Theoretical rationalization of structure of transannular bonded germanium complexes containing amide functionality

Article abstract of DOI:10.14233/ajchem.2020.22294

Penta and tetra coordinated germanium complexes have been synthesized from N,N’-bis(2-pyridyl)pyridine-2,6-dicarboxamide (H2L) and N-(pyridine-2-yl)picolinamide (HL¹) with dialkyl/aryl and trialkyl/aryl germanium halides in 1:1 molar ratios. Th

Full text of DOI:10.14233/ajchem.2020.22294

Asian Journal of Chemistry; Vol. 32, No. 5 (2020), 995-1000
A
SIAN
J
OURNAL OF HEMISTRY
C
https://doi.org/10.14233/ajchem.2020.22294
Theoretical Rationalization of Structure of Transannular
Bonded Germanium Complexes Containing Amide Functionality
1,*,
2
RAJI THOMAS
and PUSHPA PARDASANI
1
2
School of Science and Humanities, Sreenidhi Institute of Science and Technology, Hyderabad-501301, India
Department of Chemistry, University of Rajasthan, Jaipur-302055, India
*
Corresponding author: E-mail: rajithomas28@gmail.com
Received: 25 June 2019; Accepted: 12 October 2019;
Published online: 29 April 2020;
AJC-19825
Penta and tetra coordinated germanium complexes have been synthesized from N,N’-bis(2-pyridyl)pyridine-2,6-dicarboxamide (H L)
2
1
and N-(pyridine-2-yl)picolinamide (HL ) with dialkyl/aryl and trialkyl/aryl germanium halides in 1:1 molar ratios. The molecular structures
and electronic properties of complexes were well analyzed by GAUSSIAN 03 suit of programs. The transannular bonding observed in
penta coordinated complexes have been well established by natural bond orbital, Wiberg bond index and molecular electrostatic potential
analysis.
Keywords: Germanium complexes, Amide ligand, NBO, MESP.
Structures of these ligands are promising one and H L is a
2
INTRODUCTION
multifunctional bridge with two picolinamide pendants.
Germanium complexes of these ligands showed extensive
transannular bonding due to the presence of pyridine moiety.
In order to gain a better insight into the factors responsible for
the existence of these forms of bonding, in this work we studied
these systems using the Gaussian 03 [15] suit of programs.
We calculated the energies of all molecular structures and well
studied the electronic properties of these newly synthesized
complexes by density functional theory (DFT) with mixed
valence basis set.
Amide functional group, ubiquitous in biochemistry, is
important ligand construction unit for coordination chemists.
In recent years, chemists have been interested in developing
ligand systems containing pyridine carboxamide functionality
[
1,2] due to their influence on novel geometric and electronic
properties imparted onto various metal centers [3]. They have
found use in catalysis [4,5], molecular receptors [6,7] and
dendrimer synthesis [8]. Nowadays a significant amount of
research has been devoted to the elucidation of transannular
intramolecular bonding in hetero-substituted ring system [9].
There is a report on the sulfur to germanium transannular bon-
ding in spirocyclic derivative [10]. Involved in organometallic
chemistry, we are interested in the structural and pharmaco-
logical activity of metallic complexes of group 14. These elements
have shown great chemical versatility, as a result of their ability
to increase their coordination spheres. Germanium is a trace
element found in several organic substances and its compounds
are known to have a broad range of biological activities.
In the context mentioned above and in continuation to
our work on metallic complexes of group 14 [11-14], U-shaped
EXPERIMENTAL
In this work, 2-aminopyridine, picolinic acid and 2,6-
pyridine dicarbonyldichloride are purchased from Sigma-
Aldrich and used as received. Other chemicals were commer-
cially available and used without further purification. Some
reagents in ligand preparation, such as thionyl chloride and
all solvents were dried to remove water [16]. All the reactions
were carried out in presence of nitrogen atmosphere. The melting
points are recorded on a Perfit apparatus and are uncorrected.
-1
The IR spectra from 4000-400 cm were recorded on Nicolet
Shimadzu Spectrometer in KBr pellets and CCl solution. The
, DMSO, 75.5
N,N’-bis(2-pyridyl)pyridine-2,6-dicarboxamide (H
N-(pyridine-2-yl)picolinamide (HL ) are prepared as ligands.
