Structure Elucidation in Organic Chemistry E-Book

• Herausgeber: Wiley-VCH
• Kategorie: Wissenschaft und neue Technologien
• Sprache: Englisch

Seitenzahl: 975

Veröffentlichungsjahr: 2015

Beschreibung

Intended for advanced readers, this is a review of all relevant techniques for structure analysis in one handy volume.
As such, it provides the latest knowledge on spectroscopic and related techniques for chemical structure analysis, such as NMR, optical spectroscopy, mass spectrometry and X-ray crystallography, including the scope and limitation of each method. As a result, readers not only become acquainted with the techniques, but also the advantages of the synergy between them. This enables them to choose the correct analytical method for each problem, saving both time and resources. Special emphasis is placed on NMR and its application to absolute configuration determination and the analysis of molecular interactions.

Adopting a practical point of view, the author team from academia and industry guarantees both solid methodology and applications essential for structure determination, equipping experts as well as newcomers with the tools to solve any structural problem.

Leseprobe

Table of Contents

Cover

Related Titles

Title Page

Copyright

Preface

List of Contributors

Chapter 1: Interaction of Radiation with Matter

1.1 Introduction

1.2 Spectroscopy: A Definition

1.3 Electromagnetic Radiation

1.4 Electromagnetic Spectrum

1.5 Interaction of Radiation with Matter

1.6 Magnetic Spectroscopies

1.7 Pulse Techniques in NMR Spectroscopy

1.8 Line Widths

1.9 Selection Rules

1.10 Summary of Spectroscopic Techniques

References

Chapter 2: Computational Spectroscopy Tools for Molecular Structure Analysis

2.1 Introduction

2.2 Potential Energy Surface and Molecular Structure

2.3 Computational Aspects for Spectroscopic Techniques

2.4 Application and Case Studies

Acknowledgments

References

Chapter 3: Absolute Configuration and Conformational Analysis of Chiral Compounds via Experimental and Theoretical Prediction of Chiroptical Properties: ORD, ECD, and VCD

3.1 Introduction

3.2 Chirality

3.3 What is a Chiroptical Method?

3.4 Quantum Mechanical (

Ab Initio

) Methods for Predicting Chiroptical Properties

3.5 Electronic Circular Dichroism (ECD)

3.6 Vibrational Circular Dichroism (VCD)

3.7 Optical Rotatory Dispersion (ORD)

3.8 When More than One Method is Needed

3.9 Concluding Remarks

References

Chapter 4: Mass Spectrometry Strategies in the Assignment of Molecular Structure: Breaking Chemical Bonds before Bringing the Pieces of the Puzzle Together

4.1 Introduction

4.2 Instrumentation and Technology

4.3 Breaking Chemical Bonds – Fragmentation Reactions

4.4 Confirmation of Identity

4.5 Putting the Puzzle Together – Structure Elucidation of Unknowns

4.6 Conclusions and Perspectives

Abbreviations

References

Chapter 5: Basic Principles of IR/Raman: Applications in Small Molecules Structural Elucidation

5.1 Introduction

5.2 Characteristic Vibrational Modes: Diatomics and Chemical Bonds

5.3 Fundamental Vibrational Modes and Molecular Structure

5.4 Selection Rules and Finding the Number of Normal Modes in Each Symmetry Species

5.5 The Vibrational Assignment of Raman and Infrared Spectra

5.6 Conclusions

References

Chapter 6: Solid-State NMR Applications in the Structural Elucidation of Small Molecules

6.1 Introduction

6.2 Line-Narrowing and Sensitivity Enhancement Methods in ssNMR Spectroscopy

6.3 Probing Dynamics in Solids

6.4 Application of ssNMR Spectroscopy to Small Molecules

6.5 NMR of Molecules on Surfaces (DNP)

6.6 NMR Crystallography

Acronyms

References

Chapter 7: Simplified NMR Procedures for the Assignment of the Absolute Configuration

