Organic Synthesis Software

Organic Synthesis Software

Reduce the time between chemical target conception and laboratory execution with our new platform for virtual synthesis. The software allows you to filter millions of data points to suit your preferences and find optimized routes to your toughest queries in medicinal chemistry and drug discovery.

This “chemical thinking” software relies on a knowledge base of tens of thousands of expert-defined rules of chemical reactivity, combined with proprietary algorithms to scrutinize millions of synthetic pathways and choose the routes that lead to desired targets in the most cost-effective way.


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   Software and Service Offering



 Full Retrosynthetic Pathway Design of Known and Unknown Targets

Retrosynthetic analysis is an intellectually intensive process. Currently, chemists rely on their knowledge and literature databases to design a suitable synthesis for their target molecule.

The retrosynthesis module in our organic synthesis software quickly navigates back and forth through synthetic possibilities as though evaluating chess moves with a virtual assistant. Starting from a known or unknown target molecule, the module can design a synthetic pathway in times ranging from seconds to hours, depending upon its complexity, while keeping track of the chemical context of each intermediate.

Built on:
  • Reactions
  • Reaction classes
  • Conditional rules
Accounts for:
  • Indirect chemical environment
  • Substrate groups needing protection
  • Group incompatibilities
  • Stereo-and regio-chemistry

Easily filter out overly complex synthetic trees, flag cross-reactivity conflicts, and specify other custom preferences while predicting theoretical yields.


 How Does it Work?

Construction of synthetic pathways relies on advanced graph-search algorithms which "walk" gigantic trees of synthetic possibilities in intelligent ways, avoiding unpromising routes while channeling the searches to the most efficient solutions. These searches are guided by functions that define and evaluate synthetic positions. Their scores reflect the structural complexity of the synthons generated in each step, inspect creation of rings and stereocenters, and assign penalties to reactions involving selectivity issues or those requiring protection chemistries. If the user desires, penalties for protection can be set high enough to construct routes free of any protection/deprotection steps.

All along, the algorithms inspect the conformations of the intermediates, remove synthons that are too strained or otherwise synthetically unlikely, consider subtle stereoelectronic effects, and more. The algorithms come with special routines to overcome local maxima in synthetic complexity, effectively allowing for what Corey termed as tactical disconnections -- that is, counterintuitive sequences of steps that initially complexify the structure but, by doing so, can reach overall more elegant solutions.

All of these operations are supported by a vast knowledge base of 60,000+ reaction rules, each of which accounts for the full scope of substituents and molecular "context" (i.e., conflicting groups, groups to be protected, etc.), and provide suggestions for typical reaction conditions and illustrative literature references.

The program designs and displays to the user hundreds of complete and cost-ranked synthetic plans. It can handle designs for radiolabelled targets, can be told to seek starting materials meeting certain price and/or popularity criteria, and can be instructed to design routes that preserve certain bonds (e.g., those that are found in commercial patents to which one wishes to find synthetic alternatives). The entire package comes with a highly visual graphical user interface offering various 2D and 3D display modalities, "reports" on the molecular/conformational properties of each molecule in every pathway, and many more options we are sure you will enjoy exploring.


 Pathway Optimization of Known Targets using the Network of Organic Chemistry

By applying network theory to organic chemistry, the Network of Organic Chemistry module can search for optimized synthetic pathways among 10 million of chemical substances and reactions published in the literature.

Searches can be customized to:

  • include a specific intermediate,
  • avoid a toxic substrate,
  • use water soluble substances,
  • control cost,
  • favor readily available chemicals.

When the desired constraints are applied, the software evaluates each individual step to find appropriate reactions and return optimized synthetic pathways. In one real-life example, this approach allowed to optimize the syntheses for a collection of 51 products to share common intermediates, thus trimming production cost by more than 45%. (See Parallel Optimization of Synthetic Pathways within the Network of Organic Chemistry).



 What Others Are Saying

"...taught to learn new rules, as well as to restructure existing knowledge, the software might even throw up ways to make totally new compounds with useful applications.” — New Scientist

"The benefits that can be realized through the use of machine assistance need not be limited to a few specific opportunities, but rather a broader view across all synthesis environments is necessary."— ACS Central Science

"...algorithms to search for pathways quickly, and in a fraction of the time it would take to sift through a database or list."— Chemistry World


 Software and Services Offering

In 2018, customers will be able to choose one of two packages:

  • Now Available! Service: A mix of consulting- and expert-level software execution allows you to provide a target of interest and receive a fully customized route based on your synthetic style and particular needs. Consult one on one with our experienced organic chemists to receive viable synthetic pathways for your novel chemical targets under a confidential disclosure agreement (CDA). Skip the learning curve of a new software and contact us to receive your hand-picked reaction pathways today.
  • License: Allows for access to the software, training, and additional support during a defined period.

Contact us to request Information or a quote.

Our organic synthesis software is only available under limited release at this time.