Synthesis, crystal structure and theoretical investigation of two infinite two-dimensional supra-molecular compounds

Article abstract of DOI:10.1016/j.molstruc.2007.08.025

Two supra-molecular compounds: (1,1′-biphenyl)-4,4′-diammonium bis(3,5-dinitrobenzoate) (1) and 4,4′-methylene bis(benzenammonium) bis(3,5-dinitrobenzoate) monohydrate (2) were synthesized and characterized by IR spectrum, UV spectrum and element analysis. The single crystal structure analysis indicates that these compositions in two compounds are linked through N-H?O and O-H?O hydrogen bonds into infinite two-dimensional structure. Moreover, theoretical investigation was performed by using RHF/6-31G(d) method, and their stabilities, frontier molecular orbital composition and Mulliken charge distribution were discussed.

Full text of DOI:10.1016/j.molstruc.2007.08.025

Available online at www.sciencedirect.com
Journal of Molecular Structure 879 (2008) 150–155
www.elsevier.com/locate/molstruc
Synthesis, crystal structure and theoretical investigation of two
infinite two-dimensional supra-molecular compounds
a,
b
a
a,
*
Zi-Liang Wang *, Lin-Heng Wei , Ming-Xue Li , Jing-Ping Wang
a
Institute of Molecule and Crystal Engineering, College of Chemistry and Chemical Engineering, Henan University, Kaifeng 475001, China
b
College of Environment and Planning, Henan University, Kaifeng 475001, China
Received 23 June 2007; received in revised form 18 August 2007; accepted 22 August 2007
Available online 2 September 2007
Abstract
Two supra-molecular compounds: (1,10-biphenyl)-4,40-diammonium bis(3,5-dinitrobenzoate) (1) and 4,40-methylene bis(benzenam-
monium) bis(3,5-dinitrobenzoate) monohydrate (2) were synthesized and characterized by IR spectrum, UV spectrum and element anal-
ysis. The single crystal structure analysis indicates that these compositions in two compounds are linked through N–Hꢀ ꢀ ꢀO and O–Hꢀ ꢀ ꢀO
hydrogen bonds into infinite two-dimensional structure. Moreover, theoretical investigation was performed by using RHF/6-31G(d)
method, and their stabilities, frontier molecular orbital composition and Mulliken charge distribution were discussed.
Ó 2007 Elsevier B.V. All rights reserved.
Keywords: 3,5-Dinitrobenzoate; Crystal structure; Hydrogen bonds; Theoretical investigation; Mulliken
1. Introduction
can act as strong hydrogen bond acceptor. Besides, the
changing length of hydrogen bond acceptor may affect
the final structure of 1 and 2. To best of our knowledge,
some supra-molecular compounds relating to 3,5-dinitro-
benzoic acid have been reported [10–19]. However, in those
reported literatures theoretical investigation has not been
seen. Herein we present synthesis, crystal structure and the-
oretical investigation of two infinite two-dimensional
supra-molecular compounds.
In recent years, there has been increasing interest in the
use of hydrogen bonding for the design and synthesis of
supra-molecular assemblies and molecular architectures
because hydrogen bonding has long been considered to
be of importance in biological systems and molecular rec-
ognition [1–6]. Moreover, lots of literatures in which quan-
tum chemical methods were applied to analyze H-bonding
systems [7–9] have been reported, such as electronic prop-
erties, interaction energy and vibrational spectra, and so
on. It is well known that 3,5-dinitrobenzoic acid has two
strongly electron-withdrawing groups so that its carboxyl-
ate group deprotonized easily. Moreover, carboxylate
anion and two nitro groups can easily form hydrogen
bonds as hydrogen bonds acceptor with other hydrogen
bonds donors and further construct zero-, one- or higher-
dimensional structure. Herein we select (1,10-biphenyl)-
4,40-diamine and longer 4,40-methylene bis(benzenamine)
ligand because both them have two –NH2 groups and
2. Experimental
2.1. Materials and physical measurements
All chemicals were of reagent grade as received from
commercial sources and used without further purification.
C, H, N elemental analysis was performed on Perkin-Elmer
240C elemental analyzer; Infrared spectrum was recorded
as KBr pellets on a Nicolet 170SXFT-IR spectrometer in
the range of 400–4000 cmꢁ1. The UV spectrum was
performed on a Shimzu UV-250 spectrometer in the
190–350 nm range. Quantum chemical calculation of two
compounds was performed from the crystal data with
*
Corresponding author. Tel.: +86 378 3269661.
E-mail address: zlwang@henu.edu.cn (Z.-L. Wang).
0022-2860/$ - see front matter Ó 2007 Elsevier B.V. All rights reserved.
doi:10.1016/j.molstruc.2007.08.025

