Funding provided by Slippery Rock University. We would like to thank T. Boron III (Slippery Rock University) and C. Haney (University of Pennsylvania) for their insights.

1. Hydrolysis of Ni-Schiff-Base Complex
<ol>
	<li>Dissolve 1 mmol of the Ni-PBP-Schiff-base complex in 40 mL of N,N-dimethylformamide (DMF) with stirring in a 250 mL round bottom flask at room temperature.</li>
	<li>Add 60 mL of 0.2 M aqueous EDTA solution, pH 4.5.</li>
	<li>Using a magnetic stir bar and stir plate, stir the combined solution overnight. As the Schiff-base complex is hydrolyzed, the color will shift from a deep red to white.</li>
	<li>After completion of the reaction as indicated by the absence of any red coloring, transfer the reaction to a 250 mL separatory funnel.</li>
	<li>Add 50 mL dichloromethane, cap the separatory funnel, and mix. Drain the organic wash into a waste beaker. Repeat this process three times to remove PBP and any residual Ni-PBP-Schiff-base complex. Collect the remaining aqueous layer in a 250 mL round bottom flask.</li>
</ol>
2. Fmoc Protection of Hydrolyzed Amino Acid
<ol>
	<li>Adjust the isolated aqueous layer from step 1.5 described above to pH 7 using solid sodium bicarbonate. Check pH periodically using pH test strips.</li>
	<li>Add 168 mg sodium bicarbonate (2.00 mmol, 2 equiv) to the solution and stir using a magnetic stir bar and stir plate.</li>
	<li>Dissolve 337 mg Fmoc N-hydroxysuccinimide ester (1.00 mmol, 1 equiv) in a minimal amount of dioxane (roughly 4 or 5 mL) in a 10 mL vial. Transfer this solution to the aqueous solution and stir overnight.</li>
	<li>After allowing the reaction to stir overnight, acidify the resulting solution to pH 2 with 1 M hydrochloric acid. Check pH periodically using pH test strips.</li>
	<li>Transfer the reaction to a 250 mL separatory funnel and add 50 mL ethyl acetate. Cap the separatory funnel, mix well, and collect the organic layer in a 250 mL Erlenmeyer flask. Repeat this process two additional times, combining the organic extracts. Dry the combined organic extracts with roughly 3 g of magnesium sulfate.</li>
	<li>Concentrate the combined organic extracts using a rotary evaporator to afford the crude Fmoc-protected amino acid.</li>
</ol>

