Design, synthesis and spectroscopic characterization of mixed N- and O-donor Schiff base ligands (N2O3): Crystal structures of free ligands

Article abstract of DOI:10.1016/j.molstruc.2020.128106

Five Schiff base ligands containing the same bridging spacer group but differing in the substituents on the phenyl ring were synthesised and fully characterized by various spectroscopic and analytical techniques. Three of these ligands are new and all hav

Full text of DOI:10.1016/j.molstruc.2020.128106

Journal Pre-proof
Design, synthesis and spectroscopic characterization of mixed N- and O-donor Schiff
base ligands (N2O3): Crystal structures of free ligands
Hezron F.O. Ogutu, Waheed Saban, Rehana Malgas-Enus, Robert C. Luckay
PII:
S0022-2860(20)30431-2
DOI:
https://doi.org/10.1016/j.molstruc.2020.128106
MOLSTR 128106
Reference:
To appear in: Journal of Molecular Structure
Received Date: 17 January 2020
Revised Date: 9 March 2020
Accepted Date: 19 March 2020
Please cite this article as: H.F.O. Ogutu, W. Saban, R. Malgas-Enus, R.C. Luckay, Design, synthesis
and spectroscopic characterization of mixed N- and O-donor Schiff base ligands (N2O3): Crystal
structures of free ligands, Journal of Molecular Structure (2020), doi: https://doi.org/10.1016/
j.molstruc.2020.128106.
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Author Credits Statement
Hezron F. O Ogutu – student who carried out most of the work
Waheed Saban – student who carried out the rest of the work
Rehana Malgas-Enus – supervisor, person who oversaw all the synthetic work and wrote part of the
publication
Robert C. Luckay – supervisor and person who wrote most of the paper. Came up with the ideas and
senior person involved with the work.

Graphical abstract

Design, synthesis and spectroscopic characterization of
mixed N- and O-donor Schiff base ligands (N2O3): Crystal
structures of free ligands
Hezron F. O. Ogutu, Waheed Saban, Rehana Malgas-Enus and Robert C. Luckay*
Department of Chemistry & Polymer Science, Stellenbosch University, Private Bag X1,
Matieland, Stellenbosch, 7602, South Africa. Tel: +27 21 8083333, email:rcluckay@sun.ac.za.
Abstract
Five Schiff base ligands containing the same bridging spacer group but differing in the
substituents on the phenyl ring were synthesized and fully characterized by various
spectroscopic and analytical techniques. Three of these ligands are new and all have been
1
synthesized by an improved, optimised method. The H NMR spectra of these ligands were
shown to differ from that of their N-donor counterparts (ON3O-type ligands) as confirmed by
the systematic use of two-dimensional and variable temperature NMR measurements. The
effect of the added substituents were monitored via IR analysis of the ligands and showed
that the methoxy substituted ligand, L2 resulted in the highest wavenumber shift of the imine
signal whilst the naphthylaldehyde ligand, L3 was observed to cause the lowest wavenumber
shift. The crystal structures of four of these ligands showed differing low energy
conformations and in addition to all other analytical data confirms the structural analysis of
these ligands. All ligands show intramolecular hydrogen bonding while two of the ligands
show intermolecular hydrogen bonding as seen in their packing diagrams. Interestingly, the
ligand with the naphthylaldehyde group, L3, underwent tautomerism and the quinoid form of
the ligand is reported here.
INTRODUCTION
Schiff base ligands are a prominent class of ligands due to their various attractive properties
such as good flexibility and the ability to be modified by adding various donor groups.[1]
These ligands have several uses such as in making of dyes, in hydrometallurgy and in
photochromic studies.[2,3] These ligands are often synthesised via the Schiff base
condensation method that leads to the formation of the imine bond,[4] and have been
1

shown to coordinate to a wide range of metal ions, forming stable Schiff base
complexes.[1,5,6] There are many uses of these complexes, for example, they have excellent
biological properties and have thus been used in anti-cancer and anti-microbial studies, as
well as in various catalytic and gas storage studies.[7,8] We have previously published work
on the optimised synthesis of symmetrical N-donor ligands (ON3O donor groups), with one
ligand displaying both keto and enol tautomeric forms within the same compound.[2,9] In
this current work, five symmetrical O-donor Schiff base ligands (O-N-O-N-O donor groups)
have been synthesised and fully characterised. Three of these ligands, namely L2, L4 and L5
are new and two others L1 and L3 [10,11,12] shown in Figure 1 have been optimised from a
previously reported method. [10,11,12] The synthesised ligands have been studied for
electronic and inductive effects due to the different substituents. Further spectroscopic
studies have also been done to compare the effect of the central ethereal O-donor group to
the amine N-donor group. From the literature, the addition of different donor groups such as
oxygen, has been shown to initiate interesting electronic and inductive effects.[2]
Furthermore, crystal structures confirm the successful synthesis of the ligands and since the
spacer is constant with varying substituents on the phenyl rings, structures are also examined
end-on to see the influence of these effects. The synthesised ligands are shown in Figure 1.
Figure 1 Ligands synthesised and which are discussed in this work.
2

