Solving a 3D Structural Puzzle

271 Pages·2018·7.612 MB·English

by  Casper Rønn Hoeck

Springer Theses
Recognizing Outstanding Ph.D. Research
Casper Rønn Hoeck
Solving a 3D
Structural
Puzzle
Springer Theses
Recognizing Outstanding Ph.D. Research
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ø
Casper R nn Hoeck
Solving a 3D Structural
Puzzle
Doctoral Thesis accepted
by the Technical University of Denmark,
Kongens Lyngby, Denmark
123
Author Supervisor
Dr. Casper RønnHoeck Prof. Charlotte H.Gotfredsen
Department ofChemistry Department ofChemistry
Technical University of Denmark Technical University of Denmark
Kongens Lyngby,Denmark Kongens Lyngby,Denmark
ISSN 2190-5053 ISSN 2190-5061 (electronic)
SpringerTheses
ISBN978-3-319-96171-2 ISBN978-3-319-96172-9 (eBook)
https://doi.org/10.1007/978-3-319-96172-9
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’
Supervisor s Foreword
The establishment of molecular structure and configuration is central to our
understanding of chemistry and biology—and many analytical techniques provide
different structural knowledge in today’s research. Two of the techniques most
oftenemployedforfullstructureelucidationareX-raycrystallography andnuclear
magnetic resonance (NMR) spectroscopy. Which analytical technique to use
dependsonthenature,origin,andpropertiesofthecompoundbeingstudiedandthe
structural properties being researched.
NMRspectroscopyinstructuralstudiesofnaturalproductsandsmallmolecules
is an area of constant focus both in industry and academia where it is a very
importantpartofthestandardanalyticaltoolboxinresearchanddevelopment.This
requires a constant focus on developments within NMR and its applications,
including the exploration of new approaches to employ NMR parameters in 3D
structural calculations. The continued development of the entire structure elucida-
tion process calls for a multidisciplinary approach, and the use of orthogonal
experimental data is needed to increase the accuracy of the molecular structures.
The thesis by Casper Rønn Hoeck Solving a 3D Structural Puzzle describes
different topics and novel research angles on how NMR spectroscopy can be
employed in several interdisciplinary projects. The thesis describes development
and implementation of new NMR pulse sequences, new computational approaches
tostructuralcalculationsaswellasorganicpolymersynthesisofalignmentmedia—
all of which contribute to obtaining more reliable NMR-based 3D molecular
structures of small compounds.
Inhiswork,CasperhascontributedwithsignificantnewinsightsintoNMR-based
molecular structure determination and also highlighted some of the remaining
challengesfacedby3Dmolecular structure elucidationofsmallcompounds.
Kongens Lyngby, Denmark Prof. Charlotte H. Gotfredsen
March 2018
v
Abstract
Nuclear magnetic resonance (NMR) spectroscopy is a versatile tool in analytical
chemistry, highly suitable for structural elucidation of organic molecules—as well
as multiple other areas of research. The subjects covered within this thesis all
concernmethodswhichallowashiftfromcovalenttospatialstructuralinformation
using NMR spectroscopy.
Experimental distances from nuclear Overhauser effect (NOE) correlations, and
dihedral angles from 3J -coupling constants, were used to obtain 3D structural
HH
information for several natural and synthetic compounds. The stereochemistry of
novelnaturalcompoundswasdetermined,includingthatofabicyclicnon-ribosomal
peptide (a novel structural motif), a steroid, and several polyketides. Structural
insights were gained for potential anti-cancer agents; the azumamides, including
synthetic analogues. Differences in the conformational space of solution state
compounds were identified experimentally between structural analogues and com-
paredtotheinvitropotencyofthecompounds.Thestructuresoftwopeptidesthat
exhibitedahighdegreeofmolecularrecognitionwereinvestigated,resultinginthe
elucidation of a possible mode of interaction. Also, a major assumption in the
calculation of distances from NOEs, the assumption of equal rotational correlation
times between proton pairs,was investigated for molecules in organic solvents.
Two spin-state selective (S3) HMBC experiments were developed for measure-
ments of homonuclear and heteronuclear long-range coupling constants, respec-
tively. The new NMR experiments were based on two existing experiments, the
multiplicity-editedHMBCandtheHATHMBC,whichwerecombinedtoobtainS3
