Name: protocol for the synthesis of ortho-trifluoromethoxylated aniline derivatives
Uploaded: 2016-01-19T15:00:00
Description: Watch this Scientific Journal Video about Protocol for the Synthesis of Ortho-trifluoromethoxylated Aniline Derivatives at JoVE.com

We acknowledge generous start-up funds from the State University of New York at Stony Brook in support of this work. We also thank TOSOH F-Tech, Inc. for providing us TMSCF3 reagent for the synthesis of Togni reagent II.

1. Precursor Preparation: Synthesis of Methyl 4-(N-hydroxyacetamido)benzoate (1a)
<ol>
	<li>Reduction of methyl 4-nitrobenzoate.
	<ol>
		<li>Add 5.00 g of methyl 4-nitrobenzoate (27.6 mmol, 1.00 equiv), 159 mg of 5% Rhodium on carbon (Rh/C, 0.300 mol% Rh), and a magnetic stir-bar into an oven-dried 250 ml two-neck round-bottom flask (dried at 150 &#176;C for 18 hr). 
		NOTE: Reagents can be weighed out under ambient atmosphere. However, the reaction needs to be carried out under nitrogen ...

<ol>
	<li>Yagupolskii, L. M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Sintez+proizvodnykh+feniltriftormetilovogo+efira.">Sintez proizvodnykh feniltriftormetilovogo efira.</a> Dokl. Akad. Nauk SSSR. 105, 100-102 (1955).</li><li>Booth, H. S., Burchfield, P. E. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Fluorination+of+halogeno+methyl+ethers.+I.+Fluorination+of+trichlorodimethyl+ether.">Fluorination of halogeno methyl ethers. I. Fluorination of trichlorodimethyl ether.</a> J. Am. Chem. Soc. 57, 2070 (1935).</li><li>McClinton, M. A., McClinton, D. A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Trifluoromethylations+and+related+reactions+in+organic-chemistry.">Trifluoromethylations and related reactions in organic-chemistry.</a> Tetrahedron. 48, 6555-6666 (1992).</li><li>Hansch, C., Leo, A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=.">.</a> Substituent Constants for Correlation Analysis in Chemistry and Biology. , (1979).</li><li>Leroux, F., Jeschke, P., Schlosser, M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Alpha-fluorinated+ethers,+thioethers,+and+amines:+Anomerically+biased+species.">Alpha-fluorinated ethers, thioethers, and amines: Anomerically biased species.</a> Chem. Rev. 105, 827-856 (2005).</li><li>Jeschke, P., Baston, E., Leroux, F. R. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Alpha-fluorinated+ethers+as+'exotic'+entity+in+medicinal+chemistry.">Alpha-fluorinated ethers as 'exotic' entity in medicinal chemistry.</a> Mini-Rev. Med. Chem. 7, 1027-1034 (2007).</li><li>Leroux, F. R., Manteau, B., Vors, J. P., Pazenok, S. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Trifluoromethyl+ethers+-+synthesis+and+properties+of+an+unusual+substituent.">Trifluoromethyl ethers - synthesis and properties of an unusual substituent.</a> Beilstein J. Org. Chem. 4, (2008).</li><li>Fantasia, S., Welch, J. M., Togni, A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Reactivity+of+a+hypervalent+iodine+trifluoromethylating+reagent+toward+THF:+ring+opening+and+formation+of+trifluoromethyl+ethers.">Reactivity of a hypervalent iodine trifluoromethylating reagent toward THF: ring opening and formation of trifluoromethyl ethers.</a> J. Org. Chem. 75, 1779-1782 (2010).</li><li>Manteau, B., Pazenok, S., Vors, J. P., Leroux, F. R. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=New+trends+in+the+chemistry+of+alpha-fluorinated+ethers,+thioethers,+amines+and+phosphines.">New trends in the chemistry of alpha-fluorinated ethers, thioethers, amines and phosphines.</a> J. Fluorine Chem. 131, 140-158 (2010).</li><li>Landelle, G., Panossian, A., Leroux, F. R. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Trifluoromethyl+ethers+and+-thioethers+as+tools+for+medicinal+chemistry+and+drug+discovery.">Trifluoromethyl ethers and -thioethers as tools for medicinal chemistry and drug discovery.</a> Curr. Top. Med. Chem. 14, 941-951 (2014).</li><li>Liang, T., Neumann, C. N., Ritter, T. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Introduction+of+fluorine+and+fluorine-containing+functional+groups.">Introduction of fluorine and fluorine-containing functional groups.</a> Angew. Chem. Int. Ed. 52, 8214-8264 (2013).</li><li>Yarovenko, N. N., Vasileva, A. S. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=A+new+method+for+the+introduction+of+trihalomethyl+groups+into+organic+molecules.">A new method for the introduction of trihalomethyl groups into organic molecules.</a> Zh. Obshch. Khim. 28, 2502-2504 (1958).</li><li>Yagupols, L., Troitskaya, V. I. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Synthesis+of+phenyl+trifluoromethyl+ether+derivatives.">Synthesis of phenyl trifluoromethyl ether derivatives.</a> Zh. Obshch. Khim. 31, 915-924 (1961).</li><li>Yagupolskii, L. M., Orda, V. V. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Bis(triftormetoksi+I+triftormetilmerkapto)-proizvodnye+benzola.">Bis(triftormetoksi I triftormetilmerkapto)-proizvodnye benzola.</a> Zh. 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Chem. 29, 1-11 (1964).</li><li>Kuroboshi, M., Suzuki, K., Hiyama, T. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Oxidative+desulfurization-fluorination+of+xanthates+-+a+convenient+synthesis+of+trifluoromethyl+ethers+and+difluoro(methylthio)methyl+ethers.">Oxidative desulfurization-fluorination of xanthates - a convenient synthesis of trifluoromethyl ethers and difluoro(methylthio)methyl ethers.</a> Tetrahedron Lett. 33, 4173-4176 (1992).