Polyhedron 29 (2010) 1583–1587

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Polyhedron

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Copper(II) complex with tridentate N donor ligand: Synthesis, crystalstructure, reactivity and DNA binding study

Sourav Dey a, Sandipan Sarkar a, Hena Paul a, Ennio Zangrando b, Pabitra Chattopadhyay a,*

a Department of Chemistry, Burdwan University, Golapbag, Burdwan 713 104, Indiab Dipartimento di Scienze Chimiche, Via Licio Giorgieri 1, 34127 Trieste, Italy

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

Article history:Received 1 September 2009Accepted 4 January 2010Available online 2 February 2010

Keywords:Copper(II) complexTridentate N ligandCrystal structureReactivity

0277-5387/$ - see front matter � 2010 Elsevier Ltd. Adoi:10.1016/j.poly.2010.01.022

* Corresponding author. Tel.: +91 342 2558339; faxE-mail address: pabitracc@yahoo.com (P. Chattopa

Penta-coordinated mononuclear copper(II) complex of tridentate 2,6-bis-(benzimidazolyl)pyridine (L)formulated as [Cu(L)(H2O)2](NO3)2, 1 was synthesized and isolated in pure form. The complex was char-acterized by physico-chemical and spectroscopic methods, as well as single crystal X-ray diffraction anal-ysis. The structural study shows the metal in a highly distorted square pyramidal geometry [trigonalityindex s = 0.1425] that comprises two aqua molecules in the first coordination sphere. The crystal packingof 1 shows a 3D polymer formed through H-bonds involving aquo ligands, NH benzimidazole groups andnitrate anions. On reaction with pseudohalides in acetonitrile at ambient temperature complex 1 chan-ged to mono cationic copper(II) derivatives [Cu(L)(X)(H2O)]NO3 [X = SCN� (2a) and N�3 (2b)]. These cop-per(II) complexes have been isolated from the reaction mixtures and characterized by physico-chemicaland spectroscopic tools. The interaction of complex 1 with calf thymus DNA (CT-DNA) has been investi-gated by using absorption and emission spectral studies, the binding constant (Kb) and the linear Stern–Volmer quenching constant (Ksv) have been determined.

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1. Introduction

The study of copper(II) complexes with heterocyclic nitrogen-donor ligands is of great significance since they mimic active sitesof many copper-containing proteins and also for their potentialactivity as drugs [1–4]. In fact copper(II) chelates have been foundto interact with biological systems and to exhibit antineoplasticactivity [5–7], and the effectiveness of many anticancer agents de-pends on the mode and affinity of their binding with DNA [8]. Thecopper(II) complexes can interact non-covalently with nucleicacids by intercalation when they comprise planar fused aromaticring systems [9–12]. In this respect the design of functional mate-rials has received considerable attention due to their propensity totake part also in potential applications in DNA molecule probes[13–17].

Here, we report an account of the synthesis, structure, reactiv-ity and DNA binding property of a new penta-coordinated[Cu(L)(H2O)2](NO3)2 complex (1) [L = 2,6-bis(benzimidazolyl)pyr-idine]. The solid state structural analysis of the complex evi-dences a 3D polymer formed through H-bonds involving aquoligands, benzimidazole NH groups and nitrate anions. The deriva-tives [Cu(L)(X)(H2O)]NO3 [X = SCN� (2a) and N�3 (2b)] have beenobtained from complex 1 on reaction with the correspondent

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: +91 342 2530452.dhyay).

pseudohalide anions. The binding constant (Kb) and the linearStern–Volmer quenching constant (Ksv) for the interaction of 1with CT-DNA have been determined by absorption and emissionspectral studies.

2. Experimental

2.1. Materials and physical measurements

All chemicals and reagents were obtained from commercialsources and used as received. Solvents were distilled from anappropriate drying agent. Tris–HCl buffer solution and CT-DNAwere purchased from Bangalore-Genie and ethidium bromide(EB) from Sigma and were used as received.

