Humboldt State University ® Department of Chemistry

Richard A. Paselk

Chem 431	Biochemistry	Fall 2007
Lecture Notes: 5 September	© R. Paselk 2007
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Water, cont.

Water of course is a covalent structure: H-O-H. But what gives it its special properties is the polarity of its O-H bonds and the resultant dipole moments of the bonds and the molecule itself.

The water molecule itself is bent, with an angle of 104.5° between the hydrogens (compare to 109.5° for sp³ tetrahedron) as seen in text Figure 2.1

Because of the very strong dipole moments of these bonds and the very small size of the hydrogen substituents on water, a slight degree of orbital overlap occurs between adjacent water oxygens and hydrogens to give partial covalent bonds known as H-bonds (effectively, can only form with O, N, & F).

• Note that the partial covalent character means that they are directional! Text Figure 2.1c shows a representation of H-bonds in water.
• Compare the bond length of water H bonds (0.18 nm) to the covalent bond-length between O and H of 0.096 nm - notice that the bond distance is nearly twice the true covalent bond distance, but significantly less than the van der Waals radius of 0.26 nm.

In addition to covalent bonds and H-bonds there are a variety of non-covalent bonds/interactions as seen in the table below:

Interaction Type Example Average Strength, kcal/mol (kJ/mol) Range** Charge-charge (ionic)    5 (20) [in water solution] 1/r Charge-dipole     1/r2 Dipole-dipole      1/r3 Charge-induced dipole       Dipole-induced dipole*   0.1-0.2 (0.4-4)  1/r6 Dispersion*   0.1-0.2 (0.4-4) 1/r6 Hydrogen bond   3-8 (12-30)    van der Waals repulsion     1/r12

*van der Waals interactions, **from Zubay Biochemistry 3rd. Table 4.3, pg. 89.

Within solid bulk water (ice):

• every water molecule is bonded to 4 others, as in the ice structure seen in text Figure 2.2.
  • In liquid water the molecules are still bonded to a large degree (the heat of fusion for ice is only 13% of the heat of vaporization for ice, thus most of the H-bonds must survive melting).
  • Of course in liquid water the bonds are very unstable (average lifetime about 10 psec = 10^-11 sec), exchanging constantly to give a "flickering cluster" structure.
  • The various properties of water arise from this structure. (Note hi bp & mp, heat cap., viscosity, and, less obviously, that ice floats.
• Ice floats because the molecules are in an open lattice rather than close-packed. Garrett & Grisham (in their text, Biochemistry, 2nd ed) note that close-packed water molecules would only occupy about 57% of the volume of ice. This would lead one to expect that ice would float "high." It doesn't because most of the structure remains in the liquid phase at 0° C.)

Water is an excellent solvent for polar substances since its dipolar structure enables it to insulate them from each other and it can make good dipole-dipole and dipole-charge bonds. Figure 2.6 shows the hexavalent liganding of water to sodium and chloride ions to form hydration shells (For sodium ions, the waters in the inner hydration-shell exchange every 2-4 nsec.). Anything which can H-bond will also of course be quite soluble.

How does water interact with non-polar molecules?

• The problem here is that in order to dissolve in water a non-polar molecule must disrupt a series of H-bonds and no new bonds of equal strength are substituted.
• Thus water tends to exclude non-polar substances. When we forcefully disperse a non-polar substance into water then the water must form a cage around the molecule to maximize H-bonds for each water molecule. [text Figure 2.7a]
  • Now an additional problem arises-the waters hydrating the non-polar group are "locked" in place - they can't easily flip about because there is no interior bond for substitution!
• Thus the entropy of these water molecules is greatly reduced. So the insolubility of non-polar groups in water has both enthalpic and entropic factors!
• Note that many non-polar molecules may dissolve in water by the formation of micelles as in text Figure 2.7b.

Finally, recall that water is a good nucleophile and so will participate in many chemical reactions-readily hydrolyzes esters, amides, anhydrides etc.

Ionization of Water, pH & Buffers

Dissociation of water molecules: One aspect of water we have yet to talk about is its dissociation or ionization. In normal aqueous solution there is a certain probability that a hydrogen nucleus (a proton) can exchange between two hydrogen bonded molecules:

(Of course the hydronium ion, H₃O⁺, will be associated with additional water molecules as well through H-bonding. For simplicity we will just write H⁺, with the understanding that it refers in fact to hydrated hydronium ions in aqueous solution. ) Note the reaction is not highly favored, in neutral solution (no excess H⁺or OH^-) there will only be 10^-7 molar hydronium ions, in other words only about 2 of every billion water molecules will be protonated!

For aqueous solution [H⁺][OH^-]= 10^-14

Pathway Diagrams

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Last modified 5 September 2007