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Bachem AG Bachem Americas, Inc.
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AMINO ACID DERIVATIVES AND RESINS

Frequently Asked Questions on Amino Acid Derivatives and Resins

How do you abbreviate protecting groups, especially the less common ones?

The abbreviations of protecting groups used by Bachem are listed in the glossary. Most of them correspond to literature use. Benzyloxycarbonyl is abbreviated as Z (not Cbz). Allyl ester is used instead of OAll, 2-phenylisopropyl ester instead of OPp.

Substituents can be written out as well, e.g. isopropyl in place of iPr.

What is an ADS (or CofA)?

ADS stands for Analytical Datasheet, CofA Certificate of Analysis. Data listed on the ADS were determined for the actual batch.

Do you custom-synthesize amino acids and derivatives?

Yes. Please click on the tab “Custom Synthesis” to ask for a quote.

Where are the ADS available?

You can download the ADS of the currently available lot from the product entry, if the pack size you want to order is available from stock.

 

If not available for your order, the ADS can be downloaded from the Bachem website, www.bachem.com.

 

Please click on “Analytical Data Sheet“ in the lower part of our welcome page. You have to enter the product number and the lot number which is imprinted on the label of the vial and mentioned on the invoice.

 

Click on “continue” to get your ADS as pdf file.

Which analytical data do you provide for your amino acid derivatives?

The range of analytical data listed on the ADS depends on the type of product, as methods for analyzing amino acid derivatives (and very short peptides), peptides, and “non-peptidic” compounds differ somewhat.

An ADS (Analytical Datasheet) issued for an amino acid derivative can list:

  • Lot number
  • Type of product: catalog or custom-synthesized
  • Product number
  • Product designation
  • Molecular formula
  • Relative molecular mass
  • Tests performed
    • Appearance
    • Appearance of solution, solvent
    • Molecular mass, obtained by mass spectrometry
    • Elemental analysis
    • Purity (determined by TLC), TLC conditions
    • Optical rotation
    • Melting Point
    • Water content
    • Substitution (loaded resins)
How reliable is TLC-purity?

Even though it is a semi-quantitative method, thin layer chromatography (TLC) is especially suitable for analyzing amino acid derivatives. TLC is a remarkably versatile analytical tool due to the large choice of elution systems and plate development methods, which can be optimized for each individual product and/or the detection of traces of its possible contaminants (e.g. unreacted educts). Contrary to column chromatography, a number of samples can be run side by side on a TLC plate, which allows for a better comparison.

How can you be sure that the derivative is optically pure?

Certain reactions involving α-amino acids carry the risk of concomitant racemization, especially when the α-carboxy group has to be activated in the presence of bases. So a synthetic strategy avoiding racemization-prone conversions has to be developed.

If the risk of racemization exists (e.g. during loading of resins), the optical purity is controlled after performing the reaction. 

 

The optical rotation is determined only if reference values can be taken from the literature.

Which base resins do you use for obtaining loaded resins for SPPS?

Wang resin (4-alkoxybenzyl alcohol resin), SASRIN (2-methoxy-4-alkoxybenzyl alcohol resin), 2-chlorotrityl resin (Fmoc)

Merrifield resin (chloromethyl resin), PAM (phenylacetamidomethyl) resin (Boc)

All our resins are based on polystyrene cross-linked with 1% divinylbenzene.

We offer resin derivatives in two particle sizes, 200-400 mesh and 100-200 mesh.

Do you offer base resins in various loadings (LL, HL, VHL)?

Unfortunately not.
The substitutions of our resins are in the range mentioned in the catalog entry. Please ask our sales department for the loading of the currently available batch.

How to store the resins?

The storage temperature depends on the type of resin. It is mentioned in the webshop entry and on the label.
The resins have to be protected from humidity, especially 2-chlorotrityl chloride resin. PDDM has to be protected from light.

Which resins can be used for Fmoc-SPPS ?

Resins suitable for the Fmoc-SPPS of “peptide acids” (i.e. C-terminal carboxyl group):

Wang resin (4-alkoxybenzyl alcohol resin), SASRIN (2-methoxy-4-alkoxybenzyl alcohol resin), 2-chlorotrityl chloride resin.

