From metal-nucleobase chemistry towards molecular wires

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Inorganica Chimica Acta 362 (2009) 691–706

Review

From metal-nucleobase chemistry towards molecular wires

Felix Zamora a,*, M. Pilar Amo-Ochoa a,b, Pablo J. Sanz Miguel a, Oscar Castillo c

a Departamento de Quımica Inorganica, Universidad Autonoma de Madrid, 28049 Madrid, Spainb Departamento de Tecnologıa Industrial, Universidad Alfonso X ‘‘El Sabio”, 28691 Villanueva de la Canada, Madrid, Spain

c Departamento de Quımica Inorganica, Facultad de Ciencia y Tecnologıa, Universidad del Paıs Vasco, Apartado 644, E–48080 Bilbao, Spain

Received 29 November 2007; received in revised form 1 February 2008; accepted 6 February 2008Available online 20 February 2008

Dedicated to Prof. Bernhard Lippert for his continuous scientific support and friendship.

Abstract

This manuscript is a short account on the recent research developed in our Nanochemistry group. Our initial research in the field ofmetal-nucleobase chemistry, in Prof. B. Lippert’s laboratory, subsequently evolved towards exploring feasible candidates to DNA basedmolecular wires and progressed in our current investigation in 1D coordination polymers with short metal–metal distances comprisingnucleobases as terminal or bridging ligands. The selection of 1D coordination polymers is understood as a structural simplification of thenew form of DNA named M-DNA. Several aspects concerning the systematic search of new adsorption methods for coordination poly-mers on surfaces and their morphological and physical characterization as well as the use of computational methods as a tool for thedesign of suitable molecular wires are described.� 2008 Elsevier B.V. All rights reserved.

Keywords: Metal-nucleobase complexes; Coordination polymers; Molecular wires; Nanochemistry; Nanomaterials

Felix Zamora was born in Cuenca, Spain in 1967. He obtained his PhD in Inorganic Chemistry in Universidad Autonoma de

Madrid (UAM) in 1994. Afterwards, he joined and enjoined, very much, the group of Prof. B. Lippert in postdoctoral

research centered on metal-organic chemistry with mercury, gold and nucleobases. In 1996, he returned to the Department of

Inorganic Chemistry (UAM) as Assistant Professor. He became ‘‘Prof. Titular” in 2002 in the same Department. His

research interest deals with nanomaterials based on coordination polymers, in particular those using nucleobases as ligands.

Special emphasis is devoted in the development of methods to organize these nanomaterials on surfaces and the study of their

electrical, magnetical and molecular-recognition properties as ‘‘single molecules” by means of methods based on Atomic Force

Microscopy.

0020-1693/$ - see front matter � 2008 Elsevier B.V. All rights reserved.

doi:10.1016/j.ica.2008.02.029

Abbreviations: 1-MeUH, 1-methyluracil; 1,3-DiMeU, 1,3-dimethyluracil; 1-MeC, 1-methylcytosine; 9-MeA, 9-methyladenine; 9-EtA, 9-ethyladenine; 9-EtGH, 9-ethylguanine; 6-MP, 6-mercaptopurine; 9-MeHxH, 9-methylhypoxantine; dien, ethylenediamine; am, NH3 or amine; ox, oxalate; trz, 4-amino-1,2,4-triazole or 1,2,4-triazole; M-DNA, metallic DNA; AFM, atomic force microscopy; EFM, electrostatic force microscopy; DFT, density functionaltheory.

* Corresponding author. Tel.: +34 91 497 3962; fax: +34 91 497 4833.E-mail address: [email protected] (F. Zamora).

mailto:[email protected]

Ma Pilar Amo Ochoa was born in Cuenca, Spain. She obtained her BSc (1990) and Doctoral Studies (1995) in the

Autonoma University of Madrid. Afterwards, she spent one year as a postdoc working on Complexes of Mercury with

Nucleobases under the supervision of Prof. B. Lippert (1996) in Dortmund University (Germany). Presently, she is ‘‘Prof.

Titular” at the Universidad Alfonso X ‘‘El Sabio” (Madrid) and posdoctoral researcher at the Universidad Autonoma de

Madrid. Her current research interest is centered in synthesis, characterization and potencial applications as nanowires of

one-dimensional of coordination polymers, working in the Nanomaterials group of Dr. Felix Zamora.

Pablo J. Sanz Miguel was born 1974 in Zaragoza, Spain. He has his master degree from the University of Zaragoza. He then

joined the research group of Professor Bernhard Lippert, completing his Dr. rer. nat. at the University of Dortmund

(Germany, 2005) under his supervision. The title of his thesis was ‘‘Model Nucleobases and their Metal Complexes:

Hydrogen Bonding Patterns, Cytosine Deamination, Metal Migration, and Building Blocks for Architectures”. He is cur-

rently working as a post-doctoral fellow (Juan de la Cierva) with Dr. Felix Zamora at the University Autonoma of Madrid

(Spain) on nanomaterials.

Oscar Castillo was born in Vitoria, Spain, in 1974. He obtained his PhD from the Basque Country University in 2001, where

he is an associate professor at the Sience and Technology Faculty of since then. His current areas of interest include

supramolecular recognition processes between nucleobases and metal-organic frameworks, design of 1D and 2D coordination

compounds and their processability as nanomaterials, and magneto-structural correlations on coordination compounds con-

taining aromatic bridging ligands.

