high performance virtual synthesis engine
  1. acid azide synthesis
  2. acyl isocyanate from amides with oxalyl chloride
  3. Acylation of amine
  4. Addition of alcohols to alkynes
  5. Addition of hydrogen cyanide to alkynes
  6. alcohol oxidation with Corey-Kim reagent
  7. alcohol protection with Grieco reagent
  8. Aldol reaction
  9. alkanes and cycloalkanes
  10. Alkyl Lithium formation from alkyl halides
  11. Alkylation of amines with alkyl halides
  12. Alkylation of phenols with benzyl chloride
  13. Allylic halogenation of alkenes
  14. alpha-Bromination of oxocompounds
  15. alpha-Hydroxynitrile formation
  16. alpha-Iodination of oxocompounds
  17. Angeli-Rimini hydroxamic acid synth
  18. Arylation of amines
  19. Baeyer-Villiger carbonyl oxidation
  20. Barton deamination
  21. Baylis-Hillman vinyl alkylation
  22. Beckmann rearrangement
  23. Benary reaction
  24. Benzidine rearrangement
  25. Beta HX elimination (Zaitsev elimination)
  26. Biginelli pyrimidone synthesis
  27. Birch reduction
  28. Bischler-Mohlau indole synthesis
  29. Bischler-Napieralski isoquinoline synthesis
  30. Blanc chloromethylation
  31. Blum aziridine synthesis with azide
  32. Borch reductive amination
  33. Borsche-Beech aromatic carbonyl synthesis
  34. Bouveault-Locquin amino acid synthesis
  35. Bredereck imidazole synthesis from acil methyl acilates
  36. Bredereck imidazole synthesis from alpha substituted ketones
  37. Bromination of aliphatic nitro compounds
  38. Bruylants amination
  39. Bruylants amination intramolecular
  40. Bucherer-LePetit naphtol synthesis
  41. Bucherer-LePetit naphtylamine synthesis
  42. Buchwald-Hartwig cross coupling
  43. Burgess dehidration reagent
  44. Burton trifluoromethylation
  45. Carboxylic acid addition to alkynes (anti-Markovnikov)
  46. Carboxylic acid addition to alkynes (Markovnikov)
  47. carboxylic acid chloride synthesis
  48. Catalytic hydration of alkenes
  49. Catalytic hydrogenation of aromatic compounds with Rh_C or Pt_C
  50. Catalytic hydrogenation of aromatic hydrocarbons with H2/Ni or H2/Pd-C
  51. Catalytic hydrogenation of phenols
  52. Chan reduction of acetylenes
  53. Chan-Lam coupling
  54. Chapman rearrangement
  55. Chichibabin amination
  56. Clay-Kinnear-Perren phosphoryl chloride synthesis
  57. Cleavage of acyclic ethers with HI (SN1 mechanism)
  58. Cleavage of epoxides
  59. Cleavage of ethers with HI (SN2 mechanism)
  60. Cleavage of vinyl ethers
  61. Clemensen reduction
  62. Collman carbonylation reagent in aldehyde synhesis
  63. Condensation reaction of primary amines and oxocompounds
  64. Condensation reaction of secondary amines and oxocompounds
  65. Cope elimination
  66. Corey-Chaykovsky reaction
  67. Corey-Winter olefin synthesis
  68. Criege glycol cleavage
  69. Curtius rearrangement
  70. Dakin oxidation
  71. Darapsky degradation
  72. Darzens epoxide synthesis
  73. Dehalogenation of vicinal dihalides
  74. Dehydration of alcohols to alkenes
  75. Delepine aldehyde oxidation
  76. Delepine amine synthesis
  77. Dess-Martin alcohol oxidizing reagent
  78. diazoalkane acylation
  79. diazotation of aromatic amines
  80. Diazotisation of primary anilines
  81. Diels-Alder cycloaddition
  82. Diels-Alder reaction with fused aromatic hydrocarbons
  83. Direct alkylation of amines with epoxide
  84. Doering-LaFlamme allene synthesis
  85. Dondoni homologation
  86. Einhorn-Brunner triazole synthesis
  87. enamine formation with modified Mannich reaction
