Table of Contents

Cover

Related Titles

Title Page

Copyright

List of Contributors

Preface

Chapter 1: Mechanisms of Metal-Mediated C–N Coupling Processes: A Synergistic Relationship between Gas-Phase Experiments and Computational Chemistry

1.1 Introduction

1.2 From Metal-Carbon to Carbon–Nitrogen Bonds

1.3 From Metal-Nitrogen to Carbon-Nitrogen Bonds

1.4 Conclusion and Perspectives

Acknowledgments

References

Chapter 2: Fundamental Aspects of the Metal-Catalyzed C–H Bond Functionalization by Diazocarbenes: Guiding Principles for Design of Catalyst with Non-redox-Active Metal (Such as Ca) and Non-Innocent Ligand

2.1 Introduction

2.2 Theoretical Models and Methods

2.3 Design of Catalyst with Non-redox-Active Metal and Non-Innocent Ligand

2.4 Conclusions and Perspectives

Acknowledgment

References

Chapter 3: Using Metal Vinylidene Complexes to Probe the Partnership Between Theory and Experiment

3.1 Introduction

3.2 Project Planning in Organometallic Chemistry

3.3 Case Studies

3.4 The Benefits of Synergy and Partnerships

References

Chapter 4: Ligand, Additive, and Solvent Effects in Palladium Catalysis – Mechanistic Studies En Route to Catalyst Design

4.1 Introduction

4.2 The Effect of Solvent in Palladium-Catalyzed Cross Coupling and on the Nature of the Catalytically Active Species

4.3 Common Additives in Palladium-Catalyzed Cross-Coupling Reactions – Effect on (Pre)catalyst and Active Catalytic Species

4.4 Pd(I) Dimer: Only Precatalyst or Also Catalyst?

4.5 Investigation of Key Catalytic Intermediates in High-Oxidation-State Palladium Chemistry

4.6 Concluding Remarks

References

Chapter 5: Computational Studies on Sigmatropic Rearrangements via π-Activation by Palladium and Gold Catalysts

5.1 Introduction

5.2 Palladium as a Catalyst

5.3 Gold as a Catalyst

5.4 Concluding Remarks

References

Chapter 6: Theoretical Insights into Transition Metal-Catalyzed Reactions of Carbon Dioxide

6.1 Introduction

6.2 Theoretical Methods

6.3 Hydrogenation of CO₂ with H₂

6.4 Coupling Reactions of CO₂ and Epoxides

6.5 Reduction of CO₂ with Organoborons

6.6 Carboxylation of Olefins with CO₂

6.7 Hydrocarboxylation of Olefins with CO₂ and H₂

6.8 Summary

Acknowledgment

References

Chapter 7: Catalytically Enhanced NMR of Heterogeneously Catalyzed Hydrogenations

7.1 Introduction

7.2 Parahydrogen and PHIP Basics

7.3 PHIP as a Mechanistic Tool in Homogeneous Catalysis

7.4 PHIP-Enhanced NMR and Heterogeneous Catalysis

7.5 Summary and Conclusions

Acknowledgments

References

Chapter 8: Combined Use of Both Experimental and Theoretical Methods in the Exploration of Reaction Mechanisms in Catalysis by Transition Metals

8.1 Introduction

8.2 Recent DFT Developments of Relevance to Transition Metal Catalysis

8.3 Case Studies

8.4 Conclusions

Acknowledgments

References

Chapter 9: Is There Something New Under the Sun?Myths and Facts in the Analysis of Catalytic Cycles

9.1 Introduction

9.2 Kinetics Based on Rate Constants or Energies

9.3 Application: Cross-Coupling with a Bidentate Pd Complex

9.4 A Century of Sabatier's Genius Idea

9.5 Theory and Practice of Catalysis, Including Concentration Effects

9.6 RDStep , RDStates

9.7 Conclusion

References

Chapter 10: Computational Tools for Structure, Spectroscopy and Thermochemistry

10.1 Introduction

10.2 Basic Concepts

10.3 Spectroscopic Techniques

10.4 Applications and Case Studies

10.5 Conclusions and Future Developments

Acknowledgments

References

Chapter 11: Computational Modeling of Graphene Systems Containing Transition Metal Atoms and Clusters

11.1 Introduction

11.2 Quantum Chemical Modeling and Benchmarking

11.3 Representative Studies of Graphene Systems with Transition Metals

11.4 Conclusions

Acknowledgments

List of Abbreviations

References

Index

End User License Agreement

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Guide

Cover

Table of Contents

Preface

Chapter 1: Mechanisms of Metal-Mediated C–N Coupling Processes: A Synergistic Relationship between Gas-Phase Experiments and Computational Chemistry

