A close insight into the nature of intra- and intermolecular interactions in new Cu(II) Schiff base complexes derived from halogenated salicylaldehydes and allylamine: Theoretical and crystallographic studies

Article abstract of DOI:10.1016/j.poly.2018.08.023

Although numerous Schiff base complexes have been synthesized and characterized, reports on Schiff base ligands and complexes derived from amines containing terminal allyl group are rare. In this work, four halogenated Schiff base compounds were synthesized by reaction of halogenated salicylaldehydes (3,5-dichlorosalicylaldehyde, 3,5-dibromosalicylaldehyde, 3,5-diiodosalicylaldehyde and 3-bromo-5-chlorosalicylaldehyde) with allyl amine in water as green solvent at ambient temperature and characterized by elemental analyses, NMR (¹H and ¹³C), and FT-IR spectroscopy. In continue, their Cu(II) complexes were synthesized and characterized by elemental analyses, FT-IR and single-crystal X-ray diffraction. All complexes show halogen-halogen, π–π CH–π interactions and also metal–halogen secondary bonds in crystal packing. The coordination geometry around the Cu(II) in all reported compounds is best described as square planar with two axially elongated interactions named metal–halogen secondary bond (Cu…X), all beyond the sum of the corresponding vdW radii (3.421 ? for Cu…Cl in (Cl₂L)₂Cu, 3.463 ? for Cu…Br in (Br₂L)₂Cu, 3.486 ? for Cu…I in (I₂L)₂Cu and 3.467 ? for Cu…Cl in (BrClL)₂Cu). The crystal structures have also been subjected to Hirshfeld surface analysis which reveals that approximately most of the close contacts correspond to relatively weak interactions. Also, all of the interactions in crystal packing have been analyzed by theoretical calculations.

Full text of DOI:10.1016/j.poly.2018.08.023

Accepted Manuscript
A close insight into the nature of intera- and intermolecular interactions in new
Cu(II) Schiff base complexes derived from halogenated salicylaldehydes and
allylamine: Theoretical and crystallographic studies
Mahnaz Aryaeifar, Hadi Amiri Rudbari, Giuseppe Bruno
PII:
S0277-5387(18)30489-3
https://doi.org/10.1016/j.poly.2018.08.023
POLY 13346
DOI:
Reference:
Polyhedron
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Accepted Date:
10 May 2018
10 August 2018
Please cite this article as: M. Aryaeifar, H. Amiri Rudbari, G. Bruno, A close insight into the nature of intera- and
intermolecular interactions in new Cu(II) Schiff base complexes derived from halogenated salicylaldehydes and
allylamine: Theoretical and crystallographic studies, Polyhedron (2018), doi: https://doi.org/10.1016/j.poly.
2018.08.023
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A close insight into the nature of intera- and intermolecular
interactions in new Cu(II) Schiff base complexes derived from
halogenated salicylaldehydes and allylamine: theoretical and
crystallographic studies
Mahnaz Aryaeifar a, Hadi Amiri Rudbari a,*, Giuseppe Bruno b,*
a Department of Chemistry, University of Isfahan, Isfahan 81746-73441, Iran.
b Department of Chemical Sciences, University of Messina, Via F. Stagno d'Alcontres 31, 98166
Messina, Italy.
*Corresponding authors:
E-mail addresses: h.a.rudbari@sci.ui.ac.ir, hamiri1358@gmail.com (H. Amiri Rudbari);
gbruno@unime.it (G. Bruno).
1

Abstract:
Although numerous Schiff base complexes have been synthesized and characterized, reports on
Schiff base ligands and complexes derived from amines containing terminal allyl group are rare.
In this work, four halogenated Schiff base compounds were synthesized by reaction of
halogenated salicylaldehydes (3,5-dichlorosalicylaldehyde, 3,5-dibromosalicylaldehyde, 3,5-
diiodosalicylaldehyde and 3-bromo-5-chlorosalicylaldehyde) with allyl amine in water as green
solvent at ambient temperature and characterized by elemental analyses, NMR (1H and 13C), and
FT-IR spectroscopy. In continue, their Cu(II) complexes were synthesized and characterized by
elemental analyses, FT-IR and single-crystal x-ray diffraction. All complexes show halogen-
halogen, -, CH- interactions and also metal−halogen secondary bonds in crystal packing. The
coordination geometry around the Cu(II) in all reported compounds is best described as square
planar with two axially elongated interactions named metal−halogen secondary bond (Cu…X),
all beyond the sum of the corresponding vdW radii (3.421 Å for Cu…Cl in (Cl2L)2Cu, 3.463 Å
for Cu…Br in (Br2L)2Cu, 3.486 Å for Cu…I in (I2L)2Cu and 3.467 Å for Cu…Cl in
(BrClL)2Cu). The crystal structures have also been subjected to Hirshfeld surface analysis
which reveals that approximately most of the close contacts correspond to relatively weak
interactions. Also, all of the interactions in crystal packing have been analyzed by theoretical
calculations.
2

