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Welcome all seeking refuge from low carb dogma!

“To kill an error is as good a service as, and sometimes even better than, the establishing of a new truth or fact”
~ Charles Darwin (it's evolutionary baybeee!)

Thursday, March 28, 2013

The BE&HM Series ~ Part VII: Chemical Reactions


It's been a while here, and I'd really rather move forward on some other topics, but I had most of this already in the "hopper" and wish to refer to it in a coming post on calories, so a couple of shorties here.  Also since it's been a while, here are links to the other posts in this series (in order): Biophysical Electrochemistry and Human MetabolismPart II: Atoms & The Periodic TablePart III: The Main Group Elements, The Octet Rule and IonsPart IV:  Ionic Compounds, Elements & Oxidation State DefinedPart V:  Covalent Bonding & MoleculesPart VI: Electron "Ownership" & Polarity.

Most of this is copied from another post here at the Asylum, so if it seems familiar to any regular readers, that's why.  I'm going to be using the combustion of methane as an example in the next post on oxidation, so I might as well use it as an example here.  

The main characteristic of a chemical reaction is that bonds between atoms in compounds are broken and/or formed such that the composition of that matter and its properties change.   We read chemical reactions from left-to-right:

Reactants → Products

Thermodynamics tells us whether the reaction can proceed in that direction (but not if it will or the rate at which it proceeds).  Methane reacts with oxygen to form carbon dioxide and water.   

CH4 + O2 → CO2 + H2

The reactants are CH4 and O2 and the products are CO2 and H2O. The equation as written is unbalanced and incorrect because the numbers of each atom in the reactants and products are not the same. Above there are 1C, 4H and 2O in the reactants, and 1C, 2H and 3O in the products. We balance the reaction by playing with the proportions of the components:

CH4 + 2O2 → CO2 + 2H2

The numbers in front of the  O2  and H2O are like the coefficients of variables in an algebraic equation, so, for example, we have 2*2 = 4 O's on the left and 1*2 + 2*1 = 4 O's on the right.   Since we are usually dealing with billions upon billions of atoms/molecules,  we talk about a standard number of them called a mole instead of individual molecules:  1 mole = 6.02 x 1023 atoms or molecules.  So the equation reads:
  
                 1 mole CH4 reacts with  2 moles O2 to produce 1 mole CO2 and  2 moles H2O  

Stoichiometry is that strange word for this chemical math.   chemical reaction is, on the most basic level, a rearranging the atoms from one molecular arrangement to another as crudely depicted below.
image link
The above is oversimplified -- the cloud of isolated atoms in the middle is almost certainly NOT the mechanism by which this occurs -- but it's OK for the purposes of this post.  In order to convert methane and oxygen to carbon dioxide and water, we must break four C-H bonds and two O=O double bonds, and then form two C=O double bonds and four O-H bonds.  The energy to break/form bonds is referred to as enthalpy, H, and can be thought of as energy stored in the molecule.  We can determine this stored enthalpy for the components of the chemical reaction and plot it vs. the "reaction coordinate" which is the progress of the reaction.  Such a diagram looks like the one at right.  Combustion is an example of an exothermic reaction.  Essentially some of the internal enthalpy of the reactants is released to the surroundings in the form of thermal energy, heat.  In a chemistry lab one will often be asked to feel the reaction vessel after mixing some chemicals, and if it warms this is evidence of an exothermic reaction.    

We use the delta, Δ, notation to denote "the change in" something:   ΔX  = Xafter - Xbefore .  For a chemical reaction:
ΔHrxn = Hproducts - Hreactants  

For the combustion of methane (sourceΔHrxn = -890 kJ/mol methane, so one way to think of this is to write the reaction as:

CH4 + 2O2 → CO2 + 2H2O  + 890 kJ Heat

Note that energy is constant in a closed system.  If we are able to contain combustion in a thermally insulated vessel of some sort that we shall call the surroundings:   

Htotal,closed system = Hrxn + Hsurr          ΔHtotal, closed system = 0          ΔHsurr = - ΔHrxn

So the reaction components lose 890 kJ energy when they react and rearrange, and this energy "lost" by the reaction is "gained" by the surroundings as heat. 

