메뉴 건너뛰기




Volumn 47, Issue 2, 2007, Pages 686-694

Quantum mechanical energy-based screening of combinatorially generated library of tautomers. TauTGen: A tautomer generator program

Author keywords

[No Author keywords available]

Indexed keywords

COMBINATORIAL MATHEMATICS; DENSITY FUNCTIONAL THEORY; OPTIMIZATION; PERTURBATION TECHNIQUES; QUANTUM THEORY;

EID: 34247235751     PISSN: 15499596     EISSN: 1549960X     Source Type: Journal    
DOI: 10.1021/ci6002703     Document Type: Article
Times cited : (33)

References (44)
  • 1
    • 0038255018 scopus 로고    scopus 로고
    • Chemoinformatics and Drug Discovery
    • Xu, J.; Hagler, A. Chemoinformatics and Drug Discovery. Molecules 2002, 7, 566-600.
    • (2002) Molecules , vol.7 , pp. 566-600
    • Xu, J.1    Hagler, A.2
  • 2
    • 1642357706 scopus 로고    scopus 로고
    • The Many Roles of Computation in Drug Discovery
    • Jorgensen, W. L. The Many Roles of Computation in Drug Discovery. Science 2004, 303, 1813-1818.
    • (2004) Science , vol.303 , pp. 1813-1818
    • Jorgensen, W.L.1
  • 3
    • 34247257934 scopus 로고    scopus 로고
    • Perry J. K. Abstr. Pap. Am. Chem. Soc. 1997, 213(1), 176.
    • Perry J. K. Abstr. Pap. Am. Chem. Soc. 1997, 213(1), 176.
  • 4
    • 13844281250 scopus 로고    scopus 로고
    • Computational estimation of logarithm of n-octanol/air partition coefficient and subcooled vapor pressures of 75 chloronaphthalene congeners
    • Puzyn, T.; Falandysz, J. Computational estimation of logarithm of n-octanol/air partition coefficient and subcooled vapor pressures of 75 chloronaphthalene congeners. Atmos. Environ. 2005, 39, 1439-1446.
    • (2005) Atmos. Environ , vol.39 , pp. 1439-1446
    • Puzyn, T.1    Falandysz, J.2
  • 5
    • 0037152393 scopus 로고    scopus 로고
    • Hay, B. P.; Firman, T. K. HostDesigner: A Program for the de Novo Structure-Based Design of Molecular Receptors with Binding Sites that Complement Metal Ion Guests. Inorg. Chem. 2002, 41, 5502-5512.
    • Hay, B. P.; Firman, T. K. HostDesigner: A Program for the de Novo Structure-Based Design of Molecular Receptors with Binding Sites that Complement Metal Ion Guests. Inorg. Chem. 2002, 41, 5502-5512.
  • 6
    • 14844340751 scopus 로고
    • Proton Tunneling in DNA and its Biological Implications
    • Lowdin, P. O. Proton Tunneling in DNA and its Biological Implications. Rev. Mod. Phys. 1963, 35, 724-732.
    • (1963) Rev. Mod. Phys , vol.35 , pp. 724-732
    • Lowdin, P.O.1
  • 7
    • 0042117475 scopus 로고
    • Density Functional Study of Tautomerism of Uracil and Cytosine
    • Estrin, D. A.; Paglieri, L.; Corongiu, G. A. Density Functional Study of Tautomerism of Uracil and Cytosine. J. Phys. Chem. 1994, 98, 5653-5660.
    • (1994) J. Phys. Chem , vol.98 , pp. 5653-5660
    • Estrin, D.A.1    Paglieri, L.2    Corongiu, G.A.3
  • 8
    • 0031555450 scopus 로고    scopus 로고
    • Ab initio study of intramolecular proton transfer reactions in cytosine
    • Morpugo, S.; Bossa, M.; Morpugo, G. O. Ab initio study of intramolecular proton transfer reactions in cytosine. Chem. Phys. Lett. 1997, 280, 233-238.
