Intermolecular vibrations of jet-cooled (2-pyridone)2: A model for the uracil dimer

Optimizing a coarse-grained space for approximate normal-mode vibrations of molecular heterodimers

We applied the method of coarse-graining the intermolecular vibrations to molecular heterodimers assembled by double hydrogen bonding. This method is based on principal component analysis, by which the original atomic displacement vectors are projected onto a lower-dimensional space spanned by a basis set of translations, librations, and intramolecular vibrations of the constituent molecules. Compared with homodimers, the following points are particularly noted: (1) alignment of the constituent molecules in a non-symmetric atomic arrangement of the whole system and (2) the scheme of reordering the bases to construct an optimal coarse-grained space. We tested three schemes for reordering the intramolecular vibration vectors to determine that the best one is equivalent to size reduction based on the singular value decomposition. The coarse-graining analysis affords three parameters, Φ_intra, Φ_inter, and Φ_app, which are relevant to the mechanical nature of the molecular assembly. The Φ_intra values account for the internal stiffness of molecules, while the Φ_inter values are true stiffness constants of the intermolecular force and show a good correlation with the association energies of the dimers. The Φ_app values are the apparent intermolecular stiffness smaller than Φ_inter, as a result of compensation for neglecting intramolecular vibrations. All these values are consistent with each other under the coupled oscillator model, showing that the present coarse-graining analysis is valid for heterodimers as well as homodimers.

Non-conventional Hydrogen Bonding and Aromaticity: A Systematic Study on Model Nucleobases and Their Solvated Clusters

The conceptual development of aromaticity is essential to rationalize and understand the structure and behavior of aromatic heterocycles. This work addresses for the first time, the interconnection between aromaticity and sulfur/selenium centered hydrogen bonds (S/SeCHBs) involved in representative heterocycle models of canonical nucleobases (2-Pyridone; 2PY) and its sulfur (2-Thiopyridone; 2TPY) and selenium (2-Selenopyridone; 2SePY) analogs. The nucleus-independent chemical shift (NICS) and gauge induced magnetic current density (GIMIC) values suggested significant reduction of aromaticity upon replacement of exocyclic carbonyl oxygen with sulfur and selenium. However, we observed two-fold (57 %) and three-fold (80 %) enhancement in the aromaticity for 2TPY dimer, and 2SePY dimer, respectively which are connected through S/SeCHBs. Aromaticity enhancement was also noticed in 1 : 1 H-bonded complexes (heterodimers), micro hydrated clusters and for bulk hydration. It is expected that exocyclic S and Se incorporation into heterocycles without compromising aromatic loss would definitely reinforce to design new supramolecular building blocks via S/SeCH-bonded complexes.

Indices to evaluate the reliability of coarse-grained representations of mixed inter/intramolecular vibrations

We propose some methods for quantifying the reliability of coarse-grained representations of displacement vectors of normal mode vibrations. In the framework of our basic theory, the original displacement vectors are projected onto a lower-dimensional (i.e., a coarse-grained) space. Four types of functions denoted fidelity indices were introduced as measures of the similarity of the original to the restored displacement vectors. These indices were applied to several hydrogen-bonded homodimers, and the behavior of each index was examined. We found that a coarse-grained representation with high reliability resulted in the accurate restoration of properties such as eigenfrequency, modal mass, and modal stiffness.

Biomolecule Analogues 2-Hydroxypyridine and 2-Pyridone Base Pairing on Ice Nanoparticles

