Vibrational Optical Activity E-Book

Laurence A. Nafie

• Herausgeber: John Wiley & Sons
• Kategorie: Wissenschaft und neue Technologien
• Sprache: Englisch

Seitenzahl: 740

Veröffentlichungsjahr: 2011

Beschreibung

This unique book stands as the only comprehensive introduction to vibrational optical activity (VOA) and is the first single book that serves as a complete reference for this relatively new, but increasingly important area of molecular spectroscopy.

Key features:

• A single-source reference on this topic that introduces, describes the background and foundation of this area of spectroscopy.
• Serves as a guide on how to use it to carry out applications with relevant problem solving.
• Depth and breadth of the subject is presented in a logical, complete and progressive fashion.

Although intended as an introductory text, this book provides in depth coverage of this topic relevant to both students and professionals by taking the reader from basic theory through to practical and instrumental approaches.

Leseprobe

Contents

Cover

Title Page

Copyright

Dedication

Preface

Chapter 1: Overview of Vibrational Optical Activity

1.1 Introduction to Vibrational Optical Activity

1.2 Origin and Discovery of Vibrational Optical Activity

1.3 VCD Instrumentation Development

1.4 ROA Instrumentation Development

1.5 Development of VCD Theory and Calculations

1.6 Development of ROA Theory and Calculations

1.7 Applications of Vibrational Optical Activity

1.8 Comparison of Infrared and Raman Vibrational Optical Activity

1.9 Conclusions

References

Chapter 2: Vibrational Frequencies and Intensities

2.1 Separation of Electronic and Vibrational Motion

2.2 Normal Modes of Vibrational Motion

2.3 Infrared Vibrational Absorption Intensities

2.4 Vibrational Raman Scattering Intensities

References

Chapter 3: Molecular Chirality and Optical Activity

3.1 Definition of Molecular Chirality

3.2 Fundamental Principles of Natural Optical Activity

3.3 Classical Forms of Optical Activity

3.4 Newer Forms of Optical Activity

References

Chapter 4: Theory of Vibrational Circular Dichroism

4.1 General Theory of VCD

4.2 Formulations of VCD Theory

4.3 Atomic Orbital Level Formulations of VCD Intensity

4.4 Transition Current Density and VCD Intensities

References

Chapter 5: Theory of Raman Optical Activity

5.1 Comparison of ROA to VCD Theory

5.2 Far-From Resonance Theory (FFR) of ROA

5.3 General Unrestricted (GU) Theory of ROA

5.4 Vibronic Theories of ROA

5.5 Resonance ROA Theory

References

Chapter 6: Instrumentation for Vibrational Circular Dichroism

6.1 Polarization Modulation Circular Dichroism

6.2 Stokes–Mueller Optical Analysis

6.3 Fourier Transform VCD Measurement

6.4 Commercial Instrumentation for VCD Measurement

6.5 Advanced VCD Instrumentation

References

Chapter 7: Instrumentation for Raman Optical Activity

7.1 Incident Circular Polarization ROA

7.2 Scattered Circular Polarization ROA

7.3 Dual Circular Polarization ROA

7.4 Commercial Instrumentation for ROA Measurement

7.5 Advanced ROA Instrumentation

References

Chapter 8: Measurement of Vibrational Optical Activity

8.1 VOA Spectral Measurement

8.2 Measurement of IR and VCD Spectra

8.3 Measurement of Raman and ROA Spectra

References

Chapter 9: Calculation of Vibrational Optical Activity

9.1 Quantum Chemistry Formulations of VOA

9.2 Fundamental Steps of VOA Calculations

9.3 Methods and Visualization of VOA Calculations

9.4 Calculation of Electronic Optical Activity

References

Chapter 10: Applications of Vibrational Optical Activity

10.1 Classes of Chiral Molecules

10.2 Determination of Absolute Configuration

10.3 Determination of Enantiomeric Excess and Reaction Monitoring

10.4 Biological Applications of VOA

10.5 Future Applications of VOA

References

Appendix A: Models of VOA Intensity

A.1 Estimate of CD Intensity Relative to Absorption Intensity

A.2 Degenerate Coupled Oscillator Model of Circular Dichroism

A.3 Fixed Partial Charge Model of VCD

A.4 Localized Molecular Orbital Model of VCD

A.5 Ring Current Model and Other Vibrational Electronic Current Models

A.6 Two-Group and Related Models of ROA

References

Appendix B: Derivation of Probability and Current Densities from Multi-Electron Wavefunctions for Electronic and Vibrational Transitions

