Not until ...did...表示“直到...”意思.not until 提前,倒装语序,表示强调.
本句话翻译:直到19世纪初,科学家们才知道所有的物体都是由原子构成的.
the beginning of the 19th century 是个时间名词.
本句话正常语序应该是:Scientists didn't know that all matter is made up of atoms until the beginning of the 19th century .
把the beginning of the 19th century 只是为了强调突出作用.
而 at the beginning of the 19th century 搭配确实不错,但只适用在作状语的情况下.由did一词可以看出the beginning of the 19th century 在这里做的不是状语,一次不能用at.