7.1 Introduction

7.2 Single Derivatization Methods for Mono- and Polyfunctional Compounds

7.3 Resin-Bound Chiral Derivatizing Agents (Mix and Shake Method)

7.4 Non-resin in Tube Assignment (BPG and BINOL Borates)

7.5 Tandem HPLC-NMR: Simultaneous Enantioresolution and Configurational Assignment

7.6 Assignment Based on the Chemical Shifts from the Auxiliaries

7.7 Scope and Conclusions

References

Chapter 8: Structural Elucidation of Small Organic Molecules Assistedby NMR in Aligned Media

8.1 Introduction

8.2 Aligning Media

8.3 Measurement of RDCs

8.4 Computational Methodology

8.5 Data Analysis: Use of RDCs as Structural Constraints in Small Molecules

8.6 RDCs and Determination of Absolute Configuration

8.7 Conclusions and Perspectives

Acknowledgments

References

Chapter 9: NMR Techniques for the Study of Transient Intermolecular Interactions

9.1 Introduction

9.2 Nuclear Overhauser Effect

9.3 Saturation Transfer Difference NMR

9.4 Diffusion NMR

9.5 Conclusions

References

Chapter 10: Analysis of Molecular Interactions by Surface Plasmon Resonance Spectroscopy

10.1 Introduction

10.2 General Aspects of the Surface Plasmon Resonance Principle

10.3 The SPR Experiment

10.4 The Information Contained in the SPR Experiment

10.5 SPR Applications: From Large to Small Molecules

10.6 Beyond SPR–Orthogonal Interaction Biosensor Technologies

References

Chapter 11: Determination of Absolute Configurations by Electronic CD Exciton Chirality, Vibrational CD, 1H NMR Anisotropy, and X-ray Crystallography Methods – Principles, Practices, and Reliability

11.1 Introduction

11.2 Reliability in the AC Determination and Selection of Method

11.3 Non-empirical Method: AC Determination by the X-ray Bijvoet Method

11.4 Non-empirical Method: AC Determination by the ECD Exciton Chirality Method

11.5 Non-empirical Method: AC Determination by VCD Spectroscopy and DFT MO Simulation

11.6 Empirical Method: AC Determination by

1

H NMR Anisotropy Method Using MαNP Acid

11.7 Relative Method: X-ray Crystallography Using Camphorsultam Dichlorophthalic Acid (CSDP Acid)

11.8 Relative Method: X-ray Crystallography Using of MαNP Group as Internal Reference

11.9 Conclusion

11.A.1 Appendix

Acknowledgments

References

Chapter 12: An Integrated Approach to Structure Verification Using Automated Procedures

12.1 Introduction

12.2 Practical Aspects of NMR Automatic Verification

12.3 The Architecture of the Automatic Verification Expert System

12.4 Performance of the Automated Structure Verification Systems

12.5 Conclusions

Acknowledgments

References

Chapter 13: On the Search for the Appropriate Techniques for Structural Elucidation of Small Molecules

