Infrared Spectral Signature of Water as a Probe to Demystify Urea Aggregation and Force Field Accuracy
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| Format: | Preprint |
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2025
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| _version_ | 1866915416745443328 |
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| author | Adhikary, Pankaj Biswas, Rajib |
| author_facet | Adhikary, Pankaj Biswas, Rajib |
| contents | 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. |
| format | Preprint |
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arxiv_https___arxiv_org_abs_2507_21539 |
| institution | arXiv |
| publishDate | 2025 |
| record_format | arxiv |
| spellingShingle | Infrared Spectral Signature of Water as a Probe to Demystify Urea Aggregation and Force Field Accuracy Adhikary, Pankaj Biswas, Rajib Soft Condensed Matter 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. |
| title | Infrared Spectral Signature of Water as a Probe to Demystify Urea Aggregation and Force Field Accuracy |
| topic | Soft Condensed Matter |
| url | https://arxiv.org/abs/2507.21539 |