Vibronic Spectra of Jet-Cooled 2-Aminopurine·H2O Clusters Studied by UV Resonant Two-Photon Ionization Spectroscopy and Quantum Chemical Calculations

Excited-state vibrations, lifetimes, and nonradiative dynamics of jet-cooled 1-ethylcytosine

The S₁ excited-state lifetime of jet-cooled 1-ethylcytosine (1ECyt) is ∼1 ns, one of the longest lifetimes for cytosine derivatives to date. Here, we analyze its S₀ → S₁ vibronic spectrum using two-color resonant two-photon ionization and UV/UV holeburning spectroscopy. Compared to cytosine and 1-methylcytosine, the S₀ → S₁ spectrum of 1ECyt shows a progression in the out-of-plane "butterfly" mode ν₁ ^', identified by spin-component scaled-second-order coupled-cluster method ab initio calculations. We also report time-resolved S₁ state nonradiative dynamics at ∼20 ps resolution by the pump/delayed ionization technique. The S₁ lifetime increases with the number of ν₁ ^' quanta from τ = 930 ps at v₁ ^'=0 to 1030 ps at v₁ ^'=2, decreasing to 14 ps at 710 cm^-1 vibrational energy. We measured the rate constants for S₁ ⇝ S₀ internal conversion and S₁ ⇝ T₁ intersystem crossing (ISC): At the v' = 0 level, k_IC is 8 × 10⁸ s^-1 or three times smaller than 1-methylcytosine. The ISC rate constant from v' = 0 to the T₁(³ππ^*) state is k_ISC = 2.4 × 10⁸ s^-1, 10 times smaller than the ISC rate constants of cytosine, but similar to that of 1-methylcytosine. Based on the calculated S₁(¹ππ^*) state radiative lifetime τ_rad = 12 ns, the fluorescence quantum yield of 1ECyt is Φ_fl ∼ 7% and the intersystem crossing yield is Φ_ISC ∼ 20%. We measured the adiabatic ionization energy of 1-ethylcytosine via excitation of the S₁ state as 8.353 ± 0.008 eV, which is 0.38 eV lower than that of amino-keto cytosine. Measurement of the ionization energy of the long-lived T₁(ππ^*) state formed via ISC reveals that it lies 3.2-3.4 eV above the S₀ ground state.

Planarizing cytosine: The S1 state structure, vibrations, and nonradiative dynamics of jet-cooled 5,6-trimethylenecytosine

We measure the S₀ → S₁ spectrum and time-resolved S₁ state nonradiative dynamics of the "clamped" cytosine derivative 5,6-trimethylenecytosine (TMCyt) in a supersonic jet, using two-color resonant two-photon ionization (R2PI), UV/UV holeburning, and ns time-resolved pump/delayed ionization. The experiments are complemented with spin-component scaled second-order approximate coupled cluster (SCS-CC2), time-dependent density functional theory, and multi-state second-order perturbation-theory (MS-CASPT2) ab initio calculations. While the R2PI spectrum of cytosine breaks off ∼500 cm^-1 above its 0₀⁰ band, that of TMCyt extends up to +4400 cm^-1 higher, with over a hundred resolved vibronic bands. Thus, clamping the cytosine C⁵-C⁶ bond allows us to explore the S₁ state vibrations and S₀ → S₁ geometry changes in detail. The TMCyt S₁ state out-of-plane vibrations ν₁^', ν₃^', and ν₅^' lie below 420 cm^-1, and the in-plane ν₁₁^', ν₁₂^', and ν₂₃^' vibrational fundamentals appear at 450, 470, and 944 cm^-1. S₀  →  S₁ vibronic simulations based on SCS-CC2 calculations agree well with experiment if the calculated ν₁^', ν₃^', and ν₅^' frequencies are reduced by a factor of 2-3. MS-CASPT2 calculations predict that the ethylene-type S₁ ⇝ S₀ conical intersection (CI) increases from +366 cm^-1 in cytosine to >6000 cm^-1 in TMCyt, explaining the long lifetime and extended S₀ → S₁ spectrum. The lowest-energy S₁ ⇝ S₀ CI of TMCyt is the "amino out-of-plane" (OP_X) intersection, calculated at +4190 cm^-1. The experimental S₁ ⇝ S₀ internal conversion rate constant at the S₁(v^'=0) level is k_IC=0.98-2.2⋅10⁸ s^-1, which is ∼10 times smaller than in 1-methylcytosine and cytosine. The S₁(v^'=0) level relaxes into the T₁(³ππ*) state by intersystem crossing with k_ISC=0.41-1.6⋅10⁸ s^-1. The T₁ state energy is measured to lie 24 580±560 cm^-1 above the S₀ state. The S₁(v^'=0) lifetime is τ=2.9 ns, resulting in an estimated fluorescence quantum yield of Φ_fl=24%. Intense two-color R2PI spectra of the TMCyt amino-enol tautomers appear above 36 000 cm^-1. A sharp S₁ ionization threshold is observed for amino-keto TMCyt, yielding an adiabatic ionization energy of 8.114±0.002 eV.

Efficient intersystem crossing in 2-aminopurine riboside probed by femtosecond time-resolved transient vibrational absorption spectroscopy

The photophysical dynamics of 2-aminopurine, a fluorescent analogue of the canonical nucleobase adenine, has been studied by femtosecond transient vibrational absorption spectroscopy.

