DP4+App: Finding the Best Balance between Computational Cost and Predictive Capacity in the Structure Elucidation Process by DP4+. Factors Analysis and Automation

J Nat Prod. 2023 Oct 27;86(10):2360-2367. doi: 10.1021/acs.jnatprod.3c00566. Epub 2023 Sep 18.

Abstract

DP4+ is one of the most popular methods for the structure elucidation of natural products using NMR calculations. While the method is simple and easy to implement, it requires a series of procedures that can be tedious, coupled with the fact that its computational demand can be high in certain cases. In this work, we made a substantial improvement to these limitations. First, we deeply explored the effect of molecular mechanics architecture on the DP4+ formalism (MM-DP4+). In addition, a Python applet (DP4+App) was developed to automate the entire process, requiring only the Gaussian NMR output files and a spreadsheet containing the experimental NMR data and labels. The script is designed to use the statistical parameters from the original 24 levels of theory (employing B3LYP/6-31G* geometries) and the new 36 levels explored in this work (over MMFF geometries). Furthermore, it enables the development of customizable methods using any desired level of theory, allowing for a free choice of test molecules.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Automation
  • Biological Products* / chemistry
  • Magnetic Resonance Spectroscopy / methods
  • Mobile Applications*
  • Molecular Dynamics Simulation
  • Molecular Structure

Substances

  • Biological Products