메뉴 건너뛰기




Volumn 5, Issue 4, 2013, Pages

Predicting pKa values from EEM atomic charges

Author keywords

Dissociation constant; EEM; Electronegativity equalization method; Partial atomic charges; QM; QSPR; Quantitative structure property relationship; Quantum mechanics

Indexed keywords


EID: 84879945263     PISSN: None     EISSN: 17582946     Source Type: Journal    
DOI: 10.1186/1758-2946-5-18     Document Type: Article
Times cited : (18)

References (47)
  • 1
    • 0036017359 scopus 로고    scopus 로고
    • a determination of drugs using pressure-assisted capillary electrophoresis with photodiode array detection in drug discovery
    • DOI 10.1002/jps.10087
    • Ishihama Y Nakamura M Miwa T Kajima T Asakawa N: A rapid method for pKa determination of drugs using pressure-assisted capillary electrophoresis with photodiode array detection in drug discovery. J Pharm Sci 2002 91(4):933-942. (Pubitemid 34640917)
    • (2002) Journal of Pharmaceutical Sciences , vol.91 , Issue.4 , pp. 933-942
    • Ishihama, Y.1    Nakamura, M.2    Miwa, T.3    Kajima, T.4    Asakawa, N.5
  • 3
    • 72149101372 scopus 로고    scopus 로고
    • The pka distribution of drugs: Application to drug discovery
    • Manallack D: The pKa distribution of drugs: Application to drug discovery. Perspect Med Chem 2007 1:25-38.
    • (2007) Perspect Med Chem , vol.1 , pp. 25-38
    • Manallack, D.1
  • 4
    • 33846204780 scopus 로고    scopus 로고
    • a screening and prediction amenable for ADME profiling
    • DOI 10.1517/17425255.2.1.139
    • Wan H Ulander J: High-throughput pKa screening and prediction amenable for ADME profiling. Expert Opin DrugMetabx Toxicol 2006 2:139-155. (Pubitemid 46100733)
    • (2006) Expert Opinion on Drug Metabolism and Toxicology , vol.2 , Issue.1 , pp. 139-155
    • Wan, H.1    Ulander, J.2
  • 7
    • 0033915678 scopus 로고    scopus 로고
    • Recent developments in structure-based drug design
    • Klebe G: Recent developments in structure-based drug design. JMolMed 2000 78:269-281. (Pubitemid 30489711)
    • (2000) Journal of Molecular Medicine , vol.78 , Issue.5 , pp. 269-281
    • Klebe, G.1
  • 9
    • 79955711312 scopus 로고    scopus 로고
    • K orner r tetko iv: Predicting the pka of smallmolecules
    • Rupp M K orner R Tetko IV: Predicting the pKa of smallmolecules. Comb Chem High Throughput Screen 2010 14(5):307-327.
    • (2010) Comb Chem High Throughput Screen , vol.14 , Issue.5 , pp. 307-327
    • Rupp, M.1
  • 11
    • 73949145040 scopus 로고    scopus 로고
    • A universal approach for continuum solvent pka calculations: Are we there yet?
    • Ho J Coote M: A universal approach for continuum solvent pKa calculations: Are we there yet? Theor Chim Acta 2010 125(1-2): 3-21.
    • (2010) Theor Chim Acta , vol.125 , Issue.2 , pp. 3-21
    • Ho, J.1    Coote, M.2
  • 12
    • 0011786864 scopus 로고
    • Prediction of the strengths of organic bases
    • Clark J Perrin DD: Prediction of the strengths of organic bases. Q ReV Chem Soc 1964 18:295-320.
    • (1964) Q ReV Chem Soc , vol.18 , pp. 295-320
    • Clark, J.1    Perrin, D.D.2
  • 14
    • 33644855553 scopus 로고    scopus 로고
    • Decision tree methods in pharmaceutical research
    • Blower PE Cross KP: Decision tree methods in pharmaceutical research. Curr TopMed Chem 2006 6:31-39.