</li><li>Kanie, K., Tanaka, Y., Suzuki, K., Kuroboshi, M., Hiyama, T. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=A+convenient+synthesis+of+trifluoromethyl+ethers+by+oxidative+desulfurization-fluorination+of+dithio+carbonates.">A convenient synthesis of trifluoromethyl ethers by oxidative desulfurization-fluorination of dithio carbonates.</a> Bull. Chem. Soc. 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Rev. 96, 1757-1777 (1996).</li><li>Umemoto, T., Adachi, K., Ishihara, S. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=CF3+oxonium+salts,+O-(trifluoromethyl)dibenzofuranium+salts:+in+situ+synthesis,+properties,+and+application+as+a+real+CF3++species+reagent.">CF3 oxonium salts, O-(trifluoromethyl)dibenzofuranium salts: in situ synthesis, properties, and application as a real CF3+ species reagent.</a> J. Org. Chem. 72, 6905-6917 (2007).</li><li>Stanek, K., Koller, R., Togni, A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Reactivity+of+a+10-I-3+hypervalent+iodine+trifluoromethylation+reagent+with+phenols.">Reactivity of a 10-I-3 hypervalent iodine trifluoromethylation reagent with phenols.</a> J. Org. Chem. 73, 7678-7685 (2008).</li><li>Koller, R., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Zinc-mediated+formation+of+trifluoromethyl+ethers+from+alcohols+and+hypervalent+iodine+trifluoromethylation+reagents.">Zinc-mediated formation of trifluoromethyl ethers from alcohols and hypervalent iodine trifluoromethylation reagents.</a> Angew. Chem. Int. Ed. 48, 4332-4336 (2009).</li><li>Trainor, G. L. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+preparation+of+O-trifluoromethyl+carbohydrates.">The preparation of O-trifluoromethyl carbohydrates.</a> J. Carbohydr. Chem. 4, 545-563 (1985).</li><li>Nishida, M., Vij, A., Kirchmeier, R. L., Shreeve, J. M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Synthesis+of+polyfluoro+aromatic+ethers+-+a+facile+route+using+polyfluoroalkoxides+generated+from+carbonyl+and+trimethysilyl+compounds.">Synthesis of polyfluoro aromatic ethers - a facile route using polyfluoroalkoxides generated from carbonyl and trimethysilyl compounds.</a> Inorg. Chem. 34, 6085-6092 (1995).</li><li>Kolomeitsev, A. A., Vorobyev, M., Gillandt, H. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Versatile+application+of+trifluoromethyl+triflate.">Versatile application of trifluoromethyl triflate.</a> Tetrahedron Lett. 49, 449-454 (2008).</li><li>Marrec, O., Billard, T., Vors, J. P., Pazenok, S., Langlois, B. R. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=A+deeper+insight+into+direct+trifluoromethoxylation+with+trifluoromethyl+triflate.">A deeper insight into direct trifluoromethoxylation with trifluoromethyl triflate.</a> J. Fluorine Chem. 131, 200-207 (2010).</li><li>Marrec, O., Billard, T., Vors, J. P., Pazenok, S., Langlois, B. R. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=A+new+and+direct+trifluoromethoxylation+of+aliphatic+substrates+with+2,4-dinitro(trifluoromethoxy)benzene.">A new and direct trifluoromethoxylation of aliphatic substrates with 2,4-dinitro(trifluoromethoxy)benzene.</a> Adv. Synth. Catal. 352, 2831-2837 (2010).</li><li>Huang, C. H., Liang, T., Harada, S., Lee, E., Ritter, T. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Silver-mediated+trifluoromethoxylation+of+aryl+stannanes+and+arylboronic+acids.">Silver-mediated trifluoromethoxylation of aryl stannanes and arylboronic acids.</a> J. Am. Chem. Soc. 133, 13308-13310 (2011).</li><li>Rozen, S. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Selective+fluorinations+by+reagents+containing+the+OF+group.">Selective fluorinations by reagents containing the OF group.</a> Chem. Rev. 96, 1717-1736 (1996).</li><li>Venturini, F., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Direct+trifluoro-methoxylation+of+aromatics+with+perfluoro-methyl-hypofluorite.">Direct trifluoro-methoxylation of aromatics with perfluoro-methyl-hypofluorite.</a> J. Fluorine Chem. 140, 43-48 (2012).</li><li>Hojczyk, K. N., Feng, P., Zhan, C., Ngai, M. -. Y. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Trifluoromethoxylation+of+arenes:+synthesis+of+ortho-trifluoromethoxylated+aniline+derivatives+by+OCF3+migration.">Trifluoromethoxylation of arenes: synthesis of ortho-trifluoromethoxylated aniline derivatives by OCF3 migration.</a> Angew. Chem. Int. Ed. 53, 14559-14563 (2014).</li><li>Still, W. C., Kahn, M., Mitra, A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Rapid+chromatographic+technique+for+preparative+separations+with+moderate+Resolution.">Rapid chromatographic technique for preparative separations with moderate Resolution.</a> J. Org. Chem. 43, 2923-2925 (1978).</li><li>Fiederling, N., Haller, J., Schramm, H. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Notification+about+the+Explosive+Properties+of+Togni's+Reagent+II+and+One+of+Its+Precursors.">Notification about the Explosive Properties of Togni's Reagent II and One of Its Precursors.</a> Org. Process Res. 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Due to the lack of a general and user-friendly procedure for the synthesis of trifluoromethoxylated arenes, many OCF3-containing aromatic compounds are extremely expensive.34 Our strategy displaces a broad functional group tolerance and provides an easy access to various trifluoromethoxylated arenes. These compounds could serve as valuable building blocks for the discovery and development of new pharmaceuticals, agrochemicals, and materials.
Hydrazine was used as a hydrog...

