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Sulfa Drugs Related To Organic MSM

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Lecture 5
Shapes of Covalent Compounds

Tanya B. To, Ph. D.
All rights reserved 2001

Note:  This lecture covers section 7 in chapter 5.  Omit sections 8 & 9 of Chapter 5.

        In this lesson you will learn how to determine the shape of simple covalent molecules.  Here is a story to illustrate the importance of knowing the shapes of molecules.  Chemical reactions in your body would be very slow if there were no enzymes present.  Enzymes are proteins that serve to speed chemical reactions. Substances that increase the rates of chemical reactions are called catalysts.  You probably have heard of catalytic converter in your car that works to reduce the concentrations of pollutants in the exhaust fume.  Scientists hypothesized that enzymes work via a lock-and-key mechanism; that is by specific fitting or shape.  If a key has a different shape than it should, then it would fit in the lock.  The active site of each enzyme has a specific shape that only its substrate can fit (see Figure  below).  A substrate is a molecule that the enzyme works on.

        The development of sulfa drugs, a class of antibiotics, came from the discovery of the shape of a substance that bacteria use to make folic acid.  Folic acid is a coenzyme in a number of biosynthetic processes, such as synthesizing amino acids for proteins and making of nucleotides for RNA or  DNA.  Human obtain folic acid from the diet, while bacteria synthesize folic acid.   Scientists synthesized a compound (sulfa drug) that has similar shape to the one that bacteria use to make folic acid.  Both compounds that could fit in the active site of the bacterial enzyme. When the bacteria are exposed to sulfa drug, they cannot tell the difference and use our compound to make a molecule that has a folic acid type of structure but is not exactly the same. The fake folic acid does not work and prevents the bacteria from making their amino acids and nucleotides.  Consequently, the  bacteria die, and thus preventing our wounds to become  infected.  One of the synthetic compounds is called sulfanilamide (see structure on  page 634 in the text by Stoker or page 360 in the text by McMurray).  This compound is toxic to humans, but its derivatives are not and are ones used to treat infections.  These compounds are called sulfa drugs.  The discovery of sulfa drugs helped saved thousands of lives in World War I from dying of infectious wounds.

The simple difference to understand here is that sulfa drugs are anti-biotic -- that means they are against life -- they are one of that major class of medical drugs, antibiotics -- used to fight infections.  "Fighting infection" is a concept related to germs being the cause of an infection.  MSM is NOT an anti-biotic.

When a germ causes an infection, then killing that germ is the treatment.  Sulfa drugs were among the first of the now large number of antibiotics.

MSM is NOT an antibiotic -- it promotes life and living things, does not kill any living thing.  So, MSM is what is called a pro-biotic.  Traditionally a probiotic is a living organism which is useful and needed by the body -- such as acidophilus  -- most probiotics are used in the stomach and intestine and many of them involve the introduction of a small number of these living organisms which then multiply -- to the great benefit of the body.  Vitamin C is often called a probiotic since Vitamin C is so useful in the body.  MSM, finally, can be called a probiotic in this sense.  It favors life and helps all the pro-life organisms in the body survive and flourish better.  Click here for more information about Antibiotics and Probiotics.

      In covalent compounds the atoms do not form separate ions but are held together by the sharing of electrons. Chemists called a shared electron pair a bond and symbolize it by drawing a line (-)  between two atoms. A shared electron pair is also called a bonding pair, while an unshared pair (:) is called a lone pair.  For example, an oxygen molecule can be represented as any of the following:

                        ..    ..                             ..   ..
O₂      or         :O::O:           or           :O=O:

Each O has 2 bonds and 2 lone pairs.  A short-hand representation of the oxygen molecule is O=O; it is used to show only the bonding pairs and therefore the lone pairs are omited.   Since  you are learning shapes, we will NOT use the short-hand representations until after exam 1.   The number and type of bonds that each non-metallic element form in covalent compounds  are summarized in Table 5.1.
 

Table 5.1.  Elements and their bonds
 

Notes:  (1) The short -  or the long | represent a single bond, eventhough they should be equal in length.  This is the best I could do for now, until I find a better software.  (2) You can draw the lone pairs and bonds to occupy the 4 sides of a symbol in any order, as long as they add up to 8 electrons total, except for H.  for example, any of these represents the same thing:
                                          ..                           ..                        ..                    ||                           ..
                                       =S:       or              : S=         or      =S           or    :S:          or          :S
                                                                                                 ..                                                ||

The more symmetric arrangements are usually shown in text books.