2
L) and
4
1
1
13
H (CDCl
3
, DMSO, 300 MHz) and C (CDCl
3
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996 Thomas et al.
Asian J. Chem.
MHz) NMR spectra of complexes have been recorded at room
temperature on a JEOL 300AL FTNMR spectrometer using
TMS as internal standard. Germanium was estimated as
germanium oxide using platinum crucible and nitrogen was
estimated as reported in the literature method [17].
Computational details: Molecular geometries of all the
Ge(IV) complexes under study have been carried out using
Gaussian 03 suit of programs. Optimizations were done by the
DFT method. The density functional B3LYP can produce accu-
rately and economically the heats of formation for compounds
containing transition metal [18,19]. This method is combined
with a mixed valence basis set of 631-g(d) for non-metallic
atoms and LanL2DZ for metallic atoms. For essentially all
levels, the minimum character of all optimized structures was
verified by evaluation of the harmonic vibrational frequencies.
The nature of bonding and hyperconjugative interactions were
well evaluated by NBO 3.0 version incorporated in Gaussian
was added. The colour of the solution changed from light green
to yellow. After 15 min stirring, triethylamine is added drop-
wise to the stirring mixture. Then white precipitate is formed
to begin and mixture was stirred for 6 h to ensure completion
of reaction. Filtered, dried and the precipitate was washed with
saturated solution of sodium bicarbonate, water and acetone.
Dried under vacuum and ligand obtained as white powder
(60 %).
1
N-(Pyridine-2-yl)picolinamide (HL ): Pyridine carbonyl
chloride prepared from picolinic acid (0.492, 4 mmol) disso-
lved in chloroform (15 mL) and cooled to 0 °C. To this 2-amino-
pyridine (0.364 g, 4 mmol) is added and stirred. The colour of
solution changes from green to blue.After 0.5 h stirring, solu-
tion refluxed for 5 h. Colour changes to dark blue. Following
a brief period of cooling filtered and the filterate washed thrice
with water. Chloroform layer evaporated under vacuum and
the product was purified by column chromatography on silica
gel with petroleum ether/ethyl acetate (8/1 v/v) as eluent to
afford the ligand as white crystals (75 %).
03 software.Atomic charges in all the structures were obtained
using the natural population analysis (NPA) method within
the natural bond orbital approach. The relative bond strengths
have been estimated using the Wiberg bond index analysis. At
the optimized geometries, MESP topological analyses are
carried out employing the DFT/6-31G(d) wave functions and
using the UNIPROP package.
Reaction of H
(1): Sodium hydride (0.025 g, 1.168 mmol) was washed with
hexane under dinitrogen and then added to a solution of H
2
L with diphenyl germanium dichloride
2
L
(0.186 g, 0.584 mmol) in DMF. Stirred and after colour changes
diphenyl germanium dichloride (0.1738 g, 0.584 mmol) in
DMF was added to the above solution. A precipitate of NaCl
is formed, stirred and dried under vacuum following washing
the product with hexane gives a light yellow product (Scheme-I).
All other germanium complexes are produced in the same
N,N’-Bis(2-pyridyl)pyridine-2,6-dicarboxamide (H
2
L):
To a solution of 2,6-pyridine dicarbonyldichloride (0.408 g,
2
2
mmol) in dichloromethane (10 mL) at 0 °C, a solution of
-aminopyridine (0.430 g, 4.53 mmol) in the same solvent
O
N
O
N
N
Et N, CH Cl
3
2
2
+
NH
HN
1
:2 mmol
ClOC
COCl
H2L
N
NH2
N
O
N
O
N
N
N
Ge
N
R
R
R= Ph (1), Et (2), Me (3).
O
N
N
O
N
SOCl , CHCl
NaH,R GeCl
2
3
3
N
+
HN
-HCl, 1:1mmol
DMF
N
COOH
R
N
NH2
N
Ge
HL1
R
R
R= Ph (4), Et (5), Me (6).