Ice nanoparticles (H2O)N, N ≈ 450 generated in a molecular beam experiment pick up individual gas phase molecules of 2-hydroxypyridine and 2-pyridone (HP) evaporated in a pickup cell at temperatures between 298 and 343 K. The mass spectra of the doped nanoparticles show evidence for generation of clusters of adsorbed molecules (HP)n up to n = 8. The clusters are ionized either by 70 eV electrons or by two photons at 315 nm (3.94 eV). The two ionization methods yield different spectra, and their comparison provides an insight into the neutral cluster composition, ionization and intracluster ion-molecule reactions, and cluster fragmentation. Quite a few molecules were reported not to coagulate on ice nanoparticles previously. The (HP)n cluster generation on ice nanoparticles represents the first evidence for coagulating of molecules and cluster formation on free ice nanoparticles. For comparison, we investigate the coagulation of HP molecules picked up on large clusters ArN, N ≈ 205, and also (HP)n clusters generated in supersonic expansions with Ar buffer gas. This comparison points to a propensity for the (HP)2 dimer generation on ice nanoparticles. This shows the feasibility of base pairing for model of biological molecules on free ice nanoparticles. This result is important for hypotheses of the biomolecule synthesis on ice grains in the space. We support our findings by theoretical calculations that show, among others, the HP dimer structures on water clusters.

Theoretical analysis of the S2←S0 vibronic spectrum of the 2-pyridone dimer

The interplay between excitonic and vibronic coupling in hydrogen-bonded molecular dimers leads to complex spectral structures and other intriguing phenomena such as a quenching of the excitonic energy splitting. We recently extended our analysis from that of the quenching mechanism to the theoretical investigation of the complete vibronic spectrum for the ortho-cyanophenol dimer. We now apply the same approach to the vibronic spectrum of the 2-pyridone dimer and discuss the assignment of vibronic lines to gain insight into the underlying coupling mechanism. This is based on potential energy surfaces obtained at the RI-CC2/aug-cc-pVTZ level. They are used for the dynamical analysis in the framework of a multi-mode vibronic coupling approach. The theoretical results based on the quadratic vibronic coupling model are found to be in good agreement with the experimental resonant two-photon ionization spectrum.

Gas-Phase IR Spectroscopy of Nucleobases

IR spectroscopy of nucleobases in the gas phase reflects simultaneous advances in both experimental and computational techniques. Important properties, such as excited state dynamics, depend in subtle ways on structure variations, which can be followed by their infrared signatures. Isomer specific spectroscopy is a particularly powerful tool for studying the effects of nucleobase tautomeric form and base pair hydrogen-bonding patterns.

Protonation effect on the electronic properties of 2-pyridone monomer, dimer and its water clusters: a theoretical study

The CC2 (second order approximate coupled cluster method) has been applied to investigate protonation effect on electronic transition energies of 2-pyridone (2PY), 2-pyridone dimer, and micro-solvated 2-pyridone (0-2 water molecules). The PE profiles of protonated 2-pyridone (2PYH(+)) as well as monohydrated 2PYH(+) at the different electronic states have been investigated. The (1)πσ∗ state in protonated species (2PYH(+)) is a barrier free and dissociative state along the O-H stretching coordinate. In this reaction coordinate, the lowest lying (1)πσ∗ predissociates the bound S1((1)ππ∗) state, connecting the latter to a conical intersection with the S0 state. These conical intersections lead the (1)ππ∗ state to proceed as predissociative state and finally direct the excited system to the ground state. Furthermore, in presence of water molecule, the (1)πσ∗ state still remains dissociative but the conical intersection between (1)πσ∗ and ground state disappears. In addition, according to the CC2 calculation results, it has been predicted that protonation significantly blue shifts the S1-S0 electronic transition of monomer, dimer, and microhydrated 2-pyridone.

Vibrational quenching of excitonic splittings in H-bonded molecular dimers: the electronic Davydov splittings cannot match experiment

