Chemical Ligation

Chemical Ligation by Click Chemistry

Native Chemical Ligation

Staudinger Ligation

Organic Azides and Azide Sources

Functionalized Alkynes

Vol. 8, No. 1

Diphenylphosphinemethanethiol: efficacious reagent for traceless Staudinger ligation

�

Vol. 8 No. 1

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About Our Cover

IntroductionMore and more researchers face the task of selectively combining large molecules, attaching molecular probes, or covalently immobilizing substrates on surfaces. In particular when biopolymers and bioconjugates are involved there is an urgent need for mild and biocompatible reaction conditions. A toolbox of several powerful chemical ligation techniques already exists and is continually being expanded.

In this issue of ChemFiles, we provide an overview of modern chemical ligation methods and introduce highly innovative and unique new tools for research at the interface between chemistry and biology. The most prominent chemical ligation techniques (click chemistry, native chemical ligation, and Staudinger ligation) will be discussed. A comprehensive listing of available organic azides and functionalized alkynes rounds off this issue of ChemFiles with valuable building blocks for click chemistry or Staudinger ligation.

If you are unable to find the specific reagent you need, “Please Bother Us.” with your suggestions at matthias.junkers@sial.com, or contact your local Sigma-Aldrich® office (see back cover).

The cover structure depicts diphenylphosphinemethanethiol, the most efficacious reagent known today to induce traceless Staudinger ligations (Raines ligation reagent). Diphenylphosphinemethanethiol can be obtained easily from the shelf-stable precursor 670359 by removing the acetyl and borane protective groups.

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Chemical Ligation by Click Chemistry—A “Click” Away from Discovery

In an extensive study Finn and co-workers only recently showed that tris(2-benzimidazolylmethyl)amines (general structure in Figure 2) are the most promising family of accelerating ligands for the Cu catalyzed azide-alkyne cycloaddition reaction from among more than 100 mono-, bi-, and polydentate candidates.10 Under both preparative (high concentration, low catalyst loading) and dilute (lower substrate concentration, higher catalyst loading) conditions, these tripodal benzimidazole derivatives give substantial improvements in rate and yields, with convenient workup to remove residual Cu and ligand.

A new reagent developed by Carolyn R. Bertozzi and co-workers eliminates the toxicity to living cells that is usually associated with the copper catalyzed Huisgen 1,3-dipolar cycloaddition.11 By using a difluorinated cyclooctyne (Figure 3) instead of the usual terminal alkyne a rapid cycloaddition reaction takes place even without a catalyst. The ring strain and the electron-withdrawing difluoro group activate the alkyne for copper-free click chemistry. This method was used to attach fluorescent labels to cells with azide-containing sialic acid in their surface glycans. Thus, it was possible to study the dynamics of glycan trafficking in living cells over the course of 24 hours with no indication that the reaction or the labels perturb the process. This is an impressive example of how copper-free click chemistry can be used as a biologically friendly method to label and track biomolecules in living cells.

Sigma-Aldrich® proudly offers a choice of catalysts and ligands for the Huisgen cycloaddition reaction. Later sections in this issue present a comprehensive overview of available organic azides, azide sources, and alkynes that may be applied in click chemistry.

If you want to learn about hot new product additions to the click chemistry universe and other innovative areas of chemical synthesis as soon as they become available, please check our regularly updated product highlights at sigma-aldrich.com/chemicalsynthesis.

References: (1) For recent reviews, see: (a) Kolb, H. C.; Sharpless, K. B. Drug Discovery Today 2003, 8, 1128. (b) Kolb, H. C. et al. Angew. Chem. Int. Ed. 2001, 40, 2004. (2)(a) Rostovtsev, V. V.; Green, L.G.; Fokin, V.V.; Sharpless, K.B. Angew. Chem. Int. Ed. 2002, 41, 2596. (b) Tornøe, C. W. et al. J. Org. Chem. 2002, 67, 3057. (3)(a) Manetsch, R. et al. J. Am. Chem. Soc. 2004, 126, 12809. (b) Lewis, W.G. et al. Angew. Chem. Int. Ed. 2002, 41, 1053. (4) Speers, A. E. J. Am. Chem. Soc. 2003, 125, 4686. (5) Wolfbeis, O.S. Angew. Chem. Int. Ed. 2007, 46, 2980. (6) Gierlich, J.; Burley, G.A.; Gramlich, P.M.E.; Hammond, D.M.; Carell, T. Org. Lett. 2006, 8, 3639. (7) Bock, V.D.; Perciaccente, R.; Jansen, T.P.; Hiemstra, H.; Maarseveen, J.H. Org. Lett. 2006, 8, 919. (8) Lutz, J.-F. Angew. Chem. Int. Ed. 2007, 46, 1018. (9) Chan, T.R. et al. Org. Lett 2004, 6, 2853. (10) Rodionov, V. O.; Presolski, S. I.; Gardinier, S.; Lim, Y.-H.; Finn, M. G. J. Am. Chem. Soc. 2007, 129, 12696. (11) Baskin, J.M.; Prescher, J.A.; Laughlin, S.T.; Agard, N.J.; Chang, P.V.; Miller, I.A.; Lo, A.; Codelli, J.A.; Bertozzi, C.R. PNAS 2007, 104, 16793.

Ch

em

ical Lig

atio

n

by C

lick C

hem

istry

The traditional process of drug discovery based on natural secondary metabolites has often been slow, costly, and labor-intensive. Even with the advent of combinatorial chemistry and high-throughput screening in the past two decades, the generation of leads is dependent on the reliability of the individual reactions to construct the new molecular framework.

Click chemistry is a newer approach to the synthesis of drug-like molecules that can accelerate the drug discovery process by utilizing a few practical and reliable reactions. Sharpless and co-workers have defined what makes a click reaction: one that is wide in scope and easy to perform, uses only readily available reagents, and is insensitive to oxygen and water. In fact, water is in several instances the ideal reaction solvent, providing the best yields and highest rates. Reaction work-up and purification uses benign solvents and avoids chromatography.1

Of the reactions comprising the click universe, the “perfect” example is the Huisgen 1,3-dipolar cycloaddition of alkynes to azides to form 1,4-disubsituted-1,2,3-triazoles (Scheme 1). The copper(I)-catalyzed reaction is mild and very efficient, requiring no protecting groups and no purification in many cases.2 The azide and alkyne functional groups are largely inert towards biological molecules and aqueous environments, which allows the use of the Huisgen 1,3-dipolar cycloaddition in target guided synthesis3 and activity-based protein profiling,4 or the ligation of biopolymers to probes or surfaces.5 For example, Carell and co-workers demonstrated the labelling of alkyne modified DNA oligomers with fluorescence probes by click chemistry.6

The triazole has similarities to the ubiquitous amide moiety found in nature. Thus triazole formation was used for the otherwise difficult macrocyclization of a cyclic tetrapeptide analog to a potent tyrosinase inhibitor.7

Additionally triazoles are nearly impossible to oxidize or reduce. This is a main reason why material science has discovered Huisgen cycloadditions as major ligation tools in diverse areas such as polymer science or nanoelectronics.8

Using Cu(II) salts with ascorbate has been the method of choice for the preparative synthesis of 1,2,3-triazoles, but it is problematic in bioconjugation applications. However, tris[(1-benzyl-1H-1,2,3-triazol-4-yl)methyl]amine, TBTA (Figure 1), has been shown to effectively enhance the copper-catalyzed cycloaddition without damaging biological scaffolds.9

R1

N N NR2

N NN

R1

R21 mol% CuSO4

5 mol% sodium ascorbate

H2O/tBuOH 2:1rt, 8 h Scheme 1

N

NNN

N NN

NN

N

Figure 1

N

NN

N

N

N

N

R

R

R

R = H or -(CH2)4CO2K

Figure 2

F

FNH

OR

R = fluorescent dye or biotin Figure 3

�

TO ORDER: Contact your local Sigma-Aldrich office (see back cover), or visit sigma-aldrich.com/chemicalsynthesis.

