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

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 S1 ← S0 vibronic spectra of cytosine·2-pyridone (Cyt·2PY) and 1-methylcytosine·2PY are measured using UV laser resonant two-photon 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 hole-burning. 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 and wobble isomers and gives the Watson–Crick isomer exclusively. (2) The calculated ground state binding and dissociation energies, relative gas-phase abundances, 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

Excitonic Splitting and Vibronic Coupling Analysis of the m -Cyanophenol Dimer

The S1/S2 splitting of the m-cyanophenol dimer, (mCP)2 and the delocalization of its excitonically coupled S1/S2 states are investigated by mass-selective two-color resonant two-photon ionization and dispersed fluorescence spectroscopy, complemented by a theoretical vibronic coupling analysis based on correlated ab initio calculations at the approximate coupled cluster CC2 and SCS-CC2 levels. The calculations predict three close-lying ground-state minima of (mCP)2: The lowest is slightly Z-shaped (Ci-symmetric); the second-lowest is <5 cm–1 higher and planar (C2h). The vibrational ground state is probably delocalized over both minima. The S0 → S1 transition of (mCP)2 is electric-dipole allowed (Ag → Au), while the S0 → S2 transition is forbidden (Ag → Ag). Breaking the inversion symmetry by 12C/13C- or H/D-substitution renders the S0 → S2 transition partially allowed; the excitonic contribution to the S1/S2 splitting is Δexc = 7.3 cm–1. Additional isotope-dependent contributions arise from the changes of the m-cyanophenol zero-point vibrational energy upon electronic excitation, which are Δiso(12C/13C) = 3.3 cm–1 and Δiso(H/D) = 6.8 cm–1. Only partial localization of the exciton occurs in the 12C/13C and H/D substituted heterodimers. The SCS-CC2 calculated excitonic splitting is Δel = 179 cm–1; when multiplying this with the vibronic quenching factor Γvibronexp = 0.043, we obtain an exciton splitting Δvibronexp = 7.7 cm–1, which agrees very well with the experimental Δexc = 7.3 cm–1. The semiclassical exciton hopping times range from 3.2 ps in (mCP)2 to 5.7 ps in the heterodimer (mCP-h)·(mCP-d). A multimode vibronic coupling analysis is performed encompassing all the vibronic levels of the coupled S1/S2 states from the v = 0 level to 600 cm–1 above. Both linear and quadratic vibronic coupling schemes were investigated to simulate the S0 → S1/S2 vibronic spectra; those calculated with the latter scheme agree better with experiment

Gas-phase Lifetimes of Nucleobase Analogues by Picosecond Pumpionization and Streak Techniques

The picosecond (ps) timescale is relevant for the investigation of many molecular dynamical processes such as fluorescence, nonradiative relaxation, intramolecular vibrational relaxation, molecular rotation and intermolecular energy transfer, to name a few. While investigations of ultrafast (femtosecond) processes of biological molecules, e.g. nucleobases and their analogues in the gas phase are available, there are few investigations on the ps time scale. We have constructed a ps pump-ionization setup and a ps streak camera fluorescence apparatus for the determination of lifetimes of supersonic jet-cooled and isolated molecules and clusters. The ps pump-ionization setup was used to determine the lifetimes of the nucleobase analogue 2-aminopurine (2AP) and of two 2AP˙(H2O)n water cluster isomers with n=1 and 2. Their lifetimes lie between 150 ps and 3 ns and are strongly cluster-size dependent. The ps streak camera setup was used to determine accurate fluorescence lifetimes of the uracil analogue 2-pyridone (2PY), its self-dimer (2PY)2, two isomers of its trimer (2PY)3 and its tetramer (2PY)4, which lie in the 7–12 ns range

Coupling of a Jahn-Teller pseudorotation with a hindered internal rotation in an isolated molecule: 9-hydroxytriptycene

The irregular vibronic structure in the S-1&lt;--S-0 resonant two-photon ionization (R2PI) spectrum of supersonically cooled triptycene is a result of a classic Exe Jahn-Teller effect [A. Furlan et al., J. Chem. Phys. 96, 7306 (1992)]. This is well characterized and can be used as an effective probe of intramolecular perturbations. Here we examine the S-1&lt;--S-0 R2PI spectrum of 9-hydroxytriptycene and the fluorescence from various excited state vibronic levels. In this system the pseudorotation of the Jahn-Teller vibration is strongly coupled to the torsional motion of the bridgehead hydroxy group. This torsional motion results in a tunneling splitting in both the ground and excited states. The population of the upper level in the ground electronic state results in additional vibronic transitions becoming symmetry allowed in the R2PI spectrum that are forbidden in the bare triptycene molecule. The assignment of the R2PI and fluorescence spectra allows the potential energy surfaces of these vibrational modes to be accurately quantified. The full C-3v vibronic point group must be used to interpret the spectra. The time scale of the internal rotation of the-OH group and the butterfly flapping of the Jahn-Teller pseudorotation are of similar magnitude. The tunneling between the nine minima on the three dimensional potential energy surface is such that the Jahn-Teller pseudorotation occurs in concert with the-OH internal rotation. The Berry phase that is acquired during this motion is discussed. The simple physical picture emerges of the angle between two of the three benzene moieties opening in three equivalent ways in the S-1 electronic state. This geometry follows the position of the hydroxy group, which preferentially orients itself to point between these two rings. (C) 1998 American Institute of Physics. [S0021-9606(98)02348-4]