    • (2006) Curr TopMed Chem , vol.6 , pp. 31-39
    • Blower, P.E.1    Cross, K.P.2
  • 16
    • 84961978266 scopus 로고    scopus 로고
    • a calculations for carboxylic acids using complete basis set and Gaussian-n models combined with continuum solvation methods
    • DOI 10.1063/1.1337862
    • Toth AM Liptak MD Phillips DL Shields GC: Accurate relative pKa calculations for carboxylic acids using complete basis set and Gaussian-n models combined with continuum solvationmethods. J Chem Phys 2001 114:4595-4606. (Pubitemid 32287438)
    • (2001) Journal of Chemical Physics , vol.114 , Issue.10 , pp. 4595-4606
    • Toth, A.M.1    Liptak, M.D.2    Phillips, D.L.3    Shields, G.C.4
  • 18
    • 34247255912 scopus 로고    scopus 로고
    • a for druglike compounds using semiempirical and information-based descriptors
    • DOI 10.1021/ci600285n
    • Jelfs S Ertl P Selzer P: Estimation of pKa for druglike compounds using semiempirical and information-based descriptors. J Chem Inf Model 2007 47:450-459. (Pubitemid 46615947)
    • (2007) Journal of Chemical Information and Modeling , vol.47 , Issue.2 , pp. 450-459
    • Jelfs, S.1    Ertl, P.2    Selzer, P.3
  • 19
    • 11744331329 scopus 로고
    • Estimation of pka for organic oxyacids using calculated atomic charges
    • Dixon SL Jurs PC: Estimation of pKa for organic oxyacids using calculated atomic charges. J Comput Chem 1993 14:1460-1467.
    • (1993) J Comput Chem , vol.14 , pp. 1460-1467
    • Dixon, S.L.1    Jurs, P.C.2
  • 20
    • 33845768501 scopus 로고    scopus 로고
    • Klein oder t gasteiger j: Prediction of pka values for aliphatic carboxylic acids and alcohols with empirical atomic charge descriptors
    • Zhang J Klein oder T Gasteiger J: Prediction of pKa values for aliphatic carboxylic acids and alcohols with empirical atomic charge descriptors. J Chem Inf Model 2006 46:2256-2266.
    • (2006) J Chem Inf Model , vol.46 , pp. 2256-2266
    • Zhang, J.1
  • 21
    • 0032890374 scopus 로고    scopus 로고
    • Estimating the pK(a) of phenols, carboxylic acids and alcohols from semi-empirical quantum chemical methods
    • DOI 10.1016/S0045-6535(98)00172-6, PII S0045653598001726
    • Citra MJ: Estimating the pKa of phenols carboxylic acids and alcohols from semi-empirical quantum chemical methods. Chemosphere 1999 1:191-206. (Pubitemid 28537717)
    • (1999) Chemosphere , vol.38 , Issue.1 , pp. 191-206
    • Citra, M.J.1
  • 22
    • 0037026962 scopus 로고    scopus 로고
    • Comparison of different atomic charge schemes for predicting pka variations in substituted anilines and phenols
    • Gross KC Seybold PG Hadad CM: Comparison of different atomic charge schemes for predicting pKa variations in substituted anilines and phenols. Int J Quantum Chem 2002 90:445-458.
    • (2002) Int J Quantum Chem , vol.90 , pp. 445-458
    • Gross, K.C.1    Seybold, P.G.2    Hadad, C.M.3
  • 23
    • 73049111151 scopus 로고    scopus 로고
    • Correlations between quantum chemical indices and the pkas of a diverse set of organic phenols
    • Kreye WC Seybold PG: Correlations between quantum chemical indices and the pKas of a diverse set of organic phenols. Int J Quantum Chem 2009 109:3679-3684.
