Reliable vibrational wavenumbers for C=O and N-H stretchings of isolated and hydrogen-bonded nucleic acid bases.

Phys Chem Chem Phys

Scuola Normale Superiore, Piazza dei Cavalieri 7, I-56126 Pisa, Italy.

Published: March 2016

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=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=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.

Download full-text PDF

Source
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5612391PMC
http://dx.doi.org/10.1039/c5cp07386cDOI Listing

Publication Analysis

Top Keywords

n-h stretchings
12
linear regression
12
harmonic wavenumbers
12
vibrational wavenumbers
8
c=o n-h
8
training set
8
validation set
8
wavenumbers
5
n-h
5
harmonic
5

Similar Publications

The direct discharge of cationic surfactants into environmental matrices has exponentially increased due to their wide application in many products. These compounds and their degraded products disrupt microbial dynamics, hinder plant survival, and affect human health. Therefore, there is an urgent need to develop electroanalytical assessment techniques for their identification, determination, and monitoring.

View Article and Find Full Text PDF

Phormidium versicolor PC skin cream evaluation for its stability and biological activities.

Appl Microbiol Biotechnol

December 2024

Laboratory of Environmental Bioprocesses, Centre of Biotechnology of Sfax, University of Sfax, Sfax, Tunisia.

In the present investigation, 13% ± 0.84 of the extracted and purified phycocyanin from Phormidium versicolor was obtained, with a purity of 0.69 following dialysis.

View Article and Find Full Text PDF

The intermediate phase produced by the complexation of metal ions and solvent molecules usually occurs in the crystallization process of perovskite single crystal or film. Effective monitoring of intermediate-phase evolution is beneficial to the control of crystal quality. However, it is difficult to realize.

View Article and Find Full Text PDF

Three low molecular weight (LMW) sweeteners (D-tagatose, erythritol, and trehalose) were studied in yoghurt formulations to investigate their effects on syneresis, rheological properties, water distribution, and microstructural characteristics. The results indicated that trehalose improved syneresis, the fermentation process, and rheological properties compared to yoghurt fortified with sucrose, while D-tagatose and erythritol demonstrated the opposite effects on fermentation. With the addition of LMW sweeteners, the apparent viscosity and frequency sweep of yoghurt increased, with trehalose showing a better effect than sucrose or the other two LMW sweeteners.

View Article and Find Full Text PDF

KTiOPO (KTP) nanoparticles (NPs) are potential materials as biolabels for long-term imaging. Optimizing their properties can lead to higher imaging efficiency and lower cytotoxicity and side effects. In this study, these nanoparticles were synthesized using the co-precipitation method and capping agents of oxalic acid and glycine.

View Article and Find Full Text PDF

Want AI Summaries of new PubMed Abstracts delivered to your In-box?

Enter search terms and have AI summaries delivered each week - change queries or unsubscribe any time!