For over two centuries, chemists all over the world have applied their expertise and creativity to the synthesis of new molecules. By analyzing organic syntheses reported in the literature between 1700 and 2004, we show that there exist universal statistical laws that describe how molecules are made and interconverted. Here, organic chemistry is treated as a complex network of ~7 million reactions and ~6 million compounds – the result of exponential growth in chemical “activity” over the past 300 years. We describe the details of this evolution and enable predictions for the future. We also examine the structure of chemistry, which is characterized by a small set of “core” substrates from which a vast “periphery” of compounds can be made in three or less synthetic steps. In addition to fundamental interest, we describe how any chemical process may be optimized using the knowledge of chemistry as a whole. To illustrate these methods, we describe a case study of Prochemia, a small chemical company specializing in various w-functionalized alkane thiols. By applying our pathway-generating, simulated annealing algorithm, we quickly identify the globally optimal synthesis strategy, which minimizes the costs of reactions and raw materials. Interestingly, these optimal synthetic pathways are far more cost efficient than the current pathways used by the company. Thus, this algorithm should prove interesting to other specialty chemical companies as well as larger industrial chemical manufacturers.

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