Benchmarking density functional tight binding models for barrier heights and reaction energetics of organic molecules
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Qiang Cui | A. K. Jissy | Marcus Elstner | Maja Gruden | Ljubica Andjeklovic | Akkarapattiakal Kuriappan Jissy | Stepan Stepanovic | Matija Zlatar | Q. Cui | M. Elstner | M. Zlatar | M. Gruden | S. Stepanovic | Ljubica Andjeklovic
[1] J. Stewart. Optimization of parameters for semiempirical methods I. Method , 1989 .
[2] Q. Cui,et al. “Multi-Scale” QM/MM Methods with Self-Consistent-Charge Density-Functional-Tight-Binding (SCC-DFTB) , 2009 .
[3] H. Zimmerman,et al. The Stereochemistry of Allenic Enol Tautomerism – Independent Generation and Reactivity of the Enolates , 2006 .
[4] Walter Thiel,et al. Semiempirical quantum–chemical methods , 2014 .
[5] S. Grimme,et al. Efficient and Accurate Double-Hybrid-Meta-GGA Density Functionals-Evaluation with the Extended GMTKN30 Database for General Main Group Thermochemistry, Kinetics, and Noncovalent Interactions. , 2011, Journal of chemical theory and computation.
[6] J. Stewart. Optimization of parameters for semiempirical methods II. Applications , 1989 .
[7] Q. Cui. Perspective: Quantum mechanical methods in biochemistry and biophysics. , 2016, The Journal of chemical physics.
[8] F. Matthias Bickelhaupt,et al. Chemistry with ADF , 2001, J. Comput. Chem..
[9] Donald G Truhlar,et al. Benchmark database of barrier heights for heavy atom transfer, nucleophilic substitution, association, and unimolecular reactions and its use to test theoretical methods. , 2005, The journal of physical chemistry. A.
[10] Gotthard Seifert,et al. Density functional tight binding , 2014, Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences.
[11] Jan H. Jensen,et al. Distributed under Creative Commons Cc-by 4.0 towards a Barrier Height Benchmark Set for Biologically Relevant Systems , 2022 .
[12] Sándor Suhai,et al. Self-consistent-charge density-functional tight-binding method for simulations of complex materials properties , 1998 .
[13] Pavlo O. Dral,et al. Semiempirical Quantum-Chemical Orthogonalization-Corrected Methods: Benchmarks for Ground-State Properties , 2016, Journal of chemical theory and computation.
[14] M. Elstner,et al. Parametrization and Benchmark of DFTB3 for Organic Molecules. , 2013, Journal of chemical theory and computation.
[15] Burke,et al. Generalized Gradient Approximation Made Simple. , 1996, Physical review letters.
[16] Q. Cui,et al. Proton storage site in bacteriorhodopsin: new insights from quantum mechanics/molecular mechanics simulations of microscopic pK(a) and infrared spectra. , 2011, Journal of the American Chemical Society.
[17] S. Grimme,et al. How to compute isomerization energies of organic molecules with quantum chemical methods. , 2007, The Journal of organic chemistry.
[18] A. Becke. Density-functional thermochemistry. III. The role of exact exchange , 1993 .
[19] M. Frisch,et al. Ab Initio Calculation of Vibrational Absorption and Circular Dichroism Spectra Using Density Functional Force Fields , 1994 .
[20] S. Grimme,et al. A thorough benchmark of density functional methods for general main group thermochemistry, kinetics, and noncovalent interactions. , 2011, Physical chemistry chemical physics : PCCP.
[21] Krishnan Raghavachari,et al. Solving the Density Functional Conundrum: Elimination of Systematic Errors To Derive Accurate Reaction Enthalpies of Complex Organic Reactions. , 2017, Organic letters.
[22] Stefan Grimme,et al. Consistent theoretical description of 1,3-dipolar cycloaddition reactions. , 2006, The journal of physical chemistry. A.
[23] K. Houk,et al. Activation energies of pericyclic reactions: performance of DFT, MP2, and CBS-QB3 methods for the prediction of activation barriers and reaction energetics of 1,3-dipolar cycloadditions, and revised activation enthalpies for a standard set of hydrocarbon pericyclic reactions. , 2005, The journal of physical chemistry. A.
[24] Stephan Irle,et al. Density-Functional Tight-Binding Combined with the Fragment Molecular Orbital Method. , 2014, Journal of chemical theory and computation.
[25] G. Voth,et al. Benchmark Study of the SCC-DFTB Approach for a Biomolecular Proton Channel. , 2014, Journal of Chemical Theory and Computation.
[26] Q. Cui,et al. Density functional tight binding: values of semi-empirical methods in an ab initio era. , 2014, Physical chemistry chemical physics : PCCP.
[27] Stefan Grimme,et al. A General Database for Main Group Thermochemistry, Kinetics, and Noncovalent Interactions - Assessment of Common and Reparameterized (meta-)GGA Density Functionals. , 2010, Journal of chemical theory and computation.
[28] K. Morokuma,et al. Intrinsic reaction coordinate: Calculation, bifurcation, and automated search , 2015 .
[29] K. Houk,et al. Sources of error in DFT computations of C-C bond formation thermochemistries: pi-->sigma transformations and error cancellation by DFT methods. , 2008, Angewandte Chemie.
[30] James J. P. Stewart,et al. Optimization of parameters for semiempirical methods VI: more modifications to the NDDO approximations and re-optimization of parameters , 2012, Journal of Molecular Modeling.
[31] James J. P. Stewart,et al. Development and use of quantum mechanical molecular models. 76. AM1: a new general purpose quantum mechanical molecular model. [Erratum to document cited in CA103(2):11627f] , 1993 .