1.0 Synthesis and characterization
1.1 Optimization of the synthesis of ligands L1 and L3.
The ligands, L1 and L3, had previously been synthesised by the Schiff base condensation
method as reported by Wu et. al[10,11] and Yu et al[12] respectively. The yields obtained
were 68.5% for L1 and 85% for L3. These ligands were therefore synthesised through
modifications as previously discussed.[2,3] The ligand, L1 containing unsubstituted
salicylaldehyde, was synthesised by weighing 1.22 g (0.0100 moles) of the unsubstituted
salicylaldehyde and dissolving it in 40 ml methanol under reflux. 30.0 ml (0.0405 moles) of
the 2, 2-oxydiethylamine prepared as shown in the supplementary material, section S1, was
measured and immediately added dropwise to the refluxing solution. The preparation of the
3-oxapentane-1,5-diamine differed from the method by Wu et. al[10,11] and Yu et al.[12]
The prepared 3-oxapentane-1,5-diamine was added slowly to the reaction solution over 30
minutes and allowed to reflux for 24 hours. The resultant yellow solution was cooled, and the
solvent removed via rotary evaporation. A yellow crystalline powder was obtained, re-
dissolved in chloroform and washed 3 times with 10 ml water portions to remove excess
amine. The chloroform layer was dried with anhydrous sodium sulfate. The final yellow
powder was recrystallized using ethanol, to give a yellow crystalline solid which was fully
characterized as discussed. The yield obtained for the product was 72% and the remaining 4
ligands were also synthesised using the same synthetic procedure. The yields obtained for L2,
L3, L4 and L5 were 84%, 87%, 72% and 93% respectively. These results were comparable to
the yields obtained by Wu et. al[10,11] and Yu et. al[12] and the resultant products and
characterization are discussed in the supplementary, section S2.
2. Results and Discussion
2.1 IR analysis results and discussions
The electronic effect of the added donor groups and the different substituents was therefore
studied via the IR spectroscopy (ATR). For ligand L1, the observed signal at 1633 cm-1 was
assigned to the imine (C=N) functionality produced upon Schiff base condensation of the
3

aldehyde and the amine. The concomitant absence of the carbonyl peak usually observed at
1660 cm-1 for salicylaldehyde, confirmed the formation of the desired Schiff base product as
shown in Figure 2 for all five ligands. The IR band at 2855 cm-1 was assigned to the C-H
stretching bands while the peaks at 1283 cm-1 was attributed to the CAr-O stretching band.
This result compares favourably to those of our previously published N-containing ligands[2]
and the work by Wu et. al.[10,11] The wavenumber shift trend which depends on the
substituents on the phenyl ring is the same for both N2O3- and ON3O-donor type ligands.
The formation of the imine band for ligands L2, L3, L4 and L5 were observed at 1639 cm-1,
1614 cm-1, 1633 cm-1 and 1634 cm-1 respectively. The difference in the shift of the imine peak
in the series can be attributed to the difference in inductive effects of the different phenyl
substituents.[13] The IR spectra showed a higher wavenumber shift of the imine (1639 cm-1)
due to the electron-withdrawing methoxy group substituent, indicating that the introduction
of this group into the phenyl ring causes noticeable changes in the electronic properties. For
the corresponding electron donating substituents, the bulky tert-butyl group and the straight
chain nonyl group both showed relatively small shifts of the imine functionality. The presence
of the naphthylaldehyde group was shown to cause a shift to lower wavenumbers[14] (1614
cm-1) for the imine functionality as shown in Figure 2.
4

L5
L4
L3
L2
L1
3500
3000
2500
2000
1500
1000
Wavenumbers (cm-1)
Figure 2 The ATR spectra of the Schiff base products L1, L2, L3, L4 and L5.
2.2 NMR analysis and evidence of deconvolution
1
The synthesised Schiff base ligands were also analysed using H and 13C NMR spectroscopy
and the results obtained show the formation of the desired products. (see experimental
1
section and supplementary information, section S2). The H NMR spectrum of ligand L1 is
shown in Figure 3 as a representative Schiff base product. The imine signal was observed by a
strong peak at 8.30 ppm, integrating to two protons. The phenolic protons were observed by
a relatively weak signal at 13.41 ppm. The region between 6.82 ppm - 7.29 ppm shows 4
signals, which were assigned to the aromatic protons on the phenyl group. The proton signal
for C4/C20 is more shielded. The protons at C3/C19 are more deshielded. The protons at
C5/C17 and C6 /C18 are intermediate triplets as shown in the insert spectrum of Figure 3.
This together with the absence of the carbonyl signal usually observed between 9-11 ppm,
confirms the formation of the desired product. When comparing the imine signal of the five
ligands, it can clearly be seen that the signal for three of the ligands averages 8.35 ppm. For
the methoxy substituent, the imine signal is 8.26 ppm, whereas the imine signal for the
5

