Polyamines. I. Spectroscopic properties of N,N-bis-(phthalimidopropyl)-N-propylamine and supramolecular interactions in its crystals

Article abstract of DOI:10.1016/j.molstruc.2006.01.023

A new derivative of polyamine, N,N-bis-(phthalimidopropyl)-N-propylamine (1) has been synthesized and its structure studied by X-ray diffraction, FTIR, Raman, ¹H and ¹³C NMR spectroscopies. The B3LYP and DFT calculations have been carried out. The molecular structure of N,N-bis-(phthalimidopropyl)-N-propylamine (1) presents the first case of a folded conformation for this group of compounds which is stabilized by an intramolecular hydrogen bond C-H?O. Neither C-H?π, π?π or C{double bond, short}O?C{double bond, short}O interactions operate in this case. Also the supramolecular structure is stabilized by weak C-H?O and C-H?π hydrogen bonds. The optimized bond lengths as well as bond angles for 1 calculated by B3LYP/6-31G(d,p) approach are 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 have been obtained.

Full text of DOI:10.1016/j.molstruc.2006.01.023

Journal of Molecular Structure 791 (2006) 137–143
www.elsevier.com/locate/molstruc
Polyamines. I. Spectroscopic properties of N,N-bis-(phthalimidopropyl)-
N-propylamine and supramolecular interactions in its crystals
a,
a
, Iwona Kowalczyk , Justyna Werner , Teresa Borowiak , Irena Wolska
* *
a
b,
b
Bogumił Brycki
a
Laboratory of Microbiocides Chemistry, Faculty of Chemistry, Adam Mickiewicz University, Grunwaldzka 6 60-780, Pozna n´ , Poland
b
Department of Crystallography, Faculty of Chemistry, Adam Mickiewicz University, Grunwaldzka 6 60-780, Pozna n´ , Poland
Received 25 November 2005; received in revised form 16 January 2006; accepted 20 January 2006
Available online 3 March 2006
Abstract
A new derivative of polyamine, N,N-bis-(phthalimidopropyl)-N-propylamine (1) has been synthesized and its structure studied by X-ray
1
13
diffraction, FTIR, Raman, H and C NMR spectroscopies. The B3LYP and DFT calculations have been carried out. The molecular structure of
N,N-bis-(phthalimidopropyl)-N-propylamine (1) presents the first case of a folded conformation for this group of compounds which is stabilized
by an intramolecular hydrogen bond C–H/O. Neither C–H/p, p/p or CaO/CaO interactions operate in this case. Also the supramolecular
structure is stabilized by weak C–H/O and C–H/p hydrogen bonds. The optimized bond lengths as well as bond angles for 1 calculated by
1
3
1
B3LYP/6-31G(d,p) approach are compared with the X-ray data. The screening constants for C and H atoms have been calculated by the
1
13
GIAO/B3LYP/6-31G(d,p) approach and analyzed. Linear correlations between the experimental H and C chemical shifts and the computed
screening constants have been obtained.
q 2006 Elsevier B.V. All rights reserved.
Keywords: N,N-bis-(phthalimidopropyl)-N-propylamine; X-ray diffraction; B3LYP calculations; FTIR; Raman and NMR spectra
1
. Introduction
(phthalimidopropyl)-N-propylamine, a polyamine with two
terminal amine groups blocked by phthalimide moiety. Hence,
the detailed structural characterization of a new phthalimide
derivative is worthy of consideration.
Polymethylene polyamines occur naturally in all living
species and many functions of prokaryotic and eukaryotic cells
have been shown to be polyamine dependent [1,2]. On the
other hand, polyamine derivatives can be used as therapeutic
agents. For example, N-alkyl analogues of biogenic poly-
amines exhibit strong cytotoxic activity against human tumor
cell lines [3], also naphthalimide derivatives of polyamines
have potential anticancer activity [4]. Some of the polyamines
and their derivatives exhibit a very good antimicrobial activity
Polyamines and their derivatives in the most cases are
flexible molecules; however in some examples extended
conformations are observed. Crystals with phthalimide
moieties have the propensity to engage in the solid state C–
H/p, p/p, dipole/dipole and other supramolecular
interactions, depending on the detailed nature of the proximal
functional groups [8–11]. For compounds which possess
tertiary amine functions located between phthalimide moieties
the interactions mentioned above lead to a folded molecular
conformation as observed for compounds with the CSD codes
IJOKUN, REVZEX, IJOLAU [8,9,12]. For such conformation
the torsion angle N(amine)–C–C–N(phthalimide) as deter-
mined by X-ray diffraction, adopts value of about 608. Without
the possibility for C–H/p and the other interactions indicated
above as in IJOKOH or IJOKAT [8] whose amino functions
have been quaternized, an extended conformation is observed
[
5–7].
