DOI: 10.5281/zenodo.10820776
title: heat of hydrogenation for diverse organic compounds -- experimental and calculated data for 166 unique reactions

description: General remarks

The experimental data was drawn from reactions involving H2 that are available at NIST (accessed on 15/03/2024). Only reactions of type M + H2 => MH2, where M is a neutral, closed-shell organic molecule that accepts one equivalent of H2, were included in the collection. M corresponds to the oxidized form of the molecule ( => suffix '_ox'), MH2 to the reduced form (=> suffix '_red'). For reasons of clarity, the references to original publications were abbreviated in the main table (look up in separate table).

For the molecules involved, Smiles were manually assigned. From those, 3D structures were generated and evaluated in order to match the thermodynamic properties as accurately as possible (for details on the procedure refer to the related work, see below).

In addition to the experimental uncertainty, a significant scatter is seen for replicate measurements.

Please note: To compute the heat of hydrogenation from the calculated data for M/MH2 the contribution of H2 needs to be considered, take e.g. -1.164816 hartree (Energy at 298.15K, calculated at CCSD(T)=FULL/aug-cc-pVDZ) from CCCBDB (accessed on 15/03/2024).

 

Description of files

The file 01_heat_of_hydrogenation_XP+QM.csv contains experimentally measured and calculated data.



columns are separated by "|"

column names and explanations:



NIST_idx -- index of original reaction, mostly unique. In a few cases, data of the reverse reaction were subsumed under a different index

env -- if available, information about the environment a reported reaction took place in, e.g. gas phase, hexane, etc...

method -- if available, reference about the experimental technique, e.g. 'Eqk' = Heat of equilibrium, 'Cm' = Calorimetry, 'Chyd' = Calorimetry of hydrogenation

Temperature K -- if available, reported values 

reference -- Abbreviation of reference to original publication

experimental heat of reaction kJ/mol -- measured value as reported by experimentalists

experimental uncertainty -- if available, uncertainty of measurement reported by experimentalists

comments -- notes relating to identification of compounds

SMILES_ox -- isomeric canonical SMILES for oxidized form M

InChI_ox -- InChI for oxidized form M 

SMILES_red -- isomeric canonical SMILES for reduced form M

InChI_red -- InChI for reduced form M

reaction_index -- consequtively numbered for identical pairs (SMILES_ox, SMILES_red)

the calculated properties are given for the oxidized and reduced form of the molecule (in hartree)



E(B3LYP/6-31G(2df,p))

E_thermal

E(G4(MP2))@0K

E(G4(MP2))@298K

H(G4(MP2))

heat_of_formation@0K

heat_of_formation@298K






02_molecules.sdf: provides for each molecule a low-energy geometry along with some descriptors and calculated energetic properties:





coordinate block + bond information

properties



SMILES -- isomeric canonical smiles linking compound to reactions defined in 01_heat_of_hydrogenation_XP+QM.csv

radical_electrons -- number of unpaired electrons as determined by RDKit

empirical_formula -- elemental composition of molecule

molecular_weight -- as determined by RDKit in g/mol

TPSA --  topological polar surface area (TPSA) as determined by RDKit

logP -- octanol/water partition coefficient as predicted by RDKit

nof_heavy_atoms -- number of non-hydrogen atoms in molecule

degree_of_unsaturation -- sum of multiplebonds and/or rings present in the compound

rings -- number of rings in the compound as determined by RDKit

multiplicity -- spin multiplicity for use as input for QM calculations

nof_multiple_bonds -- number of multiple bonds as determined by RDKit

Std_InChI -- standard InChi

FixedH_InChI -- variant of InChI to differentiate tautomers

tag -- dataset label

total_atoms -- total number of atoms (including H)

net_charge -- total charge of molecule in units of elementary charge



energetic properties (in hartree) 





E(B3LYP/6-31G(2df,p))




E(HF/maug-cc-p(T+d)Z) 




E(HF/CBS)




E(HF/maug-cc-p(Q+d)Z) 




E(MP2/6-31G(d))




E(CCSD(T)/6-31G(d))




E(HF/G3MP2LARGEXP) 




E(MP2/G3MP2LARGEXP)




DE(MP2) hartreeDE(HF)




ZPE(B3LYP) hartree




ZPE_scale_factor hartree




E(HLC) hartree




E_thermal hartree




H_thermal hartree




E(G4(MP2))@0K hartree




E(G4(MP2))@298K hartree




H(G4(MP2)) hartree




heat_of_formation@0K kcal/mol




heat_of_formation@298K kcal/mol








03_references.csv (separated by "|") lists abbreviations and corresponding full reference to original publication of individual data points.