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            <r:String xml:lang="sv">Simuleringar av HCN polymerisation</r:String>
            <r:String xml:lang="en">Simulations of the beginnings of HCN polymerization</r:String>
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            <r:String xml:lang="sv">Data for "A Thermodynamic Landscape of Hydrogen Cyanide-Derived Molecules and Polymers"</r:String>
            <r:String xml:lang="en">Data for: "A Thermodynamic Landscape of Hydrogen Cyanide-Derived Molecules and Polymers"</r:String>
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            <a:FirstGiven>Marco</a:FirstGiven>
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              <r:String>Marco Cappelletti</r:String>
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              <r:String>Martin Rahm</r:String>
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        <r:String xml:lang="sv">Data för: "How does Adenine form from Hydrogen Cyanide?"</r:String>
        <r:String xml:lang="en">Data for: "How does Adenine form from Hydrogen Cyanide?"</r:String>
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          <r:String xml:lang="sv">Chalmers tekniska högskola</r:String>
          <r:String xml:lang="en">Chalmers University of Technology</r:String>
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      <r:Publisher>
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          <r:String xml:lang="sv">Chalmers tekniska högskola</r:String>
          <r:String xml:lang="en">Chalmers University of Technology</r:String>
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        <r:SimpleDate>2026-01-12</r:SimpleDate>
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      <r:Content xml:lang="sv">I denna studie presenterar vi en kvantkemisk utvärdering av troliga kemiska vägar från vätecyanid (HCN) till adenin.

Denna datauppsättning innehåller in- och utdatafilerna för de kvantkemiska beräkningarna, samt pythonkoden och resultaten av den mikrokinetiska modelleringen.

Geometrioptimeringar, frekvensanalys och intrinsisk reaktionskoordinat (IRC) beräkningar på DFT-nivå (B3LYP-D3BJ/6-31+G(d,p)) har utförts med programmet Gaussian16, revision B.01.
Enpunktsberäkningar med DLPNO-CCSD(T)/aug-cc-pVTZ har utförts med ORCA version 6.1.

Pythonkoden för den mikrokinetiska modelleringen har utvecklats av oss och använder LSODA-lösaren som implementerats i scipy-paketet. Koden genererar csv-filer som innehåller koncentrationerna av arterna vid olika tidpunkter.

Mappstruktur:
------------------------------------
calculations/
    species_1/
        1-expl-HCN/
        2-expl-HCN/
        ...
    species_2 /
        1-expl-HCN/
        2-expl-HCN/
        ...
    ...
    TS_1/
        1-expl-HCN/
        2-expl-HCN/
        ...
    TS_2/
        1-expl-HCN/
        2-expl-HCN/
        ...
    ...
    tautomers/
        species_4_imine-taut/
        ...
kinetic_modeling/
    KineticSolver/
    results/
        distributions/
        statistical_analysis/
------------------------------------


beräkningar/:
Den innehåller Gaussian16 och ORCA 6.1 in- och utdatafiler för beräkningar på arter (undermappar species_[n]) och övergångstillstånd (undermappar TS_[n]). Dessa undermappar innehåller beräkningar på alla solvatiseringsnivåer (upp till 5 explicita HCN-molekyler, i undermapparna [n]-expl-HCN/).
Undermappen tautomers/ innehåller beräkningar på artens imin-tautomerer, oavsett om den existerar. Dessa beräkningar har utförts med en explicit solvent HCN-molekyl.

kinetic_modeling/:
Den innehåller undermapparna KineticSolver/, med pythonkoden, och results/, där csv-filerna för resultaten finns.
distributions/ innehåller resultaten av alla (~50000) Monte Carlo-simuleringar, och statistical_analysis/ innehåller skriptet för att beräkna medianen och kvantilerna.</r:Content>
      <r:Content xml:lang="en">In this study, we present a quantum chemical evaluation of plausible chemical pathways from hydrogen cyanide (HCN) to adenine.

