Literature DB >> 27364957

molSimplify: A toolkit for automating discovery in inorganic chemistry.

Efthymios I Ioannidis1, Terry Z H Gani1, Heather J Kulik1.   

Abstract

We present an automated, open source toolkit for the first-principles screening and discovery of new inorganic molecules and intermolecular complexes. Challenges remain in the automatic generation of candidate inorganic molecule structures due to the high variability in coordination and bonding, which we overcome through a divide-and-conquer tactic that flexibly combines force-field preoptimization of organic fragments with alignment to first-principles-trained metal-ligand distances. Exploration of chemical space is enabled through random generation of ligands and intermolecular complexes from large chemical databases. We validate the generated structures with the root mean squared (RMS) gradients evaluated from density functional theory (DFT), which are around 0.02 Ha/au across a large 150 molecule test set. Comparison of molSimplify results to full optimization with the universal force field reveals that RMS DFT gradients are improved by 40%. Seamless generation of input files, preparation and execution of electronic structure calculations, and post-processing for each generated structure aids interpretation of underlying chemical and energetic trends.
© 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

Entities:  

Keywords:  chemical discovery; first-principles simulation; high-throughput screening; python; structure generation

Year:  2016        PMID: 27364957     DOI: 10.1002/jcc.24437

Source DB:  PubMed          Journal:  J Comput Chem        ISSN: 0192-8651            Impact factor:   3.376


  14 in total

1.  The (not so) simple prediction of enantioselectivity - a pipeline for high-fidelity computations.

Authors:  Rubén Laplaza; Jan-Grimo Sobez; Matthew D Wodrich; Markus Reiher; Clémence Corminboeuf
Journal:  Chem Sci       Date:  2022-05-18       Impact factor: 9.969

2.  Predicting electronic structure properties of transition metal complexes with neural networks.

Authors:  Jon Paul Janet; Heather J Kulik
Journal:  Chem Sci       Date:  2017-05-17       Impact factor: 9.825

3.  Accurate Multiobjective Design in a Space of Millions of Transition Metal Complexes with Neural-Network-Driven Efficient Global Optimization.

Authors:  Jon Paul Janet; Sahasrajit Ramesh; Chenru Duan; Heather J Kulik
Journal:  ACS Cent Sci       Date:  2020-03-11       Impact factor: 14.553

4.  Machine learning dihydrogen activation in the chemical space surrounding Vaska's complex.

Authors:  Pascal Friederich; Gabriel Dos Passos Gomes; Riccardo De Bin; Alán Aspuru-Guzik; David Balcells
Journal:  Chem Sci       Date:  2020-04-07       Impact factor: 9.825

5.  Diversifying Databases of Metal Organic Frameworks for High-Throughput Computational Screening.

Authors:  Sauradeep Majumdar; Seyed Mohamad Moosavi; Kevin Maik Jablonka; Daniele Ongari; Berend Smit
Journal:  ACS Appl Mater Interfaces       Date:  2021-12-15       Impact factor: 9.229

6.  ChemSpaX: exploration of chemical space by automated functionalization of molecular scaffold.

Authors:  Adarsh V Kalikadien; Evgeny A Pidko; Vivek Sinha
Journal:  Digit Discov       Date:  2022-01-06

Review 7.  Towards operando computational modeling in heterogeneous catalysis.

Authors:  Lukáš Grajciar; Christopher J Heard; Anton A Bondarenko; Mikhail V Polynski; Jittima Meeprasert; Evgeny A Pidko; Petr Nachtigall
Journal:  Chem Soc Rev       Date:  2018-11-12       Impact factor: 54.564

8.  A data-driven perspective on the colours of metal-organic frameworks.

Authors:  Kevin Maik Jablonka; Seyed Mohamad Moosavi; Mehrdad Asgari; Christopher Ireland; Luc Patiny; Berend Smit
Journal:  Chem Sci       Date:  2020-12-28       Impact factor: 9.825

9.  Seeing Is Believing: Experimental Spin States from Machine Learning Model Structure Predictions.

Authors:  Michael G Taylor; Tzuhsiung Yang; Sean Lin; Aditya Nandy; Jon Paul Janet; Chenru Duan; Heather J Kulik
Journal:  J Phys Chem A       Date:  2020-04-09       Impact factor: 2.781

10.  A quantitative uncertainty metric controls error in neural network-driven chemical discovery.

Authors:  Jon Paul Janet; Chenru Duan; Tzuhsiung Yang; Aditya Nandy; Heather J Kulik
Journal:  Chem Sci       Date:  2019-07-11       Impact factor: 9.825

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