[32] S. Grimme,et al. A consistent and accurate ab initio parametrization of density functional dispersion correction (DFT-D) for the 94 elements H-Pu. , 2010, The Journal of chemical physics.
[33] B. Lynch,et al. The oxidation of olefins with perbenzoic acids. A kinetic study , 1955 .
[34] George C Schatz,et al. Highly accurate first-principles benchmark data sets for the parametrization and validation of density functional and other approximate methods. Derivation of a robust, generally applicable, double-hybrid functional for thermochemistry and thermochemical kinetics. , 2008, The journal of physical chemistry. A.
[35] Satoshi Maeda,et al. Exploring Multiple Potential Energy Surfaces: Photochemistry of Small Carbonyl Compounds , 2012 .
[36] D. York,et al. Multi-scale quantum models for biocatalysis : modern techniques and applications , 2009 .
[37] Andrew G. Leach,et al. A Standard Set of Pericyclic Reactions of Hydrocarbons for the Benchmarking of Computational Methods: The Performance of ab Initio, Density Functional, CASSCF, CASPT2, and CBS-QB3 Methods for the Prediction of Activation Barriers, Reaction Energetics, and Transition State Geometries , 2003 .
[38] J. Stewart. Optimization of parameters for semiempirical methods V: Modification of NDDO approximations and application to 70 elements , 2007, Journal of molecular modeling.
[39] Stefan Grimme,et al. Effect of the damping function in dispersion corrected density functional theory , 2011, J. Comput. Chem..
[40] R. Sundberg,et al. Advanced Organic Chemistry. Part B: Reactions and Synthesis. Fourth Edition , 2001 .
[41] Walter Thiel,et al. QM/MM methods for biomolecular systems. , 2009, Angewandte Chemie.
[42] Michael Gaus,et al. Parameterization of DFTB3/3OB for Sulfur and Phosphorus for Chemical and Biological Applications , 2014, Journal of chemical theory and computation.
[43] S. Grimme. Seemingly simple stereoelectronic effects in alkane isomers and the implications for Kohn-Sham density functional theory. , 2006, Angewandte Chemie.
[44] Walter Thiel,et al. Orthogonalization corrections for semiempirical methods , 2000 .
[45] R. Hrabal,et al. An experimental and theoretical study of stereoselectivity of furan-maleic anhydride and furan-maleimide diels-alder reactions. , 2005, The Journal of organic chemistry.
[46] Walter Thiel,et al. Semiempirical Quantum-Chemical Orthogonalization-Corrected Methods: Theory, Implementation, and Parameters , 2016, Journal of chemical theory and computation.
[47] Anders S. Christensen,et al. Semiempirical Quantum Mechanical Methods for Noncovalent Interactions for Chemical and Biochemical Applications , 2016, Chemical reviews.
[48] Gotthard Seifert,et al. Density‐functional tight binding—an approximate density‐functional theory method , 2012 .
[49] Walter Thiel,et al. Beyond the MNDO model: Methodical considerations and numerical results , 1993, J. Comput. Chem..
[50] D. Truhlar,et al. Validation of electronic structure methods for isomerization reactions of large organic molecules. , 2011, Physical chemistry chemical physics : PCCP.
[51] Michele Ceriotti,et al. Beyond static structures: Putting forth REMD as a tool to solve problems in computational organic chemistry , 2015, J. Comput. Chem..
[52] Arun Rastogi,et al. Advanced Organic Chemistry: Reactions, Mechanisms and Structure , 2010 .
[53] Michael Gaus,et al. Parameterization of the DFTB3 method for Br, Ca, Cl, F, I, K, and Na in organic and biological systems. , 2015, Journal of chemical theory and computation.
[54] Seifert,et al. Construction of tight-binding-like potentials on the basis of density-functional theory: Application to carbon. , 1995, Physical review. B, Condensed matter.
[55] William L. Jorgensen,et al. PDDG/PM3 and PDDG/MNDO: Improved semiempirical methods , 2002, J. Comput. Chem..
[56] T. Dinadayalane,et al. Diels-Alder Reactivity of Butadiene and Cyclic Five-Membered Dienes ((CH)4X, X ) CH2, SiH2, O, NH, PH, and S) with Ethylene: A Benchmark Study , 2002 .
[57] D. Truhlar,et al. The DBH24/08 Database and Its Use to Assess Electronic Structure Model Chemistries for Chemical Reaction Barrier Heights. , 2009, Journal of chemical theory and computation.
[58] Michael Gaus,et al. Parametrization of DFTB3/3OB for Magnesium and Zinc for Chemical and Biological Applications , 2014, The journal of physical chemistry. B.
[59] Michael Gaus,et al. Density functional tight binding: application to organic and biological molecules , 2014 .
[60] S. Papson. “Model” , 1981 .
[61] Weitao Yang,et al. Delocalization errors in density functionals and implications for main-group thermochemistry. , 2008, The Journal of chemical physics.
[62] Michael Gaus,et al. DFTB3: Extension of the self-consistent-charge density-functional tight-binding method (SCC-DFTB). , 2011, Journal of chemical theory and computation.
[63] Julian Tirado-Rives,et al. Comparison of SCC-DFTB and NDDO-based semiempirical molecular orbital methods for organic molecules. , 2006, The journal of physical chemistry. A.
[64] S. Grimme,et al. Stereoelectronic Substituent Effects in Saturated Main Group Molecules: Severe Problems of Current Kohn-Sham Density Functional Theory. , 2007, Journal of chemical theory and computation.
[65] S. Grimme,et al. Effects of London dispersion on the isomerization reactions of large organic molecules: a density functional benchmark study. , 2010, Physical chemistry chemical physics : PCCP.
[66] R. McGibbon,et al. Discovering chemistry with an ab initio nanoreactor , 2014, Nature chemistry.