101
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Deubel DV, Lau JKC. In silico evolution of substrate selectivity: comparison of organometallic ruthenium complexes with the anticancer drug cisplatin. Chem Commun (Camb) 2006:2451-3. [PMID: 16758012 DOI: 10.1039/b601590e] [Citation(s) in RCA: 76] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A comparative quantum chemical approach helps to clarify how the selectivity of anticancer metallopharmaceuticals towards potential biological targets can be controlled by metal and ligands.
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Affiliation(s)
- Dirk V Deubel
- ETH Zurich, USI Campus, Computational Science, Via Guiseppe Buffi 13, CH-6900, Lugano, Switzerland.
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102
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Goossen LJ, Koley D, Hermann HL, Thiel W. Palladium Monophosphine Intermediates in Catalytic Cross-Coupling Reactions: A DFT Study. Organometallics 2005. [DOI: 10.1021/om050685h] [Citation(s) in RCA: 108] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Lukas J. Goossen
- Max-Planck-Institut für Kohlenforschung, D-45470 Mülheim an der Ruhr, Germany
| | - Debasis Koley
- Max-Planck-Institut für Kohlenforschung, D-45470 Mülheim an der Ruhr, Germany
| | - Holger L. Hermann
- Max-Planck-Institut für Kohlenforschung, D-45470 Mülheim an der Ruhr, Germany
| | - Walter Thiel
- Max-Planck-Institut für Kohlenforschung, D-45470 Mülheim an der Ruhr, Germany
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103
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de Jong GT, Bickelhaupt FM. Oxidative Addition of the Fluoromethane C−F Bond to Pd. An ab Initio Benchmark and DFT Validation Study. J Phys Chem A 2005; 109:9685-99. [PMID: 16866421 DOI: 10.1021/jp053587i] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We have computed a state-of-the-art benchmark potential energy surface (PES) for two reaction pathways (oxidative insertion, OxIn, and S(N)2) for oxidative addition of the fluoromethane C-F bond to the palladium atom and have used this to evaluate the performance of 26 popular density functionals, covering LDA, GGA, meta-GGA, and hybrid density functionals, for describing these reactions. The ab initio benchmark is obtained by exploring the PES using a hierarchical series of ab initio methods (HF, MP2, CCSD, CCSD(T)) in combination with a hierarchical series of seven Gaussian-type basis sets, up to g polarization. Relativistic effects are taken into account through a full four-component all-electron approach. Our best estimate of kinetic and thermodynamic parameters is -5.3 (-6.1) kcal/mol for the formation of the reactant complex, 27.8 (25.4) kcal/mol for the activation energy for oxidative insertion (OxIn) relative to the separate reactants, 37.5 (31.8) kcal/mol for the activation energy for the alternative S(N)2 pathway, and -6.4 (-7.8) kcal/mol for the reaction energy (zero-point vibrational energy-corrected values in parentheses). Our work highlights the importance of sufficient higher angular momentum polarization functions for correctly describing metal-d-electron correlation. Best overall agreement with our ab initio benchmark is obtained by functionals from all three categories, GGA, meta-GGA, and hybrid DFT, with mean absolute errors of 1.4-2.7 kcal/mol and errors in activation energies ranging from 0.3 to 2.8 kcal/mol. The B3LYP functional compares very well with a slight underestimation of the overall barrier for OxIn by -0.9 kcal/mol. For comparison, the well-known BLYP functional underestimates the overall barrier by -10.1 kcal/mol. The relative performance of these two functionals is inverted with respect to previous findings for the insertion of Pd into the C-H and C-C bonds. However, all major functionals yield correct trends and qualitative features of the PES, in particular, a clear preference for the OxIn over the alternative S(N)2 pathway.
