Cuby can be used for automation of calculations of predefined data sets. This is handled by the dataset protocol which builds and runs all the necessary calculations and processes the results, comparing them to the benchmark data provided in the definition of the data set. The calculations of the individual items can be paralellized.
Cuby is distributed with a collection of data sets described below and the users can build their own data sets.
To get the data sets featured here, you can download Cuby and extract the files you need. The data set definition files are found in directory cuby4/data/datasets
and archives of the geomtries are in cuby4/data/geometries
.
You can now download files for each data set here without downloading whole Cuby. The download links are provided at the data set pages (click on the name of the data set in the table below to get there).
New, large data sets from the Non-Covalent Interactions Atlas project.
NCIA_D1200 | London dispersion in an extended chemical space[51] |
NCIA_D442x10 | London dispersion in an extended chemical space, 10-point dissociation curves[52] |
NCIA_HB300SPXx10 | CCSD(T)/CBS interaction energies of H-bonds featuring S, P and halogens, 10-point dissociation curves[53] |
NCIA_HB375x10 | CCSD(T)/CBS interaction energies of H-bonds and decoys, 10-point dissociation curves[54] |
NCIA_IHB100x10 | CCSD(T)/CBS interaction energies of ionic H-bonds, 10-point dissociation curves[55] |
NCIA_Rep739x5 | CCSD(T)/CBS interaction energies for repulsive contacts in extended chemical space[56] |
NCIA_SH250x10 | Sigma-hole interactions, 10-point dissociation curves[57] |
3B69 | CCSD(T)/CBS three-body energies in 23x3 trimers[1] |
3B69_dimers | All dimers from the 3B69 set of trimers[2] |
A24 | Accurate CCSD(T)/CBS interaction energies in small noncovalent complexes[3] |
Bauza2013 | Halogen, chalcogen and pnicogen bonds[4] |
Charge_transfer | CCSD(T)/CBS interaction energies in charge-transfer complexes[5][6] |
HB104 | Diverse set of hydrogen bonds of O and N in organic molecules[46][47] |
Ionic_H-bonds | Ionic hydrogen bonds - dissociation curves[48] |
L7 | CCSD(T) or QCISD(T) interaction energies in large noncovalent complexes[49] |
MPCONF196 | Conformation energies of peptides and macrocyclic compounds[50] |
Pecina2015 | Chalcogen and pnicogen bonds of heteroboranes[58] |
Peptide_FGG | CSCD(T)/CBS conformation energies of FGG tripeptide[59] |
Peptide_GFA | CSCD(T)/CBS conformation energies of GFA tripeptide[60] |
Peptide_GGF | CSCD(T)/CBS conformation energies of GGF tripeptide[61] |
Peptide_WG | CSCD(T)/CBS conformation energies of WG dipeptide[62] |
Peptide_WGG | CSCD(T)/CBS conformation energies of WGG tripeptide[63] |
PLFrag547 | PLFrag547 - Protein-ligand fragments[64] |
R160x6 | Repulsive intermolecular contacts in organic molecules[65] |
S12L | Interaction energies in large noncovalent complexes derived from experiment[66] |
S66 | CCSD(T)/CBS interaction energies in organic noncovalent complexes[67][68] |
S66a8 | CCSD(T)/CBS interaction energies in organic noncovalent complexes - angular displacements[69] |
S66x8 | CCSD(T)/CBS interaction energies in organic noncovalent complexes - dissociation curves[70] |
Sulfur_x8 | CCSD(T)/CBS interaction energies in complexes featuring sulfur[71] |
W4-17 | High-level theoretical atomization energies[72] |
X40 | CSCD(T)/CBS interaction energies of halogenated molecules[73] |
X40x10 | CSCD(T)/CBS interaction energies of halogenated molecules - dissociation curves[74] |
The GMTKN30 collection of data sets by S. Grimme is available in Cuby. The original data were converted automatically to the format Cuby uses; as a result the data sets miss some fancy features such as nice names of the systems.
We have validated the GMTKN datasets against the original DFT results by Grimme (with exception of G21EA and WATER27 for which the published data were calculated in a modified basis set). Only in the SIE11 data set, there is one point (the last entry) where our result does not agree with Grimme's DFT data (but is closer to the reference).
GMTKN_ACONF | relative energies of alkane conformers[7] |
GMTKN_ADIM6 | interaction energies of n-alkane dimers[8] |
GMTKN_AL2X | dimerization energies of AlX3 compounds[9] |
GMTKN_ALK6 | fragmentation and dissociation reactions of alkaline and alkaline−cation−benzene complexes[10] |
GMTKN_BH76 | barrier heights of hydrogen transfer, heavy atom transfer, nucleophilic substitution, unimolecular, and association reactions[11][12] |
GMTKN_BH76RC | reaction energies of the BH76 set[13][14] |
GMTKN_BHPERI | barrier heights of pericyclic reactions[15] |
GMTKN_BSR36 | bond separation reactions of saturated hydrocarbons[16][17] |
GMTKN_CYCONF | relative energies of cysteine conformers[18] |
GMTKN_DARC | reaction energies of Diels−Alder reactions[19] |
GMTKN_DC9 | nine difficult cases for DFT[20] |
GMTKN_G21EA | adiabatic electron affinities[21] |
GMTKN_G21IP | adiabatic ionization potentials[22] |
GMTKN_G2RC | reaction energies of selected G2-97 systems[23] |
GMTKN_HEAVY28 | noncovalent interaction energies between heavy element hydrides[24] |
GMTKN_IDISP | intramolecular dispersion interactions[25][26] |
GMTKN_ISO34 | isomerization energies of small and medium-sized organic molecules[27] |
GMTKN_ISOL22 | isomerization energies of large organic molecules[28] |
GMTKN_MB08-165 | decomposition energies of artificial molecules[29][30] |
GMTKN_NBPRC | oligomerizations and H2 fragmentations of NH3-BH3 systems; H2 activation reactions with PH3-BH3 systems[31][32] |
GMTKN_O3ADD6 | reaction energies, barrier heights, association energies for addition of O3 to C2H4 and C2H2[33] |
GMTKN_PA | adiabatic proton affinities[34][35] |
GMTKN_PCONF | relative energies of phenylalanyl−glycyl−glycine tripeptide conformers[36] |
GMTKN_RG6 | interaction energies of rare gas dimers[37] |
GMTKN_RSE43 | radical stabilization energies[38] |
GMTKN_S22 | binding energies of noncovalently bound dimers[39][40] |
GMTKN_SCONF | relative energies of sugar conformers[41][42] |
GMTKN_SIE11 | self-interaction error related problems[43] |
GMTKN_W4-08 | atomization energies of small molecules[44] |
GMTKN_WATER27 | binding energies of water, H+(H2O)n and OH−(H2O)n clusters[45] |