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Hydrogen Bonding in Water and Biomolecules: Properties and Interactions, Exercises of Chemistry

University of Alaska SystemChemistry

The concept of hydrogen bonding in water and its impact on the properties of biomolecules. It discusses the role of hydrogen bonding in the structure and function of water, the differences between polar and nonpolar molecules, and the formation of hydrogen bonds in various biomolecules. The document also includes figures and tables to illustrate the concepts presented.

What you will learn

  • What are the differences between strong and weak interactions in biomolecules?
  • What is hydrogen bonding and how does it affect the properties of water?
  • How do polar and nonpolar molecules interact with water?
  • How does the presence of hydrogen bonding affect the melting and boiling points of molecules?
  • What role does hydrogen bonding play in the structure and function of biomolecules?

Typology: Exercises

2021/2022

Uploaded on 09/27/2022

aeinstein
aeinstein 🇺🇸

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1
Water
Attractive force between water molecules
Slight tendency of water to ionize
Structure
Function
Biomolecules
important role
Hydrogen Bond
cohesive force
favor the extreme ordering of molecules
liquid at r.t. (water)
ice (crystalline water)
Polar
Nonpolar
dissolve in water readily
dissolve in water poorly, tend to cluster together
Biomolecules
Weak interaction
Hydrogen bond
Ionic interaction
Hydrophobic & lipophilic
Van der Waals interactions
collectively
Strong impact on structures
Hydrogen bonding gives water its unusual properties
Fig. 1 The crystal structure of water in ice
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Download Hydrogen Bonding in Water and Biomolecules: Properties and Interactions and more Exercises Chemistry in PDF only on Docsity!

Water

Attractive force between water molecules Slight tendency of water to ionize Structure Function Biomolecules important role Hydrogen Bond cohesive force favor the extreme ordering of molecules liquid at r.t. (water) ice (crystalline water) Polar Nonpolar dissolve in water readily dissolve in water poorly, tend to cluster together Biomolecules Weak interaction Hydrogen bond Ionic interaction Hydrophobic & lipophilic Van der Waals interactions collectively Strong impact on structures

Hydrogen bonding gives water its unusual properties

Fig. 1 The crystal structure of water in ice

In water, the electrostatic attraction between the oxygen atom of one water molecule and

the hydrogen of another water molecule, is called hydrogen bond. In ice, each water

molecule form four hydrogen bonds with its neighboring water molecules, however, in

liquid water, some crystal lattice have been broken, and water molecules move around, so

a water molecule forms averaged 3.4 hydrogen bonds with its neighboring water

molecules. The hydrogen bonds between water molecules and the crystal structure of

solid water is shown in Fig. 1.

Table 1. Comparison of m.p., b.p. and heat of vaporization of water with other molecules

molecule Melting point (m.p.) Boiling point(b.p.) Heat of vaporization

Water 0 100 2,

Ethanol - 117 78 854

Acetone - 95 56 523

Butane - 135 - 0.5 381

Butanol - 90 117 590

* m.p. and b.p. in unit of °C, heat of vaporization in unit of J/g

Normally, for organic compound, the higher the molecule weight, the higher the melting

point, and boiling point, however, in the presence of hydrogen bond, the case might be

different, for example, ethanol has higher b.p. and m.p. than butane.

Bond dissociation energy is the energy required to break a bond, the bond

dissociation energy of hydrogen bond is only 20 kJ/mol, thus is weak comparing to the

single bond of C-C, which is 348 kJ/mol.

Hydrogen bond in liquid water is under dynamic state, because the water molecules

move very fast, once it form hydrogen bond with its neighboring molecules, the hydrogen

bond will break after that particular molecule move to other place, and form another

hydrogen bond with its neighboring molecules again. The lifetime of each hydrogen bond

is 1× 10

  • 9

s.

Vaporization heat is the energy required for a molecule to change from its liquid state

to vaporous state. H 2 O (l) ---- H 2 O (g) ΔH = + 44.0 kJ/mol. This is the reason water

has its high boiling point.

Hydrogen bond does not exist in water molecule only, other molecules with polar

functional group such as hydroxyl, carboxyl acid, and amino group can form hydrogen

bonds within these molecules also. Because of the hydrogen bond, in nucleic acid,

thymine can only form pairs with adenine, and guanine can only form pairs with cytosine,

under this circumstance, the strongest hydrogen bond can be form, and the genetic code is

secured by this kind of complementary pairs.

Water interacts electrostatically with charged solutes

Fig. 3 Water dissolves many crystalline salts by hydrating their component ions.

Term: Hydrophilic

Hydrophobic

For the molecules with positive and negative charged pairs, can dissolved in water

readily, as water has much higher dielectric constant (ε, 78.5) than many other solvents.

For example, benzene (4.6), THF (20.0). The electrostatic interaction is determined by

three factors, as shown in equation.

When charged molecules dissolve in water, the molecules will be solvated by water,

and the separated positive charge and negative charge part of the molecules will be

stabilized by many surrounding water molecules. During the process of solvation, the

entropy is increased.