naphthyl ligand is further downfield at 8.77 ppm, since these protons are more deshielded.
This mirrors the trend observed from the IR analyses.
Figure 3 The 1H NMR spectrum of ligand L1 in CDCl3 with the different protons numbered by the position of the
appearance of the carbon group it is attached to. (The insert shows the higher magnification of the aromatic
region and the alkyl region).
2.2.1 Study of the spacer (-CH2-CH2-) proton signals using 1H NMR
The protons from the diimine spacer group were observed showing a single sharp signal
(overlapping triplets) at 3.75 ppm that integrates to 8 protons (4 x 2). This was unusual since
two distinct signals were expected due to the two chemical environments that these protons
exist in. When these results are compared to the results of the analogous pentadentate N-
donor[2] (Figure 5, top), the -CH2CH2- spacer group in the backbone gave two distinct triplets
at 3.70 and 2.99 ppm with the α (group closer to the N-donor atom Figure 4) being more
shielded than the one connected to the C=N. In the present case only, the sharp single
overlapping signal at 3.75 ppm was observed for these spacer protons. The same peak signals
were observed for ligands L2, L3, L4 and L5 as shown in Figure 6. The literature results by Wu
et. al[10,11] did not show this but rather indicated an observed set of peaks from
6

approximately 3.66 ppm to 3.74 ppm integrating to 8 protons for L1. Yu et. al[12] did not
indicate the characterization of the 1H NMR spectra for these alkyl groups for the L3 ligand.
Figure 4 Representative ligands showing the explicit hydrogen of the spacer group where R = salicylaldehyde
group, X=N or O for ligand with amine at centre and L1 respectively. α and β represent expected equivalent
protons.
Figure 5 Stacked 1H NMR spectra of amine ligand (top) and L1 in CDCl3 (the two spectra are stacked at 15° angle
to show the differences in the effect of the change of donor group X on the proton signal peaks).
The analysis of our present ligands for possible molecular dynamism due to flexibility or
symmetry of the ligand solution on a higher frequency 600MHz 1H NMR and through variable
temperature 1H NMR from -25 °C to 25 °C did not show distinction of these signals as shown
7

in Figure 6. However, there was an observed small shift of the OH peak and the increase in its
intensity with reducing temperature at 13-14 ppm for ligand L1 as shown by Figure 7. The
shift and strength of the OH proton signal can be attributed to the ability of this hydrogen to
undergo tautomerism from the –C-OH to the –C=O form as had been previously discussed.[2]
Further analysis of these Schiff base ligands by 13C {1H} NMR did not show the same results as
shown in Figure 8.
L1 at 25°C
L1 at 10°C
25 °C
10 °C
Imine peak
L1 at 0°C
0 °C
L1 at -10°C
-10 °C
L1 at -25°C
-25 °C
Figure 6 The stacked 1H NMR spectra of ligand L1 in CDCl3 at temperatures -25 °C, -10 °C, 0 °C, 10 °C and 25 °C.
(The spectra are stacked at 15° angle to show the differences in the effect of the temperature on the signal
8

peaks).
The spacer protons under
different temperatures
-25 °C
-10 °C
0 °C
10 °C
25 °C
Figure 7 Superimposed 1H NMR spectra of ligand L1 in CDCl3 at temperature -25 °C, -10 °C, 0 °C, 10 °C
and 25 °C (The insert shows the magnified shift of the OH proton at different temperatures, and the magnified
stacked spectra of the spacer protons).
C9 & C13
C10 & C12
Ar H
C7 & C15
Figure 8 13C {1H} NMR spectrum for ligand L1 in CDCl3
9

From the 13C {1H} NMR spectrum, the imine signal for L1 was observed at 165 ppm, the
aromatic carbons were assigned to the signals from 117-160 ppm while the aromatic phenyl
carbon attached to the OH being the outlier between 150-160 ppm. One of the carbons
attached to the imine system in the aromatic system is overlapping to another. The two
proton decoupled spacer carbons were observed at 59 ppm and 69 ppm, as expected due to
the wider chemical shift range of the 13C {1H} NMR as compared to the 1H NMR. This was also
the case for the other ligands with different substituents as shown in the supplementary
material, section S3. Next, the 2D NMR Heteronuclear Shift Quantum Correlation analysis
(HSQC) was used to analyse the correlation of the protons and the carbons as shown in
Figure 9.
Figure 9 HSQC NMR results for ligand L1 in CDCl3.
The results from the HSQC analysis shows a correlation of the two spacer carbon signals to
the single decoupled signal for the 1H NMR while the other signals were all well resolved. The
results from these NMR studies shows that the protons of the alkyl spacer groups are
equivalent. This indicates similarity to other ethereal containing groups like the crown ether
10

