For financial support we gratefully acknowledge the EPSRC (Career Acceleration Fellowship to J.A.B.; EP/J001538/1), the Ramsay Memorial Trust (Research Fellowship 2009-2011 to J.A.B.), and Imperial College London. Thank you to Prof. Alan Armstrong for generous support and advice.

1. Preparation of Iodoaziridines with Diiodomethyllithium
<ol>
	<li>Flame dry a 100 ml round bottom flask containing a stirrer bar and fitted with a septum, under a stream of argon, then allow to cool to room temperature under an argon atmosphere. NOTE: Glassware dried in an oven overnight (125 &#176;C) and cooled to room temperature in an analogous fashion is also appropriate.</li>
	<li>To the flask, add 5.7 ml anhydrous THF and 2.7 ml anhydrous Et2O via syringe, and freshly distilled hexamethyldisilazane (1.50 mmol, 315 &#181;l) via a microsyringe.</li>
	<li>Stir the resulting solution and cool to -78 &#176;C in a dry ice/acetone bath in a suitably sized dewar to allow the flask to be well submerged. Cover the dewar with aluminum foil, to minimize exposure of the reaction vessel to light.</li>
	<li>Add nBuLi (1.50 mmol, 0.60 ml, 2.5 M in hexanes) dropwise via syringe over 2-3 min to the solution at -78 &#176;C. Allow the mixture to stir at -78 &#176;C for a further 30 min to form a 0.17 M solution of LiHMDS. CAUTION: nBuLi solution is flammable, corrosive to the skin and pyrophoric. Excess reagent in the syringe should be quenched accordingly.</li>
	<li>After 30 min, add 1 ml anhydrous THF to a flame-dried 10 ml round bottom flask via syringe, followed by diiodomethane (1.70 mmol, 135 &#181;l) via a microsyringe and ensure they are well mixed.</li>
	<li>Add the diiodomethane solution dropwise over 2 min to the solution of lithium hexamethyldisilazane at -78 &#176;C. Leave this solution for 20 min at -78 &#176;C.</li>
	<li>During this time, weigh out N-[(E)-4-methylphenylmethylidene]-4-methylbenzenesulfonamide (137 mg, 0.50 mmol) into another flame-dried 10 ml round bottom flask and dissolve in 2.0 ml anhydrous THF.</li>
	<li>After the 20 min deprotonation time, add the imine solution dropwise to the diiodomethyllithium solution over 5 min at -78 &#176;C.</li>
	<li>Immediately after the dropwise addition is complete, lift the reaction vessel out of the dry ice bath, and transfer to an ice/water bath at 0 &#176;C. Re-cover with aluminum foil and leave for 15 min at 0 &#176;C. NOTE: The solution should be orange in color.</li>
	<li>After 15 min at 0 &#176;C, quench the reaction by the addition of 30 ml saturated aqueous sodium bicarbonate solution. Transfer the mixture to a separating funnel and add 30 ml CH2Cl2. Shake the mixture and remove the lower CH2Cl2 layer. Repeat this extraction procedure two further times, and combine the CH2Cl2 layers.</li>
	<li>Add sodium sulfate to the organic layers to remove any water present in the solution, then filter off the sodium sulfate and collect the filtrate in a 250 ml round bottom flask.</li>
	<li>Remove the solvent under reduced pressure on a rotary evaporator to afford an impure sample of the desired iodoaziridine product.</li>
</ol>
2. Assessment of Product Stability to Stationary Phases for Chromatography
<ol>
	<li>Dissolve the crude aziridine sample in CH2Cl2 (16 ml) and add 1,3,5-trimethoxybenzene (28.0 mg, 0.167 mmol) as an internal standard, ensuring this is fully dissolved. Take an aliquot (2 ml) from this mixture, remove the solvent under reduced pressure and analyze this sample by 1H NMR spectroscopy.</li>
