Synthesis, crystal structure and computational studies of 4-nitrobenzylphosphonic acid

Article abstract of DOI:10.1016/j.molstruc.2014.05.052

4-Nitrobenzylphosphonic acid (1a) has been synthesized and structurally characterized by vibrational spectroscopy (IR and Raman) and single-crystal X-ray diffraction. Additionally, Hirshfeld surface analysis and computational methods have been used to com

Full text of DOI:10.1016/j.molstruc.2014.05.052

Accepted Manuscript
Synthesis, crystal structure and computational studies of 4-nitrobenzylphos-
phonic acid
Magdalena Wilk, Katarzyna N. Jarzembska, Jan Janczak, Józef Hoffmann,
Veneta Videnova-Adrabinska
PII:
S0022-2860(14)00566-3
DOI:
http://dx.doi.org/10.1016/j.molstruc.2014.05.052
MOLSTR 20651
Reference:
To appear in:
Journal of Molecular Structure
Received Date:
Revised Date:
Accepted Date:
12 December 2013
20 May 2014
23 May 2014
Please cite this article as: M. Wilk, K.N. Jarzembska, J. Janczak, J. Hoffmann, V. Videnova-Adrabinska, Synthesis,
crystal structure and computational studies of 4-nitrobenzylphosphonic acid, Journal of Molecular Structure (2014),
doi: http://dx.doi.org/10.1016/j.molstruc.2014.05.052
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Synthesis,
crystal
structure
and
computational
studies
of 4-nitrobenzylphosphonic acid
a,*
b
c
a
Magdalena Wilk , Katarzyna N. Jarzembska , Jan Janczak , Józef Hoffmann , Veneta
a,*
Videnova-Adrabinska
a
Department of Chemistry, Wrocław University of Technology, 27 Wybrzeże Wyspiańskiego
St., 50-370 Wrocław, Poland
b
Department of Chemistry, University of Warsaw, 1 Pasteura St., 02-093 Warsaw, Poland
c
Institute of Low Temperature and Structure Research, Polish Academy of Sciences, P.O. Box
1410, 2 Okólna St., 50-950 Wrocław, Poland
*Corresponding authors.
E-mail address: Veneta.Videnova-Adrabinska@pwr.edu.pl (Prof. V. Videnova-Adrabinska).
magdalena.wilk@pwr.edu.pl (Magdalena Wilk)
Abstract
4-Nitrobenzylphosphonic acid (1a) has been synthesized and structurally characterized by
vibrational spectroscopy (IR and Raman) and single-crystal X-ray diffraction. Additionally,
Hirshfeld surface analysis and computational methods have been used to compare the
intermolecular interactions in the crystal structures of 1a and its carboxylic analogue, 4-
nitrobenzylcarboxylic acid (4-NBCA). The crystal structure analysis of 1a has revealed that
the acid molecules are extended into helical chains along the b axis using one of the hydrogen
bonds established between phosphonic groups. The second (P)O–HꢀꢀꢀO(P) hydrogen bond
cross-links the inversion-related chains to form a thick monolayer with phosphonic groups
arranged inwards and aromatic rings outwards. The nitro groups serve to link the
neighbouring monolayers by weak C–HꢀꢀꢀO(N) hydrogen bonds. Computations have
confirmed the great contribution of electrostatic interactions for the crystal lattice stability.
–
1
The cohesive energy, computed for the crystal structure of 1a exceeds 200 kJ·mol in
magnitude and is nearly twice as large as that of 4-NBCA. The calculated cohesive energy
values have been further related to the results of thermal analyses.
1

Keywords
Phosphonic acid; Hydrogen-bonding interaction; Vibrational spectroscopy; Single-crystal X-
ray diffraction; Hirshfeld surface; Periodic calculations.
1. Introduction
Over the past few decades, metal phosphonates have attracted a great deal of research
interest due to their structural diversity and many potential applications in gas storage [1],
heterogeneous catalysis [2], ion exchange [3], proton conductivity [4], corrosion inhibition [5]
and sensor devices [6]. In recent years, considerable effort has been put into exploring metal
phosphonate cage compounds, as they can exhibit single molecule magnet (SMM) properties
2-
[
3
7]. Phosphonate ligands (RPO ) appear to be ideal for stabilizing polymetallic complexes as
they possess three donor O atoms and are, in principle, capable of binding up to nine metal
centers. Recently, 4-nitrobenzylphosphonic acid had been used to coordinate paramagnetic
transition metal ions, which has resulted in the formation of two new high nuclearity cage
compounds [8], but the crystal structure of the acid itself has not been determined yet.
This paper concerns the results of infrared and Raman spectroscopy studies and single-
crystal X-ray diffraction analysis of 4-nitrobenzylphosphonic acid (1a). The crystal structure
of 1a is also compared with its carboxylic analogue, namely 4-nitrobenzylcarboxylic acid (4-
NBCA, CSD refcode SEMTAF) [9], using Hirshfeld surface analysis and computational
approach supported by thermal analysis. Recently, Hirshfeld surface analysis has also been
applied for the investigation of intermolecular interactions of naphthalene-based phosphonic
acids in different protonation states [10]. However, to the best of our knowledge, no
computational studies, aimed at evaluating the strength of intermolecular interactions
responsible for the solid state organization of phosphonic acids, have been reported until now.
2

