Energies of the HOMO and LUMO Orbitals for 111725 Organic Molecules Calculated by DFT B3LYP / 6-31G*

Alberto De Luca; Alberto De Luca; Alexander Leemans; Alice Decio; Andrea Nordio; Andrea Nordio; Chiara Gagliardi; Denis Peruzzo; Filippo Arrigoni; Renato Borgatti

Energies of the HOMO and LUMO Orbitals for 111725 Organic Molecules Calculated by DFT B3LYP / 6-31G*

Authors: Alberto De Luca
Alberto De Luca
Alexander Leemans
Alice Decio
Andrea Nordio
Andrea Nordio
Chiara Gagliardi
Denis Peruzzo
Filippo Arrigoni
Renato Borgatti
Publication date: 28 December 2016
Publisher
Doi

Abstract

HOMO and LUMO orbital energies for 111725 organic molecules calculated at the B3LYP/6-31G*//PM6 or B3LYP/6-31G*//PM7 level of theory. Related publication: * Florbela Pereira, Kaixia Xiao, Diogo A. R. S. Latino, Chengcheng Wu, Qingyou Zhang and Joao Aires-de-Sousa: Machine Learning Methods to Predict Density Functional Theory B3LYP Energies of HOMO and LUMO Orbitals. J. Chem. Inf. Model. (2017) DOI: <a href="http://dx.doi.org/10.1021/acs.jcim.6b00340">10.1021/acs.jcim.6b00340</a> This data set is publicly available at http://dx.doi.org/10.6084/m9.figshare.3384184.v1 Files ----- frontier_orbitals_111725mols_sdf.tar.gz - 111275 molecules in the MDL SDFile format frontier_orbitals_111725mols.xlsx - HOMO and LUMO orbital energies for 111275 neutral organic molecules coordinates_111725mols_xyz.zip - atomic coordinates used for the DFT calculation of the 111275 molecules PM7_frontier_orbitals.xlsx - HOMO and LUMO energies calculated by the PM7 semi-empirical method. Molecules --------- For the database creation, molecular structural motifs were retrieved from organic electronics studies, and collections of dyes, metabolites and electrophiles/nucleophiles [1-5]. The database was populated by retrieval of similar examples from the ZINC database [6], the PubChem database [7] and by computationally combining motifs and lists of substituents with the ChemAxon Reactor software, JChem 15.4.6, 2015, ChemAxon (http://www.chemaxon.com). The structures were standardized with ChemAxon Standardizer (JChem 15.4.6, 2015, ChemAxon, http://www.chemaxon.com) and OpenBabel (Open Babel Package, version 2.3.1 http://openbabel.org) for neutralization and inclusion of all hydrogen atoms. The molecular structures include atomic elements C, H, B, N, O, F, Si, P, S, Cl, Se, and Br. Molecular geometries were relaxed by the PM6 or PM7 methods using the MOPAC software [8] and orbital energies were calculated by the GAMESS program [9] with the B3LYP functional and the 6-31G* basis set. Structures were calculated with the geometry obtained with the PM6 or PM7 semi-empirical method. Format ------ Each molecule is stored in its own file, ending in ".sdf". These are the starting structures, previous to geometry relaxation with the MOPAC program. The format is the standard MDL SDFile generated with ChemAxon Standardizer and OpenBabel. The atomic coordinates obtained with the PM6 and PM7 methods are stored in files ending in ".xyz", one for each molecule. Each file comprises a header line specifying the number of atoms n, a line with the id of the structure, and n lines containing the element and atomic coordinates, one atom per line. Orbital energies are stored in the frontier_orbitals_111725mols.xlsx file. Two different sheets are used for the main database and a data set used as final test set in the related publication. PM7 values are stored in the PM7_frontier_orbitals.xlsx with the same format. Column Content of .xlsx files ------ 1 Molecule ID (as appears in the corresponding .sdf file name) 2 HOMO energy in eV. 3 LUMO energy in eV. References ---------- [1] Po R, Bianchi G, Carbonera C, Pellegrino A: All that glisters is not gold: an analysis of the synthetic complexity of efficient polymer donors for polymer solar cells. Macromolecules 2015, 48:453-461. [2] Hachmann J, Olivares-Amaya R, Atahan-Evrenk S, Amador-Bedolla C, Sanchez-Carrera RS, Gold-Parker A, Vogt L, Brockway AM, Aspuru-Guzik A: The Harvard Clean Energy Project: large-scale computational screening and design of organic photovoltaics on the world community grid. J Phys Chem Lett 2011, 2:2241-2251. [3] O’Boyle NM, Campbell CM, Hutchison GR: Computational design and selection of optimal organic photovoltaic materials. J Phys Chem C 2011, 115:16200-16210. [4] Mayr H, Ofial AR: Kinetics of electrophile-nucleophile combinations: a general approach to polar organic reactivity. Pure Appl Chem 2005, 77:1807-1821. [5] Kanehisa M, Goto S: KEGG: Kyoto Encyclopedia of Genes and Genomes. Nucleic Acids Res 2000, 28:27-30. [6] Irwin JJ, Sterling T, Mysinger MM, Bolstad ES, Coleman RG: ZINC: a free tool to discover chemistry for biology. J Chem Inf Model 2012, 52:1757-1768. [7] Kim S, Thiessen PA, Bolton EE, Chen J, Fu G, Gindulyte A, Han L, He J, He S, Shoemaker BA, Wang J, Yu B, Zhang J, Bryant SH: PubChem Substance and Compound databases. Nucleic Acids Res 2016, 44(D1):D1202-13. [8] MOPAC2009 and MOPAC2012, James J. P. Stewart, Stewart Computational Chemistry, Colorado Springs, CO, USA, http://OpenMOPAC.net (2008-2012). [9] Schmidt MW, Baldridge KK, Boatz JA, Elbert ST, Gordon MS, Jensen JJ, Koseki S, Matsunaga N, Nguyen KA, Su S, Windus TL, Dupuis M, Montgomery JA: General atomic and molecular electronic structure system. J Comput Chem 1993, 14:1347-1363. GAMESS Version 1 May 2013 (R1). <br