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Data for: "How does Adenine form from Hydrogen Cyanide?"

https://doi.org/10.71870/gqyb-fj64
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.
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  • dataset-revised.zip
    794.33 MiB

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  • README.txt
    6.34 KiB

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Department of Chemistry and Chemical Engineering

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2020-04305

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Computational Astrobiology: The Rise of Macromolecules

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The goal of this project is to enhance our knowledge of chemical structures and processes that may play a role in life’s possible origins. We will apply quantum chemical calculations to study the properties and reactions of in particular hydrogen cyanide, one of the most abundant and widely distributed organic molecules in astrochemical environments. Together with collaborators, we aim to answer the following questions: How can heterocycles, including nucleobase-analogs, form from HCN polymers? What is the catalytic potential of HCN nanocrystals? What role might co-crystals have on worlds such as Saturn’s moon Titan? What are the next steps in the development of computational astrobiology? State-of-the-art computational methods, including steered ab initio molecular dynamics and structure prediction algorithms will be applied to several of these questions for the first time. Outcomes of this research will be concrete predictions of chemical structures and phenomena that will be amenable for verification by low temperature experiments by collaborating groups, by ongoing and future sample-return missions to asteroids and comets, as well as the recently selected Dragonfly mission to Saturn’s moon Titan.

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Martin Rahmmartin.rahm@chalmers.seOpens in a new tab

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doris
chalmers
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