Synthesis, separation and crystal structures of E and Z isomers of 3-(2,5-dimethoxyphenyl)-2-(4-methoxyphenyl)acrylic acid

Article abstract of DOI:10.1007/s10870-007-9288-4

Synthesis, separation and X-ray crystal structures of E and Z isomers of 3-(2,5-dimethoxyphenyl)-2-(4-methoxyphenyl)acrylic acid are reported. Separation of E and Z isomers from a 1:1 mixture has been carried out by selective acidification of their sodium

Full text of DOI:10.1007/s10870-007-9288-4

J Chem Crystallogr (2008) 38:189–194
DOI 10.1007/s10870-007-9288-4
ORIGINAL RESEARCH
Synthesis, Separation and Crystal Structures of E and Z Isomers
of 3-(2,5-Dimethoxyphenyl)-2-(4-Methoxyphenyl)Acrylic Acid
Bala Chandra Chenna Æ Bidhan A. Shinkre Æ Shweta Patel Æ Samuel B. Owens Jr. Æ
Gary M. Gray Æ Sadanandan E. Velu
Received: 13 October 2006 / Accepted: 16 October 2007 / Published online: 10 November 2007
Ó Springer Science+Business Media, LLC 2007
Abstract Synthesis, separation and X-ray crystal struc-
tures of E and Z isomers of 3-(2,5-dimethoxyphenyl)-2-(4-
methoxyphenyl)acrylic acid are reported. Separation of
E and Z isomers from a 1:1 mixture has been carried out
by selective acidification of their sodium salts carefully
controlling the pH of the solution. The structures of E
and Z isomers were confirmed by determining crystal
structures of these isomers using single crystal X-ray
diffraction. The E isomer crystallizes in the P21/c
participates in secretion and anchoring many of these cell
wall proteins by a mechanism conserved in almost the
entire class of gram-positive bacteria [1, 2]. Sortase A,
because of its control over the cellular location of multiple
virulence factors, is an attractive potential target for the
development of antibacterial drugs [1–3]. Based on a hit
from random screening, Oh et al. have recently reported a
novel small-molecule inhibitor (1), a diarylacrylonitrile
derivative for S. aureus SrtA with IC50 value of 9.2 lM
in vitro [4]. High resolution X-ray crystal structures of
S. aureus SrtA and its complex with natural substrate
(LPETG) have recently been obtained by Narayana and
coworkers [5, 6]. As a part of a project aimed at developing
inhibitors of SrtA, we were interested in making structural
modifications to the identified lead inhibitor 1 (Fig. 1).
Inhibitor 1 has a Z diarylacrylonitrile ring system. The
aryl ring (ring A) close to the CN group has a methoxy
group at the 4-position and the second aryl ring (ring B)
has two methoxy groups at the 20- and 50-positions. By
designing molecules that are variations of this template, we
hoped to discover new compounds that will inhibit SrtA
with higher binding affinities. Molecular modeling and
‘DOCKing’ efforts, using the crystal structure of SrtA,
helped us position this inhibitor in the enzyme active site.
Our computer model of inhibitor 1 in the enzyme active
site has revealed a set of interactions that could be
exploited for the design of new inhibitors. One of the key
interactions is that of the linear CN group present in
inhibitor 1 with the guanidine side chain of Arg197 moiety
in the active site. We propose to modify this CN group to a
more polar COOH group which is expected to result in a
salt bridge interaction with Arg197 side chain. This will
enhance the binding of the inhibitor in the enzyme active
site. With this goal we proposed to make the target car-
boxylic acid derivative 2. In this manuscript, we present the
˚
space group with a = 11.493(2) A, b = 5.5456(11) A,
˚
˚
c = 24.900(5) A, a = 90°, b = 92.36(3)°, c = 90°, Z = 4.
The Z isomer crystallizes in the P21/c space group with
˚
˚
˚
a = 10.192(2) A, b = 12.893(3) A, c = 13.948(3) A,
a = 90°, b = 92.18(3)°, c = 90°, Z = 4. Details of the
synthesis and structural characterization and X-ray crystal
structure determination of the title compounds are
presented.
