Structure-property relationships for self-assembled zinc chlorin light-harvesting dye aggregates

A series of zinc 3(1)-hydroxymethyl chlorins 10 a-e and zinc 3(1)-hydroxyethyl chlorins 17 with varied structural features were synthesized by modifying naturally occurring chlorophyll a. Solvent-, temperature-, and concentration-dependent UV/Vis and CD spectroscopic methods as well as microscopic investigations were performed to explore the importance of particular functional groups and steric effects on the self-assembly behavior of these zinc chlorins. Semisynthetic zinc chlorins 10 a-e possess the three functional units relevant for self-assembly found in their natural bacteriochlorophyll (BChl) counterparts, namely, the 3(1)-OH group, a central metal ion, and the 13(1) C==O moiety along the Q(y) axis, and they contain various 17(2)-substituents. Depending on whether the zinc chlorins have 17(2)-hydrophobic or hydrophilic side chains, they self-assemble in nonpolar organic solvents or in aqueous media, respectively. Zinc chlorins possessing at least two long side chains provide soluble self-aggregates that are stable in solution for a prolonged time, thus facilitating elucidation of their properties by optical spectroscopy. The morphology of the zinc chlorin aggregates was elucidated by atomic force microscopy (AFM) studies, revealing well-defined nanoscale rod structures for zinc chlorin 10 b with a height of about 6 nm. It is worth noting that this size is in good accordance with a tubular arrangement of the dyes similar to that observed in their natural BChl counterparts in the light-harvesting chlorosomes of green bacteria. Furthermore, for the epimeric 3(1)-hydroxyethyl zinc chlorins 17 with hydrophobic side chains, the influence of the chirality center at the 3(1)-position on the aggregation behavior was studied in detail by UV/Vis and CD spectroscopy. Unlike zinc chlorins 10, the 3(1)-hydroxyethyl zinc chlorins 17 formed only small oligomers and not higher rod aggregate structures, which can be attributed to the steric effect imposed by the additional methyl group at the 3(1)-position.     

Effect of carotenoids and monogalactosyl diglyceride on bacteriochlorophyll c aggregates in aqueous buffer: implications for the self-assembly of chlorosomes

Aggregation of bacteriochlorophyll (BChl) c from chlorosomes, the main light-harvesting complex of green bacteria, has been studied in aqueous buffer. Unlike other chlorophyll-like molecules, BChl c is rather soluble in aqueous buffer, forming dimers. When BChl c is mixed with carotenoids (Car), the BChl c Qy transition is further redshifted, in respect to that of monomers and dimers. The results suggest that Car are incorporated in the aggregates and induce further aggregation of BChl c. The redshift of the BChl c Qy band is proportional to the Car concentration. In contrast, the mixture of bacteriochlorophyllide (BChlide) c, which lacks the nonpolar esterifying alcohol, does not form aggregates with Car in aqueous buffer or nonpolar solvents. Instead, the position of the BChlide c Qy transition remains unshifted in respect to that of the monomeric molecule, and Car precipitates with the course of time in aqueous buffer. Similar effects on both BChl c and BChlide c are also observed when monogalactosyl diglyceride (MGDG), which forms the monolayer envelope of chlorosomes, is used instead of (or together with) Car. The results show that the hydrophobic interactions of the BChl c esterifying alcohols with themselves and the nonpolar carbon skeleton of Car, or the fatty acid tails of MGDG, are essential driving forces for BChl aggregation in chlorosomes.     

Surface-tuned assembly of porphyrin coordination oligomers

Two self-complementary phenanthroline-strapped porphyrins bearing imidazole arms and C 12 or C 18 alkyl chains were synthesized, and their surface self-assembly was investigated by atomic force microscopy (AFM) on mica and highly ordered pyrrolitic graphite (HOPG). Upon zinc(II) complexation, stable porphyrin dimers formed, as confirmed by DOSY (1)H NMR and UV-visible spectroscopy. In solution, the dimers formed J-aggregates. AFM studies of the solutions dip-coated onto mica or drop-casted onto HOPG revealed that the morphologies of the assemblies formed were surface-tuned. On mica, fiber-like assemblies of short stacks of J-aggregates were observed. The strong influence of the mica's epitaxy on the orientation of the fibers suggested a surface-assisted assembly process. On HOPG, interactions between the alkyl chains and the graphite surface resulted in the stabilization and trapping of monomer species followed by their subsequent association into coordination polymers on the surface. Interdigitation of the alkyl chains of separate polymer strands induced lateral association of wires to form islands that grew preferentially upon drop-casting and slow evaporation. Clusters of laterally assembled wires were observed for the more mobile functionalized porphyrins bearing C 12 chains.     