The trifluoromethoxy (OCF3) group has made a profound impact on life and materials science research since the first synthesis of trifluoromethyl ether in 1935.2 Due to its unique combination of high electronegativity (&#967; = 3.7)3 and excellent lipophilicity (&#928;x = 1.04),4 the trifluoromethoxy group has found broad applications in medicine, agriculture, and materials industry.5-10 However, facile introduction of the OCF3 group into organic molecules, especially aromatic compounds, remains a major challenge in synthetic chemistry.
Over the last few decades, efforts to address this challenge led to the development of a handful of transformations for the synthesis of trifluoromethoxylated arenes.5-7,9-11 These include (i) chlorine/fluorine exchange on trichlorinated precursors;1,12-17 (ii) deoxyfluorination of fluoroformates;18 (iii) oxidative fluorodesulfurization;19-21 (iv) electrophilic trifluoromethylation of alcohols;22-25 (v) nucleophilic trifluoromethoxylation;26-30, (vi) transition metal-mediated trifluoromethoxylation of aryl borates and stannanes;31 and (vii) radical trifluoromethoxylation.32,33 Nevertheless, many of these approaches either suffer from poor substrate scope or require use of highly toxic and/or thermally labile reagents. Therefore, due to the lack of a general and user-friendly method to synthesize OCF3-containing compounds, the potential of the OCF3 group has not been fully exploited in chemistry.
As part of our interest in trifluoromethoxylation reactions,34 we describe herein a two-step protocol (i.e., radical&#160;O-trifluoromethylation and thermally induced OCF3-migration) for the synthesis of methyl 4-acetamido-3-(trifluoromethoxy)benzoate (3a) from methyl 4-(N-hydroxyacetamido)benzoate (1a). The strategy is easy-to-operate and applicable to the synthesis of a wide range of ortho-trifluoromethoxylated aniline derivatives.

<table border="0" cellpadding="0" cellspacing="0" width="573">
	<tbody>
		<tr height="43">
			<td height="43" style="height:43px;width:216px;">5% Rhodium on carbon</td>
			<td style="width:71px;">Aspira Scientific</td>
			<td style="width:119px;">300835</td>
			<td style="width:167px;">5% wt% dry loading</td>
		</tr>
		<tr height="43">
			<td height="43" style="height:43px;width:216px;">hydrazine monohydrate</td>
			<td style="width:71px;">Sigma-Alderich</td>
			<td style="width:119px;">13696HMV</td>
			<td style="width:167px;">Reagent grade, 98%</td>
		</tr>
		<tr height="43">
			<td height="43" style="height:43px;width:216px;">Acetyl chloride</td>
			<td style="width:71px;">Alfa Aesar</td>
			<td style="width:119px;">10176887</td>
			<td style="width:167px;">98%</td>
		</tr>
		<tr height="43">
			<td height="43" style="height:43px;width:216px;">Sodium bicarbonate</td>
			<td style="width:71px;">Fisher Scientific</td>
			<td style="width:119px;">134826</td>
			<td style="width:167px;">Chemical pure</td>
		</tr>
		<tr height="43">
			<td height="43" style="height:43px;width:216px;">Cesium carbonate</td>
			<td style="width:71px;">Alfa Aesar</td>
			<td style="width:119px;">12887</td>
			<td style="width:167px;">99.9%, metals basis</td>
		</tr>
		<tr height="148">
			<td height="148" style="height:148px;width:216px;">Togni Reagent II</td>
			<td style="width:71px;"></td>
			<td style="width:119px;"></td>
			<td style="width:167px;">Prepared according to the literature procedure (ref 37). Caution: Pure Togni reagent II is impact and friction sensitive, treat it with great care (see ref. 36).</td>
		</tr>
		<tr height="64">
			<td height="64" style="height:64px;width:216px;">Tetrahydrofuran</td>
			<td style="width:71px;">BDH</td>
			<td style="width:119px;">BDH1149-4LG</td>
			<td style="width:167px;">Distilled from deep purple sodium benzophenone ketyl.</td>
		</tr>
		<tr height="64">
			<td height="64" style="height:64px;width:216px;">Diethyl Ether</td>
			<td style="width:71px;">Fisher Scientific</td>
			<td style="width:119px;">148221</td>
			<td style="width:167px;">Distilled from deep purple sodium benzophenone ketyl.</td>
		</tr>
		<tr height="47">
			<td height="47" style="height:47px;width:216px;">Chloroform</td>
			<td style="width:71px;">Fisher Scientific</td>
			<td style="width:119px;">141739</td>
			<td style="width:167px;">Dried over CaH2 and distilled</td>
		</tr>
		<tr height="47">
			<td height="47" style="height:47px;width:216px;">nitro methane</td>
			<td style="width:71px;">Alfa Aesar</td>
			<td style="width:119px;">J03z053</td>
			<td style="width:167px;">Dried over CaSO4 and distilled</td>
		</tr>
		<tr height="43">
			<td height="43" style="height:43px;width:216px;">Silica gel</td>
			<td style="width:71px;">SILICYCLE</td>
			<td style="width:119px;">60514</td>
			<td style="width:167px;">40-63 &#181;m (230-400 mesh)</td>
		</tr>
		<tr height="22">
			<td height="22" style="height:22px;width:216px;">Cilite</td>
			<td style="width:71px;">EMD</td>
			<td style="width:119px;">2012040674</td>
			<td style="width:167px;">Not acid washed</td>
		</tr>
	</tbody>
</table>

