Polyamines. Part II: Spectroscopic properties of N,N-dimethyl-3-phthalimidopropylammonium acetate and hydrochloride and supramolecular interactions in their crystals

Article abstract of DOI:10.1016/j.molstruc.2008.03.037

N,N-Dimethyl-3-phthalimidopropylammonium acetate and hydrochloride have been characterized by X-ray diffraction, FT-IR, Raman and NMR spectroscopy. Also B3LYP and DFT calculations have been carried out. The optimized bond lengths, bond angles and torsion angles calculated by B3LYP/6-31G(d,p) approach have been compared with the X-ray data. The screening constants for ¹³C and ¹H atoms have been calculated by the GIAO/B3LYP/6-31G(d,p) approach and analyzed. Linear correlations between the experimental ¹H and ¹³C chemical shifts and the computed screening constants confirm the optimized geometry. The packing of the both molecules is dominated by hydrogen bonds, including the weak C{single bond}H?O bonds. The supramolecular structure is organized into hydrophilic and hydrophobic segments.

Full text of DOI:10.1016/j.molstruc.2008.03.037

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Journal of Molecular Structure 891 (2008) 205–213
Contents lists available at ScienceDirect
Journal of Molecular Structure
journal homepage: www.elsevier.com/locate/molstruc
Polyamines. Part II: Spectroscopic properties of N,N-dimethyl-3-
phthalimidopropylammonium acetate and hydrochloride
and supramolecular interactions in their crystals q
b
b
Teresa Borowiak a, Irena Wolska a, Piotr Jensz a, Iwona Kowalczyk b, , Bogumił Brycki , Adrianna Sztul
*
a
´
Department of Crystallography, Faculty of Chemistry, Adam Mickiewicz University, Grunwaldzka 6, 60-780 Poznan, Poland
b Laboratory of Microbiocides Chemistry, Faculty of Chemistry, Adam Mickiewicz University, Grunwaldzka 6, 60-780 Poznan´, Poland
a r t i c l e i n f o
a b s t r a c t
Article history:
N,N-Dimethyl-3-phthalimidopropylammonium acetate and hydrochloride have been characterized by X-
ray diffraction, FT-IR, Raman and NMR spectroscopy. Also B3LYP and DFT calculations have been carried
out. The optimized bond lengths, bond angles and torsion angles calculated by B3LYP/6-31G(d,p)
approach have been compared with the X-ray data. The screening constants for 13C and 1H atoms have
been calculated by the GIAO/B3LYP/6-31G(d,p) approach and analyzed. Linear correlations between
the experimental 1H and 13C chemical shifts and the computed screening constants confirm the opti-
mized geometry. The packing of the both molecules is dominated by hydrogen bonds, including the weak
CAHꢀ ꢀ ꢀO bonds. The supramolecular structure is organized into hydrophilic and hydrophobic segments.
Ó 2008 Elsevier B.V. All rights reserved.
Received 17 January 2008
Received in revised form 13 March 2008
Accepted 18 March 2008
Available online 1 April 2008
Keywords:
N,N-Dimethyl-3-
phthalimidopropylammonium derivatives
X-ray diffraction
Supramolecular structure
Intermolecular hydrogen bonds
DFT calculations
FT-IR and NMR spectra
1. Introduction
lammonium acetate semihydrate [hereafter (1)] and hydrochloride
monohydrate [hereafter (2)] are presented. The above compounds
Quaternary aminoalkylammonium salts play an important role
in the living processes and many functions of prokaryotic and
eukaryotic cells have been shown to be alkylammonium salts
dependent [1,2]. These compounds also exhibit an excellent anti-
microbial activity, therefore they are used as antiseptics, bacteri-
cides and fungicides, and as therapeutic agents, as well. In
general, ammonium salts which show good antimicrobial activities
contain one or two alkyl chains with the lengths in the range of C8
to C14. For the use as softeners and hair conditioning agents chain
lengths between C16 to C18 are used [3,4].
belong to N,N-dimethyl-3-phthalimidopropylammonium deriva-
tives investigated in our laboratory in order to better understand
the mechanism of their biological activity.
The another aspect of our interest in N,N-dimethyl-3-phthalim-
idopropylammonium salts are their supramolecular structures and
the role of counter-ions as well as water molecules in their
formation.
