Tuesday, January 10, 2012

Go to bed. . .

Go to bed said Ms. Rabett, but Eli respectfully pointed out that someone said something wrong on the INTERNET and it's the Bunny's job to set them straight. Go to bed she replied and pulled the plug leaving Eli to hunt down the laptop.

Methane is much in the news (see Real Climate for example) and Eli wandered into a D-K moment at Judy's where one of the front pagers (notice how Judy is undercutting Tony in guest post quality?) was spitting up. Not so much wrong, as wrong for the case at hand, so the Rabett pointed to an article on methane oxidation that he had posted earlier, featuring a very nice diagram of the simplified reaction scheme from a review article by Ravishankara.

Well, harumphed the D-K poster child

So yet another Hare-brained scheme:-

H-O-O(dot) + NO(dot) (Peroxy Radical and Nitric Oxide) is generally given to generate peroxynitrous acid O=N-O-O(1-)H(1+), which then become nitric acid.

Whereas the dumb bunny has 
H-O-O(dot) + NO(dot) giving HO(Dot) + NO2(Dot).

Thus, the reaction of the peroxy radical and nitrogen dioxide is given to be a source of hydroxyl radical and nitrogen dioxide by a floppy eared fool.

Bunny actually needs the rate constants for the reaction series 

H-O-O(dot) + NO(dot) --> O=N-O-O-H

O=N-O-O-H --> HO(Dot) + NO2(Dot).
 O=N-O-O-H --> HNO3

So mister bunny, go an look up the reaction kinetics and reflect upon the implications of a bifurcated pathway where one branch is in a rapid equilibrium and the other is irreversible.
At one time or other Eli had actually looked up those rate constants for his original take, in the place to look them up the IUPAC atmospheric chemistry critical data evaluation, and surprise, the rate for the first, yielding HO and NO2 is more than two orders of magnitude faster than the second yielding HNO3, so that the relative yield of nitric acid is substantially less than 1% under atmospheric conditions. Moreover, the HO, HO2, NO and NO2 are not in a thermodynamic equilibrium, but there is a steady state situation where the sources of NOx and HOx(combustion, etc) balance the sinks such as 1a. There is an important difference between an equilibrium situation and a steady state one which Eli will get to in another post.

There are things about atmospheric chemistry (more precisely gas phase reactions) that are worth discussing because if all you have is general chemistry you miss the point as was done comprehensively by Doc Martyn, and this set of reactions is not a bad place to start.
(1) HO2 + NO --> HO + NO2

(1a) HO2 + NO --> HNO3, or nitric acid
Thus once again it becomes clear that Eli will have to stay up late correcting wrong Weblike pontifications.

The HO radical is the key reactant for atmospheric oxidation reactions, degrading stuff to water vapor and carbon dioxide. The HO2 radical acts as a reservoir species for reactive HO. Throw in some nitrogen oxides and you get

(1) HO2 + NO --> HO + NO2
(2) HO + CO --> H + CO2
(3) H + O2 + M -->HO2 + M
Reaction 2 is basic to all hydrocarbon oxidation since those schemes almost always pass through formaldehyde, H2CO which decomposes to yield CO. CO oxidation to CO2 is dominated by reaction with HO and the H atoms combine with O2 to form HO2.

What is that M you ask. Anything else. When the H and the O2 near each other, there is an attractive force between them, but it is not sufficient to stabilize HO2 unless a third body M can carry away some of the energy and stabilize the adduct. If there is no third body, the kinetic energy of the collision causes the reactants to fly apart and the addition reaction does not occur.This need for a third body to stabilize adducts is one of those things that we never get to in general chemistry, and, indeed never really need to because in solution, where general and organic chemistry are mostly done, there is always a third body provided free of charge by the solvent.

Reaction 1 has all this in spades. Looking only at the reactants, the average or sub-average chemist would say, do a Doc Martyn, clear we got nitric acid! as the product and, of course it is here that the good Doc Martyns go astray
So mister bunny, go an look up the reaction kinetics and reflect upon the implications of a bifurcated pathway where one branch is in a rapid equilibrium and the other is irreversible.
Well, true 1a is irreversible, but the rate constant is small, especially compared to 1 and the OH and NO2 products of 1 are themselves involved in a number of other fast reactions of which 1a is a termination step so real Rabetts need to be more sophisticated..

To discuss what actually happens we need a potential energy surface (PES). In the old days we did the Lamb thing and scribbled free hand, what we thought reasonable, but there are computers and ab initio chemistry programs with lots of alphabet soup (would you like a dash of DFT B3LYP/6-31 G++ with that, or perhaps some CCSD(T) sauce?) and we can get the PES, which, if not perfect, is indicative

Here the reactants start on the right, where they belong, and the products are on the left, but sometimes in the middle as will be explained. Eli has taken but slightly modified this surface from Butkovskaya, Kukui, Pouvesle, and Le Bras. J. Phys. Chem. A 2005, 109, 6509-6520

Confused? Let's take a look a some prototypes in order to gather vocabulary. There is simplification, omission and some wiggle in what follows in order to emphasize the high spots.