1
type ligands.[15] The reason for the protons not being resolved on the H NMR was
postulated to be due to the symmetry and the flexibility of the ligand which renders the
spacer protons to be equivalent as shown in Figure 10.
O
N
N
OH
HO
Figure 10 The symmetry of the ligand structure which leads to the non-resolution of the 1H NMR signals.
2.3 Mass spectrometry (MS)
The synthesised ligands were analysed by mass spectrometry (MS) and ligand L5 is used as a
representative for discussion of the results. The results indicate relative mass abundance of
the different fragments, which are obtained from the fragmentation of the molecule and
their respective isotopic pattern when bombarded by sodium ions.[16] The mass spectrum
shows that the ligand forms fragmented species (a), (b) and (c) as shown in Figure 11. The
+
different fragments can be attributed to the molecular ions [M+H] , [M-C16H26O] and [M-
C18H30N2O]+ respectively as shown in Figure 12. The base peak at 100 % abundance
represents species (a), species (b) is observed at 30 % abundance while species (c) is
observed at 40 % abundance.
From the analyses of these ligands with the different substituents L1-L4, the results show the
ionisable mass species (c) for ligand L4 and L5 only, while for ligands L1 to L3 species (c) was
observed at 100 % relative abundance while species (a) was observed at 60 % relative
abundance. These results agreed with our previous work where a similar fragmentation
pattern was observed.[2]
11

(a)
(b)
(c)
Figure 11 The fragmentation pattern of ligand L5, M represents the molecular mass of the ligand
L5=563.86g/mol.
HO36B
MS_Direct_160525_29 37 (0.179) Cm (37:44)
565.4380
100
(b)
(a)
(c)
566.4409
283.2224
335.2700
283.7239
567.4440
580.4567
336.2728
284.2257
290.7317
377.2802
609.4638
551.4226
276.2141
427.3256
379.2951
495.3592
0
200 220 240 260 280 300 320 340 360 380 400 420 440 460 480 500 520 540 560 580 600 620 640 660 680 700 720
m/z
Figure 12 Mass spectrum of ligand L5 showing the relative abundance corresponding to the m/z values as shown
in Figure 11.
12

2.4 Elemental analysis
Elemental microanalysis was carried out to study the bulk nature of the samples. All ligands
analysed were confirmed to contain the Schiff base product in high purity. Similarly, these
ligands were also observed to contain solvent (Ligands L2 and L3) that could not be
completely removed as shown in Table 1.
Table 1 Elemental analysis results.
LIGAND
FORMULAR
% CALCULATED
% OBTAINED
C
H
N
C
H
N
L1
L2
L3
L4
L5
C18H20N2O3
69.21
62.36
70.38
72.45
73.20
6.45
6.98
8.97
7.18
6.06
6.26
4.68
69.19
62.33
70.11
72.60
73.09
6.29
6.08
5.70
8.61
9.68
8.83
7.25
6.21
6.09
4.39
C20H24N2O5(CH3OH)
C26H24N3O3. (CH3O)2
C26H36N2O3(CH3CH2O)0.5
C36H50N2O3(H2O)(CH3O)0.5
6.54
8.37
10.10
3.0 DISCUSSION OF THE CRYSTAL STRUCTURES
3.1 Data collection
Suitable crystals were selected and mounted on the Bruker SMART-APEX II DUO
diffractometer instrument under liquid nitrogen stream at 100 K. For ligand L3 this was
collected at room temperature at 293 K. The results from the crystal analysis data are
therefore shown in Table 2 for all the ligands obtained. All the crystal structures discussed in
this section are to the best of our knowledge, new. All the CIF data for each of these ligands
have been deposited on the CSD. The CCDC deposition numbers are: CCDC 1905486 –
1905489.
3.1.1 Measurements
Single crystal diffraction intensity data were collected using a SMART CCD area-detector
diffractometer, using a graphite-monochromated Mo-K radiation source (λ=0.71073 Å). Data
reduction and cell refinements were carried out by SMART and SAINT programs. The
structures were solved by direct methods (Bruker SHELXTS[17]) and refined by full-matrix
13

least - squares techniques (Bruker SHELXL[17]) using all unique data. The non-H atoms in the
structure were refined anisotropically. All hydrogen atoms were placed in calculated idealised
positions. The refinement was carried out using SHELXL98.[17]
14

