The synthesis, characterization and computional investigation of?new metalloporphyrazine containing 15-membered S4donor macrocyclic moieties

Article abstract of DOI:10.1016/j.tet.2016.09.028

In this study, an improved synthesis of 1,5-bis(2-formylphenyl)-1,5-dithiapentane(3) has been performed according to the literature in a high yield. 1,5-Bis (2-benzyl alcohol)-1,5-dithia pentane (4) was prepared by the reduction reaction of precursor comp

Full text of DOI:10.1016/j.tet.2016.09.028

Accepted Manuscript
The synthesis, characterizationand computional investigation of
newmetalloporphyrazine containing 15-membered S donor macrocyclic moieties
4
Burak Yıldız, Yasemin Baygu, İzzet Kara, Hakan Dal, Yaşar Gök
PII:
S0040-4020(16)30935-8
10.1016/j.tet.2016.09.028
TET 28099
DOI:
Reference:
To appear in: Tetrahedron
Received Date: 1 July 2016
Revised Date: 30 August 2016
Accepted Date: 13 September 2016
Please cite this article as: Yıldız B, Baygu Y, Kara E, Dal H, Gök Y, The synthesis, characterizationand
computional investigation of newmetalloporphyrazine containing 15-membered S donor macrocyclic
4
moieties, Tetrahedron (2016), doi: 10.1016/j.tet.2016.09.028.
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GraphicalAbstract
The synthesis, characterization and computional investigation of new metalloporphyrazine containing 15-membered S4 donor
macrocyclic moieties
Burak Yıldız, Yasemin Baygu, İzzet Kara, Hakan Dal, Yaşar Gök
S
S
S
S
NaS
NaS
CN
CN
S
N
S
S
N
Mg
N
Mg, I2,
n-butanol
S
S
S
S
S
S
S
S
S
S
CN
CN
I
I
N
N
N
N
Ar, reflux
Ar, reflux
N
(5)
(7)
S
S
S
S
S
MgPz

ACCEPTED MANUSCRIPT
The synthesis, characterizationand computional investigation
of newmetalloporphyrazine containing 15-membered S4 donor
macrocyclic moieties
Burak Yıldıza, Yasemin Baygua, İzzet Karab, Hakan Dalc, Yaşar Göka*
aPamukkale University, Department of Chemistry, Kınıklı/Denizli-Turkey; Fax: + 90 258 2963535; E-
b
mail: gyasar@pau.edu.tr; Pamukkale University, Faculty of Education, Kınıklı/Denizli-Turkey;
cAnadolu University, Department of Chemistry, Eskişehir-Turkey
ABSTRACT:
In this study, an improved synthesis of 1,5-bis(2-formylphenyl)-1,5-dithiapentane(3)
has been performed according to the literature in a high yield. 1,5-Bis (2-benzyl
alcohol)-1,5-dithia pentane (4) was prepared by the reduction reaction of precursor
compound in high yield via solvent-free conditions. Treatment of substituted benzylic
alcohol with bromotrimethylsilane in dry acetonitrile in the presence of NaI resulted
the formation of desired iodine derivative (5) in very high yield. 7,8-dihydro-6H, 14H,
19H-dibenzo[bj][1,12,5,8]tetradithiacyclopentadecine-16,17-dicarbonitrile (7) was
synthesized by the reaction of compound 7 and dithiomaleonitrile disodium salt.
Magnesium porphyrazine carrying symmetrically four 15-membered tetrathia macro-
cycles has been synthesized by the cyclotetramerization reaction of dicarbodinitrile
compound (7) in the presence of magnesium butoxide according to the Linstead
procedure. We focused on the prediction of the geometry optimization, normal mode
frequencies, UV absorption spectra, chemical shifts and electronic properties of the
compound by using B3LYP method with 6-31G(d) basis set. These novel compounds
were characterized by a combination of elemental analysis, 1H, 13 C NMR, FT-IR, UV-
vis and MS spectral data. An X-ray crystal structure of dicarbodinitrile compound (7)
is also presented. The computed results are very close to the obtained experimental
results by spectroscopic techniques.
Keywords: Tetrathia macrocyle; Metalloporphyrazines; Macrocyclization; Green chemistry;
Template effect; Computional chemistry.
1. Introduction
One of the important cornerstones in tetrapyrrolic macrocyclic systems is the
porphyrazines.1 Porphyrazines are similar to phthalocyanines so they can also be used
in similar applications as phthalocyanines. In contrast, porphyrazines and their
1

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derivatives such as aminoporphyrazines, porphyrazinols and porphyrazine-thiolates
have been less studied since their first sythesis, which took place almost 60 years
ego.2-4 Porphyrazines have found applications in diverse areas such as industrial dyes
and pigments, electrocatalysts, electrochromic displays, PDT, chemical sensors,
Langmuir-Blodgett films, liquid crystals and non-linear optics, including their
application in material science.5-7 The first synthesis of crown-fused porphyrazines has
been accomplished by groups of Hoffman and Nolte.8-10 Porphyrazine derivatives,
which contain soft sulfur donor atoms, play an important role in affecting the solid-
state interactions and the sulfur atoms in the macrocyclic unit also give the opportunity
to bind soft transition metal cations.11-13 In addition to that, the electron-withdrawing
effect of the maleonitrile moiety may reduce the electron-donating ability of the sulfur
donors in macrocyclic unit and this kind of heteroatom strongly perturbs the
porphyrazine grand state transition shifting to the visible-to-near-IR region.14
For several decades, since their discovery and the pioneering study by Pedersen,15
innumerable studies on crown ethers and their anologues with different donor atoms
such as oxygen, nitrogen, sulfur have been carried out and their complexation ability
has been extensively studied.16 Thioether crowns are known to coordinate “soft” metal
cations such as low-valent transition metals and group IB and IIB in either an exo or
endocyclic mode.17 Thia-macrocyclic metal complexes are highly stable and have
received great attention to their biological activities including different applications
such as antitumor, antibacterial, antiviral and anticarcinogenic properties.18
Porphyrazine-linked thia macrocycles are interesting compound due to selective
extractant properties for soft metal cations and model capability for the active sites of
some enzymes.19
In recent years, Density Functional Theory (DFT) methods have widely been
used for the interpretation and prediction of complex systems behavior at an atomic
scale, the developments in the methodological, and software have transformed ab
initio and DFT approach in a completeyl interdisciplinary science from molecular
sciences to the diverse fields of chemistry.20 It is known that the DFT (B3LYP) method
adequately takes electron correlation contributions into account, which are especially
important in systems containing extensive electron conjugation and electron lone pairs.
