Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2024 Oct 7;161(13):134112.
doi: 10.1063/5.0221974.

Electrostatically embedded symmetry-adapted perturbation theory

Affiliations

Electrostatically embedded symmetry-adapted perturbation theory

Caroline S Glick et al. J Chem Phys. .

Abstract

Symmetry-adapted perturbation theory (SAPT) is an ab initio approach that directly computes noncovalent interaction energies in terms of electrostatics, exchange repulsion, induction/polarization, and London dispersion components. Due to its high computational scaling, routine applications of even the lowest order of SAPT are typically limited to a few hundred atoms. To address this limitation, we report here the addition of electrostatic embedding to the SAPT (EE-SAPT) and ISAPT (EE-ISAPT) methods. We illustrate the embedding scheme using water trimer as a prototype example. Then, we show that EE-SAPT/EE-ISAPT can be applied for efficiently and accurately computing noncovalent interactions in large systems, including solvated dimers and protein-ligand systems. In the latter application, particular care must be taken to properly handle the quantum mechanics/molecular mechanics boundary when it cuts covalent bonds. We investigate various schemes for handling charges near this boundary and demonstrate which are most effective in the context of charge-embedded SAPT.

PubMed Disclaimer

Conflict of interest statement

The authors have no conflicts to disclose.

References

    1. Cui Q., Pal T., and Xie L., “Biomolecular QM/MM simulations: What are some of the burning issues?,” J. Phys. Chem. B 125, 689–702 (2021).10.1021/acs.jpcb.0c09898 - DOI - PMC - PubMed
    1. Bondanza M., Nottoli M., Cupellini L., Lipparini F., and Mennucci B., “Polarizable embedding QM/MM: The future gold standard for complex (bio)systems?,” Phys. Chem. Chem. Phys. 22, 14433–14448 (2020).10.1039/d0cp02119a - DOI - PubMed
    1. Dohn A. O., “Multiscale electrostatic embedding simulations for modeling structure and dynamics of molecules in solution: A tutorial review,” Int. J. Quantum Chem. 120, e26343 (2020).10.1002/qua.26343 - DOI
    1. Huang J. and MacKerell A. D., “CHARMM36 all-atom additive protein force field: Validation based on comparison to NMR data,” J. Comput. Chem. 34, 2135–2145 (2013).10.1002/jcc.23354 - DOI - PMC - PubMed
    1. Maier J. A., Martinez C., Kasavajhala K., Wickstrom L., Hauser K. E., and Simmerling C., “ff14SB: Improving the accuracy of protein side chain and backbone parameters from ff99SB,” J. Chem. Theory Comput. 11, 3696–3713 (2015).10.1021/acs.jctc.5b00255 - DOI - PMC - PubMed

LinkOut - more resources