Inorganica Chimica Acta 321 (2001) 193–199

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Neutral metal complex in an ionic pocket: synthesis,physicochemical properties and X-ray structure of a copper(II)

complex containing neutral as well as cationic dafone ligands anddafonium perchlorate

Prasad Kulkarni a, Subhash Padhye a,*, Ekkehard Sinn b,*a Department of Chemistry, Uni�ersity of Pune, Pune 411 007, India

b Department of Chemistry, Uni�ersity of Missouri-Rolla, Rolla, MO 65401, USA

Received 1 March 2001; accepted 5 June 2001

Abstract

A neutral copper complex flanked by two protonated 4,5-diazafluoren-9-one (dafone, 1) ligands which are H-bonded with watermolecules and perchlorate anions has been structurally and electrochemically characterized. The capped copper compoundremains intact in solution, exhibiting a reversible Cu(II)/Cu(I) couple although undergoing a deformation along the Cu–N(2) axisand can serve as a good model of ionic pockets with metal active sites in some metalloproteins. © 2001 Elsevier Science B.V. Allrights reserved.

Keywords: Diazafluorenone; Copper(II); Crystal structures; Electrochemistry

1. Introduction

4,5-Diazafluoren-9-one (dafone, 1), which is a deriva-tive of 1,10-phenanthroline (phen), having an exocyclicketo function [1], has attracted attention of researchersdue perhaps to its DNA intercalation properties [2]. Inaddition, ruthenium complexes of 1 have been foundsuitable as building blocks for construction of photoac-tive supramolecular assemblies [3]. The reactive exo-cyclic keto function in 1 offers distinct advantages forfurther derivatization to yield multinuclear metal com-

plexes having interesting catalytic and biologicalproperties.

Unlike the case of phenanthroline ligands, coordina-tion chemistry of bidentate, neutral ligand 1 is stillrestricted to a few structurally characterized metal com-plexes [4–6]. The large N–N bite distance (2.99 A� )enforced by the rigid five-membered central ring leadsto unequal binding by the two nitrogen atoms withsmall metal ions like Cu(II) [5], although not in case oflarger metal atoms ones like ruthenium [6]. The differ-ences in the binding properties of phen and 1 may thusbe attributed to the reduced overlap of nitrogen orbitalswith the appropriate metal orbitals due to the largerbite distance in 1 [7]. A large variety of coordinationcompounds have been structurally characterized by usand others in which 1 is monoprotonated [8], biproto-nated [9] and semi/hemiprotonated with associatedhalometallate anions [8].

In an attempt to synthesize the tris–dafone complexof copper(II), we recently obtained a unique com-pound, having both neutral and cationic forms of 1 in

* Corresponding authors. Tel.: +91-20-565-6061x2076; fax: +91-20-565-1728.

E-mail address: sbpadhye@chem.unipune.ernet.in (S. Padhye).

0020-1693/01/$ - see front matter © 2001 Elsevier Science B.V. All rights reserved.

PII: S 0 0 2 0 -1693 (01 )00516 -3

P. Kulkarni et al. / Inorganica Chimica Acta 321 (2001) 193–199194

a single molecule. In the present communication wedescribe its synthesis, physicochemical properties andthe single crystal X-ray structure which shows the neu-tral copper complex flanked by two monoprotonateddafone cations in an arrangement resembling that of anionic pocket.

2. Experimental

Caution: although no problems were encountered in thepresent work, transition metal perchlorates are poten-tially explosi�e. They should be prepared in small quanti-ties and handled with care.

2.1. Materials

Dafone and Cu(dafone)2Cl2 were prepared accordingto reported methods [1,5].

2.2. Synthesis

2.2.1. Synthesis of[Cu(dafone)2Cl2][(dafoneH+H2O)]2(ClO4)2 (2)

The compound was synthesized by stirringCuCl2·2H2O (0.085 g, 0.5 mmol) with 1 (0.27 g, 1.5mmol) in 80% perchloric acid and warming the resul-tant mixture to 80 °C over a period of one hour. Slowevaporation of the reaction mixture at room tempera-ture (r.t.) yields blue green prismatic crystals in threeweeks. Anal. Calc. for C44H30N8O14Cl4Cu: C, 48.03; H,2.75; N, 10.18. Found: C, 48.15; H, 2.67; N, 10.51%. IR(Nujol, cm−1) 3390 (�N–H), 1735 (�C�O).