2. Experimental
The use of microbiocide of the same type for a long time may
cause an increase of resistance of microorganisms which is a very
serious problem. Antimicrobial resistance in bacteria comprises a
wide variety of biochemical mechanisms and processes that allow
microorganisms to grow in the presence of microbiocides. To avoid
this problem structures and types of microbiocides have to be con-
tinuously changed [5–7]. In this paper the X-ray structure as well
as results on B3LYP calculations, FT-IR, Raman and 1H NMR, 13C
NMR, 2D NMR spectroscopy of N,N-dimethyl-3-phthalimidopropy-
2.1. Synthesis
N,N-Dimethyl-3-phthalimidopropylamine was obtained by the
reaction of a commercially available N,N-dimethylpropyl-1,3-dia-
mine with phthalic anhydride in acetic acid. The reaction mixture
was heated under reflux for 4 h. The product was purified by meth-
od given in our previous paper [7]. N,N-Dimethyl-3-phthalimido-
propylamine acetate (1) was prepared by reaction of equimolar
amounts of N,N-dimethyl-3-phthalimidopropylamine and acetic
acid in anhydrous ethanol. The product was purified by crystalliza-
tion from hexane. Yield 65%, mp 40–41 °C. N,N-Dimethyl-3-phtha-
limidopropylamonium hydrochloride (2) was obtained by reaction
of N,N-dimethyl-3-phthalimidopropylamine with equimolar
q
Polyamines. I. Ref. [24].
* Corresponding author. Tel.: +48 61 829 1306; fax: +48 61 865 8008.
E-mail address: iwkow@amu.edu.pl (I. Kowalczyk).
0022-2860/$ - see front matter Ó 2008 Elsevier B.V. All rights reserved.
doi:10.1016/j.molstruc.2008.03.037

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T. Borowiak et al. / Journal of Molecular Structure 891 (2008) 205–213
amount of hydrochloric acid in anhydrous ethanol. The product
was crystallized from anhydrous ethanol. Yield 65%, mp 203–
205 °C.
determined by least-squares treatment of setting angles of high-
est-intensity reflections chosen from the whole experiment.
Intensity data were corrected for the Lorentz and polarization ef-
fects [9]. The structures were solved by direct methods by use
the SHELXS97 program [10] and refined by the full-matrix
2.2. Instrumentation
least-squares method with the SHELXL97 program [11]. The
P
2
2 2
Crystals suitable for X-ray analysis were grown by slow evap-
oration from hexane solution (1) and ethanol solution (2). All de-
tails of the measurements, crystal data and structure refinement
are given in Table 1. The data were collected on Oxford Diffrac-
tion KM4CCD diffractometer [8] at 120 K, using graphite-mono-
chromated MoKa radiation. The unit cell parameters were
function
w(jFoj ꢁ jFcj ) was minimized with wꢁ1 = [r2(Fo)2 +
(0.0500P)2 + 3.4791P] for 1 and wꢁ1 = [r2(Fo)2 + (0.0469P)2] for
2, where P ¼ ðF2o þ 2 Fc2Þ=3.
All non-hydrogen atoms were refined with anisotropic displace-
ment parameters. The coordinates of the hydrogen atoms involved
in strong hydrogen bonds, N+AHꢀ ꢀ ꢀOꢁ, OAHꢀ ꢀ ꢀOꢁ (1) and
N+AHꢀ ꢀ ꢀClꢁ, OAHꢀ ꢀ ꢀClꢁ (2), were found in difference Fourier syn-
theses and their positional and thermal parameters were refined.
The coordinates of the other hydrogen atoms were calculated from
the geometry and refined as a riding model with their displace-
ment parameters calculated as 1.2 (1.5 for methyl group) times
Ueq of the respective carrier carbon atom.
The NMR spectra in D2O were measured for 1 and 2 with a Var-
ian Gemini 300VT spectrometer, operating at 300.07 and 75.46 Hz
for 1H and 13C, respectively. Infrared spectra were recorded in the
KBr pellets using a FT-IR Bruker IFS 113v spectrometer which was
evacuated to avoid water absorption.
The calculations were performed using the GAUSSIAN 03 pro-
gram package [12] at the B3LYP [13,14] levels of theory with the
6-31G(d,p) basis set [13]. The NMR isotropic shielding constants
were calculated using the standard GIAO (Gauge-Independent
Atomic Orbital) approach [12–15] of GAUSSIAN 03 program pack-
age [16].