2. Experimental section
2
.1. Materials
4-Nitrobenzyl bromide and triethyl phosphite (98%) were purchased from Arcos
Organics. 4-Nitobenzylcarboxylic acid was obtained from Sigma-Aldrich. Hexane and
concentrated hydrochloric acid (36-38%) were supplied by POCH S.A. All reagents were
used as received without further purification.
2
2
.2. Synthesis
.2.1. (i) Diethyl 4-nitrobenzylphosphonate (3)
A flask with 4-nitrobenzyl bromide (2, 0.997 g, 4.62 mmol) and triethyl phosphite
o
(
2.5 mL, 14.08 mmol) was partially immersed in an ultrasonic bath at 25 C, the
o
temperature was gradually raised to 90 C and held at that temperature until the substrate was
completely dissolved. Stirring and heating were continued in a metal bath of Wood's alloy at
o
9
7 C for 1 h. After cooling, the excess of triethyl phosphite was removed from the reaction
mixture by extraction with hexane (4 x 3 mL). The residue was dried under reduced pressure
1
to obtain ester 3 as yellow oil. Yield: 0.626 g (55%). H NMR (300.13 MHz, CDCl
3
): δ 8.23
3
3
4
(
d, JHH = 8.8 Hz, 2H, arom. H), 7.53 (dd, JHH = 8.8 Hz, JPH = 2.5 Hz, 2H, arom. H), 3.92
3
3
2
(
dq, JPH = 7.0 Hz, JHH = 7.0 Hz, 4H, O–CH
2
–CH
3
), 3.30 (d, JPH = 22.4 Hz, 2H, CH
2
–P),
3
31
1
1
.32 ppm (t, JHH = 7.0 Hz, 6H, O–CH
2
–CH
3
). P{ H} NMR (121.50 MHz, CDCl
3
): δ 25.06
ppm (s).
2
.2.2. (ii) 4-Nitrobenzylphosphonic acid (1)
Compound 3 (0.626 g, 2.56 mmol) was hydrolyzed by refluxing with concentrated
hydrochloric acid (10 mL) for 8 h. After cooling, beige fine crystalline product 1 was
collected by vacuum filtration, washed with ice-cold water (2 x 3 mL) and dried under
1
reduced pressure. Yield: 0.348 g (62%). H NMR (300.13 MHz, D
2
O-Na
2
CO
3
): δ 7.98 (d,
3
4
3
J
HH = 8.9 Hz, 2H, arom. H), 7.31 (dd, JPH = 2.3 Hz, JHH = 8.9 Hz, 2H, arom. H), 2.92 ppm
2
31
1
(
2 2 2 3
d, JPH = 20.8 Hz, 2H, CH –P). P{ H} NMR (121.50 MHz, D O-Na CO ): δ 18.16 ppm (s).
2
.2.3. Crystallization of 4-nitrobenzylphosphonic acid (1a)
-Nitrobenzylphosphonic acid (1, 30.0 mg, 0.138 mmol) was dissolved in distilled water
4
(1 mL) and left at room temperature for slow evaporation of the solvent. After five days,
3