The elemental analyses (C, H and N) were performed on a PerkinElmer model 2400 elemental analyzer. Copper analyses were car-ried out by Varian atomic absorption spectrophotometer (AAS)model-AA55B, GTA using graphite furnace. Electronic absorptionspectra were recorded on a JASCO UV–Vis/NIR spectrophotometermodel V-570. IR spectra were recorded using JASCO FT–IR spec-trometer model 460 plus preparing KBr disk. 1H NMR spectra weremeasured on a 200 MHz Bruker-400 spectrometer. Molar conduc-tance (^M) was measured in a Systronics conductivity meter 304model using �10�3 mol L�1 solutions in appropriate solvent. Themagnetic susceptibility measurements were performed at roomtemperature by using a vibrating sample magnetometer PAR 155

Table 1Crystal data and details of refinement for complex 1.

Empirical formula C19H17CuN7O8

Formula weight 534.94Crystal system monoclinicSpace group P 21/na (Å) 8.888(3)b (Å) 14.731(4)c (Å) 16.638(4)b (�) 100.89(3)V (Å3) 2139.2(11)qcalc (g/cm3) 1.661Z 4F(0 0 0) 1092h range (�) 2.71–27.10l (Mo Ka) (mm�1) 1.086Collected/unique reflections 25414/3916Rint 0.0432Reflections [I > 2r(I)] 2214Parameters 328Goodness-of-fit (GOF) on F2 0.904Final R indices [I>2r(I)] R1 = 0.0530, wR2 = 0.1339R indices (all data) R1 = 0.0893, wR2 = 0.1519

1584 S. Dey et al. / Polyhedron 29 (2010) 1583–1587

model. The fluorescence spectra were recorded on the FluorometerHitachi-2000.

2.2. Synthesis of the ligand

The 2,6-bis(benzimidazolyl)pyridine ligand was prepared bymodifying the reported procedure [18,19]. A mixture of pyridine-2,6-dicarboxylic acid (1.67 g, 10 mmol) and 1,2-phenylenediamine(2.16 g, 20 mmol) in ethylene glycol (25 mL) was refluxed for 16 h.The volume of the resulting brown colored solution was reduced to6–8 mL by rotary evaporator. To this concentrated solution, 20 mLof water were added. A light-brown colored solid precipitated outby addition of dilute HCl and then the mixture was neutralized bysaturated sodium carbonate solution to get colorless solid of thedesired product, which was collected by filtration and washed withwater and methanol. Anal. Calc. for C19H13N5: C, 72.98; H, 4.17; N,22.68. Found: C, 73.29; H, 4.21; N, 22.50%. M.p.(�C): 294 ± 1. IR(cm�1): mC@N,1489; mN–H, 3225. 1H NMR (d, ppm in DMSO-d6):8.16–8.18 (t, 1H), 7.96–8.98 (d, 2H), 7.71–7.73 (q, 4H), 7.29–7.32(m, 4H). Yield: 65%.

2.3. Synthesis of [Cu(L)(H2O)2](NO3)2 (1)

To the suspended 2,6-bis(benzimidazolyl)pyridine (1.0 mmol,435.5 mg) in methanol, 1.0 mmol of copper(II) nitrate trihydratewas added dropwise and the mixture was stirred for 4 h at ambienttemperature. Then the resulting solution was kept aside and after afew days, deep blue colored crystalline complex was obtained byfiltration followed by washing with water, methanol and dried invacuo. Single crystals suitable for X-ray diffraction were also ob-tained from this solution. Yield: 80–85%.

(1) Anal. Calc. for C19H17CuN7O8: C, 42.75; H, 3.11; N, 18.09; Cu,11.97. Found: C, 42.62; H, 3.20; N, 18.32; Cu, 11.88%. IR (cm�1):mC@N, 1472; mNO3 , 1379. Magnetic moment (l, B.M.): 1.71. Conduc-tivity (Ko, ohm�1 cm2 mol�1) in DMF: 145.

2.4. Reactivity of 1

To a suspension of complex [Cu(L)(H2O)2](NO3)2 (1) (1.0 mmol)in acetonitrile (30 mL), a solution of potassium thiocyanate(97.1 mg) or sodium azide (65 mg) in methanol–water was addeddropwise during a period of 15 min. The mixture was stirred for4–5 h at room temperature. Then the clear filtrate was collectedfrom the resulting solution. The crystallized corresponding prod-ucts were obtained from the filtrates by allowing slow evaporationof the solvent at room temperature. Yield: 75–80%.

