Università degli Studi di Trieste Facoltà di Scienze Matematiche, Fisiche e Naturali - PDF

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Università degli Studi di Trieste Facoltà di Scienze Matematiche, Fisiche e aturali PhD Thesis in chemistry Design, preparation and structural characterization of new metalmediated supramolecular assemblies

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Università degli Studi di Trieste Facoltà di Scienze Matematiche, Fisiche e aturali PhD Thesis in chemistry Design, preparation and structural characterization of new metalmediated supramolecular assemblies of porphyrins Massimo Casanova Year 2008 UIVERSITÀ DEGLI STUDI DI TRIESTE Facoltà di Scienze Matematiche, Fisiche e aturali DIPARTIMETO DI SCIEZE CHIMICHE XX CICLO TESI DI DOTTORATO I SCIEZE CHIMICHE DESIG, PREPARATIO AD STRUCTURAL CHARACTERIZATIO OF EW METAL-MEDIATED SUPRAMOLECULAR ASSEMBLIES OF PORPHYRIS Settore scientifico disciplinare CHIM03 Massimo Casanova COORDIATORE PROF. GIULIAA PITACCO RELATORE PROF. EZO ALESSIO CORRELATORE PROF. EIO ZAGRADO A mia zia Molti pensano che l'apprendere a fare le cose, diventando uno scienziato, faccia sparire il mistero. Ciò che io sento è che il mistero motiva e nutre la scienza. La scoperta approfondisce il mistero Manfred Eigen Contents Abstract Riassunto Introduction: 1 Chapter 1: Self-assembled metallacycles with pyrazine edges 19 Chapter 2: Trinuclear metallacycles: metallatriangle and much more 37 Chapter 3: Assembly of a multiporphyrin cycles 67 Chapter 4: Photoactive assemblies of porphyrins and Re(I) complexes 89 Chapter 5: Design and metal-mediated construction of molecular cages 109 Acknowledgements Abstract Abstract The Introduction reports an overview of the metal-mediated synthetic approach to supramolecular assemblies, and focuses in particular on systems containing porphyrins. Chapter 1 describes the unexpected formation and structural characterization, both in solution and in the solid state, of a simple trinuclear metallacycle, a neutral molecular triangle featuring octahedral Ru(II) fragments as corners and pyrazine (pyz) linkers as edges. In fact, the combination of the cis bis-acceptor precursor trans-[rucl 2 (dmso-s) 4 ] with the most rigid aromatic linear linker - pyrazine - leads, under a number of different experimental conditions, to the selective formation of the neutral molecular triangle [{trans,cis-rucl 2 (dmso-s) 2 (μpyz)} 3 ], rather than to the anticipated molecular square. The X-ray structural characterization of the trinuclear metallacycle and theoretical calculations allowed us to advance some reasonable hypotheses on the reason why the molecular triangle is preferred over the expected molecular square. Intrigued by such unexpected result, we decided to perform a thorough search of the pertinent literature: Chapter 2 contains, after a comprehensive classification of the trinuclear metallacycles reported in the literature to date, an exhaustive description of those that are structurally similar to the metallatriangle described in Chapter 1, i.e. that feature cis-protected metal fragments as corners and linear linkers as sides. In Chapter 3 the preparation and characterization of two simple porphyrin molecular tweezers are reported. The two compounds, of formula [t,c,c-rucl 2 (CO) 2 (Zn 4'MPyP) 2 ] and [fac- Re(CO) 3 Br(Zn 4'MPyP) 2 ], are composed of a neutral octahedral metal fragment, either Ru(II) or Re(I), that bears two zinc mono-pyridylporphyrins in cis position. The zinc ions inside the porphyrin cores have an axial position available for further coordination. Thus, the two bis-porphyrin compounds can behave as molecular tweezers and bind appropriate - linkers in the cleft between the two porphyrins. The formation of two axial Zn bonds leads to cyclic assemblies. The two tweezers were found capable of binding a guest molecule of cis-dipyridylporphyrin (4'-cisDPyP) with good affinity, thus forming stable tris-porphyrin metallacycles. In Chapter 4 the synthesis and structural characterization of new pyridylporphyrin-re(i)-bipy