ReviewAnnual review of physical chemistry2008
Free energies of chemical reactions in solution and in enzymes with ab initio quantum mechanics/molecular mechanics methods.
Review in Annual review of physical chemistry, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 130 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
130 citing papers in PubMed.
- Benchmark Study for Calculations of pKa Values of Metal Ligands in Proteins.Journal of chemical theory and computation · 2026Article
- Solvent Stabilization of Protic Oxonium/Ammonium Intermediates in Cation Radical Cyclization Reactions Investigated via Computational Approaches.The Journal of organic chemistry · 2026Article
- Accelerating Quantum Mechanical/Molecular Mechanical (QM/MM) Simulations with Stochastic Iso-Kinetic Nosé-Hoover Multiple Time Step Integrator in CHARMM.The journal of physical chemistry. B · 2026Article
- Computational Electrosynthesis: A Perspective on Mechanistic Questions, Methodological Approaches, and Elucidating the Role of the Electrical Double Layer.The journal of physical chemistry. C, Nanomaterials and interfaces · 2025Review
- Efficient Training of Neural Network Potentials for Chemical and Enzymatic Reactions by Continual Learning.Journal of chemical theory and computation · 2025Article
- Catalytic Role of Methanol in Anodic Coupling Reactions Involving Alcohol Trapping of Cation Radicals.The Journal of organic chemistry · 2024Article
- CHARMM-GUI QM/MM Interfacer for a Quantum Mechanical and Molecular Mechanical (QM/MM) Simulation Setup: 1. Semiempirical Methods.Journal of chemical theory and computation · 2024Article
- Accelerating reliable multiscale quantum refinement of protein-drug systems enabled by machine learning.Nature communications · 2024Article
- Article
- Accurate and Efficient Multilevel Free Energy Simulations with Neural Network-Assisted Enhanced Sampling.Journal of chemical theory and computation · 2023Article
- Hybrid Quantum Mechanical/Molecular Mechanical Methods For Studying Energy Transduction in Biomolecular Machines.Annual review of biophysics · 2023Review
- Neural network potentials for chemistry: concepts, applications and prospects.Digital discovery · 2023Review
- Generalized Transition State Theory Treatment of Water-Assisted Proton Transport Processes in Proteins.The journal of physical chemistry. B · 2022Article
- Double proton transfer in hydrated formic acid dimer: Interplay of spatial symmetry and solvent-generated force on reactivity.Physical chemistry chemical physics : PCCP · 2022Article
- AcceleratingThe journal of physical chemistry. B · 2022Article
- Benchmark Study of Redox Potential Calculations for Iron-Sulfur Clusters in Proteins.Inorganic chemistry · 2022Article
- Quantum Vibrational Spectroscopy of Explicitly Solvated Thymidine in Semiclassical Approximation.The journal of physical chemistry letters · 2022Article
- AffordableThe journal of physical chemistry. A · 2021Article
- Machine-Learning-Assisted Free Energy Simulation of Solution-Phase and Enzyme Reactions.Journal of chemical theory and computation · 2021Article
- Reaction Path-Force Matching in Collective Variables: Determining Ab Initio QM/MM Free Energy Profiles by Fitting Mean Force.Journal of chemical theory and computation · 2021Article
70 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
2 authors.
Funding
Abstract
Combined quantum mechanics/molecular mechanics (QM/MM) methods provide an accurate and efficient energetic description of complex chemical and biological systems, leading to significant advances in the understanding of chemical reactions in solution and in enzymes. Here we review progress in QM/MM methodology and applications, focusing on ab initio QM-based approaches. Ab initio QM/MM methods capitalize on the accuracy and reliability of the associated quantum-mechanical approaches, however, at a much higher computational cost compared with semiempirical quantum-mechanical approaches. Thus reaction-path and activation free-energy calculations based on ab initio QM/MM methods encounter unique challenges in simulation timescales and phase-space sampling. This review features recent developments overcoming these challenges and enabling accurate free-energy determination for reaction processes in solution and in enzymes, along with applications.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.