[Cu(L)(SCN)(H2O)]NO3 (2a): Anal. Calc. for C20H15CuN7O4S: C,46.78; H, 2.84; N, 19.34; Cu, 12.27. Found: C, 46.82; H, 2.95; N,19.12; Cu, 12.40%. IR (cm�1): mC@N, 1480; mSCN, 2070; mNO3 , 1380.Magnetic moment (l, B.M.): 1.76. Conductivity (Ko, ohm�1 cm2

mol�1) in acetonitrile: 135.[Cu(L)(N3)(H2O)]NO3 (2b): Anal. Calc. for C19H15CuN9O4: C,

45.59; H, 2.96; N, 25.51; Cu, 13.01. Found: C, 45.91; H, 3.04; N,25.37; Cu, 12.79%. IR (cm�1): mC@N, 1480; mSCN, 2070; mNO3 Þ, 1380.Magnetic moment (l, B.M.): 1.78. Conductivity (Ko, ohm�1 cm2

mol�1) in acetonitrile: 140.

2.5. X-ray crystal structure analysis

Crystal data and details of refinement for the structure reportedare summarized in Table 1. Diffraction data were collected at roomtemperature on a Nonius DIP-1030H system equipped with Mo Karadiation, (k = 0.71073 Å). Cell refinement, indexing and scaling ofthe data set were performed by using programs [20]. The low com-pleteness of the dataset (83%) was mainly due to crystal damageduring data collection. The structure was solved by direct methods

using SHELXS97 [21] and subsequent Fourier analyses and refined bythe full-matrix least-squares method using SHELXL97 [21] based onF2 with all reflections. Hydrogen atoms bonded to carbon were in-cluded at calculated positions, those of water molecules were lo-cated from a D Fourier map and refined with O–H distancerestraints. All the calculations were performed using the WINGX Sys-tem, Ver 1.70.01 [22].

2.6. DNA binding experiments

The tris–HCl buffer solution (pH 8.0), used in all the experi-ments involving CT-DNA, was prepared by using deionized andsonicated HPLC grade water (Merck). The CT-DNA used in theexperiments was sufficiently free from protein, being the ratio ofUV absorbance of the DNA in tris–HCl solution at 260 and280 nm (A260/A280) of ca. �1.9 [23]. The concentration of DNAwas determined with the help of its extinction coefficient e of6600 L mol�1 cm�1 at 260 nm [24]. Stock solution of DNA was al-ways stored at 4 �C and used within 4 days. Concentrated stocksolution of complex 1 was prepared by dissolving the copper(II)complex in DMSO and diluting suitably with tris–HCl buffer tothe required concentration for all the experiments. Absorptionspectral titration experiment was performed by keeping constantthe concentration of the copper(II) polymer with varying the CT-DNA concentration. To eliminate the absorbance of DNA itself,equal solution of CT-DNA was added either to the copper(II) com-plex solution and to the reference one.

In the fluorescence displacement experiment with ethidiumbromide (EB), 5 lL of EB solution (1.0 mmol L�1) in tris–HCl wereadded to 1.0 mL of DNA solution (at saturated binding levels[25], and stored in the dark for 2.0 h. The copper(II) complex solu-tion was titrated into the DNA/EB mixture and then diluted intris–HCl buffer to 5.0 mL, making the solutions with the variedmole ratio of the copper(II) complex to CT-DNA. Prior to measure-ments, the mixture was shaken up and incubated at room temper-ature for 30 min. The fluorescence spectra of EB bound to DNAwere obtained at an emission wavelength of 584 nm.

3. Results and discussion

3.1. Synthesis and characterization

The copper(II) complex [Cu(L)(H2O)2](NO3)2 (1) was obtained ingood yield by the reaction of copper(II) nitrate trihydrate with 2,6-bis(benzimidazolyl)pyridine (L) in methanol medium in suspended

Table 2Bond lengths (Å) and angles (�) for 1.

