Lab 6 VSEPR and molecular shape “How does it look” PDF

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chemistry 106 lab 6 VSEPR and molecular shape
“How does it look”
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VSEPR and molecular shape “How does it look” Lab 6

Introduction The valence-shell electron-pair repulsion (VSEPR) model provide a method for predicting the molecular shapes. We will use Cambridge Structural Database as reference by looking up molecular geometries and molecules three-dimensions to study the particular molecules why they adopted by that shape. We have three objectives are needed to learn in this lab, first, to investigate shapes of molecules by analyzing experimental crystal structure data. Second, to understand the factors that determines the preferred shape adopted by particular molecules. Third, to use the VSEPR model to predict the shapes of given molecules.

Focus question 1 VSEPR theory is called Valence shell electron pair repulsion theory. It is a model used in chemistry to predict the geometry of individual molecules from the number of electron pairs surrounding their central atoms.

2 a) Yes. We can draw the Lewis structure of the molecule and we count the number of valence electrons and the bonds that connect two atoms. b) it would be more difficult, but it still works. Because there are more bonds and more ways to place these bonds.

3 We can see the two atoms angle and we can know about the molecular geometry , so we can know more about molecular behavior.

Procedure 1 using the website https://www.ccdc.cam.ac.uk/structures/ to search the molecule VSEPR model.

2 Enter the reference code provided under “identifier” requirement molecules about three parts.

3 Select the type of measurement we wish to make by right-clicking within the 3D viewer and selecting measure, follow by either: Distances, Angles or Torsions

4 Geometrical measurement can be made by clicking on e.g. two atoms for a distance, three atoms for an angle or four atoms for a torsion angle

5 To remove all geometrical measurement from the display right-click within the 3D viewer and select measure followed by either: Clear distances, clear angles or clear torsions.

Observation Part 1

Basic Shapes 1) Apply the VSEPR model to predict the shapes of the following molecules 2) Examine the crystal structure of the molecule the bond angles 3) Comment on how closely the observed bond angles agree with the expected ideal values. Enter the reference code provided under “identifier”

1 [PF6]-: refcode WINFAA

Figure 1, [PF6 ]^- molecule’s crystal structure. Angle between two fluorine atoms when they bind to the phosphorus atom is 90.1 degree and it is around 90 degree, and the dihedral angle is 179.6 and it is around 180 degree, and the distance between fluorine atom and the phosphorus atom is 1.58 A (Angstrom).

2 [BrF6]-: Refcode ZAQBIC

Figure 2, [BrF6]- molecule’s crystal structure. Angle between two fluorine atoms when they bind to the bromine atom is is 91.8 degree and it is around 90 degree, and the dihedral angle is 178.2 and it is around 180 degree, and the distance between fluorine atom and the phosphorus atom is 1.88A (Angstrom).

3 I3-: Refcode RIKTAG

Figure 3, I3- molecule’s crystal structure. Angle between two Iodine atoms when they bind to the Iodine atom is 180 degree, and the distance between Iodine atom and the Iodine atom is 1.88A (Angstrom).

4 In(CH3)3: Refcode TRMEIN03

Figure 4, I In(CH3)3: molecule’s crystal structure. Angle between two (CH3)- molecules when they bind to the indium is 119.6 degree, it is around 120 degree, and the distance between (CH3)- molecule and the indium atom is 2.17A (Angstrom).

5 [BeF4]^2-: Refcode KIPPEE

Figure 5, [BeF4]^2- molecule’s crystal structure. Angle between two fluorine atoms when they bind to the Beryllium is 108.6 degree, it is around 109.5 degree, and the distance between fluorine atom and the beryllium atom is 1.53A (Angstrom).

6 NH4+: Refcode ACARBM01

Figure 6, NH4+ molecule’s crystal structure. Angle between two hydrogen atoms when they bind to the Nitrogen is 109.5 degree or 110.3 degree, it is around to 109.5 degree, and the distance between nitrogen atom and the hydrogen atom is 0.93A (Angstrom).

7[SbF6]-: Refcode FUJLAX

Figure 7, [SbF6]- molecule’s crystal structure. Angle between two fluorine atoms when they bind to the antimony is 88.7 degree and it is around 90 degree, its dihedral is 179.4 degree and it is around 180 degree, it and the distance between nitrogen atom and the hydrogen atom is 1.85 A (Angstrom).

Part 2 Effect of lone pairs on the molecular shape The molecules you have encountered so far include only bonding pairs How does the presence of lone pairs will affect molecular shape?

8 XeF5-: refcode SOBWAH

Figure 8, XeF5- molecule’s crystal structure. Angle between two fluorine atoms when they bind to the Xenon is 72.3 degree and it is less than 90 , it and the distance between Xenon atom and the fluorine atom is 2.03 A (Angstrom).