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Click Catalysts and LigandsCopper(II) acetate, 98%Cupric acetate

H3C O Cu2+

O

2

C4H6CuO4 FW 181.63 [142-71-2]

326755-25G 25 g

326755-100G 100 g

Copper(I) bromide, 98%Cuprous bromide CuBr

BrCu FW 143.45 [7787-70-4]

212865-50G 50 g

212865-250G 250 g

212865-1KG 1 kg

Copper(I) iodide, 98%Cuprous iodide CuI

CuI FW 190.45 [7681-65-4]

205540-50G 50 g

205540-250G 250 g

205540-1KG 1 kg

Copper(II) sulfate, ≥99%Cupric sulfate CuSO4

CuO4S FW 159.61 [7758-98-7]

C1297-100G 100 g

C1297-500G 500 g

Copper(II) sulfate pentahydrate, ≥98.0%Cupric sulfate pentahydrate CuSO4 • 5H2O

CuO4S · 5H2O FW 249.69 [7758-99-8]98.0-102.0% (ACS specification)

209198-5G 5 g

209198-100G 100 g

209198-250G 250 g

209198-500G 500 g

209198-2.5KG 2.5 kg

Chloro(pentamethylcyclopentadienyl)(cycloocta- 8

diene)ruthenium(II)C18H27ClRu

RuCl

CH3

CH3

H3C

H3C CH3FW 379.93

667234-250MG 250 mg

667234-1G 1 g

Pentamethylcyclopentadienylbis(triphenylphosphine)ruthe-nium(II) chlorideChloro(pentamethylcyclopentadienyl)bis(triphenylphos-

Ru

CH3

CH3

CH3H3C

H3C

Cl PPh3Ph3P

phine)ruthenium(II) C46H45ClP2Ru FW 796.32 [92361-49-4]

673293-250MG 250 mg

673293-1G 1 g

(+)-Sodium L-ascorbate, ≥98%L(+)-Ascorbic acid sodium salt; Vitamin C sodium salt

O

ONaHO

O

OH

OHC6H7NaO6 FW 198.11 [134-03-2]

A7631-25G 25 g

A7631-100G 100 g

A7631-500G 500 g

A7631-1KG 1 kg

TentaGel™ TBTA 8

Tris[(1-benzyl-1H-1,2,3-

HN

O

NN

N

N

N

NN N

NN

triazol-4-yl)methyl]amine, polymer bound

696773-250MG 250 mg

Tris[(1-benzyl-1H-1,2,3-triazol-4-yl)methyl]amine, 97%TBTA

NNN N

NNN

NN

N

C30H30N10 FW 530.63

678937-50MG 50 mg

678937-500MG 500 mg

Ch

em

ical

Lig

ati

on

b

y C

lick

Ch

em

istr

y

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Native Chemical Ligation

Introduction: Chemical Synthesis of Peptides and ProteinsDespite competition by recombinant DNA techniques, the synthetic preparation of peptides and proteins offers approaches to protein engineering that are beyond the realm of biology and the limitations of the genetic code. Unlike nature, purely synthetic methods allow the design of peptides entirely from scratch and the furnishing of protein analogs with virtually any unnatural residue.

Chemical peptide synthesis faces certain limitations though. Solution-phase synthesis methods are suitable for peptides with a chain length of up to ten amino acids (Figure 1). Solid-phase peptide synthesis (SPPS) broadens the range of accessible peptides by dramatically enhancing speed and efficiency of the synthesis. Still the maximum chain length of the peptides prepared by SPPS is limited to about 50 amino acid residues.

The development of chemoselective reactions to give a native peptide bond at the site of ligation allows the synthesis of proteins by joining smaller peptides synthesized previously by SPPS. The challenge of this approach is to form an amide bond chemoselectively in the presence of amino acid side chains presenting free amines (Lys) and carboxylates (Glu/Asp). Ideally, no protecting groups should be used and all chemical transformations should take place under mild conditions that are compatible with biological environments. The most powerful technique of this kind is Native Chemical Ligation (NCL) that was introduced by Kent and co-workers in 1994 (Scheme 1).12 Prior to this work, Wieland had observed the condensation of peptide thioesters in early, pioneering investigations.13 Meanwhile, Native Chemical Ligation has enabled the synthesis of many moderate-size proteins and glycoproteins, culminating in the assembly of a 203 amino acid HIV protease covalent dimer.14 Some innovative applications and improved procedures for NCL will be presented later in this chapter.

Expressed Protein Ligation (EPL) finally combines the strengths of molecular biology and chemical synthesis by filling the gap between chemistry and biology. A protein expressed by recombinant DNA techniques can be extended with synthetic peptide fragments post-translationally. In recent examples, Cole and co-workers used EPL for the C-terminal attachment of a small phosphorylated synthetic peptide.15 Waldmann, Goody, and co-workers demonstrated the EPL synthesis of an azide-modified N-Ras protein and its site-specific immobilization onto a phosphine-functionalized glass surface by means of the Staudinger ligation.16

Native Chemical LigationNative Chemical Ligation allows the combination of two unprotected peptide segments by the reaction of a α-thioester with a cysteine-peptide (Scheme 1). The result of this reaction is a native amide bond at the ligation site, rendering this method highly attractive for the synthesis of large peptides. Usually, α-alkylthioesters are used because of their ease of preparation. Since they are rather unreactive, the ligation reaction is catalyzed by in situ transthioesterification with thiol additives. The most common thiol catalysts to date have been either a mixture of thiophenyl/benzyl mercaptan, or 2-mercaptoethanesulfonate (MESNa). In a recent study, it was shown that MESNa is a poor catalyst, requiring reaction times of typically 24–48 hours. It is outperformed by far by certain aryl thiols. Using 4-mercaptophenylacetic acid (MPAA), proteins can be synthesized much more rapidly (Figure 2). Chemical ligations are typically complete in less than an hour and with high yields.17

Native chemical ligation usually relies on the location of suitable Xaa–Cys ligation sites, spaced at intervals no greater than about 40 residues in the target amino acid sequence. However, Xaa–Cys sites in a protein’s polypeptide chain are often limiting: Cys residues are rare or even absent in many proteins, or only present in an unsuitable position. Yan and Dawson introduced an approach that allows Xaa–Ala ligation sites, with a Cys residue used in place of the native Ala residue. Subsequent desulfurization of the ligation product with freshly prepared Raney nickel produces the native target sequence.18 Recently, this methodology has been extended by Kent and co-workers to the synthesis of Cys-containing peptides by ligating fragments at Xaa–Ala junctions.19 Using acetamidomethyl (Acm) side chain protecting groups for Cys residues other than the ligation site, efficient and selective desulfurization of the ligation site is feasible.

References: (12) Dawson, P.E.; Muir, T.W.; Clark-Lewis, I.; Kent, S.B.H. Science, 1994, 266, 776. (13) Wieland, T.; Bokelmann, E.; Bauer, L.; Lang, H.U.; Lau, H. Justus Liebigs Ann. Chem. 1953, 583, 129. (14) Torbeev, V.Y.; Kent, S.B.H. Angew Chem. Int. Ed. 2007, 46, 1667. (15) Cole, P.A. J. Am. Chem. Soc. 2006, 128, 4192. (16) Watzke, A. et al. Angew. Chem. Int. Ed. 2006, 45, 1408. (17) Johnson, E.C.B.; Kent, S.B.H. J. Am. Chem. Soc. 2006, 128, 6640. (18) Yan, L.Z.; Dawson, P.E. J. Am. Chem. Soc. 2001, 123, 526. (19) Pentelute, B.L.; Kent, S.B.H. Org. Lett. 2007, 9, 687.

� Solution-phase peptide synthesisOnly small peptides (chain length < 10 aa)

� Solid-phase peptide synthesisMedium sized peptides (chain length < 50 aa)

� Native chemical ligationPeptides and smaller proteins (chain length < 200 aa)

� Expressed protein ligationChemically modifi ed proteins (chain length > 500 aa)

� Staudinger ligationModifi cation, immobilization, or combination of peptides

Figure 1

peptide1 SR

O

H2N peptide2

SH

+peptide1 S

O

NH2

peptide2

peptide1 NH

O

peptide2

SH

Scheme 1

HSS

O

O

ONa

HS

OH

O

MESNa MPAAFigure 2

Nativ

e C

hem

ical Lig

atio

n

�

TO ORDER: Contact your local Sigma-Aldrich office (see back cover), or visit sigma-aldrich.com/chemicalsynthesis.

4-Mercaptophenylacetic acid, 97%C8H8O2S OH

OHS

FW 168.21 [39161-84-7]

653152-1G 1 g

653152-5G 5 g

Sodium 2-mercaptoethanesulfonate, ≥98.0% (RT)Coenzyme M sodium salt; HS-CoM Na;

S ONa

O

O

HS

2-Mercaptoethanesulfonic acid sodium salt; MESNAC2H5NaO3S2 FW 164.18 [19767-45-4]

63705-10G 10 g

63705-50G 50 g

S-Acetamidomethyl-L-cysteine hydrochloride, ≥99.0% (AT)H-Cys(Acm).HCl

H3C

O

NH

S OH

O

NH2

• HClC6H12N2O3S · HCl FW 228.70 [28798-28-9]

00320-1G 1 g

Boc-Cys(Acm)-OH, ≥96.0% (T)Boc-S-acetamidomethyl-L-cysteine

H3C

O

NH

S OH

O

HNBoc

C11H20N2O5S FW 292.35 [19746-37-3]

15376-5G 5 g

Fmoc-Cys(Acm)-OH, ≥95.0% (HPLC, sum of enantiomers)Nα-Fmoc-S-acetaminomethyl-L-cysteine

H3C

O

NH

S OH

O

HNFmoc

C21H22N2O5S FW 414.47 [86060-81-3]

47603-5G 5 g

Fmoc-Cys(Acm)-Wang resinNα-Fmoc-S-acetaminomethyl-L-cysteine

CH3

O

NH

S

O

HNFmoc

4-benzyloxybenzyl ester polymer-bound

47613-1G-F 1 g

H-Cys(Acm)-2-ClTrt resinS-Acetamidomethyl-L-cysteine 2-chlorotrityl ester polymer-bound

94399-1G-F 1 g

TentaGel S PHB-Cys(Acm)FmocNα-Fmoc-S-acetamidomethyl-L-cysteine 4-[poly(ethylenoxy)]benzyl ester polymer-bound

86383-5G 5 g

Boc-Cys(Acm)-PAM resinBoc-S-(acetamidomethyl)-L-cysteine bound to PAM resin

61254-1G-F 1 g

Nati

ve C

hem

ical

Lig

ati

on

sigma-aldrich.com

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Staudinger Ligation

IntroductionThe reaction between an azide and a phosphine forming an aza-ylide was discovered almost a century ago by Nobel Prize laureate Herrmann Staudinger. It has found widespread application in chemical synthesis, but only recently its value as a highly chemoselective ligation method for the preparation of bioconjugates has been recognized.20 Both reactive functionalities involved in this reaction are bioorthogonal to virtually all naturally existing functionalities in biological systems and readily combine at room temperature tolerating an aqueous environment. These ideal conditions make it possible to exploit the Staudinger ligation even in the complex environment of living cells.