692 F. Zamora et al. / Inorganica Chimica Acta 362 (2009) 691–706

Contents

1. Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6932. Work on metal-nucleobase chemistry. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 693

2.1. Metal-nucleobase complexes as biological models. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 693
2.1.1. Mercury–uracil and -cytosine systems . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6932.1.2. Gold uracil system . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6942.1.3. Zn(II) and Cd(II)-nucleobase chemistry . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6952.1.4. Pt(II)–cytosine: migration and deamination. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 697
2.2. Molecular architecture with metal ions and nucleobases . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 698
2.2.1. Metalloligands: PtII(nucleobase)4 and PtII(pyrazine) systems . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6982.2.2. Discrete cages. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 699
3. Molecular wires . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 699
3.1. M-DNA and the approach to this molecule through coordination polymers . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7003.2. Development of adsorption methods for coordination polymers on surfaces . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 700
3.2.1. Casting solution from dispersions obtained by sonication and ultracentrifugation. . . . . . . . . . . . . . . . . . . . 7013.2.2. Casting solution of polyanions generated by deprotonation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7013.2.3. ‘‘In situ reaction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7023.2.4. Extrapolation to other polymeric coordination systems . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 702

3.3. Electrical characterization . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 704
3.3.1. DFT calculations to confirm electrical characterization and to assist the design . . . . . . . . . . . . . . . . . . . . . 704
4. Conclusion . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 705Acknowledgments . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 705References . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 705

F. Zamora et al. / Inorganica Chimica Acta 362 (2009) 691–706 693

1. Introduction

The aim of this article is to provide a short account ofour present research. We will focus on our main currentgoal which is the use of nucleobase coordination polymersas molecular wires. We will show how this idea came to usas the result of our initial research on metal-nucleobasechemistry, which was developed during the course of ourwork in Prof. Lippert’s laboratory. For all of us the timeworking in Dortmund was not only an amazing scientificexperience but also rather an important part of our per-sonal formation.

2. Work on metal-nucleobase chemistry

The research carried out by us in Prof. Lippert’s labora-tory can be classified in two broad groups: (i) metal-nucle-obase complexes as biological models and (ii) moleculararchitecture involving metal centers and nucleobases.

2.1. Metal-nucleobase complexes as biological models

Metal-nucleobase complex properties and their struc-tural studies can provide suitable models (biomimetic sys-tems) which might help the understanding of metal ions,biological effects. They are relatively simple models usefulto understand the role of action of metal ions in biologicalsystems; in particular, we were interested in systems involv-ing metal ions and nucleobases as models for the interac-tion of those metals with DNA. The work developed in

Scheme 1.

Fig. 1. 1H NMR spectra of Hg(NO3) (1,3-DiMeU-C5)

this field by Prof. B. Lippert during years has been mainlycentered in platinum and palladium chemistry. In addition,most of us were also working with mercury and gold.

2.1.1. Mercury–uracil and -cytosine systems

Starting out from a previous work in which the mercurycoordination to uracil and cytosine C(5) position wasreported [1], and due to the little research carried out toassess the possible biological relevance of such reactions,our first incursion in the metal-nucleobase field wasfocused in the development of basic cytosine and uracilHg(II) coordination chemistry aspects, and occasionallywith other transition metal ions. In particular, we prepared(i) complexes containing two or more metal ions simulta-neously bound and (ii) complexes containing the metalentity bound to the C(5) position of the pyrimidine ring[2]. These compounds were obtained by the metal electro-philic attack to the 5-position rendering the aromatic pro-ton substitution. We initially tried a twofold objective: (i)establish basic (1H, 199Hg) NMR aspects on relevant solu-tion species derived from (L-C5)HgII (L = 1,3-DiMeU and1-MeC); and (ii) synthesise new bis(nucleobase)complexesby replacing the acetate anion with several nucleobaseswhich were different from previously studied ‘‘metal-modi-fied base pairs” [3] containing metal–carbon bonds insteadof metal–nitrogen bonds only.

The starting compound, Hg(CH3COO)(1,3-DiMeU-C5), was obtained upon the direct reaction of the modelnucleobase 1,3-dimethyluracil with Hg(CH3COO)2

(Scheme 1). The bond formation reaction was performedin water at 50 �C in good yield. Similar reactions with1-methylcytosine were carried out. The formation of theHg–C(5) uracil/cytosine bond was clearly confirmed by1H and 199Hg NMR [2].

Substitution reactions of the acetate group proceededvery fast and allowed to obtain a variety of new derivativeswith halides and pseudohalides, HgX(L-C5). Not only X-ray crystallography strongly suggested mercury binding

with a zoom showing 199Hg satellites indicated (*).


to uracil C(5) but 1H NMR spectroscopy was also a versa-tile tool to establish mercury–carbon bond formation sinceH(6) proton resonance (i) simplifies to a singlet, which isupfield shifted, and (ii) displays 3J coupling with the199Hg isotope. The trans donor atom to the uracil/cytosinemoiety has a significant influence on the value of the cou-pling constant: NO3

� > OAc� > Cl� � Br� > I� > SCN�

> CN� > 1,3-DimeU-C5, with extremes being 222 Hz(NO3

�) and 107 Hz (1,3-DimeU-C5) (Fig. 1) [2].It is noteworthy that in the course of these substitution

reactions, disproportionation of the halide and pseudoha-lide complexes took place to form the correspondingHg(L-C5)2 complexes. The Hg(1,3-DiMeU-C5)2 complex

Fig. 3. View of the [(1,3-DiMeU-C5)Hg]3O cation showing the Hg–Hginteractions.

Fig. 2. View of the Hg(1,3-DiMeU-C5)2 molecule.

Fig. 4. View of the [(1,3-DimeU-C5)Hg(9-MeA-N6)] cation.

was isolated as single crystals and characterized by X-raycrystallography [2]. Its structure consist of a mercury atomin a linear coordination sphere coordinated to both uracilligands via C(5) (Fig. 2). The two nucleobase rings arenot coplanar (dihedral angle, 64.9�). The molecule is chiraland both enantiomers are present in the crystal lattice.

