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Comparison of parametric methods with quantum mechanics based models to estimate Clog P values Cover

Comparison of parametric methods with quantum mechanics based models to estimate Clog P values

Open Access
|May 2025

References

  1. Adamo C, Barone V (1999) The Journal of Chemical Physics 110: 6158—6170.
  2. Arnott JA, Planey SL (2012) Expert Opinion on Drug Discovery 7: 863—875.
  3. Avdeef A (1992) Quantitative Structure-Activity Relationships 11: 510—517.
  4. Avdeef A (1993) Journal of Pharmaceutical Sciences 82: 183—190.
  5. Bannwarth C, Caldeweyher E, Ehlert S, Hansen A, Pracht P, Seibert J, Spicher S, Grimme S (2020) WIREs Computational Molecular Science 11: e1493.
  6. Bannwarth C, Ehlert S, Grimme S (2019) Journal of Chemical Theory and Computation 15: 1652—1671.
  7. Becke AD (1988) Physical Review A 38: 3098—3100.
  8. Becke AD (1993) The Journal of Chemical Physics 98: 5648—5652.
  9. Bertrand B, Casini A (2014) Dalton Transactions 43: 4209—4219.
  10. Cao Y, Charisi A, Cheng L-C, Jiang T, Girke T (2008) Bioinformatics 24: 1733—1734.
  11. Carrupt P, Testa B, Gaillard P (1997) Computational Approaches to Lipophilicity: Methods and Applications. In Reviews in Computational Chemistry, Volume 11, pp. 241—315.
  12. Cheng T, Zhao Y, Li X, Lin F, Xu Y, Zhang X, Li Y, Wang R, Lai L (2007) Journal of Chemical Information and Modeling 47: 2140—2148.
  13. Clark T, Chandrasekhar J, Spitznagel GW, Von P, Schleyer R (1983) Journal of Computational Chemistry 3: 294—301.
  14. Daina A, Michielin O, Zoete V (2014) Journal of Chemical Information and Modeling 54: 3284—3301.
  15. Daina A, Michielin O, Zoete V (2017) Scientific Reports 7: 42717.
  16. Daina A, Zoete V (2016) ChemMedChem 11: 1117—1121.
  17. Donovan SF, Pescatore MC (2002) Journal of Chromatography A 952: 47—61.
  18. Egan WJ, Merz KM, Baldwin JJ (2000) Journal of Medicinal Chemistry 43: 3867—3877.
  19. Ehlert S, Stahn M, Spicher S, Grimme S (2021) Journal of Chemical Theory and Computation 17: 4250—4261.
  20. Frisch MJ, Trucks GW, Schlegel HB, Scuseria GE, Robb MA, Cheeseman JR, Scalmani G, Barone V, Petersson GA, Nakatsuji H, Li X, Caricato M, Marenich AV, Bloino J, Janesko BG, Gomperts R, Mennucci B, Hratchian HP, Ortiz JV, Izmaylov AF, Sonnenberg JL, Williams-Young D, Ding F, Lipparini F, Egidi F, Goings J, Peng B, Petrone A, Henderson T, Ranasinghe D, Zakrzewski VG, Gao J, Rega N, Zheng G, Liang W, Hada M, Ehara M, Toyota K, Fukuda R, Hasegawa J, Ishida M, Nakajima T, Honda Y, Kitao O, Nakai H, Vreven T, Throssell K, Montgomery JA, Jr. Peralta JE, Ogliaro F, Bearpark MJ, Heyd JJ, Brothers EN, Kudin KN, Staroverov VN, Keith TA, Kobayashi R, Normand J, Raghavachari K, Rendell AP, Burant JC, Iyengar SS, Tomasi J, Cossi M, Millam JM, Klene M, Adamo C, Cammi R, Ochterski JW, Martin RL, Morokuma K, Farkas O, Foresman JB, Fox DJ (2016) Gaussian Inc Wallingford CT 1: Revision B. 01.
  21. Ghose AK, Viswanadhan VN, Wendoloski JJ (1999) Journal of Combinatorial Chemistry 1: 55—68.
  22. Giaginis C, Tsopelas F, Tsantili-Kakoulidou A (2018) The Impact of Lipophilicity in Drug Discovery: Rapid Measurements by Means of Reversed-Phase HPLC. In Rational Drug Design, (Humana New York, NY), pp. 217—228.
  23. Hay M, Thomas DW, Craighead JL, Economides C, Rosenthal J (2014) Nature Biotechnology 32: 40—51. Hertzberg RP, Pope AJ (2000) Current Opinion in Chemical Biology 4: 445—451.
  24. Jinsong S, Qifeng J, Xing C, Hao Y, Wang L (2024) Communications Chemistry 7: 20.
  25. Jorgensen WL (1989) Accounts of Chemical Research 22: 184—189.
  26. Jorgensen WL, Briggs JM, Contreras MLeonor (1990) The Journal of Physical Chemistry 94: 1683—1686.
  27. Kaliszan R, Haber P, Bączek T, Siluk D, Valko K (2002) Journal of Chromatography A 965: 117—127.
  28. Karges J, Giardini MA, Blacque O, Woodworth B, Siqueira-Neto JL, Cohen SM (2023) Chemical Science 14: 711—720.
  29. Kastl A, Wilbuer A, Merkel AL, Feng L, Di Fazio P, Ocker M, Meggers E (2012) Chemical Communications 48: 1863—1865.
  30. Kim S, Chen J, Cheng T, Gindulyte A, He J, He S, Li Q, Shoemaker BA, Thiessen PA, Yu B, Zaslavsky L, Zhang J, Bolton EE (2019) Nucleic Acids Research 47: D1102—D1109.
