Computational Methods in Organometallic Catalysis

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Yu Lan. Computational Methods in Organometallic Catalysis

Table of Contents

List of Tables

List of Illustrations

Guide

Pages

Computational Methods in Organometallic Catalysis. From Elementary Reactions to Mechanisms

Foreword

Preface

Part I Theoretical View of Organometallic Catalysis

1 Introduction of Computational Organometallic Chemistry

1.1 Overview of Organometallic Chemistry

1.1.1 General View of Organometallic Chemistry

1.1.2 A Brief History of Organometallic Chemistry

1.2 Using Computational Tool to Study the Organometallic Chemistry Mechanism

1.2.1 Mechanism of Transition Metal Catalysis

1.2.2 Mechanistic Study of Transition Metal Catalysis by Theoretical Methods

References

2 Computational Methods in Organometallic Chemistry. 2.1 Introduction of Computational Methods. 2.1.1 The History of Quantum Chemistry Computational Methods

2.1.2 Post‐HF Methods

2.2 Density Functional Theory (DFT) Methods. 2.2.1 Overview of Density Functional Theory Methods

2.2.2 Jacob's Ladder of Density Functionals

2.2.3 The Second Rung in “Jacob's Ladder” of Density Functionals

2.2.4 The Third Rung in “Jacob's Ladder” of Density Functionals

2.2.5 The Fourth Rung in “Jacob's Ladder” of Density Functionals

2.2.6 The Fifth Rung in “Jacob's Ladder” of Density Functionals

2.2.7 Correction of Dispersion Interaction in Organic Systems

2.3 Basis Set and Its Application in Mechanism Studies. 2.3.1 General View of Basis Set

2.3.2 Pople's Basis Sets

2.3.3 Polarization Functions

2.3.4 Diffuse Functions

2.3.5 Correlation‐Consistent Basis Sets

2.3.6 Pseudo Potential Basis Sets

2.4 Solvent Effect

2.5 How to Choose a Method in Computational Organometallic Chemistry. 2.5.1 Why DFT Method Is Chosen

2.5.2 How to Choose a Density Functional

2.5.3 How to Choose a Basis Set

2.6 Revealing a Mechanism for An Organometallic Reaction by Theoretical Calculations

2.7 Overview of Popular Computational Programs

2.8 The Limitation of Current Computational Methods

2.8.1 The Accuracy of DFT Methods

2.8.2 Exact Solvation Effect

2.8.3 Evaluation of Entropy Effect

2.8.4 The Computation of Excited State and High Spin State

2.8.5 Speculation on the Reaction Mechanism

References

3 Elementary Reactions in Organometallic Chemistry

3.1 General View of Elementary Reactions in Organometallic Chemistry

3.2 Coordination and Dissociation. 3.2.1 Coordination Bond and Coordination

3.2.2 Dissociation

3.2.3 Ligand Exchange

3.3 Oxidative Addition

3.3.1 Concerted Oxidative Addition

3.3.2 Substitution‐type Oxidative Addition

3.3.3 Radical‐type Addition

3.3.4 Oxidative Cyclization

3.4 Reductive Elimination

3.4.1 Concerted Reductive Elimination

3.4.2 Substitution‐type Reductive Elimination

3.4.3 Radical‐Substitution‐type Reductive Elimination

3.4.4 Bimetallic Reductive Elimination

3.4.5 Eliminative Reduction

3.5 Insertion

3.5.1 1,2‐Insertion

3.5.2 1,1‐Insertion

3.5.3 Conjugative Insertion

3.5.4 Outer‐Sphere Insertion

3.6 Elimination

3.6.1 β‐Elimination

3.6.2 α‐Elimination

3.7 Transmetallation

3.7.1 Concerted Ring‐Type Transmetallation

3.7.2 Transmetallation Through Electrophilic Substitution

3.7.3 Stepwise Transmetallation

3.8 Metathesis

3.8.1 σ‐Bond Metathesis