Staudinger and Meyer first reported in 1919 that azides react smoothly with triaryl phosphines to form iminophosphoranes after elimination of nitrogen (Scheme 1).21 This imination reaction proceeds under mild conditions, almost quantitatively, and without noticeable formation of any side products.

The resulting iminophosphorane with its highly nucleophilic nitrogen atom can also be regarded as an aza-ylide (Scheme 2). It may be intercepted with almost any kind of electrophilic reagent. Common pathways include aqueous hydrolysis forming a primary amine and a phosphine(V) oxide in the so-called Staudinger reduction. Quenching with aldehydes or ketones yields imines, which is known as the aza-Wittig reaction. Even carbonyl electrophiles with low reactivity, like amides or esters, react with iminophosphoranes, especially if the reaction can take place intramolecularly (Scheme 3).

P + N N N P +N N2

Scheme 1

R3P NR'

R3P NR'

Scheme 2

PRR

RN

R1

H2OR2 R3

O

R2 NH

OR3

R2 N C O

R1NH

H R1NR2

R3

R1NR2

HN R3R2 N C N R1

- R3PO

Scheme 3

Nontraceless Staudinger LigationBertozzi et al. pioneered the application of the Staudinger reaction as a ligation method for bioconjugates. In the course of their studies on the metabolic engineering of cell surfaces they designed a phosphine with an ester moiety as an intramolecular electrophilic trap. After formation of the iminophosphorane from the newly designed phosphine reagent and an azide, the ester moiety captures the aza-ylide in a fast intramolecular cyclization reaction before hydrolysis with water can occur. This process ultimately produces a stable amide bond.22

The phosphine reagent can be synthesized from aminoterephthalic acid methyl ester by diazotization, followed by iodination and subsequent Pd-catalyzed phosphinylation (Scheme 4).

The free acid moiety allows the easy attachment of a wide choice of molecular probes to the phosphine reagent by standard esterification or amidation procedures. Thus, a fluorescence label or different detection probe can be linked to any biomolecule that has been equipped with an azide function by the Staudinger ligation even in living cells (Scheme 5).

The following paragraph shows how GlycoProfile™ azido sugars can be incorporated into glycan structures in vivo, and be used to attach a FLAG® phosphine probe chemically.

NH2

H3CO O

OHO

I

H3CO O

OHO

PPh2

H3CO O

OHO

1) NaNO2

HCl/H2O2) KI, H2O

Pd(OAc)2 (1%)Ph2PHEt3N, MeOH

57 % 69 %

393673 650064Scheme 4

PPh2

H3CO O

OO

probe

N N N

target

PPh2

O HN

OO

probe

O

target

Scheme 5

References: (20) Köhn, M.; Breinbauer, R. Angew. Chem. Int. Ed. 2004, 43, 3106. (21) Staudinger, H.; Meyer, J. Helv. Chim. Acta 1919, 2, 635. (22) Saxon, E.; Bertozzi, C.R. Science 2000, 287, 2007.

1-Methyl 2-iodoterephthalate, 90%C9H7IO4 O

OCH3

IO

HO

FW 306.05

650064-1G 1 g

650064-10G 10 g

1-Methyl-2-aminoterephthalate, 98%C9H9NO4 O

OCH3

NH2

O

HO

FW 195.17 [60728-41-8]

393673-5G 5 g

393673-25G 25 g

2-(Diphenylphosphino)terephthalic acid, 1-methyl 4-penta-fluorophenyldiester, 97%1-Methyl-4-(pentafluorophenyl)-2-(diphenyl-

O

O

O

OCH3

P

F

FF

FF

phosphino)-1,4-benzenedicarboxylateC27H16F5O4P FW 530.38

679011-25MG 25 mg

679011-100MG 100 mg

2-(Diphenylphosphino)benzoic acid, 97%C19H15O2P

P

O

OHFW 306.30 [17261-28-8]

454885-1G 1 g

454885-5G 5 g

Sta

ud

ing

er Lig

atio

n

8

TO ORDER: Contact your local Sigma-Aldrich office (see back cover), or visit sigma-aldrich.com/chemicalsynthesis.

Sta

ud

ing

er

Lig

ati

on

N-Azidoacetylmannosamine, Acetylated 8

ManNaz

O

RO

RO

OR OR

HN

ON3

R = * CH3

O

C16H22N4O10 FW 430.37

A7605-1MG 1 mg

A7605-5MG 5 mg

N-Azidoacetylgalactosamine, Acetylated 8

GalNaz

O

HN

RO

O

OR

N3

OROR

R = * CH3

O

C16H22N4O10 FW 430.37

A7480-1MG 1 mg

A7480-5MG 5 mg

N-Azidoacetylglucosamine, Acetylated 8

GlcNaz O

HN

O

RO

OR ORR = * CH3

O

N3

RO

C16H22N4O10 FW 430.37

A7355-1MG 1 mg

A7355-5MG 5 mg

GlycoProfile™ Azido SugarsThe GlycoProfile™ Azido Sugar portfolio consists of three peracetylated azido sugars that may be incorporated into glycan structures chemically or by using existing biosynthetic pathways of mammalian cells.23 Orthogonally to chemical and biological carbohydrate or peptide synthesis, the azide moiety offers an ideal anchor to attach the modified glycan to surfaces, labels, peptides, or proteins. Labelling even works in vivo by using an alternative metabolic-system approach. The acetyl groups increase cell permeability and allow the unnatural sugars to easily pass through the cell membrane. Carboxyesterases remove the acetyl groups once the monosaccharide is in the cell. Cells metabolize the azido sugars using glycosyltransferases and express the sugars on the terminus of a glycan chain both intracelullarly and on the cell surface, leaving the azido group unreacted. N-Azidoacetylmannosamine may also be introduced into the sialic acid biosynthesis pathway. A phosphine probe containing a detection epitope such as the FLAG® peptide can be selectively bound to the glycan by Staudinger Ligation, resulting in a post-translationally modified glycoprotein that is detected in vivo by using a FLAG®-specific antibody. This approach permits the analysis of pathways that are regulated by particular glycan post-translational modifications as well as the monitoring of the intracellular glycosylation process itself.

NH

O

OAcO

OAc

AcO OAc

N3

O

O

P

CH3

FLAGR

R

FLAG-Phosphine

Staudingerligation

cellMetabolic labeling

GalNAz

NH

O

OAcO

OAc

AcOO

N3

NH

OAcO

OAc

AcOO

O

H ON

O

PFLAGR

Labeled glycoprotein

..

Profiling O-type glycoproteins by metabolic labeling with an azido GalNAc analog (GalNAz) followed by Staudinger ligation with a phosphine probe (FLAG-phosphine).

Reference: (23)(a) Saxon, E.; Bertozzi, C. R. Science 2000, 287, 2007. (b) Saxon, E.; Bertozzi, C. R. Annu. Rev. Cell. Dev. Biol. 2001, 17, 1. (c) Bertozzi, C. R.; Kiessling, L. L. Science 2001, 291, 2357. (d) Dube, D. H.; Prescher, J. A.; Quang, C. N.; Bertozzi, C. R. Proc. Natl. Acad. Sci 2006, 103, 4819.

GlycoProfile FLAG–Phosphine conjugate 8

N-[4-Carbomethoxy-3-(diphenylphosphino)

P

OCH3

O

DYKDDDK

benzoyl]-Asp-Tyr-Lys-Asp-Asp-Asp-Asp-LysC62H75N10O23P FW 1359.29

GPHOS1-1MG 1 mg

GPHOS1-5X1MG 5 × 1 mg

2nd edition

Tools for Glycoproteomics and Glycomics

Glycan Labeling and Analysis

Glycoprotein Purification and Detection

Chemical and Enzymatic Deglycosylation

Enzymatic Synthesis and Degradation

Glycobiology Analysis Manual

The Glycobiology Analysis Manual is a must-have reference guide for the fields of glycoproteomics and glycomics. The Manual features:

• Innovative products and kits

• Updated and expanded technical content

• Structural and functional reviews

Whether you are an expert in carbohydrate biology and chemistry or just getting started in glycomics, the Glycobiology Analysis Manual provides the products and methods you need to solve your glycomics puzzle!

Visit sigma.com/glycomanual and request your copy.

Puzzled by Glycobiology?

sigma-aldrich.com

�

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Traceless Staudinger LigationAlthough the previously described methods for Staudinger ligations work well even in biological environments, a modification forming a native amide bond without leaving the unnatural phosphine oxide moiety in the product would be more attractive yet. In 2000, the groups of Bertozzi and Raines simultaneously introduced alternative ligation strategies.24 Based on the same working principle as the nontraceless Staudinger Ligation the auxiliary phosphine reagent can be cleaved from the product after the ligation is completed leaving a native amide bond. Thus, the total chemical synthesis of proteins and glycopeptides is enabled overcoming the limitations of native chemical ligation (NCL) of a Cys residue at the ligation juncture.