    • (2009) Int J Quantum Chem , vol.109 , pp. 3679-3684
    • Kreye, W.C.1    Seybold, P.G.2
  • 24
    • 80051968896 scopus 로고    scopus 로고
    • Predicting pka values of substituted phenols from atomic charges: Comparison of different quantum mechanical methods and charge distribution schemes
    • Svobodova Varekova R Geidl S Ionescu CM Skrehota O Kudera M Sehnal D Bouchal T Abagyan R Huber HJ Koca J: Predicting pKa values of substituted phenols from atomic charges: Comparison of different quantum mechanical methods and charge distribution schemes. J Chem Inf Model 2011 51(8):1795-1806.
    • (2011) J Chem Inf Model , vol.51 , Issue.8 , pp. 1795-1806
    • Svobodova, V.1
  • 25
    • 0000976633 scopus 로고
    • Electronic structures of molecules xi. Electroaffinity molecular orbitals and dipole moments
    • Mulliken RS: Electronic structures of molecules XI. Electroaffinity molecular orbitals and dipole moments. J Chem Phys 1935 3(9):573-585.
    • (1935) J Chem Phys , vol.3 , Issue.9 , pp. 573-585
    • Mulliken, R.S.1
  • 26
    • 36849131708 scopus 로고
    • Criteria for construction of good self-consistent-field molecular orbital wave functions and significance of lcao-mo population analysis
    • Mulliken RS: Criteria for construction of good self-consistent-field molecular orbital wave functions and significance of LCAO-MO population analysis. J Chem Phys 1962 36(12):3428-3439.
    • (1962) J Chem Phys , vol.36 , Issue.12 , pp. 3428-3439
    • Mulliken, R.S.1
  • 27
    • 16444378435 scopus 로고
    • On the non-orthogonality problem connected with the use of atomic wave functions in the theory ofmolecules and crystals
    • Lowdin PO: On the non-orthogonality problem connected with the use of atomic wave functions in the theory ofmolecules and crystals. J Chem Phys 1950 18(3):365-375.
    • (1950) J Chem Phys , vol.18 , Issue.3 , pp. 365-375
    • Lowdin, P.O.1
  • 30
    • 0001553329 scopus 로고
    • Bonded-atom fragments for describing molecular charge-densities
    • Hirshfeld FL: Bonded-atom fragments for describing molecular charge-densities. Theor Chim Acta 1977 44(2):129-138.
    • (1977) Theor Chim Acta , vol.44 , Issue.2 , pp. 129-138
    • Hirshfeld, F.L.1
  • 31
    • 84986513567 scopus 로고
    • Determining atom-centeredmonopoles from molecular electrostatic potentials - The need for high sampling density in formamide conformational-analysis
    • Breneman CM Wiberg KB: Determining atom-centeredmonopoles from molecular electrostatic potentials - the need for high sampling density in formamide conformational-analysis. J Comput Chem 1990 11(3):361-373.
    • (1990) J Comput Chem , vol.11 , Issue.3 , pp. 361-373
    • Breneman, C.M.1    Wiberg, K.B.2
  • 32
    • 84986492477 scopus 로고
    • Atomic charges derived from semiempiricalmethods
    • Besler BH Merz KM Kollman PA: Atomic charges derived from semiempiricalmethods. J Comput Chem 1990 11(4):431-439.
    • (1990) J Comput Chem , vol.11 , Issue.4 , pp. 431-439
    • Besler, B.H.1    Merz, K.M.2    Kollman, P.A.3
  • 33
    • 17744363335 scopus 로고    scopus 로고
    • Accurate partial atomic charges for high-energy molecules using class IV charge models with the MIDI! basis set
    • DOI 10.1007/s00214-004-0624-x
    • Kelly CP Cramer CJ Truhlar DG: Accurate partial atomic charges for high-energymolecules using class IV charge models with the MIDI! basis set. Theor Chem Acc 2005 113(3):133-151. (Pubitemid 40576892)
    • (2005) Theoretical Chemistry Accounts , vol.113 , Issue.3 , pp. 133-151
    • Kelly, C.P.1    Cramer, C.J.2    Truhlar, D.G.3
  • 34
    • 84986517064 scopus 로고
    • Approaches to charge calculations in molecularmechanics
    • Abraham RJ Griffiths L Loftus P: Approaches to charge calculations in molecularmechanics. J Comput Chem 1982 3(3):407-416.