3.8.2 Olefin Metathesis

3.8.3 Alkyne Metathesis

References

Part II On the Mechanism of Transition‐metal‐assisted Reactions

4 Theoretical Study of Ni‐Catalysis

4.1 Ni‐Mediated C—H Bond Activation

4.1.1 Ni‐Mediated Arene C—H Activation

4.1.2 Ni‐Mediated Aldehyde C—H Activation

4.2 Ni‐Mediated C—Halogen Bond Cleavage

4.2.1 Concerted Oxidative Addition of C—Halogen Bond

4.2.2 Radical‐Type Substitution of C—Halogen Bond

4.2.3 C—Halogen Bond Cleavage by β‐Halide Elimination

4.2.4 Nucleophilic Substitution of C—Halogen Bond

4.3 Ni‐Mediated C—O Bond Activation

4.3.1 Ether C—O Bond Activation

4.3.2 Ester C—O Bond Activation

4.4 Ni‐Mediated C—N Bond Cleavage

4.5 Ni‐Mediated C—C Bond Cleavage. 4.5.1 C—C Single Bond Activation

4.5.2 C=C Double Bond Activation

4.6 Ni‐Mediated Unsaturated Bond Activation

4.6.1 Oxidative Cyclization with Unsaturated Bonds

4.6.2 Electrophilic Addition of Unsaturated Bonds

4.6.3 Unsaturated Compounds Insertion

4.6.4 Nucleophilic Addition of Unsaturated Bonds

4.7 Ni‐Mediated Cyclization

4.7.1 Ni‐Mediated Cycloadditions

4.7.2 Ni‐Mediated Ring Substitutions

4.7.3 Ni‐Mediated Ring Extensions

References

5 Theoretical Study of Pd‐Catalysis

5.1 Pd‐Catalyzed Cross‐coupling Reactions

5.1.1 Suzuki–Miyaura Coupling

5.1.2 Negishi Coupling

5.1.3 Stille Coupling

5.1.4 Hiyama Coupling

5.1.5 Heck–Mizoroki Reaction

5.2 Pd‐Mediated C—Hetero Bond Formation

5.2.1 C—B Bond Formation

5.2.2 C—S Bond Formation

5.2.3 C—I Bond Formation

5.2.4 C—Si Bond Formation

5.3 Pd‐Mediated C—H Activation Reactions

5.3.1 Chelation‐Free C(sp3)—H Activation

5.3.2 Chelation‐Free C(sp2)—H Activation

5.3.3 Coordinative Chelation‐Assisted ortho‐ C(aryl)—H Activation

5.3.4 Covalent Chelation‐Assisted ortho‐ C(aryl)—H Activation

5.3.5 Chelation‐Assisted meta‐ C(aryl)—H Activation

5.3.6 Coordinative Chelation‐Assisted C(sp3)—H Activation

5.3.7 Covalent Chelation‐Assisted C(sp3)—H Activation

5.3.8 C—H Bond Activation Through Electrophilic Deprotonation

5.3.9 C—H Bond Activation Through σ‐Complex‐Assisted Metathesis

5.3.10 C—H Bond Activation Through Oxidative Addition

5.4 Pd‐Mediated Activation of Unsaturated Molecules

5.4.1 Alkene Activation

5.4.2 Alkyne Activation

5.4.3 Enyne Activation

5.4.4 Imine Activation

5.4.5 CO Activation

5.4.6 Isocyanide Activation

5.4.7 Carbene Activation

5.5 Allylic Pd Complex

5.5.1 Formation from Allylic Oxidative Addition

5.5.2 Formation from Allylic Nucleophilic Substitution

5.5.3 Formation from the Nucleophilic Attack onto Allene

5.5.4 Formation from Allylic C—H Activation

5.5.5 Formation from Allene Insertion

References

6 Theoretical Study of Pt‐Catalysis

6.1 Mechanism of Pt‐Catalyzed C—H Activation

6.1.1 Oxidative Addition of C—H Bond

6.1.2 Electrophilic Dehydrogenation

6.1.3 Carbene Insertion into C—H Bonds

6.2 Mechanism of Pt‐Catalyzed Alkyne Activation

6.2.1 Nucleophilic Additions

6.2.2 Cyclopropanation

6.2.3 Oxidative Cycloaddition

6.3 Mechanism of Pt‐Catalyzed Alkene Activation

6.3.1 Hydroamination of Alkenes

6.3.2 Hydroformylation of Alkenes

6.3.3 Isomerization of Cyclopropenes

References

7 Theoretical Study of Co‐Catalysis

7.1 Co‐Mediated C—H Bond Activation

7.1.1 Hydroarylation of Alkenes

7.1.2 Hydroarylation of Allenes

7.1.3 Hydroarylation of Alkynes

7.1.4 Hydroarylation of Nitrenoid