<ol>
	<li>Wang, J., Shi, T., Deng, G., Jiang, H., Liu, H. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Highly+Enantio-+and+Diastereoselective+Mannich+Reactions+of+Chiral+Ni(II)+Glycinates+with+amino+sulfones.+Efficient+asymmetric+synthesis+of+aromatic+&#945;,&#946;-diamino+acids.">Highly Enantio- and Diastereoselective Mannich Reactions of Chiral Ni(II) Glycinates with amino sulfones. Efficient asymmetric synthesis of aromatic &#945;,&#946;-diamino acids.</a> J. Org. Chem. 73 (21), 8563-8570 (2011).</li><li>Wang, J., Lin, D., Zhou, S., Ding, X., Soloshonok, V. A., Liu, H. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Asymmetric+synthesis+of+sterically+and+electronically+demanding+linear+&#969;,-trifluoromethyl+containing+amino+acids+via+alkylation+of+chiral+equivalents+of+nucleophilic+glycine+and+alanine.">Asymmetric synthesis of sterically and electronically demanding linear &#969;,-trifluoromethyl containing amino acids via alkylation of chiral equivalents of nucleophilic glycine and alanine.</a> J. Org. Chem. 76 (2), 684-687 (2011).</li><li>Wang, J., Zhou, S., Lin, D., Ding, X., Jiang, H., Liu, H. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Highly+diastereo-+and+enantioselective+synthesis+of+syn-&#946;,-substituted+tryptophans+via+asymmetric+Michael+addition+of+a+chiral+equivalent+of+nucleophilic+glycine+and+sulfonylindoles.">Highly diastereo- and enantioselective synthesis of syn-&#946;,-substituted tryptophans via asymmetric Michael addition of a chiral equivalent of nucleophilic glycine and sulfonylindoles.</a> Chem. Commun. 47 (29), 8355-8357 (2011).</li><li>Belokon, Y. N. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Highly+efficient+catalytic+synthesis+of+&#945;,-amino+acids+under+phase-transfer+conditions+with+a+novel+catalyst/substrate+pair.">Highly efficient catalytic synthesis of &#945;,-amino acids under phase-transfer conditions with a novel catalyst/substrate pair.</a> Angew. Chem. Int. Ed. 40 (10), 1948-1951 (2001).</li><li>Zhou, S., Wang, J., Lin, D., Zhao, F., Liu, H. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Enantioselective+synthesis+of+2-substituted-tetrahydroisoquinolin-1-yl+glycine+derivatives+via+oxidative+cross-dehydrogenative+coupling+of+tertiary+amines+and+chiral+nickel(II)+glycinate.">Enantioselective synthesis of 2-substituted-tetrahydroisoquinolin-1-yl glycine derivatives via oxidative cross-dehydrogenative coupling of tertiary amines and chiral nickel(II) glycinate.</a> J. Org. Chem. 78 (22), 11204-11212 (2013).</li><li>Belokon, Y. N. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Synthesis+of+&#945;,-amino+acids+via+asymmetric+phase+transfer-catalyzed+alkylation+of+achiral+nickel(II)+complexes+of+glycine-derived+Schiff+bases.">Synthesis of &#945;,-amino acids via asymmetric phase transfer-catalyzed alkylation of achiral nickel(II) complexes of glycine-derived Schiff bases.</a> J. Am. Chem. Soc. 125 (42), 12860-12871 (2003).</li><li>Ueki, H., Ellis, T. K., Martin, C. H., Soloshonok, V. A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Efficient+large-scale+synthesis+of+picolinic+acid-derived+nickel(II)+complexes+of+glycine.">Efficient large-scale synthesis of picolinic acid-derived nickel(II) complexes of glycine.</a> Eur. J. Org. Chem. 2003 (10), 1954-1957 (2003).</li><li>Dener, J. M., Fantauzzi, P. P., Kshirsagar, T. A., Kelly, D. E., Wolfe, A. B. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Large-scale+syntheses+of+Fmoc-protected+non-proteogenic+amino+acids:+useful+building+blocks+for+combinatorial+libraries.">Large-scale syntheses of Fmoc-protected non-proteogenic amino acids: useful building blocks for combinatorial libraries.</a> Org. Process Res. Dev. 5 (4), 445-449 (2001).</li><li>Cruz, L. J., Beteta, N. G., Ewenson, A., Albericio, F. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=&amp;#34;One-pot&amp;#34;,+preparation+of+N-carbamate+protected+amino+acids+via+the+azide.">&amp;#34;One-pot&amp;#34;, preparation of N-carbamate protected amino acids via the azide.</a> Org Process Res. Dev. 8 (6), 920-924 (2004).</li><li>Hart, J. R. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=.">.</a> Ullmann's Encyclopedia of Industrial Chemistry. , (2000).</li><li>Adamson, J. G., Blaskovich, M. A., Groenevelt, H., Lajoie, G. A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Simple+and+convenient+synthesis+of+tert-butyl+ethers+of+Fmoc-serine,+Fmoc-threonine,+and+Fmoc-tyrosine.">Simple and convenient synthesis of tert-butyl ethers of Fmoc-serine, Fmoc-threonine, and Fmoc-tyrosine.</a> J. Org. Chem. 56 (10), 3447-3449 (1991).</li><li>Seyfried, M. S., Lauber, B. S., Luedtke, N. W. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Multiple-turnover+isotopic+labeling+of+Fmoc-+and+Boc-protected+amino+acids+with+oxygen+isotopes.">Multiple-turnover isotopic labeling of Fmoc- and Boc-protected amino acids with oxygen isotopes.</a> Org. Lett. 12 (1), 104-106 (2010).</li><li>Bonke, G., Vedel, L., Witt, M., Jaroszewski, J. W., Olsen, C. A., Franzyk, H. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Dimeric+building+blocks+for+solid-phase+synthesis+of+&#945;,-peptide-&#946;,-peptoid+chimeras.">Dimeric building blocks for solid-phase synthesis of &#945;,-peptide-&#946;,-peptoid chimeras.</a> Synthesis. 2008 (15), 2381-2390 (2008).</li></ol>

The authors have nothing to disclose.

The protocol described above is useful in its ability to facilitate the isolation of an amino acid backbone from a Ni-Schiff-base complex under mild pH conditions and subsequent Fmoc protection of this isolated amino acid through two critical steps. The first step involves stirring a DMF/water solution containing EDTA to facilitate release of the amino acid from the complex. Residual complex or organic byproducts can easily be removed with extraction. The second step of this protocol involves an Fmoc protection of the am...

