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Journal of Molecular Structure 1035 (2013) 38–45

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Journal of Molecular Structure


journal homepage: www.elsevier.com/locate/molstruc

Synthesis, spectroscopic characterization and structural investigations of a new


charge transfer complex of 2,6-diaminopyridine with 3,5-dinitrobenzoic acid:
DNA binding and antimicrobial studies
Ishaat M. Khan a,⇑, Afaq Ahmad a, Sarvendra Kumar b
a
Department of Chemistry, Faculty of Science, Aligarh Muslim University, Aligarh 202 002, India
b
DQIAQF/INQUIMAE, Universidad de Buenos Aires, Ciudad Universitaria, Pab. II, p. 3 EHA1428 Buenos Aires, Argentina

h i g h l i g h t s

" A new H-bonded CT complex is prepared and characterized.


" Bonding modes and structural features are ascertained from various spectral techniques.
" Single-crystal X-ray studies confirmed the H-bonded network.
" DNA-binding studies of CT complex are performed.
" CT complex is also examined for antimicrobial activities.

a r t i c l e i n f o a b s t r a c t

Article history: A new charge transfer (CT) complex [(DAPH)+(DNB)] consisting of 2,6-diaminopyridine (DAP) as donor
Received 16 July 2012 and 3,5-dinitrobenzoic acid (DNB-H) as acceptor, was synthesized and characterized by FTIR, 1H and 13C
Received in revised form 1 September 2012 NMR, ESI mass spectroscopic and X-ray crystallographic techniques. The hydrogen bonding (N+–H  O)
Accepted 4 September 2012
plays an important role to consolidate the cation and anion together. CT complex shows a considerable
Available online 17 September 2012
interaction with Calf thymus DNA. The CT complex was also tested for its antibacterial activity against
two Gram-positive bacteria Staphylococcus aureus and Bacillus subtilis and two Gram-negative bacteria
Keywords:
Escherichia coli and Pseudomonas aeruginosa strains by using Tetracycline as standard, and antifungal
2,6-Diaminopyridine
3,5-Dinitrobenzoic acid
property against Aspergillus niger, Candida albicans, and Penicillium sp. by using Nystatin as standard.
Charge transfer The results were compared with standard drugs and significant conclusions were obtained. A polymeric
1
H NMR net work through H-bonding interactions between neighboring moieties was observed. This has been
13
C NMR attributed to the formation of 1:1 type CT complex.
DNA-binding Ó 2012 Elsevier B.V. All rights reserved.

1. Introduction estimations of drugs [20–22]. The protonation of the donor from


acceptors are generally root for the formation of ion pair adducts
The properties of charge-transfer (CT) complexes formed in the [23–25].
reaction of electron acceptors with donors containing nitrogen, The chemical and physical properties of CT complexes formed in
sulfur, oxygen atoms, as well as amines polysulfur and crown the reactions of p- and r-electron acceptors with different donors
ethers bases have attracted considerable attention and growing like amines, polysulfur, crown ethers bases and oxygen–nitrogen
importance in recent years [1–13]. This is owing to the important mixed bases have been the subjects of many investigations both
role of charge transfer which is played in biological systems as well in solution and in solid state [26–31]. Some researchers have
as to the significant physical properties of the CT-products such as [32–35] studied the CT interactions between the drugs and various
electrical conductivities and their applications in many forms of acceptors to throw light of the role of weak interactions in under-
electronic and solar cells and in the analysis of some drugs and standing drug–receptor mechanism. Moreover, DNA is one of the
pharmaceutical preparations [14–19]. The important role is also most important aspects in biological investigations aimed at dis-
played by the charge transfer complexes in the quantitative covering and developing new type of antiproliferative agents [36]
because DNA is one of the main molecular targets in the design of
⇑ Corresponding author. Tel.: +91 5712703515 (O), mobile: +91 9412174753. anticancer compounds [37]. In vitro DNA interaction is usually
E-mail addresses: drishaatamu@gmail.com (I.M. Khan), drafaqahmad7@gmail.
accompanied by marked fluorescence emission changes due to
com (A. Ahmad). excitation of charge transfer transitions [38] which have been