In order to better understand the mechanism of antimicro-
bial activity, we synthesized a new series of N,N-bis-
aminopropyl)-N-alkylamines and their derivatives. These
(
compounds were obtained as a part of our program to develop
synthetic routes to novel, stable polynuclear dendritic
complexes with potential biotechnical applications. In the
first step of this program, we obtained N,N-bis-
C
with the torsion angle N (amine)–C–C–N(phthalimide) of
*
Corresponding authors. Tel.: C48 61 829 1314; fax: C48 61 865 8008.
E-mail address: iwkow@amu.edu.pl (B. Brycki).
about 1708. In the folded conformation also the dipole/dipole
interactions play a crucial stabilizing role. This kind of
interaction is characterized by a short contact between OaC
(dC)/O (dK)aC dipoles [8].
0
022-2860/$ - see front matter q 2006 Elsevier B.V. All rights reserved.
doi:10.1016/j.molstruc.2006.01.023

138
B. Brycki et al. / Journal of Molecular Structure 791 (2006) 137–143
Table 1
Crystal data, data collection and structure refinement for 1
conformational preferences of 1 whose tertiary amine function
is located across longer propylene chains. Potentially, all the
conditions exist to stabilize the same kind of folded
conformation as in the case of compounds quoted above.
However, in those examples the chains between Nphthalimide and
Namine are shorter.
Compound
1
Empirical formula
Formula weight
T (K)
C
25 27 3 4
H N O
433.50
120(2)
˚
Wavelength (A)
0.71073
Crystal system, space group
Triclinic, PK1
Unit cell dimensions
˚
a (A)
˚
b (A)
2. Experimental
8.4271(5)
11.2414(6)
11.9873(7)
76.372(5)
85.758(5)
89.296(5)
1100.6(1)
2, 1.308
2.1. Synthesis
˚
c (A)
a (8)
b (8)
g (8)
N,N-bis-(phthalimidopropyl)-N-propylamine (1) was pre-
pared according to the method reported previously [13]. A
mixture N,N-bis-(3-aminopropyl)-amine (0.14 M) with phtha-
3
lic anhydride (0.31 M) were added to ice acetic acid (300 cm )
3
˚
Volume (A )
3
(Mg/m )
K1
Z, D
x
m (mm
F(000)
)
0.090
and stirred at room temperature for 2 h. At the next stage, N,N-
bis-(phthalimidopropyl)-amine was refluxed with propylbro-
mide (0.15 M) and sodium carbonate in ethanol for 18 h. The
crude product was recrystallized from anhydrous ethanol; m.p.
460
q Range for data collection (8)
hkl Range
3.05–30.01
K11%h%11
K14%k%15
K16%l%8
109–111 8C, Yield 78%. Analysis: exp. and (calc.): %C 69.20
Reflections:
(69.22); %H 6.31 (6.28); %N 9.71 (9.73).
Collected
10950
Unique (Rint
)
5560 (0.024)
3982
Observed (IO2s(I))
Data/restraints/parameters
2.2. Instrumentation
5560/0/289
1.019
2
Goodness-of-fit on F
Crystals suitable for X-ray analysis were grown by slow
evaporation from anhydrous ethanol solution. All details of the
measurements, crystal data and structure refinement are given
in Table 1. The data were collected on an Oxford Diffraction
KM4CCD diffractometer [14] at 120 K, using graphite-
R(F) (IO2s(I))
0.0423
2
wR(F ) (all data)
0.1104
3
Max/min Dr (e/A )
˚
0.212/K0.206
In the current paper, we present the X-ray structure as well
as results on B3LYP calculations, FTIR, Raman and NMR
spectroscopy of N,N-bis-(phthalimidopropyl)-N-propylamine
monochromated Mo K radiation. A total of 782 frames were
a
measured in six separate runs. The u-scan was used with a step
of 0.758, two reference frames were measured after every 50
frames, they did not show any systematic changes either in
(
hereafter 1). We have been aiming in recognizing the
Fig. 1. A perspective view of the molecular conformation of 1 together with the atom numbering scheme.