To the left is a PES for the typical gen chem reaction, A + BC --> AB + C with a barrier in the entrance channel. By entrance channel we mean that first thing, the reactants have to collide with enough energy to exceed the barrier in order to react. The transition state (TS) represents the lowest energy configuration which the reactants have to pass through in order to become products and the height of the transition state is the minimum collisional energy needed for the reaction to take place. If the collisional energy is lower, then nothing happens. ΔE is called the activation energy. If the collisional energy is above the TS barrier then the reaction will occur and the products AB + C will separate with kinetic energy which is the difference between the collisional energy and the potential energy of the products. In such a case the temperature dependence of the reaction rate constant has what is called the Ahrennius form k = A exp(-ΔE/kT) where k is Boltzmann's constant. Increasing the temperature of the system increases the average collision energy, and thus the rate of reaction.

Now let us look at something a bit more complicated

Here we have added a stable adduct, ABC in a potential well. If there are no additional encounters with third bodies (the divine molecules M) during the reaction (sub nanosecond times at the most), the reactants with collision energy above the barrier sail on through to form the products, AB + C, but if the pressure is high enough there are collisions which drop the activated complex ABC** down into the ABC potential well and the relative yields of AB or ABC depend on the number of collisions or, equivalently, the pressure

Finally there are radical (and radical-radical) reactions. Radicals, for Eli's purposes are odd electron species which are very reactive. Their reactions do not have a barrier in the entrance channel although there might be later ones as is the case for Reaction 1. The characteristic of a radical reaction is a NEGATIVE activation energy, so that the rate INCREASES with decreasing temperature. This is a measure of the strength of bond formation for the activated complex. The lower the collision energy, the more likely the complex is to form and not fall apart and thus the more likely that there will be a reaction.

In the next chapter RR will return to the HO2 + NO --> PES.


TheTracker said...

You're so kind. I don't do anything for gibbering idiots, other than some change for coffee or food. They probably benefit from certain charities I support. But you, sir, are a gentleman.

Tracy P. Hamilton said...

The rearrangement of peroxynitrous acid to nitric acid has a very high activation barrier, which mean it ain't happening. See

"An Ab Initio Study of Peroxynitrite and Peroxynitrous Acid: Important Biological Oxidants", Hui-Hsu Tsai, Tracy P. Hamilton, Jyh-Hsin M. Tsai, Mark van der Woerd, Joseph G. Harrison, Michael J. Jablonsky, Wim Koppenol and Joseph S. Beckman, J. Phys. Chem. 100, 15087 (1996).

Anonymous said...

Never go up against a chemist when radicals are on the line!


Robert Huie said...

HO2 + NO does react to produce HOONO/-OONO -- in solution. The acid either rearranges to HNO3 or splits to OH and NO2, with about even odds and a lifetime of about 1 s. The anion is basically stable. pKa is about 6.8. This is very important chemistry physiologically which can lead to some confusion about behavior in the atmosphere.

David B. Benson said...

I don't know about this radical chemistry.

Where is the conservative chemistry for balance?

Hafta be fair, don't we?

Tenney Naumer said...

Methane rising from the Arctic sea floor into the water vapor hanging over the ocean there -- thoughts on reactions? Would a large release cause precipitation in either rain or snow?

EliRabett said...

As Eli said there is always a third body in solution, and there are other surprises.

Anonymous said...

What makes a person think they know more atmospheric chemistry than a professional in the field? And a Nobel prize winner IN THAT FIELD? I am sure this Huie guy here also knows less than Doc Martyn (in spite of my instantly recognizing Huie).

Rib Smokin' Bunny AKA myoglobin + NO -> nitrosomyoglobin bunny AKA Tracy P. Hamilton

EliRabett said...

No, Eli knows Bob, and Bob knows what he is writing about:)

Anonymous said...

To cover up the damages in progress, by using methane for misleading; Warmist used another dirty trick. You will be shocked about those damages; first here is their trick:

The good Lord made, methane to be produced as a compound with other heavier elements. By itself, methane is odorless; but is very smelly, when produced. The ‘’smelly’’ bit is the organic particles, the SINKER; to make it to sink in the ground. After, those organic particles disintegrate deep in the soil. Warmist to discredit me, they point that; methane is not as heavy as air. Well, they don’t have to tell; how does it sink? Why is so much of it in the ground for fracking, how did it get their; why are they not fracking for methane in the clouds, instead deep down in the ground?! Many times they go to Antarctic, Greenland and bring lots of lies. For you is cheaper to believe them, than to go there in person and see that they are lying. But for methane is NOT necessary – because all of you are producing it! Admit that it smells, when fresh, is not pure / odourless!

Same as when the cow is belching, or releasing methane from the other end. ‘’METHANEGATE’’ is to cover up the smell. Well, unless the Green People go behind every cow, elephant, bison and instantly purify the methane = they are hiding the stench, to use methane for destroying the grazing animals. P.s. methane produced from coal doesn’t smell; that’s where the ‘’canary in the coal-mine’’ comes from. In the coal-mine the good Lord didn’t need to invent something, to make methane to sink, because is produced in the ground.

Organically produced methane above the ground, is never in a pure form. You don’t need to go and sniff the cow’s exhaust, grass clipping from the lawnmower after a week smell same as the cows methane. Simple proof of Warmist ‘’Methanegate’’. Please read the rest on my blog, to see what you are really covering up; it will knock your socks off. If you have any integrity, you will apologise to me, and most important; to the people that trust you


David B. Benson said...

Since methane removal is hydroxyl limited it seems this imples the concentration of methane continues to grow once the hydroxyl limit is reached.

[Again, I am unable to add a comment, only can reply to a prior comment.]

Robert Huie said...

Maybe that's the problem conservatives have -- most of atmospheric chemistry is radical chemistry. (Of course, all of combustion chemistry is, but they probably don't know that.)