Keywords E and Z isomers ꢀ Diarylacrylic acid ꢀ
X-ray ꢀ Single crystal structures
Introduction
Gram-positive bacteria such as staphylococci and strepto-
cocci are endowed with a multitude of cell-wall anchored
proteins that serve as an interface between the microbe
and its host. Sortase A (SrtA), a cysteine transpeptidase,
B. C. Chenna ꢀ B. A. Shinkre ꢀ S. Patel ꢀ
S. B. Owens Jr. ꢀ G. M. Gray ꢀ S. E. Velu (&)
Department of Chemistry, University of Alabama at
Birmingham, 901 14th Street South, Birmingham,
AL 35294-1240, USA
e-mail: svelu@uab.edu
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J Chem Crystallogr (2008) 38:189–194
H3CO
140 °C for 24 h. TLC (EtOAc/hexanes, 1:1) indicated the
completion of the reaction. The reaction mixture was
allowed to attain room temperature and acetic anhydride
was completely removed under reduced pressure using a
rotary evaporator. The residue obtained was stirred with 1N
NaOH solution (75 mL) for 12 h. The reaction mixture was
then diluted with water (75 mL) and washed with chloro-
form (39 30 mL). The aqueous layer was cooled to 0 °C
and acidified by slow addition of conc. HCl. The resulting
solid was filtered under suction, washed with water and
dried. This crude product was recrystallized from a mixture
of EtOAc and hexanes (1:1) to afford the E isomer of 3-
(2,5-dimethoxyphenyl)-2-(4-methoxyphenyl)acrylic acid, 3
N
A
C
OCH3
B
H3CO
1
Fig. 1 (Z)-3-(2,5-dimethoxyphenyl)-2-(4-methoxyphenyl)acrylo-
nitrile (1)
H3CO
H3CO
O
O
OH
OH
H3CO
OCH3
1
(2.5 g, 66%); m.p. 195 °C. H NMR (CDCl3) d 3.32 (s,
OCH3
H3CO
3H), 3.80 (s, 3H), 3.83 (s, 3H), 6.35 (s, 1H), 6.76–6.79 (m,
2H), 6.87–6.97 (m, 2H), 7.14–7.22 (m, 2H) and 8.25 (s,
1H); 13C NMR (CDCl3) d 55.3, 55.5, 56.4, 112.1, 114.3,
114.5, 117.8, 124.0, 127.9, 131.1, 131.5, 137.0, 152.7,
2
3
Fig. 2 Z and E isomers of 3-(2,5-dimethoxyphenyl)-2-(4-methoxy-
phenyl)acrylic acid
153.2, 159.4 and 173.6; IR (neat): m 2,459–3,329 cm-1
;
1,677 cm-1; MS (ES+) m/z 313 (M–H). Anal. Calcd for
C18H18O5: C, 68.78; H, 5.77. Found: C, 68.63; H, 5.82.
synthesis and X-ray crystals structures of the target car-
boxylic acid derivative 2 and its geometrical isomer 3
(Fig. 2).
(Z)-3-(2,5-Dimethoxyphenyl)-2-
(4-Methoxyphenyl)Acrylic Acid (2)
Experimental Section
Synthesis
The E isomer of the acid, 3 (1.2 g, 3.8 mmol) was dis-
solved in acetonitrile (100 mL) and was irradiated with UV
light (k = 254 nM, Rayonet RPR-2000 reactor) for 4 h.
Melting points were determined using an Electrothermal
9100 apparatus and are uncorrected. IR spectra were taken
with Brucker Vector-22 and Bomen MB-104 instruments.
1
TLC (CHCl3/MeOH, 9:1) and H NMR indicated that the
isomerization is complete and it is a 1:1 mixture of E–Z
isomers. The solvent was completely removed under
reduced pressure to obtain the E–Z mixture. The E–Z
mixture (750 mg, 2.39 mmol) was dissolved in 1N NaOH
(80 mL) and stirred for 30 min. The insoluble impurities
were filtered off. The filtrate was acidified by careful drop
wise addition of glacial acetic acid (The pH was monitored
using a pH meter). A light yellow solid was precipitated at
the pH of 4.8–5.0. This was filtered off and dried to furnish
285 mg (38%) of the E isomer (3). The filtrate was then
further acidified by careful drop wise addition of 6N HCl
until a pH of 3.3–3.5. An off-white solid precipitated at
this pH. This was filtered under suction and dried to furnish
the Z isomer of 3-(2,5-dimethoxyphenyl)-2-(4-methoxy-
1
All H and 13C NMR spectra were recorded on a Brucker
300 MHz spectrometer using TMS as internal standard.
The values of chemical shifts (d) are given in ppm and
coupling constants (J) in Hz. Elemental analyses were
performed by Atlantic Microlab, Norcross, Georgia and the
results are within 0.4% of theoretical values. Reactions
were monitored by TLC (Whatmann, Si gel, UV 254,
25 lM plates). The solvents used for reactions were pur-
chased as anhydrous in Sure-SealTM bottles from Aldrich
chemical company. The chemicals used are purchased from
Aldrich, Lancaster or Fisher chemical companies and used
as received.
