Problem Set Activity:  Building Molecular Models, Exercise on Lewis Structure and VSEPR

Objective:  The purpose of this experiment is: 1) draw the structural formula for a molecule based on the chemical formula 2) write the electron dot formula (Lewis Structure) corresponding to the structural formula 3) construct a computer models of the molecules (VSEPR model).

To complete this activity you will need to download Molecules-3D from Molecular Arts Corporation.  Link to http://www.ccl.net/cca/software/ and surf to molecular modeling software such as Molecule-3D.  Molecule-3D can be found at http://www.ccl.net/cca/software/MAC/index.shtml. According to the website, "... you can try Molecules-3D package FREE! No worries, no hassle, no risk. The Molecules-3D Web Edition will periodically display a registration reminder screen, but other than that it is functionally identical to the Standard Edition."  Create the 3-dimensional structure using Molecues-3D for the following compound and print a hardcopy of each structure.  You can download the molecules for this activity with this link.  The files are zipped, you will need to extract the molecules from the zip file.  The best platform for this activity will be Macintosh computers.  Molecular Inorganic Model. (MolModelInOrg_files)  You will need to go to the ILC lab in the I-building to access the Mac computers.

Finally if non of the options above work, then go to Dr. Garces Molecular Structure Library and click on the molcules of interest to see a quickTime video of molecules that are part of this activity. FOG Molecular Library: http://faculty.sdmiramar.edu/fgarces/Links_Lib/Link.htm#Molecules

Answer the questions below as your read through this activity and then use the worksheet at the end of this activity to turn in to your instructor.

Discussion;  The tether between two atoms in a molecule is called a chemical bond.  In a covalent bond, two nonmetallic elements bond to each other by sharing valence electrons.  The valence electrons are the electrons furthest from the nucleus and occupy the highest s or p sublevels (for purpose of this class).  The group number of an element indicates the number of valence electrons.  For example, fluorine is in Group VIIA/17 and has seven valence electrons (7 e-).

1.   The valence electrons for an atom is easily obtain from the periodic table.  Carbon is found in Group IVA IVA/14 and has four valence electrons.  Refer to the periodic table and find the number of valence electrons for the following elements:

Element

N

O

P

Ca

Sb

Ga

Family

            

Valence electrons

            

2    In this problem set the Lewis structure is first constructed based on the chemical formula for the molecule. From the chemical formula, the atom connectivity for the structure is established.

      Given a chemical formula, ABn, A is generally the central atom and the B atoms flanks the A atom.  i.e., NH3, NCl3, NO2.  In these examples, N is central in the atom in the structure and H, Cl and O all flank the nitrogen atom in each molecule. Sometimes there are no central atoms such as in the case of Cl2 and sometimes there is more than one central atom such in H-O-O-H.  In this structure the atom connectivity is H-O-O-H.  The two oxygen atoms are considered central. If the chemical formula contains hydrogen (H) or fluorine (F), these atoms are never central.  Determine which is the central atom for each of the following.

Chemical specie

SO2

BrO3-

CH4

PH3

HCN

CH3Cl

Central Atom

S

          

Flanking atoms

Both O

          

Atomic Connectivity

O  S  O

          

3    The Lewis structure is completed when all the valence electrons are shown in the structure and all atoms satisfy the octet rule.  Note that there are exceptions to this rule that must be taken into account.  A tutorial provides the methodology in which this is done. 

www.miramar.sdccd.cc.ca.us/faculty/fgarces/ChemComon/Tutorial/Lewis/LewisTutorial/LewisTutorial.htm

      The following example illustrates the structural formula and electron dot formula for molecular models having single, double and triple bonds.