Table 2 Crystal structure data for ligands L1, L2, L3 and L4
15

Identification code
L1
C18H20N2O3
312.36
99.98
L2
C40H48N4O10
744.82
100.77
orthorhombic
Pca21
L3
C26H26N2O4
430.49
298(2)
L4
C26H36N2O3
424.57
100(2)
Empirical formula
Formula weight
Temperature/K
Crystal system
orthorhombic
Pbcn
monoclinic
Pc
monoclinic
C2/c
Space group
a/Å
5.6768(14)
8.978(2)
31.322(8)
90
35.766(4)
4.5011(5)
22.753(3)
90
20.141(4)
6.9025(13)
7.9314(15)
90
14.407(2)
13.744(2)
24.944(4)
90
b/Å
c/Å
α/°
β/°
90
90
100.892(2)
90
91.152(2)
90
γ/°
Volume/Å3
90
90
1596.3(7)
4
3663.0(7)
4
1082.8(4)
2
4938.2(13)
8
Z
ρcalcg/cm3
1.3
1.351
1.32
1.142
μ/mm-1
0.089
664
0.098
1584
0.089
456
0.074
1840
F(000)
2Θ range for data collection/°
Index ranges
2.896 to 57.098
2.896 to 57.098
4.118 to 55.73
3.26 to 53.04
-7 ≤ h ≤ 7, -12 ≤ k ≤ 12, -40 ≤ l ≤ 41 -42 ≤ h ≤ 42, -6 ≤ k ≤ 5, -27 ≤ l ≤ 27 -24 ≤ h ≤ 26, -9 ≤ k ≤ 9, -10 ≤ l ≤ 10 -18 ≤ h ≤ 17, -12 ≤ k ≤ 17, -30 ≤ l ≤ 31
Reflections collected
Data/restraints/parameters
Goodness-of-fit on F2
15782
1855/0/108
1.034
44637
6669/37/459
1.057
12664
4998/2/306
1.036
14330
5105/0/292
1.086
Final R indexes [I>=2σ (I)]
Final R indexes [all data]
Largest diff. peak/hole / e Å-3
R1 = 0.0323, wR2 = 0.0786
R1 = 0.0388, wR2 = 0.0823
0.23/-0.16
R1 = 0.0822, wR2 = 0.2099
R1 = 0.1180, wR2 = 0.2518
0.92/-0.46
R1 = 0.0457, wR2 = 0.0961
R1 = 0.0715, wR2 = 0.1112
0.13/-0.15
R1 = 0.0606, wR2 = 0.1679
R1 = 0.0786, wR2 = 0.1827
0.60/-0.40
16

3.2 Discussion of crystal structure of ligands L1, L3 and L4
The crystal obtained for ligand L1 was in an orthorhombic crystal system and Pbcn space
group. The unit cell shows that the molecule undergoes symmetrical transition and is also
next to a glide plane perpendicular to the b-axis as shown in Figure 13. The asymmetric unit
shows half of the molecule with the other half generated by symmetry. All the bond lengths
and bond angles for this ligand were found to be consistent with previously synthesised
ligands.[2] Selected bond lengths and bond angles are given in Table 3.
Figure 13 Ortep diagram of L1 asymmetric molecule of the ligand with the insert showing the schematic
diagram. (the hydroxyl group is H-bonded to the N atom of the imine)
Table 3 Selected bond lengths and angles for ligand L1
Bond lengths
Bond Angles
bond Angle (°)
C1 C9 C8
C1 N1 C8
Torsion Angles
Atoms Length (Å)
bond
Angle °
O1 C9
O2 C3
N1 C1
1.4235(13)
1.3486(14)
1.2778(15)
108.23(9)
O2 C3 C4 C5
N1 C8 C9 O1
179.33(11)
62.17(11)
120.70(10)
For ligand L3, the crystal data was collected at room temperature and has a slight disorder.
The ligand was observed to crystallize in a monoclinic crystal system with a primitive c-
centred space group. The crystal structure shows the ligand with the protons bonded to the
17

N-atom of the amine in a quinoidal form rather than to the oxygen atom as had been
explained in previous work for the N-donor ligands.[2] This indicates that the naphthyl
containing group readily undergoes tautomerism. The Ortep diagram of this ligand is shown
in Figure 14 and the selected bond lengths and bond angles are given in Table 4. These bond
lengths and bond angles were also observed to be consistent with previous work.[2]
Figure 14 The structure of ligand L3 with the hydrogen atoms bonded to the imine rather than the phenolic
oxygen. The Ortep diagram is drawn using Olex at 50% probability.
Table 4 selected bond lengths for ligand L3
Bond Angles
Length (Å)
Bond Angles
Atoms
Length (Å)
111.3(7)
126.4(8)
Atoms
O1
O2
N5
C13
C3
1.419(11)
1.291(12)
1.278(11)
C14
C16
O1
N5
C13
C15
C16
On the other hand, the crystal structure obtained for ligand L4 was shown to crystallize in a
monoclinic crystal system with C2/c space group. The crystal shows a similar nature of
crystallization as that of L1 and L3 as shown in Figure 15. The bond lengths and bond angles
are given in Table 5 and are consistent with expected bond lengths and angles.[2]
18