1
phenyl)acrylic acid, 2 (299 mg, 40%); m.p. 102 °C; H
(E)-3-(2,5-Dimethoxyphenyl)-2-
(4-Methoxyphenyl)Acrylic acid (3)
NMR (CDCl3) d 3.73 (s, 3H), 3.78 (s, 3H), 3.84 (s, 3H),
6.80–6.83 (m, 2H), 6.86–6.94 (m, 2H), 6.95–7.0 (m, 1H),
7.14 (s, 1H) and 7.39–7.45 (m, 2H); 13C NMR (CDCl3) d
55.5, 55.8, 55.9, 111.9, 114.1, 114.7, 115.2, 125.7, 128.6,
128.9, 129.9, 134.1, 151.6, 153.4, 159.8 and 175.5; IR
(neat): m 2,452–3,312 cm-1; 1,677 cm-1; MS (ES+) m/z
313 (M–H). Anal. Calcd for C18H18O5: C, 68.78; H, 5.77.
Found: C, 68.40; H, 5.76.
To a solution of 4-methoxyphenylacetic acid, 4 (2 g,
12 mmol) in acetic anhydride (7 mL) and 2,5-dimethoxy-
benzaldehyde, 5 (2 g, 12 mmol) and Et3N (1.4 mL) were
added and the resulting mixture was stirred at room tem-
perature for 5 min. The reaction mixture was then heated at
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J Chem Crystallogr (2008) 38:189–194
X-ray Data Collection and Solution
191
All crystallographic calculations were performed with
the Siemens SHELXTL-PC program package [8]. All
heavy atom positions were located using Direct Methods
with carboxylic acid hydrogen atoms located in difference
Fourier maps. Full matrix refinement of the positional and
anisotropic thermal parameters for all these atoms versus
F2 was carried out. All other hydrogen atoms were placed
in calculated positions with the appropriate molecular
A suitable single crystal of each compound was glued on a
glass fiber with epoxy and aligned upon an Enraf Nonius
CAD4 single crystal diffractometer under aerobic condi-
tions. Standard peak search and automatic indexing
routines followed by least squares fits of 25 accurately
centered reflections resulted in accurate unit cell parame-
ters for each. The space groups of the crystals were
assigned on the basis of systematic absences and intensity
statistics. All data collection was carried out using the
CAD4-PC software [7], and details of the data collections
are given in Table 1. The analytical scattering factors of
the complex were corrected for both Df0 and iDf@ compo-
nents of anomalous dispersion. All data were corrected for
the effects of absorption and for Lorentz and polarization
effects.
˚
geometry and the d(C–H) = 0.96 A. The isotropic thermal
parameter associated with each hydrogen atom was fixed
equal to 1.2 times the Ueq of the atom to which it was
bound. Selected bond lengths and angles for complexes 2
through 3 are given in Table 2; selected dihedral angles
and torsion angles are given in Table 3. Crystallographic
data for all complexes have been deposited with the
Cambridge Crystallographic Database (2: CCDC 620355;
3: CCDC 620356).
Table 1 Crystal and structure refinement data for compounds 2 and 3
2
3
Empirical formula
CCDC deposit no.