0022-2860/$ - see front matter Ó 2012 Elsevier B.V. All rights reserved.
http://dx.doi.org/10.1016/j.molstruc.2012.09.016
I.M. Khan et al. / Journal of Molecular Structure 1035 (2013) 38–45 39

researched by fluorescence spectroscopy. Also, literature shows mounted on a glass capillary and data were collected using graph-
[16,21,39] that the CT complexes exhibit potential antimicrobial ite-monochromated Mo Ka radiation (k = 0.71073 Å) on Bruker
properties against Gram-positive as well as Gram-negative bacteria SMART APEX CCD diffractometer at 293 K. The data integration
and fungi. and reduction were processed with SAINT [44] software. An empir-
Researchers have worked on the interaction of 3,5-dinitroben- ical absorption correction was applied to the collected reflections
zoic acid with N-Methylaniline, 2,6-dimethylpyridine, norfloxacin with SADABS using XPREP [44]. All the structures were solved by
(nor) or ciprofloxacin (cip), 8-aminoquinoline [40,7,41]. Proton the direct method using SIR-97 [45] and were refined on F2 by
transfer complex of 2,6-diaminopyridine with series of nitro- the full-matrix least-squares technique using the SHELXL-97 [45]
substituted aromatic carboxylic acids and 2,4,6-trinitrobenzoic program package. A summary of crystallographic data collection
acid were also reported and studies their crystal structures and refinement parameters are given in Table 1.
[42,43]. The charge-transfer reactions of 2,6-diaminopyridine
(DAP) with 3,5-dinitrobenzoic acid (DNB) have not yet been re-
ported in literature to the best of our knowledge. In this paper, a
2.5. Pharmacology analyses
new CT complex, [(DAPH)+(DNB)] has been synthesized from
the reaction between DAP and DNB. This complex was further
Calf thymus DNA was dissolved in tris-HCl buffer (0.1 M, pH
characterized by FTIR, 1H and 13C NMR, ESI-mass spectroscopy
7.4). The purity of the DNA solution was checked from the absor-
and single crystal X-ray crystallography. The aim of the present
bance ratio A260/A280 (1.8). Fluorescence measurements were
study is to investigate interactions between acceptor and donor
made using spectrofluorophotometer Model RF-5301PC (Shima-
by X-ray crystallography and spectral analyses. The obtained re-
dzu, Japan) equipped with a 150 W Xenon lamp and a slit width
sults enabled us to ascertain the reaction stoichiometries, bonding
of 5 nm. A fixed concentration of the compound (30 lM) was taken
and structure of new [(DAPH)+(DNB)] as well as biological appli-
in a quartz cell and increasing amounts of ct-DNA solution was ti-
cations such as antimicrobial activities and DNA binding ability of
trated using increments of 5 lM. The fluorescence spectra were re-
complex.
corded in the range of 325–525 nm upon excitation at 320 nm at
310 K.
2. Experimental The antibacterial activity of newly synthesized [(DAPH)+
(DNB)] was tested in vitro against two Gram-positive bacteria
2.1. Materials Staphylococcus aureus (MSSA 22) and Bacillus subtilis (ATCC 6051)
and two Gram-negative bacteria Escherichia coli (K 12) and Pseudo-
Analytical grade DAP and DNB were employed for the synthesis monas aeruginosa (MTCC 2488) strains using disk diffusion method
of CT complexes. Chloroform (CHCl3) and DMSO were taken as [46,47]. Media with DMSO was setup as control. The disks measur-
HPLC grade. Calf thymus DNA (ct DNA) was purchased from Sigma ing 5 mm in diameter were prepared from whatmann no. 1 filter
(USA). paper sterilized by dry at heat at 140 °C for 1 h. The screening
was performed at 100 lg/ml concentration of test CT complex
2.2. Synthesis of CT complex and antibiotic disk, Tetracycline (30 lg/disk, Hi-Media) was used
as control. The present [(DAPH)+(DNB)] was also screened for its
The solid [(DAPH)+(DNB)] was prepared by mixing the satu- antifungal property against Aspergillus niger (Laboratory isolate),
rated solution of 2,6-diaminopyridine (0.108 g, 1 mmol) in CHCl3 Candida albicans (IQA-109) and Penicillium sp. (Laboratory isolate)
(25 ml) with saturated solution of 3,5-dinitrobenzoic acid in DMSO using standard agar disk diffusion method [48].
(0.636 g, 1 mmol) in CHCl3 (20 ml). An orange color solution was
formed upon the mixing and continuous stirring of these two reac-
tants produced orange precipitate. The precipitate was filtered off Table 1
and washed several times with small amounts (5 ml) of CHCl3 Crystallographic and data collection parameters for [(DAPH)+(DNB)] of DAP with
and dried under vacuum over CaCl2. DNB.