The S(1)/S(2) state exciton splittings of symmetric doubly hydrogen-bonded gas-phase dimers provide spectroscopic benchmarks for the excited-state electronic couplings between UV chromophores. These have important implications for electronic energy transfer in multichromophoric systems ranging from photosynthetic light-harvesting antennae to photosynthetic reaction centers, conjugated polymers, molecular crystals, and nucleic acids. We provide laser spectroscopic data on the S(1)/S(2) excitonic splitting Δ(exp) of the doubly H-bonded o-cyanophenol (oCP) dimer and compare to the splittings of the dimers of (2-aminopyridine)(2), [(2AP)(2)], (2-pyridone)(2), [(2PY)(2)], (benzoic acid)(2), [(BZA)(2)], and (benzonitrile)(2), [(BN)(2)]. The experimental S(1)/S(2) excitonic splittings are Δ(exp) = 16.4 cm(-1) for (oCP)(2), 11.5 cm(-1) for (2AP)(2), 43.5 cm(-1) for (2PY)(2), and <1 cm(-1) for (BZA)(2). In contrast, the vertical S(1)/S(2) energy gaps Δ(calc) calculated by the approximate second-order coupled cluster (CC2) method for the same dimers are 10-40 times larger than the Δ(exp) values. The qualitative failure of this and other ab initio methods to reproduce the exciton splitting Δ(exp) arises from the Born-Oppenheimer (BO) approximation, which implicitly assumes the strong-coupling case and cannot be employed to evaluate excitonic splittings of systems that are in the weak-coupling limit. Given typical H-bond distances and oscillator strengths, the majority of H-bonded dimers lie in the weak-coupling limit. In this case, the monomer electronic-vibrational coupling upon electronic excitation must be accounted for; the excitonic splittings arise between the vibronic (and not the electronic) transitions. The discrepancy between the BO-based splittings Δ(calc) and the much smaller experimental Δ(exp) values is resolved by taking into account the quenching of the BO splitting by the intramolecular vibronic coupling in the monomer S(1) ← S(0) excitation. The vibrational quenching factors Γ for the five dimers (oCP)(2), (2AP)(2), (2AP)(2), (BN)(2), and (BZA)(2) lie in the range Γ = 0.03-0.2. The quenched excitonic splittings Γ[middle dot]Δ(calc) are found to be in very good agreement with the observed splittings Δ(exp). The vibrational quenching approach predicts reliable Δ(exp) values for the investigated dimers, confirms the importance of vibrational quenching of the electronic Davydov splittings, and provides a sound basis for predicting realistic exciton splittings in multichromophoric systems.

Evaluation of coupling terms between intra- and intermolecular vibrations in coarse-grained normal-mode analysis: does a stronger acid make a stiffer hydrogen bond?

Using theory of harmonic normal-mode vibration analysis, we developed a procedure for evaluating the anisotropic stiffness of intermolecular forces. Our scheme for coarse-graining of molecular motions is modified so as to account for intramolecular vibrations in addition to relative translational/rotational displacement. We applied this new analytical scheme to four carboxylic acid dimers, for which coupling between intra- and intermolecular vibrations is crucial for determining the apparent stiffness of the intermolecular double hydrogen bond. The apparent stiffness constant was analyzed on the basis of a conjunct spring model, which defines contributions from true intermolecular stiffness and molecular internal stiffness. Consequently, the true intermolecular stiffness was in the range of 43-48 N m(-1) for all carboxylic acids studied, regardless of the molecules' acidity. We concluded that the difference in the apparent stiffness can be attributed to differences in the internal stiffness of the respective molecules.

The S1/S2 exciton interaction in 2-pyridone·6-methyl-2-pyridone: Davydov splitting, vibronic coupling, and vibronic quenching

