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arxiv: 2604.17357 · v1 · submitted 2026-04-19 · ⚛️ physics.chem-ph

A Chemical Space Perspective on Diastereomeric Barriers in Alkylperoxy-to-Hydroperoxyalkyl Isomerization

Raghunathan Ramakrishnan This is my paper

Pith reviewed 2026-05-10 05:39 UTC · model grok-4.3

classification ⚛️ physics.chem-ph
keywords diastereomeric barriersalkylperoxy isomerizationhydroperoxyalkyl radicalslow-temperature autooxidationsteric strainstereochemistry in combustionchemical spacetransition state energies
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The pith

Stereochemistry in low-temperature autooxidation makes some alkylperoxy isomerization barriers identical and others differ by over 60 kcal/mol due to steric strain.

A machine-rendered reading of the paper's core claim, the machinery that carries it, and where it could break.

The paper examines how the three-dimensional arrangement of atoms affects energy barriers during the isomerization of alkylperoxy radicals to hydroperoxyalkyl radicals in hydrocarbon autooxidation at low temperatures. By propagating stereochemical information through radical formation, oxygen addition, and the isomerization step across 498 small C1-C7 hydrocarbons, it generates density-functional-theory data for over five thousand species and confirms thousands of transition states. This reveals that diastereomeric pathways can be degenerate or separated by large energy gaps governed by steric effects at the peroxyl-bearing carbon. A reader would care because simplified models that ignore stereochemistry can miss kinetically relevant reaction channels and produce inaccurate rate estimates. The work supplies a concrete dataset and foundation for building stereochemistry-aware combustion mechanisms.

Core claim

Propagating stereochemical information from 498 C1-C7 hydrocarbons through radical formation, O2 addition, and ROO to QOOH isomerization produces DFT-level data for 5,356 species, including 2,324 cyclic diastereomeric transition states with connectivity verified by intrinsic reaction coordinate analysis. Explicit stereochemical treatment shows that diastereomeric pathways may be either degenerate or separated by more than 60 kcal/mol, with the magnitude of these differences governed by steric strain at the carbon bearing the peroxyl group. Constitutionally collapsed molecular representations therefore systematically miss kinetically relevant reactive channels.

What carries the argument

Diastereomeric transition states in ROO-to-QOOH isomerizations, whose energy differences are set by steric strain at the peroxyl-bearing carbon.

If this is right

  • Mechanism generation tools must retain stereochemical labels rather than collapsing to constitutional formulas.
  • Rate estimation methods need separate treatment of diastereomer-specific barriers when steric strain makes them non-degenerate.
  • Combustion models that ignore stereochemistry will overlook or misweight important reactive channels in low-temperature oxidation.
  • Predictive simulations of ignition and pollutant formation require stereochemistry-aware rate libraries built from data like this set.

Where Pith is reading between the lines

These are editorial extensions of the paper, not claims the author makes directly.

  • Extending the same stereochemical scan to larger fuel molecules could show even bigger impacts on ignition delay predictions.
  • Automated mechanism builders might incorporate rules derived from this chemical-space survey to generate diastereomer-specific pathways by default.
  • Similar steric-strain effects on diastereomeric barriers could appear in other radical isomerizations relevant to atmospheric oxidation.
  • The dataset offers a testbed for checking whether machine-learned potentials can reproduce these large stereochemical energy differences without explicit 3D input.

Load-bearing premise

The 498 C1-C7 hydrocarbons and the chosen DFT calculations with IRC confirmation are representative enough to generalize the stereochemical effects to real low-temperature autooxidation systems.

What would settle it

A laboratory measurement of product formation rates or effective barriers for a specific ROO-to-QOOH isomerization known to have non-degenerate diastereomeric paths that either matches or contradicts the predicted energy gap larger than 60 kcal/mol.

Figures

Figures reproduced from arXiv: 2604.17357 by Raghunathan Ramakrishnan.