    • (1982) J Comput Chem , vol.3 , Issue.3 , pp. 407-416
    • Abraham, R.J.1    Griffiths, L.2    Loftus, P.3
  • 35
    • 49149147973 scopus 로고
    • Iterative partial equalization of orbital electronegativity - A rapid access to atomic charges
    • Gasteiger J Marsili M: Iterative partial equalization of orbital electronegativity - a rapid access to atomic charges. Tetrahedron 1980 36(22):3219-3228.
    • (1980) Tetrahedron , vol.36 , Issue.22 , pp. 3219-3228
    • Gasteiger, J.1    Marsili, M.2
  • 36
    • 0037013378 scopus 로고    scopus 로고
    • A fastmethod for calculating geometry-dependent net atomic charges for polypeptides
    • Cho KH Kang YK No KT Scheraga HA: A fastmethod for calculating geometry-dependent net atomic charges for polypeptides. J Phys Chem B 2001 105(17):3624-3634.
    • (2001) J Phys Chem B , vol.105 , Issue.17 , pp. 3624-3634
    • Cho, K.H.1    Kang, Y.K.2    No, K.T.3    Scheraga, H.A.4
  • 37
    • 33846173582 scopus 로고    scopus 로고
    • Atomic charges via electronegativity equalization: Generalizations and perspectives
    • Oliferenko AA Pisarev SA Palyulin VA Zefirov NS: Atomic charges via electronegativity equalization: Generalizations and perspectives. Adv Quantum Chem 2006 51:139-156.
    • (2006) Adv Quantum Chem , vol.51 , pp. 139-156
    • Oliferenko, A.A.1    Pisarev, S.A.2    Palyulin, V.A.3    Zefirov, N.S.4
  • 38
    • 41749108825 scopus 로고    scopus 로고
    • Parameterization of empirical schemes of partial atomic charge calculation for reproducing themolecular electrostatic potential
    • Shulga DA Oliferenko AA Pisarev SA Palyulin VA Zefirov NS: Parameterization of empirical schemes of partial atomic charge calculation for reproducing themolecular electrostatic potential. Dokl Chem 2008 419:57-61.
    • (2008) Dokl Chem , vol.419 , pp. 57-61
    • Shulga, D.A.1    Oliferenko, A.A.2    Pisarev, S.A.3    Palyulin, V.A.4    Zefirov, N.S.5
  • 39
    • 0342876686 scopus 로고
    • Electronegativity equalization method for the calculation of atomic charges inmolecules
    • Mortier WJ Ghosh SK Shankar S: Electronegativity equalization method for the calculation of atomic charges inmolecules. J Am Chem Soc 1986 108:4315-4320.
    • (1986) J Am Chem Soc , vol.108 , pp. 4315-4320
    • Mortier, W.J.1    Ghosh, S.K.2    Shankar, S.3
  • 40
    • 33748481964 scopus 로고
    • Charge equilibration for molecular-dynamics simulations
    • Rappe AK Goddard WA: Charge equilibration for molecular-dynamics simulations. J Phys Chem 1991 95(8):3358-3363.
    • (1991) J Phys Chem , vol.95 , Issue.8 , pp. 3358-3363
    • Rappe, A.K.1    Goddard, W.A.2
  • 41
    • 33748576966 scopus 로고    scopus 로고
    • A generalization of the charge equilibrationmethod for nonmetallicmaterials
    • Nistor RA Polihronov JG Muser MH Mosey NJ: A generalization of the charge equilibrationmethod for nonmetallicmaterials. J Chem Phys 2006 125(9):094108-094118.
