Arginine, useful in protein refolding, solubilization of proteins, and suppression of protein aggregation and non-specific adsorption during formulation and purification, is a ubiquitous additive in the biotechnology and pharmaceutical industries. In order to provide a framework for analyzing the molecular level mechanisms behind arginine/protein interactions in the above context, density functional theory was used to systematically examine how arginine interacts with naturally occurring amino acids. The results show that the most favorable interaction of arginine is with acidic amino acids and arises from charge interactions and hydrogen-bond interactions. Arginine is also shown to form stacking and T-shaped structures with aromatic amino acids, the types of cation–π and N–H…π interactions, respectively, known to be important contributors to protein stability. The analysis also shows that arginine-arginine interactions lead to stable clusters, with the stability of the clusters arising from the stacking of the guanidinium part of arginine. The results show that the unique ability of arginine to form clusters with itself makes it an effective aggregation suppressant and support the interpretations of the current study using experimental and molecular dynamics results available in the literature. The results also contribute to understanding the role of arginine in increasing protein solubility, imparting thermal stability of important enzymes, and designing better additives.