Interestingly, the substitution reaction carried out onHg(CH3COO)(1,3-DiMeU-C5) with either KNO3 orAgNO3 led to substitution of the acetate by nitrate groupand subsequent hydrolysis formed the flat [(1,3-DiMeU-C5)Hg]3O pyramids [4]. The molecules display a chairlikearrangement of six mercury ions which are centrosymmet-rically related to each other and bridge via two edges of theHg3 triangles (Fig. 3). The Hg � � � Hg distances in the trinu-clear entities are 3.52 A and the distances between two ofthese entities are 3.55 A. The Hg � � � Hg interactionsbetween two pyramids are roughly orthogonal to the lineartwo-coordinate axis of each Hg, thereby generating a6-membered chair (Fig. 3).

In addition, substitution reactions of acetate by severalnucleobases, on the (1,3-DiMeU-C5)Hg(OAc), were stud-ied in order to obtain a feasible model of DNA/RNAHg(II) interaction [2]. It was particularly interesting to notethe reaction involving 9-MeA since a rare tautomer form ofthis nucleobase (imino) [5] characterized by X-ray diffrac-tion was allowed for the first time. In this compound, themercury center binds to the adenine via N6 and N1 remainsprotonated (Fig. 4). Therefore, the adenine is in its iminoform representing a rare tautomer form of this nucleobase(Scheme 2). Moreover, the X-ray crystal structure shows ananti orientation of the (1,3-DimeU-C5)Hg(II) moiety withrespect to N1 of 9-MeA, a substantial difference in nucleo-base standard geometry as compared to the amino tauto-mer form of 9-MeA [5].

2.1.2. Gold uracil system

The reaction between several uracil derivatives andKAuCl4 lead, among others, to unexpected diuracil species,by carbon–carbon bond formation (C5,C50). The mecha-nism of this process was initially unclear. To gain hintsabout the formation mechanism of this reactions, we triedthe reaction between KAuCl4 and 1,3-dimethyluracil, sincethis nucleobase presents the two nitrogen atoms blockedand, therefore, the number of reaction sites should bereduced. Thus, the reaction carried out between KAuCl4and 1,3-DimeU leads to metal binding to C5 site, followed

Scheme 2.

Scheme 3.

Scheme 4.

Fig. 5. View of the [Zn2Cl4(H2O)(l-9-EtGH-N7,O6)(9-EtGH-N7)] diho-mometallic molecule showing the intramolecular H-bond between themetallated guanines.


by oxidative dimerization to afford the di(1,3-DimeU-C5,C50) compound in good yield (Scheme 3) [6].

However, in the former reaction it was not possible toisolate any gold complex which may allow further detailsabout the mechanism of this process. To solve this prob-lem, a similar reaction was carried out but starting fromtrans-K[Au(CN)2Cl2] instead of Na[AuCl4]. In this case,the final product of the reaction was the expected 5-CN-1,3-DimeU. However, the K[Au(CN)2Cl(1,3-DimeU-C5)]species was isolated from the reaction and characterizedby X-ray diffraction. Its structure confirmed Au–C nucleo-base bond and suggested that the analogous K[AuCl3(1,3-DimeU-C5)] complex should be involved in the oxidativedimerization processes mentioned above for uracil nucleo-bases (Scheme 4) [7].

2.1.3. Zn(II) and Cd(II)-nucleobase chemistry

As a continuation of our initial works on mercury-nucleobases chemistry, we decided to extend them towardsthe rest of the 12-group metal ions, Zn(II) and Cd(II), aim-ing to obtain new DNA-interaction models. These twometal ions are of particular relevance in biological systemssince zinc is an essential biological element implicated inmany biological processes involving a large number of pro-teins and nucleic acid (DNA and RNA) interactions [8] andof special relevance in many human diseases; while cad-mium is a highly toxic metal and a potent carcinogen withan unknown mechanism of action. However, it has beensuggested that the direct or indirect binding of Cd(II) toDNA could induce its carcinogenesis activity.

In the case of Zn(II), several reactions with nucleobasemodels were carried out. The reaction between ZnCl2 and9-EtGH, in methanol, led to [Zn2Cl4(H2O)(l-9-EtGH-N7,O6)(9-EtGH-N7)] [9]. Its X-ray structure analysisrevealed that this complex consisted of a dinuclear speciesin which the two metallic centers showed a pseudotetrahe-dral coordination environment (Fig. 5). One Zn atom isbounded to guanine via N(7) acting as a bridging ligandthat coordinates to the other Zn via O(6). The second Znatom shows another guanine group, as terminal ligand,

binding to the metal center via N(7) position. The moleculeis stabilized by an intramolecular H-bond O(6)–N(1)between guanines. The Zn–Zn distance of 4.609 A is simi-lar to those found in several zinc multienzymes. This Zndimetallic complex was found to be a suitable model toexplain temperature-dependent unwinding and rewindingof DNA by guanine N(7)–Zn–N(7) guanine cross-linking,and provides structural evidences of a simultaneous Znbinding to N(7) and O(6) of guanine which could explainthat Zn(II) ions can prevent the quadruplex (G4)formation. The analogous reaction between ZnCl2 and9-methylguanine in water gives rise to [ZnCl2(H2O)-(9-MeGH-N7)] � (9-MeGH) [10]. In this compound, Zn(II)is linked to the N(7) position of guanine in a tetrahedralcoordination environment (Fig. 6a). The metalated guanineis involved in hydrogen bonding with a free 9-MeGH, whichin turn is centrosymmetrically related to itself via hydrogenbonds involving N(2)H2 and N3. This structure can be con-sidered as a model of a Zn–G �G� C triplet in DNA.

The similar reaction carried out with ZnCl2, 9-methylad-enine and 9-methylguanine affords [ZnCl2(H2O)(9-MeA-N7)] � 2(9-MeGH). The structure of this compound consists

Fig. 6. (a) View of the [ZnCl2(H2O)(9-MeGH-N7)] � (9-MeGH) with metalated and free 9-EtGH; (b) view of the [ZnCl2(H2O)(9-MeA-N7)] � 2(9-MeGH)of compound 4 with intermolecular H-bonding scheme between nucleobases.