Nowadays, it is commonly agreed that electronic structure calculations of excited
states of coordination compoundare very important complement to spectroscopic
techniques. Nevertheless, due to the size, the state degeneracies, the dynamical
correlation and relativistic effects, theoretical calculation of ground and excited state
properties of metal complexes which use computational methods confront some
difficulties. In addition to that, DFT methods are also extensively used in order to
simulate the electronic spectra of metal complexes despite the fact that the most
appropriate method to describe the ground state and excited state properties of these
kind of compounds seem to be the multiconfigurational self-consistent-field one
including relativistic effects. The most popular among them is the time-dependent
DFT (TD-DFT) approach.21
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In the present study, we synthesized and characterized a novel metalloporphyrazine
having four tetrathia crown ether moieties. X-Ray crystal structural analyses
concerning the dicyano compound has also been performed. In addition to detailed
synthesis procedures, we also theoretically investigated the geometry optimization of
precursor dicyano compound (7) and magnesium porphyrazine by means of B3LYP
method with 6-31G(d) basis set.
2. Results and Discussion
2.1. Synthesis
1,5-Bis(2-formylphenyl)-1,5-dithiapentane (3) can be prepared in high yield using a
step known synthetic routeas outlined in Scheme 1. There are many reports for the
synthesis of compound 3. One of them, the dicarboxylic acid derivative of the skeletal
framework was then reduced to the alcohol and oxidised over manganese dioxide to
form dialdehyde (3). This compound has been synthesized previously in low yields,
different ways and with different physical properties.22 Beloglazkina,22b Naeimi22c and
co-workers synthesized compound 3 under similar reaction conditions. However the
compound (3) we obtained is purer than those mentioned in the literature in terms of
spectral data. 2-Nitrobenzaldehyde, propane-1,3-dithiol and inorganic base should be
sufficient to achieve quantitative conversion of desired compound in 89% yield. The
present SNAr-reaction is high-yielding compared with similar reactions. According to
the above mentioned literature,22a,22b,22c the melting point of this compound was 56-57,
52-53 and 112-114 ºC, respectively. These data are very different from our result. The
structure of the compound produced by us was confirmed by spectroscopic data.
Compound 3 displayed the expected molecular ion peak at m/z = 317 [M+1]+. In the 1H
13
and C NMR spectra of this compound, the characteristic resonances of the aromatic-
aliphatic protons and carbons were similar to those of the literature mentioned above but
our spectra for compound 3 are the clearest of all.
The preparation of 1,5-bis(2-benzyl alcohol)-1,5-dithiapentane (4) was first carried
out by Lindoy,22a Castro23a,b and then Taylor et al.22e In these mentioned literature the
dicarboxylic acid derivative of thia ether bridge compounds were reduced to the alcohol
using a variety of reducing agents such as LiAlH4 and NaBH4. Using ecologically safe
reagents or media in organic reaction is an important paradigm in today’s chemistry.
Reduction reactions, carried out in green chemistry media, have received great attention
with advantages such as simple work-up procedure energy saving, avoidance of solvent
waste and toxicity.24 We reducted the precursor compound with an equivalent amount
of NaBH4 in the presence of wet SiO2 under solvent free conditions with 85%
1
13
conversion within 10 min. FT-IR, H and C NMR spectroscopic data concerning
structural characteristics were in accord with proposed structure and literature
mentioned above. The structure of this compound was also confirmed by its MS
spectrum, in which the peak at m/z = 320 corresponding to [M]+ was observed.
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O
S
S
S
S
SiO2, H2O
NaBH4
S
S
NaI, Me3SiBr
CH3CN
OH
OH
2
K2CO3
O
O
I
+
SH
SH
Ar, 60oC
89%
Ar, rt
92%
Ar
I
NO2
85%
(1)
(2)
(4)
(3)
(5)
S
S
S
S
S
S
N
S
S
S
NaS
CN
Mg, I2
n-Butanol
S
N
N
N
N
S
S
CN
CN
CH3CN
(5)
+
Mg
N
S
N
Ar, reflux
23%
Ar, reflux
19%
NaS
CN
S
S
(6)
N
S
S
S
(7)
S
S
MgPz
Scheme 1. The synthesis of MgPz
The conversion of alcohols into iodine derivatives is a very important
transformation process in organic chemistry. For this reason, convenient routes have been
reported in the literature.25 Examples have been reported utilizing
25c,e
KI/BF3.Et2O,25bPh3P/I2
or trimethylsilyl chloride.25a,f A comparison of the known
methods showed the bromotrimethylsilane/NaI to be more convenient due to
iodotrimethlysilane generated in situ. This reaction was found to proceed smoothly at
room temperature in 20 min. Benzylic OH groups could easily be substituted by iodide
groups in high yield (92%) using this procedure. Treatment of substituted benzylic
alcohol (4) with the three equivalent of bromotrimethylsilane in dry acetonitrile in the
presence of an equivalent amount of NaI resulted in the formation of desired iodide
1
derivative (5). The H NMR spectrum of 5 clearly showed the characteristic emerged
signals at δ = 4.61 ppm concerning iodide substitution. The other proton-NMR
resonances of 5 closely resembled those of the precursor compound (4). The proton-
13
decoupled C NMR spectrum of 5 also clearly indicated the presence of expected
signals. The disappearance of the characteristic signals concerning benzylic OH, along
with the appearance of the chemical shifts at δ = 4.66 ppm corresponding to CH2-I carbon
indicate the conversion reaction.26 A diagnostic feature of iodination formation from
compound 4 is the disappearance of the O-H resonances at 3308 cm-1 in the IR spectrum.
