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[Display omitted] Freeze-drying enables delicate, heat-sensitive biomaterials to be stored in a dry form even at room temperature. However, exposure to physicochemical stress induced by freeze-drying presents challenges for maintaining material characteristics and functionality upon reconstitution, for which reason excipients are required. Although wide variety of different excipients are available for pharmaceutical applications, their protective role in the freeze-drying is not yet fully understood. In this study, our aim was to use molecular dynamics simulations to screen the properties of different sugars and amino acids, which could be combined with plant-based nanofibrillated cellulose (NFC) hydrogel to provide protective matrix system for future freeze-drying for pharmaceuticals and biologics. The changes in the NFC-based formulations before and after freeze-drying and reconstitution were evaluated using non-invasive Timegate PicoRaman spectroscopy and traditional characterization methods. We continued to the freeze-drying with the NFC hydrogel formulations including lactose with and without glycine, which showed the highest attraction preferences on NFC surface in silico. This formulation enabled successful freeze-drying and subsequent reconstitution with preserved physicochemical and rheological properties. Raman spectroscopy gave us insights of the molecular-level changes during freeze-drying, especially the mutarotation of lactose. This research showed the potential of integrating in silico screening and non-invasive spectroscopical method to design novel biomaterial-based formulations for freeze-drying. The research provided insights of the molecular-level interactions and orientational changes of the excipients, which might be crucial in future freeze-drying applications of pharmaceuticals and biologics. [ABSTRACT FROM AUTHOR]