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Affiliation(s)
- G Theodoor de Jong
- Afdeling Theoretische Chemie, Scheikundig Laboratorium der Vrije Universiteit, De Boelelaan 1083, NL-1081 HV Amsterdam, The Netherlands
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104
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De Jong GT, Geerke DP, Diefenbach A, Solà M, Bickelhaupt FM. Oxidative addition of the ethane CC bond to Pd. Anab initiobenchmark and DFT validation study. J Comput Chem 2005; 26:1006-20. [PMID: 15880815 DOI: 10.1002/jcc.20233] [Citation(s) in RCA: 65] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
We have computed a state-of-the-art benchmark potential energy surface (PES) for the archetypal oxidative addition of the ethane C-C bond to the palladium atom and have used this to evaluate the performance of 24 popular density functionals, covering LDA, GGA, meta-GGA, and hybrid density functionals, for describing this reaction. The ab initio benchmark is obtained by exploring the PES using a hierarchical series of ab initio methods [HF, MP2, CCSD, CCSD(T)] in combination with a hierarchical series of five Gaussian-type basis sets, up to g polarization. Relativistic effects are taken into account either through a relativistic effective core potential for palladium or through a full four-component all-electron approach. Our best estimate of kinetic and thermodynamic parameters is -10.8 (-11.3) kcal/mol for the formation of the reactant complex, 19.4 (17.1) kcal/mol for the activation energy relative to the separate reactants, and -4.5 (-6.8) kcal/mol for the reaction energy (zero-point vibrational energy-corrected values in parentheses). Our work highlights the importance of sufficient higher angular momentum polarization functions for correctly describing metal-d-electron correlation. Best overall agreement with our ab initio benchmark is obtained by functionals from all three categories, GGA, meta-GGA, and hybrid DFT, with mean absolute errors of 1.5 to 2.5 kcal/mol and errors in activation energies ranging from -0.2 to -3.2 kcal/mol. Interestingly, the well-known BLYP functional compares very reasonably with a slight underestimation of the overall barrier by -0.9 kcal/mol. For comparison, with B3LYP we arrive at an overestimation of the overall barrier by 5.8 kcal/mol. On the other hand, B3LYP performs excellently for the central barrier (i.e., relative to the reactant complex) which it underestimates by only -0.1 kcal/mol.
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Affiliation(s)
- G Theodoor De Jong
- Afdeling Theoretische Chemie, Scheikundig Laboratorium der Vrije Universiteit, De Boelelaan 1083, NL-1081 HV Amsterdam, The Netherlands
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105
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de Jong GT, Geerke DP, Diefenbach A, Matthias Bickelhaupt F. DFT benchmark study for the oxidative addition of CH4 to Pd. Performance of various density functionals. Chem Phys 2005. [DOI: 10.1016/j.chemphys.2005.01.017] [Citation(s) in RCA: 74] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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106
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Goossen LJ, Koley D, Hermann HL, Thiel W. Mechanistic Pathways for Oxidative Addition of Aryl Halides to Palladium(0) Complexes: A DFT Study. Organometallics 2005. [DOI: 10.1021/om0500220] [Citation(s) in RCA: 164] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Lukas J. Goossen
- Max-Planck-Institut für Kohlenforschung, D-45470 Mülheim an der Ruhr, Germany
| | - Debasis Koley
- Max-Planck-Institut für Kohlenforschung, D-45470 Mülheim an der Ruhr, Germany
| | - Holger L. Hermann
- Max-Planck-Institut für Kohlenforschung, D-45470 Mülheim an der Ruhr, Germany
| | - Walter Thiel
- Max-Planck-Institut für Kohlenforschung, D-45470 Mülheim an der Ruhr, Germany
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107
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Diefenbach A, Bickelhaupt FM. Activation of C–H, C–C and C–I bonds by Pd and cis-Pd(CO)2I2. Catalyst–substrate adaptation. J Organomet Chem 2005. [DOI: 10.1016/j.jorganchem.2005.02.013] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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108
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Diefenbach A, De Jong G, Bickelhaupt * F. Fragment-oriented design of catalysts based on the activation strain model. Mol Phys 2005. [DOI: 10.1080/00268970412331333546] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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109
