Literature DB >> 34232033

Combining Machine Learning and Computational Chemistry for Predictive Insights Into Chemical Systems.

John A Keith1, Valentin Vassilev-Galindo2, Bingqing Cheng3, Stefan Chmiela4, Michael Gastegger4, Klaus-Robert Müller5,6,7,8, Alexandre Tkatchenko2.   

Abstract

Machine learning models are poised to make a transformative impact on chemical sciences by dramatically accelerating computational algorithms and amplifying insights available from computational chemistry methods. However, achieving this requires a confluence and coaction of expertise in computer science and physical sciences. This Review is written for new and experienced researchers working at the intersection of both fields. We first provide concise tutorials of computational chemistry and machine learning methods, showing how insights involving both can be achieved. We follow with a critical review of noteworthy applications that demonstrate how computational chemistry and machine learning can be used together to provide insightful (and useful) predictions in molecular and materials modeling, retrosyntheses, catalysis, and drug design.

Entities:  

Year:  2021        PMID: 34232033      PMCID: PMC8391798          DOI: 10.1021/acs.chemrev.1c00107

Source DB:  PubMed          Journal:  Chem Rev        ISSN: 0009-2665            Impact factor:   60.622


  377 in total

1.  Revised Basis Sets for the LANL Effective Core Potentials.

Authors:  Lindsay E Roy; P Jeffrey Hay; Richard L Martin
Journal:  J Chem Theory Comput       Date:  2008-07       Impact factor: 6.006

2.  Definition and testing of the GROMOS force-field versions 54A7 and 54B7.

Authors:  Nathan Schmid; Andreas P Eichenberger; Alexandra Choutko; Sereina Riniker; Moritz Winger; Alan E Mark; Wilfred F van Gunsteren
Journal:  Eur Biophys J       Date:  2011-04-30       Impact factor: 1.733

3.  Unsupervised word embeddings capture latent knowledge from materials science literature.

Authors:  Vahe Tshitoyan; John Dagdelen; Leigh Weston; Alexander Dunn; Ziqin Rong; Olga Kononova; Kristin A Persson; Gerbrand Ceder; Anubhav Jain
Journal:  Nature       Date:  2019-07-03       Impact factor: 49.962

4.  General-Purpose Machine Learning Potentials Capturing Nonlocal Charge Transfer.

Authors:  Tsz Wai Ko; Jonas A Finkler; Stefan Goedecker; Jörg Behler
Journal:  Acc Chem Res       Date:  2021-01-29       Impact factor: 22.384

5.  Quantum fluctuations and isotope effects in ab initio descriptions of water.

Authors:  Lu Wang; Michele Ceriotti; Thomas E Markland
Journal:  J Chem Phys       Date:  2014-09-14       Impact factor: 3.488

6.  Ab Initio Potential Energy Surfaces and Quantum Dynamics for Polyatomic Bimolecular Reactions.

Authors:  Bina Fu; Dong H Zhang
Journal:  J Chem Theory Comput       Date:  2018-04-11       Impact factor: 6.006

7.  High-throughput experimentation meets artificial intelligence: a new pathway to catalyst discovery.

Authors:  Katherine McCullough; Travis Williams; Kathleen Mingle; Pooyan Jamshidi; Jochen Lauterbach
Journal:  Phys Chem Chem Phys       Date:  2020-05-12       Impact factor: 3.676

8.  Ensemble learning of coarse-grained molecular dynamics force fields with a kernel approach.

Authors:  Jiang Wang; Stefan Chmiela; Klaus-Robert Müller; Frank Noé; Cecilia Clementi
Journal:  J Chem Phys       Date:  2020-05-21       Impact factor: 3.488

9.  Application of Generative Autoencoder in De Novo Molecular Design.

Authors:  Thomas Blaschke; Marcus Olivecrona; Ola Engkvist; Jürgen Bajorath; Hongming Chen
Journal:  Mol Inform       Date:  2017-12-13       Impact factor: 3.353

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  16 in total

1.  A focus on simulation and machine learning as complementary tools for chemical space navigation.

Authors:  Matteo Aldeghi; Connor W Coley
Journal:  Chem Sci       Date:  2022-07-11       Impact factor: 9.969

2.  BIGDML-Towards accurate quantum machine learning force fields for materials.

Authors:  Huziel E Sauceda; Luis E Gálvez-González; Stefan Chmiela; Lauro Oliver Paz-Borbón; Klaus-Robert Müller; Alexandre Tkatchenko
Journal:  Nat Commun       Date:  2022-06-29       Impact factor: 17.694

3.  Fragmentation Method for Computing Quantum Mechanics and Molecular Mechanics Gradients for Force Matching: Validation with Hydration Free Energy Predictions Using Adaptive Force Matching.

Authors:  Dong Zheng; Ying Yuan; Feng Wang
Journal:  J Phys Chem A       Date:  2022-04-14       Impact factor: 2.944

4.  Detection of multi-reference character imbalances enables a transfer learning approach for virtual high throughput screening with coupled cluster accuracy at DFT cost.

Authors:  Chenru Duan; Daniel B K Chu; Aditya Nandy; Heather J Kulik
Journal:  Chem Sci       Date:  2022-04-05       Impact factor: 9.969

5.  SpookyNet: Learning force fields with electronic degrees of freedom and nonlocal effects.

Authors:  Oliver T Unke; Stefan Chmiela; Michael Gastegger; Kristof T Schütt; Huziel E Sauceda; Klaus-Robert Müller
Journal:  Nat Commun       Date:  2021-12-14       Impact factor: 14.919

6.  Inverse design of 3d molecular structures with conditional generative neural networks.

Authors:  Niklas W A Gebauer; Michael Gastegger; Stefaan S P Hessmann; Klaus-Robert Müller; Kristof T Schütt
Journal:  Nat Commun       Date:  2022-02-21       Impact factor: 17.694

7.  Machine learning potential for interacting dislocations in the presence of free surfaces.

Authors:  Daniele Lanzoni; Fabrizio Rovaris; Francesco Montalenti
Journal:  Sci Rep       Date:  2022-03-08       Impact factor: 4.379

8.  Predicting the future of excitation energy transfer in light-harvesting complex with artificial intelligence-based quantum dynamics.

Authors:  Arif Ullah; Pavlo O Dral
Journal:  Nat Commun       Date:  2022-04-11       Impact factor: 17.694

Review 9.  Natural language processing models that automate programming will transform chemistry research and teaching.

Authors:  Glen M Hocky; Andrew D White
Journal:  Digit Discov       Date:  2022-02-03

10.  Machine learning of material properties: Predictive and interpretable multilinear models.

Authors:  Alice E A Allen; Alexandre Tkatchenko
Journal:  Sci Adv       Date:  2022-05-06       Impact factor: 14.957

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