Pauling spent most of his time in 1929 solving more molecular structures using x-ray crystallography. But here as well he found himself stymied. If a structure in which he was interested involved more than a few atoms, it was almost impossible to solve using the x-ray patterns alone. The problem again involved mathematics, this time the terrific calculations needed to translate into three-dimensional structures the patterns sprayed on photographic plates by diffracted x-rays. The more atoms involved in the molecule, the more complex the patterns and the more structures that were theoretically possible. Each added atom greatly increased the difficulty.

Pauling and other researchers faced this problem as the easier crystals were solved and they turned their attention to more complex substances. Soon Pauling was employing "human computers" — bright, diligent young mathematicians — just to do the needed calculations.

There had to be an easier way. By the late 1920s, Pauling and other researchers in the field, notably Sir William Lawrence Bragg in Britain, began to understand that basic structural patterns were often repeated in different crystals. Pauling used this observation, along with what he knew about quantum mechanics, ionic sizes, published crystal structures, and the dictates of chemistry, into a set of simple rules indicating which basic molecular patterns were most likely in complex crystals. These guidelines allowed Pauling to develop a relatively simple step-by-step procedure for eliminating scores of unlikely crystal structures and predicating the most likely ones. Soon researchers were calling his set of ideas "Pauling’s Rules."

He first published the rules in late 1928 as a contribution to a set of papers written in honor of Sommerfeld's sixtieth birthday — a fitting tribute to the man who had taught him to use whatever was needed to get to a good solution — and put them forward in more detail in the Journal of the American Chemical Society (JACS) the next year.

Pauling employed his rules with great success. In 1929 and 1930 he worked out the structure of mica, a silicate whose tendency to split into thin, flexible, transparent sheets Pauling discovered was due to a layered crystal structure with strong bonds in two directions and weak bonds in the third. He then compared mica to silicates that, while similar in chemical makeup, differed greatly in form. Talc, he found, also had a layered structure, but one that was held together so weakly in two directions that it crumbled instead of split. Another group of silicates called zeolites interested researchers because of their ability to absorb some gases, including water vapor, but not others. Pauling discovered that zeolites were honeycombed with passages so tiny that they formed molecular sieves, letting in only molecules small enough to squeeze through and keeping out others.

Before the publication of his rules for solving complex ionic crystals, Pauling had been known as a promising young crystallographer. Afterward, he was propelled into the first rank.