Synthesis, structural, spectral characterization, DFT analysis and antimicrobial studies of aquabis(L-ornithine)copper(II) picrate

Article abstract of DOI:10.1016/j.molstruc.2014.06.061

The present work consists of synthesis, spectroscopic, DFT studies and crystal structure investigation of complex [Cu(L-orn)₂(H ₂O)](PIC)₂ (where L-orn = L-ornithine, PIC = picrate anion). The molecular structure of comple

Full text of DOI:10.1016/j.molstruc.2014.06.061

Journal of Molecular Structure 1075 (2014) 43–48
Contents lists available at ScienceDirect
Journal of Molecular Structure
journal homepage: www.elsevier.com/locate/molstruc
Synthesis, structural, spectral characterization, DFT analysis and
antimicrobial studies of aquabis(L-ornithine)copper(II) picrate
a,
a
b
b
Rakesh Kumar a, , Sangeeta Obrai , Aparna Sharma , Amanpreet Kaur Jassal , Maninder Singh Hundal ,
⇑
⇑
Joyee Mitra c
a Department of Chemistry, Dr. BR Ambedkar National Institute of Technology, Jalandhar 144011, Punjab, India
b Department of Chemistry, Guru Nanak Dev University, Amritsar, Punjab 143005, India
c Department of Chemistry, University of Illinois at Urbana-Champaign, Matthews Ave., Urbana, IL 61801, United States
g r a p h i c a l a b s t r a c t
h i g h l i g h t s
ꢀ
ꢀ
ꢀ
ꢀ
Preparation and characterization of
aquabis(
picrate.
L-ornithine)copper(II)
Crystal data showed a distorted
square-pyramidal geometry for
studied complex.
Complex exhibits antimicrobial
activities against Gram-positive and
Gram-negative bacteria.
DFT/B3LYP level is capable to provide
satisfactory results for predicting
optimized geometry and vibrational
data.
a r t i c l e i n f o
a b s t r a c t
Article history:
Received 8 May 2014
Received in revised form 19 June 2014
Accepted 20 June 2014
Available online 27 June 2014
The present work consists of synthesis, spectroscopic, DFT studies and crystal structure investigation of
complex [Cu(
of complex was determined by X-ray crystallography and refined by three-dimensional least squares
techniques. Copper atom is five coordinate and two molecules of -ornithine are coordinating with it
L-orn)2(H2O)](PIC)2 (where L-orn = L-ornithine, PIC = picrate anion). The molecular structure
L
through their carboxylate oxygens and amine nitrogens whereas the fifth site is occupied by water mol-
ecule. Both of the picrate anions are present outside the coordination sphere of metal ion resulting in for-
mation of charge-separated type complex. EPR spectrum suggests about the distorted square-pyramidal
geometry of the complex and is confirmed by X-ray crystallography. The optimized structure of the pres-
ent complex has been studied using the DFT/B3LYP/6-31G*(d,p)/LANL2DZ level of theory. The vibrational
assignments and HOMO–LUMO were theoretically examined by means of the hybrid DFT method. Also
the antimicrobial properties of the title complex have been explored in the present work.
Ó 2014 Elsevier B.V. All rights reserved.
Keywords:
Crystal structure
L
-ornithine
Charge-separated
DFT study
Antimicrobial activity
Introduction
of copper is essential and beneficial whereas its excess causes tox-
icity and may produce lethal effects in all living organisms. For the
Copper is a constituent of many enzymes that act as catalysts
for a number of biochemical reactions. Presence of a small amount
last few decades, complexes of Cu(II) with amino acids have
attracted a lot of attention. There are several evidences available
of their involvement in various physiological processes. Copper-
histidine complex is useful in the treatment of Menkes disease
⇑
Corresponding authors. Tel.: +91 9888 982369.
E-mail addresses: rakesh_nitj@yahoo.co.in (R. Kumar), obrais@nitj.ac.in (S. Obrai).
