A quantum chemical approach to biological reaction with a theory of solutions
Abstract
We recently developed a novel computational methodology, referred to as QM/MM-ER, to compute free energy change associated with a chemical reaction in a condensed phase by combining the quantum mechanical / molecular mechanical (QM/MM) method with a theory of solutions. In the present review article we illustrate an outline of the QM/MM-ER method. We also present an extension of the QM/MM-ER method to compute reduction free energy of cofactor FAD (Flavin Adenine Dinucleotide) in water as well as in apoprotein by introducing a novel approach. The key of the approach is that only the excess charge involved in the reduction process is identified as a solute. The adequacy of the method is examined for the reaction in aqueous solution by comparing the result with that obtained by a conventional approach. The reduction free energy of cofactor FAD embedded in a cholesterol oxidase (PDB id = 1B4V) is computed as -163.1 kcal/mol by the QM/MM-ER approach, while it is obtained as -80.1 kcal/mol for the cofactor in water solution.
Read the paper
Related studies
- In silico toxicology protocols
- QM7-X, a comprehensive dataset of quantum-mechanical properties spanning the chemical space of small organic molecules
- Quantum Informed Machine-Learning Potentials for Molecular Dynamics Simulations of CO2's Chemisorption and Diffusion in Mg-MOF-74
- In-silico strategies in nano-drug design: Bridging nanomaterials and pharmacological applications
- mRNA codon optimization with quantum computers
- The computational power of the human brain
Go deeper in Evidence Hub
Evidence Hub adds a study data sheet (design, sample size, evidence level, key numbers), an AI summary and a chat grounded in the paper's text.