Name:______________________ Section: ________________

Energy Content of Food

Introduction:

Computational chemistry and molecular modeling are areas of theoretical chemistry used to solve
application-oriented molecular problems for a wide range of systems. Modeling calculations and
computational chemistry have thus naturally entered applied sciences such as materials science, food
science, human nutrition, pharmacology and industry. Computations can complement experiments by
offering molecular details of what is happening.

Two common models that are used in molecular modeling are quantum mechanics and molecular
mechanics. These models enable the energy of any arrangement of the considered atoms and molecules
to be calculated, and allow the modeler to determine how the energy of the system varies as the positions
of the atoms and molecules change.

Quantum mechanical calculations determine energies and other properties by solving

Schrödinger’s equation. Different methods within this group are characterized by different levels of
approximation. This leads to two main flavors of quantum calculations a) ab initio methods, based on
fundamental principles, very precise but computationally costly; and b) semi empirical methods, which –
to simplify calculations – neglect certain interactions or use experimentally derived parameters.

One semi empirical method is PM3, which we will be using for this lab. The PM3 method was built
on earlier models but the latest iterations include the Dewar et al. work from 1985 where they published
a version, naming it AM1 (Austin Model 1). This method was parameterized for H, B, C, Si, N, P, O, S, F,
Cl, Br, I, Al, Hg, Zn, Ge, Sn. This system predicts formation energies and geometries for organic molecules.
In 1989 J. J. P. Stewart re-parameterized AM1 to get PM3 (Parametric Method 3). The parameters were
evaluated differently and new atoms were added in addition to those atoms mentioned above, As, Be, Bi,
Cd, Ga, In, Mg, Pb, Sb, Se, Te, and Tl.

In the molecular mechanics model, molecules are visualized as an assembly of atoms connected
by bonds, and molecular energy is expressed as a sum of terms which correspond to bond, angle, torsion,
van der Waals and electrostatic interaction energies. The calculated potential energy of the system
depends on the relative positions of the atoms with respect to each other and it returns energy as a
function of conformation. The mathematical form of the energy terms varies among the different force
fields. We will be using the UFF (universal force field) method to quickly obtain good starting geometries
for molecules.

Simulations carried out at the atomic level start with only the atomic numbers of the elements
and the bonding between atoms (intra-molecular forces). Complex molecular structures can be drawn
and manipulated on the PC screen, and can be visualized according to different representations, e.g. balls
and sticks, overlapping spheres, tubes. In some cases, the interaction between molecules can also be
modeled effectively (inter-molecular forces), providing insights into material properties.

In this laboratory we will use the lab computers to optimize geometries and determine the
formation enthalpies of nutrients and their combustion products using a semi empirical method (PM3).
The goal is to estimate the energetic content of some common foods.
 Foods are made of many substances,
which can typically be found summarized on the
food label. For this lab we will be representing
the three main components responsible for the
energy content in food, carbohydrates, fats,
and proteins, which are listed on food labels.
Carbohydrates will be represented by glucose,
fats by stearin, and proteins by the
phenylalanine-aspartic acid dipeptide. The
structures of the compounds are shown to the
right. To model the energy available to your
body to do work we will determine the heats of
combustion and compare these to the energy
labels of food.

The combustion reaction for each of

these compounds is:

Glucose

𝐶6 𝐻12 𝑂6 + 6 𝑂2 → 6 𝐶𝑂2 + 6 𝐻2 𝑂

Phenylalanine-aspartic acid

𝐶13 𝐻16 𝑁2 𝑂5 + 13 𝑂2 → (𝑁𝐻2 )2 𝐶𝑂 + 12 𝐶𝑂2 + 6 𝐻2 𝑂

Stearin

2 𝐶57 𝐻110 𝑂6 + 163 𝑂2 → 114 𝐶𝑂2 + 110 𝐻2 𝑂

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 Recall that the enthalpy for a reaction is determined by:

∆𝐻𝑟𝑥𝑛 = ∑ 𝑛𝑚𝑜𝑙𝑒𝑐𝑢𝑙𝑒 × 𝐸𝑚𝑜𝑙𝑒𝑢𝑐𝑙𝑒 − ∑ 𝑛𝑚𝑜𝑙𝑒𝑐𝑢𝑙𝑒 × 𝐸𝑚𝑜𝑙𝑒𝑢𝑐𝑙𝑒

𝑝𝑟𝑜𝑑𝑢𝑐𝑡𝑠 𝑟𝑒𝑎𝑐𝑡𝑎𝑛𝑡

Here, 𝑛𝑚𝑜𝑙𝑒𝑐𝑢𝑙𝑒 is the molecular coefficient for the combustion reaction and 𝐸𝑚𝑜𝑙𝑒𝑐𝑢𝑙𝑒 is the energy we
will obtain from the calculations. There are also many units to describe energy and we will need to be able
to convert between a few useful forms. One especially confusing point to pay close attention to is the
difference between a thermochemical calorie (cal) and a dietary calorie (Cal).

