Jump to main content
Jump to site search
Access to RSC content Close the message box

Continue to access RSC content when you are not at your institution. Follow our step-by-step guide.


Issue 12, 2016
Previous Article Next Article

Reliable vibrational wavenumbers for C[double bond, length as m-dash]O and N–H stretchings of isolated and hydrogen-bonded nucleic acid bases

Author affiliations

Abstract

The accurate prediction of vibrational wavenumbers for functional groups involved in hydrogen-bonded bridges remains an important challenge for computational spectroscopy. For the specific case of the C[double bond, length as m-dash]O and N–H stretching modes of nucleobases and their oligomers, the paucity of experimental reference values needs to be compensated by reliable computational data, which require the use of approaches going beyond the standard harmonic oscillator model. Test computations performed for model systems (formamide, acetamide and their cyclic homodimers) in the framework of the second order vibrational perturbation theory (VPT2) confirmed that anharmonic corrections can be safely computed by global hybrid (GHF) or double hybrid (DHF) functionals, whereas the harmonic part is particularly challenging. As a matter of fact, GHFs perform quite poorly and even DHFs, while fully satisfactory for C[double bond, length as m-dash]O stretchings, face unexpected difficulties when dealing with N–H stretchings. On these grounds, a linear regression for N–H stretchings has been obtained and validated for the heterodimers formed by 4-aminopyrimidine with 6-methyl-4-pyrimidinone (4APM-M4PMN) and by uracil with water. In view of the good performance of this computational model, we have built a training set of B2PLYP-D3/maug-cc-pVTZ harmonic wavenumbers (including linear regression scaling for N–H) for six-different uracil dimers and a validation set including 4APM-M4PMN, one of the most stable hydrogen-bonded adenine homodimers, as well as the adenine–uracil, adenine–thymine, guanine–cytosine and adenine–4-thiouracil heterodimers. Because of the unfavourable scaling of DHF harmonic wavenumbers with the dimensions of the investigated systems, we have optimized a linear regression of B3LYP-D3/N07D harmonic wavenumbers for the training set, which has been next checked against the validation set. This relatively cheap model, which shows very good agreement with experimental data (average errors of about 10 cm−1), paves the route toward a reliable analysis of spectroscopic signatures for larger polynucleotides.

Graphical abstract: Reliable vibrational wavenumbers for C [[double bond, length as m-dash]] O and N–H stretchings of isolated and hydrogen-bonded nucleic acid bases

Back to tab navigation

Supplementary files

Article information


Submitted
30 Nov 2015
Accepted
17 Feb 2016
First published
17 Feb 2016

Phys. Chem. Chem. Phys., 2016,18, 8479-8490
Article type
Paper
Author version available

Reliable vibrational wavenumbers for C[double bond, length as m-dash]O and N–H stretchings of isolated and hydrogen-bonded nucleic acid bases

T. Fornaro, M. Biczysko, J. Bloino and V. Barone, Phys. Chem. Chem. Phys., 2016, 18, 8479
DOI: 10.1039/C5CP07386C

Social activity

Search articles by author

Spotlight

Advertisements