The mass spectrum of this compound shows the molecular ion peak as m/z : 541.956
[M+1]+ and the other bigger fragment ions are observed together with the corresponding
leaving groups (Fig.1).
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Figure 1.The mass spectrum of 5
The substituted tetrathia crown compound can be synthesized using a four step
synthetic route as outlined in Scheme 1. Treatment of the compound 5 with cis-1,2-
dicyano-1,2-ethylenedithiolate disodium salt (6) in dry acetonitrile resulted in the
formation of desired 15-membered macrocycle 7 in 19% yield (Scheme 1). A method for
the synthesis of thia crown ethers developed by Buter and Kellogg27 involves Cs2CO3
mediated cyclization of dithiole and a dihalide in DMF by high-dilution technique. Using
this method, tetrathia crowned macrocycles have been synthesized in low yield (10%).
This situation could be attributed an “inside-out” conformation in which the electron
densities of the sulfur atoms point out the ring.28 In addition to that, aromatic-aliphatic
chains crown thio ethers with rigid aromatic moieties adopt only a limited number of
possible ring conformations and the effective ring size is reduced.29 The macrocycle (7)
was then prepared by straightforward condensation reaction in dry acetonitrile media in
19% over all yield as shown in Scheme 1. The structure of macrocycle (7) was proven by
1
a combination of NMR, IR, elemental analysis, MS and X-ray spectral data. The H
NMR spectrum of this macrocycle is very similar to the precursor compound (5) except
for the formation of novel CH2-S chemical shifts at δ = 4.27 ppm as expected. Proton-
13
decoupled C NMR spectrum of 7 was in good agreement with proposed structure. The
characteristic signals concerning SCH2, CH2, Ar-CH2, C=C and C≡N groups at δ =34.58,
30.09, 38.31, 127.53 and 112.80 ppm, respectively, clearly suggested that
macrocyclization has occurred (Fig.2). In the IR spectrum of this compound, the
appearance of intense C≡N vibrations at 2208 cm-1 also supported the formation of
macrocycle. The ESI mass spectrum of this compound exhibited a molecular ion peakat
m/z = 426.57, which corresponds to [M]+, and also supports the structure.
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C4
C5
C3
C6
C9
C11
C2
C1
C8 C7
S
CN
C10
S
S
S
CN
Figure 2. The structure of 7
The cyclomerization of 15-membered tetrathia macrocycle substituted cis-1,2-di-
cyano-1,2-ethylene dithiolate based on a template effect of magnesium butoxide has been
used to generate the microcrystalline magnesium porphyrazine [MgPz] in 23%. An
attempt to obtain good-quality single crystals of MgPz was unsuccessful. In addition to
that, the low solubility of this compound does not permit to obtain good-quality NMR
1
spectra. The H NMR spectrum of this compound, the characteristic signals relating to
the CH2S, CH2, Ar-CH2S and aromatic group linked with tetrathia crowned macrocycle
units gave significant resonances of the proposed structure at δ = 3.21, 1.97, 5.40 and the
range of 7.40-6.76 ppm, respectively. The peak related to the C≡N group in the 13C NMR
spectrum of MgPz vanished in the case of metalloporphyrazine. In addition to that, the
appearance of C=N signals at δ = 140.05 ppm for MgPz concerning the inner core
instead of C≡N resonances in 7 supported the formation of desired compound. According
to the IR spectrum of MgPz, the stretching vibrations for the C≡N groups at 2208 cm-1
for precursor compound disappeared and a novel resonance appeared at 1626 cm-1 that is
attributed to the C=N groups in the porphyrazine core. The ESI mass spectrum of MgPz
was measured as m/z = 1728.16 [M]+ and is in good accord with the proposed structure.
The correlation analysis between the experimental and theoretical results computed in
this work has been done to observe experimental consistency with the chemical shifts
calculated by using B3LYP/6-31G(d) level. In order to check the performance of the
theoretical approach, correlation analysis has been done for full set of the chemical shifts
for compound 7 considered in gas phase and chloroform (Table 1). The correlation
par-ameters of Com.7 were calculated as R2 = 0.9935 in gas phase and R2 = 0.9937 in
solvent (Fig. 3). Theoretical 1H and 13C chemical shift values calculated with GIAO-DFT
6

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with respect to TMS of Com.7 are significantly in agreement with the experimental
values.
1
13
Table 1. Values of the H and C NMR chemical shifts of Com.7 as computed by
using B3LYP method with 6-31G(d) basis set and available experimental data
Atoms
C7
C3
C8
C10
C6
C5
C4
C11
C9
C2
Exp
134.39
127.53
136.99
123.19
128.83
132.69
130.29
112.80
38.31
34.58
30.09
7.07
7.34
7.21
7.15
4.27
2.97
1.95
Gas phase Chloroform
137.17
134.45
129.91
125.06
125.15
123.27
121.16
102.74
44.17
38.88
29.98
7.47
137.08
134.59
129.35
125.69
125.15
123.73
121.67
103.59
44.47
38.96
29.79
7.51
C1
H3
H6
H5
H4
H9
H2
H1
7.43
7.41
7.03
7.15
6.97
7.11
4.27
4.35
2.74
2.82
1.25
1.26
(a) Gas phase
(b) Chloroform
140
120
100
80
140
120
100
80
y = 0.9675x + 1.0746
R² = 0.9935
y = 0.9687x + 1.1384
R² = 0.9937
60
60
40
40
20
20
0
0
0
50
100
150
0
50
100
150
Experimental (ppm)
Experimental (ppm)
Figure 3. The correlation graphs between the experimental and calculated 1H and 13C
chemical shifts for Com.7 calculated by using B3LYP/6-31G(d) level, (a) in gas phase
(b) in solvent chloroform, respectively.