Unnatural amino acids (UAA&#39;s) bearing side chains that vary from those of the twenty naturally occurring amino acids found in nature have found utility in a wide-range of applications. Synthesis of these UAA&#39;s, however, can be difficult depending on the structure of the side-chains and the stereochemistry of the amino acid backbone. C-H bond activation of glycine in the context of a nickel Schiff-base complex has been used to produce a variety of amino acid derivatives including &#945;,&#946;-diamino acids1 and UAA&#39;s bearing fluorinated2 or heterocyclic side-chains.3
After addition of unnatural side-chains, functionalized UAA&#39;s are typically removed from the Schiff-base complex by reflux in hydrochloric acid4 and are subsequently isolated using ion-exchange chromatography. While generally efficient, this protocol generates amino acids that may be unsuitable for use in solid-phase peptide synthesis (SPPS). The nature of SPPS requires the presence of acid-labile side-chain protecting groups and the strongly acidic nature of typical Ni-Schiff-base decomposition conditions prevents isolation of UAA&#39;s with these protecting groups intact. To our knowledge, only one alternative decomposition method has been reported: use of ethylenediaminetetraacetic acid (EDTA) and hydrazine at elevated temperatures,5 conditions that themselves may not be suitable for some side-chain protecting groups such as phthalimides.
<img alt="Figure 1" src="/files/ftp_upload/55677/55677fig1.jpg" /> 
Figure 1: Synthesis of Ni-PBP-Gly from Ni2+, PBP, and Glycine (Gly). <a href="http://cloudflare.jove.com/files/ftp_upload/55677/55677fig1large.jpg" target="_blank">Please click here to view a larger version of this figure.</a>
Herein, we report a method for hydrolysis of a Ni-Schiff-base complex, Ni-PBP-Gly (Figure 1). This complex, derived from Ni2+, glycine, and pyridine-2-carboxylic acid(2-benzoyl-phenyl)-amide (PBP),6 has been demonstrated to be a useful platform for synthesis of a variety of UAA&#39;s and is easily accessible using a two-step synthetic route.7 Synthesis of this complex is literature-precedented in high yield.6 Our results described below demonstrate the applicability of hydrolysis conditions utilizing EDTA at mildly acidic to neutral pH conditions appropriate for use with UAA&#39;s bearing acid-labile side-chain protecting groups. Following hydrolysis, the resulting aqueous solution can be isolated and subjected immediately to standard Fmoc protection conditions to afford an Fmoc-protected amino acid (Figure 2).
<img alt="Figure 2" src="/files/ftp_upload/55677/55677fig2.jpg" /> 
Figure 2: Hydrolysis and Fmoc-protection of an Amino Acid Isolated from Ni-PBP-Gly. Reaction Conditions: i. EDTA (12 equiv), pH 4.5; ii. Ethyl acetate wash and adjustment to pH 7; iii. Fmoc-OSu (1 equiv), NaHCO3 (2 equiv). <a href="http://cloudflare.jove.com/files/ftp_upload/55677/55677fig2large.jpg" target="_blank">Please click here to view a larger version of this figure.</a>

<table><tbody><tr><td>Ni-PBP-Gly</td><td></td><td></td><td>Synthesized from published protocol</td></tr><tr><td>DMF</td><td>Fisher</td><td>D119-4</td><td></td></tr><tr><td>EDTA</td><td>Fisher</td><td>S311-100</td><td></td></tr><tr><td>Dichloromethane</td><td>Acros</td><td>AC610050040</td><td></td></tr><tr><td>Sodium Bicarbonate</td><td>Fisher</td><td>S233-500</td><td></td></tr><tr><td>Fmoc-OSu</td><td>Chem-Impex</td><td>&quot;00147&quot;</td><td></td></tr><tr><td>Dioxane</td><td>Fisher</td><td>D111-500</td><td></td></tr><tr><td>Hydrochloric Acid</td><td>Fisher</td><td>A144-500</td><td></td></tr><tr><td>Ethyl Acetate</td><td>Acros</td><td>AC610060040</td><td></td></tr><tr><td>Magnesium Sulfate</td><td>Fisher</td><td>M65-500</td><td></td></tr><tr><td>ZEOPrep 60ECO Silica Gel</td><td>ZEOChem</td><td></td><td></td></tr><tr><td>Hexanes</td><td>Fisher</td><td>3200250.650.443</td><td></td></tr><tr><td>Chromatography Column</td><td></td><td></td><td></td></tr><tr><td>pH Test Strips</td><td></td><td></td><td></td></tr><tr><td>Rotary Evaporator</td><td></td><td></td><td></td></tr><tr><td>250 mL Separatory Funnel</td><td></td><td></td><td></td></tr><tr><td>250 mL Round Bottom Flask</td><td></td><td></td><td></td></tr><tr><td>Stir Bar</td><td></td><td></td><td></td></tr><tr><td>Stir Plate</td><td></td><td></td><td></td></tr></tbody></table>

hydrolysis of a ni-schiff-base complex using conditions suitable for retention of acid-labile protecting groups

Unnatural amino acids, amino acids containing side-chain functionalities not commonly seen in nature, are increasingly found in synthetic peptide sequences. Synthesis of some unnatural amino acids often includes the use of a precursor consisting of a Schiff-base stabilized by a nickel cation. Unnatural side-chains can be installed on an amino acid backbone found in this Schiff-base complex. The resulting unnatural amino acid can then be isolated from this complex using hydrolysis of the Schiff-base, typically by employing reflux in strongly acidic solution. These highly acidic conditions may remove acid-labile side-chain protecting groups necessary for the unnatural amino acids to be used in microwave-assisted solid-phase peptide synthesis. In this work, we present an efficient hydrolysis and subsequent Fmoc protection of an amino acid isolated from a Ni-Schiff base complex. Hydrolysis conditions presented in this work are suitable for retention of acid-labile side-chain protecting groups and may be adaptable to a variety of unnatural amino acid substrates.