[1]. The complexes of Cu(II) with L-proline, L-leucine/isoleucine
http://dx.doi.org/10.1016/j.molstruc.2014.06.061
0022-2860/Ó 2014 Elsevier B.V. All rights reserved.

44
R. Kumar et al. / Journal of Molecular Structure 1075 (2014) 43–48
and
L
-ornithine in the presence of heterocyclic bases have shown
radiation (k = 0.7107 Å) source. The crystal structure was calcu-
lated by the direct method using the program SIR-97 [10] and
refinement was performed using full-matrix least-squares meth-
ods SHELXL-97 programme. Absorption corrections were carried
out using the multi-scan program [11]. The hydrogen atoms of
DNA binding and oxidative cleavage activity. These also have the
potential for cellular applications in chemotherapeutic agents. Effi-
cient chemical nuclease activity was shown by copper(II) com-
plexes of L-lysine [2]. Transition metal complexes of amino acids
have a significant role in cancer chemotherapy. Mixed ligand com-
plexes involving asparagine in combination with various metal
ions have been suggested as possible antimetabolites in tumor
cells [3]. Complexes of transition metals with amino acids in pro-
teins and peptides are utilized in numerous biological processes
like electron transfer, oxidation and as oxygen conveyers. In these
processes, the enzymatic active site, which is very specific, forms
complexes with divalent metal ions [4].
methylene group, terminal and
the difference
a-amino groups were located from
Fourier map and refined isotropically. Molecular drawing of the
complex was obtained with the help of ORTEP [12] and MERCURY
programme [13]. H-bonding was calculated by using PARST [14].
The crystallographic data for the complex is summarized in
Table 1.
L
-ornithine is one of the four important amino acids having
Synthesis
basic side chains, although it is not a constituent of proteins. -orni-
L
thine is effective for stimulating, production and release of growth
harmones and reducing hypertension [5]. Its function in the living
systems is very important because of its role in Krebs cycle in
the metabolism of mammals [6]. In the rapidly growing tumors,
there is decarboxylase activity, and it can be reduced by chelating
the carboxylate group of ornithine [5]. Potential medical uses of
ornithine are, its antifatigue effect, cirrhosis and as weight lifting
supplement [7].
Earlier X-ray diffraction technique was used to determine the
structure of the cupric complex of ornithine with two chloride ions
as counter anions. In this complex both the counter anions and sol-
vent molecules are present outside the coordination sphere of
metal ion and adopt square planar geometry [8]. In the previously
Copper(II) picrate was prepared by the reaction of copper car-
bonate with picric acid (1:2) in aqueous medium. The solution
was stirred for 1 h at 40 °C on a magnetic stirrer. Green color crys-
tals of copper(II) picrate were obtained on concentrating the reac-
tion mixture. The present complex [Cu(L-orn)2(H2O)](PIC)2 was
synthesized by dissolving Cu(II) picrate and ornithine (1:2) in an
aqueous solution. The mixture was stirred for 1 h at 50 °C and then
left to cool down at room temperature. Change in color of the solu-
tion confirms the completion of reaction. Slow evaporation of the
solution yielded dark green color crystals after 72 h. The melting
point of the crystals was found to be 165 °C. Yield: 80%. IR (KBr)
cmꢁ1: 3421 (
2957 ( (CAH) br), 1632 (
mas (NO2), s), 1335 (ms (NO2), vs). Elemental Analysis: Anal. Calc.
m
(OH) br), 3238 (ms (NH2, vs)), 3145 (mas (NH+3, s),
m
m
(C@O), vs), 1370 ( (CAO), m) 1563
m
reported work, [Cu(L-ornithine(phen)(Cl)]Cl.2H2O complex, the
(
square-pyramidal geometry was acquired by the metal atom with
coordination number 5 in the presence of chloride as counter anion.
In this complex, Cu(II) coordinates with two nitrogen atoms of 1,10-
phenanthroline, one nitrogen atom of an amino group, one carbox-
for C22H30CuN8O19: C, 32.94%; H, 3.54%; N, 17.51%. Found: C,
33.00%; H, 3.48%; N, 17.49%.
