Programmable conformational regulation of porphyrin dimers on geometric scaffold of duplex DNA

DNA-porphyrin conjugates were designed and synthesized in which free-base and Zn-coordinated porphyrins were introduced to the N⁶-position of the internal adenosine. Conformations of the porphyrin dimer in the major groove of duplex DNA were controlled by changing the orientation and the distance between the two porphyrin moieties. The porphyrin dimers formed a thermally favorable face-to-face conformation on the duplex DNA. In the disadvantageous geometry for porphyrin dimer formation on the duplex, the porphyrins induced the DNA duplex structures to the Z-form conformation. These results indicate that the interaction of the two porphyrins and the conformation of duplex DNA are controlled by the program of DNA sequences.     

Diastereochemically controlled porphyrin dimer formation on a DNA duplex scaffold

DNA-porphyrin conjugates were designed and synthesized for the preparation of the conformationally controlled porphyrin dimer structures constructed on a d(GCGTATACGC)2. Porphyrin derivatives were introduced to the central TATpA sequence where p represents the phosphoramidate for the attachment of the free-base porphyrin (FbP) and zinc-coordinated porphyrin (ZnP), which allows contact of the two porphyrins in the minor groove. The porphyrin dimers were characterized using CD, UV-vis, steady-state, and time-resolved fluorescence spectroscopies, indicating that the porphyrins form face-to-face conformations. Also the co-facial conformation was confirmed by comparison with spectra of the non-self-complementary duplex containing one porphyrin moiety. Introduction of zinc into porphyrin moiety destabilized the duplex formation. Two diastereomers showed different thermal stabilities and affected the conformations of porphyrin dimers. The temperature-dependent assembly and the conformational change of the porphyrin dimer on the duplex DNA were observed in the UV-vis spectra, indicating that the dynamic movement of the porphyrin dimer occurs on the duplex. The results indicate that the porphyrin dimers of DNA-FbP conjugates are overlapped clockwise and are located in the minor groove of the usual B-form DNA backbone. The interaction and conformation of two porphyrin moieties are controlled by the following three factors: (1) temperature change during and after formation of the duplex porphyrins at lower temperature; (2) diastereochemistry of the phosphoramidates where porphyrins are connected via a linker; and (3) zinc ion coordination that destabilizes the interaction of porphyrins as well duplex formation.     

Supramolecular ssDNA Templated Porphyrin and Metalloporphyrin Nanoassemblies with Tunable Helicity

Free‐base and nickel porphyrin–diaminopurine conjugates were formed by hydrogen‐bond directed assembly on single‐stranded oligothymidine templates of different lengths into helical multiporphyrin nanoassemblies with highly modular structural and chiroptical properties. Large red‐shifts of the Soret band in the UV/Vis spectroscopy confirmed strong electronic coupling among assembled porphyrin–diaminopurine units. Slow annealing rates yielded preferentially right‐handed nanostructures, whereas fast annealing yielded left‐handed nanostructures. Time‐dependent DFT simulations of UV/Vis and CD spectra for model porphyrin clusters templated on the canonical B‐DNA and its enantiomeric form, were employed to confirm the origin of observed chiroptical properties and to assign the helicity of porphyrin nanoassemblies. Molar CD and CD anisotropy g factors of dialyzed templated porphyrin nanoassemblies showed very high chiroptical anisotropy. The DNA‐templated porphyrin nanoassemblies displayed high thermal and pH stability. The structure and handedness of all assemblies was preserved at temperatures up to +85 °C and pH between 3 and 12. High‐resolution transition electron microscopy confirmed formation of DNA‐templated nickel(II) porphyrin nanoassemblies and their self‐assembly into helical fibrils with micrometer lengths.     

Self‐Sorting of Cyclic Peptide Homodimers into a Heterodimeric Assembly Featuring an Efficient Photoinduced Intramolecular Electron‐Transfer Process