1. Introduction
Halogen atoms are common substituents in a highly diverse range of molecules and subject to
noncovalent interactions in both solution and the solid state. The halogen bond occurs when
there is evidence of a net attractive interaction between an electrophilic region associated with a
halogen atom in a molecular entity and a nucleophilic region in another, or the same, molecular
entity.
The polarizable halogens exhibit electrophilic δ+ character along the axis of the C−X bond
developing “the positive σ-hole” and nucleophilic δ¯ character perpendicular to C−X bond,
referred to as the “belt” (Fig. 1) [1].
Halogen atoms undergo three kinds of weak non-covalent interactions, specifically halogen
bonding, halogen–halogen interactions, and halogen–π interactions (Scheme 1) [2, 3].
Investigation of halogen bonding (a in scheme 1) in biomolecules, halogenated alkanes,
halogenated phenols, and host molecule–polymer macromolecules by relying on crystallography
data show that halogens have a tendency to form Lewis acid-base pairs with both electron
acceptors and electron-donating heteroatoms, yielding bond angles between 140-180° and bond
lengths of less than the sum of the van der Waals radii [4].
In the halogen−halogen interactions (X···X) (b in scheme 1), both halogen bond donor and
acceptor are halogen atoms [5]. This requires one of the halogen atoms to develop a positive
electrostatic potential, i.e. a positive σ-hole interacting with an electron rich region (a negative
belt) of another [6]. The anisotropic electron distribution around the halogen atom bonded to the
carbon atom facilitates this electrophile− nucleophile pairing interaction [7]. Halogen…halogen
interactions (C―X1…X2―C) are characterized in terms of three parameters, Rij = X1…X2 and
two angles θ1 = C―X1…X2 and θ2 = X1…X2―C (b in scheme 1). Type I geometries can be
3

thought to give rise to an electrostatically repulsive arrangement since at the point of interaction
on their molecular surfaces the electrostatic potentials are approximately identical. By contrast,
type II geometries are consistent with the description of halogen bonds, wherein the two
halogens have distinct and different roles: one halogen provides the Lewis basic site (the halogen
bond acceptor) situated orthogonal to the C—X bond and this is aligned in a linear arrangement
with the Lewis acidic C—X group [8].
The strength of the halogen−halogen interactions formed by the halogen atom depends to the size
and charge of the halogen σ-hole. The size and charge of the halogen σ-hole, depends on two key
factors, namely the identity of the halogen and the chemical environment in which the halogen is
found [9]. Larger halogens tend to form larger (more positive) σ-holes, leading to stronger
interactions that are more electrostatic in nature (I > Br > Cl) [10]. By contrast, organo-fluorines
do not typically display halogen bonding properties due to the small size, extreme
electronegativity, and limited polarizability of fluorine atoms.
As mentioned in above, the size of a σ-hole is also strongly affected by the electronegativity of
the atoms (or chemical groups) that are located near the C—X bond. The electron withdrawing
effects of electronegative atoms tend to lower the overall negative charge on a halogen and,
therefore, lead to more positively charged σ-holes. For example, Halogen bonds involving
aromatically bound halogens are generally stronger than those of aliphatic halogens because
aromatic moieties have electron withdrawing properties that lead to larger σ-holes. Generally, the
hybridization of carbons to which halogens are attached affects halogen bonding ability in the
order C(sp)−X > C(sp2)−X > C(sp3)−X [11].
4

Halogen– interactions (c in scheme 1) are non-covalent interactions of aromatic donors with
halogenated organic molecules; these are similar to the more common CH– interactions [12].
These interactions are of importance in the electrophilic halogenation of aromatic systems.
Also, in another interaction for halogens, the negatively charged region can interact with the
positive charge of a transition metal. These short interactions are classified as “metal−halogen
secondary bonds,” which are formally defined as halocarbon complexes having a halogen metal
distance considerably below the sum of their van der Waals radii but longer than the metal-halide
bond length (Fig. 2)[13-15]. On the basis of nuclear quadrupole resonance (NQR) spectroscopy
results, Wulfsberg proposed the criterion that the metal−halogen distance must be shorter than
the average metal-halide distance plus 1 Å [16]. As depicted in Fig. 2, this kind of interaction
have type II geometry (b in scheme 1). Although this type of metal– halogen interaction is
known in coordination chemistry but are relatively rare, and there are few techniques capable of
detecting these bonds other than X-ray crystallography and NQR, thereupon little studied.
Although numerous Schiff base complexes with different structures have been synthesized and
characterized, reports on Schiff base ligands and complexes derived from amines containing
terminal allyl group are scanty [17,18]. We have recently reported the synthesis and structural
properties some of them [19-22]. In continuation of our research program aiming at the
understanding of the role of intra and intermolecular interactions in the allyl metal-containing
crystal structures, a series of halogenated Schiff base compounds containing allyl group, in
which the halogen atoms are in the phenyl ortho and para positions, Cl2LH, Br2LH, I2LH and
BrClLH, have been employed for the synthesis of four new Cu(II) complexes.
5