The deposition numbers CCDC 674748 for 1 and 674749 for 2
contain the supplementary crystallographic data for this paper.
These data can be obtained free of charge via www.ccdc.cam.a-
c.uk/data_request/cif, or by emailing data_request@ccdc.cam.a-
c.uk, or by contacting The Cambridge Crystallographic Data
Centre, 12, Union Road, Cambridge CB2 1EZ, UK; fax: +44 1223
336033.
Table 1
Crystal data, data collection and structure refinement for 1 and 2
Compound
1
2
Empirical formula
(C13H17N2O2)+ꢀ(C2H3O2)ꢁꢀ1/
(C13H17N2O2)+ꢀClꢁꢀH2O
2H2O
Formula weight
T (K)
301.34
120(2)
286.75
120(2)
Wavelength (Å)
Crystal system, space
group
0.71073
monoclinic, C2/c
0.71073
monoclinic, P21/c
Unit cell dimensions
a (Å)
b (Å)
33.688(7)
8.360(2)
11.561(2)
109.56(3)
3067.8(11)
8, 1.305
0.097
14.8175(8)
8.6139(4)
11.6250(5)
103.633(4)
1442.0(1)
4, 1.321
c (Å)
b(°)
Volume (Å3)
Z, Dx (Mg/m3)
l (mmꢁ1
F(000)
)
0.271
608
1288
h range for data collection 2.52–28.02
(°)
2.76–28.45
hkl range
ꢁ43 6 h 6 43
ꢁ11 6 k 6 11
ꢁ14 6 l 6 15
ꢁ19 6 h 6 19
ꢁ11 6 k 6 11
ꢁ15 6 l 6 15
Reflections
Collected
24733
23067
Unique (Rint
)
3492 (0.026)
3246
3492/0/203
3354 (0.040)
2712
3354/0/184
3. Results and discussion
Observed (I > 2r(I))
Data/restraints/
parameters
3.1. The crystal structures of 1 and 2
Absorption correction
Goodness-of-fit on F2
R(F) (I > 2r(I))
Multi-scan
1.069
0.0437
0.1102
0.390/ꢁ0.394
Multi-scan
1.146
0.0437
0.0972
0.261/ꢁ0.222
A view of the N,N-dimethyl-3-phthalimidopropylammonium
cation of 1 together with the atom numbering scheme is shown
in Fig. 1. The cation conformation in 2 is similar and for this reason
is not depicted. The phthalimide moiety in both salts is approxi-
wR(F2) (all data)
Max/min (e/Å3)
Fig. 1. A view of the N,N-dimethyl-3-phthalimidopropylammonium cation in 1.

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T. Borowiak et al. / Journal of Molecular Structure 891 (2008) 205–213
207
Table 2
mately planar, the bond lengths and angles are comparable to
those reported in the literature [17–20].
Intermolecular hydrogen bonds in crystals of 1 (Å, °)
The C(10)AC(11) bond is almost perpendicular to the phthali-
mide plane, according to the sp3 hybridization of C(10) atom and
the conformation of the aliphatic substituent can be described as
two gauche- and one anti-bond.
The supramolecular structures of 1 and 2 are unique as they
show how the supramolecular structures are influenced by small
changes, in the molecular structure. The compounds under discus-
sion differ by counter-ions, that is acetate in 1 and chloride in 2.
Probably due to imbalance between the amount of strong proton
donors and acceptors as well as for steric reasons, both compounds
crystallize with different amount of water molecules, namely 1
crystallizes as a semihydrate and 2 as a monohydrate.