Graphene功能分子在HOPG上自组装结构的密度泛函研究

Graphene自组装超分子结构,是指FTBC-Cn(n=4,6,8,12)分子有序自组装在高定向裂解石墨(HOPG)上形成的自组装超分子结构,是一种新型二维固体表面材料.其中FTBC-Cn分子是由三角形扶手椅型graphene每边添加2条含有n(n=4,6,8,12)个C原子的烷基链所形成具有曲面结构的一种分子.采用...     

Self-organization of gold-containing hydrogen-bonded rosette assemblies on graphite surface

The self-organization of supramolecular structures, in particular gold-containing hydrogen-bonded rosettes, on highly oriented pyrolytic graphite (HOPG) surfaces was investigated by tapping-mode atomic force microscopy (TM-AFM) and scanning tunneling microscopy (STM). TM-AFM and high-resolution STM results show that these hydrogen-bonded assemblies self-organize to form highly ordered domains on HOPG surfaces. We find that a subtle change in one of the building blocks induces two different orientations of the assembly with respect to the surface. These results provide information on the control over the construction of supramolecular nanoarchitectures in 2D with the potential for the manufacturing of functional materials based on structural manipulation of molecular components.     

Building-up Remarkably Stable Magnesium Porphyrin Polymers Self-Assembled via Bidentate Axial Ligands: Synthesis, Structure, Surface Morphology, and Effect of Bridging Ligands

A series of supramolecular architectures of magnesium tetranitrooctaethylporphyrins mediated by several bidentate axial ligands have been synthesized in excellent yields and structurally characterized. Six conjugated axial ligand with increasing chain lengths have been utilized in the present investigations in which the Mg···Mg nonbonding distance between successive ions also increases from 0.73 to 2.70 nm in the series. To the best of our knowledge, this is the first report where stable metallo-porphyrin polymers with such long spacers have been synthesized in one pot so easily. Linear one-dimensional (1D) polymeric chains were observed in the X-ray structure of the six-coordinated complexes in which porphyrin units are aligned parallel to each other to have so-called "shish kebab" like architectures to maintain offset-stacked overlap. However, after an optimum Mg···Mg nonbonding distance, these 1D chain do not continue, rather they form five-coordinated porphyrin dimers with "wheel-and-axle" like architectures which are then self-aggregated by π-π interactions in a perpendicular manner to fill space created by large bridging ligands more effectively which consequently results in spherical structures. The structures of the molecules in solution and their surface patterns on highly ordered pyrolytic graphite (HOPG) have also been investigated.     

Adsorption characteristic of self‐assembled corrole dimers on HOPG

Our study first focus on two types of corrole dimers oxidized and reduced forms on highly oriented pyrolytic graphite (HOPG) surface. Scanning tunneling microscopy (STM), X‐ray photoelectron spectroscopy (XPS) and contact angle measurement (CAM) were used to investigate the self‐assembled monolayers of corrole dimers adsorbed on HOPG surfaces at room temperature in air. XPS and CAM results have confirmed both two molecules adsorbed on an HOPG surface and formed self‐assembled films, and STM experiments found that the corrole dimers adsorbed on HOPG surfaces form similar lobes. The different stable space structure of the oxidized form molecule (OFM) and reduced form molecule (RFM), led to the diversity of the tetramer structural dimensions. The occurrence of molecular aggregations and assembly was controlled by the interactions between molecular–molecular and molecule–substrate. The electrostatic interactions between the molecules control the geometrical sizes and molecule–substrate interactions determine topographical shapes of the self‐assembled corrole dimers on HOPG surface. Copyright © 2009 John Wiley & Sons, Ltd.     

STM image of tungstosilicic acid molecular layer on highly oriented pyrolytic graphite

Molecular layer of tungstosilicic acid (H4SiW12O40) deposited on freshly-cleaved highly oriented pyrolytic graphite (HOPG) was observed by scanning tunneling microscopy (STM) in air at room temperature.The molecular dimension (11.5 A) of H4SiWi2O4o measured by STM is consistent with known crystallographic parameter.We also imaged the boundary of H4SiW12O40 molecular layer on HOPG showing that molecular layer of H4SiW12O40 was formed.It has been proved that individual tungstosilicic acid species is imaged.The probable reason for the formation of the molecular layer is also discussed.     