The excitonic splitting between the S(1) and S(2) electronic states of the doubly hydrogen-bonded dimer 2-pyridone[middle dot]6-methyl-2-pyridone (2PY·6M2PY) is studied in a supersonic jet, applying two-color resonant two-photon ionization (2C-R2PI), UV-UV depletion, and dispersed fluorescence spectroscopies. In contrast to the C(2h) symmetric (2-pyridone)(2) homodimer, in which the S(1) ← S(0) transition is symmetry-forbidden but the S(2) ← S(0) transition is allowed, the symmetry-breaking by the additional methyl group in 2PY·6M2PY leads to the appearance of both the S(1) and S(2) origins, which are separated by Δ(exp) = 154 cm(-1). When combined with the separation of the S(1) ← S(0) excitations of 6M2PY and 2PY, which is δ = 102 cm(-1), one obtains an S(1)/S(2) exciton coupling matrix element of V(AB, el) = 57 cm(-1) in a Frenkel-Davydov exciton model. The vibronic couplings in the S(1)/S(2) ← S(0) spectrum of 2PY·6M2PY are treated by the Fulton-Gouterman single-mode model. We consider independent couplings to the intramolecular 6a(') vibration and to the intermolecular σ(') stretch, and obtain a semi-quantitative fit to the observed spectrum. The dimensionless excitonic couplings are C(6a(')) = 0.15 and C(σ(')) = 0.05, which places this dimer in the weak-coupling limit. However, the S(1)/S(2) state exciton splittings Δ(calc) calculated by the configuration interaction singles method (CIS), time-dependent Hartree-Fock (TD-HF), and approximate second-order coupled-cluster method (CC2) are between 1100 and 1450 cm(-1), or seven to nine times larger than observed. These huge errors result from the neglect of the coupling to the optically active intra- and intermolecular vibrations of the dimer, which lead to vibronic quenching of the purely electronic excitonic splitting. For 2PY·6M2PY the electronic splitting is quenched by a factor of ~30 (i.e., the vibronic quenching factor is Γ(exp) = 0.035), which brings the calculated splittings into close agreement with the experimentally observed value. The 2C-R2PI and fluorescence spectra of the tautomeric species 2-hydroxypyridine·6-methyl-2-pyridone (2HP·6M2PY) are also observed and assigned.

Theoretical studies of proton-transfer reactions of 2-hydroxypyridine--(H2O)n (n = 0-2) in the ground and excited states

The potential energy profiles for proton-transfer reactions of 2-hydroxypyridine and its complexes with water were determined by MP2, CASSCF and MR-CI calculations with the 6-31G** basis set. The tautomerization reaction between 2-hydroxypyridine (2HP) and 2-pyridone (2PY) does not take place at room temperature because of a barrier of approximately 35 kcal/mol for the ground-state pathway. The water-catalyzed enol-keto tautomerization reactions in the ground state proceed easily through the concerted proton transfer, especially for the two-water complex. The S1 tautomerization between the 2HP and 2PY monomers has a barrier of 18.4 kcal/mol, which is reduced to 5.6 kcal/mol for the one-water complex and 6.4 kcal/mol for the two-water complex. The results reported here predict that the photoinduced tautomerization reaction between the enol and keto forms involves a cyclic transition state having one or two water molecules as a bridge.

Laser Induced Fluorescence Spectroscopy of a Mixed Dimer between 2-Pyridone and 7-Azaindole

We report here the laser induced fluorescence excitation (FE) and dispersed fluorescence (DF) spectra of a 1:1 mixed dimer between 7-azaindole (7AI) and 2-pyridone (2PY) measured in a supersonic free jet expansion of helium. Density functional theoretical calculation at the B3LYP/6-311++G** level has been performed for predictions of the dimer geometry and normal mode vibrational frequencies in the ground electronic state. A planar doubly hydrogen-bonded structure has been predicted to be the most preferred geometry of the dimer. In the FE spectrum, sharp vibronic bands are observed only for excitation of the 2PY moiety. A large number of low-frequency vibronic bands show up in both the FE and DF spectra, and those bands have been assigned to in-plane hydrogen bond vibrations of the dimer. Spectral analyses reveal Duschinsky-type mixing among those modes in the excited state. No distinct vibronic band structure in the FE spectrum was observed corresponding to excitations of the 7AI moiety, and the observation has been explained in terms of nonradiative electronic relaxation routes involving the 2PY moiety.

Fluorobenzene-nucleobase interactions: hydrogen bonding or pi-stacking?

