Vibrational and crystal structure analysis of a phenylenedioxydiacetic acid derivative

Article abstract of DOI:10.1016/j.molstruc.2010.11.055

Computationally derived data has successfully assisted the characterisation of the Raman and infrared vibrational spectra of the phenylenedioxydiacetic acid (PDA) derivative 2,2′-[(4-nitro-1,2-phenylene)bis(oxy)]diacetate (I) in the solid state. X-ray dif

Full text of DOI:10.1016/j.molstruc.2010.11.055

Journal of Molecular Structure 987 (2011) 25–33
Contents lists available at ScienceDirect
Journal of Molecular Structure
journal homepage: www.elsevier.com/locate/molstruc
Vibrational and crystal structure analysis of a phenylenedioxydiacetic
acid derivative
a
a
b
a,
⇑
Benjamin V. Cunning , Gregory A. Hope , Peter C. Healy , Christopher L. Brown
a
Queensland Micro- and Nanotechnology Centre, Griffith University, Brisbane, Qld, 4111, Australia
School of Biomolecular and Physical Sciences, Griffith University, Brisbane, Qld, 4111, Australia
b
a r t i c l e i n f o
a b s t r a c t
Article history:
Computationally derived data has successfully assisted the characterisation of the Raman and infrared
vibrational spectra of the phenylenedioxydiacetic acid (PDA) derivative 2,2 -[(4-nitro-1,2-pheny-
lene)bis(oxy)]diacetate (I) in the solid state. X-ray diffraction analysis of (I), which crystallised in the
1
non-centrosymmetric achiral space group Pca2 , revealed the computationally predicted minimum
Received 16 September 2010
Received in revised form 18 November 2010
Accepted 18 November 2010
Available online 29 November 2010
0
energy geometry differed to that observed in the solid state molecule due to significant inter-molecular
bonding, this was also confirmed computationally. Importantly, large deviations between the wavenum-
ber of predicted and experimental vibrational modes only occurred with functional groups that engaged
in inter-molecular bonding. From a comparison of the energies of the calculated and X-ray structural data
the crystal packing forces in the solid-state was estimated at ꢀ240 kJ/mol.
Keywords:
Vibrational spectroscopy
X-ray diffraction
Crystal packing forces and density
functional theory calculations
Ó 2010 Elsevier B.V. All rights reserved.
1
. Introduction
Crystal packing forces form an integral part in the three dimen-
The flexible arms substituted on the 1 and 2 positions of the
benzene ring, in addition to the nitro group located at the 4 posi-
tion, provides potential for differences in inter-molecular interac-
tions within the solid phase environment. This may result in
substantially different molecular properties (such as vibrational
mode frequencies and the minimum energy geometries) from
those predicted by single molecule gas phase quantum chemical
calculations.
sional arrangement of both biological and non-biological macro-
molecules. Understanding the nature of these interactions has
numerous applications in drug design, crystal engineering, and
understanding biological processes.
Computational chemistry packages have made the prediction of
molecular properties from small organic molecules to large pro-
teins a relatively straightforward task. The vast majority of these
packages, however, perform optimisations and calculations on a
single molecule in the gaseous phase and this may not be represen-
tative of bulk phase molecules in the solid state. Whilst these cal-
culations may fortuitously afford acceptable results for simple
systems; the subtle inter-molecular non-bonded interactions that
can often dominate in larger solid systems often result in the poor
prediction of their molecular properties.
2
. Experimental
.1. Materials
-Nitrocatechol and methyl bromoacetate were obtained from
2
4
Sigma–Aldrich (Australia). The solvents were of AR grade and ob-
tained from Merck (Australia). Potassium carbonate was obtained
from Chem-Supply (Australia). All materials were used without
further purification.
Ongoing studies into the coordination chemistry of analogues of
1
,2-phenylenedioxydiacetic acid (PDA) has resulted in the synthe-
0
sis of dimethyl 2,2 -[(4-nitro-1,2-phenylene)bis(oxy)]diacetate (I)
2.2. Synthesis of (I)
(Fig. 1). This class of molecules comprise tetradentate ligands pos-
sessing two ether oxygen atoms and two carboxylate oxygen
atoms and are capable of forming coordination complexes with
4
-Nitrocatechol (4.00 g, 25.8 mmol) was dissolved in dimethyl-
formamide (100 mL) to which potassium carbonate (9.73 g,
0.4 mmol) was subsequently added forming a slurry. A solution
ꢀ
ꢁ
2
þ
moderately hard metals, including the uranyl ion UO2 [1], lan-
7
thanides in the +3 oxidation state [2], bismuth in the +3 oxidation
state [3], and various transition metals in the +2 oxidation state [4].
of methyl bromoacetate (10.76 g 70.3 mmol) and dimethylform-
amide (10 mL) was added dropwise over a period of five minutes
at room temperature. The reaction was then stirred at 80 °C under
⇑
Corresponding author. Tel.: +61 7 37357293; fax: +61 7 37357656.
