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Electron iso-density surfaces provide a thermodynamically consistent representation of atomic and molecular surfaces

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  • Amin Alibakhshi

    (Ruhr University Bochum
    Ruhr University Bochum
    Research Alliance Ruhr
    Technical University Dortmund)

  • Lars V. Schäfer

    (Ruhr University Bochum)

Abstract

The surface area of atoms and molecules plays a crucial role in shaping many physiochemical properties of materials. Despite its fundamental importance, precisely defining atomic and molecular surfaces has long been a puzzle. Among the available definitions, a straightforward and elegant approach by Bader describes a molecular surface as an iso-density surface beyond which the electron density drops below a certain cut-off. However, so far neither this theory nor a decisive value for the density cut-off have been amenable to experimental verification due to the limitations of conventional experimental methods. In the present study, we employ a state-of-the-art experimental method based on the recently developed concept of thermodynamically effective (TE) surfaces to tackle this longstanding problem. By studying a set of 104 molecules, a close to perfect agreement between quantum chemical evaluations of iso-density surfaces contoured at a cut-off density of 0.0016 a.u. and experimental results obtained via thermodynamic phase change data is demonstrated, with a mean unsigned percentage deviation of 1.6% and a correlation coefficient of 0.995. Accordingly, we suggest the iso-density surface contoured at an electron density value of 0.0016 a.u. as a representation of the surface of atoms and molecules.

Suggested Citation

  • Amin Alibakhshi & Lars V. Schäfer, 2024. "Electron iso-density surfaces provide a thermodynamically consistent representation of atomic and molecular surfaces," Nature Communications, Nature, vol. 15(1), pages 1-7, December.
  • Handle: RePEc:nat:natcom:v:15:y:2024:i:1:d:10.1038_s41467-024-50408-8
    DOI: 10.1038/s41467-024-50408-8
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    References listed on IDEAS

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    1. Amin Alibakhshi & Bernd Hartke, 2021. "Improved prediction of solvation free energies by machine-learning polarizable continuum solvation model," Nature Communications, Nature, vol. 12(1), pages 1-7, December.
    2. Amin Alibakhshi & Bernd Hartke, 2022. "Implicitly perturbed Hamiltonian as a class of versatile and general-purpose molecular representations for machine learning," Nature Communications, Nature, vol. 13(1), pages 1-10, December.
    3. Yin Liu & Jie Wang & Sujung Kim & Haoye Sun & Fuyi Yang & Zixuan Fang & Nobumichi Tamura & Ruopeng Zhang & Xiaohui Song & Jianguo Wen & Bo Z. Xu & Michael Wang & Shuren Lin & Qin Yu & Kyle B. Tom & Ya, 2019. "Helical van der Waals crystals with discretized Eshelby twist," Nature, Nature, vol. 570(7761), pages 358-362, June.
    4. Yuan Liu & Yu Huang & Xiangfeng Duan, 2019. "Van der Waals integration before and beyond two-dimensional materials," Nature, Nature, vol. 567(7748), pages 323-333, March.
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