Z.-L. Wang et al. / Journal of Molecular Structure 879 (2008) 150–155
151
Table 1
Crystal data for 1 and 2
RHF method at 6-31G(d) level, while all the computations
have been performed using Gaussian 03 program [20]. All
the quantum chemical calculation has been done on the
Pentium IV.
1
2
Empirical formula
Formula weight
Crystal system
C26H20N6O12
608.48
C27H24N6O13
640.52
Monoclinic
C2/c
Monoclinic
P2/c
2.2. Synthesis
Space group
Unit cell dimensions
2.2.1. Synthesis of 1
˚
a (A)
27.069(15)
4.709(3)
21.732(12)
107.450(8)
2643(3)
4
1.529
0.124
6199
2366
12.548(4)
4.1444(12)
27.736(8)
101.494(5)
1413.5(7)
2
1.505
0.122
7169
2753
A 5 ml ethanol solution of (1,10-biphenyl)-4,40-diamine
(0.25 mmol, 0.045 g) was added to an aqueous solution
(25 ml) of 3,5-dinitrobenzoic acid (0.50 mmol, 0.10 g). The
mixture was stirred for 10 min at 353 K. The solution was
filtered, and the filtrate was allowed to stand at
room temperature. After 10 days, colorless single crystals
suitable for X-ray analysis were obtained. Anal. Calc. for
C26H20N6O12: C, 51.32%; H, 3.31%; N, 13.81%. Found:
C, 50.80%; H, 3.02%; N 13.40%. IR (v/cmꢁ1): 3430.44(s),
1623.75(s), 1581.66(w), 1535.21(s), 1501.12(m), 1457.23(w),
1384.04(w), 1347.49(s), 1080.39(w), 814.77(w), 725.98(m),
715.89(m). UV (kmax/nm): 201, 242.
˚
b (A)
˚
c (A)
b (°)
3
˚
V (A )
Z
Dcalcd (mg/m3)
l (mmꢁ1
)
Reflections collected
Independent reflections
Goodness-of-fit on F2
Final R indices [I > 2.0r(I)]
0.921
1.008
R1 = 0.0544
wR2 = 0.0959
R1 = 0.1305
wR2 = 0.1193
2
R1 = 0.0553
wR2 = 0.1292
R1 = 0.1101
wR2 = 0.1480
2
R indices (all data)
P
P
P
P
R = jjFoj ꢁ jFcjj/ jFoj, wR ¼ f ½wðF 2o ꢁ F c2Þ ꢂ= ½wðF o2Þ ꢂg1=2, 1, w ¼
2
2
1=½r2ðF o2Þ þ ð0:0448PÞ ꢂ, 2, w ¼ 1=½r2ðF o2Þþð0:0421PÞ ꢂ, P ¼ðF 2o þ2Fc2Þ=3.
2.2.2. Synthesis of 2
4,40-Methylene bis(benzenamine) (0.25 mmol, 0.05 g)
was added to an aqueous solution (25 ml) of 3,5-dinitroben-
zoic acid (0.50 mmol, 0.10 g). The mixture was stirred for
10 min at 353 K. The solution was filtered, and the filtrate
was allowed to stand at room temperature. After a week, col-
orless single crystals suitable for X-ray analysis were
obtained. Anal. Calc. for C27H24N6O13: C, 50.63%; H,
3.78%; N, 13.12%. Found: C, 50.11%; H, 3.47%; N,
12.83%. IR (v/cmꢁ1): 3420.98(m), 3098.48(m), 1621.01(m),
1533.60(s), 1508.51(w), 1452.01(w), 1382.47(w), 1345.19(s),
1072.64(m), 723.95(m). UV (kmax/nm): 192, 202.
Table 2
˚
Selected bond distances (A) for 1 and 2
1
N(1)–O(4)
N(2)–O(6)
O(1)–C(7)
C(1)–C(2)
C(3)–C(4)
1.218(3)
1.221(3)
1.265(3)
1.387(4)
1.373(4)
N(1)–O(3)
N(2)–O(5)
O(2)–C(7)
C(1)–C(7)
C(4)–C(5)
1.223(3)
1.205(3)
1.243(4)
1.513(4)
1.379(4)
N(1)–C(3)
N(2)–C(5)
C(1)–C(6)
C(2)–C(3)
C(5)–C(6)
1.476(4)
1.479(4)
1.385(4)
1.374(4)
1.380(4)
2
N(1)–O(4)
N(2)–O(6)
O(1)–C(7)
C(1)–C(2)
C(3)–C(4)
1.214(3)
1.209(3)
1.253(3)
1.387(3)
1.363(4)
N(1)–O(3)
N(2)–O(5)
O(2)–C(7)
C(1)–C(7)
C(4)–C(5)
1.219(3)
1.212(3)
1.235(3)
1.517(3)
1.383(4)
N(1)–C(3)
N(2)–C(5)
C(1)–C(6)
C(2)–C(3)
C(5)–C(6)
1.475(4)
1.466(4)
1.377(3)
1.374(3)
1.383(3)
2.3. X-ray crystallography
Data collections were made on Bruker SMART APEX
CCD area-detector diffractometer using graphite mono-
chromated Mo-Ka diffraction (k = 0.71073 A) at 298(2) K.
bis(3,5-dinitrobenzoate) anions. The cation herein occupies
a special position on an inversion centre. The extensive
hydrogen-bonding system, which involves all six symmetry
independent ‘active’ H atoms from two protonized amine
groups as hydrogen bonds donors and two oxygen atoms
[O(1) and O(2)] from carboxylate group as hydrogen bonds
acceptors, links the component ions into an infinite one-
dimensional chain along the [010] direction through
N–Hꢀ ꢀ ꢀO hydrogen bonds (Table 3). Adjacent chains are
further organized into two-dimensional network by
N–Hꢀ ꢀ ꢀO hydrogen bonds parallel to the (001) plane
(Fig. 2).
The compound 2 is composed of one 4,40-methylene
bis(benzenamine) cation, two bis(3,5-dinitrobenzoate)
anions and two water molecules. Here, the cation and
water molecule occupies a special position on an inversion
centre (Fig. 3), similar to that of 1. These ions and mole-
cules build an infinite one-dimensional chain via N–
Hꢀ ꢀ ꢀO and O–Hꢀ ꢀ ꢀO hydrogen bonds along the [010]
direction (Table 3). Moreover, adjacent chains result in
˚
The intensities were corrected by Lorentz-polarization
factors and empirical absorption. The structures were solved
by direct methods and refined by a full-matrix least squares
technique based on F2 using the SHELXTL-97 [21] program.
All non-hydrogen atoms were refined anisotropically.
H atoms bound to N and C atoms were positioned geomet-
rically and to water molecule were located from difference
maps.
Crystallographic data for the title compounds are listed
in Table 1. The selected bond lengths are given in Table 2.
The hydrogen bonds data are presented in Table 3.
3. Results and discussion
3.1. Structure description
As shown in Fig. 1, the compound 1 consists of
one (1,10-biphenyl)-4,40-diammonium cation and two

