Structural, spectroscopic and theoretical studies of sodium (2-carbamoylphenoxy) acetate salt

Article abstract of DOI:10.1016/j.molstruc.2019.127016

Sodium (2-carbamoylphenoxy) acetate salt crystal belongs to the P-1 space group of triclinic system, Z = 2. The asymmetric part of the unit cell consists of four (2-carbamoylphenoxy) acetate (CBA) molecules. Three Na⁺ ions are surrounded by six O atoms and one Na⁺ ion is surrounded by five O atoms. The mean Na1⁺ … O and Na2⁺ … O distance is 2.47 ? while Na3⁺ … O is 2.43 ? and Na4⁺ … O is 2.49 ?. The supramolecular self-assembly of the four (2-carbamoylphenoxy) acetate molecules is realized by hydrogen bonds, and a variety of intermolecular interactions. The interactions within the bulk of the crystal structure were highlighted with Hirshfeld surfaces. FT-IR and Raman spectra of the studied compound are reported for the first time. Assignments of the normal modes was done with the aid of density functional theory frequency calculations on the monomer and two dimers, at B3LYP/6-311 + G(2d,p) level of theory.

Full text of DOI:10.1016/j.molstruc.2019.127016

Journal Pre-proof
Structural, spectroscopic and theoretical studies of sodium (2-carbamoylphenoxy)
acetate salt
Alexandru Turza, Ana Maria Raluca Gherman, Vasile Chiꢀ, Camelia Berghian-
Grosan, Gheorghe Borodi
PII:
S0022-2860(19)31116-0
DOI:
https://doi.org/10.1016/j.molstruc.2019.127016
MOLSTR 127016
Reference:
To appear in: Journal of Molecular Structure
Received Date: 7 May 2019
Revised Date: 4 August 2019
Accepted Date: 2 September 2019
Please cite this article as: A. Turza, A.M.R. Gherman, V. Chiꢀ, C. Berghian-Grosan, G. Borodi,
Structural, spectroscopic and theoretical studies of sodium (2-carbamoylphenoxy) acetate salt, Journal
of Molecular Structure (2019), doi: https://doi.org/10.1016/j.molstruc.2019.127016.
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Structural, spectroscopic and theoretical studies of sodium (2-
carbamoylphenoxy) acetate salt
Alexandru TURZA1,2 , Ana Maria Raluca GHERMAN2,3, Vasile CHIȘ2, Camelia BERGHIAN-
GROSAN1,Gheorghe BORODI3,*
1Department of Mass Spectrometry, Chromatography and Applied Physics, National Institute of R&D of
Isotopic and Molecular Technologies, 67-103 Donat, 400293 Cluj-Napoca, Romania
2Faculty of Physics, Babeș-Bolyai University, 1 Kogălniceanu, 400084 Cluj-Napoca, Romania
3Department of Molecular and Biomolecular Physics, National Institute of R&D of Isotopic and Molecular
Technologies, 67-103 Donat, 400293 Cluj-Napoca, Romania
*Corresponding author at Department of Molecular and Biomolecular Physics, National Institute of R&D
of Isotopic and Molecular Technologies, Donat 67-103, 400293 Cluj-Napoca, Romania
E-mail address: gheorghe.borodi@yahoo.com (Gheorghe Borodi)
1

ABSTRACT
Sodium (2-carbamoylphenoxy) acetate salt crystal belongs to the P-1 space group of triclinic system, Z =
2. The asymmetric part of the unit cell consists of four (2-carbamoylphenoxy) acetate (CBA) molecules.
Three Na+ ions are surrounded by six O atoms and one Na+ ion is surrounded by five O atoms. The mean
Na1+…O and Na2+…O distance is 2.47 Å while Na3+…O is 2.43 Å and Na4+…O is 2.49 Å. The
supramolecular self-assembly of the four (2-carbamoylphenoxy) acetate molecules is realized by
hydrogen bonds, and a variety of intermolecular interactions. The interactions within the bulk of the
crystal structure were highlighted with Hirshfeld surfaces. FT-IR and Raman spectra of the studied
compound are reported for the first time. Assignments of the normal modes was done with the aid of
density functional theory frequency calculations on the monomer and two dimers, at B3LYP/6-
311+G(2d,p) level of theory.
Keywords: algamon, sodium (2-carbamoylphenoxy) acetate, crystal structure, density functional theory,
raman, FT-IR
INTRODUCTION
Sodium (2-carbamoylphenoxy) acetate salt, with the chemical formula C9H8NNaO4 (Scheme 1),
produced by Microsin (Bucharest, Romania) under the name of algamon [1], is the salt of the active
substance o-carbamoyl-phenoxyacetic acid, used for its analgesic activity [2]. To our knowledge, the
crystal structure of the product, further denoted as AGM, is not contained in the CSD 2018 database yet.
The compound is appearing as solid white powder at room temperature, with a 263o C melting point,
and 419o C boiling point.
Scheme 1 – Molecular scheme of sodium (2-carbamoylphenoxy) acetate.
The pharmacokinetics of sodium (2-carbamoylphenoxy) acetate was studied in 9 healthy male
subjects following a single intramuscular administration and the plasma concentration of o-
carbamoylphenoxyacetic acid and metabolised salicylamide was analysed. The plasma concentration
profiles (AUC) were also monitored. It has been shown that there are moderate rates of metabolic
conversion and only small amounts of salicylamide appear in the circulatory system [3].
The literature shows a lack of studies referring to this compound. In this paper, we report for
the first time its structural characterization by X-ray single crystals diffraction, XRPD, and the
characterization of intermolecular interactions with the surfaces Hirshfeld [4-8]. Vibrational properties
of AGM are also reported herein. Its FT-IR and Raman spectra were registered for the first time. A full
assignment of both spectra is listed. This was achieved with the aid of frequency calculations, by using
density functional theory (DFT) methods. The calculated spectra, both IR and Raman, were performed
on AGM monomer and two dimers, as being present in the crystal packing. Dimer models, able to
capture intermolecular interactions, bring supplementary useful information related to vibrational
features of molecules [9, 10].
2

