To explain the large, opposite effects of urea and glycine betaine (GB) on stability of folded proteins and protein complexes, we quantify and interpret preferential interactions of urea with 45 model compounds displaying protein functional groups and compare with a previous analysis of GB. This information is needed to use urea as a probe of coupled folding in protein processes and to tune molecular dynamics force fields. Preferential interactions between urea and model compounds relative to their interactions with water are determined by osmometry or solubility and dissected using a unique coarse-grained analysis to obtain interaction potentials quantifying the interaction of urea with each significant type of protein surface (aliphatic, aromatic hydrocarbon (C); polar and charged N and O). Microscopic local-bulk partition coefficients K p for the accumulation or exclusion of urea in the water of hydration of these surfaces relative to bulk water are obtained. K p values reveal that urea accumulates moderately at amide O and weakly at aliphatic C, whereas GB is excluded from both. These results provide both thermodynamic and molecular explanations for the opposite effects of urea and glycine betaine on protein stability, as well as deductions about strengths of amide NH-amide O and amide NH-amide N hydrogen bonds relative to hydrogen bonds to water. Interestingly, urea, like GB, is moderately accumulated at aromatic C surface. Urea m-values for protein folding and other protein processes are quantitatively interpreted and predicted using these urea interaction potentials or K p values. U rea and glycine betaine (GB) rank at opposite ends of a series of small nonelectrolyte solutes in terms of their effects on protein folding and other protein processes. Stabilities (ΔG o obs ) of folded proteins and of site-specific protein-DNA complexes decrease linearly with increasing urea molarity and increase with increasing GB molarity (1-5). This solute series parallels the Hofmeister anion and cation series of non-Coulombic effects of salt ions on protein processes; guanidinium cation and thiosulfate or iodide anions are highly destabilizing but alkali metal cations are not destabilizing and sulfate or fluoride anions are stabilizing (6-8). Similar rank orders but smaller ranges of solute and nonCoulombic salt effects are observed on DNA and RNA duplex formation; urea and salt ions that greatly destabilize proteins when added at molar concentrations also greatly destabilize DNA duplexes, but GB and Hofmeister salt ions that stabilize proteins do not stabilize nucleic acids duplexes (4,5,(8)(9)(10)(11). Another range of solute effects is observed for the series of solutes from ethylene glycol (EG) to PEG, where the monomer EG destabilizes both hairpin and duplex DNA helices, whereas polymeric PEGs greatly stabilize the duplex and eliminate the destabilization of the hairpin helix (12). In our research, we use molecular thermodynamic analyses of model compound data to interpret and predict the effects of these solutes an...