Structure Elucidation in Organic Chemistry

The Search for the Right Tools

Maria-Magdalena Cid, Jorge Bravo

• Publisher: Wiley-VCH
• Year: 2015
• Print ISBN: 9783527333363
• eBook ISBN: 9783527664634
• Edition: 1
• Topic: Physical Sciences
• Subtopic: Organic Chemistry

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.

1
Interaction 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.).

However, the chemical properties of the visual pigments in our retinas, together with the structure of the eye, limit our perceptions to light wavelengths between 390 and 750 nm and objects larger than 0.1 mm. Application of our knowledge about the interaction of light with matter and the development of optical instruments allowed us very early to use optical devices to immensely expand the range of objects accessible to our study, from the organelles in cells to faraway galaxies. In parallel, the discovery of electromagnetic radiation outside of the visible range provided incentives and tools for the elaboration of unifying concepts about light and for a myriad of technological applications.

In this chapter, we summarize the main laws that govern the interaction of electromagnetic radiation with matter, and the way in which these laws can be applied to the different phenomena that can arise from this interaction. This information is necessarily limited, and will be developed in more detail as needed in each of the following chapters on specific techniques.

1.2 Spectroscopy: A Definition

Spectroscopy is the study of the interaction of electromagnetic radiation with matter involving either absorption, emission, or scattering of radiation by the system under study. Atomic and molecular spectra can provide detailed information about the structure and chemical properties of the system. Spectroscopic techniques are one of the main sources of molecular geometries, that is, bond lengths, bond angles, and torsion angles, and can also yield, as will be seen, significant information about molecular symmetry, energy level distributions, electron densities, or electric and magnetic properties [1–15].

Spectroscopy has been an essential tool in the development of models for atomic and molecular structure, prompting scientists to refine existing models to accurately reproduce the experimentally observed spacing between energy states. A dramatic example of this is the birth of quantum theory (to explain the discrete nature of electronic transitions in atoms) or the discovery of the element helium in the spectrum of the Sun, well before it was found on Earth [16–19]. Nowadays, spectroscopic tools are routinely used in quantitative and qualitative chemical analysis and in the characterization of new molecules and materials, and play an essential role in such diverse fields as the elaboration and testing of theoretical models, synthetic chemistry, the study of reaction mechanisms, or biochemistry and materials science [20–23].

Atomic and molecular spectroscopies are mainly related to the absorption or emission of electromagnetic radiation and the changes taking place in those systems as a consequence of the energy of the radiation. Diffraction methods, however, involve the wave nature of the radiation, and rely on the interpretation of the interference patterns between waves upon their encounter with obstacles of dimensions roughly close to their wavelength. When these waves correspond to electromagnetic waves in the X-ray region of the spectrum or particles such as electrons or neutrons, their wavelengths are similar to the spacing between atoms in condensed phases such as liquids or crystals and they can be employed to obtain useful information about the atomic positions in these materials. X-ray diffraction produced the key images for unraveling the double-helix structure of DNA, and is routi...

Table of contents

• Cover
• Related Titles
• Title Page
• Copyright
• Preface
• List of Contributors
• Chapter 1: Interaction of Radiation with Matter
• Chapter 2: Computational Spectroscopy Tools for Molecular Structure Analysis
• Chapter 3: Absolute Configuration and Conformational Analysis of Chiral Compounds via Experimental and Theoretical Prediction of Chiroptical Properties: ORD, ECD, and VCD
• Chapter 4: Mass Spectrometry Strategies in the Assignment of Molecular Structure: Breaking Chemical Bonds before Bringing the Pieces of the Puzzle Together
• Chapter 5: Basic Principles of IR/Raman: Applications in Small Molecules Structural Elucidation
• Chapter 6: Solid-State NMR Applications in the Structural Elucidation of Small Molecules
• Chapter 7: Simplified NMR Procedures for the Assignment of the Absolute Configuration
• Chapter 8: Structural Elucidation of Small Organic Molecules Assistedby NMR in Aligned Media
• Chapter 9: NMR Techniques for the Study of Transient Intermolecular Interactions
• Chapter 10: Analysis of Molecular Interactions by Surface Plasmon Resonance Spectroscopy
• 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
• Chapter 12: An Integrated Approach to Structure Verification Using Automated Procedures
• Chapter 13: On the Search for the Appropriate Techniques for Structural Elucidation of Small Molecules
• Index
• EULA