EXPERIMENTAL
Algamon was obtained from Microsin, a Romanian producer of active pharmaceutical
ingredients, and was used without further purification.
A suitable single crystal (0.3 x 0.2 x 0.1 mm) was selected from the bulk of crystalline powder; it
was coated in inert oil (Paratone N), and mounted on a fine nylon loop. X-ray single crystal data
collection was acquired by a SuperNova diffractometer equipped with dual microsources, Eos CCD
detector with the tube operating at 50 kV and a current of 0.8 mA using Cu Kα radiation, the crystal
being kept at room temperature during data acquisition.
Powder X-ray diffraction pattern was recorded on a Bruker D8 Advance diffractometer,
equipped with a germanium (1 1 1) monochromator in the incident beam to get a monochromatic
radiation (Cu Kα1). Data acquisition was made with DIFFRAC plus XRD Commander software, having a
scan speed of 0.02o s-1 in 3-40o 2θ range.
Crystallographic data for the structure reported in this paper have been deposited with the
Cambridge Structural Database as Supplementary Publication CCDC No 1909666.
Raman spectrum was collected with a Raman JASCO NRS 3300 spectrometer, equipped with a
CCD detector (-69 °C), a diffraction grating of 600/mm, and a 100x Olympus objective. 785 nm laser line
was used as an excitation source, its power being set at 137.6 mW. The resulted Raman spectrum is an
addition of three acquisitions of 120 s each. It was recorded with a resolution of 6.45 cm-1.
FT-IR spectrum of AGM was collected with a JASCO 6100 spectrometer, with a resolution of 2
cm-1, using KBr pellet technique. The spectrum was recorded in the range of 350-4000 cm-1.
Influence of acidic media onto the sodium (2-carbamoylphenoxy) acetate: the salt was treated
with 0.2 M hydrochloric acid, considering a 1: 1.1 molar ratio between salt and HCl. Thus, to 100 mg of
salt, 2.53 mL solution of 0.2 M hydrochloric acid is added. In a very short time a white precipitate was
obtained. It was analyzed by X-ray diffraction and the presence of NaCl was detected in the obtained
mixture. Further, the precipitate was washed with double distilled water to remove the sodium chloride.
COMPUTATIONAL DETAILS
Single crystal diffraction data were collected using CrysAlis PRO software and crystal structure
was solved with Olex2 [11], by olex2.solve [12] structure solution program using Charge Flipping and
refined with the ShelXL [13] refinement package by least Squares minimization. Absorption correction
was made by multi-scan method in CrysAlis PRO software using spherical harmonics, implemented in
SCALE3 ABSPACK scaling algorithm [14].
Hydrogen atoms attached to C, N and O atoms were positioned geometrically and refined as
riding atoms, considering Uiso(H)=1.2Ueq(C,N) for all CH, CH2 and NH2 groups and 1.5Ueq(O) for all OH2
groups. Water molecule was refined as rotating group with O-H=0.878 Å. Secondary CH2 were refined
with riding coordinates, with C-H=0.97 Å, aromatic H atoms were refined as riding with C-H=0.93 Å,
while primary amide with riding coordinates and N-H=0.86 Å.
Hirshfeld analysis was used to provide data about interactions within the bulk of a crystal
structure, which are mapped on a 3D surface [15, 16]. Based on the CIF file obtained by single crystal X-
ray diffraction, Crystal Explorer software [17] was used to calculate the Hirshfeld surface and color
mapping. During the computation, the X-H bond lenghts (where X = C, O, or N) were normalized at
standard bond lenghts determined by neutron diffraction (C-H=1.083 Å, O-H=0.983 Å and N-H=1.009 Å).
Fingerprints [18, 19] are 2D representations designed to visualize different interactions in a quantitative
manner, as percentages. Every individual molecule has an unique Hirshfeld surface and fingerprint plot
which are influenced by its environment. Fingerprint plot was done using dnorm function, where dnorm (Eq.
(1)) is a ratio encompassing the distances of any surface point to the nearest interior (di) and exterior
(de) nucleus, and the van der Waals radii of the atoms. For each point on the Hirsfeld surface, de and di
are both determined, each point on the 2D fingerprint plot corresponding to a unique pair (de and di).
3

Red spots on the Hirshfeld surface denote that dnorm has a negative value, thus the sum of di and de is
less than the sum of the van der Waals radii. White spots indicate that the sum of di and de is equal to
zero, and intermolecular connections are close to the sum of van der Waals radii. Finally, blue indicates
a positive value for dnorm function, where the intermolecular contacts are longer compared to the sum of
van der Waals radii.
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Density Functional Theory (DFT) methods, implemented in Gaussian 09, Revision E.01 software
package [20], were employed on both geometry optimizations and frequency calculations. The level of
theory used is a joining of B3LYP [21-24] hybrid exchange-correlation functional and 6-311+G(2d,p)
triple-zeta basis set. Wavefunction convergence and geometry optimization were met using tight criteria
and an ultrafine grid. Both geometry optimization and frequency calculations were performed on
algamon monomer (Figure 1) and two of its dimers (Figure 2). There are two ways in which two algamon
molecules can form hydrogen bonds in the crystallographic network, thus the two dimers. All starting
geometries were taken from the crystallographic data. Frequency calculations confirmed that the
geometries correspond to true minima on the potential energy surface. Calculated bond lenghts, angles
and dihaedrals of AGM monomer, dimer I, and dimer II are listed in Table S3, S4, and S5. The calculated
wavenumbers were scaled by the corresponding scaling factor of the used level of theory (0.967) as
suggested by Andersson and Uvdal [25]. Normal modes assignment to their specific IR and Raman bands
was made by observation of animated modes by using GaussView, Version 5 [26] software. We took into
account both the relative intensities and peaks’ position of the resulted calculated Raman and IR
spectra. All calculations were performed in gaseous phase.
Molecular structures of AGM monomer and the dimers were pictured in Mercury [27], as well as
crystal packing, hydrogen bonds and short range interactions.
All Raman and IR spectra, both calculated and experimental, were ploted in Origin (OriginLab,
Northampton, MA).
Figure 1 – Optimized geometry of AGM molecule at B3LYP/6-311+G(2d,p) level of theory, in gas phase.
4