Among the suitable phosphine reagents for traceless Staudinger ligations, diphenylphosphinemethanethiol (Figure 1), developed by Raines and co-workers, exhibits the best reactivity profile and has already found widespread application. This Raines ligation reagent is first acylated. Treatment with an azide leads to the formation of an aza-ylide. The nucleophilic nitrogen atom of the aza-ylide then attacks the carbonyl group, cleaving the thioester. Hydrolysis of the rearranged product finally produces a native amide and liberates the auxiliary as its phosphine(V) oxide (Scheme 6).25

It’s recommended to use a freshly prepared Raines ligation reagent because it has only a limited stability. In this issue of ChemFiles, Sigma-Aldrich® proudly introduces new product 670359 as a shelf-stable, convenient source for this highly useful reagent (sold under license for research and development purposes only. U.S. Patent 6,974,884 and related patents apply). In the acetylthiomethyldiphenylphosphine borane complex 670359, the thiol and phosphine moiety are protected as acetyl ester and borane adduct, respectively. The active Raines ligation reagent can be liberated easily by treatment with DABCO® at 40 °C followed by basic ester cleavage (Scheme 7). Hackenberger and co-workers showed that acidic deprotection of the phosphine-borane was advantageous in glycopeptide and cyclopeptide preparations.26 In the latter case, a linear peptide with terminal azide and phosphine-borane groups was synthesized by SPPS. 95% TFA was used to deprotect the phosphine and the amino acid side chains simultaneously in a single step. Diisopropylethylamine (DIPEA) was then added to trigger the peptide macrocyclization by traceless Staudinger ligation, yielding cyclic Microcin J25 with 21 amino acids.

Other Staudinger ligation induced macrocyclizations have been published previously by Maarseveen and co-workers, who successfully used the Raines ligation reagent for the synthesis of a series of medium-sized lactams.27 Wong and co-workers reported the synthesis of 14 different glycopeptides through the traceless Staudinger Ligation.28 For this work, they also developed a protease-catalyzed method to selectively introduce an N-terminal azido group into an unprotected polypeptide, as it was needed for the subsequent ligation reaction.

Most recently, Raines and co-workers introduced a water-soluble variant of their reagent carrying dimethylamino groups (Figure 2). This substrate mediates the rapid ligation of equimolar substrates in water. In a pilot experiment, traceless Staudinger ligation was integrated with expressed protein ligation (EPL), revealing future opportunities in modern protein chemistry.29

References: (24)(a) Saxon, E.; Armstrong, C.R.; Bertozzi, C.R. Org. Lett. 2000, 2, 2141. (b) Nilsson, B.L.; Kiessling, L.L.; Raines, R.T. Org. Lett. 2000, 2, 1939. (25) Soellner, M.B.; Nilsson, B.L.; Raines, R.T. J. Am. Chem. Soc. 2006, 128, 8820. (26) Kleineweischede, R.; Jaradat, D.; Hackenberger, P.R. Contributions at the 8th German Peptide Symposium 2007, Heidelberg, Germany. (27) David, O.; Meester, W.J.N.; Bieräugel, H.; Schoemaker, H.E.; Hiemstra, H.; van Maarseveen, J.H. Angew. Chem. Int. Ed. 2003, 42, 4373. (28) Liu, L.; Hong, Y.-Y., Wong, C.-H. ChemBioChem 2006, 7, 429. (29) Tam, A.; Soellner, M.B.; Raines, R.T. J. Am. Chem. Soc. 2007, 129, 11421.

Sta

ud

ing

er Lig

atio

n

HS P

Figure 1

R1 SR'

O

HS PPh2+

R1 S

O

PPh2

R2N3

R1 S

O

P+Ph2

-NR2

R1 NH

OR2 H2O

- HSCH2POPh2

Scheme 6

S PPh2

O BH3NaOMe, MeOH

rt, 95%HS PPh2

BH3

HS PPh2S PPh2

O NaOH, MeOH

94%

1) 95% TFA, 1 h2) DIPEA, rt95%

DABCO®

toluene, 40 °C95%

670359

Scheme 7

PH+

HS

H+

NH+

N x 3 Cl-

Figure 2

Acetylthiomethyl-diphenylphosphine 8

borane complex, ≥98.0%

C15H18BOPS

P S CH3

O

H3B

FW 288.15 [446822-71-5]

670359-250MG 250 mg

670359-1G 1 g

1,4-Diazabicyclo[2.2.2]octane, 98%DABCO; TED; Triethylenediamine

NNC6H12N2

FW 112.17 [280-57-9]

D27802-25G 25 g

D27802-100G 100 g

D27802-500G 500 g

D27802-2KG 2 kg

1,4-Diazabicyclo[2.2.2]octane hydrochloride, polymer-boundDabco chloride resin; TED-Cl resin

NN Cl

578282-5G 5 g

578282-25G 25 g

Dabco 33-LV1,4-Diazabicyclo[2.2.2]octane solution

NNC6H12N2

FW 112.17 [280-57-9]

290734-100ML 100 mL

290734-500ML 500 mL

10

TO ORDER: Contact your local Sigma-Aldrich office (see back cover), or visit sigma-aldrich.com/chemicalsynthesis.

Organic Azides and Azide SourcesSince the preparation of the first organic azide, phenyl azide, by Peter Griess in 1864 this energy-rich and versatile class of compounds has enjoyed considerable interest. In more recent years, completely new perspectives have emerged, notably the use of organic azides for peptide synthesis, combinatorial synthesis, heterocycle synthesis, and the ligation or modification of biopolymers.30 The most prominent fields of application today are Huisgen 1,3-dipolar cycloadditions, and different variants of the Staudinger ligation.

The azido group can also be regarded as a protecting group for coordinating primary amines, especially in sensitive substrates like complex carbohydrates or peptidonucleic acids (PNA).31 For example, it is stable to alkene metathesis conditions.32

Sigma-Aldrich® is offering a broad range of organic azides for your research. Additionally a wide choice of azide sources facilitates the preparation of tailor-made organic azides.

An elegant way to produce organic azides from unactivated olefins was recently reported by Carreira and co-workers. A catalyst, that is easily prepared from Co(BF4)2 · 6H2O and a Schiff base, allows hydroazidation with p-toluenesulfonyl azide (TsN3) to yield alkyl azides. Mono-, di-, and trisubstituted olefins are tolerated in this reaction, and complete Markovnikov selectivity is observed (Scheme 1).33

References: (30) Bräse, S.; Gil, C.; Knepper, K.; Zimmermann, V. Angew. Chem. Int. Ed. 2005, 44, 5188. (31) Debaene, F.; Winssinger, N. Org. Lett. 2003, 5, 4445. (32) Kane-mitsu, T.; Seeberger, P.H. Org. Lett. 2003, 5, 4541. (33) Waser, J.; Nambu, H.; Carreira, E.M. J. Am. Chem. Soc. 2005, 127, 8294.

R''R

R'

+ TsN3

R''R

R'N3

t-Bu

t-BuOH

N CO2K

Ph Ph

6 mol%

6 mol% Co(BF4)2 · 6 H2O30 mol% t-BuOOH, silane

EtOH, 23 °C, 2-24 hScheme 1

Azide Sources4-Acetamidobenzenesulfonyl azide, 97%p-ABSA

S N3

O

ONH

O

H3C

C8H8N4O3S FW 240.24 [2158-14-7]

404764-5G 5 g

404764-25G 25 g

Azide exchange resin,azide on Amberlite IRA-400

368342-10G 10 g

368342-50G 50 g

Azidotrimethylsilane, 95%Trimethylsilyl azide

SiH3C N3

CH3

CH3

C3H9N3Si FW 115.21 [4648-54-8]

155071-10G 10 g

155071-50G 50 g

Azidotrimethyltin(IV), 97%C3H11N3Sn FW 207.85 [1118-03-2]

349488-1G 1 g

349488-5G 5 g

Azidotris(diethylamino)phosphonium bromideC12H30BrN6P

NPN N

N3H3C CH3

CH3

CH3CH3

H3C

BrFW 369.28 [130888-29-8]

≥97.0% (AT)11556-1G 1 g

11556-5G 5 g

98%380822-1G 1 g

Benzenesulfonyl azide, functionalized silica gel

Si SO

ON3

590274-5G 5 g

Benzenesulfonyl azide, polymer-bound

S N3

O

O

572977-5G 5 g

4-Carboxybenzenesulfonazide, 97%4-(Azidosulfonyl)benzoic acid

S N3

O

O

O

HO

C7H5N3O4S FW 227.20 [17202-49-2]

340138-2.5G 2.5 g

Cesium azide, 99.99%CsN3 CsN3

FW 174.93 [22750-57-8]

510181-5G 5 g

510181-25G 25 g

Cobalt(II) tetrafluoroborate hexahydrate, 99%B2CoF8 · 6H2O Co(BF4)2 • 6H2O

FW 340.63 [15684-35-2]

399957-25G 25 g

399957-100G 100 g

Diphenyl phosphoryl azideDPPA; Phosphoric acid diphenyl ester azide O

PO ON3

C12H10N3O3P FW 275.20 [26386-88-9]

97%178756-5G 5 g

178756-25G 25 g

178756-100G 100 g

≥90% (HPLC)79627-50ML 50 mL

Diphenylphosphoryl azide, polymer-boundDPPA polymer-bound; PS-DPPA

O P O

O

N3

668168-1G 1 g

668168-5G 5 g

668168-25G 25 g

Lithium azide solutionLiN3 LiN3

FW 48.96[19597-69-4]

20 wt. % in H2O480525-25G 25 g

480525-100G 100 g

Org

an

ic A

zid

es

an

d A

zid

e S

ou

rces

11

Ready to scale up? For competitive quotes on larger quantities or custom synthesis, contact your local Sigma-Aldrich office, or visit safcglobal.com.

