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Find my institution Log In Journal of Chemical Information and Modeling ACS Publications …
Find my institution Log In Journal of Chemical Information and Modeling ACS Publications …
Combined QM/MM, machine learning path integral approach to compute free energy profiles and kinetic isotope effects in RNA cleavage reactions
We present a fast, accurate, and robust approach for determination of free energy profiles
and kinetic isotope effects for RNA 2′-O-transphosphorylation reactions with inclusion of …
and kinetic isotope effects for RNA 2′-O-transphosphorylation reactions with inclusion of …
Perspective: Reference-Potential Methods for the Study of Thermodynamic Properties in Chemical Processes: Theory, Applications, and Pitfalls
In silico investigations of enzymatic reactions and chemical reactions in condensed phases
often suffer from formidable computational costs due to a large number of degrees of …
often suffer from formidable computational costs due to a large number of degrees of …
How many conformations need to be sampled to obtain converged QM/MM energies? The curse of exponential averaging
U Ryde - Journal of chemical theory and computation, 2017 - ACS Publications
Combined quantum mechanical and molecular mechanical (QM/MM) calculations is a
popular approach to study enzymatic reactions. They are often based on a set of minimized …
popular approach to study enzymatic reactions. They are often based on a set of minimized …
[HTML][HTML] Recent developments in multiscale free energy simulations
Physics-based free energy simulations enable the rigorous calculation of properties, such as
conformational equilibria, solvation or binding free energies. While historically most …
conformational equilibria, solvation or binding free energies. While historically most …
Multireference generalization of the weighted thermodynamic perturbation method
We describe the generalized weighted thermodynamic perturbation (gwTP) method for
estimating the free energy surface of an expensive “high-level” potential energy function …
estimating the free energy surface of an expensive “high-level” potential energy function …
Accelerated computation of free energy profile at ab initio quantum mechanical/molecular mechanics accuracy via a semi-empirical reference potential. I. Weighted …
Free energy profile (FE Profile) is an essential quantity for the estimation of reaction rate and
the validation of reaction mechanism. For chemical reactions in condensed phase or …
the validation of reaction mechanism. For chemical reactions in condensed phase or …
Predicting Octanol–Water Partition Coefficients: Are Quantum Mechanical Implicit Solvent Models Better than Empirical Fragment-Based Methods?
In this work, we examined the performance of contemporary quantum mechanical implicit
solvent models (SMD, SM8, SM12, and ADF-COSMO-RS) and empirical fragment-based …
solvent models (SMD, SM8, SM12, and ADF-COSMO-RS) and empirical fragment-based …
Force field benchmark of amino acids. 2. Partition coefficients between water and organic solvents
The partitioning of amino acids between water and apolar environments is of vital
importance in protein function and drug delivery. Here we present an extensive benchmark …
importance in protein function and drug delivery. Here we present an extensive benchmark …
Accelerated computation of free energy profile at ab initio quantum mechanical/molecular mechanical accuracy via a semi-empirical reference potential. II …
An efficient and accurate reference potential simulation protocol is proposed for producing
ab initio quantum mechanical/molecular mechanical (AI-QM/MM) quality free energy profiles …
ab initio quantum mechanical/molecular mechanical (AI-QM/MM) quality free energy profiles …