beige needle-shaped crystals of 1a were obtained. Yield: 12.4 mg (41%). The phase purity of
a was confirmed by comparison of simulated and experimental powder XRD patterns (Fig.
S1).
1
2
.2.4. Crystallization of 4-nitrobenzylcarboxylic acid (4-NBCA)
-Nitrobenzylcarboxylic acid (30.0 mg, 0.166 mmol) was dissolved in distilled water (4
4
mL) and left at room temperature for slow evaporation of the solvent. The next day, white
needle-shaped crystals of 4-NBCA were obtained. Yield: 22.5 mg (75%). The phase purity of
4
-NBCA was confirmed by comparison of simulated and experimental powder XRD patterns
(Fig. S2).
2
.3. NMR spectroscopy in solution
1
31
1
The H and P{ H} NMR spectra were acquired at room temperature on a Bruker
1
31
Avance DRX-300 spectrometer, operating at 300.13 MHz ( H) and 121.50 MHz ( P). NMR
samples were prepared by dissolving 50 μL of 3 in CDCl (500 μL ) and 20 mg of 1 and 13 mg
of sodium carbonate in D O (500 μL ).
3
2
2
.4. Vibrational spectroscopy
The FT-IR spectrum of 1a was recorded on a Bruker Vertex 70v FT-IR spectrometer in
–
1
–1
the range of 4000–370 cm with a resolution of 2 cm using the KBr pellet technique. The
Raman spectrum of 1a was collected on a Bruker MultiRAM FT-Raman spectrometer in the
–
1
–1
range of 3600–50 cm with a resolution of 2 cm using the Nd:YAG laser line at 1064 nm.
Instrument control, spectra analysis and correction for fluorescence effect in the case of
Raman measurement were performed using the Bruker OPUS software.
2
.5. Single-crystal X-ray data collection and structure determination
Single-crystal X-ray diffraction measurement of 1a was carried out at 295 K on a four-
circle KUMA KM4 diffractometer equipped with two-dimensional CCD area detector.
Graphite monochromatized Mo-Kαradiation (λ= 0.71073 Å) and ω-scan technique (Δω = 1°)
were used for data collection. Data collection and reduction along with absorption correction
were performed using CrysAlis software package [11]. The structure was solved by direct
methods using SHELXS-97 [12], which revealed the positions of almost all non-hydrogen
4

atoms. The remaining atoms were located from subsequent difference Fourier syntheses. The
positions of H atoms attached to benzene C atoms were constrained (C–H = 0.93 Å) with
U
iso(H) = 1.2Ueq(C). The positions of H atoms of the methylene group were constrained (C–H
0.97 Å) with Uiso(H) = 1.5Ueq(C). The positions of H atoms of the phosphonic group were
=
refined with Uiso(H) = 1.5Ueq(O). The structure was refined using SHELXL-97 [12] with the
anisotropic thermal displacement parameters. Visualizations of the structure were made with
the Diamond 3.1 program [13]. Details of the data collection parameters, crystallographic data
and final agreement parameters are collected in Table 1.
Table 1. Crystal data and details of the structure determination for compound 1a.
Empirical formula
O
2
6 4 2 3 2
NC H CH PO H
–
1
Formula weight (g·mol )
217.11
Crystal system, space group
Monoclinic, P2
12.910(3)
8.627(2)
1
/c (No. 14)
a (Å)
b (Å)
c (Å)
α(°)
8.355(2)
90.00
β(°)
γ(°)
104.090(10)
90.00
3
V (Å )
902.5(4)
4
Z
–
3
D
calc/Dobs (g·cm )
1.598/1.59
0.300
–
1
μ(mm )
F(000)
448
Crystal size (mm)
Radiation type, wavelength, λ (Å)
0.28 × 0.23 × 0.19
Mo K α, 0.71073
Temperature (K)
θ range (°)
295(2)
2.87–29.31
Absorption correction
Numerical, CrysAlis Red
0.9206/0.9451
11145/2331/1220
0.0668
Tmin /Tmax
Reflections collected / unique / observed
R
int
5

2
Refinement on
F
2
2
R[F > 2 σ( F )]
0.0555
2
a)
wR(F all reflections)
0.0885
Goodness-of-fit, S
1.001
–3
Δρ max, Δρ min, (e·Å )
+0.275, –0.307
a)
2
2 2
4
½
–1
2
2
2
2
wR = {Σ[w(F
o
– F
c
) ]/ΣwF
o
o o
} ; w = [σ(F ) + (aP) ] where a = 0.0200 and P = (F +
2
c
2F
)/3.
2
.6. Powder X-ray diffraction data collection
The experimental powder XRD patterns of 1a and 4-NBCA were acquired on a
PANalytical X’Pert diffractometer equipped with a Cu Kαradiation source (λ= 1.54182 Å),
and operated at 40 kV and 30 mA. The data were collected at room temperature in the range
o
of 2θ= 5–40 . On the other hand, the corresponding simulated powder XRD patterns were
generated using Diamond 3.1 software.
2
.7. Simultaneous thermal analysis
The combined TG-DTA-MS analyses were performed using a simultaneous thermal
analyzer NETZSCH STA 449 F3 Jupiter coupled with a quadrupole mass spectrometer QMS
03 C Aëolos. The samples (17.3 mg of 1a and 20.4 mg of 4-NBCA) were placed inside
Al crucibles. The measurements were carried out in the range of 35–600°C with a heating
rate of 4°C⋅min and under dynamic air atmosphere (N
4
2
O
3
-1
2
2
/O 80:20) with a gas flow of 20
-1
mL·min . The data acquisition and processing were realized using NETZSCH Proteus
software.
2
.8. Computational details
Two sets of coordinates were used for the purpose of the energetic analysis, i.e. the
experimentally determined structure with the X–H bonds (where X stands for any atom
different from hydrogen) elongated to neutron-normalized values, and the computationally
optimized crystal geometry. Geometry optimization was carried out at the
DFT(B3LYP)/pVTZ level of theory [14-16] in CRYSTAL09 [17]. During the optimization
procedure atomic coordinates were varied, while cell parameters were kept fixed at the
6

