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QM40, Realistic Quantum Mechanical Dataset for Machine Learning in Molecular Science.
Sci Data
December 2024
Southern Methodist University Department of Chemistry, Dallas, TX, USA.
The growing popularity of machine learning (ML) and deep learning (DL) in scientific fields is hindered by the scarcity of high-quality datasets. While quantum mechanical (QM) predictions using DL techniques such as graph neural networks (GNNs) and generative models are gaining traction, insufficient training data remains a bottleneck. The QM40 dataset addresses this challenge by representing 88% of the FDA-approved drug chemical space.
View Article and Find Full Text PDFIon solvation free energy calculations based on first-principles molecular dynamics thermodynamic integration.
J Chem Phys
May 2024
State Key Laboratory of Superlattices and Microstructures, Institute of Semiconductors, Chinese Academy of Science, Beijing 100083, People's Republic of China.
Numerous electrochemistry reactions require the precise calculation of the ion solvation energy. Despite the significant progress in the first-principles calculations for crystals and defect formation energies for solids, the liquid system free energy calculations still face many challenges. Ion solvation free energies can be calculated via different semiempirical ways, e.
View Article and Find Full Text PDFA Very "Distilled" Emblem in Baroque Rome: Natural Philosophy, Alchemy, and Atomism in the Academy of the Umoristi.
Ambix
May 2024
Center for the History of Philosophy and Science, Faculty of Philosophy, Theology and Religious studies, Radboud University, Nijmegen, The Netherlands.
Created and published in a printed volume in 1611, the emblem chosen by the literary Academy of the Umoristi is intriguing at multiple levels. At a time when the water cycle was still unknown, the image engaged the thorny question of how the evaporation of salty seawater, condensed into clouds, could subsequently pour down as sweet rain. Additionally, the Lucretian motto "Redit agmine dulci" audaciously evoked the philosophy of atoms.
View Article and Find Full Text PDFLithium Storage Mechanism: A Review of Perylene Diimide N-Substituted with a 1,2,4-Triazol-3-yl Ring for Organic Cathode Materials.
ACS Appl Mater Interfaces
December 2023
Department of Chemistry and Research Institute of Molecular Alchemy, Gyeongsang National University, Jinju 52828, South Korea.
The demand for lithium-ion batteries (LIBs) has increased rapidly. However, commercial inorganic-based cathode materials have a low theoretical capacity and inherent disadvantages, such as high cost and toxicity. Redox-active organic cathodes with a high theoretical capacity, eco-friendly properties, and sustainability have been developed to overcome these limitations.
View Article and Find Full Text PDFFlexible Topology: A Dynamic Model of a Continuous Chemical Space.
J Chem Theory Comput
August 2023
Department of Computational Mathematics, Science & Engineering, Michigan State University, East Lansing, Michigan 48824, United States.
Ligand design problems involve searching chemical space for a molecule with a set of desired properties. As chemical space is discrete, this search must be conducted in a pointwise manner, separately investigating one molecule at a time, which can be inefficient. We propose a method called "Flexible Topology", where a ligand is composed of a set of shapeshifting "ghost" atoms, whose atomic identities and connectivity can dynamically change over the course of a simulation.
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