B. Brycki et al. / Journal of Molecular Structure 791 (2006) 137–143
139
P
2
2 2
[
17]. The function
2
w(jF j KjF j ) was minimized with
o c
Table 2
Hydrogen-bonding geometry (A and deg) for 1
o
2
c
K1
2
2
2
˚
w Z½s ðF Þ Cð0:0605PÞ ꢀ, where PZðF C2F Þ=3. All
o
non-hydrogen atoms were refined with anisotropic thermal
parameters. The coordinates of the hydrogen atoms were
calculated in idealized positions and refined as a riding model
with their thermal parameters calculated as 1.2 (1.5 for methyl
group) times Ueq of the respective carrier carbon atom.
D–H/A
d(D–H)
d(H/A)
d(D/A)
!(DHA)
0
0
0
0
C4 –H4 1/O13
0.97
0.93
0.93
0.97
0.93
0.97
2.60
2.53
2.55
2.55
2.59
2.78
3.300(2)
3.461(2)
3.241(2)
3.404(2)
3.133(2)
3.570(2)
129
178
132
147
118
139
i
C8 –H8 /O13
0
0
ii
C10 –H10 /O13
C15–H15B/O6
C10 –H10 /O6
C14–H14A/Cg
iii
0
0
iv
The NMR spectra were recorded in CDCl on a Varian
3
v
Gemini 300VT spectrometer, operating at 300.07 and
13
75.46 MHz for H and C, respectively.
1
0
0
0
0
0
0
Cg represents the centroid of six-membered ring C7 /C8 /C9 /C10 /C11 /C12
Symmetry codes: (i) xK1, y, z; (ii) Kx, KyC1, Kz; (iii) KxC1, Ky, KzK1;
iv) xK1, y, zC1; (v) Kx, Ky, Kz.
The FTIR spectra were recorded in Nujol and Fluorolube
K1
(
emulsion at 2 cm
resolution on a Bruker IFS 113v
spectrometer, which was evacuated to avoid water and CO2
absorption. Raman spectra were recorded on a Nicolet Magna
760 spectrometer operating at the 1064 nm exciting line of an
Nd;YAG laser. Each spectrum consists of 250 scans at 31 8C.
The calculations were performed using the GAUSSIAN 98
package [18] at the B3LYP [19,20] levels of theory with the
6-31G(d,p) basis set [21]. The molecular parameters were
optimized in ab initio calculations at density-functional (DFT)
peak positions or in their intensities. The unit cell parameters
were determined by least-squares treatment of setting angles of
5
837 highest-intensity reflections chosen from the whole
experiment. Intensity data were corrected for the Lorentz and
polarization effects [15]. The structure was solved by direct
methods with the SHELXS 97 program [16] and refined by the
full-matrix least-squares method with the SHELXL 97 program
Fig. 2. The structure of one molecular sheet: centrosymmetric dimers form molecular tapes which are connected into sheets. Two tapes have been shown. Hydrogen
bonds have been indicated by dashed lines.

140
B. Brycki et al. / Journal of Molecular Structure 791 (2006) 137–143
levels of the theory using the split-valence polarized
6
worthy of mention that the attractive interaction energies for
the perpendicular motif of the CaO dipoles are comparable in
strength to a C–H/O hydrogen bond [22].
-31G(d,p) basis set.
CCDC 290791 for 1 contains the supplementary crystallo-
graphic data for this paper. These data can be obtained free of
charge via www.ccdc.cam.ac.uk/data_request/cif, or by email-
ing data_request@ccdc.cam.ac.uk, or by contacting The
Cambridge Crystallographic Data Centre, 12, Union Road,
Cambridge CB2 1EZ, UK; fax: C44 1223 336033.