Figure 1
Figure 1. Figure 1: Workflow for generating cyclic transition states for the [PITH_FULL_IMAGE:figures/full_fig_p005_1.png] view at source ↗
Figure 2
Figure 2. Figure 2: Workflow used to generate stereochemically resolved SMILES of the species studied [PITH_FULL_IMAGE:figures/full_fig_p007_2.png] view at source ↗
Figure 3
Figure 3. Figure 3: Workflow for the quantum chemistry data generation and characterization of [PITH_FULL_IMAGE:figures/full_fig_p009_3.png] view at source ↗
Figure 4
Figure 4. Figure 4: Workflow used to diagnose connectivity mapping in 2,356 IRC calculations for [PITH_FULL_IMAGE:figures/full_fig_p012_4.png] view at source ↗
Figure 5
Figure 5. Figure 5: Joint distribution of reaction energies and forward barrier heights for 1,162 [PITH_FULL_IMAGE:figures/full_fig_p014_5.png] view at source ↗
Figure 6
Figure 6. Figure 6: Histogram of difference in electronic energies between diastereomeric transition [PITH_FULL_IMAGE:figures/full_fig_p015_6.png] view at source ↗
Figure 7
Figure 7. Figure 7: Energy difference between diastereomeric transition states, ∆∆ [PITH_FULL_IMAGE:figures/full_fig_p016_7.png] view at source ↗
Figure 8
Figure 8. Figure 8: Violin-plot distribution of diastereomeric barrier differences for [PITH_FULL_IMAGE:figures/full_fig_p017_8.png] view at source ↗
Figure 9
Figure 9. Figure 9: Ratio of the total rate constant for two parallel pathways, [PITH_FULL_IMAGE:figures/full_fig_p019_9.png] view at source ↗
Figure 10
Figure 10. Figure 10: Energy profiles for selected R • + O2 → ROO• → •QOOH reactions, showing the relative energies of R • + O2, all located ROO• conformers, the two diastereomeric transition￾state structures, and all located •QOOH conformers. Numbers in parentheses indicate the number of conformers identified for the corresponding ROO• and •QOOH wells. In the transition-state drawings, N is used in place of the abstracted H a… view at source ↗
read the original abstract

Low-temperature hydrocarbon autooxidation involves radical intermediates whose reactivity depends not only on the stereochemistry of the intermediates themselves, but also on that of the transient species encountered along the reaction path. This study offers large-scale evidence for the importance of stereochemistry in low-temperature autooxidation by propagating stereochemical information from 498 C1-C7 hydrocarbons through radical formation, $\mathrm{O_2}$ addition, and the isomerization of alkylperoxy ROO radicals to hydroperoxyalkyl QOOH radicals. The resulting dataset comprises density-functional-theory-level data for 5,356 species, including 2,324 cyclic diastereomeric transition states associated with 1,162 unique ROO -> QOOH isomerization reactions, with transition-state connectivity confirmed by intrinsic reaction coordinate analysis. Explicit stereochemical treatment reveals that diastereomeric pathways may be either degenerate or separated by more than 60 kcal/mol, with the magnitude of these differences governed by steric strain at the carbon bearing the peroxyl group. These results show that constitutionally collapsed molecular representations can systematically miss kinetically relevant reactive channels and provide a foundation for stereochemistry-aware mechanism generation, rate estimation, and predictive combustion modeling.

Editorial analysis

A structured set of objections, weighed in public.

Desk editor's note, referee report, simulated authors' rebuttal, and a circularity audit. Tearing a paper down is the easy half of reading it; the pith above is the substance, this is the friction.

Referee Report

2 major / 2 minor

Summary. The paper performs a large-scale DFT survey of stereochemical effects in ROO-to-QOOH isomerization for 498 C1-C7 hydrocarbons, producing data on 5,356 species and 2,324 IRC-confirmed cyclic diastereomeric transition states. It reports that diastereomeric pathways are either degenerate or separated by >60 kcal/mol, with the magnitude controlled by steric strain at the peroxyl-bearing carbon, and concludes that constitutionally collapsed representations systematically miss kinetically relevant channels.

Significance. If the reported energy separations hold, the work provides a valuable foundation for stereochemistry-aware mechanism generation and rate estimation in low-temperature autooxidation. The breadth of the 498-molecule survey and the consistent use of IRC verification for all 2,324 TS constitute clear strengths that could support improved predictive combustion models.

major comments (2)
  1. [Methods] Methods section: no benchmarking or error estimation is reported for the chosen DFT functional/basis set against higher-level methods (e.g., CCSD(T) single points) on the high-strain diastereomeric TS subset. Standard DFT errors of 4-10 kcal/mol in relative TS energies for sterically crowded peroxyl systems directly affect the load-bearing claim of separations >60 kcal/mol.
  2. [Results] Results on diastereomeric energy differences: the assertion that steric strain at the peroxyl carbon governs gaps >60 kcal/mol is presented without accompanying statistical distribution, error bars, or sensitivity analysis to functional choice, leaving the quantitative magnitude unsecured for the 1,162 unique reactions.
minor comments (2)
  1. [Abstract] The abstract and dataset description would benefit from explicit statement of the DFT functional, basis set, and dispersion correction employed.
  2. [Figures] Figure captions for the energy-difference distributions could clarify the binning and whether degenerate cases are included.

