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.     

双卟啉化合物的构象平衡及π-π作用研究

制备并表征了一系列以柔韧烷氧化相连的自由双卟啉及其锌配合物,以＾１Ｈ－ＮＭＲ考察了烷氧链长度及锌离子对双卟啉构象平衡的影响。结果表明,双卟啉存在开放式及闭合式构象平衡,随烷氧链的增长,构象平衡由开放式向闭合式移动,当链上碳原子数为４时最有利于双卟啉形成闭合式构象。     

Photophysical properties of a C6 hydrocarbon linked porphyrin dimer

The synthesis and characterisation of a C₆ hydrocarbon linked porphyrin dimer and its zinc complex is described. From fluorescence quantum yields and excited singlet and triplet state lifetimes, recorded for the dimers and the corresponding monomer species, it is suggested that the dimeric porphyrins exist in solution in open and closed conformations. The open conformations retain photophysical properties similar to those of the relevant monomeric species but the closed conformations do not fluoresce.     

Introducing structural flexibility into porphyrin-DNA zipper arrays

A more flexible nucleotide building block for the synthesis of new DNA based porphyrin-zipper arrays is described. Changing the rigid acetylene linker between the porphyrin substituent and the 2'-deoxyuridine to a more flexible propargyl amide containing linkage leads in part to an increased duplex stability. The CD spectra reveal different electronic interactions between the porphyrins depending on the type of linker used. Molecular modelling suggests large variation of the relative orientation of the porphyrins within the major groove of the DNA. The porphyrins can be metallated post-synthetically with different metals as shown with zinc, cobalt and copper. The spectroscopic features do not alter drastically upon metallation apart from the CD spectra, and the stability of the metal complex is highly dependent on the nature of the metal. As shown by CD spectroscopy, the zinc porphyrin is rapidly demetallated at high temperatures. Globular structure determination using SAXS indicates that a molecular assembly comprised of a two to four helical bundle dominates in solution at higher concentrations (≥50 μM) which is not observed by spectroscopy at lower concentrations (≤1 μM).     

Investigation of tightly coupled porphyrin arrays comprised of identical monomers for multibit information storage

Our prior designs for molecular-based information storage devices have employed multiple redox-active units organized in weakly coupled, covalently linked arrays. To explore a simpler design, we report here the synthesis of porphyrin arrays where porphyrins with identical oxidation potentials are directly linked to one another instead of joined via a molecular linker. Oxidative coupling with AgPF(6) of zinc(II)-5,15-bis(4-tert-butylphenyl)-10-phenylporphyrin, obtained by a rational synthesis, afforded the expected dimer joined by a meso-meso linkage and an unexpected trimer joined by meso-meso linkages. For attachment to an electroactive surface we synthesized a meso-linked porphyrin dimer with a thiol-linker in one of the meso positions. The S-acetyl protecting group was used to avoid handling free thiol groups. Coupling of zinc(II)-5,10,15-tris(3, 5-di-tert-butylphenyl)porphyrin ("upper half") and zinc(II)-5-[4-(S-acetylthio)phenyl]-10,20-bis(3, 5-di-tert-butylphenyl)porphyrin ("lower half") afforded three different meso-linked dimers with the desired dimer as the main product. Electrochemical examination of the meso-linked dimer in solution shows that the first two oxidation potentials of the array differ by approximately 0.15 V and straddle the value exhibited by the monomeric constituents. The third and fourth oxidation potentials of the array are also split although to a lesser extent ( approximately 0.08 V) than the first and second. For the meso-linked trimer, the first three oxidation waves are also split; however, these waves are severely overlapped. The electrochemical behavior of the dimers and trimer is indicative of strong electronic interactions among the porphyrins. The thiol-derivatized meso-linked dimers form self-assembled monolayers (SAMs) on gold via in situ cleavage of the S-acetylthio protecting group. The porphyrin SAM exhibits four well-resolved oxidation waves. Regardless, the meso-meso linkage is relatively unstable upon formation of the pi-cation radical(s). This characteristic indicates that the structural motif is of limited utility for molecular information storage elements.     