protocol for the synthesis of ortho-trifluoromethoxylated aniline derivatives

Molecules bearing trifluoromethoxy (OCF3) group often show desired pharmacological and biological properties. However, facile synthesis of trifluoromethoxylated aromatic compounds remains a formidable challenge in organic synthesis. Conventional approaches often suffer from poor substrate scope, or require use of highly toxic, difficult-to-handle, and/or thermally labile reagents. Herein, we report a user-friendly protocol for the synthesis of methyl 4-acetamido-3-(trifluoromethoxy)benzoate using 1-trifluoromethyl-1,2-benziodoxol-3(1H)-one (Togni reagent II). Treating methyl 4-(N-hydroxyacetamido)benzoate (1a) with Togni reagent II in the presence of a catalytic amount of cesium carbonate (Cs2CO3) in chloroform at RT afforded methyl 4-(N-(trifluoromethoxy)acetamido)benzoate (2a). This intermediate was then converted to the final product methyl 4-acetamido-3-(trifluoromethoxy)benzoate (3a) in nitromethane at 120 &#176;C. This procedure is general and can be applied to the synthesis of a broad spectrum of ortho-trifluoromethoxylated aniline derivatives, which could serve as useful synthetic building blocks for the discovery and development of new pharmaceuticals, agrochemicals, and functional materials.

Methyl 4-(N-hydroxyacetamido)benzoate (1a) was synthesized in 92% isolated yield through a two-step procedure (i.e., reducing methyl 4-nitrobenzoate with hydrazine using 5% Rh/C as a catalyst to form methyl 4-(N-hydroxyamino)benzoate, followed by acetyl protection of the resulting hydroxylamine). O-Trifluoromethylation of 1a with Togni reagent II in the presence of catalytic amount of cesium carbonate (Cs2CO<...

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Protocol for the Synthesis of Ortho-trifluoromethoxylated Aniline Derivatives

An operationally simple procedure for the synthesis of ortho-trifluoromethoxylated aniline derivatives via a two-step sequence of O-trifluoromethylation of N-aryl-N-hydroxyacetamide followed by thermally induced intramolecular OCF3-migration is reported.

Protocol for the Synthesis of Ortho-trifluoromethoxylated Aniline Derivatives

Molecules bearing trifluoromethoxy (OCF3) group often show desired pharmacological and biological properties. However, facile synthesis of ...