We describe the thermodynamic characterisation of the self‐sorting process experienced by two homodimers assembled by hydrogen‐bonding interactions through their cyclopeptide scaffolds and decorated with Zn–porphyrin and fullerene units into a heterodimeric assembly that contains one electron‐donor (Zn–porphyrin) and one electron‐acceptor group (fullerene). The fluorescence of the Zn–porphyrin unit is strongly quenched upon heterodimer formation. This phenomenon is demonstrated to be the result of an efficient photoinduced electron‐transfer (PET) process occurring between the Zn–porphyrin and the fullerene units of the heterodimeric system. The recombination lifetime of the charge‐separated state of the heterodimer complex is in the order of 180 ns. In solution, both homo‐ and heterodimers are present as a mixture of three regioisomers: two staggered and one eclipsed. At the concentration used for this study, the high stability constant determined for the heterodimer suggests that the eclipsed conformer is the main component in solution. The application of the bound‐state scenario allowed us to calculate that the heterodimer exists mainly as the eclipsed regioisomer (75–90 %). The attractive interaction that exists between the donor and acceptor chromophores in the heterodimeric assembly favours their arrangement in close contact. This is confirmed by the presence of charge‐transfer bands centred at 720 nm in the absorption spectrum of the heterodimer. PET occurs in approximately 75 % of the chromophores after excitation of both Zn–porphyrin and fullerene chromophores. Conversely, analogous systems, reported previously, decorated with extended tetrathiafulvalene and fullerene units showed a PET process in a significantly reduced extent (33 %). We conclude that the strength (stability constant (K)×effective molarity (EM)) of the intramolecular interaction established between the two chromophores in the Zn–porphyrin/fullerene cyclopeptide‐based heterodimers controls the regioisomeric distribution and regulates the high extent to which the PET process takes place in this system.     

Synthesis of non-covalent BODIPY–metalloporphyrin dyads and triads

Boron-dipyrromethenes (BODIPY) containing oxypyridine substituents at 3- and 3,5-positions and metalloporphyrins (Zn(II), Ru(II)) were used to synthesize four non-covalent BODIPY–metalloporphyrin dyads and four BODIPY–metalloporphyrin triads assembled using metal–pyridine ‘N’ interaction. The formation of BODIPY–metalloporphyrin assemblies was confirmed by 1D and 2D NMR methods and X-ray crystal structure obtained for one of the BODIPY–metalloporphyrin dyad. In ¹H NMR, the signals of oxypyridine group(s) of BODIPY unit showed significant upfield shifts supporting the coordination of oxypyridine group of BODIPY unit to metalloporphyrin unit. The NMR study also indicated that Zn(II) porphyrin forms relatively weak BODIPY–Zn(II) porphyrin conjugates, whereas Ru(II) porphyrin forms strong BODIPY–Ru(II) porphyrin conjugates. The X-ray structure solved for BODIPY–Zn(II)porphyrin dyad revealed that the Zn(II) porphyrin coordinated to the BODIPY unit obliquely and the angle between the Zn(II) porphyrin and the pyridyl ring is 70°. The absorption properties of stable BODIPY–Ru(II) porphyrin conjugates showed the overlapping absorption features of both the components and the fluorescence studies indicated that the BODIPY unit emission was significantly quenched on coordination with RuTPP(CO) unit. The electrochemical studies exhibited the features of both BODIPY and metalloporphyrin units in dyads and traids.     

Sequence and linker dependent chiral dimerization of DNA–porphyrin conjugates

Circular dichroism (CD), UV–vis absorption, fluorescence, and resonance light scattering (RLS) spectroscopies were used to elucidate the role of the DNA sequence, linkers between DNA and porphyrin, and metal in the porphyrin coordination center on the self-assembly of DNA–porphyrin conjugates. A series of eight non-self-complementary DNA–porphyrin conjugates have been synthesized with zinc and free-base porphyrins covalently attached to the short ODNs (A₈ or T₈) via amide or phosphate linker. A small structural modification (e.g., amide linker replaced by the phosphate linker) showed a dramatic effect on the aggregation properties of DNA–porphyrin conjugates and greatly altered their spectroscopic properties. At low ionic strength, porphyrin aggregation was not observed for any conjugate. An increase in the ionic strength caused two out of eight conjugates to form chiral porphyrin dimers.     

Control of Energy Transfer Between Pyrene- and Perylene-Nucleosides by the Sequence of DNA-Templated Supramolecular Assemblies

DNA was used as supramolecular scaffold to order chromophores and control their optical properties. Ethynylpyrene as energy donor was attached to 2′-desoxy-2-aminoadenosine that binds selectively to thymidines (T) in the template. Ethynylperylene as acceptor was attached to 2′-desoxyuridine that is complementary to 2′-desoxyadenosine (A). This donor-acceptor pair was assembled along single-stranded DNA templates of different A−T sequences to investigate the sequence control of the energy transfer between the chromophores. The fluorescence intensities increase in the mixed assemblies along the DNA templates from A₁₀T₁₀ over (AATT)₅ to (AT)₁₀, although these templates provide equal numbers of potential binding sites for the two different nucleoside chromophore conjugates and exhibit similar absorbances. This shows that the sequence selective assembly of the two building blocks along DNA templates is programmable and alters the fluorescence readout. Such sequence-controlled supramolecular chemistry represents the key element for future functional π-systems in materials for light harvesting of solar energy.     