B.1 Transition Probability Density

B.2 Transition Current Density

B.3 Conservation of Transition Probability and Current Density

B.4 Conservation Equation for Vibrational Transitions

References

Appendix C: Theory of VCD for Molecules with Low-Lying Excited Electronic States

C.1 Background Theoretical Expressions

C.2 Lowest-Order Vibronic Theory Including Low-Lying Electronic States

C.3 Vibronic Energy Approximation

C.4 Low-Lying Magnetic-Dipole-Allowed Excited Electronic States

Reference

Appendix D: Magnetic VCD in Molecules with Non-Degenerate States

D.1 General Theory

D.2 Combined Complete Adiabatic and Magnetic-Field Perturbation Formalism

D.3 Vibronic Coupling B-Term Derivation

D.4 MCD from Transition Metal Complexes with Low-Lying Electronic States

References

Index

This edition first published 2011

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Library of Congress Cataloging-in-Publication Data

Nafie, Laurence A.

Vibrational optical activity : principles and applications / Laurence A. Nafie.

p. cm.

Includes bibliographical references and index.

ISBN 978-0-470-03248-0 (cloth)

1. Vibrational spectra. I. Title.

QC454.V5N34 2011

539.6–dc22

2011012255

Print ISBN: 9780470032480

ePDF ISBN: 9781119976509

oBook ISBN: 9781119976516

ePub ISBN: 9781119977537

Mobi: 9781119977544

This book is dedicated to the loving, nurturing, and inspiring support of both my parents, Marvin Daniel and Edith Fletcher Nafie and my mother's parents Frederic Stark and Edith Webster Fletcher, and to my loving wife Rina Dukor who, for the last 15 years, has been my business and scientific partner in helping me to bring vibrational optical activity to the world, and who recently became, as well, my life's partner in marriage.

Preface

During the years surrounding the new millennium, the field of vibrational optical activity (VOA), comprised principally of vibrational circular dichroism (VCD) and vibrational Raman optical activity (ROA), underwent a transition from a specialized area of research that had been practiced by a handful of pioneers into an important new field of spectroscopy practiced by an increasing number of scientists worldwide. This transition was made possible by the development of commercial instrumentation and software for the routine measurement and quantum chemical calculation of VOA. This development in turn was fueled by the growing focus among chemists for controlling and characterizing molecular chirality in synthesis, dynamics, analysis, and natural product isolation. The emphasis on chirality was particularly important in the pharmaceutical industry, where the most effective new drugs were single enantiomers and where new federal regulations required specifying proof of absolute configuration and enantiomeric purity for each new drug molecule developed. Today, more than a decade beyond the start of this renaissance, chemists and spectroscopists are discovering the power of VOA to provide, directly, the stereo-specific information needed to further enhance the ongoing revolution in the application of chirality across all fields of molecular science.

The impact of VOA has not been restricted to applications centered on molecular chirality. A concurrent revolution is currently taking place in the field of biotechnology. All biological molecules are chiral, where the chirality is specified by the homochirality of our biosphere, for example l-amino acids and d-sugars. The role of chirality here is not with the specification of absolute configuration but with the specification of the solution-state conformation of biological molecules in native environments. VOA has been found to be hypersensitive to the conformational state in all classes of biological molecules, including amino acids, peptides, proteins, sugars, nucleic acids, glycoprotiens, in addition to fibrils, viruses, and bacteria. Now that the human genome has been coded, emphasis has shifted to understanding what proteins and related molecules are specified in the genetic code. What is their structure and function? Thus VOA is particularly useful as a sensitive new probe of the solution structure of these new protein molecules by classification of their folding family in solution.

What is it about VOA that allows it to determine absolute configuration and molecular conformation in new ways? It is simply that the field of VOA is fulfilling its promise of combining the detailed structural sensitivity of vibrational spectroscopy with the three-dimensional stereo-sensitivity of traditional forms of optical activity. The actual realization of the foreseen potential of VOA has been delivered by sweeping advances in the last two decades of both instrumentation for the measurement of VOA, and software for its calculation and accurate spectral simulation. As will be seen in the chapters of this book, VOA spectra are accompanied by their parent normal vibrational spectra, vibrational absorption, and Raman scattering, and the additional VOA spectrum, linked to a traditional spectrum, is what confers the specific new spectral information.