Scheme-I: Preparation of germanium complexes

Vol. 32, No. 5 (2020)
Theoretical Rationalization of Structure of Transannular Bonded Germanium Complexes 997
1
13
manner in 1:1 molar ratio with H
2
L and HL reacting with diffe-
(q, Ge-CH
2
CH
3
). C NMR (CDCl
3
, 75 MHz): δ 162.50 (1,
rent R
2
GeCl
2
and R GeCl, respectively.All complexes are soluble
3
C=O), 151.09 (2, C=N), 149.24-122.32 (4, C=C), 7.81 (3, Ge-
in organic solvents like benzene, hexane, chloroform, etc.
CH
2
CH
3
), 12.16 (3, Ge-CH
2
CH
3
). Anal. calcd. (found) (%)
for C17
H
23
N
3
OGe: C, 57.03 (59.02); H, 6.48 (6.33); N, 11.74
Spectral data
(
11.39); Ge, 20.28 (20.13).
Compound 6: Brown solid, yield ~ 55 %, m.p.: 154 °C, IR
N,N’-Bis(2-pyridyl)pyridine-2,6-dicarboxamide (H L):
White solid, yield ~ 60 %, m.p.: 215°C, IR (KBr, νmax, cm ):
2
–1
–1
1
(
KBr, νmax, cm ): 1695 (C=O), 528 (Ge-C). H NMR (CDCl ,
3
1
1
(
1
691 (C=O), 3354 (N-H). H NMR (CDCl
3
, 300 MHz): δ 10.55
s, NH), 8.63-7.31 (m, ArH). C NMR (CDCl , 75 MHz): δ
62.68 (2, C=O), 150.88 (3, C=N), 149.08-123.54 (6, C=C).
13
3
00 MHz): δ 8.58-7.20 (m, ArH), 0.31 (s, Ge-Me). C NMR
, 75 MHz): δ 162.50 (1, C=O), 151.07 (2, C=N), 149.23-
22.02 (4, C=C), 4.85 (3, Ge-Me). Anal. calcd. (found) (%) for
OGe: C, 53.23 (53.08); H, 5.42 (5.83); N, 13.30 (13.33);
Ge, 22.98 (22.13).
1
3
3
(CDCl
3
1
C
Anal. calcd. (found) (%) for C17
H
13
N
5
O
2
: C, 63.94 (63.11); H,
H
14 17
N
3
4
.10 (4.03); N, 21.93 (21.98).
1
N-(Pyridine-2-yl)picolinamide (HL ):White crystal, yield
–
1
~
(
(
1
(
(
75 %, m.p.: 102°C, IR (KBr, νmax, cm ): 1698 (C=O), 3350
RESULTS AND DISCUSSION
1
N-H). H NMR (CDCl
3
, 300 MHz): δ 10.59 (s, NH), 8.57-7.36
m, ArH). C NMR (CDCl , 75 MHz): δ 162.11 (1, C=O),
50.24 (2, C=N), 149.83-123.94 (4, C=C).Anal. calcd. (found)
O: C, 66.32 (66.21); H, 4.55 (4.73); N, 21.09
In the IR spectra of the ligands there is a peak in the range
13
3
-1
3
354-3350 cm which is assigned to ν(N-H) of amide ligand
which disappears on complex formation. Peak corresponding
%) for C11
9
H N
3
to ν(C=O) remains almost unchanged in all the complexes
20.98).
Compound 1: Yellow solid, yield ~ 42 %, m.p.: 232 °C, IR
1
13
which means there is no coordination from it. The H and C
NMR spectra of all the germanium complexes exhibited charac-
teristic signals and multiplicities for R-Ge and ligand protons.
–
1
1
(
3
KBr, νmax, cm ): 1688 (C=O), 524 (Ge-C). H NMR (CDCl ,
3
13
00 MHz): δ 8.61-7.32 (m,ArH). C NMR (CDCl
3
, 75 MHz):
1
In H NMR spectrum of ligand, deuterium exchangeable amide
δ 162.45 (2, C=O), 149.99 (3, C=N), 149.77-122.14 (12, C=C).
Anal. calcd. (found) (%) for C29 Ge: C, 64.01 (64.22);
H, 3.89 (3.73); N, 12.87 (12.58); Ge, 13.34 (13.11).
protons resonated in the region 10.58-10.59 ppm which dis-
appears on complex formation suggesting deprotonation
of amide protons and subsequent Ge-N formation. C NMR
H
21
N
5
O
2
13
Compound 2: Cream solid, yield ~ 68 %, m.p.: 225 °C, IR
spectrum gives characteristic signals for R-Ge resonances.
