Sayle RA (2010) So You Think You Understand Tautomerism? J Comput Aided Mol Des 24:485–496
Article CAS PubMed Google Scholar
Taylor PJ, van der Zwan G, Antonov L (2014) Tautomerism: introduction, history, and recent developments in experimental and theoretical methods. In: Antonov L (ed) Tautomerism. Wiley VCH, Weinheim
Martin Y (2010) Tautomerism, Hammett σ, and QSAR. J Comput Aided Mol Des 24:613–616
Article CAS PubMed Google Scholar
Martin Y (2009) Let’s Not Forget Tautomers. J Comput Aided Mol Des 23:693–704
Article CAS PubMed PubMed Central Google Scholar
Pospisil P, Ballmer P, Scapozza L, Folkers G (2003) Tautomerism in computer-aided drug design. J Rec Signal Transd 23:361–371
Clark T (2010) Tautomers and reference 3D-structures: the orphans of in silico drug design. J Comput Aided Mol Des 24:605–611
Article CAS PubMed Google Scholar
Cavasin AT, Hillisch A, Uellendahl F, Schneckener S, Göller AH (2018) Reliable and performant identification of low-energy conformers in the gas phase and water. J Chem Inf Model 58:1005–1020
Article CAS PubMed Google Scholar
Seep L, Bonin A, Meier K, Diedam H, Göller AH (2021) Ensemble completeness in conformer sampling: the case of small macrocycles. J Cheminform 13:55
Article PubMed PubMed Central Google Scholar
Fraczkiewicz R, Lobell M, Göller AH, Krenz U, Schoenneis R, Clark RD, Hillisch A (2015) Best of both worlds: combining pharma data and state of the art modeling technology to improve in silico pKa prediction. J Chem Inf Model 55:389–397
Article CAS PubMed Google Scholar
Sitzmann M, Ihlenfeldt WD, Nicklaus MC (2010) Tautomerism in Large Databases. J Comput aided mol des 24:521–551
Article CAS PubMed PubMed Central Google Scholar
Tautomerism, ed. Antonov, L., Wiley VCH, Weinheim, 2014.
Wieder M, Fass J, Chodera JD (2021) Fitting quantum machine learning potentials to experimental free energy data: predicting tautomer ratios in solution. Chem Sci 12:11364–11381
Article CAS PubMed PubMed Central Google Scholar
Warr WA (2010) Tautomerism in chemical information management systems. J Comput Aided Mol Des 24:497–520
Article CAS PubMed Google Scholar
Sayle R, Delany JJ (1999) Canonicalization and Enumeration of Tautomers. Daylight EMUG99.
RDKit: Open-source cheminformatics. http://www.rdkit .org
Kochev NT, Paskaleva VH, Jeliazkova N (2013) Ambit-tautomer: an open source tool for tautomer generation. Mol Inf 32:481–504
Guasch L, Peach ML, Nicklaus MC (2015) Tautomerism of warfarin: combined chemoinformatics, quantum chemical, and NMR investigation. J Org Chem 80:9900–9909
Article CAS PubMed PubMed Central Google Scholar
Oziminski WP, Wiśniewski I (2021) Quantum-chemical study on the relative stability of sildenafil tautomers. Struct Chem 32:1733–1743
Goerigk L, Grimme S (2011) Efficient and accurate double-hybrid-meta-GGA density functionals-evaluation with the extended GMTKN30 database for general main group thermochemistry, kinetics, and Noncovalent Interactions. J Chem Theory Comput 7:291–309
Article CAS PubMed Google Scholar
Geballe MT, Skillman AG, Nicholls A, Guthrie J, Taylor PJ (2010) The SAMPL2 blind prediction challenge: introduction and overview. J Comput Aided Mol Des 24:259–279
Article CAS PubMed Google Scholar
Fogarasi G (2010) Studies on tautomerism: benchmark quantum chemical calculations on formamide and formamidine. J Mol Struct 978:257–262
Milletti F, Vulpetti A (2010) Tautomer preference in PDB complexes and its impact on structure-based drug discovery. J Chem Inf Model 50:1062–1074
Article CAS PubMed Google Scholar
Milletti F, Storchi L, Sforna G, Cross S, Cruciani G (2009) Tautomer enumeration and stability prediction for virtual screening on large chemical databases. J Chem Inf Model 49:68–75
Article CAS PubMed Google Scholar
Pipeline Pilot, client version 21.2.0.2574, server version 21.2.0.2575, Dassault Systemes Biovia Corp, 2020
Settings: Enumerate all Tautomers; maximally 1000; defaults.
