TD-DFT Investigation of the Magnetic Circular Dichroism Spectra of Some Purine and Pyrimidine Bases of Nucleic Acids

Abstract

We present a computational study of the magnetic circular dichroism (MCD) spectra in the 200-300 nm wavelength region of purine and its derivative hypoxanthine, as well as of the pyrimidine bases of nucleic acids uracil, thymine, and cytosine, using the B3LYP and CAM-B3LYP functionals. Solvent effects are investigated within the polarizable continuum model and by inclusion of explicit water molecules. In general, the computed spectra are found to be in good agreement with the experimental ones, apart from some overall blue shifts. Both the pseudo-A term shape of the MCD spectra of the purines and the B term shape of the spectra of pyrimidine bases are reproduced. Our calculations also correctly reproduce the reversed phase of the MCD bands in purine compared to that of its derivatives present in nucleic acids. Solvent effects are sizable and system specific, but they do not in general alter the qualitative shape of the spectra. The bands are dominated by the bright π → π* transitions, and our calculations in solution nicely reproduce their energy differences, improving the estimates obtained in the gas phase. Shoulders are predicted for purine and uracil due to n → π* excitations, but they are too weak to be observed in the experiment.

Resolving Electronic Transitions in Synthetic Fluorescent Protein Chromophores by Magnetic Circular Dichroism

“…[10b, 23] We find it efficient with respect to the required computer time, althoughe fficient implementations of other procedures,s uch as the complex polarization propagator( CPP) methods, [9b] have also been reported and tested. [24] As shown below the SOS calculations reproduce the main trends observed in the experimental spectra.…”

“…The sum‐over‐state methodology (SOS) [9 h, 22] is used for simulations of MCD intensities, which has been successfully applied for fullerene derivatives . We find it efficient with respect to the required computer time, although efficient implementations of other procedures, such as the complex polarization propagator (CPP) methods, have also been reported and tested . As shown below the SOS calculations reproduce the main trends observed in the experimental spectra.…”

Modeling magnetic circular dichroism within the polarizable embedding approach

“…However, the MCD spectrum may also be determined directly with use of the complex polarization propagator (CPP) method developed by Norman and coworkers. [24,25,26,27,28,29] The CPP approach introduces a finite lifetime of the excited states directly in the response calculations, thereby avoiding the unphysical divergence of the standard response equations at resonance frequencies. By this, the CPP equations are well-defined throughout the entire spectral region.…”

“…Therefore, a proper description of the environmental effects is a key component for predicting reliable spectroscopic parameters. Regarding computation of MCD parameters, environmental effects have previously been included using either a polarizable continuum model (PCM) [18] and/or by including a small number of solvent molecules in the QM description, the so-called super-molecular approach [31,29,32]. One advantage of using a PCM approach to model the effects of the solvent is that the solvent dynamics is implicitly included.…”

“…[36,61,62] The MCD spectra of the nucleobases occurring in DNA have been studied both from a theoretical and an experimental point of view, where the theoretical results typically have been used to assign and interpret the experimentally recorded spectrum. [29,63,64,65,31] In a recent paper, the MCD spectra of various nucleobases have been calculated by means of quantum chemical methods based on TDDFT calculations. [29] Especially the role of solvent effects -included either through use of the PCM or super-molecular approach -was discussed, and it was found that the intensities for the MCD signal typically show an enhancement compared to similar calculations for the molecule in isolation.…”