Synthesis of Calix[6]arene-Porphyrin Receptors and Study on their Catalytic Performance in Epoxidation of Styrene

The artificial receptors with multiple recognition site had been synthesized by linking two unsymmetrical monofunctionalized porphyrin to p-tert-butyl calix[6]-arene via two flexible chain, followed by inserting metal ion into the porphyrin species.The structures (see Fig 1) of these calix[6]arene-diporphyrins and their metal complexes were confirmed by UV-vis spectra, IR spectra, mass spectra, ¹NMR spectra(600 MHz) and/or ¹³C NMR. Their conformations were investigated preliminarily by UV-vis spectra and computer simulation. In constrast with the correspounding porphyrin monomer, the soret bond of calix[6]arene-diporphyrins in UV-vis spectra showed hypsochromic shift. This phenomenon suggested that two porphyrin rings maintain a face to face parallel conformation, as confirmed by computer simulation that showed the conformation energy is the lowest as two porphyrin rings hold such a conformation. Besides, simplicity of the ¹NMR spectra indicates that the conformation of calix[6]arene-diporphyrin possesses high symmetry. Therefore,the calix[6]arene must be cone conformation.     

Conformation Analysis and Thermodynamics of Binding Behavior of DABCO to p/p type Dimeric Porphyrin Hosts

Covalently linked metalloporphyrin dimers have attracted considerably interest among chemists as models for metalloenzymes, which derive from their remarkable electron, energy transfer and special conformation properties1,2. Metalloporphyrins with large cavities have been designed and assembled with the idea of creating multisite complexing hosts incorporating functionalized subunits for binding organic substrates and transition metals so as to mimic metalloenzymes, as well as supermolecular ph…     

Facile formation of a meso-meso linked porphyrin dimer catalyzed by a manganese(IV)-oxo porphyrin

A manganese(IV)-oxo porphyrin catalyzes C-C bond formation between zinc porphyrins at the meso-position with a two-electron oxidant to afford the meso-meso linked porphyrin dimer efficiently. The meso-meso linked dimer is formed via formation of the porphyrin radical cation, and the rate-determining step in the catalytic cycle is the formation of a manganese(IV)-oxo porphyrin with a two-electron oxidant.     

Fusing Porphyrins and Phospholes: Synthesis and Analysis of a Phosphorus‐Containing Porphyrin

A phosphole‐fused porphyrin dimer, as a representative of a new class of porphyrins with a phosphorus atom, was synthesized for the first time. The porphyrin dimer exhibits remarkably broadened absorption, indicating effective π‐conjugation over the two porphyrins through the phosphole moiety. The porphyrin dimer possesses excellent electron‐accepting character, which is comparable to that of a representative electron‐accepting material, [60]PCBM. These results provide access to a new class of phosphorus‐containing porphyrins with unique optoelectronic properties.     

Scanning tunneling microscopy observation of self-assembled monolayers of strapped porphyrins

In this paper, we reveal that the free-base and zinc strapped porphyrins possessing long alkyl chains, C 24OPP-HQ and Zn(C 24OPP-HQ), respectively, can be arranged on surfaces. We used scanning tunneling microscopy (STM) to observe alkyl-chain-assisted self-assembled monolayers (SAMs) of these strapped porphyrins at the solid-liquid interface. STM images revealed that the strapped benzene moiety was detectable on the porphyrin core: that is, the strapped porphyrins could be differentiated from nonstrapped analogues. We compared the population of the nonstrapped porphyrin (C 24OPP) and either of the strapped porphyrins C 24OPP-HQ or Zn(C 24OPP-HQ) in the mixed SAMs. We then confirmed that Zn(C 24OPP-HQ) is more favorably incorporated in the mixed SAMs than C 24OPP-HQ. From (1)H NMR spectroscopic and X-ray crystallographic analyses, we concluded that the factors increasing the population of Zn(C 24OPP-HQ) in the mixed SAMs are the enhanced rigidity of the porphyrin core by the zinc coordination and the flat structure of the porphyrin moiety in the saddle conformation. This study demonstrates that strapped porphyrins possessing long alkyl chains are available to arrange the functional modules on the surface via chemical modification on the strapped moiety.     