	<li>Open the recorded 1H NMR spectrum using standard NMR processing software. In Mestrenova, right click the spectrum and chose &#8220;integration&#8221;, then &#8220;manual&#8221; to provide the integration tool. Click and drag to cover the width of the peaks at 6.08 ppm and at 4.87 ppm to integrate the signals of the internal standard and the aziridine CHI signal respectively. Right-click on the integral for the peak at 6.08 ppm, select &#8220;edit integral&#8221; and change the &#8220;normalized&#8221; value to 3.0. NOTE: Similar steps can be applied with other software packages.</li>
	<li>Use the updated value of integral for the aziridine CHI signal (4.87 ppm) to determine the yield of the iodoaziridine, here using (100/3) &#215; (the integral of the CHI signal), which affords a calculated yield of 59%. NOTE: Given the known quantity of internal standard (0.167 mmol), and the product peak corresponding to 1 proton, the yield of iodoaziridine is calculated by the following equation:100 &#215; (integral of product peak) &#215; (moles of internal standard) / moles starting material.</li>
	<li>Prepare slurries of the following stationary phases (25 g): silica, silica + 1% NEt3 (triethylamine), neutral alumina, basic alumina (activity I), basic alumina (activity IV) and Florisil, each in 5% EtOAc/hexane (50 ml), in six separate 250 ml conical flasks containing stirrer bars. In another conical flask prepare a 5% EtOAc/hexane solution (50 ml), to be used as a control experiment. CAUTION: silica gel, alumina and other stationary phases employed are dangerous if inhaled, therefore should always be handled in an effective fume hood.</li>
	<li>Add 2 ml aliquots of the iodoaziridine/internal standard solution to each of the conical flasks at RT. Stir the slurry mixtures for 30 min. NOTE: this represents the duration the compound may be exposed to the stationary phase during a normal flash column chromatography procedure.</li>
	<li>Filter the slurry mixtures using a sintered funnel, and collect the filtrate in a 250 ml round bottom flask. Wash the residue on the sintered funnel with CH2Cl2 (2 &#215; 30 ml). Repeat this filtering process for the remaining slurries. NOTE: It is appropriate to offset the commencement of each stationary phase to allow time for filtration and so maintain the same time for each of the stationary phase materials.</li>
	<li>Remove the solvent from the resulting samples under reduced pressure, and analyze by 1H NMR spectroscopy to calculate the amount of iodoaziridine recovered in each case, as described in Section 2.2.</li>
	<li>Compare the yields of iodoaziridine obtained from each stationary phase tested with that obtained in Section 2.1. NOTE: The sample giving the highest yield, ideally the same as in 2.1, indicates the optimal stationary phase for chromatography. In this example, basic alumina (activity IV) was deemed the best stationary phase for purification.</li>
</ol>
3. Deactivation of Basic Alumina and Purification of the Iodoaziridine
<ol>
	<li>Repeat Section 1 to generate the crude iodoaziridine mixture.</li>
	<li>To generate basic alumina (activity IV), add 100 g of basic alumina (activity I) to a 500 ml round bottom flask and then add 10 ml water to the flask and fit with a glass stopper.</li>
	<li>Shake the flask vigorously until no lumps are visible, indicating even spreading of water throughout the alumina. Allow the alumina to cool to RT. CAUTION: the adsorption of water is exothermic, so the flask may get hot and may result in a build up of pressure. Release any pressure build up frequently.</li>
	<li>Purify the crude iodoaziridine by column chromatography using the basic alumina (activity IV) as the stationary phase, eluting with hexane, grading to 5% EtOAc/hexane. NOTE: high concentrations of EtOAc should not be used with basic alumina. In these cases, diethyl ether can be used instead.</li>
	<li>Combine the product containing fractions and remove the solvent under reduced pressure to obtain the pure iodoaziridine.</li>
</ol>