E-mail address: c.l.brown@griffith.edu.au (C.L. Brown).
a drying tube (CaCl
and the retentate rinsed with acetone (3 ꢁ 50 mL portions). The
2
) for 12 h. The reaction slurry was filtered,
0
022-2860/$ - see front matter Ó 2010 Elsevier B.V. All rights reserved.
doi:10.1016/j.molstruc.2010.11.055

2
6
B.V. Cunning et al. / Journal of Molecular Structure 987 (2011) 25–33
methods and refined by full matrix least squares refinement on
2
F after application of empirical absorption corrections. Anisotropic
thermal parameters were refined for non-hydrogen atoms; (x, y, z,
U ) were included and constrained at estimated values. Conven-
iso H
tional residuals at convergence are quoted; statistical weights
were employed. Computation used the teXsan [5] CrysAlis [6],
SHELXL97 [7], ORTEP-3 [8] and PLATON [9] program and software
systems. A full .cif deposition resides in both the supplementary
data and the Cambridge Crystallographic Data Centre with CCDC
number 791829. Copies of the data may be obtained free of charge
from the Director, CCDC, 12 Union Road, Cambridge, CB2 1EZ. UK at
the following address: http://www.ccdc.cam.ac.uk/cgi-bin/catreq.
cgi.
Fig. 1. A representative view of (I).
solvents from the combined organic phase were removed under re-
duced pressure and the residue partitioned between ethyl acetate
and water (75 mL of each). The organic layer separated and subse-
quently washed twice with water (50 mL), and then dried using
anhydrous sodium sulphate. The residue after solvent removal
was recrystallised twice from pure ethanol yielding 4.32 g
14.4 mmol, 56%) of material (long needle-like crystals of up to
cm in length). Single crystals suitable for X-ray analysis were
grown by slowly cooling a warm ethanol solution in an insulated
vessel followed by slow evaporation of the ethanol solvent.
Crystal Data for C12
group Pca2 a = 11.5978(8), b = 14.7402(11), c = 7.7831(6) Å,
U = 1330.5(2) Å , Z = 4, D
size: 0.33 ꢁ 0.15 ꢁ 0.14 mm. Tmin/max = 0.96, 0.98.
153 Reflections collected, 1275 unique (Rint = 0.030), R = 0.025
8
H13NO M = 299.23, orthorhombic, space
1
,
(
1
3
ꢂ3
ꢂ1
c
= 1.49 g cm , l = 0.128 mm , Crystal
6
2
[
938 reflections with I > 2
r(I)], wRF = 0.045 (all data). A thermal
1H NMR (400 MHz, CDCl
J = 2.6 Hz, 2H), 6.88 (d, J = 9.0 Hz, 2H), 4.83 (s, 2H), 4.80 (s, 2H),
) d 7.92 (dd, J = 9.0, 2.6 Hz, 2H), 7.74 (d,
ellipsoid plot is shown in Fig. 2.
3
3
.83 (s, 3H), 3.81 (s, 3H).
C NMR (100 MHz, CDCl
2.4. Vibrational spectroscopy
1
3
3
) d 168.48, 168.32, 153.20, 147.59,
1
42.40, 118.89, 113.23, 110.09, 66.37, 66.24, 52.66.
Raman spectra of (I) were collected on a Renishaw InVia spec-
MS(ES+) calculated M + Na 322.05 m/z; found M + Na 321.83 m/z.
trometer, excited using a 632.8 nm HeNe laser. The radiation was
focused through a 50ꢁ Leica N Plan lens, and was measured at
ꢃ10 mW. The samples for Raman were prepared by focusing the
radiation directly onto the crystalline material. The resultant spec-
trum is shown in Fig. 3.
2
.3. X-ray crystallography
A unique data set for (I) was measured on an Oxford-Diffraction
GEMINI S Ultra CCD diffractometer at 200 ± 1 K (Mo–K
k = 0.71069 Å) to 2hmax = 50°. The structure was solved by direct
a
radiation
IR spectroscopy was performed using a Thermo Nicolet Nexus
FT-IR spectrometer equipped with EverGlo IR source optics at a
Fig. 2. A thermal ellipsoid plot of (I).

B.V. Cunning et al. / Journal of Molecular Structure 987 (2011) 25–33
27
Fig. 3. The Raman spectrum of (I).
ꢂ1
resolution of 2 cm . The samples for infrared were dispersed
minimum energy geometry structure are available in the supple-
mentary data.
within KBr forming a thin disc. The spectrum is shown in Fig. 4.
