The structural dynamics of a molecule are determined by the underlying potential energy landscape. Conical intersections are funnels connecting otherwise separate potential energy surfaces. Posited almost a century ago, conical intersections remain t...
The journal of physical chemistry letters
Oct 27, 2021
The utilization of artificial neural networks (ANNs) provides strategies for accelerating molecular simulations. Herein, ANNs are implemented as propagators of the time-dependent Schrödinger equation to simulate the quantum dynamics of systems with t...
Since the discovery of penicillin, the development and use of antibiotics have promoted safe and effective control of bacterial infections. However, the number of antibiotic-resistance cases has been ever increasing over time. Thus, the drug discover...
The journal of physical chemistry letters
Oct 21, 2021
Diabatization of one-electron states in flexible molecular aggregates is a great challenge due to the presence of surface crossings between molecular orbital (MO) levels and the complex interaction between MOs of neighboring molecules. In this work, ...
International journal of molecular sciences
Oct 12, 2021
A successful passage of the blood-brain barrier (BBB) is an essential prerequisite for the drug molecules designed to act on the central nervous system. The logarithm of blood-brain partitioning (LogBB) has served as an effective index of molecular B...
Human interaction with the world is dominated by uncertainty. Probability theory is a valuable tool to face such uncertainty. According to the Bayesian definition, probabilities are personal beliefs. Experimental evidence supports the notion that hum...
The journal of physical chemistry letters
Sep 23, 2021
We present an approach that extends the theory of targeted free energy perturbation (TFEP) to calculate free energy differences and free energy surfaces at an accurate quantum mechanical level of theory from a cheaper reference potential. The converg...
Despite their rich information content, electronic structure data amassed at high volumes in ab initio molecular dynamics simulations are generally under-utilized. We introduce a transferable high-fidelity neural network representation of such data i...
Journal of chemical theory and computation
Sep 1, 2021
Despite recent advances in the development of machine learning potentials (MLPs) for biomolecular simulations, there has been limited effort on developing stable and accurate MLPs for enzymatic reactions. Here we report a protocol for performing mach...
Chemical compound space (CCS), the set of all theoretically conceivable combinations of chemical elements and (meta-)stable geometries that make up matter, is colossal. The first-principles based virtual sampling of this space, for example, in search...