  88. Erlenmeyer amino acid synthesis
  89. Eschenmoser fragmentation
  90. Eschenmoser methylenation
  91. Eschweiler-Clarke amine methylation
  92. Ether formation from alcohols
  93. Feist-Benary furane synthesis
  94. Finnegan tetrazole synthesis
  95. Fischer indole synthesis
  96. Fischer oxazole synthesis from cyanohydrins
  97. Fischer oxazole synthesis from hydroxyamides
  98. Formation of acetals and ketals
  99. Formation of alkylated, alpha unsaturated nitro compound
  100. Formation of cyclic acetals and ketals
  101. Forster diazo synthesis
  102. Freund-Gustavson cyclopropane synthesis
  103. Friedel-Crafts acylation
  104. Friedel-Crafts alkylation
  105. Friedlander quinoline synthesis
  106. Fritsch-Buttenberg-Wiechell acetylene synthesis (rearrangement)
  107. Fukuyama coupling
  108. Gabriel amine synthesis
  109. Gewald aminofurane synthesis
  110. Gewald aminopyrrole synthesis
  111. Gewald aminothiophene synthesis
  112. Goldberg coupling
  113. Grignard addition to carbonyl compounds
  114. Grignard compound addition to carbonyl compounds
  115. Grignard reaction to carbonyl compounds
  116. Grignard reagent formation
  117. Guaresky-Thorpe pyridone synthesis
  118. Guy-Lemaire-Guette ortho chlorination
  119. Guy-Lemaire-Guette para chlorination
  120. Halogen addition to alkenes
  121. Halogen addition to alkynes
  122. Halogenation of alcohols with hydrogen halides
  123. Halogenation of alkanes (substitution)
  124. Halogenation of alkanes (UV light)
  125. Halogenation of aromatic hydrocarbons
  126. Halogenation of primary anilines
  127. Hass-Bender carbonyl synthesis
  128. Heck reaction
  129. Heck reaction (intermolecular)
  130. Heck reaction (intramolecular)
  131. Hell-Volhardt-Zelinski bromination
  132. Henry nitro condensation
  133. Herz benzothiazole synthesis
  134. Hiyama coupling
  135. Hofmann amide degradation
  136. Hofmann elimination
  137. Hofmann-Löffler-Freytag reaction
  138. Horner-Wadsworth-Emmons olefination
  139. Horner-Wadsworth-Emmons reaction
  140. Houben-Hoesch phenol acylation
  141. Houben-Hoesch phenol formylation
  142. Hunsdiecker-Borodin-Cristol-Firth decarboxylation bromination
  143. Hydration of alkenes
  144. Hydration of alkynes (Markovnikov’s addition)
  145. Hydration of terminal alkynes (anti-Markovnikov’s addition)
  146. Hydrogen bromide addition to alkenes (anti-Markovnikov)
  147. Hydrogen halide addition to alkenes (Markovnikov)
  148. Hydrogen halide addition to alkynes
  149. Hydrolytic carbon monoxide addition to alkynes
  150. Hydroxyation of alkenes with potassium permanganate
  151. Hydroxymethylation of phenols
  152. imino ester synthesis
  153. Intramolecular amine alkylation
  154. isocyanate synthesis from amines with phosgene
  155. isocyanate with nucleophile
  156. Isomerisation of alkenes
  157. Isonitril formation
  158. Isothiocyanate formation from primary aromatic or aliphatic amines
  159. Jones oxidation of primer alcohols
  160. Jones oxidation of secunder alcohols
  161. Keinan silane reagent for reductive iodination
  162. Kendall-Mattox dehydrohalogenation
  163. Knoevenagel condensation
  164. Knoevenagel condensation Doebner modification
  165. Knorr quinoline synthesis
  166. Kolbe-Schmitt synthesis
  167. Kornblum aldehyde synthesis
  168. Kuhn-Winterstein olefination
  169. Kumada coupling
  170. Kumada-Negishi coupling
  171. Lawesson thiacarbonylation
  172. Leuckart-Wallach reductive amination