152
Z.-L. Wang et al. / Journal of Molecular Structure 879 (2008) 150–155
Table 3
Hydrogen bonds for 1 and 2
D–Hꢀ ꢀ ꢀAa
Dꢀ ꢀ ꢀH (A) Hꢀ ꢀ ꢀA (A) Dꢀ ꢀ ꢀA (A) D–Hꢀ ꢀ ꢀA (°)
˚
˚
˚
1
N3–H3Aꢀ ꢀ ꢀO2
N3–H3Bꢀ ꢀ ꢀO1i
N3–H3Cꢀ ꢀ ꢀO1ii
0.89
0.89
0.89
1.89
1.93
1.91
2.762
2.791
2.768
168
163
162
2
N3–H3Aꢀ ꢀ ꢀO1
N3–H3Bꢀ ꢀ ꢀO7
0.89
0.89
2.39
2.08
1.75
2.01
1.94
2.981
2.962
2.631
2.734
2.734
124
172
170
144
160
N3–H3Cꢀ ꢀ ꢀO1iii 0.89
O7–H7Aꢀ ꢀ ꢀO2
O7–H7Bꢀ ꢀ ꢀO2iv
a
0.84
0.83
Symmetry codes: i = ꢁx + 2, ꢁy + 1, ꢁz + 1; ii = ꢁx + 2, ꢁy + 2,
ꢁz + 1; iii = x, y ꢁ 1, z; iv = ꢁx + 1, y, ꢁz + 1/2.
an infinite two-dimensional network by N–Hꢀ ꢀ ꢀO hydro-
gen bonds propagating in (001), as presented in Fig. 4.
Although 4,40-methylene bis(benzenamine) has more a
methylene group than that of (1,10-biphenyl)-4,40-diammo-
nium cation, the structure of 2 is similar to that of 1, indi-
cating the length changing of hydrogen bonding acceptor
here has little influences on their structure. In addition,
we can see from Table 2 that the different cation has little
influences on the structure of bis(3,5-dinitrobenzoate)
anions through hydrogen bonding and static electric inter-
actions. During our investigation we found pH value has
little influences on the information of 1 and 2. Whereas
the mole ratio of 3,5-dinitrobenzoic acid and (1,10-biphe-
nyl)-4,40-diamine (or 4,40-methylene bis(benzenamine) play
an important role in the products of 1 and 2. When the
mole ratio was close to 2:1, the two compounds can be
obtained easily. Unexpectedly, under similar reaction con-
ditions, compound 2 combine one water molecule of crys-
tallization. However, the appearance of water molecule
takes an important role in the structure of 2, which acts
a bridge via hydrogen bonds links these ions into a two-
dimensional network. If there are no water molecules, these
ions only build a one-dimensional chain, as shown in
Fig. 5.
Fig. 2. The crystal packing of 1. Hydrogen bonds are indicated by dashed
lines. For clarity, H atoms not involved in the hydrogen bonds have been
omitted.
3.2. Theoretical calculation
3.2.1. Stability
The total energy for two compounds is ꢁ2220.33 a.u. (1)
and ꢁ2411.37 a.u. (2), respectively. Whereas the energy of
HOMO is ꢁ0.35896 a.u. (1) and ꢁ0.16189 a.u. (2), and the
energy of LUMO is ꢁ0.02798 a.u. (1) and 0.02958 a.u. (2)
Fig. 1. The crystal structure of 1, with the atomic numbering of the asymmetric unit. Displacement ellipsoids are drawn at the 50% probability level.
Unlabelled atoms are related to labeled atoms by the symmetry code (3/2 ꢁ x, 3/2 ꢁ y, 1 ꢁ z).

