Ab Initio Anharmonic Analysis of Vibrational Spectra of Uracil Using the Numerical-Analytic Implementation of Operator Van Vleck Perturbation Theory

Abstract

The numerical-analytic implementation of the operator version of the canonical Van Vleck second-order vibrational perturbation theory (CVPT2) is employed for a purely ab initio prediction and interpretation of the infrared (IR) and Raman anharmonic spectra of a medium-size molecule of the diketo tautomer of uracil (2,4(1H,3H)-pyrimidinedione), which has high biological importance as one of the four RNA nucleobases. A nonempirical, semidiagonal quartic potential energy surface (PES) expressed in normal coordinates was evaluated at the MP2/cc-pVTZ level of theory. The quality of the PES was improved by replacing the harmonic frequencies with the "best" estimated CCSD(T)-based values taken from the literature. The theoretical method is enhanced by an accurate treatment of multiple Fermi and Darling-Dennison resonances with evaluation of the corresponding resonance constants W and K (CVPT2+WK method). A prediction of the anharmonic frequencies as well as IR and Raman intensities was used for a detailed interpretation of the experimental spectra of uracil. Very good agreement between predicted and observed vibrational frequencies has been achieved (RMSD ∼4.5 cm(-1)). The model employed gave a theoretically robust treatment of the multiple resonances in the 1680-1790 cm(-1) region. Our new analysis gives the most reliable reassignments of IR and Raman spectra of uracil available to date.

Anharmonic Effects on Vibrational Spectra Intensities: Infrared, Raman, Vibrational Circular Dichroism, and Raman Optical Activity

“…An important difficulty to their correct evaluations is the potential presence of Fermi resonances in those equations. In order to treat consistently those occurrences already noted by others,99,102 an adapted version of our hybrid degeneracy-corrected PT2/VPT2 method (HDCPT2), introduced for the calculation of vibrational energies65 was chosen. The idea behind the degeneracy-corrected approach (DCPT2) is to replace all potentially resonant terms by a non-divergent form, following the transformation, Sk22Δω→Sfalse(Δω2+k2−Δωfalse)where S is the sign of “ k 2 Δ ω ”, k 2 is a term containing a product of cubic force constants, and Δ ω is a frequency difference, which can be very small in case of Fermi resonances.…”

“…for details). It should be noted that Krasnoshchekov and collaborators have proposed an alternative approach directly embedded in their on-the-fly canonical Van Vleck perturbation calculations 102,103…”

Simulated NIR spectra as sensitive markers of the structure and interactions in nucleobases

“…Deperturbed and generalized variants of VPT2 method (DVPT2/GVPT2) have been adopted for detailed studies of IR features of numerous molecules 58 , including nucleobases 59–63 . For example, uracil has been examined by the second-order operator canonical Van Vleck perturbation theory (CVPT2) 64 . On the other hand, accurate but computationally highly expensive variational approach has recently been optimized in resource usage by Thomas et al .…”

Vibrational investigation of nucleobases by means of divide and conquer semiclassical dynamics

“…Specifically, we will compare our semiclassical vibrational estimates with experimental values [103][104][105] and GVPT2 and CVPT2 calculated energy levels. 30,31 As a first evaluation of the level of theory, we report in Table I the force field, where harmonic CCSD(T) estimates have been corrected using GVPT2 estimates at the level of B3LYP theory for anharmonicities. We can observe a good agreement between these two column values, suggesting that our computational setup is a good harmonic estimate for a possible accuracy and feasibility of the semiclassical simulations.…”