MolModa: accessible and secure molecular docking in a web browser.

Molecular docking advances early-stage drug discovery by predicting the geometries and affinities of small-molecule compounds bound to drug-target receptors, predictions that researchers can leverage in prioritizing drug candidates for experimental testing. Unfortunately, existing docking tools often suffer from poor usability, data security, and maintainability, limiting broader adoption. Additionally, the complexity of the docking process, which requires users to execute a series of specialized steps, often poses a substantial barrier for non-expert users.

From Byte to Bench to Bedside: Molecular Dynamics Simulations and Drug Discovery.

Molecular dynamics (MD) simulations and computer-aided drug design (CADD) have advanced substantially over the past two decades, thanks to continuous computer hardware and software improvements. Given these advancements, MD simulations are poised to become even more powerful tools for investigating the dynamic interactions between potential small-molecule drugs and their target proteins, with significant implications for pharmacological research.

Quantum alchemy beyond singlets: Bonding in diatomic molecules with hydrogen.

Bonding energies play an essential role in describing the relative stability of molecules in chemical space. Therefore, methods employed to search chemical space need to capture the bonding behavior for a wide range of molecules, including radicals. In this work, we investigate the ability of quantum alchemy to capture the bonding behavior of hypothetical chemical compounds, specifically diatomic molecules involving hydrogen with various electronic structures.

Evaluating quantum alchemy of atoms with thermodynamic cycles: Beyond ground electronic states.

Due to the sheer size of chemical and materials space, high-throughput computational screening thereof will require the development of new computational methods that are accurate, efficient, and transferable. These methods need to be applicable to electron configurations beyond ground states. To this end, we have systematically studied the applicability of quantum alchemy predictions using a Taylor series expansion on quantum mechanics (QM) calculations for single atoms with different electronic structures arising from different net charges and electron spin multiplicities.

Quantifying Uncertainties in Solvation Procedures for Modeling Aqueous Phase Reaction Mechanisms.

Computational quantum chemistry provides fundamental chemical and physical insights into solvated reaction mechanisms across many areas of chemistry, especially in homogeneous and heterogeneous renewable energy catalysis. Such reactions may depend on explicit interactions with ions and solvent molecules that are nontrivial to characterize. Rigorously modeling explicit solvent effects with molecular dynamics usually brings steep computational costs while the performance of continuum solvent models such as polarizable continuum model (PCM), charge-asymmetric nonlocally determined local-electric (CANDLE), conductor-like screening model for real solvents (COSMO-RS), and effective screening medium method with the reference interaction site model (ESM-RISM) are less well understood for reaction mechanisms.

First-principles modeling of chemistry in mixed solvents: Where to go from here?

Mixed solvents (i.e., binary or higher order mixtures of ionic or nonionic liquids) play crucial roles in chemical syntheses, separations, and electrochemical devices because they can be tuned for specific reactions and applications.