2. Experimental Section
2.1. Chemicals and instrumentation
All the chemicals were purchased from Sigma-Aldrich Co. and used without further purification.
The FT-IR spectra were recorded on a JASCO, FT/IR-6300 spectrometer (4000–400 cm-1) in
KBr pellets. 1H and 13C NMR spectra were recorded on a Bruker Avance 400 spectrometer using
CDCl3 as solvents for the ligands. The elemental analyses were performed on Leco, CHNS-932
and Perkin-Elmer 7300 DV elemental analyzers.
2.2. Crystallographic refinement details
The X-ray data of (Cl2L)2Cu, (Br2L)2Cu, (I2L)2Cu and (BrClL)2Cu were collected at room
temperature with a Bruker APEX II CCD area detector diffractometer using Mo K radiation (
= 0.71073 Å). Data collections, cell refinements, data reductions and absorption corrections
were performed using multiscan methods with Bruker software [23]. The structures were solved
by direct methods using SIR2004 [24]. The non-hydrogen atoms were refined anisotropically by
the full matrix least squares method on F2 using SHELXL [25]. All hydrogen atoms were added
at ideal positions and constrained to ride on their parent atoms. Crystallographic data for
complexes are listed in Table 1. Selected bond distances and angles are summarized in Table 2.
2.3. Computational study
Theoretical calculations were made in order to understand solid-state interactions that determine
molecular packing of our compounds and attempt to quantify the energies of the individual
interactions that are predominantly made up by several halogen bond. The Density Functional
Theory approach it was also used to test the relatively inexpensive validity of quasi-relativistic
6

effective core potential. DFT calculations were performed by using the GAUSSIAN 09 program
package [26] on i7 processor personal computer. The effect of electron correlation on the
molecular geometry was taken into account by using Becke's three-parameter hybrid, and the
gradient corrected Lee-Yang-Parr correlational functional (B3LYP) [27] employing the quasi-
relativistic effective core potential (RECP) SDD and valence basis sets recommended by
Stuttgart group [28]. B3LYP and several other functionals such as HSEH1PBE [29], PBEPBE
[30], HCTH [31] were used in conjunction with the standard basis sets (SDD) in order to test
their ability to reproduce the interactions energy. Among those, the functional HSEH1PBE, in
conjunction with SDD basis sets and the AUTO fitting set it seems to be the best in simulating
the regular proceeding of the potential energy curve of the interactions. Energy interaction
calculations, as single point energy (SPE), for dimeric couples was computed, starting from the
crystal structures geometry of all samples as coming from the x-ray determination, varying the
appropriate distance from 2 Å to ∞. The energy of dimers at infinite distance it was placed equal
two time the monomer's energy; this energy was taken as zero. The counterpoise correction [32]
is employed to reduce basis set superposition error (BSSE).
2.4. Hirshfeld surface analysis
Hirshfeld surfaces (HSs) and 2D fingerprint plots (FPs) were generated using Crystal Explorer
3.1 [33] based on results of single crystal X-ray diffraction studies. The function dnorm is a ratio
encompassing the distances of any surface point to the nearest interior (di) and exterior (de) atom
and the van der Waals radii of the atoms [34,35]. The negative value of dnorm indicates the sum of
di and de is shorter than the sum of the relevant van der Waals radii, which is considered to be a
closest contact and is visualized as red color in the HSs. The white color denotes intermolecular
7

distances close to van der Waals contacts with dnorm equal to zero whereas contacts longer than
the sum of van der Waals radii with positive dnorm values are colored with blue. A plot of di
versus de is a 2D fingerprint plot which recognizes the existence of different types of
intermolecular interactions.
2.5. Synthesis of the Schiff-base ligands
All Schiff base ligands, Cl2LH: allylamine and 3,5-dichlorosalicylaldehyde; Br2LH: allylamine
and 3,5-dibromosalicylaldehyde; I2LH: allylamine and 3,5-diiodosalicylaldehyde; BrClLH:
allylamine and 3-bromo-5-chlorosalicylaldehyde, were synthesized using identical reaction
conditions. Therefore, only the synthesis of Cl2LH will be described in detail. The addition of 10
mmol of 3,5-dichlorosalicylaldehyde to a distilled water solution (20 mL) of allylamine (12
mmol) at room temperature yielded a yellow precipitate almost immediately. The reaction
mixture was stirred overnight, then the yellow precipitate was collected by filtration, washed
with 50 mL of distilled water, and dried in air.
Cl2LH: Yield 95%, Anal. calc. for C10H9Cl2NO: C: 52.20, H: 3.94, N: 6.09. Found: C: 52.23, H:
1
3.95, N: 6.07. FT-IR (KBr, cm-1): 1625 (vs, C=N). H NMR (CDCl3, 400 MHz, 298 K) δ/ppm:
14.51 (s, 1H, OH); 8.28 (s, 1H, N=CH); 7.42 (d, 1H, ClC-CH-CC); 7.17 (s, 1H, ClC-CH-CCl);
6.01 (m, 1H, CH=CH2); 5.28 (d of q, 1H, CH=CHH); 5.25 (d of q, 1H, CH=CHH), 4.29 (d of q,
CH2CH=CH2). 13CNMR (CDCl3, 400 MHz, 298 K) δ/ppm: 163.96, 157.43, 133.48, 132.37,
129.00, 123.15, 122.28, 119.38, 117.63, 60.12.
8