experimental values. Structure optimization prior to further computational studies is
particularly important in the case of low-resolution crystal structures, since it allows to obtain
reliable values for the X–H bond distances and for the bond directionality (which cannot be
achieved by simple X–H elongation to neutron-normalized values). Indeed, this is visible
when we compare the experimental and optimized crystal structures of 1a (Fig. S3). Both
structures are generally very similar with largest discrepancies observed for the positions of
the hydrogen atoms, especially for those involved in strong hydrogen bonds. In the case of our
study, structure optimization additionally helped to relate the structure of 1a with the
literature structure of 4-NBCA at the common ground.
Cohesive energy computations were performed using the CRYSTAL09 program package
[17] at the DFT(B3LYP) level of theory [14, 15] with the pVTZ molecular all-electron basis
set [16]. Both Grimme dispersion correction [18, 19] and correction for basis set superposition
error (BSSE) were applied [20]. Ghost atoms were selected up to 5 Å distance from the
considered molecule in a crystal lattice, and were used for the BSSE estimation. The
evaluation of Coulomb and exchange series was controlled by five thresholds, set arbitrarily
-7
-7
-7
-7
-25
to the values of 10 , 10 , 10 , 10 , 10 . Shrinking factor was equal to 8, which refers to 170
k-points in the irreducible Brillouin zone and assures the full convergence of the total energy.
The cohesive energy (Ecoh) was calculated as described below [21]:
1
Ecoh
=
Ebulk − Emol
Z
where Ebulk is the total energy of the system (calculated per unit cell) and Emol is the energy of
the molecule extracted from the bulk. Z stands for the number of molecules in the unit cell.
Additionally, the optimized geometry was subjected to crystal interlayer interaction
computation. All of the calculation parameters were set identical as for the purpose of the
cohesive energy estimation. The only difference was introduced to ghost atom definition,
where an upper and lower molecular layers were additionally used as ghost function sets in
order to obtain BSSE. The interlayer interaction energy (Eintl) calculation formula is
analogous to that for cohesive energy [22]:
1
Eintl
=
Ebulk − Eslab
n
where Eslab is the energy of a molecular slab extracted from the bulk, while n indicates the
slab number per a unit cell. Therefore, the resulting stabilization energy falls on a part of a
7

slab belonging to the unit cell. CRYSTAL09 automatically assigns the slab group symmetry
and cuts out the repeatable fragment.
Finally, dimer interaction energies were evaluated within the supramolecular approach.
Alike above, the calculations were carried out at the DFT(B3LYP)/pVTZ level of theory with
the BSSE and Grimme corrections applied.
3. Results and discussion
Although 4-nitrobenzylphosphonic acid (1) was first synthesized by Litthauer in 1889
[23], its crystal structure has not been determined to date. In current work 1 has been prepared
according to the modified literature procedure of Coogan and Harger [24]. Diethyl 4-
nitrobenzylphosphonate (3), obtained via Michaelis-Arbuzov reaction of 4-nitrobenzyl
bromide (2) and triethyl phosphite, has been transformed into 1 by means of acidic hydrolysis
(Scheme 1). Single crystals of 4-nitrobenzylphosphonic acid (1a) have been achieved by
recrystallization of 1 from water.
2 5 3
Scheme 1. Synthetic route to compound 1. Reagents: (i) P(OC H ) and (ii) HCl.
IR and Raman spectroscopy studies have confirmed the presence of nitro and phosphonic
functional groups in the structure of 1a. The nitro group exhibits two very strong bands at
–
1
1
521 and 1345 cm arising from the asymmetric and symmetric stretching vibrations. In turn,
–
1
the phosphonic group gives rise to a series of strong bands in the region 1300–900 cm . The
–
1
well resolved band, observed at 1268 cm , is associated with the P=O stretching vibration,
–
1
while the two broad bands at 1077 and 950 cm correspond to the asymmetric and symmetric
stretching vibrations of PO group. Additional not well resolved bands, observed in this
2
region, are connected with the deformation vibrations of (P)O–H groups. The presence of two
very strong (P)O–H···O(P) hydrogen bonds with the O···O distance lower than 2.6 Å is
–
1
manifested also by the medium absorption, extended in the whole region 3500–1650 cm ,
which is connected with the O–H stretching vibrations. The complementary IR and Raman
8

spectra of 1a are shown in Fig. 1. The positions and intensities of all observed vibrational
modes together with their tentative assignments are given in Table 2.
Figure 1. Complementary IR (red) and Raman (green) spectra of compound 1a.
Table 2. Positions and assignments of vibrational bands, observed in FTIR and Raman
spectra of compound 1a.
a)
IR
Raman
Band assignment
3
3
2
111 m
ν( C–H)
085 m
971 m
3084 vw
2970 vw
ν (CH )
as
2
2936 m
2932 vw
ν(CH )
s
2
2
2
850 m
764 m, br
ν( O–H)
ν( O–H)
2
2
450 m
213 m, br
1
1
1
1
1
941 w
808 w
698 w
610 m
599 m
ν( C=C)
1599 w
9