–
1
1
(
3
(
KBr, νmax, cm ): 1690 (C=O), 529 (Ge-C). H NMR (CDCl ,
3
Computational calculations
00 MHz): δ 8.56-7.12 (m, ArH), 0.61 (t, Ge-CH
2
CH
, 75 MHz): δ 162.35 (2,
C=O), 151.99 (3, C=N), 149.26-122.62 (6, C=C), 7.99 (2, Ge-
CH CH ), 12.73 (2, Ge-CH CH ). Anal. calcd. (found) (%)
Ge: C, 56.30 (56.12); H, 4.72 (4.23); N, 15.63
16.58); Ge, 16.21 (16.99).
Compound 3: White solid, yield ~ 53 %, m.p.: 195 °C, IR
3
), 0.93
13
q, Ge-CH
2
CH
3
). C NMR (CDCl
3
Structural studies: The structures of ligands and com-
plexes were well studied by different computational methods
using Gaussian 03 suite of programs. All the structures are
optimized by DFT-B3LYP method using mixed valence basis
set (6-31g(d) + LanL2DZ). The optimized parameters of the
complexes are listed in Table-1.
In the ligand (H
interaction between two pyridyl rings with a distance of 4.02
Å between the centeres and an angle of 22.5°. In Fig. 1, H
shows the attractive electrostatic interaction between the σ
framework and the π electron density in the ligand. This is
mainly due to the presence of nitrogen in the ring which has
an electron withdrawing effect that reduces the π electron
density and thus increases π–π interactions. In HL, anti-anti
conformation is the most stable one because in cis form there
is lone pair repulsion between N and O. In anti form there is
an intramolecular hydrogen bonding and this conformation
remains unchanged in complexes also.
2
3
2
3
for C21
H
21
N O
5 2
(
–
1
1
(
3
(
1
KBr, νmax, cm ): 1692 (C=O), 521 (Ge-C). H NMR (CDCl
3
,
2
L), there is a parallel displaced π-πstacking
13
00 MHz): δ 8.55-7.22 (m, ArH), 0.13 (s, Ge-Me). C NMR
, 75 MHz): δ 162.31 (2, C=O), 149.98 (3, C=N), 149.44-
23.62 (6, C=C), 4.32 (2, Ge-Me). Anal. calcd. (found) (%) for
Ge: C, 54.34 (54.22); H, 4.08 (4.12); N, 16.68
CDCl
3
2
L
C
19
H
17
N
5
O
2
(
16.34); Ge, 17.29 (17.99).
Compound 4: Off white solid, yield ~ 54 %, m.p.: 132 °C,
IR (KBr, νmax, cm ): 1697 (C=O), 528 (Ge-C). H NMR (CDCl ,
–1
1
3
13
3
00 MHz): δ 8.65-7.26 (m,ArH). C NMR (CDCl
δ 162.45 (1, C=O), 150.93 (2, C=N), 148.44-128.32 (13, C=C).
Anal. calcd. (found) (%) for C29 OGe: C, 69.37 (69.72);
3
, 75 MHz):
H
23
N
3
H, 4.62 (4.33); N, 8.37 (8.39); Ge, 14.23 (Ge, 14.46).
Compound 5: Cream solid, yield ~ 45 %, m.p.: 171 °C, IR
After complexation, a new H-bond interaction is observed
in complexes 1-3 between carbonyl oxygen and hydrogens
from two pyridyl rings. The pyridine-2,6-dicarboxamido unit
–1
1
(
3
KBr, νmax, cm ): 1697 (C=O), 523 (Ge-C). H NMR (CDCl ,
3
00 MHz): δ 8.60-7.01 (m, ArH), 0.67 (t, GeCH
2
CH ), 0.99
3
TABLE-1
OPTIMIZED PARAMETERS OF COMPLEXES 1-6
r
R
R
R
θ
θ
θ
1
Compound
1
2
3
E (Kcal/mol)
1
2
2
3
3
(
C=O)
(Ge-N )
2.070
2.141
2.044
3.760
3.290
3.580
(Ge-N )
2.010
2.046
2.046
1.930
1.960
1.960
(Ge-N )
2.070
2.140
2.044
4.040
3.860
4.010
(N ,Ge,N )
77.18
(N ,Ge,N )
77.18
(N ,Ge,N )
146.90
151.06
153.58
102.38
103.53
102.84
1
2
3
4
5
6
1.227
1.235
1.224
1.229
1.231
1.231
-3617.353
-3312.540
-3233.883
-2993.274
-2976.537
-2858.597
75.58
76.50
69.44
65.25
75.59
76.51
46.69
52.81
63.93
53.80

998 Thomas et al.
Asian J. Chem.