Assembly of Multi‐Phthalocyanines on a Porphyrin Template by Fourfold Rotaxane Formation

A stacked assembly composed of a porphyrin and two phthalocyanines was prepared through fourfold rotaxane formation. Two phthalocyanine molecules, bearing four 24‐crown‐8 units, were assembled onto a porphyrin template incorporating four sidechains with two dialkylammonium ions each through pseudorotaxane formation between crown ether units and ammonium ions. The Staudinger phosphite reaction, as the stoppering reaction, resulted in the formation of the stacked heterotrimer composed of a porphyrin and two phthalocyanines connected through a fourfold rotaxane structure. UV/Vis spectroscopic and electrochemical studies of the heterotrimer indicated that there is a significant electronic interaction between the two phthalocyanine units due to the close stacking. The electrochemical oxidation process of the stacked heterotrimer was studied by cyclic voltammetry and spectroelectrochemistry. Electron paramagnetic resonance (EPR) spectroscopy of a dinuclear Cu^II complex, in which two Cu^II phthalocyanines were assembled on a metal‐free porphyrin template, revealed that two Cu^II phthalocyanines were located within the stacking distance, which resulted in an antiferromagnetic interaction between the two S= spins in the ground state of the Cu²⁺ ions in the heterotrimer.     

Use of a porphyrin platform and 3,4-HPO chelating units to synthesize ligands with N4 and O4 coordination sites

Piperazine and 1,2-diaminobenzene have been previously used as anchoring molecules to synthesize 3-hydroxy-4-pyridinone (3,4-HPO) tetradentate ligands affording ligands with different flexibility and coordination properties. In order to have a relatively rigid and hindered structure, a porphyrin platform was selected to anchor one or two 3,4-HPO chelating units. This platform provides an additional N₄ coordination sphere and also very interesting optical properties to the synthesized conjugates. Depending on the metal ion present in the porphyrin core, conjugates with different spectroscopic properties are obtained. EPR spectroscopy has been used to characterize the copper(II) metalloporphyrins and to monitor and identify the species formed upon addition of copper(II) to solutions of two porphyrin conjugates with one and two 3,4-HPO arms. The porphyrin conjugates having two 3,4-HPO units are ligands that provide two separate binding sites with N₄ and O₄ coordination spheres, which allow accommodation of two metal ion centers that may be distinguished by spectroscopic methods.     

Bridging and Conformational Control of Porphyrin Units through Non-Traditional Rigid Scaffolds

Connecting two porphyrin units in a rigid linear fashion, without any undesired electron delocalization or communication between the chromophores, remains a synthetic challenge. Herein, a broad library of functionally diverse multi-porphyrin arrays that incorporate the non-traditional rigid linker groups cubane and bicyclo[1.1.1]pentane (BCP) is described. A robust, reliable, and versatile synthetic procedure was employed to access porphyrin-cubane/BCP-porphyrin arrays, representing the largest non-polymeric structures available for cubane/BCP derivatives. These reactions demonstrate considerable substrate scope, from utilization of small phenyl moieties to large porphyrin rings, with varying lengths and different angles. To control conformational flexibility, amide bonds were introduced between the bridgehead carbon of BCP/cubane and the porphyrin rings. Through varying the orientation of the substituents around the amide bond of cubane/BCP, different intermolecular interactions were identified through single crystal X-ray analysis. These studies revealed non-covalent interactions that are the first-of-their-kind including a unique iodine-oxygen interaction between cubane units. These supramolecular architectures indicate the possibility to mimic a protein structure due to the sp³ rigid scaffolds (BCP or cubane) that exhibit the essential conformational space for protein function while simultaneously providing amide bonds for molecular recognition.     