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E. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Highly+diastereoselective+aziridination+of+imines+with+trimethylsilyldiazomethane.+Subsequent+silyl+substitution+with+electrophiles,+ring+opening,+and+metalation+of+C-silylaziridines+&#8722;+a+cornucopia+of+highly+selective+transformations.">Highly diastereoselective aziridination of imines with trimethylsilyldiazomethane. Subsequent silyl substitution with electrophiles, ring opening, and metalation of C-silylaziridines &#8722; a cornucopia of highly selective transformations.</a> J. Org. Chem. 67 (7), 2335-2344 (2002).</li><li>Nelson, J. 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The authors declare that they have no competing financial interests.

A procedure for the diastereoselective preparation of cis-N-Ts-iodoaziridines is described, along with a stability study protocol to quantitatively indicate the best stationary phase for purification of potentially unstable compounds by flash column chromatography. It is envisaged that access to iodoaziridines through this approach will enable methods to access to a wide range of aziridines to be developed, by derivatization of the intact ring.
An appropriate modification to ...

The aim of this method is to prepare iodoaziridines that offer potential for further functionalization to aziridine derivatives. The method incorporates a protocol for the quantitative selection of the optimal stationary phase for chromatography.
Aziridines, as three-membered rings, posses inherent ring strain that makes them important building blocks in organic chemistry1. They display a vast array of reactivity often involving aziridine ring opening2,3, particularly as intermediates in the synthesis of functionalized amines4,5, or the formation of other nitrogen containing heterocycles6,7. The synthesis of a range of aziridine derivatives by functionalization of a precursor containing an intact aziridine ring has emerged as a viable strategy8. Functional group&#8211;metal exchange, to generate an aziridinyl anion, and reaction with electrophiles has been shown to be effective9,10,11, and recently regio- and stereoselective deprotonation of N-protected aziridines has also been achieved12-15. Very recently, palladium catalyzed cross-coupling methods to form aryl aziridines from functionalized aziridine precursors has been developed by Vedejs16,17, and ourselves18.
The chemistry of heteroatom substituted aziridines opens up fascinating questions of reactivity and stability19. We have been interested in the preparation of iodoaziridines as a novel functional group that offers the potential to provide precursors to a wide range of derivatives with complementary reactivity to existing aziridine functionalization reactions. In 2012 we reported the first preparation of aryl N-Boc-iodoaziridines20, and very recently reported the preparation of aryl and alkyl substituted N-Ts-iodoaziridines21.
The method to access iodoaziridines uses diiodomethyllithium, a reagent which has recently also been employed in the preparation of diiodoalkanes22,23, diiodomethylsilanes22,24, and vinyl iodides25-27. The carbenoid-like nature of this reagent requires preparation and use at low temperatures22,28. The techniques and conditions used for the generation of diiodomethyllithium in the preparation of iodoaziridines are described below.
While silica has emerged as the material of choice for chromatography29, it proved to be unsuitable for the purification of the N-Ts-iodoaziridines. Silica gel is generally the first and only solid phase material employed in flash chromatography in organic chemistry due to the availability and effective separations. However, the acidic nature of silica gel can cause the decomposition of sensitive substrates during purification, preventing isolation of the desired material. While other stationary phases or modified silica gels are available for chromatography30, there was no way to assess compatibility of the target molecule to these different materials. Due to the sensitive nature of the iodoaziridines, we established a protocol to assess the stability of a compound to an array of stationary phases21, which is demonstrated here. This has potential for application in the synthesis of a wide range of compounds with sensitive functional groups. The following protocol provides efficient access to N-Ts iodoaziridines, allowing the diastereoselective synthesis of both alkyl and aromatic cis-iodoaziridines in high yield.

<table border="0" cellpadding="0" cellspacing="0" width="871">
	<tbody>
		<tr height="42">
			<td height="42" style="height:42px;width:209px;">Hexamethyldisilazane</td>
			<td style="width:273px;">999-97-3</td>
			<td style="width:197px;">Alfa Aesar</td>
			<td style="width:192px;">Distill from KOH under argon prior to use.</td>
		</tr>
		<tr height="42">
			<td height="42" style="height:42px;width:209px;">n-Butyllithium</td>
			<td style="width:273px;">109-72-8</td>
			<td style="width:197px;">Sigma Aldrich</td>
			<td style="width:192px;">2.5 M in hexanes, titrate prior to use.</td>
		</tr>
		<tr height="42">
			<td height="42" style="height:42px;width:209px;">Diiodomethane</td>
			<td style="width:273px;">75-11-6</td>
			<td style="width:197px;">Alfa Aesar</td>
			<td style="width:192px;">Contains copper as a stabilizer.</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:209px;">1,3,5-Trimethoxybenzene</td>
			<td style="width:273px;">621-23-8</td>
			<td style="width:197px;">Sigma Aldrich</td>
			<td style="width:192px;"></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:209px;">Silica</td>
			<td style="width:273px;">112945-52-5</td>
			<td style="width:197px;">Merck</td>
			<td style="width:192px;"></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:209px;">Basic alumina</td>
			<td style="width:273px;">1344-28-1</td>
			<td style="width:197px;">Sigma Aldrich</td>
			<td style="width:192px;"></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:209px;">Neutral alumina</td>
			<td style="width:273px;">1344-28-1</td>
			<td style="width:197px;">Merck</td>
			<td style="width:192px;"></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:209px;">Florisil</td>
			<td style="width:273px;">1343-88-0</td>
			<td style="width:197px;">Sigma Aldrich</td>
			<td style="width:192px;"></td>
		</tr>
		<tr height="22">
			<td height="22" style="height:23px;width:209px;">THF</td>
			<td colspan="3" rowspan="3" style="width:663px;">All anhydrous solvents were dried through activated alumina purification columns.&#160;</td>
		</tr>
		<tr height="25">
			<td height="25" style="height:25px;width:209px;">Et2O</td>
		</tr>
		<tr height="25">
			<td height="25" style="height:25px;width:209px;">CH2Cl2</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">NMR spectrometer</td>
			<td>Bruker AV 400&#160;</td>
			<td>n/a</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:209px;">NMR processing software</td>
			<td>MestReNova&#160;</td>
			<td>7.0.2-8636</td>
			<td></td>
		</tr>
	</tbody>
</table>

synthesis and purification of iodoaziridines involving quantitative selection of the optimal stationary phase for chromatography

