NMR Spectroscopy: Processing Strategies, Second Updated Edition

267 Pages·2000·6.52 MB·English

by  Dr. Peter Bigler(auth.)

Peter Bigler
NMR Spectroscopy:
Processing Strategies
Second Updated Edition
@WILEY-VCH
Spectroscopic Techniques:
An Interactive Course
Pre tsch/Clerc
Spectra Interpretation of Organic Compounds
Bigler
NMR Spectroscopy: Processing Strategies,
Second Updated Edition
Weber/Thiele
NMR Spectroscopy: Modern Spectral Analysis
In Preparation:
Schorn/Bigler
NMR Spectroscopy: Data Acquisition
Frohlich/Thiele
NMR Spectroscopy: Intelligent Data Management
Peter Bigler
NMR Spectroscopy:
Processing Strategies
Second Updated Edition
w
@ I LEY-VCH
Weinheim . New York . Chichester . Brisbane . Singapore . Toronto
Dr. Peter Bigler
Department of Chemistry and Biochemistry
IJiiiversity of Berne
Freiestrasse 3
CH-3012 Bern
Switzerland
A CD-ROM containing a teaching version of the program WIN-NMR (0B ruker Analytik GmbH) is
included with this book. Readcrs can obtain further information on this softwarc by contacting:
Brukcr Analytik GmbH, Silberstreifen, D-76287 Rheinstettcn. Germany.
This book was carefully produced. Nevertheless, author and publisher do not warrant the informa-
tion contained therein to be free of errors. Readers are advised to keep in mind that statements,
data, illustrations, procedural details or other items may inadvertently be inaccurate.
Library of Congress Card No. applied for
A catalogue record for this book is available from the British Library
Die Deutsche Bibliothck - CIP Cataloguing-in-Publication-Data
A catalogue record for this publication is available from Die Deutsche Bibliothek
0W ILEY-VCH Verlag GmbH, D-69469 Weinheim (Federal Republic of Germany), 2000
Printed on acid-free and chlorine-free paper
All rights reserved (including those of translation into other languages). No part of this book may be
reproduced in any form - by photoprinting, microfilm, or any other means - nor transmitted or trans-
lated into a machine language without written permission from the publishers. Registered names, trade-
marks, etc. used in this book, even when not specifically marked as such are not to be considered unpro-
tected by law.
Composition: Kuhn & Weyh, D-79111 Freiburg
Printing: Betzdruck GmbH, D-64291 Darmstadt
Bookbinding: Schaffer GmbH & Co. KG, D-67269 Grunstadt
Printed in the Federal Republic of Germany
Preface to the Second Edition
The popularity of high resolution NMR is ctill unbroken and is based on its excellent
information content with respect to molecular structures. New experimental techniques
have opened new areas of application and improvements in spectrometer hard- and
software not only fascilitate daily work of spectroscopists but bring NMR closer to the
non-experienced user.
It is nowadays common practice in many NMR environments that NMR data is acquired
in automation and remote processing of the corresponding data is performed on a “do it
yourself’ basis by non-experts. It was therefore the aim of the first book, published in
1997, to introduce newcomers in the fascinating field of NMR into the central step of
data processing.
Encouraged by the wide acceptance and the good resonance of the book this second
edition was published, taking into account the newest versions of the powerful BRUKER
data processing software ID WIN-NMR, 2D WIN-NMR and GETFILE, running in a
MS-WINDOWS environment (e.g. WINDOWS 98 or WINDOWS NT), and adding a
further established 2D NMR experiment of practical importance. Suggestions of users
and reviewers of the first book were taken up, a few text passages were clarified, the
graphical layout was improved, mistakes/typing errors were removed and the procedure
for software and data base installation has been simplified.
Users are encouraged to send comments, suggestions for improvements or hints on
mistakes to:
Prof. Dr. Peter Bigler
Department of Chemistry and Biochemistry
University of Berne
Freiestrasse 3
CH-3012 Berne
e-mail: [email protected]
Fax: [phone]
Berne, November 1999 P. Bigler
Acknowledgements
I am deeply indebted to Dr. B. F. Taylor, University of Sheffield, for checking and
proofreading the entire manuscript, for many valuable comments and his encouragement
in preparing this volume.