adducts, in which a porphyrin bears either one or four Re(I)-bipy fragments in peripheral position, are described in detail. A summary of their photophysical characterization (performed by the group of Franco Scandola at the University of Ferrara) is also reported. Abstract Our interest in this field was stimulated by recent papers from the group of Perutz that described complexes of formula [fac-re(co) 3 (3-pic)(bipy-M porph)] + (3-pic = 3-picoline, M = Zn or Mg), in which the porphyrin is connected to the bipy moiety through an amidic bond. Upon irradiation of the porphyrin chromophore, a fast photoinduced electron transfer process from the metalloporphyrin to the Re(I)-bipy fragment was observed. In our compounds, the dimer [fac-re(co) 3 (bipy)(4'mpyp)](cf 3 SO 3 ) and the pentamer [fac- {Re(CO) 3 (bipy)} 4 (μ-4'tpyp)](cf 3 SO 3 ) 4, the porphyrins are directly coordinated to the Re fragments through the pyridyl moieties. We also prepared the corresponding geometrical isomers obtained with 3' rather than 4' porphyrins: [fac-re(co) 3 (bipy)(3'mpyp)](cf 3 SO 3 ) and [fac-{re(co) 3 (bipy)} 4 (μ-3'tpyp)](cf 3 SO 3 ) 4. All new compounds were structurally characterized in the solid state by X-ray crystallography. The preliminar investigation showed that, despite the structural similarity between our systems and those described by Perutz (they are basically composed by the same fragments even though assembled differently), their photophysical behaviour is quite different. In the fifth and last Chapter of this thesis the synthesis of a new fascinating metal-mediated supramolecular cage of porphyrins of cylindrical shape and its structural characterization, both in solution and in the solid state, are described in detail. The molecular cylinder, whose X-ray structure is also reported, is composed by three metallacycles of zinc porphyrins, of formula [t,c,c-rucl 2 (CO) 2 (Zn 4'-cisDPyP)] 2, that are axially connected to two tridentate 1,3,5- pyridyl-2,4,7-triazine (TPT) linkers through six (pyridyl) Zn coordination bonds. This supramolecular architecture represents a further example, after the molecular sandwiches of porphyrins described by our group a few years ago, of how metallacycles of zinc-porphyrins can be conveniently used as building blocks for the facile construction of stable higher-order supramolecular assemblies. Chapter 5 also reports a preliminary investigation of the synthesis of a new slipped molecular sandwich of porphyrins. The newly-shaped supramolecular multiporphyrin assembly is formed by two slipped-cofacial, rather than flat, metallacycles of zincporphyrins axially connected through two linear linkers. Riassunto Riassunto ell'introduzione si riporta una panoramica sulla sintesi di supramolecole mediata da metalli e, in particolare, si focalizza l'attenzione sui sistemi contenenti porfirine. Il Capitolo 1 descrive l'inattesa formazione, per assemblaggio di frammenti lineari ed angolari a 90, di un semplice metallaciclo trinucleare neutro avente ai vertici frammenti ottaedrici di Ru(II) e, ai lati, molecole di pirazina (pyz). Il triangolo molecolare [{trans,cis-rucl 2 (dmso- S) 2 (μ-pyz)} 3 ], ottenuto per reazione tra il precursore cis bis-accettore [trans-rucl 2 (dmso-s)4] e la pirazina, il più corto e rigido dei leganti aromatici lineari, è stato caratterizzato sia in soluzione che allo stato solido. L atteso quadrato molecolare è stato osservato soltanto come specie transiente. La caratterizzazione strutturale ai raggi X del triangolo molecolare e successivi calcoli teorici hanno permesso di avanzare alcune ipotesi sulle ragioni per le quali l'addotto triangolare risulta favorito rispetto al quadrato. In seguito a questi risultati inattesi, è stata svolta una approfondita ricerca bibliografica sulla letteratura pertinente. Il Capitolo 2 contiene, oltre ad una classificazione dei numerosi tipi di metallacicli trinucleari riportati in letteratura, un'esauriente descrizione di quelli strutturalmente simili al caso riportato nel Capitolo 1, cioè aventi frammenti metallici cisprotetti ai