Formula weight
Temperature
C21H21O5
620355
C18H18O5
620356
353.38
314.32
293(2) K
293(2) K
˚
˚
0.71073 A
Wavelength
0.71073 A
Monoclinic
P21/c
Crystal system
Space group
Monoclinic
P21/c
˚
a = 11.493(2) A
˚
a = 10.192(2) A
Unit cell dimensions
˚
b = 12.893(3) A
˚
b = 5.5456(11) A
˚
c = 13.948(3) A
˚
c = 24.900(5) A
b = 92.18(3)°
1831.6(6) A
b = 92.36(3)°
1585.6(5) A
3
˚
3
˚
Volume
Z
4
4
Density (calculated)
Absorption coefficient
F(000)
1.175 mg/m3
0.085 mm-1
685
1.317 mg/m3
0.096 mm-1
664
Crystal size
0.4 9 0.5 9 0.8 mm3
0.2 9 0.2 9 0.7 mm3
h range for data collection
Index ranges
2.00–22.46°
-10 B h B 10, -13 B k B 0, -14 B l B 1
2.36–22.48°
-12 B h B 12, -5 B k B 0, -1 B l B 26
Reflections collected
Independent reflections
Completeness to h = 22.48°
Absorption correction
Refinement method
Data/restraints/parameters
Goodness-of-fit on F2
Final R indices [I [ 2r(I)]
R indices (all data)
Extinction coefficient
Largest diff. peak and hole
2717
2222
2379 [R(int) = 0.0340]
100.00%
2062 [R(int) = 0.0565]
99.90%
None
Full-matrix least-squares on F2
None
Full-matrix least-squares on F2
2379/0/244
2062/0/216
1.03
1.002
R1 = 0.0453, wR2 = 0.1200
R1 = 0.0776, wR2 = 0.1373
0.015(2)
R1 = 0.0662, wR2 = 0.1565
R1 = 0.1639, wR2 = 0.1913
0.0023(17)
-3
-3
˚
0.189 and -0.185 e A
˚
0.207 and -0.188 e A
123

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J Chem Crystallogr (2008) 38:189–194
˚
the isomerization of the product from an E to Z form would
be a necessary step. We used a modified literature proce-
dure [11] to make the E isomer (3) by the condensation of
4-methoxyphenyl acetic acid (4) and 2,5-dimethoxybenz-
aldehyde (5) in the presence of triethyl amine in acetic
anhydride (Scheme 1).
Table 2 Selected bond lengths (A) and angles (°) for 2 and 3
2
3
C(3)–C(4)
1.473(3)
1.294(3)
1.497(3)
1.332(3)
1.486(3)
1.226(3)
125.2(2)
121.9(2)
115.3(2)
119.5(2)
115.3(2)
127.2(2)
122.0(2)
121.4(2)
121.9(2)
119.3(2)
122.8(2)
1.469(6)
1.305(5)
1.485(6)
1.340(6)
1.475(6)
1.227(5)
124.3(4)
121.3(4)
116.5(5)
119.3(4)
116.4(4)
129.6(4)
118.8(4)
121.5(4)
121.9(5)
123.5(5)
122.3(5)
C(1)–O(1)
C(1)–C(2)
C(2)–C(3)
H3CO
CHO
C(2)–C(10)
H3CO
Et3N
C(1)–O(2)
+
COOH
Ac2O
140oC
OCH3
C(3)–C(2)–C(10)
O(2)–C(1)–C(2)
O(1)–C(1)–C(2)
C(3)–C(2)–C(1)
C(10)–C(2)–C(1)
C(2)–C(3)–C(4)
C(5)–C(4)–C(3)
C(11)–C(10)–C(2)
C(15)–C(10)–C(2)
C(9)–C(4)–C(3)
O(2)–C(1)–O(1)
4
5
H3CO
H3CO
H3CO
O
O
OH
OH
UV irradiation
220nM
OCH3
OCH3
H3CO
3
2
Scheme 1 Synthesis of E and Z isomers of 3-(2,5-dimethoxyphenyl)-
2-(4-methoxyphenyl)acrylic acid
This reaction resulted in the formation of only E isomer
(3) in excellent yield. A solution of 3 in acetonitrile was
irradiated with UV light (k = 254 nM, Rayonet RPR-2000
reactor) for 4 h to obtain a 1:1 mixture of E and Z isomers
of 3-(2,5-dimethoxyphenyl)-2-(4-methoxyphenyl)acrylic
acid. This mixture was converted to corresponding sodium
salts by dissolving in 1N NaOH solution. This solution was
then acidified with acetic acid by carefully controlling the
pH of the solution by using a pH meter. The E isomer (3)
precipitated out at the pH of 4.8–5.0. This was filtered off
and the filtrate was further acidified with 6N HCl. The Z
isomer (2) precipitated out at the pH of 3.3–3.5. In order
to confirm the stereochemistry of the isomers, they were
crystallized by slow evaporation from the solvent combi-
nation of benzene and hexanes and structures were
determined by X-ray crystallography.