As esterification of the C-terminal Fmoc-amino acid can be accompanied by concomitant racemization, we recommend using preloaded resins. They are produced under conditions optimized for minimal racemization and tested for chiral purity.

Resins suitable for the Fmoc-SPPS of peptide amides:

Fmoc-Rink amide AM resin (Fmoc-2,4-dimethoxy-4'-(carboxymethyloxy)-benzhydrylamine linked to Aminomethyl resin), Tricyclic amide linker resin, PAL resin (4-Alkoxy-2,6-dimethoxybenzylamine resin), Xanthenyl linker resin (Sieber amide resin). As removal of Fmoc and loading of the C-terminal amino acid can be easily included in standard Fmoc-SPPS protocols, we do not offer preloaded amide resins.

Which amino acid derivatives can be used for Fmoc-SPPS?

The side-chain protecting groups have to withstand repetitive treatments with piperidine.

 

Derivatives of trifunctional amino acids used in "standard" Fmoc-SPPS:

 

Fmoc-Arg(Pbf)-OH, Fmoc-Arg(Pmc)-OH

Fmoc-Asp(OtBu)-OH

Fmoc-Asn(Trt)-OH, Fmoc-Asn(Mtt)-OH (for N-terminal Asn)

Fmoc-Cys(Trt)-OH (single S-S-bridge, or "folding")

Fmoc-Gln(Trt)-OH

Fmoc-Glu(OtBu)-OH

Fmoc-His(1-Trt)-OH (Fmoc-His(Trt)-OH)

Fmoc-Lys(Boc)-OH

Fmoc-Ser(tBu)-OH

Fmoc-Thr(tBu)-OH

Fmoc-Trp(Boc)-OH

Fmoc-Tyr(tBu)-OH

 

All lateral protecting groups can be removed with TFA.

Which resins can be used for Boc-SPPS?

Resins suitable for the Boc-SPPS of “peptide acids” (i.e. C-terminal carboxyl group):

Merrifield resin (chloromethyl resin) and hydroxymethyl resin, PAM (phenylacetamidomethyl) resin (only available in preloaded form)

As esterification of the C-terminal Boc-amino acid can be accompanied by concomitant racemization, we recommend using preloaded resins. They are produced under conditions optimized for minimal racemization and tested for optical purity.

Resins suitable for the Boc-SPPS of peptide amides:

MBHA resin (4-methyl-benzhydrylamine resin), BHA resin (benzhydrylamine resin)

Both resins are offered as hydrochlorides, the amino group has to be liberated before coupling the C-terminal Boc-amino acid.

As the loading step can be easily included in standard Boc-SPPS protocols, we do not offer preloaded amide resins.

Which amino acid derivatives can be used for Boc-SPPS?

The side-chain protecting groups have to withstand repetitive treatment with trifluoroacetic acid in methylene chloride.

Derivatives of trifunctional amino acids for "standard" Boc-SPPS:

 

Boc-Arg(Tos)-OH

Boc-Asp(OcHex)-OH

Boc-Asn(Xan)-OH

Boc-Cys(Mob)-OH, Boc-Cys(MBzl)-OH

Boc-Gln(Xan)-OH

Boc-Glu(OcHex)-OH

Boc-His(Tos)-OH

Boc-Lys(2-chloro-Z)-OH

Boc-Ser(Bzl)-OH

Boc-Thr(Bzl)-OH

Boc-Trp-OH, Boc-Trp(For)-OH

Boc-Tyr(2-bromo-Bzl)-OH, Boc-Tyr(2,6-dichloro-Bzl)-OH

 

All lateral protecting groups can be removed with HF (removal of For only in the presence of a thiol)

Which resins can be used for the synthesis of peptide acids?

Resins suitable for Fmoc-SPPS:

Wang resin (4-alkoxybenzyl alcohol resin), SASRIN (2-methoxy-4-alkoxybenzyl alcohol resin), 2-chlorotrityl chloride resin.

