Quantum Mechanical Methods Predict Accurate Thermodynamics of Biochemical Reactions.
ACS Omega
; 6(14): 9948-9959, 2021 Apr 13.
Article
en En
| MEDLINE
| ID: mdl-33869975
Thermodynamics plays a crucial role in regulating the metabolic processes in all living organisms. Accurate determination of biochemical and biophysical properties is important to understand, analyze, and synthetically design such metabolic processes for engineered systems. In this work, we extensively performed first-principles quantum mechanical calculations to assess its accuracy in estimating free energy of biochemical reactions and developed automated quantum-chemistry (QC) pipeline (https://appdev.kbase.us/narrative/45710) for the prediction of thermodynamics parameters of biochemical reactions. We benchmark the QC methods based on density functional theory (DFT) against different basis sets, solvation models, pH, and exchange-correlation functionals using the known thermodynamic properties from the NIST database. Our results show that QC calculations when combined with simple calibration yield a mean absolute error in the range of 1.60-2.27 kcal/mol for different exchange-correlation functionals, which is comparable to the error in the experimental measurements. This accuracy over a diverse set of metabolic reactions is unprecedented and near the benchmark chemical accuracy of 1 kcal/mol that is usually desired from DFT calculations.
Texto completo:
1
Colección:
01-internacional
Base de datos:
MEDLINE
Tipo de estudio:
Prognostic_studies
/
Risk_factors_studies
Idioma:
En
Revista:
ACS Omega
Año:
2021
Tipo del documento:
Article
País de afiliación:
Estados Unidos
Pais de publicación:
Estados Unidos