I am very grateful to Dr H. Thiele, Dr. A. Germanus and Dipl. lng. J. Skarbek
(BRUKER-Franzen Analytik) who developed the WIN-NMR software modules for their
helpful advices and the excellent collaboration.
I would also like to express my gratitude to BRUKER/SPECTROSPIN for their
interest in this project, helpful advice and support, and to Wiley-VCH for their assistance
and patience when waiting for the final manuscript.
Finally I thank my family and my research group who had to put up with far less
attention than they deserved, for much longer than they, or I, expected.
Preface
High resolution NMR spectroscopy is currently the most popular technique in
unravelling molecular structures. The main reason for this popularity are the various
interactions between nuclei which may be detected and determined quantitatively by
corresponding NMR experiments. Whether the aim is to elucidate the structure of an
unknown pure compound, to measure proton-proton distances in a protein or to detect
and quantify the signals of metabolites from a biological extract, it is those properties
relating one nucleus with another, which makes NMR such an indispensable tool not
only in chemistry but also in biology, medicine and related sciences. As a consequence,
numerous pulse experiments have been designed to exploit these nuclear interactions and
as a result the structural information now available with high resolution NMR
spectroscopy is probably greater and more readily obtainable than with any other single
technique.
Over the last few years there has been a tremendous technical improvement in NMR
spectrometer design. The increasing number of modern research and low-cost FT NMR
spectrometers and the powerful NMR software available today have lead to new areas of
application and new perspectives of how to use and exploit NMR spectroscopy. New
concepts have to be introduced and proved which should not only include the
maximisation of sample through put, but should also encourage NMR users to undertake
part of the tasks usually done exclusively by the NMR specialist. Reassigning the various
jobs among users and specialists, taking into consideration the users and the specialists
theoretical background and NMR expertise, should increase overall efficiency and bring
the beauties of modern NMR closer to the interested user. This reassigning of
responsibilities can take two forms,
Routine NMR spectrometers can be operated either in automation mode or “hands-
on” mode by specially trained users, allowing the specialist NMR operators to
concentrate on more demanding spectroscopic problems.
The enormous amount of NMR raw data produced by a modem spectrometer can be
processed on remote computers. The power and capacity of even low-cost personal
computers, the versality of corresponding NMR software and the availability of local
networks for rapid data transfer allow the non-specialised user to efficiently process
and analyse their own NMR data on a remote computer station. This will increase the
sample through put and give the NMR specialists more time to use the spectrometer
computer for testing and optimising new sophisticated experiments or to do time-
consuming and more demanding processing.
These ideas and perspectives were thc origin for the series entitled Spectroscopic
Techniques: An Znteractive Course. The section relating to NMR Spectroscopy consists
of four volumes
Volume 1 P rocessiiig Sti-ate<qie.s
~
Volume 2 - Datcr Acquisition
Volume 3 - Modern Specti-alA nalysis
Volume 4 Intelligent Dato Management
-
and deals with all the aspects of a standard NMR investigation, starting with the
definition of the structural problem and ending - hopefully - with the unravelled
structure. This sequence of events is depicted on the next page. The central step is the
transformation of the acquired raw data into a NMR spectrum which may then be used in
two different ways. The NMR spectrum can be analysed and the NMR parameters such
as chemical shifts, coupling constants, peak areas (for proton spectra) and relaxation
times can be extracted. Using NMR parameter data bases and dedicated software tools
these parameters may then be translated into structural information. The second way
follows the strategy of building up and making use of NMR data bases. NMR spectra
serve as the input for such data bases, which are used to directly compare the measured
spectrum of an unknown compound either with the spectra of known compounds or with
the spectra predicted for the expected chemical structure. Which of the two approaches is
followed depends on the actual structural problem. Each of them has ist own advantages,
limitations and field of application. However, it is the combined application of both
techniques that makes them such a powerful tool for structure elucidation.