Br2LH: Yield 92%, Anal. calc. for C10H9Br2NO: C: 37.65, H: 2.84, N: 4.39. Found: C: 37.64, H:
1
2.86, N: 4.39. FT-IR (KBr, cm-1): 1629 (vs, C=N). H NMR (CDCl3, 400 MHz, 298 K) δ/ppm:
14.69 (s, 1H, OH); 8.24 (s, 1H, N=CH); 7.71 (d, 1H, ClC-CH-CC); 7.34 (s, 1H, ClC-CH-CCl);
5.99 (m, 1H, CH=CH2); 5.27 (d of q, 1H, CH=CHH); 5.25 (d of q, 1H, CH=CHH), 4.28 (d of q,
CH2CH=CH2). 13CNMR (CDCl3, 400 MHz, 298 K) δ/ppm: 163.80, 159.07, 137.83, 133.37,
132.76, 119.63, 117.76, 112.88, 108.97, 59.82.
I2LH: Yield 92%, Anal. calc. for C10H9I2NO: C: 29.08, H: 2.20, N: 3.39. Found: C: 29.11, H:
1
2.23, N: 3.40. FT-IR (KBr, cm-1): 1623 (vs, C=N). H NMR (CDCl3, 400 MHz, 298 K) δ/ppm:
14.90 (s, 1H, OH); 8.14 (s, 1H, N=CH); 8.06 (d, 1H, ClC-CH-CC); 7.51 (s, 1H, ClC-CH-CCl);
5.98 (m, 1H, CH=CH2); 5.28 (d of q, 1H, CH=CHH); 5.25 (d of q, 1H, CH=CHH), 4.27 (d of q,
CH2CH=CH2).13CNMR (CDCl3, 400 MHz, 298 K) δ/ppm: 163.49, 162.38, 148.88, 139.90,
133.26, 119.36, 117.93, 89.05, 78.24, 59.40.
BrClLH: Yield 90%, Anal. calc. for C10H9BrClNO: C: 43.75, H: 3.30, N: 5.10. Found: C: 43.74,
H: 3.31, N: 5.08. FT-IR (KBr, cm-1): 1627 (vs, C=N).1H NMR (CDCl3, 400 MHz, 298 K) δ/ppm:
14.64 (s, 1H, OH); 8.25 (d, 1H, N=CH); 7.59 (d, 1H, ClC-CH-CC); 7.22 (s, 1H, ClC-CH-CCl);
6.01 (m, 1H, CH=CH2); 5.30 (d of t, 1H, CH=CHH); 5.25 (d of t, 1H, CH=CHH), 4.29 (d of t,
CH2CH=CH2). 13CNMR (CDCl3, 400 MHz, 298 K) δ/ppm: 163.85, 158.40, 135.26, 133.44,
129.74, 122.67, 119.05, 117.69, 112.38, 60.00.
2.6. Preparation of the complexes
9

Similar to ligands, the four complexes were synthesized using identical reaction conditions,
therefore only the synthesis of (Cl2L)2Cu will be described in detail. A solution of triethylamine
(3 mmol) in MeOH (5 mL) was added to the MeOH solution (20 mL) of ligand Cl2LH (2 mmol),
the solution turned dark yellow and was stirred for 10 min, then addition of 1 mmol of
CuCl2.2H2O to this solution yielded a green precipitate almost immediately. The resulting was
refluxed for 3 h to preparation of the (Cl2L)2Cu complexes. Then the green precipitate was
collected by filtration, washed with methanol, and dried in air. For all four complexes the green
crystals were obtained in tetrahydrofuran by recrystallization.
(Cl2L)2Cu: Yield 89%, Anal. calc. for C20H16Cl4CuN2O2: C: 46.04, H: 3.09, N: 5.37. Found: C:
46.03, H: 3.10, N: 5.37., FT-IR (KBr, cm-1): 1619 (vs,C=N).
(Br2L)2Cu: Yield 87%, Anal. calc. for C20H16Br4CuN2O2: C: 34.34, H: 2.31, N: 4.00. Found: C:
34.35, H: 2.33, N: 3.99., FT-IR (KBr, cm-1): 1618 (vs, C=N).
(I2L)2Cu: Yield 93%, Anal. calc. for C20H16CuI4N2O2: C: 27.07, H: 1.82, N: 3.16. Found: C:
27.07, H: 1.83, N: 3.16., FT-IR (KBr, cm-1): 1616 (vs,C=N).
(BrClL)2Cu: Yield 91%, Anal. calc. for C20H16Br2Cl2CuN2O2: C: 39.34, H: 2.64, N: 4.59.
Found: C: 39.33, H: 2.65, N: 4.61., FT-IR (KBr, cm-1): 1619 (vs,C=N).
3. Result and Discussion
3.1. IR and NMR spectra
10

Synthesis of Schiff base ligands and their Cu(II) complexes are shown in Schemes 2 and 3. All
of complexes were obtained in good yield (more than 90%). The elemental analyses of the
complexes were consistent with their proposed compositions. Stability of all ligands and
complexes in the most common polar and non-polar solvents including H2O, MeOH, EtOH,
CH3CN, CHCl3, DMSO and DMF was tested and the results showed the stability of complexes
in solvents. The most characteristic feature in the IR spectra of the ligands comes from the C=N
stretching vibrations. This band appeared at 1625, 1629, 1623 and 1627 cm-1 for Cl2LH, Br2LH,
I2LH and BrClLH, respectively [36].
Compared to the free Schiff base ligands, this band was shifted to lower wavenumber upon
coordination (1619, 1618, 1616 and 1619 cm-1 for (Cl2L)2Cu, (Br2L)2Cu, (I2L)2Cu and
(BrClL)2Cu, respectively) [37]. Formation of M-N bonds leads to weakening of C=N band and
this can be explained by the donation of electrons from the nitrogen atom to the empty orbitals of
the metal atom. Additional support for the formation of the complexes were provided by the
existence of weak intensity bands at ~ 480 cm-1 and ~ 520 cm-1 attributed to the formation of M-
N and M-O bonds, respectively.
1
The H NMR and 13C NMR spectra of the Schiff base ligands, Cl2LH, Br2LH, I2LH and
BrClLH were measured in CDCl3, with TMS as internal standard. The data is depicted in
1
13
experimental section and spectra in Figs. S1-S7 and 1H NMR of I2LH in Fig. 3. The H and C
NMR spectra of all ligands obtained after 12, 24 and 120 h were similar to the initial spectrum,
1
indicating that the ligands are stable in deuterated chloroform. The H NMR spectra of all
ligands show one peak as triplet at ~ 8.2 ppm corresponding to the imine proton (CH=N), and a
sharp O―H signal at ~14.5 ppm (for example see the 1H NMR spectrum of I2LH in Fig. 3). The
very sharp peak for the phenolic (-OH) proton in the prepared Schiff bases can be ascribed to the
11