vertici e leganti ditopici lineari ai lati. el Capitolo 3 sono riportate la sintesi e la caratterizzazione di due semplici esempi di pinze molecolari. I due sistemi, aventi rispettivamente formula [t,c,c-rucl 2 (CO) 2 (Zn 4'MPyP) 2 ] e [fac- Re(CO) 3 Br(Zn 4'MPyP) 2 ], sono entrambi composti da frammenti metallici neutri, Ru(II) o Re(I), con due zinco-monopiridilporfirine coordinate in posizione cis. Dal momento che lo ione zinco predilige la pentacoordinazione, la sua inserzione nelle due porfirine adiacenti introduce nel sistema due nuovi siti di coordinazione assiali sfruttabili per ulteriori reazioni. Questi complessi possono quindi essere considerati come pinze molecolari capaci di coordinare appropriati guest azotati, tramite due legami assiali Zn, con la conseguente formazione di sistemi ciclici di porfirine. I due complessi studiati si sono dimostrati capaci di coordinare una molecola di cis-dipiridilporfirina (4'-cisDPyP) con buona affinità, formando metallacicli trisporfirinici stabili. el Capitolo 4 vengono riportate la sintesi e la caratterizzazione di nuovi sistemi piridilporfirina-re(i)-bipy, nei quali le piridilporfirine possiedono uno o quattro frammenti luminescenti Re(I)-bipy coordinati perifericamente. È inoltre riportata una breve descrizione Riassunto della loro caratterizzazione fotofisica (effettuata presso il gruppo di ricerca del Prof. Franco Scandola dell'università di Ferrara). Il nostro interesse nei confronti di questi sistemi è stato stimolato dalle recenti pubblicazioni di Perutz e collaboratori nelle quali vengono descritti diadi di formula generale [fac-re(co) 3 (3-pic)(bipy-M porph)] + (3-pic = 3-picolina, M = Zn o Mg): in tali composti la metallo-porfirina è connessa, tramite un legame ammidico, ad un frammento bipy che si coordina al renio. In questi sistemi l'irradiazione del cromoforo porfirinico induce un rapido trasferimento elettronico dalla porfirina al frammento Re(I)- bipy. I complessi da noi preparati e caratterizzati, sia in soluzione che allo stato solido, sono il dimero [fac-re(co) 3 (bipy)(4'mpyp)](cf 3 SO 3 ), il pentamero [fac-{re(co) 3 (bipy) 4 (μ-4'tpyp)] (CF 3 SO 3 ) 4 e i corrispettivi isomeri geometrici, [fac-re(co) 3 (bipy)(3'mpyp)](cf 3 SO 3 ) e [fac- {Re(CO) 3 (bipy)} 4 (μ-3'tpyp)](cf 3 SO 3 ) 4, ottenuti utilizzando le 3' invece delle 4'- piridilporfirine. In tutti i casi la porfirina è direttamente coordinata ai frammenti metallici Rebipy tramite i gruppi piridilici. Studi preliminari dimostrano che, malgrado le analogie strutturali tra i due tipi di composti, che sono costituiti essenzialmente dagli stessi cromofori seppure assemblati in modo differente, il loro comportamento fotofisico è differente. el quinto ed ultimo Capitolo di questa tesi vengono descritte la sintesi mediata da metalli e la caratterizzazione, sia in soluzione che allo stato solido, di una nuova gabbia molecolare di porfirine di forma cilindrica. Il cilindro molecolare ottenuto, del quale è riportata anche la struttura ai raggi X, è composto da tre metallacicli di zinco-porfirine di formula [t,c,c- RuCl 2 (CO) 2 (Zn 4'-cisDPyP)] 2 connessi assialmente a due molecole di legante tritopico azotato 1,3,5-piridil-2,4,7-triazina (TPT) tramite la formazione di sei legami Zn (piridile). Questo sistema supramolecolare è un ulteriore esempio, dopo i molecular sandwich di porfirine descritti dal nostro gruppo in precedenti pubblicazioni, di come i metallacicli di zinco-porfirine siano degli ottimi componenti per la facile costruzione modulare di elaborati sistemi supramolecolari contenenti numerosi cromofori porfirinici. Inoltre, in questo capitolo è riportato uno studio preliminare sulla sintesi di nuovi sandwich di porfirine aventi geometria sfalsata. Questa nuova tipologia di addotti è formata da metallacicli di zinco-porfirine con geometria a scalino, anziché planare, coordinati assialmente tramite connettori lineari. Introduction Metal-mediated self-assembly of supramolecular systems Central to supramolecular chemistry 1 is the concept that assemblies of molecular components (supramolecular structures) can be designed to perform relatively elaborate and useful tasks. The concept is currently being applied to the design of supramolecular systems capable of mimicking, at the molecular level, functions normally performed by natural systems or by artificial macroscopic devices (e.g. molecular-level machines). 