editing of long-range homonuclear coupling constants. The output of the first S3
HMBCexperimentwasHMBC-typespectrawithnJ correlatedcross-peaks,from
CH
which n+1J -coupling constants were sign-selectively determined with high
HH
accuracy.Verysmallcouplingconstants,includingpreviouslyunreportedcoupling
constants from strychnine, were extracted, with all experimental values correlating
verywelltotheoreticalcouplingconstantsfromDFTcalculation.Apulsesegment
wasdevelopedtochangethepolarizationoftheCH-HpairsinthehomonuclearS3
HMBC, to gain S3 edited nJ -coupling constants in the cross-peaks. While only
CH
determining coupling constants to methine carbons, the extracted experimental
vii
viii Abstract
coupling constants correlated very well to theoretical coupling constants, thus
extending the S3 HMBC methodology to include both n+1J - and nJ -coupling
HH CH
constants.
Residual dipolar couplings (RDCs) are a relatively late addition to the small
molecularNMRcommunity,wherealignmentmediaareusedtoobtainanisotropic
samples, which allow for RDCs to be extracted. The number of inter-nuclear
vectors for the correlation of RDCs to 3D structures is often limited for small
molecules. Homonuclear RDCs were extracted by use of the homonuclear S3
HMBC that correlated well to alignment tensors from 1D -coupling constants,
CH
thus increasing the number of internuclear vectors. The topic of enantiodiscrimi-
nationbyRDCmeasurementsofrigidorganicmoleculeswasalsoinvestigated,and
newalignmentmediaweredevelopedtoallowslightdiscriminationofenantiomers
bystretchedpolymers.Finally,anewmethodofback-calculationofRDCsfrom3D
structures was developed and tested, which copes better with multiple conformers
than the commonly used SVD methodology. The approach thus resulted in good
conformer populations for several small molecules, including multiple cinchona
alkaloids.
Preface
Theworkpresentedinthisthesiswascarriedoutduringmythreeyearsofresearch
as a Ph.D. student at the Department of Chemistry, Technical University of
Denmark. The work was supervised by Associate Professor Charlotte Held
Gotfredsen and funded by the Department of Chemistry. A three-month external
stay was conducted in the group of Dr. Craig Butts at the School of Chemistry,
University of Bristol, UK.
The thesis is divided into nine chapters, covering three main topics. The first
topic is nuclear Overhauser effect correlations and 3J -coupling constants in 3D
HH
structural investigations of organic compounds (Chap. 3). This is followed by a
chapter concerning structural information from long-range coupling constants and
new pulse sequences to determine these (Chap. 4). The final topic covers multiple
chapters and focuses on 3D structural information from residual dipolar coupling
constants, from increasing the number of available inter-nuclear vectors by
long-range coupling constants (Chap. 6) to enantiodiscrimination (Chap. 7), and a
chapter on structural flexibility and a new method of back-calculating (Chap. 8).
Kongens Lyngby, Denmark Dr. Casper Rønn Hoeck
ix
Parts of this thesis have been published in the following journal articles:
I. Maolanon,AlexR;Villadsen,JesperS;Christensen,NielsJ;Hoeck,Casper;
Friis, Tina; Harris, Pernille; Gotfredsen, Charlotte H; Fristrup, Peter; Olsen,
Christian A. Methyl Effect in Azumamides Provides Insight Into Histone
Deacetylase Inhibition by Macrocycles. Journal of Medicinal Chemistry,
2014, 57, 9644–9657.
II. Petersen, Lene M; Hoeck, Casper; Frisvad, Jens C; Gotfredsen, Charlotte H;
Larsen,ThomasO.DereplicationGuidedDiscoveryofSecondaryMetabolites
of Mixed Biosynthetic Origin from Aspergillus aculeatus. Molecules, 2014,
19, 10898–10921.
III. Kjaerulff,Louise;Benie,AndrewJ;Hoeck,Casper;Gotfredsen,CharlotteH;
Sørensen, Ole W. S3 HMBC: Spin-State-Selective HMBC for accurate mea-
surement of homonuclear coupling constants. Application to strychnine
yielding thirteen hitherto unreported J . Journal of Magnetic Resonance,
HH
2016, 263, 101–107.
IV. Li, Ming; Hoeck, Casper; Schoffelen, Sanne; Gotfredsen, Charlotte H;
Meldal, Morten. Specific Electrostatic Molecular Recognition in Water.
Chemistry - A European Journal, 2016, 22, 7206–7214.
V. Hoeck,Casper;Gotfredsen,CharlotteH;Sørensen,OleW.S3HMBChetero:
Spin-State-Selective HMBC for accurate measurement of heteronuclear cou-
pling constants. Journal of Magnetic Resonance, 2017, 275, 68–72.
xi