Bond lengthsCu–N(1) 1.997(3) Cu–O(1w) 1.999(3)Cu–N(2) 1.979(3) Cu–O(2w) 2.145(3)Cu–N(3) 1.985(3)

Bond anglesN(1)–Cu–N(2) 79.62(13) N(3)–Cu–O(1w) 98.76(12)N(1)–Cu–N(3) 158.82(13) N(1)–Cu–O(2w) 98.17(15)

S. Dey et al. / Polyhedron 29 (2010) 1583–1587 1585

condition. The complex (1) is insoluble in water and methanol,moderately soluble in DMF and DMSO, and fully insoluble in com-mon organic solvents. In the solid state the complex is fairly stablein air so as to allow physical measurements. The conductivity of 1in DMF was measured to be 145 Ko mol�1 cm�1 at 300 K, whichsuggests that the complex exists as 1:2 electrolyte. At room tem-perature the magnetic moment l of 1.71 B.M. corresponds to oneunpaired electron.

N(2)–Cu–N(3) 79.26(13) N(2)–Cu–O(2w) 122.39(15)N(1)–Cu–O(1w) 98.79(13) N(3)–Cu–O(2w) 94.40(16)N(2)–Cu–O(1w) 150.27(14) O(1w)–Cu–O(2w) 87.31(14)

Fig. 2. Crystal packing of 1, [CuL(H2O)2](NO3)2: 3D polymer built by H-bondsoccurring among aquo ligands, benzimidazole NH and nitrate anions.

3.2. Structural description of 1

The ORTEP views of complex [Cu(L)(H2O)2](NO3)2 (1) with theatom numbering scheme is illustrated in Fig. 1, and a selection ofbond distances and angles are listed in Table 2. The coordinationsphere around the metal ion can be described as a very distortedsquare pyramidal geometry, comprising the 2,6-bis(benzimidazol-yl)pyridine moiety, acting as a tridentate ligand, and two watermolecules. The organic ligand has almost coplanar atoms (maxi-mum displacement from the mean plane being ±0.078(3) Å), andof the three N donor sites, two comes from the two benzimidazolylunits and the third from the central pyridine nitrogen donor.

All the Cu–N distances present comparable values within theire.s.d.’s and fall in the range 1.979(3)–1.997(3) Å, although nitrogendonors pertain to different heterocycle rings (namely benzimid-azole and pyridine). On the other hand the Cu–O distances are sig-nificant different of 1.999(3) and 2.145(3) Å, being the latterrelative to the water O(2w) at the ‘‘pseudo-apical” position of thepyramid. In fact the distortions from the ideal geometry are clearlyevidenced from the N(2)–Cu–O(2w) angle of 122.39(15)�, while theother X–Cu–O(2w) angles deviate utmost by 8� from the right. Thisparticular arrangement accomplishes the H-bonds interactions(see below) with a nitrate anion (Fig. 1). In the basal plane theN(2)–Cu–O(1w) and N(1)–Cu–N(3) angles of 150.27(14) and158.82(13)�, respectively, leads to a trigonality index s of 0.1425[26].

The crystal packing shows a 3D polymer formed by the self-assembly of the [Cu(L)(H2O)2]2+ complex units and nitrate anionsthrough a H-bonding scheme (Fig. 2). In fact the aqua ligandsand the benzimidazole NH groups act as H donors towards the ni-trate oxygens. The Ow–H� � �O(nitrate) and the NH� � �O(nitrate) dis-tances are within 2.717(4)–2.860(6) and 2.855(6)–2.896(5) Å,respectively (Table 3). The shortest Cu� � �Cu separation in the net-work is of 6.836(2) Å.

Fig. 1. ORTEP drawing (40% probability ellipsoid) of the molecular cation of 1,showing the H-bond interactions with a nitrate anion.

It is interesting to compare the present crystal and molecularstructure with the closely related [Cu(L)(H2O)2(NO3)](NO3)�H2Ocomplex. In this case a 3D crystal packing is still formed througha H-bonding scheme, but the metal is enclosed in a very elongatedoctahedral environment, being weakly coordinated to a nitrate an-ion (Cu–ONO2 distance of 2.8 Å) [27].

Complex 1 suspended in acetonitrile at ambient temperaturereacts with pseudohalides yielding a new type of monocationicpenta-coordinated copper(II) species formulated as [Cu(L)(X)(H2O)]NO3 [X= SCN� (2a) and N�3 (2b)]). It may be expected thatof the two water molecules, that located at apical position (longerCu–O distance) has been replaced by the thiocyanate or azide li-gand. However, a possible rearrangement of ligands in the coordi-nation sphere of 2a and 2b, which leads the aqua and the anion ataxial and equatorial position, respectively, is not to be excluded[28].