Interatomic distances and angles within the phthalimide
residues are normal [9]. Looking at the torsion angles in the
aliphatic part of the molecule, one finds four gauche and two
antibonds, although some of them are highly distorted from the
ideal values. The ranges for the gauche–torsion angles are from
about K63 to K868, whereas these for antibonds are equal to
about 150 and 1798. Such a broad spread is probably caused
certain tension in the molecule which is caused off by the
intramolecular C–H/O hydrogen bond. The packing forces
influence on the conformation should be also considered (see
Section 3.2.).
3
. Results and discussion
3
.1. The crystal structure of 1
A perspective view of the molecular conformation together
The supramolecular structure of 1 is unique. The molecules
are organized into three-dimensional network by weak
intermolecular interactions. Thus, within the crystal, centro-
symmetric molecular dimers are formed via a pair of hydrogen
with the atom numbering scheme is shown in Fig. 1.
The molecule of 1 adopts a folded conformation with an
angle between its phthalimide residues of 78.1(2)8. It is
0
stabilized by the weak intramolecular hydrogen bond C(4 )–
0
0
0
bonds C10 –H10 /O13 (Table 2, Fig. 2).
H(4 )/O(13) (Table 2) and there are no indications for the
The dimers are further linked via very weak C–H/p
hydrogen bonds (C14–H14A/Cg where g is the centroid of a
other kind of intramolecular interactions as CaO/CaO
electrostatic interactions, C–H–p or p–p interactions [8].
The reason for that lies in the propyl groups which cause that
the distances between the amine function and phthalimide parts
as well as the both phthalimide moieties are too long. The weak
hydrogen bond C–H/O is apparently competitive to the
CaO/CaO electrostatic interactions for steric reasons. It is
0
0
0
0
0
six-membered ring C7 /C8 /C9 /C10 /C11/C12 ) thus forming
infinite tapes along [010] axis. The tapes in turn, form two-
dimensional sheets by hydrogen bonds C15–H15B/O6 and
0
0
C10 –H10 /O6 (Fig. 2, Table 2). Three-dimensional supra-
molecular structure results from combination of sheets via
0
0
hydrogen bonds C8 –H8 /O13 (Fig. 3). Surprisingly, neither
Table 3
Selected X-ray and B3LYP parameters of N,N-bis-(phthalimidopropyl)-N-
propylamine (1)
Parameters
X-ray
B3LYP 6-31G(d,p)
Bond lengths
N(1)–C(2)
N(1)–C(14)
C(4)–N(5)
N(5)–C(6)
1.471(1)
1.478(2)
1.457(2)
1.395(1)
1.399(2)
1.394(2)
1.397(2)
1.210(1)
1.212(1)
1.461
1.468
1.464
1.405
1.420
1.405
1.420
1.215
1.216
0
0
N(5 )–C(6 )
N(5)–C(13)
0
0
N(5 )–C(13 )
C(6)–O(6)
C(13)–O(13)
Bond angles
0
C(2 )–N(1)–C(2)
111.6(1)
110.1(1)
123.9(1)
124.3(1)
106.1(1)
124.8(1)
114.1
115.0
124.5
124.6
106.7
125.1
C(2)–N(1)–C(14)
C(13)–N(5)–C(4)
C(6)–N(5)–C(4)
N(5)–C(6)–C(7)
O(13)–C(13)–N(5)
Torsion angles
0
C(2 )–N(1)–C(2)–C(3)
K75.1(1)
160.7(1)
179.3(1)
K83.0(1)
93.1(1)
43.9
C(14)–N(1)–C(2)–C(3)
C(2)–C(3)–C(4)–N(5)
C(3)–C(4)–N(5)–C(13)
C(3)–C(4)–N(5)–C(6)
C(13)–N(5)–C(6)–O(6)
O(6)–C(6)–C(7)–C(8)
N(5)–C(6)–C(7)–C(8)
K91.8
68.6
60.8
K122.5
178.9
0.8
179.1(1)
K0.6(2)
179.8(1)
Fig. 3. The supramolecular three-dimensional structure of 1. Molecular sheets
are connected by C–H/O hydrogen bonds (dashed lines).