Figure 2 – Optimized geometry of AGM dimer I, and II at B3LYP/6-311+G(2d,p) level of theory, in gas phase. Labels
from the monomer are kept the same for both dimers
RESULTS AND DISCUSSIONS
1. Crystal structure
1.1 Single crystal data and molecular configuration
Crystals of sodium (2-carbamoylphenoxy) acetate (C9H8NNaO4; M = 217.154 g/mol) are triclinic, belong
to the space group P-1 and have the following unit cell parameters: a = 10.8538(4) = Å, b = 13.6231(6) Å,
c = 13.8545(6) Å, α = 103.770(4)°, β = 103.723(3)°, γ = 100.065(3)°. No restraints and constraints were
used during refinement procedure. All information about crystal structure and refinement are displayed
in Table 1.
Table 1 - Crystal data and structure refinement for sodium (2-carbamoylphenoxy) acetate.
Identification code
Empirical formula
Formula weight
Temperature/K
Crystal system
Space group
a/Å
sodium (2-carbamoylphenoxy) acetate
C36H34N4Na4O17
886.63
293(2)
triclinic
P-1
10.8538(4)
13.6231(6)
13.8545(6)
103.770(4)
103.723(3)
100.065(3)
1873.95(13)
2
b/Å
c/Å
α/°
β/°
γ/°
Volume/Å3
Z
ρcalcg/cm3
μ/mm-1
1.571
1.460
F(000)
916.0
Crystal size/mm3
0.3 × 0.2 × 0.1
CuKα (λ = 1.54184)
Radiation
2Θ range for data collection/° 6.89 to 142.896
Index ranges -13 ≤ h ≤ 10, -16 ≤ k ≤ 16, -17 ≤ l ≤ 14
5

Reflections collected
11851
Independent reflections
7113 [Rint = 0.0170, Rsigma = 0.0224]
Data/restraints/parameters 7113/0/551
Goodness-of-fit on F2
1.038
Final R indexes [I>=2σ (I)]
R1 = 0.0343, wR2 = 0.0974
Final R indexes [all data]
R1 = 0.0380, wR2 = 0.1009
Largest diff. peak/hole / e Å-3 0.29/-0.24
The four molecules in the asymmetric unit were overlapped (Figure 3) using Olex2 software in
order to highlight the differences between their configurations. It can be observed that these
differences are not very large. The most notable are present in the acetate group and the oxygen atoms
(O11, O25, O39, and O53) between the acetate group and the carbamoylphenoxy benzene ring. Small
configuration differences, but still noticeable, can be observed are in the amide group. Finally, in the
unit cell, three of the four AGM molecules exhibit similar configuration, one of them being slightly
different, as it can be seen in Figure 3. The O43, O39 oxygen atoms and C36 carbon belong to the same
molecule, and all of them have different position, compared with the corresponding O atoms from the
other three molecules.
Figure 3 – Overlay of the four sodium (2-carbamoylphenoxy) acetate molecules forming the asymmetric unit
1.2 Na cations coordination
In the crystal structure, the asymmetric unit for sodium (2-carbamoylphenoxy) acetate is
composed of four such molecules, being coordinated to four Na atoms. The sodium cations are
coordinated to oxygen atoms, coordination being five or six, as seen in Figure 4b, together with their
geometries. All O-Na distances and O-Na-O angles are listed in Table S1 and S2, respectively. The Na-O
coordination distances values are within a fairly narrow range 2.317 – 2.738 Å, the maximum difference
being slightly over 0.4 Å. Three of the four Na atoms are coordinated by oxygen atoms belonging to the
acetate fragment, while the last is linked by the oxygen from amide group. Mean Na-O bond lengths are
comparable to those in similar compounds [28, 29].
Na cations are positioned on both sides of the crystallographic plane (0 0 1), in proximity of this
plane, as seen in Figure S1. The atoms with the same label are connected one by one through inversion
operation.
1.3 Hydrogen bonds and short range interactions
Among the three (2-carbamoylphenoxy) acetate molecules from the asymmetric unit, for which the
acetate fragments coordinates the sodium cations, one of them forms the N46-H…O45 intermolecular
hydrogen bond with the amide group. The second molecule forms a hydrogen bond with the amide
6

group N18-H…O15, while the last one does not interact at all with its neighbours by intermolecular
hydrogen bonds. This is the AGM monomer for which the oxygen from amide coordinates one Na atom.
Two intermolecular hydrogen bonds starting from the water molecule (O61), where O61 is the donor,
form the O61-H61B ... O43 and O61-H61A ... O45 intermolecular bonds. There are also nine
intramolecular hydrogen bonds bridging the nitrogen atoms of the amides with the acetate and amide
oxygens of (2-carbamoylphenoxy) anions, which are presented in the second part of Table 2. All the
above mentioned hydrogen bonds can be seen in Figure 4a.
Table 2 – Intermolecular (* - red doted lines in Figure 4a) and intramolecular (^ - blue dotted lines in Figure 4a)
hydrogen bond lengths, within the asymmetric unit of sodium (2-carbamoylphenoxy) acetate
D-H…A
d(D-H) d(H…A)
0.860 2.0982(17) 2.9455(17) 168.30(5)
0.860 2.306(6) 3.0271(16) 139.4(8)
0.878 2.0878(15) 2.9208(15) 162.92(5)
0.878 1.895(4) 2.7606(16) 168.3(16)
d(D…A)
<(DHA)
*(amide)N46-H46A…O45
*(water)O61-H61A…O45
*(amide)N18-H18A…O15
*(water)O61-H61B…O43
^N60-H60B…O53
^N60-H60B…O57
^N60-H60A…O29
^N18-H18B…O11
^N18-H18B…O15
^N32-H32B…O25
^N32-H32A…O57
^N46-H46B…O39
^N46-H46B…O43
0.860 1.9637(16) 2.6282(16) 133.19(5)
0.860 2.5239(16) 3.3404(16) 158.85(4)
0.860
2.102(16) 2.9295(16) 161.25(5)
0.860 1.9433(15) 2.6105(15) 133.44(5)
0.860 2.5518(16) 3.3659(16) 158.29(3)
0.860 1.9362(16) 2.6077(16) 133.96(5)
0.860 2.1529(17) 2.9654(17) 157.42(5)
0.860 1.9296(17) 2.5981(17) 133.57(5)
0.860 2.4085(17) 3.2060(17) 154.47(4)
7