We hypothesized that removal of the Ni2+ from the Ni-PBP-Gly complex could allow an efficient aqueous hydrolysis of the Schiff-base without the need for harsh pH conditions. As EDTA is an inexpensive and well-studied chelating agent,10 we hypothesized that addition of EDTA to a solution of Ni-PBP-Gly would facilitate chelation of Ni2+ ions, thereby promoting hydrolysis of the complex.
<p class="jove_content" fo:keep-together.within-page="1...

Watch this Scientific Journal Video about Hydrolysis of a Ni-Schiff-Base Complex Using Conditions Suitable for Retention of Acid-labile Protecting Groups at JoVE.com

Hydrolysis of a Ni-Schiff-Base Complex Using Conditions Suitable for Retention of Acid-labile Protecting Groups

Here, we present an efficient hydrolysis and subsequent Fmoc protection of an amino acid isolated from a Ni-Schiff-base complex. Hydrolysis conditions presented here are suitable for use when retention of acid-labile side-chain protecting groups is required. This technique may be adaptable to a variety of unnatural amino acid substrates.

Unnatural amino acids, amino acids containing side-chain functionalities not commonly seen in nature, are increasingly found in synthetic peptide ...

hydrolysis-ni-schiff-base-complex-using-conditions-suitable-for

Research

JoVE Journal

Biochemistry

9.6K Views.  Slippery Rock University.  Hier presenteren we een efficiënte hydrolyse en daaropvolgende Fmoc bescherming van een aminozuur geïsoleerd uit een Ni-Schiff-base complex. Hydrolyseomstandigheden die hier geschikt zijn voor gebruik retentie zuur-labiele zijketen beschermende groepen vereist. Deze techniek kan worden aangepast aan een verscheidenheid van niet-natuurlijke aminozuur substraten. 

Video: Hydrolysis of a Ni-Schiff-Base Complex Using Conditions Suitable for Retention of Acid-labile Protecting Groups

Separation of Aldehydes and Reactive Ketones from Mixtures Using a Bisulfite Extraction Protocol

The purification of organic compounds is an essential component of routine synthetic operations. The ability to remove contaminants into an aqueous layer by generating a charged structure provides an opportunity to use extraction as a simple purification technique. By combining the use of a miscible organic solvent with saturated sodium bisulfite, aldehydes and reactive ketones can be successfully transformed into charged bisulfite adducts that can then be separated from other organic components of a mixture by the introduction of an immiscible organic layer. Here, we describe a simple protocol for the removal of aldehydes, including sterically-hindered neopentyl aldehydes and some ketones, from chemical mixtures. Ketones can be separated if they are sterically unhindered cyclic or methyl ketones. For aliphatic aldehydes and ketones, dimethylformamide is used as the miscible solvent to improve removal rates. The bisulfite addition reaction can be reversed by basification of the aqueous layer, allowing for the re-isolation of the reactive carbonyl component of a mixture.

Here, we present a protocol to remove aldehydes and reactive ketones from mixtures by a liquid-liquid extraction protocol directly with saturated sodium bisulfite in a miscible solvent. This combined protocol is rapid and facile to perform. The aldehyde or ketone can be re-isolated by the basification of the aqueous layer.

The purification of organic compounds is an essential component of routine synthetic operations. The ability to remove contaminants into an aqueous layer ...

Chemistry

Preparation of SNS Cobalt(II) Pincer Model Complexes of Liver Alcohol Dehydrogenase

Chemical model complexes are prepared to represent the active site of an enzyme. In this protocol, a family of tridentate pincer ligand precursors (each possessing two sulfur and one nitrogen donor atom functionalities (SNS) and based on bis-imidazole or bis-triazole compounds) are metallated with CoCl2&#183;6H2O to afford tridentate SNS pincer cobalt(II) complexes. Preparation of the cobalt(II) model complexes for liver alcohol dehydrogenase is facile. Based on a quick color change upon adding the CoCl2&#183;6H2O to acetonitrile solution that contains the ligand precursor, the complex forms rapidly. Formation of the metal complex is complete after allowing the solution to reflux overnight. These cobalt(II) complexes serve as models for the zinc active site in liver alcohol dehydrogenase (LADH). The complexes are characterized using single crystal X-ray diffraction, electrospray mass spectrometry, ultra-violet visible spectroscopy, and elemental analysis. To accurately determine the structure of the complex, its single crystal structure must be determined. Single crystals of the complexes that are suitable for X-ray diffraction are then grown via slow vapor diffusion of diethyl ether into an acetonitrile solution that contains the cobalt(II) complex. For high quality crystals, recrystallization typically takes place over a 1 week period, or longer. The method can be applied to the preparation of other model coordination complexes and can be used in undergraduate teaching laboratories. Finally, it is believed that others may find this recrystallization method to obtain single crystals beneficial to their research.