DAH
Hꢀ ꢀ ꢀA
1.58(2)
1.94(2)
2.69
2.58
2.65
Dꢀ ꢀ ꢀA
<DAHꢀ ꢀ ꢀA
175(2)
165(2)
151
154
147
N+(13)AH(13)ꢀ ꢀ ꢀO2ꢁ (2R) (i)
O(3W)AH(1W)ꢀ ꢀ ꢀO2ꢁ(1R) (ii)
C(14)AH(14A)ꢀ ꢀ ꢀO(3W) (iii)
C(15)AH(15C)ꢀ ꢀ ꢀO(3W) (iii)
C(1R)AH(1CR)ꢀ ꢀ ꢀO2ꢁ(1R) (iv)
C(7)AH(7)ꢀ ꢀ ꢀO(2) (v)
1.03(2)
0.86(2)
0.96
0.96
0.96
2.608(2)
2.780(1)
3.562(2)
3.468(2)
3.494(2)
3.421(2)
3.426(2)
0.93
0.97
2.50
2.46
171
177
C(11)AH(11B)ꢀ ꢀ ꢀO(9) (vi)
Symmetry codes: (i) ꢁx + 1/2, ꢁy + 1/2, ꢁz + 1; (ii) ꢁx + 1/2, y + 1/2, ꢁz + 1/2; (iii)
ꢁx, ꢁy + 1, ꢁz + 1; (iv) ꢁx + 1, ꢁy + 1, ꢁz + 1; (v) x, ꢁy + 1, z ꢁ 1/2; (vi) x, ꢁy + 1,
z + 1/2.
The packing of the molecules 1 and 2 is dominated by hydro-
gen bonds, which form in crystals of 1 a synthon consisting of
two N,N-dimethyl-3-phthalimidopropylammonium cations, two
acetate anions and one water molecule (Fig. 2) with the own
crystallographic symmetry of a twofold axis along [010] direc-
tion (Tables 2 and 3). Surprisingly, the synthon in crystals of 2,
which is built of two cations, two chloride anions and two water
molecules, is a fragment of a catemer motif, with a chain run-
Table 3
Intermolecular hydrogen bonds in crystals of 2 (Å, °)
DAH
Hꢀ ꢀ ꢀA
Dꢀ ꢀ ꢀA
<DAHꢀ ꢀ ꢀA
N+(13)AH(13)ꢀ ꢀ ꢀClꢁ(1)
O(W)AH(1W)ꢀ ꢀ ꢀClꢁ(1) (i)
O(W)AH(2W)ꢀ ꢀ ꢀClꢁ(1) (ii)
C(12)AH(12A)ꢀ ꢀ ꢀO(W) (iii)
C(11)AH(11A)ꢀ ꢀ ꢀO(2) (iv)
C(4)AH(4)ꢀ ꢀ ꢀO(9) (iii)
0.93(2)
0.98(3)
0.94(4)
0.97
0.97
0.93
2.15(2)
2.21(3)
2.30(4)
2.34
2.41
2.52
3.069(1)
3.172(2)
3.236(1)
3.273(2)
3.349(2)
3.450(2)
170(1)
169(3)
176(3)
161
162
177
ning along
a twofold screw axis of symmetry along [010]
(Fig. 3). The chain in 2 resembles the catemer motif in the pack-
ing of carboxylic acids which possess also other functionalities
able to compete with the carboxylic group in the formation of
intermolecular hydrogen bonds [21]. The detailed structure of
the synthon is in 1 as follows: each cation is hydrogen bonded
with an anion by a N+(13)AH(13)ꢀ ꢀ ꢀO2ꢁ(2R) (acetate) bond. The
water molecule, located on a twofold axis of symmetry glues
two acetate anions of the synthon by two hydrogen bonds
O(3W)AH(1W)ꢀ ꢀ ꢀO2ꢁ(1R). There are also four weak hydrogen
bonds CAHꢀ ꢀ ꢀOW within the synthon, namely two bonds
Symmetry codes: (i) ꢁx + 1, ꢁy, ꢁz; (ii) x, ꢁy ꢁ 1/2, z ꢁ 1/2; (iii) x, ꢁy + 1/2, z + 1/2;
(iv) x, ꢁy + 1/2, z ꢁ 1/2.
C(15)AH(15C)ꢀ ꢀ ꢀO(W) and two bonds C(14)AH(14A)ꢀ ꢀ ꢀO(W),
each pair related by the twofold axis of symmetry. All the de-
scribed interactions cause a closed character of the synthon of
1 which is also a consequence of its own symmetry consistent
with the twofold axis. The synthons of 1 are then joined only
Fig. 2. The supramolecular structure of 1. A supramolecular synthon is depicted in red, water molecules occupy special positions on a twofold axis of symmetry. (For
interpretation of the references to color in this figure legend, the reader is referred to the web version of this article.)

