Rafał A. Bachorz

Strong N-H pi Hydrogen Bonding in Amide-Benzene Interactions

Among the weak intermolecular interactions found in proteins, the amide N--H...pi interaction has been widely observed but remains poorly characterized as an individual interaction. We have investigated the isolated supersonic-jet-cooled dimer of the cis-amide and nucleobase analogue 2-pyridone (2PY) with benzene and benzene-d6. Both MP2 and SCS-MP2 geometry optimizations yield a T-shaped structure with a N--H...pi hydrogen bond to the benzene ring and the C=O group above, but far from the C--H bonds of benzene. The CCSD(T) calculated binding energy at the optimum geometry is De = 25.2 kJ/mol (dissociation energy D0 = 21.6 kJ/mol), corresponding to the H-bond strength of the water dimer or of N--H...O hydrogen bonds. The T-shaped geometry is supported by the infrared-ultraviolet depletion spectra of 2PY x benzene: The N--H stretch vibrational frequency is lowered by 56 cm(-1), and the C=O stretch vibration is lowered by 10 cm(-1), relative to those of bare 2PY, indicating a strong N--H...pi interaction and a weak interaction of the C=O group. The benzene C--H infrared stretches exhibit very small shifts (approximately 2 cm(-1)) relative to benzene, signaling the absence of interactions with the benzene C--H groups. The infrared spectral shifts are consistent with a strong nonconventional pi hydrogen bond and a T-shaped structure for 2PY x benzene. Symmetry-adapted perturbation theory calculations show that the N--H...pi interaction is by far the dominant stabilization factor.

Coupled-cluster and explicitly correlated perturbation-theory calculations of the uracil anion

A valence-type anion of the canonical tautomer of uracil has been characterized using explicitly correlated second-order Moller-Plesset perturbation theory (RI-MP2-R12) in conjunction with conventional coupled-cluster theory with single, double, and perturbative triple excitations. At this level of electron-correlation treatment and after inclusion of a zero-point vibrational energy correction, determined in the harmonic approximation at the RI-MP2 level of theory, the valence anion is adiabatically stable with respect to the neutral molecule by 40 meV. The anion is characterized by a vertical detachment energy of 0.60 eV. To obtain accurate estimates of the vertical and adiabatic electron binding energies, a scheme was applied in which electronic energy contributions from various levels of theory were added, each of them extrapolated to the corresponding basis-set limit. The MP2 basis-set limits were also evaluated using an explicitly correlated approach, and the results of these calculations are in agreement with the extrapolated values. A remarkable feature of the valence anionic state is that the adiabatic electron binding energy is positive but smaller than the adiabatic electron binding energy of the dipole-bound state.

Photoelectron spectroscopy of adiabatically bound valence anions of rare tautomers of the nucleic acid bases

Anionic states of nucleic acid bases (NABs) are involved in DNA damage by low-energy electrons and in charge transfer through DNA. Previous gas phase studies of free, unsolvated NAB parent anions probed mostly dipole-bound states, which are not present in condensed phase environments. Recently, we demonstrated that very rare tautomers of uracil (U), cytosine (C), adenine (A), and guanine (G), which are obtained from canonical tautomers through N-to-C proton transfers, support valence anionic states. Here we report the photoelectron spectrum of the final member of the NABs series: the valence state of the thymine (T) anion. Additionally, we summarized the work of all five NABs. All of the newfound anionic tautomers of the NABs may be formed via dissociative electron attachment followed by hydrogen atom reattachment to a carbon atom. Furthermore, these unusual tautomers may affect the structure and properties of DNA and RNA exposed to low-energy electrons. The new valence states observed here, unlike dipole bound states, could exist in condensed phases and may be relevant to radiobiological damage.