(a) Sadowski J, Gasteiger J, Klebe G (1994) Comparison of Automatic Three-Dimensional Model Builders Using 639 X-ray Structures. J Chem Inf Comput Sci 34:1000–1008; (b) CORINA, Molecular Networks GmbH, Erlangen, Germany (http://www.molecular-networks.com).
Bannwarth C, Ehlert S, Grimme S (2019) GFN2-xTB: an accurate and broadly parametrized self-consistent tight-binding quantum chemical method with multipole electrostatics and density-dependent dispersion contributions. J Chem Theory Comput 15:1652–1671
Article CAS PubMed Google Scholar
Riplinger C, Neese F (2013) An efficient and near linear scaling pair natural orbital based local coupled cluster method. J Chem Phys 138:34106
Piecuch P, Kucharski SA, Kowalski K, Musial M (2002) Efficient computer implementation of the renormalized coupled-cluster methods: The R-CCSD[T], R-CCSD(T), CR-CCSD[T], and CR-CCSD(T) approaches. Comp Phys Commun 149:71–96
Neese F (2012) The ORCA PROGRAM SYSTEM. WIREs Comput Mol Sci 2:73–78
Dewar MJS, Zoebisch EG, Healy EF, Stewart JJP (1985) Development and use of quantum mechanical molecular models. 76. AM1: a new general purpose quantum mechanical molecular model. J Am Chem Soc 107:3902–3909
Stewart JJP (1989) Optimization of parameters for semiempirical methods I. Method J Comput Chem 10:209–220
Lu C, Wu C, Ghoreishi D, Chen W, Wang L, Damm W, Ross GA, Dahlgren MK, Russell E, Von Bargen CD, Abel R, Friesner RA, Harder ED (2021) OPLS4: improving force field accuracy on challenging regimes of chemical space. J Chem Theory Comput 17:4291–4300
Article CAS PubMed Google Scholar
Maestro Version 13.0.135, MMshare Version 5.6.135, Platform Linux-x86_64, Small-Molecule Drug Discovery Suite 2021–4, Schrodinger, LLC, New York, 2021.
Ernzerhof M, Scuseria GE (1999) Assessment of the Perdew Burke Ernzerhof exchange-correlation functional. J Chem Phys 110:5029–5036
Adamo C, Barone V (1999) Toward reliable density functional methods without adjustable parameters: The PBE0 model. J Chem Phys 110:6158–6170
Grimme S, Antony J, Ehrlich S, Krieg H (2010) A consistent and accurate ab initio parametrization of density functional dispersion correction (DFT-D) for the 94 elements H-Pu. J Chem Phys 132:154104
Becke AD, Johnson ER (2005) A density-functional model of the dispersion interaction. J Chem Phys 123:154101
Weigend F, Ahlrichs R (2005) Balanced basis sets of split valence, triple zeta valence and quadruple zeta valence quality for H to Rn: design and assessment of accuracy. Phys Chem Chem Phys 7:3297–3305
Article CAS PubMed Google Scholar
Weigend F (2006) Accurate coulomb-fitting basis sets for H to Rn. Phys Chem Chem Phys 8:1057–1065
Article CAS PubMed Google Scholar
Hellweg A, Hättig C, Höfener S, Klopper W (2007) Optimized accurate auxiliary basis sets for RI-MP2 and RI-CC2 calculations for the atoms Rb to Rn. Theor Chem Acc 117:587–597
Perdew JP, Burke K, Ernzerhof M (1996) Generalized gradient approximation made simple. Phys Rev Lett 77:3865–3868
Article CAS PubMed Google Scholar
Tao J, Perdew JP, Staroverov VN, Scuseria GE (2003) Climbing the density functional ladder: nonempirical meta-generalized gradient approximation designed for molecules and solids. Phys Rev Lett 91:146401
Furness JW, Kaplan AD, Ning J, Perdew JP, Sun J (2020) Accurate and numerically efficient r2SCAN meta-generalized gradient approximation. J Phys Chem Lett 11:8208–8215
Article CAS PubMed Google Scholar
Chai JD, Head-Gordon M (2008) Long-range corrected hybrid density functionals with damped atom-atom dispersion corrections. Phys Chem Chem Phys 10:6615–6620
Article CAS PubMed Google Scholar
Zhao Y, Truhlar DG (2008) The M06 suite of density functionals for main group thermochemistry, thermochemical kinetics, noncovalent interactions, excited states, and transition elements: two new functionals and systematic testing of four m06-class functionals and 12 other functionals. Theor Chem Acc 120:215–241
留言 (0)