Table 3 Selected dihedral angles (°) and torsion angles (°) for
compounds 2 and 3
2
3
C(4)–C(9) ring, C(10)–C(15) ring
C(10)–C(15) ring, alkenea
C(4)–C(9) ring, alkenea
Alkenea, carboxylic acidb
C(2)–C(3)–C(4)–C(5)
a
53.87
16.62
37.28
66.85
70.37
73.88
19.00
6.74
-37.82
161.40
Alkene defined by plane through C(2)–C(3)–H(3)
b
Carboxylic acid defined by plane through O(2)–C(1)–O(1)
Results and Discussion
Synthesis
X-ray Crystal Structures
Our initial attempt to make compound 2 was by directly
hydrolyzing the CN group present in inhibitor 1. Inhibitor 1
was prepared according to the reported literature procedure
[4]. Attempts were made to hydrolyze the cyanide group
present in inhibitor 1 to corresponding carboxylic acid by
treatment with con HCl [9]. However, this reaction did not
yield the expected product possibly because the staring
material underwent polymerization under strongly acidic
conditions. Basic hydrolytic conditions were also attemp-
ted for this transformation without significant success.
We then decided to make the target compound 2 by a
more traditional method of condensing 4-methoxyphenyl
acetic acid with 2,5-dimethoxybenzaldehyde in the pres-
ence of a base [10]. The literature indicates that this
reaction leads only to the formation of the E isomer (3). So,
The crystal structures of 2 and 3 exhibit a number of
features that differ from one another as shown in Figs. 3
and 4.
However, one important feature that the two compounds
share is the presence of intermolecular hydrogen bonding
between the carboxylic acid groups in adjacent molecules
in the crystal lattice (Figs. 5 and 6). In contrast, there is no
intramolecular hydrogen bonding between the carboxylate
groups and the adjacent methoxy groups in either com-
pound that would possibly affect the conformation of their
enzymatic binding sites.
When investigating the relative conformations of the
two compounds, several differences are seen. Table 3 gives
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J Chem Crystallogr (2008) 38:189–194
193
Fig. 3 ORTEP [13] drawing of the molecular structure of the Z
Isomer, 2. Thermal ellipsoids are drawn at 50% and nonspecific
hydrogens are omitted for clarity
Fig. 5 ORTEP [13] Packing Diagram of the molecular structure of
the Z Isomer, 2, showing intermolecular hydrogen bonding. Thermal
ellipsoids are drawn at 50%
selected dihedral angles and torsion angles for specific
sections of each molecule. From this data, one can see that
the E isomer (3) is considerably more sterically hindered
by the interaction between the two rings causing them to
twist out of plane with one another. This is demonstrated
by the 70.37° dihedral angle between the planes of the two
rings as well as the torsion angle of 161.40° about the
C(3)–C(4) bond. This conformation also shows little or no
interaction between the dimethoxy ring and the carboxylate
group which results in the alkene double bond and the
carboxylate group being coplanar (dihedral angle = 6.74°)
and thus conjugated. In contrast, the Z isomer (2) is much
more planar overall. However, increased interaction
between the dimethoxy ring and the carboxylate group
results in the carboxylate group twisting out of plane
and thus lessens the amount of conjugation (dihedral
angle = 66.85°).
Fig. 4 ORTEP [13] drawing of the molecular structure of the E
Isomer, 3. Thermal ellipsoids are drawn at 50% and nonspecific
hydrogens are omitted for clarity
123

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J Chem Crystallogr (2008) 38:189–194
One final point of interest is the manner in which these
compounds stack in the crystal lattice with respect to the
two rings. The Z isomer (2) exhibits p–p stacking (Fig. 7)
between adjacent molecules in the unit cell whereas this is
not seen in the E isomer (3). The interplanar distance
˚
between interacting rings of 3.423 A is consistent with
previous work done on purine rings by Bugg et al., who
found the distances of interacting rings in stacked struc-
˚
tures to be 3.879 A [12]. The presence of this interaction in
the Z isomer (2) is likely due to the increased planarity of
the molecule, which allows for the rings to orient them-
selves on one another to stack throughout the lattice. The E
isomer (3) has the rings twisted much more out of plane
with one another preventing adjacent molecules from p–p
stacking.
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Fig. 6 ORTEP [13] Packing Diagram of the molecular structure of
the E Isomer, 3, showing intermolecular hydrogen bonding. Thermal
ellipsoids are drawn at 50%
`
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123