7

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2.2. Electronic properties
Figure 4 shows the absorption spectrum of symmetrically 15-membered S4-
macrocycles tetra substituted porphyrazinato magnesium complex. Metal porphyrazines
show an intense Soret (B) band at around λmax.<400 nm and a significant sharp bands that
have their principal absorptions at around λmax.>600 nm.30 The absorption spectrum of
MgPz taken in chloroform at room temperature exhibits a strong absorption at λ max.= 685
nm which is because of the π → π* transition and is referred to as a Q band which relates
to a strong low-energy absorbance. The other absorption is accompanied by a slightly
higher energy shoulder at λ = 625 nm. The sharp single band at λmax. = 685 nm is
characteristic of tetrapyrrolic systems such as porphyrazine, phthalocyanine and
derivatives with D4h symmetry.8,31 However, another intense absorption at around λ = 383
nm can be attributed to the so-called N-band, which is strengthened with respect to the
Soret band. The Q and Soret band absorptions should be related to π→π* transition from
a2u HOMO to the double degenerate eg LUMO orbitals.32 The very broad absorption at
around λmax.= 519 nm is assigned to an n→π* transition of the non bonding electrons of
the peripheral sulfur and nitrogen atoms, which are associated with porphyrazine core π
system. This strong coupling of the nonbonding electrons with the π-system also resulted
in considerable broadening because of vibrational fine structure.33
2
1.8
1.6
1.4
1.2
1
0.8
0.6
0.4
0.2
0
300
500 700
Wavelenght (nm)
900
Figure 4. The UV-vis spectrum of MgPz (1x10-5 M in chloroform)
8

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The highest occupied molecular orbital (HOMO) and the lowest unoccupied
molecular orbital (LUMO) energies are important parameters in molecular orbital theory.
The energy gap between the HOMO-LUMO orbitals characterizes the electron
conductivity and the spectroscopic properties of the molecules.
The electronic gap values are calculated as 3.8374 eV for Com.7 and 2.1560 eV for
MgPz at B3LYP/6-31G(d) level as seen in Table 2. The optic gap values are calculated
as 3.7547 eV for Com.7 and 1.8644 eV for MgPz. These energy gap values show that
charge transfer in the molecule exists. The high electron density is mostly localized on
the N atom as can be seen in Figure 5a,b. Typically, organic semiconductors with a band-
gap of about 3 eV are applied as photoactive materials, but the observed open-circuit
voltages are only in the range of 0.5–1 V.34 The inorganic semiconductor materials used
to make photovoltaic cells have energy band gaps within the range 1.1-1.7 eV ,that is
they are near to the optimum energy band gap (1.5 eV) for photovoltaic solar energy
conversion by a single junction solar cell.35 Accordingly, the molecule is a candidate for
inorganic semiconductor materials. In addition, the calculated self-consistent field (SCF)
energies of Com.7 and MgPz are calculated as -2513.178 a.u. and -10253.588 a.u.,
respectively.
Table 2. Electronic parameters of the compounds.
Electronic parameters
HOMO (eV)
LUMO (eV)
ꢀE=LUMO-HOMO (eV)
TD/LUMO-HOMO (eV)
I (eV)
Com. 7
-6.3876
-2.5503
3.8374
3.7547
6.3876
2.5503
4.4689
1.9187
0.5212
MgPz
-5.8589
-3.7029
2.1560
1.8644
5.8589
3.7029
4.7809
1.0780
0.9277
A (eV)
χ (eV)
Hardness (η)
Softness (S)
The electrostatic Surface Potential (ESP) that is associated with partial charge and
electronegativity plots exhibit the distribution of charge of compounds with respect to the
difference between positive and negative charge.36 The ESP map of the surface presented
in molecular size shows the shape and electrostatic potential value. Colours seen on the
ESP surfaces indicate different values of the electrostatic potentials. Red colour
represents the regions carrying the most electronegative potentials, i.e. electron rich
regions, blue colour represents regions of most positive potentials, i.e. electron poor
regions and green colour means zero potential. Mentioned potentials increase in the
following order: red<orange<yellow<green<blue. The deepest blue region defines
strongest attraction and the deepest red describes strongest repulsion. However, the
electrophilic reactivity has been presented by negative (red) regions but nucleophilic
reactivity has been shown by the positive (blue) regions. The ESP of Com.7 and MgPz
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changes from -0.04368 a.u. to 0.04368 a.u. for Com.7 and from -0.007525 a.u. to
0.007525 a.u. for MgPz, respectively, as seen in Figure 5a,b. The energy gap [(∆E =
LUMO-HOMO)calcd.] = 2.1560 eV] of MgPz is significantly smaller than Com.7 which
can be attributed the introduction of electron donating sulfur atoms at the α positions of
porphyrazine. Especially sulfur moieties at the α positions in porphyrazine can destabilize
the HOMO energy,37 so that the HOMO-LUMO value becomes smaller than Com.7.
As shown in Figure 6 for Com.7, LUMO electrons are mostly localized on double and
triple bonded groups such as C=C and C≡N. On the other hand, HOMO electrons are
mostly localized on the aromatic and thia ether groups. The LUMO electrons of MgPz
(Fig. 7) are mostly localized on C-N moieties. However, the HOMO electrons are mostly
localized on carbon and sulfur atoms which are linked pyrrole units.
Also the chemical hardness (η) and electron affinity (A) of the molecules can be
calculated from the HOMO-LUMO orbitals. The chemical hardness values of Com.7 and
the MgPz are 1.9187eV and 1.0780 eV, respectively. The electron affinity (A),
electronegativity (χ), chemical hardness (η) and softness (σ) of the molecules are given in
Table 2. Hardness (η) data of Com.7 and MgPz are calculated as 1.9187 and 1.0780,
re-
Figure 5a. The molecular electrostatic potential surface map calculated at B3LYP/6-
31G(d) level of Com.7.
spectively. The hardness character of MgPz decreases according to the precursor com-
pound and on the contrary, the softness character increases because of the decrease of
absolute electronegativity of porphyrazine core.38
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Figure 5b. The molecular electrostatic potential surface map calculated at B3LYP/6-
31G(d) level of MgPz.