Studies on modified DNA oligomers and polymerase reactions have previously demonstrated that canonical nucleobases can exhibit stable and even selective pairing with shape-complementary fluorobenzene nucleotides. Because of the fluorination of the pairing edges, hydrogen bonds are believed to be absent, and the local DNA stability has been attributed to pi-stacking and shape complementarity. Using two-color resonant two-photon ionization and fluorescence emission spectroscopies, we show here that supersonically cooled complexes of the nucleobase analogue 2-pyridone with seven substituted fluorobenzenes (1-fluorobenzene, 1,2- and 1,4-difluorobenzene, 1,3,5- and 1,2,3-trifluorobenzene, 1,2,4,5- and 1,2,3,4-tetrafluorobenzene) are hydrogen-bonded and not pi-stacked. The S1 <--> S0 vibronic spectra show intermolecular vibrational frequencies that are characteristic for doubly hydrogen bonded complexes. The bands shift to the blue with increasing hydrogen-bond strength; the measured spectral blue shifts deltanu are in excellent agreement with the ab initio calculated shifts. The spectral shifts are also linearly correlated with the calculated hydrogen-bond dissociation energies D0, published in a companion paper (Frey, J. A.; Leist, R.; Leutwyler, S. J. Phys. Chem. A 2006, 110, 4188). This correlation allows us to reliably estimate the ground-state dissociation energies as D0 approximately 6 kcal/mol of the 2-pyridone.fluorobenzene complexes from the observed spectral shifts.

Reaction paths of tautomerization between hydroxypyridines and pyridones

Tautomerization paths of 2(and 4)-hydroxypyridine (called here HP) to 2(and 4)-pyridone (called here PY) with water molecules were investigated by the use of density functional theory calculations. Potential energies were compared for a number of water molecules. The 2-HP molecule was found to be isomerized most readily and concertedly to the 2-PY one via proton relays with two water molecules. The reaction pattern is invariant even when outer water molecules are added. The 4-HP(H(2)O)(n) --> 4-PY(H(2)O)(n) reaction model did not give small activation energies. However, a reaction of (4-HP)(2)(H(2)O)(2) --> (4-PY)(2)(H(2)O)(2) was found to occur readily through a transient ion-pair intermediate. The conversion processes of (2-PY)(2) to the tautomerization reacting system were discussed. The hydrogen-bond directionality regulates the tautomerization paths.

Ab initio/DFT and AIM studies on dual hydrogen-bonded complexes of 2-hydroxypyridine/2-pyridone tautomerism

The second-order Møller-Plesset (MP2) and density functional theory (DFT) calculations have been carried out to investigate the structures and stabilities of hydrogen (H-) bonded 2-hydroxypyridine (2HP)/2-pyridone (2PY) dimeric forms as well as 2HP-2PY complexes. The results on single-point counterpoise (CP) correction of these complexes were compared against CP-optimized correction. The nature of the intermolecular contacts in the sense of normal H-bond or blue-shifting H-bond was determined on the basis of harmonic vibrational, atom-in-molecule (AIM), and natural bond orbital (NBO) analysis. A blue-shifting C-H...N H-bond was found and NBO analysis revealed a slight decrease in the population of the contacting sigmaC-H* antibonding orbital as the primary reason of the C-H contraction. Good correlations have been established between the interaction energies and the H-bond distances versus other characteristic H-bond parameters.

Picosecond water dynamics adjacent to charged paramagnetic ions measured by magnetic relaxation dispersion

Measurements of water-proton spin-lattice relaxation rate constants as a function of magnetic field strength [magnetic relaxation dispersion (MRD)] in aqueous solutions of paramagnetic solutes reveal a peak in the MRD profile. These previously unobserved peaks require that the time correlation functions describing the water-proton-electron dipolar coupling have a periodic contribution. In aqueous solutions of iron(III) ion the peak corresponds to a frequency of 8.7 cm-1, which the authors ascribe to the motion of water participating in the second coordination sphere of the triply charged solute ion. Similar peaks of weaker intensity in the same time range are observed for aqueous solutions of chromium(III) chloride as well as for ion pairs formed by ammonium ion with trioxalatochromate(III) ion. The widths of the dispersion peaks are consistent with a lifetime for the periodic motion in the range of 5 ps or longer.