K179.7

B. Brycki et al. / Journal of Molecular Structure 791 (2006) 137–143
141
Table 4
Chemical shifts (d, ppm) in CDCl
3
and calculated GIAO nuclear magnetic shielding tensors (scal) for N,N-bis-(phthalimidopropyl)-N-propylamine (1)
d
exp.
d
calc.
s
calc.
d
exp.
d
calc.
s
calc.
C (2)
51.5
26.3
36.5
48.8
31.2
36.7
46.9
30.0
H (2)
2.49
1.80
3.74
7.81
7.72
2.36
1.41
0.88
2.72
1.91
3.73
7.83
7.61
2.42
1.43
0.75
2.31
1.59
3.36
7.57
7.38
2.08
1.07
0.36
C (3)
H (3)
C (4)
35.3
H (4)
C (6,13)
C (7,12)
C (8,11)
C (9,10)
C (14)
C (15)
C (16)
168.4
133.8
132.2
123.0
55.6
171.8
133.5
129.7
121.4
53.4
165.2
128.4
124.7
116.7
51.4
H (8,11)
H (9,10)
H (14)
H (15)
H (16)
20.1
23.2
22.3
11.9
9.5
9.1
(a)
(b)
8
6
4
2
0
1
1
1
80
50
20
9
6
3
0
0
0
0
0
30
60
90 120 150 180
0
2
4
6
8
σ (calc)
σ (calc)
13
13
Fig. 4. The relationship (a) between the experimental C chemical shifts (d) and the GIAO computed C screening constants (s) and (b) between the experimental
1
1
H chemical shifts (d) and the GIAO computed H screening constants (s).
(a)
2
2
1
1
5
0
5
0
5
0
(b) 1.2
1
0
0
0
0
0
.0
.8
.6
.4
.2
.0
3
500
3000 2500
2000
1500
1000
500
–
1
Wavenumbers/cm
Fig. 5. The spectra of N,N-bis-(phthalimidopropyl)-N-propylamine: (a) Raman spectrum in the solid state; and (b) FTIR spectrum in Nujol and Fluorolube emulsion.

142
B. Brycki et al. / Journal of Molecular Structure 791 (2006) 137–143
K1
1710 cm . In the Raman spectrum, this absorption is very
K1
intermolecular interactions CaO/CaO nor p/p have been
found.
small and lies at 1705 cm
[27]. The difference between
intensities of symmetric and asymmetric stretching vibrations
of carbonyl groups is connected with the symmetry of the
molecule. When two CaO bonds are not coplanar the intensity
3
.2. B3LYP calculations
of n CaO should be lower than that of the n CaO [24]. The
as
The optimized geometry parameters computed by using of
s
the B3LYP are compared with the X-ray diffraction data in
Table 3. The experimental and calculated bond lengths and
bond angles are comparable in the most cases.
split of nasCaO band suggests the non-equivalence of carbonyl
groups in phtalimide moiety which is confirmed by X-ray data.
According to the dihedral angles presented in Table 3, the
molecules in the gas-phase are more folded in comparison to
those in the crystal. The conformation differences are probably
caused by intermolecular interactions in crystals. It is well
known that intermolecular interactions may cause the
molecular geometry in the crystals to be different from that
of the free molecules [23].
Table 5
FTIR and Raman frequencies of N,N-bis-(phthalimidopropyl)-N-propylamine
(1)
Raman
FTIR
Proposed assignment
3091
3061
2947
2925
nCH
nCH
2974
2952
2924
2871
2854
2822
1771
1764
1710
1610
1465
1447
1430
1396
nCH
nCH
nCH
nCH
nCH
2
2
2
2
2
1 13
.3. H NMR and C NMR spectra
2873
3
2
2
856
822
The proton chemical shift assignments are based on the 2D
1774
n CO
as
asCO
CO
1763
1705
1610
1467
1456
n
n
COSY experiments, in which the proton–proton connectivity is
observed through the off-diagonal peaks in the counter plot.
The 2D heteronuclear shifts correlated counter map
s
nCC
nCC
(
HETCOR) has been used to identify resonance signals in the
3
d
asCH
3
1
C NMR spectra.
