Accurate prediction of <sup>11</sup>B NMR chemical shift of BODIPYs <i>via</i> machine learning

Ksenofontov, Alexander A.; Isaev, Yaroslav; Lukanov, Michail M.; Makarov, Dmitriy M.; Eventova, Varvara; Khodov, Ilya A.; Березин, М. Б.

doi:10.1039/d3cp00253e

Cited by 5 publications

(3 citation statements)

References 79 publications

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“…More specifically, in Bruker NMR systems, having two spectra, for example, 1 H and, e.g., 14 N or 19 F, after referencing the first (in Method A or, much better, using Method B), the second spectrum is usually standardized indirectly [73] with respect to the 1 H frequency using the xiref referencing macro implemented in TopSpin software. Importantly, it avoids the widespread, but now not-recommended, use of primary external standards, namely 15% BF 3 •OEt 2 in CDCl 3 , neat CH 3 NO 2 , neat CFCl 3 , and 85% H 3 PO 4 , respectively [12,[77][78][79], which is usually less accurate and sometimes very dangerous. In fact, it can be assumed that the death of an academic chemist as a result of exposure to liquid Me 2 Hg (external reference for 199 Hg NMR spectroscopy) accelerated the introduction of this universal procedure at the expense of using the highly problematic Method E [80][81][82].…”

Section: Methods For 1 H/ 13 C Chemical Shift Referencementioning

confidence: 99%

On the Use of Deuterated Organic Solvents without TMS to Report 1H/13C NMR Spectral Data of Organic Compounds: Current State of the Method, Its Pitfalls and Benefits, and Related Issues

Nazarski

2023

Molecules

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The quite popular, simple but imperfect method of referencing NMR spectra to residual 1H and 13C signals of TMS-free deuterated organic solvents (referred to as Method A) is critically discussed for six commonly used NMR solvents with respect to their δH and δC data that exist in the literature. Taking into account the most reliable data, it was possible to recommend ‘best’ δX values for such secondary internal standards. The position of these reference points on the δ scale strongly depends on the concentration and type of analyte under study and the solvent medium used. For some solvents, chemically induced shifts (CISs) of residual 1H lines were considered, also taking into account the formation of 1:1 molecular complexes (for CDCl3). Typical potential errors that can occur as a result of improper application of Method A are considered in detail. An overview of all found δX values adopted by users of this method revealed a discrepancy of up to 1.9 ppm in δC reported for CDCl3, most likely caused by the CIS mentioned above. The drawbacks of Method A are discussed in relation to the classical use of an internal standard (Method B), two ‘instrumental’ schemes in which Method A is often implicitly applied, that is, the default Method C using 2H lock frequencies and Method D based on Ξ values, recommended by the IUPAC but only occasionally used for 1H/13C spectra, and external referencing (Method E). Analysis of current needs and opportunities for NMR spectrometers led to the conclusion that, for the most accurate application of Method A, it is necessary to (a) use dilute solutions in a single NMR solvent and (b) to report δX data applied for the reference 1H/13C signals to the nearest 0.001/0.01 ppm to ensure the precise characterization of new synthesized or isolated organic systems, especially those with complex or unexpected structures. However, the use of TMS in Method B is strongly recommended in all such cases.

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Section: Methods For 1 H/ 13 C Chemical Shift Referencementioning

confidence: 99%

On the Use of Deuterated Organic Solvents without TMS to Report 1H/13C NMR Spectral Data of Organic Compounds: Current State of the Method, Its Pitfalls and Benefits, and Related Issues

Nazarski

2023

Molecules

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“…In this context, it is essential to know the properties and possible use of emerging compounds, so that they can be of benefit for different applications. It should be noted that recent studies have implemented a machine learning algorithm to predict 11 B NMR chemical shifts in emerging organic compounds, adding techniques and methodology for spectral studies [28]. In this sense, it is important to have a detailed knowledge of the physical and chemical characteristics of the molecule, as well as its electronic properties.…”

Section: Introductionmentioning

confidence: 99%

Optoelectronic Response to the Fluor Ion Bond on 4-(4,4,5,5-Tetramethyl-1,3,2-dioxoborolan-2-yl)benzaldehyde