    • (1997) Chem. Phys. Lett , vol.280 , pp. 233-238
    • Morpugo, S.1    Bossa, M.2    Morpugo, G.O.3
  • 9
    • 0037149133 scopus 로고    scopus 로고
    • Relative Stabilities of Three Low-Energy Tautomers of Cytosine: A Coupled-Cluster Electron Correlation Study
    • and references cited therein
    • Fogarasi, G. Relative Stabilities of Three Low-Energy Tautomers of Cytosine: A Coupled-Cluster Electron Correlation Study. J. Phys. Chem. A 2002, 106, 1381-1390, and references cited therein.
    • (2002) J. Phys. Chem. A , vol.106 , pp. 1381-1390
    • Fogarasi, G.1
  • 10
    • 34247190213 scopus 로고    scopus 로고
    • Canonicalization and Enumeration of Tautomers, in Innovative Computational Applications
    • San Francisco, October 25-27
    • Sayle, R.; Delany, J. Canonicalization and Enumeration of Tautomers, in Innovative Computational Applications. Institute for International Research, Sir Francis Drake Hotel, San Francisco, October 25-27, 1999.
    • (1999) Institute for International Research, Sir Francis Drake Hotel
    • Sayle, R.1    Delany, J.2
  • 13
    • 84961975587 scopus 로고    scopus 로고
    • Stabilization of very rare tautomers of 1-methylcytosine by an excess electron
    • Harańczyk, M.; Rak, J.; Gutowski, M. Stabilization of very rare tautomers of 1-methylcytosine by an excess electron. J. Phys. Chem. A 2005, 109, 11495-11503.
    • (2005) J. Phys. Chem. A , vol.109 , pp. 11495-11503
    • Harańczyk, M.1    Rak, J.2    Gutowski, M.3
  • 14
    • 84961976877 scopus 로고    scopus 로고
    • Stabilization of very rare tautomers of uracyl by an excess electron
    • Bachorz, R. A.; Rak, J;. Gutowski, M. Stabilization of very rare tautomers of uracyl by an excess electron. Phys. Chem. Chem. Phys. 2005, 7, 2116-2125.
    • (2005) Phys. Chem. Chem. Phys , vol.7 , pp. 2116-2125
    • Bachorz, R.A.1    Rak, J.2    Gutowski, M.3
  • 15
    • 84961978388 scopus 로고    scopus 로고
    • On the unusual stability of valence anions of thymine based on very rare tautomers. A computational study
    • Mazurkiewicz, K.; Bachorz, R. A.; Gutowski, M.; Rak, J. On the unusual stability of valence anions of thymine based on very rare tautomers. A computational study. J. Phys. Chem. B 2006, 110, 24696-24707.
    • (2006) J. Phys. Chem. B , vol.110 , pp. 24696-24707
    • Mazurkiewicz, K.1    Bachorz, R.A.2    Gutowski, M.3    Rak, J.4
  • 16
    • 0000617357 scopus 로고    scopus 로고
    • Dipole bound, nucleic acid base anions studied via negative ion photoelectron spectroscopy
    • Hendricks, J. H.; Lyapustina, S. A.; de Clercq, H. L.; Snodgrass, T. J.; Bowen, K. H. Dipole bound, nucleic acid base anions studied via negative ion photoelectron spectroscopy. J. Chem. Phys. 1996, 104, 7788-7791.
    • (1996) J. Chem. Phys , vol.104 , pp. 7788-7791
    • Hendricks, J.H.1    Lyapustina, S.A.2    de Clercq, H.L.3    Snodgrass, T.J.4    Bowen, K.H.5
  • 17
    • 0036770134 scopus 로고    scopus 로고
    • Barrier-free intermolecular proton transfer in the uracil-glycine complex induced by excess electron attachment
    • Gutowski, M.; Dabkowska, I.; Rak, J.; Xu, S.; Nilles, J. M.; Radisic, D.; Bowen, K. H., Jr. Barrier-free intermolecular proton transfer in the uracil-glycine complex induced by excess electron attachment. Eur. Phys. J. D 2002, 20, 431-439.
