Experiment 5 Models to the Rescue

Experiment 5: Models to the Rescue ~ Introduction: We always visualize molecules in a two-dimensional aspect during general chemistry but never in a three-dimensional aspect. This prevents us from fully seeing all the properties that the molecule has, as well as understanding those properties. A three-dimensional structure can help us determine chemical and physical properties as well as the bonds they have. In this lab, the molecules we are going to work on include H2O, NH3, CH4, OCl2, CS2, BF3, NF3 and SF6. Using the Avogadro Program, we will be able to verify the molecular geometries predicted from the VSEPR theory, visualize molecular structures in 3D, and obtain the bond distances and bond angles from the calculations. ~ Materials: ● Laptop w/ Avogadro Program: helps us verify the molecular geometries predicted from VSEPR ● Lab manual ● Notebook for drawing Lewis Structures ~ Observations and Experimental: Part 1: Predictions of Molecules using VSEPR Molecules H2O NH3 Lewis Structure Prediction Electron Geometry: Tetrahedral Molecular Geometry: Bent Bond Angles: 109.5° Electron Geometry: Tetrahedral Molecular Geometry:Trigonal Pyramidal Bond Angles: 109.5° CH4 Electron Geometry: Tetrahedral Molecular Geometry: Tetrahedral Bond Angles: 109.5° OCl2 Electron Geometry: Tetrahedral Molecular Geometry: Bent Bond Angles: 109.5° CS2 BF3 Electron Geometry: Linear Molecular Geometry: Linear Bond Angles: 180° Electron Geometry: Trigonal Planar Molecular Geometry: Trigonal Planar Bond Angles: 180° Electron Geometry: Tetrahedral Molecular Geometry: Trigonal Pyramidal Bond Angles: 109.5° NF3 Electron Geometry: Octahedral Molecular Geometry: Octahedral Bond Angles: 90° SF6 Part 2: Using “Avogadro” to verify molecular structures. Molecules H2O NH3 Structures CH4 OCl2 CS2 BF3 NF3 SF6 ~ Discussion and Conclusion: This lab helped us properly see and understand the components of molecules in a three-dimensional aspect. We used the Avogadro Program to look at the geometric shape of the molecule and concluded that if the amount of lone pairs decreases, the bond angle increases. The VSEPR model allowed us to see what water’s bonds angle as 104.5 degrees with a bent shape. Methane was a tetrahedral resulting in a bond angle of 109.5 degrees. With the ability of the Avogadro Program, these molecules can be seen to show a trend between bond angles. ~ References: ● Smeureanu, G. & Geggier, S. (2019). General Chemistry Laboratory . New York, NY Zumdahl, S. (2014). Chemistry. 9 th ed. Belmont, California: Cengage Learning ● “Avogadro Chemistry.” Avogadro, July 2018, avogadro.cc/. Accessed 3 Oct. 2020. ● “Periodic Table - Ptable.” Ptable.Com, 2020, ptable.com/?lang=en#Properties. Accessed 9 Oct. 2020. ● Creative Chemistry, Tetrahedral molecules. “Tetrahedral Molecules | Creative Chemistry.” Creative Chemistry, 8 June 2017, www.creative-chemistry.org.uk/molecules/tetrahedral#:~:text=The%20H%E2%80%94C %E2%80%94H%20bond,the%20tetrahedral%20angle%2C%20109.5%C2%B0.&text=T he%20bond%20angles%20in%20ammonia,their%20lone%20pairs%20of%20electrons. Accessed 9 Oct. 2020. ~ Focus Questions: 1. What is an element? A pure substance which cannot be broken down by chemical means, consisting of atoms which have identical numbers of protons in their atomic nuclei. 2. What is a molecule? A molecule is a group of atoms bonded together. 3. How can you construct a model of a molecule based on a chemical formula? The chemical formula tells us the type and number of atoms that are in the molecule. We can construct a model by calculating the number of bonds and how they are bonded. When we do this, we have to keep the octet and duet rule in mind as most elements (except Hydrogen) are most stable when they have eight electrons. 4. Do these images look like what you expected? (i.e. compared to images you’ve seen in lectures or in your textbook?). The images came out like I expected because all the shapes that I predicted were shown. The images that I see in textbooks are also the same as what I saw on the program. 5. What does such a picture of an orbital represent? Explain this as clearly and concisely as you can. Each picture of the orbitals represents the orbitals bonding. They show the region between the nucleus where the electrons orbit. The models illustrate the bonding and ant-bonding electrons whether its pi and/or sigma bonds. ~ Post Lab Questions: 1. Fill in the following table using data calculated by Avogadro’s software in the lab: Compounds Angle VSPER predicted (degrees) Angle before optimization (degrees) Angle after optimization (degrees) Angle Literature value (degrees) Bond Length before optimization (Å) Bond Length after optimization (Å) Water 109.5 109.471 104.5 104.5 0.97 0.99 Ammonia 109 109.47 108.32 107 1.02 1.04 Methane 109.5 109.47 109.47 109.5 1.07 1.11 2. Do you see a trend for water, ammonia, and methane bond angles? Explain your answer in terms of their VSEPR structures. In the data collected, I did not observe any trends. However, a trend can be found using the VSEPR theory. We see that water has 2 bonding groups and 2 lone pairs and can conclude that it has a bond angle of 104.5 degrees. Ammonia has 1 lone pair and 3 bonding groups and has a bond angle of 107.8 degrees. As we observe methane we know that it has 4 bonding groups and no lone pair. This means that we should’ve seen a difference in their angle column, but we did not. 3. What is the main idea behind the VSEPR theory? The main idea behind the VSEPR theory is electron repulsion. Their theory tells us how atoms are bonded to a central atom and how the number of bonding groups affect the shape and bond angle of a molecule. If there are more lone pairs, there would be a stronger electron repulsion causing the bond angles to shrink. 