Benchmarking Electronic Excitation Energies and Transitions in Peptide Radicals

Abstract

Excited electronic states in several radical chromophores representing photochemically active groups in peptide and protein radicals and cation radicals were investigated computationally using equation-of-motion coupled cluster (EOM-CCSD) and time-dependent density functional theory (TD-DFT) methods. The calculations identified the main transitions responsible for photodissociations of gas-phase peptide cation radicals in the near-UV region of the spectrum. Analysis of the EOM-CCSD benchmarks showed that no TD-DFT method was universally accurate across the various radical motifs that included Cα-amide, aminoketyl, formamidyl, guanidyl, carbamyl, benzyl, phenoxy, and tautomeric dihydrophenyl and imidazolyl radicals. Overall, the ωB97XD, M06-2X, and LC-BLYP hybrid functionals showed acceptable performance when benchmarked against EOM-CCSD calculations. However, the performance of these TD-DFT methods depended on the nature of the radical chromophore, emphasizing the need for benchmarking and careful analysis.

Ground and Excited-Electronic-State Dissociations of Hydrogen-Rich and Hydrogen-Deficient Tyrosine Peptide Cation Radicals

“…1). Arginine radicals formed by electron transfer have been shown to be moderately efficient hydrogen atom acceptors [55,57] Guanidinium radicals are strong chromophores absorbing light at 320, 341, and 357 nm, with the corresponding oscillator strength factors of 0.07, 0.18, and 0.01 [58]. This is consistent with the efficient photodepletion of the charge-reduced hydrogen-rich cation radicals at 355 nm (Supplementary Figure S4a-d).…”

“…Based on the analysis of peptide radical chromophores [58] +• are most straightforward in that they both result in a dominant loss of the Tyr side chain. This is consistent with the Tyr-O radical structure of this ion where loss of C 7 H 6 O is the lowest energy process in CID and the Tyr-O radical is the absorbing chromophore for UVPD [43].…”

Critical Assessment of TD-DFT for Excited States of Open-Shell Systems: I. Doublet–Doublet Transitions

“…To the best of our knowledge, up to now, the benchmarking of TD-DFT on excited states of open-shell systems has only been performed for some peptide radicals, 46,47 where only transitions involving open-shell orbitals were considered and the spin contamination problem was not addressed at all. The lack of benchmarks is largely due to the lack of reliable reference dataaccurate experimental results are very rare for open-shell systems.…”

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

“…Combined, the major bands calculated for Gly‐2 CE and Lys‐3 CE account for the action spectrum features at 260 and 300 nm. The LC‐BLYP spectra gave very similar results when accounted for the 15–20 nm blue shift of the major lines . In summary, the action spectrum of the z 3 (CE) ion from ETD points to a mixture of radical isomers.…”

“…[28] The TD-DFT calculations that we used, M06-2X, LC-BLYP and ωB97XD, all with the 6-311++G(2d,p) basis set, were previously benchmarked on equation-of-motion coupled cluster (single and double excitations) calculations for simpler model radical chromophores analogous to those in z-ions, and the best fit was found for M06-2X and LC-BLYP excitation energies and oscillator strengths. [29] The calculations showed that the experimental action spectra cannot be accounted for by considering only the terminal α-Gly 1 radicals, • CH 2 CONH-GK + -CE (Gly-1 CE ). The calculated spectra for Gly-1 CE showed a weak band at 360 nm (M06-2X/6-311++G(2d, p) [ Fig.…”