    • (2002) Eur. Phys. J. D , vol.20 , pp. 431-439
    • Gutowski, M.1    Dabkowska, I.2    Rak, J.3    Xu, S.4    Nilles, J.M.5    Radisic, D.6    Bowen Jr., K.H.7
  • 19
    • 0037187138 scopus 로고    scopus 로고
    • Li, X.; Cai, Z.; Sevilla, M. D. DFT Calculations of the Electron Affinities of Nucleic Acid Bases: Dealing with Negative Electron Affinities. J. Phys. Chem. A 2002, 106, 1596-1603.
    • Li, X.; Cai, Z.; Sevilla, M. D. DFT Calculations of the Electron Affinities of Nucleic Acid Bases: Dealing with Negative Electron Affinities. J. Phys. Chem. A 2002, 106, 1596-1603.
  • 20
    • 27144487451 scopus 로고    scopus 로고
    • Finding Adiabatically Bound Anions of Guanine through Combinatorial-Computational Approach
    • Harańczyk, M.; Gutowski, M. Finding Adiabatically Bound Anions of Guanine through Combinatorial-Computational Approach. Angew. Chem. Int. Ed. 2005, 44, 6585-6588.
    • (2005) Angew. Chem. Int. Ed , vol.44 , pp. 6585-6588
    • Harańczyk, M.1    Gutowski, M.2
  • 22
    • 34247181248 scopus 로고    scopus 로고
    • Gaussian 03, Revision C.02; Frisch, M. J, Trucks, G. W, Schlegel, H. B, Scuseria, G. E, Robb, M. A, Cheeseman, J. R, Montgomery, J. A, Jr, Vreven, T, Kudin, K. N, Burant, J. C, Millam, J. M, Iyengar, S. S, Tomasi, J, Barone, V, Mennucci, B, Cossi, M, Scalmani, G, Rega, N, Petersson, G. A, Nakatsuji, H, Hada, M, Ehara, M, Toyota, K, Fukuda, R, Hasegawa, J, Ishida, M, Nakajima, T, Honda, Y, Kitao, O, Nakai, H, Klene, M, Li, X, Knox, J. E, Hratchian, H. P, Cross, J. B, Bakken, V, Adamo, C, Jaramillo, J, Gomperts, R, Stratmann, R. E, Yazyev, O, Austin, A. J, Cammi, R, Pomelli, C, Ochterski, J. W, Ayala, P. Y, Morokuma, K, Voth, G. A, Salvador, P, Dannenberg, J. J, Zakrzewski, V. G, Dapprich, S, Daniels, A. D, Strain, M. C, Farkas, O, Malick, D. K, Rabuck, A. D, Raghavachari, K, Foresman, J. B, Ortiz, J. V, Cui, Q, Baboul, A. G, Clifford, S, Cioslowski, J, Stefanov, B. B, Liu, G, Liashenko, A, Piskorz, P, Komaromi, I
    • Gaussian 03, Revision C.02; Frisch, M. J.; Trucks, G. W.; Schlegel, H. B.; Scuseria, G. E.; Robb, M. A.; Cheeseman, J. R.; Montgomery, J. A, Jr.; Vreven, T.; Kudin, K. N.; Burant, J. C.; Millam, J. M.; Iyengar, S. S.; Tomasi, J.; Barone, V.; Mennucci, B.; Cossi, M.; Scalmani, G.; Rega, N.; Petersson, G. A.; Nakatsuji, H.; Hada, M.; Ehara, M.; Toyota, K.; Fukuda, R.; Hasegawa, J.; Ishida, M.; Nakajima, T.; Honda, Y.; Kitao, O.; Nakai, H.; Klene, M.; Li, X.; Knox, J. E.; Hratchian, H. P.; Cross, J. B.; Bakken, V.; Adamo, C.; Jaramillo, J.; Gomperts, R.; Stratmann, R. E.; Yazyev, O.; Austin, A. J.; Cammi, R.; Pomelli, C.; Ochterski, J. W.; Ayala, P. Y.; Morokuma, K.; Voth, G. A.; Salvador, P.; Dannenberg, J. J.; Zakrzewski, V. G.; Dapprich, S.; Daniels, A. D.; Strain, M. C.; Farkas, O.; Malick, D. K.; Rabuck, A. D.; Raghavachari, K.; Foresman, J. B.; Ortiz, J. V.; Cui, Q.; Baboul, A. G.; Clifford, S.; Cioslowski, J.; Stefanov, B. B.; Liu, G.; Liashenko, A.; Piskorz, P.; Komaromi, I.; Martin, R. L.; Fox, D. J.; Keith, T.; Al-Laham, M. A.; Peng, C. Y.; Nanayakkara, A.; Challacombe, M.; Gill, P. M. W.; Johnson, B.; Chen, W.; Wong, M. W.; Gonzalez, C.; Pople, J. A. Gaussian, Inc.: Wallingford, CT, 2004.