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.     

Synthesis and photodynamics of fluorescent blue BODIPY-porphyrin tweezers linked by triazole rings

Novel zinc porphyrin tweezers in which two zinc porphyrins were connected with π-conjugated boron dipyrromethenes (BDP meso-Por(2) and BDP β-Por(2)) through triazole rings were synthesized to investigate the photoinduced energy transfer and electron transfer. The UV-vis spectrum of BDP β-Por(2) which has less bulky substituents than BDP meso-Por(2) exhibits splitting of the Soret band as a result of the interaction between porphyrins of BDP β-Por(2) in the excited state. Such interaction between porphyrins of both BDP β-Por(2) and BDP meso-Por(2) is dominant at room temperature, while the coordination of the nitrogen atoms of the triazole rings to the zinc ions of the porphyrins occurs at low temperature. The conformational change of the BDP-porphyrin composites was confirmed by the changes in UV-vis and fluorescence spectra depending on temperature. Photodynamics of BDP meso-Por(2) and BDP β-Por(2) has also been investigated by laser flash photolysis. Efficient singlet-singlet energy transfer from the ZnP to the π-conjugated BDP moiety of both BDP meso-Por(2) and BDP β-Por(2) occurred in opposite direction as compared to energy transfer from conventional BDP to ZnP due to the π-conjugation in nonpolar toluene. In polar benzonitrile, however, additional electron transfer occurred along with energy transfer.     

Red shifting due to nonplanarity in alkylporphyrins: solid-state polarized UV-vis spectra and ZINDO calculations of two nickel(II)octaethylporphyrins

We present the first demonstration of red shifting upon nonplanarity in alkylporphyrins using two pure conformations having known structures with identical substituents. The traditional view about the relationship of spectral red shifting to nonplanar deformation in porphyrins has been that the deformation from planar to nonplanar forms is in itself the cause of the shifting, but recently this view has been challenged. Among the new arguments is that the substituents required to effect conformational change also bring about nuclear rearrangements in the porphyrin complex which is the actual cause of the red shifting. Octaethylporphyrinatonickel(II), however, exists in both planar and ruffled forms which are determined only by the crystal structure, thus making the issue of different substituents moot. Using a polarized specular reflectance UV-vis microspectrophotometer, we have obtained polarized spectra of pure, solid samples of both forms of NiOEP. We find Soret band red shifting in the solid state that is much larger than previous reports of solution spectra and also report Q-band red shifting. We performed ZINDO calculations on monomers and dimers of both forms of NiOEP, based upon reported structures, and have reproduced the reported solution transition energies and our solid-state spectra as well as the red shifts that we and others have found experimentally. We conclude that, at least in this system, red shifting does indeed result primarily from conformation changes in the porphyrin.     

Binding of meso-tetrakis(N-methylpyridium-4-yl)porphyrin to triplex oligonucleotides: evidence for the porphyrin stacking in the major groove

Induced CD spectra of meso-tetrakis(N-methylpyridium-4-yl)porphyrin (TMPyP) complexed with d(A)12.d(T)12, d(G)12.d(C)12 duplex and d(A)12.[d(T)12]2, d(G)12.d(C)12.d(C)12+ triplex in the Soret band were compared in this study. When TMPyP is complexed with the duplex, a monomeric CD spectrum at a low [TMPyP]/[oligomer] ratio was apparent, while at a high mixing ratio, the excitonic CD was dominant. In contrast, when TMPyP was complexed with the triplex, the excitonic CD disappears at a relatively high mixing ratio, indicating the TMPyP exciton formation is inhibited by the third strand, which is located in the major groove. This observation indicates that the exciton is formed at the major groove of both AT- and GC-rich DNA, while the monomeric TMPyP binds at (or near) the minor groove of the AT site.     