1
1
521 vs
492 m
1515 vw
ν (NO )
as
2
δ(CH )
s
2
1
1
1
1
422 vw
407 vw
393 vw
345 vs
1345 vs
1268 vw
1200 vw
ν(NO )
s
2
1
268 s
ν( P=O)
1
1
1
1
1
203 w
183 m
156 m
109 s
δ(O–H)
1109 vw
077 s
ν (PO )
as
2
9
8
8
7
50 vs
59 vs
22 s
ν(PO )
s
2
863 vw
774 vw
ν( C–N)
δ(NO2)
72 s
ν( P–C)
727 vw
ρ( CH2)
6
6
95 s
out-of-plane ring def. vib.
41 m
630 vw
5
41 s
δ(NO2)
478 m
430 s
407 s
390 s
2
δ(PO )
2
90 vw
00 m
1
a)
Abbreviations: vs – very strong, s – strong, m – medium, w – weak, vw – very weak, br –
broad, ν– stretching, as – asymmetric, s – symmetric, δ– in-plane deformation vibration, ρ–
rocking.
1
0

The single-crystal X-ray diffraction analysis has revealed that 1a crystallizes in the
monoclinic P2 /c space group with one molecule in the asymmetric part of the unit cell (Fig.
). All N–O and P–O bond lengths (Table 3) are typical for the nitro group and the non-
1
2
dissociated phosphonic group, respectively [25]. The nitro group is coplanar with the benzene
o
ring, as indicated by the dihedral angle of 1.903(293) formed by the O41/N4/O42 plane with
the C1–C6 ring.
Figure 2. The asymmetric part of the unit cell of compound 1a, showing the atom-labelling
scheme. Displacement ellipsoids are drawn at the 50% probability level.
Table 3. Selected geometric parameters (Å, °) for compound 1a.
C7–P1
1.779(3)
1.506(2)
1.541(2)
1.542(2)
C4–N4
1.481(5)
1.214(4)
1.218(3)
P1–O11
P1–O12
P1–O13
N4–O41
N4–O42
C1–C7–P1
115.8(2)
O12–P1–O13
O41–N4–O42
109.69(13)
123.7(4)
O11–P1–O12
O11–P1–O13
108.50(12)
115.12(14)
1
1

Figure 3. A side view of two monolayers of compound 1a, demonstrating the intralayer O–
H···O hydrogen-bonding interactions.
The acid molecules are organized into thick molecular monolayers with phosphonic groups
located inside and aromatic rings arranged outside from both sides of the layer. The two-
dimensional hydrogen-bonded network of the monolayer is created merely by phosphonic-
phosphonic interactions (Fig. 3). Formally it can be disentangled into C(4) helical chains,
i
extended along the b axis and formed by O12–H12···O11 hydrogen bonds. The neighbouring,
ii
opposite running chains are further interlinked by O13–H13···O11 hydrogen bonds. The
(
P)O–H···O(P) hydrogen-bonded network is characterized by two centrosymmetric ring
2
4
motifs denoted as R (12) and R (16) (Fig. 4) [26]. A search in the Cambridge Structural
4
4
Database (CSD version 5.35 of November 2013) [27] using the Solid Form Module of
Mercury 3.3 revealed that a similar two-dimensional hydrogen-bonded pattern is observed in
the crystal structures of only six more phosphonic acids (CALGON, FECTOW, NISPAH,
OLOPUA, RIGNUR, YOJTAT).
1
2

Figure 4. The two-dimensional hydrogen-bonded network of compound 1a, formed between
the phosphonic groups. Aromatic rings, nitro and methylene groups are omitted for clarity.
1
1
[
2 2
Symmetry codes: (vi) –x+1, –y+1, –z+1; (vii) –x+1, y+ / , –z+ / ; (viii) –x+1, –y+2, –z+1.]
Two weak C–H···O hydrogen bonds, donated from the methylene group toward the O-atoms
of the nitro group and the phosphonic group, additionally stabilize the two-dimensional
iv
network. One of them, C7–H71···O41 , established between translation-related molecules
iii
along the chain, is responsible for the pitch of the helix, while the other, C7–H72···O12 ,
connects the chains. The 4-nitrobenzyl groups are arrayed from both sides of the monolayer.
o
The benzene rings are inclined at an angle of 56.087(61) versus bc plane. The distal nitro
v
groups are used to interlink the neighbouring monolayers via a weak C5–H5···O42 hydrogen
bond, donated from an aromatic C–H group to the O-atom of the nitro group (Fig. 5).
1
3