Preparation of SNS CobaltII Pincer Model Complexes of Liver Alcohol Dehydrogenase

The preparation of SNS pincer cobalt(II) model complexes of liver alcohol dehydrogenase is presented here. The complexes can be prepared by reacting the ligand precursor with CoCl2&#183;6H2O and can then be recrystallized by allowing diethyl ether to slowly diffuse into an acetonitrile solution that contains the cobalt complex.

Chemical model complexes are prepared to represent the active site of an enzyme. In this protocol, a family of tridentate pincer ligand precursors (each ...

Targeted Antibody Blocking by a Dual-Functional Conjugate of Antigenic Peptide and Fc-III Mimetics (DCAF)

Elimination of harmful antibodies from organisms is a valuable approach for the intervention of antibody-associated diseases, such as Dengue hemorrhagic fever and autoimmune diseases. Since thousands of antibodies with different epitopes are circulating in blood, no universal method, except for the dual-functional conjugate of antigenic peptide and Fc-III mimetics (DCAF), was reported to target specific harmful antibodies. The development of DCAF molecules makes significant contribution to the progress of targeted therapy, which were demonstrated to eliminate the antibody dependent enhancement (ADE) effect in a Dengue virus (DENV) infection model and to boost the acetylcholine receptor activity in a myasthenia gravis model. Here, we describe a protocol for the synthesis of a DCAF molecule (DCAF1), which can selectively block 4G2 antibody to attenuate ADE effect during Dengue virus infection, and illustrate the binding of DCAF1 to 4G2 antibody by an ELISA assay. In our method, DCAF1 is synthesized by the conjugation of a hydrazine derivative of a Fc-III peptide and a recombinant expressed long &#945;-helix with antigenic sequence through native chemical ligation (NCL). This protocol has been successfully applied to DCAF1 as well as other DCAF molecules for targeting their cognate antibodies.

Targeted Antibody Blocking by a Dual-Functional Conjugate of Antigenic Peptide and Fc-III Mimetics DCAF

Development of a dual-functional conjugate of antigenic peptide and Fc-III mimetics (DCAF) is novel for the elimination of harmful antibodies. Here, we describe a detailed protocol for the synthesis of DCAF1 molecule, which can selectively block 4G2 antibody to eliminate antibody dependent enhancement effect during Dengue virus infection.

Elimination of harmful antibodies from organisms is a valuable approach for the intervention of antibody-associated diseases, such as Dengue hemorrhagic ...

Immunology and Infection

Molecular Orbital (MO) Theory

Source: Tamara M. Powers, Department of Chemistry, Texas A&#38;M University
This protocol serves as a guide in the synthesis of two metal complexes featuring the ligand 1,1&#39;-bis(diphenylphosphino)ferrocene (dppf): M(dppf)Cl2, where M = Ni or Pd. While both of these transition metal complexes are 4-coordinate, they exhibit different geometries at the metal center. Using molecular orbital (MO) theory in conjunction with 1H NMR and Evans method, we will determine the geometry of these two compounds.

Molecular Orbital MO Theory: Predicting Geometry of Transition Metal Complexes

Source: Tamara M. Powers, Department of Chemistry, Texas A&#38;M University
This protocol serves as a guide in the synthesis of two metal complexes ...

