Comparative analysis of QSAR models for predicting pKa of organic oxygen acids and nitrogen bases from molecular structure

Journal of Chemical Information and Modeling

Volumn 50, Issue 11, 2010, Pages 1949-1960

  Yu, Haiying ^a,b   Kühne, Ralph ^a   Ebert, Ralf Uwe ^a   Schüürmann, Gerrit ^a,b  

^a HELMHOLTZ CENTRE FOR ENVIRONMENTAL RESEARCH UFZ   (Germany)

^b TU BERGAKADEMIE FREIBERG   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

ANILINE; CHEMICAL ANALYSIS; COMPUTATIONAL CHEMISTRY; FORECASTING; HYDROGEN BONDS; MEAN SQUARE ERROR; MOLECULAR GRAPHICS; MOLECULAR OXYGEN; NITROGEN; PHENOLS; QUANTUM CHEMISTRY;

ALIPHATIC CARBOXYLIC ACIDS; COMPARATIVE ANALYSIS; INTRAMOLECULAR H-BONDING; PREDICTION PERFORMANCE; ROOT MEAN SQUARE ERRORS; SQUARED CORRELATION COEFFICIENTS; SUBSTANTIAL VARIATIONS; SUBSTITUTION PATTERNS;

SET THEORY;

EID: 78649513581     PISSN: 15499596     EISSN: 1549960X     Source Type: Journal    
DOI: 10.1021/ci100306k     Document Type: Article

References (38)

