Synthesis and characterization of two new macrobicyclic salts containing hexahydropyrimidine moieties: experimental and density functional theory studies

Article abstract of DOI:10.1007/s13738-017-1189-7

Two macrocyclic Schiff base ligands (L¹, L²) and their related reduced forms (L³ and L⁴) have been prepared. In the presence of nickel(II) perchlorate in methanol, the reinforced macrobicyclic salts containing h

Full text of DOI:10.1007/s13738-017-1189-7

J IRAN CHEM SOC
DOI 10.1007/s13738-017-1189-7
ORIGINAL PAPER
Synthesis and characterization of two new macrobicyclic
salts containing hexahydropyrimidine moieties: experimental
and density functional theory studies
Hassan Keypour1 · Simin Babeli1 · Hamid Zeynali1 · Mehdi Bayat1 · Majid Rezaeivala2
Received: 13 April 2017 / Accepted: 23 August 2017
© Iranian Chemical Society 2017
Abstract Two macrocyclic Schif base ligands (L1, L2) and
their related reduced forms (L3 and L4) have been prepared.
In the presence of nickel(II) perchlorate in methanol, the
reinforced macrobicyclic salts containing hexahydropyrimi-
dine cation moiety have been developed. Here, it seems that
Ni(II) perchlorate acts as oxidizing agent converting metha-
nol to the formaldehyde which in turn bridges two nitro-
gen atoms of reduced forms of macrocycle producing fnal
products. All Schif base ligands and their reduced forms
together with related salts were characterized by elemental
analysis, IR spectroscopy, 1H and 13C NMR, EI-Mass and
in the case of [L3′](ClO4) salt by X-ray crystallography. The
proposed mechanism for the formation of macrobicyclic
ligand [L3′] from the reaction of macrocyclic ligand L3 and
formaldehyde has also been studied via density functional
theory (DFT).
Introduction
Reinforced macrocycles are prepared by the inclusion of
bridging alkyl groups between nitrogen atoms in the mac-
rocyclic ring. Reinforced macrocycles showed much greater
rigidity than those non-reinforced analogues [1]. The addi-
tion of an extra bridging group between nitrogen donors on
macrocyclic ligands (to give a piperazine-like structure)
leads to much more rigid ligands displaying selectivity for
metal ions due to the match between the size of the metal
ion and that of the macrocyclic cavity in comparison with
conventional macrocyclic ligands [2].
Macrocyclic Schif base ligands have gained favour due
to both their relatively straightforward synthesis and their
multidentate nature which results in very high binding con-
stants for many d- and f-block metals [3]. Macrocyclic Schif
base ligands containing nitrogen donor groups have received
particular attention because of their mixed hard–soft donor
character, versatile coordination behaviour [4, 5] and biolog-
ical activities, i.e. toxicity against bacterial growth [6], anti-
cancerous [7] and other biochemical properties [8]. In some
works, the presence of metal ion could change the struc-
ture of ligand and open the rings due to reversible nature
of imines linkage [9], even in some cases not only open the
rings but also rearrange the structure of ligands because of
streak hindrance as a result of metal ion coordination [10].
In other work, the presence of various metal ion salts such
as Ni(II) perchlorate has been oxidized methanol to formal-
dehyde [11] which in turn bridges two nitrogen atoms and a
new ring has been formed in the structure of product [12].
We have also studied mono- and binuclear complexes of
transition metal ions containing nitrogen and oxygen donors
atoms in macrocyclic or macroacyclic ligands [13–16]. As
an extension of this idea, we report in this work synthe-
sis and characterization of four potentially tetradentate
Keywords Macrocyclic ligand · Hexahydropyrimidine
moieties · X-ray crystal structure · Macrobicyclic ligand ·
Density functional theory
Electronic supplementary material The online version of this
article (doi:10.1007/s13738-017-1189-7) contains supplementary
material, which is available to authorized users.