13.1 Introduction

13.2 The Challenge of Structural Determination

13.3 Tools: Mass Spectrometry (MS)

13.4 Tools: Solution NMR Spectroscopy

13.5 Tools: Solid-State NMR Spectroscopy

13.6 Chiroptical Spectroscopies

13.7 Theoretical Calculations:

Ab initio

Calculations of NMR Shifts

13.8 Theoretical Calculations: Computer-Assisted Structure Elucidation

13.9 Summary

Acknowledgments

References

Index

EULA

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Guide

Cover

Table of Contents

Preface

Chapter 1: Interaction of Radiation with Matter

List of Illustrations

Figure 1.1

Figure 1.2

Figure 1.3

Figure 1.4

Figure 1.5

Figure 1.6

Figure 2.1

Figure 2.2

Figure 2.3

Figure 2.4

Figure 2.5

Figure 2.6

Figure 2.7

Figure 2.8

Figure 2.9

Figure 3.1

Figure 3.2

Figure 3.3

Figure 3.4

Figure 3.5

Figure 3.6

Figure 3.7

Figure 3.8

Figure 3.9

Figure 3.10

Figure Scheme 3.1

Figure 3.11

Figure 3.12

Figure 3.13

Figure 3.14

Figure 3.15

Figure 3.16

Figure 3.17

Figure 3.18

Figure 3.19

Figure 3.20

Figure 3.21

Figure 3.22

Figure 3.23

Figure 3.24

Figure 3.25

Figure 3.26

Figure 3.27

Figure 3.28

Figure 3.29

Figure 3.30

Figure 3.31

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 4.9

Figure 4.10

Figure 4.11

Figure 4.12

Figure 4.13

Figure 4.14

Figure 4.15

Figure 4.16

Figure 4.17

Figure 5.1

Figure 5.2

Figure 5.3

Figure 5.4

Figure 5.5

Figure 5.6

Figure 5.7

Figure 5.8

Figure 5.9

Figure 5.10

Figure 6.1

Figure 6.27

Figure 6.2

Figure 6.3

Figure 6.4

Figure 6.5

Figure 6.6

Figure 6.7

Figure 6.8

Figure 6.9

Figure 6.10

Figure 6.11

Figure 6.12

Figure 6.13

Figure 6.14

Figure 6.15

Figure 6.16

Figure 6.17

Figure 6.18

Figure 6.19

Figure 6.20

Figure 6.21

Figure 6.22

Figure 6.23

Figure 6.24

Figure 6.25

Figure 6.26

Figure 6.28

Figure 6.29

Figure 6.30

Figure 6.31

Figure 6.32

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

Figure 7.12

Figure 7.13

Figure 7.14

Figure 7.15

Figure 7.16

Figure 7.17

Figure 7.18

Figure 7.19

Figure 7.20

Figure 7.21

Figure 7.22

Figure 7.23

Figure 7.24

Figure 7.25

Figure 7.26

Figure 7.27

Figure 8.1

Figure 8.2

Figure 8.3

Figure 8.4

Figure 8.5

Figure 8.6

Figure 8.7

Figure 8.8

Figure 8.9

Figure 8.10

Figure 8.11

Figure 8.12

Figure 8.13

Figure 8.14

Figure 8.15

Figure 8.16

Figure 8.17

Figure 8.18

Figure 8.19

Figure 8.20

Figure 8.21

Figure 8.22

Figure 8.23

Figure 8.24

Figure 9.1

Figure 9.2

Figure 9.3

Figure 9.4

Figure 9.5

Figure 9.6

Figure 9.7

Figure 9.8

Figure 9.9

Figure 9.10

Figure 9.11

Figure 9.12

Figure 9.13

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 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