Theoretical calculations
ylate oxygen atom of L-ornithine in the equatorial positions and
Clꢁ at the elongated apical position. Two water molecules present
outside the coordination sphere [2c]. Here, we have presented the
In the present investigation, geometry optimization of the title
complex was carried out using the B3LYP/6-31G*(d,p)/LANL2DZ
level of theory. 6-31G (d,p) is a popular polarized basis set which
crystal and molecular structure of cupric complex of L-ornithine
in the presence of picrate as counter anions. The structure is solved
to elucidate the influence of counter anions and solvent on the
bonding and the geometry of the metal ions. The presence of
electron-withdrawing group of the picrate ion makes it good pi-
acceptor for cations as well as neutral carrier donor molecules [9].
Table 1
Crystallographic data for complex [Cu(L-orn)2(H2O)](PIC)2.
Compound
[Cu(L-orn)2(H2O)](PIC)2
Empirical formula
Formula weight
Crystal system
Crystal size
Color
Shape
C22 H30Cu N10 O19
802.11
Orthorhombic
0.13 ꢂ 0.11 ꢂ 0.09
Green
Experimental
Material and instrumentation
Rectangular
P 21 21 21
Space group
Unit cell dimensions (Å), (°)
All chemicals, solvents used in this study were of high purity.
a = 7.816 (4)
a = 90.000
L-ornithine was supplied by Loba Chemie and used without purifi-
b = 14.506 (8) b = 90.000
cation. Picric acid was used after recrystallization. The IR absorption
spectrum of the complex was recorded in the range of 450–
4000 cmꢁ1 by means of a Perkin Elemer FTIR RX I spectrometer with
KBr pellets (Sigma Aldrich). The elemental analyses was performed
on Flash 2000 Organic Elemental Analyzer. EPR measurement was
c = 27.880(14)
3161(3), 4
1.686
0.793
1652.0
1.46–32.38
ꢁ11 6 h 6 8
ꢁ21 6 k 6 21
ꢁ41 6 l 6 39
27153
c = 90.000
Volume (Å3), Z
qcalc (g cmꢁ3
)
l
(cmꢁ1
F (000)
)
Range of data collection
Limiting frequency
carried out at room temperature using
a Bruker EMX EPR
spectrometer. For antimicrobial activity, pathogenic bacteria Serra-
tia marcescens (MTCC-97), Sphingobium japonicum (MTCC-6362),
Stenotrophomonas maltophilia (MTCC- 2446) and Staphylococcus
aureus (MTCC-3160) were procured from Microbial Type Culture
Collection (MTCC), Institute of Microbial Technology, Chandigarh.
Total reflections
Independent reflections
Completeness to theta = 25.00
Refinement method
11286 [R(int) = 0.0280]
99.8%
Full matrix least squares on F2
11286/12/505
Data/restraints/parameters
Goodness of fit on F2
Final R indices [I > 2 (I)]
R indices (all data)
1.033
R1 = 0.0533, wR2 = 0.1439
R1 = 0.0668, wR2 = 0.1529
1.029 and ꢁ0.825
CCDC 894386
X-ray diffraction
Largest diff. peak & hole (e Å3)
Deposition number
X-ray diffraction data was collected with ‘‘Bruker APEX-II CCD’’
area detector diffractometer with graphite monochromated Mo K
a

R. Kumar et al. / Journal of Molecular Structure 1075 (2014) 43–48
45
Fig. 1. (a) ORTEP diagram of the complex with atom labeling scheme. Picrate anions and hydrogen atoms have been removed for clarity, (b) distorted square-pyramidal view
of the complex and (c) optimized structure of the complex using the B3LYP/6-31G*/LANL2DZ level of theory.
Table 2
Selected geometric parameters from X-ray and DFT-B3LYP calculations for
[Cu(L-orn)2(H2O)](PIC)2.