List of Illustrations

Figure 1.1

Scheme 1.1

Figure 1.2

Figure 1.3

Scheme 1.2

Figure 1.4

Figure 1.5

Scheme 2.1

Scheme 2.2

Scheme 2.3

Scheme 2.4

Scheme 2.5

Figure 2.2

Scheme 2.6

Scheme 2.7

Scheme 2.8

Figure 2.1

Figure 2.3

Figure 2.4

Scheme 3.1

Scheme 3.2

Scheme 3.3

Scheme 3.4

Scheme 3.5

Scheme 3.6

Scheme 3.7

Scheme 3.8

Scheme 3.9

Scheme 3.10

Figure 3.1

Scheme 3.11

Figure 4.1

Figure 4.2

Figure 4.3

Figure 4.4

Figure 4.5

Figure 4.6

Figure 4.7

Figure 4.8

Figure 4.10

Figure 4.9

Figure 4.11

Figure 4.12

Figure 4.13

Figure 4.14

Figure 5.1

Figure 5.2

Figure 5.3

Figure 5.4

Figure 5.5

Scheme 5.1

Figure 5.6

Figure 5.7

Figure 5.8

Scheme 5.2

Scheme 5.3

Figure 5.9

Figure 5.10

Figure 5.11

Figure 5.12

Scheme 5.4

Scheme 5.5

Figure 5.13

Figure 5.14

Figure 5.16

Figure 5.15

Scheme 5.6

Figure 5.17

Figure 5.18

Scheme 5.7

Figure 5.19

Scheme 5.8

Figure 5.20

Scheme 6.1

Scheme 6.2

Figure 6.1

Scheme 6.3

Figure 6.2

Scheme 6.4

Figure 6.3

Figure 6.4

Scheme 6.5

Scheme 6.6

Figure 6.5

Scheme 6.7

Figure 6.6

Scheme 6.8

Figure 6.7

Figure 6.8

Scheme 6.9

Figure 6.9

Figure 7.1

Figure 7.2

Figure 7.3

Figure 7.4

Figure 7.5

Figure 7.6

Figure 7.7

Figure 7.8

Figure 7.9

Figure 7.10

Figure 7.11

Scheme 8.1

Figure 8.1

Figure 8.2

Figure 8.3

Figure 8.4

Figure 8.5

Scheme 8.2

Scheme 8.3

Figure 8.6

Scheme 8.4

Scheme 8.5

Scheme 8.6

Figure 8.7

Scheme 8.7

Scheme 8.8

Figure 8.8

Scheme 8.9

Scheme 8.10

Figure 8.9

Figure 8.10

Scheme 8.11

Scheme 8.12

Figure 8.11

Scheme 9.1

Scheme 9.2

Scheme 9.3

Scheme 9.4

Scheme 9.5

Scheme 9.6

Figure 9.1

Scheme 9.7

Scheme 9.8

Scheme 9.9

Scheme 9.10

Figure 9.2

Figure 9.3

Scheme 9.11

Scheme 9.12

Scheme 9.13

Scheme 9.14

Scheme 9.15

Scheme 9.16

Scheme 9.17

Figure 10.1

Figure 10.2

Figure 10.3

Figure 10.4

Figure 10.5

Figure 10.6

Figure 10.7

Figure 10.8

Figure 10.9

Figure 10.10

Figure 10.11

Figure 10.12

Figure 10.13

Figure 10.14

Figure 10.15

Figure 10.16

Figure 11.1

Figure 11.2

Figure 11.3

Figure 11.4

Figure 11.5

Figure 11.6

Figure 11.7

Figure 11.8

Figure 11.9

Figure 11.10

Figure 11.11

List of Tables

Table 2.1

Table 2.2

Table 2.3

Table 1.4

Table 1.5

Table 2.6

Table 2.7

Table 2.8

Table 2.9

Table 3.1

Table 10.1

Table 10.2

Table 10.3

Table 10.4

Table 10.5

Table 10.6

Table 10.7

Table 10.8

Table 10.9

Table 11.1

Table 11.2

Table 11.3

Table 11.4

Table 11.5

Table 11.6

Table 11.7

Table 11.8

Table 11.9

Table 11.10

Table 11.11

Table 11.12

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Edited by Valentine P. Ananikov

