Data for paper "Enhanced Quantum Simulations Reveal Conformation-Controlled, Site-Resolved Proton Binding in Biliverdin"

This archive contains the data and scripts behind the paper "Enhanced Quantum Simulations Reveal Conformation-Controlled, Site-Resolved Proton Binding in Biliverdin". The paper computes the site-resolved (microscopic) pKa values of the four pyrrole nitrogens of biliverdin (BV) in explicit water, the populations of its neutral tautomers, and their dependence on the conformation of the molecule (locked and open helix), and tests the approach on histidine, propionic acid, and malonaldehyde. Contents: - Metadynamics (DC-DFTB, explicit water): the deprotonation trajectories used for histidine, propionic acid, and BV, with the analysis data from which each microscopic pKa is read, the report on the selection of the 200 BV ring C trajectories by four filters, and the four trajectories in which a lactam carbonyl captured the departing proton.- Umbrella sampling (DC-DFTB): free-energy profiles, window time series, and block-bootstrap results for malonaldehyde, the syn-anti rotation of propionic acid, the proton transfers between the BV rings, and the rotation of BV ring D from the locked to the open helix.- Unbiased DC-DFTB trajectories: Mulliken charges and water radial distribution functions of the BV nitrogens.- Absorption spectra: excitation energies and oscillator strengths (CAM-B3LYP/cc-pVDZ) for 150 QM/MM geometries of each of 11 BV microstates, and the script that builds the spectrum of each microstate.- Digitized literature data used for comparison (Shang et al., Biochemistry 2010; Liu et al., Phys. Chem. Chem. Phys. 2020).- Scripts that recompute the microstate networks (all microscopic and macroscopic pKa values, cycle closures, and populations), the water density around BV used to define bulk water, and the figures of the paper and its Supporting Information.- Simulation inputs: structures, topologies, force fields, and input files for the DC-DFTB, classical MD, QM/MM, and TDDFT calculations. README.md describes every folder, the conventions (units, how each pKa and free energy is obtained, microstate names), and how to run the scripts (Python 3.10 or later with numpy, scipy, pandas, matplotlib, and pillow). MANIFEST.tsv lists every file with its size and SHA-256 checksum. DFTB Slater-Koster parameter files are not included; obtain the 3OB set from dftb.org.