Performing solvation free energy calculations in LAMMPS using the decoupling approach

Heterogeneous and Allosteric Role of Surface Hydration for Protein-Ligand Binding

Atomistic-level understanding of surface hydration mediating protein-protein interactions and ligand binding has been a challenge due to the dynamic nature of water molecules near the surface. We develop a computational method to evaluate the solvation free energy based on the density map of the first hydration shell constructed from all-atom molecular dynamics simulation and use it to examine the binding of two intrinsically disordered ligands to their target protein domain. One ligand is from the human protein, and the other is from the 1918 Spanish flu virus. We find that the viral ligand incurs a 6.9 kcal/mol lower desolvation penalty upon binding to the target, which is consistent with its stronger binding affinity. The difference arises from the spatially fragmented and nonuniform water density profiles of the first hydration shell. In particular, residues that are distal from the ligand-binding site contribute to a varying extent to the desolvation penalty, among which the "entropy hotspot" residues contribute significantly. Thus, ligand binding alters hydration on remote sites in addition to affecting the binding interface. The nonlocal effect disappears when the conformational motion of the protein is suppressed. The present results elucidate the interplay between protein conformational dynamics and surface hydration. Our approach of measuring the solvation free energy based on the water density of the first hydration shell is tolerant of the conformational fluctuation of protein, and we expect it to be applicable to investigating a broad range of biomolecular interfaces.

Influence of Pore Size in Benzoin Condensation of Furfural Using Heterogenized Benzimidazole Organocatalysts

A designed N-heterocyclic carbene (NHC) catalyst was covalently anchored on a range of mesoporous and hierarchical supports, to study the influence of pore size in the benzoin condensation of furfural. The structural and spectroscopic characteristics of the anchored catalysts were investigated, also with the help of molecular dynamics simulations, in order to rationalize the degree of stability and recyclability of the heterogenized organocatalysts. Quantitative yields (99 %) and complete recyclability were maintained after several cycles, vindicating the design rationale.

A New Formulation for the Concerted Alchemical Calculation of van der Waals and Coulomb Components of Solvation Free Energies

Alchemical free energy calculations via molecular dynamics have been widely used to obtain thermodynamic properties related to protein-ligand binding and solute-solvent interactions. Although soft-core modeling is the most common approach, the linear basis function (LBF) methodology [Naden, L. N.; et al. J. Chem. Theory Comput.2014, 10 (3), 1128; 2015, 11 (6), 2536] has emerged as a suitable alternative. It overcomes the end-point singularity of the scaling method while maintaining essential advantages such as ease of implementation and high flexibility for postprocessing analysis. In the present work, we propose a simple LBF variant and formulate an efficient protocol for evaluating van der Waals and Coulomb components of an alchemical transformation in tandem, in contrast to the prevalent sequential evaluation mode. To validate our proposal, which results from a careful optimization study, we performed solvation free energy calculations and obtained octanol-water partition coefficients of small organic molecules. Comparisons with results obtained via the sequential mode using either another LBF approach or the soft-core model attest to the effectiveness and correctness of our method. In addition, we show that a reaction field model with an infinite dielectric constant can provide very accurate hydration free energies when used instead of a lattice-sum method to model solute-solvent electrostatics.

Structure and stability of 7-mercapto-4-methylcoumarin self-assembled monolayers on gold: an experimental and computational analysis

Self-assembled monolayers (SAM) of 7-mercapto-4-methylcoumarin (MMC) on a flat gold surface were studied by molecular dynamics (MD) simulations, reference-free grazing incidence X-ray fluorescence (GIXRF) and X-ray photoelectron spectroscopy (XPS), to determine the maximum monolayer density and to investigate the nature of the molecule/surface interface. In particular, the protonation state of the sulfur atom upon adsorption was analyzed, since some recent literature presented evidence for physisorbed thiols (preserving the S-H bond), unlike the common picture of chemisorbed thiyls (losing the hydrogen). MD with a specifically tailored force field was used to simulate either thiol or thiyl monolayers with increasing number of molecules, to determine the maximum dynamically stable densities. This result was refined by computing the monolayer chemical potential as a function of the density with the bennet acceptance ratio method, based again on MD simulations. The monolayer density was also measured with GIXRF, which provided the absolute quantification of the number of sulfur atoms in a dense self-assembled monolayer (SAM) on flat gold surfaces. The sulfur core level binding energies in the same monolayers were measured by XPS, fitting the recorded spectra with the binding energies proposed in the literature for free or adsorbed thiols and thiyls, to get insight on the nature of the molecular species present in the layer. The comparison of theoretical and experimental SAM densities, and the XPS analysis strongly support the picture of a monolayer formed by chemisorbed, dissociated thiyls.

A unified approach for calculating free energies of liquid and defective crystals based on thermodynamic integration

The free energy calculation is fundamentally important in the research of physics, chemistry and materials. Thermodynamic integration is the most common way to estimate free energies. In the research, we proposed a unified approach using atomic simulations to calculate the free energies of liquid and defective crystals. The new approach is based on thermodynamic integration (TI) using two alchemical pathways. Softcore potentials are developed for three-body interatomic potentials to realize the alchemical pathways. Employing the new approach, the free energy of the liquid can be calculated without requiring another reference system. The free energy of the defective crystal can be calculated directly at high temperature. It avoids the singularity at the integration endpoint caused by the defect diffusion which is a serious problem in the widely used Einstein crystal method. In addition, the new approach can capture the whole free energy of the defective crystal including the contribution of anharmonic and configurational entropy which are particularly important at high temperature. The new method is simple yet effective and can be extended to different materials and more complex liquid and defective crystal systems.

Toward Physics-Based Solubility Computation for Pharmaceuticals to Rival Informatics

We demonstrate that physics-based calculations of intrinsic aqueous solubility can rival cheminformatics-based machine learning predictions. A proof-of-concept was developed for a physics-based approach via a sublimation thermodynamic cycle, building upon previous work that relied upon several thermodynamic approximations, notably the 2RT approximation, and limited conformational sampling. Here, we apply improvements to our sublimation free-energy model with the use of crystal phonon mode calculations to capture the contributions of the vibrational modes of the crystal. Including these improvements with lattice energies computed using the model-potential-based Ψ_mol method leads to accurate estimates of sublimation free energy. Combining these with hydration free energies obtained from either molecular dynamics free-energy perturbation simulations or density functional theory calculations, solubilities comparable to both experiment and informatics predictions are obtained. The application to coronene, succinic acid, and the pharmaceutical desloratadine shows how the methods must be adapted for the adoption of different conformations in different phases. The approach has the flexibility to extend to applications that cannot be covered by informatics methods.