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arXiv · 2507.21539

Infrared Spectral Signature of Water as a Probe to Demystify Urea Aggregation and Force Field Accuracy

Pankaj Adhikary·Rajib Biswas
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Abstract

Urea is widely used as a protein denaturant. However, the potential of urea to form self-assembled structures at higher concentrations and the influence of its self-interactions on water structure and dynamics remains elusive. This open question demands tracking of molecular-level rearrangements. In this work, we explore the influence of urea on local structure of water and dynamics and relate it to urea self-association. We correlate vibrational spectral response and orientational dynamics of water with concentration-dependent self-association of urea by looking at the interface surface area, hydrogen bond strength, and population of relevant donor-acceptor pairs. We compare the response of four urea force fields (KBFF, OPLS-S, OPLS-AA-D, GAFF-D3) with simple point charge extented water. The KBFF model reproduces experimental IR spectra. Both variants of the Duffy model (OPLS-S, OPLS-AA-D) show blue shifts with reasonable broadening and intense concentration-dependent responses, while GAFF-D3 shows random peak shifts with prominent broadening. Regarding urea self-aggregation, KBFF is mildly repulsive, Duffy models are attractive, and GAFF-D3 is neutral with high variability. Only KBFF and GAFF-D3 capture the expected deceleration in water-orientational dynamics. We conclude urea does not self-aggregate significantly in water, even at higher concentrations. KBFF emerges as the most reliable classical non-polarizable model of urea for capturing both structural and dynamic properties of water.

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Pankaj Adhikary, Rajib Biswas. 2025-07-29. Infrared Spectral Signature of Water as a Probe to Demystify Urea Aggregation and Force Field Accuracy. https://arxiv.org/abs/2507.21539

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