We report the generation of gas-phase cation radicals of unusual nucleobases 5-aza-7-deazaguanine (P) and 6-amino-5-nitro-(
)pyrid-2-one (Z) that have been used as building blocks of base-expanded ...(hachimoji) DNA. The cation radicals were generated by collision-induced intramolecular electron transfer and dissociation of ternary copper-terpyridine complexes. The cation radicals were characterized by deuterium labeling and tandem mass spectrometry including MS
collision-induced dissociation, UV-vis photodissociation, and action spectroscopy. Vibronic absorption UV-vis spectra were calculated by time-dependent density functional theory (TD-DFT) and compared with the action spectra to unequivocally assign the most closely matching structures for the gas-phase cation radicals. Ab initio calculations up to the coupled clusters-complete basis set (CCSD(T)/CBS) level of theory were used to rank by energy the P and Z neutral molecules and cation-radical isomers and provided transition-state and dissociation energies. The 5-aza-7-deazaguanine cation radicals were determined to have the canonical N-1-H, 6-oxo structure (
) that was the global energy minimum within this group of isomers. The Z cation radicals were found to have the 1
-pyrid-2-one structure (
). The formation of
and
was shown to be controlled by the solution thermodynamics of the Cu-terpyridine complexes and the kinetics of their dissociations. We also report and compare CCSD(T)/CBS-calculated adiabatic recombination energies of cation radicals for the entire hachimoji set of eight nucleobases,
(7.92 eV),
(8.51 eV),
(8.51 eV),
(7.76 eV),
(8.98 eV),
(8.62 eV),
(8.32 eV), and
(7.97 eV), to assess the thermodynamics of base-to-base electron transfer following random ionization.
Oxidation of nontraditional nucleobases 1-methylcytosine (hachimoji base S) and isoguanine (hachimoji base B) in gas-phase ternary complexes with CuII(terpyridine)2+ formed cation radicals that were ...characterized by tandem mass spectrometry, UV–vis photodissociation action spectroscopy in the 210–700 nm region, and ab initio calculations up to the CCSD(T)/complete basis set level of theory. Oxidation of S was accompanied by exothermic isomerization in the 1-methylcytosine ion (1 +• ), forming 1-methylene-2-hydroxy-4-aminopyrimidine cation radical (9 +• ) as a noncanonical distonic isomer of the nucleobase. Ion 9 +• was characterized by deuterium exchange experiments and provided a matching UV–vis action spectrum with the vibronic absorption spectrum from time-dependent density functional theory calculations. Oxidation of B resulted in the formation of a canonical isoguanine cation radical (12 +• ) as judged from the match of the experimental action spectrum with the calculated vibronic absorption spectrum. The calculated adiabatic ionization energies of canonical S and B, 8.51 and 7.76 eV, respectively, indicated exothermic electron transfer from B to S +• to proceed in an ionized base pair. Contrasting this, the lowest energy tautomer of ionized S (9 +• ) had a low adiabatic recombination energy, REadiab = 5.70 eV, that would prevent it from oxidizing other nucleobases. Recombination energies of several nucleobase tautomers are reported and discussed.
Cation radicals of adenine (A
) and 9-methyladenine (MA
) were generated in the gas phase by collision-induced intramolecular electron transfer in copper-terpyridine-nucleobase ternary complexes and ...characterized by collision-induced dissociation (CID) mass spectra and UV-vis photodissociation action spectroscopy in the 210-700 nm wavelength region. The action spectra of both A
and MA
displayed characteristic absorption bands in the near-UV and visible regions. Another tautomer of A
was generated as a minor product by multistep CID of protonated 9-(2-bromoethyl)adenine. Structure analysis by density functional theory and coupled-clusters ab initio calculations pointed to the canonical 9-H-tautomer
as the global energy minimum of adenine cation radicals. The canonical tautomer
was also calculated to be a low-energy structure among methyladenine cation radicals. However, two new noncanonical tautomers were found to be energetically comparable to
. Vibronic absorption spectra were calculated for several tautomers of A
and MA
and benchmarked on equation-of-motion coupled-clusters excited-state calculations. Analysis of the vibronic absorption spectra of A
tautomers pointed to the canonical tautomer
as providing the best match with the action spectrum. Likewise, the canonical tautomer
was the unequivocal best match for the MA
ion generated in the gas phase. According to potential-energy mapping,
was separated from energetically favorable noncanonical cation radicals by a high-energy barrier that was calculated to be above the dissociation threshold for loss of a methyl hydrogen atom, thus preventing isomerization. Structures and energetics of all four DNA nucleobase cation radicals are compared and discussed.