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Diefenbach A, de Jong GT, Bickelhaupt FM. Activation of H−H, C−H, C−C and C−Cl Bonds by Pd and PdCl-. Understanding Anion Assistance in C−X Bond Activation. J Chem Theory Comput 2005; 1:286-98. [PMID: 26641300 DOI: 10.1021/ct0499478] [Citation(s) in RCA: 129] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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110
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Bento AP, Solà M, Bickelhaupt FM. Ab initio and DFT benchmark study for nucleophilic substitution at carbon (SN2@C) and silicon (SN2@Si). J Comput Chem 2005; 26:1497-504. [PMID: 16092145 DOI: 10.1002/jcc.20261] [Citation(s) in RCA: 119] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
To obtain a set of consistent benchmark potential energy surfaces (PES) for the two archetypal nucleophilic substitution reactions of the chloride anion at carbon in chloromethane (S(N)2@C) and at silicon in chlorosilane (S(N)2@Si), we have explored these PESes using a hierarchical series of ab initio methods [HF, MP2, MP4SDQ, CCSD, CCSD(T)] in combination with a hierarchical series of six Gaussian-type basis sets, up to g polarization. Relative energies of stationary points are converged to within 0.01 to 0.56 kcal/mol as a function of the basis-set size. Our best estimate, at CCSD(T)/aug-cc-pVQZ, for the relative energies of the [Cl(-), CH(3)Cl] reactant complex, the [Cl-CH(3)-Cl](-) transition state and the stable [Cl-SiH(3)-Cl](-) transition complex is -10.42, +2.52, and -27.10 kcal/mol, respectively. Furthermore, we have investigated the performance for these reactions of four popular density functionals, namely, BP86, BLYP, B3LYP, and OLYP, in combination with a large doubly polarized Slater-type basis set of triple-zeta quality (TZ2P). Best overall agreement with our CCSD(T)/aug-cc-pVQZ benchmark is obtained with OLYP and B3LYP. However, OLYP performs better for the S(N)2@C overall and central barriers, which it underestimates by 2.65 and 4.05 kcal/mol, respectively. The other DFT approaches underestimate these barriers by some 4.8 (B3LYP) to 9.0 kcal/mol (BLYP).
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Affiliation(s)
- A Patrícia Bento
- Afdeling Theoretische Chemie, Scheikundig Laboratorium der Vrije Universiteit, De Boelelaan 1083, NL-1081 HV Amsterdam, The Netherlands
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111
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de Jong GT, Solà M, Visscher L, Bickelhaupt FM. Ab initio benchmark study for the oxidative addition of CH4 to Pd: Importance of basis-set flexibility and polarization. J Chem Phys 2004; 121:9982-92. [PMID: 15549873 DOI: 10.1063/1.1792151] [Citation(s) in RCA: 67] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
To obtain a state-of-the-art benchmark potential energy surface (PES) for the archetypal oxidative addition of the methane C-H bond to the palladium atom, we have explored this PES using a hierarchical series of ab initio methods (Hartree-Fock, second-order Møller-Plesset perturbation theory, fourth-order Møller-Plesset perturbation theory with single, double and quadruple excitations, coupled cluster theory with single and double excitations (CCSD), and with triple excitations treated perturbatively [CCSD(T)]) and hybrid density functional theory using the B3LYP functional, in combination with a hierarchical series of ten Gaussian-type basis sets, up to g polarization. Relativistic effects are taken into account either through a relativistic effective core potential for palladium or through a full four-component all-electron approach. Counterpoise corrected relative energies of stationary points are converged to within 0.1-0.2 kcal/mol as a function of the basis-set size. Our best estimate of kinetic and thermodynamic parameters is -8.1 (-8.3) kcal/mol for the formation of the reactant complex, 5.8 (3.1) kcal/mol for the activation energy relative to the separate reactants, and 0.8 (-1.2) kcal/mol for the reaction energy (zero-point vibrational energy-corrected values in parentheses). This agrees well with available experimental data. Our work highlights the importance of sufficient higher angular momentum polarization functions, f and g, for correctly describing metal-d-electron correlation and, thus, for obtaining reliable relative energies. We show that standard basis sets, such as LANL2DZ+1f for palladium, are not sufficiently polarized for this purpose and lead to erroneous CCSD(T) results. B3LYP is associated with smaller basis set superposition errors and shows faster convergence with basis-set size but yields relative energies (in particular, a reaction barrier) that are ca. 3.5 kcal/mol higher than the corresponding CCSD(T) values.