Potassium 2-(3,5-di-tert-butyl-2-hydroxybenzylideneamino)-2,2-diphenylacetate, 95%Potassium N-(3,5-di-tert-butylsalicylidene)-2-

CH3H3C CH3

CH3H3CH3C

OH

NO

OK

amino-2,2-diphenylacetateC29H32KNO3

FW 481.67

676551-250MG 250 mg

676551-1G 1 g

Sodium azideN3Na NaN3

FW 65.01 [26628-22-8]

99.99+% (metals basis)438456-5G 5 g

438456-25G 25 g

≥99.0% (T)71290-10G 10 g

71290-100G 100 g

71290-500G 500 g

≥99%13412-100G-R 100 g

13412-6X100G-R 6 × 100 g

13412-250G-R 250 g

13412-1KG-R 1 kg

13412-6X1KG-R 6 × 1 kg

13412-20KG-R 20 kg

Tetrabutylammonium azideC16H36N4

NCH3

CH3

H3C

H3CN3

-FW 284.48 [993-22-6]

651664-5G 5 g

651664-25G 25 g

Organic Azides1-Azidoadamantane, 97%C10H15N3 N3

FW 177.25 [24886-73-5]

276219-1G 1 g

276219-5G 5 g

4-Azidoaniline hydrochloride, 97%4-Aminophenyl azide hydrochloride

N3

NH2

• HClC6H6N4 · HClFW 170.60[91159-79-4]

359556-250MG 250 mg

359556-1G 1 g

(4S)-4-[(1R)-2-Azido-1-(benzyloxy)ethyl]-2,2-dimethyl-1,3-dioxolaneC14H19N3O3

O O

H3C CH3

O

N3

FW 277.32

573213-1G 1 g

[3aS-(3aα,4α,5β,7aα)]-5-Azido-7-bromo-3a,4,5,7a-tetra-hydro-2,2-dimethyl-1,3-benzodioxol-4-ol, 99%C9H12BrN3O3 Br

OHN3

O

O CH3

CH3

FW 290.11 [171916-75-9]

493406-500MG 500 mg

Org

an

ic Azid

es

an

d A

zide S

ou

rces

α-Azidoisobutyric acid solution2-Azido-2-methylpropionic acid

OHH3C

N3H3C

O

C4H7N3O2 FW 129.12 [2654-97-9]

~15% in heptane (T)52916-10ML-F 10 mL

52916-50ML-F 50 mL

~15% in heptane (T)59955-10ML-F 10 mL

Azidomethyl phenyl sulfide, 95%Phenylthiomethyl azide S N3

C7H7N3S FW 165.22 [77422-70-9]

244546-1G 1 g

6-(4-Azido-2-nitrophenylamino)hexanoic acid N-hydroxy-succinimide ester, ≥90%N-Succinimidyl 6-(4-azido-

NO

OO

ONH

O2N N32-nitroanilino)hexanoateC16H18N6O6 FW 390.35 [64309-05-3]

A3407-50MG 50 mg

(2S,3R,4E)-2-Azido-4-octadecene-1,3-diolD-Sphingosine azide

CH(CH2)12CH3HO

OH

N3

C18H35N3O2 FW 325.49 [103348-49-8]

A0456-1MG 1 mg

A0456-5MG 5 mg

4-Azidophenacyl bromide4’-Azido-2-bromoacetophenone; 4-Azido-

N3

OBrα-bromoacetophenone

C8H6BrN3O FW 240.06 [57018-46-9]

A6057-500MG 500 mg

≥98.0% (HPLC)11550-250MG-F 250 mg

11550-1G-F 1 g

4-Azidophenyl isothiocyanate, 97%C7H4N4S

N3

NCS

FW 176.20 [74261-65-7]

359564-500MG 500 mg

2,6-Bis(4-azidobenzylidene)-4-methylcyclohexanoneC21H18N6O

CH3

O

N3N3

FW 370.41 [5284-79-7]

97%283029-5G 5 g

≥90% (HPLC, calc. based on dry substance)14528-10G 10 g

4,4’-Diazido-2,2’-stilbenedisulfonic acid disodium salt hydrate, 97%C14H8N6Na2O6S2 · xH2O

SO3–

SO3– N3

N3

Na+

Na+

• xH2OFW 466.36 (Anh)

363227-10G 10 g

1�

TO ORDER: Contact your local Sigma-Aldrich office (see back cover), or visit sigma-aldrich.com/chemicalsynthesis.

7-(Diethylamino)coumarin-3-carbonyl azide, ≥95% (HPLC)C14H14N4O3

O O

O

N3

NH3C

CH3

FW 286.29 [157673-16-0]

31755-25MG 25 mg

Ethidium bromide monoazide, ≥95% (HPLC)3-Amino-8-azido-5-ethyl-6-phenylphenanthridinium bromide; Ethidium monoazide bromideC21H18BrN5 FW 420.31 [58880-05-0]

E2028-5MG 5 mg

Ethyl azidoacetate solutionC4H7N3O2

O

ON3 CH3

FW 129.12 [637-81-0]

~30% in methylene chloride (NMR)88539-50ML-F 50 mL

~25% in toluene (NMR)77213-25ML-F 25 mL

~25% in ethanol (NMR)93528-25ML-F 25 mL

4-Methoxybenzyloxycarbonyl azide, 95%4-Methoxybenzyl azidoformate

H3CO

O

O

N3C9H9N3O3 FW 207.19 [25474-85-5]

152854-5G 5 g

152854-25G 25 g

Photobiotin acetateBiotin {3-[3-(4-azido-2-nitroanilino)-N-methylpropylamino]propyl-amide} acetate; N-(4-Azido-2-nitrophenyl)-N’-(3-biotinylaminopropyl)-N’-methyl-1,3-propanediamine acetateC23H35N9O4S · C2H4O2

S

NHHN

O

HN

O

N

CH3HN

O2N

N3

HH

CH3HO

O

FW 593.70 [96087-38-6]

≥95% (HPLC)79728-1MG 1 mg

≥98.0% (TLC)56385-1MG-F 1 mg

Ro 15-4513Ethyl 8-azido-6-dihydro-5-methyl-6-oxo-

N

N

NO CH3

O

OCH3

N3

4H-imidazo[1,5-a][1,4]benzodiazepine- 3-carboxylateC15H14N6O3 FW 326.31 [91917-65-6]

R109-25MG 25 mg

R109-100MG 100 mg

PEG AzidesO-(2-Aminoethyl)-O′-(2-azidoethyl)heptaethylene glycol,≥90% (oligomer purity)Azido-PEG-amine (n=8)

H2NO

N38C18H38N4O8 FW 438.52 [857891-82-8]

76318-500MG-F 500 mg

Org

an

ic A

zid

es

an

d A

zid

e S

ou

rces

O-(2-Aminoethyl)-O′-(2-azidoethyl)nonaethylene glycol, ≥90% (oligomer purity)Azido-PEG-amine (n=10)

H2NO N3

10C22H46N4O10 FW 526.62 [912849-73-1]

77787-500MG-F 500 mg

O-(2-Aminoethyl)-O′-(2-azidoethyl)pentaethylene glycol, ≥90% (oligomer purity)Azido-PEG-amine (n=6)

H2NO

N36C14H30N4O6 FW 350.41

76172-500MG-F 500 mg

O-(2-Azidoethyl)-O-[2-(diglycolyl-amino)ethyl]heptaethylene glycol, ≥90% (oligomer purity)Azido-PEG-acid (n=8)

HON

ON3

O

8HO

O

C22H42N4O12 FW 554.59 [846549-37-9]

71613-500MG-F 500 mg

11-Azido-3,6,9-trioxaundecan-1-amine, ≥90% (GC)1-Amino-11-azido-3,6,9-trioxaundecane; O-(2-Aminoethyl)-O’-(2-azidoethyl)diethylene glycol; 2-{2-[2-(2-

N3H2NOO

O

Azidoethoxy)ethoxy]ethoxy}ethylamineC8H18N4O3 FW 218.25 [134179-38-7]

17758-1ML 1 mL

17758-5ML 5 mL

Azido Carbohydrates2-Acetamido-2-deoxy-β-D-glucopyranosyl azide 3,4,6- 8

triacetate, ≥98.0% (HPLC)

2-Acetamido-3,4,6-tri-O-acetyl-2-deoxy-β-D- O

HN

OR

RO

N3RO

CH3

O

CH3

O

R = *

glucopyranosyl azide[6205-69-2]

671118-250MG 250 mg

671118-1G 1 g

2-Acetamido-3,4,6-tri-O-benzyl-2-deoxy-β-D- 8

glucopyranosyl azide, ≥98.0% (HPLC)

C29H32N4O5 O

HN

OR

RO

N3RO

CH3

O

R = *FW 516.59 [214467-60-4]

671215-100MG 100 mg

8-Azidoadenosine 3′:5′-cyclic monophosphate, ~95%C10H11N8O6P

N

N N

N

NH2

O

O

O

OH

N3

POOH

FW 370.22 [31966-52-6]

A1262-5MG 5 mg

8-Azido-cyclic adenosine diphosphate-ribose, ≥95% (HPLC)Cyclic adenosine diphosphate-ribose 8-azide

POO

O O

OH

O

N

N N

N

NH

OH

O

OHOH

PHOO

OH

N3

C15H20N8O13P2 FW 582.31 [150424-94-5]

A6830-.1MG 0.1 mg

1�

Ready to scale up? For competitive quotes on larger quantities or custom synthesis, contact your local Sigma-Aldrich office, or visit safcglobal.com.