The highly diastereoselective preparation of cis-N-Ts-iodoaziridines through reaction of diiodomethyllithium with N-Ts aldimines is described. Diiodomethyllithium is prepared by the deprotonation of diiodomethane with LiHMDS, in a THF/diethyl ether mixture, at -78 &#176;C in the dark. These conditions are essential for the stability of the LiCHI2 reagent generated. The subsequent dropwise addition of N-Ts aldimines to the preformed diiodomethyllithium solution affords an amino-diiodide intermediate, which is not isolated. Rapid warming of the reaction mixture to 0 &#176;C promotes cyclization to afford iodoaziridines with exclusive cis-diastereoselectivity. The addition and cyclization stages of the reaction are mediated in one reaction flask by careful temperature control.
Due to the sensitivity of the iodoaziridines to purification, assessment of suitable methods of purification is required. A protocol to assess the stability of sensitive compounds to stationary phases for column chromatography is described. This method is suitable to apply to new iodoaziridines, or other potentially sensitive novel compounds. Consequently this method may find application in range of synthetic projects. The procedure involves firstly the assessment of the reaction yield, prior to purification, by 1H NMR spectroscopy with comparison to an internal standard. Portions of impure product mixture are then exposed to slurries of various stationary phases appropriate for chromatography, in a solvent system suitable as the eluent in flash chromatography. After stirring for 30 min to mimic chromatography, followed by filtering, the samples are analyzed by 1H NMR spectroscopy. Calculated yields for each stationary phase are then compared to that initially obtained from the crude reaction mixture. The results obtained provide a quantitative assessment of the stability of the compound to the different stationary phases; hence the optimal can be selected. The choice of basic alumina, modified to activity IV, as a suitable stationary phase has allowed isolation of certain iodoaziridines in excellent yield and purity.

The procedure described affords cis-(&#177;)-2-iodo-3-(4-tolyl)-1-(4-tolylsulfonyl)aziridine as a single diastereoisomer and with excellent purity (Figure 1). Prior to purification, a yield of 59% of the iodoaziridine product was calculated by 1H NMR spectroscopy. However, this iodoaziridine was particularly challenging to purify and underwent significant decomposition on silica. Purification on basic alumina (activity IV) as determined by the stationary phase screen allowed the produ...

Watch this Scientific Journal Video about Synthesis and Purification of Iodoaziridines Involving Quantitative Selection of the Optimal Stationary Phase for Chromatography at JoVE.com

Synthesis and Purification of Iodoaziridines Involving Quantitative Selection of the Optimal Stationary Phase for Chromatography

A protocol for the diastereoselective one-pot preparation of cis-N-Ts-iodoaziridines is described. The generation of diiodomethyllithium, addition to N-Ts aldimines and cyclization of the amino gem-diiodide intermediate to iodoaziridines is demonstrated. Also included is a protocol to rapidly and quantitatively assess the most appropriate stationary phase for purification by chromatography.

The highly diastereoselective preparation of cis-N-Ts-iodoaziridines through reaction of diiodomethyllithium with N-Ts aldimines is described. ...

synthesis-purification-iodoaziridines-involving-quantitative

Research

JoVE Journal

Chemistry

12.5K Views.  Imperial College London.  Un protocollo per la diastereoselettiva preparazione di un piatto di cis - N-TS-iodoaziridines è descritto. La generazione di diiodomethyllithium, oltre a N-Ts aldimines e ciclizzazione della gemma amino-diioduro intermedio iodoaziridines è dimostrata. È incluso anche un protocollo di rapidamente e quantitativamente valutare la fase stazionaria più appropriato per la purificazione mediante cromatografia. 

