Experiment 6 - Lecture notes 6 PDF

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3D Structure of Molecules Danielle M. Carrasquillo Experiment 6- VSEPR and molecular shape SUMMARY During this lab, we will investigate the shapes of molecules by analyzing data, understand the factors that help us determine the shape of the molecules, and use the VESPR model to predict shapes of given molecules. We will use an online site for looking up molecule 3D models. We will analyze the molecular shape and characteristics using the online tool. This will help us to understand different characteristics that are studied by chemists, as well as learn the different types of crystal structures associated with the molecules we will look at. Doing this lab, we will be able to identify the geometric shape of each model. INTRODUCTION The structure and measurement of molecules are important for chemists to study because molecules hold a lot of responsibility for performing specific tasks in their chemical being. The molecule structure acts as a buildings blueprint. It remains responsible for operating the correct way to keep the chemical bonds going. Learning how to measure these molecule angles are important because the measurement of angels will determine how a compound reacts with another compound. Although very small, molecules have many different characteristics to be studied and there are many different important factors involved in molecule bonding and reactions. Without knowing the geometric shape of the molecules, you will not be able to identify the properties that may further help you understand different parts of chemistry. MATERIALS AND METHOD  Angle chart from lab 5 instructions  https://www.ccdc.cam.ac.uk/structures/? ccdccheck=e235e279638c2a32af29d1e7030d52b6 

Excel spreadsheet  For each of the 3 parts of this lab, get the below information according to each part of the lab and what is required.  Using the given molecules, predict the geometry and angles of the molecules using a Lewis dot drawing, the given formulas, and the chart given from lab 5.  For each of the given molecules, use the website above to link the molecule identifier. This will bring you to a crystal structure of that molecule. Evaluate the structure and identify the shape of each molecule.  Using the “angle measurement tool” on the website, get all the possible bond angles for each of the molecules. (remember to attach hydrogen as needed)

RESULT AND DISCUSSION Part 1:

Molecule Name

Molecule Identifier

Shape

Bond Angle

PF6[BrF6]I3ln(CH3)3 [BeF4]2NH4+ [SbF6]-

WINFAA ZAQBIC RIKTAG TRMEIN03 KIPPEE ACARBM01 FUJLAX

Octahedral Pyramidal Linear Bent Trigonal Planar Tetrahedral Octahedral

91.0, 179.6 89.7, 178.2 180 109.5, 124.01 109.7 123.9 89, 179.3

Predicted Bond Angle 60 60 120 109 120 120 90

In this part of the lab, we measured all the different possible bond angles. We saw that some of these bond angles remained similar depending on which bond angle we measured from. We want to note the angles with major differences such as: PF6-, [BrF6]-, ln(CH3)3 and [SbF6]-. These all show that the structure includes multiple angles. Understanding the different bond angles helps us to figure out how to identify the geometric shape. Part 2: Molecule Name

Molecule Identifier

Shape

XeF5H2O [ClF4]-

SOBWAH MUSIMO01 ROLSEQ

Pentagonal Pyramidal Bent Trigonal Bipyramidal

SbBr52-

CLPYSB

T-Shaped

For this part of the lab, we looked up each molecule identifier to physically see and identify the shape of the molecule based on the structure of the 3D model given. Figuring out the shapes are tricky when you do not have bond angles to reference. Just looking at the molecule alone, without measuring the angles, makes it difficult to correctly identify the shape. Part 3: Molecule

Molecule Identifier

Predicted Geometry

Predicted Angles

SO2 NH3 Dichloro-diphenylselenium Boric Acid

DADXOW KATLAT

Bent Trigonal Pyramidal

120 90

Actual Angles 114 101.3

PHSECL01

Tetrahedral

180

92.4, 175

JAGREP

Trigonal Planar

109.5

107.2

Predicting the geometry of the molecules are more involved than it seems. Using the chart of shapes and the given molecule, it is not easy to identify the geometry because a big part of the geometry involves the bond angles. The bond angles are important for identifying the configuration and actual molecular function. Although bond angles are easy to get through the online tool, it is the most important step in figuring out the actual geometry as well as predicted factors when looking at different molecules.