  173. Lieben hypohalide oxidation haloform reaction
  174. Madelung indole synthesis
  175. Mannich reaction
  176. McFadyen-Stevens reduction
  177. Meerwein-Ponndorf-Verley reduction
  178. Menshutkin reaction
  179. Methylation of phenols with diazomethane
  180. Milas olefin hydroxylation
  181. Miller-Loudon-Snyder nitrile synthesis
  182. Miyaura borylation reaction
  183. Negishi coupling
  184. Nitration of alcohols with nitric acid
  185. Nitration of alkanes
  186. Nitration of aromatic amines
  187. Nitration of aromatic hydrocarbons
  188. Nitrosation of secondary amines
  189. Noyori asymmetric hydrogenation of carbonyls
  190. nucleophile acylation with acid halide
  191. Nucleophile acylation with carboxylic acid or anhydride
  192. Nucleophilic aromatic substitution (SN2)
  193. O’Donnell amino acid synthesis
  194. Oppenauer oxidation
  195. Oxidation of alcohols
  196. Oxidation of alkanes to alcohols
  197. Oxidation of alkanes to ketones
  198. Oxidation of alkenes with peracids
  199. Oxidation of alkenes with potassium permanganate
  200. Oxidation of alkynes with potassium permanganate(basic medium)
  201. Oxidation of alkynes with potassium permanganate(neutral medium)
  202. Oxidation of alpha methyl aromatic hydrocarbons with KMnO4 to benzoic acid
  203. Oxidation of anilines to ortho quinones
  204. Oxidation of anilines to para quinones
  205. Oxidation of phenols to ortho or para quinones
  206. Oxidation of tertiary amine to amine oxide
  207. Oxidation of vicinal diols to aldehydes or ketones
  208. Oxime from active CH with nitrosation
  209. Oxime from carbonyls with hydroxylamine
  210. Ozonolysis of alkenes
  211. Paal-Knorr furane synthesis
  212. Paal-Knorr pyrrole synthesis
  213. Paal-Knorr thiophene synthesis
  214. Passerini condensation
  215. Perkin reaction
  216. Perkin rearrangement
  217. Petasis reaction
  218. Pfitzinger quinoline synthesis
  219. Phenol formation from primary anilines
  220. Quellet chloroalkylation
  221. Reaction of alkynes with oxo compounds (Reppe like reaction)
  222. Reaction of amines with alcohols
  223. Reaction of primary aliphatic amines with nitrous acid
  224. Reduction of alkyl halides (Zn/H+,LiAlH4,Pd/C,HI)
  225. Reduction of nitro arenes to azo arenes
  226. Reduction of nitro compounds to amines or anilines
  227. Reformatsky reaction
  228. Reformatsky reaction intramolecular
  229. Reformatsky reaction of thiocarbonyls
  230. Ring closure by halogen elimination from alkyl halides
  231. Ritter reaction intramolecular
  232. Ritter reaction of alcohols
  233. Ritter reaction of alkenes
  234. Schotten-Baumann reaction with phenols
  235. SN1 substitution of alkyl halides
  236. SN2 substitution of alkyl halides
  237. Stille carbonyl synthesis
  238. Stille coupling
  239. Sulfation of alcohols with sulfuric acid
  240. Sulfonation of aromatic amines
  241. Sulfonation of aromatic hydrocarbons
  242. Suzuki coupling
  243. Symmetric coupling of 1-alkynes
  244. Symmetric coupling of di-alkynes
  245. THP group cleavage
  246. Tosylation with Koser’s reagent
  247. Ullmann condensation
  248. Ullmann reaction
  249. Voight α-aminoketone synthesis
  250. Volhardt-Erdmann thiophene synthesis
  251. von Braun degradation of tertiary amines
  252. Wacker-Tsuji olefine oxidation
  253. Water addition to carbonyl compounds
  254. Williamson ether synthesis
  255. Wittig reaction
  256. Wolff rearrangement
  257. Wolff-Kishner reduction
  258. Wurtz reaction