* Hassan Keypour
haskey1@yahoo.com
1
Faculty of Chemistry, Bu-Ali Sina University,
Hamedan 65174, Iran
2
Department of Chemical Engineering, Hamedan University
of Technology, Hamedan 65155, Iran
Vol.:(0123456789)
1 3

J IRAN CHEM SOC
macrocyclic Schif base ligands and their corresponding
reduced forms, L1, L2, L3 and L4 (Fig. 1). After addition of
the nickel(II) perchlorate to the reduced form of ligands (L3
or L4) solutions, surprisingly two reinforced macrobicyclic
ligands have been isolated (Scheme 1). We also reported the
crystal structure of [L3′](ClO4) (Fig. 2).
sodium hydroxide in (10 mL) water was added (0.125 g,
3.125 mmol). The resulting mixture was magnetically
stirred and heated for 30 min. Then, α,α′-dibromo-
m-xylene (0.411 g, 1.56 mmol) and sufficient ethanol
(20 mL) were added. Refuxing was continued for 48 h.
The solution was then allowed to cool and the product
formed as colourless crystals which were fltered of and
recrystallized from acetonitrile.
Experimental
Yield: 0.630 g (64.1%). Mp; 118 °C, IR (KBr, cm−1
)
1682 ν(C=O), 1H NMR (CDCl3, ppm) 5.24 (4H, 2-OCH2),
7.09–7.84 (12H, Ar–H), 10.56 (2H, CHO), 13C NMR
(CDCl3, ppm) 70.26, 113.114, 121.19, 126.09, 127.10,
130.87, 135.93, 141.39, 161.14 (Ar–C), 189.57 (2C,
C=O).
Chemical and starting materials
α,α′-Dibromo-m-xylene, 1,3-diaminopropane, 1,4-diamin-
obutane, ethanol, methanol, acetonitrile and metal salts were
obtained from the Merck Company and were used without
further purifcation.
General synthesis of the Schif base ligands (2)
Caution α,α′-Dibromo-m-xylene is a very caustic and it
should be treated and handled with caution.
1, 3-Diaminopropane or 1, 4-diaminobutane (0.3 mmol) in
dry methanol (10 mL) was added dropwise to a boiling solu-
tion of 1, 3-bis(2-formyl phenoxy methyl) benzene (0.104 g,
0.3 mmol) in methanol (15 mL). Refuxing continued for
24 h. We concentrated the solution to a volume 5 mL, which
led to the deposition of a powdery precipitate washed with
diethyl ether and dried in vacuum.
General synthesis of the 1, 3‑bis(2‑formyl phenoxy
methyl)benzene
To a refluxing solution of salicylaldehyde (0.381 g,
3.125 mmol) in absolute ethanol (20 mL), a solution of
O
O
N
O
O
O
O
N
N
O
O
N
1, 3- bis(2-formylphenoxy methyl)benzene
L1
L2
O
O
O
O
NH
NH
NH
HN
L3
L4
Fig. 1 The structure of aldehyde and synthesized ligands
1 3

J IRAN CHEM SOC
Scheme 1 Schematic pattern
for the formation of macrobicy-
clic ligand
-
ClO4
O
O
O
O
N
Ni(ClO4)2 .6H2O
CH3OH
+
NH
HN
NH
H
O
H
H
H
Ni(ClO4)2 .6H2O
H
C
OH
O
O
O
O
H
O
H
NH
NH
NH
N
-
ClO4
L2
Yield: 0.177 g (46%). IR (KBr, cm−1) 1640 ν(C=N), Anal.
Calc. for C24H22N2O2: C, 78.6; H, 6.8; N, 6.8. Found:
1
C, 78.1; H, 6.41; N, 6.13%, H NMR (CDCl3, ppm)
1.23–1.47(4H, CH2–CH(22,3)), 3.72–3.84(4H, CH2–CH(21,4)),
5.09–5.26 (4H, 2CH2O), 6.83–7.98 (12H, Ar–H), 8.65, 8.72
(2H, 2CH=N), 13C NMR (CDCl3, ppm) 26.86 (C2, C3),
52.07 (C1, C4), 69.42 (C5, C6) 116.87–136.56 (12C, Ar–C),
161.75 (C7, C8). EI-MS (m/z, %): 398 (Fig. 1).
