Dry Lab

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Coastal Alabama Community College - Bay Minette *

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111

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Chemistry

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Dec 6, 2023

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docx

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Dry Lab – Computer Models of Chemical Structures For this dry lab you will be using a website to help you visualize the very abstract concepts of chemical structures, their shapes (VSEPR theory) and polarity. You will work through the directions step by step to draw various molecules, take some measurements and come to some conclusions on the trends you observe. Introduction Drawing a molecule on a piece of paper can help you visualize what it might look like, but it can only go so far. Molecules are three-dimensional objects. That is sometimes hard to keep in mind when you simply draw them on paper. It doesn’t help that molecules are so small that we can’t see them even in a standard microscope. There are many computer programs available to help visualize molecules. Many are very advanced programs that will do calculations to determine the best structure for a molecule. These programs have advanced significantly over the last few years, and they have also been simplified and made to be user friendly for all people. You will be using several aspects of the online tools called “CheMagic.” These tools were developed at Illinois State University. The tools are pretty easy to use, and the directions provided in the lab will walk you step by step through how to complete the lab. All of the concepts covered in this lab are discussed in chapters 8 and 9 of your textbook. As a quick review, here are some terms that will be helpful to recall: Lewis structures : method of showing the location of the atoms and electrons in an atom or molecule. If you need a refresher on how to draw Lewis structures, see your text book. Bonding electrons : electrons that are involved in a covalent bond between two atoms. Lone pairs : two paired electrons that are not involved in a bond. Single bond : sharing of two electrons between two atoms. Double bond : sharing of four electrons between two atoms. Triple bond : sharing of six electrons between two atoms. Electronegativity : the degree to which an atom attracts electrons. Dipole : difference in electronegativity between two atoms causing an unequal sharing of electrons and therefore a partial positive and partial negative charge. Hydrogen bonding : attractive force between two molecules that contain H-N, H-O, or H-F bonds. VSEPR theory : method of determining molecular shape based on the idea that all electron groups want to be as far apart from each other as possible.

Here are a few new, but closely related terms you will explore in this lab: Bond length : the distance between the centers of two atoms involved in a bond. Bond angle : the angle formed between three consecutive atoms in a molecule. Bond order : description of the number of bonds between a pair of atoms. A single bond has a bond order of 1; a double bond had a bond order of 2; and a triple bond has a bond order of 3. Reality Check While you will be doing some simple visualizations of some very basic molecules, computer programs are frequently used in areas such as drug design. Before attempting to make a new drug molecule, Computational Chemists will use computer programs to optimize the target structure. This will provide them with many details about the proposed molecule and help them determine if it is worth spending the time and money to try to synthesize it in the laboratory. This is just one example. What other areas do you think it would be useful to know what a molecule looks like and/or some of its properties before synthesizing it?  Answer the questions in the procedure as you go. They are indicated by italics. Exploring the CheMagic Tools with Chloromethane 1. Using a web browser (I know Chrome and Firefox work well, but others likely do, too), open up the “CheMagic Model Kit.” It can be found at https://chemagic.org/molecules/amini.html? pid=off 2. When you first open the Model Kit you will see there are three sections. There is a blue box in the middle. This is where you will see the model in 3D. I will call this the “ 3D Box .” This program uses the standard colors for atoms. a. What is the color that represents carbon? Grey b. What color is hydrogen? WHite 3. The left hand column is where you will draw and/or look up your molecules. I will call this the “ Drawing Tools .” The right hand portion is what I will call the “ Tool Bar .” This is where you will find different functions you will use throughout the experiment. To pull up a particular molecule, click on “name” in the Load Models portion of the Drawing Tools. The pop-up window will always have aspirin listed in the textbox. You will have to delete it before putting in the name of the molecule you want to look at. 4. The first molecule you will need to look at is chloromethane. Type chloromethane into the box and click on “OK.” 5. Once the molecule is in the window, click on the “Optimize” button in the Other Model Actions on the bottom left. This will generate the best structure for the molecule. ***YOU MUST DO

