NMR Spectroscopy: Data Acquisition (Book & CD-ROM)

358 Pages·2001·1.84 MB·English

by  Christian Schorn

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Preface
The application of NMR spectroscopy into new fields of research continues on an
almost daily basis. High-resolution NMR experiments on compounds of low molecular
mass in the liquid phase are now routine and modern NMR spectroscopy is aimed at
overcoming some of the inherent problems associated with the technique. Thus higher
magnetic field strengths can be used to help overcome the problems associated with low
sample concentration enabling the analysis of complex spectra of large macromolecules
such as proteins whilst also helping to advance the study of non liquid samples by MAS
and solid state NMR spectroscopy. Apart from the chemical and physical research fields
NMR spectroscopy has become an integral part of industrial production and medicine,
e.g. by MRI (magnetic resonance imaging) and MRS (magnetic resonance spectroscopy).
The basic principles of acquiring the raw time domain data, processing this data and then
analysing the spectra is similar irrespective of the particular technique used. The
diversity of NMR is such that a newcomer to NMR spectroscopy might train in the field
of high resolution NMR and establish his career in solid state NMR. A distinct advantage
of NMR spectroscopy is that the basic knowledge of acquisition, processing and analysis
may be transferred from one field of endeavour to another. These ideas and perspectives
were the origin for the series entitled Spectroscopic Techniques: An Interactive Course.
The section relating to NMR Spectroscopy, consists of four volumes
• Volume 1 – Processing Strategies
• Volume 2 – Data Acquisition
• Volume 3 – Modern Spectral Analysis
• Volume 4 – Intelligent Data 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 databases 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 databases. 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
VI Preface
the two approaches is followed depends on the actual structural problem. Each of them
has its 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 1 – 4 may 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.
This also includes the graphical layout for the 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.
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 1D WIN-NMR, 2D WIN-NMR and GETFILE software
tools, together with a set of experimental data for two carbohydrate compounds 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 l’ 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
Preface VII
STRUCTURAL PROBLEM
(cid:1)

EVALUATION OF EXPERIMENTS
AND DATA ACQUISITION
Volume 2: Data Acquisition
(cid:1)
RAW DATA

(cid:1)
DATA PROCESSING
Volume 1: Processing Strategies
(cid:1)
SPECTRA
(cid:2) (cid:1)

DATA ANALYSIS DATA ARCHIVING
Volume 3: Modern Spectral Analysis Volume 4: Intelligent Data Management
(cid:1) (cid:1)
NMR-PARAMETER NMR DATA BASE
(cid:1) (cid:1)
DATA INTERPRETATION DATA MANAGEMENT
Volume 4: Intelligent Data Management
(cid:1) (cid:1)

