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eChem: A Notebook Exploration of Quantum Chemistry
Thomas Fransson, Mickael G. Delcey, Iulia Emilia Brumboiu, Manuel Hodecker, Xin Li, Zilvinas Rinkevicius, Andreas Dreuw, Young Min Rhee, and Patrick Norman (2023)Highlighted by Jan JenseneChem is an...
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Virtual Ligand Strategy in Transition Metal Catalysis Toward Highly Efficient...
Wataru Matsuoka, Yu Harabuchi, and Satoshi Maeda (2023)Highlighted by Jan JensenThis perspective shows how an old computational tool can be adapted to serve a new purpose. When I started in compchem...
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Seeing is Believing: Brain-Inspired Modular Training for Mechanistic...
Ziming Liu, Eric Gan, Max Tegmark (2023)Highlighted by Jan JensenAdapted from Figures 1 and 3 in the paper. (c) 2023 the authors While this fascinating paper is not about chemistry it could easily be...
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Evolutionary Multiobjective Optimization of Multiligand Metal Complexes in...
Hannes Kneiding, Ainara Nova, David Balcells (2023)Highlighted by Jan JensenFigure 5 from the paper. (c) 2023 the authors. Reproduced under the CC BY ND licenseThe authors show that an NBO analysis can...
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Real-World Molecular Out-Of-Distribution: Specification and Investigation
Prudencio Tossou, Cas Wognum, Michael Craig, Hadrien Mary, Emmanuel Noutahi (2023)Highlighted by Jan JensenPart of Figure 1 from this reportWhy do ML models perform much worse different test sets?...
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Accelerated dinuclear palladium catalyst identification through unsupervised...
Julian A. Hueffel, Theresa Sperger, Ignacio Funes-Ardoiz, Jas S. Ward, Kari Rissanen, Franziska Schoenebeck (2021)Highlighted by Jan JensenFigure 1 from the paper. (c) 2021 the authors.I've been...
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Ranking Pareto optimal solutions based on projection free energy
Ryo Tamura, Kei Terayama, Masato Sumita, and Koji Tsuda (2023)Highlighted by Jan JensenFigure 1 from the paper. (c) APS 2023. Reproduced under the CC-BY license.One of the main challenges in...
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Few-Shot Learning for Low-Data Drug Discovery
Daniel Vella and Jean-Paul Ebejer (2023)Highlighted by Jan JensenTOC graphic from the articleThis paper is an update and expansion to this seminal paper by Pande and co-workers (you should definitely...
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Growing strings in a chemical reaction space for searching retrosynthesis...
Federico Zipoli, Carlo Baldassari, Matteo Manica, Jannis Born, and Teodoro Laino (2023)Highlighted by Jan JensenPart of Figure 10 from the paper. (c) The authors 2023. Reproduced under the...
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Accurate transition state generation with an object-aware equivariant...
Chenru Duan, Yuanqi Du, Haojun Jia, and Heather J. Kulik (2023)Highlighted by Jan JensenPart of Figure 1 from the paper. As anyone who has tried it will know, finding TSs is one of the most difficult,...
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TS-Tools: Rapid and Automated Localization of Transition States Based on a...
Thijs Stuyver (2024)Highlighted by Jan JensenFigure 2 from the paper. (c) the author 2024 reproduced under the CC-BY-NC-ND licenceThis paper caught my eye for several reasons. It's an open source...
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AiZynth Impact on Medicinal Chemistry Practice at AstraZeneca
Jason D. Shields, Rachel Howells, Gillian Lamont, Yin Leilei, Andrew Madin, Christopher E. Reimann, Hadi Rezaei, Tristan Reuillon, Bryony Smith, Clare Thomson, Yuting Zhengc and Robert E. Ziegler...
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An evolutionary algorithm for interpretable molecular representations
Philipp M. Pflüger, Marius Kühnemund, Felix Katzenburg, Herbert Kuchen, and Frank Glorius (2024)Highlighted by Jan JensenParts of Figures 2 and 6 combined. (c) 2024 Elsevier, IncThis paper presents a...
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Invalid SMILES are beneficial rather than detrimental to chemical language...
Michael A. Skinnider (2024)Highlighted by Jan JensenFigure 3c from the paper. (c) The author. Reproduced under the CC-BY LicenseLanguage models (LMs) don't always produce valid SMILES and while for...
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FragGT: Fragment-based evolutionary molecule generation with gene types
Joshua Meyers and Nathan Brown (2024)Highlighted by Jan JensenFigure 1 from the paper. (c) The authors. Reproduced under the CC-BY licenseGenetic algorithms (GAs) allow for changes at the atom level...
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Using GNN property predictors as molecule generators
Félix Therrien, Edward H. Sargent, and Oleksandr Voznyy (2024)Highlighted by Jan JensenFigure 1 from the paper. (c) 2024 the authorsNow this is a very neat idea. Normally, we use back propagation to...
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Reproducing Reaction Mechanisms with Machine Learning Models Trained on a...
Joonyoung F. Joung, Mun Hong Fong, Jihye Roh, Zhengkai Tu, John Bradshaw, and Connor Wilson Coley (2024)Highlighted by Jan JensenFigure 1 from the paper. (c) the authors 2024If you don't follow this...
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Variational Pair-Density Functional Theory: Dealing with Strong Correlation...
Mikael Scott, Gabriel L. S. Rodrigues, Xin Li, and Mickael G. Delcey (2024)Highlighted by Jan JensenAs I've said before, one of the big problems in quantum chemistry is that we still can't routinely...
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Toy Models of Superposition
Nelson Elhage, Tristan Hume, Catherine Olsson, Nicholas Schiefer, Tom Henighan, Shauna Kravec, Zac Hatfield-Dodds, Robert Lasenby, Dawn Drain, Carol Chen, Roger Grosse, Sam McCandlish, Jared Kaplan,...
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Lifelong Machine Learning Potentials
Marco Eckhoff and Markus Reiher (2023)Highlighted by Jan JensenWhile machine learning potentials (MLPs) can give you DFT accuracy at FF costs, they also come with some practical problems: they often...
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The vDZP Basis Set Is Effective For Many Density Functionals
Corin C. Wagen and Jonathon E. Vandezande (2024)Highlighted by Jan JensenWhile this is an interesting paper, a cursory reading (like the one I did initially) can leave you with the wrong impression....
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dxtb —An efficient and fully differentiable framework for extended tight-binding
Marvin Friede, Christian Hölzer, Sebastian Ehlert, and Stefan Grimme (2024)Highlighted by Jan JensenWhen I first saw this paper on SoMe I was incredibly excited because I first thought it was the...
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Applying statistical modeling strategies to sparse datasets in synthetic...
Brittany C. Haas, Dipannita Kalyani, Matthew S. Sigman (2025)Highlighted by Jan JensenA few weeks ago I listened to an online talk by Matt Sigman and one thing that really surprised me was the...
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GOAT: A Global Optimization Algorithm for Molecules and Atomic Clusters
Bernardo de Souza (2025)Highlighted by Jan JensenIf you want to predict accurate reaction energies and barrier heights of typical organic molecules then you are spending a significant portion of CPU...
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Designing Target-specific Data Sets for Regioselectivity Predictions on...
Jules Schleinitz, Alba Carretero-Cerdán, Anjali Gurajapu, Yonatan Harnik, Gina Lee, Amitesh Pandey, Anat Milo, and Sarah Reisman (2025)Highlighted by Jan JensenHave you ever looked at a poorly...
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