lization, the electron density on nitrogen increases and the
positive charge on carbon decrease on complex formation. The
MESP plot and NPA charges of respective atoms are shown in
Fig. 3.
2
.49Å
2
.63Å
2.24Å
In addition there is an increase in the carbonyl carbon to
oxygen bonds of ~ 0.002 Å and a decrease in the carbonyl
carbon to nitrogen bond length of ~ 0.023 Å indicate binding
of amide functionality to metal ions through nitrogen atom
[20]. In complexes 1-3, Ge-NPy (central) and Ge-NPy (sides)
bond distances are in the order 2.01-2.04 Å and ~ 4.01 Å,
respectively. In complexes 4-6, two Ge-NPy distances are in
the order 3.29-4.04 Å. This indicates, in the case of complexes
1-3, the coordination is from the central NPy out of three pyri-
dine rings and from the amide nitrogens, whereas in the case of
4-6, only amide nitrogen is involved in bonding to germanium.
The participation and non-participation of lone pair of
nitrogen from pyridine ring in complexes 1-3 and 4-6, respec-
tively have been confirmed from Wiberg bond index analysis
and the important bond indexes for complexes 3 and 6 are
2
.16
2.37
1
2
Fig. 1. Optimized structure of ligands H L and HL
is a strong chelator. This is reflected in the short Ge-Npy and
Ge-Namido bond distances 2.04-2.01 Å and 2.14-2.04 Å, respec-
tively and this remains almost same in all the germanium
complexes. In these complexes, the two carboxamido nitrogens
are trans to each other with equal Ge-N bond lengths and have
a mirror plane along. Due to the close bite of the pyridine-2-
carboxamido units, both five membered rings force the Namido
-
Ge-Npy angles very close to 76° (Table-1). Thus there forms
transannular interaction from the pyridyl nitrogens with a bond
distances 2.04-2.14 in these complexes. The intramolecular
shown in Fig. 4. The C=O bond index in H L is 1.6861 which is
2
slightly lowered after complexation and C-N bond index is
1.1253 which is slightly increased in complex. From the figure
it is clear that in diamide complex, the coordination is only
from central pyridine ring and in the case of monoamide complex,
there is no coordination from pyridine ring nitrogens.
From NBO analysis it is observed that the significant donor
acceptor interactions are occurred between germanium and
two amide nitrogens (103.07-92.50 kcal/mol) and germanium
1
hydrogen bonding observed in HL as shown in Fig. 1 have
no significant differences after complexes formation (4-6). The
optimized structures of complexes are shown in Fig. 2.
In the MESP plot of ligand, the electron density is concen-
trated on the oxygen atom, whereas in complexes this is spread
around O-C-N region due to hyperconjugation. By this deloca-
1
2
3
4
5
Fig. 2. Optimized structure of germanium complexes 1-6
6

Vol. 32, No. 5 (2020)
Theoretical Rationalization of Structure of Transannular Bonded Germanium Complexes 999
O: -0.594; C: 0.688; N: -0.642
O: -0.600; C: 0.654; N: -0.759
L and complex 3
Fig. 3. MESP plot and NPA charges of respective atoms for H
2
CONFLICT OF INTEREST
The authors declare that there is no conflict of interests
regarding the publication of this article.
O
2
O
N
1
O
1
.2227
N1
1.2227
N
0.4293
N 3
0
.0480
N 2
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LP* Ge
LP* Ge
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LP N2
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103.07
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LP N1
LP N3
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LP* Ge
LP* Ge
LP* Ge
LP* Ge
1
1
LP N2
LP N2
116.43
82.67
3.98
LP N
1
LP N3
1.58

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