ViSCa: A computational toolbox for vibrational spectral calculations-Application to sum frequency generation...

Accurate spectral calculations are essential for interpreting the complex vibrational spectra of proteins, but high-level quantum chemical methods are computationally prohibitive for large proteins. This tutorial introduces the Vibrational Spectra Calculation (ViSCa) toolbox, a computational suite of methods for sum frequency generation (VSFG) spectral calculations. This article guides potential users through generating protein conformations and simulating the corresponding VSFG spectra to facilitate structural studies at interfaces. We use a frequency-mapping approach to construct an excitonic Hamiltonian of the amide-I modes of the protein backbone, which offers a functional balance between computational efficiency and accuracy. Included are several illustrative examples that showcase the different functionalities of ViSCa, including determining the orientation of a known protein structure at an interface ("ViSCa-Orient"), as well as coupling the calculations to molecular dynamics simulations to determine distinct changes in protein structure driven by the interfacial environment ("ViSCa-Select").