Theoretical Study of the pH-Dependent Photophysics Of N1,N6-Ethenoadenine and N3,N4-Ethenocytosine

Comparing ultrafast excited state quenching of flavin 1,N6-ethenoadenine dinucleotide and flavin adenine dinucleotide by optical spectroscopy and DFT calculations

Flavins are photoenzymatic cofactors often exploiting the absorption of light to energize photoinduced redox chemistry in a variety of contexts. Both flavin adenine dinucleotide (FAD) and flavin mononucleotide (FMN) are used for this function. The study of these photoenzymes has been facilitated using flavin analogs. Most of these analogs involve modification of the flavin ring, and there is recent evidence that adenine (Ade)-modified FAD can affect enzyme turnover, but so far this has only been shown for enzymes where the adenine and flavin rings are close to each other in a stacked conformation. FAD is also stacked in aqueous solution, and its photodynamics are quite different from unstacked FAD or FMN. Oxidized photoexcited FAD decays rapidly, presumably through PET with Ade as donor and Fl* as acceptor. Definitive identification of the spectral signatures of Ade^∙+ and Fl^∙- radicals is elusive. Here we use the FAD analog Flavin 1,N⁶-Ethenoadenine Dinucleotide (εFAD) to study how different photochemical outcomes depend on the identity of the Ade moiety in stacked FAD and its analog εFAD. We have used UV-Vis transient absorption spectroscopy complemented by TD-DFT calculations to investigate the excited state evolution of the flavins. In FAD*, no radicals were observed, suggesting that FAD* does not undergo PET. εFAD* kinetics showed a broad absorption band that suggests a charge transfer state exists upon photoexcitation with evidence for radical pair formation. Surprisingly, significant triplet flavin was produced from εFAD* We hypothesize that the dipolar (ε)Ade moieties differentially modulate the singlet-triplet energy gap, resulting in different intersystem crossing rates. The additional electron density on the etheno group of εFAD supplies better orbital overlap with the flavin S₁ state, accelerating charge transfer in that molecule.

The Excited State Dynamics of a Mutagenic Cytidine Etheno Adduct Investigated by Combining Time-Resolved Spectroscopy and Quantum Mechanical Calculations

Joint femtosecond fluorescence upconversion experiments and theoretical calculations provide a hitherto unattained degree of characterization and understanding of the mutagenic etheno adduct 3,N4-etheno-2'-deoxycytidine (εdC) excited state relaxation. This endogenously formed lesion is attracting great interest because of its ubiquity in human tissues and its highly mutagenic properties. The εdC fluorescence is modified with respect to that of the canonical base dC, with a 3-fold increased lifetime and quantum yield at neutral pH. This behavior is amplified upon protonation of the etheno ring (εdCH⁺). Quantum mechanical calculations show that the lowest energy state ππ*1 is responsible for the fluorescence and that the main nonradiative decay pathway to the ground state goes through an ethene-like conical intersection, involving the out-of-plane motion of the C5 and C6 substituents. This conical intersection is lower in energy than the ππ* state (ππ*1) minimum, but a sizable energy barrier explains the increase of εdC and εdCH⁺ fluorescence lifetimes with respect to that of dC.

Tricyclic nitrogen base 1,N6-ethenoadenine and its ribosides as substrates for purine-nucleoside phosphorylases: Spectroscopic and kinetic studies

The title compound is an excellent substrate for E. coli PNP, as well as for its D204N mutant. The main product of the synthetic reaction is N9-riboside, but some amount of N7-riboside is also present. Surprisingly, 1,N⁶-ethenoadenine is also ribosylated by both wild-type and mutated (N243D) forms of calf PNP, which catalyze the synthesis of a different riboside, tentatively identified as N6-β-D-ribosyl-1,N⁶-ethenoadenine. All ribosides are susceptible to phosphorolysis by the E. coli PNP (wild type). All the ribosides are fluorescent and can be utilized as analytical probes.

Cytosine in Context: A Theoretical Study of Substituent Effects on the Excitation Energies of 2-Pyrimidinone Derivatives

The ultrafast radiationless decay mechanism for cytosine has been shown to be in part dependent upon high vertical excitation, while slower fluorescence displayed in some cytosine analogs is generally linked to lower vertical excitation energies. To probe how excitation energies relate to pyrimidine structure, substituent effects on the vertical excitation energies for a number of derivatives of 2-pyrimidin-(1H)-one (2P) have been calculated using multireference configuration-interaction ab initio methods. Substitutions using groups with pi electron donating, withdrawing and conjugation-extending properties at the C(4) and C(5) positions on the 2P system give predictive trends for the first three singlet excited-state energies. The S(1) pipi* energies of 2P derivatives involving C4 substitution vary linearly with the Hammett substituent parameter sigma(P)+. Cytosine is shown to have the highest bright pipi* energy of the 2P derivatives presented, with that energy being strongly dependent on the position, orientation, and geometry of the C4-amino. A simple description of the predictive energetic trends for the bright pipi* energies using frontier molecular orbital theory is presented, based on the character of the HOMO and LUMO orbitals for each derivative. The results of this study expand the current understanding of the photophysical behavior of the DNA pyrimidine bases and could be useful in the design of analogs where particular spectral properties are desired.