General synthesis of reduced forms of the ligands
Fig. 2 View of [L3′](ClO4) in the asymmetric unit showing the num-
bering scheme. Thermal ellipsoids are drawn at 30% probability level,
while hydrogen size is arbitrary
NaBH4 (2.4 g) was added slowly to the stirred solution of
ligands (L1, L2), in dry methanol (10 mL). After the reac-
tion had ceased, the solution was cooled and then fltered.
On addition of ice to the fltrate, oily phase separated, which
was extracted with chloroform (three times). The chloroform
was removed by using a rotary evaporator. That eventually
crystallized to form a white solid.
L1
Yield: 0.118 g (32%). Anal. Calc. for C24H22N2O2.: C,
78.1; H, 6.29; N, 7.28. Found: C, 79.0; H, 6.38; N, 7.34%.
IR (KBr, cm−1) 1641 ν(C=N), 1H NMR (CDCl3, ppm)
3.51–3.63 (4H, CH2–CH(22,3)), 5.17–5.32 (4H, 2CH2O),
6.91–7.99(12H, Ar–H), 8.56, 8.58 (2H, 2CH=N), 13C
NMR (CDCl3, ppm) 29.17 (C1), 58.23 (C2, C3) 70.05 (C4,
C5) 117.04–158.99 (12C, Ar–C), 159.68 (C6, C7). EI-MS
(m/z, %): 384 (Fig. 1).
L3
Yield: 0.19 g (40%). Anal. Calc. for C25H28N2O2: C, 77.30;
H, 7.26; N, 7.21. Found: C, 77.96; H, 7.85; N, 7.67%. IR
1
(KBr, cm−1) 1600 ν(N–H), H NMR (CDCl3, ppm) 1.72
(2H, CH2(2)), 1.91 (2H, 2NH), 2.64 (4H, 2CH(21,3)), 3.80 (4H,
1 3

J IRAN CHEM SOC
2CH2(6,7)), 5.17 (4H, 2CH2(4,5)), 7.02–7.54 (12H, Ar–H), 13
C
Bruker software [17–19]. The structures were solved by
direct methods using SIR2004 [20]. The non-hydrogen
atoms were refned anisotropically by the full-matrix least
squares method on F2 using SHELXL [21]. The hydrogen
atoms of NH2 groups were found in diference Fourier map
and refned isotropically. The other hydrogen (H) atoms were
placed at the calculated positions and constrained to ride on
their parent atoms. Details concerning collection and analy-
sis are reported in Table 1.
NMR (CDCl3, ppm) 30.11 (C2), 47.91 (C1, C3) 50.10 (C6,
C7) 72.50 (C4, C5) 112.03–151.8 (12C, Ar–C). EI-MS (m/z,
%): 388 (Fig. 1).
L4
Yield: 0.19 g (42%). Anal. Calc. for C26H30N2O2.: C, 77.58;
H, 7.51; N, 6.96. Found: C, 78.15; H, 8.27; N, 7.55%. IR
1
(KBr, cm−1) 1600 ν(N–H), H NMR (CDCl3, ppm) 1.35
(4H, CH2(2,3)), 2.15 (2H, 2NH), 2.50 (4H, 2CH2(1,4)), 3.76
(4H, 2CH2(7,8)), 5.05 (4H, 2CH(25,6)), 6.93–7.58 (12H, Ar–H).
EI-MS (m/z, %): 402 (Fig. 1).
Theoretical studies
The calculations were done with the Gaussian 03 suite of
programs [22]. The reactants, intermediates, transition states
and product were optimized at BP86/Def2-SVP level of
theory. The frequencies were computed at BP86/Def2-SVP
General method of synthesis of ligand salts
Ni(ClO4)2 (0.25 mmol) was dissolved in dry methanol
(10 mL) and slowly added to a stirred boiling solution
(20 mL) of L3 or L4 (0.3 mmol) in the same solvent with
refuxing continuing for 6 h. The solution was reduced to
ca. 5 mL, and the precipitate was fltered and washed with
diethyl ether and dried in vacuum. Crystals suitable of [L3′]
(ClO4) for X-ray difraction studies were obtained by slow
difusion of Et2O vapour into the MeOH/MeCN solution of
the above solid.
