Lecture 10: Shapes of Molecules

Lecture 10: Shapes of Molecules Summary This lecture focused on the Valence Shell Electron Pair Repulsion (VSEPR) model. This model allows us to predict the shapes of molecules—a precursor to more fully understanding their properties. VSEPR is based around electron repulsion, and gives the most stable structures as those that minimize these repulsions. To find the VSEPR representation of a molecule, follow these steps: 1. Write Lewis structure 2. Classify each electron pair as bonding or nonbonding 3. Maximize separation between domains 4. Give more space to non-bonding domains and to bonding domains with higher bond order A bonding pair (BP) of electrons is any two electrons that take part in a bond. A double bond is made up of 2 BPs, and a triple bond is made up of 3 BPs. A lone pair (LP) of electrons is any two electrons that are not part of a bond. The strength of repulsion between electron pairs, in ascending order, goes as follows: BP-BP, BP-LP, LP-LP. Also, the repulsion of a single BP is less than that of 2 BPs or 3 BPs. VSEPR Geometries by Boundless Chemistry. License: CC BY-SA. This content is excluded from our Creative Commons license. For information, see https://ocw.mit.edu/fairuse. 4 Why this matters The average human can discriminate between 4,000 and 10,000 different odors. (Before we get excited about how awesome that is, consider that a dog can smell between 10 and 100 thousand times better than a human!). But what is smell, from a chemistry perspective? Taste and smell are related, and thinking about what’s behind them goes back to the ancient Greeks. None other than our friend Democritus (atomism!) speculated that the taste Diagrams of tongue, taste of a substance was due to the shape of its component papilla and taste bud removed particles. He thought that acidic particles would be due to copyright restrictions. sharp, since they felt like they attacked your mouth, while sweet stuff was made of nice cuddly soft shapes. While his reasoning was quite simple, the idea that taste and smell were governed by shape was amazingly prescient. Fast forward 2500 years and we now know that the ability to taste and smell works through “receptor sites” in the tongue and nose. Here’s the tongue broken down, showing the receptor site on the right, and below that is a larger view of receptor site with various parts labeled. Note that the receptor site is also what we call a taste bud. Signals that get sent from this receptor site to the brain through the nerve fibers determine what you taste, Labeled diagram of a taste and the signal is deeply dependent not just on the bud removed due to copyright restrictions. composition of the molecule itself, but also on its shape. Take a look at the two molecules below, glucose which tastes sweet, and quinine which tastes bitter. Their chemistries are different and the way the chemistry of the molecule bonds to the sensory cell is crucial, but the way the shape fits into the pore itself and impacts the orientation of the molecule on the sensory cell can be equally important. If we didn’t know the shapes of these molecules, we’d write them out as simple 2D Lewis structures, but it’s those 3D shapes that you see in the figure that distinguish their tastes! In the case of the carvone molecule, or C10 H14 O, we have an even more striking example of the role of shape on smell. This molecule forms two mirror images, denoted R and S in the figure below. The R form smells like spearmint while the S form smells like caraway seeds. Same exact chemistry, different shape, different smell. Many molecules can take on two forms like this with mirror symmetry but that aren’t the same, and such pairs are called enantiomers. Actually, beyond molecules, enan5 Glucose and quinine molecules © source unknown. All rights reserved. This content is excluded from our Creative Commons license. For information, see https://ocw.mit.edu/fairuse. tiomers can be anything. Your hands, for example, are enantiomers. If you hold them up facing one another you’ll see they have mirror symmetry, and if you try to rotate one around the other you’ll see you can’t superimpose them. For this reason, the property of havSpearmint and caraway seed ing mirror symmetry but not being superimposable is called molecules removed due to handedness, or chirality. The fact that the two enantiomers copyright restrictions. are perceived as smelling different shows that those receptor cells must contain chiral groups, allowing them to respond more strongly to one enantiomer than to the other. Thus, both for the molecule being smelled and for the molecules used to do the smelling, molecular shape holds the key! Why this employs It’s about time we talk about enzymes. These are molecules, often proteins, folded into a specific (and complicated!) shape, that speed up chemical reactions in your body. Enzymes are absolutely essential for so many crucial functions of our body, including respiration, digestion, muscle and nerve function, and many more. In digestion, the role of an enzyme molecule can speed up a needed reaction by a factor of a million times! That lets you digest your dinner in hours rather than, well, a thousand years. Enzymes work by binding to molecules in a specific way, and you may have already guessed that shape is crucial. In fact, way back in 1894 it was the Nobel Laureate Emil Fischer who came "Lock and Key" model synthesis diagram up with the ”lock and key” model to explain removed due to copyright restrictions. how enzymes work. The idea in this model is pretty much how it sounds: an enzyme’s active site is a specific shape, and only the substrate will fit into it, like a lock and key. Here’s a cartoon to illustrate how the enzyme perfectly fits, because of its shape, into a substrate, giving the substrate the power to make reactions happen faster (also called catalysis). The model has been updated over the past 100 years, for example to include the fact that the substrate and enzyme itself are dynamic and can change shape when they interact, or that the effects of the surrounding solvent are important, but the key feature that shape is crucial remains the foundational principle upon which enzymes operate. 6 As you may have noticed by just going to the grocery store, there’s a big market for new foods with new enzymes. There are so many enzymes involved in digestion, like lipases that help digest fats in the gut. amylase helps change starches into sugars. Maltase breaks the sugar maltose into glucose (it’s in potatoes, pasta, and beer, for example). Trypsin breaks proteins down into amino acids. Lactase breaks down lactose, the sugar in milk, into glucose and galactose, and on and on. Which brings me to the job market: here, specifically the food industry. The synthesis and use of new enzymes in the preparation of food have seen tremendous growth not only in digestion but also in the taste and texture of the food, as well as possible economic benefits. There are many jobs related to food science (check out this article in the NatureJobs pages, which is a cool site in case you haven’t seen it: https : //www.nature.com/naturejobs/science/articles/10.1038/nj7422 − 149a?W T.eci d = N AT U REjobs − 20121106). But jobs related to enzymes having to do with food also relate to the future of humanity itself. How will we feed our population in the future? Will all protein need to be plant-based? Or will we eat insect-meat? Or meat grown in a lab? Will food be 3D-printed, and will it be served by robots? All of these topics have recently received vast amounts of attention, research funding, led to start-ups, and a lot of interest from larger companies, and all of that spells jobs. Specifically, jobs involving knowledge about enzymes, which in the end only function because of their shape (VSEPR!). Example Problems 1. Draw the Lewis structure of H2 N-SH and determine the VSEPR geometry around (a) the nitrogen atom, and (b) the sulfur atom. 2. Determine the VSPER geometry for each of the following and predict whether each will be polar or nonpolar a) BF3 b) F OF c) CCl4 7 Solutions 1. a) Geometry around the nitrogen atom: trigonal pyramidal b) Geometry around the sulfur atom: bent 2. a) BF3 : Difference in N-F electronegativity: polar bonds. Trigonal planar: dipoles cancel! Nonpolar b) F OF : Difference in O-F electronegativity: dipole moment: polar c) CCl4 : Difference in C-Cl electronegativity: dipole moments; tetrahedral structure: cancel out, so nonpolar! 8 Example 2a © source unknown. All rights reserved. This content is excluded from our Creative Commons license. For information, see https://ocw.mit.edu/fairuse.