Intermolecular dissociation energies of hydrogen-bonded 1-naphthol complexes

We have measured the intermolecular dissociation energiesD0of supersonically cooled 1-naphthol(1NpOH) complexes with solvents S = furan, thiophene, 2,5-dimethylfuran, and tetrahydrofuran. Thenaphthol OH forms non-classical H-bonds with the aromaticπ-electrons of furan, thiophene, and2,5-dimethylfuran and a classical H-bond with the tetrahydrofuran O atom. Using the stimulated-emission pumping resonant two-photon ionization method, the ground-stateD0(S0) values werebracketed as 21.8±0.3 kJ/mol for furan, 26.6±0.6 kJ/mol for thiophene, 36.5±2.3 kJ/mol for2,5-dimethylfuran, and 37.6±1.3 kJ/mol for tetrahydrofuran. The dispersion-corrected density func-tional theory methods B97-D3, B3LYP-D3 (using the def2-TZVPP basis set), andωB97X-D [usingthe 6-311++G(d,p) basis set] predict that the H-bonded (edge) isomers are more stable than the faceisomers bound by dispersion; experimentally, we only observe edge isomers. We compare the cal-culated and experimentalD0values and extend the comparison to the previously measured 1NpOHcomplexes with cyclopropane, benzene, water, alcohols, and cyclic ethers. The dissociation energiesof the nonclassically H-bonded complexes increase roughly linearly with the average polarizabilityof the solvent, ̄α(S). By contrast, theD0values of the classically H-bonded complexes are larger,increase more rapidly at low ̄α(S), but saturate for large ̄α(S). The calculatedD0(S0) values forthe cyclopropane, benzene, furan, and tetrahydrofuran complexes agree with experiment to within1 kJ/mol and those of thiophene and 2,5-dimethylfuran are∼3 kJ/mol smaller than experiment. TheB3LYP-D3 calculatedD0values exhibit the lowest mean absolute deviation (MAD) relative toexperiment (MAD = 1.7 kJ/mol), and the B97-D3 andωB97X-D MADs are 2.2 and 2.6 kJ/mol,respectively

Planarizing cytosine: The S 1 state structure, vibrations, and nonradiative dynamics of jet-cooled 5,6-trimethylenecytosine

We measure theS0→S1spectrum and time-resolvedS1state nonradiative dynamics of the “clamped”cytosine derivative 5,6-trimethylenecytosine (TMCyt) in a supersonic jet, using two-color resonanttwo-photon ionization (R2PI), UV/UV holeburning, and ns time-resolved pump/delayed ionization.The experiments are complemented with spin-component scaled second-order approximate cou-pled cluster (SCS-CC2), time-dependent density functional theory, and multi-state second-orderperturbation-theory (MS-CASPT2)ab initiocalculations. While the R2PI spectrum of cytosine breaksoff∼500 cm1above its 000band, that of TMCyt extends up to +4400 cm1higher, with over a hun-dred resolved vibronic bands. Thus, clamping the cytosine C5–C6bond allows us to explore theS1state vibrations andS0→S1geometry changes in detail. The TMCytS1state out-of-plane vibra-tionsν′1,ν′3, andν′5lie below 420 cm1, and the in-planeν′11,ν′12, andν′23vibrational fundamentalsappear at 450, 470, and 944 cm1.S0→S1vibronic simulations based on SCS-CC2 calculationsagree well with experiment if the calculatedν′1,ν′3, andν′5frequencies are reduced by a factorof 2–3. MS-CASPT2 calculations predict that the ethylene-typeS1S0conical intersection (CI)increases from +366 cm1in cytosine to>6000 cm1in TMCyt, explaining the long lifetime andextendedS0→S1spectrum. The lowest-energyS1S0CI of TMCyt is the “amino out-of-plane”(OPX) intersection, calculated at +4190 cm1. The experimentalS1S0internal conversion rateconstant at theS1(v′=0) level iskIC=0.98–2.2·108s1, which is∼10 times smaller than in1-methylcytosine and cytosine. TheS1(v′=0) level relaxes into theT1(3ππ∗) state by intersystemcrossing withkISC=0.41–1.6·108s1. TheT1state energy is measured to lie 24 580±560 cm1above theS0state. TheS1(v′=0) lifetime isτ=2.9 ns, resulting in an estimated fluorescencequantum yield ofΦfl=24%. Intense two-color R2PI spectra of the TMCyt amino-enol tautomersappear above 36 000 cm1. A sharpS1ionization threshold is observed for amino-keto TMCyt,yielding an adiabatic ionization energy of 8.114±0.002 eV

Gas-Phase Cytosine and Cytosine-N 1 -Derivatives Have 0.1–1 ns Lifetimes Near the S 1 State Minimum

Ultraviolet radiative damage to DNA is inefficient because of the ultrafast S1 ⇝ S0 internal conversion of its nucleobases. Using picosecond pump–ionization delay measurements, we find that the S1(1ππ*) state vibrationless lifetime of gas-phase keto-amino cytosine (Cyt) is τ = 730 ps or ∼700 times longer than that measured by femtosecond pump–probe ionization at higher vibrational excess energy, Eexc. N1-Alkylation increases the S1 lifetime up to τ = 1030 ps for N1-ethyl-Cyt but decreases it to 100 ps for N1-isopropyl-Cyt. Increasing the vibrational energy to Eexc = 300–550 cm–1 decreases the lifetimes to 20–30 ps. The nonradiative dynamics of S1 cytosine is not solely a property of the amino-pyrimidinone chromophore but is strongly influenced by the N1-substituent. Correlated excited-state calculations predict that the gap between the S2(1nOπ*) and S1(1ππ*) states decreases along the series of N1-derivatives, thereby influencing the S1 state lifetime