Fast NMR data acquisition : beyond the Fourier transform

324 Pages·2017·10.74 MB·English

by  Mehdi Mobli

Fast NMR Data Acquisition
Beyond the Fourier Transform
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New Developments in NMR
Editor-in-chief:
William S. Price, University of Western Sydney, Australia
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0 Series editors:
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F Sharon Ashbrook, University of St Andrews, UK
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6 Bruce Balcom, University of New Brunswick, Canada
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2 Istv´an Furo´, Industrial NMR Centre at KTH, Sweden
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8 Masatsune Kainosho, Tokyo Metropolitan University, Japan
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8 Maili Liu, Chinese Academy of Sciences, Wuhan, China
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10 Titles in the series:
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oi:1 1: Contemporary Computer-Assisted Approaches to Molecular Structure
d Elucidation
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or 2: New Applications of NMR in Drug Discovery and Development
sc. 3: Advances in Biological Solid-State NMR
s.r
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on 6: Gas Phase NMR
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1 7: Magnetic Resonance Technology: Hardware and System
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8: Biophysics and Biochemistry of Cartilage by NMR and MRI
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n 1 9: Diffusion NMR of Confined Systems: Fluid Transport in Porous Solids
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d and Heterogeneous Materials
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ubli 11: Fast NMR Data Acquisition: Beyond the Fourier Transform
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Fast NMR Data Acquisition
Beyond the Fourier Transform
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7 The University of Queensland, Brisbane, Australia
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F Foreword
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0.1 Few branches of spectroscopy match the versatility, applicability and im-
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oi: plications of Magnetic Resonance. In its molecular analysis mode, NMR, it
g | d provides structural and dynamic information in the widest range of situ-
or ations: solids, organics, pharmaceuticals, proteins and nucleic acids, cells,
c.
s.rs and metabolism in living organisms. In its imaging mode, MRI, it provides
ub one of the most widely used forms for understanding biological function
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p:// andfornon-invasivediagnosisofdisease.Acommondenominatorofnearly
htt allcontemporaryNMRandMRIexperimentsrelatestotheirneedtounravel
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o complex, overlapping information. This challenge is solved via one of
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01 magnetic resonance’s most insightful propositions: the multidimensional
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y NMR/MRI experiment. By spreading and correlating information onto sev-
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8 eral dimensions, multidimensional NMR/MRI stands as one of the intel-
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n lectual jewels of modern spectroscopy. While originally proposed by Jeener
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d as a tool to assign J-coupled peaks in a spectrum, Ernst and others rapidly
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s realizedthevalueofmultidimensionalmagneticresonancetoobtainimages
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u of opaque objects, to detect invisible coherence states, to provide the reso-
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lutionneededtoelucidatecomplexchemicalsystems,andtodeterminethe
spatialstructureofbiologicalmachinesundernearphysiologicalconditions.
Multidimensionalapproacheshavesincebeenadoptedbyotherbranchesof
spectroscopy—electronparamagneticresonance,massspectrometry,IRand
visible optics—and thereby taken an additional number of unique roles in
chemistry and biochemistry. But in no area of scientific research have
multidimensional experiments retained such central roles as in NMR and
MRI. Just to give an idea of the breadth of these applications, suffice it to
mention that 2D-mediated observations ofradiation-less multiple-quantum
transitions is essential to understand the structure of complex materials,
that2Dcorrelationsbetweendistantnucleiinsmallmoleculesoftenserveas
the ‘‘eyes’’ with which organic and pharmaceutical chemists identify their
NewDevelopmentsinNMRNo.11
FastNMRDataAcquisition:BeyondtheFourierTransform
EditedbyMehdiMobliandJeffreyC.Hoch
rTheRoyalSocietyofChemistry2017
PublishedbytheRoyalSocietyofChemistry,www.rsc.org
v
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vi Foreword
products, that correlations of low-g evolutions with 1H spin detection have
been essential to endow NMR with the sensitivity needed by the structural
biologist seeking to understand biochemical function in situ, that tens of
millions of yearly 3D MRI scans are at the core of radiological exams pre-
ventingandtreatingthewidestrangeofmaladies,andthatneitherbiology’s
05 nor psychology’s contemporary understanding of living bodies and minds
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61- correlations.