Guevara,

Núñez,

Pérez

et al. 2024

IJMS

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Boronate esters are a class of compounds containing a boron atom bonded to two oxygen atoms in an ester group, often being used as precursors in the synthesis of other materials. The characterization of the structure and properties of esters is usually carried out by UV-visible, infrared, and nuclear magnetic resonance (NMR) spectroscopic techniques. With the aim to better understand our experimental data, in this article, the density functional theory (DFT) is used to analyze the UV-visible and infrared spectra, as well as the isotropic shielding and chemical shifts of the hydrogen atoms 1H, carbon 13C and boron 11B in the compound 4-(4,4,5,5-tetramethyl-1,3,2-dioxoborolan-2-yl)benzaldehyde. Furthermore, this study considers the change in its electronic and spectroscopic properties of this particular ester, when its boron atom is coordinated with a fluoride anion. The calculations were carried out using the LSDA and B3LYP functionals in Gaussian-16, and PBE in CASTEP. The results show that the B3LYP functional gives the best approximation to the experimental data. The formation of a coordinated covalent B–F bond highlights the remarkable sensitivity of the NMR chemical shifts of carbon, oxygen, and boron atoms and their surroundings. Furthermore, this bond also highlights the changes in the electron transitions bands n→π* and π→π* during the absorption and emission of a photon in the UV-vis, and in the stretching bands of the C=C bonds, and bending of BO2 in the infrared spectrum. This study not only contributes to the understanding of the properties of boronate esters but also provides important information on the interactions and responses optoelectronic of the compound when is bonded to a fluorine atom.

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“…Park et al found that isotropic 11 B NMR chemical shifts from the borosilicate minerals correlated with the local geometric parameters of the tetrahedrally coordinated B sites [8]. Ksenofontov et al provide a convenient tool and database that we collected for all researchers, that allows us to predict the 11 B NMR chemical shift of boron-containing dyes [9]. Reto Horst et al describe NMR spectroscopy as the Swiss army knife of drug discovery [10].…”

Section: Introductionmentioning

confidence: 99%

11B NMR of the Morphological Evolution of Traditional Chinese Medicine Borax

Li,

Yang,

Wang

et al. 2024

Molecules

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This article applies nuclear magnetic resonance technology to the study of boron-containing traditional Chinese medicine, in order to explore the morphological evolution of boron elements in traditional Chinese medicine. Borax is a traditional Chinese medicine with anti-corrosion, anti-inflammatory, antibacterial, and anticonvulsant effects. It is made by boiling, removing stones, and drying borax minerals like borate salts. This article introduces an 11B nuclear magnetic resonance method for identifying and characterizing boron-containing compounds in TCM. We applied this technology to borax aqueous solutions in different chemical environments and found that with boron mixed in the form of SP2 hybridization in equilateral triangles and SP3 hybridization in equilateral tetrahedra, the pH changes in alkaline environments significantly affected the ratio of the two. At the same time, it was found that in addition to the raw material peak, boron signals of other boron-containing compounds were also detected in 20 commercially available boron-containing TCM preparations. These new boron-containing compounds may be true pharmaceutical active ingredients, and adding them directly to the formula can improve quality and safety. This article describes the detection of 11B NMR in boron-containing traditional Chinese medicine preparations. It is simple, non-destructive, and can provide chemical fingerprint studies for boron-containing traditional Chinese medicine.

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Accurate prediction of ¹¹B NMR chemical shift of BODIPYs via machine learning

Abstract: In this article, we present the results of developing a model based on RFR machine learning method using the ISIDA fragment descriptors for predicting the 11B NMR chemical shift of...

Cited by 5 publications

References 79 publications

On the Use of Deuterated Organic Solvents without TMS to Report 1H/13C NMR Spectral Data of Organic Compounds: Current State of the Method, Its Pitfalls and Benefits, and Related Issues

On the Use of Deuterated Organic Solvents without TMS to Report 1H/13C NMR Spectral Data of Organic Compounds: Current State of the Method, Its Pitfalls and Benefits, and Related Issues

Optoelectronic Response to the Fluor Ion Bond on 4-(4,4,5,5-Tetramethyl-1,3,2-dioxoborolan-2-yl)benzaldehyde

11B NMR of the Morphological Evolution of Traditional Chinese Medicine Borax

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Accurate prediction of 11B NMR chemical shift of BODIPYs via machine learning

Abstract: In this article, we present the results of developing a model based on RFR machine learning method using the ISIDA fragment descriptors for predicting the 11B NMR chemical shift of...

Cited by 5 publications

References 79 publications

On the Use of Deuterated Organic Solvents without TMS to Report 1H/13C NMR Spectral Data of Organic Compounds: Current State of the Method, Its Pitfalls and Benefits, and Related Issues

On the Use of Deuterated Organic Solvents without TMS to Report 1H/13C NMR Spectral Data of Organic Compounds: Current State of the Method, Its Pitfalls and Benefits, and Related Issues

Optoelectronic Response to the Fluor Ion Bond on 4-(4,4,5,5-Tetramethyl-1,3,2-dioxoborolan-2-yl)benzaldehyde

11B NMR of the Morphological Evolution of Traditional Chinese Medicine Borax

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Accurate prediction of ¹¹B NMR chemical shift of BODIPYs via machine learning