2.2.2. Synthesis of [dafoneH+(ClO4)] (3)The compound was prepared by crystallizing 1 from

80% perchloric acid in aqueous medium. The crystalstructure revealed it to contain protonated dafonecations with perchlorate counter anions. Anal. Calc. forC11H7N2O5Cl: C, 46.75; H, 2.49; N, 9.91. Found: C,47.24; H, 2.35; N, 10.13%. IR (Nujol, cm−1) 3300(�N–H), 1737 (�C�O).

2.3. Instrumental measurements

Elemental analyses were performed on HOSLYCHN analyzer, while IR spectra were recorded on aPerkin–Elmer IR1615 instrument. Cyclic voltam-mograms were recorded on a BAS CV-27 instrument inDMF solvent with tetraethyl ammonium perchlorate asthe supporting electrolyte using a three electrode systemconsisting of platinum disc electrode (2 mm diameter)as working electrode and saturated calomel and plat-inum wire as the reference and auxiliary electrodes,respectively.

2.4. Crystal Structure determination and refinements

The measurements on single crystals were made asdescribed previously [10] using a Rigaku AFC6S dif-fractometer with graphite monochromated Mo K� ra-diation. The crystal data and details of data collectionfor compounds 2 and 3 are included in Table 1.

2.4.1. Structure solution and refinement for 2The stoichiometry clearly requires Cu atom lie at the

cell origin; the halogen positions can then be read fromthe 3D Patterson map. This procedure phased the datasufficiently to locate the other atoms from differenceFourier maps. The non-hydrogen atoms were refinedanisotropically. Full-matrix least-squares refinement[11] was carried out using the TEXRAY [12] program set,giving unweighted and weighted agreement factors ofR=���Fo�− �Fc��/��Fo�=0.040. Rw= [� w(�Fo�− �Fc�)2/� wFo

2]1/2=0.043.The standard deviation of an observation of unit

weight [13] was 2.19. The weighing scheme was basedon counting statistics and included a factor (P=0.01)to downweigh the intense reflections. Plots of �w(�Fo�−�Fc�)2 versus �Fo�, reflection order in data collection,sin �/�, and various classes of indices showed no un-usual trends. Neutral atom scattering factors weretaken from Cromer and Waber [14]. Anomalous disper-sion effects were included in Fcalc [15]; the values of �fand �f � were those of Cromer [16].

2.4.2. Structure and refinement for 3Following similar procedure as described above the

unweighted and weighted agreement factors of R andRw for the crystals of 3 were found to be 0.043 and0.045, respectively.

3. Results and discussion

3.1. Crystal structure[Cu(dafone)2Cl2(dafoneH+H2O)2(ClO4)2] (2)

The molecular structure of the [Cu(dafone)2Cl2-(dafoneH+H2O)2(ClO4)2] (2) complex is shown in Fig. 1and selected bond distances and bond angles are givenin Table 2.

The unit cell contains just one formula unit of 2 withtwo distinct parts, viz. the central, neutral Cu(d-afone)2Cl2 compound and the two capping protonateddafone molecules associated with the perchlorate an-ions. In the central copper compound, the two nitrogendonor atoms (shown by the thick lines) and the twocoordinated chloride ions constitute an equatorial planewhile the remaining two nitrogen atoms (denoted bythin lines) occupy axial positions. The average equato-rial Cu–N distance is 1.998(2) A� , while the average

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Table 1Crystal data and data collection for compounds 2 and 3

32

Empirical formula CuCl4O14N8C44H30 ClO5N2C11H7

Formula weight 1100.1 282.6pink, fragmentgreen, prismsCrystal color, habit

0.55×0.25×0.20Crystal dimensions (mm3) 0.90×0.50×0.50triclinicCrystal system monoclinic25 (28.3–41.5°) 25 (30.4–47.5°)No. of reflections used for unit cell

determination (2� range)0.35Omega scan peak width at half-height 0.35

Lattice parameters9.182(2)a (A� ) 5.590(2)

17.508(2)b (A� ) 16.211(3)10.649(2)7.928(2)c (A� )

96.66(2)� (°)102.50(2)� (°) 105.80(1)

77.37(2)� (°)1106.1(8)V (A� 3) 1083.0(5)

P21/cSpace group P1�41Z

1.65Dcalc (g cm−3) 1.73F000 559 576

3.688.14� (Mo K�) (cm−1)Rigaku AFC6SDiffractometer Rigaku AFC6S

0.71069Radiation (Mo K�, �) (A� ) 0.710692120Temperature (°C)

