Webb Annual Reports on NMR Spectroscopy

1. Auflage 2010
ISBN: 978-0-12-381354-1
Verlag: Elsevier Science & Techn.
Format: EPUB
Kopierschutz: 6 - ePub Watermark

E-Book, Englisch, Band Volume 69, 256 Seiten

Reihe: Annual Reports on NMR Spectroscopy

In recent years, no other technique has gained such significance as NMR spectroscopy. It is used in all branches of science in which precise structural determination is required and in which the nature of interactions and reactions in solution is being studied. Annual Reports on NMR Spectroscopy has established itself as a premier means for the specialist and non-specialist alike to become familiar with new techniques and applications of NMR spectroscopy. - Provides updates on the latest developments in NMR spectroscopy - Includes comprehensive review articles - Highlights the increasing importance of NMR spectroscopy as a technique for structural determination

Autoren/Hrsg.

Webb, Graham A.

Inhaltsverzeichnis

1;Front Cover;1
2;Annual Reports on NMR Spectroscopy;4
3;Copyright Page;5
4;Contents;6
5;Contributors;8
6;Preface;10
7;Chapter 1: 129Xe NMR Studies of Xenon Adsorption;12
7.1;1. Introduction;13
7.2;2. Basic Approaches of 129Xe NMR Spectroscopy;14
7.2.1;2.1. Chemical shift of adsorbed xenon;14
7.2.2;2.2. Variation of the 129Xe chemical shift due to porosity and temperature;16
7.2.3;2.3. Xenon exchange spectroscopy;19
7.2.4;2.4. NMR of adsorbed species as a probe for metal clusters in porous materials;20
7.3;3. Microporous Carbon Materials;21
7.3.1;3.1. Commercially available amorphous carbon materials;22
7.3.2;3.2. Pitch-based activated carbon modified by air oxidation/pyrolysis cycles;25
7.4;4. Mesoporous Carbon Materials;29
7.4.1;4.1. Testing the nanoparticles surface: Diamond and onion-like carbon aggregates;29
7.4.2;4.2. Filamentous carbon: Surface, porosity and paramagnetic impurities;31
7.4.3;4.3. Multi-wall carbon nanotubes;37
7.5;5. Conclusions;45
7.6;References;46
8;Chapter 2: NMR Studies for Mapping Structure and Dynamics of Nucleosides in Water;50
8.1;1. Introduction;51
8.2;2. Overview, Trends and Opinions;53
8.3;3. Nomenclature and Symbols;54
8.4;4. About Stacking of Nucleosides in Water;60
8.5;5. Structure in Water;61
8.5.1;5.1. Proton and carbon-13 data;80
8.5.2;5.2. Investigations by other nuclei;102
8.5.3;5.3. Quantum mechanical calculations;109
8.6;6. Dynamics in Water;114
8.6.1;6.1. Rotation barrier about the glycosidic bond;114
8.6.2;6.2. Sugar pseudo-rotation barrier;116
8.6.3;6.3. Rotation barrier about the exocyclic hydroxymethyl bond;117
8.6.4;6.4. Rotation barrier about the exocyclic amino bond;117
8.6.5;6.5. Chemical exchange with water;119
8.6.6;6.6. Relaxation time measurements;122
8.6.7;6.7. Diffusion experiments;131
8.6.8;6.8. Microdynamics in water: A tentative interpretation;136
8.7;7. Conclusion;139
8.8;Acknowledgements;139
8.9;References;140
9;Chapter 3: Time-Domain NMR Applied to Food Products;156
9.1;1. Introduction;158
9.2;2. History;160
9.3;3. Equipment;161
9.3.1;3.1. Magnets;161
9.3.2;3.2. Electronics;162
9.4;4. One-Dimensional Relaxometry and Diffusometry;163
9.4.1;4.1. Relaxometry;163
9.4.2;4.2. Diffusometry;164
9.5;5. Two-Dimensional NMR Relaxometry and Diffusometry;165
9.5.1;5.1. T1(.)–T2 correlations;165
9.5.2;5.2. T2–D correlations using pulsed-field gradients;166
9.5.3;5.3. T1–T2 and T2–D correlations in inhomogeneous fields;167
9.5.4;5.4. 2D exchange experiments;167
9.6;6. Data-Analysis Approaches;168
9.6.1;6.1. Signal processing;168
9.6.2;6.2. Model-driven analysis;168
9.6.3;6.3. Discrete relaxometric and diffusometric decays;172
9.6.4;6.4. Continuously distributed relaxometric and diffusometric decays;173
9.6.5;6.5. Multi-variate data analysis approaches;174
9.7;7. Benchtop Time-Domain NMR Applications;174
9.7.1;7.1. Solid fat content;174
9.7.2;7.2. Shelf-life stability of foods;176
9.7.3;7.3. Moisture and fat content;176
9.7.4;7.4. Microstructural features in food emulsions;177
9.7.5;7.5. Functionality of food ingredients;179
9.7.6;7.6. Functionality of heterogeneous food products;188
9.8;8. Mobile Time-Domain NMR Applications;196
9.8.1;8.1. Unilateral NMR sensors;196
9.8.2;8.2. Online quality inspection;196
9.9;9. Perspectives and Conclusions;197
9.9.1;9.1. Hardware;197
9.9.2;9.2. Fast measurements;197
9.9.3;9.3. In situ measurements;198
9.9.4;9.4. Enhancing information yield from the time-domain;198
9.10;Acknowledgement;198
9.11;References;198
10;Chapter 4: From Helical Jump to Chain Diffusion: Solid-State NMR Study of Chain Dynamics in Semi-Crystalline Polymers;210
10.1;1. Introduction;211
10.2;2. NMR Strategies for Probing Chain Dynamics in Solid Polymeric Materials;211
10.2.1;2.1. Spin–lattice relaxation measurement;212
10.2.2;2.2. Probing motionally modulated/averaged NMR interaction;212
10.2.3;2.3. Longitudinal spin exchange experiment;214
10.3;3. Helical Jump and Chain Diffusion in Semi-Crystalline Polymers;215
10.3.1;3.1. Helical jump in polymer crystals;216
10.3.2;3.2. Chain diffusion in semi-crystalline polymers and its influencing factors;219
10.3.3;3.3. The correlation between helical jump and chain diffusion;229
10.4;Acknowledgements;234
10.5;References;234
11;Subject Index;236
12;Color Plates;244

