Computer

software Software is a set of computer programs and associated software documentation, documentation and data (computing), data. This is in contrast to Computer hardware, hardware, from which the system is built and which actually performs the work. ...

for computer-assisted organic synthesis (CAOS) are used in

organic chemistry Organic chemistry is a subdiscipline within chemistry involving the science, scientific study of the structure, properties, and reactions of organic compounds and organic materials, i.e., matter in its various forms that contain carbon atoms.Clay ...

in tandem with

computational chemistry Computational chemistry is a branch of chemistry that uses computer simulation to assist in solving chemical problems. It uses methods of theoretical chemistry, incorporated into computer programs, to calculate the structures and properties of mo ...

to help facilitate the tasks of designing, predicting, and producing

chemical reactions A chemical reaction is a process that leads to the IUPAC nomenclature for organic transformations, chemical transformation of one set of chemical substances to another. Classically, chemical reactions encompass changes that only involve the pos ...

. CAOS aims to identify a series of chemical reactions which, from a starting compound, can produce a desired

molecule A molecule is a group of two or more atoms held together by attractive forces known as chemical bonds; depending on context, the term may or may not include ions which satisfy this criterion. In quantum physics, organic chemistry, and bio ...

. CAOS algorithms typically use two

database In computing, a database is an organized collection of data stored and accessed electronically. Small databases can be stored on a file system, while large databases are hosted on computer clusters or cloud storage. The design of databases spa ...

s: a first one of known chemical reactions and a second one of known starting materials (i.e., typically molecules available commercially). Desirable synthetic plans cost less, have high yield, and avoid using hazardous reactions and intermediates. Typically cast as a planning problem, significant progress has been made in CAOS. Examples of CAOS applications include: * Spaya
Retrosynthesis planning tool freely accessible provided by Iktos
* IBM Rxn

* AiZynthFinder
A freely accessible open source retrosynthetic planning tool
developed as a collaboration between AstraZeneca and the University of Bern. AiZynthFinder predicts synthetic routes to a given target compound, and can be retrained on a users own dataset whether from public or proprietary sources. * Manifold
Compound searching and retrosynthesis planning tool freely accessible to academic users, developed by PostEra
* WODCA – no trial version;

proprietary software Proprietary software is computer software, software that is deemed within the free and open-source software to be non-free because its creator, publisher, or other rightsholder or rightsholder partner exercises a legal monopoly afforded by modern ...

* Organic Synthesis Exploration Tool (OSET) –

open-source software Open-source software (OSS) is computer software that is released under a license in which the copyright holder grants users the rights to use, study, change, and distribute the software and its source code to anyone and for any purpose. Ope ...

, abandoned * CHIRON – no trial version;

* SynGen – demo version;

; a unique program for automatic organic synthesis generation; focuses on generating the shortest, lowest cost synthetic routes for a given target organic compound, and is thus a useful tool for synthesis planning * LHASA – demo available but not linked (?);

* SYLVIA – demo version;

; rapidly evaluates the ease of synthesis of organic compounds; can prioritize thousands of structures (e.g., generated by de novo design experiments or retrieved from large virtual compound libraries) according to their synthetic complexity * ChemPlanner (formerly ARChem – Route Designer) - is an

expert system In artificial intelligence, an expert system is a computer system emulating the decision-making ability of a human expert. Expert systems are designed to solve complex problems by reasoning through bodies of knowledge, represented mainly as if� ...

to help chemists design viable synthetic routes for their target molecules; the

knowledge base A knowledge base (KB) is a technology used to store complex structured and unstructured information used by a computer system. The initial use of the term was in connection with expert systems, which were the first knowledge-based systems. ...

of reaction rules is algorithmically derived from reaction databases, and commercially available starting materials are used as termination points for the retrosynthetic search * ICSYNTH – demo available;

; A computer aided synthesis design tool that enables chemists to generate synthetic pathways for a target molecule, and a multistep interactive synthesis tree; at its core is an algorithmic chemical knowledge base of transform libraries that are automatically generated from reaction databases. *

Chematica Chematica is a software that uses algorithms and a collective database to predict synthesis pathways for molecules. The software development, led by Bartosz A. Grzybowski, was publicized in August 2012. In 2017, the software and database were whol ...

(Now known as Synthia) * ASKCOS – Open-source suite of synthesis planning and computational chemistry tools.https://askcos.mit.edu/

References

{{DEFAULTSORT:Computer-assisted organic synthesis software Organic chemistry Computational chemistry software Molecular modelling software Physics software Lists of software

See also

References