Spectroscopy and Modeling of Biomolecular Building Blocks
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Table of contents
- Cover
- Contentsv
- Prefacexiii
- Chapter 1. Modelling1
- General Features1
- 1.1 Interactions Responsible for Biomolecular Structures and Biospecific Recognition1
- 1.2 Quantum Mechanics Modelling8
- 1.3 Molecular Mechanics: Force-Fields18
- 1.4 Semi-Empirical Methods22
- 1.5 Exploration of Potential Energy Landscapes24
- 1.6 Mixed Approaches QM/MM36
- 1.7 Excited States38
- References45
- Chapter 2. Spectroscopy59
- General Features59
- 2.1 Frequency-Resolved Spectroscopy60
- 2.2 Time-Resolved Spectroscopy101
- 2.3 Electron Spectroscopy103
- References115
- Chapter 3. Experimental Methods129
- 3.1 Bringing Biomolecules into Gas-Phase129
- General Features129
- 3.2 Mass-Spectrometry146
- General Features146
- 3.3 Determination of Structures of Mass-Selected Gas-Phase Biomolecular Systems171
- References189
- Case Studies209
- Chapter 4.1. Nucleobases, Nucleosides and Oligonucleotides211
- General Features211
- References237
- Chapter 4.2. Amino Acids, Peptides and Proteins251
- General Features251
- References282
- Chapter 4.3. Sugars297
- General Features297
- References305
- Chapter 4.4. Neuromolecules309
- General Features309
- References318
- Chapter 4.5. Non-Covalent Complexes323
- General Features323
- References331
- Chapter 4.6. Chiral Molecular Systems339
- References346
- Chapter 4.7. Low-Energy Electron–Molecule Interactions351
- General Features351
- References367
- Chapter 4.8. Large Biomolecular Systems in the Gas-Phase373
- General Features373
- References384
- Chapter 5. From Gas-Phase to Solution389
- General Features389
- 5.1 Modelling of Solvation392
- 5.2 Solvents399
- 5.3 Hydrophobicity408
- 5.4 Hydration of Nucleobases, Oligonucleotides, DNA and RNA410
- 5.5 Hydration of Amino Acids, Peptides and Proteins417
- 5.6 Hydration of Saccharides434
- 5.7 Hydration of Neuromolecules438
- References444
- Conclusion467
- References471
- Subject Index475
This book presents an overview of recent advances in the intertwining of the following research fields: photon and electron spectroscopy, quantum chemistry, modelling and mass-spectrometry. The coupling of these disciplines offers a new point of view to the understanding of isolated elementary building blocks of biomolecules and their assemblies. It allows the unambiguous separation between intrinsic properties of biomolecular systems and those induced by the presence of their environment.
The first chapters provide background in modelling (I), frequency-resolved spectroscopy using microwave, infrared and UV photons, time-resolved spectroscopy in the femtosecond domain and energy-resolved electron spectroscopy (II) and production of gas-phase neutral and ionic biomolecular species, mass-spectrometry, ion mobility and BIRD techniques (III).
Chapter IV is devoted to case studies of gas-phase experimental investigations coupled to quantum or classical calculations. The topics are structural studies of nucleobases and oligonucleotides, peptides and proteins, sugars; neuromolecules; non-covalent complexes; chiral systems, interactions of low-energy electrons with biomolecules in the radiation chemistry context and very large gas-phase biomolecular systems.
The fifth chapter concerns the link between gas-phase and liquid-phase. Different treatments of solvation are illustrated through examples pointing out the influence of progressive addition of water molecules upon properties of nucleobases, peptides, sugars and neuromolecules.
Offer a new perspective to the understanding of isolated elementary building blocks of bio molecules
Includes case studies of experimental investigations coupled to quantum or classical calculations
The first chapters provide background in modelling (I), frequency-resolved spectroscopy using microwave, infrared and UV photons, time-resolved spectroscopy in the femtosecond domain and energy-resolved electron spectroscopy (II) and production of gas-phase neutral and ionic biomolecular species, mass-spectrometry, ion mobility and BIRD techniques (III).
Chapter IV is devoted to case studies of gas-phase experimental investigations coupled to quantum or classical calculations. The topics are structural studies of nucleobases and oligonucleotides, peptides and proteins, sugars; neuromolecules; non-covalent complexes; chiral systems, interactions of low-energy electrons with biomolecules in the radiation chemistry context and very large gas-phase biomolecular systems.
The fifth chapter concerns the link between gas-phase and liquid-phase. Different treatments of solvation are illustrated through examples pointing out the influence of progressive addition of water molecules upon properties of nucleobases, peptides, sugars and neuromolecules.
Offer a new perspective to the understanding of isolated elementary building blocks of bio molecules
Includes case studies of experimental investigations coupled to quantum or classical calculations