Fig. 7. View of the polymeric chain and with the H-bonds in [Zn(9-EtA-N7)Cl3](9-EtAH).


of a tetrahedral Zn(II) complex in which Zn(II) is bound tothe N(7) of adenine instead of the expected coordination tothe N(7) of guanine, while two guanines remain uncoordi-nated. The metalated adenine base interacts via its Wat-son–Crick edge (N1, N(6)H2) with the sugar edge(N(2)H2, N3) of one of the free guanine nucleobase ofthe GG pair. Therefore, in both compounds the guanine–guanine hydrogen bonds involving the Watson–Crick edge(N(1)H, N(2)H2) of one base and the Hoogsteen edge[N(7), O(6)] of the other guanine–guanine are the predom-inant interaction in the solid state phase. The GG interac-tions lead to infinite ribbons. It is likely that the unusualbehavior of Zn(II) towards the N(7) position of adenineinstead of guanine could be due to the stability of theseguanine ribbons.

The compound [Zn(9-EtA-N7)Cl3](9-EtAH) was pre-pared by an unusual reaction between the [ZnCl2(6-MP)2]

(6-MP = 6-mercaptopurine) compound with 9-EtA(Fig. 7) [11]. While the reactions performed with severalZn(II) salts and adenine did not allow isolation or identifi-cation of any complex. The compound structure consists ofan anionic Zn(II) complex in which adenine coordinates tothe Zn atom of the ZnCl3 entity, via N(7), while an adeni-nium is acting as counterion. The metalated adenine isassociated by H-bonding: N(6)–H � � � N(1) and N(6)–H � � � N(7), leading to a polymeric ribbon-like 1Dsupramolecular arrangement. DFT calculations showedthe stability of the adenine–adeninium interaction due tothe coordination of the Zn(II) to the N(7) site of adenine.

The reactions carried out between two different Zn(II)salts and 1-MeC lead to two new Zn(II)-pyrimidine dimer.The [Zn2Cl4(l-1-MeC-O2,N3)2] in which the 1-MeCligands are bridging two ZnCl2 moieties and [Zn2(1-MeC-N3)4(l-SO4)2] � 2H2O in which the sulfates act as bridging


ligands. These complexes represent new models of Zn(II)–DNA/RNA interaction, opening the possibility to twoZn(II) ions connecting a base pair (Fig. 8) [12].

Two new complexes of Cd(II) with 9-alkylguanine,trans-[Cd(9-RGH-N7)2(H2O)4](NO3)2(R = Me, Et), havebeen prepared by the reaction of Cd(II) salts with the cor-responding 9-alkylguanine. The structures of these cationiccomplexes show the Cd(II) ions in a regular octahedralgeometry linked to N(7) position of two 9-alkylguanineligands in trans. Four water molecules coordinated toCd(II) in the equatorial plane complete its coordinationsphere (Fig. 9). This coordination mode led us to suggestthat GG bifunctional adducts may be involved in the car-cinogenesis of Cd(II), increasing the probability of muta-tions [13].

2.1.4. Pt(II)–cytosine: migration and deamination

The platinum–cytosine chemistry was widely studied inLippert’s laboratory. Our contribution was centered intwo main aspects observed on this metal nucleobase sys-tem: deamination of cytosine and N(3) ? N(4) metalmigration. To understand these observations, several PtII-N3-cytosine models were studied.

The reaction of [(dien)Pt(1-MeC-N3)]2+, at high pHand room temperature, results in [(dien)Pt(1-MeU-N3)]+

as a deamination product and in syn-[(dien)Pt(1-MeC�-N4)]+ andanti-[(dien)Pt(1-MeC-N4)]+ [14]. Analogous

Fig. 8. View of the two Zn(II) dimer complexes with 1-MeC [Zn2Cl4(

Fig. 9. View of the intra- and intermolecular H-bonding inter

reactions were observed in similar models. For instance,[(NH3)3Pt(N3-1-MeC)]2+ under the same conditionsundergoes only deamination, with [(NH3)3Pt(N3-1-MeU)]+ as the resulting product. Introduction of othermetal in the system, palladium, which reacts kineticallymore rapidly, allows only the migration product:[(dien)Pd(1-MeC-N3)]2+ suffers metal migration to form[(dien)Pd(1-MeC-N4)]+. Combinations of these tasksallow for different pathways to [(dien)M(N3-1-MeC-N4)M(dien)]3+ dinuclear species [15]. Therefore, deamina-tion of cytosine nucleobases is greatly facilitated by metalcoordination to the N(3) position. The detailed study ofthe platinum-assisted deamination of cytosine in somesystems reveals that the reaction does not require hightemperatures. Rather, after ca. 30 min at the temperatureof the human body (37 �C), the cytosine is fully con-verted into uracil [16]. In this context, we also demon-strated that metal migration processes do not requirehigh pH. The main product obtained from [Pt(1-MeC-N3)3I]I after several days at low pH was found to betrans-[Pt(1-MeC-N3)2I2] [17]. As a minor product, trans-[Pt(1-MeC-N3)(1-MeC-N4)I2] was also isolated, accordingto a postulated migration mechanism [18]. Evidently, therole of the exocyclic amino group in the different plati-num–cytosine systems seems to be essential, involvingnot only deamination and migration reactions, but alsopKa variation (acidification) of the sites [19].

l-1-MeC-O2,N3)2] (a) and [Zn2(1-MeC-N3)4(l-SO4)2] � 2H2O (b).

actions between trans-[Cd(9-MeGH-N7)2(H2O)4] cations.


