1Voet and Voet, Biochemistry, 3rdFigure 2-1 Structure of the water molecule.Solid LiquidFigure 2-3 The crystal structure of ice demonstrates the tetrahedral dipole structure of water molecules. In liquid water, less then 3 hydrogen bonds are formed per water molecule at any given time.Figure 2-4 Theoretically predicted and spectroscopically confirmed structures of the water trimer, tetramer, and pentamer.Voet and Voet, Biochemistry, 3rd2Figure 2-6 Hydrogen bonding by functional groups.Voet and Voet, Biochemistry, 3rdO – H bond distances:Covalent = 0.958ÅHydrogen = 1.8ÅVan der Waals = 2.6Å[1Å = 0.1nm = 10-10m]Although the hydrogen atoms are shown along lines connecting the oxygen atoms, this is now thought unlikely even in ice. K. Modig, B. G. Pfrommer and B. Halle, Temperature-dependent hydrogen-bond geometry in liquid water, Phys. Rev. Lett. 90 (2003) 075502. Figure 2-2 Hydrogen bond between two water molecules.Voet and Voet, Biochemistry, 3rd3Dipole moment (δ+Æδ-)µ = Q r µ(H2O) = 1.85 Debye1 Debye = 3.33x10-30CmAsymmetries in electron distributions.http://www.lsbu.ac.uk/water/molecule.htmlJ. L. Finney, The water molecule and its interactions: the interaction between theory, modelling and experiment, J. Mol. Liquids, 90(2001) 303-312. δ+δ+δ−δ−Cox, Lehninger Principles in Biochemistry, chapter 3Molecular dipoles are the result of covalent bond formation between atoms of different electronegativity. Electronegativity is a property of atoms within molecules and quantifies the relative attraction of shared electrons in covalent bonds for an atom.4Cox, Lehninger Principles in Biochemistry, chapter 4The dipole structure of molecules determines water solubilityKnow the Macroscopic and the Microscopic5Cox, Lehninger Principles in Biochemistry, chapter 4Polarity is a measure of a physical property of a molecular structure and is a microscopic property.Hydrophilicity is a measure of solubility in liquid water and is a macroscopic property.Macroscopic Microscopic Dielectric constantDipole momentAmphipathic (amphiphilic)Polar&Non-polarHydrophobic Non-polarHydrophilic PolarHydration –the solvation of ions in water6Voet and Voet, Biochemistry, chapter 2, figure 5Ion Crystal radius (Å) Hydrated radius (Å) Hydration number Li+ 0.60 3.82 6 Na+ 0.95 3.58 4 K+ 1.33 3.31 4 Table Ionic radii and average hydration numbers (from Conway, p.73, 302; crystal radii determined from salt crystals; hydration number obtained from dielectric decrement measurements). The hydration shell – a microscopic structureqa+×qa-F = k× -------D×r2Coulomb's law for an ion pair a+a-D = dielectric constant or relative permittivity D (also e in the literature, is a dimensionless factor indicating the relative permittivity of the medium with respect to the permittivity of vacuum; the permittivity of vacuum eo= 8.854x10-12farad/m). The dielectric constant is a measure of the polarizability of the solvent (responsiveness of a localized charge distribution (dipole) to an external electric field), a property which is related to the polarity of the solvent molecules. Note that the dielectric constant of a solvent is a better indicator of its ‘miscibility with water’ than the molecular dipole moment (chloroform is a non-polar solvent even though its m(molecule)=1.1 and not zero).The dielectric constant as a measurement of solubility of charges7Table 2-1 Dielectric Constants and Permanent Molecular Dipole Moments of Some Common Solvents.Voet and Voet, Biochemistry, chapter 2The Hydrophobic Effect8Voet&Voet, Biochemistry, chapter 8Figure 8-58 The orientational preference of water molecules next to a nonpolar solute.Cox, Lehninger Principles in Biochemistry, chapter 4, figure 79Cox, Lehninger Principles in Biochemistry, chapter 4, figure 7The Hydrophobic EffectSelf-assembly of amphipathic molecules (e.g. fatty acids) in liquid water. The driving force is the hydrophobic effect due to the increase in entropy of the bulk water phase (flickering cluster structure).The Hydrophobic EffectSelf-assembly of amphipathic molecules (e.g. fatty acids) in liquid water. The driving force is the hydrophobic effect due to the increase in entropy of the bulk water phase (flickering cluster structure).Acids and Bases, pH10Cox, Lehninger Principles in Biochemistry, chapter 4, figure 13Cox, Lehninger Principles in Biochemistry, chapter 4, figure 17The acid – base chemical equilibrium11Figure 2-11 Distribution curves for acetic acid and acetate ion.Voet and Voet, Biochemistry, chapter 2Figure 2-10Acid-base titration curves of 1-L solutions of 1M acetic acid, H2PO4–, and NH4+ by a strong base.Voet and Voet, Biochemistry, chapter
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