Hydrogen-rich cation radicals (GATT + 2H)
+
&z.rad; and (AGTT + 2H)
+
&z.rad; represent oligonucleotide models of charged hydrogen atom adducts to DNA. These tetranucleotide cation radicals were ...generated in the gas phase by one-electron reduction of the respective (GATT + 2H)
2+
and (AGTT + 2H)
2+
dications in which the charging protons were placed on the guanine and adenine nucleobases. We used wavelength-dependent UV/Vis photodissociation in the valence-electron excitation region of 210-700 nm to produce action spectra of (GATT + 2H)
+
&z.rad; and (AGTT + 2H)
+
&z.rad; that showed radical-associated absorption bands in the near-UV (330 nm) and visible (400-440 nm) regions. Born-Oppenheimer molecular dynamics and density-functional theory calculations were used to obtain and rank by energy multiple (GATT + 2H) dication and cation-radical structures. Time-dependent density functional theory (TD-DFT) calculations of excited-state energies and electronic transitions in (GATT + 2H)
+
&z.rad; were augmented by vibronic spectra calculations at 310 K for selected low-energy cation radicals to provide a match with the action spectrum. The stable product of one-electron reduction was identified as having a 7,8-dihydroguanine cation radical moiety, formed by intramolecular hydrogen atom migration from adenine N-1-H. The hydrogen migration was calculated to have a transition state with a low activation energy,
E
a
= 96.5 kJ mol
−1
, and positive activation entropy, Δ
S
‡
= 75 J mol
−1
K
−1
. This allowed for a fast isomerization of the primary reduction products on the ion-trap time scale of 150 ms that was substantially accelerated by highly exothermic electron transfer.
Hydrogen-rich cation radicals (GATT + 2H)
+
&z.rad; and (AGTT + 2H)
+
&z.rad; represent oligonucleotide models of charged hydrogen atom adducts to DNA.
We report the generation and spectroscopic study of hydrogen-rich DNA tetranucleotide cation radicals (GATC+2H)+• and (AGTC+2H)+•. The radicals were generated in the gas phase by one-electron ...reduction of the respective dications (GATC+2H)2+ and (AGTC+2H)2+ and characterized by collision-induced dissociation and photodissociation tandem mass spectrometry and UV–vis photodissociation action spectroscopy. Among several absorption bands observed for (GATC+2H)+•, the bands at 340 and 450 nm were assigned to radical chromophores. Time-dependent density functional theory calculations including vibronic transitions in the visible region of the spectrum were used to provide theoretical absorption spectra of several low-energy tetranucleotide tautomers having cytosine-, adenine-, and thymine-based radical chromophores that did not match the experimental spectrum. Instead, the calculations indicated the formation of a new isomer with the 7,8-H-dihydroguanine cation radical moiety. The isomerization involved hydrogen migration from the cytosine N-3–H radical to the C-8 position in N-7-protonated guanine that was calculated to be 87 kJ mol–1 exothermic and had a low-energy transition state. Although the hydrogen migration was facilitated by the spatial proximity of the guanine and cytosine bases in the low-energy (GATC+2H)+• intermediate formed by electron transfer, the reaction was calculated to have a large negative activation entropy. Rice–Ramsperger–Kassel–Marcus (RRKM) and transition state theory kinetic analysis indicated that the isomerization occurred rapidly in hot cation radicals produced by electron transfer with the population-weighed rate constant of k = 8.9 × 103 s–1. The isomerization was calculated to be too slow to proceed on the experimental time scale in thermal cation radicals at 310 K.