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28 Despite these invaluable and extraordinarily diverse roles of one and the
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82 same experiment, a grand challenge stands in the road of these MR imple-
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81 mentations: the additional time that multidimensional experiments de-
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9/9 mand vis-a`-vis their 1D counterparts. This is a demand that was ‘‘built-in’’
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0 andacceptedfromthegenesisofthesemethodsonwards,butwhichisoften
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10. onerousandfarfrominconsequential.Indeed,extendedacquisitionshavea
oi: penalty that goes far beyond the ‘‘time is money’’ concept: by increasing
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c. dimensions involved, high-dimensional experiments on the complex sys-
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s.r tems on which they are most essential rapidly become incompatible with
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http:// own,andcan rarelywithstand extremely long examinations intheirnatural
n conditions. In few instances did this become as apparent as in the medical
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2 subjecttohigh-definitionthree-orfour-dimensionalacquisitionslastingfor
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Ma hours on end. This triggered a slow but steady departure from the discrete
18 FouriertransformprinciplesthatdominatedthenDMRIacquisitionoverits
on first two decades. To this end, phycisists joined efforts with computer sci-
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he entists, leading eventually to the kind of sparse sampling techniques that
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bli nowadays enable the delivery of 2563 or 5123 3D images in a matter of
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experiments, suffering as they do from the additional sensitivity penalties
associated with lower spin concentrations and to mixing processes that,
active in-between the various dimensions, tax this kind of acquisition even
further. The results of these efforts within the field of NMR, particularly as
they have shaped over the last decade, are summarized in the pages of this
monograph. These include the use of fast-switching gradients to unravel
indirect spectral dimensions, the introduction of regularization procedures
inordertobypasstheotherwiseovertlystrictsamplingdemandsofthefast
Fouriertransformalgorithm,thejointsamplingofmultipledimensionsina
‘‘back-projected’’ fashion, and the design of metrics to assess the reliability
of all these techniques. Coming to the aid of the much lower sensitivities
characterizing NMR vis-a`-vis MRI are relaxation-enhanced methods, which
over recent years have become an indispensible tool in multidimensional
biomolecular NMR.
WhileitisclearthatacceleratednDNMRacquisitionsarerapidlybecome
a mature topic, I would like to challenge the reader by venturing to say
that their final form is far from settled. Additional improvements and
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Foreword vii
combinations of new spin physics and data processing will surely keep en-
hancing the performance of high-dimensional NMR, including perhaps
spectroscopic-orientedanaloguesofcommonMRImodalities,suchasmulti-
bandexcitationsandparallelreceiving,whichsofarhavenotreceivedallthe
NMR attention they might deserve. Furthermore, it is unlikely that one
05 singleapproachwillfitbestthehundredsofmultidimensionalexperiments
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61- dimensions and interactions is much higher than that occupying our MR
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28 imaging colleagues. I therefore conclude by thanking the authors and edi-
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82 tors of this volume for offering its material as timely ‘‘food for thought’’,
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81 while encouraging all of us to read these pages with a critical, open mind.
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9/9 Chances are that the ultimate treatise on fast multidimensional NMR still
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0.1 NMR spectroscopy is ubiquitous in structural elucidation of synthetic
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oi: compounds, metabolites, natural products and materials in chemistry, as
g | d well as structural and functional characterisation of biomolecules and
or macromolecular complexes. The versatility of NMR spectroscopy derives
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s.rs frommultiple-pulseexperiments,wherenuclearcorrelationsareencodedin
ub multidimensionalspectra.However,thedirectresultofanNMRexperiment
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p:// is not a spectrum, but a time series. The NMR spectrum is generated from
htt the time response of the pulsed experiment through the application of a
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01 trum from, or consistent with, the time-domain empirical data. Signal pro-
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y cessing and pulsed NMR therefore go hand-in-hand in modern NMR
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8 spectroscopy.TheinherentlyweakNMRsignalhasmadesignalprocessinga
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n vital step in the varied applications of NMR. Basic understanding of signal
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discrete Fourier transform (DFT) that was seminal in the development of
modern pulsed NMR experiments. Prime among these limitations is the
difficulty (using the DFT) of obtaining high-resolution spectra from short
datarecords.AninherentlimitationoftheDFTistherequirementthatdata
be collected at uniform time intervals; many modern methods of spectrum
analysis circumvent this requirement to enable much more efficient
sampling approaches. Other modern methods of spectrum analysis obtain
high-resolutionspectrabyimplicitlyorexplicitlymodellingtheNMRsignals.