Stabilization of very rare tautomers of uracil by an excess electron

We characterized valence-type and dipole-bound anionic states of uracil using various electronic structure methods. We found that the most stable anion is related to neither the canonical 2,4-dioxo nor a rare imino-hydroxy tautomer. Instead, it is related to an imino-oxo tautomer, in which the N1H proton is transferred to the C5 atom. This valence anion is characterized by an electron vertical detachment energy (VDE) of 1267 meV and it is adiabatically stable with respect to the canonical neutral by 3.93 kcal mol(-1). It is also more stable by 2.32 and 5.10 kcal mol(-1) than the dipole-bound and valence anion, respectively, of the canonical tautomer. The VDE values for the former and the latter are 73 and 506 meV, respectively. Another, anionic, low-lying imino-oxo tautomer with a VDE of 2499 meV has a proton transferred from N3H to C5. It is less stable than the neutral canonical tautomer by 1.38 kcal mol(-1). The mechanism of formation of anionic tautomers with the carbon C5 protonated may involve intermolecular proton transfer or dissociative electron attachment to the canonical neutral tautomer followed by a barrier-free attachment of a hydrogen atom to C5. The six-member ring structure of anionic tautomers with carbon atoms protonated might be unstable upon an excess electron detachment. Indeed, the neutral systems resulting from electron detachment from anionic tautomers with carbon atoms protonated evolve along barrier-free decomposition pathways to a linear or a bicyclo structure, which might be viewed as lesions to RNA. Within the PCM hydration model, the low-lying valence anions become adiabatically bound with respect to the canonical neutral and the two most stable tautomers have carbon atoms protonated.

Electron-Driven Acid-Base Chemistry : Proton Transfer from Hydrogen Chloride to Ammonia

In contrast to widely familiar acid-base behavior in solution, single molecules of NH3 and HCl do not react to form the ionic salt, NH+4Cl–, in isolation. We applied anion photoelectron spectroscopy and ab initio theory to investigate the interaction of an excess electron with the hydrogen-bonded complex NH3···HCl. Our results show that an excess electron induces this complex to form the ionic salt. We propose a mechanism that proceeds through a dipole-bound state to form the negative ion of ionic ammonium chloride, a species that can also be characterized as a deformed Rydberg radical, NH4, polarized by a chloride anion, Cl–.

Explicitly Correlated Coupled-Cluster Theory

The theoretical prediction of molecular energies and properties to chemical accuracy is often achieved using coupled-cluster methods and large orbital basis sets. Through recent advances in F12 explicitly correlated methods it is now possible to obtain the same high accuracy far more efficiently, using much smaller orbital basis sets. In CCSD(T)-F12 methods, the basis set truncation error is almost entirely eliminated by introducing a small set of two-particle basis functions that depend explicitly on the inter-electronic distances and closely resemble the correlation hole. The computational expense of including the F12 geminals can be reduced to a fraction of that of the underlying CCSD(T) calculation through judicious insertions of resolution of the identity approximations and further simplifications. In this chapter we present CCSD(T)-F12 theory and review the simplified models CCSD(T)(F12), CCSD(T)-F12x and CCSD(T) \(_{\overline{F12}}\), demonstrating their utility for practical applications. In contrast to standard CCSD(T), the Hartree–Fock basis set error may limit the accuracy of a CCSD(T)-F12 calculation and we therefore also describe methods for improving the Hartree–Fock energy within an F12 calculation. A brief discussion on the extension of F12 theory to reduce basis set errors in connected triples and response properties is also presented.

Photoelectron spectrum of valence anions of uracil and first-principles calculations of excess electron binding energies

The photoelectron spectrum (PES) of the uracil anion is reported and discussed from the perspective of quantum chemical calculations of the vertical detachment energies (VDEs) of the anions of various tautomers of uracil. The PES peak maximum is found at an electron binding energy of 2.4 eV, and the width of the main feature suggests that the parent anions are in a valence rather than a dipole-bound state. The canonical tautomer as well as four tautomers that result from proton transfer from an NH group to a C atom were investigated computationally. At the Hartree-Fock and second-order Moller-Plesset perturbation theory levels, the adiabatic electron affinity (AEA) and the VDE have been converged to the limit of a complete basis set to within +/-1 meV. Post-MP2 electron-correlation effects have been determined at the coupled-cluster level of theory including single, double, and noniterative triple excitations. The quantum chemical calculations suggest that the most stable valence anion of uracil is the anion of a tautomer that results from a proton transfer from N1H to C5. It is characterized by an AEA of 135 meV and a VDE of 1.38 eV. The peak maximum is as much as 1 eV larger, however, and the photoelectron intensity is only very weak at 1.38 eV. The PES does not lend support either to the valence anion of the canonical tautomer, which is the second most stable anion, and whose VDE is computed at about 0.60 eV. Agreement between the peak maximum and the computed VDE is only found for the third most stable tautomer, which shows an AEA of approximately -0.1 eV and a VDE of 2.58 eV. This tautomer results from a proton transfer from N3H to C5. The results illustrate that the characteristics of biomolecular anions are highly dependent on their tautomeric form. If indeed the third most stable anion is observed in the experiment, then it remains an open question why and how this species is formed under the given conditions.