Z.-L. Wang et al. / Journal of Molecular Structure 879 (2008) 150–155
153
Fig. 3. The crystal structure of 2, with the atomic numbering of the
asymmetric unit. Displacement ellipsoids are drawn at the 50% probability
level. Unlabeled atoms are related to labeled atoms by the symmetry code
(ꢁx, y, 1/2 ꢁ z).
Fig. 5. An infinite one-dimensional chain when water molecules have been
omitted in 2.
the frontier molecular orbits were expressed as the atomic
orbital coefficient square sum in the type of atomic orbits
and corrected by normalizing the specific molecule orbital
[22]. The stereographs of frontier molecular orbits of two
compounds are shown in Figs. 6 and 7, respectively.
Orbital contribution investigation indicate: for 1, the
composition of HOMO comes mainly from orbits of two
carboxyl oxygen O(1#) and O(2#) (70.74%), six carbon
Fig. 4. The packing diagram of 2. Hydrogen bonds are shown as dashed
lines. For clarity, H atoms not involved in the hydrogen bonding have
been omitted.
with the HOMO–LUMO gaps 0.38658 a.u. (1) and
0.19147 a.u. (2), respectively. These results mean two com-
pounds have better stability.
3.2.2. Frontier molecular orbital composition
In order to study their electronic structure, frontier
molecular orbital populations have been analyzed. The
atomic orbital composition for varies type of atoms in
Fig. 6. The frontier molecular orbits (HOMO and LUMO) in 1.

