Structures of three chalcones derived from 6-methoxy-2-naphthaldehyde

Article abstract of DOI:10.1007/s10870-008-9446-3

In the molecular structures of three new structurally related chalcone derivatives, namely (2E)-1-(2-hydroxyphenyl)-3-(6-methoxy-2-naphthyl)prop-2-en- 1-one, C₂₀H₁₆O₃, I, (2E)-1-(2-chloropyridin-4- yl)-3-(6-methoxy-2-napht

Full text of DOI:10.1007/s10870-008-9446-3

J Chem Crystallogr (2009) 39:157–162
DOI 10.1007/s10870-008-9446-3
ORIGINAL PAPER
Structures of Three Chalcones Derived from
6-Methoxy-2-naphthaldehyde
Jerry P. Jasinski Æ Ray J. Butcher Æ
Anil N. Mayekar Æ H. S. Yathirajan Æ
B. Narayana
Received: 9 March 2008 / Accepted: 10 July 2008 / Published online: 25 July 2008
ꢀ Springer Science+Business Media, LLC 2008
Abstract In the molecular structures of three new
structurally related chalcone derivatives, namely (2E)-1-(2-
hydroxyphenyl)-3-(6-methoxy-2-naphthyl)prop-2-en-1-one,
C20H16O3, I, (2E)-1-(2-chloropyridin-4-yl)-3-(6-methoxy-
2-naphthyl)prop-2-en-1-one, C19H14ClNO2, II, and (2E)-3-
(6-methoxy-2-naphthyl)-1-pyridin-4-ylprop-2-en-1-one,
III, C19H15NO2, the configuration of the keto group is syn
with respect to the olefinic double bond. In all three struc-
tures the molecules pack with weak intermolecular C–HÁÁÁO
interactions utilizing both the methoxy and keto oxygen’s in
I, the methoxy oxygen in II and the keto oxygen in III. These
interactions link the molecules into chains diagonally along
the (011) plane of the unit cell in I and III and along the (010)
plane in II. The dihedral angle between the phenyl and
2-napthyl rings in I is 31.7(3)ꢁ. In II and III the dihedral
angle between the pyridyl and 2-naphthyl rings is 14.4(9)ꢁ
and 1.8(9)ꢁ, respectively. C–HÁÁÁO hydrogen bonding inter-
actions influence these twist angles of these rings in I–III
while weak p–p stacking interactions between naphthyl
rings in I and III and also between pyridyl and naphthyl rings
in II help stabilize crystal packing. [I: P21/c, a = 7.6635(4)
˚
˚
˚
A, b = 11.8047(6) A, c = 16.7584(7) A, b = 99.271(5)ꢁ,
3
V = 1496.25(13) A ; II: Pbca, a = 14.1424(4) A, b =
3
6.0957(2) A, c = 33.1458(11) A, V = 2857.43(16) A ; III:
˚
˚
˚
˚
˚
˚
P21/c, a = 11.5155(4) A, b = 6.0020(2) A, c = 22.4645(8)
˚
3
˚
˚
A, b = 103.002(4)ꢁ, V = 1512.85(9) A ].
