An automated framework for NMR chemical shift calculations of small organic molecules.
An automated framework for NMR chemical shift calculations of small organic molecules.
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DOI：
10.1186/s13321-018-0305-8
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发表时间：
2018-10-26
影响因子：
8.6
通讯作者：
Renslow RS
中科院分区：
文献类型：
--
作者：
Yesiltepe Y;Nuñez JR;Colby SM;Thomas DG;Borkum MI;Reardon PN;Washton NM;Metz TO;Teeguarden JG;Govind N;Renslow RS
当使用核磁共振（NMR）来协助复杂样品的化学鉴定时，研究人员通常依赖于化学位移谱的数据库。然而，真实的标准通常依赖于实验性地构建文库。考虑到复杂的生物样品，如血液和土壤，由于可用标准品和实验处理时间的限制，无法确定所有可能化合物所需的全部NMR光谱。作为替代方案，我们引入了计算机化学库引擎（ISiCLE）NMR化学位移模块，通过使用量子化学计算来精确和自动计算小有机分子的NMR化学位移。ISiCLE通过开源高性能计算化学软件NWChem进行基于密度泛函理论（DFT）的计算，用于预测化学性质-特别是NMR化学位移。ISiCLE使用DFT方法、溶剂和NMR活性核的任何可用组合，使用用户选择的参比化合物和/或线性回归方法计算分子组的NMR化学位移。计算的NMR化学位移提供给用户的每一个分子，沿着比较相对于文献中常用的一些指标。在这里，我们使用一组312个分子来演示ISiCLE，这些分子的大小范围高达90个碳原子。对于每一个，NMR化学位移的计算已经进行了8个不同层次的DFT理论，并与溶剂化效应使用隐式溶剂导体样屏蔽模型。DFT方法的依赖性的计算化学位移已被系统地研究，通过基准测试和随后的文献中的实验数据进行比较。此外，ISiCLE已被应用到一组80甲基环己烷构象，通过玻尔兹曼加权相结合，并与实验值相比。我们证明，我们的协议显示的承诺，在自动化的化学位移计算，并最终扩大化学位移库。 本文的在线版本（10.1186/s13321-018-0305-8）包含补充材料，可供授权用户使用。
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. The online version of this article (10.1186/s13321-018-0305-8) contains supplementary material, which is available to authorized users.
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影响因子：
4.4
作者：
BECKE, AD
通讯作者：
BECKE, AD
影响因子：
2.9
作者：
Baldridge, KK;Siegel, JS
通讯作者：
Siegel, JS
影响因子：
1.6
作者：
Alver, Ozgur
通讯作者：
Alver, Ozgur
DOI：
10.1039/p29800000255
发表时间：
1980-01-01
期刊：
JOURNAL OF THE CHEMICAL SOCIETY-PERKIN TRANSACTIONS 2
影响因子：
--
作者：
BOOTH, H;EVERETT, JR
通讯作者：
EVERETT, JR
影响因子：
--
作者：
Aliev, Abil E.;Courtier-Murias, Denis;Zhou, Shen
通讯作者：
Zhou, Shen