9 H2O: refcode MUSIMO01

Figure 9, H2O molecule crystal structure. Angle between two hydrogen atoms when they bind to the oxygen atom is 100.6 degree, less than 109.5 and the distance between hydrogen atom and the oxygen atom is 0.96 A (Angstrom).

10 [ClF4]-: refcode ROLSEQ

Figure 10, [ClF4]- molecule’s crystal structure. Angle between two fluorine atoms when they bind to the chlorine is 90 degree and its dihedral is 178.4 degree less than 180 degree , and the distance between chlorine atom and the fluorine atom is 1.77 A (Angstrom).

11 SbBr5^2-: refcode CLPYSB

Figure 11, SbBr5^2- molecule’s crystal structure. Angle between two bromine atoms when they bind to the antimony is 92.9 degree and it is it is around to 90 degree, and its dihedral is 179.3 and it is around to 180 degree and the distance between bromine atom and the antimony atom is 2.68 A (Angstrom).

Part 3 Effect of lone pairs on bond angles 12 Di-bromodimethylselenium: refcode RIZMIW

Figure 12, Di-bromodimethylselenium molecule’s crystal structure. Angle between two bromine atoms when they bind to the selenium is 90.6 degree and it is it is around to 90 degree, and its dihedral is 177.7 degree and it is around to 180 degree and the distance between bromine atom and the selenium atom is 2.55A (Angstrom). Angle between two CH3 molecules when they bind to the selenium is 98 degree and the distance between CH3 molecule and the selenium atom is 1.92A (Angstrom). Angle between CH3 molecule and bromine when they bind to the selenium is 91.7 degree.

13 SO2: Refcode DADXOW

Figure 13, SO2 molecule crystal structure. Angle between two oxygen atoms when they bind to the sulfur atom is 113 degree, less than 120 degree and the distance between sulfur atom and the oxygen atom is 1.46 A (Angstrom).

14 NH3:refcode KATLAT

Figure 14, NH3 molecule crystal structure. Angle between two hydrogen atoms when they bind to the nitrogen atom is 102. 9degree, less than 109.5 degree and the distance between sulfur atom and the oxygen atom is 0.9 A (Angstrom).

15 Dichloro-diphenyl-selenium: refcode PHSECL01

Figure 15, Dichloro-diphenyl-selenium molecule’s crystal structure. Angle between two chlorine molecules when they bind to the selenium is 90.4 degree and it is it is around to 90 degree, and its dihedral is 175 degree and it is around to 180 degree and the distance between chlorine atom and the selenium atom is 2.39 (Angstrom). Angle between two phenyl molecules when they bind to the selenium is 100.4 degree and the distance between phenyl molecules and the selenium atom is 1.94A (Angstrom). Angle between phenyl molecule and chlorine when they bind to the selenium is 90.8 degree.

16 Boricacid: refcode JAGREP

Figure 16, Boricacid molecule crystal structure. Angle between two HO- groups when they bind to the boron atom is 119.9 degree, less than 120 degree and the distance between HO- group and the boron atom is 1.38 A (Angstrom).

Conclusion Figure 1, It is close to the angle degree that predict in VSEPR theory, its molecule has zero lone pairs so its molecular geometry and its electron geometry are the same geometry--Octahedral. There are 6 electron groups in [PF6 ]^- electron geometry. The angle between two fluorine atoms when they bind to the phosphorus atom are 180 and 90 degree. Figure 2, It is close to the angle degree that predict in VSEPR theory, its molecule has zero lone pairs so its molecular geometry and its electron geometry are the same geometry--Octahedral. There are 6 electron groups in [BrF6]- electron geometry. The angle between two fluorine atoms when they bind to the bromine atom are 90 degree and its dihedral is 180 degree. Figure 3,I3-, It is the same angle degree that predict in VSEPR theory, its molecule has three lone pairs so its molecular geometry is linear, and its electron geometry has 5 electron groups, so it is trigonal bipyramidal. The angle between two iodine atoms when they bind to the iodine atom are 90 degree and its dihedral is 120 degree. Figure4 In(CH3)3: It is close to the angle degree that predict in VSEPR theory, its molecule has zero lone pairs so its molecular geometry and its electron geometry are the same geometry— trigonal planar and its electron geometry has three electron groups. The angle between two (CH3)- molecules when they bind to the indium atom is 120 degree. Figure5 [BeF4]^2-, It is close to the angle degree that predict in VSEPR theory, its molecule has zero lone pairs so its molecular geometry and its electron geometry are the same geometry— tetrahedral and its electron geometry has four electron groups. The angle between two fluorine atoms when they bind to the beryllium atom is 109.5 degree. Figure6 NH4+, It is close to the angle degree that predict in VSEPR theory, its molecule has zero lone pairs so its molecular geometry and its electron geometry are the same geometry— tetrahedral and its electron geometry has four electron groups. The angle between two hydrogen atoms when they bind to the nitrogen atom is 109.5 degree. Figure 7, [SbF6]-, It is close to the angle degree that predict in VSEPR theory, its molecule has zero lone pairs so its molecular geometry and its electron geometry are the same geometry Octahedral. There are 6 electron groups in [BrF6]- electron geometry. The angle between two fluorine atoms when they bind to the antimony atom is 109.5 degree. Figure 8, [SbF6]-, It is less than the angle degree that predict in VSEPR theory, its molecule has one lone pairs so its molecular geometry is square pyramidal and there are 6 electron groups in [BrF6]- electron geometry, so its electron geometry is octahedral. The angle between two fluorine atoms when they bind to the xenon is less than 90 degree in the molecular geometry. Figure 9, In the VSEPR theory, water molecule has two lone pairs so its molecular geometry is bent and it has four electron groups so its electron geometry is tetrahedral. The angle between