Keywords Chalcones Á Crystal structure Á
Hydrogen bonds Á Naphthyl Á Pyridyl Á Phenyl Á
Syn Á Trans
Introduction
The present investigation is a continuation of our broad
programme work on the synthesis and structural study of
chalcones and its derivatives and to understand the geo-
metrical features and the underlying intermolecular
interactions which hold the assembly of molecules in the
crystalline lattice. Chalcones exhibit various biological
activities like insecticidal, antimicrobial, antichorniviral,
antipicorniviral and bacteriostatic properties. Azachal-
cones, the derivatives of chalcones with an annular nitrogen
atom in the phenyl ring, were reported to have a wide range
of biological activities, such as antibacterial, antitubercu-
lostatic and anti-inflammatory. The 4-azachalcones and
their N-alkyl derivatives were reported to be the most potent
of the chalcone series as inhibitors of myeloperoxidase
release from rat polymorphonuclear leukocytes and
microtubule polymerization inhibitors which bind to the
colchicines-binding site of microtubules [1–5]. We report
here the crystal structures of three chalcones derived from
6-methoxy-2-naphthaldehyde, namely, (2E)-1-(2-hydroxy-
phenyl)-3-(6-methoxy-2-naphthyl)prop-2-en-1-one, C20H16O3,
J. P. Jasinski (&)
Department of Chemistry, Keene State College, 229 Main Street,
Keene, NH 03435-2001, USA
e-mail: jjasinski@keene.edu
R. J. Butcher
Department of Chemistry, Howard University,
525 College Street NW, Washington, DC 20059, USA
A. N. Mayekar Á H. S. Yathirajan
Department of Studies in Chemistry, University of Mysore,
Manasagangotri, Mysore 570 006, India
B. Narayana
Department of Studies in Chemistry, Mangalore University,
Mangalagngotri, Mangalore 574 199, India
123

158
J Chem Crystallogr (2009) 39:157–162
I, (2E)-3-(6-methoxy-2-naphthyl)-1-pyridin-4-ylprop-2-en-
1-one, II, C19H15NO2, and (2E)-1-(2-chloropyridin-4-yl)-3-
(6-methoxy-2-naphthyl)prop-2-en-1-one, C19H14ClNO2, III.
4.28(4.33), 437–439 K, THF:Acetonitrile (1:1); Chalcone
III: C19H15NO2, C: 78.80(78.87); H: 5.18(5.23); N:4.39
(4.44), 450–452 K, THF: acetonitrile (1:1). The elemental
analysis was measured using the instrument ELEMENTAR
VARIO EL III, Hanau, Germany.
Experimental
Synthesis of compounds I–III were carried out by adding
to a mixture of 6-methoxy-2-naphthaldehyde (0.01 mol)
and substituted ethanones (0.01 mol) in 40 mL of ethyl
alcohol, 10–15 mL of 25% KOH drop wise with vigorous
stirring for about 6–10 h. The crude products obtained in
all three cases (Fig. 1) were filtered and recrystallized. The
molecular formulae, compositions (Calculated), melting
points and recrystallization solvents of each of the three
chalcones are: Chalcone I: C20H16O3, C: 78.86(78.93); H:
5.26(5.30); 371–373 K, Ethyl acetate; Chalcone II:
C19H14ClNO2, C: 70.39(70.48); H: 4.30(4.36.00);N:
Structure Determination and Refinement
X-ray analysis including data collection, cell refinement and
data reduction was carried out with an Oxford Diffraction
Gemini CCD using the CrysAlisPro software package [6].
Non-H atoms were refined anisotropically by full-matrix
least-squares on F2. Structure solution and refinement was
completed with SHELXS97 [7] and SHELXL97 [7] and
molecular graphics were carried out with SHELXTL [8]. In
all three compounds [I, II and III] the H atoms were placed
in their geometrically calculated places and refined using a
˚
riding model with C–H = 0.95 A, and Uiso(H) = 1.18–
1.21Ueq(C) for aromatic, CH3 (AFIX 137 in SHELXTL)
and CH. This worked well for normal C–H bonds since
most of the geometric parameters for these molecules are
very similar to standard values [9]. In I the hydroxyl
hydrogen, H10, was located in a difference map and then
˚
refined using a riding model with O–H = 0.84 A, and with
U
iso(H) = 1.19Ueq(O) as this gives a true location of the
atom bonded to a sp3 hybridized oxygen (Table 1).
Results and Discussion
In the title compounds I (C20H16O3), II (C19H15NO2), and
III (C19H14ClNO2), the configuration of the keto group is
syn with respect to the olefinic double bond [C7–C8–C(9)–
C10 (II, III) = + 10.3(3); -0.69(19), C8–C9–C10–C11
(I) = - 13.68(16)ꢁ] (Figs. 2–4). The dihedral angle
between the phenyl and 2-naphthyl rings in I is 31.7(3)ꢁ.