6.0Take-off angle (°) 6.06.0 mm horizontal, 6.0 mm verticalDetector aperture 6.0 mm horizontal, 6.0 vertical

4040Crystal to detector distance (cm)�–2�Scan type �–2�

8°/min (in �)Scan rate 8°/min (in �)(1.73+0.30 tan �)(1.73+0.30 tan �)Scan width (°)54.12�max (°) 54.2total 2687, unique 2463 (Rint=0.033)total 5156, unique 4851 (Rint=0.024)No. of reflections measured

Lorentz-polarization, absorption (transCorrections Lorentz-polarization, absorption (transfactors: 0.77–1.32) factors: 0.94–1.00)

Fig. 1. Molecular structure of [Cu (dafone)2Cl2(dafoneH+

H2O)2(ClO4)2] (2).

axial Cu–N bond length is 2.650(2) A� . This arrange-ment is presumed to result from the large N(1)–N(2)bite distance (2.991(3) A� ). The Cu–Cl distance is2.3105(9) A� constituting an overall tetragonally dis-torted octahedral geometry around the central copperatom.

The chlorides are H-bonded to water molecules asso-ciated with the capping protonated dafone species withthe Cl(1)–O(7) distance of 3.190(3) A� . The outerdafone ligands are protonated and H-bonded to watermolecules while undergoing weak H-bonding interac-tions with the associated perchlorate anions. This ar-rangement can be correctly described as a neutralcopper complex in an ionic pocket with hydrogenbonds governing the intermolecular interactions. Simi-lar arrangements are often found at the metalloproteinactive sites, where the active site containing metal cen-ter is made available to a substrate through an ionicchannel [17].

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Table 2Selected bond lengths (A� ) and bond angles (°) for 2

Bond lengthsCu–Cl(1) Cl(2)–O(5)2.3105(9) 1.412(3)

Cl(2)–O(6)Cu–N(1) 1.414(3)1.998(2)O(1)–C(8)2.650(2) 1.212(3)Cu–N(2)

1.431(2)Cl(2)–O(3) O(2)–C(19) 1.200(4)Cl(2)–O(4) 1.425(3)

Intermolecular distancesO(5)–O(5) 3.181(6)(d)Cl(1)–O(7) 3.190(3)(a)O(6)–C(21)3.194(4)(b) 3.188(4)(e)O(1)–C(21)

3.004(4)(c)O(2)–C(19) O(7)–N(4) 2.680(4)(f)3.010(5)(c)O(2)–O(2) O(7)–N(3) 2.978(5)(f)3.164(4)(a)O(4)–C(11)

Bond anglesCu–N(1)–C(1)–128.8(2)180.00Cl(1)–Cu–Cl(1)�

90.00(7)Cl(1)–Cu–N(1) Cu–N(1)–C(5) 115.2(2)90.00(7)Cl(1)–Cu–N(1)� C(1)–N(1)–C(5) 115.9(2)

C(6)–N(2)–Cu180.00 95.9(2)N(1)–Cu–N(1)�N(1)–Cu–N(2) 78.73(8) C(6)–N(2)–C(11) 114.4(2)

C(11)–N(2)–Cu101.27(8) 149.7(2)N(1)–Cu–N(2)�86.52(6)Cl(1)–Cu–N(2) C(12)–N(3)–C(16) 113.7(3)93.48(6)Cl(1)–Cu–N(2)� C(17)–N(4)–C(22) 119.6(3)

180.00N(2)–Cu–N(2)

Symmetry operators: (a) −x, −y, −1−z ; (b) 1+x, y, z ; (c) −x,1−y, −z ; (d) −1−x, 1−y, −1−z ; (e) x, y, z−1; (f) x, y, z.

It is obvious that since capping is along the equato-rial chloride positions, Cu–Cl and Cu–N(1) distancesare elongated while axial Cu–N(2) distances are com-pressed in compound 2 resulting in reduction of thetetragonal distortion. Consequently bond angles in thepresent compound are modified to achieve more sym-metric structure.

3.3. Physicochemical properties

Compound 1 shows characteristic carbonyl stretchingfrequency at 1717 cm−1 which upon copper complexa-tion is slightly shifted to 1720 cm−1 in Cu (dafone)2Cl2.In compound 2, this frequency appears at 1735 cm−1

and is ascribed to the carbonyl moiety of the proto-nated dafone ligand. A similar increase in the frequencyis also observed in compound 3. The stretching fre-quency expected around 1720 cm−1 for the neutraldafone ligand is masked probably due to closeness ofthe two frequencies. Additionally both compounds 2and 3 show N–H stretching frequency around 3300cm−1.