Simulated Author's Rebuttal

2 responses · 0 unresolved

We thank the referee for their constructive and detailed review of our manuscript. We have addressed each major comment below and describe the revisions that will be incorporated to improve the work.

read point-by-point responses

  1. Referee: [Methods] Methods section: no benchmarking or error estimation is reported for the chosen DFT functional/basis set against higher-level methods (e.g., CCSD(T) single points) on the high-strain diastereomeric TS subset. Standard DFT errors of 4-10 kcal/mol in relative TS energies for sterically crowded peroxyl systems directly affect the load-bearing claim of separations >60 kcal/mol.

    Authors: We acknowledge that the manuscript does not include explicit benchmarking of the chosen DFT functional and basis set against higher-level methods such as CCSD(T) for the diastereomeric transition states. The scale of the study (2,324 IRC-confirmed transition states) renders comprehensive higher-level calculations computationally prohibitive. However, the reported separations exceed 60 kcal/mol, which remains substantially larger than typical DFT errors of 4-10 kcal/mol even after accounting for such uncertainties; this preserves the conclusion that diastereomeric channels are kinetically distinct. In the revised manuscript, we will add a dedicated discussion of expected error ranges drawn from literature benchmarks on similar peroxyl and hydroperoxyl systems and will include a limited benchmark study on a representative subset of high-strain diastereomeric TS pairs to provide quantitative support for the error estimates. revision: partial

  2. Referee: [Results] Results on diastereomeric energy differences: the assertion that steric strain at the peroxyl carbon governs gaps >60 kcal/mol is presented without accompanying statistical distribution, error bars, or sensitivity analysis to functional choice, leaving the quantitative magnitude unsecured for the 1,162 unique reactions.

    Authors: We agree that a statistical presentation of the energy differences would strengthen the results section. The manuscript currently highlights the maximum observed separation (>60 kcal/mol) and links it to steric strain at the peroxyl-bearing carbon through structural inspection of the IRC-verified transition states. We will revise the manuscript to include a histogram (or cumulative distribution) of the diastereomeric barrier differences across all 1,162 reactions, together with summary statistics (mean, median, and standard deviation). Because all data were generated at a single consistent level of theory, relative comparisons within the dataset remain reliable; we will explicitly note this and discuss the absence of a full functional-sensitivity analysis as a limitation while emphasizing that the large magnitude of the observed gaps supports the qualitative conclusions. revision: yes

Circularity Check

0 steps flagged

No significant circularity; forward computational survey

full rationale

The manuscript is a large-scale DFT computational survey that propagates stereochemical labels through radical formation, O2 addition, and ROO→QOOH isomerization for 498 C1–C7 hydrocarbons, producing 5356 species and 2324 IRC-confirmed diastereomeric transition states. No equations, fitted parameters, or self-citations are invoked to derive the central claim; the reported energy gaps (including >60 kcal/mol separations) are direct numerical outputs of the chosen level of theory applied to explicitly enumerated stereoisomers. The work therefore contains no self-definitional, fitted-input, or self-citation-load-bearing reductions and is self-contained against external benchmarks.

Axiom & Free-Parameter Ledger

0 free parameters · 1 axioms · 0 invented entities

The central claim depends on the accuracy of DFT for relative transition-state energies and on the representativeness of the chosen hydrocarbon set; no explicit free parameters or new entities are introduced in the abstract.

axioms (1)
  • domain assumption Density functional theory calculations yield reliable relative energies for the diastereomeric transition states in ROO to QOOH isomerizations.
    Invoked by the use of DFT-level data without further validation details in the abstract.

pith-pipeline@v0.9.0 · 5508 in / 1262 out tokens · 34075 ms · 2026-05-10T05:39:16.376102+00:00 · methodology

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