Hydrogen-bond vibrations in the S1↔S0 spectra of a nucleobase pair analog: A mixed dimer between 2-pyridone and formamide

The vibronically resolved electronic spectra for S(1)<-->S(0) transitions of a mixed dimer between 2-pyridone (2PY) and formamide have been measured in a supersonic free jet expansion using laser-induced fluorescence spectroscopy. Quantum chemistry method at different levels of theory has been used to optimize the geometries of the dimer for the S(0) and S(1) electronic states and also to calculate the normal vibrational modes. Assignments for the vibronic bands observed in the dispersed fluorescence spectrum of the 0(0) (0) band have been suggested with the aid of the ground state frequencies calculated by density functional theoretical method. Spectral analysis reveals that electronic excitation causes extensive mixing of the low-frequency intermolecular vibrational modes of the dimer with some of the intramolecular modes of the 2PY moiety. This spectral behavior is consistent with the complete active space self-consistent field theoretical prediction that with respect to a number of geometrical parameters the dimer geometry in S(1) is significantly distorted from the geometry of the S(0) state.

Double proton transfer in the isolated and DNA-embedded guanine-cytosine base pair

The energetics and dynamics of double proton transfer (DPT) is investigated theoretically for the Watson-Crick conformation of the guanine-cytosine (GC) base pair. Using semiempirical density functional theory the isolated and DNA-embedded GC pair is considered. Differences in the energetics and dynamics of DPT thus addresses the question of how relevant studies of isolated base pairs are for the understanding of processes occurring in DNA. Two-dimensional potential energy surfaces involving the transferring hydrogen atoms and the proton donors and acceptors are presented for both systems. The DPT reaction is accompanied by a contraction of the distance between the two bases with virtually identical energetic barriers being 18.8 and 18.7 kcal/mol for the isolated and DNA-embedded system, respectively. However, the transition state for DPT in the DNA-embedded GC pair is offset by 0.1 A to larger N-H separation compared to the isolated GC pair. Using activated ab initio molecular dynamics, DPT is readily observed for the isolated base pair with a minimal amount of 21.4 kcal/mol of initial average kinetic energy along the DPT normal mode vector. On a time scale of approximately 100 fs DPT has occurred and the excess energy is redistributed. For the DNA-embedded GC pair considerably more kinetic energy is required (30.0 kcal/mol) for DPT and the process is completed within one hydrogen vibration. The relevance of studies of isolated base pairs and base pair analogs in regard of reactions or properties involving DNA is discussed.

2-pyridone: The role of out-of-plane vibrations on the S1↔S0 spectra and S1 state reactivity

The S(1)<-->S(0) vibronic spectra of supersonic jet-cooled 2-pyridone [pyridin-2-one (2PY)] and its N-H deuterated isotopomer (d-2PY) have been recorded by two-color resonant two-photon ionization, laser-induced fluorescence and emission, and fluorescence depletion spectroscopies. By combining these methods, the B origin of 2PY at 0(0) (0)+98 cm(-1) and the bands at +218 and +252 cm(-1) are identified as overtones of the S(1) state out-of-plane vibrations nu(1) (') and nu(2) ('), as are the analogous bands of d-2PY. Anharmonic double-minimum potentials are derived for the respective out-of-plane coordinates that predict further nu(1) (') and nu(2) (') overtones and combinations, reproducing approximately 80% of the vibronic bands up to 600 cm(-1) above the 0(0) (0) band. The fluorescence spectra excited at the electronic origins and the nu(1) (') and nu(2) (') out-of-plane overtone levels confirm these assignments. The S(1) nonplanar minima and S(1)<--S(0) out-of-plane progressions are in agreement with the determination of nonplanar vibrationally averaged geometries for the 0(0) (0) and 0(0) (0)+98 cm(-1) upper states by Held et al. [J. Chem. Phys. 95, 8732 (1991)]. The fluorescence lifetimes of the S(1) state vibrations show strong mode dependence: Those of the out-of-plane levels decrease rapidly above 200 cm(-1) excess vibrational energy, while the in-plane vibrations nu(5) ('), nu(8) ('), and nu(9) (') have longer lifetimes, although they are above or interspersed with the "dark" out-of-plane states. This is interpreted in terms of an S(1) (') state reaction with a low barrier towards a conical intersection with a prefulvenic geometry. Out-of-plane vibrational states can directly surmount this barrier, whereas in-plane vibrations are much less efficient in this respect. Analysis of the fluorescence spectra allows to identify nine in-plane S(0) (') state fundamentals, overtones of the S(0) state nu(1) (") and nu(2) (") out-of-plane vibrations, and >30 other overtones and combination bands. The B3LYP6-311++G(d,p) calculated anharmonic wave numbers are in very good agreement with the observed fundamentals, overtones, and combinations, with a deviation Delta(rms)=1.3%.