The virtual enumeration of chemical reactions is a powerful tool in virtual compound library design or combinatorial chemistry. Reactor is the virtual reaction enumeration engine of ChemAxon’s JChem technology that supports generic reaction equations combined with reaction rules and hence is capable of generating chemically feasible products without pre-selection of reagents. Reactor is able to carry out highly automated reaction enumeration as well as the manual selection of main products for a given chemical reaction is supported.

Product Type:component
Interfaces:CLIGUI ( Desktop )API ( Java, .NET )

Predicting products of chemical reactions

Reaction synthesis on your desktop

Reactor is a high performance, integratable reaction enumeration engine. It works with generic reaction equations that can be defined and imported in various formats, including among others SMIRKS/SMARTS strings, RDF, RXN and MRV files or be drawn in MarvinSketch.

The Reactor package includes a large and constantly increasing library of organic chemical reactions that can be used directly, without any further configuration.

Reaction scheme

Define your chemical reactions

Using the generic reaction equations virtual synthetic compound libraries can be generated under full manual control. When doing so, users have the opportunity to draw and edit reactants directly and to select chemically meaningful products from the output of the enumeration process by using their chemical intuition on the fly. This approach is particularly advantageous for enumerating small, focused libraries.

Manual product selection

Get synthesizable molecules by proper reaction rules

The reaction rules are defined in Chemical Terms, ChemAxon’s scripting language that is designed to add chemical intelligence to cheminformatics applications. Through Chemical Terms a large number of calculated properties can be included in the reaction rules to produce valid compound libraries. Besides calculating physicochemical properties on the fly, Chemical Terms language also supports importing of arbitrary fields from the input reactant files to be used for the evaluation of the reaction rules.

Reaction rules

Intelligent and flexible reaction enumeration

Stereochemically aware reactions

Reaction schemes can include stereochemical information. Reactor is capable of handling both tetrahedral and double bond stereochemistry flexibly; inversion and retention centers as well as cis-trans configuration changes can be determined within Reactor’s smart reaction schemes. Prochiral reaction schemes are also supported since version 5.5, allowing the user to manage syn/anti additions.

Stereo change

Library design

Reactor can be set up to carry out simple sequential enumeration, in which case reactants are virtually reacted with each other in the order as they are present in the input files. Reactor is also capable of combinatorial enumeration, generating combinatorial virtual synthetic libraries. Users also have the option to exclude unwanted products from the enumeration results manually, restricting the outcome of the reaction enumeration process to the desired main products only. Reactor supports the generation of product or reaction libraries in a large variety of different output formats.

Create rich molecular libraries

Reactor has the option to copy arbitrary property fields from the input reactant files to the results. These can include e.g. solubility or availability information of the reactants. Also, Reactor can generate synthesis codes for each reaction in the enumeration process containing selected information from the reaction scheme and the reactants.

Information dump

Ease of access

A wizard-like user interface

The standalone version of Reactor has a clean and straightforward graphical user interface for configuring the reaction enumeration process. The GUI leads users step by step through the whole configuration process of the virtual chemical reaction.


Accessibility on various platforms

Reactor is available as a standalone application and has also been integrated into Instant JChem and JChem for Excel. It is also available in the workflow management tools KNIME and Pipeline Pilot. In its standalone version it can be used through the GUI, as a command line application and also through a full featured Java API. Reactor offers full platform independence, it is equally available for Microsoft Windows®, Mac OS and Linux platforms.

Create and test your reactions

Reactor has an integrated reaction sketcher and editor tool. Users can create their own reaction schemes and add corresponding reaction rules to them using the Chemical Terms language. The prepared reaction schemes can be tested and the reaction rules can be validated using the integrated reaction testing tool of Reactor.

Ligand Alignment

Articles in the library

AMRI Leverages Instant JChem for Compound Libraries

Sep 15, 2016 - Presentation
AMRI recently launched a Compound Library Consortium (CLC), to deliver 70,000 compounds within 2.5 years for three different partners. AMRI selected Instant JChem (IJC) from ChemAxon to …

Experiences with Reactor in Pipeline Pilot

Sep 15, 2009 - Presentation
Virtual libraries are potentially a source of novel compounds which could be used in virtual screening, lead optimization and lead hopping. In order for a virtual compound library to be …

Making “Real” Molecules in Virtual Space

Jan 13, 2006 - Publication
Predicting “realistic” compounds of given chemical reactions with virtual synthesis tools usually requires the manual intervention of experienced chemists in the enumeration p…

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