Molecular dynamics-guided reaction discovery reveals endoperoxide-to-alkoxy radical isomerization as key branching point in α-pinene ozonolysis

Huan Yang; Umberto Raucci; Siddharth Iyer; Galib Hasan; Thomas Golin Almeida; Shawon Barua; Anni Savolainen; Juha Kangasluoma; Matti Rissanen; Hanna Vehkamäki; Theo Kurtén

doi:10.1038/s41467-025-55985-w

Molecular dynamics-guided reaction discovery reveals endoperoxide-to-alkoxy radical isomerization as key branching point in α-pinene ozonolysis

Huan Yang^*, Umberto Raucci^*, Siddharth Iyer, Galib Hasan, Thomas Golin Almeida, Shawon Barua, Anni Savolainen, Juha Kangasluoma, Matti Rissanen, Hanna Vehkamäki, Theo Kurtén^*

^*Corresponding author for this work

Research output: Contribution to journal/Conference contribution in journal/Contribution to newspaper › Journal article › Research › peer-review

Abstract

Secondary organic aerosols (SOAs) significantly impact Earth’s climate and human health. Although the oxidation of volatile organic compounds (VOCs) has been recognized as the major contributor to the atmospheric SOA budget, the mechanisms by which this process produces SOA-forming highly oxygenated organic molecules (HOMs) remain unclear. A major challenge is navigating the complex chemical landscape of these transformations, which traditional hypothesis-driven methods fail to thoroughly investigate. Here, we explore the oxidation of α-pinene, a critical atmospheric biogenic VOC, using a novel reaction discovery approach based on molecular dynamics and state-of-the-art enhanced sampling techniques. Our approach successfully identifies all established reaction pathways of α-pinene ozonolysis, as well as discovers multiple novel species and pathways without relying on a priori chemical knowledge. In particular, we unveil a key branching point that leads to the rapid formation of alkoxy radicals, whose high and diverse reactivity help to explain hitherto unexplained oxidation pathways suggested by mass spectral peaks observed in α-pinene ozonolysis experiments. This branching point is likely prevalent across a variety of atmospheric VOCs and could be crucial in establishing the missing link to SOA-forming HOMs.

Original language	English
Article number	661
Journal	Nature Communications
Volume	16
Issue	1
Number of pages	12
ISSN	2041-1723
DOIs	https://doi.org/10.1038/s41467-025-55985-w
Publication status	Published - Dec 2025
Externally published	Yes

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Yang, H., Raucci, U., Iyer, S., Hasan, G., Golin Almeida, T., Barua, S., Savolainen, A., Kangasluoma, J., Rissanen, M., Vehkamäki, H., & Kurtén, T. (2025). Molecular dynamics-guided reaction discovery reveals endoperoxide-to-alkoxy radical isomerization as key branching point in α-pinene ozonolysis. Nature Communications, 16(1), Article 661. https://doi.org/10.1038/s41467-025-55985-w

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title = "Molecular dynamics-guided reaction discovery reveals endoperoxide-to-alkoxy radical isomerization as key branching point in α-pinene ozonolysis",

abstract = "Secondary organic aerosols (SOAs) significantly impact Earth{\textquoteright}s climate and human health. Although the oxidation of volatile organic compounds (VOCs) has been recognized as the major contributor to the atmospheric SOA budget, the mechanisms by which this process produces SOA-forming highly oxygenated organic molecules (HOMs) remain unclear. A major challenge is navigating the complex chemical landscape of these transformations, which traditional hypothesis-driven methods fail to thoroughly investigate. Here, we explore the oxidation of α-pinene, a critical atmospheric biogenic VOC, using a novel reaction discovery approach based on molecular dynamics and state-of-the-art enhanced sampling techniques. Our approach successfully identifies all established reaction pathways of α-pinene ozonolysis, as well as discovers multiple novel species and pathways without relying on a priori chemical knowledge. In particular, we unveil a key branching point that leads to the rapid formation of alkoxy radicals, whose high and diverse reactivity help to explain hitherto unexplained oxidation pathways suggested by mass spectral peaks observed in α-pinene ozonolysis experiments. This branching point is likely prevalent across a variety of atmospheric VOCs and could be crucial in establishing the missing link to SOA-forming HOMs.",

author = "Huan Yang and Umberto Raucci and Siddharth Iyer and Galib Hasan and {Golin Almeida}, Thomas and Shawon Barua and Anni Savolainen and Juha Kangasluoma and Matti Rissanen and Hanna Vehkam{\"a}ki and Theo Kurt{\'e}n",