噻吩基卟啉衍生物的单光子和双光子吸收性质的理论研究

本文理论上研究了两个系列的噻吩基卟啉衍生物,这种衍生物在可见光区具有大的双光子吸收截面。用密度泛函理论和ZINDO-SOS方法,计算了分子的几何构型、电子结构,单光子和双光子吸收性质。结果显示噻吩单元的数目影响分子的单光子和双光子吸收性质。具有两个或三个噻吩基团的噻吩基卟啉衍生物在较大范围内具有可用于实际应用中的双光子吸收响应,这一性质有利于这类分子在光限幅中的应用。插入乙炔基有利于扩大共轭范围,增加分子的双光子吸收截面。同时,乙炔基团的加入导致了单光子和双光子波长的红移。从高透明性和相对大的非线性光学响应考虑,噻吩基卟啉衍生物是一类有应用前景的双光子吸收材料。     

Programmed‐Assembly System Using DNA Jigsaw Pieces

A novel method for assembling multiple DNA origami structures has been developed by using designed 2D DNA origami rectangles, so‐called “DNA jigsaw pieces” that have sequence‐programmed connectors. Shape and sequence complementarity were introduced to the concavity and convex connectors in the DNA rectangles for selective connection with the help of nonselective π‐stacking interactions between the side edges of the DNA jigsaw piece structures. Single DNA jigsaw piece units were assembled into unidirectional nanostructures with the correct alignment and uniform orientation. Three and five different DNA jigsaw pieces were assembled into predesigned and ordered nanostructures in a programmed fashion. Finally, three‐, four‐, and five‐letter words have been displayed by using this programmed DNA jigsaw piece system.     

Supramolecular Light‐Harvesting Antennas of Metal‐Coordinated Bis(8‐Hydroxyquinoline)‐Substituted Porphyrin Networks

Artificial antenna complexes of metal‐coordinated bis(8‐hydroxyquinoline)‐substituted porphyrin networks that mimic antenna chromophores in plants were organized on titanium dioxide electrodes in photoelectrochemical cells. The generated photocurrents can be optimized according to the two ways of porphyrin self‐assembly due to the “antenna effect”: changing the number of assembled porphyrin monolayers and the number of generations of the metal‐coordinated porphyrin networks.     

DNA-mediated exciton coupling and electron transfer between donor and acceptor stilbenes separated by a variable number of base pairs

The synthesis, steady-state spectroscopy, and transient absorption spectroscopy of DNA conjugates possessing both stilbene electron donor and electron acceptor chromophores are described. These conjugates are proposed to form nicked DNA dumbbell structures in which a stilbenedicarboxamide acceptor and stilbenediether donor are separated by variable numbers of A-T or G-C base pairs. The nick is located either adjacent to one of the chromophores or between two of the bases. Thermal dissociation profiles indicate that stable structures are formed possessing as few as two A-T base pairs. Circular dichroism (CD) spectra in the base pair region are characteristic of B-DNA duplex structures, whereas CD spectra at longer wavelengths display two bands attributed to exciton coupling between the two stilbenes. The sign and intensity of these bands are dependent upon both the distance between the chromophores and the dihedral angle between their transition dipoles [Deltaepsilon approximately Rda(-2) sin(2theta)]. Pulsed laser excitation of the stilbenediamide results in creation of the acceptor-donor radical ion pair, which decays via charge recombination. The dynamics of charge separation and charge recombination display an exponential distance dependence, similar to that observed previously for systems in which guanine serves as the electron donor. Unlike exciton coupling between the stilbenes, there is no apparent dependence of the charge-transfer rates upon the dihedral angle between donor and acceptor stilbenes. The introduction of a single G-C base pair between the donor and acceptor results in a change in the mechanism for charge separation from single step superexchange to hole hopping.     

Excitation energy transport processes of porphyrin monomer,dimer, cyclic trimer,and hexamer probed by ultrafast fluorescence anisotropy decay

Femtosecond fluorescence anisotropy measurements for a variety of cyclic porphyrin arrays such as Zn(II)porphyrin m-trimer and hexamer are reported along with o-dimer and monomer as reference molecules. In the porphyrin arrays, a pair of porphyrin moieties are joined together via triphenyl linkage to ensure cyclic and rigid structures. Anisotropy decay times of the porphyrin arrays can be well described by the F?rster incoherent excitation hopping process between the porphyrin units. Exciton coupling strengths of 74 and 264 cm(-1) for the m-trimer and hexamer estimated from the observed excitation energy hopping rates are close to those of B800 and B850, respectively, in the LH2 bacterial light-harvesting antenna. Thus, these cyclic porphyrin array systems have proven to be useful in understanding energy migration processes in a relatively weak interaction regime in light of the similarity in overall structures and constituent chromophores to natural light-harvesting arrays.     

