Automated calculation of data sets

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.

Downloading individual data sets

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).

Data sets available

Non-Covalent Interactions Atlas data sets

New, large data sets from the Non-Covalent Interactions Atlas project.

NCIA_D1200London dispersion in an extended chemical space[118]
NCIA_D442x10London dispersion in an extended chemical space, 10-point dissociation curves[119]
NCIA_HB300SPXx10CCSD(T)/CBS interaction energies of H-bonds featuring S, P and halogens, 10-point dissociation curves[120]
NCIA_HB375x10CCSD(T)/CBS interaction energies of H-bonds and decoys, 10-point dissociation curves[121]
NCIA_IHB100x10CCSD(T)/CBS interaction energies of ionic H-bonds, 10-point dissociation curves[122]
NCIA_Rep739x5CCSD(T)/CBS interaction energies for repulsive contacts in extended chemical space[123]
NCIA_SH250x10Sigma-hole interactions, 10-point dissociation curves[124]

Other data sets

3B69CCSD(T)/CBS three-body energies in 23x3 trimers[1]
3B69_dimersAll dimers from the 3B69 set of trimers[2]
A24Accurate CCSD(T)/CBS interaction energies in small noncovalent complexes[3]
Bauza2013Halogen, chalcogen and pnicogen bonds[4]
Charge_transferCCSD(T)/CBS interaction energies in charge-transfer complexes[5][6]
Dipoles152Benchmark CCSD(T)/CBS dipole moments in fixed equilibrium geometries[7]
HB104Diverse set of hydrogen bonds of O and N in organic molecules[113][114]
Ionic_H-bondsIonic hydrogen bonds - dissociation curves[115]
L7CCSD(T) or QCISD(T) interaction energies in large noncovalent complexes[116]
MPCONF196Conformation energies of peptides and macrocyclic compounds[117]
Pecina2015Chalcogen and pnicogen bonds of heteroboranes[125]
Peptide_FGGCSCD(T)/CBS conformation energies of FGG tripeptide[126]
Peptide_GFACSCD(T)/CBS conformation energies of GFA tripeptide[127]
Peptide_GGFCSCD(T)/CBS conformation energies of GGF tripeptide[128]
Peptide_WGCSCD(T)/CBS conformation energies of WG dipeptide[129]
Peptide_WGGCSCD(T)/CBS conformation energies of WGG tripeptide[130]
PL-REX_1kPL-REX protein-ligand complexes - small model (~ 1000 atoms)[131]
PLA15PLA15 - protein-ligand interactions in active site model[132]
PLFrag547PLFrag547 - Protein-ligand fragments[133]
R160x6Repulsive intermolecular contacts in organic molecules[134]
S12LInteraction energies in large noncovalent complexes derived from experiment[135]
S66CCSD(T)/CBS interaction energies in organic noncovalent complexes[136][137]
S66a8CCSD(T)/CBS interaction energies in organic noncovalent complexes - angular displacements[138]
S66x8CCSD(T)/CBS interaction energies in organic noncovalent complexes - dissociation curves[139]
Sulfur_x8CCSD(T)/CBS interaction energies in complexes featuring sulfur[140]
W4-17High-level theoretical atomization energies[141]
X40CSCD(T)/CBS interaction energies of halogenated molecules[142]
X40x10CSCD(T)/CBS interaction energies of halogenated molecules - dissociation curves[143]

GMTKN55 data sets

The GMTKN55 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. The conversion was validated bu comparing calculations in Cuby to the the DFT results from the original paper, and in all data sets no or negligible difference was observed.

