Accurate Prediction of 1H NMR Chemical Shifts of Small Molecules Using Machine Learning (2024)

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Metabolites

Volume 14

Issue 5

10.3390/metabo14050290

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Article

by

Tanvir Sajed

Accurate Prediction of 1H NMR Chemical Shifts of Small Molecules Using Machine Learning (5)Tanvir Sajed

1,

Zinat Sayeeda

Accurate Prediction of 1H NMR Chemical Shifts of Small Molecules Using Machine Learning (6)Zinat Sayeeda

1,

Brian L. Lee

Accurate Prediction of 1H NMR Chemical Shifts of Small Molecules Using Machine Learning (7)Brian L. Lee

1,

Mark Berjanskii

Accurate Prediction of 1H NMR Chemical Shifts of Small Molecules Using Machine Learning (8)Mark Berjanskii

1,

Fei Wang

2,

Vasuk Gautam

Accurate Prediction of 1H NMR Chemical Shifts of Small Molecules Using Machine Learning (10)Vasuk Gautam

1Accurate Prediction of 1H NMR Chemical Shifts of Small Molecules Using Machine Learning (11) and

David S. Wishart

Accurate Prediction of 1H NMR Chemical Shifts of Small Molecules Using Machine Learning (12)David S. Wishart

1,2,3,4,*Accurate Prediction of 1H NMR Chemical Shifts of Small Molecules Using Machine Learning (13)

1

Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada

2

Department of Computing Science, University of Alberta Edmonton, AB T6G 2E8, Canada

3

Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, AB T6G 2B7, Canada

4

Faculty of Pharmacy and Pharmaceutical Sciences, University of Alberta, Edmonton, AB T6G 2H7, Canada

*

Author to whom correspondence should be addressed.

Metabolites 2024, 14(5), 290; https://doi.org/10.3390/metabo14050290

Submission received: 16 April 2024/Revised: 11 May 2024/Accepted: 16 May 2024/Published: 19 May 2024

(This article belongs to the Special Issue Metabolomics and Machine Learning for Improved Diagnostics and as a Tool to Accelerate Drug Development)

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Abstract

NMR is widely considered the gold standard for organic compound structure determination. As such, NMR is routinely used in organic compound identification, drug metabolite characterization, natural product discovery, and the deconvolution of metabolite mixtures in biofluids (metabolomics and exposomics). In many cases, compound identification by NMR is achieved by matching measured NMR spectra to experimentally collected NMR spectral reference libraries. Unfortunately, the number of available experimental NMR reference spectra, especially for metabolomics, medical diagnostics, or drug-related studies, is quite small. This experimental gap could be filled by predicting NMR chemical shifts for known compounds using computational methods such as machine learning (ML). Here, we describe how a deep learning algorithm that is trained on a high-quality, “solvent-aware” experimental dataset can be used to predict 1H chemical shifts more accurately than any other known method. The new program, called PROSPRE (PROton Shift PREdictor) can accurately (mean absolute error of <0.10 ppm) predict 1H chemical shifts in water (at neutral pH), chloroform, dimethyl sulfoxide, and methanol from a user-submitted chemical structure. PROSPRE (pronounced “prosper”) has also been used to predict 1H chemical shifts for >600,000 molecules in many popular metabolomic, drug, and natural product databases.

Keywords: NMR; chemical shift; machine learning; graph neural network; predictor

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MDPI and ACS Style

Sajed, T.; Sayeeda, Z.; Lee, B.L.; Berjanskii, M.; Wang, F.; Gautam, V.; Wishart, D.S.Accurate Prediction of 1H NMR Chemical Shifts of Small Molecules Using Machine Learning. Metabolites 2024, 14, 290.https://doi.org/10.3390/metabo14050290

AMA Style

Sajed T, Sayeeda Z, Lee BL, Berjanskii M, Wang F, Gautam V, Wishart DS.Accurate Prediction of 1H NMR Chemical Shifts of Small Molecules Using Machine Learning. Metabolites. 2024; 14(5):290.https://doi.org/10.3390/metabo14050290

Chicago/Turabian Style

Sajed, Tanvir, Zinat Sayeeda, Brian L. Lee, Mark Berjanskii, Fei Wang, Vasuk Gautam, and David S. Wishart.2024. "Accurate Prediction of 1H NMR Chemical Shifts of Small Molecules Using Machine Learning" Metabolites 14, no. 5: 290.https://doi.org/10.3390/metabo14050290

Note that from the first issue of 2016, this journal uses article numbers instead of page numbers. See further details here.

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MDPI and ACS Style

Sajed, T.; Sayeeda, Z.; Lee, B.L.; Berjanskii, M.; Wang, F.; Gautam, V.; Wishart, D.S.Accurate Prediction of 1H NMR Chemical Shifts of Small Molecules Using Machine Learning. Metabolites 2024, 14, 290.https://doi.org/10.3390/metabo14050290

AMA Style

Sajed T, Sayeeda Z, Lee BL, Berjanskii M, Wang F, Gautam V, Wishart DS.Accurate Prediction of 1H NMR Chemical Shifts of Small Molecules Using Machine Learning. Metabolites. 2024; 14(5):290.https://doi.org/10.3390/metabo14050290

Chicago/Turabian Style

Sajed, Tanvir, Zinat Sayeeda, Brian L. Lee, Mark Berjanskii, Fei Wang, Vasuk Gautam, and David S. Wishart.2024. "Accurate Prediction of 1H NMR Chemical Shifts of Small Molecules Using Machine Learning" Metabolites 14, no. 5: 290.https://doi.org/10.3390/metabo14050290

Note that from the first issue of 2016, this journal uses article numbers instead of page numbers. See further details here.