Beyond the practical benefits to those needing information about the stereochemical structure of chiral molecules, VOA is also providing deep insights into our understanding of the theoretical and computational basis of chemistry. At the theoretical level, VOA intensities require contributions from the interaction of radiation with matter that lie beyond the normal electric-dipole interaction, which by itself is blind to chirality. The new interactions manifested in VOA spectra are the interference of the electric-dipole mechanism with the magnetic-dipole mechanism, and in the case of ROA, the electric-quadrupole mechanism, as well. In addition, VCD in particular requires a theoretical description that lies beyond the Born–Oppenheimer approximation and gives new information about the correlation of the nuclear velocities with molecular electron current density. This is new terrain that lies beyond the traditional Born–Oppenheimer base view of conceptualizing molecules in terms of correlations between nuclear positions and electron probability density. VOA spectra are also proving to be delicate points of reference for quantum chemists who are seeking to improve the accuracy of descriptions of molecules from small organics to proteins and nucleic acids with increasingly realistic models of solvent and intermolecular interactions.

Although VCD and ROA were discovered about the same time in the early to mid-1970s, they have evolved along distinctly different paths in terms of instrumentation and theoretical description. VCD progressed dramatically by taking advantage of Fourier transform infrared spectrometers while ROA gained enormously in efficiency by using advanced solid-state lasers and multi-channel charge-coupled device detectors. ROA theory emerged early and directly from within the Born–Oppenheimer approximation, while VCD theory had to await a deeper understanding of the theory beyond the Born–Oppenheimer approximation for its complete formulation. On the other hand, VCD is simpler and more efficient to calculate whereas ROA is more challenging and requires more intensive calculations. Owing to differences in the relative advantages of infrared absorption and Raman scattering, VCD and ROA tend to be applied to different types of molecules in different types of sampling environments. As a result, papers on VOA, with a few recent exceptions, tend to involve either VCD or ROA, but not both. Nevertheless, despite these relatively separate lines of development, VCD and ROA have a great deal in common, and taken together contain complementary and reinforcing spectral information.

The goal of this book is to bring together, in one place, a comprehensive description of the fundamental principles and applications of both VCD and ROA. An effort has been made to describe these two fields using a unified theoretical description so that the similarities and differences between VCD and ROA can most easily be seen. Both of these fields rest on the foundations of vibrational spectroscopy and the science of describing the vibrational motion of molecules, and both are forms of molecular optical activity sensitive to chirality in molecules. After a basic and somewhat historical introduction to VOA in Chapter 1, the fundamentals of vibrational spectroscopy are presented in Chapter 2 where the formalism of the complete adiabatic approximation, needed for the theoretical description of VCD and a refined description of ROA, is provided. Chapter 3 contains the fundamentals of molecular chirality and the mathematical formalism needed for understanding the theory of both VCD as given in Chapter 4 and ROA as given in Chapter 5. Having completed the necessary theoretical basis of VOA, the focus of the book shifts to instrumentation. The language of describing optical instrumentation and measured VOA intensities, including interfering intensities from birefringence, is the Stokes–Mueller formalism. This is introduced in Chapter 6 for a description of fundamental and advanced methods of VCD instrumentation and is continued in Chapter 7 as a basis for describing ROA instrumentation. The focus of Chapter 8 is the measurement of VOA spectra followed by a description of the methods used for calculating VOA spectra in Chapter 9. In Chapter 10, the final chapter of the book, highlights and selected examples of VOA applications are described. Here VCD and ROA applications are interwoven to better gain an appreciation for both the differences and features in common between these two areas of VOA.

As can be seen from this description of the contents of the book, the material flows from basic principles through theoretical and experimental methods to applications. An effort has been made with the book as a whole, as well as with the individual chapters, to begin with an overview of contents. Thus, Chapter 1 gives a bird's eye view of the entire book and each chapter begins with a descriptive overview at an elementary level of the contents of that chapter. Continued reading in the book or in each chapter carries the reader deeper into the subject with the most advanced material presented usually in last parts of each chapter.

The intended readership for the book is the complete range from beginner to expert in the field of VOA. The book attempts to bridge the gap between the fundamentals of vibrational spectroscopy, chirality, and optical activity and the frontier of research and applications of VOA. The book could serve both as a textbook for graduate courses in chemistry or biophysics as well as a reference for the experienced researcher or scientist. A basic understanding of spectroscopy and quantum mechanics is assumed, but beyond that, nothing further is needed besides patience and a desire to learn new concepts and ideas. Hopefully, the book can serve as a foundation for the continued advancement and development of the exciting new field of VOA.