THIS WITH EACH STRUCTURE OR YOUR VALUES WILL BE INCORRECT!!*** 6. Play around with the model a bit. Click on it and drag to rotate. 7. To measure the distance between two atoms, or the bond length , click on “Length” in the right hand Tool Bar. Then click on the two atoms you want to measure the distance between. The number is then indicated on the structure. Measure one C-H bond and the C-Cl bond. a. Are they the same or different? The two atoms are not quite the same but are very close. The difference between the two is 0.02mm. 8. To measure the angle between three atoms, or the bond angle , click on “Angle” in the right hand Tool Bar. Then click on the three atoms that make up the angle you wish to measure. Measure a H-C-H angle and the H-C-Cl angle. a. Are they the same or different? They angle between the three atoms are not the same. 9. Now click on the “MEP” button in the left side Other Model Actions. You will see some colors appear around your molecule. The MEP function is showing you the electron density around the molecule. Remember that atoms have electronegativity values. The greater that value, the more likely electrons are to be close to or on that atom. The difference in electronegativity throughout the molecule will determine if a molecule is polar or non-polar. The colors will range from Red (negative, high electron density) to Blue (positive, low electron density) with green being neutral. a. Which atom in chloromethane is the most electronegative? Cl b. What color is it in the MEP image? Red c. Is chloromethane a polar or non-polar molecule? Polar 10. Click Clear/Reset Exploring Bond Lengths and Bond Angles with Respect to Atomic Radius Trends and Polarity with Respect to Electronegativity Trends 1. Draw the Lewis structures for the molecules in Data Table 1. Be sure to show all lone pairs. 2. Click on “Names” and enter the first molecule name listed on Data Table 1 (methane). 3. Click on the “Optimize” button. 4. Rotate the molecule around and observe its molecular shape. Write the name of the shape in the report form (see table 9.2 in your book). Note that lone pairs are not shown in the model. But the molecules still follow VSPER and have the proper molecular shape. When observing the molecules, think about where the lone pairs would be located. 5. Measure the bond length and record it in your table. Click Clear/Reset to remove the values.

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6. Next measure the bond angle and record it in your table. Click Clear/Reset to remove values. 7. Click on “MEP”. Record whether the molecule is polar or non-polar 8. Repeat steps 2-7 for ammonia and water. Answer the following after completing the above steps for methane, ammonia, and water. a. Do your predictions of what the molecular shape of the molecules match what you are seeing with CheMagic? My predictions of what the molecular shape of the molecules match mostly to what I see. b. As you move from left to right on the periodic table, the size of your atoms decreases. Can you use this to explain the trend in the bond lengths you are measuring? (Answer this question after taking measurements for all three molecules.) When you are moving left to right on the periodic table, the size of your atoms do decrease. The decrease of the bond lengths is due to the radii of the atom which projects different measurements of the molecules. c. What happens to the bond angle as the number of lone pairs increases? i. Why do you think that is? The reason the bond angle as the number of lone pairs increase is because of the increasing distance between pairs that are added to the molecule. Exploring Bond Length with Respect to Bond Order 1. Draw Lewis structures for Data Table 2. Carefully double check them when you view them. 2. Click on “Name” in the Load Models. Type in ethane and click “OK”. a. Does the Lewis structure you drew match what you see? If not, correct your structure. 3. Click on “Optimize”. 4. From the introduction: What is the bond order? To determine the bond order, you look at the number of electron pairs or bonds that are present when in between two atoms. 5. You can determine the shape around any atom in a larger molecule. Looking at one of the carbon atoms, a. What is the shape of the atoms attached to it? The shape the atom is attached to is a triangular shape. 6. Measure the C-H and C-C bonds and record them. Also measure the H-C-H and H-C-C angles and record them.

7. Click on “Clear/Reset” to remove your measurements. Then click on MEP. a. Do some areas have higher electron density than others? According to the model we see that some electrons do have higher electron density than the others. 8. For ethane, rotate the molecule so you are looking down the C-C bond. You should only be able to see one carbon atom as the other should be directly behind it. a. What do you notice about the hydrogen atoms? Are they aligned or staggered? When I look at the hydrogen atoms, they look more staggered than aligned and it is around two carbon atoms b. Why do you think that is? One reason I think that it is staggared is because it most likely helps stabilize the energy in the atom. 9. Repeat steps 2-7 for ethene and ethyne. Note the small difference in the names of these molecules . a. In the double and triple bonds where is the greatest electron density located? Between the double and triple bond, the triple bond has the greatest electron density. b. As the bond order increases, what happens to the length of the bond? When the bond order increases, the length of the bond decreases c. Which bond do you think would be stronger (harder to break)? (Answer this question after taking measurements for all three molecules.) After measuring the three molecules of ethane, the triple bond of ethyne is the stronger bond which is going to be harder to break than the others. Data Table 1 Molecule Lewis Structure Molecular Shape Bond Length (Å) Bond Angle (°) Polar or Non-Polar CH 4 Methane H H-C-H H tetrahedron 0.109A 110 Non-polar NH 3 Ammonia H H-N-H trigonalplanar 0.102A 107 polar H 2 O Water H-O-H angular 0.097A 104.5 polar

Data Table 2 Molecule Lewis Structure Bond Order Molecular Shape around Each Carbon Atom Bond Length (Å) Bond Angle (°) C 2 H 6 Ethane H. H H-C-C-H H H 1 tetrahedron C-H 0.109 C-C 0.151nm H-C-C 110.6 H-C-H 108.3 C 2 H 4 Ethene H H C=C H H 2 trigonal planar C-H 0.108 C-C 0.133nm H-C-C 120.7 H-C-H 118.5 C 2 H 2 Ethyne H-C= C-H - - 3 linear C-H 0.107 C-C 0.120 H-C-C 180

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