Empirical formula C12H11N5O6


2.3. Single crystal growth Formula weight (Mr) 321.26
Crystal description Prism
A saturated solution of the synthesized title [(DAPH)+(DNB)] Temperature (K) 100(2)
was prepared in methanol, stirred well for about 1 h and heated Wavelength (Å) 0.71073

slightly to dissolve well. Then the solution was filtered through a Crystal system Triclinic
Space group P-1
Whatmann: 41 grade filter paper to remove the suspended impu- a = 6.859(3)
Unit cell dimensions (Å)
rities. The clear filtrate was collected in 50 ml conical flask and b = 12.505(5)
kept unperturbed in a dust free chamber for the growth of single c = 15.776(6)
crystal of the [(DAPH)+(DNB)]. Well defined, bright colored, trans- a = 95.327(7)
parent and needle shaped crystals were harvested at the end of the b = 93.426(7)
c = 102.753(7)
fifth day. 3 1309.5(9)
V ðÅ Þ
Z 4
2.4. Spectral and crystal structure analyses Dx (g cm3) 1.629
F(0 0 0) 664
The 1H NMR spectra and 13C NMR spectra of the reactants and h, k, l max 8, 15, 19
h range (°) 2.60–26.85
the crystal of [(DAPH)+(DNB)] were recorded in DMSO using the N ref 5295
Bruker DRX-300 NMR spectrometer. The FTIR spectra were re- Min and max transmission 0.968, 0.976
corded employing spectroscopic 2020 FTIR spectrometer using Refinement method Full matrix least squares on F2
the KBr pellet technique. The ESI mass spectrum of [(DAPH)+ Goodness of fit on F2 1.076
R1, wR2 [I > 2r (I)] 0.0678, 0.1712
(DNB)] was recorded using LC–MS Q-ToF Micro, Amino Acid
R1, wR2 (all data) 0.0945, 0.2258
Analyser (Shimadzu). A single crystal of the CT compound was
40 I.M. Khan et al. / Journal of Molecular Structure 1035 (2013) 38–45

broad band observed in the region 3200–3500 cm1 may be as-


signed to the presence of hydrogen bonded O–H and N–H bonds
present in [(DAPH)+(DNB)] [49]. The band at 3160 cm1 in
[(DAPH)+(DNB)] is due to the aromatic C–H stretching vibration
but the same was observed at 3134 cm1 and 3092 cm1 in free do-
nor and acceptor, respectively. The [(DAPH)+(DNB)] was character-
ized by an absent or shifted to lower intensities of the band [49].
This shows an acid–base interaction involving a proton transfer
from the acceptor to donor or electron transfer from donor to accep-
tor which favors a strong hydrogen bonding, is likely to occur [50].
The –NH2 deformation mode is observed by the absorption at
1643 cm1 (very strong) in [(DAPH)+(DNB)] but the same was ob-
served at 1618 cm1 (broad and strong) in free donor. The asym-
metric and symmetric stretching vibration of the NO2 group is
observed at 1531 cm1 and 1445 cm1, respectively. Therefore, it
has been realized that the shift to the lower frequency of masym
(NO2) vibration (1531 cm1) in the spectrum of the [(DAPH)+
(DNB)] compared with free DNB (1629 cm1,very strong) is due
to the increased electron density on the acceptor moiety owing to
the charge transfer interaction in the [(DAPH)+(DNB)] [51]. It was
Fig. 1. FTIR spectra of (A) DAP (Donor); (B) DNB (Acceptor) and (C)
[(DAPH)+(DNB)].
concluded that the withdrawing groups on DNB facilitate to liberate
the protons of COOH to make intermolecular hydrogen bonds with
lone pair of electrons on pyridyl nitrogen atom of DAP. This fact is
3. Result and discussion also supported by X-ray crystallographic studies of [(DAPH)+
(DNB)]. Therefore, the complexation between DAP and DNB is
3.1. FTIR spectra strongly supported by FTIR spectral data.