 

 

Download the Molecular 3D structure of water, chlorofor, formaldehyde and hydrogen cyanide by clicking on this link.  Molecules  You need not download this file if you have already down loaded the MolModelInOrg_files

Example 1   The model of a water molecule is sketched below.  Draw (a) the structural formula and (b) the electron dot formula corresponding to the model and (c) verify the electron dot formula by checking the total number of electron dots against the sum of all valence electrons.  The model is shown at the end (to be discussed later).  The chemical formula for water is H2O.  In panel 1, the oxygen is central and the hydrogen atoms flank the oxygen.  Panel 2 shows a line between the oxygen and hydrogen atom, which represent the bond between the two atoms.  A bond forms by two shared electrons, as shown in panel 3.  Panel 4 takes into account all the valence electrons of water (8) and shows that all atoms satisfy the octet rule (hydrogen being satisfied with two.  Finally, panel 5 shows the molecular geometry of water.  The molecular geometry is determined by VSEPR analysis.

1

Water, H2O

2

3

4

5

To verify the above Lewis structure the valence electrons are added from each atom in the molecule.  Recall that hydrogen is in Group IA/1 and oxygen is in Group VIA/6.

 2 Hydrogen (2 * 1 e- ) = 2 e-
1 Oxygen (1 * 6 e- ) = 6 e-
Sum of valence electrons 8 e-

There are eight dots used to write the electron dot formula.  Since this equals the number of valence electrons, the electron dot formula is correct.

Example 2  The Lewis structure analysis for chloroform is shown below. Chloroform possesses a total of 26 electrons.                                          

1 Hydrogen (1 * 1 e- ) = 1 e-
1 Carbon (1 * 4 e- ) = 4 e-
1 Chlorien (3 * 7 e- ) = 21 e-
Sum of valence electrons 26 e-

           1

Chloroform, CHCl3

2

3

4

5

The procedure requires the establishment of the atomic connectivity (2) the addition of electrons to the central atom such that the octet rule is satisfied (3) and completion of the Lewis structure by adding the remaining 18 electrons such that the octet rule is satisfied for all atoms in the structure, excluding H which is satisfied with two electrons.

Example 3  The Lewis structure analyses for formaldehyde is shown below. Formaldehyde possesses a total of 12 electrons.

1 Hydrogen (2 * 1 e- ) = 2 e-
1 Carbon (1 * 4 e- ) = 4 e-
1 Oxygen (1 * 6 e- ) = 6 e-
Sum of valence electrons 12 e-

1

Formaldehyde, H2CO

2

3

4

5

For formaldehyde, two bonds are placed between the carbon and the oxygen in order for the central atom, carbon, to posses an octet (2).  Carbon shares a total of eight electrons (3) while the remaining four electrons are added on oxygen so that oxygen too satisfies the octet rule (4).  The final Lewis structure shows all 12 valence electrons distributed such that all atoms (except H) satisfy the octet rule.

Example: 4   The Lewis structure analysis for hydrogen cyanide is shown below. Hydrogen cyanide possesses a total of 10 electrons

1 Hydrogen (2 * 1 e- ) = 1 e-
1 Carbon (1 * 4 e- ) = 4 e-
1 Nitrogen (1 * 5 e- ) = 5 e-
Sum of valence electrons 10 e-

1

Hydrogen cyanide, HCN

2

3

4

5

For hydrogen cyanide, three bonds are placed between the carbon and the nitrogen in order for the central atom, carbon, to posses an octet (2).  Carbon shares a total of eight electrons (3) while an additional two electrons are added on nitrogen so that nitrogen too satisfies the octet rule (4).  The final Lewis structure shows all 10 valence electrons distributed such that all atoms (except H) satisfy the octet rule.

 

 

Download the Molecular 3D structure of for this section with the link:  Lewis Structure. You need not download this file if you have already down loaded the MolModelInOrg_files

Complete the Lewis structure for the following.  Use separate sheet of paper if you need more room.