Understanding Organometallic Reaction Mechanisms and Catalysis

Computational and Experimental Tools

The Editor

Prof. Dr. Valentine P. Ananikov

Russian Academy of Sciences, Zelinsky

Institute of Organic Chemistry

47 Leninski Prospect

119991 Moscow

Russia

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List of Contributors

Valentine P. Ananikov

Russian Academy of Sciences

Zelinsky Institute of Organic Chemistry

Leninsky Prospekt 47

Moscow, 119991

Russia

and

Lomonosov Moscow State University

Department of Chemistry

Leninskie Gory

Moscow, 119991

Russia

Vincenzo Barone

Scuola Normale Superiore

Piazza dei Cavalieri 7

Pisa I-56126

Italy

Danila A. Barskiy

International Tomography Center

SB RAS, 3A Institutskaya Street

Novosibirsk, 630090

Russia

and

Novosibirsk State University

Department of Natural Sciences

Pirogova Street

Novosibirsk, 630090

Russia

Malgorzata Biczysko

Scuola Normale Superiore

Piazza dei Cavalieri 7

Pisa I-56126

Italy

Ivan Carnimeo

Scuola Normale Superiore

Piazza dei Cavalieri 7

I-56126 Pisa

Italy

Niels Johan Christensen

Technical University of Denmark

Department of Chemistry

Kemitorvet, building 207

Lyngby, DK-2800

Denmark

Ting Fan

The Hong Kong University of Science and Technology

Department of Chemistry

Clear Water Bay

Kowloon

Hong Kong

Natalie Fey

University of Bristol

School of Chemistry

Cantock's Close

Bristol, BS8 1TS

UK

Peter Fristrup

Technical University of Denmark

Department of Chemistry

Kemitorvet, building 207

Lyngby, DK-2800

Denmark

Osvaldo Gutierrez

University of Pennsylvania

Department of Chemistry

Roy and Diana Vagelos

Laboratories

231 S. 34 Street

Philadelphia

19104-6323 PA

USA

Igor V. Koptyug

International Tomography Center

SB RAS, 3A Institutskaya Street

Novosibirsk, 630090

Russia

and

Novosibirsk State University

Department of Natural Sciences

Pirogova Street

Novosibirsk, 630090

Russia

Kirill V. Kovtunov

International Tomography Center

SB RAS, 3A Institutskaya Street

Novosibirsk, 630090

Russia

and

Novosibirsk State University

Department of Natural Sciences

Pirogova Street

Novosibirsk, 630090

Russia

Marisa C. Kozlowski

University of Pennsylvania

Department of Chemistry

Roy and Diana Vagelos Laboratories

S. 34 Street

Philadelphia

19104-6323 PA

USA

Sebastian Kozuch

University of North Texas

Department of Chemistry

Center for Advanced Scientific Computing and Modeling (CASaM)

Denton

TX 76203-5070

USA

Robert Kretschmer

Technische Universität Berlin

Institut für Chemie

Straße des 17. Juni 115

Berlin, 10623

Germany

Zhenyang Lin

The Hong Kong University of Science and Technology

Department of Chemistry

Clear Water Bay

Kowloon

Hong Kong

Daniel Lupp

Technical University of Denmark

Department of Chemistry

Kemitorvet, building 207

Lyngby, DK-2800

Denmark

Jason M. Lynam

University of York

Department of Chemistry

Heslington

York, YO10 5DD

UK

Djamaladdin G. Musaev

Emory University

Cherry L. Emerson Center for Scientific Computation

Dickey Drive

Atlanta

Georgia 30322

USA

Mikhail V. Polynski

Russian Academy of Sciences

Zelinsky Institute of Organic Chemistry

Leninsky Prospekt 47

Moscow, 119991

Russia

and

Lomonosov Moscow State University

Department of Chemistry

Leninskie Gory

Moscow, 119991

Russia

Oleg G. Salnikov

International Tomography Center

SB RAS, 3A Institutskaya Street

Novosibirsk, 630090

Russia

and

Novosibirsk State University

Department of Natural Sciences

Pirogova Street

Novosibirsk, 630090

Russia

Maria Schlangen

Technische Universität Berlin

Institut für Chemie

Straße des 17. Juni 115

Berlin, 10623

Germany

Franziska Schoenebeck

RWTH Aachen University

Institute of Organic Chemistry

Landoltweg 1

Aachen, 52056

Germany

Helmut Schwarz

Technische Universität Berlin

Institut für Chemie

Straße des 17. Juni 115

Berlin, 10623

Germany

Ivan V. Skovpin

International Tomography Center

SB RAS, 3A Institutskaya Street

Novosibirsk, 630090

Russia

and

Novosibirsk State University

Department of Natural Sciences

Pirogova Street

Novosibirsk, 630090

Russia

John M. Slattery

University of York

Department of Chemistry

Heslington

York, YO10 5DD

UK

Adrian Varela-Alvarez

Emory University

Cherry L. Emerson Center for Scientific Computation

Dickey Drive

Atlanta

Georgia 30322

USA

Vladimir V. Zhivonitko

International Tomography Center

SB RAS, 3A Institutskaya Street

Novosibirsk, 630090

Russia

and

Novosibirsk State University

Department of Natural Sciences

Pirogova Street

Novosibirsk, 630090

Russia

Preface

Understanding electronic structure and reactivity of organometallic compounds remains the problem of fundamental importance in modern chemistry. Development of catalysis and organic chemistry was largely governed by elucidation of reaction mechanisms and utilization of this knowledge to control selectivity and improve yields in synthetic applications dealing with medicinal chemistry, preparation of pharmaceutical and biologically active molecules, industrial processes, fine organic synthesis, new generation of smart materials and organic electronics. In recent decades research in these areas was stimulated by rapid progress in quantum chemistry and utilization of theoretical calculations to reveal correlations between molecular structure, properties, and reactivity.