Leseproben

3. Nomenclature and Symbols

For atom numbering and torsion angle definition in nucleosides, we follow the IUPAC/IUB guidelines. 41 , and 73 Accordingly, the chemical structure and atom numbering of the most common nucleosides, viz., the four purine nucleosides, abbreviated hereafter Pus, adenosine A, guanosine G, Inosine I, xanthosine X and the four pyrimidine nucleosides, abbreviated hereafter Pys, cytidine C, thymidine T, orotidine O and uridine U, are given, respectively, in Figure 2 and Figure 3 . Notation of the furanoside-type sugar (?- d ribose r in RNA and ?- d-2? deoxyribose d in DNA) is also pictured on A in Figure 2 and on C in Figure 4 .

Figure 2 Chemical structure of the most common purine nucleosides (Pus).

Figure 3 Chemical structure of the most common pyrimidine nucleosides (Pys).

Figure 4 (A) The torsion angle ? in uridine U and the definition of the torsion angles ? 0, ? 1, ? 2, ? 3 and ? 4 in the ribose ring. (B) Conformational model for the glycosidic torsion angle ? in nucleosides for Pys (O 2) and for Pus (N 3) showing the anti and syn ranges and denoting the four symmetric quadrants (dashed lines).

The nucleoside flexibility is fully characterised by three internal modes of motion:

• ?
  The glycosidic linkage torsion angle ?, O4??C1??N1?C2 (?, Pys) and O4??C1??N9?C4 (?, Pus), is pictured in Figure 4A , Section 5.1.1.1 , for U. According to this definition, the syn conformation is in the range ? = 0 ± 90°, whereas the anti conformation is in the range ? = 180 ± 90° ( Figure 4B ).
• ?
  The pseudo-rotation of the furanose ring or sugar puckering mode is illustrated in Figure 5A , with the two most common states of the ribose cycle, the C2? endo (referred to as 2E, or S-type) and the C3? endo (referred to as 3E, or N-type) represented in Figure 5B . Endocyclic torsion angles of the sugar are denoted ? 0 to ? 4, P is the pseudo-rotation phase angle and ? m is the maximum torsion angle which describes the maximum out-of-plane pucker, according to the usual convention. 41 , and 73 They are exemplified on U in Figure 4A .

  Figure 5 (A) The pseudo-rotational wheel of the ribose sugar in nucleosides. The dashed angle represents the phase angle of 36°. Envelope E and twist T alternate every 18°. After rotation by 180°, the mirror image of the starting position is found as schematised for the North position and the South position in the hatched part. (B) Schematic representation of the ribose equilibrium between the two states N and S: C3?, endo ( 3E, N) ? C2?, endo (2E, S). P = 0° and P = 180° are the phases along the pseudo-rotation cycle.

• ?
  The three main rotamers in staggered conformations gg, gt and tg as obtained by rotation about the exocyclic C4? ?C5? bond in the ribose moiety are drawn in Figure 6 , as Newman projections about this bond.