2.5. Computational studies
3
. Results and discussion
Single point calculations, geometry optimisation and vibra-
The vibrational assignments subsequently discussed are sum-
marised below in Table 1.
tional calculations were performed using the hybrid functional
B3LYP as implemented in Gaussian 03 [10]. Interaction energy cal-
culations were performed at the MP2 level, with basis set superpo-
sition error taken into account via counterpoise correction. The
basis set used was 6-31G augmented with diffuse functions given
by the parameter ‘‘++’’ in the Gaussian 03 command file. A fre-
quency factor of 0.96 was applied to all frequencies [11]. Potential
energy distribution (PED) analysis was performed with the aid
of the VEDA4 package [12]. The geometric coordinates of the
3.1. Vibrations attributed to C–H bonds
A tri-substituted benzene ring gives rise to three aromatic C–H
stretches, which were calculated to occur at 3145, 3136 and
ꢂ1
3108 cm . Analysis of the infrared spectrum of (I) locates these
ꢂ1
bands at 3096 and 3042 and 3021 cm . Analysis of the Raman
Fig. 4. The infrared spectrum of (I).

2
8
B.V. Cunning et al. / Journal of Molecular Structure 987 (2011) 25–33
Table 1
Summary of the various vibrational modes observed in (I). Format: vibration(atoms or group) – minimum descriptive elements (PED%)
c
= out of plane deformation, b = in-plane
deformation,
s = torsion, m = stretch, s = symmetric, as = asymmetric.
IR
Raman
Calcd
%PEDs
3
3
3
3
3
3
3
3
2
096
042
021
126
096
064
042
022
981
3099
3047
3024
3145
3136
3108
3092
3086
3059
3054
3049
2985
2985
2966
2962
2929
m
m
m
m
m
m
m
m
m
m
m
m
m
(CH) (94)
(CH) (89)
(CH) (91)
as(CH
as(CH
as(CH
as(CH
as(CH
as(CH
3
) (97)
3
) (81)
2
) (90)
3
) (99)
3
) (99)
2
) (88)
3100
m
m
(CH
(CH
3
) (19)
) (10)
2
3046
3025
2985
2963
(CH
(CH
2
) (84)
) (97)
2
2
951
925
2953
2929
3
3
as(CH ) (19)
m(CH
3
) (80)
2897
2856
2847
2795
(CH ) (95)
2
1775
1761
1738
1761
1734
1660
1626
m
m
(OC) (85)
(OC) (85)
1642
1617
1595
1587
1619
1595
1585
1577
1573
m
m
(Ph) (62)
(Ph) (57)
m(Ph) (11)
1534
1
1
495
466
1482
1465
1465
1457
1456
1454
m
c
c
c
c
c
c
(PhC–O) (12) b(Ph–H) (37)
m
(Ph) (20)
(CH
(CH
(CH
(CH
(CH
(CH
2
3
2
2
3
3
) (61)
) (13)
) (58)
) (10)
) (71)
) (67)
s
c
c
c
s
c
(HCOC) Ph–O (21)
1
460
1460
455
(CH
(CH
(CH
3
) (64)
2
) (13)
3
) (13)
s
s
c
(HCOH) ester (22)
(HCOH) ester (25)
(CH ) (48)
2
1
1
1
451
434
1451
1438
(HCOH) ester (21)
1
451
1425
422
(CH ) (10)
2
1425
b(CH
3
) (80)
1
c
m
s
(CH ) (64)
3
1410
1375
1351
1516
1419
1368
(Ph) (33)
(HCOC) Ph–O (56)
1375
1510
1358
m
m
m
2
as(NO ) (78)
1
345
(Ph) (15)
(Ph) (17)
s(HCOC) Ph–O (54)
1320
1330
1
1
305
286
1302
1286
1271
1259
1239
1213
1207
1203
1181
1170
b(Ph–H) (50)
(CO) ester (14) b(Ph–H) (53)
(PhC–O) (29) (Ph) (16) b(Ph–H) (10)
(NO ) (67) b(NO ) (10)
(CO) – ester C, methoxy O (26) b(Ph–H) (14)
(CH ) (68) (HCOH) Ph–O (10)
(CO) – phenyl O (30) b(Ph–H) (17) Bing (Ph) (16)
(CO) – ester C, methoxy O (53) (HCOC) Ph–O (10)
(HCOC) Ph–O (49)
(HCOH) ester (66)
1276
m
m
m
m
c
m
m
c
c
m
c
c
m
m
s
c
m
c
m
m
c
m
1
1
1
1
263
341
227
211
1263
1342
1229
m
s
2
2
2
s
1189
1
179
1180
s
s
1
1
151
149
(CH
(CH
2
) (17)
) (10)
s
c
(HCOC) Ph–O (13)
(CH ) (16)
3
3
s
1
1
