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diff --git a/data/qm9_readme.txt b/data/qm9_readme.txt new file mode 100644 index 000000000..efd3af9c4 --- /dev/null +++ b/data/qm9_readme.txt @@ -0,0 +1,114 @@ + +Data set dsgdb9nsd +================== + +Thermochemical properties for 133885 small organic molecules at the DFT/B3LYP level of theory. + +Please cite this publication if you use this data set: +* Raghunathan Ramakrishnan, Pavlo O. Dral, Matthias Rupp, O. Anatole von Lilienfeld: + Quantum chemistry structures and properties of 134 kilo molecules + Scientific Data (2014) + +Related publications: +* Raghunathan Ramakrishnan, Pavlo O. Dral, Matthias Rupp, O. Anatole von Lilienfeld: + Learning the error: Augmenting legacy quantum chemistry with machine learning. + submitted (2014) + +* Matthias Rupp, Alexandre Tkatchenko, Klaus-Robert Mueller, O. Anatole von + Lilienfeld: Fast and Accurate Modeling of Molecular Atomization Energies with + Machine Learning, Physical Review Letters, 108(5): 058301, 2012. + DOI: 10.1103/PhysRevLett.108.058301 + +This data set is publicly available at +* http://dx.doi.org/10.6084/m9.figshare.XXXX + +Files +----- + +dsgdb9nsd.xyz.tar.bz2 - 133885 molecules with properties in XYZ-like format +dsC7O2H10nsd.xyz.tar.bz2 - 6095 isomers of C7O2H10 with properties in XYZ-like format +validation.txt - 100 randomly drawn molecules from the 133885 set with enthalpies of formation +uncharacterized.txt - 3054 molecules from the 133885 set that failed a consistency check +atomref.txt - Atomic reference data +readme.txt - Documentation + +Molecules +--------- + +For a subset of the GDB-9 database [1] consisting of 133885 neutral organic +molecules composed from elements H,C,N,O,F, molecular geometries were relaxed +and properties calculated at the DFT/B3LYP/6-31G(2df,p) level of theory. + +For a subset of 6095 isomers of C7O2H10, energetics were calculated +at the G4MP2 [2] level of theory. + +For a validation set of 100 randomly drawn molecules from the 133885 molecules set, +enthalpies of formation were additionally calculated at the +DFT/B3LYP/6-31G(2df,p), G4MP2, G4 and CBS-QB3 levels of theory. + +3054 molecules from the 133885 GDB9 molecules failed a consistency check where the Corina generated +Cartesian coordinates and the B3LYP/6-31G(2df,p) equilibrium geometry lead to different SMILES strings. + +Format +------ + +Each molecule is stored in its own file, ending in ".xyz". +The format is an ad hoc extension of the XYZ format [3]. + +Line Content +---- ------- +1 Number of atoms na +2 Properties 1-17 (see below) +3,...,na+2 Element type, coordinate (x,y,z) (Angstrom), and Mulliken partial charge (e) of atom +na+3 Frequencies (3na-5 or 3na-6) +na+4 SMILES from GDB9 and for relaxed geometry +na+5 InChI for GDB9 and for relaxed geometry + +The properties stored in the second line of each file: + +I. Property Unit Description +-- -------- ----------- -------------- + 1 tag - "gdb9"; string constant to ease extraction via grep + 2 index - Consecutive, 1-based integer identifier of molecule + 3 A GHz Rotational constant A + 4 B GHz Rotational constant B + 5 C GHz Rotational constant C + 6 mu Debye Dipole moment + 7 alpha Bohr^3 Isotropic polarizability + 8 homo Hartree Energy of Highest occupied molecular orbital (HOMO) + 9 lumo Hartree Energy of Lowest occupied molecular orbital (LUMO) +10 gap Hartree Gap, difference between LUMO and HOMO +11 r2 Bohr^2 Electronic spatial extent +12 zpve Hartree Zero point vibrational energy +13 U0 Hartree Internal energy at 0 K +14 U Hartree Internal energy at 298.15 K +15 H Hartree Enthalpy at 298.15 K +16 G Hartree Free energy at 298.15 K +17 Cv cal/(mol K) Heat capacity at 298.15 K + +I. = Property index (properties are given in this order) +For the 6095 isomers, properties 12-16 were calculated at the G4MP2 level of theory. +All other calculations were done at the DFT/B3LYP/6-31G(2df,p) level of theory. + +Notes +----- + +Out of the 133885 molecules, geometries of the 11 molecules with indices +21725, 87037, 59827, 117523, 128113, 129053, 129152, 129158, 130535, 6620, 59818 +were difficult to converge. +Low threshold convergence was possible for 21725, 59827, 128113, 129053, 129152, 130535. +Molecules 6620 and 59818 converged to very low-lying saddlepoints, with lowest frequency < 10i cm^-1. + +References +---------- + +[1] Lorenz C. Blum, Jean-Louis Reymond: 970 Million Druglike Small Molecules + for Virtual Screening in the Chemical Universe Database GDB-13, Journal of + the American Chemical Society 131(25): 8732-8733, 2009. DOI: 10.1021/ja902302h +[2] Larry A. Curtiss, Paul C. Redfern, Krishnan Raghavachari: Gaussian-4 theory + using reduced order perturbation theory, Journal of Chemical Physics 127(12): + 124105, 2007. DOI: 10.1063/1.2770701 +[3] The XYZ format, originally developed for the XMol program by the Minnesota + Supercomputer Center, is a widespread plain text format for exchange of molecules + (atomic coordinates and annotation). There is no formal specification. See, e.g., + http://openbabel.org/wiki/XYZ, or, http://wiki.jmol.org/index.php/File_formats/Formats/XYZ |