Annual Reports on NMR Spectroscopy (eBook)

Graham A. Webb (Herausgeber)

eBook Download: PDF | EPUB

2010 | 1. Auflage
256 Seiten
Elsevier Science (Verlag)
978-0-12-381354-1 (ISBN)

Infos

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

Inhalt

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

Textauszug

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...

Produkt-Details

• Erscheint lt. Verlag: 12.4.2010
• Sprache: englisch
• Themenwelt: Naturwissenschaften ► Chemie ► Analytische Chemie
• Themenwelt: Naturwissenschaften ► Physik / Astronomie ► Elektrodynamik
• Themenwelt: Technik
• ISBN-10: 0-12-381354-9 / 0123813549
• ISBN-13: 978-0-12-381354-1 / 9780123813541