[minimal]

Ok, I think I have some conflicting data about what the effects of increasing heat will have on producing weak bonds, or removing weak bonds.  Now, weak bonds will obviously be broken easier under heat, as they cannot handle the stress.  However, isn't a greater amount of heat needed to yield products that are not favored? (higher energy states?)  Aren't these higher energy states synonymous with weaker bonds?
I'm a little confused, because I have asked (on this site) about PCR, and if you have the primer annealing to unwanted areas, whether you would raise or lower the temperature.  The answer given to me on this site was that you would raise the temperature, in order to break the wobble bonds.  However, I'm looking at a Roche applied sciences PCR manual, and it says if the Primer Annealing parameter value (50-65 C, 30-60 s) is higher than optimal, you would get formation of nonspecific products.  Is this not to say that this non specific higher energy (essentially weaker) bonds would occur?

edit: Ok, reading further into the Roche applied sciences requirements for the primer annealing temperature, it says if the temperature is too low, non-specific annealing will increase dramatically.  That being said, I'm still a bit confused, because I was under the impression if you wanted 'weird' products to form, you'd have to crank the temperature up, or do something similar (use of enzymes or other catalysts) to generate these products.

[enahs]

I have no comment on your specific question about the annealing (I am not even sure if that is a chemical process, just a physical one).

But with regards to this question:

However, isn't a greater amount of heat needed to yield products that are not favored? (higher energy states?)

First, I assume you mean Thermodynamically non-favored. Kinetics and Entropy play a large role, as in being kinetically and entropically favorable also determines if a reaction occurs or not .

However, with regards to the thermodynamics, you should probably look into the concept of Activation Energy.


All the above (Thermodynamics, Activation Energy, Entropy and Kinetics) are crucial into what will form and why and at what conditions, etc. But the activation energy concept is what I think you might be lacking.

[minimal]

Sorry, what I mean is that to produce reactive products (such as a peroxide), it requires adding more heat, not less, correct? But then more heat would also destroy that bond (assuming there are other options for the products - such as an alkene). 
I'm not sure what you mean between the difference of chemical and physical processes, but what I am referring to is done in vitro, and is the hydrogen bonding of a primer (complementary sequence), to a particular strand of dna.

edit: nevermind I think I just figured it out.  If you want products that are reactive and unfavored, you have to have the solution hot enough to break the bonds of the favored reactants and products, and some unfavored product will be produced.  However, if you want to remove the unfavored product, you must go hot enough to disrupt its bonds, but not high enough to disrupt the favored bonds.

[minimal]

can I just get some confirmation from someone that that last statement (the edit) of mine is indeed correct?