note = "Publisher Copyright: {\textcopyright} The Author(s) 2025.",

year = "2025",

month = dec,

doi = "10.1038/s41467-025-55985-w",

language = "English",

volume = "16",

journal = "Nature Communications",

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Yang, H, Raucci, U, Iyer, S, Hasan, G, Golin Almeida, T, Barua, S, Savolainen, A, Kangasluoma, J, Rissanen, M, Vehkamäki, H & Kurtén, T 2025, 'Molecular dynamics-guided reaction discovery reveals endoperoxide-to-alkoxy radical isomerization as key branching point in α-pinene ozonolysis', Nature Communications, vol. 16, no. 1, 661. https://doi.org/10.1038/s41467-025-55985-w

Molecular dynamics-guided reaction discovery reveals endoperoxide-to-alkoxy radical isomerization as key branching point in α-pinene ozonolysis. / Yang, Huan; Raucci, Umberto; Iyer, Siddharth et al.
In: Nature Communications, Vol. 16, No. 1, 661, 12.2025.

Research output: Contribution to journal/Conference contribution in journal/Contribution to newspaper › Journal article › Research › peer-review

TY - JOUR

T1 - Molecular dynamics-guided reaction discovery reveals endoperoxide-to-alkoxy radical isomerization as key branching point in α-pinene ozonolysis

AU - Yang, Huan

AU - Raucci, Umberto

AU - Iyer, Siddharth

AU - Hasan, Galib

AU - Golin Almeida, Thomas

AU - Barua, Shawon

AU - Savolainen, Anni

AU - Kangasluoma, Juha

AU - Rissanen, Matti

AU - Vehkamäki, Hanna

AU - Kurtén, Theo

PY - 2025/12

Y1 - 2025/12

N2 - Secondary organic aerosols (SOAs) significantly impact Earth’s climate and human health. Although the oxidation of volatile organic compounds (VOCs) has been recognized as the major contributor to the atmospheric SOA budget, the mechanisms by which this process produces SOA-forming highly oxygenated organic molecules (HOMs) remain unclear. A major challenge is navigating the complex chemical landscape of these transformations, which traditional hypothesis-driven methods fail to thoroughly investigate. Here, we explore the oxidation of α-pinene, a critical atmospheric biogenic VOC, using a novel reaction discovery approach based on molecular dynamics and state-of-the-art enhanced sampling techniques. Our approach successfully identifies all established reaction pathways of α-pinene ozonolysis, as well as discovers multiple novel species and pathways without relying on a priori chemical knowledge. In particular, we unveil a key branching point that leads to the rapid formation of alkoxy radicals, whose high and diverse reactivity help to explain hitherto unexplained oxidation pathways suggested by mass spectral peaks observed in α-pinene ozonolysis experiments. This branching point is likely prevalent across a variety of atmospheric VOCs and could be crucial in establishing the missing link to SOA-forming HOMs.

AB - Secondary organic aerosols (SOAs) significantly impact Earth’s climate and human health. Although the oxidation of volatile organic compounds (VOCs) has been recognized as the major contributor to the atmospheric SOA budget, the mechanisms by which this process produces SOA-forming highly oxygenated organic molecules (HOMs) remain unclear. A major challenge is navigating the complex chemical landscape of these transformations, which traditional hypothesis-driven methods fail to thoroughly investigate. Here, we explore the oxidation of α-pinene, a critical atmospheric biogenic VOC, using a novel reaction discovery approach based on molecular dynamics and state-of-the-art enhanced sampling techniques. Our approach successfully identifies all established reaction pathways of α-pinene ozonolysis, as well as discovers multiple novel species and pathways without relying on a priori chemical knowledge. In particular, we unveil a key branching point that leads to the rapid formation of alkoxy radicals, whose high and diverse reactivity help to explain hitherto unexplained oxidation pathways suggested by mass spectral peaks observed in α-pinene ozonolysis experiments. This branching point is likely prevalent across a variety of atmospheric VOCs and could be crucial in establishing the missing link to SOA-forming HOMs.

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U2 - 10.1038/s41467-025-55985-w

DO - 10.1038/s41467-025-55985-w

M3 - Journal article

C2 - 39809821

AN - SCOPUS:85215757644

SN - 2041-1723

VL - 16

JO - Nature Communications

JF - Nature Communications

IS - 1

M1 - 661

ER -

Molecular dynamics-guided reaction discovery reveals endoperoxide-to-alkoxy radical isomerization as key branching point in α-pinene ozonolysis

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