1  Compound, Chemical formula

2

Total Valence electron

3

Connectivity

4

Lewis Structure

Ammonia,

NH3

 

8

H

H   N   H

Methylene chloride,

CH2Cl2

 

      

Formic acid,

HCOOH

 

      

Hydroxylamine,

NH2OH

 

      

Nitrate ion,

NO2-

 

      

Acetate ion,

CH2COO-

 

      

4   The shape of a molecule has a tremendous impact on the physical properties and chemical reactivity of that molecule.  The molecular shape of a molecule can be determine from its chemical formula by applying the Valence Shell Electron Pair Repulsion Theory (VSEPR) analysis.  The core assumption of VSEPR is that the valence electrons around the central atom of the molecule are responsible for its shape via their mutual repulsion, i.e., the shape of the molecule is determined by the arrangement of the central valence electrons which possesses the lowest electronic repulsion and hence the lowest energy.  VSEPR works well for main group covalent compounds and ions, less well for transition metal compounds, and not well at all for ionic compounds.  In this class we will work with mostly main group covalent compounds.

A terminology, which must be clear, is the distinction made between electronic and molecular geometry.  Electronic geometry refers to the distribution of the electron pairs around the central atom.  Thus if a molecule has 3 electron domain (regions of electron density) around its central atom, its electronic geometry is trigonal planar, regardless of how many of the pairs are bonding or lone pair electrons.  Molecular geometry refers to the arrangement of the atoms in the molecule.  It is the molecular geometry that influences the physical property of the molecule. 

The use of VSEPR clearly requires knowledge of how many electron domains (regions of electron density) are around the central atom and also whether these pairs are bonding or lone pairs.  The simplest method for determining this is to draw the Lewis structure of the molecule and then count the number of electron domains surrounding the central atom.

 


The application of the VSEPR theory can be summarize by the following table.  In this table, A represents the central atom, E represents electron domains, and B represents the bonded atom.

e- Regon

AEn

Electronic Geometry

Bond Pair (Coord #)

non-bond pair

AEnBm

Molecular Geometry

Bond angle
Hybrid

2

AE2


Linear

2

0

AB2


Linear

180 °

sp

3

AE3

 Trigonal

3

0

AB3

   Trigonal

120 °

sp2

2

1

AB2E

   Bent

< 120 °

sp2

4

AE4

Tetrahedral

4

0

AB4

   Tetrahedral

109.5 °

sp3

3

1

AB3E

   Pyramidal

< 109.5 °

sp3

2

2

AB2E2

    Bent

< 109.5 °

sp3

A tutorial provides the methodology in which the molecular geometry is determined from VSEPR. 

www.miramar.sdccd.net/faculty/fgarces/ChemComon/Tutorial/VSEPR/VSEPRTutorial/VSEPRTutorial.htm

A summary on how to use VSEPR to determine molecular geometry is provided here.

A) Determine the Lewis Structure.

      i) Valence electrons for each atom in the structure.

      ii) Determine the number of bonds in the molecule and identify the central atom

B) Determine electronic geometry (AEn system) from Lewis structure.

            i) Count the electron domain (region) around the central atom.

            ii) Arrange electron domain in order to minimize electron-electron repulsion.

               This occurs when electron pair are far apart as possible.

      iii) 2-domain yields a linear, 3-domains yield a trigonal, and 4-domains yield a tetrahedral

C) Determine the molecule geometry (ABmEn system) from its electronic geometry.

i) The molecular geometry is based on the final position of the atoms.

ii) The lone pair electrons are ignored when determining the molecular geometry.

1) AE2; Electronic geometry (linear) with this designation will yield a molecular geometry designation of (AB2) which is linear. This is accomplished by replacing all two-electron domains by 2 bonded atoms.  Example BeH2

2-a) AE3; Electronic geometry (trigonal) with this designation will yield a molecular geometry designation of (AB3) which is trigonal.  This is accomplished by replacing all three-electron domains by 3 bonded atoms.  Example BH3

2-b) AE3; Electronic geometry (trigonal) with this designation will yield a molecular geometry designation of (AB2E) which is bent.  This is accomplished by replacing two of the three electron domains by 2 bonded atoms. Example SO2

3-a) AE4 Electronic geometry (tetrahedral) with this designation will yield a molecular geometry designation of (AB4) which is tetrahedral.  This is accomplished by replacing all four-electron domains by 4 bonded atoms. Example CH4

3-b) AE4 Electronic geometry (tetrahedral) with this designation will yield a molecular geometry designation of (AB3E) which is pyramidal.  This is accomplished by replacing three of the four electron domains by 3 bonded atoms. Example NH3

