Related papers: Predicting binding free energies in solution
Free energies of ionic solvation calculated from computer simulations exhibit a strong system size dependence. We perform a finite-size analysis based on a dielectric-continuum model with periodic boundary conditions. That analysis results…
Predictions of relative stabilities of (competing) molecular crystals are of great technological relevance, most notably for the pharmaceutical industry. However, they present a long-standing challenge for modeling, as often minuscule free…
Determining the solvation free energies of single ions in water is one of the most fundamental problems in physical chemistry and yet many unresolved questions remain. In particular, the ability to decompose the solvation free energy into…
Free energy calculations are widely used tools in computational chemistry, but their dependence on the assignment of partial charges during force field parametrization reduces their accuracy and reproducibility. In this work, we highlight…
Host-guest binding plays a crucial role in the functionality of various systems, and its efficiency is often quantified using the binding free energy, which represents the free-energy difference between the bound and dissociated states.…
We demonstrate that with two small modifications, the popular dielectric continuum model is capable of predicting, with high accuracy, ion solvation thermodynamics in numerous polar solvents, and ion solvation free energies in…
Solvation free energy is an important quantity in Computational Chemistry with a variety of applications, especially in drug discovery and design. The accurate prediction of solvation free energies of small molecules in water is still a…
We present relativistic many-body calculations of total electron binding energy of neutral atoms up to element $Z=120$. Binding energy for ions may be found by subtracting known ionization potentials. Accuracy of the results for $17<Z…
The thesis focuses on the prediction of solvation thermodynamics using integral equation theories. Our main goal is to improve the approach using a rational correction. We achieve it by extending recently introduced pressure correction, and…
A recently developed statistical mechanical Quasi-Chemical Theory (QCT) has led to significant insights into solvation phenomena for both hydrophilic and hydrophobic solutes. The QCT exactly partitions solvation free energies into three…
Quantitative prediction of thermodynamic properties in solution is essential for translating atomistic simulations into reliable chemical insight. As an exemplar system, the behaviour of CaCO$_3$ in water has been widely studied to…
Treating water as a linearly responding dielectric continuum on molecular length scales allows very simple estimates of solvation structure and thermodynamics for charged and polar solutes. While this approach can successfully account for…
A rigorous formalism for estimating noncovalent binding free energies and thermodynamic expectations from calculations in which receptor configurations are sampled independently from the ligand is derived. Due to this separation, receptor…
Free energies govern the behavior of soft and liquid matter, and improving their predictions could have a large impact on the development of drugs, electrolytes or homogeneous catalysts. Unfortunately, it is challenging to devise an…
We present a simulation scheme to calculate defect formation free energies at a molecular crystal/water interface based on force-field molecular dynamics (MD) simulations. To this end we adopt and modify existing approaches to calculate…
The accurate prediction of solvation free energy is of significant importance as it governs the behavior of solutes in solution. In this work, we apply a variety of machine learning techniques to predict and analyze the alchemical free…
We consider the prediction of a basic thermodynamic property---hydration free energies---across a large subset of the chemical space of small organic molecules. Our in silico study is based on computer simulations at the atomistic level…
The principles behind the computation of protein-ligand binding free energies by Monte Carlo integration are described in detail. The simulation provides gas-phase binding free energies that can be converted to aqueous energies by solvation…
Experimental studies on ion-water clusters have provided insights into the microscopic aspects of hydration phenomena. One common view is that extending those experimental studies to larger cluster sizes would give the single ion absolute…
The high-energy tail of the distribution of solute-solvent interaction energies is poorly characterized for condensed systems, but this tail region is of principal interest in determining the excess free energy of the solute. We introduce…