Table 1 Crystal data and structure refnement for [L3′] (ClO4)
Empirical formula
C26H29ClN2O6
Formula weight
Temperature (K)
500.96
293
Wavelength (Å)
Crystal system
Space group unit cell dimensions
a (Å)
b (Å)
c (Å)
0.71073
Orthorhombic
Pna2(1)
16.8734 (6)
9.2665 (3)
30.5482 (15)
90
[L3′](ClO4)
Yield: 49%. Anal. Calc. for: C26 H29 Cl N2 O6: C, 62.33; H,
5.83; N, 5.59. Found: C, 62.40; H, 581; N, 5.78%. IR (KBr,
α (°)
−
cm−1): 1601 υ(N–H), 1100 υ(ClO4 ). EI-MS (m/z, %): 501.
β (°)
90
γ (°)
90
[L4′](ClO4)
V (Å3)
Z
4776.4 (3)
8
1.393
0.206
2112
Dcalc (mg/m3)
Yield: 42%. Anal. Calc. for: C27 H31 Cl N2 O6: C, 62.96; H,
6.06; N, 5.44. Found: C, 62.87; H, 6.22; N, 5.78%. IR (KBr,
Absorption coefcient (mm−1
F (000)
)
−
cm−1): 1602 υ(N–H), 1100 υ(ClO4 ). EI-MS (m/z, %): 515.
Index ranges
−20 ≤ h ≤ 20, −11 ≤ k ≤ 11,
−33 ≤ l ≤ 36
Physical measurements
Refections collected/unique [R(int)
29.16° (%) = Completeness to θ
Refnement method
]
0.206
99.60%
IR spectra were measured on a PerkinElmer FT-IRGX spec-
trophotometer. Mass spectra were recorded using VARIAN
3400 GC-Mass spectrometer. NMR spectra were measured
on Bruker DPX 400 spectrometers. Elemental analyses were
performed in a Carlo-Erba EA microanalyser.
Full-matrix least squares on F2
8227/73/602
0.83
Data/restraints/parameters
Goodness-of-fta on F2
Final Rb indices [I > 2 s (I)]
R1 = 0.0763
wR2 = 0.0905
R1 = 0.1270
wR2 = 0.2201
0.263/− 0.193
Rb indices (all data)
X‑ray crystal structure determination
e.A−3 (largest dif. peak and hole)
Single-crystal data for [L3′](ClO4) were collected at room
temperature with a Bruker APEX II CCD area detector dif-
fractometer using Mo Ka radiation (λ = 0.71073 Å). Data
collection, cell refnement, data reduction and absorption
correction were performed using multiscan methods with
GOF is defned as {∑[w(F20 − Fc2)]/(n − p)}1/2 where n is the num-
a
ber of data and p is the number of parameters
�
�
/
}
1∕2
(
)
(
)
∑
∑
∑
∑
2
bR =
∕
F0 , wR2
=
w F02 − Fc2
w F02
��
�
F0 − Fc
�
���
�
�
��
���
�
�
1 3

J IRAN CHEM SOC
level. All minima and transition structures were confrmed to
anion. Supramolecular involves weak C–H···π interactions
between the H atoms of the –CH2 group of one macrobicy-
clic and the aromatic ring of another macrobicyclic, which
is further reinforced by strong non-covalent H-bonding
interactions involving lattice perchlorate anion, to form an
overall 2D structure. The C–N(2)–C bond angle is smaller
than C–N(1)–C in the six-membered ring and C–O(1)–C in
another ring is smaller than C–O(2)–C. In the case of bond
lengths C(1)–N(2) have taller, and C(2)–O(2) have shorter
bond length in this compound (Tables 2 and 3).
have none and one imaginary frequency, respectively.
