The title of this experiment is patterns in molecular structure molecular structure journal, journal of molecular structure and shape and it really focuses on drawing and interpreting lewis structure molecular structure journal, journal of molecular structures which are molecular level representations of the structure molecular structure journal, journal of molecular structures of chemical compounds typically in an introductory chemistry course drawing. Lewis structure molecular structure journal, journal of molecular structures focuses on being given a chemical formula and drawing the structure molecular structure journal, journal of molecular structure from that but I’m actually not a big fan of this kind of problem because it’s not a very well formed and well understood quite frankly type of problem. It’s not easy for an introductory student to get a handle on it and in fact. It isn’t what expert chemists do which is the main thing that frustrates me about it. Actually the main thing that expert chemists do is interpret given structure molecular structure journal, journal of molecular structures and expand abbreviations. And that’s really where we focus our attention in this experiment in terms of drawing. Lewis structure molecular structure journal, journal of molecular structures rather than drawing a structure molecular structure journal, journal of molecular structure from scratch with absolutely no information. It’s much more common for a practicing chemist to have to expand a given sub structure molecular structure journal, journal of molecular structure so for example here. We see co2 co2. H embedded within this structure molecular structure journal, journal of molecular structure. This is a sub structure molecular structure journal, journal of molecular structure found within this molecule. This molecule by the way is the drug lyrica this is one of the top selling drugs in the United States at least as of this video recording and to really understand what’s going on with the co2 age group it’s important for us to be able to expand it into a full. Luud lewis structure molecular structure journal, journal of molecular structure to see how things are connected where the double and triple bonds are where the non-bonding lone pairs are that kind of thing. And that’s where the first part of this experiment focuses and so just to continue with. This example of lyrica is highlighted group here. This is called a carboxylic acid and we can take this group and really blow it up into its constituent atoms. One thing that we can tell immediately from this is that the carbon is connected to this atom here which is an implied carbon atom with two hydrogen’s connected to it. This carbon is connected to this carbon.
You can tell that because the c is adjacent to this line indicating a single bond so to begin to expand this structure molecular structure journal, journal of molecular structure. We can start by drawing that see just connected me a single line to the rest of the structure molecular structure journal, journal of molecular structure which we could represent just with a squiggly line here. Oh in terms of the two oxygens in the remaining hydrogen. It’s not actually entirely clear how we expand this. We could do this a couple of different ways by connecting the two oxygens together and then putting a hydrogen on the end or we could imagine putting one oxygen here and one oxygen here in connecting hydrogen this way and if we think through how we would have to add additional electrons here and the fact that we have no atoms left we would realize that a big problem comes in at this carbon which is violating the octet rule in the structure molecular structure journal, journal of molecular structure drawn. This way and this tells us that this first connectivity that we drew is not the connectivity of this group. These are decisions that you’ll have to make as you work through this experiment and there are important decisions to make. There are decisions that practicing chemists. Make all the time when interpreting abbreviations so. Let’s assume that this is the so called. Sigma skeleton or skeletal structure molecular structure journal, journal of molecular structure of this functional group. And now we have to figure out how to add electrons onto this we could store it. For example by adding lone pairs to this oxygen atom to satisfy the octet rule and lone pairs to this oxygen to satisfy the octet rule. This looks good except this carbon is violating the octet rule and we have formal charges shoes since this carbon is formally posited in this oxygen formally negative to fix this situation. We can simply erase this nonbonding pair of electrons on oxygen and create a double bond here. Now everything’s looking good. Everything’s satisfying the octet rule. So in the first part of the experiment you’ll work through a number of these abbreviated structure molecular structure journal, journal of molecular structures found primarily within molecules of pharmaceutical interest and expand them into full doiis structure molecular structure journal, journal of molecular structures containing multiple bonds and lone pairs.
Like this in the second part of the experiment you’ll begin interpreting these expanded lewis structure molecular structure journal, journal of molecular structures to draw interesting conclusions or recognize interesting things about the atoms involved in the structure molecular structure journal, journal of molecular structure and the first thing we’ll look at is the geometry from a given. Lewis structure molecular structure journal, journal of molecular structure through the use of Vesper theory. We can infer the arrangements of electrons in space around each atom and the molecular geometry that results the basic idea behind this the basic starting point is to first focus our attention on one of the atoms and here in the carboxylic acid functional group. We’re gonna focus on the carbon which is kind of the most central of the atoms and we want to identify the number of so-called electron pair domains in this thing and electron pair. Domains has a variety of different names electron pair domains electron domains charge clouds. These are regions of space. Where electrons reside kind of common regions of space for different groups of electrons and each double or triple bond counts as a single domain as do pairs of nonbonding electrons and single bonds. And so if we focus on this carbon you can see that we have 1 2 3 electron pair domains around that carbon by applying. Vesper Theory we can go immediately from that number of electron pair domains to what I like to call the electron group arrangement and this is essentially the arrangement of the electron pair domains around the central atom in space. This is directly implied by the number of electron pair domains based on the Vesper principle and here the electron group arrangement based on three domains is trigonal planar. The electron group arrangement doesn’t really pay attention to whether the electron domain is a bond or a lone pair when we start paying attention to that or we start just asking where the atoms located in space kind of ignoring the positions of the lone pairs on some level.