3′-Azido-2′,3′-dideoxyuridine, ≥98% (TLC)C9H11N5O4

ON3

HO N

HN

O

O

FW 253.21 [84472-85-5]

A4810-10MG 10 mg

N-Azidoacetylgalactosamine, Acetylated 8

GalNaz

O

HN

RO

O

OR

N3

OROR

R = * CH3

O

C16H22N4O10 FW 430.37

A7480-1MG 1 mg

A7480-5MG 5 mg

N-Azidoacetylglucosamine, Acetylated 8

GlcNaz O

HN

O

RO

OR ORR = * CH3

O

N3

RO

C16H22N4O10 FW 430.37

A7355-1MG 1 mg

A7355-5MG 5 mg

N-Azidoacetylmannosamine, Acetylated 8

ManNaz

O

RO

RO

OR OR

HN

ON3

R = * CH3

O

C16H22N4O10 FW 430.37

A7605-1MG 1 mg

A7605-5MG 5 mg

1-O-tert-Butyldimethylsilyl 2-azido-2-deoxy-β-D-glucopyranoside 3,4,6-triacetate, 97%C18H31N3O8Si

OO

O

O

O

H3C

O

H3C

N3

SiCH3

CH3

CH3

CH3

CH3

O

H3C O

FW 445.54 [99049-65-7]

510947-1G 1 g

α-D-Mannopyranosyl azide, ≥90% (TLC)C6H11N3O5

O

HOOH HO

N3

HO

FW 205.17

M6691-100MG 100 mg

α-D-Mannopyranosyl azide tetraacetate, ≥90% (TLC)2,3,4,6-Tetra-O-acetyl-α-D-mannopyranosyl azide

R= * CH3

OO

RO

OR RO

N3

RO

C14H19N3O9 FW 373.32

G4168-100MG 100 mg

2,3,4-Tri-O-acetyl-β-D-xylopyranosyl azide, 8 ≥98.0% (HPLC)

C11H15N3O7 ON3

O CH3

O

OH3C

O

O

O

H3CFW 301.25 [53784-33-1]

670790-1G 1 g

670790-5G 5 g

1-Azido-1-deoxy-β-D-galactopyranoside, 97%C6H11N3O5

ON3

OH

HO

HO

OHFW 205.17 [35899-89-9]

513989-500MG 500 mg

1-Azido-1-deoxy-β-D-galactopyranoside tetraacetate, 97%C14H19N3O9

ON3RO

R= * CH3

OOR

OR

RO

FW 373.32 [13992-26-2]

513970-1G 1 g

1-Azido-1-deoxy-β-D-glucopyranosideC6H11N3O5

ON3

OH

OH

HO

HO

FW 205.17 [20379-59-3]

514004-500MG 500 mg

1-Azido-1-deoxy-β-D-glucopyranoside tetraacetateC14H19N3O9

ON3RO

R= * CH3

OOR

OR

RO

FW 373.32 [13992-25-1]

513997-1G 1 g

1-Azido-1-deoxy-β-D-lactopyranoside, 97%C12H21N3O10

OO

OH

HO

HO

OH

O

OH

HO

OH

N3FW 367.31 [69266-16-6]

514012-500MG 500 mg

3′-Azido-3′-deoxythymidineAZT; Azidothymidine

O

N3

HO

HN

N

O

O

CH3C10H13N5O4 FW 267.24 [30516-87-1]

≥98% (HPLC)A2169-25MG 25 mg

A2169-100MG 100 mg

A2169-250MG 250 mg

A2169-1G 1 g

≥99.0% (HPLC)11546-100MG 100 mg

11546-500MG 500 mg

2′-Azido-2′-deoxyuridine, ≥98.0% (N)C9H11N5O5

O

OH

HO

HN

N

O

O

N3

FW 269.21 [26929-65-7]

11544-5MG 5 mg

3-Azido-2,3-dideoxy-1-O-(tert-butyldimethylsilyl)-β-D-arabino-hexopyranose, 98%C12H25N3O4Si

ON3

O

HO

Si

CH3

CH3

OH

CH3

CH3

CH3FW 303.43 [189454-43-1]

497029-250MG 250 mg

Org

an

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TO ORDER: Contact your local Sigma-Aldrich office (see back cover), or visit sigma-aldrich.com/chemicalsynthesis.

Functionalized AlkynesAlkynes contain a highly versatile functional group that may be utilized for numerous reactions such as electrophilic additions of hydrogen, halogens, hydrogen halides, or water; metathesis; hydroboration; oxidative cleavage; C–C coupling; and cycloadditions. Terminal alkynes may be transformed into metal acetylides and can then be submitted to nucleophilic substitution with alkyl halides, forming new C–C bonds, or nucleophilic addition, e.g., the Favorskii reaction.

Sigma-Aldrich® furnishes a broad portfolio of alkynes consisting of more than 250 products. To see the full listing, please visit the organic building blocks section on Chem Product Central at: sigma-aldrich.com/chemprod.

From the class of cycloaddition reactions that can be performed with alkynes, the Huisgen 1,3-dipolar cycloaddition stands out and has found tremendous interest in recent years as the best representative of a “click” reaction. Alkyne building blocks with a second functionality are particularly useful in click chemistry. The second functional group allows the attachment of a molecule of interest that subsequently can be “clicked” conveniently to the target azide. The following product list contains alkynes with a free or protected hydroxyl functional group, halogen-bearing alkynes, and miscellaneous other alkynes with an additional functional group.

Hydroxylated Alkynestert-Butyldimethyl(2-propynyloxy)silane, 97%C9H18OSi

HCO Si

CH3

CH3

CH3

CH3

CH3

FW 170.32 [76782-82-6]

495492-5ML 5 mL

495492-25ML 25 mL

2-tert-Butyldimethylsiloxybut-3-yne, 97%tert-Butyl-dimethyl-(methyl-prop-2-ynloxy)silane

HCO Si

CH3CH3

CH3

CH3

CH3CH3

667579-1G 1 g

667579-10G 10 g

4-(tert-Butyldimethylsilyloxy)-1-butyne, 97%C10H20OSi

HC O SiCH3

CH3 CH3

CH3

CH3FW 184.35 [78592-82-2]

541672-5ML 5 mL

541672-25ML 25 mL

3-Butyn-1-ol, 97%C4H6O HC OH

FW 70.09 [927-74-2]

130850-5G 5 g

130850-25G 25 g

130850-100G 100 g

3-Butyn-2-ol, 97%C4H6O

HCOH

CH3FW 70.09 [2028-63-9]

447986-25ML 25 mL

447986-100ML 100 mL

3,5-Dimethyl-1-hexyn-3-ol, 99%C8H14O

HCOH

CH3 CH3

CH3

FW 126.20 [107-54-0]

278394-100ML 100 mL

278394-500ML 500 mL

[(1,1-Dimethyl-2-propynyl)oxy]trimethylsilane, 98%C8H16OSi

HCO

H3C

CH3

SiCH3

CH3

CH3FW 156.30 [17869-77-1]

495239-5ML 5 mL

495239-25ML 25 mL

1,1-Diphenyl-2-propyn-1-ol, 99%C15H12O

CCH

HOFW 208.26 [3923-52-2]

477443-5G 5 g

477443-25G 25 g

2-Ethynylbenzyl alcohol, 97%C9H8O OH

CHFW 132.16 [10602-08-1]

520039-5G 5 g

4-Ethynylbenzyl alcohol, 97%C9H8O

HOCH

FW 132.16 [10602-04-7]

519235-5G 5 g

1-Ethynyl-1-cyclohexanol, ≥99%C8H12O

CHOH

FW 124.18 [78-27-3]

E51406-5ML 5 mL

E51406-100ML 100 mL

E51406-5L 5 L

E51406-20L 20 L

1-Ethynylcyclopentanol, 98%C7H10O

CHOH

FW 110.15 [17356-19-3]

130869-5G 5 g

2-(3-Fluorophenyl)-3-butyn-2-ol, 90%C10H9FO CH3

OHCH

F

FW 164.18

648930-1G 1 g

1-Heptyn-3-ol, 97%C7H12O HC

OHCH3

FW 112.17 [7383-19-9]

666963-1G 1 g

666963-10G 10 g

1-Hexyn-3-ol, 90%C6H10O HC

CH3

OHFW 98.14 [105-31-7]

537764-5G 5 g

537764-25G 25 g

5-Hexyn-1-ol, 96%C6H10O HC OHFW 98.14 [928-90-5]

302015-1G 1 g

302015-5G 5 g

302015-25G 25 g

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Ready to scale up? For competitive quotes on larger quantities or custom synthesis, contact your local Sigma-Aldrich office, or visit safcglobal.com.

