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Updated: Mar 29, 2026

An Efficient Method for the Synthesis of Peptoids with Mixed Lysine-type/Arginine-type Monomers and Evaluation of Their Anti-leishmanial Activity

An Efficient Method for the Synthesis of Peptoids with Mixed Lysine-type/Arginine-type Monomers and Evaluation of Their Anti-leishmanial Activity

Published on: November 2, 2016

Performance Evaluation of the Three-Layer ONIOM Method: Case Study for a Zwitterionic Peptide.

Keiji Morokuma¹, Qingfang Wang¹, Thom Vreven¹

¹Cherry L. Emerson Center for Scientific Computation and Department of Chemistry, Emory University, Atlanta, Georgia 30322, and Gaussian, Inc., 340 Quinnipiac Street, Building 40, Wallingford, Connecticut 06492.

Journal of Chemical Theory and Computation

|December 3, 2015

Summary

The three-layer ONIOM method offers a reliable and stable approach for studying zwitterionic peptide molecules. This computational chemistry technique provides the best balance between accuracy and cost for deprotonation energy calculations.

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Published on: September 7, 2019

Area of Science:

Computational Chemistry
Biophysical Chemistry

Background:

The ONIOM (Our Own N-layered Integrated molecular Orbital and molecular Mechanics) method is a powerful tool for modeling large molecular systems.
Accurate calculation of deprotonation energies in zwitterionic peptides is crucial for understanding their biochemical behavior.

Purpose of the Study:

To systematically investigate the performance of the three-layer ONIOM method for zwitterionic peptide calculations.
To compare different ONIOM combinations for optimized geometries and deprotonation energies.

Main Methods:

The study employed the three-layer ONIOM method with various combinations of high-level quantum (B3LYP/6-31G*), low-level quantum (AM1), and molecular mechanics (Amber) methods.
Optimized geometries and deprotonation energies of a model zwitterionic peptide were calculated.

Main Results:

The three-layer ONIOM(HQ:LQ:MM) method demonstrated superior reliability and stability compared to QM:MM:MM or generic QM/MM approaches.
This method effectively accounts for electronic effects and mitigates issues at the QM-MM boundary.

Conclusions:

The three-layer ONIOM method, incorporating a medium-level quantum method, represents the optimal compromise between accuracy and computational efficiency for zwitterionic peptide deprotonation energy calculations.
This approach enhances the predictive power of computational studies in biophysical chemistry.