(a)
(b)
Figure 4 – (a) Inter (red dotted lines) and intramolecular (blue dotted lines) hydrogen bonds within the asymmetric
unit of sodium (2-carbamoylphenoxy) acetate; (b) coordination of the four Na ions
By omitting the sodium cations within the structure it is observed that the crystal structure may be
reduced to three synthons held by N-H…O and O-H…O hydrogen bonds between the (2-
carbamoylphenoxy) acetate anions.
Two (2-carbamoylphenoxy) acetate anions are coupled by double N46-H46A…O45 hydrogen bond,
2
characterized by a R2 (8) intermolecular descriptor. Also the two (2-carbamoylphenoxy) acetate (CBA)
molecules are linked by bridged water molecules through the O61-H61B ... O43 bond with acetate group
and O61-H61A ... O45 hydrogen bond from the amide group. The (2-carbamoylphenoxy) acetate anions
and water molecules are related by an inversion operation, having the centroid coordinates at (0, ½, ½)
and which is a special position and an inversion point of the P-1 space group (Figure S2 A).
2
A different supramolecular synthon, forming a R2 (18) motif is built via double N18-H18A…O15
intermolecular hydrogen bonds. The synthon is generated by the inversion of a (2-carbamoylphenoxy)
acetate anion, having the centroid positioned on the center of oa edge (½, 0, 0), which is an inversion
point of the P-1 space group and a special position (Figure S2 B).
Another supramolecular synthon is generated by coupling two (2-carbamoylphenoxy) acetate
anions from asymmetric unit via N32-H32A…O57, respectively N60-H60A…O29 hydrogen bonds. The
8

2
assembly is characterized by a R2 (18) descriptor having the anions related by pseudo-inversion with the
centroid localized in general positions (0.576, 0.76, 0.063) (Figure S2 C).
Besides the hydrogen bonds, the crystal structure stability is also held by short range interactions, as
given in Table 3.
Table 3 – Distances (in Å) for the different types of short range interactions in the crystal packing
Interaction
Na-Na
No/asymm unit
Distances (Å)
3.485-3.991
3.140-3.821
2.871-3.498
3.079-3.393
3.046-3.240
4
4
8
4
3
Na-π
Na-C
C-H…Na
N-H…Na
1.4 Hirshfeld analysis
The analysis was conducted individually for each fragment of (2-carbamoylphenoxy) acetate in the
asymmetric unit and the water molecule as well. Hirshfeld surfaces were generated presenting front and
back views, with the Na ions being always outside of the surfaces.
The Hirshfeld surface mapped with dnorm for (2-carbamoylphenoxy) acetate fragment (Figure 5a, 5b)
2
which include the N18 atom shows two red spots which are included in the formation of R2 (18)
supramolecular synthon via the N18-H18A…O15 hydrogen bond (Figure S2 B). These two hydrogen
bonds are identified on the fingerprint plot by H…O and O…H interactions as two sharp spikes labeled by
1 and 2 (Figure 5c). Five deep red spots are present on the Hirshfeld surface and are associated with the
coordinative interaction with Na1, Na2 and Na4 cations (Figures 5a, 5b). This feature is signaled on the
fingerprint plot by an intense green area labeled by 4.
(a)
(b)
9

(c)
Figure 5 – Front view (a), back view (b) of the Hirshfeld surface mapped with dnorm over the range -0.6842 to
+1.1678 arbitrary units and fingerprint plot (c) for the CBA molecule including N18 atom.
The (2-carbamoylphenoxy) acetate fragment which include N32 atom exhibits two red spots
mapped on the Hirshfeld surface (Figures 6a, 6b), indicating the formation of two intermolecular
hydrogen bonds, namely N32-H32A…O57 (N32-H32 being inside the Hirshfeld surface) respectively N60-
2
H60A…O29 (O29 being inside the Hirshfeld surface), which participate to the formation of the R2 (18)
synthon (Figure S 2C). Six deep red spots are present on the surface and are characteristic to Na-O (Na1,
Na2, and Na3) coordinative interactions (seen on the fingerprint plot in Figure 6c as label 4).
(a)
(b)
10

(c)
Figure 6 – Front view (a), back view (b) of the Hirshfeld surface mapped with dnorm over the range -0.6903 to
+1.1672 arbitrary units and fingerprint plot (c) for the CBA molecule including N32 atom.
The amide group of the (2-carbamoylphenoxy) acetate fragment, including the N46 atom, builds
2
a R2 (8) graph set motif via the two N46-H46A…O45 hydrogen bonds (Figure S2 A), which are seen as
two adjacent red spots on the Hirshfeld surface (Figures 7a, 7b). Additionally, two hydrogen bonds O61-
H61B...N43 and O61-H61A…O45 are identified on the surface as red areas, O61 being the oxygen from
water. Four coordinative interactions with the Na2, Na3 and Na4 cations are also seen on the surface.
(a)
(b)
11

(c)
Figure 7 – Front view (a), back view (b) of the Hirshfeld surface mapped with dnorm over the range -0.6595 to
+1.2012 arbitrary units and fingerprint plot (c) for the CBA molecule including N46 atom
.
The Hirshfeld surface mapped on the fragment containing the N60 atom shows two red spots as
an indication of N32-H32A…O57 respectively N60-H60B…O29 hydrogen bonds formation (Figures 8a, 8b)
2
which builds a R2 (18) graph set motif (Figure S 2C) between the two (2-carbamoylphenoxy) acetate
anions. The coordination with five Na cations (Na1, Na3 and Na4) is represented as deep red spots on
the surface.
(a)
(b)
12