Video: Synthesis and Purification of Iodoaziridines Involving Quantitative Selection of the Optimal Stationary Phase for Chromatography

Determination of the Gas-phase Acidities of Oligopeptides

Amino acid residues located at different positions in folded proteins often exhibit different degrees of acidities. For example, a cysteine residue located at or near the N-terminus of a helix is often more acidic than that at or near the C-terminus 1-6. Although extensive experimental studies on the acid-base properties of peptides have been carried out in the condensed phase, in particular in aqueous solutions 6-8, the results are often complicated by solvent effects 7. In fact, most of the active sites in proteins are located near the interior region where solvent effects have been minimized 9,10. In order to understand intrinsic acid-base properties of peptides and proteins, it is important to perform the studies in a solvent-free environment.
We present a method to measure the acidities of oligopeptides in the gas-phase. We use a cysteine-containing oligopeptide, Ala3CysNH2 (A3CH), as the model compound. The measurements are based on the well-established extended Cooks kinetic method (Figure 1) 11-16. The experiments are carried out using a triple-quadrupole mass spectrometer interfaced with an electrospray ionization (ESI) ion source (Figure 2). For each peptide sample, several reference acids are selected. The reference acids are structurally similar organic compounds with known gas-phase acidities. A solution of the mixture of the peptide and a reference acid is introduced into the mass spectrometer, and a gas-phase proton-bound anionic cluster of peptide-reference acid is formed. The proton-bound cluster is mass isolated and subsequently fragmented via collision-induced dissociation (CID) experiments. The resulting fragment ion abundances are analyzed using a relationship between the acidities and the cluster ion dissociation kinetics. The gas-phase acidity of the peptide is then obtained by linear regression of the thermo-kinetic plots 17,18.
The method can be applied to a variety of molecular systems, including organic compounds, amino acids and their derivatives, oligonucleotides, and oligopeptides. By comparing the gas-phase acidities measured experimentally with those values calculated for different conformers, conformational effects on the acidities can be evaluated.

The determination of the gas-phase acidities of cysteine-containing oligopeptides is described. The experiments are performed using a triple quadrupole mass spectrometer. The relative acidities of the peptides are measured using collision-induced dissociation experiments, and the quantitative acidities are determined using the extended Cooks kinetic method.

Amino acid residues located at different positions in folded proteins often exhibit different degrees of acidities. For example, a cysteine residue ...

Split-and-pool Synthesis and Characterization of Peptide Tertiary Amide Library

Peptidomimetics are great sources of protein ligands. The oligomeric nature of these compounds enables us to access large synthetic libraries on solid phase by using combinatorial chemistry. One of the most well studied classes of peptidomimetics is peptoids. Peptoids are easy to synthesize and have been shown to be proteolysis-resistant and cell-permeable. Over the past decade, many useful protein ligands have been identified through screening of peptoid libraries. However, most of the ligands identified from peptoid libraries do not display high affinity, with rare exceptions. This may be due, in part, to the lack of chiral centers and conformational constraints in peptoid molecules. Recently, we described a new synthetic route to access peptide tertiary amides (PTAs). PTAs are a superfamily of peptidomimetics that include but are not limited to peptides, peptoids and N-methylated peptides. With side chains on both &#945;-carbon and main chain nitrogen atoms, the conformation of these molecules are greatly constrained by sterical hindrance and allylic 1,3 strain. (Figure 1) Our study suggests that these PTA molecules are highly structured in solution and can be used to identify protein ligands. We believe that these molecules can be a future source of high-affinity protein ligands. Here we describe the synthetic method combining the power of both split-and-pool and sub-monomer strategies to synthesize a sample one-bead one-compound (OBOC) library of PTAs.

Peptide tertiary amides (PTAs) are a superfamily of peptidomimetics that include but are not limited to peptides, peptoids and N-methylated peptides. Here we describe a synthetic method which combines&#160;both split-and-pool and sub-monomer strategies to synthesize a one-bead one-compound library of PTAs.

Peptidomimetics are great sources of protein ligands. The oligomeric nature of these compounds enables us to access large synthetic libraries on solid ...

Quantitative Detection of Trace Explosive Vapors by Programmed Temperature Desorption Gas Chromatography-Electron Capture Detector

The direct liquid deposition of solution standards onto sorbent-filled thermal desorption tubes is used for the quantitative analysis of trace explosive vapor samples. The direct liquid deposition method yields a higher fidelity between the analysis of vapor samples and the analysis of solution standards than using separate injection methods for vapors and solutions, i.e., samples collected on vapor collection tubes and standards prepared in solution vials. Additionally, the method can account for instrumentation losses, which makes it ideal for minimizing variability and quantitative trace chemical detection. Gas chromatography with an electron capture detector is an instrumentation configuration sensitive to nitro-energetics, such as TNT and RDX, due to their relatively high electron affinity. However, vapor quantitation of these compounds is difficult without viable vapor standards. Thus, we eliminate the requirement for vapor standards by combining the sensitivity of the instrumentation with a direct liquid deposition protocol to analyze trace explosive vapor samples.