HOMO
LUMO
Figure 6. The HOMO and LUMO energies for Com.7 with B3LYP/6-31G(d) basis set in
gas phase.
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HOMO
LUMO
Figure 7. The HOMO and LUMO energies for MgPz with B3LYP/6-31G(d) basis set
in gas phase
2.3. X-ray structure
The X-ray structural determination of the title compound confirms the assignments of
its structure from spectroscopic data (Table 3). The molecular structure along with the
atom numbering Scheme is depicted in Figs. 8a and 8b, where the asymmetric unit
contains two crystallographically independent molecules and the bond lengths and angles
are within normal ranges. The selected bond lengths, bond angles and torsion angles and
the hydrogen-bond geometry are given in Tables 4 and S1 (see Table S1 in the
Sopporting Information), respectively. The average C-S bond lengths and C-S-C bond
angles are 1.787(4) Å and 101.59(19)o (for molecule I) and 1.789(4) Å and 101.26(19)o
(for molecule II) (Table S1), respectively. The ligand cavities may play important roles in
the complexations and metal-ion selectivities. The intramolecular S1…C5 [6.454(3) Å],
S2…C21 [6.603(3) Å],C11…C21 [6.210(3) Å],C5…C15 [6.019(3) Å], C5…C21
[6.068(3) Å], C6…C21 [6.005(3) Å] (in molecule I) and S7...C42 [6.506(4) Å], S8…C26
[6.475(4) Å], S8…C27 [6.004(3) Å], C32…C42[6.064(3) Å], S7C41 [5.990(3) Å],
C26…C42 [5.967(3) Å],(in molecule II) distances may indicate the hole sizes of the
rings. The planar rings A(C6-C11), B(C15-C20),C(C27-C32) and D(C36-C41) are
oriented at dihedral angles of A/B=24.50(13)o, A/C = 11.77(12)o, A/D = 43.56(11)o, B/C
= 15.89(14)o, B/D = 21.40(12)o and C/D = 32.29 (12)o. In the crystal structure,
intermolecular C-H··S interactions (Table 4) link the molecules into infinite chains along
the a-axis (see Figure S22 in Supporting Information), while the molecules are stacked
12

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along the a-axis and elongated along the c-axis (see Figure S21 in Supporting
Information).39
Figure 8a. ORTEP-3 [3] drawing (for molecule I) of the title compound with the atom-
numbering Scheme. Displacement ellipsoids are drawn at the 50% probability level.
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Figure 8b.ORTEB-3 [3] drawing (for molecule II) of the title compound with the
atomnumbering Scheme. Displacement ellipsoids are drawn at the 50% probability
level.
Table 3. Crystallographic data for Com. 7.
C21H18N2S4
colorless/plate
426.61
Empirical formula
Colour/shape
Formula weight
120(2)
T (K)
Radiation used, graphite monochr.
Mo Kα (λ = 0.71073 Å)
monoclinic
P 21/n
Crystal system
Space group
a (Å)
10.9323 (2)
16.1929 (3)
23.1279 (5)
90
b (Å)
c (Å)
α
(o)
β(o)
97.186 (3)
90
γ(o)
V (Å3)
4062.07 (14)
8
Z
Absorption coefficient (mm-1)
0.477
calc (mg mm-3)
1.395
ρ
0.09 x 0.19 x 0.24
25.68
Crystal dimensions (mm)
θ
θ
(Max.) (o)
(Min.) (o)
2.95
7673
Reflections measured
-13 <h < 11
-19 <k < 19
-28 <l < 28
4899
Range of h, k, l
No of reflections with I>2
Corrections applied
Structure solution
Treatment of H atoms
No. of parameters var
Goodness-of-fit S
R = ||Fo| - |Fc|||/|Fo|
Rw
σ(I)
Lorentz-polarization
Direct methods
Geometric calculations
487
1.044
0.0564
0.1442
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0.0696
0.991
Rint
(∆/ρ)max (e Å-3)
Table 4. Hydrogen-bond geometry (Å, o) for Com.7.
D-H···A
D-H
H···A
2.67
2.84
D···A
D-H···A
148
C21-H21B···S8i 0.99
C42-H42A···S1ii 0.99
3.546(4)
3.572(4)
131
Symmetry codes: (i) ½ -x, ½ + y, ½ - z, (ii)3/2 -x, -½ + y, ½ - z.
Selected theoretical bond lengths, bond angles and torsion angles of the Com.7 and
MgPz compounds computed from B3LYP/6-31G(d) are given in Table S2 (see Table
S2 in the Supporting Information) with the experimental data as a supplementary
material. The computed bond lengths, bond angles and torsion angles, as shown in
Table S2, help us to understand the molecular structure of the Com.7 and MgPz
compounds. For example, the mean bond length of the N-C is measured as 1.141 Å
while it is computed as 1.165 Å for Com.7 and 1.336 Å for MgPz by using B3LYP/6-
31G(d) level. Also, the mean length value of the S-C is measured as 1.7877 Å while it is
computed as 1.824 Å for Com.7 and 1.821 Å for MgPz by using B3LYP/6-31G(d)
level.
The mean bond angle of the C–S–C is measured as 101.423° it is calculated as
104.133° for Com.7 and 104.739° for MgPz using B3LYP/6-31G(d) level. The mean
bond angle of the C–C–C is measured as 112.450° it is calculated as 110.159° for
Com.7 and 110.665° for MgPz. The mean bond angle of the N–C–C is measured as
177.725° it is calculated as 177.988° for Com.7. It is calculated as 124.345° for MgPz.
Additionally, the selected dihedral angles for the compounds are also given in Table S2.
