The large chemical suppliers mainly sell popular, often bought products. Since there are many orders for these chemicals, they have local warehouses; products from these warehouses can be shipped quickly and cheaply. The rare chemicals in their catalogs are very expensive that hides shipping expenses.

Novell, unique and rare compounds are bought less often. Their suppliers keep a centralized warehouse. Products then are shipped from this warehouse to wherever the buyer works. And that can be anywhere in the world. An order might be shipped from Germany to United States or Japan. Such shipping is more expensive than the local shipping for the basic chemicals. See shipping rate comparison. 

Why don’t rare chemical suppliers simply add shipping expenses to product prices? Then their shipping and molecule prices would be comparable to the large chemical supplier prices.

If you order just one or two compounds, then there is little difference if shipping charges are already included in the product price or are charged separately. But what is you need 5, 10 or even 100 compounds? In this case it is best to list prices of products and shipping separately.

For example, if you want to order 10 screening compounds that each cost 1 mg USD 26.00, you will pay USD 260 for the compounds, and USD 120 for shipping and handling. The total will be USD 380. Similar rare compounds sold by the basic chemical suppliers might cost USD 200 for each compound. The shipping might be free, but the total cost would be USD 2000. So even with the expensive shipping rare compound suppliers deliver products cheaper. You just see explicitly how they arrive at USD 146 for one compound compared to free shipping price of USD 200 at the basic chemical supplier.