Rge calculationWe calculated QM atomic charges for each of the combinations of QM theory level, basis set and population evaluation for which we have EEM parameters (see Table 1). Specifically, atomic charges were calculated for these eight QM approaches: HF/STO3G/MPA, HF/61G/MK, and B3LYP/61G with MPA, NPA, Hirshfeld, MK, CHELPG and AIM). The QM charge calculations had been carried out utilizing Gaussian09 [54]. Inside the case of AIM population evaluation, the output from Gaussian09 was additional processed by the software program package AIMAll [55].Information set for phenolsAn aspect that is very important for the applicability in the pKa prediction method is its transferability to other chemical classes. In this perform, we present a case study displaying the performance on the method on carboxylic acids, that are also quite popular testing molecules for pKa prediction approaches [1921,43]. The data set consists of 71 distinct molecules of carboxylic acids and their dissociated forms. The 3D structures of those molecules were obtained within the same way as for the phenols.Trifluridine Data Sheet The list of the molecules, which includes their names, NCS numbers, CAS numbers and experimental pKa values can be discovered inside the (Added file 3: Table S1b). The SDF files using the 3D structures in the molecules and their dissociated forms are also included in the (More file 2: Molecules).pKa valuesThere are two main methods to build a QSPR model for a function to be predicted. The first should be to produce as generalThe experimental pKa values were taken in the Physprop database [61].SvobodovVaekovet al. Journal of Cheminformatics 2013, 5:18 a r a http://www.jcheminf.com/content/5/Page 4 ofTable 1 Summary information regarding the EEM parameter sets utilized in the present studyQM theory level basis set HF/STO3G MPA PA EEM parameter set name Svob2007 cbeg2 Svob2007 cmet2 Svob2007 chal2 Svob2007 hm2 Baek1991 Mort1986 HF/61G B3LYP/61G MK MPA NPA Jir2008 hf Chaves2006 Bult2002 mul Ouy2009 Ouy2009 elem Ouy2009 elemF Bult2002 npa Hir. MK CHELPG AIM Bult2002 hir Jir2008 mk Bult2002 mk Bult2002 che Bult2004 aim Svobodova et al. [44] Svobodova et al. [44] Svobodova et al. [44] Svobodova et al. [44] Baekelandt et al.Buy1196145-01-3 [45] Mortier et al.PMID:24360118 [39] Jirouskova et al. [46] Chaves et al. [47] Bultinck et al. [48] Ouyang et al. [49] Ouyang et al. [49] Ouyang et al. [49] Bultinck et al. [48] Bultinck et al. [48] Jirouskova et al. [46] Bultinck et al. [48] Bultinck et al. [48] Bultinck et al. [50] Published by Year of publication 2007 2007 2007 2007 1991 1986 2008 2006 2002 2009 2009 2009 2002 2002 2008 2002 2002 2004 C, O, N, H, S C, O, N, H, S, Fe, Zn C, O, N, H, S, Br, Cl, F, I C, O, N, H, S, F, Cl, Br, I, Fe, Zn C, O, N, H, P, Al, Si C, O, N, H C, O, N, H, S, F, Cl, Br, I, Zn C, O, N, H, F C, O, N, H, F C, O, N, H, F C, O, N, H, F C, O, N, H, F C, O, N, H, F C, O, N, H, F C, O, N, H, S, F, Cl, Br, I, Zn C, O, N, H, F C, O, N, H, F C, O, N, H, F Elements includedDescriptors and QSPR models for phenolsOur descriptors had been atomic charges. We analyzed two kinds of QSPR models, namely QSPR models with three descriptors (3d QSPR models) and QSPR models with 5 descriptors (5d QSPR models). The 3d QSPR models used these descriptors which proved to become probably the most relevant for pKa prediction in our previous study [24]. Therefore these descriptors had been the atomic charge in the hydrogen atom from the phenolic OH group (qH ), the charge around the oxygen atom from the phenolic OH group (qO ), along with the charge around the carbon atom binding the phenolic OH gr.