Electrospray tandem mass spectrometry of new porphyrin amino acid conjugates

Porphyrin amino acid conjugates with one or two porphyrin units were analyzed by electrospray ionization tandem mass spectrometry (ESI-MS/MS). The ESI-MS spectra of all the porphyrins studied, obtained in positive ion mode, show the presence of the corresponding protonated molecule [M+H]+; ESI-MS spectra of diporphyrinyl compounds also show the doubly charged ions [M+2H]2+. The fragmentations of these ions induced by collision with argon were studied (ESI-MS/MS). ESI-MS/MS gives detailed structural information about the amino acids associated with the porphyrin. Cleavage of the bonds in the vicinity of the porphyrin moiety and those involving the side chain of amino acid residues gives structural information about this type of association. A fragmentation common to all derivatives corresponds to the cleavage of the phenyl-CO bond. The expected cleavage of the amide bond, that links the porphyrin to the amino acid moiety, is a minor fragmentation, which in some cases is even absent. The MS/MS spectra of the monoporphyrinyl derivatives show product ions characteristic of the amino acid linked to the porphyrin; the fragmentation also indicates when the amino acids has a terminal carboxylic group or a terminal ester group. The fragmentations of the diporphyrinyl compounds occur mainly by the cleavage of the spacer, leading, in the case of the doubly charged ions, to predominantly mono-charged ions, indicating a preferential location of the two protons in separated porphyrinic units.     

The synthesis of covalently linked tetraarylporphyrin dimers

A new and general synthesis of porphyrin dimers is described. The synthesis involves the reaction of dibromoalkanes with phenolic porphyrins, such as 5(4-hydroxyphenyl)-10,15,20-tritolylporphyrin, to form σ-bromoalkyl porphyrin ethers. The latter compounds are then reacted with a second phenolic porphyrin to give porphyrin dimers. A mixed metalloporphyrin dimer has been prepared which contains both V(IV) and Cu(II). The compounds have been examined spectroscopically. The free-base porphyrin dimers show a splitting of the intense Soret band. This is interpreted as indicative of weak singlet energy transfer between the covalently linked porphyrins.     

Study on the interaction of new water-soluble porphyrin with DNA

A porphyrin meso-tetrakis{[4-(1-pyridyl)propoxy]phenyl}porphyrin (TPyPP) and its Ni complex (TPyPP(Ni)) have been synthesized and characterized by 1H NMR, UV-vis spectra. The interaction of two porphyrins with calf thymus-DNA (CT-DNA) has been explored by UV-vis, fluorescence and circular dichroic spectroscopy and viscosity measurements. The results suggest that these porphyrins can bind to DNA by the same binding mode. TPyPP outside binds by self-stack with DNA both at low drug load r (=[porphyrin]/[DNA]) and high drug load. Though TPyPP(Ni) has center metal nickel, binding mode with DNA has little difference compared with TPyPP, dominating out-binding mode with different direction along DNA. The binding constants of the TPyPP and TPyPP(Ni) to DNA were 4.65 x 10(5) M(-1) and 3.2 x 10(5) M(-1), respectively. A colored precipitate was found after time in two porphyrin's viscosity measurement. The reasonable interpretation is the porphyrins with alkyl connected N-position of pyridine can strongly interact with the anionic phosphates of DNA and lead to hydrophobic complex.     

Chiral recognition by CD-sensitive dimeric zinc porphyrin host. 1. Chiroptical protocol for absolute configurational assignments of monoalcohols and primary monoamines.