MOLECULAR STRUCTURE MOLECULAR STRUCTURE
VIII Preface
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 NMR-SIM. Together with 1D WIN-NMR and
2D WIN-NMR, NMR-SIM 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.
Volume 3: Modern Spectral Analysis
Following the strategy of spectral analysis, the evaluation of a whole unknown
structure, of the local stereochemistry in a molecular fragment or of molecular dynamic
properties, depends on NMR parameters. Structural information can be obtained from
chemical shifts, homonuclear and heteronuclear spin-spin connectivities and
corresponding coupling constants and from relaxation data such as NOEs, ROEs, Ts or
1
Ts. It is assumed that the user is aware of the typical ranges of these NMR parameters
2
and of the numerous correlation’s between the NMR and structural parameters, i.e.
between coupling constants, NOE enhancements or linewidths and dihedral angles,
internuclear distances and exchange rates. However, the extraction of these NMR
parameters from the corresponding spectra is not always straightforward,
• The spectrum may exhibit extensive signal overlap, a problem common with
biomolecules.
• The spectrum may contain strongly coupled spin systems.
• The molecule under investigation may be undergoing dynamic or chemical exchange.
Modern Spectral Analysis discusses the strategies needed to efficiently and
competently extract the NMR parameters from the corresponding spectra. You will be
shown how to use the spectrum simulation package WIN-DAISY to extract chemical
shifts, coupling constants and individual linewidths from even highly complex NMR
spectra. In addition, the determination of Ts, Ts or NOEs using the special analysis
1 2
tools of 1D WIN-NMR will be explained. Sets of spectral data for a series of
Preface IX
representative compounds, including the two carbohydrates mentioned in volume 1 are
used as instructive examples and for problem solving. NMR analysis often stops with the
plotting of the spectrum thereby renouncing a wealth of structural data. This part of the
series should encourage you to go further and fully exploit the valuable information
“hidden” in the carefully determined NMR parameters of your molecule.
Volume 4: Intelligent Data Management
The evaluation and interpretation of NMR parameters to establish molecular
structures is usually a tedious task. An alternative way to elucidate a molecular structure
is to directly compare its measured NMR spectrum – serving here as a fingerprint of the
investigated molecule – with the corresponding spectra of known compounds. An expert
system combining a comprehensive data base of NMR spectra with associated structures,
NMR spectra prediction and structure generators not only facilitates this part of the NMR
analysis but makes structure elucidation more reliable and efficient.
In Intelligent Data Management, an introduction to the computer-assisted
interpretation of molecular spectra of organic compounds using the Bruker WIN-
SPECEDIT software package is given. This expert system together with the Bruker
STRUKED software tool is designed to follow up the traditional processing of NMR
spectra using 1D WIN-NMR and 2D WIN-NMR in terms of structure-oriented spectral
interpretation and signal assignments. WIN-SPECEDIT offers not only various tools for
automatic interpretation of spectra and for structure elucidation, including the prediction
of spectra, but also a number of functions for so-called "authentic" archiving of spectra
in a database, which links molecular structures, shift information and assignments with
original spectroscopic data. You will learn to exploit several interactive functions such as
the simple assignment of individual resonances to specific atoms in a structure and about
a number of automated functions such as the recognition of signal groups (multiplets) in
1H NMR spectra. In addition, you will also learn how to calculate and predict chemical
shifts and how to generate a local database dedicated to your own purposes. Several
examples and exercises, including the two carbohydrate compounds from volume 1,
serve to apply all these tools and to give you the necessary practice for your daily
spectroscopic work.
It is the primary aim of the series Spectroscopic Techniques: An Interactive Course
to teach the user how NMR spectra may be obtained from the data acquired on a
spectrometer and how these spectra may be used to establish molecular structure
following one of the two strategies outlined before. The series of volumes therefore
emphasises the methodical aspect of NMR spectroscopy, rather than the more usual
analytical aspects i.e. the description of the various NMR parameters and of how they
depend on structural features, presented in numerous textbooks.
This series of books is to give the newcomer to physical NMR spectroscopy the
necessary information, the theoretical background and the practice to acquire NMR
spectra and to process the measured raw data from modern routine homonuclear and
heteronuclear 1D and 2D NMR experiments. They will also enable the user to evaluate
NMR parameters, to generate and exploit dedicated databases and finally to establish the
molecular structure.
X Preface
Each of the four volumes consists of three parts:
• A written part covers the theoretical background and explains why things are done in
particular manner. Practical hints, examples, exercises and problems are also
included.
• Software tools dedicated to the items discussed in the corresponding volume are
supplied on CD-ROM.
• The most popular 1D and 2D pulse sequences together with the corresponding NMR
raw data and spectra are supplied on CD-ROM. They are used to simulate NMR
experiments, to exercise data processing and spectral analysis and serve as a database
for spectral interpretation.
It is this combination of written text, the software tools and supplied data, that make it
different from other books on NMR spectroscopy and which should draw your attention
to the many possibilities and the enormous potential of modern NMR. Sitting in front of
your PC , which becomes your personal “PC-NMR spectrometer”, you experience in a
very direct and practical way, how modern NMR works. According to the approved rule
“Learning by Doing” you perform NMR experiments without wasting valuable
spectrometer time, handle experimental data in different ways, plot 1D and 2D spectra,
analyse spectra and extract NMR parameters and learn to build up and use NMR data
bases.

TEXTBOOK PC
THEORY SOFTWARE TOOLS
PRACTICAL HINTS PULSE SEQUENCES
EXERCISES NMR DATA
PROBLEMS
It is recommended that you use all these educational tools in a complementary and
interactive way switching from textbook to the software tools and the sets of data stored
on the PC and back again and that you proceed at your own rate. It is assumed that you
verify the numerous examples and solve the exercises in order to improve your skill in
Preface XI
using the various software tools and to consolidate the theoretical background. In this
way, the strongly interconnected components of this series of books are best utilised and
will guarantee the most efficient means to become an expert in this field.
Furthermore it is recommended that NMR newcomers start with the central volume
Processing Strategies and complete their education in modern NMR spectroscopy
according to their special needs by working through the appropriate volumes, Data
Acquisition, Modern Data Analysis and Intelligent Data Management.
This interactive course in practical NMR spectroscopy may be used in dedicated
courses in modern NMR spectroscopy at universities, technical schools or in industry, or
may be used in an autodidactic way for those interested in this field.