  • 23
    • 4243553426 scopus 로고
    • Density-functional exchange-energy approximation with correct asymptotic behavior
    • (a) Becke, A. D. Density-functional exchange-energy approximation with correct asymptotic behavior. Phys. Rev. A 1988, 38, 3098-3100.
    • (1988) Phys. Rev. A , vol.38 , pp. 3098-3100
    • Becke, A.D.1
  • 24
    • 0000189651 scopus 로고
    • Density-functional thermochemistry. III. The role of exact Exchange
    • (b) Becke, A. D. Density-functional thermochemistry. III. The role of exact Exchange. J. Chem. Phys. 1993, 98, 5648-5652.
    • (1993) J. Chem. Phys , vol.98 , pp. 5648-5652
    • Becke, A.D.1
  • 25
    • 0345491105 scopus 로고
    • Development of the Colle-Salvetti correlation-energy formula into a functional of the electron density
    • (c) Lee, C.; Yang, W.; Paar, R. G. Development of the Colle-Salvetti correlation-energy formula into a functional of the electron density. Phys. Rev. B 1988, 37, 785-789.
    • (1988) Phys. Rev. B , vol.37 , pp. 785-789
    • Lee, C.1    Yang, W.2    Paar, R.G.3
  • 26
    • 11744256643 scopus 로고
    • Molecular Interactions in Solution: An Overview of Methods Based on Continuous Distributions of the Solvent
    • Tomasi, J.; Persico, M. Molecular Interactions in Solution: An Overview of Methods Based on Continuous Distributions of the Solvent. Chem. Rev. 1994, 94, 2027-2094.
