A simple synthesis of photolabile α-methyl nitrobenzyl compounds

Article abstract of DOI:10.1081/SCC-120039491

α-Methyl nitrobenzyl compounds have demonstrated superior photochemical release properties when compared to nitrobenzyl compounds lacking α-methyl substitution at the benzylic position. The synthesis of 4-(1-hydroxy-ethyl)-3-nitro-benzoic acid ethyl ester

Full text of DOI:10.1081/SCC-120039491

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A Simple Synthesis of
Photolabile α‐Methyl
Nitrobenzyl Compounds
Charles P. Salerno a & Henderson J. Cleaves a
a The Scripps Institution of Oceanography, UCSD ,
9500 Gilman Drive, Svedrup Hall, La Jolla,
California, 92093‐0212, USA
Published online: 10 Jan 2011.
To cite this article: Charles P. Salerno & Henderson J. Cleaves (2004) A
Simple Synthesis of Photolabile α‐Methyl Nitrobenzyl Compounds, Synthetic
Communications: An International Journal for Rapid Communication of Synthetic
Organic Chemistry, 34:13, 2379-2386, DOI: 10.1081/SCC-120039491
To link to this article: http://dx.doi.org/10.1081/SCC-120039491
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SYNTHETIC COMMUNICATIONSw
Vol. 34, No. 13, pp. 2379–2386, 2004
A Simple Synthesis of Photolabile a-Methyl
Nitrobenzyl Compounds
*
Charles P. Salerno and Henderson J. Cleaves
The Scripps Institution of Oceanography, UCSD,
La Jolla, California, USA
ABSTRACT
a-Methyl nitrobenzyl compounds have demonstrated superior photo-
chemical release properties when compared to nitrobenzyl compounds
lacking a-methyl substitution at the benzylic position. The synthesis of
4-(1-hydroxy-ethyl)-3-nitro-benzoic acid ethyl ester and 4-(1-amino-
ethyl)-3-nitro-benzoic acid ethyl ester was each carried out in four steps.
The efficient oxidation of 4-ethyl-3-nitro-benzoic acid to 4-acetyl-3-nitro-
benzoic acid by 3 mol% chromium trioxide/periodic acid in acetonitrile
provides a common, crystallizable precursor from which both hydroxy
and amine substituted a-methyl nitrobenzyl compounds may be
*
Correspondence: Henderson J. Cleaves, The Scripps Institution of Oceanography,
UCSD, 9500 Gilman Drive, Svedrup Hall, La Jolla, CA 92093-0212, USA; E-mail:
hcleaves@ucsd.edu.
2379
DOI: 10.1081/SCC-120039491
0039-7911 (Print); 1532-2432 (Online)
www.dekker.com
Copyright # 2004 by Marcel Dekker, Inc.

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Salerno and Cleaves
synthesized. This oxidative methodology will be useful in synthesizing a
broad array of nitrobenzyl protecting groups.
Key Words: Nitrobenzyl compounds; Oxidation; Photolabile protecting
groups; a-Methyl groups; Ultraviolet light; Caged compounds; Hemi-
acetal; Hemiaminal.
INTRODUCTION
Nitrobenzyl photolabile protecting groups provide a mild, noninvasive
means by which small molecules may be photolytically deprotected under a
wide variety of solvents and conditions. The versatility of nitrobenzyl groups
has encouraged their use as linkers and protecting groups in chemical
synthesis as well as biological applications. Polyfunctional nitrobenzyl
protecting groups provide the broadest range of potential applications.
In 1975, Rich and Gurawa introduced the 4-(amino-methyl)-3-
nitro-benzoic acid class of groups for use as photolabile linkers in solid
phase applications, Fig. 1.[1] The compact size of these compounds and the
presence of a carboxylic acid group for enhancing water solubility also make
variants of these compounds attractive from the standpoint of protecting
biologically relevant substrates. Over the last two decades there has been a
mounting body of data that suggests nitrobenzyl compounds with methyl
groups at the a-benzyl position possess faster rates of release and higher quan-
tum efficiencies of product release.[2] In addition, a-methyl groups result in
the formation of a nitroso ketone byproduct, which is intrinsically less reactive
than the corresponding nitroso aldehyde. This has the advantage of increasing
photolytic yields due to the preservation of released product. Furthermore, the
mechanism by which commonly used thiol scavengers react with the a-methyl
nitroso ketone has been fully characterized.[3] The suggested mechanism for
Figure 1. A selection of photolabile protecting groups/linkers.