  31. Kim S, Chen J, Cheng T, Gindulyte A, He J, He S, Li Q, Shoemaker BA, Thiessen PA, Yu B, Zaslavsky L, Zhang J, Bolton EE (2021) Nucleic Acids Research 49: D1388—D1395.
  32. Klopman G, Li J-Y, Wang S, Dimayuga M (1994) Journal of Chemical Information and Computer Sciences 34: 752—781.
  33. Krishnan R, Binkley JS, Seeger R, Pople JA (1980) The Journal of Chemical Physics 72: 650—654.
  34. Langenaeker W, Gert T, Winter DH (2010) Silicos-it. Lee C, Yang W, Parr RG (1988) Physical Review B 37: 785—789.
  35. Lipinski CA, Lombardo F, Dominy BW, Feeney PJ (2001) Advanced Drug Delivery Reviews 46: 3—26.
  36. Mannhold R, Poda GI, Ostermann C, Tetko IV (2009) Journal of Pharmaceutical Sciences 98: 861—893.
  37. Marenich AV, Cramer CJ, Truhlar DG (2009) The Journal of Physical Chemistry B 113: 6378—6396.
  38. MarvinSketch was used for drawing displaying and characterizing chemical structures and reactions; Marvin 17.21.0; Chemaxon (2020).
  39. McLean AD, Chandler GS (1980) The Journal of Chemical Physics 72: 5639—5648.
  40. Meylan WM, Howard PH (1995) Journal of Pharmaceutical Sciences 84: 83—92.
  41. Meylan WM, Howard PH (2000) Perspectives in Drug Discovery and Design 19: 67—84.
  42. Michalík M, Lukeš V (2016) Acta Chimica Slovaca 9: 89—94.
  43. Miertuš S, Scrocco E, Tomasi J (1981) Chemical Physics 55: 117—129.
  44. Miertuš S, Tomasi J (1982) Chemical Physics 65: 239—245.
  45. Moriguchi I, Hirono S, Liu Q, Nakagome I, Matsushita Y (1992) Chemical and Pharmaceutical Bulletin 40: 127—130.
  46. Moriguchi I, Hirono S, Nakagome I, Hirano H (1994) Chemical and Pharmaceutical Bulletin 42: 976—978.
  47. Muegge I, Heald SL, Brittelli D (2001) Journal of Medicinal Chemistry 44: 1841—1846.
  48. Nedyalkova MA, Madurga S, Tobiszewski M, Simeonov V (2019) Journal of Chemical Information and Modeling 59: 2257—2263.
  49. O’Boyle NM, Banck M, James CA, Morley C, Vandermeersch T, Hutchison GR (2011) Journal of Cheminformatics 3: 33.
  50. OECD 107 Method (1995) OECD guideline for the testing of chemicals adopted by the Council on 27th July 1995 Partition Coefficient (n-octanol/water): Shake Flask Method.
  51. Pages BJ, Ang DL, Wright EP, Aldrich-Wright JR (2015) Dalton Transactions 44: 3505—3526.
  52. Pascual‐ahuir JL, Silla E, Tuńon I (1994) Journal of Computational Chemistry 15: 1127—1138.
  53. Perdew JP, Burke K, Ernzerhof M (1996) Physical Review Letters 77: 3865—3868.
  54. Perdew JP, Burke K, Ernzerhof M (1997) Physical Review Letters 78: 1396—1396.
  55. Petersson GA, Al-Laham MA (1991) The Journal of Chemical Physics 94: 6081—6090.
  56. Petersson GA, Bennett A, Tensfeldt TG, Al-Laham MA, Shirley WA, Mantzaris J (1988) The Journal of Chemical Physics 89: 2193—2218.
  57. Rassolov VA, Pople JA, Ratner MA, Windus TL (1998) The Journal of Chemical Physics 109: 1223—1229.
  58. Rassolov VA, Ratner MA, Pople JA, Redfern PC, Curtiss LA (2001) Journal of Computational Chemistry 22: 976—984.
  59. Thompson MA (2004) Molecular Docking Using ArgusLab, an Efficient Shape-Based Search Algorithm and the a Score Scoring Function (Philadelphia).
  60. US EPA (1996) EPA Product properties test guideline. OPPTS 830.7550 Partition coefficient (n-octanol/H2O), shake flask method.
  61. Vosko SH, Wilk L, Nusair M (1980) Canadian Journal of Physics 58: 1200—1211.
  62. Wang R, Fu Y, Lai L (1997) Journal of Chemical Information and Computer Sciences 37: 615—621.
  63. Wildman SA, Crippen GM (1999) Journal of Chemical Information and Computer Sciences 39: 868—873.
  64. Zhao Y, Truhlar DG (2008) Theoretical Chemistry Accounts 120: 215—241.
DOI: https://doi.org/10.2478/acs-2025-0002 | Journal eISSN: 1339-3065 | Journal ISSN: 1337-978X
Language: English
Page range: 8 - 23
Published on: May 20, 2025
Published by: Slovak University of Technology in Bratislava
In partnership with: Paradigm Publishing Services
Publication frequency: 2 issues per year
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© 2025 Dávid Zajaček, Andrej Hlinčík, Lukas Bucinsky, Matej Uhliar, published by Slovak University of Technology in Bratislava
This work is licensed under the Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 License.