ArticleACS omega2021
Quantum Mechanical Methods Predict Accurate Thermodynamics of Biochemical Reactions.
Article in ACS omega, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 7 papers.
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Who cites it
7 citing papers in PubMed.
- ReaxFF Parameter Set for Boron Clusters and Icosahedral Boron Crystals: Comparison with Density Functional Theory and Machine-Learning Potentials.The journal of physical chemistry. C, Nanomaterials and interfaces · 2025Article
- A comprehensive DFT study on piroxicam transition metal complexes (Mn, Fe, Co, Ni, and Zn): implications for computational drug design.Journal of molecular modeling · 2025Article
- CACTUS: Chemistry Agent Connecting Tool Usage to Science.ACS omega · 2024Article
- Improving pathway prediction accuracy of constraints-based metabolic network models by treating enzymes as microcompartments.Synthetic and systems biotechnology · 2023Article
- Benchmarking Density Functional Theory Methods for Metalloenzyme Reactions: The Introduction of the MME55 Set.Journal of chemical theory and computation · 2023Article
- The isothermal Boltzmann-Gibbs entropy reduction affects survival of the fruit fly Drosophila melanogaster.Scientific reports · 2023Article
- Artificial Intelligence for Autonomous Molecular Design: A Perspective.Molecules (Basel, Switzerland) · 2021Review
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Authors and funding
7 authors.
Funding
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Abstract
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.
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Registered trials
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