Watson–Crick and Sugar-Edge Base Pairing of Cytosine in the Gas Phase: UV and Infrared Spectra of Cytosine·2-Pyridone

Abstract

While keto-amino cytosine is the dominant species in aqueous solution, spectroscopic studies in molecular beams and in noble gas matrices show that other cytosine tautomers prevail in apolar environments. Each of these offers two or three H-bonding sites (Watson-Crick, Wobble, Sugar-edge). The mass-and isomer-specific S 1 ← S 0 vibronic spectra of cytosine·2-pyridone (Cyt·2PY) and 1-methylcytosine·2PY are measured using UV laser resonant twophoton ionization (R2PI), UV/UV depletion and IR depletion spectroscopy. The UV spectra of the Watson-Crick and Sugar-edge isomers of Cyt·2PY are separated using UV/UV spectral holeburning. Five different isomers of Cyt·2PY are observed in a supersonic beam. We show that the Watson-Crick and Sugar-edge dimers of keto-amino cytosine with 2PY are the most abundant in the beam, although keto-amino-cytosine is only the third most abundant tautomer in the gas phase. We identify the different isomers by combining three different diagnostic tools: (1) Methylation of the cytosine N1-H group prevents formation of both the Sugar-edge * To whom correspondence should be addressed 1 and Wobble isomers and gives the Watson-Crick isomer exclusively. (2) Calculation of ground state binding and dissociation energies, the relative gas-phase abundances, the excitation and the ionization energies are in agreement with the assignment of the dominant Cyt·2PY isomers to the Watson-Crick and Sugar-edge complexes of keto-amino cytosine. (3) The comparison of calculated ground state vibrational frequencies to the experimental IR spectra in the carbonyl stretch and NH/OH/CH stretch ranges strengthen this identification.

Microhydration Effects on the Ultrafast Photodynamics of Cytosine: Evidences for a Possible Hydration‐Site Dependence

“…Our calculations also predict that monohydration of keto‐Cy at site A is more stable than at site B by about 2.0–2.7 kJ mol −1 . This result is consistent with a recent study that experimentally confirmed that 2‐pyridone binds more strongly at site A than at site B of keto‐Cy 53. Because of the lower barriers involved, the distributions of binding‐site isomers are expected to approach those near the low temperature limit (<100 K), suggesting that the Cy⋅H 2 O transient arises mostly (>90 %) from keto‐Cy⋅H 2 O with the water bound at site A .…”

Microhydration Effects on the Ultrafast Photodynamics of Cytosine: Evidences for a Possible Hydration‐Site Dependence

“…1mCy exists predominately as the keto form in the gas phase, and as such, 1mCy has often been used to identify the keto contributions in Cy tautomeric mixtures. [12,53,54] Thepresumption that the excited-state energetics and dynamics of 1mCy closely resemble those of keto-Cy has been discussed previously [12,54] and is supported by more recent theoretical studies. [14,15] As shown in Figure 2, the 1mCy monomer transient does exhibit the characteristic 0.5 ps decay of keto-Cy at 267 nm excitation.…”

“…[52] Our calculations also predict that monohydration of keto-Cy at site A is more stable than at site B by about 2.0-2.7 kJ mol À1 .T his result is consistent with arecent study that experimentally confirmed that 2-pyridone binds more strongly at site A than at site B of keto-Cy. [53] Because of the lower barriers involved, the distributions of binding-site isomers are expected to approach those near the low temperature limit (< 100 K), suggesting that the Cy•H 2 O transient arises mostly (> 90 %) from keto-Cy•H 2 Ow ith the water bound at site A.A ni mmediate conclusion is that monohydration of keto-Cy at site A does not alter its excitedstate deactivation dynamics much, because the decay time is essentially the same as that of keto-Cy monomer at the same excitation energy.…”

How nature covers its bases

“…68,70 This finding suggests for the GC base pair, that the triply H-bonded Watson-Crick base pair has much faster internal conversion than other GC cluster structures and that for GG and CC dimers the lowest energy, symmetrically Hbound, structures exhibit short excited state lifetimes as well. 37,[117][118][119][120][121] For the GC base pair, Domcke and Sobolewski predict a rapid internal conversion following coupling with a charge transfer state, which causes a proton transfer of the central hydrogen from G to C. 122 The chargetransfer state couples with the ground state with a CI leading to a return of the proton to the guanine, completing the deactivation. A similar process may occur in intramolecularly hydrogen bonded nucleosides.…”