  Figure 6 Newman projections showing the three main staggered conformations about the C4?–C5? exocyclic bond.

Other more detailed nomenclature and symbols about inter-atomic bond distances, hydrogen bonding and base stacking, bond angles and torsion angles can be found in original publications, 74 , 75 , 76 , 77 , and 78 in classical texbooks 41 , and 79 and in previous NMR reviews in this field. 80 , 81 , 82 , 83 , and 84 So far, in this review, and in order to avoid possible misunderstandings, all the (ribo)nucleosides are quoted by a one letter symbol (A, C, G, I, O, T, U, X,...), whereas for the deoxy(ribo)nucleosides the first lower-case letter d indicates the ?- d-2? deoxyribose-type sugar and where the second capital letter (A, C, G, I, O, T, U, X,...) refers to the nucleobase. For example, dT means the deoxythymidine, which is unfortunately and often yet named as thymidine, whereas T is the “true” thymidine which is also named ribothymidine to avoid confusion with deoxythymidine dT because this latter was discovered before the “true” thymidine T. and was erroneously named “thymidine”. As stated above, there is a large number of common nucleosides and we describe below only the most frequently reported, namely:

• (a)
  C-Nucleosides such as pseudo-uridine (? uridine, symbolised as ?U hereafter) which occurs ubiquitously as a minor component in various tRNAs. 85 , 86 , and 87 and a large number of C-analogues which have been the cornerstone of antiviral and anticancer chemotherapy over the past three decades. 72 , 86 , 87 , and 88
• (b)
  Azanucleosides which are also powerful chemotherapeutic agents with, for example, anti-human immunodeficiency virus (HIV) activity. 89 , 90 , and 91
• (c)
  Thionucleosides which are often found in the wobble position of transfer RNA anticodon and occur exclusively in the N anti form. 92 , and 93
• (d)
  Halogeno-nucleosides which have anti-herpes virus activity and are also used in anticancer chemotherapy. 94 , and 95
• (e)
  2?,3?-Dideoxynucleosides such as 3?-azido-2?,3?-dideoxyribosylthymine (AZT) with also anti-HIV activity and cytopathic effect on human T-lymphotropic virus type. 96 , 97 , and 98
• (f)
  Bicyclic heterocyclic nucleosides which possess a base ring fused to various membered heterocyclic systems and are known for their reported in vitro and in vivo inhibition of various tumour cell lines. 99 , 100 , and 101
• (g)
  5?- O-Amino-2?-deoxy-nucleosides which are building blocks for antisense oligonucleotides and have recently gained much attention for their usefulness in antisense therapy. 102
• (h)
  ?-Nucleosides which are conformational enantiomers of the common nucleosides with the anomeric carbon C1? in an inverted configuration and are found in vitamin B-12 and in arabino-nucleosides which differ from their ribo analogues in the altered configuration at C2? and exhibit broad antiviral activity against DNA-containing viruses as well as against RNA tumour viruses. 103

From these preliminary considerations, it emerges that most nucleosides are generally in the anti conformation around the glycosidic linkage with the ribose in the N state, C3? endo form and the gg arrangement around the C4?–C5? exocyclic bond. 7 , 8 , 9 , and 10 Nevertheless, it should be stressed that the presence of electronegative substituents either on the ribose moiety 76 , 94 , 104 , 105 , 106 , 107 , 108 , 109 , and 110 or/and on the aromatic ring 76 , 89 , 109 , 110 , 111 , 112 , 113 , 114 , 115 , 116 , 117 , and 118 as well as the presence of bulky groups on either one or the other cycle 76 , 112 , and 113 can dramatically change the anti/ syn geometry and/or the N/S puckering with also important modifications in the proportions of the gg, gt and tg rotamers. In some well-defined cases, hydrogen bonding between the C5? hydroxyl group and a particular acceptor group on the ribose or on the base can increase the proportion of the syn conformation. 76 , 109 , 113 , 116 , 119 , 120 , 121 , 122 , 123 , 124 , 125 , and 126 In other well-defined cases, changes in the solvent or pH can also change the conformation and the furanose pucker. 114 , 121 , and 127 Finally, it has also been shown that the S (C2? endo) form appears to be greater in deoxynucleoside as compared to ribonucleoside. This variability in flexibility, structure shaping and biological functions has been tentatively estimated, mainly, by Pullman and co-workers 128 , and 129 in the 1970s by using (old) semi-empirical MO-SCF calculations and also by others 130 , 131 , 132 , 133 , 134 , 135 , and 136 with often some recourse to molecular mechanics (MM). Today, this theoretical field has opened the way to the state of the art for the sugar puckering and the conformation simulated by MD and/or Car–Parrinello molecular dynamics (CPMD) and/or BD, 37 , 137 , and...