The FTIR spectra of the donor, acceptor and resulting complex are 3.2. 1H NMR spectra
depicted in Fig. 1 showing the presence of characteristic absorption
bands due to the varied force constant in the donor and the acceptor 1
H NMR spectra of the DNB, DAP and the [(DAPH)+(DNB)] were
species on account of the prevalent proton transfer mechanism. A taken to investigate the environments of various protons as shown

Fig. 2. 1H NMR spectrum of [(DAPH)+(DNB)] of DAP with DNB.


I.M. Khan et al. / Journal of Molecular Structure 1035 (2013) 38–45 41

between NH2 and d6-dmso. A broad signal of range d = 6–7 ppm


is attributed to the protons of NH2 on C2 and C6 whereas this
was observed as a singlet at d = 5.54 ppm in free DAP. The doublet
at d = 5.79 ppm is attributed to the protons on C3 and C5 carbon
atoms in DAP moiety whereas this was observed at d = 5.90 ppm
in free DAP Fig. 1S (b). The triplet centered at d = 7.31 ppm is due
to the proton on C4 carbon atom of DAP moiety but it was observed
at d = 7.22 ppm in free DAP. The singlet is splitted into triplet by
two neighborhood protons on C3 and C5 carbon atoms in DAP
[53]. The protons present at C2 and C4 positions show two different
singlets at d = 8.95 ppm and d = 8.91 ppm, respectively, whereas in
free DNB these protons were observed at d = 8.77 ppm and at
d = 9.01 ppm, respectively [52]. This downfield shift in frequency
has been attributed to an increased electron density on DNB part
of the charge transfer interaction between the donor and the
acceptor molecules.

13
3.3. C NMR spectra
13 + 
Fig. 3. C NMR spectrum of [(DAPH) (DNB) ] of DAP with DNB. The resonance signals of aromatic ring carbons appear in the
119–166 ppm range as shown in Fig. 2S (a and b) and Fig. 3. The
sharp signal at d = 128 ppm is due to the C3 and C5 atoms of the
in Fig. 1S (a and b) and Fig. 2 respectively. The spectrum of DAP moiety in the [(DAPH)+(DNB)] but same was observed at
[(DAPH)+(DNB)] was recorded in DMSO (An internal reference), d = 111 ppm in free DAP. A signal observed at d = 141 ppm is as-
which exhibited a signal at d = 2.50 ppm (Fig. 2). Strong to medium signed to the C2 and C6 carbons while a medium intensity signal
intensity resonance signals due to the protons present in the at 119 ppm is attributed to C4 carbon of DAP moiety [54]. The
[(DAPH)+(DNB)] was observed at the expected positions. The sig- DNB moiety of [(DAPH)+(DNB)] shows resonance signals at
nal due to the COOH proton [52] was absent in the spectrum of the 147 ppm characteristic of the C3 and C5 carbons bearing the NO2
[(DAPH)+(DNB)] confirming the transfer of proton from DNB to groups [55] but this was observed at 148 ppm in free DNB as
DAP. A broad signal or multiplet of moderate intensity at shown in Fig. 2S (a). The high intensity resonance signal at
3.56 ppm observed in the spectrum of [(DAPH)+(DNB)] may be 166 ppm is assigned to the ipso carbon (C1), which in free DNB
due to residual water in d6-dmso or proton/deuterium exchange was observed at 163 ppm Fig. 2S (a) while signal at 143 ppm is

Fig. 4. Mass spectrum of [(DAPH)+(DNB)] of DAP and DNB.


42 I.M. Khan et al. / Journal of Molecular Structure 1035 (2013) 38–45

Fig. 5. ORTEP view of crystal of [(DAPH)+(DNB)] showing the numbering scheme.

due to the C4 carbon of the DNB moiety in [(DAPH)+(DNB)] and at m/z = 202 indicates ultimately the formation of [CTC-COOH–
same was present at 122 ppm in free DNB. NO2+4H]+ species. Thus the ESI-mass data is in line with the
proposed molecular formula of CT complex which was further
3.4. ESI-Mass Spectrum corroborated from X-ray studies.