The contents of volumes I 4m ay be summarized as follows:
Volume 1: Processing Strategies
Processing NMR data transforms the acquired time domain signal(s) depending on
-
the experiment into 1D or 2D spectra. This is certainly the most central and important
-
step in the whole NMR analysis and is probably the part, which is of interest to the vast
majority of NMR users. Not everyone has direct access to an NMR spectrometer, but
most have access to some remote computer and would prefer to process their own data
according to their special needs with respect to their spectroscopic or structural problem
and their ideas concerning the graphical layout i.e. for presentation of reports, papers or
thesis. It is essential for the reliability of the extracted information and subsequent
conclusions with respect to molecular structure, that a few general rules are followed
when processing NMR data. It is of great advantage that the user is informed about the
many possibilities for data manipulation so they can make the best use of their NMR
data. This is especially true in more demanding situations when dealing with subtle, but
nevertheless important spectral effects. Modern NMR data processing is not simply a
Fourier transformation in one or two dimensions, it consists of a series of additional steps
in both the time and the frequency domain designed to improve and enhance the quality
of the spectra.
Preface vii
I
EVALUATION OF EXPERIMENTS
AND DATA ACQUISITION
Volume 2: Data Acauisition
I
DATA PROCESSING
Volume 1: Processing Strategies
f2
I
DATA ANALYSIS DATA ARCHIVING
Volume 3: Modern Spectral Analysis Volume 4: Intelligent Data Management
U U
U U
I I
r D A T AI NTERPRETATION DATA MANAGEMENT
Volume 4: Intelligent Data Management
U U
Processing Strategies gives the theoretical background for all these individual
processing steps and demonstrates the effects of the various manipulations on suitable
examples. The powerful Bruker 1 D WIN-NMR, 2D WIN-NMR and GETFILE software
tools, together with a set of experimental data for two carbohydrate coinpounds allow
you to carry out the processing steps on your own remote computer, which behaves in
some sense as a personal “NMR processing station”. You will learn how the quality of
NMR spectra may be improved, experience the advantages and limitations of the various
processing possibilities and most important, as you work through the text, become an
expert in this field. The unknown structure of one of the carbohydrate compounds should
stimulate you to exercise and apply what you have learnt. The elucidation of this
unknown structure should demonstrate, how powerful the combined application of
several modern NMR experiments can be and what an enormous and unexpected amount
of structural information can thereby be obtained and extracted by appropriate data
processing. It is this unknown structure which should remind you throughout this whole
educational series that NMR data processing is neither just “playing around” on a
computer nor some kind of scientific “l’art pour I’ art”. The main goal for measuring and
processing NMR data and for extracting the structural information contained in it, is to
get an insight into how molecules behave.
Furthermore, working through Processing Strategies should encourage you to study
other topics covered by related volumes in this series. This is particularly important if
you intend to operate a NMR spectrometer yourself, or want to become familiar with
additional powerful software tools to make the best of your NMR data.
Volume 2: Data Acquisition
Any NMR analysis of a structural problem usually starts with the selection of the
most appropriate pulse experiment(s). Understanding the basic principles of the most
common experiments and being aware of the dependence of spectral quality on the
various experimental parameters are the main prerequisites for the successful application
of any NMR experiment. Spectral quality on the other hand strongly determines the
reliability of the structural information extracted in subsequent steps of the NMR
analysis. Even if you do not intend to operate a spectrometer yourself, it would be
beneficial to acquire some familiarity with the interdependence of various experimental
parameters e.g. acquisition time and resolution, repetition rate, relaxation times and
signal intensities. Many mistakes made with the application of modern NMR
spectroscopy arise because of a lack of understanding of these basic principles. Data
Acquisition covers these various aspects and exploits them in an interactive way using
the Bruker software package NMRSIM. Together with ID WIN-NMR and 2D WIN-
NMR, NMRSIM allows you to simulate routine NMR experiments and to study the
interdependence of a number of NMR parameters and to get an insight into how modern
multiple pulse NMR experiments work.