The overall goal of this protocol is to synthesize novel ortho-trifluoromethoxylated anilines with the discovery and development of new drugs, agrochemicals, and functional materials. This method can help to answer key questions in the field of foreign chemistry such as how incorporation of trifluoromethoxy group into a molecule effects its physical, chemical, and biological properties. The main advantage of this technique that our method uses easy-to-handle reagents.It's amendable to gram-scale synthesized and it has broad substrate scope and high tolerance of functional groups. For the reduction of methyl 4-nitrobenzoate, add 5.00 grams of methyl 4-nitrobenzoate, 159 milligrams of 5%Rhodium on carbon, and a magnetic stir-bar into an oven-dried 250 milliliter two-neck round-bottom flask. Connect one neck of the flask to a nitrogen-vacuum manifold and cap the other neck with a septum.Perform three vacuum-refill cycles to replace the air in the flask with nitrogen gas, then add 138 milliliters of anhydrous tetrahydrofuran to the reaction flask using an airtight syringe. Cool and stir the reaction mixture at zero degrees Celsius for 15 minutes. Next, add 1.47 milliliters of hydrazine monohydrate drop-wise to the reaction mixture at zero degrees Celsius using an airtight syringe.At this point, Rhodium on carbon will start aggregation to form larger particles. Monitor the reaction using thin-layer chromatography or TLC. Use a mixture of hexane and ethyl acetate as an element to develop the TLC.When methyl 4-nitrobenzoate is completely consumed, filter the reaction mixture through a short pad of Celite in a 60 milliliter frit Buchner funnel using vacuum filtration. Wash the filter with 20 milliliters of ethyl acetate three times. Concentrate the filtrate in vacuo using a rotary evaporator to afford the crude methyl 4-hydroxyamino benzoate which is used directly without further purification.To perform acetyl protection of methyl 4-hydroxyamino benzoate, add 2.55 grams of sodium bicarbonate, all the crude methyl 4-hydroxyamino benzoate obtained in the previous step, and a stir-bar into an oven-dried 500 milliliter two-neck round-bottom flask. Cap one neck with a septum, and connect another neck to a nitrogen-vacuum manifold. Perform three vacuum-refill cycles to replace the air in the flask with nitrogen gas.Add 138 milliliters of anhydrous diethyl ether to the reaction flask using an airtight syringe. Cool and stir the reaction mixture at zero degrees Celsius for 15 minutes. Prepare a solution of 2.17 milliliters of acetyl chloride and 138 milliliters of anhydrous diethyl ether.Add the solution to the reaction mixture at zero degrees Celsius using a syringe pump at a rate of 10.0 milliliters per hour. At the end of the addition, filter the reaction mixture through a short pad of Celite in a 16 milliliter frit Buchner funnel using vacuum filtration. After washing the filter with 20 milliliters of ethyl acetate three times, concentrate the filtrate in vacuo using a rotary evaporator.Purify the crude product with flash-column chromatography eluting with a mixture of hexane and ethyl acetate to afford 5.31 grams of methyl 4-hydroxy acetamido benzoate as a light yellow solid. Add 2.00 grams of methyl 4-hydroxy acetamido benzoate, 311 milligrams of cesium carbonate 3.63 grams of Togni reagent II, and a magnetic stir-bar into an oven-dried 250 milliliter round-bottom flask inside a glove box. This reaction can also be performed using Schlenk techniques outside the glove box, then add 95.6 milliliters of dried and degassed chloroform to the reaction flask.Cap the flask with a septum and stir the reaction mixture at 23 degrees Celsius under nitrogen atmosphere either inside or outside the glove box for 16 hours. Filter the reaction mixture through a filter funnel to remove any solid residue before concentrating the filtrate in vacuo using a rotary evaporator. Next, purify the crude product using flash-column chromatography eluting with a mixture of hexane and dichloromethane to afford 2.51 grams of methyl 4-trifluoromethoxy acetamido benzoate To synthesize the final product at 2.51 grams of methyl 4-trifluoromethoxy acetamido benzoate, a magnetic stir-bar, and 9.05 milliliters of anhydrous nitromethane into a 15 milliliter pressure vessel.Cap the vessel with a screw cap, stir the reaction mixture at 120 degree Celsius behind the safety shield for 20 hours. After cooling the reaction mixture to room temperature, transfer to a 100 milliliter round-bottom flask. Concentrate the reaction mixture in vacuo using a rotary evaporator.Purify the crude product with flash-column chromatography eluding with a mixture of hexanes and ethyl acetate to afford 2.13 grams of methyl 4-acetamido 3-trifluoromethoxy benzoate. Characterize all the new compounds by proton-carbon-13 nuclear magnetic resonance or NMR spectroscopy and high-resolution mass spectroscopy. Use fluorine-19 NMR spectroscopy to characterize compounds containing fluorine atoms.Representative results of Togni reagent II mediated intermolecular trifluoromethoxylation of arenes are shown here. This protocol is general and applicable to a wide array of aromatic compounds. The reaction tolerates a broad spectrum of functional groups.In addition, high levels of ortho over para selectivity are observed, for example, substrates, 3f, 3k, and 3l. In the presence of two non-identical ortho positions, low levels of Regio-control are obtained as in substrates, 3d.3e. 3k, and 3m.Furthermore, the reaction temperature for the trifluoromethoxy migration step depends on the electronic nature of the arenes. Generally, more electron-deficient arenes require higher reaction temperature. After its development, this technique paved the way for researchers in the field of chemistry and biology to explore trifluoromethoxylated arenes, and the discovery, and the development of new technique molecules.

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Synthesis of Antiviral Tetrahydrocarbazole Derivatives by Photochemical and Acid-catalyzed C-H Functionalization via Intermediate Peroxides (CHIPS)

The direct functionalization of C-H bonds is an important and long standing goal in organic chemistry. Such transformations can be very powerful in order to streamline synthesis by saving steps, time and material compared to conventional methods that require the introduction and removal of activating or directing groups. Therefore, the functionalization of C-H bonds is also attractive for green chemistry. Under oxidative conditions, two C-H bonds or one C-H and one heteroatom-H bond can be transformed to C-C and C-heteroatom bonds, respectively. Often these oxidative coupling reactions require synthetic oxidants, expensive catalysts or high temperatures. Here, we describe a two-step procedure to functionalize indole derivatives, more specifically tetrahydrocarbazoles, by C-H amination using only elemental oxygen as oxidant. The reaction uses the principle of C-H functionalization via Intermediate PeroxideS (CHIPS). In the first step, a hydroperoxide is generated oxidatively using visible light, a photosensitizer and elemental oxygen. In the second step, the N-nucleophile, an aniline, is introduced by Br&#248;nsted-acid catalyzed activation of the hydroperoxide leaving group. The products of the first and second step often precipitate and can be conveniently filtered off. The synthesis of a biologically active compound is shown.

Synthesis of Antiviral Tetrahydrocarbazole Derivatives by Photochemical and Acid-catalyzed C-H Functionalization via Intermediate Peroxides CHIPS

A two-step procedure for the synthesis of pharmaceutically active indole-derivatives by C-H functionalization with anilines is described, using photo- and Br&#248;nsted acid catalysis.

The direct functionalization of C-H bonds is an important and long standing goal in organic chemistry. Such transformations can be very powerful in order ...