Figure 5. The three-dimensional packing arrangement of compound 1a. The hydrogen bonds
are drawn as dashed lines (red for O–H···O, green for intralayer C–H···O and pink for
interlayer C–H···O).
Table 4. Hydrogen bond geometry (Å, °) for compound 1a.
D–HꢀꢀꢀA
d(D–H)
d(HꢀꢀꢀA)
d(DꢀꢀꢀA)
<D–HꢀꢀꢀA
i
O12–H12ꢀꢀꢀO11
0.90 (3)
0.81 (3)
0.97
1.66 (3)
1.81 (3)
2.57
2.550 (3)
2.581 (3)
3.356 (4)
3.453 (4)
3.255 (4)
173 (3)
159 (3)
138
ii
O13–H13ꢀꢀꢀO11
iii
C7–H72ꢀꢀꢀO12
iv
C7–H71ꢀꢀꢀO41
0.97
2.58
150
v
C5–H5ꢀꢀꢀO42
0.93
2.58
130
1
1
3
1
Symmetry codes: (i) −x+1, y− /
2
, −z+ /
2
; (ii) x, −y+ /
2
, z+ /
2
; (iii) −x+1, −y+1, −z; (iv) x, y+1,
1
1
2 2
z; (v) −x, y+ / , −z+ / .
In order to profoundly examine the strength and role of the above listed hydrogen bonds
and other intermolecular contacts, and to estimate their importance for the crystal lattice
stability, Hirshfeld surface analysis and computational study have been conducted. Hirshfeld
surface constitutes a useful tool in crystal engineering. It allows for crystal packing
investigations and for certain quantification of the contributions coming from different close
contacts present in a crystal lattice (Supplementary Materials). The Hirshfeld surface for 1a
1
4

mapped with dnorm property is visualised in Fig. 6a. It reflects interatomic contact distances in
respect to atom van der Waals radii (red colour stands for the close contacts, while blue for
the distant ones). On the basis of such a Hirshfeld surface, the related fingerprint plot has been
derived (Fig. 6b). The Hirshfeld surface around the phosphonic group is coated with three
large red spots of the same size, which means that it participates in strong O–H···O hydrogen-
bonding interactions. On the other hand, much smaller pale red spots on the dnorm surface are
related to almost every H-atom coming from the hydrocarbon fragment and both O-atoms
belonging to the nitro group, which indicates that the crystal lattice is rich in weak C–H···O
hydrogen bonds. Two long broadening spikes at the sides of the main body of the fingerprint
plot correspond not only to the O–H···O hydrogen-bonding interactions but also, at higher d
i
and d values, reveal the contribution from C–H···O hydrogen bonds. Consequently, the total
e
percentage share of H···O contacts constitutes over 50% of the total number of intermolecular
contacts, which demonstrates their importance for the structure stability (Fig. 6c). In turn, the
second most numerous contacts, H···H, which are very common in the case of crystal
structures of organic molecules, contribute to about 20% of the total (Fig. 6d). The Hirshfeld
surface analysis shows the existence of other weak intermolecular contacts, for which the
percentage participations to the Hirshfeld surface area are presented in Fig. 6e.
1
5

Figure 6. (a) The Hirshfeld surface for compound 1a mapped with dnorm function; (b) The
corresponding 2D fingerprint plot; (c-d) The fingerprint plots, broken down into contributions
from H···O and H···H contacts; (e) The percentage contributions of various close
intermolecular contacts to the Hirshfeld surface area. Other contacts constitute H···N, N···O,
C···N.
The energy studies have confirmed the importance of the hydrogen-bonded network for
–
the crystal lattice stability. Periodically calculated cohesive energy amounts to −226.2 kJ·mol
1
.
In the case of crystal structure of such a small organic molecule, this result indicates a great
electrostatic nature of the strongest contacts [22, 28]. Two main hydrogen bonds, namely
i
ii
O12–H12···O11 and O13–H13···O11 , involving the neighbouring phosphonic groups,
constitute the principal intermolecular interaction in D1 and D2 dimer motifs, respectively
(Fig. 7). The estimated interaction energies of these and other dimers are given in Table 5. As
2
4
it was mentioned previously, the dimeric units are further connected into R (12) and R (16)
4
4
ring motifs leading to the formation of a molecular layer parallel to the bc plane. Both ring
motifs are characterized by significant stabilization energy values reaching from −222.0 to
–
1
−
365.0 kJ·mol . Another interesting and relatively strong interacting molecular configuration
16