Cation radicals of DNA nucleosides, 2′-deoxyadenosine, 2′-deoxyguanosine, 2′-deoxycytidine, and 2′-deoxythymidine, can exist in standard canonical forms or as noncanonical isomers in which the charge ...is introduced by protonation of the nucleobase, whereas the radical predominantly resides in the deoxyribose moiety. Density functional theory as well as correlated ab initio calculations with coupled clusters (CCSD(T)) that were extrapolated to the complete basis set limit showed that noncanonical nucleoside ion isomers were thermodynamically more stable than their canonical forms in both the gas phase and as water-solvated ions. This indicated the possibility of exothermic conversion of canonical to noncanonical forms. The noncanonical isomers were calculated to have very low adiabatic ion–electron recombination energies (REad) for the lowest-energy isomers 2′-deoxy-(N-3H)adenos-1′-yl (4.74 eV), 2′-deoxy-(N-7H)guanos-1′-yl (4.66 eV), 2′-deoxy-(N-3H)cytid-1′-yl (5.12 eV), and 2′-deoxy-5-methylene-(O-2H)uridine (5.24 eV). These were substantially lower than the REad value calculated for the canonical 2′-deoxyadenosine, 2′-deoxy guanosine, 2′-deoxy cytidine, and 2′-deoxy thymidine cation radicals, which were 7.82, 7.46, 8.14, and 8.20 eV, respectively, for the lowest-energy ion conformers of each type. Charge and spin distributions in noncovalent cation-radical dA⊂dT and dG⊂dC nucleoside pairs and dAT, dCT, dTC, and dGC dinucleotides were analyzed to elucidate the electronic structure of the cation radicals. Born–Oppenheimer molecular dynamics trajectory calculations of the dinucleotides and nucleoside pairs indicated rapid exothermic proton transfer from noncanonical T+ · to A in both dAT+ · and dA⊂dT+ ·, leading to charge and radical separation. Noncanonical T+ · in dCT+ · and dTC+ · initiated rapid proton transfer to cytosine, whereas the canonical dCT+ · dinucleotide ion retained the cation radical structure without isomerization. No spontaneous proton transfer was found in dGC+ · and dG⊂dC+ · containing canonical neutral and noncanonical ionized deoxycytidine.
Noncanonical nucleobases and nucleosides represent newly discovered species of relevance for DNA ionization. We report a targeted synthesis of gas-phase 9-methylene(1
)adenine cation radical (
) as a ...low-energy isomer of ionized 9-methyladenine. Ion
showed unique collision-induced dissociation and UV-vis photodissociation action spectra that distinguished it from other cation radical isomers. Ab initio energy calculations with coupled cluster theory extrapolated to the complete basis set limit, CCSD(T)/CBS, identified cation radical
as the global energy minimum of the adenine-related C
H
N
isomers. The action spectrum of
was assigned on the basis of vibronic absorption spectra that were calculated with time-dependent density functional theory for multiple vibrational configurations of thermal ions. The major dissociation of
proceeded by hydrogen loss that was elucidated by deuterium labeling at the exchangeable N-1 and NH
positions and C-8 position and by kinetic analysis. The dissociation involved a reversible rearrangement to intermediate dihydropteridine structures, yielding a protonated aminopteridine as the product, which was identified by multistep UV-vis action spectroscopy. We also report a computational study of related noncanonical isomers of 2'-deoxyadenosine cation radical having the radical defect at C-1' that were found to be thermodynamically more stable than the canonical isomer in both the gas phase and aqueous solution. The noncanonical isomers were calculated to have extremely low ion-electron recombination energies of 4.42-5.10 eV that would make them dead-end hole traps if produced by DNA ionization.