148
107
1149
1109
1133
1116
(Ph) (13) b(Ph–H) (42)
(CH
(CH
2
) (19)
) (28)
s
s
(HCOH) ester (66)
(HCOH) ester (49)
1
114
3
1
1
1
085
050
028
1085
1052
1029
1070
1018
1014
(Ph) (10)
(CO) O attached to Ph, non Ph C (51)
(HCOC) Ph–O (18) (C–C('O)–O) (11)
(CH ) (18) (HCOH) Ph–O (43) (C–C('O)–O) (15)
m(CN) (17) b(Ph–H) (23)
c
1
002
2
s
c
9
9
9
84
51
99
986
953
1001
984
960
947
(CO) O attached to Ph, non Ph C (41)
(Ar–C[5,6]H) (out of sync) (78)
(CO) ester-methylC (72)
(CO) ester-methylC (69)
(Ar–C[2]H) lone H wag (81)
9
29
9
8
8
7
8
7
7
06
72
54
19
16
97
87
908
873
858
719
816
799
788
920
877
(CN) (12)
b(NO
m(CO) – phenyl O (10) m(CO) O attached to Ph, non Ph C (16)
2
)
856
815
782
766
m
c
m
m
m
c
c
(COC) – ester C, methoxy O, methyl C, simultaneous stretch (40) b (Ph) (12)
(Ar–C[5,6]H) – (in sync) (79)
(CO) – ester C, methoxy O (56)
(COC) – ester C, methoxy O, methyl C, simultaneous stretch (15) b(NO ) (25)
2
2
(C–O) – Ph–C, Ph–O (11) Ph ring breath (12) b(NO ) (22)
7
40
711
708
696
675
(Ph) (58)
(NO ) (75)
2
7
6
45
78
746
683
b(OCO) carbonyl C'O, methoxy O (25)

B.V. Cunning et al. / Journal of Molecular Structure 987 (2011) 25–33
29
Table 1 (continued)
IR
Raman
Calcd
%PEDs
6
6
6
5
39
33
07
83
640
634
608
587
662
631
603
581
569
554
530
480
462
428
410
354
330
302
294
265
226
209
201
177
166
157
b(COC) (ester) (11) c(CCO) – ester C, methoxy O (20)
b(Ph) – ring breath (22) b(NO
2
) (17)
b(Ph) (41)
s
c
(HCOC) – methylene C, Ph–O (19)
(CCO) – methylene C, ester C, carbonyl O (11) c
c
(CCO) – methylene C, ester C, carbonyl O
5
73
(CCO) – methylene C, ester C, carbonyl O
5
4
4
4
31
88
66
16
531
488
468
418
b(Ph) (10)
c(Ph) (10) c(Ph) (32)
b(Ph) (54)
c
c
(CCO) – methoxy O, ester C (10) b(COC) – methoxy O (14) c(Ph) (21)
(Ph) (39)
373
362
341
312
286
257
242
216
204
185
168
144
111
b(CCO) – ester C, methoxy O (33) c(Ph) (12)
m
m
c
(CN) (11) b(Ph) (38)
(CN) (10) b(CCO) – methoxy O, ester C, methylene C (13)
(Ph) (53)
c (Ph) (13)
b(COC) – methoxy O (27) b(COC) – methoxy O (27)
b(COC) – methoxy O (66)
b(COC) – Ph–O (36)
b(COC) – methoxy O (21) b(CCO) – ester C, methylene C, Ph–O (12)
b(NO ) (45)
b(OCC) – Ph–O, Ph–C (46)
(CCOC) – ester C, methoxy O (38)
b(NO ) (26) (CCOC) – ester C, methoxy O (17)
b(CCO) – ester C, methoxy O (16) (Ph) (34)
(Ph) (11)
(Ph) (14)
(HCOC) methylene C, Ph–O (15)
(HCOC) methyl C, methoxy O (69)
2
s
s(CCOC) – ester C, methoxy O (18)
2
s
c
1
1
1
1
9
6
5
3
3
2
2
36
24
06
00
4
1
4
9
8
s
s
s
s
s
(CCOC) – ester C, methoxy O (21)
(OCCO) – methylene C, ester C (42)
(HCOC) methyl C, methoxy O (65)
(HCOC) – methyl C, methoxy O (13)
c
c
s
s
(CCOC) – Ph–C, Ph–C, Ph–O, methylene C (70)
b(CCO) ester C, methylene C, Ph–O (23) b(COC) – Ph–C, Ph–O, methylene C (37)
(NO ) (70)
2
b(COC) – Ph–C, Ph–O, methylene C (10) ) (13) s(OCCO) – methylene C, ester C (52)
c
2
c(NO
s
s
s
(CCOC) – ester C, ester O (10) s(OCCO) – methyleneC, esterC (52)
(OCCO) – methylene C, ester C (70)
(OCCO) – methylene C, esterC (54)
5
3
ꢂ1
spectrum displays the three bands at 3099, 3047 and 3024 cm
.
C–O ether stretch. The twist was coupled in computationally de-
rived vibrations between 1271 and 1203 cm , with the exception
of the symmetric nitro stretch.