iii
iii
is D3. It is built up from the C7–H72···O12 hydrogen bond and the C2–H2···O11 contact,
established between the hydrocarbon fragment and the phosphonic group. These interactions
iv
iv
iv
together with the C7–H71ꢀꢀꢀO41 hydrogen bond and the C3 –H3 ···O11 contact,
constituting the two times weaker D4 dimer, contribute supplementary to the stability of the
layered structure. As a consequence, the interactions within the layers are much stronger than
those keeping the layers together. It is also clearly seen from the calculated interlayer
–
1
interaction energy, which is equal to −22.2 kJ·mol . The interlayer interactions are based
v
mainly on the weak C5–H5ꢀꢀꢀO42 hydrogen bond, donated from the aromatic C–H group to
the O-atom of the nitro group, (D5) and the contact formed between the nitro groups (D7).
This may be reflected in the crystal morphology and mechanical properties, as for example, in
the tendency of crystal to stratify in a particular crystallographic direction [29, 30]. It is also
worth noting that the D6 and D7 dimers are quite well stabilized, however, no regular
hydrogen bonds are formed. D6 is created by face-to-face (FF) π- π interactions between
ix
aromatic rings and the C3–H3ꢀꢀꢀO13 contact, whereas D7 is held mainly by the interlayer
interaction of the nitro groups located anti-parallel one above another (weak N4···O42
electrostatic contacts).
Table 5. Interaction energy values calculated for selected structural motifs of compound 1a.
a)
a)
Interaction energy
Interaction energy
Structural motif
Structural motif
–
1
–1
(
kJ·mol )
(kJ·mol )
i
ix
D1 [C(4)]
−64.6
−70.7
D6
−19.3
−21.0
ii
x
D2 [C(4)]
D7
iii
2
2
D3 [ R (8) ]
−54.3
R (12)
−222.0
−365.0
2
4
iv
2
4
D4 [ R (9)]
−25.5
−9.3
R (16)
2
4
v
D5 [D(3)]
a)
for optimized geometry with usage of periodic optimization in the CRYSTAL09 package
1
1
2 2
Symmetry codes: (ix) –x, y− / , −z+ / ; (x) −x, −y, −z.
1
7

Figure 7. Schematic representation of dimer motifs related to interaction energy values given
in Table 5.
The comparison of the crystal structures of 1a and the 4-nitrobenzylcarboxylic acid (4-
NBCA), especially in terms of their hydrogen bond connectivity patterns, constitutes another
interesting aspect of the research. The compound 1a can be considered as an analogue of 4-
NBCA, where the flat carboxyl group is replaced by the nonplanar phosphonic group. Both
compounds display layered structures in the solid state, but the organization of their layers is
different. The functional groups of the compounds are provided with good donors and
acceptors capable to form strong hydrogen bonds, which are decisive for the self-recognition
and control the self-organization process. However, the compounds differ in number, the
1
8

spatial orientation and approachability of the hydrogen bond sides, which has burden
consequences for the supramolecular architectures. On the other hand, the weak C–H···O
hydrogen bonds are also important for the packing patterns. The hydrogen-bonded network of
the monolayer in 1a is formed via two strong (P)O–H···O(P) hydrogen bonds, one of which
extends the molecules into C(4) helical chains, and the other cross-links the chains to form a
gird network with 12- and 16-membered ring motifs. The C–H···O hydrogen bonds, donated
from the methylene group are only used to stabilize the monolayer. Another C–H···O
hydrogen bond, donated toward the nitro group serves to connect the layers in three-
dimensional network. As far as the 4-NBCA is concerned, the basic molecular extension
formed explicitly by the use of (C)O–H···O(C) hydrogen bonds is the centrosymmetric dimer
2
with R (8) ring motif. This structural motif is obviously characterized by the most
2
–
1
significant interaction energy of −81.1 kJ·mol . Two weak C–H···O hydrogen bonds, donated
toward the hydroxyl O-atom of the carboxyl group, are utilized to expand the dimers in two
dimensions, forming double-stranded zig-zag chains that are further interconnected in the
monolayer. The O-atoms of the nitro group due to greater interatomic distances are
inaccessible as hydrogen bond acceptors and do not participate in any hydrogen-bonding
interactions. Thus, the nitro group is much less involved in the structure stabilization than it is
in 1a (Supplementary Materials). The corresponding Hirshfeld surface and fingerprint plot for
4
-NBCA are presented in Figs. 8a and 8b. In comparison to 1a, a minor part of the Hirshfeld
surface of 4-NBCA is covered with red spots, indicating a lower number of close contacts
such as hydrogen-bonding interactions (compare Figs. 6a and 8a). Additionally, two long
spikes in the fingerprint plot of 4-NBCA, related to H···O contacts, are narrower, which
suggests a smaller contribution from weak C–H···O hydrogen bonds to the total dnorm surface
area (compare Figs. 6b and 8b). Generally, the supramolecular network of 4-NBCA is less
developed with a greater participation of H···H dispersion forces at the expense of H···O
contacts. As a result, the cohesive energy is almost twice less advantageous than that of 1a
–
1
and amounts to −128.9 kJ·mol .
1
9