3-c) AE4 Electronic geometry (tetrahedral) with this designation will yield a molecular geometry designation of (AB2E2) which is bent.  This is accomplished by replacing two of the four electron domains by 2 bonded atoms. Example H2O
 


 

 

Problem Set Activity:  Building Molecular Models: Exercise on Lewis Structure and VSEPR
___/ ___ Score
Name (Last)_______________(First)_______________ Date _______


1. Refer to the periodic table and find the family (i.e., Group I) and the number of valence electrons for the following elements:

Element

N

O

P

Ca

Sb

Ga

Family

            

Valence electrons

            


2. Determine which is the central atom, which are the flanking atoms and how the atoms are connected for each of the following.

Chemical specie

SO2

BrO3-

CH4

PH3

HCN

CH3Cl

Central Atom

S

          

Flanking atoms

Both O

          

Atomic Connectivity

O  S  O

          


3. Complete the Lewis structure for the following. Use separate sheet of paper if you need more room.

1  Compound, Chemical formula

2

Total Valence electron

3

Connectivity

4

Lewis Structure

Ammonia,

NH3

 

8

H

H   N   H

Methylene chloride,

CH2Cl2

 

      

Formic acid,

HCOOH

 

             O
       H    C   O-H		  

Hydroxylamine,

NH2OH

 

                H
       H   N   O-H 		 

Nitrate ion,

NO2-

 

      

Acetate ion,

CH2COO-

 

              H   O
    H    C    C  O-H 		 


 

 

4. Putting it all together. Complete the table below for each molecule or polyatomic ion by:
a) writing the Lewis structure. b) determining the AE-system, the electronic geometry and sketching the shape.
c) determining the ABE-system, the molecular geometry and sketching the shape of the molecule.
d) and designating all the bond angle in the chemical. See the example for ammonia.

Example

Lewis Structure

AEn

Electronic Geometry

ABmEn

Molecular Geometry

Bond angles

NH3

AE4, Tetrahedral

AB3E Pyramidal

H-N-H angle
 < 109.5 °

CS2

 

        

HOCl

 

        

O3

 

        

SiH4

 

        

CO2

 

        

NO2-

 

        

F2O

 

        

SCN-

 

        

NO3-

 

        


 

 

5 Computer exercise.
Your instructor will need to provide you more information for this activity. To complete this activity you will need to download Molecules-3D from Molecular Arts Corporation. Link to http://www.ccl.net/cca/software/ and surf to molecular modeling software for your platform such as Windows 98 or Mac. WinChem for windows can be found at http://www.ccl.net/cca/software/MS-WIN3/MolecModelling_for_Windows/index.shtml and Molecule-3D for Macs at http://www.ccl.net/cca/software/MAC/index.shtml. According to the website, “… you can try Molecules-3D package FREE! No worries, no hassle, no risk. The Molecules-3D Web Edition will periodically display a registration reminder screen, but other than that it is functionally identical to the Standard Edition.” Create the 3-dimensional structure using Molecues-3D for the following compound and print a hardcopy of each structure. In order to create the correct structure the molecular geometry must first be determine using the VSEPR analysis.

If appropriate software cannot be found then go to
http://chemfinder.cambridgesoft.com and use the database to look up the structure of the chemicals below.

Finally if non of the options above work, then go to Dr. Garces Molecular Structure Library and click on the molecules of interest to see a quickTime video of molecules that are part of this activity.
FOGMolecularLibrary: http://faculty.sdmiramar.edu/fgarces/Links_Lib/Link.htm#Molecules

Other links to 3D Molecular modeling software:
http://www.faidherbe.org/site/cours/dupuis/vseprev.htm
http://www.liv.ac.uk/Chemistry/Links/refmodl.html
http://gsaix2.cc.gasou.edu/chemdept/general/molecule/tutorial/  

Explain why nitrogen dioxide, NO2, a component of smog, is predicted to be an unstable molecule. 

(Hint:  Draw the electron dot formula).