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Structure and dynamics of supramolecular assemblies studied by advanced solid-state NMR spectroscopy [Elektronische Ressource] / Almut Rapp

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Structure and Dynamics ofSupramolecular Assemblies Studied byAdvanced Solid-State NMR SpectroscopyDissertationzur Erlangung des Grades,,Doktor der Naturwissenschaften“am Fachbereich Chemie und Pharmazieder Johannes Gutenberg-Universitat¨in MainzAlmut Rappgeboren in BerlinMainz 2003Jahr der mundlichen¨ Prufung:¨ 2003ContentsIntroduction 11 Fundamentals 41.1 Supramolecular chemistry . . ......................... 41.2 NMR Spectroscopy . . ............................. 61.2.1 Interactions . . ............................. 71.2.2 Dipole-dipole couplings . . . . . . .................. 81.2.3 Line broadening . . . ......................... 11.2.4 Fast Magic Angle Spinning . . . . .................. 121.2.5 Concept of Recoupling ......................... 1311.2.6 H-decoupling in general . . . . . . .................. 131.2.7 Coherence . . ............................. 151.2.8 Spin-pair approximation . . . . . . .................. 161.2.9 Quantum Chemical description . . . .................. 172 NMRmethodsandpulsesequences 212.1 Two dimensional experiments in general . . .................. 2112.2 2D H Double-Quantum Spectroscopy . . . .................. 222.3 Heteronuclear experiments . . ......................... 252.3.1 REDOR . . . . ............................. 25III CONTENTS2.3.2 2D REPT-HSQC . . . . ........................ 262.3.3 TEDOR . . ............................... 312.4 Spinning sideband patterns . . . ........................ 322.

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Published 01 January 2003
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Structure and Dynamics of
Supramolecular Assemblies Studied by
Advanced Solid-State NMR Spectroscopy
Dissertation
zur Erlangung des Grades
,,Doktor der Naturwissenschaften“
am Fachbereich Chemie und Pharmazie
der Johannes Gutenberg-Universitat¨
in Mainz
Almut Rapp
geboren in Berlin
Mainz 2003Jahr der mundlichen¨ Prufung:¨ 2003Contents
Introduction 1
1 Fundamentals 4
1.1 Supramolecular chemistry . . ......................... 4
1.2 NMR Spectroscopy . . ............................. 6
1.2.1 Interactions . . ............................. 7
1.2.2 Dipole-dipole couplings . . . . . . .................. 8
1.2.3 Line broadening . . . ......................... 1
1.2.4 Fast Magic Angle Spinning . . . . .................. 12
1.2.5 Concept of Recoupling ......................... 13
11.2.6 H-decoupling in general . . . . . . .................. 13
1.2.7 Coherence . . ............................. 15
1.2.8 Spin-pair approximation . . . . . . .................. 16
1.2.9 Quantum Chemical description . . . .................. 17
2 NMRmethodsandpulsesequences 21
2.1 Two dimensional experiments in general . . .................. 21
12.2 2D H Double-Quantum Spectroscopy . . . .................. 22
2.3 Heteronuclear experiments . . ......................... 25
2.3.1 REDOR . . . . ............................. 25
III CONTENTS
2.3.2 2D REPT-HSQC . . . . ........................ 26
2.3.3 TEDOR . . ............................... 31
2.4 Spinning sideband patterns . . . ........................ 32
2.4.1 REPT-HDOR sideband patterns . . . ................. 34
2.4.2 REREDOR sideband patterns . . . . ................. 36
2.4.3 DQ sideband patterns . . ........................ 38
2.4.4 Calculating spinning sideband patterns . . . ............. 39
12.5 H NMR shift calculations . . . ........................ 41
3 YellowFilterDye 44
3.1 Color film dyes and their properties . . . . . ................. 46
3.2 Rhombic polymorph: Structural investigation ................. 47
3.3 Needle Structural investigation . ................. 58
3.4 Molecular Dynamics of Yellow Filter Dye Polymorphs . . . . . . ...... 6
3.4.1 Local Dynamics of Rhombic Polymorph . . ............. 6
3.4.2 Local Dynamics of Needle polymorph................. 69
3.4.3 Conclusion ............................... 72
4 Helicalshape-persistentdendriticpolymers 73
1 134.1 Structural features of G1-PMA below T :2D H- C correlation spectrum . . 74g
1 13 1 14.2 Segmental dynamics of G1-PMA below T : H- C and H- H sideband pat-g
terns . ...................................... 80
4.3 Segmental dynamics of G1-PMA above T – intermediate motional regime . 87g
4.4 G1-PS vs. G1-PMA............................... 8
4.5 G2-PMA vs. G1-PMA . . . . . ........................ 90