Conformational structures of jet-cooled acetaminophen-water clusters: a gas phase spectroscopic and computational study

Jet-cooled acetaminophen (AAP)-water clusters, AAP-(H₂O)₁, were investigated by mass-selected resonant two-photon ionization (R2PI), ultraviolet-ultraviolet hole-burning (UV-UV HB), infrared-dip (IR-dip), and infrared-ultraviolet hole-burning (IR-UV HB) spectroscopy. Each syn- and anti-AAP rotamer has three distinctive binding sites (-OH, >CO, and >NH) for a water molecule, thus 6 different AAP-(H₂O)₁ conformers are expected to exist in the molecular beam. The origin bands of the AAP(OH)-(H₂O)₁ and AAP(CO)-(H₂O)₁ conformers (including their syn- and anti-conformers) in the R2PI spectrum are shifted to red and blue compared to those of the AAP monomer, respectively. These frequency shifts upon complexation between a water molecule and a specific binding site of AAP are also predicted by theoretical calculations. The spectral assignments of the origin bands in the R2PI spectra and the IR vibrational bands in the IR-dip spectra of the four lowest-energy conformers of AAP-(H₂O)₁, [syn- and anti-AAP(OH)-(H₂O)₁ and syn- and anti-AAP(CO)-(H₂O)₁], are aided by ab initio and time-dependent density functional theory (TDDFT) calculations. Further investigation of the IR-dip spectra has revealed a hydrogen-bonded NH stretching mode, supporting the presence of the syn-AAP(NH)-(H₂O)₁ conformer. Moreover, by employing IR-UV HB spectroscopy, we have reconfirmed the existence of the syn-AAP(NH)-(H₂O)₁ conformer, which happened to be buried underneath the broad background contributed by the AAP(OH)-(H₂O)₁ conformers. These observations have led us to conclude that all of the possible conformers of AAP-(H₂O)₁ have been found in this study.

2-aminopurine as a fluorescent probe of DNA conformation and the DNA–enzyme interface

Nearly 50 years since its potential as a fluorescent base analogue was first recognized, 2-aminopurine (2AP) continues to be the most widely used fluorescent probe of DNA structure and the perturbation of that structure by interaction with enzymes and other molecules. In this review, we begin by considering the origin of the dramatic and intriguing difference in photophysical properties between 2AP and its structural isomer, adenine; although 2AP differs from the natural base only in the position of the exocyclic amine group, its fluorescence intensity is one thousand times greater. We then discuss the mechanism of interbase quenching of 2AP fluorescence in DNA, which is the basis of its use as a conformational probe but remains imperfectly understood. There are hundreds of examples in the literature of the use of changes in the fluorescence intensity of 2AP as the basis of assays of conformational change; however, in this review we will consider in detail only a few intensity-based studies. Our primary aim is to highlight the use of time-resolved fluorescence measurements, and the interpretation of fluorescence decay parameters, to explore the structure and dynamics of DNA. We discuss the salient features of the fluorescence decay of 2AP when incorporated in DNA and review the use of decay measurements in studying duplexes, single strands and other structures. We survey the use of 2AP as a probe of DNA-enzyme interaction and enzyme-induced distortion, focusing particularly on its use to study base flipping and the enhanced mechanistic insights that can be gained by a detailed analysis of the decay parameters, rather than merely monitoring changes in fluorescence intensity. Finally we reflect on the merits and shortcomings of 2AP and the prospects for its wider adoption as a fluorescence-decay-based probe.

Conformational preferences of monohydrated clusters of imidazole derivatives revisited

IR-UV double resonance spectroscopy was used to identify the conformers of monohydrated benzimidazole andN-methylbenzimidazole in a supersonic jet. A new OH–N bound conformer relevant to histidine containing proteins was discovered. The long standing differences in the literature about the relative energies and abundance of the monohydrated imidazole derivatives have also been resolved.

Why water makes 2-aminopurine fluorescent?

Depending on where it binds, a water molecule may change the excited-state lifetime of 2-aminopurine by a factor of 100. We explain why?

Reactive pathways in the chlorobenzene-ammonia dimer cation radical: new insights from experiment and theory

Building upon our recent studies of noncovalent interactions in chlorobenzene and bromobenzene clusters, in this work we focus on interactions of chlorobenzene (PhCl) with a prototypical N atom donor, ammonia (NH3). Thus, we have obtained electronic spectra of PhCl···(NH3)n (n = 1-3) complexes in the region of the PhCl monomer S0 -S1 (ππ*) transition using resonant 2-photon ionization (R2PI) methods combined with time-of-flight mass analysis. Consistent with previous studies, we find that upon ionization the PhCl···NH3 dimer cation radical reacts primarily via Cl atom loss. A second channel, HCl loss, is identified for the first time in R2PI studies of the 1:1 complex, and a third channel, H atom loss, is identified for the first time. While prior studies have assumed the dominance of a π-type complex, we find that the reactive complex corresponds instead to an in-plane σ-type complex. This is supported by electronic structure calculations using density functional theory and post-Hartree-Fock methods and Franck-Condon analysis. The reactive pathways in this system were extensively characterized computationally, and consistent with results from previous calculations, we find two nearly isoenergetic arenium ions (Wheland intermediates; denoted WH1, WH2), which lie energetically below the initially formed dimer cation radical complex. At the energy of our experiment, intermediate WH1, produced from ipso-addition, is not stable with respect to Cl or HCl loss, and the relative branching between these channels observed in our experiment is well reproduced by microcanonical transition state theory calculations based upon the calculated parameters. Intermediate WH2, where NH3 adds ortho to the halogen, decomposes over a large barrier via H atom loss to form protonated o-chloroaniline. This channel is not open at the (2-photon) energy of our experiments, and it is suggested that photodissociation of a long-lived (i.e., several ns) WH2 intermediate leads to the observed products.