2.2. Molecular architecture with metal ions and nucleobases

Apart from the complex formation, the structural char-acteristic of nucleobases allows to extend their coordina-tion chemistry towards the construction of more complexmolecular architectures based on supramolecule formationvia new metal-nucleobase bond formation using the initialmonomeric complexes as suitable building blocks to extendits nuclearity or connecting the mononuclear metal-nucleo-base complexes via multiple H-bonding using the availableH-bond donor–acceptor positions.

2.2.1. Metalloligands: PtII(nucleobase)4 and PtII(pyrazine)

systemsSome metal-nucleobase complexes have the ability to

behave as metalloligands towards metal ions. This suggeststheir potential to act as building blocks for molecular

Scheme

Scheme

architectures. In particular, PtII (nucleobase)4 and PtII

(pyrazine) systems have been successfully tested regardingthis purpose. Firstly, series of pyrazine (pyz) complexesderived from cis-(NH3)2PtII, (tmeda)PtII, and trans-(NH3)2PtII species [20]. Secondly, cations [PtII(9-EtGH-N7)4]2+, trans-[Pt(1-MeC-N3)2(9-EtGH-N7)2]2+, [Pt(9-MeHxH-N7)4]2+, and {[(H2O)Cu(O6-9-MeHxH-N7)4Pt]2Cu(ClO4)4}6+ [21].

A clear aqueous solution is obtained by the addition ofHClO4 to a suspension of trans-[Pt(NH3)2(1-MeU-N3)2], acompound of very low water solubility in water. The 1HNMR resonances of the uracil ligands are downfield fromthose of the starting trans-platinum complex with the for-mation of the trans-[Pt(NH3)2(1-MeUH)2](ClO4)2 � 2H2O.The former complex was isolated and characterized byX-ray crystallography. Its structure shows that Pt(II) isbound to the N(3) positions of the two 1-MeUH, which

6.

5.


are oriented head–head and are almost co-planar. Compar-ison of C–O bond lengths shows a lengthening of C(4)–O(4) suggesting that O(4) is protonated. The structuralanalysis suggests that the two neutral 1-MeUH ligandscoordinated to platinum are in the rare 4-hydroxo, 2-oxotautomeric form. Unfortunately, the errors in the bondlengths and angles of the two uracil rings do not permit adetailed structural discussion as well, which was possiblepreviously for the related complexes of 1-methyluracil hav-ing cis-geometries (Scheme 5). On the other hand, thetrans-[Pt(NH3)2(1-MeU-N3)2] has proved to behave as ametalloligand toward several metal ions (Ag+, Na+,Hg2+), binding these via exocyclic oxygen atoms, i.e.,O(4) [22]. Subsequently, HgII also binds to the C(5) sitewith the substitution of the aromatic proton and theformation of a Hg–C bond. Metal binding to O(4) of1-MeUH is feasible due to the residual basicity of thisoxygen atom as a consequence of deprotonation and Ptcoordination at N(3) (Scheme 5).

2.2.2. Discrete cages

The mixed dinuclear Pt–Hg complex trans-[Pt(am)2-(1-MeC2�-N3,N4,C5)Hg3X2]n+ synthesized by the reactionof trans-[Pt(am)2L2]2+ (am = NH3 or amine; L = 1-methyl-cytosine) followed by the exocyclic amino group deproto-

Scheme

Fig. 10. Spacefill representation of the octanuclear cation[{Pt(CH3NH2)2(C5H3N3O)2Hg 3(OH)}2].

nation and heterometallic ion binding represents suitablestarting materials for the preparation of larger aggregatessuch as tetranuclear complexes of the type trans-[Pt(CH3NH2)2(1-MeC2�-N3,N4,C5)Hg3X2]n+. Complexesof this type with various combinations of X were prepared.

The tetranuclear PtHg3 complexes (with X = H2O/OH�) undergo dimerization to produce the octanuclearcomplex {Pt(CH3NH2)2(C5H3N3O)2Hg3(OH)(NO3)}2]-(NO3)4 (Scheme 6) [23]. This molecular hexagon wasobtained by the electrophilic attack of the excess ofHg(OAc)2 at the C(5) position of both cytosine ligands giv-ing the tetranuclear PtHg3complex.

In this octanuclear structure, the tetranuclear PtHg3

entities are connected via OH bridges. The basic form ofthe centrosymmetric cation (+6) consists of a compressedhexagon, of 7 A (two sides) and 5.5 A (four sides) withall six metal (four Hg(II) and two Pt(II)) ions being copla-nar and forming the sides of the hexagon. The four nucle-obases and the two hydroxo groups represent the cornersof the hexagon. All metal ions and OH groups are almostcoplanar. In the crystal, Pt2Hg6 cations form infinite inter-lacing staircases. The intermolecular separation betweenthe platinum ions is 4.929(2) A (Fig. 10).

3. Molecular wires

A molecular wire is defined as a molecule (long andone-dimensional) which transports electrical charges withlow resistivity. Several candidates to molecular andnano-wires have been proposed in the last years with dif-ferent results. Currently, carbon nanotubes and DNAhave been the most promising candidates. Carbon nano-tubes are good electricity conductors; however, they pres-ent poor functionalization chemistry, and their synthesisstill encounter with the not well-controlled preparations.In contrast, DNA is a molecule with increasing impor-tance in material sciences. As a nanowire candidate, itpresents a well-known chemistry that allows the forma-tion of controlled architectures based on the sequencesself-assembly [24]; still, DNA behave as insulator, at leastfor lengths up to 30 nm [25,26]. The high structural capa-bility of DNA enables the formation of circuits on a tubeby the combination of selected DNA fragments. However,its none or low conductance has to be increased to be use-ful to this end.

7.


3.1. M-DNA and the approach to this molecule through

coordination polymers

Recently, we have started a new research project. Thebackground of this project is our initial formation onmetal-nucleobase chemistry; however, the main goal isfocused on the search of new perspectives towards poten-tial applications of these types of compounds.