    • (2006) J Chem Phys , vol.125 , Issue.9 , pp. 094108-094118
    • Nistor, R.A.1    Polihronov, J.G.2    Muser, M.H.3    Mosey, N.J.4
  • 42
    • 33749021099 scopus 로고    scopus 로고
    • a values of functional groups in protein-ligand complexes
    • DOI 10.1002/prot.21110
    • Czodrowski P Dramburg I Sotriffer CA Klebe G: Development validation and application of adapted PEOE charges to estimate pKa values of functional groups in protein-ligand complexes. Proteins Struct Funct Bioinf 2006 65:424-437. (Pubitemid 44454114)
    • (2006) Proteins: Structure, Function and Genetics , vol.65 , Issue.2 , pp. 424-437
    • Czodrowski, P.1    Dramburg, I.2    Sotriffer, C.A.3    Klebe, G.4
  • 43
    • 34247208582 scopus 로고    scopus 로고
    • a values
    • DOI 10.1021/ci600295z
    • Gieleciak R Polanski J: Modeling robust QSAR. 2. Iterative variable elimination schemes for CoMSA: Application for modeling benzoic acid pKa values. J Chem Inf Model 2007 47:547-556. (Pubitemid 46615956)
    • (2007) Journal of Chemical Information and Modeling , vol.47 , Issue.2 , pp. 547-556
    • Gieleciak, R.1    Polanski, J.2
  • 44
    • 34547615155 scopus 로고    scopus 로고
    • Electronegativity equalization method: Parameterization and validation for large sets of organic organohalogene and organometalmolecule
    • Svobodova V Electronegativity equalization method: Parameterization and validation for large sets of organic organohalogene and organometalmolecule. Int J Mol Sci 2007 8:572-582.
    • (2007) Int J Mol Sci , vol.8 , pp. 572-582
    • Svobodova, V.1
  • 45
    • 85013533965 scopus 로고
    • Probing the reactivity of different sites within amolecule or solid by direct computation ofmolecular sensitivities via an extension of the electronegativity equalization method
    • Baekelandt BG Mortier WJ Lievens JL Schoonheydt RA: Probing the reactivity of different sites within amolecule or solid by direct computation ofmolecular sensitivities via an extension of the electronegativity equalization method. J AmChemSoc 1991 113(18):6730-6734.
    • (1991) J AmChemSoc , vol.113 , Issue.18 , pp. 6730-6734
    • Baekelandt, B.G.1    Mortier, W.J.2    Lievens, J.L.3    Schoonheydt, R.A.4
  • 46
    • 65949085814 scopus 로고    scopus 로고
    • Electronegativity equalization method: Parameterization and validation for organic molecules using the merz-kollman-singh charge distribution scheme
    • Jirouskova Z Svobodova Varekova R Vanek J Koca J: Electronegativity equalization method: Parameterization and validation for organic molecules using the Merz-Kollman-Singh charge distribution scheme. J Comput Chem 2009 30:1174-1178.
    • (2009) J Comput Chem , vol.30 , pp. 1174-1178
    • Jirouskova, Z.1    Svobodova, V.R.2    Vanek, J.3    Koca, J.4
  • 47
    • 33746865286 scopus 로고    scopus 로고
    • Toward an alternative hardness kernel matrix structure in the Electronegativity Equalization Method (EEM)
    • DOI 10.1021/ci050505e
    • Chaves J Barroso JM Bultinck P Carbo-Dorca R: Toward an alternative hardness kernelmatrix structure in the Electronegativity Equalization Method (EEM). J Chem Inf Model 2006 46(4):1657-1665. (Pubitemid 44185692)
    • (2006) Journal of Chemical Information and Modeling , vol.46 , Issue.4 , pp. 1657-1665
    • Chaves, J.1    Barroso, J.M.2    Bultinck, P.3    Carbo-Dorca, R.4


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.