1 𝑘𝐽 = 0.239 𝑘𝑐𝑎𝑙
1 𝑘𝑐𝑎𝑙 = 1 𝐶𝑎𝑙
𝑘𝐽
1 𝐻𝑎𝑟𝑡𝑟𝑒𝑒 = 2625.499
𝑚𝑜𝑙

Procedure:

Drawing water

1. Open the program Avogadro

2. Under Draw Settings select oxygen

3. Left click somewhere in the large drawing area (in the View 1 tab) to place an oxygen atom. The
program automatically places two hydrogen atoms bonded to the oxygen. Congratulations you
have drawn water! You can fully enjoy this rich 3-D structure looking at it from different views by
selecting the navigation tool ( ) and left clicking and dragging in the black
area.
4. Now we want to make sure we have a good guess geometry. To quickly do this select the icon for
energy minimization ( ). Then Start the optimization, this should take
about 1 second. The progress of the optimization can be monitored by the energy values in the
top left window where the molecule is drawn. When the values no longer change make sure to
stop the calculation by clicking the Stop button.

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5. We now need to prepare the input for a semi empirical PM3 quantum mechanical calculation. We
can do this in the menu under Extensions  Orca  Generate Orca Input.

Save the file by selecting the Generate… button. We want to remember what the file is called and
where it is for later, so save the file in Data (D:), perhaps naming it h2o.inp
6. Now we need to specify the calculation to run in the input file. Open the location in Windows
Explorer and navigate to Data (D:). Open ‘h2o.inp’ by right clicking on the file and selecting Open.
In the popup that appears choose Select a program from a list of installed programs. Then select
OK. Scroll down to the bottom of the list and select WordPad, then click OK. The file should be
open in WordPad now. Edit the file to look like the below input (you only need to change the line
beginning with an exclamation point !). Now save the file and it is ready to calculate.
# avogadro generated ORCA input file
# Basic Mode
#
! pm3 opt

* xyz 0 1
O 0.94650 1.48999 0.00986
H 1.91438 1.53037 -0.01306
H 0.66765 2.29706 -0.44823
*

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Submitting A Calculation to Run (a file called h2o.inp in this case)

7. We now need to tell the calculation to run. To do this we need to open a command prompt by
going to the Start menu and searching for cmd and opening cmd.exe. We need to go to to our
input file by changing to its directory by typing
d:
and then press enter. We can now run the calculation by typing
C:\Orca\orca h2o.inp > h2o.out
and then pressing enter. This will take a few seconds to complete. You will know it is done when
D:\> shows up again.
Example of calculation still running

Example of calculation complete

8. The calculation is now complete and we can analyze the results. Open ‘h2o.out’ by right clicking
on the file and selecting Open. In the popup that appears choose Select a program from a list of
installed programs. Then select OK. Scroll down to the bottom of the list and select WordPad,
then click OK. The output text might look messy, to fix this in WordPad make sure ‘No wrap’ is
selected for word wrapping (see below).

Scroll down to the bottom and make sure you can find the line that contains:
****ORCA TERMINATED NORMALLY****
This tells us everything went as planned. If you cannot find this line ask your instructor for help. If
you have found this line we can now get the energy from the calculation by scrolling up a bit from
the bottom until you see:

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 ------------------------- --------------------
FINAL SINGLE POINT ENERGY -75.960123535056
------------------------- --------------------

Write down the energy you see on the lab report sheet. The unit of this energy is Hartrees.

Draw and Calculate O2

O2 is a bit more challenging than water. We need to tell the programs which atoms are where and
what type of bond connects the atoms (See pictures below for reference). First, change the atom
to Oxygen (8) for the Element and change the Bond Order to Double. Left click and hold
somewhere on the black screen, when you drag the cursor you should see a second oxygen atom.
Release the left click. If the newly placed atom looks strange (bond too short or long) you can do
a quick optimization to make things look reasonable by pressing Ctrl + Alt + o . Remember to do a
quick optimization ( ) before saving, editing the file, and running the
calculation. One thing that will need to be changed for only the oxygen input file is the multiplicity,
this is done by changing the 1 to 3 to specify a triplet, see just below for what the input file should
look like. The calculation can now be run, referring to above for doing this.

