# Limiting Chemical Reactions

#### January 1, 2015

Figuring out the limiting reactant in a chemical reaction integrates many of the basic chemistry concepts including: unit conversions from moles to mass and vice versa; the meaning of chemical formulas; and understanding the stoichiometry of chemical reactions. So, since we’ll need a number of these, I wrote a python program to help me design the questions (and figure out the answers).

Program examples come zipped because they require the program file and the elements_database.py library:

# Baking Powder and Vinegar (Common Molecules)

Limiting_component-Common.py: This has the baking powder and vinegar reaction limited by 5 g of baking soda. It’s nice because it uses a few pre-defined “common molecules” (which are defined in the elements_database.py library.

You enter the reactants and products and the program checks if the reaction is balanced, then calculates the moles and masses based on the limiting component, and finally double checks to make sure the reaction is mass balanced.

Limiting_component-Common.py

```from elements_database import *
import sys

print "LIMITING REACTANT PROGRAM"
print
print "  Determines the needed mass and moles of reactants and products if reaction is limited by one of the components"

c = common_molecules()

'''Create Reaction'''
rxn = reaction()
#       molecule: from molecule class in elements_database
#       stoichiometry: integer number

'''Print out the reaction'''
print
print "Chemical Formula"
print "  " + rxn.print_reaction()
print

'''Check if reaction is balanced'''
balanced = rxn.check_for_balance(printout=True)

'''Calculate limits of reaction'''
if balanced:
rxn.limited_by_mass(c.baking_soda, 5, printout=True)

```

Outputs results in the Results table (using scientific notation):

```LIMITING REACTANT PROGRAM

Determines the needed mass and moles of reactants and products if reaction is limited by one of the components

Chemical Formula
NaHCO3 + HCl  --> CO2 + H2O + NaCl

Check for balance
---------------------------------------------
| Element | Reactants | Products | Difference |
---------------------------------------------
|   Na    |    1      |    -1    |     0      |
|   H     |    2      |    -2    |     0      |
|   C     |    1      |    -1    |     0      |
|   O     |    3      |    -3    |     0      |
|   Cl    |    1      |    -1    |     0      |
---------------------------------------------
Balance is:  True

Given: Limiting component is 5 g of NaHCO3.
Molar mass = 84.00676928
Moles of NaHCO3 = 0.0595190130849

Results
------------------------------------------------------------------
| Molecule | Stoich.*| Molar Mass (g) | Moles req. |    Mass (g)   |
------------------------------------------------------------------
|NaHCO3    |    1    |    84.0068     |  5.952e-02 |   5.000e+00   |
|HCl       |    1    |    36.4602     |  5.952e-02 |   2.170e+00   |
|CO2       |    -1   |    44.0096     |  5.952e-02 |   2.619e+00   |
|H2O       |    -1   |    18.0156     |  5.952e-02 |   1.072e+00   |
|NaCl      |    -1   |    58.4418     |  5.952e-02 |   3.478e+00   |
------------------------------------------------------------------
* negative stoichiometry means the component is a product

Final Check: Confirm Mass balance:
Reactants:    7.1701 g
Products:    -7.1701 g
--------------------------
=      0.0000 g
--------------------------
```

# General Example

If not using the common molecules database, you need to define the components in the reaction as molecules yourself. This example reacts magnesium sulfate and sodium hydroxide, and limits the reaction with 20 g of magnesium sulfate.

Limiting_component-General.zip

The main file is:

Chem_Exam-limiting.py

```from elements_database import *
import sys

print "LIMITING REACTANT PROGRAM"
print
print "  Determines the needed mass and moles of reactants and products if reaction is limited by one of the components"

# create reaction

rxn2 = reaction()
#       molecule: from molecule class in elements_database
#       stoichiometry: integer number

'''Print out the reaction'''
print
print "Chemical Formula"
print "  " + rxn2.print_reaction()
print

'''Check if reaction is balanced'''
balanced = rxn2.check_for_balance(printout=True)

'''Calculate limits of reaction'''
if balanced:
rxn2.limited_by_mass(molecule("Mg:1,S:1,O:4"), 20, True)

# print out masses
print "Masses Involved in Reaction"
print "  Reactants:"
for i in rxn2.reactants:
#print "rxn", i
print "    {m}: {g} g".format(m=i.molecule.print_formula().ljust(10), g=i.mass)
print "  Products:"
for i in rxn2.products:
#print "rxn", i
print "    {m}: {g} g".format(m=i.molecule.print_formula().ljust(10), g=-i.mass)

```

This program is slightly different from the common molecules example in that, at the end, it prints out masses calculated in a more easily readable format in addition to the other data.

```Masses Involved in Reaction
Reactants:
MgSO4     : 20.0 g
NaOH      : 13.2919931774 g
Products:
MgO2H2    : 9.69066512026 g
Na2SO4    : 23.6013280571 g
```

When I have some time I’ll convert this to JavaScript like the molecular mass example.