The book contains many equations, and as a result, alas, it won't ever make the New York Times Bestseller's List. In fact, at the theoretical level, the book is essentially a carefully crafted set of explained equations. Equations are numbered by chapter. When an equation is presented that is based on a previously presented equation, even if it is the same equation, reference to the earlier equation is given to allow the reader to go back and see in more detail the equation's origin in the book. References are provided in the text in a format that identifies authors and years of publication. In the electronic version of the book these are, where possible, live HTML links that take the reader to the source of electronic publication. For the most part, chapters are written to be self-consistent and thus can be read individually in any order depending on the particular interests and background knowledge of the reader.

As with any book requiring years of preparation, the author is deeply grateful for the help, collaboration and support of many individuals without whom this book could not have been written. Gratitude begins with my Ph.D. advisor Warner L. Peticolas, who sadly passed away in 2009, and my postdoctoral advisor Philip J. Stephens who started me off on the road to VCD. Warner taught me the excitement of scientific discovery and opened the doors for me to the world of Raman spectroscopy, and Philip taught me the importance of precision and discipline in the way science is practiced and gave me the opportunity to explore and discover the world of infrared vibrational optical activity. I am also grateful to Gershon Vincow, Chairman of the Chemistry Department at Syracuse University who in 1975 hired me as a new Assistant Professor and supported the beginning and growth of my research program in VCD and ROA, and to then Assistant Professor William (Woody) Woodruff who welcomed me to the department and shared his facilities with me to help jump start the construction of my first ROA spectrometer.

I owe endless gratitude to my many graduate students and postdoctoral associates who have worked with me over the years at Syracuse University. Of particular importance are my first postdoctoral associates, Max Diem and Prasad Polavarapu, both of whom went on to distinguished academic careers. I also give very special acknowledgment to Teresa (Tess) Freedman who, as a Research Professor at Syracuse University, collaborated with me on VOA for nearly three decades and helped guide my research program from 1984 to 2000, when I was busy as Chair of the Chemistry Department. Her talent for planning VOA experiments, writing papers, advising students, and carrying out calculations complemented my own love of developing VOA theory and new methods of VOA instrumentation. Without her daily support over those many years, my research in VOA could not have progressed as broadly as it did. Special thanks also go to my former postdoctoral associate, Xiaolin Cao, now a research scientist at Amgen, Inc., who contributed significantly to the optimization of the first dual-PEM, dual-source FT-VCD spectrometer at Syracuse University.

I would like to thank Dr. Rina K. Dukor for being my partner in founding BioTools, Inc., starting in 1996, with the central goal of commercializing VCD and ROA instrumentation. This was achieved in stages, first with VCD in 1997 and then with ROA in 2003. With Rina, my focus on VOA changed from Syracuse University to the world, from pure academic pursuit to facilitating the measurement and calculation of VOA by anyone who wanted to explore this new field of spectroscopy. For the birth of commercial VCD instrumentation, special thanks go Henry Buijs, Gary Vail, Jean-René Roy, Allan Rilling, and many others at Bomem for helping to bring dedicated VCD instrumentation to commercial availability, and again to Philip Stephens for purchasing this first VCD instrument and helping to refine its testing and performance. For ROA instrumentation, special thanks go to Werner Hug for his unfailing encouragement and providing, with help from Gilbert Hangartner, the details of his revolutionary new design for the measurement of ROA. I would also like to thank Omar Rahim and David Rice of Critical Link, LLC for working with BioTools to design and build the first generation of commercial ROA spectrometers, and to Laurence Barron of Glasgow University for purchasing the first of these spectrometers and assisting with Lutz Hecht in the improvement of its performance.

I owe a debt of gratitude to all the employees and close customers of BioTools, Inc. who helped advance the cause of VOA, with special thanks to Oliver McConnell, Doug Minick, Anders Holman, Hiroshi Izumi, Don Pivonka, Ewan Blanch, and Salim Abdali. I would also like to thank those at Gaussian Inc., specifically Mike Frisch and Jim Cheeseman, for being the first to bring VCD and ROA software to commercial availability.

Finally, I would like to thank all other colleagues and collaborators not yet mentioned, who have joined with me in helping to explore and extend the frontiers of VCD and ROA.