Rillema and coworkers have examined the electro-chemical profiles of 1 and ruthenium complexes in

Fig. 2. Crystal structure of 3 (A) and crystal packing diagram for 3(B).

3.2. Crystal structure of [dafoneH+(ClO4)] (3)

The molecular structure and the packing diagram for3 are shown in Fig. 2 and selected bond distances andbond angles are summarized in Table 3.

The protonated dafone molecule in this compoundappears to be very much planar, the angles betweenadjacent fused rings being only 1°. One of the nitro-gens, N(1), is protonated and is hydrogen-bonded tothe oxygen, O(2), of the perchlorate anion at a distanceof 2.876(3) A� . The Cl–O bonds in the perchlorateanion show very little variation except for the Cl–O(2)bond which shows little lengthening (1.450(2) A� ) obvi-ously due to its association with the neighboring N(1)atom. The carbonyl bond length(C(13)–O(1)) in thiscompound is shorter (1.203(3) A� ) than that found inthe parent dafone molecule (1.212(3) A� ).

The crystal packing diagram for 3 is shown in Fig. 2which indicates four molecules of the compound in aunit cell. However, there are no significant intermolecu-lar interactions due perhaps to the absence of anypolarizable protons or lattice water molecules in thesecrystals.

It would be relevant to compare structural differ-ences between the free, neutral copper complex de-scribed by Rajasekharan et al. [5] and the presentcompound 2 (Table 4) as it can indicate constraintsimposed by the ionic pockets on metal active sites inproteins.

P. Kulkarni et al. / Inorganica Chimica Acta 321 (2001) 193–199 197

Table 3Selected bond lengths (A� ) and bond angles (°) for [dafoneH+(ClO4)](3)

Bond lengthsO(1)–C(13) 1.203(3) N(1)–N(8) 3.091(3)

N(1)–C(6)1.339(3) 1.335(3)N(1)–C(2)1.319(3)N(8)–C(7) N(8)–C(9) 1.352(3)

Cl–O(3)Cl–O(2) 1.421(2)1.450(2)Cl–O(5) 1.430(2)1.427(2)Cl–O(4)

Interionic distancesO(4)–C(4)2.876(3)(a) 3.001(3)(c)O(2)–N(1)O(5)–C(13)O(2)–N(8) 3.119(4)(c)3.095(3)(b)

Bond anglesN(1)–C(6)–C(7) 128.7(2)O(2)–Cl–O(3) 109.1(1)C(5)–C(6)–C(7)109.0(1) 110.5(2)O(2)–Cl–O(4)

O(2)–Cl–O(5) 108.2(1) N(8)–C(7)–C(6) 126.3(2)N(8)–C(7)–C(12)110.0(1) 126.3(2)O(3)–Cl–O(4)C(6)–C(7)–C(12)O(3)–Cl–O(5) 107.4(2)110.2(1)N(8)–C(9)–C(10)110.4(1) 124.6(3)O(4)–Cl–O(5)

120.3(2)C(2)–N(1)–C(6) C(9)–C(10)–C(11) 120.3(2)C(10)–C(11)–C(12)113.8(2) 116.5(2)C(7)–N(8)–C(9)

121.0(2)N(1)–C(2)–C(3) C(7)–C(12)–C(11) 118.6(2)120.2(2)C(2)–C(3)–C(4) C(7)–C(12)–C(13) 109.2(2)

C(11)–C(12)–C(13)117.4(2) 132.2(2)C(3)–C(4)–C(5)120.4(2)C(4)–C(5)–C(6) O(1)–C(13)–C(5) 127.0(2)

O(1)–C(13)–C(12) 128.2(2)C(4)–C(5)–C(13) 131.5(2)C(5)–C(13)–C(12)108.1(2) 104.8(2)C(6)–C(5)–C(13)

120.8(2)N(1)–C(6)–C(5)

Symmetry transformations: (a) x, y, z ; (b) −x, −y, 1−z ; (c) x,1/2−y, z−1/2.

served in case of protonated dafone ligand, which isabsent in the compounds containing neutral dafoneligand. (Fig. 3B)

