We demonstrate the capability of creating robust density functional tight binding (DFTB) models for chemical reactivity in prebiotic mixtures through force matching to short time scale quantum free energy estimates. Molecular dynamics using density functional theory (DFT) is a highly accurate approach to generate free energy surfaces for chemical reactions, but the extreme computational cost often limits the time scales and range of thermodynamic states that can feasibly be studied. In contrast, DFTB is a semiempirical quantum method that affords up to a thousandfold reduction in cost and can recover DFT-level accuracy. Here, we show that a force-matched DFTB model for aqueous glycine condensation reactions yields free energy surfaces that ...
The fully analytic gradient is developed for density-functional tight-binding (DFTB) combined with t...
We present a method for the creation of classical force fields for water under dissociative thermody...
Lately, there has been great interest in performing free-energy perturbation (FEP) at the combined q...
Accurate determination of reaction barrier is crucial in chemical reaction engineering since it is d...
International audienceApplication of ab initio molecular dynamics to study free energy surfaces (FES...
In solution chemical reaction, we often need to consider a multidimensional free energy (FE) surface...
In this thesis, we present novel computational methods and frameworks to address the challenges asso...
We develop a new method combining replica exchange transition interface sampling with two distinct p...
Kohn-Sham density functional theory (DFT) is a standard tool in most branches of chemistry, but a...
Metadynamics calculations of large chemical systems with ab initio methods are computationally prohi...
Thesis (Ph.D.)--University of Washington, 2015The study of chemical reactions is a foundation of che...
Density Functional Tight Binding (DFTB) models are two to three orders of magnitude faster than ab i...
International audienceThe hydration or binding free energy of a drug-like molecule is a key data for...
Recent developments in physical and computer sciences enable quantitative predictions of chemical re...
The dimerization of glycine is the simplest oligomerization of amino acids and plays an important ro...
The fully analytic gradient is developed for density-functional tight-binding (DFTB) combined with t...
We present a method for the creation of classical force fields for water under dissociative thermody...
Lately, there has been great interest in performing free-energy perturbation (FEP) at the combined q...
Accurate determination of reaction barrier is crucial in chemical reaction engineering since it is d...
International audienceApplication of ab initio molecular dynamics to study free energy surfaces (FES...
In solution chemical reaction, we often need to consider a multidimensional free energy (FE) surface...
In this thesis, we present novel computational methods and frameworks to address the challenges asso...
We develop a new method combining replica exchange transition interface sampling with two distinct p...
Kohn-Sham density functional theory (DFT) is a standard tool in most branches of chemistry, but a...
Metadynamics calculations of large chemical systems with ab initio methods are computationally prohi...
Thesis (Ph.D.)--University of Washington, 2015The study of chemical reactions is a foundation of che...
Density Functional Tight Binding (DFTB) models are two to three orders of magnitude faster than ab i...
International audienceThe hydration or binding free energy of a drug-like molecule is a key data for...
Recent developments in physical and computer sciences enable quantitative predictions of chemical re...
The dimerization of glycine is the simplest oligomerization of amino acids and plays an important ro...
The fully analytic gradient is developed for density-functional tight-binding (DFTB) combined with t...
We present a method for the creation of classical force fields for water under dissociative thermody...
Lately, there has been great interest in performing free-energy perturbation (FEP) at the combined q...