The six-membered pyridyl ring in II is disordered with the
slightly less predominant component (N–C3A–C2A–C1–
C5A–C4A) forming a distorted chair configuration with
Cremer & Pople [10] puckering parameters Q, h and u of
˚
0.053(1)A, 23.9(7)ꢁ and 314.954(5)ꢁ, respectively. In II
and III the dihedral angle between the pyridyl (A com-
ponent in II) and 2-naphthyl rings is 14.4(9)ꢁ and 1.8(6)ꢁ
respectively. Geometric parameters are in normal ranges
[9] (Table 2). Among the three compounds, weak intra-
molecular O–HÁÁÁO interactions are only seen in I (Fig. 2).
In all three structures the molecules pack with weak
intermolecular C–HÁÁÁO interactions utilizing both the
methoxy and keto oxygen’s in I, the methoxy oxygen in II
and the keto oxygen in III, respectively (Table 3). These
link the molecules into chains diagonally along the (011)
plane of the unit cell in I and III and along the (101) plane
Fig. 1 Scheme for (I), (II) and (III)
123

J Chem Crystallogr (2009) 39:157–162
159
Table 1 Crystal and Experimental Data for I, II and III
I
II
III
Formula
C20H16O3
C19H15NO2
289.32
C19H14ClNO2
323.76
Formula weight
Crystal color, habit
Crystal size (mm)
Crystal System
Space Group
304.33
Yellow-orange, chunk
Colorless, prism
0.51 9 0.45 9 0.22
Orthorhombic
Pbca
Colorless, prism
0.48 9 0.37 9 0.25
0.49 9 0.44 9 0.31
Monoclinic
P 21/c
Monoclinic
P 21/c
Temperature (K)
200 (2)
200 (2)
200 (2)
11.5155 (4)
6.0020 (2)
22.4645 (8)
90
˚
a (A)
7.6635 (4)
14.1424 (4)
6.0957 (2)
33.1458 (11)
90
˚
b (A)
11.8047 (6)
˚
c (A)
16.7584 (7)
a (ꢁ)
b (ꢁ)
c (ꢁ)
90
99.271 (5)
90
103.002 (4)
90
90
90
3
˚
Volume A
1496.25 (13)
2857.43 (16)
8
1512.85 (9)
4
Z
4
Dcalc (g cm-3
)
1.351
1.345
1.421
F (0 0 0)
640
1216
672
No. of Reflections [I [ 2r(I)]
2hmax/ꢁ with Mo Ka
R,Rw [I [ 2r(I)]
4952
4870
4985
64.84
65.04
64.98
0.0435, 0.1092
0.0715, 0.1757
1.060
0.0391, 0.1053
1.031
Goodness of fit on F2
0.925
(Dr)max
0.000
0.000
0.000
-3
˚
(Dq)max/e A
0.259
0.206
0.361
-3
˚
(Dq)min/e A
-0.231
-0.327
-0.198
Measurement
GEMINI (Oxford Diffraction, 2007)
CrysAlisPro
Program System
Structure Determination
Refinement
SHELXS97
Full-matrix least-squares on F2 (SHELXL97)
CCDC 680465 (I), 680467 (II), 680466 (III) contains supplementary crystallographic data for this paper. These data can be obtained free of
charge from The Cambridge Crystallographic Data Centre via www.ccdc.cam.ac.uk/data_request/cif, or by emailing data_r-
equest@ccdc.cam.ac.uk, or by contacting The Cambridge Crystallographic Data Centre, 12, Union Road, Cambridge CB2 1EZ, UK; fax: +44-
1223-336033
between the centroids of interacting rings is Cg2(I)ÁÁÁ
˚
Cg2(I) = 3.644(9) A (-x, 1-y, 1-z), Cg1(III)ÁÁÁC-
˚
g1(III) = 3.998(3) A (2-x, 1-y, -z) and Cg1(III)ÁÁÁ
˚
Cg2(III) = 3.797(8) A (1-x, 1-y, -z), respectively
[Cg2(I) = center of gravity of the 1st 2-naphthyl ring in I
(C10–C11–C12–C13–C18–C19); Cg1(III) & Cg2(III) =
center of gravity of the pyridyl and 1st 2-naphthyl ring in
III (N–C3–C2–C1–C5–C4 and C9–C10–C11–C12–C17–
C18)].