3.3. Spectral characterization

The IR spectrum of the complex 1 shows an intense band at1380 cm�1 assigned to mNO3, in addition to a characteristic bandat 1478 cm�1 assignable to the mC@N stretching frequency. In theinfrared spectra of 2, the characteristic strong band at 2085 cm�1

along with a weak band at 776 cm�1 indicate the presence of theN-bonded SCN (2a), while an intense band at 2035 cm�1, attribut-able to the terminal end-on azide, was observed in 2b [29].

The electronic spectrum of the copper(II) polymer was recordedin the UV–Vis region using DMSO as solvent. Three absorption

Table 3Hydrogen bond geometry (Å/�).

D–H d(D–H) d(H� � �A) <DHA d(D� � �A) A Symmetry code

O1w–H11 0.88(5) 1.88(5) 158(4) 2.717(4) O2O1w–H12 0.86(3) 1.91(3) 163(4) 2.741(6) O4O2w–H21 0.90(5) 1.96(5) 175(3) 2.860(6) O5O2w–H22 0.84(4) 1.91(4) 165(5) 2.732(6) O3 �x + 1/2, y + 1/2, �z + 1/2N4–H4 0.86 2.12 142 2.855(6) O6 x � 1/2, �y + 3/2, z � 1/2N5–H5 0.860 2.04 170 2.896(5) O1 �x + 1, �y + 1, �z

1586 S. Dey et al. / Polyhedron 29 (2010) 1583–1587

bands with varied intensity were observed. An intense band at224 nm (s, e = 9,512 dm3 mol�1 cm�1) is assigned to p–p* intra-li-gand transition along with the less intense band at 330 nm (s,e = 3012 dm3 mol�1 cm�1) corresponding to the charge transfer li-gand to metal transition. A broad band observed at the 627 nm (b,e = 112 dm3 mol�1 cm�1) is well in agreement with the d–d transi-tion for copper(II) in the square pyramidal geometry.

3.4. DNA binding studies

3.4.1. Electronic absorption titrationTo examine the binding mode of copper(II) complex with DNA,

the absorption spectra of the copper(II) complex 1, were recordedduring the titration with CT-DNA. As shown in Fig. 3, the spectraindicate a significant hyperchromism effect centered at the330 nm absorption maximum, suggesting that a strong interactionbetween the copper(II) complex and DNA is operative. This spectralchange might be demonstrating in terms of groove binding [30].

Groove binding molecules contain unfused aromatic ring sys-tems connected by bonds with torsional freedom in order to adoptappropriate conformation that closely matches the helical turn ofDNA grooves, while fused polyaromatic systems containing pro-tonated nitrogen atoms or having protonated side chains attachedto the ring system are typically intercalators [31]. Here, the organicligand L, having coplanar atoms upon copper coordination, likelyfacilitates the formation of van der Waals contacts or hydrogenbonds during interaction with DNA grooves. The spectral titrationdata allows determining the intrinsic binding constant Kb of 1 withCT-DNA by using the following equation [32]:

½DNA�=ðea � ef Þ ¼ ½DNA�=ðeb � ef Þ þ 1=½Kbðeb � ef Þ�

where [DNA] is the DNA concentration, ef and eb represent theextinction coefficients for the free and fully bound copper(II)complex, respectively, and ea the copper(II) complex extinction

0.04

0.08

0.12

0.16

0.20g

a

Abso

rban

ce

Wave length (nm)250 300 350 400 450

Fig. 3. Electronic spectral of 1 through titration with CT-DNA in tris–HCl buffer;[Complex] = 1.64 � 10�6; [DNA]: (a) 0.0, (b) 0.94 � 10�6, (c) 2.00 � 10�6, (d)4.82 � 10�6, (e) 7.76 � 10�6, (f) 9.7 � 10�6, (g) 1.2 � 10�5 mol L�1. The increase ofDNA concentration is indicated by an arrow.

coefficient during each addition of DNA. The [DNA]/(ea � ef) plotagainst [DNA] gave a linear relationship (Fig. 4), from the slope ofwhich the intrinsic binding constant Kb for the complex 1 was cal-culated to be 0.8 � 105 M�1 (R = 0.99376 for six points). This valueis comparable well with that of the well-established groove bindingrather than classical intercalator agent [33].