CONCLUSION This lab really offered good strategies for figuring out VSEPR model evaluations as well as using the VSEPR method to figure out the shapes of the molecules. Combined with the

3D online tool, we were able to understand how our predictions correlate with the actual shape. It was interesting to find that the angle predictions were almost always wrong because I could not visualize the setting of the molecules until looking at the 3d model. I believe now, with knowing how to correctly use the Lewis dot structure and following the VSEPR rules, I would have an easier time with predicting angles correctly. Although the shapes can be tricky, I learned that each shape name is very important because it also correlates with the actual angle. For the next lab, I would spend more time on my Lewis dot structures while looking at the 3D model together to help me get a better understanding. REFRENCES 1. J.Lewinski, J.Zachara, K.B.Starowieyski, I.Justyniak, J.Lipkowski, W.Bury, P.Kruk, R.Wozniak CCDC 287085: Experimental Crystal Structure Determination, 2006, DOI: 10.5517/cc9mqtf 2. Wikipedia contributors. (2020, October 6). Molecular geometry. In Wikipedia, The Free Encyclopedia. Retrieved 13:51, October 10, 2020, from https://en.wikipedia.org/w/index.php? title=Molecular_geometry&oldid=982228836 FOCUS QUESTIONS 1. What is VSEPR theory, and how can it be used to predict molecular shapes? – The VSEPR theory is Valance shell electron pair repulsion theory that is used to predict the shape of the molecules based on the number of pairs surrounding the central atom. When you know how many molecules surround the central atom, you can easily look on a chart and match it to the same shape given and you will then know the predicted shape. 2. a. Can the structure of a simple molecular substance be illustrated by drawing or building models? Why and why not? - You can predict molecular substances by drawing them out and building models on an online source like we used for this lab. You first would get started by drawing out the Lewis dot structure, so you know how many bonds are involved and how many molecules are connected to an atom. b. What about more complex molecules? Explain. – For complex molecules, you would be able to also predict the molecular shape by drawing and building models. However, it could get tricky and making a Lewis dot structure would be difficult to interpret. I would not attempt a more complex molecule shape prediction without an online 3D tool just because it would probably be too confusing otherwise. 3. How are models and theories useful in helping to explain the structure and behavior of matter? – Theories are helpful for giving us a guide to figuring out certain characteristics that are helpful to know and make it easier to predict other characteristics. Models are useful for helping us figure out helpful characteristics of structures such as bond length, bond angle, shape, and number of bonds. POST-LAB QUESTIONS

1. What are molecular geometries and how do they differ from domain geometry? – Molecular geometries are the shape and 3D structure arrangement of molecules within an atom, it includes lone pairs, bonds, and angles. Domain geometry is different because it includes the electron pairs. 2. What is the electronic geometry about a central atom which has the following number of regions of electron density? a. Three regions of electron density- Trigonal Planar b. Four regions of electron density- Tetrahedral c. Five regions of electron density- Trigonal Bipyramidal 3. Is PH3 molecule symmetrical or unsymmetrical? What about BI3? Explain your reasoning for both. -PH3 does not appear to be symmetrical even though they all the moleculers have the same bond angle of 93.5 because the molecules collect on one side of the atom, causing asymmetry. BI3 appears to be symmetrical because it is flat, and each molecule have the same angles of 120. 4. Keeping VSEPR model in mind, draw the Lewis structures for ethanol, (C5H5OH) and dimethyl ether (CH3OCH3). Determine the electron pair geometry and molecular geometry around the oxygen atom in each. – (C5H5OH), (CH3OCH3). (not sure how to do the lewis structure via word document) both are: Tetrahedral, and Bent 5. Cubane C8H8(s) is a cubic shaped hydrocarbon with a carbon atom at each corner of the cube. Cubane is very unstable…. a. According to the VSEPR theory, what should be the shape around each carbon atom? What bond angle is associated with this shape? - This has 3 carbon atoms and the angle associated with this shape is tetrahedral with angle of 109.5. b. If you assume an ideal cubic shape, what are the actual bond angles around each carbon? – The cubic shape would involve 90 degree, 120degree and 178 degrees. It would still have the tetrahedral shape. c. Explain how your answers to question 5A and 5B suggest why the molecule is so unstable. - This is unstable because there are many different ways of coming to the same molecule. The angles for predicted are different than the actual angle making it not very simple to read or predict. 6. What are the steps to determine the shape of a molecule given a formula? Explain and show a few examples. – Lewis dot structure, evaluate pairs and line pairs, estimate geometries. SO2 has 1 S atom connected to 2 O atoms. Since there are 3 total atoms, making it bent with the estimated angle 120....