(c)
Figure 8 – Front view (a), back view (b) of the Hirshfeld surface mapped with dnorm over the range -0.7055 to
+1.2092 arbitrary units and fingerprint plot (c) for the CBA molecule including N60 atom
.
For water molecule, the Hirshfeld surface mapped with dnorm shows the coordinative contact as
an intense red spot in the proximity of Na4 cation (Figures 9a, 9b). The O61-H61B…O43 and O61-
H61A…O45 hydrogen bonds are illustrated as two red spots, O61 being the oxygen from water. The 2D
representation of the Hirshfeld surface (the fingerprint plot,) shows a sharp spike characteristic to O-
H…O hydrogen bonding (label 1, Figure 9c). The O61-Na4 coordination is represented on the Hirshfeld
surface as a red spot and transposed on the fingerprint plot as label 4.
It can be noted that the fingerprint plots for the four molecules are quite similar; spike 1 and 2
represents the H…O and O…H contacts, label 3 indicates the H…H contacts while the O…Na contacts are
shown by label 4.
(a)
(b)
13

(c)
Figure 9 – Front view (a), back view (b) of the Hirshfeld surface mapped with dnorm over the range -0.6566 to
+1.0870 arbitrary units and fingerprint plot (c) for the water molecule.
Therefore, Hirshfeld analysis for all four CBA molecules and water revealed that the strongest
interactions are hydrogen bonds that contribute to the formation of supramolecular synthons and the
interactions between oxygen atoms and Na cations. However, the percentage contributions of
interatomic contacts to the Hirshfeld surface shows that the highest number of interactions correspond
to H…H contacts, followed by O…H/H…O, C…H/H…C and O…Na contacts, as shown in Figure 10. Yet, for
the water molecule, the number of H…H and O…H/H…O interactions is almost equal.
Figure 10- Percentage contributions to the Hirshfeld surface area for the various close intermolecular contacts for
the different CBA fragments and water molecule. N60, N46, N31, N18 represents the molecules which include
these atoms
.
2. Vibrational spectroscopy. IR and Raman spectra
14

Vibrational (especially Raman) spectroscopy is an important tool for the pharmaceutical field,
both in the development and manufacturing stages, proving significant information in the process of
drug production [30]. Thus, a full description of both Raman and IR bands are very important for any
pharmaceutical drug. The AGM Raman and IR bands are presented in Table 4, along with a full
assignment of the normal modes. The observed bands (Figure 11 and 12) are classified by their
intensities as very weak, weak, medium, strong, and very strong.
In the high wavenumber region (above 1800 cm-1) the vibrational spectrum has been recorded
by using FT-IR spectroscopy, Figure 11. We assigned symmetric and asymmetric stretching of NH2 group
to the medium 3414 cm-1 and small 3590 cm-1 IR bands. They are very well approximated by frequency
calculations on AGM monomer, at 3417 and 3565 cm-1.The very small IR bands above 2900 cm-1
represent different stretches of CH and CH2 units. Most of the corresponding calculated wavenumbers
are in better agreement for dimer II. This fitting is in accordance with the one between the calculated
and XRD geometrical parameters (bond lengths, angles and dihedrals) for dimer II, as seen in Table S3 –
S5.
There are several bands in the 1500 – 1700 cm-1 range, which correspond mainly to NH2 bending
moiety, one of them being the 1560 cm-1 frequency; it is of medium intensity in the Raman spectrum,
Figure 12, and a weak shoulder, in the IR spectrum, slightly shifted to 1567 cm-1. In Table 4 we report a
set of two wavenumbers for each mode, corresponding to both NH2 groups, one for each molecule in a
dimer. NH2 chemical group is involved in both inter and intramolecular hydrogen bonds, what brings the
differences in corresponding calculated bonds of the monomer and two dimers. The other one is one of
the strongest Raman band, at 1591 cm-1, and has an IR correspondent shifted to 1600 cm-1. The
calculated bands of both dimers perfectly match the experimental values (1591 and 1594 cm-1 for dimer
I; 1590 and 1596 cm-1 for dimer II). In the IR spectrum, for the moieties grouped in a broad band with
several peaks, all calculated correspondents are underestimated with a significant amount. 1625 cm-1 is
one of the strongest intensities in the whole spectrum, and does not have a Raman correspondent. Best
calculated results were obtained in the case of the two dimers.
The bands between 1250 and 1500 cm-1, of complementary IR/Raman medium or weak
intensity, are mainly due to either CC stretching, or CH2 wagging.
The weak band at 1446 cm-1 (Raman) or 1442 cm-1 (IR) is due to the bending vibration of NH2
unit.
CH2 twisting is assigned to the weak Raman 1222 cm-1, or IR 1224 cm-1 peak. It is best
reproduced by the two dimers, with a difference of 17 and 19 cm-1.
The two strong Raman bands at 1153 cm-1 and 1167 cm-1, and their IR correspondents, at 1152
and 1163 cm-1, are due to an in plane bending of CH groups.
NH2 rocking is assigned to the strong Raman band at 1117 cm-1, with very weak IR intensity.
CN stretching is assigned to the medium Raman and weak IR band, observed at 1095 cm-1, and
1097 cm-1, respectively. The calculated values are best reproduced for the two dimers, with shifts from
experimental counterparts between 2 and 10 cm-1. We obtained a set of two values for each dimer. CO
stretching is assigned to the weak Raman shoulder at 1054 cm-1, and weak IR band at 1053 cm-1.
Moreover, this band represents an in plane deformation of benzene ring.
Benzene ring breathing can be observed as a strong Raman band at 1042 cm-1, and a weak IR, at
1044 cm-1. The results for all three systems present close values, 1030 cm-1 being the best.
C11C12 stretching, coupled with O=C-O bending, can be observed as a strong Raman band at
935 cm-1, and a very weak IR band, at 934 cm-1. This band is best reproduced in the case of dimer I (937
cm-1), as expected, since the mentioned atoms are involved in hydrogen bonds between two AGM
molecules, bonds that are always present in AGM crystal, as seen in Figure 4a.
The weak band at 850 cm-1, existing in both Raman and IR spectrum, is attributed to an in plane
deformation of the benzene ring, more specifically, it consists of a CCC bending and an in plane bending
15

