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Molecular beacon is a DNA probe containing a sequence complementary to the target that is flanked by self-complementary termini, and carries a fluorophore and a quencher at the ends. We used the fluorescein and dabcyl as fluorophore and quencher respectively, and studied with DFT calculations at the GGA/DNP level, and taking into account DFT dispersion corrections by the Grimme and Tkatchenko-Scheffler (TS) schemes, the distance, where the most favorable energetic interaction between the fluorophore and quencher in conjugated form occurs. This distance occurs at a separation distance of 29.451 Å between the centers of Dabcyl and fluorescein employing the TS DFT dispersion correction scheme, indicating FRET efficiency around 94.28 %. The calculated emission spectra of the conjugated pair in water indicated that the emission and absorption spectrum overlap completely and thus no fluorescence can be observed due to the fluorescence resonance energy transfer (FRET) effect. The DFT results confirmed the experimentally observing fluorescence quenching of the fluorescein-dabcyl conjugated system by FRET.

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Comparison between the molecular mechanics calculated energy of interaction of lignan dimers and trimers with a cellulose I crystallite and the experimental values of Young's modulus obtained by thermomechanical analysis (TMA) of cellulose paper impregnated with low molecular weight lignins showed good correlation between calculated and experimental results. The oligomer composition of the four low molecular weight lignins tested was obtained by MALDI-TOF mass spectrometry. This showed that these lignins were predominantly composed of dimers and trimers rendering them ideal for correlation testing. The lignan/cellulose crystallite interaction energy is determined by the oligomer molecular weight as well as the type of linkage within the lignan oligomers. Lignans with higher molecular weight in which the units are linked as β-O-4 give interaction energy values indicating stronger attraction with cellulose. two molecules repel each other. Thus, the more negative is the energy of interaction, the more strongly attracted to each other are the two molecules.