2-Hydroxypyridine ↔ 2-Pyridone Tautomerization: Catalytic Influence of Formic Acid

A 1:1 hydrogen-bonded complex between 2-pyridone and formic acid has been characterized using laser-induced-fluorescence excitation and dispersed fluorescence spectroscopy in a supersonic jet expansion. Under the same expansion condition, the fluorescence signal of the tautomeric form of the complex (2-hydroxypyridine...formic acid) is absent, although both the bare tautomeric molecules exhibit well-resolved laser-induced-fluorescence spectra. Quantum chemistry calculation at the DFT/B3LYP/6-311++G** level predicts that in the ground electronic state the activation barrier for tautomerization from hydroxy to keto form in bare molecules is very large (approximately 34 kcal/mol). However, the process turns out to be nearly barrierless when assisted by formic acid, and double proton transfer occurs via a concerted mechanism.

Gas-Phase Watson-Crick and Hoogsteen Isomers of the Nucleobase Mimic 9-Methyladenine⋅2-Pyridone

2-Pyridone (pyridin-2-one) is a mimic of the uracil and thymine nucleobases, with only one N--H and C==O group. It provides a single H-bonding site, compared to three for the canonical pyrimidine nucleobases. Employing the supersonically cooled 9-methyladenine2-pyridone (9MAd x 2PY) complex, which is the simplest base pair to mimic adenine-uracil or adenine-thymine, we show that its gas-phase UV spectrum consists of contributions from two isomers. Based on the H-bonding sites of 9-methyladenine, these are the Watson-Crick and Hoogsteen forms. Combining two-color two-photon ionisation (2C-R2PI), UV-UV depletion and laser-induced fluorescence spectroscopies allows separation of the two band systems, revealing characteristic intermolecular in-plane vibrations of the two isomers. The calculated S(0) and S(1) intermolecular frequencies are in good agreement with the experimental ones. Ab initio calculations predict the Watson-Crick isomer to be slightly more stable (D(0)=-16.0 kcal mol(-1)) than the Hoogsteen isomer (D(0)=-15.0 kcal mol(-1)). The calculated free energies Delta(f)G(0) of the Watson-Crick and Hoogsteen isomers agree qualitatively with the experimental isomer concentration ratio of 3:1.

Probing the Watson−Crick, Wobble, and Sugar-Edge Hydrogen Bond Sites of Uracil and Thymine