The length of esterifying alcohol affects the aggregation properties of chlorosomal bacteriochlorophylls

Abstract Chlorosomes, the main light-harvesting complexes of green photosynthetic bacteria, contain bacteriochlorophyll (BChl) molecules in the form of self-assembling aggregates. To study the role of esterifying alcohols in BChl aggregation we have prepared a series of bacteriochlorophyllide c (BChlide c) derivatives differing in the length of the esterifying alcohol (C(1), C(4), C(8) and C(12)). Their aggregation behavior was studied both in polar (aqueous buffer) and nonpolar (hexane) environments and the esterifying alcohols were found to play an essential role. In aqueous buffer, hydrophobic interactions among esterifying alcohols drive BChlide c derivatives with longer chains into the formation of dimers, while this interaction is weak for BChlides with shorter esterifying alcohols and they remain mainly as monomers. All studied BChlide c derivatives form aggregates in hexane, but the process slows down with longer esterifying alcohols due to competing hydrophobic interactions with hexane molecules. In addition, the effect of the length of the solvent molecules (n-alkanes) was explored for BChl c aggregation. With an increasing length of n-alkane molecules, the hydrophobic interaction with the farnesyl chain becomes stronger, leading to a slower aggregation rate. The results show that the hydrophobic interaction is the driving force for the aggregation in an aqueous environment, while in nonpolar solvents it is the hydrophilic interaction.     

β-联碳酰基类衍生物有序自组装膜的STM研究

在大气条件下, 利用扫描隧道显微镜研究了四个β-联碳酰基类衍生物在高定向裂解石墨(HOPG)表面的自组装结构. 研究分子的结构中均包含π电子共轭体系和烷基链. 实验研究了分子结构对自组装结构的影响, 并利用分子结构的变化实现了自组装膜结构的调控. 结果表明, 在甲苯溶剂中制备的这些自组装结构均长程有序, 分子间氢键和偶极相互作用是影响自组装膜结构变化的重要因素.     

Synthetic Zinc and Magnesium Chlorin Aggregates as Models for Supramolecular Antenna Complexes in Chlorosomes of Green Photosynthetic Bacteria

Abstract— A comparison of the spectra of in vitro (3-hydroxymethyl-13¹-oxometallochlorin) and in vivo chlorosomal (bacterio-chlorophyll- c ) aggregates suggests a similar supramolecular structure for the artificial oligomers and the bacte-riochlorophyll- c aggregates in the extramembranous antenna complexes (chlorosomes) of green photosynthetic bacteria. Synthetic zinc and magnesium chlorins have been found to aggregate in 1 % (vol/vol) tetrahydrofuran and hexane solutions and in thin films to form oligomers with the Q_y absorption bands shifted to longer wavelengths by about 1900 (Zn chlorins) and 2100 cm⁻¹ (Mg) relative to the corresponding monomer bands. Visible absorption and circular dichroism spectra of various zinc chlorins establish that a central metal, a 3¹-hydroxy and a 13¹-keto group are functional prerequisites for the aggregation. Vibrational bands measured by IR spectroscopy of solid films reveal two characteristic structural features of the oligomers: (1) a five-coordinated metallochlorin macrocycle with an axial ligand (bands at 1500-1630 cm⁻¹), and (2) a hydrogen bond between the keto oxygen of one chlorin and the hydroxy group of a second chlorin, the oxygen of which is chelated to the metal atom of a third molecule, i.e . C=O…H-O…M (=Zn or Mg).     