7.1.5 Oxidative C—H Alkoxylation

7.2 Co‐Mediated Cycloadditions

7.2.1 Co‐Mediated Pauson–Khand Reaction

7.2.2 Co‐Catalyzed [4+2] Cyclizations

7.2.3 Co‐Catalyzed [2+2+2] Cyclizations

7.2.4 Co‐Catalyzed [2+2] Cyclizations

7.3 Co‐Catalyzed Hydrogenation

7.3.1 Hydrogenation of Carbon Dioxide

7.3.2 Hydrogenation of Alkenes

7.3.3 Hydrogenation of Alkynes

7.4 Co‐Catalyzed Hydroformylation

7.4.1 Direct Hydroformylation by H2 and CO

7.4.2 Transfer Hydroformylation

7.5 Co‐Mediated Carbene Activation

7.5.1 Arylation of Carbene

7.5.2 Carboxylation of Carbene

7.6 Co‐Mediated Nitrene Activation

7.6.1 Aziridination of Olefins

7.6.2 Amination of Isonitriles

7.6.3 Amination of C—H Bonds

References

8 Theoretical Study of Rh‐Catalysis

8.1 Rh‐Mediated C—H Activation Reactions

8.1.1 Rh‐Catalyzed Arylation of C—H Bond

8.1.2 Rh‐Catalyzed Alkylation of C—H Bond

8.1.3 Rh‐Catalyzed Alkenylation of C—H Bond

8.1.4 Rh‐Catalyzed Amination of C—H Bond

8.1.5 Rh‐Catalyzed Halogenation of C—H Bond

8.2 Rh‐Catalyzed C—C Bond Activations and Transformations

8.2.1 Strain‐driven Oxidative Addition

8.2.2 The Carbon—Cyano Bond Activation

8.2.3 β‐Carbon Elimination

8.3 Rh‐Mediated C—Hetero Bond Activations

8.3.1 C—N Bond Activation

8.3.2 C—O Bond Activation

8.4 Rh‐Catalyzed Alkene Functionalizations

8.4.1 Hydrogenation of Alkene

8.4.2 Diboration of Alkene

8.5 Rh‐Catalyzed Alkyne Functionalizations

8.5.1 Hydroacylation of Alkynes

8.5.2 Hydroamination of Alkynes

8.5.3 Hydrothiolation of Alkynes

8.5.4 Hydroacetoxylation of Alkynes

8.6 Rh‐Catalyzed Addition Reactions of Carbonyl Compounds

8.6.1 Hydrogenation of Ketones

8.6.2 Hydrogenation of Carbon Dioxide

8.6.3 Hydroacylation of Ketones

8.7 Rh‐Catalyzed Carbene Transformations

8.7.1 Carbene Insertion into C—H Bonds

8.7.2 Arylation of Carbenes

8.7.3 Cyclopropanation of Carbenes

8.7.4 Cyclopropenation of Carbenes

8.8 Rh‐Catalyzed Nitrene Transformations

8.8.1 Nitrene Insertion into C—H Bonds

8.8.2 Aziridination of Nitrenes

8.9 Rh‐Catalyzed Cycloadditions

8.9.1 (3+2) Cycloadditions

8.9.2 Pauson–Khand‐type (2+2+1) Cycloadditions

8.9.3 (5+2) Cycloadditions

8.9.4 (5+2+1) Cycloadditions

References

9 Theoretical Study of Ir‐Catalysis

9.1 Ir‐Catalyzed Hydrogenations

9.1.1 Hydrogenation of Alkenes

9.1.2 Hydrogenation of Carbonyl Compounds

9.1.3 Hydrogenation of Imines

9.1.4 Hydrogenation of Quinolines

9.2 Ir‐Catalyzed Hydrofunctionalizations

9.2.1 Ir‐Catalyzed Hydroaminations

9.2.2 Ir‐Catalyzed Hydroarylations

9.2.3 Ir‐Catalyzed Hydrosilylations

9.3 Ir‐Catalyzed Borylations

9.3.1 Borylation of Alkanes

9.3.2 Borylation of Arenes

9.4 Ir‐Catalyzed Aminations

9.4.1 Amination of Alcohols

9.4.2 Amination of Arenes

9.5 Ir‐Catalyzed C—C Bond Coupling Reactions

References

10 Theoretical Study of Fe‐Catalysis

10.1 Fe‐Mediated Oxidations

10.1.1 Alkane Oxidations

10.1.2 Arene Oxidations

10.1.3 Alkene Oxidations

10.1.4 Oxidative Catechol Ring Cleavage

10.2 Fe‐Mediated Hydrogenations

10.2.1 Hydrogenation of Alkenes

10.2.2 Hydrogenation of Carbonyls

10.2.3 Hydrogenation of Imines

10.2.4 Hydrogenation of Carbon Dioxide

10.3 Fe‐Mediated Hydrofunctionalizations

10.3.1 Hydrosilylation of Ketones

10.3.2 Hydroamination of Allenes

10.4 Fe‐Mediated Dehydrogenations

10.4.1 Dehydrogenation of Alcohols