Synthesis of Photolabile a-Methyl Nitrobenzyl Compounds
2381
release of amines, amides, carboxylic acids, alcohols, and phosphates pro-
ceeds via the photoinduced formation of hemiacetal or hemiaminal type inter-
mediates that decomposes to release the product and nitroso aromatic group.[4]
Several authors have attempted to improve upon Rich and Gurawa’s nitro-
benzyl compounds by the incorporation of alkyl groups at the a-benzyl position.
Photolabile groups incorporating the a-methyl nitrobenzyl element have also
been developed based upon the 6-nitroveratryl substructure, Fig. 1.[5] A draw-
back of dimethoxy substitution is that despite greater absorption at longer
wavelengths, quantum efficiencies of product release are typically orders of
magnitude lower.[6] Furthermore, their absorption extends into the visible spec-
trum and may complicate their use under standard lighting. Other a-alkyl
benzyl variants include the 3-amino-3-(2-nitrophenyl)-propionic linker.[7]
Although the synthesis of this groups was highly efficient it is prone to undergo
acid and base catalyzed beta-elimination, Fig. 1.[8] This prompted the develop-
ment of the 3-amino-3-(20-nitrophenyl)-2,2-dimethyl propionic acid protecting
group, Fig. 1. The 4-(1-amino-ethyl)-3-nitro-benzoic acid photolabile group is
the closest in structure to the first compounds developed by Rich and Gurawa,
Fig. 1. The compact size of this compound and stability under basic conditions
allowed its efficient use as a water soluble amide protecting group.[9]
RESULTS
The well established benefits of a-benzyl methyl substitution thus prompted
the development of a practical, scalable synthesis of a-methyl compounds 1 and
2 to serve as needed references in the growing family of nitrobenzyl protecting
groups and linkers, Fig. 2. This work demonstrates the first synthesis of 2.
A frustrating aspect of nitro aromatic compounds is their relative sensi-
tivity to strongly reducing chemistry and organometallic reagents. This limits
the means by which substituents may be introduced following nitration.
When attempting a highly efficient, scalable synthesis of such compounds intro-
duction of the nitro group should proceed so as to achieve nearly quantitative
regioselective conversion to the desired nitro substituted isomer. Originally 1
was synthesized via the coupling of potassium phthalimide with 4-(1-bromo-
ethyl)-benzoic acid-ethyl ester in refluxing DMF followed by nitration using
fuming nitric acid, 2108C.[9] The synthesis of 1 was problematic in that it
generated an 80 : 20 mixture of ortho : meta isomers that required silica column
chromatography. The synthesis of 2 was attempted via nitration of 4-acetyl
benzoic acid and 4-(1-acetoxy-ethyl)-benzoic acid using a variety of nitrating
conditions. In each case a mixture of isomers or decomposition occurred, Sch. 1.a
aNitrating conditions included fuming HNO3 at 2108C, HNO3/H2SO4, HNO3/Ac2O.

2382
Salerno and Cleaves
Figure 2. 1 ¼ R ¼ NH2, 2 ¼ R ¼ OH.
The synthesis of 1 and 2 was thus to follow a route in which the nitro group
was introduced first, followed by the oxidative introduction of a ketone which
could be easily converted to either the alcohol or amine, Sch. 2. The photolabile
groups were to be synthesized as their ethyl ester derivatives to aid in purification
and incorporation. The synthesis proceeded via the nitration of commercially
available 4-ethyl-benzoic acid using fuming nitric acid at 2108C. The presence
of strongly directing alkyl and carboxy groups in 4-ethyl-benzoic acid promotes
its near quantitative conversion to 3 (. 95%) as a crystalline solid. The selective
oxidation of 3 to 4 was carried out using the delightful chromium based chemi-
stry of Yamazaki.[10] The oxidation uses only a catalytic amount of CrO3
(3 mol%) in the presence of an excess of periodic acid, which serves as the termi-
nal oxidant. The reaction proceeds smoothly and cleanly in MeCN to produce
ketone 4 in 85% yield as a crystalline solid. This is the first example demonstrat-
ing the efficiency of Yamazaki’s chemistry in the presence of both o-nitro and
carboxylic acid groups. Compound 4 was then converted to 5 via p-TsOH
catalyzed esterfication. Compound 5 may then be used to produce 6 or 7.
Compound 6 was generated via NaBH4 of 5 in 93% yield while reductive ammi-
nation using NaCNBH3/NH4OAc in MeOH produced 7 in 30% yield.
In conclusion, a-methyl photolabile protecting groups suitable for pro-
tecting both amino and hydroxy containing molecules have been synthesized
from a common, inexpensive starting material in good yields.
Scheme 1.