4. Which bond angle was the closest to the literature value (after “clean up” or “ab initio optimization”)? Explain your answer. The bond angle closest to its bond angle after cleanup is methane. Methane has 4 bonding pairs to its central atom resulting in its tetrahedral’s structure. This tetrahedral shape is stable and after we cleaned it up, the bond angle remained the same (109.47). 5. What is the bond order in the nitrogen molecule as predicted by the MO theory? Is this in agreement with the Lewis Structure? Explain and show calculations of bond order. The bond order in a nitrogen molecule is 3. There is a triple bond between the diatomic nitrogen after drawing the lewis structure and following the octet rule. We can see a triple bond between nitrogen. (Bonding Order = # of bonding electrons - # of antibonding electrons) / 2) (Bonding Order = (6-0)/2 = 3) Experiment 6: How does it look? ~ Introduction: The VSEPR theory is a model used to determine the geometry of individual molecules from the number of electron pairs surrounding their central atoms. The central atom is the one who is most electronegative relative to the other atoms in the molecule. The theory also assumes that each atom in a molecule will achieve a geometry that minimizes the repulsion between electrons in the valence shell of that atom. In this experiment, we will use the VSEPR model to determine the shape, bond length, and bond angle specific molecules had. The experiment will also introduce the specific lone pairs and electron density for the specific molecules. ~ Materials: ● Laptop ● Lab Manual ● Notebook for drawing Lewis Structures ~ Observations and Experimental: Part 1: Basic Shapes Molecule Shape PF Octahedral [BrF ]Octahedral Bond Angles Observed Predicted Bond Angle (degrees) 89.9 90.1 90 89.4 90 90 (2) 91.1 86.6 90 The bond angles from observed are all close to or exactly 90. We see 2 angles that are exactly 90 degrees. 180 Predicted is the exact angle measurement as the observed molecule. 180 I Linear In(CH ) Trigonal Planar Observations based on VSEPR 109.4 (2) 109.5 109.5 VSEPR predicts that the bond angle for an octahedral would be 90 degrees and the bond angles observed are all close to 90 and exactly 1 is 90 degrees. The bond angles observed are all extremely close to the predicted bond angle that a trigonal planar shape would have. Tetrahedral 108.6 109.7 108.6 109.5 Tetrahedral 114.9 110.3 109.5 109.5 [BeF ]^2- NH + [SbF ]Tetrahedral 92.1 88.2 91 88.7 90 Generally we see that the bond angle observed is close to the bond angle predicted from a tetrahedral shape of 109.5. We have one observed angle that is fairly close to the The observed bond angles are fairly close to the expected bond values. Part 2: Effect of lone pairs on the molecular shape Molecule Name Shape XeF - Pentagonal Planar H O Bent [CIF ]- Square Planar SbBr ^2- Square Pyramidal How will the presence of lone pairs affect molecular shape? The presence of lone pairs changed the geometry of the molecule. The more lone pairs the molecule has, the more it will repel which causes the change in shape and angles. An example would be water (H2O) because without the 2 lone pairs, the molecule would have been linear but with the 2 lone pairs, the molecular geometry became bent. Part 3: Effect of lone pairs on bond angles Molecule Predicted Geometry Actual Geometry Predicted Bond Angle (degrees) Actual Bond Angles Di-bromodimethylselenium Seesaw Seesaw 90 90 90.6 91.7 SO Bent Bent 120 109.5 NH Trigonal Pyramidal Trigonal Pyramidal 109.5 100.4 101.3 102.9 Dichloro-diphenyl-selenium Trigonal Bipyramidal Trigonal Bipyramidal 90 90.8 92.4 100.4 Boric Acid Trigonal Planar Trigonal Planar 120 119 120.2 120.7 Comment on how closely the observed bond angles agree with the expected idea values? Can you account for any deviations for the idea values? The observed angles were fairly close to the expected idea values (ex: boric acid where it was <1 standard deviation). The only molecule that has a big deviation from the expected would be SO but that might be an anomaly or human error. Every other molecule has a standard deviation of less than < 3. ~ Discussion and Conclusion: In part 1 of our experiment, we saw the bond angles of our observed being in very close range with our predicted bond angles because they were simple molecules with no lone pairs. As we increased the complexity in part 2 and 3, we began to see a large shift in bond angles where it wasn’t close to the expected bond angles. This is due to the fact that there were lone pairs present which causes a repulsion. We concluded that having lone pairs changes the molecular geometry of the molecule. The more lone pairs you have, the smaller the bond angle becomes. ~ References: ● Smeureanu, G. & Geggier, S. (2019). General Chemistry Laboratory . New York, NY Zumdahl, S. (2014). Chemistry. 