A general microscale protocol for the determination of absolute configurations of primary amino groups or secondary hydroxyl groups linked to a single stereogenic center is described. The chiral substrates are linked to the achiral trifunctional bidentate carrier molecule (3-aminopropylamino)acetic acid (1, H(2)NCH(2)CH(2)CH(2)NHCH(2)COOH) and the resultant conjugates are then complexed with dimeric zinc porphyrin host 2 giving rise to 1:1 host/guest sandwiched complexes. These complexes exhibit exciton-coupled bisignate CD spectra due to stereodifferentiation leading to preferred porphyrin helicity. Since the chiral sense of twist between the two porphyrins in the complex is dictated by the stereogenic center of the substrate, the sign of the couplet determines the absolute configuration at this center. The twist of the porphyrin tweezer in the complex can be predicted from the relative steric sizes of the groups flanking the stereogenic center, such that the bulkier group protrudes from the complex sandwich. In certain alpha-hydroxy esters and alpha-amino esters, electronic factors and hydrogen bonding govern the preferred conformation of the complex, and hence the CD spectra.     

Light-harvesting heptadecameric porphyrin assemblies

New porphyrin assemblies containing 17 porphyrin molecules are constructed by using free base TPP-type porphyrins having eight pyrazine moieties 1. Spectroscopic titration of dimeric [meso-tetrakis(2-carboxy-4-nonylphenyl)porphyrinato]zinc(II) 2 with these porphyrins shows that the processes of the formation of the heptadecameric porphyrin assemblies may be analyzed as eight independent equilibrium processes with an identical binding constant. All binding constants are larger than 5 x 107 M-1 which is the determinable upper limit of the present titration method. In all cases, the fluorescence spectrum of the 1:8 mixture of 1 and 2 consists of the major fluorescence of 1 and the minor one of 2.pyrazine complex even in the presence of the large excess of the antenna pigments. The observed spectra are well reconstructed by the form of faF1 + fbF2, where F1 and F2 are the fluorescence of 1 and the 2.pyrazine complex measured separately at the corresponding concentrations. Interestingly, the general trend that values of fa are nearly equal to those of r564 x (1 - fb) in all cases is found, where r564 is the absorption ratios of the 2.pyrazine moiety and the central free base porphyrin in the assemblies at 564 nm. The observation indicates the excitation of the central porphyrin is directly enhanced by the absorption of the antenna pigments even in such large scale assemblies. Thus, the antenna effect for 1 having largest r564 results in 77 times fluorescence enhancement of the central free base porphyrin. The systems also show interesting dependency of energy-transfer efficiencies on the topological arrangement of the antenna elements.     

Synthesis of Linear Amphipathic Porphyrin Dimers and Trimers: An Approach to Bilayer Lipid Membrane Spanning Porphyrin Arrays

A modular building-block approach has been developed for the construction of linear amphipathic porphyrin arrays. The reaction of meso-(trifluoromethyl)dipyrromethane and an aldehyde under the conditions of the two-step room temperature porphyrin synthesis affords the trans-substituted porphyrin (13-56% yields). A similar reaction with two different aldehydes provides access to porphyrins bearing two different functional groups. An ethyne porphyrin and an iodo porphyrin (either free base or zinc) are selectively joined via Pd(0)-catalyzed coupling reactions, affording a linear array with porphyrins in defined metalation states. Coupling of a zinc-porphyrin bearing iodo and ester groups with a free base porphyrin bearing ethyne and ester groups yielded the zinc-free base porphyrin dimer. Coupling of a bis-ethyne porphyrin with a porphyrin bearing iodo and ester groups afforded the porphyrin trimer. Cleavage of the esters yielded the amphipathic porphyrin dimer and trimer arrays. The arrays with adjacent zinc and free base porphyrins undergo efficient electronic energy transfer. Both amphipathic porphyrin arrays have been incorporated into L-alpha-phosphatidylcholine vesicles. This versatile synthetic strategy provides access to a family of porphyrin arrays for studies of photophysical processes in supramolecular assemblies.