154
Z.-L. Wang et al. / Journal of Molecular Structure 879 (2008) 150–155
at the (x, y, z) position. The suggestions can be reflected
in Fig. 7. On the other hand, these results indicate that car-
boxyl group oxygen in 1 and water molecule in 2 are poten-
tially active sites and can react with metal centers or
hydrogen bonds donors [22,23].
3.2.3. Mulliken atomic charge distribution
The Mulliken atomic charge distribution of the labeled
atoms for two compounds are listed in Table 4. In 1, the
negative charges of 3,5-dinitrobenzoate anion are mainly
populated on two carboxyl oxygen O(1) and O(2), which
further suggests that these atoms are potentially active sites
and can react with metal centers or hydrogen bonds donors
[22,23], consistent with the above-mentioned conclusion. In
contrast, positive charges of (1,10-biphenyl)-4,40-diammo-
nium cation are not localized on the protonated nitrogen
(N3 and N3#) [symmetry code #: 3/2 ꢁ x, 3/2 ꢁ y, 1 ꢁ z]
atom but populated on six hydrogen atoms bound to them,
suggesting that the positive charges in the cation are delo-
calized between the nitrogen and hydrogen atoms. The
Mulliken atomic charge distribution of the atoms in 2 is
similarly to that of 1, the negative charges of 3,5-dini-
trobenzoate anion are populated on deprotonated O(1)
and O(2) [O(1#), O(2#)] (symmetry code #: ꢁx, y, 1/
2 ꢁ z). Positive charges of 4,40-methylene bis(benzenamine)
cation are mainly populated on six hydrogen atoms bound
to two protonated nitrogen atoms, too.
Fig. 7. The frontier molecular orbits (HOMO and LUMO) in 2.
atoms of benzene ring from 3,5-dinitrobenzoate anion
(24.62%) at the symmetry position (3/2 ꢁ x, 3/2 ꢁ y,
1 ꢁ z). In contrast, the components of LUMO come
mainly from 10 carbon atoms of (1,10-biphenyl)-4,40-diam-
monium cation (85.48%), six hydrogen atoms bound to two
protonated N(3) and N(3#) atoms (3.41%) (symmetry code
#: 3/2 ꢁ x, 3/2 ꢁ y, 1 ꢁ z). The suggestions can be repre-
sented in Fig. 6. For 2, the composition of HOMO comes
mainly from orbits of water oxygen O(7) (39.23%) and
O(7#) (14.32%) [symmetry code #: ꢁx, y, 1/2 ꢁ z]. The
components of LUMO come mainly from six carbon
atoms (57.86%) of benzene ring, four nitro group oxygen
(23.89%) and two N atoms of two nitro groups (16.43%)
4. Supplementary material
Crystallographic data for the structural analysis of have
been deposited with the Cambridge Crystallographic Data
Center, CCDC number 651810 for complex 1 and CCDC
number 651811 for complex 2. Copies of this information
may be obtained free of charge from the Director, CCDC,
12 Union Road, Cambridge CB2 1EZ, UK (fax: +44 1223
336033; e-mail: deposit@ccdc.cam.ac.uk or website: http://
www.ccdc.cam.ac.uk).
Table 4
Mulliken charges for 1 and 2
Atom
Charge
Atom
Charge
Atom
Charge
Atom
Charge
Atom
Charge
Atom
Charge
1
N(1)
O(4)
C(4)
C(10)
H(3B)
H(12)
0.487485
ꢁ0.451535
ꢁ0.070615
ꢁ0.156874
0.429996
N(2)
O(5)
C(5)
C(11)
H(3C)
H(13)
0.495149
ꢁ0.45515
0.119151
0.047567
0.435024
0.207433
N(3)
O(6)
C(6)
C(12)
H(4)
ꢁ0.758518
ꢁ0.450591
ꢁ0.05105
ꢁ0.135241
0.265148
O(1)
C(1)
C(7)
C(13)
H(6)
ꢁ0.704482
ꢁ0.172651
0.818078
O(2)
C(2)
C(8)
H(2)
H(9)
ꢁ0.79538
ꢁ0.086608
0.04774
0.228931
0.209942
O(3)
C(3)
C(9)
H(3A)
H(10)
ꢁ0.490975
0.129418
ꢁ0.170266
0.498334
0.201857
ꢁ0.165679
0.264485
0.229767
2
N(1)
O(4)
C(3)
C(9)
H(2)
H(7A)
H(14A)
0.490219
ꢁ0.45061
0.129777
ꢁ0.18049
0.255815
0.274001
0.217582
N(2)
O(5)
C(4)
C(10)
H(3A)
H(7B)
H(14B)
0.493068
ꢁ0.45651
ꢁ0.06273
ꢁ0.11901
0.458746
ꢁ0.452056
0.217599
N(3)
O(6)
C(5)
C(11)
H(3B)
H(9)
ꢁ0.74411
ꢁ0.45554
0.1194
0.027393
0.425987
0.201178
O(1)
O(7)
C(6)
C(12)
H(3C)
H(10)
ꢁ0.746
O(2)
C(1)
C(7)
C(13)
H(4)
H(12)
ꢁ0.72151
ꢁ0.21118
0.807865
ꢁ0.18727
0.274286
0.214806
O(3)
C(2)
C(8)
C(14)
H(6)
H(13)
ꢁ0.45407
ꢁ0.06712
0.019988
ꢁ0.32759
0.250226
0.201089
0.227747
ꢁ0.07404
ꢁ0.14167
0.425478
0.188447

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