Bond distances (Å)
Experimental
Theoretical
Deviation
CuAN1
CuAN3
CuAO1
CuAO3
CuAO1 W
2.002 (2)
2.000 (2)
1.951 (19)
1.955 (18)
2.280 (2)
2.093
2.064
1.975
1.980
2.307
ꢁ0.091
ꢁ0.064
ꢁ0.024
ꢁ0.025
ꢁ0.027
Bond angles (°)
N1ACuAN3
N1ACuAO1
N1ACuAO3
N3ACuAO1
N3ACuAO3
N1ACuAO1W
100.26 (9)
83.66 (8)
158.64(9)
169.97 (9)
83.63 (8)
100.68
79.59
169.59
179.41
81.16
ꢁ0.42
4.07
ꢁ10.95
ꢁ9.44
2.47
103.26 (10)
107.99
ꢁ4.73
adds p functions to hydrogen atoms in addition to the d functions
on heavy atoms, while LANL2DZ is a basis set for post-third row
atoms. The comparison of data obtained from theoretically opti-
mized structure and crystallographic determined structure was
carried out. All the DFT calculations were performed by using
Gaussian 03 program on a personal computer and Gauss View
was used for visualization of the structure, simulated vibrational
spectra and molecular orbitals [15–18]. HOMO and LUMO analysis
have been used to elucidate the information regarding the charge
transfer within the molecule. These calculations are valuable for
providing insight into the vibrational spectrum and molecular
parameters like bond distances and bond angles.
Fig. 2. Molecular structure of the complex with hydrogen bonding interactions.
Antimicrobial activity
The antimicrobial activities of picric acid (PIC), copper(II) pic-
rate and the present complex [Cu(
L-orn)2(H2O)](PIC)2 were tested
against pathogenic Gram ꢁve (S. marcescens, S. japonicum, S.

46
R. Kumar et al. / Journal of Molecular Structure 1075 (2014) 43–48
Table 3
maltophilia) and Gram +ve (S. aureus) bacterial strains using the
broth microdilution method. The procedure to carry out the mini-
mum inhibitory concentration of the metal complexes was
described earlier in the copper(II) and silver(I)picrate complexes
[19]. The antimicrobial activities of metal complexes were evalu-
ated as minimum inhibitory concentration where no viability of
bacteria was observed after incubation of 48 h.
Selected hydrogen bonding interactions in [Cu(L-orn)2(H2O)](PIC)2 complex.
Hydrogen bonding geometry
D–H. . .A
d(D–H)
d(H–A)
d(D–A)
\(DHA)
N1AH1B. . .O11E
N2AH2C. . .O1B
N2AH2B. . .O5C
N3AH13A. . .O18F
N4AH14A. . .O4G
N4AH14B. . .O12
N4AH14B. . .O13
O1WAH1W. . .O2B
O1WAH2W. . .O11C
O1WAH2W . . .O15D
0.87
0.87
0.89
0.82
0.84
0.86
0.86
0.83
0.83
0.83
2.630
2.091
1.960
2.513
2.023
1.987
2.542
2.020
2.760
2.368
3.015 (4)
2.940(3)
2.790(4)
2.513 (4)
2.862(3)
2.766(6)
3.139(8)0
2.839 (4)
3.261 (4)
2.890 (4)
107.96
163.60
153.52
121.33
178.40
149.92
127.23
166.29
120.56
121.54
Results and discussion
Description of the crystal structure
The crystal structure of the complex [Cu(L-orn)2(H2O)](PIC)2
was determined by a single crystal X-ray diffraction method. The
molecular structure of the copper complex is shown in Fig. 1a. It
crystallized in the orthorhombic P21 21 21 space group and is sim-
ilar in many ways of other Cu(II) complexes of amino acids whose
crystal structure have already determined [2]. The geometry
around Cu(II) can be best described as distorted square-pyramidal
Table 4
Selected experimental and theoretical IR frequencies of [Cu(L-orn)2(H2O)](PIC)2
complex.