Figure 8. (a) The Hirshfeld surface for 4-NBCA mapped with dnorm function; (b) The
corresponding 2D fingerprint plot; (c-d) The fingerprint plots, broken down into contributions
from H···O and H···H contacts; (e) The percentage contributions of various close
intermolecular contacts to the Hirshfeld surface area. Other contacts constitute H···N, N···O,
C···N.
The calculated cohesive energy of a crystal should reflect its enthalpy of sublimation.
Furthermore, the cohesive energy controls to a great extent also the melting point of a solid.
Generally, the higher the cohesive energy of a crystal is, the higher should be its melting
point. Metal crystals, are a good illustration to this statement, since there is almost a linear
correlation between both parameters in them. In the case of the studied crystals, the calculated
values for cohesive energy strongly suggest that 1a should be characterized by the higher
melting point than 4-NBCA. In order to verify this presumption, the derived cohesive energy
values have been further related to the results of thermal analyses. The obtained TG-DTA
curves for 1a and 4-NBCA are shown in Figs S5 and S6, respectively. The first endothermic
peak on the DTA curves is attributed to the melting process. Compound 1a displays a melting
o
o
point of 226.2 C, while 4-NBCA of 155.0 C. These results are in agreement with the
2
0

expectations. Obviously the energetically favourable 1a is characterized with higher melting
temperature compared to the carboxylic analogue, 4-NBCA.
4. Conclusion
4
-Nitrobenzylphosphonic acid (1a) has been synthesized and structurally characterized.
The solid state organization of 1a demonstrates a layered structure with C–H···O(N)
hydrogen-bonding interactions between the layers. The two-dimensional hydrogen-bonded
2
4
network consists of R (12) and R (16) ring motifs, which reveal considerable stabilization
4
4
–
1
energy values reaching from −222.0 to −365.0 kJ·mol . The adjacent monolayers are held
together via weak interactions involving the nitro group and this is reflected by the interlayer
–
1
interaction energy of −22.2 kJ·mol . In comparison to 4-nitrobenzylcarboxylic acid (4-
NBCA), the supramolecular architecture of 1a is more complicated and richer in stronger
intermolecular interactions in large part because of the phosphonic group, which is more
productive in hydrogen bond formation than the carboxyl group. As a result, the cohesive
–
1
energy of 1a is equal to −226.2 kJ·mol and is almost twice as big as that of 4-NBCA. The
o
experimental melting point of 1a is also ca. 70 C higher than that of 4-NBCA.
Acknowledgements
This work was financed by a statutory activity subsidy from the Polish Ministry of
Science and Higher Education for the Department of Chemistry of Wrocław University of
Technology. MW and VVA also gratefully acknowledge the instrumental grant no.
6
221/IA/119/2012 from Polish Ministry of Science and Higher Education, which supported
the Integrated Departmental Laboratory for Engineering and Research of Advanced Materials,
where the measurements of the IR and Raman spectra were performed. Calculations were
carried out using resources provided by the Wrocław Centre for Networking and
Supercomputing (http://wcss.pl, grant no. 285). KNJ was supported by the Foundation for
Polish Science within the START program.
MW wishes to acknowledge helpful discussions with Professor M. Soroka.
2
1

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Appendix A. Supplementary materials
Details on data collection and refinement, fractional atomic coordinates, anisotropic
displacement parameters and full list of bond lengths and angles in CIF format have been
deposited at the Cambridge Crystallographic Data Centre, No. CCDC 950613. Copies of this
information can be obtained free of charge from The Director, CCDC, 12 Union Road,
Cambridge, CB2 1EZ, UK (fax: +44 1223 336 033; email: deposit@ccdc.cam.ac.uk or www:
http://www.ccdc.cam.ac.uk).
2
3

Graphical abstract
2
4

Highlights
•
•
4-Nitrobenzylphosphonic acid (1a) has been synthesized and characterized.
1a displays a layered structure with weak C–H···O(N) hydrogen bonds between layers.
2
4
•
The layer is composed of R (12) and R (16)ring motifs, exhibiting large stabilization
4 4
energies.
The cohesive energy of 1a is much more advantageous than that of its carboxylic analogue.
•
2
5