 

Resins suitable for Boc-SPPS:

Merrifield resin (chloromethyl resin) and hydroxymethyl resin, PAM (phenylacetamidomethyl) resin (only available in preloaded form)

As esterification of the C-terminal amino acid can be accompanied by concomitant racemization, we recommend using preloaded resins. They are produced under conditions optimized for minimal racemization and tested for optical purity.

Why should I use preloaded resins?

As esterification of the C-terminal amino acid can be accompanied by concomitant racemization, especially with Cys and His derivatives, we recommend using preloaded resins. They are produced under conditions optimized for minimal racemization and tested for optical purity.

Racemization can be suppressed when reacting the carboxylate of the protected amino acid with a resin halogenide (2-chlorotrityl chloride resin, Merrifield resin)

How to store preloaded resins?

The storage temperature depends on the type of base resin. It is mentioned in the webshop entry and on the label.
The resins have to be protected from humidity.

Do you offer preloaded resins in various loadings (LL, HL, VHL)?

We offer a broad choice of LL and a number of HL preloaded 2-chlorotrityl resins. The substitutions of our resins are in the range mentioned in the catalog entry. Please ask our sales department for the loading of the currently available batch. The ADS of the resin listing the substitution you have ordered can be downloaded from our homepage.

How to avoid problems with a C-terminal proline during Boc-SPPS?

Diketopiperazine formation may occur after deblocking the second amino acid, the penultimate residue of the peptide to be synthesized, especially in case of a C-terminal proline (generally: in case of Nα-alkylated amino acids). Losses due to this reaction resulting in premature cleavage from the resin can be considerably reduced by simultaneous coupling and liberation of the amino group from the trifluoroacetate.

Why use Pro-chlorotrityl resin for obtaining peptides with C-terminal Pro?

Diketopiperazine formation may occur after deblocking the second amino acid, especially in case of a C-terminal proline (generally: in case of Nα-alkylated amino acids).  The bulky chlorotrityl group prevents this cyclization resulting in premature cleavage.

Fmoc-Pro-DHPP-® (D-1830) represents a more acid-stable alternative to 2-chlorotrityl resin.

I can't find a resin loaded with the amino acid I need. What can I do?

We can prepare it for you. Please click on the tab “Custom Synthesis” to ask for a quote.
Or, Fmoc amino acids can be coupled smoothly and practically devoid of racemization to diphenyldiazomethane resin (PDDM resin). Fmoc Asp- and Glu-derivatives can be easily attached to this resin by their side chains.

Do you offer preloaded resins with a reduced loading?

We offer a broad choice of LL (low load) 2-chlorotrityl resins. The loading of other resins can be reduced during the first coupling steps.

Which resins can be used for the synthesis of peptide amides?

Resins suitable for the Fmoc-SPPS of peptide amides:

Fmoc-Rink amide AM resin (Fmoc-2,4-dimethoxy-4'-(carboxymethyloxy)-benzhydrylamine linked to Aminomethyl resin), Tricyclic amide linker resin, PAL resin, Xanthenyl linker resin (Sieber amide resin).

Resins suitable for the Boc-SPPS of peptide amides:

4-Methyl-benzhydrylamine resin (MBHA resin), benzhydrylamine resin (BHA resin)

Both are offered as hydrochlorides, the amino group has to be liberated before coupling the C-terminal Boc-amino acid.

Which resins allow obtaining fully protected peptides?

Resins suitable for Fmoc-SPPS of protected peptides:

SASRIN (2-methoxy-4-alkoxybenzyl alcohol resin) and 2-Chlorotrityl resin

Xanthenyl linker resin (for protected peptide amides)

SASRIN-carbazate (for protected peptide hydrazides)

Bachem does not offer resins specifically designed for the Boc-SPPS of protected peptides. Such peptides can also be obtained by Boc-SPPS on e.g. Merrifield resin followed by cleavage with nucleophiles.

Do you offer resins suitable for the synthesis of peptide alcohols?

Yes, we do.

2-Chlorotrityl resin has been used for the Fmoc-SPPS of peptide alcohols.

