Water-mediated interactions between non-polar moieties play a crucial role in driving self-assembly processes such as surfactant micellization, protein folding, and many other diverse phenomena. Among a variety of forces contributing to the self assembly, hydrophobic interactions play a dominant role. Historically, thermodynamic models describing hydrophobic effects have invariably relied on macroscopic thermodynamic properties to infer this molecular behavior. Experimental studies help to probe the spatial correlations between model hydrophobic solutes and to measure their waters of hydration in order to examine structural perturbations in the surrounding water induced by the solute, or to measure directly the attractive forces between hydrophobic surfaces. Further, molecular simulations can be used to derive entropic and enthalpic contributions to the free energy of hydrophobic hydration in terms of water structure surrounding simple, model hydrophobic solutes, such as methane. Based on the results for simple solutes, these methods can now be extended to investigate the hydrophobic hydration of more complex molecular solutes of arbitrary size and shape such as micelles. Atomistic simulations of chemical systems provide a new perspective towards testing the theories behind the ubiquitous phenomenon of hydrophobic effect, and probe the underlying thermodynamic signatures. In this context, my research work delves into the water-mediated interactions leading to the hydrophobic hydration of short chain alkanes, volumetric properties of unfolded polypeptides and self-assembly mechanism in polymer-surfactant systems. The first part of my research involves re-optimization of existing force field interaction parameters for the CHn alkane sites (n=0 to 4) to accurately reproduce the experimental hydration free energies of linear and branched chain alkanes over a range of temperatures. This Hydrophobic Hydration-Alkane (HH-Alkane) model accounts for polarization effects in the alkane hydration and can be extended to polypeptides in water. Subsequent discussions will focus on the results from extensive molecular simulations of tri- and tetrapeptides to quantify the accuracy of the simulation model in capturing the volumetric properties of unfolded polypeptides. Group additivity correlation was used to calculate the partial molar volumes of the neutral sidechains of amino acids, glycine backbone unit and both zwitterionic and N-acetyl/amide terminal units. The simulation results will be compared to the experimental results to validate these observations. In addition, the research explores the self-assembly and aggregation mechanism in anionic sodium dodecyl sulfate (SDS) surfactant- non-ionic Polyethylene Oxide (PEO) and Poly vinyl pyrrolidone (PVP) polymer systems. Potential of mean force calculations at multiple temperatures show an increasing trend in hydrophobic attractions within the polymer-micelle system. Also, these simulations provide interesting insights into the experimentally observed phenomena between the polymers and the micelles starting from pre-formed structure as well as random configurations. / 1 / Lalitanand N. Surampudi

Hydrophobic interactions guide important molecular self-assembly processes such as protein folding. On the macroscale, hydrophobic interactions consist of the aggregation of "oil-like" objects in water by minimizing the interfacial energy. However, the hydration mechanism of small hydrophobic molecules on the nanoscale (~1 nm) differs fundamentally from its macroscopic counterpart. Theoretical studies over the last two decades have pointed to an intricate dependence of molecular hydration mechanisms on the length scale. The microscopic-to-macroscopic cross-over length scale is critically important to hydrophobic interactions in polymers, proteins and other macromolecules. Accurate experimental determination of hydration mechanisms and their interaction strengths are needed to understand protein folding. This thesis reports the development of experimental and analytical techniques that allow for direct measurements of hydrophobic interactions in a single molecule. Using single molecule force spectroscopy, the mechanical unfolding of a single hydrophobic homopolymer was identified and modeled. Two experiments examined how hydrophobicity at the molecular scale differ from the macroscopic scale. The first experiment identifies macroscopic interfacial tension as a critical parameter governing the molecular hydrophobic hydration strength. This experiment shows that the solvent conditions affect the microscopic and macroscopic hydrophobic strengths in similar ways, consistent with theoretical predictions. The second experiment probes the hydrophobic size effect by studying how the size of a non-polar side-chain affects the thermal signatures of hydration. Our experimental results reveal a cross-over length scale of approximately 1 nm that bridges the transition from entropically driven microscopic hydration mechanism to enthalpically driven macroscopic hydration mechanism. These results indicate that hydrophobic interactions at the molecular scale differ from macroscopic scale, pointing to potential ways to improve our understanding and predictions of molecular interactions. The system established in this thesis forms the foundation for further investigation of polymer hydrophobicity.

Hydrophobic interactions guide important molecular self-assembly processes such as protein folding. On the macroscale, hydrophobic interactions consist of the aggregation of "oil-like" objects in water by minimizing the interfacial energy. However, the hydration mechanism of small hydrophobic molecules on the nanoscale (~1 nm) differs fundamentally from its macroscopic counterpart. Theoretical studies over the last two decades have pointed to an intricate dependence of molecular hydration mechanisms on the length scale. The microscopic-to-macroscopic cross-over length scale is critically important to hydrophobic interactions in polymers, proteins and other macromolecules. Accurate experimental determination of hydration mechanisms and their interaction strengths are needed to understand protein folding. This thesis reports the development of experimental and analytical techniques that allow for direct measurements of hydrophobic interactions in a single molecule. Using single molecule force spectroscopy, the mechanical unfolding of a single hydrophobic homopolymer was identified and modeled. Two experiments examined how hydrophobicity at the molecular scale differ from the macroscopic scale. The first experiment identifies macroscopic interfacial tension as a critical parameter governing the molecular hydrophobic hydration strength. This experiment shows that the solvent conditions affect the microscopic and macroscopic hydrophobic strengths in similar ways, consistent with theoretical predictions. The second experiment probes the hydrophobic size effect by studying how the size of a non-polar side-chain affects the thermal signatures of hydration. Our experimental results reveal a cross-over length scale of approximately 1 nm that bridges the transition from entropically driven microscopic hydration mechanism to enthalpically driven macroscopic hydration mechanism. These results indicate that hydrophobic interactions at the molecular scale differ from macroscopic scale, pointing to potential ways to improve our understanding and predictions of molecular interactions. The system established in this thesis forms the foundation for further investigation of polymer hydrophobicity.

Raman multivariate curve resolution (Raman-MCR) spectroscopy is used to study water-mediated interactions by decomposing Raman spectra of aqueous solutions into bulk water and solute-correlated (SC) spectral components. The SC spectra are minimum-area difference spectra that reveal solute-induced perturbations of water structure, including changes in water hydrogen-bonding strength, tetrahedral structure, and formation of dangling (non-hydrogen-bonded) OH defects in a solute's hydration shell. Additionally, Raman-active intramolecular vibrational modes of the solute may be used to uncover complementary information regarding solute--solute interactions. Herein, Raman-MCR is applied to address fundamental questions related to: (1) confined cavity water and its connection to host-guest binding, (2) hydrophobic hydration of fluorinated solutes, (3) specific ion effects on nonionic micelle formation, and (4) ion pairing in aqueous solutions.