Figure 15 Ortep diagram of L4 asymmetric molecule of the ligand. (The hydroxyl group is H-bonded to the N
atom of the imine).
Table 5 Selected bond lengths and angles for ligand L4
Bond lengths
Bond Angles
bond Angle (°)
C8 O1 C9
C7 N1 C6
Torsion Angles
Atoms Length (Å)
bond
O1 C9 C10 N2 174.39(17)
N1 C7 C8 O1 74.6(2)
Angle °
O1 C9
O2 C20
N1 C6
1.422(3)
1.357(2)
1.277 (3)
113.90(16)
118.75(18)
Since all these ligands are synthesized with the 2,2-dioxy ethylamine spacer, these ligands
therefore show a bend if viewed sideways from the perspective of the spacer atoms as
shown by Figure 16 for L1. This bend is also observed for all these ligands. This bent structure
can be as a result of forces of crystallinity, the ligands resistance to forming the pseudo-linear
molecules as had been previously observed for the N-donor ligands, i.e. does the N-donor
atom lend itself moreso to linearity compared to the O-donor atom or is it due to a
contribution from the substituents on the phenyl ring.[2] It can be hypothesized that the bent
shape, once dissolved in a solution like CDCl3 might be able to show dynamism that leads to
the proton overlap as discussed earlier. The overlay calculation of these ligands through root
mean square calculation (R.M.S) shown by Figure 17 for L1 and L3 shows a deviation of 0.693
Å
and 0.797 Å for the L3 and L4 compared to the L1 ligand. It is interesting to note that the
phenyl and naphthyl groups are in a trans-configuration towards each other.
19

Figure 16 Ortep diagram of L1 ligand viewed sideways on indicating the V-shaped bend of the ligand.
L1 crystal in trans configuration
L3 crystal in trans configuration
Amine spacer completely
overlaid
Figure 17 Ortep diagram of L1 and L3 ligand overlaid with the spacer atoms completely overlaid and the
naphthyl group and the salicylaldehyde group in a trans configuration showing a rotation opposite to each
other. Overlay was done by Olex and the R.M.S obtained was 0.693 Å.
20

Bend angle due to substituent
One side of L1 and L3 on the
same plane
L1 ligand crystal
L3 ligand crystal
Figure 18 Ortep diagram of L1 and L3 ligand overlaid with the spacer atoms completely overlaid and viewed
from the spacer carbon perspective (same diagram as that of Figure 17 viewed from below indicated by the
green arrow) to show the degree of bend.
Figure 19 The asymmetric unit cell of L1 ligand showing the ordered packing system in the unit cell with the
ligands lying in different directions. The Z unit represents only 4 asymmetric unit molecules in the cell. The O-
atoms are represented by the red ellipsoids, the N-atoms are represented by the blue ellipsoids. C-atoms are
represented by the grey ellipsoids. Figure generated by ORTEP at 50% probability.
Further analysis of this crystal shows that all these molecules have intramolecular hydrogen
bonding between the imine nitrogen and the hydroxyl proton. There was no observed inter
21

molecular bonding in the packing of these ligands. For the ligand L1 the unit cell contains four
molecules of the above asymmetric molecule (Figure 13) lying parallel to each other as
shown in Figure 19. For ligands L3 and L4 the packing diagrams are shown in the
supplementary information, section S5.
3.3 Discussion of crystal structure of Ligand L2
The crystal was obtained and crystallised in an orthorhombic crystal system, Pca21 space
group. The crystal system indicates a body centred ligand with two-fold screw axis and a glide
plane perpendicular to the c-plane as illustrated by the asymmetric unit with two molecules
lying parallel and rotated. This is shown by Figure 20 which displays the position of the O6
atom that seems to undergo a simple rotation lying almost opposite to the other.
06 Rotated
by 180°
O1
Figure 20 The two-unit molecules in the asymmetric unit of the crystal (insert shows the schematic diagram of
L2
The crystal structure of the ligand also proves that there is intramolecular hydrogen bonding
between the imine N-atom and the hydroxyl group in the system as shown by Figure 20. This
is consistent with the structures of L1 and L4. The position of one of the H-atoms bound to
the O2 atom is shown to be twisted outwards and therefore is not H-bonded to the N-atom
of the imine. The analysis of the packing of the crystal indicates that the two asymmetric
units in the unit cell are lying opposite to each other as shown by Figure 21. The selected
22

bond lengths and angles are shown in Table 6 and are consistent with the previously
synthesised ligands.[2]
Table 6 Selected bond lengths and bond angles for ligand L2
Bond lengths
Bond Angles
Angle (˚)
Torsion Angles
Atoms
Length (Å)
1.419(6)
1.359(6)
1.436(7)
bond
Angle (˚)
bond
O1 C9
O2 C4
N1 C1
C9 O1 C10 112.2(4)
C1 N2 O8 119.8(4)
C1O C11 N6 110.1(4)
O1 C11 N6 C12
O1 C9 C8 N2
-120.4(5)
62.17(11)
N
C8 C9 113.2(5)
Figure 21 Packing diagram of ligand L2 showing an ordered packed ligand viewed from AC-plane. The O-atoms
are represented by the red ellipsoids, the N-atoms are represented by the blue ellipsoids. C-atoms are
represented by the grey ellipsoids. Figure generated by ORTEP at 50% probability.
4.0 Conclusion
Five different Schiff base ligands containing the N2O3 donor sets were synthesised and fully
characterised using several different analytical techniques. Three of these ligands L2, L4 and
L5 are new, whilst L1 and L3 have been synthesised and extensively used before. The
analyses of these ligands indicated that the O-donor group’s linker (ethylene protons)
23

