Support Materials:

•  Goal:
  To define and characterize the properties of small molecules, continued...
   
•  Objectives:
  Students will be able to...
   
  • use their calculator to solve pH = - log₁₀[H⁺]. Click here to review logarithms and to take a practice quiz.
  • identify whether a functional group is an acid (H⁺ donor) or a base (H⁺ acceptor).
    Comprehension: The charge on a N or O atom (+1, -1, or 0) is determined by whether H⁺ is bound to that atom or not.
    N compounds are typically neutral (base) or positive (acid).
    O compounds are typically neutral (acid) or negative (base).
    Remember: Not all O- or N-containing compounds bind and lose protons. Exceptions include amides (found, for example, in DEET - N,N-diethyl-m-toluamide), esters, and alcohols.
    Examples of acid / base compounds:
    Coniine, the toxin in hemlock oil, has an amine function.
    Dettol, a skin-safe disinfectant, has a hydroxyl group. Context is important: The hydroxyl group in Dettol can lose a proton because it is bonded to an aromatic carbon group (a benzene ring). The hydroxyl group in an alcohol, such as ethanol, cannot lose a proton because it is bonded to an aliphatic carbon group (an ethyl group).
    
    Practice problems given in class:
    Methyl jasmonate: Contains three functional groups: a ketone, an alkene (olefin), and an ester. Students had to circle these groups, given the structural formula. None of these groups have acid / base properties.
    
    Applications:
    Charge has two important biological effects: it increases solubility and decreases membrane permeability. Examples:
    1) Urushiol, the active ingredient in poison ivy, is a mixture of catechol compounds. (The antioxidant 3,4-dihydroxybenzoic acid - Introduction - is also an example of a catechol). Catechols can be neutral (acid) or negative (base). The base form is more soluble in water. Use a basic solution (pH >> 7) to remove urushiols from the skin.
    2) Nicotine, the addictive ingredient in tobacco smoke, can be neutral (base) or positive (acid). The addition of ammonia to tobacco smoke will increase pH and make more nicotine base, by shifting the following reaction to the right:
    nicotineH⁺ (acid)   ⇌   nicotine (base)  +   H⁺
    Increasing the fraction of base nicotine will increase its addictive potential. More base nicotine, which is neutral, will increase its rate of diffusion across cell membranes and, ultimately, its rate of entry into the brain.
    3) Aspirin: See textbook: problem 35, p. 56).
     
    • list and identify examples of intermolecular forces.
      Application: Polyamines: This type of compound is found in some spider venoms. The structure that I showed in class has a single amide group and three amine groups. The amine nitrogens can acquire a + charge when they bind a proton. The pK_a values for these amine groups are >> 7, which means that they'll be bound with a proton at physiological pH. This creates a "patch" of positive charge that can interact with nerve cell proteins that have a complementary "patch" of negative charge. This charge-charge interaction (opposite charges attract) inhibits the nerve cell protein, leading to paralysis.
      
       
  • to understand Le Chatelier's effect:
    Application: Effect of hyperventilation and hypoventilation on blood pH - textbook problem 34, p.56.
    
     

Other information:

•  Water is the solvent of life. Despite its simple structure, water's chemical properties are still being researched. Many of water's unusual properties are due to hydrogen bonding interactions, a type of intermolecular force. Click here to find out more about the structure of water, hydrogen bonding, and why water is an excellent solvent. A summary of noncovalent (intermolecular) forces that are important in biochemistry can be found here. (From Interactive Concepts in Biochemistry by Rodney Boyer).
  Also: textbook problem 7, p.55, is on how to recognize the ingredients to make a hydrogen bond. The effect of H-bonding can be seen in a series of small molecules of similar molecular weight - companion guide problem 3, p. 24. The strength of a bond, whether it's covalent or noncovalent, can be measured in kJ / mol (kJ, or kilojoule, is a measure of potential energy). Covalent bonds are typically 350 - 450 kJ / mol. Noncovalent bonds are much weaker. Problem 7 in the companion guide gets you thinking about this.
   
•  Many important molecules, such as drugs, come in two flavors: charged and neutral. Here's a link that examines one of the practical implications of this molecular property.
  Blood-brain barrier: http://www.soton.ac.uk/~jrc3/chudler/bbb.html.