ꢂ1
The methyl and methylene units both have asymmetric and sym-
metric stretches which are assigned as follows; (Raman followed
by infrared)
951 and 2953,
The methyl group associated with the ester single bonded oxy-
m
asCH
3
2984 and 2982,
m
asCH
2
2962 and 2960,
.
m
s
CH
3
There are a number of modes in the region between 1300–
950 cm which are attributed to Ar–X and Ar–H in-plane defor-
mations, however these are often coupled with aromatic ring
stretching and bending modes [16]. Two significant benzene C–H
in-plane deformation modes were, according to potential energy
ꢂ1
ꢂ1
2
m
s
CH 2928 and 2925 cm
2
gen gives rise to symmetric and asymmetric deformations, the lat-
ter being linearly correlated with the symmetric deformation [13].
The computational calculations predicted the symmetric deforma-
distribution analysis, not coupled to
C–H in-plane deformation mode was weakly coupled to a
m
(Ph) modes, and one benzene
(Ph)
ꢂ1
tions to be present at 1422 and 1425 cm whilst four asymmetric
m
deformation modes were present at 1454, 1457, and two at
mode. These absorbencies were observed in the calculated spec-
trum at 1271, 1259, and 1133 cm . All three of these modes were
ꢂ1
ꢂ1
1
465 cm , which is expected for methyl groups attached to an
oxygen atom with little symmetry [14]. The asymmetric deforma-
assigned in the Raman spectrum, to bands at 1286, 1276, and
ꢂ1
ꢂ1
tion of the CH
3
group was assigned experimentally at 1460 cm
1149 cm . One of the modes did not appear to be infrared active;
ꢂ1
ꢂ1
and its asymmetric deformation as a shoulder at 1434 cm in
the infrared spectrum. The symmetric deformation was assigned
these were assigned to 1286 and 1148 cm respectively. 1,2,4-Tri-
ꢂ1
substituted benzenes show absorbances in the 1125–1090 cm
ꢂ1
ꢂ1
at 1437 cm in the Raman spectrum and the asymmetric deforma-
range and also absorb weakly in the 1000–960 cm range [17].
tion was not present. The rocking mode of the methyl group on the
ester is often seen as a shoulder on the C(@O)–O stretch [15] and
this is the case with the title compound. The shoulder is observed
The out of plane of aromatic C–H deformation modes, of which
1,2,4 tri-substituted benzenes have three [15], were observed in
the predicted spectrum as follows: two adjacent hydrogen atoms,
ꢂ1
ꢂ1
ꢂ1
at 1182 cm in the infrared spectrum, and is absent from the Ra-
out of sync., 960 cm , in sync., 815 cm . The lone hydrogen lo-
cated in the ‘5’ position on the benzene ring was observed at
man spectrum. The two individual methyl group rocking modes
ꢂ1
ꢂ1
were observed in the predicted spectrum at 1149 and 1150 cm
.
920 cm . These theoretical values agreed well with those assigned
The methylene deformation or scissoring mode was assigned in
in the experimental spectra, in which the two adjacent hydrogen
ꢂ1
ꢂ1
the infrared and Raman spectrum at 1451 cm . This mode was
atoms were observed at 953 and 816 cm respectively in the Ra-
ꢂ1
ꢂ1
predicted computationally at 1456 and 1451 cm . The associated
man spectrum and 951 and 816 cm in the infrared spectrum. The
ꢂ1
methylene ‘wagging’ mode was assigned experimentally at
lone hydrogen ‘wag’ was assigned at 908 and 906 cm in the Ra-
ꢂ1
1
375 cm in both infrared and Raman spectrums and was pre-
man and infrared spectra respectively.
ꢂ1
dicted computationally at 1368 and 1345 cm . The methylene
‘
twist’ when bonded to an ether oxygen is typically reported to
3.2. Ester vibrations
ꢂ1
be in the region of 1270 ± 40 cm [15]. In the calculated spectrum
of (I) the methylene twists were predicted much lower, at
The characterisation of carbonyl group vibrations was simpli-
fied due to the fingerprint region being absent of commonly found
vibrational modes, and the strong intensity of the carbonyl mode in
ꢂ1
1
203 cm for one arm. In the other arm, the twists were coupled
strongly to other vibrations, namely the C–O ester stretch and the

3
0
B.V. Cunning et al. / Journal of Molecular Structure 987 (2011) 25–33
infrared [18]. Esters are found at the higher frequency range of car-
bonyl groups due to the electronegativity of the proximal oxygen
attached to the carbonyl carbon [19] and also due to contributions
from the mesomeric effect [13]. The C1 symmetry of the molecule
results in one vibrational mode for each of the two groups with a
stretch owing to its proximity to its peak in the IR spectrum. The
symmetric stretch was observed as a strong peak in both the infra-
red and Raman spectra at 1341 and 1342 cm respectively, again
ꢂ1
in accordance with the previous observation. Interestingly the
computationally predicted vibrational modes occurred at a signif-
icantly lower wavenumber for both symmetric and asymmetric
ꢂ1
wavenumber difference of 34 cm , similar to that observed exper-
ꢂ1
imentally. The two separate modes were distinct in the experimen-
modes of vibration, calculated at 1358 and 1213 cm respectively.