Figure 11.12

Figure 11.13

Figure 11.14

Figure 11.15

Figure 11.16

Figure 11.17

Figure 11.18

Figure 11.19

Figure 11.20

Figure 11.21

Figure 11.22

Figure 11.23

Figure 11.24

Figure 11.25

Figure 11.26

Figure 11.27

Figure 11.28

Figure 11.29

Figure 11.30

Figure 11.31

Figure 11.32

Figure 11.33

Figure 11.34

Figure 11.35

Figure 11.36

Figure 11.37

Figure 11.38

Figure 11.39

Figure 11.40

Figure 11.41

Figure 11.44

Figure 11.42

Figure 11.43

Figure Scheme 12.1

Figure Scheme 12.2

Figure 12.1

Figure 12.2

Figure 12.3

Figure 12.4

Figure 12.5

Figure 12.6

Figure 12.7

Figure 12.8

Figure 12.9

Figure 12.10

Figure 12.11

Figure 12.12

Figure 12.13

Figure 12.14

Figure 12.15

Figure 12.16

Figure 12.17

Figure 13.1

Figure 13.2

Figure 13.3

Figure 13.4

Figure 13.5

Figure 13.6

Figure 13.7

Figure 13.8

List of Tables

Table 1.1

Table 1.2

Table 2.1

Table 2.2

Table 2.3

Table 2.4

Table 4.1

Table 4.2

Table 4.3

Table 5.1

Table 5.2

Table 5.3

Table 6.1

Table 6.2

Table 6.3

Table 10.1

Table 10.2

Table 11.A.1

Table 12.1

Table 12.2

Table 12.3

Table 12.4

Table 12.5

Table 12.6

Table 12.7

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Edited by

María-Magdalena Cid and Jorge Bravo

Structure Elucidation in Organic Chemistry

The Search for the Right Tools

The Editors

Prof. Dr. María-Magdalena Cid

University of Vigo

Organic Chemistry Department

Lagoas-Marcosende

36310 Vigo

Spain

Prof. Dr. Jorge Bravo

University of Vigo

Inorganic Chemistry Department

Campus Universitario

Lagoas Marcosende

36310 Vigo

Spain

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© 2015 Wiley-VCH Verlag GmbH & Co. KGaA, Boschstr. 12, 69469 Weinheim, Germany

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Preface

The correct structural determination of a given molecule is not only a matter of building up a puzzle with more or less academic interest but also a complex exercise with aftermaths that sometimes go well beyond. A well-documented example is the repercussions at different levels that the resolution of the DNA structure in 1954 had, a landmark that merited the Nobel Prize for Medicine in 1962. However, it is not necessary to go back to those years to be aware of the importance of correct structure determination. In this regard, a recent article published by C&EN, reports on the first legal case in which a structural reassignment puts in trouble a patent and clinical trials of the promising anticancer agent TIC10. In this article Nick Levinson, the Stanford University postdoc who discovered the bosutinib problem, says, “I find it astonishing that a drug candidate can get this far through regulatory controls and into trials without the key players actually having done the proper quality control. It points to a serious hole in the whole process.”

The application of spectroscopy for structure determination and analysis has seen a big growth during the last decades and is now an important part of every chemistry course, as spectroscopic methods are nowadays used at some point in the solution of almost all problems in chemistry, including those at the frontier of life sciences. Besides, determining the molecular structure of materials is an essential step in understanding their properties and how they are formed.

This book is intended to provide the readers with the advantages of the synergy among all the involved techniques in structural elucidation to solve a particular target, bridging the gap among mass spectrometry, optical and X-ray spectroscopies, and nuclear magnetic and surface plasmon resonances (SPRs) by providing the needed knowledge and applicability of all of them. Because most of the advances in these techniques required the use of computational tools, computational spectroscopy is another subject included in the book.

This book provides the advanced student or practicing chemist with a comprehensive and up-to-date perspective on structural elucidation studies of pure substances and mixtures, in molecular or supramolecular architectures. It starts with an introductory chapter describing the different manifestations of light-matter interactions. Chapter 2 is devoted to computational spectroscopy, providing an overview of the theoretical background and computational requirements needed for molecular structure analysis by means of spectroscopic techniques. Chapters about the use of mass spectrometry (Chapter 4) and infrared/Raman spectroscopy (Chapter 5) for characterizing, identifying, or determining a structure provide qualitative and quantitative information not available from any other techniques.

Several chapters are devoted to nuclear magnetic resonance (NMR), because, since its discovery, it is the analytical method that has had the greatest impact, particularly in chemistry. In fact, developments in NMR have been the motive behind the award of two Nobel prizes for chemistry. NMR is used in all branches of science in which precise structural determination is required and in which the nature of interactions and reactions in solution are being studied. Thus, part of the book focuses on topics of current interest in solid and solution NMR in isotropic and anisotropic media. Transfer nuclear Overhauser effect and saturation transfer difference (STD) allowing the detection of transient binding of small molecules to macromolecular receptors is also treated along with automatic verification system (ASV) applied to assess the correctness of a proposed structure.