of CH groups. This band’s shape is very well reproduced in the calculated Raman spectrum of both
dimers, together with the very weak shoulder.
NH2 twisting is assigned to the very strong Raman band at 763 cm-1, and the very weak shoulder,
at 796 cm-1. In the IR spectrum, this band is of weak intensity. Again, the correspondent calculated on
dimer I is in the best agreement (762 cm-1) with the experimental data, the NH2 groups in this
configuration being involved in inter and intramolecular hydrogen bonds.
In phase out of plane bending of CH group is assigned to the medium band at 750 cm-1. This
band is present only in the IR spectrum.
O=C-O bending can be observed in the Raman spectrum with medium intensity (701 cm-1) and
with weak intensity in the IR spectrum (699 cm-1). The calculated wavenumber corresponding to dimer I
is in the best agreement with experimental data, hydrogen bonds which involve the above mentioned
atoms being satisfied in this configuration.
The weak Raman and medium IR band observed at 623 cm-1 is due to an in plane deformation of
the benzene ring, a combination of NH2 rocking and CCC bending. Its very weak Raman shoulder or the
medium IR band, observed at 612 cm-1, and 617 cm-1 respectively, are assigned to CH2 rocking and O=C-
O wagging.
The band at 474 cm-1 presents medium intensity in the Raman spectrum and weak intensity in
the IR spectrum. In the latter case, it can be observed slightly shifted, at 480 cm-1. This band is assigned
to NH2 rocking. The corresponding value calculated on the AGM monomer is in a closer proximity with
the Raman value, while those calculated on dimers are in better agreement with the value in the IR
spectrum.
Raman band observed at 412 cm-1 is the strongest and is attributed to an in plane deformation
of AGM molecule. In the IR spectrum, this band is of very weak intensity. Rocking of AGM molecule is
attributed to the 358 cm-1 band, with medium Raman and weak IR intensity. In both cases, the
correspondent wavenumbers calculated on dimer II have the smallest difference relative to the
experimental data. Both values are underestimated.
Another very strong band in the Raman spectrum is the one present at 269 cm-1. We assigned a
twisting of the benzene ring to this band – an out of plane deformation of the ring.
The medium Raman band observed at 154 cm-1 is broad. We assigned this band to a
combination of CH2 rocking and the same twisting of the benzene ring.
On a first glance, the overall shapes of the calculated IR and Raman spectra of AGM are not a
facsimile of the experimental ones. Some of the FT-IR and Raman bands were very well reproduced by
our calculations, such as 1591 cm-1 (Raman) and 1600 cm-1 (IR), 1329/1326 cm-1, 1278/1279 cm-1,
1095/1097 cm-1, 935/934 cm-1, 796/799 cm-1, 763/765 cm-1, etc (see Table 4). This made assigning their
normal modes much easier. While for other bands, the differences in position/intensity are more
notable, but not troubling, especially in the 1000 – 1700 cm-1 range, because of the approximations we
took on choosing the models and level of theory. The models for which one wants to perform frequency
calculations by using DFT methods are limited to the number of atoms. When a monomer is used, the
vibrations corresponding to functional groups involved in intermolecular interactions (such as hydrogen
bonds) will differ significantly because these interactions are not taken into account. This is the reason
why we chose to different models of dimmers (Figure 1 and 2). The four molecules of AGM from a unit
cell are involved in three intermolecular hydrogen bonds – one between two of them, forming a dimer I,
and the others, interacting with AGM molecules outside the unit cell, forming another dimer I, and a
dimer II (Figure 4a). As a result, the vibrational spectra should be a combination of the two dimmers’.
Models consisting AGM molecules which present π-π stacking interactions (Figure 4a) were not
considered either. On the other hand, we did not take into account the anharmonicity when we
performed the frequency calculations. This usually comes with discrepancies between our results and
experimental data.
16