The nucleobases uracil (U) and thymine (T) offer three hydrogen-bonding sites for double H-bond formation via neighboring N-H and C=O groups, giving rise to the Watson-Crick, wobble and sugar-edge hydrogen bond isomers. We probe the hydrogen bond properties of all three sites by forming hydrogen bonded dimers of U, 1-methyluracil (1MU), 3-methyluracil (3MU), and T with 2-pyridone (2PY). The mass- and isomer-specific S1 <-- S0 vibronic spectra of 2PY.U, 2PY.3MU, 2PY.1MU, and 2PY.T were measured using UV laser resonant two-photon ionization (R2PI). The spectra of the Watson-Crick and wobble isomers of 2PY.1MU were separated using UV-UV spectral hole-burning. We identify the different isomers by combining three different diagnostic tools: (1) Selective methylation of the uracil N3-H group, which allows formation of the sugar-edge isomer only, and methylation of the N1-H group, which leads to formation of the Watson-Crick and wobble isomers. (2) The experimental S1 <-- S0 origins exhibit large spectral blue shifts relative to the 2PY monomer. Ab initio CIS calculations of the spectral shifts of the different hydrogen-bonded dimers show a linear correlation with experiment. This correlation allows us to identify the R2PI spectra of the weakly populated Watson-Crick and wobble isomers of both 2PY.U and 2PY.T. (3) PW91 density functional calculation of the ground-state binding and dissociation energies De and D0 are in agreement with the assignment of the dominant hydrogen bond isomers of 2PY.U, 2PY.3MU and 2PY.T as the sugar-edge form. For 2PY.U, 2PY.T and 2PY.1MU the measured wobble:Watson-Crick:sugar-edge isomer ratios are in good agreement with the calculated ratios, based on the ab initio dissociation energies and gas-phase statistical mechanics. The Watson-Crick and wobble isomers are thereby determined to be several kcal/mol less strongly bound than the sugar-edge isomers. The 36 observed intermolecular frequencies of the nine different H-bonded isomers give detailed insight into the intermolecular force field.

Density Functional Study on the Reaction Mechanism of Proton Transfer in 2-Pyridone: Effect of Hydration and Self-Association

The proton-transfer mechanism in the isolated, mono, dehydrated forms and dimers of 2-pyridone and the effect of hydration or self-assistance on the transition state structures corresponding to proton transfer from the keto form to the enol form have been investigated using B3LYP and BH-LYP hybrid density functional methods at the 6-311++G (2d, 2p) basis set level. The barrier heights for both H2O-assisted and self-assisted reactions are significantly lower than that of the bare tautomerization reaction from 2-pyridone to 2-hydroxypyridine, implying the importance of the superior catalytic effect of H2O and (H2O)2 and the important role of 2-pyridone itself for the intramolecular proton transfer. Long-range solvent effects have also been taken into account by using the continuum model (Onsager model and polarizable continuum model (PCM)) of water. The tautomerization energies and the potential energy barriers are increased both for the water-assisted and for the self-assisted reaction because of the bulk solvent, which imply that the tautomerization of PY becomes less favorable in the polar solvent.

Infrared depletion spectra of 2-aminopyridine⋅2-pyridone, a Watson–Crick mimic of adenine⋅uracil

The 2-aminopyridine2-pyridone (2AP2PY) dimer is linked by N-H...O=C and N-H...N hydrogen bonds, providing a model for the Watson-Crick hydrogen bond configuration of the adenine.thymine and adenine.uracil nucleobase pairs. Mass-specific infrared spectra of 2AP2PY and its seven N-H deuterated isotopomers have been measured between 2550 and 3650 cm(-1) by IR laser depletion combined with UV two-color resonant two-photon ionization. The 2PY amide N-H stretch is a very intense band spread over the range 2700-3000 cm(-1) due to large anharmonic couplings. It is shifted to lower frequency by 710 cm(-1) or approximately 20% upon H bonding to 2AP. On the 2AP moiety, the "bound" amino N-H stretch gives rise to a sharp band at 3140 cm(-1), which is downshifted by 354 cm(-1) or approximately 10% upon H bonding to 2PY. The amino group "free" N-H stretch and the H-N-H bend overtone are sharp bands at approximately 3530 cm(-1) and 3320 cm(-1). Ab initio structures and harmonic vibrations were calculated at the Hartree-Fock level and with the PW91 and B3LYP density functionals. The PW91/6-311++G(d,p) method provides excellent predictions for the frequencies and IR intensities of all the isotopomers.