Experimental and Theoretical Determination of Dissociation Energies of Dispersion-Dominated Aromatic Molecular Complexes.

The dissociation energy (D0) of an isolated and cold molecular complex in the gas-phase is a fundamental measure of the strength of the intermolecular interactions between its constituent moieties. Accurate D0 values are important for the understanding of intermolecular bonding, for benchmarking high-level theoretical calculations, and for the parametrization of force-field models used in fields ranging from crystallography to biochemistry. We review experimental and theoretical methods for determining gas-phase D0 values of M·S complexes, where M is a (hetero)aromatic molecule and S is a closed-shell "solvent" atom or molecule. The experimental methods discussed involve M-centered (S0 → S1) electronic excitation, which is often followed by ionization to the M(+)·S ion. The D0 is measured by depositing a defined amount of vibrational energy in the neutral ground state, giving M(‡)·S, the neutral S1 excited state, giving M*·S, or the M(+)·S ion ground state. The experimental methods and their relative advantages and disadvantages are discussed. Based on the electronic structure of M and S, we classify the M·S complexes as Type I, II, or III, and discuss characteristic properties of their respective potential energy surfaces that affect or hinder the determination of D0. Current theoretical approaches are reviewed, which comprise methods based on a Kohn-Sham reference determinant as well as wave function-based methods based on coupled-cluster theory.

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.

Probing for non-statistical effects in dissociation of the 1-methylallyl radical.

The 1-methylallyl radical loses a hydrogen atom following photoexcitation to its lowest valence electronically excited state and displays statistical behavior in decomposition, implying that the presence of methyl rotors cannot be depended upon as an indicator for non-statistical dissociation dynamics in hydrocarbon radicals.

Vibronic structure of the 3s and 3p Rydberg states of the allyl radical.

Resonance-enhanced multiphoton ionization combined with electronic ground state depletion spectroscopy of jet-cooled allyl radicals (C(3)H(5)) provides vibronic spectra of the 3s and 3p Rydberg states. Analysis of the vibronic structure following two-photon excitation of rovibrationally cold allyl radicals reveals transitions to the 3p(z) ((2)A(1)) Rydberg state with an electronic origin at 42230 cm(-1). More than 40 transitions to vibrational levels in the partially overlapping spectra of the 3p(y) ((2)B(2)) Rydberg state and the 3s ((2)A(1)) Rydberg state are identified and reassigned on the basis of predictions from ab initio calculations and results and simulations of pulsed-field-ionization zero-kinetic-energy photoelectron spectra obtained recently using resonant multiphoton excitation via selected vibrational levels of these two Rydberg states (J. Chem. Phys. 2009, 131, 014304). Depletion spectroscopy reveals that the transition to the short-lived 3p(x) ((2)B(1)) Rydberg state in vicinity of three-state same symmetry conical intersections predicted theoretically carries most of the oscillator strength of these coupled 3s and 3p Rydberg states. The results allow for the first time to experimentally derive the energetic ordering of the 3p Rydberg states of the allyl radical.

Jet-cooled 2-aminopyridine dimer: conformers and infrared vibrational spectra.

The 2-aminopyridine dimer, (2AP)(2), is linked by two N-H...N hydrogen bonds, providing a model for the Watson-Crick configurations of the adenine or cytosine self-dimers. Structure optimization of (2AP)(2) at the MP2 level with the aug-cc-pVQZ basis set establishes the existence of two nearly degenerate conformers with C(i) and C(2) symmetry. Adding complete basis set extrapolation and DeltaCCSD(T) corrections gives binding energies D(e) = 10.70 and 10.72 kcal/mol, respectively. Both isomers are chiral, each giving rise to a pair of enantiomers. The potential energy surface of (2AP)(2) is calculated along the 2AP amino flip coordinates, revealing a 4-fold minimum low-energy region with a planar C(2h) symmetric and four asymmetric transition structures. The mass-selective resonant two-photon ionization (R2PI) spectra of supersonically cooled (2AP)(2) were remeasured. Three different species (A-C) were separated and characterized by UV/UV depletion spectroscopy and by infrared (IR) depletion spectroscopy in the 2600-3800 cm(-1) range. The R2PI and IR spectra of species A and B are very similar, in agreement with the prediction of two conformers of (2AP)(2). The IR bands are assigned to the H-bonded N-H(b) stretch, the N-H(2) bend overtone, and the free N-H(f) stretch of (2AP)(2), based on the calculated IR spectra, thereby extending and correcting previous assignments. Conformer A is tentatively assigned as the C(2) conformer. The UV spectrum of species C is very different from those of A and B, its IR spectrum exhibiting additional O-H stretching bands. C is assigned to the (2AP)(2).H(2)O cluster, based on the agreement of its IR spectrum with calculated IR spectra. Complete dissociation into the (2AP)(2)(+) ion occurs upon ionization.