10.4.2 Dehydrogenation of Formaldehyde

10.4.3 Dehydrogenation of Formic Acid

10.4.4 Dehydrogenation of Ammonia‐Borane

10.5 Fe‐Catalyzed Coupling Reactions

10.5.1 C—C Cross‐Couplings with Aryl Halide

10.5.2 C—N Cross‐Couplings with Aryl Halide

10.5.3 C—C Cross‐Couplings with Alkyl Halide

10.5.4 Iron‐Mediated Oxidative Coupling

References

11 Theoretical Study of Ru‐Catalysis

11.1 Ru‐Mediated C—H Bond Activation

11.1.1 Mechanism of the Ru‐Mediated C—H Bond Cleavage

11.1.2 Ru‐Catalyzed C—H Bond Arylation

11.1.3 Ru‐Catalyzed ortho‐Alkylation of Arenes

11.1.4 Ru‐Catalyzed ortho‐Alkenylation of Arenes

11.2 Ru‐Catalyzed Hydrogenations

11.2.1 Hydrogenation of Alkenes

11.2.2 Hydrogenation of Carbonyls

11.2.3 Hydrogenation of Esters

11.2.4 Hydrodefluorination of Fluoroarenes

11.3 Ru‐Catalyzed Hydrofunctionalizations

11.3.1 Hydroacylations

11.3.2 Hydrocarboxylations

11.3.3 Hydroborations

11.4 Ru‐Mediated Dehydrogenations

11.4.1 Dehydrogenation of Alcohols

11.4.2 Dehydrogenation of Formaldehyde

11.4.3 Dehydrogenation of Formic Acid

11.5 Ru‐Catalyzed Cycloadditions

11.5.1 Ru‐Mediated (2+2+2) Cycloadditions

11.5.2 Ru‐Mediated Pauson–Khand Type (2+2+1) Cycloadditions

11.5.3 Ru‐Mediated Click Reactions

11.6 Ru‐Mediated Metathesis

11.6.1 Ru‐Mediated Intermolecular Olefin Metathesis

11.6.2 Ru‐Mediated Intramolecular Diene Metathesis

11.6.3 Ru‐Mediated Alkyne Metathesis

References

12 Theoretical Study of Mn‐Catalysis

12.1 Mn‐Mediated Oxidation of Alkanes

12.1.1 C—H Hydroxylations

12.1.2 C—H Halogenations

12.1.3 C—H Azidations

12.1.4 C—H Isocyanations

12.2 Mn‐Mediated C—H Activations

12.2.1 Electrophilic Deprotonation

12.2.2 σ‐Complex‐Assisted Metathesis

12.2.3 Concerted Metalation–Deprotonation

12.3 Mn‐Mediated Hydrogenations

12.3.1 Hydrogenation of Carbon Dioxide

12.3.2 Hydrogenation of Carbonates

12.4 Mn‐Mediated Dehydrogenations

12.4.1 Dehydrogenation of Alcohols

12.4.2 Dehydrogenative Couplings

References

13 Theoretical Study of Cu‐Catalysis

13.1 Cu‐Mediated Ullmann Condensations

13.1.1 C—N Bond Couplings

13.1.2 C—O Bond Couplings

13.1.3 C—F Bond Couplings

13.2 Cu‐Mediated Trifluoromethylations

13.2.1 Trifluoromethylations Through Cross‐Coupling

13.2.2 Trifluoromethylations Through Oxidative Coupling

13.2.3 Radical‐Type Trifluoromethylations

13.3 Cu‐Mediated C—H Activations

13.3.1 C—H Arylations

13.3.2 C—H Aminations

13.3.3 C—H Hydroxylation

13.3.4 C—H Etherifications

13.4 Cu‐Mediated Alkyne Activations

13.4.1 Azide–Alkyne Cycloadditions

13.4.2 Nucleophilic Attack onto Alkynes

13.4.3 Alkynyl Cu Transformations

13.5 Cu‐Mediated Carbene Transformations

13.5.1 [2+1] Cycloadditions with Alkenes

13.5.2 Carbene Insertions

13.5.3 Rearrangement of Carbenes

13.6 Cu‐Mediated Nitrene Transformations

13.6.1 [2+1] Cycloadditions with Alkenes

13.6.2 Amination of Nitrenes

13.6.3 Nitrene Insertions

13.7 Cu‐Catalyzed Hydrofunctionalizations

13.7.1 Hydroborylations

13.7.2 Hydrosilylation

13.7.3 Hydrocarboxylations

13.8 Cu‐Catalyzed Borylations

13.8.1 Borylation of Alkenes

13.8.2 Borylation of Alkynes

13.8.3 Borylation of Carbonyls

References

14 Theoretical Study of Ag‐Catalysis

14.1 Ag‐Mediated Carbene Complex Transformations

14.1.1 Silver–Carbene Formation

14.1.2 Carbene Insertion into C—Cl Bond

14.1.3 Carbene Insertion into O—H Bond

