bond cleavage, which leads to side-chain abstraction by the radical.     

Experimental and Theoretical Investigation of One‐pot Synthesis of 2‐Amino‐4H‐chromenes Catalyzed by Basic‐functionalized Ionic Liquids

An efficient and environmentally benign procedure for the reactions of three components condensation of salicylaldehyde and two different CH acids to give 2‐amino‐4H‐chromenes catalyzed by a series of basic‐functionalized ionic liquids was reported. The most possible reaction pathway was proposed for the first time by performing density functional theory (DFT) calculations. Both cation and anion of [Bmim]OH have a cooperative effect on the reaction. [Bmim]⁺ increases the electrophilicity of salicylaldehyde via intermolecular hydrogen bonds, while OH^? deprives proton of two CH acids to strengthen their nucleophilic ability.     

Modeling competitive reaction mechanisms of peroxynitrite oxidation of guanine

5-Guanidino-4-nitroimidazole is a stable product from the peroxynitrite induced one-electron oxidation of guanine. Reaction mechanisms to form the 5-guanidino-4-nitroimidazole as well as 8-nitroguanine, through the combination of the guanine radical cation and nitrogen dioxide radical and through the combination of the deprotonated neutral guanine radical and nitrogen dioxide radical, have been investigated by the use of the B3LYP method of density functional theory. Our calculations suggest that the guanine radical cation mechanism is preferred over the neutral guanine radical mechanism and that a water molecule is involved in the reaction as a catalyst or as a reactant.     

Noninnocence of the ligand atoms in iron‐porphine: Chemical consequences of the delocalized electron spin

It is well recognized that the electronic spin density in transition metal complexes in high‐spin states, tends to delocalize from the metal ion itself to the donor atoms of the ligand. In square planar iron‐porphine [PFe]⁺ the delocalization occurs even further and spin corresponding to roughly one electron is delocalized over a large part of the ligand. In this article, density functional theory is applied to explore the chemical consequences of the delocalized spin in four‐coordinate iron‐porphine. It is shown that the porphine ligand has a moderate affinity for radicals, and that covalent bonds can form through spin‐pairing of the unpaired delocalized electron on the porphine ligand and the unpaired electron of another radical species. The hydrogen atom is used as a probe to evaluate the radical affinity of the different nitrogen and carbon atoms that constitute the porphine ligand. It is computationally predicted that the porphine ligand of four‐coordinate iron‐porphine is kinetically capable of activating weak C? H bonds of, for example, unsaturated organic compounds. Hydrogen atom transfer becomes spontaneous via subsequent homo‐coupling of the organic radical created. Whether or not the radical affinity of the porphine ligand has any mechanistic implications for heme‐containing enzymes is left as an open question.     

Recognition of Free Tryptophan in Water by Synthetic Pseudopeptides: Fluorescence and Thermodynamic Studies

Pseudopeptidic receptors containing an acridine unit have been prepared and their fluorescence response to a series of amino acids was measured in water. Free amino acids, not protected either at the C or the N terminus, were used for this purpose. The prepared receptors display a selective response to tryptophan (Trp) versus the other assayed amino acids under acidic conditions. The macrocyclic nature of the receptor is important as the fluorescence quenching is higher for the macrocyclic compound than for the related open‐chain receptor. Notably, under the experimental acidic conditions used, both the receptor and guest are fully protonated and positively charged; thus, the experimental results suggest the formation of supramolecular species that contain two positively charged organic molecular components in proximity stabilized through aromatic–aromatic interactions and a complex set of cation‐anion‐cation interactions. The selectivity towards Trp seems to be based on the existence of a strong association between the indole ring of the monocharged amino acid and the acridinium fragment of the triprotonated form of the receptor, which is established to be assisted by the interaction of the cationic moieties with hydrogen sulfate anions.     

Photoinduced Interactions Between Oxidized and Reduced Lipoic Acid and Riboflavin (Vitamin B2)

As a powerful natural antioxidant, lipoic acid (LipSS) and its reduced form dihydrolipoic acid (DHLA) exert significant antioxidant activities in vivo and in vitro by deactivation of reactive oxygen and nitrogen species (ROS and RNS). In this study the riboflavin (RF, vitamin B₂) sensitized UVA and visible‐light irradiation of LipSS and DHLA was studied employing continuous irradiation, fluorescence spectroscopy, and laser flash photolysis (LFP). Our results indicate that LipSS and DHLA quench both the singlet state (¹RF*) and the triplet state (³RF*) of RF by electron transfer to produce the riboflavin semiquinone radical (RFH^.) and the radical cation of LipSS and DHLA, respectively. The radical cation of DHLA is rapidly deprotonated twice to yield a reducing species; the radical anion of LipSS (LipSS^.?). When D₂O was used as solvent, it was confirmed that the reaction of LipSS with ³RF* consists of a simple electron‐transfer step, while loss of hydrogen occurs in the case of DHLA oxidation. Due to the strong absorption of RFH^. and the riboflavin ground state, the absorption of the radical cation and the radical anion of LipSS can not be observed directly by LFP. N,N,N′,N′‐tetramethyl‐p‐phenylenediamine (TMPD) and N,N,N′,N′‐tetramethyl benzidine (TMB) were added as probes to the system. In the case of LipSS, the addition resulted in the formation of the radical cation of TMPD or TMB by quenching of the LipSS radical cation. If DHLA is the reducing substrate, no formation of probe radical cation is observed. This confirms that LipSS^.+ is produced by riboflavin photosensitization, and that there is no oxidizing species produced after DHLA oxidization.