In contrast, the crystal structures of related chalcone
Fig. 2 Molecular structure of (I), drawn with 50% probability
displacement ellipsoids and showing the atom labeling scheme. The
dashed line indicates an intramolecular hydrogen bond, O1–H10ÁÁÁO2
derivatives C18H14O2S [11], C20H16O2 [12], and
C27H25NO4 [13], show that these compounds are essen-
tially planar with the central C=C double bond trans-
configured and geometric parameters in normal ranges. In
C20H16O2 [12], its two C=C atoms are slightly twisted out
of the naphthyl plane with the dihedral angle between the
in II (Figs. 5–7). In addition weak p–p stacking interac-
tions are observed between naphthyl rings in I and III and
also between pyridyl and naphthyl rings in II. The distance
123

160
J Chem Crystallogr (2009) 39:157–162
˚
Table 2 Selected bond lengths (A), Bond angles (ꢁ), and Torsion
angles (ꢁ) for (I), (II) and (III)
(I) C20H16O3
C6–C7
1.4817 (15) C7–O2
1.4612 (15) C8–C9
1.4559 (15) C15–O3
1.3473 (14) C20–O3
1.2429 (13)
1.3342 (14)
1.3674 (13)
1.4272 (14)
C7–C8
C9–C10
C1–O1
(II) C19H15NO2
C1–C6
Fig. 3 Molecular structure of (II), drawn with 50% probability
displacement ellipsoids and showing the atom labeling scheme.
Disordered C2–C3, C4–C5 atoms in the pyridine ring are shown as
PART A (C2A, C3A, C4A, C5A)
1.503 (2)
1.472 (2)
1.457 (2)
C6–O1
C7–C8
C14–O2
1.226 (2)
1.335 (2)
1.369 (2)
C6–C7
C8–C9
(III) C19H14ClNO2
C1–C6
1.5096 (16) C6–O1
1.4727 (16) C7–C8
1.4568 (15) C14–O2
1.2219 (14)
1.3430 (16)
1.3670 (14)
C6–C7
C8–C9
(I) C20H16O3
C5–C6–C7
C9–C10–C11
O2–C7–C6
C15–O3–C20
O1–C1–C2
(II) C19H15NO2
C5A–C1–C6
C8–C9–C10
O1–C6–C1
C14–O2–C19
(III) C19H14ClNO2
C5–C1–C6
C8–C9–C10
O1–C6–C1
C14–O2–C19
(I) C20H16O3
C5–C6–C7–C8
C5–C6–C7–O2
O1–C1–C6–C5
(II) C19H15NO2
122.34 (9)
121.82 (9)
C7–C8–C9
C6–C7–C8
121.85 (10)
119.38 (9)
120.85 (10)
124.53 (10)
122.19 (10)
119.75 (10) O2–C7–C8
117.38 (8) C14–C15–O3
117.56 (10) O1–C1–C6
Fig. 4 Molecular structure of (III), drawn with 50% probability
displacement ellipsoids and showing the atom labeling scheme
125.9 (2)
C1–C6–C7
118.82 (16)
120.86 (15)
121.91 (17)
125.15 (16)
aromatic groups being 14.09(8)ꢁ. But the chalcone, viz.,
1-(3-bromo-2-thienyl)-3-(6-methoxy-2-naphthyl)prop-2-en-1-
one, C18H13BrO2S [14], is chiral due to the twist of the
naphthalene and thienyl rings about the chalcone backbone
[dihedral angle = 17.75 (10)ꢁ]. In addition, there are weak
C–HÁÁÁO interactions which link the molecules into chains
along the b direction.
122.48 (15) C9–C10–C11
119.27 (16) O1–C6–C7
117.80 (15) C13–C14–O2
124.17 (10) C1–C6–C7
122.72 (10) C9–C10–C11
118.60 (10) O1–C6–C7
117.78 (10) C13–C14–O2
119.22 (10)
121.21 (10)
122.18 (11)
124.90 (11)
The role of the keto group in stabilizing the structure
within the crystal environment as well packing effects can
be examined by looking at its orientation relative to the
methoxy napthaldehyde group and to its twist angles with
the phenyl and pyridyl rings when compared to a theoret-
ical semi empirical model based on atom sizes and bonding
tendencies such as that provided by MOPAC [15].
