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

Abstract

Near-infrared (near-IR; NIR) spectroscopy is continuously advancing in biophysical and biochemical fields of investigation. For instance, recent progresses in NIR hyperspectral imaging of biological systems may be noted. However, interpretation of NIR bands for biological samples is difficult and creates a considerable barrier in exploring the full potential of NIR spectroscopy in bioscience. For this reason, we carried out a systematic study of NIR spectra of adenine, cytosine, guanine, and thymine in polycrystalline state. Interpretation of NIR spectra of these nucleobases was supported by anharmonic vibrational analysis using Deperturbed Vibrational Second-Order Perturbation Theory (DVPT2). A number of molecular models of nucleobases was applied to study the effect of the inter-molecular interactions on the NIR spectra. The accuracy of simulated NIR spectra appears to depend on the intra-layer interactions; in contrast, the inter-layer interactions are less influential. The best results were achieved by combining the simulated spectra of monomers and dimers. It is of particular note that in-plane deformation bands are far more populated than out-of-plane ones and the importance of ring modes is relatively small. This trend is in contrast to that observed in mid-IR region. As shown, the local, short-range chemical neighborhood of nucleobase molecules influence their NIR spectra more considerably. This suggests that NIR spectra are more sensitive probe of the nucleobase pairing than mid-IR ones. The obtained results allow, for the first time, to construct a frequency correlation table for NIR spectra of purines and pyrimidines.

Near-Infrared Spectroscopy in Bio-Applications

“…Often, assignments of only selected NIR band are available, e.g., intense and fairly isolated OH stretching bands. Recent advances in quantum chemical calculation of NIR spectra of biomolecules should be highlighted [9,[91][92][93][94], which bring significant progress in the interpretability of their NIR absorption, as well as the insight into how it is influenced by intermolecular interactions. These approaches are essential in improving speculative nature of NIR band assignments (Section 3.7).…”

“…This yields significantly improved interpretation of the complex NIR spectra, including biomolecules. In addition, NIR spectra of several biomolecules were successfully reproduced with these methods and their absorption bands were comprehensively explained [9,[91][92][93][94]. This approach was also helpful in interpreting the meaningful wavenumbers in PLS regression models of bio-active compounds in plant medicines.…”

“…Nucleic acids are typically minor constituents, and hence a clear appearance of their bands in NIR spectra is unlikely. Detailed assignments of NIR bands of nucleobases (nucleic acid bases) are essential for the possibility to unveil the characteristic wavenumbers as markers for nucleic acids present in the sample [94]. It was possible to construct a frequency correlation table for NIR spectra of purines and pyrimidines.…”

Anharmonic DFT Study of Near-Infrared Spectra of Caffeine: Vibrational Analysis of the Second Overtones and Ternary Combinations

“…It was demonstrated that very accurate reproduction of NIR spectra of small- to medium-sized molecules in liquid phase and in solutions is possible [ 28 , 29 , 30 ], including very fine spectral details resulting from the conformational populations [ 31 , 32 , 33 ]. NIR spectra simulations were also performed for biologically-relevant molecules, e.g., short- [ 34 , 35 ], medium- [ 36 ], and long-chain fatty acids [ 37 ], amino acids [ 38 , 39 ] or nucleobases [ 40 ]. The theoretical calculations of the spectra were used to directly aid analytical applications of NIR spectroscopy, where the interpretation of the multivariate regression models and understanding of the instrumental difference between various benchtop and miniaturized NIR spectrometers has been made available this way.…”

Characterization of thymine microcrystals by CARS and SHG microscopy

“…The nucleic acid bases—thymine (5-methyluracil), adenine, cytosine, uracil and guanine through hydrogen bonds and stacking interactions self-assemble into nanostructures of different dimensionality 1 , 2 . While such structures are not found in Nature, detailed information on intermolecular forces which hold the DNA structure, becomes encoded in crystal forms, formation energies as well as in thermodynamic properties of the crystals 3 – 5 . The ordering of this self-arrangement depends on the type of substrate used for the assembly.…”