1
showed that all ligands through H NMR analysis, displayed these protons as one signal. To
the best of our knowledge, this had not been observed before. Carbon signals were observed
as two separate signals in the 13C NMR spectrum. The HSQC analysis was therefore used to
show the correlation of the 1H NMR signals to the 13C NMR signals.
The analyses of these ligands for the effect of the added substituents proved that the
methoxy substituted ligand, L2 showed the highest wavenumber shift of the imine signal
while the naphthylaldehyde ligand, L3 was observed to cause a lower wavenumber shift. Both
the previously synthesised and the new ligand crystal structures had not been previously
studied. This complements all other analytical data indicating that these ligands were
obtained with a detailed structural analysis. Different ligands show different crystallizations
with different crystal systems. The ligand with the naphthylaldehyde group, L3 underwent
tautomerism and the quinoid form of the ligand is shown here.
5.0 Experimental
5.1 Reagents
The following aldehydes were used, 2-hydroxyl phenylaldehyde (salicylaldehyde) for the
synthesis of L1 ligand, 5-methoxy-2-hydroxylphenylaldehyde for L2 ligand, 2-hydroxyl
naphthylaldehyde for L3 ligand and were all purchased from Sigma Aldrich and used without
further purification. The 5-tert butyl-2-hydroxyl phenylaldehyde for L4 and 5-nonyl-2-
hydroxyl phenylaldehyde for L5 were synthesized using a modified literature method and
obtained in high yield.[3,18] The two corresponding alcohols 4-tert butyl-phenol and 4-nonyl-
phenol together with paraformaldehyde were all purchased from Sigma Aldrich. The
magnesium turnings used were purchased from Merck Schuchardt OHG. The toluene solvent,
sulfuric acid (H2SO4) and nitric acid (HNO3) were bought from Merck laboratory supplies. All
these reagents were used without further purification. The corresponding diamine bearing
the added O-donor group; 2,2-oxydiethylamine dihydrochloride, was purchased from Sigma
Aldrich and was prepared using the procedure highlighted in the supplementary material,
section S1. The D-chloroform used for NMR studies was bought from Sigma Aldrich. The 99 %
pure ethanol solution and 99 % methanol were bought from B & M Scientific and were used
24

after dry distillation. The cold ethanol was obtained by placing the dried ethanol (in a sealed
250 ml volumetric flask) in an ice bath for 24 hours. All aqueous solutions were prepared
using double distilled deionized water from an econoPure16 reverse osmosis system.
5.2 Instrumentation
The infrared analysis, mass spectral analysis and the elemental analysis were carried out as
1
discussed in previous work[2]. The H NMR and the 13C NMR were carried out using the
Varian Unity Inova 400 MHz liquid State NMR Spectrometer and the higher magnitude Varian
Unity Inova 600 MHz liquid State NMR Spectrometer. Approximately 20 mg of the
synthesized samples were weighed and dissolved in CDCl3 in an NMR tube. The same
procedure was used for the variable temperature analysis and the HSQC analysis. The
program MestReNova was used to process the spectrum. Crystalline samples or powder
samples were analysed for melting points on a Stuart Scientific Melting Point apparatus
SMP30. All the crystal structural analysis was carried out using a Bruker SMART-APEX II DUO
diffractometer Instrument under liquid nitrogen stream at 100 K except the L3 ligand which
was analysed at room temperature.
All the ligands previously made are given in the supplementary material, however, that of the
new ligands are given below:
5.3 Characterization of previously made ligands
The characterization results for the synthesised ligands L1 and L3 are in the supplementary
information, section S2.
5.3.1 Characterization of 5-methoxy salicylaldehyde and 2,2'-[ethane-1,2-
diylbis(oxy)]diethanamine (Ligand L2).
O
O
O
N
N
OH
HO
Figure 22 Schematic diagram of ligand L2
25