Palm Beach Gardens, Florida, USAFebruary, 2011

Chapter 1

Overview of Vibrational Optical Activity

1.1 Introduction to Vibrational Optical Activity

Vibrational optical activity (VOA) is a new form of natural optical activity whose early history dates back to the nineteenth century. We now know that the original observations of optical activity, the rotation of the plane of linearly polarized radiation, termed optical rotation (OR), or the differential absorption of left and right circularly polarized light, circular dichroism (CD), have their origins in electronic transitions in molecules. Not until after the establishment of quantum mechanics and molecular spectroscopy in the twentieth century was the physical basis of natural optical activity revealed for the first time.

1.1.1 Field of Vibrational Optical Activity

Vibrational optical activity, as the name implies, is the area of spectroscopy that results from the introduction of optical activity into the field of vibrational spectroscopy. VOA can be broadly defined as the difference in the interaction of left and right circularly polarized radiation with a molecule or molecular assembly undergoing a vibrational transition. This definition allows for a wide variety of spectroscopies, as will be discussed below, but the most important of these are the forms of VOA associated with infrared (IR) absorption and Raman scattering. The infrared form is known as vibrational circular dichroism, or VCD, while the Raman form is known as vibrational Raman optical activity, VROA, or usually just ROA (Raman optical activity). VCD and ROA were discovered experimentally in the early 1970s and have since blossomed independently into two important new fields of spectroscopy for probing the structure and conformation of all classes of chiral molecules and supramolecular assemblies.

VCD has been measured from approximately 600 cm−1 in the mid-infrared region, into the hydrogen stretching region and through the near-infrared region to almost the visible region of the spectrum at 14 000 cm−1. The infrared frequency range of up to 4000 cm−1 is comprised mainly of fundamental transitions, while higher frequency transitions in the near-infrared are dominated by overtone and combination band transitions. ROA has been measured to as low as 50 cm−1, a distinct difference compared with VCD, but ROA is more difficult to measure beyond the range of fundamental transitions and is typically only measured for vibrational transitions below 2000 cm−1. VCD and ROA can both be measured as electronic optical activity in molecules possessing low-lying electronic states, although in the case of VCD it is appropriate to refer to these phenomena as infrared electronic circular dichroism, IR-ECD or IRCD, and electronic ROA, or EROA.

VCD and ROA are typically measured for liquid or solution-state samples. VCD has been measured in the gas phase and in the solid phase as mulls, KBr pellets and films of various types. When sampling solids, distortions of the VCD spectra due to birefringence and particle scattering need to be avoided. To date, ROA has not been measured in gases or diffuse solids, but nothing precludes this sampling option, although technical issues may arise, such as sufficient Raman intensity for gases and competing particle scattering for diffuse solids.

At present, there is only one form of VCD, namely the one-photon differential absorption form, although recently, a second manifestation of VCD, the differential refractive index, termed the called vibrational circular birefringence (VCB), has been measured. A VCB spectrum is the Kramers–Kronig transform of a VCD spectrum and is also known as vibrational optical rotatory dispersion (VORD). As we shall see, ORD is the oldest form of optical activity and the form of VOA that was sought in the 1950s and 1960s before the discovery of VCD. By comparison, ROA is much richer in experimental possibilities. Because one can consider circular (or linear) polarization differences in Raman scattering intensity associated with the incident or scattered radiation, or both, in-phase and out-of-phase, there are four (eight) distinct forms of ROA. Further, for ROA there are choices of scattering geometry and the frequency of the incident radiation, both of which give rise to different ROA spectra. As a result, there is in principle a continuum of different types of VOA measurements that can be envisioned for a given choice of sample molecule.

Beyond this, many other forms of VOA are possible. One form is reflection vibrational optical activity, which would include VCD measured as specular reflection, diffuse reflection or attenuated total reflection (ATR). In principle, VCD could also be measured in fluorescence. Because fluorescence depends on the third power of the exciting frequency, infrared fluorescence VOA would be very weak relative to VCD and thus very difficult to measure. As with fluorescence in the visible and ultraviolet regions of the spectrum, fluorescence VCD could be measured in two forms, fluorescence detected VCD or circularly polarized emission VCD. In the former, one would measure all the fluorescence intensity resulting from the differential absorbance of left and right circularly polarized infrared radiation (VCD) or measure the difference in left and right circularly polarized infrared emission from unpolarized exciting infrared radiation. Finally, we note the various manifestations of nonlinear or multi-photon VCD, such as two-photon infrared absorption VCD.