Assignment
Experimental
Theoretical
ms (NH2), mas (NH+3)
3238 vs 3145 s
1632 vs
1370 m
3421 br
2957 br
3422, 3434
1626
1369
3533
2966
based on structural parameter (
cules. The axial position around the metal ion is occupied by water
molecule whereas basal positions are occupied by an -amino
s = 0.18) for five-coordinate mole-
m
m
m
m
(C@O)
(CAO)
(OH)
a
nitrogen and a carboxyl oxygen of each of the two symmetrically
related bidentate ornithine ligand. The metal-axial ligand (water)
bond length is larger than metal-basal (ornithine) distance
(Table 2). Both of the picrate anions remain outside the coordina-
tion sphere of the metal ion and are interacting with carboxylate
(CAH)
mas (NO2)
ms (NO2)
1563 s
1335 vs
1557
1338
br = Broad, m = medium; s = strong; vs = very strong.
oxygens, nitrogen atoms of terminal and
a-amino group through
hydrogen bonding interactions. The selected bond lengths and
angles are summarized in Table 2.
The terminal as well as
a-amino group, carboxylate oxygens
and water molecules are involved in extensive hydrogen bonding
interactions in 3-dimensional network. Amino groups are donating
hydrogen bonds to one of the carboxylate oxygens, phenolic oxy-
gens and oxygen of the o-nitro group of picrate anion in an inter-
molecular way. Intramolecular hydrogen bonding interactions
have also been observed between terminal amino group and phe-
nolic oxygen. Water molecules are donors of hydrogen bonds to
carboxylate oxygen and oxygen of the p-nitro group of picrate
anion of neighbouring units (Fig. 2, Table 3).
Theoretical calculations
The ground-state structure of the studied complex has been
carefully optimized using the B3LYP/6-31G*/LANL2DZ level of the-
ory as shown in Fig. 1c. The copper atom is five coordinate with
distorted square-pyramidal geometry. The optimized structural
data is in well consistence with the X-ray crystal structure data.
As shown in Table 2, the bond lengths and bond angles calculated
by the DFT studies are in good agreement with that obtained from
crystal structure data. The maximum deviation of bond length
0.091 (Å) for CuAN1 and of bond angle is 10.95° for N1ACuAO3.
The characteristic vibrational bands of complex are presented in
Table 4. The vibrational bands at 3238 cmꢁ1 and 3053 cmꢁ1 belong
Fig. 3. Atomic orbital compositions of the frontier molecular orbital for complex.
correspond to the asymmetric and symmetric stretching of the NO2
group of picrate anions (Fig. S1), respectively while theoretically
to
m
s(NH2) and (
m
as(NH+3) and the corresponding signals appear at
calculated vibration bands appear at 1557 cmꢁ1 and 1338 cmꢁ1
.
3422 cmꢁ1 and 3434 cmꢁ1 in the theoretical IR spectrum. The
The total energy, energy gap and dipole moment have an influ-
ence on the stability of molecule. The frontier orbitals HOMO and
LUMO are very important parameters for chemical reaction and
take part in chemical stability [21]. The transitions can be
described from HOMO to LUMO which determine the way in which
one molecule interacts with other species. It also determines the
molecular electron transport properties because it is a measure
of electron conductivity also. In the present complex, the highest
occupied molecular orbital (HOMO) is localized over the terminal
amino group whereas LUMO is most distributed over the metal
appearance of signals at 1632 cmꢁ1 and 1370 cmꢁ1 correspond to
the coordinating (
m (C@O) with Cu(II) ion) and non-coordinating
part of ( (CAO)) stretching bands. The latter is hydrogen bonded
m
either with the water molecule or the neighbouring molecule.