Scope and limitations of the SCS-MP2 method for stacking and hydrogen bonding interactions.

Fluorobenzenes are pi-acceptor synthons that form pi-stacked structures in molecular crystals as well as in artificial DNAs. We investigate the competition between hydrogen bonding and pi-stacking in dimers consisting of the nucleobase mimic 2-pyridone (2PY) and all fluorobenzenes from 1-fluorobenzene to hexafluorobenzene (n-FB, with n = 1-6). We contrast the results of high level ab initio calculations with those obtained using ultraviolet (UV) and infrared (IR) laser spectroscopy of isolated and supersonically cooled dimers. The 2PY.n-FB complexes with n = 1-5 prefer double hydrogen bonding over pi-stacking, as diagnosed from the UV absorption and IR laser depletion spectra, which both show features characteristic of doubly H-bonded complexes. The 2-pyridone.hexafluorobenzene dimer is the only pi-stacked dimer, exhibiting a homogeneously broadened UV spectrum and no IR bands characteristic for H-bonded species. MP2 (second-order Møller-Plesset perturbation theory) calculations overestimate the pi-stacked dimer binding energies by about 10 kJ/mol and disagree with the experimental observations. In contrast, the MP2 treatment of the H-bonded dimers appears to be quite accurate. Grimme's spin-component-scaled MP2 approach (SCS-MP2) is an improvement over MP2 for the pi-stacked dimers, reducing the binding energy by approximately 10 kJ/mol. When applied to explicitly correlated MP2 theory (SCS-MP2-R12 approach), agreement with the corresponding coupled-cluster binding energies [at the CCSD(T) level] is very good for the pi-stacked dimers, within +/- 1 kJ/mol for the 2PY complexes with 1-fluorobenzene, 1,2-difluorobenzene, 1,2,4,5-tetrafluorobenzene, pentafluorobenzene and hexafluorobenzene. Unfortunately, the SCS-MP2 approach also reduces the binding energy of the H-bonded species, leading to disagreement with both coupled-cluster theory and experiment. The SCS-MP2-R12 binding energies follow the SCS-MP2 binding energies closely, being about 0.5 and 0.7 kJ/mol larger for the H-bonded and pi-stacked forms, respectively, in an augmented correlation-consistent polarized valence quadruple-zeta basis. It seems that the SCS-MP2 and SCS-MP2-R12 methods cannot provide sufficient accuracy to replace the CCSD(T) method for intermolecular interactions where H-bonding and pi-stacking are competitive.

Isomers of the uracil dimer: an ab initio benchmark study.

Benchmark ab initio calculations at the correlated level are reported for ten isomers of the uracil dimer (U.U): six are doubly N-H...O hydrogen bonded, three have a C-H...O and an N-H...O hydrogen bond, and one is doubly C-H...O hydrogen bonded. Their structures were optimized at the correlated level by using second-order Møller-Plesset perturbation theory (MP2), resolution of identity MP2 (RIMP2), and the binding energies D(e) calculated with the coupled-cluster method with singles, doubles, and iterative triples, CCSD(T). The MP2 and RIMP2 binding energies D(e) are extrapolated to the complete basis set (CBS) limit, using the aug-cc-pVXZ (X = D, T, Q) basis sets, giving binding energies accurate to +/-0.07 kcal/mol. With one exception, the correlation energy contributions at the CCSD(T) level increase the binding energies, although the changes are small, +0.03 to -0.27 kcal/mol (or 0.1% to 2.2%). The most stable isomer is the doubly N1-H...O hydrogen-bonded HB4 form, with D(e)[CCSD(T)]= -19.04 kcal/mol. The biologically relevant HB2 dimer has D(e)[CCSD(T)] = -12.64 kcal/mol, and the HB5 dimer that constitutes the main structural motif of the uracil crystal has -13.20 kcal/mol. The "Calcutta" dimer, which occurs in an RNA hexamer, is among the weakest isomers, with D(e)[CCSD(T)] = -9.81 kcal/mol. We compare to the binding energies calculated with the B3LYP, PBE, and PW91 density functionals; the PW91/6-311++G(d,p) binding energies agree with the CBS benchmark values, to within <2%. A useful single-molecule descriptor for the strengths of the individual hydrogen bonds can be derived from the gas-phase acidity DeltaE(0)(A-H) of the N-H or C-H donor groups and the gas-phase proton affinity PA(0)(B) of the C=O groups of the uracil monomer. The calculated hydrogen bond energies D(e)(infinity) correlate well with the difference between gas-phase acidity and basicity, DeltaE(0)(A-H) - PA(0)(B).