Two separate chapters are devoted to optical spectroscopy (electronic and vibrational circular dichroism and optical rotatory dispersion) (Chapter 3) and X-ray analysis (Chapter 11), as they are essential techniques for determination of relative and absolute configuration of natural products.

The book also aims at introducing the reader to the applications of SPR technology (Chapter 10), emphasizing on a practical point of view since SPR sensors have become a central tool for the study of biomolecular interactions and the detection of chemical and biological species.

Finally, Chapter 13 tries to emphasize that the structural determination of chemical compounds is commonly a difficult task and frequently entails the combined use of several tools. To illustrate the power of this combination, randomly chosen representative cases of misassigned structures are discussed.

We hope this book provides experts and untrained researchers with the needed tools to solve structural problems and also with the current state of development in other not so common techniques.

We thank those who made this book a reality either by proofreading the manuscripts or by giving interesting suggestions to improve them. We would like to make a special mention of all the authors for their commitment in this project and also to Dr. Carlos Silva for his invaluable assistance in the design of the cover and Dr. Reinhold Weber for all his support without which this project would not have reached the end.

Vigo, December 2014

María Magdalena Cid

Jorge Bravo

List of Contributors

José Lorenzo Alonso-Gómez

Universidade de Vigo

Departamento de Quimica Orgánica

Edificio de Ciencias Experimentais

Campus Lagoas-Marcosende

Vigo

Spain

Jesús Angulo

Instituto de Investigaciones Quimicas

CSIC-US

Glycosystems Laboratory

Avenida Americo Vespucio 49

Sevilla

Spain

Ana Ardá

Centro de Investigaciones Biológicas

Chemical and Physical Biology

Ramiro de Maeztu 9

Madrid

Spain

Ricardo F. Aroca

University of Windsor

Department of Chemistry and Biochemistry

Windsor, N9B 3P4

Ontario

Canada

Michael Bernstein

Mestrelab Research

S.L., Feliciano Barrera

Baixo

Santiago de Compostela

Spain

Nina Berova

Columbia University

Department of Chemistry

Havemeyer Hall

3114

Broadway

New York 10027

USA

Malgorzata Biczysko

Istituto Italiano di Tecnologia

Center for Nanotechnology Innovation @NEST

Piazza San Silvestro 12

Pisa

Italy

and

Scuola Normale Superiore

Piazza dei Cavalieri 7

Pisa

Italy

Jorge Bravo

Universidade de Vigo

Departamento de Quimica Inorganica

Edificio de Ciencias Experimentais

Campus Lagoas-Marcosende

Vigo

Spain

Eurico J. Cabrita

Universidade Nova de Lisboa

Departamento de Quimica

Faculdade de Ciencias e Tecnologia

2829-516 Caparica

Portugal

María Magdalena Cid

Universidade de Vigo

Departamento de Quimica Organica

Edificio de Ciencias Experimentais

Campus Lagoas-Marcosende

Vigo

Spain

Juan Carlos Cobas Gómez

Mestrelab Research

S.L., Feliciano Barrera

Baixo

Santiago de Compostela

Spain

Roberto R. Gil

Carnegie Mellon University

Department of Chemistry

Mellon Institute

Room 302

Fifth Avenue

Pittsburgh

PA 15213-3890

USA

Christian Griesinger

Max-Planck-Institut für Biophysikalische Chemie

Abteilung 030

Am Fassberg 11

Göttingen

Germany

Nobuyuki Harada

Tohoku University

Institute for Multidisciplinary Research for Advanced Materials

2-1-1 Katahira

Aoba

Sendai 980-8577

Japan

Maarten Honing

VU University Amsterdam

Department of BioMolecular Analysis

De Boelelaan 1083

HV Amsterdam

The Netherlands

Jesús Jiménez-Barbero

Centro de Investigaciones Biológicas

C/Ramiro de Maeztu 9

Madrid

Spain

Luís Mafra

University of Aveiro

Department of Chemistry

CICECO

3810-193 Aveiro

Portugal

Manuel Martín-Pastor

Universidade de Santiago de Compostela

Unidade de RMN.RIAIDT

Edificio CACTUS

Campus Vida s/n

Santiago de Compostela

Spain

Eva Muñoz

Universidade de Santiago de Compostela

Departamento de Quimica Organica

Facultade de Quimica y Centro Investigacion en Quimica Bilogica y Materiales Moleculares (CIQUS)