14.1.4 Nucleophilic Attack by Carbonyl Groups

14.1.5 Carbene Insertion into C—H Bond

14.2 Ag‐Mediated Nitrene Transformations

14.2.1 Silver–Nitrene Complex Formation

14.2.2 Nucleophilic Attack by Unsaturated Bonds

14.2.3 Nucleophilic Attack by Amines

14.3 Ag‐Mediated Silylene Transformations

14.4 Ag‐Mediated Alkyne Activations

14.4.1 π‐Activation of Alkynes

14.4.2 C—H Activation of Alkynes

References

15 Theoretical Study of Au‐Catalysis

15.1 Au‐Mediated Alkyne Activations

15.1.1 Isomerization of Alkynes

15.1.2 Nucleophilic Attack by Oxygen‐Involved Nucleophiles

15.1.3 Nucleophilic Attack by Nitrogen‐Involved Nucleophiles

15.1.4 Nucleophilic Attack by Arenes

15.2 Au‐mediated Alkene Activations

15.2.1 Nucleophilic Addition of Alkenes

15.2.2 Allylic Substitutions

15.3 Au‐mediated Allene Activations

15.3.1 Hydroamination of Allenes

15.3.2 Hydroalkoxylation of Allenes

15.3.3 Cycloisomerization of Allenyl Ketones

15.4 Au‐mediated Enyne Transformations

15.4.1 1,5‐Enyne Cycloisomerizations

15.4.2 1,6‐Enyne Cycloisomerizations

15.4.3 Allenyne Cycloisomerizations

15.4.4 Conjugative Enyne Cycloisomerizations

References

Index. a

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d

e

f

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i

k

l

m

n

o

p

q

r

s

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v

w

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Yu Lan

The 1960s saw remarkable advances in methods, approximations, and the beginnings of the flowering of computers for chemical calculations. The dawn of the modern hybrid density functional theory in the mid‐1990s, borrowing exact exchange from wavefunction theory, made it possible to begin the quantitative calculations of structure, mechanics, and mechanisms, including the incredibly useful organometallic reactions. Both Ru and Mo catalysts for olefin metathesis, and Pd catalysis for cross‐coupling reactions, have led to Nobel prizes for their discoverers.

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Scheme 2.3 The combination of Gaussian‐type orbitals (GTOs) for the construction of Slater‐type orbital (STO). (a) STO. (b) GTO. (c) The combination of GTOs.

Following a suggestion of Boys, Pople decided to use a combination of Gaussian‐type functions to mimic the STO, which was named Gaussian‐type orbital (GTO). These orbitals have a different spatial function, X′Y‴Z′e−ζr2; therefore, the integrals required to build the Fock matrix can be evaluated exactly (Scheme 2.3b). The tradeoff is that GTOs do differ in shape from the STOs, particularly at the nucleus where the STO has a cusp, but the GTO is continually differentiable. The computational advantage is so substantial that it is more efficient to represent a single atomic orbital as a combination of several GTOs rather than a single STO (Scheme 2.3c). When a few GTOs with differing shapes are added, the result is a function that resembles an STO. Now, the basis set is not just the atomic orbitals, but is instead all the GTOs that are used to make up the atomic orbitals. The minimum Gaussian‐type basis set is STO‐3G, in which “STO” is the abbreviation of STO, and “3G” means that each STO is obtained by a linear combination of three GTOs [66, 67].

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