intramolecular hydrogen-bonding interaction of this functional group with nitrogen heteroatom
1
of imine functionality. The H NMR spectra also show a multiplet peak for –CH-CH=CH2
proton at ~6.0 ppm. The reason for splitting of –CH peak is coupling of hydrogen of –CH with –
CH2 and =CH hydrogens.
3.2. X-ray Crystal Structure
The molecular structures of all complexes were determined by single crystal X-ray diffraction
technique. View of the molecular structures of (Cl2L)2Cu, (Br2L)2Cu, (I2L)2Cu and
(BrClL)2Cu complexes with common atom numbering scheme are shown in Fig. 4.
Crystallographic data and selected bond distances and angles of complexes are listed in Tables 1
and 2, respectively. Single crystal X-ray analysis reveals all complexes crystallize in
centrosymmetric space groups (monoclinic P21/c for (Br2L)2Cu, (I2L)2Cu and (BrClL)2Cu;
triclinic P-1 for (Cl2L)2Cu). The crystallographic data also reveal that in all complexes the metal
center is four coordinated by two phenolate oxygen and two imine nitrogen atoms of two moles
of Schiff base ligand. The coordination geometry around the Cu(II) in all reported compounds is
best described as square planar with two axially elongated interactions named metal−halogen
secondary bonds (Cu…X).
Examination of the main metal-ligand distances in all complexes, Table 2, shows that the Cu—N
distances are longer than the Cu—O distances due to stronger ability of the oxygen atom to bond
to the metal than the nitrogen atom [38,39]. The Cu—N distances are 2.0002(3), 2.0002(3),
2.019(8) and 2.007(2) Å, while, the Cu—O distances are 1.895(2), 1.901(2), 1.919(7) and
1.9055(17) Å for (Cl2L)2Cu, (Br2L)2Cu, (I2L)2Cu and (BrClL)2Cu, respectively. These bond
lengths (Cu—O and Cu—N) and bond angles (N—Cu—O) (Table 2) are similar to those seen in
12

related complexes [17,40,41]. For instance, in our previous work, distances of 1.902(2) and
1.896(2) Å for the Cu—O bond and 2.014(3) and 2.003(3) Å for Cu—N bond and angles of
88.14(13) and 88.44(12) for N—Cu—O are found in a copper(II) complex derived from
salicylaldehyde and allylamine [21].
As shown in Figs. 5-8, there are halogen-halogen type I interactions in all of the complexes. A
statistical study proved that at distances inferior to the sum of van der Waals radii type I
interactions are dominant, while at distances close to the value of that sum halogen bonds
prevail. However, when the contact distance is superior to the van der Waals radii sum, type I
becomes more frequent, particularly for I…I contacts [42].
As we can see for (Cl2L)2Cu in Fig. 5, only halogens in para position (Cl2) can involve in
intermolecular halogen-halogen interaction. The Cl2…Cl2 interaction length is 3.5639 Å that is
little more than the sum of van der Waals radii (3.52 Å) (Table 3). In the (Br2L)2Cu and
(I2L)2Cu, the halogen atom in the ortho position (X1) also involve in halogen-halogen interaction
with para halogen of another molecule with Br1…Br2 distance of 3.8922 Å for (Br2L)2Cu and
with I1…I2 distance of 4.0633 Å for (I2L)2Cu (Figs. 6 and 7 and Table 3). Then, in (Br2L)2Cu
and (I2L)2Cu complexes, each para-halogen (Br or I) acts as both halogen bond donor and an
acceptor in the generation of bifurcated X…X halogen bonding interactions. The para-halogen-
para-halogen interaction for Cl…Cl in (Cl2L)2Cu is 3.5639, for Br…Br in (Br2L)2Cu is 3.8610
Å and for I…I in (I2L)2Cu is 3.8260 Å. These X...X contacts, except one I…I in (I2L)2Cu, are
just a little longer than the sum of Bondi’s van der Waals radii of halogens (Table 3). The vdW
radii for Cl, Br, and I atoms are 1.76, 1.87, and 2.03 Å, respectively, and the corresponding sum
of the vdW radii are Cl + Cl = 3.52; Br + Br = 3.74 and I + I = 4.06 Å. In (BrClL)2Cu complex,
only Br in ortho-positian have a very week interaction with the chlorine atom of neighbor
13