Campus Vida s/n

Santiago de Compostela

Spain

Armando Navarro-Vázquez

Universidade de Vigo

Departamento de Quimica Organica

Edificio de Ciencias Experimentais

Campus Lagoas-Marcosende

Vigo

Spain

Wilfried M.A. Niessen

VU University Amsterdam

Department of BioMolecular Analysis

De Boelelaan 1083

HV Amsterdam

The Netherlands

Pedro M. Nieto

Instituto de Investigaciones Quimicas

CSIC-US

Glycosystems Laboratory

Avenida Americo Vespucio 49

Sevilla

Spain

Olalla Nieto Faza

Universidade de Vigo

Departamento de Química Física

Facultad de Química

Edificio de Ciencias Experimentais

Campus Lagoas-Marcosende

Vigo

Spain

Ignacio Pérez-Juste

Universidade de Vigo

Departamento de Química Física

Facultad de Química

Edificio de Ciencias Experimentais

Campus Lagoas-Marcosende

Vigo

Spain

Ana G. Petrovic

New York Institute of Technology

Broadway

Office 405A

New York

NY 10023-7692

USA

Cristina Puzzarini

Universitá di Bologna

Dipartimento di Chimica ``Giacomo Ciamician''

Via Selmi 2

Bologna

Italy

Emilio Quiñoá Cabana

Universidade de Santiago de Compostela

Departamento de Quimica Organica

Facultade de Quimica y Centro Investigacion en Quimica Bilogica y Materiales Moleculares (CIQUS)

Campus Vida s/n

Santiago de Compostela

Spain

Daniel Ricklin

University of Pennsylvania

Department of Pathology and Laboratory Medicine

Stellar Chance Laboratories

Curie Boulevard

Philadelphia

PA 19104

USA

Ricardo Riguera Vega

Universidade de Santiago de Compostela

Departamento de Quimica Organica

Facultade de Quimica y Centro Investigacion en Quimica Bilogica y Materiales Moleculares (CIQUS)

Campus Vida s/n

Santiago de Compostela

Spain

João Rocha

University of Aveiro

Department of Chemistry

CICECO

3810-193 Aveiro

Portugal

Mariana Sardo

University of Aveiro

Department of Chemistry

CICECO

3810-193 Aveiro

Portugal

José Manuel Seco

Universidade de Santiago de Compostela

Departamento de Quimica Organica

Facultade de Quimica y Centro Investigacion en Quimica Bilogica y Materiales Moleculares (CIQUS)

Campus Vida s/n

Santiago de Compostela

Spain

Han Sun

Abteilung NMR-basierte Strukturbiologie

Max-Planck-Institut für biophysikalische Chemie

Am Fassberg 11

Göttingen

Germany

Stanislav Sýkora

Extra Byte

Via Raffaello Sanzio 22C

Castano Primo

Italy

1Interaction of Radiation with Matter

Ignacio Pérez-Juste and Olalla Nieto Faza

1.1 Introduction

The interaction of light with matter is at the basis of one of the primary participants in human perception, because a significant part of the cerebral cortex is dedicated to visual processing. This complex mechanism starts with the light-induced isomerization of a retinal molecule that triggers a messenger cascade to produce the transmission of a nerve impulse from the retina. And it is through sight that we gather most of our knowledge of our environment (sizes, colors, shapes, etc.).