Education

JoVE Science Education

Inorganic Chemistry

Protection of Alcohols

This lesson delves into the concept of protection and deprotection of a functional group fundamental to synthetic organic chemistry. These phenomena are explained in the context of aliphatic and aromatic alcohols.
<h4>Protection</h4>
It defines a protecting group as the masking agent to make the more reactive species inert to a given set of conditions. This concept is depicted via the illustration of liquid flow through different outlets in an assembly of pipes. The analogy helps to understand the role of a protecting group in reaction selectivity, as in the case of the organolithium alkylation of a halide in the presence of a competing acidic alcohol group. The example shows how protection of the alcohol group helps to achieve the alkylation of the halide. Popular protecting groups for alcohols include the trialkylsilyl family for nucleophiles or carbon and nitrogen bases and the tetrahydropyranyl (THP) group for strong bases. In the former example, the halide of the trialkylsilyl derivative reacts with the alcohol in the presence of a nucleophilic catalyst to generate a trialkylsilyl ether.
<h4>Deprotection</h4>
Every protection is followed by deprotection after the intended reaction. The deprotection restores the system to its native state. In protection with trialkylsilyl groups, deprotection is achieved using fluoride salts like tetra-n-butylammonium fluoride (TBAF) that are soluble in organic solvents. Here, the re-protonation of the oxygen regenerates the native alcohol. In the case of protection with THP, deprotection is achieved using acid hydrolysis.
<h4>Principle of design</h4>
The lesson also elucidates the principles behind the design of a protecting group using an illustration of a house under varying external weather conditions. It demonstrates the selectivity offered by a protecting group in a specific environment. For instance, THP protects alcohol from strong bases. The acetal formed in this case is stable towards bases but susceptible to acid hydrolysis.
Apart from the reaction conditions, the reactivity of the molecule to be protected also plays a key role in designing a suitable protecting group. For example, methyl ethers&#8217; ability to protect phenols is found inappropriate for aliphatic alcohols. Here, the stability of the corresponding leaving groups during deprotection plays a key role. For example, the alkoxides, unlike phenoxides, are poor leaving groups for deprotection with hydrogen bromide.
The following table summarizes the various protection/deprotection groups for different types of alcohols and related conditions:
<table style="margin-left: auto; margin-right: auto;">
	<tbody style="border: 1px solid black;">
		<tr>
			<td style="color: black; border: 1px solid black; text-align: center;">Protecting group</td>
			<td style="color: black; border: 1px solid black; text-align: center;">Structure</td>
			<td style="color: black; border: 1px solid black; text-align: center;">Protects</td>
			<td style="color: black; border: 1px solid black; text-align: center;">From</td>
			<td style="color: black; border: 1px solid black; text-align: center;">Protection</td>
			<td style="color: black; border: 1px solid black; text-align: center;">Deprotection</td>
		</tr>
		<tr>
			<td style="color: black; border: 1px solid black; text-align: center;">Trialkylsilyl (R3Si&#8211;), 
			e.g., TBDMS</td>
			<td style="color: black; border: 1px solid black; text-align: center;">Me3Si&#8211;OR 
			(Me3C)Me2Si&#8211;OR</td>
			<td style="color: black; border: 1px solid black; text-align: center;">Alcohols 
			(OH in general)</td>
			<td style="color: black; border: 1px solid black; text-align: center;">Nucleophiles, 
			C or N bases</td>
			<td style="color: black; border: 1px solid black; text-align: center;">R3SiCl, 
			base</td>
			<td style="color: black; border: 1px solid black; text-align: center;">H+, H2O, 
			or F&#8722;</td>
		</tr>
		<tr>
			<td style="color: black; border: 1px solid black; text-align: center;">Tetrahydropyranyl 
			(THP)</td>
			<td style="color: black; border: 1px solid black; text-align: center;"><img alt="Figure1" src="/files/ftp_upload/11927/Figure_1-11927.svg" style="text-align: center; height: 50px;" /></td>
			<td style="color: black; border: 1px solid black; text-align: center;">Alcohols 
			(OH in general)</td>
			<td style="color: black; border: 1px solid black; text-align: center;">Strong bases</td>
			<td style="color: black; border: 1px solid black; text-align: center;">3,4-Dihydropyran, 
			H+</td>
			<td style="color: black; border: 1px solid black; text-align: center;">H+, H2O</td>
		</tr>
		<tr>
			<td style="color: black; border: 1px solid black; text-align: center;">Benzyl ether 
			(OBn)</td>
			<td style="color: black; border: 1px solid black; text-align: center;"><img alt="Figure2" src="/files/ftp_upload/11927/Figure_2-11927.svg" style="text-align: center; height: 50px;" /></td>
			<td style="color: black; border: 1px solid black; text-align: center;">Alcohols 
			(OH in general)</td>
			<td style="color: black; border: 1px solid black; text-align: center;">Almost everything</td>
			<td style="color: black; border: 1px solid black; text-align: center;">NaH, BnBr</td>
			<td style="color: black; border: 1px solid black; text-align: center;">H2, Pd/C, 
			or HBr</td>
		</tr>
		<tr>
			<td style="color: black; border: 1px solid black; text-align: center;">Methyl ether 
			(ArOMe)</td>
			<td style="color: black; border: 1px solid black; text-align: center;"><img alt="Figure3" src="/files/ftp_upload/11927/Figure_3-11927.svg" style="text-align: center; height: 50px;" /></td>
			<td style="color: black; border: 1px solid black; text-align: center;">Phenols 
			(ArOH)</td>
			<td style="color: black; border: 1px solid black; text-align: center;">Bases</td>
			<td style="color: black; border: 1px solid black; text-align: center;">NaH, MeI, or 
			(MeO)2SO2</td>
			<td style="color: black; border: 1px solid black; text-align: center;">BBr3, HBr, HI, 
			Me3SiI</td>
		</tr>
	</tbody>
</table>

Protection and Deprotection of Alcohols and Phenols

This lesson delves into the concept of protection and deprotection of a functional group fundamental to synthetic organic chemistry. These phenomena are ...