3-Hydroxyphenylacetylene3-Ethynylphenol

HO

CHC8H6O FW 118.13 [10401-11-3]

632023-1G 1 g

632023-5G 5 g

2-Methyl-3-butyn-2-ol, 98%Dimethyl ethynyl carbinol

HCCH3

CH3OHC5H8O

FW 84.12 [115-19-5]

129763-5ML 5 mL

129763-100ML 100 mL

129763-1L 1 L

5-Methyl-1-hexyn-3-ol, 97%C7H12O HC

OH

CH3

CH3FW 112.17 [61996-79-0]

666971-1G 1 g

666971-5G 5 g

3-Methyl-1-penten-4-yn-3-ol, 98%Ethynyl methyl vinyl carbinol

HC CH2

HO

CH3

C6H8O FW 96.13 [3230-69-1]

493023-5G 5 g

3-Methyl-1-pentyn-3-ol, 98%Ethyl ethynyl methyl carbinol; Meparfynol

HC CH3CH3

HO

C6H10O FW 98.14 [77-75-8]

137561-100ML 100 mL

137561-500ML 500 mL

1-Octyn-3-ol, 96%C8H14O

HCCH3

OH

FW 126.20 [818-72-4]

127280-10G 10 g

127280-50G 50 g

127280-250G 250 g

1-Pentyn-3-ol, 98%C5H8O HC CH3

OHFW 84.12 [4187-86-4]

E28404-1G 1 g

E28404-10G 10 g

4-Pentyn-1-ol, 97%C5H8O

HCOH

FW 84.12 [5390-04-5]

302481-5G 5 g

302481-25G 25 g

4-Pentyn-2-ol, ≥98%(±)-4-Pentyn-2-ol

HC CH3

OH

C5H8O FW 84.12 [2117-11-5]

268992-1G 1 g

268992-5G 5 g

268992-25G 25 g

2-Phenyl-3-butyn-2-ol, ≥98%C10H10O CH3

OHCHFW 146.19

[127-66-2]

212997-5G 5 g

212997-25G 25 g

212997-100G 100 g

1-Phenyl-2-propyn-1-ol, 98%(±)-α-Ethynylbenzyl alcohol; (±)-3-Hydroxy-3-phenyl-1- HO

CH

propyne; 1-Phenylpropargyl alcohol; (±)-1-Phenyl-2- propyn-1-olC9H8O FW 132.16 [4187-87-5]

226610-1G 1 g

226610-10G 10 g

Propargyl alcohol, 99%2-Propyn-1-ol HC

OHC3H4O FW 56.06 [107-19-7]

P50803-5ML 5 mL

P50803-100ML 100 mL

P50803-500ML 500 mL

P50803-1L 1 L

1,1,1-Trifluoro-2-phenyl-3-butyn-2-ol, 96%C10H7F3O CF3

OHCHFW 200.16

[99727-20-5]

553298-500MG 500 mg

553298-1G 1 g

3-Trimethylsiloxy-1-propyne, 98%(Propargyloxy)trimethylsilane; Trimethyl(propargyloxy)

HCO Si

CH3

CH3

CH3

silane; Trimethyl(2-propynyloxy)silane; O-(Trimethylsilyl)propargyl alcoholC6H12OSi FW 128.24 [5582-62-7]

374423-1G 1 g

374423-10G 10 g

3-(Trimethylsilyloxy)-1-butyne, 97%2-(Trimethylsilyloxy)-3-butyne

HCCH3

O SiCH3

CH3

CH3C7H14OSi FW 142.27 [17869-76-0]

632031-5G 5 g

632031-25G 25 g

10-Undecyn-1-ol, ≥95.0% (GC)C11H20O HC

OHFW 168.28 [2774-84-7]

94195-1ML 1 mL

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TO ORDER: Contact your local Sigma-Aldrich office (see back cover), or visit sigma-aldrich.com/chemicalsynthesis.

Halogenated Alkynes(3,5-Bis(trifluoromethyl)phenylethynyl)trimethylsilane, 97%C13H12F6Si

Si

CH3

CH3

CH3

F3C

F3C

FW 310.31 [618092-28-7]

597805-5G 5 g

1-Bromo-2-butyne, 99%C4H5Br H3C

BrFW 132.99 [3355-28-0]

427292-1G 1 g

427292-5G 5 g

1-Bromo-2-ethynylbenzene, 95%C8H5Br

CH

Br

FW 181.03 [766-46-1]

494178-1G 1 g

1-Bromo-4-ethynylbenzene, 97%C8H5Br Br CHFW 181.03 [766-96-1]

206512-1G 1 g

1-Bromo-2-pentyne, 97%C5H7Br

H3C

Br

FW 147.01 [16400-32-1]

429538-1G 1 g

429538-10G 10 g

(2-Bromophenylethynyl)trimethylsilane, 98%C11H13BrSi

Br

Si CH3

CH3

CH3

FW 253.21 [38274-16-7]

484695-5G 5 g

(3-Bromophenylethynyl)trimethylsilane, 97%C11H13BrSi

Si

CH3

CH3

CH3

Br

FW 253.21 [3989-13-7]

510971-5G 5 g

(4-Bromophenylethynyl)trimethylsilane, 98%C11H13BrSi

Si CH3BrCH3

CH3

FW 253.21 [16116-78-2]

494011-5G 5 g

494011-25G 25 g

1-Chloro-2-ethynylbenzene, 98%(2-Chlorophenyl)acetylene

CH

ClC8H5Cl FW 136.58 [873-31-4]

465305-1G 1 g

465305-5G 5 g

1-Chloro-4-ethynylbenzene, 98%(4-Chlorophenyl)acetylene

CHClC8H5Cl FW 136.58 [873-73-4]

206474-1G 1 g

3-Chloro-1-ethynylbenzene, 97%C8H5Cl

CH

Cl

FW 136.58 [766-83-6]

630268-1G 1 g

630268-5G 5 g

6-Chloro-1-hexyne, 98%C6H9Cl HC Cl

FW 116.59 [10297-06-0]

469777-5ML 5 mL

469777-25ML 25 mL

3-Chloro-3-methyl-1-butyne, 97%C5H7Cl

HCCH3

CH3

ClFW 102.56 [1111-97-3]

301345-1G 1 g

301345-5G 5 g

301345-25G 25 g

1-Chloro-2-octyne, 98%C8H13Cl

CH3(CH2)3CH2

Cl

FW 144.64 [51575-83-8]

442860-1G 1 g

442860-10G 10 g

5-Chloro-1-pentyne, 98%C5H7Cl HC

Cl

FW 102.56 [14267-92-6]

244376-5G 5 g

244376-25G 25 g

(5-Chloro-1-pentynyl)trimethylsilylsilane, 97%1-Chloro-5-trimethylsilyl-4-pentyne

Si

CH3

CH3

CH3Cl

C8H15ClSi FW 174.74 [77113-48-5]

595918-5G 5 g

1-Chloro-4-(phenylethynyl)benzene, 98%C14H9Cl

ClFW 212.67 [5172-02-1]

510750-1G 1 g

510750-5G 5 g

(3-Chlorophenylethynyl)trimethylsilane, 98%C11H13ClSi

Si

CH3

CH3

CH3

Cl

FW 208.76 [227936-62-1]

597708-1G 1 g

597708-5G 5 g

(4-Chlorophenylethynyl)trimethylsilane, 97%C11H13ClSi

Si

CH3

CH3

CH3ClFW 208.76 [78704-49-1]

563447-5G 5 g

563447-25G 25 g

1,4-Dichloro-2-butyne, 99%C4H4Cl2

Cl

Cl

FW 122.98 [821-10-3]

D59607-5G 5 g

D59607-25G 25 g

D59607-100G 100 g

Fun

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Ready to scale up? For competitive quotes on larger quantities or custom synthesis, contact your local Sigma-Aldrich office, or visit safcglobal.com.