As a result, the experimental value of bond lengths, bond angles and torsion angles
of the compounds were compared with theoretical method. The correlation (R2 = 0.9985
and R2 = 0.9903) between the experimental and theoretical bond lengths of the Com.7
and MgPz is good, as shown in Figure 9. There is compatibility between experimental
and theoretical results for the geometric parameters of the chemical compounds.
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1.9
1.9
1.8
1.7
1.6
1.5
1.4
1.3
1.2
1.1
Com.7
MgPz
y = 1.0201x + 0.0003
R² = 0.9985
1.8
1.7
1.6
1.5
1.4
1.3
y = 0.7563x + 0.4697
R² = 0.9903
1
1.2
1.4
1.6
1.8
1
1.2
1.4
1.6
1.8
Experimental (Å)
Experimental (Å)
(a) selected bond lengths (Å)
130
180
150
120
90
Com.7
MgPz
y = 0.94x + 8.4295
R² = 0.9915
y = 1.084x - 5.5999
R² = 0.9091
120
110
100
90
120
150
180
90
100
110
120
130
Experimental (o)
Experimental (o)
(b) selected bond angles (o)
MgPz
180
120
60
180
120
60
Com.7
0
0
-180 -120 -60
-60
0
60 120 180
-180 -120 -60
-60
0
60 120 180
y = 0.9562x + 1.5159
R² = 0.9445
-120
-180
-120
-180
y = 0.9644x + 1.3026
R² = 0.9462
Experimental (o)
Experimental (o)
(c) selected torsion angles (o)
Figure 9. The correlation graphs between the experimental and calculated geometric
parameters of the Com.7 and MgPz calculated by using B3LYP/6-31G(d).
16

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3. Conclusions
Here, a novel porphyrazinato magnesium (II) complex derived from 7,8-dihydro-
6H,14H, 19H-dibenzo[bj][1,12,5,8]tetradithiacyclopentadecine-16,17-dicarbonitrile has
been synthesized in a multi-step reaction sequence and characterization. The optimized
conditions for some reaction steps such as SNAr (3) reduction (4) and iodination (5)
reactions have been achieved. The 15-membered tetrathia macrocycle (7) was
synthesized and the X-ray structure of this compound showed that it crystallizes in the
monoclinic system with a P21/n space group. In addition, we also investigated the
geometry optimization of tetrathia macrocycle (7) and magnesium porphyrazine by
means of B3LYP method with 6-31G(d) basis set. Some X-ray data such as bond
lenghts, bond angles and structure concerning macrocyclic compound were compared
with theoretical results in Figure 9. Theoretical calculation of Com.7 and MgPz
compounds obtained by using B3LYP/6-31G(d) level are reported here for the first
time. It is seen that there is compatibility between experimental and theoretical results
for characterizing the compounds. The HOMO and LUMO orbitals of Com.7 and
MgPz have also been predicted. Macrocylic precursor compound (7) and metallo
porphyrazine (MgPz) containing symmetrically four macrocyclic units provide an
opportunity of these compounds for heavy metal extraction, especially soft metals, in
extractions from water media to organic phase. Some steps of the synthesis of
macrocycle could be completed on green chemistry area.
4. Experimental Section
4.1. General: All organic solvents used were analytical grade and dried over
standard drying agent and procedures prior to use.40Anhydrous butanol was stored over
magnesium butoxide and distilled before. Unless otherwise stated, all reactions were
carried out under argon atmosphere in a vacuum line or using standard Schlenk
techniques. TLC was performed on Merck aluminum sheets with silica gel 60 F254.
Merck silica gel 60 (0.063-0200 mm) was used for column chromatography. Melting
points were determined on an electrothermal melting point apparatus in a sealed
capillary and are uncorrected. Infrared and UV-vis spectra were recorded with on a
Perkin Elmer UATR Two spectrometer and on a Shimadzu UV-1601
1
13
spectrophotometer, respectively. H and C NMR spectra were recorded with a Varian
Mercury plus 300 MHz spectrometer. The reported chemical shifts are given relative to
Si(CH3)4 and were locked to the signal of the solvent. Mass spectra of compounds were
obtained a Thermo TSQ Quantum Access MAX. LC-MS/MS and in linear modes with
average of 50 shots on a Bruker Daltonicis Microflex mass spectrometer equipped with
a nitrogen UV-Laser operating at 337 nm. cis-1,2-Dicyano-1,2-ethylenedithiolate was
prepared according to the literature.41
4.2. X-ray crystallography
Suitable crystals of the title compound was crystallized from ethanol.
Crystallographic data were recorded on a Bruker Kappa APEXII CCD area-detector
diffractometer using
17

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Mo Kα radiation (λ=0.71073 Å) at T=120(2) K. Absorption correction by multiscan42
was applied. Structure was solved by direct methods and refined by full-matrix least
squares against F2 using all data.43 All non-H atoms were refined anisotropically.
Aromatic and methylene H atoms were positioned geometrically at distances of 0.95
(aromatic) and 0.99 (CH2) from the parent C atoms; a riding model was used during the
refinement process and the Uiso(H) values were constrained to be 1.2Ueq (for aromatic
and methylene carrier atoms).39 The crystallographic data are given in Table 3. CCDC-
1499665 for com.7 contain the supplementary crystallographic data for this
paper.
4.3. Theoretical calculations
DFT methods account for electron correlation by estimating the interaction of an
electron with the total electron density. DFT orbitals are formed from basis functions
like those used in SCF or MP2. The most popular DFT method is B3LYP (Becke3-
Parameter method for calculating that part of the molecular energy due to overlapping
orbitals plus the Lee–Yang–Parr method of accounting for correlation).44 The
theoretical calculations were performed to determine whether they are compatible with
the experimental and theoretical results.