Rovibrational energy levels of H3(+) with energies above the barrier to linearity.

The H(3)(+) potential energy surface is sampled at 5900 geometries with the emphasis on the nonequilibrium and asymptotic points. Apart from the Born-Oppenheimer energy converged to the accuracy better than 0.02 cm(-1), the adiabatic and the leading relativistic corrections are computed at each geometry. To represent analytically the potential energy surface, the parameters of a power series are determined by fitting to the computed energy points. Possible choice of nuclear masses simulating the nonadiabatic effects in solving the nuclear Schrodinger equation is analyzed. A set of theoretically predicted rovibrational transitions is confronted with the experimental data in the 10,700-13,700 cm(-1) window of the spectra.

Large-amplitude vibrations of an N-H center dot center dot center dot pi hydrogen bonded cis-amide-benzene complex

The ground-state N-H...pi interaction of 2-pyridone.benzene (2PY.Bz) has been studied by infrared-UV depletion spectroscopy of the supersonic-jet cooled complex [P. Ottiger et al., J. Phys. Chem. B (2009) 113, 2937]. Here, we investigate the large-amplitude vibrations of 2PY.Bz and its d(1)-2PY and benzene-d(6) isotopologues in the S(1) state, using two-color resonant two-photon ionization and UV-holeburning spectroscopies, complemented by RI-CC2 and SCS-RI-CC2 calculations of the S(1) state. The latter predict a tilted T-shaped structure with an N-H...pi hydrogen bond to the benzene ring, similar to the S(0) state. The binding energy is predicted to increase by 1.5 kJ mol(-1) upon S(1)<--S(0) excitation, in close agreement with the experimental value of 1.2 kJ mol(-1). The vibronic band structure up to 60 cm(-1) above the 0 band is dominated by large-amplitude delta tilting excitations, reflecting a change in the tilt angle of the T-shaped complex. The S(0) and S(1) state delta potentials were fitted to experiment, yielding a single minimum in the S(0) state and a double-minimum S(1) potential with delta(min) = +/-13 degrees. The second large-amplitude vibration is the theta twisting or benzene internal-rotation mode. Due to the C(6) symmetry of the benzene moiety the S(0) and S(1) state theta potentials are sixfold symmetric. Analysis of the theta band structure reveals that the S(0) and S(1)theta potentials are mutually aligned and that the internal rotation barriers are V(6)(S(0)) < 0.2 kJ mol(-1) and V(6)(S(1)) = 0.10(1) kJ mol(-1), in close agreement with the calculations. Weaker excitations of the totally symmetric intermolecular vibrations chi (shear), omega (bend) and sigma (stretch) vibrations are also observed. The 2PY intramolecular nu(1) overtone, corresponding to an 2PY amide out-of-plane twist distortion, lies approximately 30% higher than in bare 2PY, reflecting the hindrance of this motion by the strong N-H...pi interaction.

Accurate Coupled Cluster Calculations of the Reaction Barrier Heights of Two CH3• + CH4 Reactions†

We have computed barrier heights of 71.8 +/- 2.0 and 216.4 +/- 2.0 kJ mol(-1) for the reactions CH4 + CH3* --> CH3* + CH4 and CH4 + CH3* --> H* + C2H6, respectively, using explicitly correlated coupled cluster theory with singles and doubles combined with standard coupled cluster theory with up to connected quadruple excitations. Transition-state theory has been used to compute the respective reaction rate constants in the temperature interval of 250-1500 K. The computed rates for the reaction to ethane are orders of magnitude slower than those used in the mechanism of Norinaga and Deutschmann (Ind. Eng. Chem. Res. 2007, 46, 3547.) for the modeling of the chemical vapor deposition of pyrolytic carbon.