A Direct, Early Stage Guanidinylation Protocol for the Synthesis of Complex Aminoguanidine-containing Natural Products

The guanidine functional group, displayed most prominently in the amino acid arginine, one of the fundamental building blocks of life, is an important structural element found in many complex natural products and pharmaceuticals. Owing to the continual discovery of new guanidine-containing natural products and designed small molecules, rapid and efficient guanidinylation methods are of keen interest to synthetic and medicinal organic chemists. Because the nucleophilicity and basicity of guanidines can affect subsequent chemical transformations, traditional, indirect guanidinylation is typically pursued. Indirect methods commonly employ multiple protection steps involving a latent amine precursor, such as an azide, phthalimide, or carbamate. By circumventing these circuitous methods and employing a direct guanidinylation reaction early in the synthetic sequence, it was possible to forge the linear terminal guanidine containing backbone of clavatadine A to realize a short and streamlined synthesis of this potent factor XIa inhibitor. In practice, guanidine hydrochloride is elaborated with a carefully constructed protecting array that is optimized to survive the synthetic steps to come. In the preparation of clavatadine A, direct guanidinylation of a commercially available diamine eliminated two unnecessary steps from its synthesis. Coupled with the wide variety of known guanidine protecting groups, direct guanidinylation evinces a succinct and efficient practicality inherent to methods that find a home in a synthetic chemist&#39;s toolbox.

Here, we present a protocol for direct, early stage guanidinylation that enables rapid total synthesis of aminoguanidine-containing small organic molecules. An advanced synthetic intermediate used in the synthesis of a blood coagulation factor XIa inhibitor was prepared using this protocol.

The guanidine functional group, displayed most prominently in the amino acid arginine, one of the fundamental building blocks of life, is an important ...

Synthesis of Protein Bioconjugates via Cysteine-maleimide Chemistry

The chemical linking or bioconjugation of proteins to fluorescent dyes, drugs, polymers and other proteins has a broad range of applications, such as the development of antibody drug conjugates (ADCs) and nanomedicine, fluorescent microscopy and systems chemistry. For many of these applications, specificity of the bioconjugation method used is of prime concern. The Michael addition of maleimides with cysteine(s) on the target proteins is highly selective and proceeds rapidly under mild conditions, making it one of the most popular methods for protein bioconjugation.
We demonstrate here the modification of the only surface-accessible cysteine residue on yeast cytochrome c with a ruthenium(II) bisterpyridine maleimide. The protein bioconjugation is verified by gel electrophoresis and purified by aqueous-based fast protein liquid chromatography in 27% yield of isolated protein material. Structural characterization with MALDI-TOF MS and UV-Vis is then used to verify that the bioconjugation is successful. The protocol shown here is easily applicable to other cysteine - maleimide coupling of proteins to other proteins, dyes, drugs or polymers.

Synthesis of Protein Bioconjugates via Cysteine-maleimide Chemistry

This protocol details the important steps required for the bioconjugation of a cysteine containing protein to a maleimide, including reagent purification, reaction conditions, bioconjugate purification and bioconjugate characterization.

The chemical linking or bioconjugation of proteins to fluorescent dyes, drugs, polymers and other proteins has a broad range of applications, such as the ...

Facile Synthesis of Worm-like Micelles by Visible Light Mediated Dispersion Polymerization Using Photoredox Catalyst

Presented herein is a protocol for the facile synthesis of worm-like micelles by visible light mediated dispersion polymerization. This approach begins with the synthesis of a hydrophilic poly(oligo(ethylene glycol) methyl ether methacrylate) (POEGMA) homopolymer using reversible addition-fragmentation chain-transfer (RAFT) polymerization. Under mild visible light irradiation (&#955; = 460 nm, 0.7 mW/cm2), this macro-chain transfer agent (macro-CTA) in the presence of a ruthenium based photoredox catalyst, Ru(bpy)3Cl2 can be chain extended with a second monomer to form a well-defined block copolymer in a process known as Photoinduced Electron Transfer RAFT (PET-RAFT). When PET-RAFT is used to chain extend POEGMA with benzyl methacrylate (BzMA) in ethanol (EtOH), polymeric nanoparticles with different morphologies are formed in situ according to a polymerization-induced self-assembly (PISA) mechanism. Self-assembly into nanoparticles presenting POEGMA chains at the corona and poly(benzyl methacrylate) (PBzMA) chains in the core occurs in situ due to the growing insolubility of the PBzMA block in ethanol. Interestingly, the formation of highly pure worm-like micelles can be readily monitored by observing the onset of a highly viscous gel in situ due to nanoparticle entanglements occurring during the polymerization. This process thereby allows for a more reproducible synthesis of worm-like micelles simply by monitoring the solution viscosity during the course of the polymerization. In addition, the light stimulus can be intermittently applied in an ON/OFF manner demonstrating temporal control over the nanoparticle morphology.

This article describes a process for producing polymeric self-assembled nanoparticles using visible light mediated dispersion polymerization. Using low energy visible light to control the polymerization allows for the reproducible formation of self-assembled worm-like micelles at high solids content.

Presented herein is a protocol for the facile synthesis of worm-like micelles by visible light mediated dispersion polymerization. This approach begins ...

