SpectroIBIS:多共形量子化学光谱计算的自动数据处理。

IF 3.6 2区 生物学 Q2 CHEMISTRY, MEDICINAL
Journal of Natural Products Pub Date : 2025-02-28 Epub Date: 2025-02-07 DOI:10.1021/acs.jnatprod.4c01321
Brodie W Bulcock, Yit-Heng Chooi, Gavin R Flematti
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引用次数: 0

摘要

量子化学光谱计算在天然产物研究中越来越流行,以帮助阐明化学结构,特别是它们的立体化学构型。随着现代计算速度的提高,这些计算变得越来越快,但随后的数据处理、检查和表示仍然是许多研究人员面临的关键瓶颈。在本文中,我们将介绍SpectroIBIS计算机程序,它是一种用户友好的工具,可以自动执行该工作流中常见的繁琐任务。通过简单的图形用户界面,研究人员可以拖放高斯或ORCA输出文件,以在几秒钟内产生玻尔兹曼平均ECD, VCD, UV-vis和IR数据,光学旋转和/或1H和13C NMR化学位移。此外,还生成了格式化的、具有出版质量的补充数据表,其中包含共形能量和原子坐标,并保存到与Microsoft Word和LibreOffice兼容的DOCX文件中。重要的是,SpectroIBIS可以通过自动检查冗余构象和虚频率来帮助研究人员发现常见的计算问题。其他有用的功能包括识别在更高的理论水平的构象能量重新计算,并自动生成输入文件的量子化学程序与可选的高能构象排除。最后,我们证明了SpectroIBIS对五种天然产物的光谱计算的适用性。SpectroIBIS是一个开源软件,可以作为免费的桌面应用程序获得(https://github.com/bbulcock/SpectroIBIS)。
本文章由计算机程序翻译,如有差异,请以英文原文为准。
SpectroIBIS: Automated Data Processing for Multiconformer Quantum Chemical Spectroscopic Calculations.

Quantum chemical spectroscopic calculations have grown increasingly popular in natural products research for aiding the elucidation of chemical structures, especially their stereochemical configurations. These calculations have become faster with modern computational speeds, but subsequent data handling, inspection, and presentation remain key bottlenecks for many researchers. In this article, we introduce the SpectroIBIS computer program as a user-friendly tool to automate tedious tasks commonly encountered in this workflow. Through a simple graphical user interface, researchers can drag and drop Gaussian or ORCA output files to produce Boltzmann-averaged ECD, VCD, UV-vis and IR data, optical rotations, and/or 1H and 13C NMR chemical shifts in seconds. Also produced are formatted, publication-quality supplementary data tables containing conformer energies and atomic coordinates, saved to a DOCX file compatible with Microsoft Word and LibreOffice. Importantly, SpectroIBIS can assist researchers in finding common calculation issues by automatically checking for redundant conformers and imaginary frequencies. Additional useful features include recognition of conformer energy recalculations at a higher theory level, and automated generation of input files for quantum chemistry programs with optional exclusion of high-energy conformers. Lastly, we demonstrate the applicability of SpectroIBIS with spectroscopic calculations for five natural products. SpectroIBIS is open-source software available as a free desktop application (https://github.com/bbulcock/SpectroIBIS).

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来源期刊
CiteScore
9.10
自引率
5.90%
发文量
294
审稿时长
2.3 months
期刊介绍: The Journal of Natural Products invites and publishes papers that make substantial and scholarly contributions to the area of natural products research. Contributions may relate to the chemistry and/or biochemistry of naturally occurring compounds or the biology of living systems from which they are obtained. Specifically, there may be articles that describe secondary metabolites of microorganisms, including antibiotics and mycotoxins; physiologically active compounds from terrestrial and marine plants and animals; biochemical studies, including biosynthesis and microbiological transformations; fermentation and plant tissue culture; the isolation, structure elucidation, and chemical synthesis of novel compounds from nature; and the pharmacology of compounds of natural origin. When new compounds are reported, manuscripts describing their biological activity are much preferred. Specifically, there may be articles that describe secondary metabolites of microorganisms, including antibiotics and mycotoxins; physiologically active compounds from terrestrial and marine plants and animals; biochemical studies, including biosynthesis and microbiological transformations; fermentation and plant tissue culture; the isolation, structure elucidation, and chemical synthesis of novel compounds from nature; and the pharmacology of compounds of natural origin.
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