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Accurate Prediction of 1H NMR Chemical Shifts of Small Molecules Using Machine Learning (14)

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Accurate Prediction of 1H NMR Chemical Shifts of Small Molecules Using Machine Learning (2024)

FAQs

Accurate Prediction of 1H NMR Chemical Shifts of Small Molecules Using Machine Learning? ›

The new program, called PROSPRE (PROton Shift PREdictor) can accurately (mean absolute error of <0.10 ppm) predict 1H chemical shifts in water (at neutral pH), chloroform, dimethyl sulfoxide, and methanol from a user-submitted chemical structure.

How to predict NMR chemical shift? ›

When predicting chemical shifts, you need to watch for remote (not geminal) electronegative group/s. If a substituent has a remote electronegative group, an asterisk (*) is add to the chemical shift increment indicating that the chemical shift increment will be increased.

How to find chemical shift h nmr? ›

H NMR Chemical Shifts

Tetramethylsilan[TMS;(CH3)4Si] is generally used for standard to determine chemical shift of compounds: δTMS=0ppm. In other words, frequencies for chemicals are measured for a 1H or 13C nucleus of a sample from the 1H or 13C resonance of TMS.

What does a high chemical shift mean? ›

When a signal is found with a higher chemical shift: the applied effective magnetic field is lower, if the resonance frequency is fixed (as in old traditional CW spectrometers) the frequency is higher, when the applied magnetic field is static (normal case in FT spectrometers) the nucleus is more deshielded.

What is the symbol for chemical shift? ›

The chemical shift (δ) is therefore a small number, expressed in units of parts per million (ppm). The suffix ppm is interchangeable with x10 6, just as the symbol % is interchangeable with x0.

How do you predict H NMR splitting pattern? ›

To find the NMR splitting pattern, for a given hydrogen atom, count how many identical hydrogen atoms are adjacent, and then add one to that number. For example, in CH2ClCH3 below, the red hydrogen atoms are adjacent to three identical hydrogen atoms (marked in blue).

What is the formula for chemical shift of NMR? ›

NMR Chemical Shift

Formula V. 2.1, νeff = γ⋅Beff = γ⋅(1-σ )⋅Bo, indicates that the resonance frequency of a target spin-½ nucleus is defined by its intrinsic magnetic shielding property σ and the externally generated magnetic field Bo.

What is the N 1 rule for H NMR? ›

Splitting pattern reveals the N+1 Rule, which states that a peak's splitting pattern will be the number of neighboring protons (N) + 1. For example, a triplet peak indicates the hydrogen represented has 2 neighboring hydrogens.

What are the three major factors that influence chemical shifts? ›

Factors affecting the chemical shift include the molecular weight of the atom, the temperature of the reaction, the concentration of catalysts, and the solubility of the atom.

What causes low chemical shift in NMR? ›

There are two major factors that cause different chemical shifts (a) deshielding due to reduced electron density (due electronegative atoms) and (b) anisotropy (due to π bonds). Coupling = Due to the proximity of "n" other equivalent H atoms, causes the signals to be split into (n+1) lines.

Which proton will have the greatest chemical shift? ›

Aromatic protons have the highest chemical shift values because of their unique electronic environme...

Why is 1H NMR spectroscopy such a widely used technique? ›

1H NMR spectroscopy is widely used for determining the structure of chemical compounds because the spectra obtained contain the following characteristics: (1) resonance signals that are usually observed in different regions depending on the chemical structure of the analyte, (2) signals are split (3JH–H) by spin–spin ...

How does 1H NMR work? ›

An H-NMR (proton nuclear magnetic resonance) spectrum is generated by applying a strong magnetic field to a sample containing protons, such as a liquid or solid organic compound. The sample is placed in a magnetic field, and then a pulse of radio frequency energy is applied.

What does NMR tell you? ›

NMR spectra provide us with important information: The number of different absorptions (signals, peaks) implies how many different types of protons are present. The amount of shielding shown by these absorptions implies the electronic structure of the molecule close to each type of proton.

What is the formula for the chemical shift of NMR? ›

shift = δ × spectrometer frequency = 7.27 × 10⁻⁶ × 300 × 10⁶ Hz = 2181 Hz.

What determines chemical shift in C NMR? ›

C NMR Chemical Shifts

C chemical shift is affect by electronegative effect and steric effect. If an H atoms in an alkane is replace by substituent X, electronegative atoms (O, N, halogen), ?-carbon and ?-carbon shift to downfield (left; increase in ppm) while ?-carbon shifts to upfield.

What determines NMR shift? ›

The proton NMR chemical shift is affect by nearness to electronegative atoms (O, N, halogen.) and unsaturated groups (C=C,C=O, aromatic). Electronegative groups move to the down field (left; increase in ppm).

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