The electrical characterization of DNA has been contro-versial. This molecule has been described from conductor[28] to insulator [29]. Currently, it is widely accepted thatit behaves as insulator up to 30 nm length. Severalapproaches try to increase conductivity on DNA by themodification of its electronic structure. A new molecularwire candidate based on DNA is the so-called M-DNA[27]. This DNA form was first described by Prof. Lee,and it consists of a substitution of the protons betweenguanine–cytosine and adenine–thymine by Zn(II), Ni(II)or Co(II) cations (Scheme 7). They reported that this sub-stitution is only achieved at a high pH (pH 8), and at lowestvalues this form reverses to DNA. However, its structure isnot clear and the electrical characterization is againcontroversial.

To overcome the well-known problems concerning thelow stability, unclear structure and controversial electricalproperties of the M-DNA, we decided to study this prob-lem from the simplest point of view using a M-DNAmodel. Our approach was based on the selection of a

Fig. 11. Representations of the suggested M-DNA structure with metal ionspolymer (left).

one-dimensional coordination polymer with a relatedstructure to that of M-DNA. The polymer selected wasthe 1D-coordination polymer [Cd(6-MP)2]n (6-MP =6-mercaptopurinate). The X-ray structure of this polymerwas well established by X-ray diffraction [30], and severalsynthetic pathways around the Cd-6MP system were stud-ied by us [31]. The structure of this polymer, while preserv-ing many of the features of M-DNA, is simpler and allowsaffordable modeling with ab initio techniques (Fig. 11).

3.2. Development of adsorption methods for coordination

polymers on surfaces

The processability of coordination polymers towardsnanosized entities is an essential step for any future nano-technological application. Coordination polymer architec-tures are well designed to be processed as nanomaterialssince a single polymeric complex chain falls into thenanometric size. In the initial steps on supramolecularcoordination chemistry, Prof. Lehn suggested the use ofcoordination polymers as promising nanomaterials [32].However, studies of the properties of such supramoleculesrequire their isolation and the use of suitable techniques fortheir physical and chemical characterization. In principle,this is not an easy task since most of the coordination poly-mers are described as insoluble materials with restrictedprocessability and in some cases with rapid degradationin solution and decomposition upon heating. Therefore,

inserted between the base pairs (right) and the [Cd(6-MP)2]n coordination


their manipulation towards suitable forms to study thesepotential nanomaterials seemed not trivial [33].

The first goal was clearly defined by the necessity ofappropriate adsorption methods for coordination polymersas ‘‘single” molecules on surfaces. As mentioned above, the[Cd(6-MP)2]n coordination polymer was selected for itsstructural similarities to M-DNA. A revision of theliterature concerning adsorption methods for coordinationpolymers was very scarce and restricted to few samples ontwo-dimensional systems. The few methods reported forthe adsorption of 2D coordination polymers are based onthe sublimation and deposition in separate stages of theirbuilding blocks and subsequent self-reaction and assem-bling by temperature annealing to provide the 2D networkon the surface [34]. This is a technically complicatedmethod which is only available under specific conditionsin ultrahigh vacuum experiments, as our objective wasthe electrical characterization of the molecules once theyare suitably adsorbed on the surfaces.

3.2.1. Casting solution from dispersions obtained by

sonication and ultracentrifugationThe [Cd(6-MP)2 � 2H2O]n framework shows none or

very low solubility in organic and inorganic solvents. ItsX-ray structure shows that the 1D coordination polymerchains are connected to one another by means of indirecthydrogen bonds comprising crystallization water mole-cules. As the thermal decomposition profile of this polymerindicated that the crystal lost the water molecules withoutdecomposition between 150 and 350 �C, the polymer wastreated at 200 �C to furnish the anhydrous [Cd(6-MP)2]nspecies. Once the water molecules were removed, weassumed that the interchain connections should be mini-mized, leading to van der Waals interchain interactionssolely. Therefore, to disperse the chains of [Cd(6-MP)2]n,

Fig. 12. AFM topography image of the distribution of individual chains of [Cdthe X-ray diffraction crystal structure. Topographic AFM image of the polyacentrifugation on mica surface previously treated with ATPS (c) and height p

we decided to use ultrasounds. Thus, the crystals were sus-pended in dry ethanol and dispersed in an ultrasonic bath.The energy provided by the sonication led to the breakageof the intermolecular interactions, and probably some ofthe coordination bonds, leading to chain fragments. Thefinal solution was prepared by the deposition of a centri-fuged suspension droplet on a mica surface. The AFMtopographic characterization of the surface (Fig. 12a andb) shows the distribution of individual chains with a meanheight of 5.3 ± 1.4 A, which is in good agreement with theexpected diameter based on the X-ray diffraction studies.Using this simple procedure, large discrete chains (withlengths as long as 10 lm) were obtained.

3.2.2. Casting solution of polyanions generated by

deprotonation

Treatment of a homogeneous suspension of [Cd(6-MP)2]n with NaOH formed the soluble anionic coordina-tion polymer ½Cdð6-MP2�Þ2�n2n�. The polyanion wasisolated as single crystals, and X-ray diffraction analysescorroborated deprotonation on N(1) and N(9) positionsin the 6-MP ligands leading to the self-assembly of the gen-erated dimetallic subunits composed by parallel packed½Cdð6-MP2�Þ2�n2n� polyanions and ½CaðOH2Þ6�n2nþ polyca-tions, which are joined together by means of electrostaticinteractions and hydrogen bonds. For [Cd(6-MP)2]n, thepH of the synthetic media allows only single deprotonationof the 6-MP ligand. Linear neutral chains of formula[Cd(6-MP)2]n were obtained, which are packed togetherwith crystallization water molecules by an extensive hydro-gen-bond network (Fig. 12c and d). Therefore, the solubi-lization of [Cd(6-MP)2 � 2H2O]n in water in a basic mediumwas used as an alternative method to study the adsorptionon surfaces. Moreover, taking into account the effects ofthe deprotonation on a crystal of [Cd(6-MP)2 � 2H2O]n,

(6-MP)2]n on mica (a) with typical height of 6 A (b) in good agreement withnion obtained by deprotonation of [Cd(6-MP)2]n with NaOH and furtherrofile across the molecule (d).


where all the chains are neutral, one can easily realize thatthe negative charge acquired by the chains will generateintra-chain repulsive forces, leading to a disaggregationof the new anionic polymeric chains. AFM topographyimage of a droplet of this solution adsorbed on mica (pre-viously treated with aminopropyltriethoxy-silane), show alinear molecule of �0.5 nm height (value in agreement withthe X-ray height of a single polymer).