Table 4 – Experimental Raman and FT-IR bands of AGM molecule, together with full assignments based on DFT
calculations, performed on the monomer and the two considered dimers of the molecule of interest. All
calculations were done in gas-phase, at B3LYP/6-311+G(2d,p) level of theory.
Experimental
Calculated
monomer
152
Assignments
Raman
IR
dimer I
145
160
173; 181
234; 244
270
284
306
371; 380
427
dimer II
156
154 m
-
-
-
-
-
-
ρ(CH2), τ(benzene ring)
-
-
ρ(CH2), τ(benzene ring) in phase monomers
ρ(benzene ring), β(side chains) (vHB(O10H20))
ρ(benzene ring), β(side chains) (vHB(O13H20))
τ(benzene ring)
ρ(benzene ring), ρ(formamide), ν(O14Na15), ρ(O13C12O14)
ρ(AGM) – ρ(NH2), ρ(benzene ring), ρ(O13C12O14)
ρ(AGM) – ω(CH2), β(C1C7N9), ρ(NH2)
in plan def. of AGM – ν(C1C7), ρ(NH2), β(O8C7N9), δ(CH), ω(CH2)
ω(NH2)
181
214
252
286
338
359
401
412
183; 188
214; 216
258
269 vs
294
358 m
-
412 vs
354 w
364 w
408 vw
349; 350
364; 376
402; 421
-
-
-
474 m
526 vw
580 w
428 vw
480 w
529 vw
567 w
-
448
477
539
580
446
481; 485
543
582
599
-
ω(NH2), τ(CH) out of phase
ρ(NH2), ρ(O13C12O14), ω(CH2), δ(CH)
τ(CH) out of phase, τ(NH2)
β(C6O10C11), δ(CH), ρ(NH2), ω(CH2)
β(C1C6C5), β(C2C3C4) – in plane deformation of benzene ring, ν(C11C12), ρ(NH2),
β(O13C12O14), β(O8C7N9)
481; 488
542; 543
581; 585
609; 610
591 sh w
606
612 sh vw
623 w
617 m
623 sh m
623
625
-
656
714
617
642
655
694
708
622
645
640
ρ(CH2), ω(C12O13O14)
ρ(NH2), β(C1C2C3), β(C4C5C6) – in plane deformation of benzene ring
ω(NH2)
τ(NH2), τ(CH) out of phase
β(O13C12O14), ρ(NH2), β(C2C1C6), β(C3C4C5) – in plane deformation of benzene
ring
681 sh vw
701 m
675 w
699 w
-
719; 722
-
721
773
762; 786
-
ω(NH2)
τ(CH) in phase
-
750 m
767
764
766
774; 778
763 s
765 sh w
τ(NH2), ν(C1C7), β(C2C1C6), β(C3C4C5), δ(CH) – in plane deformation of benzene
ring, β(O13C12O14), β(C6O10C11)
τ(NH2), τ(CH) out of phase, ω(C1C7O8)
β(C2C3C4), δ(CH) – in plane deformation of benzene ring, β(C5C6O10), ρ(NH2)
τ(CH) out of phase – out of lane deformation of benzene ring
ν(C11C12), β(O13C12O14), ω(CH2)
benzene ring breathing, δ(CH)
ν(O10C11), β(C3C4C5), δ(CH) – in plane deformation of benzene ring
ν(C7N9), ρ(NH2), δ(CH), ν(C11O10)
ρ(NH2), β(C1C6C5), δ(CH)
796 vw
850 w
798 vw
850 sh w
805
862
868
819
861
877
937
1030
799; 800
864
874
945
1030
935 s
1042 s
1054 sh w
1095 m
1117 s
1153 s
1167 s
1222 w
1252 m
934 vw
1044 w
1053 w
1097 w
1117 vw
1152 w
1163 w
1224 w
1252 m
945
1029
1042
1083
1060
1125
1147
1208
1227
1252
1280
1312
1329
1392
1016
1041
1093; 1103
1075; 1079
1130
1147
1205
1227; 1230
1256; 1257
1279
1311
1374
1101; 1105
1075; 1076
1130; 1132
1146
δ(CH), ρ(NH2)
δ(CH)
τ(CH2)
1205
1229; 1230
1256; 1257
1279; 1280
1311
1361; 1375
1393
ν(C6O10), ν(C1C2), ν(C4C5), δ(CH), ω(CH2)
β(C5C1C7), δ(CH), ρ(NH2), ω(CH2)
ν(C1C2), ν(C3C4), ν(C5C6), δ(CH) – in plane deformation of benzene ring, β(NH2)
ω(CH2), δ(C5H9)
ν(C1C7), β(C7N9H20), δ(CH)
ν(C11C12), ω(CH2), νsym(O13C12O14)
1278 w
1301 w
1329 w
1406 sh m
1423 m
1446 w
1463 m
1482 w
1560 m
1591 vs
1600sh m
1631sh vw
1653sh vw
1684 w
-
1279 m
1301 sh w
1326 w
1390 sh w
1421 m
1442 w
1461 m
1483 m
1567 sh w
1600 vs
1388; 1392
1432
1438
1467
1557
1584
1563
1541
1429
1441; 1442
1464
1532; 1536
1591; 1594
1565
1594
1617
1653
2936
1431
1436; 1438
1467
β(NH2), δ(CH)
ν(C1C2), ν(C5C6), δ(CH), β(CH2)
ν(C1C6), ν(C3C4), δ(CH), β(CH2)
β(NH2), ν(C1C2), ν(C3C4), δ(CH), ν(C7=O8), νas(O13C12O14)
β(NH2), ν(C2C3), ν(C5C6), δ(CH)
β(NH2), ν(C1C6), ν(C3C4), δ(CH)
β(NH2), νas(O13C12O14), ω(CH2)
β(NH2), ν(C7=O8), ν(C1C2), ν(C4C5), δ(CH)
β(NH2), ν(C7=O8), ν(C1C2), ν(C4C5), δ(CH)
νsym(CH2)
1553 (R); 1554 (IR)
1590 (R); 1596 (IR)
1567 (R); 1572 (IR)
1541 (R); 1549 (IR)
1642
1625 vs
1654 s
1685sh w
2917
1650
2921
2961
-
1563
2920
2960
-
-
-
2946
2979
2982
-
νas(CH2)
-
-
3051
3060
3063
3058
νas(CH) out of phase
17

-
-
-
-
-
-
-
-
-
-
3079
3078
3095
3099
-
-
-
-
-
3080
3091
3099
-
-
-
-
-
3075
3095
3098
-
-
-
-
-
νsym(CH2) out of phase
νas(CH2) in phase
νsym(CH2) out of phase
-
-
-
-
-
3199
3254
3301
3356
3386
3414
3590
3416
3565
3318
3444
3251
3475
νsym(NH2)
νas(NH2)
ν – stretching; β – bending; δ – in plane bending; ρ – rocking; τ – twisting; ω – wagging; as – asymmetric; sym – symmetricș; vw – very weak; w –
weak; m – medium; s – strong; vs – very strong; IR – only IR active; R – only Raman active;
Figure 11 – Experimental FT-IR spectrum of AGM molecule in solid state, compared to calculated IR spectra on
AGM monomer, dimer I, and dimer II. All calculations were performed at B3LYP/6-311+G(2d,p) level of theory, in
gas-phase.
18