The stoichiometry of the novel [(DAPH)+(DNB)] was ascer- 3.5. X-ray crystallography of CT complex
tained from electron spray ionization (ESI)-mass spectral analysis.
The ES-mass spectrum of the compound is consistent with the for- The single crystal X-ray studies were performed on CT complex.
mation of the proposed molecular structure of the compound as The Ortev view and H-bonding scheme in extended structure are
shown in Fig. 4. The spectrum exhibited a molecular ion peak at shown in Fig. 5 and 6. It is clear from the crystal structure of the
m/z = 318 assignable to molecular ion fragment [CTC-3H]+, which complex that proton transfer phenomenon has taken place between
confirmed the formation of [(DAPH)+(DNB)] between DAP and the donor and the acceptor. A proton from the COOH group of DNB is
DNB. The peak at m/z = 110 is characteristic of the fragmented spe- transferred to the pyridyl nitrogen of DAP. This has been ascertained
cies [CTC-DNB+H]+. The remaining weak intensity peak at m/ further from the bond distance of N1-H101 or N5-H202 i.e., 0.982 Å,
z = 166 is due to the formation of [CTC-DAP-NO2]+. The peak at which is a normal covalent bond. The hydrogen bonding distances
m/z = 274 corresponds to the formation of [CTC-NO2–H]+. A peak present in CT complex are [N1H101  O5 = (2.593 Å)] and

Fig. 6. H-bonding scheme in extended structure of [(DAPH)+(DNB)].


I.M. Khan et al. / Journal of Molecular Structure 1035 (2013) 38–45 43

Table 2
Selected atomic parameters and equivalent isotropic thermal parameters. 2.0
0
Atom X Y Z
Beq (Å
A)
O2 0.3695(4) 0.62813(18) 0.16438(15) 0.0246(5)
O8 0.0026(3) 0.56996(18) 0.70680(15) 0.0245(5)
1.5
O9 0.2165(3) 0.51437(17) 0.99071(15) 0.0237(5)
N1 0.7972(4) 0.8467(2) 0.38955(17) 0.0156(6)

F /F
o
N3 0.7995(4) 0.7551(3) 0.50900(18) 0.0210(6)
1.0
N4 0.7157(5) 0.9183(2) 0.7716(2) 0.0252(7)
N7 0.0297(4) 0.6701(2) 0.72580(16) 0.0187(6)
C1 0.7990(5) 0.8555(3) 0.3048(2) 0.0179(7)
C2 0.8177(5) 0.7652(3) 0.2500(2) 0.0190(7) 0.5
C3 0.8294(5) 0.6689(2) 0.2838(2) 0.0184(7)
C4 0.8228(4) 0.6595(2) 0.3706(2) 0.0182(7)
C5 0.8072(4) 0.7520(2) 0.4245(2) 0.0173(7)
H01 0.811(7) 0.708(4) 0.529(3) 0.038(13) 0.0
H02 0.808(5) 0.820(3) 0.545(2) 0.019(9) 0 10 20 30 40 50
H03 0.781(6) 0.958(4) 0.225(3) 0.042(12)
DNA (µM)
H04 0.768(6) 1.005(4) 0.316(3) 0.038(12)
H05 0.445(6) 0.650(3) 1.019(2) 0.031(10)
Fig. 8. Stern–Volmer plot for the binding of [(DAPH)+(DNB)] of DAP and DNB, with
H06 0.553(6) 0.766(4) 1.021(3) 0.030(12)
DNA.
H07 0.753(7) 0.973(4) 0.808(3) 0.043(13)

Dynamic quenching results from collision between fluorophore


[N3H02  O6 = (2.930 Å)], which are quite short or comparable to and quencher whereas static quenching is due to ground-state
the normal hydrogen bonding distances indicating a strong interac- complex formation between fluorophore and quencher [59]. How-
tion between donor acceptor [21]. The important H-bond angles ob- ever, the characteristic Stern–Volmer plot of combined quenching
served in the [(DAPH)+(DNB)] are N3H02  O6 (161.29°) and (both static and dynamic) is an upward curvature. The binding of
N1H101  O5 (165.37°). The H-bonds in the extended structure CT complex with Calf thymus DNA, was studied by monitoring
of [(DAPH)+(DNB)] are shown in Fig. 6. The C–N–C in the present the changes in the intrinsic fluorescence of CT complex at varying
complex is 123° which is different from free C–N–C aromatic bond DNA concentrations. Fig. 7 gives the representative fluorescence
angles of pyridine (i.e., 115°) showing the attachment of proton [56]. emission spectra of the complex upon excitation at 250 nm. The
The aromatic rings are not parallel to each other indicating the ab- addition of DNA caused a gradual decrease in the fluorescence
sence of pp interactions. The selected structural parameters, emission intensity of the CT complex suggesting changes in the
atomic parameters and equivalent isotropic thermal parameters microenvironment of the fluorophore upon interaction with DNA
are summarized in Tables 1 and 2. as the CT complex was observed to bind the DNA. To determine
the DNA binding ability of the compound, fluorescence intensity
3.6. DNA binding studies data were analyzed by the Stern–Volmer equation [60].

