Caledon said:
So a mole is just a number, and that number coincides with the atoms in 12g of C12 at rest
More precisely, it is the number of atoms in 12 g of C12
assuming that all of the atoms are at rest. (And also, to be precise, assuming that the binding energies between the atoms are insignificant.) In other words, it is 12 g divided by the mass number of the carbon-12 nucleus.
Caledon said:
The connection I'm having trouble making is, how can this be used to stoichiometrically calculate the atoms in a given sample that is not at rest
First of all, once again, don't confuse the individual atoms being in motion with the sample being in motion. Do you do stoichiometry on samples that are flying around your lab? I'm betting the samples are sitting at rest on a table in your lab.
The fact that the individual atoms in the sample are not at rest does introduce a (very small) inaccuracy into the calculation of the number of atoms in the sample, yes. (So do the binding energies between the atoms.) But for practical purposes this inaccuracy is much too small to matter.
For example, suppose I have a lump of pure coal that is exactly 12 grams of carbon-12 atoms, as measured while it's sitting at rest in the lab. How many atoms will there be in the lump? It won't be exactly Avogadro's number (12 grams divided by the mass number of carbon-12); it will be a bit smaller, because the sample is at some finite temperature and there are binding energies associated with the covalent bonds between the carbon atoms. How much smaller? (That is, how much error am I making if I assume there are exactly one Avogadro's number of atoms in the sample?) Well, we just write down an equation similar to what I wrote above:
$$
M_0 = N \left( m_{12} + T \right) - U
$$
where ##M_0 = 12## is the rest mass of the sample (note that I'm using units in which ##c = 1##, so mass and energy have the same units), ##N## is the actual number of atoms in the sample, ##m_{12}## is the mass number of carbon-12, ##T## is the absolute temperature of the sample (measured in energy units), and ##U## is the total of all the chemical bond energies. Rearrange this as follows:
$$
N = \frac{M_0 + U}{m_{12} + T} = \frac{M_0}{m_{12}} \left( \frac{1 + U / M_0}{1 + T / m_{12}} \right)
$$
So the size of the error is just the factor in parentheses on the right. How big is that? Let's plug in some numbers.
##U / M_0## can be estimated from the heat of combustion of coal, which varies with the type of coal; the highest value I've found online is 32 kilojoules per gram, which equates to 32,000 times 10,000,000 ergs per Joule, divided by ##c^2## to get "grams per gram" of binding energy. This is a very small number, about ##3.6 \times 10^{-10}##.
##T## is just the absolute temperature in mass units, which for ##T## in Kelvins is just ##k_B T / c^2##, where ##k_B = 1.38 \times 10^{-23}## is Boltzmann's constant (again in SI units, so we have to correct for that as well to get ##T## in grams). For an ordinary temperature of 300 K, this gives ##T = 4.6 \times 10^{-35}## in grams.
##m_{12}## is exactly 12 atomic mass units, by definition, and an a.m.u is ##1.66 \times 10^{-24}## grams. This gives another very small number for ##T / m_{12}##, about ##2.3 \times 10^{-12}##. This is less than 1 percent of ##U / M_0##, so it will, at best, reduce the error slightly (since it appears in the denominator) compared to the effect of ##U / M_0##. So the total error involved in not counting the kinetic temperature or binding energy when estimating the number of atoms in the sample is at most a few parts in ten billion, i.e., way too small to matter in practical terms.