INTERCONVERSION OF BACTERIOCHLOROPHYLL c AGGREGATES IN SOLID FILMS UPON ORGANIC VAPOR TREATMENT

Bacteriochlorophyll c (BChl c) solid films were prepared from a carbon tetrachloride solution on CaF₂ plates as artificial aggregates. Effects of organic vapor such as acetone and tetrahydrofuran (THF) on the BChl c films were studied by absorption and Fourier-transform infrared spectroscopy. Two major homologs (R[E,E]BChl c_F and R[P,E]BChl c_F) and one minor homolog (S[I,E]BChl c) isolated from the green photosynthetic bacterium Chlorobium limicola strain 6230 were examined for the experiments. The BChl c polymeric aggregates absorbing at739–753 nm similar to those in the chlorosome were induced for all homologs upon the treatment of BChl c solid film with acetone vapor. The 13¹-keto C=O stretching band in the R[E,E]BChl c_F solid film showed a downward shift from 1651 cm^?1to 1643 cm^?1 with a concomitant shift of the 3¹-OH stretching bands from 3337 and 3238 cm^?1 to 3163 cm^?1. It was suggested that the lower aggregates brought about by Mg…O=C(13¹) and (3¹)O…O=C(13¹) bonds were transformed into the higher aggregates strongly hydrogen-bonded in a Mg…(3¹)O-H…O=C(13^l) interaction. They were transformed to a monomer-like form absorbing at 667 nm upon exposure to THF vapor and were reversibly converted to the higher aggregates upon removal of THF molecules in vacuo.     

Self-aggregation of synthetic protobacteriochlorophyll-d derivatives

3(1)-Racemically pure zinc 3(1)-hydroxy-13(1)-oxo-porphyrins (zinc methyl 17,18-dehydro-bacteriopheophorbides-d) as well as their 3(1)-demethyl form were prepared by modifying chlorophyll-a through oxidation by 2,3-dichloro-5,6-dicyano-benzoquinone. From visible, circular dichroism and infrared spectral analyses, these synthetic pigments self-aggregated in 1%(vol/vol) tetrahydrofuran and cyclohexane to give large oligomers by an intermolecular bonding of 13-C=O...H-O(3(1))...Zn(central) and pi-pi interaction of the porphyrin chromophores. The supramolecular structures are similar to those of the corresponding chlorins and a core part of extramembranous light-harvesting antennas of photosynthetic green bacteria. The 17,18-dehydrogenation of a chlorin to porphyrin moiety did not disturb its self-aggregation and the synthetic zinc porphyrins are good models for naturally occurring self-aggregative bacteriochlorophylls.     

Optical spectroscopy of a highly fluorescent aggregate of bacteriochlorophyll c

Bacteriochlorophyll (BChl) c and a similar model compound, Mg-methyl bacteriopheophorbide d, form several types of aggregates in nonpolar solvents. One of these aggregates is highly fluorescent, with a quantum yield higher than that of the monomer. This aggregate is also unusual in that it shows a rise time in its fluorescence emission decay at certain wavelengths, which is ascribed to a change in conformation of the aggregate. An analysis of fluorescence depolarization data is consistent with either a linear aggregate of four or five monomers or preferably a cyclic arrangement of three dimers.     

Nanopatterning of donor/acceptor hybrid supramolecular architectures on highly oriented pyrolytic graphite: a scanning tunneling microscopy study

Hybrid supramolecular architectures have been fabricated with acceptor 1,4-bis(4-pyridylethynyl)-2,3-bis-dodecyloxy-benzene (PBP) and donor 2,6-bis(3,4,5-tris-dodecyloxy-phenyl)dithieno[3,2-b:2',3'-d]thiophene (DTT) compounds on highly oriented pyrolytic graphite (HOPG) surfaces, and their structures and molecular conductance are characterized by scanning tunneling microscopy/spectroscopy (STM/STS). Stable, one-component adlayers of PBP and DTT are also investigated. The coadsorption of two-component mixtures of PBP and DTT results in a variety of hybrid nanopattern architectures that differ from those of their respective one-component surface assemblies. Adjusting the acceptor/donor molar ratio in mixed adlayer assemblies results in dramatic changes in the structure of the hybrid nanopatterns. STS measurements indicate that the HOMO and LUMO energy levels of PBP and DTT on an HOPG surface are relatively insensitive to changes in the hybrid supramolecular architectures. These results provide important insight into the design and fabrication of two-dimensional hybrid supramolecular architectures.     

Self-assembly of amphiphilic hexapyridinium cations at the air/water interface and on HOPG surfaces.