卟啉和酞菁修饰的单壁碳纳米管的合成及光谱性质

利用5-(4-氨基苯基)-10,15,20-三(3,5-二辛氧基苯基)卟啉和2,9,16-三叔丁基-23-氨基锌(Ⅱ)酞菁通过酰胺键连接方式同时对单壁碳纳米管进行共价修饰, 通过红外光谱、拉曼光谱、X射线光电子能谱和透射电镜对所得碳纳米管复合物进行了表征, 证实了其结构. 紫外-可见吸收光谱和荧光光谱分析表明, 光活性分子卟啉和酞菁均与单壁碳纳米管之间存在较强的电子效应. 经卟啉和酞菁共同修饰的单壁碳纳米管复合物比卟啉和酞菁单独修饰的碳纳米管复合物的吸光范围更宽, 而且分散性较好(309 mg/L), 是潜在的光电转换材料.     

Toward reliable gold nanoparticle patterning on self-assembled DNA nanoscaffold

Assembly of gold nanoparticles (AuNP) into designer architectures with reliablity is important for nanophotonics and nanoelectronics applications. Toward this goal we present a new strategy to prepare AuNPs monofunctionalized with lipoic acid modified DNA oligos. This strategy offers increased bonding strength between DNA oligos and AuNP surface. These conjugates are further selectively mixed with other DNA strands and assembled into fixed sized DNA nanostructures carring a discrete number of AuNPs at desired positions. Atomic force microscopy imaging reveals a dramatically improved yield of the AuNPs on DNA tile structure compared to the ensembles using monothiolate AuNP-DNA conjugates.     

Self-assembling of the porphyrin-linked acyclic penta- and heptapeptides in aqueous trifluoroethanol

The conjugates of porphyrin with links to the acyclic penta- and heptapeptides were synthesized to mimic natural multiple porphyrin systems. The linear penta- and heptapeptide with hydrophilic/hydrophobic alternative sequences took a random structure in aqueous trifluoroethanol (TFE). However, these polypeptides took a beta-sheet structure in the same solvent when the N-terminal Cys linked to the porphyrin, suggesting that the conjugates self-assembled via the intermolecular hydrophobic interaction between the porphyrins. The circular dichroism (CD) spectra, UV/vis spectra, size exclusion chromatography (SEC), and (1)H NMR spectroscopy supported the self-assembling. In the self-assembled structure of the pentapeptide linking porphyrin at the p-phenyl position (9), the porphyrins were involved in two porphyrin-porphyrin interactions, i.e., the side-by-side interaction between the neighboring polypeptide chains and the face-to-face interaction between the first and the third peptide chains. The CD spectra of 9 showed two sets of Cotton effects probably arising from these two interactions. The UV/vis spectra also supported the above interpretation, showing multiple absorptions in the longwave and shortwave shifted regions. The SEC analyses showed the assembled structure of the conjugates. The (1)H NMR signals of the porphyrin rings of 9 were hardly observed in D(2)O-CD(3)OD because of the shortened spin-spin relaxation time T(2)().     

Chiroptical transcription of helical information through supramolecular harmonization with dynamic helices

With biologically important "peptide bundling" as the motif, new chromophoric cyclic host 1 was designed, which consists of two zinc porphyrin units that are connected by dynamic peptide helices of nonameric aminoisobutyric acid (Aib) units. Upon inclusion of pyridine-anchored helical peptides between the zinc porphyrin units, 1 displayed an intense exciton-coupled circular dichroism (CD) band at 410-450 nm, whose sign reflected the helical sense of the guest peptides. Studies with conformationally defined dehydrophenylalanine-containing analogues indicated that the dynamic helical chains in the host are stereochemically harmonized with right- or left-handed helices of the guest peptides in a confined nano space, leading to either clockwise- or anticlockwise-twisted geometry (chiroptical output) of the connecting zinc porphyrin chromophores.     

2,2′‐Bipyridine‐Based Dendritic Structured Compounds for Second Harmonic Generation

Parallel alignment of dipolar electron‐donor–π‐bridge‐electron‐acceptor entities can strongly enhance their nonlinear optical properties. This favorable arrangement can be in principle achieved by linking these units covalently or through metal coordination. Four dipolar single‐strand chromophores decorated with a 5‐electron‐donor–5′‐electron‐acceptor‐modified 2,2′‐bipyridine functionality were synthesized. For two of these chromophores triple‐stranded dendritic structures were successfully formed. All of the compounds were characterized with respect to their linear and nonlinear optical properties. For the aldehyde derivatives an enhancement of the first hyperpolarizability of 4.5 rather than 3 was obtained when going from single to triple strands. Theoretical calculations with density functional theory suggest that interstrand transitions contribute to the optical properties of the dendritic structures.