Diazirine-tagged d- and l-adrenaline derivatives formed abundant noncovalent gas-phase ion complexes with peptides
-Ac-SSIVSFY-NH
(peptide S) and
-Ac-VYILLNWIGY-NH
(peptide V) upon electrospray ...ionization. These peptide sequences represent the binding motifs in the β
-adrenoreceptor. The structures of the gas-phase complexes were investigated by selective laser photodissociation of the diazirine chromophore at 354 nm, which resulted in a loss of N
and formation of a transient carbene intermediate in the adrenaline ligand without causing its expulsion. The photolyzed complexes were analyzed by collision-induced dissociation (CID-MS
and CID-MS
) in an attempt to detect cross-links and establish the binding sites. However, no cross-linking was detected in the complexes regardless of the peptide and d- or l-configuration in adrenaline. Cyclic ion mobility measurements were used to obtain collision cross sections (CCS) in N
for the peptide S complexes. These showed identical values, 334 ± 0.9 Å
, for complexes of the l- and d-adrenaline derivatives, respectively. Identical CCS were also obtained for peptide S complexes with natural l- and d-adrenaline, 317 ± 1.2 Å
, respectively. Born-Oppenheimer molecular dynamics (BOMD) in combination with full geometry optimization by density functional theory calculations provided structures for the complexes that were used to calculate theoretical CCS with the ion trajectory method. A close match (337 Å
) was found for a single low Gibbs energy structure that displayed a binding pocket with Ser 2 and Ser 5 residues forming hydrogen bonds to the adrenaline catechol hydroxyls. Analysis of the BOMD trajectories revealed a small number of contacts between the incipient carbene carbon atom in the ligand and X-H bonds in the peptide, which was consistent with the lack of cross-linking. Temperature dependence of the internal dynamics of peptide S-adrenaline complexes as well as the specifics of the adrenaline carbene reactions are discussed. In particular, peptide amide hydrogen transfer to the carbene carbon atom was calculated to require crossing a potential energy barrier, which may hamper cross-linking in competition with carbene internal rearrangements.
Non-covalent complexes of the short amyloid peptide motif Gly-Asn-Asn-Gln-Gln-Asn-Tyr (GNNQQNY) with peptide counterparts that were tagged with a diazirine ring at the N-termini (*GNNQQNY) were ...generated as singly charged ions in the gas phase. Specific laser photodissociation (UVPD) of the diazirine tag in the gas-phase complexes at 355 nm generated transient carbene intermediates that underwent covalent cross-linking with the target GNNQQNY peptide. The crosslinking yields ranged between 0.8 and 4.5%, depending on the combinations of peptide C-terminal amides and carboxylates. The covalent complexes were analyzed by collision-induced dissociation tandem mass spectrometry (CID-MS3), providing distributions of cross-links at the target peptide amino acid residues. A general preference for cross-linking at the target peptide Gln-4-Gln-5-Asn-6-Tyr-7 segment was observed. Born-Oppenheimer molecular dynamics calculations were used to obtain 100 ps trajectories for nine lowest free-energy conformers identified by ωB97X-D/6-31+G(d,p) gradient geometry optimizations. The trajectories were analyzed for close contacts between the incipient carbene atom and the X-H bonds in the target peptide. The close-contact analysis pointed to the Gln-5 and Tyr-7 residues as the most likely sites of cross-linking, consistent with the experimental CID-MS3 results. Non-covalent binding in the amide complexes was evaluated by DFT calculations of structures and energies. Although antiparallel arrangements of the GNNQQNY and *GNNQQNY peptides were favored in low-energy gas-phase and solvated complexes, the conformations and peptide-peptide interface surfaces were found to differ from the secondary structure of the dry interface in GNNQQNY motifs of amyloid aggregates.
Sixty DNA trinucleotide cation radicals covering a large part of the genetic code alphabet were generated by electron transfer in the gas phase, and their chemistry was studied by collision-induced ...dissociation tandem mass spectrometry and theoretical calculations. The major dissociations involved loss of nucleobase molecules and radicals, backbone cleavage, and cross-ring fragmentations that depended on the nature and position of the nucleobases. Mass identity in dissociations of symmetrical trinucleotide cation radicals of the (XXX+2H)+• and (XYX+2H)+• type was resolved by specific 15N labeling. The specific features of trinucleotide cation radical dissociations involved the dominant formation of d 2 + ions, hydrogen atom migrations accompanying the formation of ( w 2 +H)+•, ( w 2 +2H)+, and ( d 2 +2H)+ sequence ions, and cross-ring cleavages in the 3′- and 5′-deoxyribose moieties that depended on the nucleobase type and its position in the ion. Born–Oppenheimer molecular dynamics (BOMD) and density functional theory calculations were used to obtain structures and energies of several cation-radical protomers and conformers for (AAA+2H)+•, (CCC+2H)+•, (GGG+2H)+•, (ACA+2H)+•, and (CAA+2H)+• that were representative of the different types of backbone dissociations. The ion electronic structure, protonation and radical sites, and hydrogen bonding were used to propose reaction mechanisms for the dissociations.