The experimental chemical shifts in CDCl and the GIAO
shielding constants calculated for 1 are listed in Table 4. The
1
corelations between the experimental H and C chemical
1432
396
nCC
nCC
1
3
1
374
dasCH
3
13
1366
330
1311
1366
1329
1311
1294
nCC, dCH
dCH
2
1
2
shifts (dexp) and the computed screening constants (scalc.) are
13
dCH2
nCC
nCC
nCC
1
shown in Fig. 4. For H and C the correlation is linear and
described by the following equation:
1
286
1
278
1279
1250
dexp Z Ascalc CB
1249
dCH
nCC
nCN
nCN
2
1
212
Values of the slope (A Z1.0401, A Z0.9904) and
1188
1170
1187
1178
1113
1099
1087
1065
1050
1038
1021
984
C
H
intercept (B ZK6.8923, B Z0.3423) were determined
C
H
1113
1110
1083
1066
bCH
bCH
gCH
gCH
nCC
through a fit of the computed shielding constants to the
experimental chemical shifts.
2
1
The very good correlation coefficients (r Z0.999) for H
2
13
and (r Z0.998) for C correlations confirm the optimized
geometry of 1.
1035
dCH
bCC
gCH
gCH
2
1
9
016
85
3
.4. FTIR and Raman spectra
970
976
9
49
950
dCH
dCO
gCH
bCC
gCH
nCC
2
9
11
97
The IR and Raman spectra of 1 in the solid state are
8
presented in Fig. 5 and the assignments proposed are given in
Table 5. These assignments are partly based on the calculated
spectrum of N-aminophthalimide [24].
8
8
83
69
883
869
857
819
795
856
819
K1
In general, the bands around 1650–1350 cm
spectra are assigned to skeletal C–C stretching modes of
in FTIR
nCC
7
92
gCH
tring
dCO
bCC
bring
gCH
gCC
tring
tring
7
7
59
23
benzene ring. The C–N stretching vibrations of 1 are observed
K1
at 1187 and 1178 cm
.
The FTIR spectrum of 1 shows characteristic bands at 1771
7
16
713
691
628
531
692
629
K1
and 1764 cm
vibrations of carbonyl group n CaO in a phthalimide
which are due to asymmetric stretching
5
31
as
4
83
moiety [25,26]. The symmetric stretching vibration n CaO
s
appears in the FTIR spectrum as a broad and intensive band at
4
61
472

B. Brycki et al. / Journal of Molecular Structure 791 (2006) 137–143
143
4
. Conclusions
[9] D.M.Y. Barrett, I.A. Kahwa, J.T. Mague, G.L. McPherson, J. Org. Chem.
0 (1995) 5946.
10] D.M.Y. Barrett, I.A. Kahwa, D.J. Williams, Acta Crystallogr. C52 (1996)
069.
6
[
[
The molecular and crystal structures of N,N-bis-(phthalimi-
2
dopropyl)-N-propylamine (1) have been determined by X-ray
diffraction and by the B3LYP calculations. The crystal
structure of 1 presents the first case of a folded conformation
of N-alkylamine-phthalimides which is stabilized by an
intramolecular hydrogen bond C–H/O. Also the supramole-
cular structure is stabilized by the C–H/O and C–H/p
hydrogen bonds. No CaO/CaO interactions have been
found.
11] D.M.Y. Barrett, I.A. Kahwa, B. Rad u¨ chel, A.J.P. White, D.J. Williams,
J. Chem. Soc. Perkin Trans. 2 (1998) 1851.
[12] F.H. Allen, Acta Crystallogr. B58 (2002) 380.
[
[
13] B. Brycki, J. Werner, I. Kowalczyk, Pol. J. Chem, in press.
14] Oxford Diffraction Poland, CrysAlisCCD, CCD Data Collection GUI,
Version 1.171, 2003.
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1
Good correlations between the experimental C and H
3
1
chemical shifts in CDCl solution of 1 and GIAO/B3LYP/6-
3
3
1G(d,p) calculated isotropic shielding tensors ðd ZAscalc
exp
C
BÞ have confirmed the optimized geometry of 1.
Acknowledgements
This work was supported by the funds from Adam
Mickiewicz University, Faculty of Chemistry.
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