The Hydrogen Bond and the Water Molecule

The hydrogen bond and the water molecule: the physics and chemistry of water, aqueous and bio media

Acknowledgments Preface Part I: The hydrogen bond

Chapter 1 The hydrogen bond: formation, thermodynamic properties, classification Chemical bonds Intermolecular bonds Van der Waals interactions, Hydrogen bonds The H-bond: historical and prospective aspects, general bibliography Intermolecular and intramolecular H-bonds Electronic structures of H-bonds Thermodynamics of H-bonds: electronic and vibrational contributions to enthalpies Examples of weak, intermediate strength and strong H-bonds Weak H-bonds Medium-strength H-bonds Strong H-bonds Non-conventional H-bonds H/D substitutions in H-bonds Appendix A: energies and related quantities.

Chapter 2 Geometrical properties of H-bonds and H-bonded organized supramolecular structures

Geometries of H-bonds at equilibrium

Equilibrium angles 0 and 0 Equilibrium distances Q0 Equilibrium distances q0 Organized supramolecular structures of macromolecules Cellulose and amylose Proteins Composition: polypeptide backbone Primary, secondary and tertiary structures of a protein Pleated -sheets -helices tertiary structures and beyond Stability of secondary structures and denaturation of proteins DNA Conclusion

Chapter 3 Methods to observe and describe H-bonds Calorimetry

Modern experimental methods Absorption of an electromagnetic wave Microwave spectroscopy IR spectra: rotational bonds NMR spectroscopy Principles NMR of H-bonds established by small or medium-size molecules NMR of macromolecules Conclusion X-ray absorption spectroscopy Scattering of electromagnetic waves or particles Coherent scattering (X-rays and neutrons) Incoherent scattering Incoherent light scattering Incoherent neutron scattering (INS) Theoretical descriptions of the electronic structures of H-bonds Summary

Chapter 4 Infrared spectroscopy of H-bonded systems: experimental point of view

IR spectroscopy and H-bond vibrations Intermonomer vibrations in the FIR region Description anharmonicities of intermonomer modes. Intramonomer vibrations in the mid-infrared region

Stretching bands s Introduction Integrated intensities

s band centres

Shifts  of s and enthalpies H of H-bonds

Shifts  of s and H-bond distances Evidence of cooperativity between H-bonds Conclusion

Widths of s bands

The s band of H-bonds: conclusion. Other intramonomer bands Stretching and bending vibrations of the donating X-H group Carbonyl and carboxyl C=O groups Multiphoton vibrational spectroscopy: Raman and nonlinear IR spectroscopies Raman spectra Time resolved non linear IR spectroscopies Sum-frequency generation (SFG) spectroscopy Conclusion

Chapter 5 Infrared spectroscopy of H-bonded systems: theoretical descriptions

Introduction

Integrated intensities of s bands s bandshapes of isolated H-bonds: modulation by intermonomer modes Modulation by intermonomer stretching modes Modulation by intermonomer bending modes

s bandshapes of non-isolated H-bonds s bandshapes of H-bonds: Fermi resonances conclusion on s bands Appendix: IR spectroscopy Experimental spectroscopy: measured quantities and set-ups First moments of a distribution or of a spectral band Normal modes in the harmonic approximation Reduced masses, force constants and vibrational amplitudes

Centre and width of s

Chapter 6 Reactivity of H-bonds: transfers of protons and of H-atoms

Great amplitude motions in isolated H-bonds Proton transfers in a H-bond network Ionization mechanism of an acid or a base + - Diffusion of H3O and OH ions in liquid water Proton transfers in the electronic excited state Photoacids ESPT's in biology: photosynthesis and vision mechanisms. H-bonded ferroelectrics Hydrogen atom transfers by tautomerism Conclusion

Chapter 7 H/D isotopic substitution in H-bonds The H and D atoms: similarities and differences Geometries and therrmodynamics of H-bonds and D-bonds Geometries of H-bonds and D-bonds Enthalpies of H-bonds and D-bonds Dynamic properties of H-bonds and D-bonds Vibrational spectra of H-bonds and D-bonds Partial H/D substitution and isotopic dilution H/D substitution in biology: a dramatic effect on reactivity H-bonds and D-bonds as seen by methods sensitive to nuclear spins Conclusion Appendix

Part II: The water molecule

Chapter 8 The H2O molecule in water vapour and ice H2O : an exceptional molecule. Water vapour The major greenhouse gas and its strong IR bands Formation of rain drops. Ice(s) Ice Ih and Ice Ic Crystal structures IR spectrum Structures of ice surfaces. Other crystalline phases of ice. Ice Ih/ liquid water interfaces. Amorphous phases of ice. Reactivity of ice Ice in the atmosphere Ozone depletion and polar stratospheric clouds Mechanisms of ozone destruction. Conclusion

Chapter 9 The H2O molecule in liquid water

H-bonds in liquid water Thermodynamics IR spectroscopy O-H free groups? IR spectra of liquid water and of ice intermonomer bands intramonomer bands Structure of the H-bond network of liquid water. The exceptional properties of liquid water Exceptional chemical properties Ionization and solvation of acids and bases Ionization and solvation of salts Solvation of organic molecules Organized structures of amphiphile molecules Micelles Biological membranes Langmuir-Blodgett layers Exceptional physical properties Our understanding of liquid water Conclusion

Chapter 10 The water molecule in (bio)macromolecules

Water molecules and their dense hydrogen bond networks Arrangements of water molecules in macromolecules Hydration mechanisms Hydration of a model biopolymer: hyaluronane (HA) Dried state of HA Successive hydration mechanisms First hydration mechanism H1 Subsequent hydration mechanisms at higher hygrometries Hydration of a synthetic polymer: a sulfonated polyimide General features for hydration mechanisms? Protection of biomacromolecules against external stress (cryo- and lyo-protections) Survival under freezing temperatures or hydric stress Protection mechanisms Protein folding Reactivity of water molecules in macromolecules Conclusion

Chapter 11 Observing the water molecule

A difficult to observe molecule Global methods Classical molecular methods other than vibrational spectroscopy X-ray scattering Neutron scattering NMR spectroscopy Molecular Dynamics (MD) Vibrational spectroscopy

IR spectroscopy to observe H2O molecules ATR (Attenuated Total Reflection) IR spectrometry on thin samples: hydration of macromolecules Hydration spectra of hyaluronane HA Analysis of hydration spectra Bands due to H2O molecules: measurement of the water uptake Intensities of the difference bands due to the macromolecule Time-resolved non-linear IR spectroscopy NIR and Raman spectroscopies Conclusion

Part III: General conclusion

Chapter 12 Conclusion: the H-bond, the water molecule and life