Figure 12 – Experimental Raman spectrum of AGM molecule in solid state (excitation laser line: 785 nm), compared
to the calculated Raman spectra on AGM monomer, dimer I, and dimer II. All calculations were performed at
B3LYP/6-311+G(2d,p) level of theory, in gas-phase.
3. Influence of acidic media onto the sodium (2-carbamoylphenoxy) acetate salt
Being the salt of an active substance from the group of the salicylic acid derivatives, namely o-
carbamoyl-phenoxyacetic acid, it is interesting to investigate the influence of slight amounts of
hydrochloric acid onto the sodium salt structure.
Thus, the salt was treated with 0.2 M hydrochloric acid, considering a 1: 1.1 molar ratio between
salt and HCl. The X-ray diffraction pattern, FT-IR and Raman spectra of the final compound are
presented in Figure 14 (for comparison and a better understanding of the changes, the spectra of the
initial structure are also presented).
(a)
(b)
19

(c)
Figure 13 – X-ray diffraction (XRD) (a), FT-IR (b) and Raman (c) spectra of AGM before and after the treatment with
1.1 equivalents of 0.2 M hydrochloric acid
From Figure 14, it can be observed that after treatment, a new structure was obtained and
there are not at all traces of the starting material. The new compound was indexed by several indexing
methods: TREOR90 [31], DICVOL96 [32] and X-Cell [33] using the Reflex module incorporated in the
Biovia Materials Studio software [34]. Through all three indexing techniques, a monoclinic common
solution (a= 17.5567 Å, b= 4.8948 Å, c= 16.7413 Å, β=114.68°) with a relatively high figure of merit
(F.O.M.) was obtained
The vibrational data (both FT-IR and Raman) indicate the transformation of sodium salt in the
corresponding acid: the appearing of new bands in the IR spectra, at 1713 and 3210 cm-1, assigned to
C=O and O-H stretching vibrations from the –COOH group, Figure 14b, and the shift of the asymmetric
stretching vibration of CO2 to higher frequency after the COOH formation (from 1684 to 1729 cm-1),
-
Figure 14c [35].
CONCLUSIONS
The sodium (2-carbamoylphenoxy) acetate salt (denoted as AGM) crystallizes in triclinic system,
and belongs to the P-1 space group, having four molecules in the asymmetric unit. The crystal structure
of AGM shows that the compound comprises (2-carbamoylphenoxy) acetate (CBA) anions, sodium
cations and one water molecule. Three cations of Na from the asymmetric unit are coordinated with six
O atoms, while one Na cation with five oxygen atoms. The (2-carbamoylphenoxy) acetate anions and
water molecules are held in the crystal structure also by N-H…O, O-H…O hydrogen bonds, four being
intermolecular and nine intramolecular hydrogen bonds.
From the Hirshfeld analysis conducted on the four molecules of CBA and water, it appears that the
strongest interactions which aggregate the structure are the coordination bonds between O--Na+ and
the hydrogen bonds that contribute to the formation of the synthons. Fingerprint breakdown shows
that the most numerous interactions are van der Waals (H…H, O…H/H…O, C…H/H…C) and coordinative
(O…Na).
Two of (2-carbamoylphenoxy) acetate molecules from the asymmetric unit are coupled by inversion
2
2
with neighbouring equivalent molecules, forming R2 (8) and R2 (18) supramolecular assemblies and the
other two molecules of the asymmetric unit are coupled to each other by pseudo inversion forming a
2
R2 (18) synthon. If only the sodium cations are considered, they lay on both sides of the crystallographic
plane (0 0 1), in the proximity of it.
20

FT-IR and Raman spectra of AGM are reported for the first time. We used calculated vibrational spectra
on AGM monomer and two configurations of dimers for assigning the normal modes. In general,
calculated modes on the two dimers are in better agreement with experimental data, especially for the
normal modes belonging to the functional groups involved in hydrogen bonds. Dimer II provides better
computational results above 1300 cm-1, while dimer I performs a better fit for the modes below 1000
cm-1. In between, both dimers present similar results. This emphasizes the importance of choosing a
starting geometry that mimics as much as possible the real molecular interactions when calculating
vibrational properties of molecules.
ACKNOWLWDGEMENTS
This work was supported by a grant of Romanian Ministry of Research and Innovation, under Core
Program, project number 19 35 02 02 (ATT, CBG) and 19 35 02 01 (AMRG, GB).
V. Chiş highly acknowledges the support of the CNCS-UEFISCDI Romania, grant PN-III-P4_ID-PCCF-2016-
0112.
All calculations were performed on the high performance cluster supported by project POS CEE COD
SMIS CSNR 48806/1862.
The authors would like to thank Sorina CIUPE for AGM’s FT-IT spectrum.
Declarations of interest: none
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23

Structural, spectroscopic and theoretical studies of sodium (2-
carbamoylphenoxy) acetate salt
Alexandru TURZA1,2 , Ana Maria Raluca GHERMAN2,3, Vasile CHIȘ2, Camelia BERGHIAN-
GROSAN1,Gheorghe BORODI3,*
1Department of Mass Spectrometry, Chromatography and Applied Physics, National Institute of R&D of
Isotopic and Molecular Technologies, 67-103 Donat, 400293 Cluj-Napoca, Romania
2Faculty of Physics, Babeș-Bolyai University, 1 Kogălniceanu, 400084 Cluj-Napoca, Romania
3Department of Molecular and Biomolecular Physics, National Institute of R&D of Isotopic and Molecular
Technologies, 67-103 Donat, 400293 Cluj-Napoca, Romania
*Corresponding author at Department of Molecular and Biomolecular Physics, National Institute of R&D
of Isotopic and Molecular Technologies, Donat 67-103, 400293 Cluj-Napoca, Romania
E-mail address: gheorghe.borodi@yahoo.com (Gheorghe Borodi)
•
•
Crystal structure of sodium (2-carbamoylphenoxy) acetate has been reported.
The Hirshfeld analysis shows that the strongest interactions are due to the coordination
2
2
of Na...O and the hydrogen bonds involved in the formation of R2 (8) and R2 (18)
synthons.
•
•
FT-IR and Raman spectra are reported for the first time, together with a full assignment
of vibrational bands.
Two possible dimer conformations are chosen for calculating the vibrational spectra by
DFT methods.
1