2,3 Thus, supramolecular chemistry can be viewed as the basis for a bottom-up approach to the challenging fields of molecular electronics and nanotechnology. 4 Moreover, the formation of supramolecular entities represents an abiological analogue of numerous biological processes mediated by collective interactions and recognition events between large molecules. In synthetic supramolecular chemistry the structural complexity is achieved by self-assembly and self-organization of predetermined fragments through non-covalent bonds; in this modular approach the synthetic effort concerns the preparation of relatively small and simple units (building blocks). Self-assembly is a highly convergent synthetic approach and it has been employed to design a variety of discrete supramolecular assemblies, making use of molecular recognition through hydrogen bonds, electrostatic and π-π stacking interactions, and coordination bonds to transition metal ions. 1,5 Indeed, recent years have witnessed a growing number of supramolecular systems that incorporate metal ions as assembling and organizing centers. 5 Metal-ligand coordinative bonding offers a series of advantages over the other non-covalent interactions, 5 including: 1) thermodynamic features: metal-ligand bonding interactions are strong (bond energies of kj/mol per interaction) and have a greater directionality compared to electrostatic and π-π stacking interactions or even hydrogen bonding; 2) kinetic features: the relative inertness (or lability) of coordinative bonds can be fine-tuned according to the nature and oxidation state of the metal centers. Kinetically inert metal centers provide access to those assemblies which form most rapidly, while kinetically labile metal centers allow for the generation of supramolecular architectures at thermodynamic equilibrium. Since self-assembled discrete supramolecules are normally favoured thermodynamically over oligomeric or polymeric systems, both by enthalpic and entropic effects, the equilibrium between the constituent building blocks and the final product produces, in principle, self-healing assemblies that are relatively defect-free; 3) great versatility: the large and diverse number of coordination geometries of transition-metal ions can be exploited in the construction of elaborate assemblies; 4) precise control over the 1 Introduction architecture (shape and size) as well as of the charge and polarity (and thus solubility) of the assemblies; 5) good yields, inherent in the convergent self-assembly process; 6) ease of introduction of functionalities into the supramolecular assembly through the metal centers (e.g. redox, photophysical, magnetic properties) and/or through the ancillary ligands (e.g. chirality). 3, 5 Within this modular approach, defined by Mirkin and Holliday as the directionalbonding approach, 6 the structural units of the supramolecular assemblies can be reduced to simple rigid geometric figures with their ends acting as linkage points. In addition to their shape, the building blocks can be usefully classified in terms of their electron donor/acceptor properties. In fact, most of the metal-mediated assemblies reported to date have been obtained by treatment of metal complexes (acceptor building blocks) with bi- or polydentate organic linkers with suitable donor atoms (mainly nitrogen) in a desired spatial orientation (donor building blocks). Thus, the final shape, dimension, and topology of the self-assembled architecture will be defined by the coordination numbers and geometries of the metal centers as well as by the shape and geometry of the linkers, including the number and relative orientations of the peripheral basic sites (Scheme 1). Building blocks Blocks Scheme 1. Molecular polygons and polyhedra created via systematic combination of polytopic building blocks with predetermined angles: acceptor building blocks are depicted in red whereas donor building blocks are depicted in blue. The metal centers utilized can be either naked ions (in which case the coordination number and the geometry are embedded in the nature of the ion) or coordination compounds in which the number and geometry of the coordination sites available for the construction of the macromolecule are controlled by the other non-participating ligands. 