Synthesis of Photolabile a-Methyl Nitrobenzyl Compounds
2383
Scheme 2.
EXPERIMENTAL SECTION
General
All 1H NMR and 13C NMR were taken on Varian 400 and 500 MHz spectro-
meters. Mass spectra were taken at Numega Resonance Labs, San Diego, CA.
MeCN was HPLC grade (Fisher Scientific). Elemental analysis was carried
out by Desert Analytics, Tucson AZ.
Synthetic Procedures
4-Ethyl-3-nitro-benzoic acid (3). Fuming HNO3 (50 mL) was placed in
a round-bottomed flask and cooled to 2108C using a slurry of dry ice/
saturated NaCl solution and ice. 4-Acetyl-benzoic acid (10 g, 67 mmol),
Fluka, was slowly added over the course of 30 min. After an additional

2384
Salerno and Cleaves
30 min stirring the reaction was completed. A fritted funnel was placed in a
filter flask. Finely crushed ice (200 g) was placed on a fritted funnel and the
acid solution poured over it. The ice was vigorously stirred followed by
the application of vacuum to the filter flask. The precipitated ice/solid mixture
was filtered until the ice had melted. The remaining white solid was
then washed with 100 mL of H2O. The solid was dried under vacuum then
crystallized from EtOAc/hexane to yield 12.3 g of 3 as white crystals. Yield:
95%. M.p. ¼ 145–1468C. 1H NMR (500 MHz, d6-DMSO):
d 8.26
(d, J ¼ 1.5 Hz, 1H), 8.02 (dd, J ¼ 1.5 Hz, J ¼ 8 Hz, 1H), 7.50 (d, J ¼ 8.5 Hz,
1H), 2.78 (q, J ¼ 15Hz, 2H), 1.14 (t, J ¼ 15Hz, 3H). 13C NMR (500 MHz,
d6-DMSO): d 165.6, 148.8, 142.7, 133.5, 131.8, 130.2, 125.1, 25.6, 14.5. ESI
MS: m/z calcd for C9H9NO4 (M–1) ¼ 194, found 194. Anal. Calcd. for
C9H9NO4 (%): C, 55.38; H, 4.65; N, 7.17; O, 32.79; Found: C, 55.21; H, 4.50.
4-Acetyl-3-nitro-benzoic acid (4). Compound 3 (10 g, 51.3 mmol) was
added to 44 mL of MeCN. A 0.1 M solution of CrO3 in MeCN was prepared
by pulverizing 1 g of CrO3 solid using a mortar and pestle followed by dissol-
ving in 100 mL acetonitrile with the assistance of mild heating (ꢀ508C). Over
the course of 3 hr, 15.5 mL of the 0.1 M CrO3/MeCN solution was slowly
added along with H5IO6 (35 g, 154 mmol) accompanied by vigorous stirring.
After 12 hr an additional 3.9 mL of 0.1 M CrO3 solution was added along with
11.7 g of H5IO6. The solution was allowed to stir for an additional 12 hr after
which the solvent was decanted and then removed under reduced pressure.
The remaining solid was suspended in 500 mL EtOAc and extracted with
H2O, then with a 5% sodium thiosulfate solution. The organic layer was
dried with NaSO4 and the solvent evaporated. The remaining solid was crys-
tallized using EtOAc/hexane to result in 9.1 g of 4 as pale yellow crystals.
1
Yield: 85%. M.p. ¼ 1628C. H NMR (500 MHz, d6-DMSO): d 8.33 (s, 1H),
8.17 (d, J ¼ 8 Hz, 1H), 7.69 (d, J ¼ 7.5 Hz), 2.50 (s, 3H). 13C NMR
(500 MHz, d6-DMSO): d 199.7, 165.2, 145.8, 140.0, 135, 133.9, 128.7,
125.1, 30.30. ESI MS: m/z calcd for C9H7NO5 (M–1) ¼ 208, found 208.
Anal. Calcd. for C9H7NO5 (%): C, 51.68; H, 3.37; N, 6.70; O, 38.25;
Found: C, 51.86; H, 3.56.
4-Acetyl-3-nitro-benzoic acid ethyl ester (5). Compound 4 (8.9 g,
42.8 mmol) was added to 250 mL anhydrous EtOH along with p-toluene-
sulfonic acid monohydrate (16.3 g, 85.6 mmol). The solution was refluxed
for 4 hr under nitrogen followed by removal of the EtOH under reduced press-
ure. The remaining solid was dissolved in ethyl acetate then extracted with
H2O, then 5% NaCO3H. The organic layer was dried with NaSO4, filtered,
and the solvent evaporated to give 9.5 g of 5 as a waxy yellow white solid.
Yield: 93%. M.p. ¼ 57–608C: 1H NMR (400 MHz, CDCl3): d 8.70
(d, J ¼ 1.6 Hz, 1H), 8.35 (dd, J ¼ 1.6 Hz, J ¼ 8 Hz, 1H), 7.49 (d, J ¼ 8 Hz,
1 H), 4.45 (q, J ¼ 7.2 Hz, 2H), 2.58 (s, 3H), 1.44 (t, J ¼ 7.2 Hz, 3H). 13C