Citing this post: Urbano, L., 2015. Limiting Chemical Reactions, Retrieved March 27th, 2017, from Montessori Muddle: http://MontessoriMuddle.org/ .
Attribution (Curator's Code ): Via: Montessori Muddle; Hat tip: Montessori Muddle.

# Molar Mass of Molecules

#### December 5, 2014

Calculate the molar mass of a molecule:

The notation for the chemical formula is a little funky: you put the element symbol and then the number of atoms separated by a colon; each element/number of atoms pair are separated by commas, so sodium chloride (NaCl) would be “Na:1,Cl:1“.

This will have to do until I can write something to parse the regular chemical formula notation.

On the plus side, you can link to a specific molecular mass calculation by adding the formula to the url. So magnesium chloride (MgCl2) can be found with this url:

http://soriki.com/js/chem/chem_db/molecular_mass.html?formula=Mg:1,Cl:2

Citing this post: Urbano, L., 2014. Molar Mass of Molecules, Retrieved March 27th, 2017, from Montessori Muddle: http://MontessoriMuddle.org/ .
Attribution (Curator's Code ): Via: Montessori Muddle; Hat tip: Montessori Muddle.

# Updated Atom Builder

#### September 5, 2014

A couple of my students asked for worksheets to practice drawing atoms and electron shells. I updated the Atom Builder app to make sure it works and to make the app embedable.

So now I can ask a student to draw 23Na+ then show the what they should get:

# Worksheet

Draw diagrams of the following atoms, showing the number of neutrons, protons, and electrons in shells. See the example above.

I guess the next step is to adapt the app so you can hide the element symbol so student have to figure what element based on the diagram.

Citing this post: Urbano, L., 2014. Updated Atom Builder, Retrieved March 27th, 2017, from Montessori Muddle: http://MontessoriMuddle.org/ .
Attribution (Curator's Code ): Via: Montessori Muddle; Hat tip: Montessori Muddle.

# DNA Writer: Storing Information in DNA Exercise

#### February 2, 2013

DNA Writer: Translate text into a DNA code (and back again) using a simple lookup table.

I created this little DNA Writer webpage after seeing the article on scientists recording one of Shakespeare’s sonnets on DNA, I was inspired to put together something similar as an assignment for my middle-school science class to demonstrate how DNA records information. With the website to do quick translations for me, I’ll give each student the translation table and a simple message in DNA code and have them figure out the message.

Update: I’ve adapted the code to add a two to five letter sequence of non-coding DNA to the beginning and end of the message code. There’s also start and stop code as well.

The DNA sequence (or RNA in this figure) can be broken down into groups of three nucleotides called codons. Each codon codes for a specific amino acid, so the order of codons gives the sequence of amino acids in the proteins created by the DNA strand. Image by TransControl via Wikipedia.

The DNA Writer code uses a simple look-up table where each letter in the English alphabet is assigned a unique three letter nucleotide code. The three letters are chosen from the letters of the DNA bases – AGCT – similar to the way codons are organized in mRNA. Any unknown characters or punctuation are ignored.

Also, with a little tweaking, I think I can adapt this assignment to show how random mutation can be introduced into DNA sequences during transcription. Maybe break the class into groups of 4, give the first student a message as a nucleotide sequence have them copy and pass it on to the next student and so on. If I structure this as a race between the groups, then someone’s bound to introduce some errors, so when they translate the final code back into English they should see how the random mutation affected their code.

UPDATE: Non-Coding (junk) DNA: I’ve updated the code so that you have the option of adding a short (2-5 character) string of non-coding DNA to the beginning and end of each sequence.

A more personalized and printer friendly format for output.

UPDATE 2: Personalized and Printable output: Since I’m using the DNA writer to give each student a personalized message, I’ve created a button that gives “Printer Friendly Output” which will produce an individualized page with the code, the translation table, and some information on how it works, so I can print off individualized assignments more easily.

UPDATE 3: You can now get a color coded version of the sequence.

Ravenclaw’s DNA sequence color coded, and translated back to English.

Update 4: Now you can embed the nucleobase color patterns into other websites. Like so:

Citing this post: Urbano, L., 2013. DNA Writer: Storing Information in DNA Exercise, Retrieved March 27th, 2017, from Montessori Muddle: http://MontessoriMuddle.org/ .
Attribution (Curator's Code ): Via: Montessori Muddle; Hat tip: Montessori Muddle.

# Atom Builder

#### January 22, 2013

This app lets you drag and drop electrons, protons, and neutrons to create atoms with different charges, elements, and atomic masses. You can also enter the element symbol, charge and atomic mass and it will build the atom for you.

Note, however, it only does the first 20 elements.

Citing this post: Urbano, L., 2013. Atom Builder, Retrieved March 27th, 2017, from Montessori Muddle: http://MontessoriMuddle.org/ .
Attribution (Curator's Code ): Via: Montessori Muddle; Hat tip: Montessori Muddle.