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3,4-Dichlorophenylacetylene, 97%1,2-Dichloro-4-ethynylbenzene; 3,4-Dichloro-

CHCl

Cl

1-ethynylbenzeneC8H4Cl2 FW 171.02 [556112-20-0]

672890-1G 1 g

(2,4-Difluorophenylethynyl)trimethylsilane, 96%C11H12F2Si

Si

CH3

CH3

CH3F

F

FW 210.30 [480438-92-4]

563471-1ML 1 mL

563471-5ML 5 mL

(3,5-Difluorophenylethynyl)trimethylsilane, 98%C11H12F2Si

Si

CH3

CH3

CH3

F

F

FW 210.30 [445491-09-8]

589330-5G 5 g

1-Ethynyl-3,5-bis(trifluoromethyl)benzene, 97%C10H4F6

CH

F3C

F3C

FW 238.13 [88444-81-9]

630241-1G 1 g

1-Ethynyl-2,4-difluorobenzene, 97%C8H4F2 CH

F

FFW 138.11 [302912-34-1]

556440-5G 5 g

1-Ethynyl-3,5-difluorobenzene, 97%C8H4F2

CH

F

F

FW 138.11 [151361-87-4]

590177-1G 1 g

1-Ethynyl-2-fluorobenzene, 97%C8H5F

CH

FFW 120.12 [766-49-4]

467006-250MG 250 mg

467006-1G 1 g

1-Ethynyl-3-fluorobenzene, 98%C8H5F

CH

FFW 120.12 [2561-17-3]

519405-5G 5 g

1-Ethynyl-4-fluorobenzene, 99%C8H5F

CHFFW 120.12 [766-98-3]

404330-1G 1 g

404330-5G 5 g

4-Ethynyl-1-fluoro-2-methylbenzene, 97%C9H7F

CHF

H3C

FW 134.15 [351002-93-2]

521205-1G 1 g

521205-5G 5 g

2-Ethynyl-α,α,α-trifluorotoluene, 97%1-Ethynyl-2-trifluoromethylbenzene

CH

CF3

C9H5F3 FW 170.13 [704-41-6]

521183-1G 1 g

3-Ethynyl-α,α,α-trifluorotoluene, 97%C9H5F3 CH

F3CFW 170.13 [705-28-2]

557331-5G 5 g

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• More than 750 new products

• Over 3,000 chemical listings

• 13C, 15N, D, 18O, 17O labeled products

• Enriched noble gases

• Application sections and literature references

Now Available!The New ISOTEC® 2008–2010 Stable Isotopes Catalog

from Aldrich Chemistry

To receive your FREE copy of the catalog, visit sigma-aldrich.com/sicat

18

TO ORDER: Contact your local Sigma-Aldrich office (see back cover), or visit sigma-aldrich.com/chemicalsynthesis.

4-Ethynyl-α,α,α-trifluorotoluene, 97%C9H5F3 CHF3CFW 170.13 [705-31-7]

556432-5G 5 g

(2-Fluorophenylethynyl)trimethylsilane, 96%C11H13FSi

Si

CH3

CH3

CH3

F

FW 192.30 [480439-33-6]

571407-5G 5 g

571407-25G 25 g

(4-Fluorophenylethynyl)trimethylsilane, 97%C11H13FSi

Si

CH3

CH3

CH3FFW 192.30 [130995-12-9]

563463-5ML 5 mL

563463-25ML 25 mL

(4-Iodophenylethynyl)trimethylsilane, 97%C11H13ISi

Si

CH3

CH3

CH3IFW 300.21 [134856-58-9]

640751-1G 1 g

640751-5G 5 g

Propargyl bromide solution3-Bromo-1-propyne HC

BrC3H3Br FW 118.96 [106-96-7]

80 wt. % in xylene530409-50G 50 g

530409-125G 125 g

Propargyl chloride, 98%3-Chloro-1-propyne HC

ClC3H3Cl FW 74.51 [624-65-7]

143995-5G 5 g

143995-25G 25 g

Propargyl chloride solution3-Chloro-1-propyne HC

ClC3H3Cl FW 74.51 [624-65-7]

70 wt. % in toluene384321-100ML 100 mL

4-(Trifluoromethoxy) phenylacetylene, 97%4-Ethynyl-1-(trifluoromethoxy) benzene

CHF3COC9H5F3O FW 186.13 [160542-02-9]

672858-1G 1 g

1-[(Trimethylsilyl)ethynyl]-3-fluorobenzene, 97%C11H13FSi

Si

CH3

CH3

CH3

F

FW 192.30 [40230-96-4]

563269-5G 5 g

1-[(Trimethylsilyl)ethynyl]-3-(trifluoromethyl)benzene, 98%1-(3’-Trifluoromethylphenyl)-2-(trimethylsilyl)acetylene C12H13F3Si

Si

CH3

CH3

CH3

F3C

FW 242.31 [40230-93-1]

562661-5ML 5 mL

562661-25ML 25 mL

1-[(Trimethylsilyl)ethynyl]-4-(trifluoromethyl)benzene, 97%[4-(Trifluoromethyl)phenyl](trimethylsilyl)acetylene

Si

CH3

CH3

CH3F3CC12H13F3Si FW 242.31 [40230-95-3]

563439-5ML 5 mL

563439-25ML 25 mL

Miscellaneous AlkynesN-tert-Amyl-1,1-dimethylpropargylamine, 98%C10H19N

HC

HN

CH3H3C

CH3

CH3

CH3

FW 153.26 [2978-40-7]

514934-5G 5 g

N-tert-Butyl-1,1-dimethylpropargylamine, 97%C9H17N

HC

HN CH3

CH3CH3

CH3H3CFW 139.24 [1118-17-8]

513695-5G 5 g

Cyclopropylacetylene, 97%Ethynylcyclopropane HC

C5H6 FW 66.10 [6746-94-7]

663018-5G 5 g

663018-25G 25 g

1,3-Diethynylbenzene, 97%C10H6 CH

HC

FW 126.15 [1785-61-1]

632104-1G 1 g

632104-5G 5 g

1,4-Diethynylbenzene, 96%C10H6 CHHCFW 126.15 [935-14-8]

632090-5G 5 g

3-Dimethylamino-1-propyne, 97%N,N-Dimethylpropargylamine;

HCN

CH3

CH3 N,N-Dimethyl-2-propynylamineC5H9N FW 83.13 [7223-38-3]

143065-5G 5 g

143065-25G 25 g

1,1-Dimethyl-N-tert-octylpropargylamine, 96%C13H25N

HC

HN

CH3H3C CH3

CH3

CH3

CH3

CH3

FW 195.34 [263254-99-5]

513709-1G 1 g

2-Ethynylaniline, 98%C8H7N

CH

NH2

FW 117.15 [52670-38-9]

597651-1G 1 g

597651-5G 5 g

3-Ethynylaniline, ≥98%C8H7N

CH

H2N

FW 117.15 [54060-30-9]

498289-5G 5 g

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Ready to scale up? For competitive quotes on larger quantities or custom synthesis, contact your local Sigma-Aldrich office, or visit safcglobal.com.

4-Ethynylaniline, 97%1-Amino-4-ethynylbenzene

CHH2NC8H7N FW 117.15 [14235-81-5]

481122-5G 5 g

4-Ethynylbiphenyl, 97%C14H10 CHFW 178.23 [29079-00-3]

521175-5G 5 g

1-Ethynylcyclohexene, 99%C8H10 CHFW 106.17 [931-49-7]

316571-5G 5 g

316571-25G 25 g

1-Ethynylcyclohexylamine, 98%C8H13N NH2

CHFW 123.20 [30389-18-5]

177024-1G 1 g

177024-5G 5 g

1-Ethynyl-3,5-dimethoxybenzeneC10H10O2

H3CO

H3CO

CHFW 162.19 [171290-52-1]98% (CP)

588520-1G 1 g

588520-5G 5 g

4-Ethynyl-N,N-dimethylaniline, 97%4-Dimethylaminophenylacetylene;

CHNH3C

H3C

1-Ethynyl-4-dimethylanilineC10H11N FW 145.20 [17573-94-3]

592609-1G 1 g

592609-5G 5 g

1-Ethynyl-2-nitrobenzene, 98%C8H5NO2 CH

NO2

FW 147.13 [16433-96-8]

519456-5G 5 g

1-Ethynyl-4-nitrobenzene, 97%C8H5NO2 CHO2NFW 147.13 [937-31-5]

519294-1G 1 g

519294-5G 5 g

1-Ethynyl-4-phenoxybenzene, 97%C14H10O

HC OFW 194.23 [4200-06-0]

521213-1G 1 g

521213-5G 5 g

1,6-Heptadiyne, 97%C7H8 HC CH

FW 92.14 [2396-63-6]

407437-1G 1 g

2-Methyl-3-butyn-2-amine, 95% 8

3-Amino-3-methyl-1-butyne; HC

CH3

NH2CH3

1,1-DimethylpropargylamineC5H9N FW 83.13 [2978-58-7]

687189-5G 5 g

N-Methylpropargylamine, 95%3-Methylamino-1-propyne

HC

HN

CH3C4H7N FW 69.11 [35161-71-8]

150223-1G 1 g

150223-5G 5 g

N-Methyl-N-propargylbenzylamine, 97%Pargyline N

CH3

CH

C11H13N FW 159.23 [555-57-7]

M74253-5G 5 g

M74253-25G 25 g

1,8-Nonadiyne, 98%C9H12 HC CH

FW 120.19 [2396-65-8]

161306-10G 10 g

1,7-Octadiyne, 98%C8H10 CH

HCFW 106.17 [871-84-1]

161292-1G 1 g

161292-10G 10 g

Propargylamine, 98%3-Amino-1-propyne; 2-Propynylamine HC

NH2C3H5N FW 55.08 [2450-71-7]

P50900-1G 1 g

P50900-5G 5 g

P50900-25G 25 g

Propargylamine hydrochloride, 95%3-Amino-1-propyne hydrochloride; HC

NH2

• HCl 2-Propynylamine hydrochlorideC3H5N · HCl FW 91.54 [15430-52-1]

P50919-1G 1 g

P50919-10G 10 g

Tripropargylamine, 98%C9H9N N

HC CHCH

FW 131.17 [6921-29-5]

T84964-5G 5 g

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