An ab initio benchmark study of hydrogen bonded formamide dimers.

The five singly and doubly hydrogen bonded dimers of formamide are calculated at the correlated level by using resolution of identity Møller-Plesset second-order perturbation theory (RIMP2) and the coupled cluster with singles, doubles, and perturbative triples [CCSD(T)] method. All structures are optimized with the Dunning aug-cc-pVTZ and aug-cc-pVQZ basis sets. The binding energies are extrapolated to the complete basis set (CBS) limit by using the aug-cc-pVXZ (X = D, T, Q) basis set series. The effect of extending the basis set to aug-cc-pV5Z on the geometries and binding energies is studied for the centrosymmetric doubly N-H...O bonded dimer FA1 and the doubly C-H...O bonded dimer FA5. The MP2 CBS limits range from -5.19 kcal/mol for FA5 to -14.80 kcal/mol for the FA1 dimer. The DeltaCCSD(T) corrections to the MP2 CBS limit binding energies calculated with the 6-31+G(d,p), aug-cc-pVDZ, and aug-cc-pVTZ basis sets are mutually consistent to within < or =0.03 kcal/mol. The DeltaCCSD(T) correction increases the binding energy of the C-H...O bonded FA5 dimer by 0.4 kcal/mol or approximately 9% over the distance range +/-0.5 Angstrom relative to the potential minimum. This implies that the ubiquitous long-range C-H...O interactions in proteins are stronger than hitherto calculated.

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%.

Gas-phase Watson-Crick and Hoogsteen isomers of the nucleobase mimic 9-methyladenine x 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.

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.

Hydrogen bonding of the nucleobase mimic 2-pyridone to fluorobenzenes: an ab initio investigation.

The hydrogen-bonded complexes of the nucleobase mimic 2-pyridone (2PY) with seven different fluorinated benzenes (1-, 1,2-, 1,4-, 1,2,3-, 1,3,5-, 1,2,3,4-, and 1,2,4,5-fluorobenzene) are important model systems for investigating the relative importance of hydrogen bonding versus pi-stacking interactions in DNA. We have shown by supersonic-jet spectroscopy that these dimers are hydrogen bonded and not pi-stacked at low temperature (Leist, R.; Frey, J. A.; Leutwyler, S. J. Phys. Chem. A 2006, 110, 4180). Their geometries and binding energies D(e) were calculated using the resolution of identity (RI) Møller-Plesset second-order perturbation theory method (RIMP2). The most stable dimers are bound by antiparallel N-H...F-C and C-H...O=C hydrogen bonds. The binding energies are extrapolated to the complete basis set (CBS) limit, , using the aug-cc-pVXZ basis set series. The CBS binding energies range from -D(e,CBS) = 6.4-6.9 kcal/mol and the respective dissociation energies from -D(0,CBS) = 5.9-6.3 kcal/mol. In combination with experiment, the latter represent upper limits to the dissociation energies of the pi-stacked isomers (which are not observed experimentally). The individual C-H...O=C and N-H...F-C contributions to D(e) can be approximately separated. They are nearly equal for 2PY.fluorobenzene; each additional F atom strengthens the C-H...O=C hydrogen bond by approximately 0.5 kcal/mol and weakens the C-F...H-N hydrogen bond by approximately 0.3 kcal/mol. The single H-bond strengths and lengths correlate with the gas-phase acid-base properties of the C-H and C-F groups of the fluorobenzenes.

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.

Infrared depletion spectra of 2-aminopyridine2-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.