This dataset contains the input and output files of the quantum chemical calculations, as well as the python code, and the results, of the microkinetic modeling. 

Geometry optimizations, frequency analysis, and intrinsic reaction coordinate (IRC) calculations at the DFT level (B3LYP-D3BJ/6-31+G(d,p)) have been performed with the program Gaussian16, revision B.01.
Single-point calculations with DLPNO-CCSD(T)/aug-cc-pVTZ have been carried out using ORCA version 6.1. 

The python code for the microkinetic modeling has been developed by us, and it uses the LSODA solver as implemented in the scipy package. The code generates csv files containing the concentrations of the species at different times.

Folder structure:
------------------------------------
calculations/
    species_1/
        1-expl-HCN/
        2-expl-HCN/
        ...
    species_2 /
        1-expl-HCN/
        2-expl-HCN/
        ...
    ...
    TS_1/
        1-expl-HCN/
        2-expl-HCN/
        ...
    TS_2/
        1-expl-HCN/
        2-expl-HCN/
        ...
    ...
    tautomers/
        species_4_imine-taut/
        ...
kinetic_modeling/
    KineticSolver/
    results/
        distributions/
        statistical_analysis/
------------------------------------

calculations/:
It contains Gaussian16 and ORCA 6.1 input and output files of the calculations on species (species_[n] subfolders) and transition states (TS_[n] subfolders). These subfolder contains calculations on all solvation levels (up to 5 explicit HCN molecules, in the [n]-expl-HCN/ subsubfolders).
The tautomers/ subfolder contains the calculations on the imine tautomers of the species, whether it exists. These calculations have been performed with one explicit solvent HCN molecule.

kinetic_modeling/:
It contains the sub-folders KineticSolver/, with the python code, and results/, in which are the csv files of the results. 
distributions/ contains the results of all (~50000) Monte Carlo simulations, and statistical_analysis/ contains the script to calculate the median and the quantiles.</r:Content>
    </r:Abstract>
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        <r:URN>urn:ddi:se.researchdata:2025-163.TopicalCoverage:2.0</r:URN>
        <r:Subject xml:lang="en" controlledVocabularyID="10402" controlledVocabularyName="Standard för svensk indelning av forskningsämnen 2025">Physical Chemistry</r:Subject>
        <r:Subject xml:lang="sv" controlledVocabularyID="10402" controlledVocabularyName="Standard för svensk indelning av forskningsämnen 2025">Fysikalisk kemi</r:Subject>
        <r:Subject xml:lang="en" controlledVocabularyID="10407" controlledVocabularyName="Standard för svensk indelning av forskningsämnen 2025">Theoretical Chemistry</r:Subject>
        <r:Subject xml:lang="sv" controlledVocabularyID="10407" controlledVocabularyName="Standard för svensk indelning av forskningsämnen 2025">Teoretisk kemi</r:Subject>
        <r:Keyword xml:lang="en" controlledVocabularyID="af157837-bdbd-4a9a-b24e-6a79adfef57f" controlledVocabularyName="GCMD">HYDROGEN CYANIDE</r:Keyword>
        <r:Keyword xml:lang="en" controlledVocabularyID="p2870" controlledVocabularyName="YSO">origin of life</r:Keyword>
        <r:Keyword xml:lang="sv" controlledVocabularyID="p2870" controlledVocabularyName="YSO">livets uppkomst</r:Keyword>
        <r:Keyword xml:lang="en" controlledVocabularyID="37974" controlledVocabularyName="NASA Thesaurus">adenines</r:Keyword>
        <r:Keyword xml:lang="en" controlledVocabularyID="182673" controlledVocabularyName="NASA Thesaurus">chemical kinetics</r:Keyword>
        <r:Keyword xml:lang="en" controlledVocabularyID="50387" controlledVocabularyName="NASA Thesaurus">quantum chemistry</r:Keyword>
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