4.6 Benz-G2-PMA vs. G1-PMA and G2-PMA . . ................. 92
4.7 G1-4EO-PMA vs. G1-PMA . . ........................ 96
4.8 Conclusion . . . . ............................... 9CONTENTS III
5 Self-assemblyofdendriticmoleculeswithapolycyclicaromaticcore 101
5.1 Structural investigation .............................102
15.1.1 Assignment of H chemical shifts . ..................105
5.1.2 Analysis of π-shifts . . .........................108
5.1.3 Separation of aromatic and aliphatic region . . . ...........11
5.2 Investigation of molecular dynamics . . . . ..................13
6 Moleculardynamicsofaliquidcrystallineshape-persistentmacrocycle 118
6.1 Dynamical properties in the columnar liquid crystalline phase . . . . . ....19
6.2 Dynamical properties of the extraannular oligo-alkyl chains in the solid phase 123
7 Summary 125
Appendix 129
A Experimental details . .............................129
BT relaxation of Yellow Filter Dye molecules in the rhombic and the needle
1
morphology . . . . . . .............................130
C G1-dendron – NOESY experiment . . . . . ..................130IV CONTENTSIntroduction
Supramolecular chemistry has established itself during the last 35 years as one of the ma-
jor fields in chemistry and is still advancing very rapidly [Lehn 95, Atwood 96, Steed 00,
Ciferri 00]. Itsfirst aims were to mimic biology but up to now a vast number of novel species
have been synthesized, and the principles of supramolecular organization are increasingly
used for designing new functional materials. The underlying principles are self-assembling
processes via non-covalent interactions. Despite the knowledge gained so far about the design
rules of supramolecular chemistry, many aspects of non-covalent interactions and the result-
ing self-organization are still poorly understood and yet to be discovered. Deeper insight
can be gained by determining the structure as well as by identifying the structure-driving and
structure-directing features of supramolecular systems, such as hydrogen bonds and molec-
ular functional units capable of aggregating via π-π interactions. These questions represent
important challenges for modern characterization techniques, where solid-state nuclear mag-
netic resonance (NMR) spectroscopy proves to be a very powerful tool, especially when a
lack of long range order makes single-crystal investigations impossible, as is the case for
many supramolecular systems. In addition to structural information, solid-state NMR can
also elucidate dynamical properties of the materials.
1 1 1 13Recent advances in homonuclear H- H and heteronuclear H- C dipolar recou-
pling techniques under fast magic angle spinning (MAS) [Schnell 01b, Saalwachter¨ 01a,
Saalwachter¨ 02b] provide new means to investigate structure and dynamics in the solid state
by NMR spectroscopy, without being reliant on isotopic enrichment. The NMR methods used
1 1 1 13in this work are all based on a selective suppression and/or measurement of H- H and H- C
dipole-dipole couplings. Since dipole-dipole couplings act through space and depend on the
distance between the coupled nuclei, as well as on the orientation of the coupling vector with
respect to the magnetic field, they provide access to both structural and dynamic information
1about the material. Moreover, H chemical shifts have been shown to be very sensitive to
ring current effects of adjacent aromatic moieties and, in this way, serve as means to eluci-
date molecular packing arrangements [Brown 01b]. Dipole-dipole couplings are, however,
1also responsible for the poor resolution in H solid-state spectra because they broaden the
resonance lines significantly. A straight-forward approach to reduce dipole-dipole couplings
in the solid state is MAS [Andrew 58, Lowe 59]. Spinning speeds of 30 kHz, which have
12 CONTENTS
become routinely available within the last few years, usually provide sufficient homonuclear
1dipolar decoupling to resolve the relevant H resonances. While removing dipole-dipole cou-
plings during the course of the experiment with MAS to achieve sufficient resolution, it is,
at the same time, necessary to access the structural and dynamic information inherent to the
individual dipole-dipole couplings. Therefore, selected homo- or heteronuclear dipole-dipole
couplings are re-introduced by so-called recoupling techniques [Dusold 00]. A detailed de-
scription of the different homonuclear and heteronuclear dipolar recoupling NMR techniques
employed in this work is found in Chapter 2.