2 Introduction A topic of particular interest is the construction of supramolecular two-dimensional and three-dimensional macrocycles through a modular metal-mediated synthetic approach. The general self-assembly principle has been applied to the design of three-dimensional architectures such as molecular cages and cage-type receptors of controllable size and shape. Fujita and Biradha coined the term molecular paneling to describe the construction of three-dimensional structures by linking two-dimensional, multidentate, planar organic components (panels) through metal coordination complexes. 7 Relatively small changes in the nature of the linkers may lead to final assemblies with very different architectures; for example, Fujita and coworkers described two compounds formed by self-assembly of the ditopic cis-protected acceptor building block [Pd(en)] 2+ (en = ethylenediamine), with two very similar tridentate triazine-based linkers, L1 = 2,4,6-tris(3- pyridyl)-1,3,5-triazine and L2 = 2,4,6-tris(4-pyridyl)-1,3,5-triazine, which differ only in the position of the peripheral atoms. The resulting assemblies share the same M 6 L 4 stoichiometry but have quite different structures: [{Pd(en)} 6 (L1) 4 ][O 3 ] 12 is a nanometersized macrotricycle, while [{Pd(en)} 6 (L2) 4 ][O 3 ] 12 is an adamantoid nanocage. 4,5,7,8 It may happen that the combination of a pair of donor/acceptor building blocks leads to a series of products that may, or may not, be in equilibrium. This phenomenon has been described as resulting in a «combinatorial library» When these products are in equilibrium, the system is described to form a «dynamic library». 13 Often single products can be isolated from a dynamic library by means of specific host-guest interactions. There are also examples of metal-containing donor fragments, i.e. complexed bridging ligands, in which the unbound termini of polydentate linkers are available for further coordination to other metal centers, thus leading to multi-metal assemblies The effectiveness and versatility of the metal-mediated self-assembly approach toward the synthesis of elaborate architectures is astonishing. In slightly more than two decades from the first report of a metal-mediated molecular square as described by Fujita and coworkers, 22 exciting tridimensional nanoscale assemblies, such as cuboctahedra and dodecahedra, 23,24 hexahedral capsules and nanotubes, 7b, 25, 26 nanometer-sized cubes, 27 and multicompartmental cylindrical nanocages 28 have been described. Metal-mediated assemblies of porphyrins The interaction between light and natural supramolecular systems is of paramount importance for life on earth, principally because plants and bacteria, by means of 3 Introduction sophisticated supramolecular arrays of chromophores, convert solar energy into chemical energy. These supramolecular systems are based on sets of several chlorophylls or related chromophores arranged in a well-controlled geometry and displaying precisely defined electronic properties. These assemblies of tetrapyrrolic chromophores (i.e. porphyrins) are found both in the photosynthetic reaction centers (RCs) and in the various light harvesting complexes of plants and photosynthetic bacteria (Figure 1). 29,30 Figure 1. Top left: X-ray structure of an integral membrane light-harvesting complex from photosynthetic purple bacterium Rhodopseudomonas acidophyla. Right: Schematic picture of a photosynthetic reaction center from the bacteri
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