two hydrogen atoms when they bind to the oxygen atom is less than 109.5 degree in molecular geometry.

Figure 10, [ClF4]-, It is the same angle degree that predict in VSEPR theory, its molecule has one lone pairs so its molecular geometry is trigonal bipyramidal and there are 5 electron groups in [ClF4]- electron geometry, so its electron geometry is seesaw. The angle between two fluorine atoms when they bind to the chlorine is equal to 90 degree and its dihedral is less than 180 degree in the molecular geometry. Figure11, SbBr5^2-,It is close to the angle degree that predict in VSEPR theory, its molecule has zero lone pairs so its molecular geometry and its electron geometry are the same geometry— Trigonal bipyramidal and its electron geometry has five electron groups. The angle between two bromine atoms when they bind to the antimony atom is 90 degree and its dihedral is 180 degree. Figure12, Di-bromodimethylselenium ,It is close to the angle degree that predict in VSEPR theory, its molecule has one lone pairs so its molecular geometry seesaw and its electron geometry geometry—Trigonal has five electron groups, so it is trigonal bipyramidal. The angle between two atoms or molecules when they bind to the selenium atom is close to 90 degree and its dihedral is close to 180 degree. Figure 13, In the VSEPR theory, SO2 molecule has one lone pairs so its molecular geometry is bent and it has three electron groups so its electron geometry is trigonal planar. The angle between two oxygen atoms when they bind to the sulfur atom is less than 120 degree in molecular geometry. Figure 14, In the VSEPR theory, NH3 molecule has one lone pairs so its molecular geometry is trigonal pyramidal and it has four electron groups so its electron geometry is tetrahedral. The angle between two hydrogen atoms when they bind to the nitrogen atom is less than 109.5 degree in molecular geometry. Figure15, Dichloro-diphenyl-selenium, It is close to the angle degree that predict in VSEPR theory, its molecule has one lone pairs so its molecular geometry is seesaw and it has five electron groups, so it is trigonal bipyramidal. The angle between two atoms or molecules when they bind to the selenium atom is close to 90 degree and its dihedral is close to 180 degree. Figure 16, In the VSEPR theory, Boricacid molecule has zero lone pairs so its molecular geometry and its electron geometry are the same—trigonal planar. They have three electron groups. The angle between two HO- group when they bind to the boron atom is less than 120 degree in molecular geometry.

Post lab question 1 Molecular geometry is the name of the geometry used to describe the shape of a molecule. According to VSEPR, electron pairs distribute themselves around a central atom in such a way as to maximize their distance from each other. Electron domain geometries are based on the total number of electron pairs, while molecular geometries describe the arrangement of atoms and bonding pairs in a molecule. 2 A) trigonal planar B) tetrahedral C) trigonal bipyramidal 3 PH3 has a lone pair and does not have a trigonal planar geometry, so it is not symmetrical.

BI3 has no pair and it has a trigonal planar geometry, so it is symmetrical. 4.

H-C-C-O-H

In Ethanol oxygen has two lone pairs so it has bent electron geometry, and it has tetrahedral molecular geometry.

H-C-O-C-H

In Dimethyl ether oxygen has two lone pairs so it has bent electron geometry, and it has tetrahedral molecular geometry. 5 A) It is tetrahedral shape and 109.5° bond angle. B) 90 C) Carbon has 4 single bond, and no lone pairs so the electron domain geometry is tetrahedral.

The molecule has a cubic shape, that every C-C-C bond angle will be 90°. The cubic shape requires the carbon atoms to adopt an unusually sharp 90° bonding angle, which against the 109.45° angle of a tetrahedral carbon in VSEPR theory....