     The shape of  a molecule is determined by the number of electron groups attached to the central atom and the number of atoms attached to the central atom. Each electron group is a single bond (-), a double bond (=), a triple bond, or a lone pair   Use Table 1 to determine the shapes of molecules from structural formulas.  The chemical formulas that you have been using, for example CCl₄, is called molecular formulas because they show what the molecule is made of.  When a formula shows how the atoms are attached to the central atom, it is called a structural formula because it shows the structure of the molecule.  Examples of molecular formulas and structural formulas are shown in Table 1.   Molecular formulas of covalent compounds are generally written in this order:  first C, second H, and last all other elements.  See examples in Table 5.2.  You will be given the structural formulas and asked to determine the shapes and write molecular formulas.
 

Table 5.2.   Rules for Molecular Shapes from structural formulas.
 

No. of electron groups on the central atoms (single, double, triple bond or a lone pair)	No. atoms attached  to the central atom	Molecular Shape of the central atom	Example Molecular Formula	Example Structural Formula	3-D shape
4	4	tetrahedral	CCl4 the central atom C is surrounded by  4 single bonds  = 4 electron groups	..          :Cl:   ..      |      .. :Cl -  C - Cl:   ..      |      ..         :Cl:           ..
4	3	pyramidal	NF3 the central atom N is surrounded by 1 lone pair and 3 single bonds = 4 electron groups	..    ..    .. :F - N - F:         |       :F:        ..
4	2	bent	H2O the central atom O is surrounded by 2 single bonds and 2 lone pairs =  4 electron groups	..   H-O-H        ..
3	3	planar triangular	COCl2 the central atom C  is surrounded by 2 single bonds and  1 double bond =  3 electron groups	:O:   ..     ||     .. :Cl - C - Cl :   ..           ..
3	2	bent	HNO the central atom N has 1 single bond, 1 double bond, and 1 lone pair =  3 electron groups	..   .. H-N=O :
2	2	linear	CO2 the central atom C  is surrounded by  2 double bonds =  2 electron groups	..        .. O=C=O  ..        ..

        All diatomic molecules are linear, because two atoms make a straight line.  For example, the shape of H-H is linear.

       To illustrate the use of Table 5.2, let's determine the shape for the following structural formula:
                                                                                                        ..   ..
                                                                                                   H-N=O:

The central atom is N.  It has 1 lone pair, 1 single bond, and 1 double bond, which add up to a total of 3 electron groups.  It is attached to 2 atoms (H and O).  Find the row in Table 5.2  that contains 3 electron groups and 2 atoms attached;  you will find that the shape of HNO is bent.

    Molecular shape dictates many physical properties and chemical specificity. For example, a water (H₂O) molecule has a bent shape because its central atom (O) has 4 electron groups (2 lone pairs &  2 single bonds) and 2 atoms attached.  The bent structure results in a net polarity, which makes water a polar molecule. Carbon dioxide (CO₂) molecule, on the other hand, has a linear shape because its central atom (C) has 2 electron groups (zero lone pairs and 2 double bonds) and 2 atoms attached.  Carbon dioxide Lewis structure is :O=C=O:    The linear structure results in zero net polarity and thus makes CO₂ a non-polar molecule.  You are not responsible for determining the polarity of molecules.  When you need polarity information, I will tell you if a compound is polar or nonpolar.

           Since water is polar, it can only dissolve polar and soluble ionic substances, such as, salt and ethyl alcohol. Similarly, the non-polar CO₂ can only be dissolved in non-polar solvent, such as carbon tetrachloride (CCl₄).  Both gasoline and oil are non-polar substances and, thus, do not mix with water, a polar substance. This observation gives rise to the general rule for solubility "like dissolves like."  This general rule finds many applications. The delivery method of some drug depends on its polarity.  If a drug is polar, this means it will be soluble in water and can be taken orally or injected into the blood stream.  If a drug is non-polar, this means it is fat-soluble and may be injected in the fatty tissue.  The polarity of a compound  also has a dramatic effect on its toxicity. For example, fat-soluble vitamins or pollutants can accumulate in fatty tissues and can reach dangerously high concentrations, while water-soluble substances are excreted in urine. For this reason, water-soluble vitamins are not as toxic as fat-soluble ones.

The End!
 

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