Results and discussion
The free Schif base macrocyclic ligands, L1 and L2, were
prepared from [1 + 1] cyclocondensation of 1, 3-diaminopro-
pane or 1, 4-diaminobutane and 1, 3-bis (2-formyl phenoxy
methyl)benzene. These ligands were precipitated as air-stable
solid compounds. Then, these macrocyclic ligands reduced
by sodium borohydride and diamine macrocyclic ligands
L3 or L4 were obtained. All ligands were characterized by
elemental analyses, EI-Mass, IR spectroscopy, 1H NMR and
13C NMR. In the presence of Ni(ClO4)2, in methanol solu-
tion, macrobicyclic ligand salts [L3′](ClO4) and [L4′](ClO4)
were isolated from their reduced forms. These compounds
were characterized by elemental analyses, EI-Mass and IR
spectroscopy in two cases and X-Ray crystallography in the
case of [L3′](ClO4). In this compound, nickel(II) perchlorate
acts vital role in converting methanol to formaldehyde and
formaldehyde can form a new cycle in macrocyclic ligand
and result in fnal compound instead of macrocyclic complex.
In previous work, in similar structures, we have reported the
closure of macrocyclic ring in the presence of Co(II) and
Zn(II) metal ions [9] and in another work, because of the
preferential structural requirement caused by exerting extra
force due to steric hindrance imposed by the electronic nature
of the copper(II) ion, polymeric open chain complexes were
obtained instead of macrocyclic ones [10] and in this work
we observed that Ni(II) perchlorate acts as oxidant, and the
new macrobicyclic ligand salt was characterized.
Computational studies
The proposed mechanism for the formation of macrobicyclic
ligand [L3ʹ] from the reaction of macrocyclic ligand L3 and
formaldehyde has been investigated using density functional
theory (DFT) (see Fig. 3). The geometries of all compounds
investigated here were optimized at the BP86/Def2-SVP
level as given in Fig. S1. The calculated structural data
for [L3ʹ] were compared with corresponding X-ray crystal
structure (see Table S1). The result shows that there is good
agreement between the calculated structural data with those
derived with X-ray crystal structure for [L3ʹ] (see Table S1).
The relative Gibbs free energy (See Table S2) profle for the
reaction pathway is shown in Fig. 3.
At frst, according to experimental data derived in this study,
oxidation of methanol to formaldehyde was observed. The
Table 2 A comparison between selected calculated bond lengths (Å)
and bond angles for macrobicyclic ligand salt, and the corresponding
experimental values
The IR spectra of the compound show a sharp band in
the range 1601 cm−1, attributed to (N–H) and a wide band
in the range 2600–2886 cm−1, attributed to ʋ(N–H+). This is
indicative of the linking nitrogen atoms per carbon, and six-
and seven-membered rings in the skeleton of macrocycle
were obtained and separated as ligand salt’s from metal ions.
Bond lengths (Å)
Experimental
1.430
BP86/def2-SVP
1.430
C(1)–N(2)
In six-membered aliphatic ring
C(1)–N(1)
1.520
1.520
In six-membered aliphatic ring
C(1)–N(2)
C(1)–N(1)
C(1)–O(2)
C(2)–O(2)
C(1)–O(1)
C(2)–O(1)
1.522
1.484
1.431
1.369
1.377
1.449
1.522
1.484
1.431
1.369
1.377
1.449
Crystal structures
X‑ray crystal structures of [L3ʹ](ClO4)
Suitable crystals of [L3ʹ](ClO4) were obtained from an
acetonitrile/methanol solution by slow difusion of diethyl
ether. The ORTEP view of the compound is shown in Fig. 2.
Crystallographic data, structure refnement parameters and
selected bond distances and angles are given in Table 1.