Mono- and multilayers of a novel amphiphilic hexapyridinium cation with six eicosyl chains (3) are spread at the air/water interface as well as on highly ordered pyrolytic graphite (HOPG). On water, the monolayer of 3 is investigated by recording surface pressure/area and surface potential/area isotherms, and by Brewster angle microscopy (BAM). Self-organized tubular micelles with an internal edge-on orientation of molecules form at the air/water interface at low surface pressure whereas multilayers are present at high surface pressure, after a phase transition. Packing motifs suggesting a tubular arrangement of the constituting molecules were gleaned from atomic force microscopy (AFM) investigations of Langmuir-Blodgett (LB) monolayers being transferred on HOPG at different surface pressures. These LB film structures are compared to the self-assembled monolayer (SAM) of 3 formed via adsorption from a supersaturated solution, which is studied by scanning tunnelling microscopy (STM). On HOPG the SAM of 3 consists of nanorods with a highly ordered edge-on packing of the aromatic rings and an arrangement of alkyl chains which resembles the packing of molecules at the air/water interface at low surface pressure. Additional details of the molecular packing were gleaned from single-crystal X-ray structure analysis of the hexapyridinium model compound 2b, which possesses methyl instead of eicosyl residues.     

Effect of molecular mass on supramolecular organisation of poly(4,4'-dioctyl-2,2':5',2'-terthiophene)

The effect of the chain length on the type and extent of the 2D supramolecular organization in poly(4,4'-dioctyl-2,2':5',2'-terthiophene) (PDOTT) monomolecular layers deposited on highly oriented pyrolytic graphite (HOPG) is studied by scanning tunneling microscopy (STM) and analyzed in terms of molecular modeling. The strictly monodispersed fractions of increasing molecular mass used in this study were obtained by chromatographic fractionation of the crude product of 4,4'-dioctyl-2,2':5',2'-terthiophene oxidative polymerization. STM investigations of PDOTT layers, deposited on HOPG from poly- and monodispersed fractions, show that polydispersity can be considered as a key factor seriously limiting supramolecular ordering. This is a consequence of significant differences in the type of supramolecular order observed for molecules of different chain length. It has been demonstrated that shorter molecules (consisting of 6 and 9 thiophene units) form well-defined two-dimensional islands, while the interactions between longer molecules (consisting of 12 and 15 thiophene units) become anisotropic. Consequently, for higher molecular mass fractions, the supramolecular organization is one-dimensional and consists of more or less separated rows of ordered macromolecules. In this case an increase of the chain length leads to amplification of the intermolecular interactions proceeding via interdigitation of the alkyl substituents of adjacent molecules. Polydispersed fractions show much less ordered organization because of the incompatibility of the supramolecular structures of molecules of different molecular masses. This finding is of crucial importance for the application of polythiophene derivatives in organic and molecular electronics since ordered supramolecular organization constitutes the condition sine qua non of good electrical transport properties.     

Protein Structural Characterization by Scanning Tunneling Microscopy with Electrochemistry

The structure characterization of native and unfolded enzymes and redox proteins like hemoglobin(Hb), myoglobin(Mb), cytochrome c and beef liver catalase etc. by STM on an electrochemically prepared HOPG surface has been studied with the help of electrodeposition. The capability of electrochemical method to prepare stable Hb samples for STM image and for unfolding of this protein has been successfully developed. STM images show an oval-shaped pattern for the native structure of Hb and two dimers consisting of one Hb molecule is clearly discerned. The dimension of folded molecule is determined as 6.4×5.3×0.7 nm³.     

Selective effect of guest molecule length and hydrogen bonding on the supramolecular host structure

A host supramolecular structure consisting of bis-(2,2':6',2' '-terpyridine)-4'-oxyhexadecane (BT-O-C16) is shown to respond to guest molecules in dramatic ways, as observed by using scanning tunneling microscopy (STM) on a highly oriented pyrolytic graphite surface under ambient conditions. It is observed that small linear molecules can be encapsulated within the host supramolecular lattice. The characteristics of the host structure were nearly unaffected by the encapsulated guest molecules of terphthalic acid (TPA) dimers, whereas appreciable changes in cavity dimension can be observed with azobenzene-4,4'-dicarboxylic acid. The STM study and density functional theory (DFT) analysis reveal that intermolecular hydrogen bonding interaction plays an essential role in forming the assembling structures. The difference in guest molecule length is considered the important cause for the different guest-host complexes.     

Pd–Cu/HOPG and Pd–Ag/HOPG Model Catalysts in CO and Methanol Oxidations at Submillibar Pressures

Kinetics and Catalysis - The regularities of formation of alloyed Pd–Cu bimetallic particles deposited on highly oriented pyrolytic graphite (HOPG) were studied by STM and...