    • (1994) Chem. Rev , vol.94 , pp. 2027-2094
    • Tomasi, J.1    Persico, M.2
  • 27
    • 34247201651 scopus 로고    scopus 로고
    • Straatsma, T. P, Aprà, E, Windus, T. L, Bylaska, E. J, de Jong, W, Hirata, S, Valiev, M, Hackler, M, Pollack, L, Harrison, R, Dupuis, M, Smith, D. M. A; Nieplocha, J, Tipparaju V, Krishnan, M, Auer, A. A, Brown, E, Cisneros, G, Fann, G, Früchtl, H, Garza, J, Hirao, K, Kendall, R, Nichols, J, Tsemekhman, K, Wolinski, K, Anchell, J, Bernholdt, D, Borowski, P, Clark, T, Clerc, D, Dachsel, H, Deegan, M, Dyall, K, Elwood, D, Glendening, E, Gutowski, M, Hess, A, Jaffe, J, Johnson, B, Ju, J, Kobayashi, R, Kutteh, R, Lin, Z, Littlefield, R, Long, X, Meng, B, Nakajima, T, Niu, S, Rosing, M, Sandrone, G, Stave, M, Taylor, H, Thomas, G, van Lenthe, J, Wong, A, Zhang, Z, NWChem, A Computational Chemistry Package for Parallel Computers, Version 4.6; Pacific Northwest National Laboratory: Richland, WA 99352-0999, U.S.A, 2004
    • (a) Straatsma, T. P.; Aprà, E.; Windus, T. L.; Bylaska, E. J.; de Jong, W.; Hirata, S.; Valiev, M.; Hackler, M.; Pollack, L.; Harrison, R.; Dupuis, M.; Smith, D. M. A; Nieplocha, J.; Tipparaju V.; Krishnan, M.; Auer, A. A.; Brown, E.; Cisneros, G.; Fann, G.; Früchtl, H.; Garza, J.; Hirao, K.; Kendall, R.; Nichols, J.; Tsemekhman, K.; Wolinski, K.; Anchell, J.; Bernholdt, D.; Borowski, P.; Clark, T.; Clerc, D.; Dachsel, H.; Deegan, M.; Dyall, K.; Elwood, D.; Glendening, E.; Gutowski, M.; Hess, A.; Jaffe, J.; Johnson, B.; Ju, J.; Kobayashi, R.; Kutteh, R.; Lin, Z.; Littlefield, R.; Long, X.; Meng, B.; Nakajima, T.; Niu, S.; Rosing, M.; Sandrone, G.; Stave, M.; Taylor, H.; Thomas, G.; van Lenthe, J.; Wong, A.; Zhang, Z.; NWChem, A Computational Chemistry Package for Parallel Computers, Version 4.6; Pacific Northwest National Laboratory: Richland, WA 99352-0999, U.S.A., 2004.
  • 29
    • 34247187495 scopus 로고    scopus 로고
    • GOT:, Available at
    • GOT: Gaussian Output Tools. Available at http://gaussot.sf.net.
    • Gaussian Output Tools
  • 30
    • 0033963034 scopus 로고    scopus 로고
    • Schaftenaar, G.; Noordik. J. H. Molden: a pre- and post-processing program for molecular and electronic structures. J. Comput.-Aided Mol. Des. 2000, 14, 123-34.
    • Schaftenaar, G.; Noordik. J. H. Molden: a pre- and post-processing program for molecular and electronic structures. J. Comput.-Aided Mol. Des. 2000, 14, 123-34.
  • 31
    • 4143095330 scopus 로고    scopus 로고
    • Kendall, R. A.; Dunning, T. H., Jr.: Harrison, R. J. Electron affinities of the first-row atoms revisited. Systematic basis sets and wave functions. J. Chem. Phys. 1992, 96, 6796-6806.
    • Kendall, R. A.; Dunning, T. H., Jr.: Harrison, R. J. Electron affinities of the first-row atoms revisited. Systematic basis sets and wave functions. J. Chem. Phys. 1992, 96, 6796-6806.
  • 33
    • 36449001370 scopus 로고
    • Coupled cluster theory for high spin, open shell reference wave functions
    • (a) Knowles, P. J.; Hampel, C.; Werner, H.-J. Coupled cluster theory for high spin, open shell reference wave functions. J. Chem. Phys. 1994, 99, 5219-5227.
    • (1994) J. Chem. Phys , vol.99 , pp. 5219-5227
    • Knowles, P.J.1    Hampel, C.2    Werner, H.-J.3
  • 34
    • 0011006010 scopus 로고
    • Perturbative corrections to account for triple excitations in closed and open shell coupled cluster theories
    • (b) Deegan, J. J. O.; Knowles, P. J. Perturbative corrections to account for triple excitations in closed and open shell coupled cluster theories. Chem. Phys. Lett. 1994, 227, 321-326.
