Literature DB >> 33428408

Predicting Density Functional Theory-Quality Nuclear Magnetic Resonance Chemical Shifts via Δ-Machine Learning.

Pablo A Unzueta1, Chandler S Greenwell1, Gregory J O Beran1.   

Abstract

First-principles prediction of nuclear magnetic resonance chemical shifts plays an increasingly important role in the interpretation of experimental spectra, but the required density functional theory (DFT) calculations can be computationally expensive. Promising machine learning models for predicting chemical shieldings in general organic molecules have been developed previously, though the accuracy of those models remains below that of DFT. The present study demonstrates how much higher accuracy chemical shieldings can be obtained via the Δ-machine learning approach, with the result that the errors introduced by the machine learning model are only one-half to one-third the errors expected for DFT chemical shifts relative to experiment. Specifically, an ensemble of neural networks is trained to correct PBE0/6-31G chemical shieldings up to the target level of PBE0/6-311+G(2d,p). It can predict 1H, 13C, 15N, and 17O chemical shieldings with root-mean-square errors of 0.11, 0.70, 1.69, and 2.47 ppm, respectively. At the same time, the Δ-machine learning approach is 1-2 orders of magnitude faster than the target large-basis calculations. It is also demonstrated that the machine learning model predicts experimental solution-phase NMR chemical shifts in drug molecules with only modestly worse accuracy than the target DFT model. Finally, the ability to estimate the uncertainty in the predicted shieldings based on variations within the ensemble of neural network models is also assessed.

Entities:  

Year:  2021        PMID: 33428408     DOI: 10.1021/acs.jctc.0c00979

Source DB:  PubMed          Journal:  J Chem Theory Comput        ISSN: 1549-9618            Impact factor:   6.006


  3 in total

1.  HMDB 5.0: the Human Metabolome Database for 2022.

Authors:  David S Wishart; AnChi Guo; Eponine Oler; Fei Wang; Afia Anjum; Harrison Peters; Raynard Dizon; Zinat Sayeeda; Siyang Tian; Brian L Lee; Mark Berjanskii; Robert Mah; Mai Yamamoto; Juan Jovel; Claudia Torres-Calzada; Mickel Hiebert-Giesbrecht; Vicki W Lui; Dorna Varshavi; Dorsa Varshavi; Dana Allen; David Arndt; Nitya Khetarpal; Aadhavya Sivakumaran; Karxena Harford; Selena Sanford; Kristen Yee; Xuan Cao; Zachary Budinski; Jaanus Liigand; Lun Zhang; Jiamin Zheng; Rupasri Mandal; Naama Karu; Maija Dambrova; Helgi B Schiöth; Russell Greiner; Vasuk Gautam
Journal:  Nucleic Acids Res       Date:  2022-01-07       Impact factor: 16.971

2.  NP-MRD: the Natural Products Magnetic Resonance Database.

Authors:  David S Wishart; Zinat Sayeeda; Zachary Budinski; AnChi Guo; Brian L Lee; Mark Berjanskii; Manoj Rout; Harrison Peters; Raynard Dizon; Robert Mah; Claudia Torres-Calzada; Mickel Hiebert-Giesbrecht; Dorna Varshavi; Dorsa Varshavi; Eponine Oler; Dana Allen; Xuan Cao; Vasuk Gautam; Andrew Maras; Ella F Poynton; Pegah Tavangar; Vera Yang; Jeffrey A van Santen; Rajarshi Ghosh; Saurav Sarma; Eleanor Knutson; Victoria Sullivan; Amy M Jystad; Ryan Renslow; Lloyd W Sumner; Roger G Linington; John R Cort
Journal:  Nucleic Acids Res       Date:  2022-01-07       Impact factor: 16.971

3.  A Machine Learning Model of Chemical Shifts for Chemically and Structurally Diverse Molecular Solids.

Authors:  Manuel Cordova; Edgar A Engel; Artur Stefaniuk; Federico Paruzzo; Albert Hofstetter; Michele Ceriotti; Lyndon Emsley
Journal:  J Phys Chem C Nanomater Interfaces       Date:  2022-09-23       Impact factor: 4.177

  3 in total

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