Protocol for the Solid-phase Synthesis of Oligomers of RNA Containing a 2'-O-thiophenylmethyl Modification and Characterization via Circular Dichroism

Solid-phase synthesis has been used to obtain canonical and modified polymers of nucleic acids, specifically of DNA or RNA, which has made it a popular methodology for applications in various fields and for different research purposes. The procedure described herein focuses on the synthesis, purification, and characterization of dodecamers of RNA 5&#39;-[CUA CGG AAU CAU]-3&#39; containing zero, one, or two modifications located at the C2&#39;-O-position. The probes are based on 2-thiophenylmethyl groups, incorporated into RNA nucleotides via standard organic synthesis and introduced into the corresponding oligonucleotides via their respective phosphoramidites. This report makes use of phosphoramidite chemistry via the four canonical nucleobases (Uridine (U), Cytosine (C), Guanosine (G), Adenosine (A)), as well as 2-thiophenylmethyl functionalized nucleotides modified at the 2&#39;-O-position; however, the methodology is amenable for a large variety of modifications that have been developed over the years. The oligonucleotides were synthesized on a controlled-pore glass (CPG) support followed by cleavage from the resin and deprotection under standard conditions, i.e., a mixture of ammonia and methylamine (AMA) followed by hydrogen fluoride/triethylamine/N-methylpyrrolidinone. The corresponding oligonucleotides were purified via polyacrylamide electrophoresis (20% denaturing) followed by elution, desalting, and isolation via reversed-phase chromatography (Sep-pak, C18-column). Quantification and structural parameters were assessed via ultraviolet-visible (UV-vis) and circular dichroism (CD) photometric analysis, respectively. This report aims to serve as a resource and guide for beginner and expert researchers interested in embarking in this field. It is expected to serve as a work-in-progress as new technologies and methodologies are developed. The description of the methodologies and techniques within this document correspond to a DNA/RNA synthesizer (refurbished and purchased in 2013) that uses phosphoramidite chemistry.

Protocol for the Solid-phase Synthesis of Oligomers of RNA Containing a 2'-O-thiophenylmethyl Modification and Characterization via Circular Dichroism

This article provides a detailed procedure on the solid-phase synthesis, purification, and characterization of dodecamers of RNA modified at the C2&#39;-O-position. UV-vis and circular dichroism photometric analyses are used to quantify and characterize structural aspects, i.e., single-strands or double-strands.

Solid-phase synthesis has been used to obtain canonical and modified polymers of nucleic acids, specifically of DNA or RNA, which has made it a popular ...

Synthesis and Mass Spectrometry Analysis of Oligo-peptoids

Peptoids are sequence-controlled peptide-mimicking oligomers consisting of N-alkylated glycine units. Among many potential applications, peptoids have been thought of as a type of molecular information storage. Mass spectrometry analysis has been considered the method of choice for sequencing peptoids. Peptoids can be synthesized via solid phase chemistry using a repeating two-step reaction cycle. Here we present a method to manually synthesize oligo-peptoids and to analyze the sequence of the peptoids using tandem mass spectrometry (MS/MS) techniques. The sample peptoid is a nonamer consisting of alternating N-(2-methyloxyethyl)glycine (Nme) and N-(2-phenylethyl)glycine (Npe), as well as an N-(2-aminoethyl)glycine (Nae) at the N-terminus. The sequence formula of the peptoid is Ac-Nae-(Npe-Nme)4-NH2, where Ac is the acetyl group. The synthesis takes place in a commercially available solid-phase reaction vessel. The rink amide resin is used as the solid support to yield the peptoid with an amide group at the C-terminus. The resulting peptoid product is subjected to sequence analysis using a triple-quadrupole mass spectrometer coupled to an electrospray ionization source. The MS/MS measurement produces a spectrum of fragment ions resulting from the dissociation of charged peptoid. The fragment ions are sorted out based on the values of their mass-to-charge ratio (m/z). The m/z values of the fragment ions are compared against the nominal masses of theoretically predicted fragment ions, according to the scheme of peptoid fragmentation. The analysis generates a fragmentation pattern of the charged peptoid. The fragmentation pattern is correlated to the monomer sequence of the neutral peptoid. In this regard, MS analysis reads out the sequence information of the peptoids.

A protocol is described for the manual synthesis of oligo-peptoids followed by sequence analysis by mass spectrometry.

Peptoids are sequence-controlled peptide-mimicking oligomers consisting of N-alkylated glycine units. Among many potential applications, peptoids have ...

The MPLEx Protocol for Multi-omic Analyses of Soil Samples

Mass spectrometry (MS)-based integrated metaproteomic, metabolomic, and lipidomic (multi-omic) studies are transforming our ability to understand and characterize microbial communities in environmental and biological systems. These measurements are even enabling enhanced analyses of complex soil microbial communities, which are the most complex microbial systems known to date. Multi-omic analyses, however, do have sample preparation challenges, since separate extractions are typically needed for each omic study, thereby greatly amplifying the preparation time and amount of sample required. To address this limitation, a 3-in-1 method for the simultaneous extraction of metabolites, proteins, and lipids (MPLEx) from the same soil sample was created by adapting a solvent-based approach. This MPLEx protocol has proven to be both simple and robust for many sample types, even when utilized for limited quantities of complex soil samples. The MPLEx method also greatly enabled the rapid multi-omic measurements needed to gain a better understanding of the members of each microbial community, while evaluating the changes taking place upon biological and environmental perturbations.

A protocol is presented for simultaneously extracting metabolites, proteins, and lipids from a single soil sample, allowing reduced sample preparation times and enabling multi-omic mass spectrometry analyses of samples with limited quantities.

Mass spectrometry (MS)-based integrated metaproteomic, metabolomic, and lipidomic (multi-omic) studies are transforming our ability to understand and ...