    • (1994) Chem. Phys. Lett , vol.227 , pp. 321-326
    • Deegan, J.J.O.1    Knowles, P.J.2
  • 35
    • 34247232734 scopus 로고    scopus 로고
    • Amos, R. D, Bernhardsson, A, Berning, A, Celani, P, Cooper, D. L, Deegan, M. J. O, Dobbyn, A. J, Eckert, F, Hampel, C, Hetzer, G, Knowles, P. J, Korona, T, Lindh, R, Lloyd, A. W, McNicholas, S. J, Manby, F. R, Meyer, W, Mura, M. E, Nicklass, A, Palmieri, P, Pitzer, R, Rauhut, G, Schütz, M, Schumann, U, Stoll, H, Stone, A. J, Tarroni, R, Thorsteinsson, T, Werner, H.-J. MOLPRO, a package of ab initio programs designed by H.-J. Werner and P. J. Knowles, version 2002.1
    • Amos, R. D.; Bernhardsson, A.; Berning, A.; Celani, P.; Cooper, D. L.; Deegan, M. J. O.; Dobbyn, A. J.; Eckert, F.; Hampel, C.; Hetzer, G.; Knowles, P. J.; Korona, T.; Lindh, R.; Lloyd, A. W.; McNicholas, S. J.; Manby, F. R.; Meyer, W.; Mura, M. E.; Nicklass, A.; Palmieri, P.; Pitzer, R.; Rauhut, G.; Schütz, M.; Schumann, U.; Stoll, H.; Stone, A. J.; Tarroni, R.; Thorsteinsson, T.; Werner, H.-J. MOLPRO, a package of ab initio programs designed by H.-J. Werner and P. J. Knowles, version 2002.1.
  • 36
    • 34247225593 scopus 로고    scopus 로고
    • Academic Computer Center in Gdañsk TASK
    • Academic Computer Center in Gdañsk (TASK), http://www.task.gda.pl.
  • 39
    • 0031187388 scopus 로고    scopus 로고
    • Langevin Dipoles Model for ab Initio Calculations of Chemical Processes in Solution: Parametrization and Application to Hydration Free Energies of Neutral and Ionic Solutes and Conformational Analysis in Aqueous Solution
    • Florian, J.; Warshel, A. Langevin Dipoles Model for ab Initio Calculations of Chemical Processes in Solution: Parametrization and Application to Hydration Free Energies of Neutral and Ionic Solutes and Conformational Analysis in Aqueous Solution. J. Phys. Chem. B 1997, 101, 5583-5595.
    • (1997) J. Phys. Chem. B , vol.101 , pp. 5583-5595
    • Florian, J.1    Warshel, A.2
  • 40
    • 0029584358 scopus 로고
    • The Meaning of Component Analysis: Decomposition of the Free Energy in Terms of Specific Interactions
    • Boresch, S.; Karplus, M. The Meaning of Component Analysis: Decomposition of the Free Energy in Terms of Specific Interactions. J. Mol. Biol. 1995, 254, 801-807.
    • (1995) J. Mol. Biol , vol.254 , pp. 801-807
    • Boresch, S.1    Karplus, M.2
  • 43
    • 2142813682 scopus 로고
    • Computer Simulation of Molecular Dynamics: Methodology, Applications, and Perspectives in Chemistry
    • van Gunsteren, W. F.; Berendsen, H. J. C. Computer Simulation of Molecular Dynamics: Methodology, Applications, and Perspectives in Chemistry. Angew. Chem. Int. Ed. 1990, 29, 992-1023.
    • (1990) Angew. Chem. Int. Ed , vol.29 , pp. 992-1023
    • van Gunsteren, W.F.1    Berendsen, H.J.C.2
  • 44
    • 34247219234 scopus 로고    scopus 로고
    • E.g. there are 4 sites connected to N4 of adenine, but 2 sites that describe the amino group (2 hydrogen atoms at N4) overlap with another 2 sites describing rotamers of the N4 imino group.
    • E.g. there are 4 sites connected to N4 of adenine, but 2 sites that describe the amino group (2 hydrogen atoms at N4) overlap with another 2 sites describing rotamers of the N4 imino group.


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.