-4.82 (15)
C8–C9–C10–C11
-13.68 (16)
-3.63 (16)
-2.48 (15)
173.88 (10) C14–C14–O3–C20
179.63 (10) O1–C1–C6–C7
MOPAC calculations on I and III were performed with
WebMO ProTM as implemented by WeMO [16]. The dis-
ordered pyridyl ring in II did not allow for a converged
result, therefore will not be used in the subsequent analysis.
The PM-3 (Parametric Model 3) approximation together
with the Hartree-Fock closed-shell (restricted) wavefunc-
tion was used for I and III and minimizations were
C5A–C1–C6–C7 -23.7 (4)
C5A–C1–C6–O1 155.9 (3)
(III) C19H14ClNO2
C7–C8–C9–C10
10.3 (3)
7.6 (3)
C13–C14–O2–C19
C5–C1–C6–C7
C5–C1–C6–O1
6.03 (18)
C7–C8–C9–C10
-0.69 (19)
-4.96 (18)
-174.4 (12) C13–C14–O2–C19
teminnated at an r.m.s. gradient of less than 0.01 kJ mol-1
˚
bonding effects influence these twist angle values for the
molecule in this crystal. The repulsion of the H atoms at C8
and C11 is balanced by the p conjugation of the carbonyl
and aryl groups as well as from intermolecular hydrogen
bonding effects. The slight difference between the C7–O2
A
-1. When the refined atom coordinates in I are subjected
to a MOPAC calculation the angle between the mean
planes of the phenyl and 2-naphthyl groups become 54.018
(vs. 31.738 in crystal) and the angle between the mean
planes of the keto group (C6–C7–O2–C8) and the phenyl
and 2-napthyl groups become 27.248 and 36.268 (vs. 4.628
and 27.838 in crystal), respectively, in the local minimized
structure. It is clear that inter and intramolecular hydrogen
˚
˚
bond length (1.2429(13) A crystal vs 1.245 A MOPAC)
indicates only slightly different degrees of conjugation of
the sp3 hybridized O2 atom. In III, the angle between the
mean planes of the phenyl and 2-naphthyl groups becomes
123

J Chem Crystallogr (2009) 39:157–162
161
Table 3 Hydrogen bonds for (I) C20H16O3, (II) C19H15NO2 and (III)
˚
C19H14ClNO2 [A and ꢁ]
D–H…A
d(D–H) d(HÁÁÁA) d(DÁÁÁA)
\(DHA)
I
O(1)–H(1O)…O(2)
C(8)–H(8A)…O(3)#1
C(11)–H(11A)…O(3)#1 0.95
C(20)–H(20C)…O(2)#2 0.98
0.84
0.95
1.80
2.56
2.59
2.63
2.5403(11) 146.0
3.4810(13) 163.0
3.5381(13) 173.6
3.3164(16) 127.6
II
C(3A)–H(3AA)…O(2)#3 0.95
III
2.52
2.58
3.314(4)
141.5
C(8)–H(8A)…O(1)#4
0.95
3.4518(15) 153.2
Fig. 5 Packing diagram of (I), viewed down the a axis. Dashed lines
indicate intermolecular (C8–H8AÁÁÁO3) and intramolecular (O1–
H10ÁÁÁO2) hydrogen-bonding interactions
Symmetry transformations used to generate equivalent atoms: (I) #1
x, -y + 3/2, z - 1/2, #2 -x,-y + 2,-z, (II) #3 x, -y + 3/2,
z + 1/2, (III) #4 -x + 1,-y + 2,-z
58.438 (vs. 1.868 in crystal) and the angle between the
mean planes of the keto group (C1–C6–O1–C7) and the
phenyl and 2-naphthyl groups becomes 56.788 and 1.608
(vs. 56.788 and 1.608 in crystal), respectively, in the local
minimized structure when subjected to the MOPAC cal-
culation. These results indicate a pattern of similar effects
due to hydrogen bonding interactions on the twist angle of
these groups. The difference between the C6–O1, bond
Fig. 6 Packing diagram of (II), viewed down the b axis. Dashed lines
indicate intermolecular (C3A–H3AAÁÁÁO2) hydrogen-bonding
interactions
˚
˚
length [1.2219(14) A crystal vs 1.218 A MOPAC] also
indicates only slightly different degrees of conjugation of
the hydrogen bonded sp3 hybridized O1 atom.