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On the other hand, in the crystal of 2 the chloride anions partic-
ipate in chains: waterꢀ ꢀ ꢀClꢁꢀ ꢀ ꢀwaterꢀ ꢀ ꢀClꢁꢀ ꢀ ꢀwaterꢀ ꢀ ꢀ [via
O(W)AH(1W)ꢀ ꢀ ꢀClꢁ(1) and O(W)AH(2W)ꢀ ꢀ ꢀClꢁ(1) hydrogen
bonds] and the N,N-dimethyl-3-phthalimidopropylammonium
cations are connected with the chains via N+(13)AH(13)ꢀ ꢀ ꢀClꢁ(1)
hydrogen bonds (Figs. 3 and 5). Surprisingly, due to steric reasons
oxygen atoms of the water molecules participate only in weak
hydrogen bonds CAHꢀ ꢀ ꢀO [C(12)AH(12A)ꢀ ꢀ ꢀO(W)]. The chains de-
scribed above and the ammonium fragments of the cations form
hydrophilic segments, whereas the phthalimidopropyl – parts
form hydrophobic ones, as in the structure of 1.
The hydrophilic segments both, in 1 and 2, are arranged alter-
nately with the hydrophobic ones (Figs. 4 and 5) which are similar
in both crystals with the phthalimide units oriented mutually in a
herringbone fashion with a head-to-head overlap of their five-mem-
bered rings and thread also by weak CAH. . .O hydrogen bonds to the
carbonyl groups of the phthalimide units (see Tables 2 and 3).
3.2. B3LYP calculations
The optimized geometry parameters were computed by using
the B3LYP and compared with the X-ray diffraction data in Table
4. The experimental and calculated bond lengths and bond angles
are comparable in the most cases and slightly longer than the X-
ray values. The average deviation, X-ray–B3LYP, is ꢁ0.008 Å. Some
discrepancies in the values of torsion angles between the X-ray and
theoretical data are caused by the packing forces which are af-
fected by anion. In the optimized structure of 2 there is one inter-
molecular hydrogen bond (Clꢁꢀ ꢀ ꢀHAOH 3.108 Å) in contrast to
crystal, where Clꢁ anion form two intermolecular bonds,
Clꢁꢀ ꢀ ꢀHAOH and N+AHꢀ ꢀ ꢀClꢁ (Table 3). In 1 the acetate anion is en-
gaged with the water molecule via hydrogen bond HOH ꢀ ꢀ ꢀ
Fig. 3. The catemer motif in the supramolecular structure of 2. The molecular ch-
ain: ꢀ ꢀ ꢀwaterꢀ ꢀ ꢀClꢁꢀ ꢀ ꢀwaterꢀ ꢀ ꢀClꢁꢀ ꢀ ꢀ runs along a twofold screw axis of symmetry in
the [010] direction. The N,N-dimethyl-3-phthalimidopropylammonium cations are
connected with the chain via N+AHꢀ ꢀ ꢀClꢁ hydrogen bonds. A molecular synthon is
depicted in red. (For interpretation of the references to color in this figure legend,
the reader is referred to the web version of this article.)
ꢀ
ꢁOOCCH3 ¼ 2:714 Å, but in crystal only intermolecular hydrogen
bonds HOHꢀ ꢀ ꢀꢁOOCCH3 and N+ꢀ ꢀ ꢀ ꢁOOCCH3 are present (Table 2).
The calculated bond lengths and bond angles for N,N-dimethyl-3-
phthalimidopropylamonium chloride monohydrate and its anhy-
drous analogue are very similar, however the torsion angles are
substantially different what shows a crucial role of water molecule
in the structure of cation 2 (Table 4). The high tendency to form
hydrates by cations 1 and 2 arises from much lower energy of hy-
drates in comparison to anhydrous analogues. For N,N-dimethyl-3-
phthalimidopropylamonium chloride monohydrate the calculated
energy is about 7% lower than for anhydrous form (Table 4).
be weak intermolecular hydrogen bonds CAHꢀ ꢀ ꢀO [two hydrogen
bonds C(1CR)AH(1CR)ꢀ ꢀ ꢀO2ꢁ(1R)] thus forming a hydrophilic seg-
ment (Fig. 4). The phthalimidopropyl – parts of the cations are in
consequence directed outside the hydrophilic segment giving
rise to hydrophobic segments.
Fig. 4. The supramolecular structure of 1. Alternate hydrophilic and hydrophobic segments.