Jann A. Frey

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. Grimmes 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.

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.

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.

Binding energies of hydrogen-bonded cis-amide and nucleobase dimers : An evaluation of DFT performance

The understanding of biological processes at the molecular level demands accurate knowledge of the nonbonded interactions that control the geometries, binding energies and dynamics of the supramolecular structures involved. High level ab initio methods are still prohibitively expensive for large systems, but certain density functional (DFT) methods can provide cost-effective alternatives. The performance of six different functionals (BLYP, B3LYP, X3LYP, PBE, PW91, and mPW91) for the calculation of the doubly hydrogen-bonded cis-amide dimers (formamide)2 and (2-pyridone)2 have been tested. Their N-H...O hydrogen bond motifs occur between many nucleobases, peptides, and proteins. Binding energy benchmarks using ab initio MP2 calculations and basis set extrapolations to the complete basis set (CBS) limit with the Dunning aug-cc-pVXZ (X=D,T,Q) basis set series have been established. These yield D ∞ e = -14.80 kcal/mol for (formamide)2 and -22.63 kcal/mol for (2PY) 2 . Of the six functionals, PW91 consistently gives the best agreement with the MP2 basis-set limit binding energies, closely followed by PBE. The mPW91, B3LYP and the recently proposed X3LYP functionals are in less good agreement. The BLYP functional underestimates the interaction strengths by 20-25% and is not recommended. As an application the hydrogen-bond isomerization equilibria for the Sugar-edge, Watson-Crick and Wobble isomers of the dimers 2-pyridone-uracil and 2-pyridone-thymine from first principles are computed and compared to experiment.

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.