F =F ¼ 1 þ Ksv ½Q
The fluorescence quenching technique is often used to monitor
the molecular interactions because of its high sensitivity [38,57]. In where F and F0 are the fluorescence intensity with and without the
order to obtain the DNA binding nature of CT complex, the interac- quencher (CT-DNA), Ksv the Stern-Volmer quenching constant, and
tions of CT complex with Calf thymus DNA by fluorescence spec- [Q] the concentration of the quencher. The Ksv for the CT complex
troscopy were investigated. Fluorescence quenching is usually was obtained as the slope of the Stern–Volmer graph are
classified as dynamic quenching and static quenching [58]. shown Fig. 8 and was found to be 2.411  104 l M1 which is more

Fig. 7. Fluorescence emission spectra of [(DAPH)+(DNB)] of DAP and DNB in the absence (—) and presence of increasing amount (5 lM) of DNA from top second spectra to
bottom.
44 I.M. Khan et al. / Journal of Molecular Structure 1035 (2013) 38–45

Table 3
Antibacterial and antifungal activity of synthesized 100 lg/ml concentration of novel [(DAPH)+(DNB)] of DAP and DNB.

Bacteria CT complex Tetracycline Fungi CT complex Nystatin


Diameter of zone of inhibition in mm at 100 lg/ml and DMSO as control
Staphylococcus aureus 22.3 (±1.09) 20 (±0.83) Aspergillus niger 20 (±1.14) 24 (±0.24)
Bacillus subtilis 21.7 (±1.50) 21 (±0.95) Candida albicans 15 (±1.28) 23 (±0.58)
Escherichia coli 24.0 (±1.72) 25 (±0.88) Penicillium sp. 30 (±1.63) 25 (±0.88)
Pseudomonas aeruginosa 19.5 (±1.43) 20 (±0.83)

appreciable in comparison to earlier reported CT complexes of 2,6- Acknowledgements


diaminopyridine (DAP) with picric acid and 1,10-phenanthroline
with p-Nitrophenol [53,39]. The data plotted as emission intensity The Chairman, Department of Chemistry, AMU is thanked for
against quencher concentration (Fig. 8) gives an upward curve in providing research facilities at Physical Chemistry Lab and Instru-
our case as well, thus indicating the incidences of both static mentation Center. Thanks for Mr. Avtar, SAIF, Chandigarh, Punjab
and dynamic quenching. One of the cardinal features of this CT for the analysis of sample.
complex bearing the NH2 with COOH is its enhanced DNA binding
ability. This study will be beneficial in developing a variety of anti Appendix A. Supplementary material
neoplastic drugs. It is concluded in our work that CT complex shows
the binding with DNA which is one of the main molecular targets in Crystallographic data (exclusive structure factors) have been
the design of anticancer compounds [37]. deposited at the Cambridge Crystallographic Data Center as sup-
plementary publication no. CCDC-. 752972 Copies of the data can
3.7. Antibacterial activity be obtained free of charge on application to CCDC 12 Union Road,
Cambridge, CB2 1EZ, UK, E-mail: depodeposit@ccdc.cam.ac.uk.
[(DAPH)+(DNB)] was studied for its antibacterial and anti- Supplementary data associated with this article can be found, in
fungal activities using disk diffusion method [46,47] in vitro against the online version, at http://dx.doi.org/10.1016/j.molstruc.2012.09.
two Gram-positive bacteria Staphylococcus aureas (MSSA 22) and B. 016.
subtilis (ATCC 6051) and two Gram-negative bacteria E. coli (K 12)
and P. aeruginosa (MTCC 2488) at concentration of 100 lg/ml. Tet- References
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