JoVE Core

Organic Chemistry

Unit 1

Alcohols and Phenols

KEY TERMS AND CONCEPTS

Preparation of Carboxylic Acids: Hydrolysis of Nitriles

Nitriles (R–CN) can be converted into carboxylic acids (R–COOH) upon treatment with aqueous acids, i.e., upon hydrolysis of nitriles. Under base-catalyzed conditions, carboxylate anions (R–COO−) are formed.
<img alt="Hydrolysis reaction mechanism diagram, showing conversion of nitrile to carboxylic acid with arrows." src="/files/ftp_upload/13085/13085_PT_Figure_1.svg" style="text-align: center; height: 56px;" data-altupdatedat="1747908711000" data-alt="Figure1">
The reaction facilitates a two-step conversion of haloalkanes to carboxylic acids. Here, haloalkanes are first converted to nitriles using sodium cyanide via an SN2 reaction. The resultant nitrile is then hydrolyzed to yield carboxylic acids bearing one more carbon than the haloalkane used. The reaction uses dimethyl sulfoxide, alcohols, or water as solvents. As the process involves the SN2 mechanism, tertiary alkyl halides are seldom used.
<img alt="Organic synthesis reaction sequence; diagram illustrating nucleophilic substitution to carboxylic acid." src="/files/ftp_upload/13085/13085_PT_Figure_2.svg" style="text-align: center; height: 46px;" data-altupdatedat="1747908711000" data-alt="Figure2">

Nitriles (R&#8211;CN) can be converted into carboxylic acids (R&#8211;COOH) upon treatment with aqueous acids, i.e., upon hydrolysis of nitriles. Under ...

Carboxylic Acids

Acid Halides to Carboxylic Acids: Hydrolysis

Hydrolysis of acid halides is a nucleophilic acyl substitution reaction in which acid halides react with water to give carboxylic acids. The reaction occurs readily and does not require acid or a base catalyst.
As shown below, the mechanism involves a nucleophilic attack by water at the carbonyl carbon to form a tetrahedral intermediate. This is followed by the reformation of the carbon–oxygen π bond along with the departure of a halide ion. A final proton transfer step yields carboxylic acid as the substitution product. 
<img alt="Organic reaction mechanism, diagram, showing nucleophilic substitution and product formation steps." src="/files/ftp_upload/12361/12361_PT_Figure_1_.svg" style="text-align: center; height: 200px;" data-altupdatedat="1747908711000" data-alt="Figure1">
The reaction produces a very strong acid, HCl, as a by-product. Therefore, a base such as pyridine is used in the reaction, which reacts with HCl to form pyridinium chloride. This process neutralizes the acid and prevents undesired side reactions.

Hydrolysis of acid halides is a nucleophilic acyl substitution reaction in which acid halides react with water to give carboxylic acids. The reaction ...

Carboxylic Acid Derivatives

Protecting Groups for Aldehydes and Ketones: Introduction

Protecting groups are compounds that can bind to a specific functional group in the presence of other functional groups to protect them from undesired chemical reactions. These compounds can selectively bind to particular functional groups and advance chemoselective reactions in polyfunctional systems (Figure 1). After the functional group has served its purpose, it is removed by reacting it with specific compounds.
<img alt="Chemical structure of malonic acid, diagram showing bonding, central CH2 group, molecular geometry." src="/files/ftp_upload/12844/12844_PT_Figure_1.svg" style="text-align: center; height: 60px;" data-altupdatedat="1747908711000" data-alt="Chemical structure of malic acid, diagram, showing molecular arrangement, functional groups.">
The aldehydes and ketones can be selectively protected in the presence of other carbonyl groups such as esters or acids based upon their reactivity. This is important for the manipulation of one functional group over the other.
For instance, when carrying out a reduction reaction in the presence of an ester and a ketone, the ketone will always be preferentially reduced to alcohol. In order to achieve the selective reduction of an ester to an alcohol while keeping the ketone unaffected, the ketone group needs to be protected (Figure 2, first step). After the ketone is protected, the ester is reduced to an alcohol using LiAlH4 (Figure 2, second step). Finally, the ketone is regenerated by removing the protecting group (Figure 2, third step).
<img alt="Organic synthesis diagram, ketone protection with cyclic acetal and reduction with LiAlH4." src="/files/ftp_upload/12844/12844_PT_Figure_2.svg" style="text-align: center; height: 215px;" data-altupdatedat="1747908711000" data-alt="Chemical reaction diagram; acetal formation, protection, and reduction; TsOH, LiAlH4 used.">
Acetals and thioacetals are the most commonly used protecting groups for aldehydes and ketones and can be easily removed. In addition, they are resistant to chemical species such as nucleophiles, or reducing and oxidizing agents.