Synthesis of Photolabile a-Methyl Nitrobenzyl Compounds
2385
NMR (400 MHz, CDCl3): d 198.8, 163.4, 145.5, 150.0, 134.8, 132.8, 127.5,
124.2, 62.2, 30.2, 14.3. Anal. Calcd. for C11H11NO5 (%): C, 55.70; H, 4.67;
N, 5.90; O, 33.72; Found: C, 55.98; H, 4.62; N, 5.87.
4-(1-Hydroxy-ethyl)-3-nitro-benzoic acid ethyl ester (6). Compound 5
(5.0 g, 0.021 mmol) was dissolved in 200 mL of anhydrous EtOH. NaBH4
(0.93 g, 25.2 mmol) was added and the solution heated to 608C for 90 min.
The solvent was then removed under reduced pressure and the remaining
solid dissolved in EtOAc, which was then extracted with brine and
H2O. The organic layer was dried with NaSO4, filtered, and the solvent
removed under reduced pressure to result in 4.65 g of 6 as a waxy white
1
solid. Yield: 93%. M.p. ¼ 51–538C: H NMR (500 MHz, CDCl3): d 8.58
(d, J ¼ 1.5 Hz, 1H), 8.28 (dd, J ¼ 8.5 Hz, 1H), 7.96 (d, J ¼ 8 Hz, 1H), 5.48
(q, J ¼ 6 Hz, 1H), 4.42 (q, J ¼ 7.5 Hz, 2H), 1.58 (d, J ¼ 6 Hz, 3H), 1.42
(t, 3 H, J ¼ 7 Hz): 13C NMR (500 MHz, CDCl3): d 164.4, 147.5, 145.6,
134.0, 130.6, 128.0, 125.4, 65.7, 63.1, 24.7, 14.5. ESI MS: m/z calcd for
C11H13NO5 (M 2 1) ¼ 238, found 238. Anal. Calcd. for C11H12NO5 (%):
C, 55.46; H, 5.08; N, 5.88; O, 33.58; Found: C, 54.90; H, 5.15; N, 6.02.
4-(1-Amino-ethyl)-3-nitro-benzoic acid ethyl ester (7). Compound
5 (4 g, 16.9 mmol) was dissolved in 160 mL of anhydrous MeOH. Ammonium
acetate (19.5 g, 0.25 mmol), .99.9% Aldrich, was added followed by
NaCNBH3 (4.7 g, 76 mmol). The solution was refluxed under nitrogen for
7 hr followed by cooling and addition of 340 mL of 0.5 M NaHCO3. The
solution was then stirred for 24 hr followed by acidification to pH ꢀ3 using
an aqueous 5% HCl solution. The solution was then extracted with CHCl3,
the aqueous layer separated and brought to ꢀ pH 8.0 with 0.5 M NaHCO3.
The solution was then extracted 3 ꢀ with chloroform. The chloroform layer
was dried with NaSO4, filtered, and the solvent evaporated to result in
1
1.22 g of 7 as a light yellow oil. Yield: 30% H NMR (500 MHz, CDCl3): d
8.42 (d, J ¼ 2.0 Hz, 1H), 8.24 (dd, J ¼ 8.5 Hz, 1H), 7.92 (d, J ¼ 8 Hz, 1H),
4.65 (q, J ¼ 6.5 Hz, 1H), 4.42 (q, J ¼ 7.0 Hz, 2H), 1.87 (2H), 1.47
(d, J ¼ 6.5 Hz, 3H), 1.41 (t, 3 H, J ¼ 7 Hz). Anal. Calcd. for C11H14N2O4
(%): C, 55.46; H, 5.92; N, 11.76; O, 26.86; Found: C, 54.44; H, 6.03;
N, 11.37.
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Received in the USA March 2, 2004