It is noted that the length of the c-axis of the unit cell of
˚
III (22.4645(8) A) is much longer than that in I
˚
(16.7584(7) A) even though they have the same space
group (P21/c). Based on that fact that they both link the
molecules into chains diagonally along the (011) plane of
the unit cell and with the a and b axis of similar length, it
would appear that this increase could be attributed to the
presence of two intermolecular hydrogen bond interactions
from the keto oxygen in I as well as a methoxy H-bond as
compared to one keto oxygen H-bond interaction in III
along with the presence of a chloro atom bonded to the
pryidyl ring in the plane of the linked molecules in the bc
plane (Figs. 5 and 7).
Fig. 7 Packing diagram of (III), viewed down the a axis. Dashed
lines indicate intermolecular (C8–H8AÁÁÁO1) hydrogen-bonding
interactions
˚
C4BÁÁÁC4B = 2.871(3) A (1 - x, 1 - y, - z)]. Therefore it
would seem that additional crystal packing effects such as
those described here also contribute to the influence of
geometric and spatial orientation of the molecules in the unit
cells of all three compounds. The remaining geometric
parameters in all three structures are similar to standard
values [9]. These observations support the data outlined
above as well as the conclusions from the MOPAC calcula-
tions on I and III.
Further analysis of crystal packing in the title compounds
reveals that there are short intermolecular steric contacts in
all three structures between atoms of the naphthyl fragments
of neighboring molecules in I [C(11)ÁÁÁC(19) (-x, 1-y,
˚
1-z) = 2.540(5) A], between the methoxy oxygen atom
and chloro groups in III [ClÁÁÁO(2) (1 + x, ‘ - y,
˚
-1/2 + z) = 3.036(2) A] and between a naphthyl fragment
and keto oxygen atom in II [C(15)ÁÁÁO(1) (1 - x, 1/2 + y,
˚
1/2 - z) = 3.147(0) A] [17]. In II disordered carbon atoms
Acknowledgements ANM thanks University of Mysore for use of
their research facilities. RJB acknowledges the NSF MRI program
(grant No. CHE-0619278) for funds to purchase the X-ray
diffractometer.
of pyridyl groups of neighboring molecules also form short
˚
interatomic steric interactions [C2AÁÁÁC2A = 3.393(0) A;
˚
˚
C3AÁÁÁC3A = 3.113(9) A; C2AÁÁÁC3A = 2.897(3) A;
123

162
J Chem Crystallogr (2009) 39:157–162
10. Cremer D, Pople JA (1975) J Am Chem Soc 97:1354–1358
11. Yathirajan HS, Narayana B, Ashalatha BV, Sarojini BK, Bolte M
(2006) Acta Cryst E62:o4440–o4441
12. Yathirajan HS, Mayekar AN, Sarojini BK, Narayana B, Bolte M
(2007) Acta Cryst E63:o1012–o1013
13. Yathirajan HS, Mayekar AN, Sarojini BK, Narayana B, Bolte M
(2007a) Acta Cryst E63:o1140–o1141
14. Butcher RJ, Yathirajan HS, Ashalatha BV, Narayana B, Sarojini
BK (2007) Acta Cryst E63:o1430–o1431
15. Stewart JJ (1990) MOPAC, A General Molecular Orbital Pack-
age, Frank J. Seiler Research Lab, United States Air Force
Academy, No. ADA233489
16. Schmidt JR, Polik WF (2007) WebMO Pro, version 8.0.010e;
WebMO, LLC, Holland, MI, USA.Eur J. Med. Chem. Available
from http://www.webmo.net
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