Since the periodic arrangement of molecules in a crystal is induced by non-covalent inter-
actions, molecular crystals can be understood as a supramolecular entity with an exceptionally
high order [Desiraju 95b]. Due to the long-range order, an X-ray crystal structure can be eas-
ily determined. Chapter 3 deals with such a molecular crystal (Yellow Filter Dye molecule
[Deroover ]), which exists in two different morphologies and whose chromophore system in-
duces π-shift effects. Due to the relatively small size of the molecule, a nucleus independent
chemical shift (NICS) map can be calculated using density functional theory (DFT), which
1predicts the H chemical shift effect induced by the π-electrons of the chromophore system
at a certain location relative to the molecule. Since the two crystal structures are known, it
1is possible to relate the H chemical shifts predicted by the NICS map to specific structural
features and packing phenomena of the molecules in the two polymorphs. In this way, the
applicability of the NMR experiments and the DFT calculations is tested.
Supramolecular helices and other columnar assemblies of molecules are well known from
nature, one of the most famous examples being the Tobacco Mosaic Virus [Klug 83]. In ad-
dition, a lot of effort has been devoted to synthesizing novel columnar architectures, see e.g.,
[Bushby 02, Ciferri 02, Brundveld 01, Percec 98b, Chandrasekhar 98]. Such architectures are
promising with respect to a variety of applications such as biocatalysis or optics and electron-
ics. In Chapters 4 and 5 several related supramolecular dendritic molecules are investigated
[Percec 98a, Percec 02b], which self-assemble in a columnar fashion below as well as above
their glass transitions. The core of the nanometer-scale columns may be a polymer chain
(Chapter 4) or consist of stacked polycyclic aromatic rings (Chapter 5), to which the dendrons
are attached via a linker group (depicted schematically in Figure 0.1). The study is carried
out over a representative selection of systems with characteristic differences, such as different
polymer backbone or polycyclic aromatic core, size of dendritic groups or length andflexibil-
ity of linker units (Chapter 4). By solid-state NMR valuable information can be gained about
the impact that different building blocks have on the self-assembly process and the resulting
local structure and dynamics of the columnar arrangement. In particular, local dynamics of
1CH groups are obtained and characteristic H chemical shifts are analyzed in combinationn
with NICS maps. In this way, the structure-driving and structure-directing moieties of the
assembly can determined. It’s to be noted that the dynamic properties of the polycyclic aro-
matic cores in the center of the columns (Chapter 5) are of special interest with respect to theirCONTENTS 3
promising optoelectronical properties, due to their significant charge-carrier mobility.
Figure 0.1: Schematic representation of dendritic molecules which self-organize in a columnar fash-
ion. The core of the column consists either of a polymer backbone (left) or a stack of polycyclic
aromatic rings (right).
Chapter 6 focuses on a quite different supramolecular columnar assembly where shape-
persistent macrocycles with intra- and extraannular substituents stack on top of each other
to build hollow nanotubes [Fischer 03]. To achieve a stable thermotropic liquid crystalline
phase a correct balance of rigid and flexible parts in the molecule is required. The degree of
segmental dynamics of the different moieties is determined by NMR, such that space require-
ments can also be estimated. In this way, the columnar phase and packing behavior can be
understood on a molecular level.