Alternatively,wehavewitnessedthedevelopmentofapproachesthatcollect
multidimensional data via multiplexing in space—exploiting the physical
dimensionsofthesample—ratherthanviasamplingaseriesofindirecttime
dimensions,orapproachesthattailorthepulsesequenceinwaysthatenable
NewDevelopmentsinNMRNo.11
FastNMRDataAcquisition:BeyondtheFourierTransform
EditedbyMehdiMobliandJeffreyC.Hoch
rTheRoyalSocietyofChemistry2017
PublishedbytheRoyalSocietyofChemistry,www.rsc.org
viii
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Preface ix
drasticallyfastersamplingintime.Together,methodsbasedonnonuniform
sampling in time or sampling in space enable a class of experiments de-
scribedasFastNMRDataAcquisition.Themethodsthatincreasethespeed
ofdataacquisitionthroughnon-conventionalpulsesequencedesigninclude
SOFAST-NMRandSingleScanNMR,coveredinthefirsttwochaptersofthis
08 book. Methods based on modelling the signal to obtain high resolution
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61- are described in Chapters 3–4 and Chapters 5–10, respectively. The latter
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28 are further categorized by those that sample in a deterministic matter,
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82 i.e. uniformly along radial or concentric patterns (Chapters 5 and 6) or
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81 those that seek incoherence in the distribution of the sampling times
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9/9 (Chapters 7–10).
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10. scientists in the development of Fast NMR Data Acquisition to provide a
oi: comprehensive reference text on this rapidly growing field. The popularity
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c. Forexample,asearchfornon-uniformsampling(NUS)terms(non-uniform,
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s.r non-linear,projection,radial,etc.)andNMRrevealed185publicationssince
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p 2000 (Scopus). 13 of these were published between 2000 and 2005, when
http:// projection reconstruction and reduced dimensionality experiments were
n being developed. In 2005–2010 the impact of these experiments and their
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7 relationship to data sampling led to 44 publications, and in 2010–2015 the
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2 field further expanded with 105 publications, with the introduction of
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Ma various ‘‘compressed sensing’’ techniques and the elucidation of their re-
18 lationshiptoestablishedmethods.Similarly, citationsofthesearticleshave
on risenfrom237citationsin2010toB800citationsin2015.Thesenumbers,
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he although crude, nevertheless show how interest in fast acquisition techni-
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bli queshasexplodedoverthepasttwodecades,movingfromrelativeobscurity
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perhaps most evident in the rapid adaptation of modern spectrometers
to these methods. In2005, purpose-written pulse sequences had tobe used
to perform NUS, whilst today it is treated as simply another standard ac-
quisition parameter during experimental setup by most commercial NMR
instruments.
Thereisnodoubtthatfastacquisitionmethodsarenowfirmlyestablished
asapartof modern NMR spectroscopy andwe hope thatthistextbookwill
serve to orient the spectroscopist in this new era, providing improved
understanding of the many methods on offer and enabling informed de-
cisions on how to make the most of the faint nuclear signals to resolve
complex chemical and biological problems.
Wearedeeplyindebtedtoourcolleagueswhocontributedtothisvolume,
and we express special thanks to Professor Lucio Frydman for contributing
his perspective in the Foreword. We are also grateful to the editorial staff
of the Royal Society of Chemistry for their enthusiasm for this project and
their tireless efforts during editing and production. Finally, MM wishes to
acknowledge support from the Australian Research Council in establishing
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x Preface
fast acquisition methods towards the automation of protein structure
determination by NMR (FTl10100925). JCH wishes to acknowledge the
generous support of the US National Institutes of Health via the grant
P41GM111135, which enabled the establishment of NMRbox.org: National
Center for Biomolecular NMR Data Processing and Analysis. All of
08 the authors of computer codes for non-Fourier methods represented in
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61- NMRbox.org.
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