Rs, CAS numbers and experimental pKa values, might be found in the (Extra file 1: Table S1a). The SDF files together with the 3D structures of molecules and their dissociated forms are also in the (Additional file two: Molecules).Information set for carboxylic acidsThe EEM charges had been calculated by the system EEM SOLVER [53] using each and every in the 18 EEM parameter sets.QM charge calculationWe calculated QM atomic charges for all of the combinations of QM theory level, basis set and population evaluation for which we have EEM parameters (see Table 1). Especially, atomic charges had been calculated for these eight QM approaches: HF/STO-3G/MPA, HF/61G*/MK, and B3LYP/61G* with MPA, NPA, Hirshfeld, MK, CHELPG and AIM). The QM charge calculations were carried out employing 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 from the pKa prediction approach is its transferability to other chemical classes. In this perform, we give a case study displaying the functionality on the strategy on carboxylic acids, that are also very typical testing molecules for pKa prediction approaches [19-21,43]. The information set includes 71 distinct molecules of carboxylic acids and their dissociated types. The 3D structures of these molecules were obtained in the exact same way as for the phenols. The list of your molecules, which includes their names, NCS numbers, CAS numbers and experimental pKa values could be found inside the (Extra file 3: Table S1b). The SDF files with the 3D structures in the molecules and their dissociated forms are also integrated within the (More file 2: Molecules).Polymyxin B pKa valuesThere are two key strategies to develop a QSPR model to get a feature to become predicted.Theophylline The very first should be to generate as generalThe experimental pKa values have been taken from the Physprop database [61].PMID:24275718 SvobodovVaekovet al. Journal of Cheminformatics 2013, five:18 a r a http://www.jcheminf/content/5/Page 4 ofTable 1 Summary details about the EEM parameter sets employed in the present studyQM theory level + basis set HF/STO-3G 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. [45] Mortier et al. [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 have been atomic charges. We analyzed two varieties of QSPR models, namely QSPR models with 3 descriptors (3d QSPR models) and QSPR models with five descriptors (5d QSPR m.