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Affiliation(s)
- G Theodoor de Jong
- Afdeling Theoretische Chemie, Scheikundig Laboratorium der Vrije Universiteit, De Boelelaan 1083, NL-1081 HV Amsterdam, The Netherlands
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112
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Diefenbach A, Bickelhaupt FM. Activation of H−H, C−H, C−C, and C−Cl Bonds by Pd(0). Insight from the Activation Strain Model. J Phys Chem A 2004. [DOI: 10.1021/jp047986+] [Citation(s) in RCA: 107] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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113
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Senn HM, Ziegler T. Oxidative Addition of Aryl Halides to Palladium(0) Complexes: A Density-Functional Study Including Solvation. Organometallics 2004. [DOI: 10.1021/om049963n] [Citation(s) in RCA: 189] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Hans Martin Senn
- Department of Chemistry, University of Calgary, Calgary, Alberta T2N 1N4, Canada
| | - Tom Ziegler
- Department of Chemistry, University of Calgary, Calgary, Alberta T2N 1N4, Canada
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114
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Tai HC, Krossing I, Seth M, Deubel DV. Organometallics versus P4 Complexes of Group 11 Cations: Periodic Trends and Relativistic Effects in the Involvement of (n−1)d, ns, and np Orbitals in Metal−Ligand Interactions. Organometallics 2004. [DOI: 10.1021/om034246z] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Hui-Chung Tai
- Academia Sinica, Taipei, Taiwan 11529, Republic of China, Department of Chemistry, University of Karlsruhe, 76128 Karlsruhe, Germany, Department of Chemistry, University of Calgary, Canada T2N 1N4, Swiss Center for Scientific Computing, ETH Zürich, 6928 Manno, Switzerland, and Department of Chemistry and Applied Biosciences, Computational Science Laboratory, ETH Zürich, 6900 Lugano, Switzerland
| | - Ingo Krossing
- Academia Sinica, Taipei, Taiwan 11529, Republic of China, Department of Chemistry, University of Karlsruhe, 76128 Karlsruhe, Germany, Department of Chemistry, University of Calgary, Canada T2N 1N4, Swiss Center for Scientific Computing, ETH Zürich, 6928 Manno, Switzerland, and Department of Chemistry and Applied Biosciences, Computational Science Laboratory, ETH Zürich, 6900 Lugano, Switzerland
| | - Michael Seth
- Academia Sinica, Taipei, Taiwan 11529, Republic of China, Department of Chemistry, University of Karlsruhe, 76128 Karlsruhe, Germany, Department of Chemistry, University of Calgary, Canada T2N 1N4, Swiss Center for Scientific Computing, ETH Zürich, 6928 Manno, Switzerland, and Department of Chemistry and Applied Biosciences, Computational Science Laboratory, ETH Zürich, 6900 Lugano, Switzerland
| | - Dirk V. Deubel
- Academia Sinica, Taipei, Taiwan 11529, Republic of China, Department of Chemistry, University of Karlsruhe, 76128 Karlsruhe, Germany, Department of Chemistry, University of Calgary, Canada T2N 1N4, Swiss Center for Scientific Computing, ETH Zürich, 6928 Manno, Switzerland, and Department of Chemistry and Applied Biosciences, Computational Science Laboratory, ETH Zürich, 6900 Lugano, Switzerland
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115
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116
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Goossen LJ, Koley D, Hermann H, Thiel W. The mechanism of the oxidative addition of aryl halides to Pd-catalysts: a DFT investigation. Chem Commun (Camb) 2004:2141-3. [PMID: 15467842 DOI: 10.1039/b409144b] [Citation(s) in RCA: 86] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Based on DFT calculations, a new mechanism for the oxidative addition of aryl halides to Pd-catalysts is presented. The key intermediate is an anionic Pd-species in which the aryl halide coordinates to the palladium via the halide atom.
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Affiliation(s)
- Lukas J Goossen
- Max-Planck-Institut fur Kohlenforschung, Kaiser-Wilhelm-Platz 1, D-45470, Mulheim an der Ruhr, Germany.
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117
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Hinrichs RZ, Schroden JJ, Davis HF. Competition between C-C and C-H insertion in prototype transition metal-hydrocarbon reactions. J Am Chem Soc 2003; 125:860-1. [PMID: 12537471 DOI: 10.1021/ja0278842] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The competition between C-C and C-H insertion in model transition-metal reactions with cyclopropane and propene (C3H6) was studied as a function of total energy. Insertion of neutral transition metal atoms M (= Y, Zr, Nb, and Mo*) into the C-C bonds of cyclopropane led to formation of MCH2 + C2H4, whereas C-H insertion produced MC3H4 + H2. The measured product branching ratios verify the relative potential energy barrier heights for C-C and C-H insertion predicted by ab initio calculations.
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Affiliation(s)
- Ryan Z Hinrichs
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14583, USA
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118
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