The reversible redox couple at +0.54 V in com-pound 2 (Fig. 3B) is assigned to the Cu(II)/Cu(I) oneelectron process corresponding to the inner neutralcopper complex. The Cu(II)/Cu(I) redox couples forcopper complexes of phenanthroline derivatives gener-ally appears in the range of +0.1 to +0.8V dependingupon substitution [19,20]. The Cu(II)/Cu(I) redox po-tential for compound 2 is close to that for Cu(dmp)2

+

(+0.58 V) (where, dmp=2,9-dimethyl-1,10-phenan-throline) suggesting that 1 is as efficient as dmp instabilizing +1 oxidation state for copper ions [21].However, the reduction of Cu(II) to Cu(I) is not com-pletely reversible and small amount of Cu(I) is furtherreduced to Cu(0), which is plated on the electrodesurface. This can be easily concluded from the largestripping wave observed around −0.30 V upon succes-sive scans indicating dissolution of adsorbed copper dueto reoxidation reaction [22]. The peak at −0.57 V incompound 2 is assigned to the reduction of Cu(I) toCu(0) based on the isolation of cathodic peaks one byone. The oxidation peak at −0.30 V appears only afterscans were made up to −0.8 V on the negative direc-tion [23].

On the other hand, the Cu(dafone)2Cl2 complexshows Cu(II)/Cu(I) couple at +0.51 V which is slightlyshifted towards positive side compared to compound 2(Fig. 3A). The prominent peak at −0.73 V is assignedto reduction of Cu(I) to Cu(0) based on the peakisolation studies. Thus capping with two protonateddafone ligands seems to affect reduction of Cu(I) toCu(0) by stabilizing intermediate Cu(I) species as indi-cated by an increase in reversibility of Cu(II)/Cu(I)redox couple in compound 2. (Table 5) It is noteworthythat redox potentials of the metalloenzymes are simi-larly sensitive to the surrounding protein environmentand indicative of the reactivity of the metal centers [24].Thus capping of the central metal complex seems tohave a small but significant effect on the Cu(II)/Cu(I)redox couple in the present case, indicative of therelative stability of 2 towards redox reactions.

Table 4Structural differences in copper complexes of dafone

Cu(dafone)2Cl2aCompound 2

2.310(9)2.292Cu–Cl (A� )1.998(2)1.978Cu–N1 (A� )

Cu–N2 (A� ) 2.773 2.650(2)1.197C–O (A� ) 1.212(3), 1.200(4) b

N1–Cu–Cl (°) 91.30 90.00(7)93.11N2–Cu–Cl (°) 86.52(6)

N1–Cu–N2 (°) 78.73(8)76.60

a Ref. [5].b For protonated dafone cation.

detail [18]. Accordingly the first redox couple observedin 1 around −1.0 V is ascribed to the reversiblereduction of the exocyclic carbonyl group while theother observed at −1.6 V, is attributed to the reduc-tion of the phenanthroline moiety. The redox potentialsof the related dafone compounds in DMF solvents aresummarized in Table 5. All compounds showed a lig-and-based reversible redox couple around –1.0 V. Thisreduction is completely reversible in compound 1 and 3as calculated from scan rate dependence studies. Al-though in case of copper complexes the peaks do notshow any shift, its reversibility is considerably affected.An additional reduction peak around −0.35 V is ob-

Table 5Electrochemical data for dafone compounds

E° (for Cu(II)/Cu(I)) (V)E° (for carbonyl) (V)Compound

1 −1.00(97)+0.51(86)−0.99(65)Cu(dafone)2Cl2+0.54(92)−1.00(70)2

3 −1.03(94)

The numbers in parentheses are percent chemical reversibilities calcu-lated using variable scan speeds.

P. Kulkarni et al. / Inorganica Chimica Acta 321 (2001) 193–199198

Fig. 3. Cyclic voltammogram of Cu(dafone)2Cl2 (A) and compound 2(B).

result of energy minimization processes during latticepacking. IR spectroscopic data and electrochemicalprofiles are particularly able to differentiate betweenthe neutral and cationic forms of the dafone ligand.The capping also offers a thermodynamic stability tothe inner [Cu(dafone)2Cl2] center against decompositionand hence compound 2 can be regarded as a goodmodel for the ionic pocket with active metal sites foundin many metalloproteins [17].

5. Supplementary material

Atomic coordinates, details of bond lengths and an-gles and thermal parameters are available from theauthors on request.

Acknowledgements

PPK would like to acknowledge financial assistance(SRF) from CSIR (New Delhi, INDIA) while SBPwould like to thank the British Council for thevisitorship.

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