molecule. The distance for this week halogen-halogen interaction is 3.91 Å. This should be noted
that the vdW radii for Cl and Br atoms are 1.76 and 1.87 Å, respectively, and the corresponding
sum of the vdW radii is Cl + Br = 3.63 Å.
Another interesting interaction in these complexes is metal−halogen secondary bonds. As shown
in Figs. 5-8, two axial directions of Cu atom occupied by two para-halogen atoms of two
different complexes. The closest separation is 3.421 Å for Cu…Cl in (Cl2L)2Cu, 3.463 Å for
Cu…Br in (Br2L)2Cu and 3.486 Å for Cu…I in (I2L)2Cu. For comparison, the sum of the
Bondi’s van der Waals radii of copper with chlorine, bromine and iodine are 3.16 (1.40 +1.76),
3.27 (1.40 + 1.87) and 3.43 (1.40 +2.03) Å, respectively. In the complex (BrClL)2Cu, para-
chlorine atoms have interaction with Cu with Cu…Cl distance of 3.467 Å. The Cu–Halogen–
Cphen angle is 92.26(13), 92.26(13), 92.26(13) and 92.26(13)° in (Cl2L)2Cu, (Br2L)2Cu,
(I2L)2Cu and (BrClL)2Cu complexes, respectively, which is close to the expected angle of 90°
that would ideally position the region of negative electrostatic potential on the halogen atom to
interact with the metal center. Hence, we can say in all reported complexes, the coordination
geometry around the Cu(II) can be described in best way as square planar plus two axially
elongated interactions.
Interaction between terminal hydrogen of allyl group (RHC=CHH) with one carbon atom of
benzene group of the nearest neighbor molecule is another interesting intermolecular interaction
in these complexes. The terminal H atoms in Ally group attached to Csp2 and for this reason is
approximately positive. These positive hydrogen atoms can have interaction with  system of
benzene group of neighbor molecule (Fig. 9). This interaction involves the atom of H(10B)
pointing directly to the system π C1-C2 in (Cl2L)2Cu with distance of 2.898 and 3.112 Å, and
14

H(10A) to the system π C1-C2 with distance of 2.905 and 2.966 Å in (Br2L)2Cu, 3.053 and
3.182 Å in (I2L)2Cu and 2.870 and 2.877 Å in (BrClL)2Cu.
In the all complexes, the –CH=CH2 group is almost perpendicular to plane of molecule. The
angle between created plane of N1-O1-Cu1-O1′-N1′ atoms and N1-C8-C9 atoms is 92.26(13),
92.26(13), 92.26(13) and 92.26(13)° in (Cl2L)2Cu, (Br2L)2Cu, (I2L)2Cu and (BrClL)2Cu
complexes, respectively. This arrangement allows to the –N–CH2 and –N–CH2–CH hydrogen
atoms having suitable intramolecular interaction with oxygen atom (Fig. 10). We saw this kind
of arrangement of allyl group also in our previous work in preparation of Cu(II), Co(II) and
Zn(II) complexes from salicylaldehyde and allylamine [21]. These two intramolecular
interactions can be described as S1 (5) [43].
2
Another important intermolecular interaction is these complexes is … interactions. As shown
in Table 4 and Scheme 4, … interactions are exist between Cg(1)…Cg(2) with centroid–
centroid distance of 3.6502 and 3.5273 Å for (Cl2L)2Cu, 3.6593 and 3.5870 Å for (Br2L)2Cu,
3.7488 and 3.5638 Å for (I2L)2Cu and 3.6465 and 3.5918 Å for (BrClL)2Cu in which Cg(1) and
Cg(2) are centers of Cu(1)/O(1)/C(1)/C(6)/C(7)/N(1) and C(1)/C(6) rings, respectively.
3.3. Hirshfeld surface analysis
Hirshfeld surface (HS) based tools represent a unique approach to the crystal structure prediction
and this method offers a facile way of obtaining information on trends in crystal packing [34].
Hirshfeld surfaces and their associated finger print plots for synthesized complexes were
calculated using CrystalExplorer 3.1 and are illustrated in Figs. 11 and 12 [33,35]. The distances
from the Hirshfeld surface to the nearest atoms outside and inside the surface are the quantities
de and di, respectively, and the normalized contact distance based on these, dnorm = (di-
15

rivdw)/rivdw+(de-revdw)/revdw, is symmetric in de and di, with divdw and devdw being the van der Waals
radii of the atoms. The mapping of dnorm on the Hirshfeld surface highlights the donor and
acceptor equally and it is a powerful tool for analyzing directional intermolecular interactions, as
it displays a surface where contacts shorter than the sum of their van der Waals radii have
negative values of dnorm and appear as conspicuous red spots; contacts longer than the van der
Waals distances have positive values of dnorm and are mapped in blue. Hirshfeld surface of
synthesized copper complexes bear a lot of similarities (due to similar structure of the complex
compounds) and will be therefore described together.
According to the Hirshfeld surface analysis, Fig. 13, for all four complexes, the intermolecular
Hal⋯H contacts, comprising 31.6 (Cl…H), 30.5 (Br…H), 31.4 (I…H) and 31.1% (for both
Cl…H and Br…H) of the total number of contacts for (Cl2L)2Cu, (Br2L)2Cu, (I2L)2Cu and
(BrClL)2Cu respectively, are major contributors to the crystal packing. The shortest H∙∙∙Hal
contacts are shown on the fingerprint plots as a pair of spikes at de + di ≈ 2.8 Å for (Cl2L)2Cu, ~
3.0 Å for (Br2L)2Cu, ~ 3.1 Å for (I2L)2Cu and ~ 3.1-3.2 Å for (BrClL)2Cu (Fig. 12).
According to the Hirshfeld surface analysis also intermolecular H…H contacts, comprising ~ 29
% of the total number of contacts, are one of major contributors to the crystal packing (Fig. 13).
As shown in Fig. 12, the shortest H…H contacts in the fingerprint plots of all complexes are at
de+ di = 2.3–2.5 Å. The H…H contacts are characterized by broader spikes in (Cl2L)2Cu and
(BrClL)2Cu and relatively sharper spikes in (Br2L)2Cu. Furthermore, a subtle feature, splitting
in the fingerprint plots of H…H, is evident in the fingerprint plot of (I2L)2Cu. This splitting
occurs when the shortest contact is between three atoms, rather than for a direct two-atom
contact.
16