Trace explosive vapors of TNT and RDX collected on sorbent-filled thermal desorption tubes were analyzed using a programmed temperature desorption system coupled to GC with an electron capture detector. The instrumental analysis is combined with direct liquid deposition method to reduce sample variability and account for instrumentation drift and losses.

The direct liquid deposition of solution standards onto sorbent-filled thermal desorption tubes is used for the quantitative analysis of trace explosive ...

Supercritical Nitrogen Processing for the Purification of Reactive Porous Materials

Supercritical fluid extraction and drying methods are well established in numerous applications for the synthesis and processing of porous materials. Herein, nitrogen is presented as a novel supercritical drying fluid for specialized applications such as in the processing of reactive porous materials, where carbon dioxide and other fluids are not appropriate due to their higher chemical reactivity. Nitrogen exhibits similar physical properties in the near-critical region of its phase diagram as compared to carbon dioxide: a widely tunable density up to ~1 g ml-1, modest critical pressure (3.4 MPa), and small molecular diameter of ~3.6 &#197;. The key to achieving a high solvation power of nitrogen is to apply a processing temperature in the range of 80-150 K, where the density of nitrogen is an order of magnitude higher than at similar pressures near ambient temperature. The detailed solvation properties of nitrogen, and especially its selectivity, across a wide range of common target species of extraction still require further investigation. Herein we describe a protocol for the supercritical nitrogen processing of porous magnesium borohydride.

Nitrogen is an effective supercritical fluid for extraction or drying processes due to its small molecular size, high density in the near-liquid supercritical regime, and chemical inertness. We present a supercritical nitrogen drying protocol for the purification treatment of reactive, porous materials.

Supercritical fluid extraction and drying methods are well established in numerous applications for the synthesis and processing of porous materials. ...

A Quantitative Glycomics and Proteomics Combined Purification Strategy

There is a growing desire in the biological and clinical sciences to integrate and correlate multiple classes of biomolecules to unravel biology, define pathways, improve treatment, understand disease, and aid biomarker discovery. N-linked glycosylation is one of the most important and robust post-translational modifications on proteins and regulates critical cell functions such as signaling, adhesion, and enzymatic function. Analytical techniques to purify and analyze N-glycans have remained relatively static over the last decade. While accurate and effective, they commonly require significant expertise and resources. Though some high-throughput purification schemes have been developed, they have yet to find widespread adoption and often rely on the enrichment of glycopeptides. One promising method, developed by Thomas-Oates et al., filter aided N-glycan separation (FANGS), was qualitatively demonstrated on tissues. Herein, we adapted FANGS to plasma and coupled it to the individuality normalization when labeling with glycan hydrazide tags strategy in order to achieve accurate relative quantification by liquid chromatography mass spectrometry and enhanced electrospray ionization. Furthermore, we designed new functionality to the protocol by achieving tandem, shotgun proteomics and glycosylation site analysis on hen plasma. We showed that N-glycans purified on filter and derivatized by hydrophobic hydrazide tags were comparable in terms of abundance and class to those by solid phase extraction (SPE); the latter is considered a gold standard in the field. Importantly, the variability in the two protocols was not statistically different. Proteomic data that was collected in-line with glycomic data had the same depth compared to a standard trypsin digest. Peptide deamidation is minimized in the protocol, limiting non-specific deamidation detected at glycosylation motifs. This allowed for direct glycosylation site analysis, though the protocol can accommodate 18O site labeling as well. Overall, we demonstrated a new in-line high-throughput, unbiased, filter based protocol for quantitative glycomics and proteomics analysis.

A high-throughput protocol was developed for combined proteomics and glycomics purification and LC-MS/MS quantification in plasma. Deamidation analysis of N-linked glycosylation motifs was specific to deglycosylated sites. Accurate quantitation of N-glycans was achieved by coupling filter aided N-glycan separation to the individuality normalization when labeling with glycan hydrazide tags strategy.

There is a growing desire in the biological and clinical sciences to integrate and correlate multiple classes of biomolecules to unravel biology, define ...

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.

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.

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

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&#039;-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 ...