Nonpolar compounds dissolve in water poorly

For nonpolar gas, such as oxygen, nitrogen, carbon dioxide, dissolve very poorly in

water.

For other nonpolar molecules, such as benzene, hexane, cannot dissolve in water

either, and will form two phases.

Any molecules dissolve into water, will disturb the spatial orientation of water, and

break down some of the hydrogen bond between water molecules. For charged or polar

molecules, when they dissolve into water, although part of hydrogen bond is broken, the

charged or polar molecule can form hydrogen bond with water molecules, or can form

electrostatic interaction, and these new formed interaction will compensate the broken

hydrogen bond present originally in water. However, for nonpolar molecules, they are

hydrophobic. When they meet with water molecules, the water molecules are forced to

form a cage around these nonpolar molecules, and the partially lost hydrogen bond

cannot be compensated, in addition, entropy is reduced also, because water molecules

form ordered constitution.

When a molecule contains both hydrophilic (polar) part and hydrophobic (nonpolar)

part, this kind of molecules has intermediate solubility in water. When this kind of

molecules is called amphipathic (amphiphilic) compounds.

Fig 4. Long chain fatty acid is surrounded by a layer of water molecules, because of

lower solubility of alkyl chain in water

Fig. 6 Amphipathic molecules can form micelles in bilayers, like cellular plasma

membrane

Forming micelles has many applications in our daily life. For example, soap is a

kind of molecules (potassium or sodium salt of carboxylic acids, first generation), which

has polar part (carboxylic acid) and nonpolar part (hydrocarbon chain up to 17 carbon

atoms). Soap is used to clean many oil stains on clothes and so on.

Paint

Weak interactions are crucial to macromolecular structures and functions

All the biomolecules are composed of monomeric subunits, with many functional

groups such as amino, carbonyl, hydroxyl, ester, phosphate and so on. The four kinds of

weak interactions including hydrogen bond, ionic interaction, hydrophobic and lipophilic

interaction (HLI), and van der Waals interactions all exist within these molecules.

Although these interactions are very weak, comparing to covalent bond interaction, these

weak interaction collectively will control the interaction between the biomolecules. And

it is this kind of weak interactions between biomolecules, that the interactions between

the biomolecules are highly specific, selective and reversible. For example, the

interactions exist in the antibody-antigen, enzyme-substrate and ligand-receptor couples.

The conformation of biomolecules in aqueous solution will take the specific

conformation where all the weak-bonding possibilities can be maximized.

After binding of enzyme with ligand, both enzyme and ligand will release some

water molecules that associate with them originally, and the entropy is increased.

Solutes affect the colligative properties of aqueous solutions

Colligative property describes the property of solution of which the change is

depending on the number of particles (as molecules) and not on the nature of the

particles, this kind of property includes vapor pressure, boiling point, melting point

(freezing point), and osmotic pressure.

Dissolved solutes alter the colligative properties of aqueous solution by lowering

the effective concentration of water. (1.86 °C for m.p., 0.543 °C for b.p. at 1M solution).

Osmotic pressure is determined by Π = icRT, where ic is the osmolarity of the

solution. When more than one solute dissolves in the solution, the osmotic pressure is the

sum of all the contribution of each solutes.

Π = RT (i 1 c 1 + i 2 c 2 + …. + incn)

Many membranes allow all or none of the constituents of a solution to pass through;

only a few allow a selective flow. In classic demonstration of osmosis, a vertical tube

containing a solution of sugar, with its lower end closed off by a semipermeable

membrane, is placed in a container of water. As the water passes through the membrane

into the tube, the level of sugar solution in the tube rises visibly. A semipermeable

membrane that may be used for such a demonstration is the membrane found just inside

the shell of an egg, that is, the film that keeps the white of the egg from direct contact

with the shell.

Three mechanisms for cell to prevent the osmotic lysis:

Fig. 7 the proton hopping

(55.5 M)(Keq) = [H+][OH-] = Kw = (55.5 M)(1.8× 10 -^16 M) = 1.0 × 10 -^14 M^2

when water is neutral, where [H+] = [OH-], so, [H+] = √Kw =√ 1 × 10 -^14 M^2

[H+] = [OH-] = 10-^7 M

The pH scale designates the H

and OH

concentrations

The term pH is defined by the expression

Note: the ion product of water will vary with temperature, at 25°C, when water is neutral,

pH = 7. When temperature increases to around 100 °C, Kw = 10

  • 12

M

2

, at that

temperature, when water is neutral, pH = 6.

Weak acids and bases have characteristic dissociation constants

The weak acis and bases are those acids and bases that are ionized partially in dilute

aqueous solution. Acids are defined as proton donors, and bases are defined as proton

acceptors. Proton donor and its corresponding proton acceptor make up a conjugate acid-

base pair.

pKa = - log Ka

Fig. 8 The titration curve of acetic acid