The C…C contacts are shown on the fingerprint plots of all complexes as the characteristic pale
blue/green, mixed with yellow points, area on the diagonal at de = di ≈ 1.7–2.1 Å (Fig. 12), and
attributed to the formation of the above mentioned strong … stacking interactions (Table 4).
However, this … stacking interactions is less than 6% of the total Hirshfeld surface area of
complexes.
The fingerprint plots of all copper complexes features spike of various lengths and thickness, and
the most prominent being the presence of wing- like peripheral spikes for C…H contact at the
top left and bottom right of each plot (Fig. 12). The spike at the top left corresponds to the points
on the surface around the C–H donor, while those at the bottom right correspond to the surface
around the  acceptor [44]. As shown in Fig 3, the shortest C…H distance (de+ di) is ≈ 2.8–2.9
Å. The most important C–H… interaction in the packing of all copper complexes is related to
interaction of hydrogen of allyl group (RHC=CHH) with one carbon of benzene group of the
nearest neighbor molecule. Hirshfeld surface analysis show this short interaction as red spot
(Fig. 11). For the (BrClL)2Cu, we can see two red spots for this interaction. This splitting occurs
when the shortest contact is between three atoms, rather than for a direct two-atom contact. As
shown in Fig 11, the hydrogen of ally group (H10A) in complex (BrClL)2Cu have short
interaction with C1 and C6 of benzene group of the nearest neighbor molecule.
It is worth to mention that, the molecular surface of (Cl2L)2Cu and (BrClL)2Cu complexes is
also populated by Hal…N contact (2.1%) and C…O contacts (1.9 and 2.3% for (Cl2L)2Cu, and
(BrClL)2Cu, respectively). The contribution of C…O contacts for (Br2L)2Cu and (I2L)2Cu is
2.1 and 1.7%, respectively.
17

Close inspection of other intermolecular contacts in the structures of all copper complexes also
revealed a negligible proportion of Cu…C (0.2–0.3%), Cu…H (0.1–0.2%), Hal…O (0.7–1.4%),
C…N (0.3–0.4%), O…H (0.6–1.2%) and N…H (1.2–1.3%) (Fig. 13).
3.4. Theoretical calculations
As can be seen in Fig. S8, the four compounds are all engaged in a series of intermolecular
interactions that determine the whole molecular packing. Three of the four complexes are
isomorphic while the fourth: (Cl2L)2Cu, it crystallizes in the P-1 space group with a halved cell
volume with respect to others.
Compound (Cl2L)2Cu is the only compound that, thanks to Cl…Cl and H…Cl interactions, it
forms a series of 2D supramolecular aggregates that extend according to the (-424)
crystallographic plans as depicted in Fig. 14. The chlorine-chlorine interaction makes an angle
C-Cl ... Cl of 152.63 ° and a Cl…Cl distance of 3.5639 Å, just above the sum of van der Waals
radii (3.52 Å), although is not in the optimal geometry that provides an interaction between the
negative belt and the positive hole at 90°. However, is an interaction which brings a positive
contribution (0.42 kcal mol-1) to the overall reticular energy (See Fig. S9 and S10). The same
halogen-halogen interaction is present in the (I2L)2Cu and (Br2L)2Cu compounds. The geometry
of the interaction is almost the same as that observed with the chlorine compound, with the
interaction energy of 0.65 and 0.56 kcal mol-1 for (I2L)2Cu and (Br2L)2Cu, respectively. (Fig.
S10).
Also, all the complexes show metal-halogen interaction along with π-π stacking interaction that
leads to a head to tail coupling between two centrosymmetric compounds. The range of energy is
from 6.04 kcal mol-1 for (Br2L)2Cu, until 7.94 kcal mol-1 for (Cl2L)2Cu as reported in Fig. 15.
18

