Journal article
An automated framework for NMR chemical shift calculations of small organic molecules
Journal of cheminformatics, Vol.10(1), pp.1-16
12/2018
Handle:
https://hdl.handle.net/2376/103622
PMCID: PMC6755567
PMID: 30367288
Abstract
When using nuclear magnetic resonance (NMR) to assist in chemical identification in complex samples, researchers commonly rely on databases for chemical shift spectra. However, authentic standards are typically depended upon to build libraries experimentally. Considering complex biological samples, such as blood and soil, the entirety of NMR spectra required for all possible compounds would be infeasible to ascertain due to limitations of available standards and experimental processing time. As an alternative, we introduce the in silico Chemical Library Engine (ISiCLE) NMR chemical shift module to accurately and automatically calculate NMR chemical shifts of small organic molecules through use of quantum chemical calculations. ISiCLE performs density functional theory (DFT)-based calculations for predicting chemical properties—specifically NMR chemical shifts in this manuscript—via the open source, high-performance computational chemistry software, NWChem. ISiCLE calculates the NMR chemical shifts of sets of molecules using any available combination of DFT method, solvent, and NMR-active nuclei, using both user-selected reference compounds and/or linear regression methods. Calculated NMR chemical shifts are provided to the user for each molecule, along with comparisons with respect to a number of metrics commonly used in the literature. Here, we demonstrate ISiCLE using a set of 312 molecules, ranging in size up to 90 carbon atoms. For each, calculation of NMR chemical shifts have been performed with 8 different levels of DFT theory, and with solvation effects using the implicit solvent Conductor-like Screening Model. The DFT method dependence of the calculated chemical shifts have been systematically investigated through benchmarking and subsequently compared to experimental data available in the literature. Furthermore, ISiCLE has been applied to a set of 80 methylcyclohexane conformers, combined via Boltzmann weighting and compared to experimental values. We demonstrate that our protocol shows promise in the automation of chemical shift calculations and, ultimately, the expansion of chemical shift libraries.
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Details
- Title
- An automated framework for NMR chemical shift calculations of small organic molecules
- Creators
- Yasemin Yesiltepe - Pullman, WA USAJamie R Nuñez - Richland, WA USASean M Colby - Richland, WA USADennis G Thomas - Richland, WA USAMark I Borkum - Richland, WA USAPatrick N Reardon - Corvallis, OR 97331 USANancy M Washton - Richland, WA USAThomas O Metz - Richland, WA USAJustin G Teeguarden - Richland, WA USANiranjan Govind - Richland, WA USARyan S Renslow - Pullman, WA USA
- Publication Details
- Journal of cheminformatics, Vol.10(1), pp.1-16
- Academic Unit
- Chemical Engineering and Bioengineering, School of
- Publisher
- Springer International Publishing; Cham
- Grant note
- Microbiomes in Transition (MinT) Initiative / ;
- Identifiers
- 99900546617801842
- Language
- English
- Resource Type
- Journal article