We are asking a question now about the molecular geometry about that central atom and so the idea behind molecular geometry really is just where are the atoms in space based on the electron group arrangement and the number of non-bonding lone pairs linked to the central atom. Now this carbon has no non-bonding lone pairs linked to it from that. We can immediately conclude that its molecular. Geometry is also trigonal planar in the second part of this experiment you’ll identify the number electron-pair domains bonding and non-bonding and then infer the electron group arrangements and molecular geometries for these sub structure molecular structure journal, journal of molecular structures that we drew in. Part A in the next stage of the experiment. We’ll determine whether the functional group is polar or nonpolar and get a rough idea for the direction of the dipole moment if the structure molecular structure journal, journal of molecular structure is polar recalled that by polarity we mean a situation within a molecule in which one side one end of the molecule has net positive charge due to a lack of electrons and the other end of the molecule has a net negative charge due to an excess of electrons. This sets up a situation with partial positive charge on one end and partial negative charge on the other end and we can represent that using either these Delta plus and Delta minus symbols or using an arrow with a cross on one end to indicate the positively charged in this is the so-called dipole vector in Part C of the experiment. We’re going to again interpret our full. Lewis structure molecular structure journal, journal of molecular structure from Part. A this time using the full Lewis structure molecular structure journal, journal of molecular structure to determine whether the functional group is polar or nonpolar. And we’re gonna do that. By first analyzing the bonds dipoles so a very systematic way to analyze polarity involves looking at the electronegativities of linked atoms and deciding where the electrons are within each pair of bonded atoms so for example we could look at carbon and oxygen and the carbon oxygen double bond and ask which of these two atoms is more electronegative.
Well oxygen being more electronegative will tend to pull electrons towards itself or tend to hold on to a larger electron density and this implies that the carbon oxygen bond is polarized toward oxygen with negative charge on the oxygen end and positive charge on the carbon end and in fact the same is true of the other carbon oxygen bond the carbon oxygen single bond is polarized toward oxygen with the positive end at carbon and the negative end and oxygen. Finally we can look at the oxygen hydrogen bond and again ask about electronegativity which is more electronegative. Oxygen or hydrogen while oxygen is quite a bit more electronegative than hydrogen. And so this bond will be polarized toward the oxygen from these three bonds dipole vectors we can get a sense of the overall dipole vector just by adding the bonds dipoles and. Let’s actually draw that overall dipole vector and purple so that we can distinguish it from the individual bond dipole vectors so roughly speaking. If we were to add these three vectors together we would get a resultant vector that’s somewhat in this general direction and this purple vector roughly speaking represents the overall polarity of the functional group because of the length of that vector the fact that it is definitely nonzero due to these strong bond. Dipoles this tells us that the functional group overall is most definitely polar and one last thing. I’ll mention about this. Determining polarity is that we’ve essentially ignored the influence of whatever. This functional group is attached to because this is typically carbon which is more or less electro neutral in most cases if a strongly electronegative atom like oxygen or nitrogen is connected. Here it may be worth considering but in this case where we had just carbon connected to carbon we could safely ignore it so in. Part C of the experiment you’ll determine bond dipoles and an overall dipole vector roughly speaking for each functional group that we drew in Part A and you’ll determine whether the functional groups overall are polar or nonpolar a very important determination for reasoning about properties that are based on whether the molecule as a whole is polar or nonpolar finally in Part D of the experiment will explore the hybridization of the central atom within each functional group and so as we did previously when looking at the geometry.
We’re going to focus our attention here. On the central carbon atom now hybridization you should recall is an orbital concept involving a modified or hybrid set of atomic orbitals used to make bonds to the atoms that surround the central atom hybridization is a way of describing the orbital overlap and valence bond. Theory turns that leads to the bonds that we see in the Lewis structure molecular structure journal, journal of molecular structure because the central adamant only means enough hybrid atomic orbitals to hold the electrons in the electron pair domains. That surround it. The number of electron pair domains can be used to directly reason about the hybridization in most cases. And that’s certainly the case here. And in all the functional groups you’ll see in this experiment we previously determined that this carbon atom is surrounded by three electron pair domains. This means that that carbon atom is associated with three hybrid orbitals in essence. One is involved in this bond to the doubly bonded. Oxygen one is involved in this bond to the singly bonded. Oxygen and what is involved to the bond to the carbon atom. That’s kind of off-screen right here. So we need three hybrid orbitals or hybrid atomic orbitals here at this point. We apply the idea that when hybridizing the number of atomic orbitals n is equal to the number of hybrid atomic orbitals out and the atomic orbitals here refers to the valence atomic orbitals. Which are involved in bonding and so carbon. Being in the second row of the periodic table has valence orbitals that include the two as 2px 2py and 2pz atomic orbitals because we only need 3 hybrid atomic orbitals to form these 3 bonds or 3 electron pair domains.
If you like we only need to use the 2s and two of the 2p orbitals. Let’s say the 2px and 2py. It actually doesn’t matter which two we choose to form the hybrids. This means that the hybrids are constructed by mixing an s and 2 P orbitals and we represent that using s P and a superscript 2 in conclusion we say that the hybridization of this carbon atom within this structure molecular structure journal, journal of molecular structure with 3 electron pair domains associated with it is sp2 each of the hybrids involved in a sigma bond to oxygen oxygen and carbon can be called an sp2 hybrid. So in the last part of the experiment you’ll work out the hybridization of the central atom in each of those sub structure molecular structure journal, journal of molecular structures that we drew in part a this is an important interpreted result of the full Lewis structure molecular structure journal, journal of molecular structure hybridization gives us insight into the nature of electrons around the central atom their energies their reactivity and their locations in space.
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