Protecting groups are compounds that can bind to a specific functional group in the presence of other functional groups to protect them from undesired ...

Aldehydes and Ketones

Acetals and Thioacetals as Protecting Groups for Aldehydes and Ketones

Acetals are formed by reacting two equivalents of alcohol with carbonyl compounds like aldehydes or ketones. Acetals are unaffected by bases, nucleophiles, oxidizing agents, and reducing agents. They serve as protecting groups for aldehydes and ketones. Acetals can be easily formed and also easily removed via mild acid hydrolysis.
In the presence of multiple functional groups, when selective reduction of one group over the other is desired, groups like aldehydes and ketones that form acetals readily can be protected from undergoing undesirable reactions. For instance, if a compound contains a ketone and an ester group, the ketone can be protected by converting it into acetal. On the other hand, the ester does not form acetal; hence it can be subjected to the desired reaction, and in the end, the ketone can be deprotected.
<img alt="Chemical reaction process, acetal formation and reduction, organic chemistry mechanism diagram." src="/files/ftp_upload/12333/12333_Figure_1.svg" style="opacity: 0.9; text-align: center; height: 200px;" data-altupdatedat="1747908711000" data-alt="Figure1">
The sulfur-containing analogs of acetals are called thioacetals that can act as an efficient protecting group for aldehydes and ketones. The thioacetals are stable in acidic conditions. Due to this, they cannot be deprotected by acid hydrolysis. Instead, mercuric chloride in aqueous acetonitrile is used for its deprotection.
<img alt="Chemical reaction: Dithiolane to Acetone transformation; HgCl₂ catalyst; reaction mechanism diagram." src="/files/ftp_upload/12333/12333_Figure_2.svg" style="text-align: center; height: 55px;" data-altupdatedat="1747908711000" data-alt="Figure2">
Apart from acting as protecting groups, thioacetals also play a major role in organic synthesis, especially in reduction reactions. Thioacetals can undergo desulfurization in the presence of Raney nickel and hydrogen to form hydrocarbons.
<img alt="Organic reaction diagram, hydrogenation using H2, Raney Ni; forming hydrocarbons, thiols." src="/files/ftp_upload/12333/12333_Figure_3.svg" style="text-align: center; height: 55px;" data-altupdatedat="1747908711000" data-alt="Figure3">

Acetals are formed by reacting two equivalents of alcohol with carbonyl compounds like aldehydes or ketones. Acetals are unaffected by bases, ...

Amides to Carboxylic Acids: Hydrolysis

Amides can undergo either acid-catalyzed hydrolysis or base-promoted hydrolysis through a typical nucleophilic acyl substitution. Each hydrolysis requires severe conditions.
Acid-catalyzed hydrolysis:
Hydrolysis of amides under acidic conditions yields carboxylic acids. Since the reaction occurs slowly, hydrolysis requires the conditions of heat.
The mechanism begins with the protonation of the carbonyl oxygen by the acid catalyst. The protonation makes the amide carbonyl carbon more electrophilic. Next, water acts as a nucleophile and attacks the carbonyl carbon to form a tetrahedral intermediate. Further, deprotonation of the tetrahedral intermediate gives a neutral tetrahedral addition intermediate. Subsequent protonation of the amino nitrogen converts the amino group into a better leaving group. In the next step, the carbonyl group is re-formed with the departure of ammonia as a leaving group. A final deprotonation step yields a carboxylic acid.
<img alt="Figure1" src="/files/ftp_upload/12372/12372_PT_Figure_1_.svg" style="text-align: center; height: 225px;" />
The formation of ammonium ion drives the equilibrium favoring the product formation.
Base-promoted hydrolysis: 
Base-promoted hydrolysis is another nucleophilic acyl substitution reaction, where hydroxide acts as a nucleophile. Amides undergo hydrolysis when heated under basic aqueous solutions to produce carboxylic acid.
The base-promoted mechanism involves a nucleophilic attack by the hydroxide ion at the amide carbonyl carbon to form a tetrahedral intermediate. In the second step, the carbonyl group is reconstructed with the departure of an amide ion as a leaving group. Next, deprotonation yields a carboxylate ion and ammonia. This step drives the reaction to completion, which pushes the equilibrium towards the product. A final step involves acidification of the carboxylate ion to give free acid.
<img alt="Figure2" src="/files/ftp_upload/12372/12372_PT_Figure_2.svg" style="text-align: center; height: 200px;" />

Amides can undergo either acid-catalyzed hydrolysis or base-promoted hydrolysis through a typical nucleophilic acyl substitution. Each hydrolysis requires ...

Hydrolysis of a Ni-Schiff-Base Complex Using Conditions Suitable for Retention of Acid-labile Protecting Groups

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