ꢂ1
tal spectra, visible at 1761 and 1734 cm with Raman, and at 1762
Inspection of other vibrational analysis articles [22,23] which
examined molecules containing nitro groups indicated that our
calculation was anomalous in its substantial deviation from exper-
imental observations.
ꢂ1
and 1738 cm in the infrared spectrum. Examination of the X-ray
structure reveals that the carbonyl groups are located in substan-
tially differing chemical environments, which is likely to account
ꢂ1
ꢂ1
for the ca. 100 cm differences between the predicted and exper-
The Ar C–N stretch was assigned to 1085 cm in both infrared
ꢂ1
imental models.
and Raman, whilst it was calculated at 1070 cm . Nitro groups
ꢂ1
The oxygen-methyl carbon stretch in esters usually appears in
have a characteristic absorption in the 850 cm
region which
ꢂ1
the region of 980 ± 80 cm [15]. This mode was physically ob-
was originally attributed to a C–N vibration [24] however, is now
ꢂ1
ꢂ1
served at 999 cm in the infrared spectrum and 1001 cm in
the Raman spectrum, whilst in the predicted spectrum two bands
often attributed to the NO
2
scissor vibration. [25] The scissor mode
ꢂ1
was observed in (I) at 858 and 854 cm in the Raman and the
infrared spectra respectively. In the predicted spectrum this mode
is coupled strongly to ring vibrations and actually appears twice
ꢂ1
attributable to each of the individual arms at 947 and 921 cm
were observed.
ꢂ1
The in plane deformations of the carbonyl group appear in the
coupled with differing ring vibrations at 766 and 740 cm . The
ꢂ1
wide region of 715 ± 115 cm whilst the out of plane deformation
‘wagging’ and ‘rocking’ modes are seen in benzene rings with an
ꢂ1
appear from 635 ± 130 cm
[15]. The in plane deformation as
electron donating group in the meta or para position at 760 ± 30
ꢂ1
ꢂ1
calculated by PED was present in both modes at 856 and
and 540 ± 30 cm
[15]. The wag was assigned at 745 cm
in
ꢂ1
ꢂ1
ꢂ1
7
66 cm . The mode at 856 cm however had a much stronger
the infrared and 746 cm in the Raman spectrum. The rocking
mode was assigned at 531 cm in Raman and 530 cm in the
infrared spectrum.
ꢂ1
ꢂ1
contribution despite lying outside the range given by the reference.
ꢂ1
Experimentally, this mode was assigned to the bands at 719 cm
in both infrared and Raman. The out of plane deformation was
ꢂ1
3.5. Aromatic carbon vibrations
observed in the calculated spectrum at 675 cm and assigned to
ꢂ1
the bands at 683 and 678 cm in the Raman and infrared spectra
In benzene there are two ring carbon–carbon vibrations that oc-
respectively.
ꢂ1
ꢂ1
cur at 1588 cm and 1486 cm respectfully. These modes are
doubly degenerate in benzene systems that possess a threefold
plane of symmetry and are split in systems lacking this property
3.3. Phenolic vibrations
[
13]. In the title compound the two higher frequency modes are as-
The presence of the oxygen atoms located in the meta and para
ꢂ1
signed at 1595 cm in both infrared and Raman spectra, and at
1
two modes were calculated at 1577 cm
respective bands for the lower carbon–carbon vibration is seen as
a very weak mode in the Raman spectrum located at 1495 cm
and is likely lost under the very intense NO
spectrum. This mode was computationally predicted at 1482 cm
The second low frequency mode was assigned to 1410 cm in the
infrared and was absent in the Raman spectrum. This mode was
positions of the aryl unit gives rise to band associated with aryl and
alkyl C–O stretching vibrations. Aryl–alkyl ethers have strong
ꢂ1
585 and 1587 cm in infrared and Raman respectively. These
ꢂ1
ꢂ1
ꢂ1
and 1573 cm . The
bands in the region 1350–1240 cm which is attributed to the
ꢂ1
aromatic carbon–oxygen stretch, and 1050–1010 cm attributed
ꢂ1
to the alkyl carbon–oxygen stretch [15]. The higher frequency of
the aromatic carbon–oxygen is attributed to the resonance effect
which gives the bond some partial double bond character increas-
ing its force constant [20]. We suspect that this character is also
responsible for the substantially differing frequencies attributed
to carbon oxygen stretches at the para and meta positions. This
2
mode in the infrared
ꢂ1
.