3.2.3. ‘‘In situ” reaction

The reaction between the 6-mercaptopurine and aCd(II) salt on a highly oriented pyrolytic graphite (HOPG)surface led to the formation of [Cd(6-MP)2]n upon heating.AFM images recorded immediately after solution deposi-tion did not show the organized structures. However, afterheating this surface at 80 �C for 1 h, the AFM topographyimage showed fibrous structures with a height ranging from0.5 to 5 nm, proving that in situ reaction leads to singlechains and fibers of [Cd(6-MP)2]n.

Fig. 14. AFM image of a homogeneous distribution of nanoobjects of [Mn(l-oheight profile (b). High pass AFM filtered image of [Mn(l-ox)(4-amino-1,2,4widths (c) and their height profiles (d). AFM topography image on mica otriazole)2] with NaOH (e) and a height profile (f).

Fig. 13. View of a chain of [Mn(l

3.2.4. Extrapolation to other polymeric coordination systems

Once the success on CdII/mercaptopurine system iso-lated chain adsorption was achieved, the group decidedto ensure that the adsorption methods employed wereof broader application. With this aim, a three-componentM/ox/trz (M = Mn(II), Co(II); ox = oxalate; trz = 4-amino-1,2,4-triazole or 1,2,4-triazole) 1D polymeric sys-tem was selected (Fig. 13). In both complexes, the metalcenters are linked by oxalate anions in a bisbidentatefashion. The remaining positions in the octahedral coor-dination environment are filled by two monodentatedtrz molecules in a trans arrangement. These features leadto linear polymeric chains which are linked together bydirect hydrogen bonding interactions between the aminogroup of the terminal ligand and the oxygen atoms ofthe oxalato bridge of an adjacent chain in the case ofthe 4-amino-1,2,4-triazole compound, and through non-direct hydrogen bonds involving crystallization watermolecules to connect the N4–H donor group and the

x)(4-amino-1,2,4-triazole)2] on mica (a) with a zoom of one particle and its-triazole)2] on HPOG showing a large number of rods with non-uniformf single chains obtained after the treatment of [Mn(l-ox)(4-amino-1,2,4-

-ox)(4-amino-1,2,4-triazole)2].


oxygen atoms of the oxalate as acceptors in the 1,2,4-tri-azole compound.

Sonication of a suspension of a [Mn(l-ox)(4-amino-1,2,4-triazole)2] in ethanol provides a homogeneous nano-particle distribution of 4 nm in height on mica surface, asevidenced by AFM topography. However, a high densityof linear chains was obtained upon adsorption of the sameethanolic suspension on HOPG with height values rangingbetween 0.5 and 1.0 nm, which is in agreement with theexpected diameter of a single polymer (Fig. 14). Con-versely, coordination polymer deprotonation with dilutedNaOH causes the chain liberation. The AFM images ofthe resulting solution deposited on mica indicated a lowchain density and it was also observed that as the lengthof the molecules increased, the probability of finding a mol-ecule dropped, indicating that NaOH treatment was prob-ably cutting the molecules by the oxidation of the Mn(II)cations (Fig. 14).

Following this work, we tried to exploit the coordina-tion polymer metal–ligand bond reversibility by thermal

Fig. 15. AFM topographic image showing different structures obtained by thesurface: rods (a), fibers and rings (c), with their height profiles. Isolation of single c

or mechanical (ultrasound) forces to give smaller oligomers[35]. In the following steps, the new generated fragmentscould be reassembled in solution and/or surface affordingthe original arrangement or new architectures. Sonicatedsuspensions of [Co(l-ox)(1,2,4-triazole)2] � 2H2O in ethanol(1 mg/mL) showed unspecific aggregates formation as wellas some chains of 3–6 nm height when deposited on HOPG(Fig. 15a). However, less concentrated solutions lead in thesame surface to well-ordered chains with heights rangingfrom 0.60 nm (the expected value for an isolated chain)to 35 nm and lengths as high as 20 lm with other typesof ordered structures such as rings, tailed rings and dots(Fig. 15b and c). These circular motifs were attributed toa lower concentration of the solution that makes an oligo-meric fragments recombination towards the original one-dimensional architecture more difficult. As previously men-tioned for the Mn(II) compound, deposition on a mica sur-face of sonicated suspensions in ethanol does not give anyorganization. However, using water as solvent fibers withlengths of several microns and heights ranging from 5 to

deposition of a solution of [Co(l-ox)(1,2,4-triazole)2] � 2H2O on a HOPGhains of [Co(l-ox)(1,2,4-triazole)2] � 2H2O on mica with its height profile (d).


13 A is generated on mica (with or without poly-L-lysinetreatment) (Fig. 15d). Furthermore, poly-L-lysine treat-ment of the mica surface increases its hydrophobicity,entailing a higher density of adsorbed molecules. All thesefacts are a clear indication that the natures of substrate,solvent, and coordination polymer play an important rolein the formation of nanostructures derived from thesesupramolecules. Finally, an in situ reaction with the threebuilding blocks from the one-dimensional coordinationpolymer was attempted: when a HOPG surface was dippedin a low concentrated solution containing stoichiometricquantities of Co(II), ox, and 1,2,4-triazole (1:1:2), longfibrous structures with heights ranging from 0.6 to 10 nmwere obtained (Fig. 15).