A 1.56 g (0.0103 moles) of 5-methoxy-salicylaldehyde and 0.00516 moles of 2, 2’-[ethane-1,
2-diylbis (oxy)]diethanamine in ethanol were refluxed in ethanol. A yellow precipitate was
obtained from the yellow solution in a yield of 84.0 %. mp 86.5-87.4 °C. For C20H24N2O5:
(CH3O) EA calculated (%) C (62.36) H (6.98) N (7.18) EA Found (%); C (62.33%), H (6.78),
N(7.25); 1H NMR ppm (400 MHz, CDCl3) δ H 12.85 (2 H, s OH), 8.26 (2 H, s NCH), 6.94 – 6.83 (4
H, m ArH), 6.69 (2 H, d, J 2.8Hz, ArH), , 3.77 – 3.70 (8 H, m, NCH2CH2), 2.16 (6 H, s, OCH3). 13C
{1H} NMR (101 MHz, CDCl3) 166.23 (s, ArCN), 155.31 (s, CArOH), 152.03 (s, CArOCH3), 119.35 (s,
CArH), 118.51 (s, CArH), 117.72 (s, CArH), 114.98 (s, CArH), 70.48 (s, OCH2CH2), 59.24 (s,
CH2CH2O), 31.03 (s, OCH3). IR (ATR, neat, cm-1); 2886 (w, CH), 1639 (s, C=N), 1587 (w, C=C),
1490 (s, C-H), 1259 cm-1 (s, CAr-O): ESI-MS (ES+); Expected m/z (%) 372.17, obtained m/z (%)
373.17(100), [M+H]+
.
5.3.2 Characterization of 5-t-butyl salicylaldehyde and 2,2'-[ethane-1,2-
diylbis(oxy)]diethanamine (Ligand L4).
CH3
H3C
H3C
H3C
CH3
CH3
O
N
N
OH
HO
Figure 23 Schematic diagram of Ligand L4.
A 2.76 g (0.00774 moles) of 2-hydroxy 4-tert butyl aldehyde and 26.0 ml (0.00387) moles of 2,
2’-[ethane-1, 2-diylbis (oxy)]diethanamine were refluxed in ethanol. A brownish yellow oil was
obtained which slowly solidified, yield 72.0 % for C26H36N2O3 (CH3CH2O)0.5 EA calculated (%) C
1
(72.45) H (8.78) N (6.26). EA Found (%) C (72.60) H (8.61) N (6.09) H NMR (400 MHz, CDCl3)
δ H 8.37 (2 H, m, NCH), 7.34 (2 H, dd, J 8.7Hz, 2.5Hz, ArH), 7.23 (2 H, d, J 2.5Hz, ArH), 6.89 (2
H, d, J 8.7Hz, ArH), 3.80 – 3.70 (8H, OCH2CH2), 1.31 – 1.29 (18 H, m, C(CH3)3). 13C {1H} NMR
(101 MHz, CDCl3) δ C; 166.86 (s, ArCN), 158.96 (s, CArOH), 141.35 (s, CArCH3), 129.71 (s, CArH),
127.91 (s, CArCN), 116.64 (s, CArH), 70.82 (s, NCH2 CH2), 59.33 (s, NCH2 CH2), 31.41 (s, CCH3).
IR (ATR, neat, cm-1); 2865 (s, C-H); 1633 (s, C=N); 1589 (s,C=C), 1494 (m, C-H), 1265 cm-1 (m,
CAr-O), ESI-MS (ES+); Expected m/z(%) 424.28 Obtained m/z (%) 425.28 (100)[M+H]+.
26

5.3.3 Characterization of 5-nonyl salicylaldehyde and 2,2'-[ethane-1,2-
diylbis(oxy)]diethanamine (ligand L5).
H 3
C
C H 3
O
N
N
O H
H O
Figure 24 Schematic diagram of Ligand L5
A 1.98 g (0.00797 moles) of 2-hydroxy 4-nonylaldehyde and 26.7ml (0.00400 moles) of 2, 2’-
[ethane-1,2-diylbis(oxy)]diethanamine were refluxed in ethanol. A brownish yellow less
viscous oil was obtained. Yield 93.0 %. FM C36H50N2O3.(H2O) (CH3O)0.5 EA calculated (%) C
1
(73.20), H (10.10), N (4.68), Found (%) C (73.09), H (9.68), N (4.39) H NMR ppm (600MHz,
CDCl3) δ 8.37 (1 H, m), 7.52 – 6.68 (3 H, m), 4.47 – 2.96 (4H, m), 2.32 – 0.11 (19 H, m). 13C
{1H} NMR (400 MHz, CDCl3) δ 166.91(s, ArCN), 158.83(s, CArOH), 140.76(s, CArH), 140.09(s,
CArC), 137.93(s, CArH), 130.46(s, CArH), 118.08(s, CArH), 116.49(s, CArH), 70.85(s, NCH2 CH2),
59.24(s, NCH2 CH2), 51.88-8.75((CH2)8CH3). IR (ATR, neat, cm-1); 3005 (w, OH), 2926(m, C-H),
2868 (m, C-H), 1633 (m, C=N); 1588 (s,C=C); 1491 (m, CH); 1280 cm-1 (m, CAr-O): ESI-MS
(ES+); Expected m/z(%) 564.84, obtained m/z (%) 283.32 (40) [(M/2)+H]+, 335.27 (30) [M-
C16H26O], 566.44 (100) [M+2H]+.
6.0 Acknowledgements
We wish to thank Stellenbosch University and the National Research Foundation (NRF),
grant number 111701 for financial support for this work.
7.0 Conflict of Interest
There is no conflict of interest for this work.
8.0 References
[1]
A.M. Abu-dief, I.M.A. Beni-Suef Univ. J. Basic Appl. Sci. 4 (2015) 119–133.
27