ꢂ1
ꢂ1
predicted at 1419 cm in the computational spectrum. The fifth
aromatic carbon–carbon stretch which in 1,2,4-trisubstituted rings
substituted with two ‘light’ and one ‘heavy’ substituent is usually
observed in the 1295 ± 35 region [15]. This mode was observed
mode was assigned for both infrared and Raman spectra at
ꢂ1
1
263 cm in the para position whilst the meta mode was only
ꢂ1
present in the Raman spectrum at 1189 cm . In the predicted
spectrum this mode was assigned at 1239 cm for the oxygen
ꢂ1
ꢂ1
in the calculated spectrum at 1330 cm and assigned in the Ra-
ꢂ1
ꢂ1
man at 1319 cm and was absent in the infrared spectrum.
para to the nitro group, and 1181 cm for the oxygen meta to
the nitro group. The alkyl-O stretches were observed at
ꢂ1
ꢂ1
ꢂ1
1
050 cm in the infrared spectrum and 1052 cm in the Raman
4. Geometries
spectrum for the para position and 984 and 986 cm for the meta
position. In the predicted spectrum the modes were observed for
The single crystal X-ray structure determination for (I) revealed
that the compound crystallised as discrete molecules in the non-
ꢂ1
ꢂ1
the para position at 1018 cm and meta position 984 cm
.
1
centrosymmetric, achiral space group Pca2 . An image of the X-
3
.4. Nitro vibrations
ray structure in comparison to the computationally derived struc-
ture is shown in Fig. 5. In the solid state the nitro group of the mol-
ecule, is twisted with respect to the plane of the benzene ring with
the torsion angle C3–C4–N4–O42 = ꢂ11.9(4)°. This twist results in
co-planarity with the benzene ring of an adjacent molecule in the
The asymmetric stretch of the nitro group was observed in the
ꢂ1
infrared spectra as a very strong mode located at 1516 cm which
agreed well with the observation that nitro groups para to an elec-
tron donating group are located toward the lower frequency range
typical of nitro groups [21]. We note that despite both the twisting
crystal, facilitating a p–p stacking interaction which is detailed in
Fig. 6. This contrasts to the planarity observed across the nitro
of the nitro-benzene torsion angle and the p–p stacking effect (de-
group and aromatic ring in the predicted model.
scribed below), the frequency of the vibrational mode does not dif-
Again in the solid state the 2-methoxy-2-oxoethanolate (2m2o)
group in the meta position, with respect to the nitro group, is
essentially co-planar with the benzene ring with the torsion angles
fer with respect to that usually observed. The Raman spectrum had
ꢂ1
a very weak signal at 1510 cm which we attributed to the same

B.V. Cunning et al. / Journal of Molecular Structure 987 (2011) 25–33
31
Fig. 5. (a) The predicted minimum energy geometry of (I). (b) The molecular structure of (I) as revealed by single crystal X-ray diffraction.
C3–C2–O2–C10 O2–C10–C11–O11 and O11–C11–O12–C12 being
ꢂ0.6(4)°, 1.8(4)°, 0.9(5)° respectively. In contrast, the 2m2o group
in the para position lies approximately perpendicular to the ben-
zene ring (the C1–O1–C7–C8 torsion angle being ꢂ78.2(3)°).
The carbonyl oxygen (O8) located on the para 2m2o group pos-
sesses short-range interactions along the screw axis to two hydro-
gen atoms (H6 and H7B) with distances 2.718 and 2.380 Å for
O8ꢄ ꢄ ꢄH6 and O8ꢄ ꢄ ꢄH7B respectively (Fig. 6). The carbonyl oxygen
located on the meta group (O11) possesses only one short range
interaction with H7A with symmetry operation x ꢂ 1/2, 2 ꢂ y, z.
Each carbonyl group exists in substantially different chemical
environments.
Computational analysis, using differences in single point poten-
tial energies of the X-ray and theoretical gas phase geometry opti-
mised structures can approximate the crystal packing forces [26]
required to maintain the molecule in its solid state conformation.
Our initial analysis using this simplistic approach suggested that
the compound was indeed stabilized by substantial inter-molecu-
lar forces which when calculated at the B3LYP 6-31++G level affor-
ded a value of approximately 630 kJ/mol.
The magnitude of this crystal packing force raised a number of
questions relating to both the accuracy of the computationally pre-
dicted structure as well as the magnitude of the individual short-
range interactions located in the crystal structure. On closer
inspection, the differences in bond lengths between the crystal
structure and the computationally optimised structure differ by a
small, but not insignificant amount (see Table 2). It is likely that
the bond lengths in the crystal structure which differ from the pre-
dicted bond lengths could potentially have a large impact on the
single point energy calculation. To address this, we adjusted the
bond lengths of the geometry derived from the crystal structure
to the values in the predicted structure while maintaining the bond
It can be postulated that the crystal growth along the crystallo-
graphic ‘c’ axis was facilitated by the aforementioned
action between the nitro group and an adjacent aromatic ring,
p
ꢄ ꢄ ꢄ
p inter-
the para carbonylꢄ ꢄ ꢄH interactions, a C–H10Aꢄ ꢄ ꢄ
p
interaction and
the potential overlapping of adjacent benzene
p orbitals. These
interactions, along with the absence of strong interactions repeat-
ing along the ‘a’ or ‘b’ axis, explains why (I) crystallises easily as
long thin needles.