3.3. Electrical characterization

Conductivity studies of coordination polymers in bulkmaterial (single crystals or powder) suggest about thepotential metallic and semi-conducting behavior of the iso-lated chains [36–38].

However, it is essential to measure the electrical trans-port in individual polymers or nanofibers in order to testpotential applications for nano-electronics. Electricalproperties of isolated chains are the key for potential appli-cations as molecular wires, towards nanocircuits construc-tion. To perform an electrical characterization of molecularchains, these have to be isolated in a good density on aninsulated surface (i.e., mica). For this purpose, severalexperiments can be achieved. In the case of the [Cd(6-MP)2]n coordination polymer, its electrical characterizationwas carried out both by electrostatic force microscopy(EFM) and by conductance AFM. Using a metallizedAFM tip, a topographic image of several individual chainswas taken and compared with an electrostatic image of thesame region at 4 V. No differences were observed, indicat-ing that the chains are good insulators [39]. In a secondEFM experiment, a gold sharp electrode edge was placed

Fig. 16. High pass AFM filtered image of a single chain of [Cd(6-MP)2]n conapplying a tip-sample bias of 4 V (right) is shown.

on the surface by sublimation of a macroscopic gold elec-trode and further deposition using a mask [26]. Topo-graphic AFM images along the electrode edge showedsome polymer chains, which were partially covered by thegold electrode (Fig. 16). By grounding the electrode andapplying a bias of 4 V to the AFM tip, a clear electrostaticeffect on the gold electrode was observed. Nevertheless,molecules connected to the gold electrode remained unaf-fected (Fig. 16) [40], a result that also suggests that thechains are insulators.

Finally, direct measurement of the current along thepolymers was performed. If the metallic AFM tip isbrought into direct contact with the gold electrode, witha bias voltage of 100 mV, a current higher than 100 lAwas measured. In contrast, when the chains connected tothe gold electrode were contacted by the tip, no currentwas measured within our detection limits (�10 pA), eventhough the experimental setup allows to make the contactand to measure I–V characteristics at distances to the elec-trode as close as 50 nm, with the bias voltage rangingbetween ±8 V. Thus, it can be concluded that [Cd(6-MP)2]n chains are good insulators. To our best knowledge,this is the only study that deals with the electric propertiesof isolated chains of a coordination polymer.

3.3.1. DFT calculations to confirm electrical characterization

and to assist the design

Experimental measurements carried out for [Cd(6-MP)2]n were reinforced with DFT calculations, which indi-cate a large bandgap of 2.30 eV, small bandwidths (0.32 eVfor the highest occupied molecular orbital, HOMO) andthat the states with a large weight in the metal ions arelow in energy, well below the Fermi level [39]. Thus, metalatoms do not behave as a conducting metallic wire, butrather as a chain of cations in an ionic compound.

The high potential of DFT calculations as a tool for thedesign of new conductor coordination polymers has beenrecently investigated [41]. We have used first principle cal-

nected to a macroscopic gold electrode (left). The same AFM image but


culations for one-dimensional coordination polymers ofthe formula [M(6-MP)2]n (6-MP = 6-mercaptopurinate,M = Fe, Co, Ni, Cu, Ru, Pd, and Pt). Common stablestructures consistent with the experimental data have beenproposed. Polymers containing FeII, NiII, and CoII werefound to be ferromagnetic semiconductors, with magneticmoments of 4, 2, and 1 B, respectively. [Cu(6-MP)2]n showsa Peierls-unstable metallic phase that undergoes a transi-tion from paramagnetic metal to ferromagnetic semicon-ductor under small stretching. Calculated gaps indicatethat the polymer with Cu(II) may behaves as a metallicconductor, and the one with Fe(II) as a semiconductor.These results give a valuable suggestion for the design ofnew molecular wires based on one-dimensional coordina-tion polymers. Current efforts are centered on the synthesisof those polymers with smaller calculated gaps.

4. Conclusion

The emergent area of nanotechnology requires new pro-cedures to organize materials at the nanometer scale. In thecase of nanofibers with (nanowires) or without electricalconductivity, the 1D polymeric coordination compoundsare well suited.

This manuscript is a short account of our currentresearch centered on the search of new nanomaterialsbased on coordination polymers, towards their potentialuse as molecular wires. We described the adsorption meth-ods on several surfaces developed so far, which allow orga-nizing 1D coordination polymers as nanoobjects of diverseshapes. In particular, we have been able to isolate individ-ual chains from several coordination polymers followingdifferent procedures. The electrical characterization of thefirst isolated individual chains has shown to be insulated.However, developed adsorption methods have been provedto be satisfactory in several 1D coordination polymers.Current DFT calculations have been performed to designnew candidates with suitable electrical properties. Ourinterest concerning the use of nucleobases as terminalligands goes directly to our final goal: construction ofnanocircuits based on molecules. With this aim, we believethat the use of nucleobases is of interest since they mightallow to organized the molecular wires of the1D coordina-tion polymers on well-organized nanoarrays of DNA via

H-bonding formation [24]. Therefore, DNA will act astemplates of new molecular wires allowing the constructionof nanocircuits on a test-tube.

Acknowledgments

We acknowledge the financial support by the MEC(Projects No. CTQ2006-02840, MAT2004-05589-C02-01/02, MAT2007-66476-C02-02, NAN2004-09183-C10-06,FP6-029192 and CTQ2006-027185-E) and Comunidad deMadrid (Project S-0505/MAT/0303). We also to acknowl-edge Dr. G. Givaja for valuable comments. P.J.S.M.

thanks the Spanish MEC for a research contract (progra-ma Juan de la Cierva).

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