Theoretical calculations using modern quantum chemical methods provided an outstanding opportunity to make a valuable insight into the problem and allowed reliable description of reaction mechanisms in catalysis from the first principles. Application of informative and flexible computational procedures on numerous examples has demonstrated accurate computational modeling – often within the accuracy achieved in experimental measurements.

Not surprisingly, there is a remarkable interest in modern experimental chemistry to understand computational methods and to apply these methods in the everyday research. In fact, the number of publications that contain both – experiment studies and theoretical calculations – was tremendously increased over the last years. It is not uncommon for purely experimental research groups to learn theoretical methods and facilitate mechanistic studies, especially in the fields where experimental capabilities alone are not sufficient to solve the problem. Rapid increase in the computational power of modern personal computers and easy availability of high performance CPUs even further stimulate this tendency. What is important nowadays, is to transfer the knowledge about state-of-the-art theoretical methods and fascinating opportunities they open in the studies of transition metal chemistry and catalysis.

The role of this book is to highlight new horizons in the studies of reaction mechanisms that open joint application of experimental studies and theoretical calculations. The book is aimed to provide first hand experience from known experts that are practically familiar with such complex studies involving both computational and experimental tools.

The present book chapters review organometallic and catalytic reactions in the gas phase, model systems for studying reactions in solution under homogeneous conditions with soluble metal complexes, as well as complex chemical transformations involving heterogeneous systems. Few chapters are dedicated to describe methodology of computational studies for exploration of catalytic cycles and mechanisms of organometallic reactions.

I would like to express my great thanks to the authors that accepted to contribute to the book for their excellent chapters. Finally, I thank Anne Brennfuehrer and Lesley Belfit from Wiley for continuous help and assistance during development of this book project.

Moscow, Russia, 2014

Valentine Ananikov

Chapter 1
Mechanisms of Metal-Mediated C–N Coupling Processes: A Synergistic Relationship between Gas-Phase Experiments and Computational Chemistry

Robert Kretschmer, Maria Schlangen, and Helmut Schwarz

1.1 Introduction

As a consequence of the key positions that the elements carbon and nitrogen occupy in nature, C–N bond formation constitutes an important issue in the synthesis of various products ranging from chemical feedstocks to pharmaceuticals. Not surprisingly, over the last few decades, intensive research has been devoted to this timely topic [1], and the use of ammonia as a relatively inexpensive reagent for C–N coupling reactions has been found to be highly desirable [2]. However, despite the impressive progress reported on the development of new synthetic methodologies, there exists a lack of information on the precise, atomistic-level derived mechanisms in particular for the metal-mediated formation of nitrogen-containing organic molecules generated directly from ammonia. One way to gain such insight is to perform gas-phase experiments on “isolated” reactants. These studies provide an ideal arena for probing experimentally the energetics and kinetics of a chemical reaction in an unperturbed environment at a strictly molecular level without being obscured by difficult-to-control or poorly defined solvation, aggregation, counterion, and other effects. Thus, an opportunity is provided to reveal the intrinsic feature(s) of a catalyst, to explore directly the concept of single-site catalysts, or to probe in detail how mechanisms are affected by factors such as cluster size, different ligands, dimensionality, stoichiometry, oxidation state, degree of coordinative saturation, and charge state. In short, from these experiments, one may learn what determines the outcome of a chemical transformation [3]. In addition, thermochemical and kinetic data derived from these experiments provide a means to benchmark the quality of theoretical studies.

While the study of “naked” gas-phase species will, in principal, never account for the precise kinetic and mechanistic details that prevail at a surface, in an enzyme, or in solution, when complemented by appropriate, computationally derived information, these gas-phase experiments prove meaningful on the ground that they permit a systematic approach to address the above-mentioned questions; moreover, they provide a conceptual framework. The DEGUSSA process, which is the rather unique, platinum-mediated, large-scale coupling of CH and NH to generate HCN [4], serves as a good example. Mass spectrometry-based experiments [5] suggested both the key role of CHNH as a crucial gas-phase transient and also pointed to the advantage of using a bimetallic system rather than a pure platinum-based catalyst for the C–N coupling step to diminish undesired, catalyst-poisoning “soot” formation [6, 7]. The existence of CHNH was later confirmed by photoionization studies [8] and catalysts that are currently employed contain silver-platinum alloys rather than pure platinum.

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