Concept: Shape is important to
determining how a molecule functions, and interacts with other
molecules.
These images are from quizzes taken in Organic Chemistry I, and Organic Chemistry II.
The first is a quiz question for which I had to rank several alkanes according to boiling point, from highest to lowest. Shape is important in determining which boiling point corresponds with which molecule, because the length of the chain, and the number of substituents determines how closely the molecules pack, thus how much surface area comes in contact with the other molecules, thus how much intermolecular forces come into play. The more IMF, the harder it is to break them apart, thus the higher the temperature needs to be to have enough energy available to break the molecules apart from each other.
This second question
addresses the importance of shape in relationship to the function of
polyethylene. In this case, while both are long chain
molecules, one type is more crystalline in structure (the unbranched),
while one is less crystalline in structure (the branched). The
difference causes a difference in rigidity in the resulting material,
so that one would be good for beach balls (less crystalline, more
branched), and one would be good for beach chairs (more crystalline,
not branched).
This is an image of a portion of a PIM that I completed for Environmental Chemistry. For this PIM, we were asked to research a specific greenhouse gas, and I was assigned methane. All of the greenhouse gasses contribute to the warming of Earth by taking heat tht is reflected off of the Earth's surface, and bouncing it back towards the Earth's surface, rather than releasing it into space. For all of the greenhouse gasses, the reason this occurs is due to each molecule's shape. In the case of methane, as you can see below, the high degree of symmetry in the structure is what causes methane to capture and release the IR back towards the Earth's surface. In fact, while many people know that carbon dioxide is the most prevalent of the greenhouse gasses, in actuality, methane is the most powerful of the greenhouse gasses, because it is able to bend and stretch in so many more ways than carbon dioxide.
These images are from quizzes
taken in Biochemistry.
The first is a question that addresses the importance of the structure of the peptide bond in a protein. In this case, the rigidity of the bond, which causes a planar shape, forces the whole bond to rotate as a plane. This introduces steric hindrance as a factor, since the adjacent R-groups then influence the bond to rotate at particular angles to reduce unfavorable sterics.
The first is a question that addresses the importance of the structure of the peptide bond in a protein. In this case, the rigidity of the bond, which causes a planar shape, forces the whole bond to rotate as a plane. This introduces steric hindrance as a factor, since the adjacent R-groups then influence the bond to rotate at particular angles to reduce unfavorable sterics.
The second question addresses the shape-specific
function of enzymes. It addresses the fact that we cannot
digest cellulose, because it has beta 1,4 glycosidic bonds, which are
axial, and the enzyme alpha-amylase only cleaves alpha-1,4 glycosidic
bonds, which are equatorial.
These are images from my thesis, which was about pectin. Pectin's function is wholly related to the shape of the molecules in its different forms.
This first image is from the portion of the thesis that discusses the alternating beta 1,4 and beta 1,2 linkages between the sugars in one type of pectin chain, called Rhamnogalacturonan. These alternating links cause kinking in the sugar chains, which changes the way that particular type of pectin gels.
This second image is from the section that discusses pectin's use as a hydrocolloid. The long chains create pockets. The interaction between the chains can be changed through manipulating several factors, including the shape of the pecitn molecule itself.
This third image is from a section that discusses medical uses of pectin. Studies show that the shape of the pectin molecule is able to grab onto a particular type of cancer cell. The cancer cells then pass out of the system, attached to the pectin.
This is only a small sample of the instances when I learned that shape was important to function and interaction with other molecules. There are several different scenarios that can affect function and interaction, but all of them come down, ultimately to molecular shape.
In some cases, it is uniformity, or lack-thereof in structure of the molecule that helps to determine its intermolecular interactions, as seen in situations represented by the two examples in artifact #1, where I discuss the effect of branching and substituents on rigidity and boiling points, and the second example in artifact #4, where I discuss the creation of pockets from the intermolecular bonding in pectin chains. Regularity in pattern, without branching, allows closer nesting in intermolecular bonding, particularly with longer chain molecules. The addition of substituents introduces branching that disrupts the regularity, and interferes with the ability for the molecules to nest closely, thus reducing the strength of the intermolecular bonds. In cases represented by the first example in artifact #1, the result is changes in boiling point. In cases represented by the second example in artifact #1, the result is a change in the rigidity of the resulting material. In cases represented by the second example in artifact #4, the result is pockets created within one molecule when branched portions are prohibited from bonding due to steric hindrance, and smooth, unbranched portions are able to experience strong intermolecular forces. These three results can be seen as analagous, because all three are determined by the strength of the intermolecular bonds, and as stated previously, the intermolecular bonds are affected by the addition of branching and/or substiuents. Steric hindrance is also a factor in situations represented by the first example in artifact #3 and the first example in artifact #4. These represent situations in which molecules are forced into particular shapes, because of steric hindrance causing one conformation to have lower steric hindrance, and thus lower potential energy, and thus higher stability than other conformations with higher steric hindrance, potential energy, and thus lower stability. Potential energy is also important in cases, such as those represented by artifact #2. The shape of the molecule determines the amount of potential energy that it can absorb and convert into heat/kinetic energy. The greater the symmetry, the greater the amount of energy can be absorbed and released through the different vibrational actions as heat/kinetic energy. Finally, IMF, steric hindrance, and energy conversion in all molecules, such as those represented by the second example in artifact #3 and the third example in in artifact #4 determine the actual function of the molecule. When the strength/weakness of intermolecular forces, the steric hindrance increases/decreases from various bonding/interactions, and the amount of energy absorbed and used/converted is taken into account, what an individual molecule can do becomes very specific, as determined by its shape, size and substituents.