1. a Prediction for Organic Acids and Bases; Chapman & Hall: London, 1981.
2. a J. Chem. Inf. Model. 2009, 49, 2013-2033
3. ACD/Labs, version 12.0; Advanced Chemistry Development Inc.: Toronto, Ontario, Canada, 2009.
4. Karickhoff, S. W.; Mcdaniel, V. K.; Melton, C.; Vellino, A. N.; Nute, D. E.; Carreira, L. A. Predicting Chemical Reactivity by Computer Environ. Toxicol. Chem. 1991, 10, 1405-1416
5. as Quant. Struct.-Act. Relat. 1995, 14, 348-355
6. Hilal, S. H.; Karickhoff, S. W.; Carreira, L. A. Prediction of Chemical Reactivity Parameters and Physical Properties of Organic Compounds from Molecular Structure Using SPARC; EPA/600/R-03/030 March 2003; US Environmental Protection Agency, National Exposure Research Laboratory, Office of Research and Development: Research Triangle Park, NC, 2003.
7. a Values of Drugs Based on Their Molecular Structures Anal. Bioanal. Chem. 2007, 389, 1267-1281
8. a Values of Pharmaceutical Substances J. Chem. Inf. Model. 2009, 49, 2801-2812
9. a of Carboxylic Acids and Chlorinated Phenols Quant. Struct.-Act. Relat. 1996, 15, 121-132
10. a of Carboxylic Acids Using the Ab initio Continuum-Solvation Model PCM-UAHF J. Phys. Chem. A 1998, 102, 6706-6712
11. a calculations for carboxylic acids using Complete Basis Set and Gaussian-n models combined with CPCM continuum solvation methods J. Am. Chem. Soc. 2001, 123, 7314-7319
12. Takano, Y.; Houk, K. N. Benchmarking the conductor-like polarizable continuum model (CPCM) for aqueous solvation free energies of neutral and ionic organic molecules J. Chem. Theory Comput. 2005, 1, 70-77
13. a Scale J. Phys. Chem. A 2003, 107, 9380-9386
14. Eckert, F.; Klamt, A. Accurate Prediction of Basicity in Aqueous Solution with COSMO-RS J. Comput. Chem. 2006, 27, 11-19
15. 2O in the Gas Phase and in Aqueous Solution J. Chem. Phys. 1998, 109, 9523-9528
16. a Using Semiempirical Molecular Orbital Methods. Part 1: Application to Phenols and Carboxylic Acids Quant. Struct.-Act. Relat. 2002, 21, 457-472
17. a Using Semiempirical Molecular Orbital Methods. Part 2: Application to Amines, Anilines and Various Nitrogen Containing Heterocyclic Compounds Quant. Struct.-Act. Relat. 2002, 21, 473-485
18. a for Druglike Compounds Using Semiempirical and Information-Based Descriptors J. Chem. Inf. Model. 2007, 47, 450-459
19. a, and logD J. Chem. Inf. Comput. Sci. 2002, 42, 796-805
20. a by Molecular Tree Structured Fingerprints and PLS J. Chem. Inf. Comp. Sci. 2003, 43, 870-879
21. Lee, A. C.; Shedden, K.; Rosania, G. R.; Crippen, G. M. J. Chem. Inf. Model. 2008, 48, 1379-1388
22. Howard, P.; Meylan, W. Physical/Chemical Property Database (PHYSPROP); Syracuse Research Corporation, Environmental Science Center: North Syracuse NY, 1999.
23. a of Phenols in Different Solvents QSAR Comb. Sci. 2007, 26, 385-397
24. a Prediction Using Group Philicity J. Phys. Chem. A 2006, 110, 6540-6544
25. a Prediction Method Using Grid Molecular Interaction Fields J. Chem. Inf. Model. 2007, 47, 2172-2181
26. Habibi-Yangjeh, A.; Danandeh-Jenagharad, M.; Nooshyar, M. Prediction Acidity Constant of Various Benzoic Acids and Phenols in Water Using Linear and Nonlinear QSPR Models Bull. Korean Chem. Soc. 2005, 26, 2007-2016
27. a for Benzoic Acids in Different Solvents QSAR Comb. Sci. 2008, 27, 563-581
28. a Values Using Intermolecular Structure and Properties of Hydrogen-Bonded Complexes J. Phys. Chem. A 2008, 112, 775-782
29. Silverman, B. D.; Platt, D. E. Comparative Molecular Moment Analysis (CoMMA): 3D-QSAR without Molecular Superposition J. Med. Chem. 1996, 39, 2129-2140
30. a Values of Protonated Benzimidazoles (part 1) J. Phys. Chem. B 2006, 110, 9270-9279 (Pubitemid 43829023)
31. Halle, J. C.; Lelievre, J.; Terrier, F. Solvent effect on preferred protonation sites in nicotinate and isonicotinate anions Can. J. Chem. 1996, 74, 613-620
32. Schüürmann, G. Quantum Chemical Descriptors in Structure-Activity Relationships-Calculation, Interpretation and Comparison of Methods. In Predicting Chemical Toxicity and Fate. Cronin, M. T. D.; Livingstone, D. J., Eds.; CRC Press: Boca Raton, FL, 2004, pp 85 - 149.
33. Dewar, M. J. S.; Zoebisch, E. G.; Healy, E. F.; Stewart, J. J. P. The Development and Use of Quantum-Mechanical Molecular-Models. 76. AM1-A New General-Purpose Quantum-Mechanical Molecular-Model J. Am. Chem. Soc. 1985, 107, 3902-3909
34. Karickhoff, S. W.; Carreira, L. A.; Hilal, S. H. SPARC Performs Automated Reasoning in Chemistry; University of Georgia: Athens, GA; http://ibmlc2.chem. uga.edu/sparc/. Accessed September 4, 2010.
35. Schüürmann, G.; Ebert, R.-U.; Chen, J.; Wang, B.; Kühne, R. External Validation and Prediction Employing the Predictive Squared Correlation Coefficient - Test Set Activity Mean vs Training Set Activity Mean J. Chem. Inf. Model. 2008, 48, 2140-2145
36. Schwöbel, J.; Ebert, R.-U.; Kühne, R.; Schüürmann, G. Modeling the H bond Donor Strength of -OH, -NH, and -CH Sites by Local Molecular Parameters J. Comput. Chem. 2009, 30, 1454-1464
37. Schwöbel, J.; Ebert, R.-U.; Kühne, R.; Schüürmann, G. Prediction of the Intrinsic Hydrogen Bond Acceptor Strength of Organic Compounds by Local Molecular Parameters J. Chem. Inf. Model. 2009, 49, 956-962
38. Schwöbel, J.; Ebert, R.-U.; Kühne, R.; Schüürmann, G. Prediction of the Intrinsic Hydrogen Bond Acceptor Strength of Chemical Substances from Molecular Structure J. Phys. Chem. A 2009, 113, 10104-10112