The molecular structure of the compound was optimized to get the global minima
using B3LYP/6-31G(d) level. The same calculation procedure is also used to predict the
1H and 13C NMR chemical shielding constants in gas phase by applying the GIAO-
B3LYP. After that, the same basis set and computational method are used for the
vibrational spectra of the compound by using the optimized structure. Moreover, TD-
DFT/B3LYP/6-31G(d) computations of the compound were used to predict the
electronic absorption spectra in gas phase. All the calculations were performed in gas
phase by using Gaussian 09. Revision C1 program on TUBİTAK clusters.45 In addition,
GaussView 5.0.9 was used for the visualization of the structure.46
4.4. Synthesis
Synthesis of 1,5-Bis(2-formylphenyl)-1,5-dithiapentane (3)
Propane-1,3-dithiol (2.16 g, 20 mmol) was added to a solution of 2-nitro benzaldehyde
(6.16 g, 40 mmol) inside a round-bottom flask in dry DMF (50 mL) under argon
atmosphere at room temperature. Finally powdered anhydro potassium carbonate (6 g,
43.47 mmol) was added portion-wise and the reaction mixture was stirred at 60 ºC for
27 h. The reaction was monitored by a thin layer chromatography [silica gel
(chloroform)]. The mixture was filtered off while hot and then cooled to room
temperature. The cooled solution was poured into crashed ice (150 g) and resulting
mixture was filtered, washed with cooled water and the dried in vacuo. The pale yellow
solid product was recrystallized from ethanol that afforded desired compound
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inexcellent yield. Yield: 5.65 g (89%), mp. 83-85 ºC (lit.data1: mp.56-57 ºC, lit data2:
1
mp.51-53 ºC, lit. data3: mp.112-114 ºC). H NMR (300 M Hz,CDCl3): δ 10.36 (s, 2H,
HC=O), 7.84 (d, J = 7.83 Hz, 2H, ArH), 7.49 (t, J = 7.63 Hz, ArH, 2H), 7.41 (d, J =
7.83 Hz, 2H, ArH), 7.31 (t, J = 7.43 Hz, 2H, ArH), 3.12 (t, J = 7.04 Hz, 4H, CH2S),
2.12-2.06 (m, 2H, CH2). 13C NMR (75.MHz, CDCl3): δ 191.39, 140.96, 134.12, 133.98,
132.34, 128.23, 125.61, 31.98,27.28. FT-IR (cm-1): 3064 (Ar-H), 2963-2841 (C-H),
1674 (HC=O), 1583, 1558, 1456, 1195, 742. MS (ESI) m/z = 317 [M+1]+. Anal. calc.
for C17H16O2S2: C, 64.55, H, 5.06. Found: C, 64.38; H, 5.20.
Synthesis of 1,5-Bis(2-benzyl alcohol)-1,5-dithiapentane (4)
In a round-bottom flask (25 mL) charged with SiO2 (0.836 g, 13.92 mmol) and water
(0.42 mL) was added and stirred to obtain homogenize mixture. Precursor compound
(3) (1.32 g, 4.18 mmol) was added to wet SiO2 and this reaction mixture was stirred
for 10 min. NaBH4 (0.159 g, 4.18 mmol) as a fine powder was then aded. The reaction
mixture was turned waxy within 1-2 min. and then dichloro methane (60 mL) was
added and stirred at room temperature for overnight. The mixture was filtered, washed
with dichloromethane and dried over MgSO4 and then the solvent was removed to give
a pale yellow oily product, which was used without further purification. Yield: 1.14 g
(85%) (lit. data4: 70%, lit. data5: 85%).1H NMR (300 MHz,CDCl3): δ 7.36 (d, J = 6.65
Hz, 4H, Ar-H), 7.32-7.30 (m, 4H, Ar-H), 4.71 (s, 4H, CH2OH), 2.99 (t, J = 7.04 Hz,
4H, SCH2), 2.87 (br, 2H, OH), 1.94-1.87 (m, 2H, CH2). 13C NMR (75 MHz, CDCl3): δ
140.93, 134.00, 130.05, 128.25, 128.17, 126.74, 63.35, 32.86, 28.32. FT-IR (cm-1):
3308 (O-H), 3057-3014 (Ar-H), 2917-2870 (C-H), 1599, 1439, 1192, 1032, 745. MS
(ESI) m/z : 320 [M]+. Anal. calc. for C17H20O2S2: C, 63.75; H, 6.25. Found: C, 63.59;
H, 6.10.
Synthesis of 1,5-Bis(2-iodomethyl)phenyl-1,5-dithiapentane (5)
A round bottom flask which contained compound 4 (1.26 g, 3.94 mmol) and NaI (3.53
g, 23.52 mmol) in dry acetonitrile (50 mL) and which was fitted with a condenser was
evacuated, refilled three times with argon and connected to the vacuum line. To a
solution of the corresponding alcohol, bromotrimethylsilane (3.57g, 23.36 mmol) was
added with continuous stirring. The reaction mixture was stirred at room temperature
for 20 min. and monitored by thin layer chromatography [silica gel(chloroform)]. A
mixture of dichloromethane and water [100 mL (1:1)] was added to the reaction
mixture and the organic phase was further treated with water, saturated Na2S2O3 (20
mL) and water and then dried over MgSO4. The organic phase was evaporated to
dryness under reduced pressure, yielding pale yellow crystal solid. Yield: 1.95 g
1
(92%), mp.73-74 ºC. H NMR (300 MHz, CDCl3): δ 7.35 (d, J = 1.57 Hz, 2H, Ar-H),
7.29 (d, J = 1.17 Hz, 2H, Ar-H), 7.22 (d, J = 1.57 Hz, 2H, Ar-H), 7.13 (d, J = 1.56 Hz,
2H, Ar-H), 4.61 (s, 4H, CH2-I), 3.16 (t, J = 7.04 Hz, 4H, CH2S), 2.08-2.01 (m, 2H,
13
CH2). C NMR (75 MHz, CDCl3): δ 138.78, 135.49, 130.16, 129.82, 128.73, 126.60,
32.32, 28.24, 4.66. FT-IR (cm-1): 3053, 3036, 2952-2941, 1594, 1467, 1150, 1034,
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752. MS (ESI) m/z : 541.956 [M+1]+, 413 [M-I]+, 284.9 [M-2I-2]+, 163.2 [M-
C7H6SI2]+, 137 [M-C8H8SI2]+. Anal. calc. for C17H18S2I2: C, 37.79; H, 3.33. Found: C,
37.97; H, 3.17.