The Cu…X separations are all in a narrow range: 3.421Å ((Cl2L)2Cu); 3.467Å ((BrClL)2Cu);
3.463 Å ((Br2L)2Cu) and 3.486 Å for iodine compound (I2L)2Cu. All separations are slightly
above the sum of the van der Waals radii. The interaction can arise from a strong connection
between the halogen lone pair (HOMO’s) and the empty 4pz orbital of copper atoms, metal-
halogen interactions as depicted in Fig. 16 where the three involved MO from single monomers
are pictorially put together.
There is a HB-π interaction involving the terminal hydrogen atom of the ethylenic fragment and
the phenyl ring in all four complexes. This interaction involves the atom of H(10B) pointing
directly to the system π C1-C2 with distance of 2.898 and 3.112 Å for (Cl2L)2Cu and atom
H(10A) to the system π C1-C2 for (Br2L)2Cu with distance of 2.905 and 2.966 Å, for
(BrClL)2Cu with distance of 2.870 and 2.877 Å and for (I2L)2Cu with distance of 3.053 and
3.182 Å. These interactions, whose energy diagrams are depicted in Fig. 17, contributes
significantly to molecular packing with an energy that varies from a minimum of 2.05 kcal mol-1
in (Cl2L)2Cu to a maximum of 3.15 kcal mol-1 in the complex (I2L)2Cu. For the two remaining
compounds, it has the value of 2.61 and 2.62 kcal mol-1 for (Br2L)2Cu and (BrClL)2Cu,
respectively. Last attractive interaction is observed in the compounds (BrClL)2Cu and (I2L)2Cu
(Fig. 18), in it the halogen atoms I1 and Br1 point towards the π system of the phenyl ring. In the
solid state the two distances are just below the sum of the van der Waals radii (I…C3: 3.627 Å
(3.680 Å) and Br…C3: 3.567 Å (3.670 Å)). The computed energies show minimum energy of
0.66 and 0.55 kcal mol-1 for (BrClL)2Cu and (I2L)2Cu, respectively. The low energy for both
interactions depends on the non-perfect geometry of this kind of interaction (C-I…C3 153.73°
and C-Br…C3 158.35°).
19

Generally, minimum energy distance computed with SPE procedure don’t correspond to the
distance found at experimental observed position in the solid state. This is because in the solid
state the crystallographic minimum energy results from a suitable balance of all attractive and
repulsive interactions. While with the calculation we explore a single interaction, at most, as in
the case of metal halogen interaction and π- π staking are two interactions that determine the total
energy.
4. Conclusions
To summarize, we have presented the preparation, structural and computational analysis of four
new Cu(II) coordination compounds based on new halogenated Schiff base ligands derived from
halogenated salicylaldehydes (3,5-dichlorosalicylaldehyde, 3,5-dibromosalicylaldehyde, 3,5-
diiodosalicylaldehyde and 3-bromo-5-chlorosalicylaldehyde) and allyl amine. All complexes
show halogen-halogen of type I, -, CH- interactions and also metal−halogen secondary bonds
in crystal packing. The coordination geometry around the Cu(II) in all reported compounds is
best described as square planar plus two axially elongated interactions (Cu…X) named
metal−halogen secondary bonds. According to the Hirshfeld surface analysis, the intermolecular
Hal⋯H and H…H and C…H contacts, are major contributors in the crystal packing. Also, all of
the interactions in crystal packing have been analyzed by theoretical calculations.
Appendix A. Supplementary data
CCDC 1839638, 1839639, 1839640 and 1839641 contain the supplementary crystallographic
data for (BrCl2L)2Cu, (Br2L)2Cu, (I2L)2Cu and (Cl2L)2Cu, respectively. These data can be
20

obtained free of charge via http://www.ccdc.cam.ac.uk/conts/retrieving.html, or from the
Cambridge Crystallographic Data Centre, 12 Union Road, Cambridge CB2 1EZ, UK. Fax: +44
1223 336 033; or e-mail: deposit@ccdc.cam.ac.uk
Acknowledgements
The authors are grateful to the Research Council of the University of Isfahan for financial
support of this work and also university of Messina for determination of structures by SCXRD
instrument.
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24

Scheme 1 Schematic representations of three intermolecular halogen interactions, halogen
bonding, halogen-halogen interaction, halogen- interaction.
25

OH
X2
N
X1
CHO
H2O
r.t
OH
X2
H2N
+
X1
Cl2LH X1= X2= Cl
Br2LH X1= X2= Br
I2LH X1= X2= I
BrClLH X1= Br; X2= Cl
Scheme 2 Preparation of ligands
26

OH
X2
X1
CHO
+
H2N
a
b
c
X1
X2
O
N
N
Cu
O
X2
X1
Scheme 3 Synthetic routes for the preparation of the complexes: (a) stirring of allylamine and
haloganated salicylaldehydes (3,5-dichlorosalicylaldehyde, 3,5-dibromosalicylaldehyde, 3,5-
diiodosalicylaldehyde, 3-Bromo-5-chlorosalicylaldehyde) in MeOH at ambient temperature; (b)
adding of trimethylamine to solution and stirring for 10 minutes; (c) adding of CuCl2 and stirring
in ambient temperature and then reflux for 3 hours (X1=X2=Cl in (Cl2L)2Cu; X1=X2=Br in
(Br2L)2Cu; X1=X2=I in (I2L)2Cu and X1= Br, X2=Cl in (BrClL)2Cu).
27

doffset
offset angle
N
Cu
O
dplane-plane
dCg-Cg
O
Cu
N
Scheme 4. Schematic representation of geometrical parameters for definition of π–π stacking
28

Negative electrostatic potential


X
Positive electrostatic potential
Fig. 1 Regions of positive and negative electrostatic potential highlighting the anisotropy
associated with the electron density distribution around the covalently bonded X (halogen) atom.

R

n+
M
Fig. 2 Illustration of the type of anisotropic charge distribution found for polarizable halogen
atoms, which can lead to metal–halogen secondary bonding.
29