Your needs it is to generate a diagram. You do not need to use powerpoint which is a presentation software. 

To generate your diagram programmatically you can use perl/python or whatever as programming language and graphviz to make a diagram.

Using dot language to describe your diagram and circo as graphviz engine to get your expecting rendering.

As example copy this:

digraph G {

  node [shape=box];

  "Compounds 1"[ label="Compounds 1" color="red" ];

  "Compounds 2"[ label="Compounds 2" color="blue" ];

  "Compounds 3"[ label="Compounds 3" color="blue" ];

  "Compounds 4"[ label="Compounds 4" color="blue" ];

  "Compounds 5"[ label="Compounds 5" color="blue" ];

  "Compounds 1" -> "Compounds 2"

  "Compounds 1" -> "Compounds 3"

  "Compounds 3" -> "Compounds 4"

  "Compounds 3" -> "Compounds 5"

}

Paste it on http://sandbox.kidstrythisathome.com/erdos/

Note: For your purpose use twopi or circo as graphviz engine

https://paste.fedoraproject.org/461827/