9 th ed. Belmont, California: Cengage Learning ● “Search - Access Structures.” Cam.Ac.Uk, 2020, www.ccdc.cam.ac.uk/structures/?ccdc-check=7ea82042c672f568d05300a2b462c0d0. Accessed 3 Oct. 2020. ~ Focus Questions: 1. What is VSEPR theory, and how can it be used to predict molecular shapes? The VSEPR theory (Valence Shell Electron Pair Repulsion) is a model used to find the geometry of molecules by the number of electron pairs (bonds) surrounding the central atoms. The goal of this theory is to be as far away as possible from one another so that repulsion can be minimal. It can be used to predict molecular shapes due to the amount of electron pairs it predicts as well as lone pairs that it has. For example if it has 2 lone pairs, it can have a shape of a tetrahedral of other shapes that have 2 electron pairs. 2. A. Can the structure of a simple molecular substance be illustrated by drawing or building models? Why and why not? The structure of a simple molecular substance can be illustrated by drawing or building models because the ball-stick model (example) shows their shape and bond angle while the Lewis structure shows lone pairs and amount of bonds. The structure can be illustrated to show important information that can be used for a conclusion. B. What about more complex molecules? Explain. Complex molecules can also be illustrated by drawing or building models because the ball-and-stick model works best when multiple compounds are involved/ combined onto different elements. 3. How are models and theories useful in helping to explain the structure and behavior of matter? Models and theories are helpful because they simplify complex ideas. They can also help explain the structures of things so it is easier to understand as well as help you visually comprehend what is going on in the structure. The VSEPR theory is one example that helps you visually comprehend what is going on in the structure by showing us how the valence electrons are bonded with its central atom. ~ Post Lab Questions: 1. What are molecular geometries and how do they differ from electron domain geometry? Molecular geometries are the 3D arrangement of atoms that considers electron densities, lone pairs, and bonds around the central atom. Electron domain geometry only uses the number of electron groups (central atom’s density) and is named exactly like the electron group geometry without considering other factors. 2. What is the electronic geometry about a central atom which has the following number of regions of electron density? a. 3 regions of electron density : Trigonal Planar b. 4 regions of electron density : Tetrahedral c. 5 regions of electron density : Trigonal Bipyramidal 3. Is the PH3 molecule symmetrical or unsymmetrical? What about BI3? Explain your reasoning for both. PH3 is not symmetrical because it has a lone pair causing it to have a repulsion between the lone and bonded pairs. It also does not have a trigonal planar geometry. BI3 is symmetrical because it has a trigonal planar geometry and no lone pairs so there is no repulsion going on. 4. Keeping the VSEPR model in mind, draw the lewis structure for ethanol (C2H5OH) and dimethyl (CH3OCH3). Determine the electron pair geometry and molecular geometry around the oxygen atom in each. The Lewis structure for ethanol has the oxygen atom with 2 lone pairs bonds to carbon and hydrogen. The Lewis structure for dimethyl ether has the oxygen atom in the middle of 2 bonds with carbon and 2 lone pairs. 5. Cubane (C8H8) is a cubic-shaped hydrocarbon with a carbon atom at each corner of the cube. Cubane is very unstable. Some researchers have been seriously injured when the crystals of the compound exploded while being scooped out of a bottle. Not surprisingly, cubane has been the subject of some research as an explosive. a. According to the VSEPR theory, what should be the shape around each carbon atom? What bond angle is associated with this shape? According to the VSEPR theory, there should be a tetrahedral shape around each carbon atom (4 bonds). b. If you assume an ideal cubic shape, what are the actual bond angles around each carbon? If you assume an ideal cubic shape, the bond angles would be 90 degrees since a cube has perfect 90 degree right angles. c. Explain how your answer to question 5a and 5b suggest why this molecule is so unstable. This molecule is so unstable because the bond angles are 109.5 degrees instead of 90 degrees causing a strain. There are 4 single bonds in a tetrahedral shape with bond angles of 109.5 but carbon atoms only have 90 degree angles. The bonds are strained to 109.5 degrees instead of 90 degrees. 6. What are the steps to determine the shape of a molecule given the formula? Explain and show a few examples. The steps to determine the shape of a molecule given the formula would be to first draw a simple lewis structure of the molecule. Then using that structure, determine the SN (steric number = # of lone electrons + # of atoms bonded to central atom). After that, you would use the steric number and the VSEPR theory to determine the electron geometry of the molecule. Finally, you would use the VSEPR shape to determine the shapes and bond angles between all the bonding pairs.