Biologically active molecules (proteins, nucleic acids, etc.) have distinct three-dimensional structures that match and fit, and thereby determine their behavior and interactions with other molecules within their native solvated environment. Moreover, in order to successfully apply molecular structural information in areas such as drug discovery, and disease therapy, one must also be able to take into account energetic factors such as electrostatic potentials and hydrophobicity for more comprehensive biomolecular interactions. In this talk I shall present, irregular fast Fourier algorithms to compute error-bounded approximations of solvation molecular surfaces and skins, (dielectric interfaces), along with area and volume derivatives, starting from the molecules atomic coordinate data. For a molecule with M atoms in R3, the time complexity for point and derivatives estimation, is near linear in M. Similarly, we use a combination of irregular fast Fourier methods and higher order cubature, to rapidly estimate the generalized Born solvation energy for scoring binding affinities in molecular docking, and polarization force fields for fast molecular dynamics. This is joint work with my two Ph.D. students, Vinay Siddhanavalli, and Wenqi Zhao.