A friend helped me to understand the chemistry behind these characteristic sake parameters; san-do (acid level) and amino san-do (amino acid level). It is not that complicated once the basics are explain but without understanding the basics it is impossible to really know what is going on.
Foundational concept: the mole. A mole is a quantity of objects like a dozen. It allows us to map reactions between individual molecules and atoms and more manageable quantities like grams and liters. One mole of hydrogen is 1 gram. Hydrogen is the simplest and lightest atom with one proton and one electron. The electron weight is so small it is insignificant in comparison to the proton. So the proton as hydrogen itself has an atomic weight of 1. Each atom has an atomic weight, ignoring electrons, equal to the number of protons and neutrons it contains. The neutron weighs the same as the proton.
A carbon atom has 6 protons and 6 neutrons and thus has an atomic weight of 12. Because the carbon atom is 12 times that of hydrogen one mole of carbon would also be 12 times the weight of hydrogen or 12 grams.
Foundational concept: molarity or moles/Liter. To create a one molar solution (solution of one molarity) of carbon in water simply place 12 grams of carbon in a one liter container and add water until reaching the one liter level. When we talk about the concentration of elements based on chemical reaction equations we do so in molarity or moles per liter.
Foundational concept: pH, a measure of acidity. The pH of a solution is a measure of how acid or base a solution is with a pH of 7.0 being neutral. Technically speaking
pH = -log(aH+)
where aH+ is the effective H+ or hydrogen ion concentration. A hydrogen ion is hydrogen minus its electron (or a naked proton if you will). The higher the concentration above 10-7 the more acid the solution and the farther below 10-7 the more base the solution. While a pH of 7.0 is considered neutral, a pH value of 8.2 is used for titration. As near as I understand, the reason is because of the use of phenolphthalein as an indicator of neutrality. Phenolphthalein changes color in a solution that reaches a pH of 8.2. Given this “neutral” point is used when using the indicator, it is also used when using a pH meter so that the results will be the same either way.
Now what does all this have to do with measuring the san-do of sake? Well, we can use pH and some basic analytical chemistry to estimate the amount of acid in sake. To do this the first thing we do is choose a representative acid to estimate. This is important because it gives us a chemical compound description and an atomic weight. Given this the more similar the acid is to other acids in the item to be measured the more accurate the estimate will be. The acid used for sake is succinic acid which can be written as SuH2. For wine tartaric acid is used and is written as H2C4H4O6. Given the acid we can consider reactions that will provide an indication needed to estimate the concentration.
SuH2 + 2NaOH –> 2H2O + SuNa2 which is a reaction of an acid + base –> water + salt.
The two hydrogen ions in SuH2 combine with the 2OH in 2NaOH to form water while the Su and 2Na combine to form SuNa2 a salt which provides all H+ with an electron to neutralize them. Hence, by using NaOH we can change the pH of our sample in direct relation to the amount of SuH2 present. So, the amount of NaOH needed to bring the sample to neutral will be the amount needed in the above reaction to remove all SuH2. This gives a direct indication of the amount of SuH2 present and hence the estimate we want. The formula used for this is:
Which says that the concentration of acid (C1) in the sample volume (V1) divided by the molar ratio (n1) is equal to the known concentration (C2) of NaOH added (V2) to make the combined solution neutral divided by its molar ratio (n2). In the reaction above for succinic acid, n1 and n2 are 1 and 2 respectively because for each SuH2, 2 NaOH are needed for the reaction (see the reaction equation).
We can rewrite this equation to give the estimated value we want, the concentration of succinic acid (C1):
Recall that concentrations are in moles per liter or molarity. To convert the moles per liter to grams of succinic acid per liter the atomic weight of succinic acid is multiplied by its molarity. The molecular mass of succinic acid is 118. Given this to go from molarity to grams per liter we just multiply C1 by 118 to get the grams of succinic acid per liter. Given this and the values of n1 and n2, our estimate is:
That is all there is to finding the san-do or acid level as succinic acid in sake. Finding the amino san-do requires a little more work. As with san-do, amino san-do follows a similar procedure. In fact the first step in estimating amino san-do is to follow the same procedure as that for san-do. However, if you are not interested in san-do there is no need to go to the work to generate the actual estimate. On the other hand if you would like to have estimates for both the san-do and amino san-do then collecting the needed information to estimate san-do while doing the procedure for amino san-do estimation is a trivial addition.
The first step in estimating the amino san-do is to follow the same titration procedure as estimating san-do. This neutralizes the sake sample so the acids are no longer present. Recall they are converted to water and salts.
As we did with the acid above we need to choose an amino acid to represent the overall amino acids in the sample. For sake, glycin, CH2NH2 COOH, is used. Glycin is chosen because it is the simplest of amino acids. Amino acids. In general, amino acids have the structure CHRNH2 COOH. Notice that one of the H in glycin has been replaced with R for the general structure. R can be a very complicated structure so it is just a place holder for whatever sets in this position. For example, R is an H in the case of glycin. Anyway, COOH is the organic acid component of the amino acid and what makes it an acid. This first titration step remove the hydrogen ion from COOH
CH2NH2 COOH + NaOH –> CH2NH2 COONa + H2O
As before, this reaction is an acid + base –> water + salt but where the salt is an amino salt. So at the end of step 1 the interesting component remaining is CHRNH2.
The second step is to add formalin solution that has been adjusted to pH 8.2 and doubled in volume with distilled water to the sample. Formalin is a saturated solution of formaldehyde (37% by mass) in water. The formalin solution converts one of the hydrogen atoms to a hydrogen ion. Basically, the following reaction:
CHRNH2 –by formalin–> CHRNHH+
By exposing the hydrogen ion we can now, in the next step, use a reaction through titration to understand how much CHRNH2 is in the sample. Since the amount of CHRNH2 is the same as the amount of glycin we will have an estimate of the glycin in the sake sample.
In the third step we again titrate with an NaOH solution to estimate the number of glycin molecules based on the following reaction:
CHRNHH + NaOH –> CHRNH + Na + H2O
As before we use the equation for estimating the molar concentration, repeated here:
However, unlike before, only one NaOH is required in the reaction equation for every CHRNHH+ so both n1 and n2 equal 1 and hence they can be removed from the estimating equation:
As glycin has an atomic weight of 75 the final equation to estimate the amount of amino acids as glycin (that is the amino san-do) in the sake sample is:
That is the chemistry behind the san-do and amino san-do measurement procedures. I hope I have been able to explain this in a way that is clearer then nigori
 My fried is Jonathan Musther of New Zealand.
 Here I am using SuH2 to represent C4H6O4 to emphasize the two hydrogen ions present.