Fig. 6. The inter-molecular interactions along the crystallographic C axis. Inset: A view illustrating the O ꢄ ꢄ ꢄ H interactions.

3
2
B.V. Cunning et al. / Journal of Molecular Structure 987 (2011) 25–33
Table 2
Summary of short contacts in the molecule.
Table 4
Interactions energies of selected dimer assemblies using the X-ray
crystal structure geometries.
Short contacts
Distance (Å)
Crystal dimer assembly
Interaction energy (kJ/mol)
O42 H5
O8–H7
O8–H6
O1–H12
O1–H10
2.53
2.38
2.72
2.67
2.57
1
2
3
ꢂ37.4
ꢂ13.6
ꢂ7.0
for the variations observed between the vibrational modes of
experiment and theory.
Table 3
Total bond lengths of the various parts of the molecule.
Total distance (Å)a
Total distance (Å)b
5. Conclusion
Benzene ring
Para arm
Meta arm
Total
8.335
7.080
7.075
8.401
7.188
7.212
This study reports both the solid state vibrational and X-ray
structural analysis of a derivative of phenylenedioxydiacetic acid
and compares these data to the molecules computationally pre-
dicted properties. X-ray analysis revealed the presence of numer-
ous short-range inter-molecular forces. The theoretical method
utilised, which does not take these interactions into consideration,
predicted the bulk of the vibrational modes for the title compound.
Two notable exceptions, however, were the nitro group symmetric
and asymmetric stretches and the carbonyl symmetric stretches.
This may be attributable to the observation that both of these
groups are engaged in significant inter-molecular bonding as re-
vealed by X-ray analysis and favourable interaction energy calcula-
tions. The application of potential energy distribution analysis
allowed the assignment of the various vibrational modes, including
the mixed modes, unambiguously.
22.490
22.801 (ꢃ1.4% difference)
a
Crystal structure.
Predicted structure.
b
angles and torsions, thus normalising the bond lengths. This re-
sulted in a reduction of the difference in the single energy point
calculations to a more realistic value of 240 kJ/mol (see Table 3).
We also calculated interaction energies of three dimer assem-
blies of (I) (Fig. 7) as they appear in the crystal structure. This re-
vealed that all three interactions result in attractive forces
(
Table 4), however they were quite weak. We attributed this obser-
vation to a combination of basis set incompleteness for interaction
energies [27] and the non-optimised geometries of the initial
structures. Despite these shortcomings, the computational calcula-
tions predicted favourable interactions that may have accounted
We have revealed that the optimised geometry, as predicted
computationally, deviated quite considerably from the geometry
shown in the crystal structure. Subsequent analysis of the X-ray
Fig. 7. The geometries of the dimer systems for the three interaction energy calculations.

B.V. Cunning et al. / Journal of Molecular Structure 987 (2011) 25–33
33
structure demonstrated significant numbers of inter-molecular
crystal packing forces in the solid state. These forces were estimated
by calculating the two energies of the bond length normalised X-ray
and computationally derived minimum energy geometries. The
magnitude of this force was approximately 240 kJ/mol.
Yazyev, A.J. Austin, R. Cammi, C. Pomelli, J.W. Ochterski, P.Y. Ayala, K.
Morokuma, G.A. Voth, P. Salvador, J.J. Dannenberg, V.G. Zakrzewski, S.
Dapprich, A.D. Daniels, M.C. Strain, O. Farkas, D.K. Malick, A.D. Rabuck, K.
Raghavachari, J.B. Foresman, J.V. Ortiz, Q. Cui, A.G. Baboul, S. Clifford, J.
Cioslowski, B.B. Stefanov, G. Liu, A. Liashenko, P. Piskorz, I. Komaromi, R.L.
Martin, D.J. Fox, T. Keith, M.A. Al-Laham, C.Y. Peng, A. Nanayakkara, M.
Challacombe, P.M.W. Gill, B. Johnson, W. Chen, M.W. Wong, C. Gonzalez, J.A.
Pople, Gaussian, Inc., Wallingford CT, 2004.
Acknowledgement
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[
[
12] M.H. Jamróz, Warsaw, 2004.
13] N.B. Colthup, L.H. Daly, S.E. Wiberley, Introduction to Infrared and Raman
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The authors thank the Australian Government for an Australian
Postgraduate Award (BVC).
[14] G. Socrates, Infrared and Raman Characteristic Group Frequencies: Tables and
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[
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