[L3ʹ](ClO4) crystallizes in the orthorhombic Pna2 space
group. The asymmetric unit consists of two L3ʹ unit and
Bond angle (°)
C–O(2)–C
C–O(1)–C
119.57
118.25
112.29
119.569
118.249
112.297
C–N(1)–C
In six-membered aliphatic ring
C–N(2)–C
109.50
109.496
In six-membered aliphatic ring
C–N(1)–C
C–N(2)–C
−
two crystallized perchlorates (ClO4 ) anions. Interestingly,
114.15
113.83
114.93
112.96
each macrobicyclic unit is stabilized by an intricate array of
H-bonding interactions with crystallized lattice perchlorate
1 3

J IRAN CHEM SOC
Table 3 Calculated frst vibrational frequency and zero point correction as well as thermal correction to Gibbs free energy and sum of elec-
tronic and thermal free energies (G) for the compounds investigated here at BP86/Def2-SVP
L3
TS-1
Int1
TS-2
Product
First vibrational frequency (cm−1
Zero point correction(ZPE) (Hartree)
Thermal correction to Gibbs free energy (Hartree)
)
25.26
0.470476
0.414818
−1141.22
0.496946
0.438854
21.70
0.501412
0.441817
−165.77
0.496336
0.440518
33.48
0.476294
0.422383
Sum of electronic and thermal free energies (G) (Hartree) −1228.136971 −1342.489687 −1342.541899 −1342.484583 −1266.204544
TS-2
Fig. 3 Energy profle cal-
TS-1
culated for the synthesis of
macrobicyclic ligand [L3′].
The relative Gibbs free energy
obtained at B3LYP/Def2-SVP
40.46
37.26
4.50
0
-7.77
+ H2O
CH2O+
Reactant
Int1
Product
calculations show that the reaction starts with a nucleophilic
attack of one of the amine groups of macrocyclic ligand L3
to formaldehyde via transition structure TS1 which led to the
formation of Int1.
forms (L3 and L4). The synthesis of all ligands was carried
out in dry methanol. The precipitated products which are
air-stable solids and moderately insoluble in most common
organic solvents were characterized by physical techniques.
After the addition of nickel(II) perchlorate to L3 and L4
ligands in methanol, surprisingly instead of forming corre-
sponding complexes the macrocyclic salts containing hexa-
hydropyrimidine moieties have been isolated. Here, Ni(II)
perchlorate acts as oxidizing agent converting methanol to the
formaldehyde which, in turn, bridges two nitrogen atoms of
reduced forms of macrocycle producing hexahydropyrimi-
dine cation. Similar work and also our computational study
have confrmed our conclusion. The density functional theory
(DFT) result confrms that the formation of [L3ʹ] from the reac-
tion of macrocyclic ligand L3 and formaldehyde is exothermic.
The barrier energies for the calculated Int1 and corre-
sponding TS1 are about 4.5 and 37.5 kcal mol−1 (see Fig. 3).
In continuation, the next nucleophilic attack in Int1
would give macrobicyclic ligand salt, [L3′](ClO4) (see
Fig. 3). The energy barrier for the calculated TS2 is about
40.50 kcal mol−1 (see Fig. 3), and these data are about
+3.0 kcal mol−1 greater than that derived for TS1. The
results show that the formation of macrobicyclic ligand salt
[L3ʹ] from the reaction of macrocyclic ligand L1 and for-
maldehyde is exothermic and corresponding product [L3ʹ] is
about −7.8 kcal mol−1 more stable than reactant.
Conclusion
Supplementary material
In summary, we report the successful synthesis of two mac-
CCDC 1450551 contains the supplementary crystallo-
graphic data for complex [L3ʹ](ClO4) that had been deposited
rocyclic Schif base ligands (L1, L2) and their related reduced
1 3

J IRAN CHEM SOC
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with the Cambridge Crystallographic Data Centre. These
data can be obtained free of charge via http://www.ccdc.cam.
ac.uk/conts/retrieving.html or from the Cambridge Crystal-
lographic Data Centre, 12 Union Road, Cambridge CB2
1EZ, UK; fax: (+44) 1223-336-033; or e-mail: deposit@
ccdc.cam.ac.uk.
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Acknowledgements We are grateful to the Faculty of Chemistry of
Bu-Ali Sina University, Ministry of Science, Research and Technology
of Iran for fnancial support.
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