The assignments of the vibrational bands at 3421 cmꢁ1 belonging
to the
m (OH) stretching vibrations while theoretical calculation
shows the corresponding bands at 3533 cmꢁ1 that suggest the
presence of water molecule in the complex [20]. The strong bands
in the frequency range 1563 cmꢁ1 and 1335 cmꢁ1 for the complex

R. Kumar et al. / Journal of Molecular Structure 1075 (2014) 43–48
47
Fig. 4. (a) EPR spectrum of copper complex and (b) a probable splitting pattern for the d orbitals in a square-pyramidal complex.
a panel of pathogenic bacterial strains using the microbroth dilu-
tion method. Compounds with -amino acids like -ornithine con-
a
L
taining terminal amine moiety easily penetrate through cell walls
due to their ionic character [5]. The antimicrobial screening data
indicate that the metal salt, free acid as well as the complex are
displaying fairly good antimicrobial activity against all the four
mentioned bacteria. The complex is most effective antimicrobial
agent against S. marcescens and S. japonicum bacterial strains
(Fig. 5). MIC values (
lg/ml) for the metal salt and its complex with
L-ornithine were summarized in Table 5. The amino acid complex
was active against bacteria under very low concentration, and min-
imizing the possible toxic effects.
Conclusion
Fig. 5. Antimicrobial activity of the picric acid, metal salt and complex with
minimum inhibitory concentration (MIC) in ( g/ml).
l
The copper amino acid complex [Cu(L-orn)2(H2O)](PIC)2 was
prepared and structurally characterized as charge-separated com-
plex. The coordination number of metal ion is five, having distorted
square - pyramidal geometry. An EPR study suggests that the
center (Fig. 3). Lower HOMO–LUMO energy gap confirms the
charge transfer takes place within the complex.
unpaired electron is present in dx2
orbital indicating distorted
ꢁy2
EPR spectral study
square-pyramidal geometry of the complex. Comparison between
the experimental and theoretical results indicates that density
functional B3LYP/6-31G*/LanL2DZ method is able to provide satis-
factory results for predicting structural parameters and vibrational
wavenumbers. HOMO–LUMO energy gap suggests the charge-
transfer interactions taking place within the complex. The antimi-
crobial results show that complex has good inhibitory effect
without causing any toxicity against all four bacterial strains but
it is most effective antimicrobial agent against S. marcescens than
metal salt and free picric acid.
The EPR spectrum of the copper complex was recorded at room
temperature on X-band frequency of 9.86 GHz under the magnetic
field strength varying from 2400 to 4400 G. Intense absorption sig-
nal appeared in the high field at 3400 G (Fig 4a). As is apparent in
the spectrum of copper complex, gII (2.23) > g\(2.07) indicating
that the unpaired electron is in dx2
orbital (Fig. 4b) of square
ꢁy2
pyramidal complexes [22]. The anisotropy in g indicates the pres-
ence of a fairly large component of low symmetry in the ligand
field.
Acknowledgements
Antimicrobial activity
Authors are highly thankful to Ministry of Human Resource and
Development (MHRD), New Delhi for providing research assistant-
ship to Mr. Rakesh Kumar, one of the authors and Dr. BR Ambedkar
The antimicrobial activity of picric acid, copper(II) picrate and
synthesized complex [Cu(L-orn)2(H2O)](PIC)2 was screened against
Table 5
Minimum inhibitory concentrations for the picric acid, metal salt and complex on bacterial strains by microbroth dilution method (
lg/ml).
Complexes
Serratia marcescens
Sphingobium japonicum
Stenotrophomonas maltophilia
Staphylococcus aureus
PIC
25
25
25
12.5
50
12.5
6.2
12.5
1.5
Cu (PIC)
Complex
Ciprofloxacin
12.5
6.2
3.2
6.2
6.2
3.2
6.2

48
R. Kumar et al. / Journal of Molecular Structure 1075 (2014) 43–48
(e) G.M. Fogelholm, H.K. Näveri, K.T. Kiilavuori, M.H. Härkönen, Int. J. Sport
Nutr. 3 (1993) 290–297.
National Institute of Technology, Jalandhar for providing research
infrastructure. Rakesh Kumar is also thankful to Dr. A.K. Jana and
Hermanpreet Meehnian for their help during the course of this
present work.
[8] By S. Guha, N.N. Saha, Acta Cryst. B26 (1970) 2073–2079.
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Appendix A. Supplementary material
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