GMTKN55_ACONFRelative energies of alkane conformers[47]
GMTKN55_ADIM6Interaction energies of n-alkane dimers[48]
GMTKN55_AHB21Interaction energies in anion–neutral dimers[49]
GMTKN55_AL2X6Dimerisation energies of AlX3 compounds[50]
GMTKN55_ALK8Dissociation and other reactions of alkaline compounds[51]
GMTKN55_ALKBDE10Dissociation energies in group-1 and -2 diatomics[52]
GMTKN55_Amino20x4Relative energies in amino acid conformers[53]
GMTKN55_BH76Barrier heights of hydrogen transfer, heavy atom transfer, nucleophilic substitution, unimolecular and association reactions[54]
GMTKN55_BH76RCReaction energies of the BH76[55]
GMTKN55_BHDIV10Diverse reaction barrier heights[56]
GMTKN55_BHPERIBarrier heights of pericyclic reactions[57]
GMTKN55_BHROT27Barrier heights for rotation around single bonds[58]
GMTKN55_BSR36Bond-separation reactions of saturated hydrocarbons[59]
GMTKN55_BUT14DIOLRelative energies in butane-1,4-diol conformers[60]
GMTKN55_C60ISORelative energies between C60 isomers[61]
GMTKN55_CARBHB12Hydrogen-bonded complexes between carbene analogues and H2O, NH3, or HCl[62]
GMTKN55_CDIE20Double-bond isomerisation energies in cyclic systems[63]
GMTKN55_CHB6Interaction energies in cation–neutral dimers[64]
GMTKN55_DARCReaction energies of Diels-Alder reactions[65]
GMTKN55_DC1313 difficult cases for DFT methods[66][67]
GMTKN55_DIPCS10Double-ionisation potentials of closed-shell systems[68]
GMTKN55_FH51Reaction energies in various (in-)organic systems[69][70]
GMTKN55_G21EAAdiabatic electron affinities[71]
GMTKN55_G21IPAdiabatic ionization potentials[72]
GMTKN55_G2RCReaction energies of selected G2/97 systems[73]
GMTKN55_HAL59Binding energies in halogenated dimers (incl. halogen bonds)[74][75]
GMTKN55_HEAVY28Noncovalent interaction energies between heavy element hydrides[76]
GMTKN55_HEAVYSB11Dissociation energies in heavy-element compounds[77]
GMTKN55_ICONFRelative energies in conformers of inorganic systems[78]
GMTKN55_IDISPIntramolecular dispersion interactions[79]
GMTKN55_IL16Interaction energies in anion–cation dimers[80]
GMTKN55_INV24Inversion/racemisation barrier heights[81]
GMTKN55_ISO34Isomerisation energies of small and medium-sized organic molecules[82]
GMTKN55_ISOL24Isomerisation energies of large organic molecules[83][84]
GMTKN55_MB16-43Decomposition energies of artificial molecules[85]
GMTKN55_MCONFRelative energies in melatonin conformers[86]
GMTKN55_NBPRCOligomerisations and H2 fragmentations of NH3/BH3 systems, H2 activation reactions with PH3/BH3 systems[87]
GMTKN55_PA26Adiabatic proton affinities (incl. of amino acids)[88][89][90]
GMTKN55_PArelRelative energies in protonated isomers[91]
GMTKN55_PCONF21Relative energies in tri- and tetrapeptide conformers[92][93][94]
GMTKN55_PNICO23Interaction energies in pnicogen-containing dimers[95]
GMTKN55_PX13Proton-exchange barriers in H2O, NH3, and HF clusters[96]
GMTKN55_RC21Fragmentations and rearrangements in radical cations[97]
GMTKN55_RG18Interaction energies in rare-gas complexes[98]
GMTKN55_RSE43Radical-stabilisation energies[99]
GMTKN55_S22Binding energies of noncovalently bound dimers[100]
GMTKN55_S66Binding energies of noncovalently bound dimers[101]
GMTKN55_SCONFRelative energies of sugar conformers[102]
GMTKN55_SIE4x4Self-interaction-error related problems[103]
GMTKN55_TAUT15Relative energies in tautomers[104]
GMTKN55_UPU23Relative energies between RNA-backbone conformers[105][106]
GMTKN55_W4-11Total atomisation energies[107]
GMTKN55_WATER27Binding energies in (H2O)n, H+(H2O)n and OH-(H2O)n[108][109]
GMTKN55_WCPT18Proton-transfer barriers in uncatalysed and water-catalysed reactions[110]
GMTKN55_YBDE18Bond-dissociation energies in ylides[111][112]

GMTKN30 data sets

Although superseeded by GMTKN55, the GMTKN30 data sets are also kept in Cuby for backward compatibility. These were previously named just GMTKN. Please note that data sets with the same name may use different reference data in GMTKN30 and GMTKN55. The dsata sets were validsated agains 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).

GMTKN30_ACONFrelative energies of alkane conformers[8]
GMTKN30_ADIM6interaction energies of n-alkane dimers[9]
GMTKN30_AL2Xdimerization energies of AlX3 compounds[10]
GMTKN30_ALK6fragmentation and dissociation reactions of alkaline and alkaline−cation−benzene complexes[11]
GMTKN30_BH76barrier heights of hydrogen transfer, heavy atom transfer, nucleophilic substitution, unimolecular, and association reactions[12][13]
GMTKN30_BH76RCreaction energies of the BH76 set[14][15]
GMTKN30_BHPERIbarrier heights of pericyclic reactions[16]
GMTKN30_BSR36bond separation reactions of saturated hydrocarbons[17][18]
GMTKN30_CYCONFrelative energies of cysteine conformers[19]
GMTKN30_DARCreaction energies of Diels−Alder reactions[20]
GMTKN30_DC9nine difficult cases for DFT[21]
GMTKN30_G21EAadiabatic electron affinities[22]
GMTKN30_G21IPadiabatic ionization potentials[23]
GMTKN30_G2RCreaction energies of selected G2-97 systems[24]
GMTKN30_HEAVY28noncovalent interaction energies between heavy element hydrides[25]
GMTKN30_IDISPintramolecular dispersion interactions[26][27]
GMTKN30_ISO34isomerization energies of small and medium-sized organic molecules[28]
GMTKN30_ISOL22isomerization energies of large organic molecules[29]
GMTKN30_MB08-165decomposition energies of artificial molecules[30][31]
GMTKN30_NBPRColigomerizations and H2 fragmentations of NH3-BH3 systems; H2 activation reactions with PH3-BH3 systems[32][33]
GMTKN30_O3ADD6reaction energies, barrier heights, association energies for addition of O3 to C2H4 and C2H2[34]
GMTKN30_PAadiabatic proton affinities[35][36]
GMTKN30_PCONFrelative energies of phenylalanyl−glycyl−glycine tripeptide conformers[37]
GMTKN30_RG6interaction energies of rare gas dimers[38]
GMTKN30_RSE43radical stabilization energies[39]
GMTKN30_S22binding energies of noncovalently bound dimers[40][41]
GMTKN30_SCONFrelative energies of sugar conformers[42][43]
GMTKN30_SIE11self-interaction error related problems[44]
GMTKN30_W4-08atomization energies of small molecules[45]
GMTKN30_WATER27binding energies of water, H+(H2O)n and OH−(H2O)n clusters[46]