Before moving on, note that there is a threshold energy, Ea = activation energy, that must be exceeded before the reaction proceeds.  This is a very generic depiction of reaction energetics and the implication that there is a relationship between the magnitudes of ΔH and Eis misleading  in the diagram.  You can have reactions with small  Ea and large ΔH, and we can have reactions with large Ea  and small  ΔH, both small, both large, you get the picture.  The reactants "transform" to what is called the "activated complex" or "transition state" at the peak of the curve and then proceed downhill.  One can draw the analogy to a car at some higher elevation than another, it will roll downhill given a path to do so.  If it's on the other side of a hill, it must make it to the top of the hill requiring gas to get there, but once over the top, you can shut off the engine and coast down to the bottom.

Reactions can also be endothermic.  Both are shown below:


In this direction, there's a greater "hump" to overcome as well as energy being "required" .   But all chemical reactions require overcoming a threshold before the reaction proceeds spontaneously.  If this were not so there would be no stable molecules.  

Enthalpy is not the only energetic term in consideration, or otherwise only exothermic reactions would likely ever occcur!   The whole picture includes an entropy term, ΔS that combines with enthalpy to determine "free" energy  ΔG:     G = H - TS   or    ΔGrxn =  ΔHrxn  - TΔSrxn



Biochemistry Note:  I may revisit this and flesh out the full energetics, or address it elsewhere at some point.  It is my position that we don't really need to bother with the entropy in the types of discussions I'm about to enter into, and here's why:
  1. The major energy "currency" of the human body is adenosine triphosphate, ATP
  2. The vast majority of ATP production from the breakdown of all three macronutrients is from the point of acetyl CoA onward (Krebs/TCA and the ETC) through common pathways, and 
  3. ATP subsequently fuels energy requiring processes.  
In these processes, we have interconversion of chemical energies.  There are many who are generally first (and perhaps only) exposed to thermodynamics in the physics/MechE context of the steam engine/Carnot cycle.  In that context, the heat energy released is converted to mechanical work -- a conversion that is never 100% efficient -- this loss is chalked up to entropy.  This is not a knock on those to whom I refer, it is merely a statement of fact.  In the ATP (and related) coupled reactions scenarios, we don't have these losses because humans do NOT work by trying to convert thermal energy to mechanical energy like steam engines.

20 comments:

Nigel Kinbrum said...

Ooh, science! Will you be blogging about catalysts, enzymes etc?

Princess Dieter aka Mir said...

Good. I was great at my chemistry and microbiology classes in college--even won some contest thingy-- but that was 1982/83, and I've forgotten most. Refreshing is good. :D

T said...

At about the 33-minute mark of this: http://www.fatburningman.com/mat-lalonde-on-nutrient-density/

Sounds like you guys are similar.

blogblog said...

Animals, including humans, don't burn food in pure oxygen (calorimetry). We absorb nutrients after food has been processed by our gut microbiota. The variations in our gut microbiota largely determine how much energy we absorb and whether we become obese or diabetic.

The Caloric content of our food is really nothing more than a convenient convention with little basis in reality. eg PUFA and MCTs are metabolised in a totally different manner despite having an identical caloric value.

Evelyn aka CarbSane said...

A bit ... going more in the redox direction here.

Evelyn aka CarbSane said...

:)

Evelyn aka CarbSane said...

Kraken fan here :) I must disagree a bit with the part you cite in that I don't see a whole lot of DOCUMENTED deficiencies in our country. Even a lot of our junk is fortified.

Evelyn aka CarbSane said...

Our gut microbiota play a very small role in our nutrient processing and absorption.

Evelyn aka CarbSane said...

Charles feel free to repost your comment in a more appropriate thread. :)

Harry's Acolyte said...

Charles is now slamming you on the "Saner" blog. If that's him, he needs to get a life (maybe I do too). If it's not, he needs to know that he's being imped.

Evelyn aka CarbSane said...

I think it is him. Ironic that he posted links to paleodrama in this thread.

Jane said...

Evelyn, did you see a comment I tried to post here about fortification of junk? There was another on an earlier thread about meat making the colon alkaline. It doesn't matter at all, I just need to know whether I pressed the wrong button.

Evelyn aka CarbSane said...

I may have missed it.

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