# avogadro generated ORCA input file

# Basic Mode
#
! pm3 opt

* xyz 0 3
O -0.44959 -0.39087 0.00000
O 0.83166 -0.43461 0.00000
*

Draw and Calculate CO2

CO2 is a bit more challenging than water. We need to tell the program which atoms are where and
the type of bond connecting the atoms (See pictures below for reference). First add the carbon
atom. Now select Oxygen (8) for the Element and change the Bond Order to Double. Left click and
hold somewhere near the carbon and drag the bond to carbon. Repeat this for the second oxygen
on the opposite side (remember if things looks strange you can do a quick optimization to make
things look reasonable by pressing Ctrl + Alt + o ). Remember to do a quick optimization (
) before saving, editing, and running the calculation (referring to above
for doing this if necessary).

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Draw and Calculate Urea

Draw, optimize, create input, edit the input and run the calculation for urea. The blue spheres
are nitrogen atoms.

Draw and Calculate Glucose

This structure is a bit more complex than we have drawn so far. Sometimes when things get too
complicated you can obtain structural information from somewhere. To get the glucose structure
Select Build > Insert > Fragment… as shown below. Under cyclic_sugars select
alpha-D-glucopyranose.cml and press Insert. It probably looks strange since all atoms are selected
and appear blue, to make it look normal select Edit > Select none. Now we have a good starting
structure to create the input file with, edit the calculation method, and run the calculation.

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Draw and Calculate Phenylalanine-aspartic acid

To speed up the drawing of this structure there is an input file ready to go. The file is located in
L:\Departments\Math-Science-Engineering\BRose\phenasp.inp . Copy this file to D: and run the
calculation. You can look at the output structure in Avogadro by opening the output file, likely
phenasp.out, to take a look and make sure all atoms are there and properly connected.

Draw and Calculate Stearin

This structure takes some time to build and would be an exercise in tedium. To make things easier
the file is located L:\Departments\Math-Science-Engineering\BRose\stearin.inp . Copy the file to
D:\ and then run the calculation. This will take a few minutes, use this time to start the conversions
and calculations on the report sheet.

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 Report Sheet
Enter the energy from each molecule, only 5 digits to the right of the decimal point are needed.

molecule Energy (Hartrees) Energy (kJ/mol)

𝐻2 𝑂

𝑂2

𝐶𝑂2

Urea, (𝑁𝐻2 )2 𝐶𝑂

Glucose (𝐶6 𝐻12 𝑂6)

Phenylalanine-aspartic
acid (𝐶13 𝐻16 𝑁2 𝑂5)

Stearin (𝐶57 𝐻110 𝑂6)

𝒌𝑱 𝒌𝑱 𝑪𝒂𝒍
Combustion of X ∆𝑯𝒓𝒙𝒏 ( ) ∆𝑯𝒓𝒙𝒏 ( ) ∆𝑯𝒓𝒙𝒏 ( )
𝒎𝒐𝒍 𝒎𝒐𝒍 𝒐𝒇 𝑿 𝒈 𝒐𝒇 𝑿

Glucose (𝐶6 𝐻12 𝑂6)

Phenylalanine-aspartic
acid (𝐶13 𝐻16 𝑁2 𝑂5)

Stearin (𝐶57 𝐻110 𝑂6)

Show conversions for the combustion of glucose:

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Additional Calculation Space:

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Now get a nutrition label from your instructor.

1) What is the food?

2) Use the energies calculated above and the amounts listed on the nutrition label for one serving
to determine the energy content in one serving of your food.

One serving Energy Content, from Energy Content, from label

amount (g) calculations (Cal) (Cal)

Carbohydrate

Protein

Fat

Total

3) % relative error between calculation and label.

4) Discuss one reason for the error between the label and your results. (Hint: What could
contribute to accuracy being a large source of error?)

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 Prelab

The combustion reaction for acetylene (𝐶2 𝐻2 ), commonly used for welding, is:

2 𝐶2 𝐻2 + 5 𝑂2 → 4 𝐶𝑂2 + 2 𝐻2 𝑂
The energy of each component has been calculated and is given below

Molecule Energy (kJ/mol)

𝐶2 𝐻2 -203015.8

𝑂2 -394683.4

𝐶𝑂2 -495163.7

𝐻2 𝑂 -200657.56

1) Determine the enthalpy change for this reaction (∆𝐻𝑟𝑥𝑛 ) in kJ/mol. Show your work.

2) What is the enthalpy change per mole of acetylene? Show your work.

3) If 32 g of acetylene are burnt how many kJ of energy will be released? Show your work.

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