Synthesisof 7,8-dihydro-6H,14H,19H-dibenzo[bj][1,12,5,8]tetradithiacyclopenta-
decine-16,17-dicarbonitrile (7)
A mixture of 1,5-bis(2-iodomethyl)phenyl-1,5-di-thiapentane (2.7 g, 5 mmol) and 1,2-
dicyano-1,2-ethylenedithiolate disodium salt (0.93 g, 5 mmol) in dry acetonitrile (170
mL) in around-bottom two necked flask was heated and stirred at reflux temperature
under argon atmosphere for 24 h. The reaction was monitored by thin layer
chromatography [silica gel (chloroform:hexane) (1:1)] and then allowed to cool to
room temperature. The solvent was evaporated to dryness under reduced pressure and
the residue was solidified by stirring water (80 ml) at room temperature overnight. The
brown solid was filtered and the solids washed with water and then dried in vacuo. The
solid was chromatographed on silica gel [(chloroform:hexane)(1:1)] and recrystallized
1
from ethanol to give 7 as a yellow crystals. Yield: 0.4 g (19%), mp.156-158 ºC. H-
NMR (300 MHz, CDCl3): δ 7.34 (d, J = 7.83 Hz, 2H, Ar-H6), 7.21 (d, J = 7.43 Hz,
2H, Ar-H5), 7.15 (t, J = 6.85 Hz, 2H, Ar-H4), 7.08 (t, J = 6.85 Hz, 2H, Ar-H3), 4.27 (s,
4H, Ar-CH2S, H9), 2.97 (t, J = 7.85 Hz, 4H, CH2S, H2), 1.96-1.92 (m, 2H, CH2, H1).
13C- NMR (75 MHz, CDCl3): δ 136.99 (C8), 134.39 (C7), 132.69 (C5), 130.29 (C4),
128.83 (C6), 127.53 (C3), 123.19 (C10), 112.80 (C11), 38.31 (C9), 34.58 (C2), 30.09
(C1). FT-IR (cm-1): 3064, 3012, 2967-2920, 2208, 1588, 1469, 1421, 1260, 1167, 734,
663. MS (ESI) m/z: 426.57 [M]+. Anal. calc. for C21H18N2S4. C, 59.15; H, 4.22; N,
6.57. Found: C, 59.06; H, 4.30; N, 6.47.
Synthesis of Magnesium porphyrazine (MgPz)
Mg powder (0.0148 g,0.616 mmol) and I2 (one small crystal) and 1-butanol was (5
mL) charged in a Schlenk system connected with vacuum line under argon
atmosphere. The reaction mixture was refluxed and stirred for 12 h till all metal was
dissolved. The suspension was cooled to room temperature and dicyano compound (6)
(0.426 g, 1 mmol) in dry butanol (2 mL) was added and then the mixture was further
heated at reflux temperature for 28 h. The reaction was monitored by thin layer
chromatography [silica gel (chloroform:hexane) (1:1)]. The deep dark blue suspension
was cooled to room temperature, filtered and washed with methanol. The solution was
concentrated in vacuo and the residue was purified by column chromatography over
silica gel [(chloroform: hexane) (1:1)] to obtain dark blue crystals. Yield: 0.10 g
1
(23%), mp>300 ºC. H-NMR (300 MHz, CDCl3+DMSO-d6): δ 7.42-7.40 (m, 8H, Ar-
H), 7.12-7.10 (m, 8H, Ar-H), 7.04-7.01 (m, 8H, Ar-H), 6.78-6.75 (m, 8H, Ar-H), 5.40
(s, 16H, Ar-CH2S), 3.22-3.18 (m, 16H, CH2S), 1.98-1.95 (m, 8H, CH2). 13C- NMR (75
MHz, CDCl3): δ 140.05, 134.73, 134.34, 130.32, 128.07, 127.68, 115.75, 38.82, 35.02,
28.53. FT-IR (cm-1): 3053, 3003, 2963-2911, 1626, 1586, 1467, 1439, 1418, 1291,
1209, 1034, 757. MS (ESI) m/z: 1728.16 [M]+. Anal. calc. for C84H72N8S16Mg. C,
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58.33; H, 4.16; N, 6.48. Found: C, 58.44; H, 4.07; N, 6.59. UV-vis (CHCl3): λmax (log
ε): 685 (5.25), 625 (4.76), 519 (4.39), 383 (5.12).
Supporting Information
Selected crystallographic data, experimental bond lengths (Å), bond angles (o) and
torsion angles (o) for Com.7. Calculated structural data for Com.7 and selected bond
lengths (Å), bond angles (o) and torsion angles (o) for Com.7 and MgPz. A partial
packing diagram of Com.7. Hydrogen bonds are shown as dashed lines. A partial
packing diagram viewed down the a-axis. Copies of the 1H, 13C NMR, IR, MS spectral
data of all compounds and UV-vis data of MgPz.
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Acknowledgements
The numerical calculations reported in this paper were partially performed at
TUBITAK ULAKBIM, High Performance and Grid Computing Center (TRUBA
resources). One of the author (B.Y) is also indepted to TUBİTAK for financial support
as scholoarship. We are also grateful to Gebze Technical University X-Ray Center for
the X-Ray data they provided.
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Highlights
•The convenient synthesis of substituted benzyl alcohol from substituted aldehyde
form in green chemistry conditions.
•Synthesis of iodinated derivative of subtituted benzyl alcohol with excellent yield,
short reaction time, simple work up and fairly mild conditions.
•X-ray characterization of 15-membered S4 macrocycle.
•The compatibility between experimental and theoretical results of S4-macrocycle and
MgPz.