Vibrational spectral signature of water to probe the mystery of urea aggregation and validation of force fields

Abstract

Urea is a widely used 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 remain elusive. This open question demands tracking of molecular-level rearrangements. In this work, we explore the influence of urea on water’s local structure and dynamics and relate it to urea self-association. We correlate the vibrational spectral response and orientational dynamics of water with concentration-dependent self-association of urea by examining 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, and GAFF-D3) with SPC/E water. The KBFF–SPC/E pair best reproduces the experimental IR spectra. Both variants of the Duffy model (OPLS-S and OPLS-AA-D) show blue shifts with reasonable broadening and strong 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 the KBFF–SPC/E pair captures the expected deceleration in water-orientational dynamics. We conclude that urea does not self-aggregate significantly in water, even at higher concentrations; urea aggregation, when present, arises from the accumulation of weak, short-lived contacts rather than from strong pairwise association. KBFF emerges as the most reliable classical non-polarizable model of urea for capturing both structural and dynamic properties of water.