3.4.2. Ethidium bromide fluorescence displacement experimentsEthidium bromide (EB) fluorescence displacement experiments

were also performed in order to investigate the interaction mode of1 with CT-DNA. EB has been used to probe the interaction of thecomplex with DNA. In fact the EB fluorescence intensity will be en-hanced in the presence of DNA because of its intercalation into thehelix, and it is quenched by the addition of another molecule thatdisplaces EB from DNA [34]. Here, a significant decrease of the fluo-rescence intensity of EB bound to DNA at 584 nm was recorded byincreasing the concentration of 1 (Fig. 5).

This observation of EB fluorescence quenching leads us to de-duce that the copper(II) complex may interact with DNA throughthe groove binding mode, releasing some EB molecules from theEB-DNA system [35]. The quenching of EB bound to DNA by thecopper(II) complex is in agreement with the linear Stern–Volmerequation:

I0=I ¼ 1þ Ksv ½complex�

where I0 and I represent the fluorescence intensities in the ab-sence and presence of quencher, respectively. Ksv is the linearStern–Volmer quenching constant and [complex] the concentra-tion of the quencher. From the slope of the regression line inthe derived plot of I0/I versus [complex] (Fig. 6), the Ksv valuefor the copper(II) complex was found to be 10.0 � 104

(R = 0.99596 for five points), indicating a strong affinity of the cop-per(II) complex to CT-DNA.

0 2 4 6 8 10 122.5

3.0

3.5

4.0

4.5

5.0

5.5

[DN

A]/(ε

a-εf)x

1010

[DNA]x106

Fig. 4. Plot of [DNA]/(ea � ef) vs. [DNA] for the titration of CT-DNA with 1 in tris–HClbuffer; binding constant Kb = 0.8 � 105 M�1 (R = 0.99376 for six points).

400

800

1200

1600

2000

2400

edcba

e

a

Inte

nsity

Wave length (nm)550 600 650 700 750

Fig. 5. Emission spectra of the CT-DNA–EB system in tris–HCl buffer based on thetitration of copper(II) complex 1. kex = 522 nm; [EB] = 0.96 � 10�6 mol L�1;[DNA] = 2.07 � 10�5; [Complex]: (a) 0.0, (b) 0.82 � 10�6, (c) 1.64 � 10�6, (d)2.46 � 10�6, (e) 3.28 � 10�6 mol L�1. The arrow indicates the increase of thecomplex concentration.

0.00 0.75 1.50 2.25 3.00 3.75

1.0

1.1

1.2

1.3

1.4

I 0/I

[Complex]×106

Fig. 6. Plot of I0/I vs. [complex] for the titration of CT-DNA–EB system with 1 usingspectrofluorimeter; linear Stern–Volmer quenching constant (Ksv) for 1 = 10.0 �104; (R = 0.99596 for five points).

S. Dey et al. / Polyhedron 29 (2010) 1583–1587 1587

4. Conclusion

We synthesized a highly distorted square pyramidal penta-coordinated copper(II) complex having tridentate 2,6-bis-(benzim-idazolyl)pyridine ligand (L) and two water molecules in thecoordination sphere, formulated as [Cu(L)(H2O)2](NO3)2 (1). Thecrystal structure shows a 3D inorganic polymer through an H-bonding scheme involving aquo ligands and NH benzimidazolegroups. On reaction with pseudohalides in acetonitrile at roomtemperature, the more labile water molecule at axial position ofthe complex 1 was probably replaced to form penta-coordinatedmononuclear copper(II) complexes of formula [Cu(L)(X)(H2O)]NO3

[X = SCN� or N�3 ]. The interaction of 1 with CT-DNA has been stud-ied by using absorption and emission spectral techniques indicat-ing groove binding mode interaction.

5. Supplementary material

CCDC 740841 contains the supplementary crystallographic datafor this paper. These data can be obtained free of charge from

CCDC, 12, Union Road, Cambridge, CB21EZ, UK (fax: +44-1223-336-033; e-mail: deposit@ccdc.ac.uk or www.ccdc.cam.ac.uk).

Acknowledgements

Financial support from Department of Science and Technol-ogy (DST), New Delhi, India is gratefully acknowledged. E. Zangr-ando thanks MIUR-Rome, PRIN N 2005035123 for financialsupport.

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