Diphenyldiazomethane resin (PDDM resin) can be used as a carrier for the Fmoc-SPPS of peptides, but it is especially suitable for the synthesis of peptide alcohols, which may also be obtained in protected form.

Bachem also offers Ellman's dihydropyrane resin.

Which amino acid derivatives are used in solution synthesis?

The choice of Nα- and side-chain protection depends on the sequence of the peptide and the synthetic strategy, which is far more complex than in SPPS. In most cases, Z or Boc are chosen as Nα-protecting groups. Z cannot be cleaved by catalytic hydrogenolysis (the standard method for removing this protecting group) in the presence of sulfur-containing amino acids. Blocking the side-chains of Cys and Lys is mandatory. Choice and extent of additional lateral protection depend on the synthetic strategy.

How do you determine the loading of a resin?

The substitution (loading) of resins carrying Fmoc amino acids is assessed by cleavage and spectrophotometric determination of the piperidine adduct. Loading with Boc-amino acids is determined following removal of the protecting group by the picric acid method.

Why are certain amino acid derivatives sold as salts?

Amino acid derivatives have to be sufficiently shelf-stable and preferably crystalline to be marketed.
In most cases, lack of crystallinity is the reason for converting amino acid derivatives into DCHA, DEA, or CHA salts. N-protected Amino acid derivatives carrying very acid-labile protecting are offered as salts as to avoid premature cleavage during storage (e.g. Bpoc-Gly-OH • DCHA). For a protocol describing the liberation of the acid please see the Technical Note downloadable from our homepage.
Esters of amino acids have to be converted into salts of strong acids as to prevent oligomerization (e.g. H-Ala-OMe • HCl) and increase shelf-stability.

Do I have to convert DCHA and CHA salts into the free acids?

Yes.
Please see our Technical Note "Conversion of a DCHA salt to the free acid" downloadable from our homepage. Special care has to be taken when liberating amino acids carrying highly acid-sensitive groups as Bpoc.

Do you offer stable phosphotyrosine mimics?

We offer 4-phosphonophenylalanine derivatives suitable for Fmoc- and Boc-SPPS:

 

Fmoc-4-phosphono-Phe(Bzl)-OH

Boc-4-phosphono-Phe(Et)2-OH

and the

O-malonyltyrosine derivative Fmoc-Tyr(malonyl-di-OtBu)-OH.

Do you offer pseudoproline dipeptides and isoacyl dipeptides?

Yes. As both are buiding blocks used in Fmoc-SPPS, our steadily increasing offer of pseudoproline dipeptides and isoacyl dipeptides is filed under “Amino Acid Derivatives”. Click on the tab “Amino Acids” and set the second filter on “Isoacyl Dipeptides” or “Pseudoproline Dipeptides”, respectively. The product contained in the families “Fmoc-Dipeptides” and “Dmb and Hmb Dipeptides” could be of interest as well.

Do you offer heavy isotope labeled amino acid derivatives?

Yes, we offer a number of 2H- and 15N-labeled derivatives.
You will find two families, one containing our 15N-labeled derivatives and the other consisting of our deuterated derivatives, in the amino acids section of our online catalog.

Do you offer spacers?

Spacers which can be incorporated during Fmoc-SPPS:

Fmoc-εAhx-OH, Fmoc-8-aminooctanoic acid (Fmoc-8-Aoc-OH) (both non-polar)

Fmoc-AEEAc-OH (polar)

For Boc-SPPS:

Boc-εAhx-OH, 11-(Boc-amino)-undecanoic acid

 

N-terminal FITC requires a spacer.

How to store amino acid derivatives?

The recommended storage temperature is mentioned in the product entry of the derivative. Generally, amino acids derivatives should be stored in a tightly closed vessel. They should be protected from humidity and light.

How long can I store amino acid derivatives?

Most amino acid derivatives can be stored for years at the recommended storage temperature, if protected from humidity and light.

Can I check the loading before buying the resin?

Yes. The loading of the currently available lot can be found on the ADS which can be downloaded, but only for pack sizes available from stock. The substitutions of our preloaded resins are in the range mentioned in the catalog entry.