Synthesis of Substrate-Bound Au Nanowires Via an Active Surface Growth Mechanism

Advancing synthetic capabilities is important for the development of nanoscience and nanotechnology. The synthesis of nanowires has always been a challenge, as it requires asymmetric growth of symmetric crystals. Here, we report a distinctive synthesis of substrate-bound Au nanowires. This template-free synthesis employs thiolated ligands and substrate adsorption to achieve the continuous asymmetric deposition of Au in solution at ambient conditions. The thiolated ligand prevented the Au deposition on the exposed surface of the seeds, so the Au deposition only occurs at the interface between the Au seeds and the substrate. The side of the newly deposited Au nanowires is immediately covered with the thiolated ligand, while the bottom facing the substrate remains ligand-free and active for the next round of Au deposition. We further demonstrate that this Au nanowire growth can be induced on various substrates, and different thiolated ligands can be used to regulate the surface chemistry of the nanowires. The diameter of the nanowires can also be controlled with mixed ligands, in which another &#34;bad&#34; ligand could turn on the lateral growth. With the understanding of the mechanism, Au nanowire-based nanostructures can be designed and synthesized.

We report a solution-based method to synthesize substrate-bound Au nanowires. By tuning the molecular ligands used during the synthesis, the Au nanowires can be grown from various substrates with different surface properties. Au nanowire-based nanostructures can also be synthesized by adjusting the reaction parameters.

Advancing synthetic capabilities is important for the development of nanoscience and nanotechnology. The synthesis of nanowires has always been a ...

Facile Protocol for the Synthesis of Self-assembling Polyamine-based Peptide Amphiphiles (PPAs) and Related Biomaterials

Polyamine-based Peptide Amphiphiles (PPAs) are a new class of self-assembling amphiphilic biomaterials-related to the peptide amphiphiles (PAs). Traditional PAs possess charged amino acids as solubilizing groups (lysine, arginine), which are directly connected to a lipid segment or can contain a linker region made of neutral amino acids. Tuning the peptide sequence of PAs can yield diverse morphologies. Similarly, PPAs possess a hydrophobic segment and neutral amino acids, but also contain polyamine molecules as water solubilizing (hydrophilic) groups. As is the case with PAs, PPAs can also self-assemble into diverse morphologies, including small rods, twisted nano-ribbons, and fused nano-sheets, when dissolved in water. However, the presence of both primary and secondary amines on a single polyamine molecule poses a significant challenge when synthesizing PPAs. In this paper, we show a simple protocol, based on literature precedents, to achieve a facile synthesis of PPAs using solid phase peptide synthesis (SPPS). This protocol can be extended to the synthesis of PAs and other similar systems. We also illustrate the steps that are needed for cleavage from the resin, identification, and purification.

Facile Protocol for the Synthesis of Self-assembling Polyamine-based Peptide Amphiphiles PPAs and Related Biomaterials

The synthesis of polyamine-based peptide amphiphiles (PPAs) is a significant challenge due to the presence of multiple amine nitrogens, which requires judicious use of protecting groups to mask these reactive functionalities. In this paper, we describe a facile method for the preparation of these new class of self-assembling molecules.

Polyamine-based Peptide Amphiphiles (PPAs) are a new class of self-assembling amphiphilic biomaterials-related to the peptide amphiphiles (PAs). ...

Automation of a Positron-emission Tomography (PET) Radiotracer Synthesis Protocol for Clinical Production

The development of new positron-emission tomography (PET) tracers is enabling researchers and clinicians to image an increasingly wide array of biological targets and processes. However, the increasing number of different tracers creates challenges for their production at radiopharmacies. While historically it has been practical to dedicate a custom-configured radiosynthesizer and hot cell for the repeated production of each individual tracer, it is becoming necessary to change this workflow. Recent commercial radiosynthesizers based on disposable cassettes/kits for each tracer simplify the production of multiple tracers with one set of equipment by eliminating the need for custom tracer-specific modifications. Furthermore, some of these radiosynthesizers enable the operator to develop and optimize their own synthesis protocols in addition to purchasing commercially-available kits. In this protocol, we describe the general procedure for how the manual synthesis of a new PET tracer can be automated on one of these radiosynthesizers and validated for the production of clinical-grade tracers. As an example, we use the ELIXYS radiosynthesizer, a flexible cassette-based radiochemistry tool that can support both PET tracer development efforts, as well as routine clinical probe manufacturing on the same system, to produce [18F]Clofarabine ([18F]CFA), a PET tracer to measure in vivo deoxycytidine kinase (dCK) enzyme activity. Translating a manual synthesis involves breaking down the synthetic protocol into basic radiochemistry processes that are then translated into intuitive chemistry &#34;unit operations&#34; supported by the synthesizer software. These operations can then rapidly be converted into an automated synthesis program by assembling them using the drag-and-drop interface. After basic testing, the synthesis and purification procedure may require optimization to achieve the desired yield and purity. Once the desired performance is achieved, a validation of the synthesis is carried out to determine its suitability for the production of the radiotracer for clinical use.

Automation of a Positron-emission Tomography PET Radiotracer Synthesis Protocol for Clinical Production

Positron-emission tomography (PET) imaging sites that are involved in multiple early clinical research trials need robust and versatile radiotracer manufacturing capabilities. Using the radiotracer [18F]Clofarabine as an example, we illustrate how to automate the synthesis of a radiotracer using a flexible, cassette-based radiosynthesizer and validate the synthesis for clinical use.

The development of new positron-emission tomography (PET) tracers is enabling researchers and clinicians to image an increasingly wide array of biological ...