"Polytopal Rearrangement Model of Stereoisomerization" and Its Potential as the Basis for a Systematic Model of All Stereoisomerism.

The term "polytopal rearrangement" describes any shape changing process operating on a coordination "polyhedron"-the solid figure defined by the positions of the ligand atoms directly attached to the central atom of a coordination entity. Developed in the latter third of the last century, the polytopal rearrangement model of stereoisomerization is a general mathematical approach for analyzing and accommodating the complexity of such processes for any coordination number. The motivation for the model was principally to deal with the complexity, such as Berry pseudorotation in pentavalent phosphorus species, arising from rearrangements in inorganic coordination complexes of higher coordination numbers. The model is also applicable to lower coordination centers, for example, thermal "inversion" at nitrogen in NH3 and amines. We present the history of the model focusing on its essential features, and review some of the more subtle aspects addressed in recent literature. We then introduce a more detailed and rigorous modern approach for describing such processes using an assembly of existing concepts, with the addition of formally described terminology and representations. In our outlook, we contend that the rigorous and exhaustive application of the principles of the polytopal rearrangement model, when combined with torsional isomerism, will provide a basis for a mathematically complete, general, and systematic classification for all stereoisomerism and stereoisomerization. This is essential for comprehensively mapping chemical structure and reaction spaces.

Publisher Correction: A new fundamental type of conformational isomerism.

In the version of this Article originally published, the word 'stereoisomerism' was erroneously included in the label of the upper-right box of Fig. 1. The label within the box has been corrected and it now reads: "Constitutional isomerism (same formula, different connectivity)". This has been corrected in the online version of the Article.

A new fundamental type of conformational isomerism.

Isomerism is a fundamental chemical concept, reflecting the fact that the arrangement of atoms in a molecular entity has a profound influence on its chemical and physical properties. Here we describe a previously unclassified fundamental form of conformational isomerism through four resolved stereoisomers of a transoid (BF)O(BF)-quinoxalinoporphyrin. These comprise two pairs of enantiomers that manifest structural relationships not describable within existing IUPAC nomenclature and terminology. They undergo thermal diastereomeric interconversion over a barrier of 104 ± 2 kJ mol-1, which we term 'akamptisomerization'. Feasible interconversion processes between conceivable synthesis products and reaction intermediates were mapped out by density functional theory calculations, identifying bond-angle inversion (BAI) at a singly bonded atom as the reaction mechanism. We also introduce the necessary BAI stereodescriptors parvo and amplo. Based on an extended polytope formalism of molecular structure and stereoisomerization, BAI-driven akamptisomerization is shown to be the final fundamental type of conformational isomerization.

Improved peroxide biosensor based on Horseradish Peroxidase/Carbon Nanotube on a thiol-modified gold electrode.

A new 3-dimensional (3D) network of crosslinked Horseradish Peroxidase/Carbon Nanotube (HRP/CNT) on a thiol-modified Au surface has been described in order to build up the effective electrical wiring of the enzyme units with the electrode. The synthesized 3D HRP/CNT network has been characterized with cyclic voltammetry and amperometry which results the establishment of direct electron transfer between the redox active unit of HRP and the Au surface. Electrochemical measurements reveal that the high biological activity and stability is exhibited by the immobilized HRP and a quasi-reversible redox peak of the redox centre of HRP was observed at about -0.355 and -0.275V vs. Ag/AgCl. The electron transfer rate constant, KS and electron transfer co-efficient α were found as 0.57s-1 and 0.42, respectively. Excellent electrocatalytic activity for the reduction of H2O2 was exhibited by the developed biosensor. The proposed biosensor modified with HRP/CNT 3D network displays a broader linear range and a lower detection limit for H2O2 determination. The linear range is from 1.0×10-7 to 1.2×10-4M with a detection limit of 2.2.0×10-8M at 3σ. The Michaelies-Menten constant Kapp M value is estimated to be 0.19mM. Moreover, this biosensor exhibits very high sensitivity, good reproducibility and long-time stability.

Endothermic singlet fission is hindered by excimer formation.

Singlet fission is a process whereby two triplet excitons can be produced from one photon, potentially increasing the efficiency of photovoltaic devices. Endothermic singlet fission is desired for a maximum energy-conversion efficiency, and such systems have been considered to form an excimer-like state with multiexcitonic character prior to the appearance of triplets. However, the role of the excimer as an intermediate has, until now, been unclear. Here we show, using 5,12-bis((triisopropylsilyl)ethynyl)tetracene in solution as a prototypical example, that, rather than acting as an intermediate, the excimer serves to trap excited states to the detriment of singlet-fission yield. We clearly demonstrate that singlet fission and its conjugate process, triplet-triplet annihilation, occur at a longer intermolecular distance than an excimer intermediate would impute. These results establish that an endothermic singlet-fission material must be designed to avoid excimer formation, thus allowing singlet fission to reach its full potential in enhancing photovoltaic energy conversion.

Time-resolved and temperature tuneable measurements of fluorescent intensity using a smartphone fluorimeter.

A smartphone fluorimeter capable of time-based fluorescence intensity measurements at various temperatures is reported. Excitation is provided by an integrated UV LED (λex = 370 nm) and detection obtained using the in-built CMOS camera. A Peltier is integrated to allow measurements of the intensity over T = 10 to 40 °C. All components are controlled using a smartphone battery powered Arduino microcontroller and a customised Android application that allows sequential fluorescence imaging and quantification every δt = 4 seconds. The temperature dependence of fluorescence intensity for four emitters (rhodamine B, rhodamine 6G, 5,10,15,20-tetraphenylporphyrin and 6-(1,4,8,11-tetraazacyclotetradecane)2-ethyl-naphthalimide) are characterised. The normalised fluorescence intensity over time of the latter chemosensor dye complex in the presence of Zn2+ is observed to accelerate with an increasing rate constant, k = 1.94 min-1 at T = 15 °C and k = 3.64 min-1 at T = 30 °C, approaching a factor of ∼2 with only a change in temperature of ΔT = 15 °C. Thermally tuning these twist and bend associated rates to optimise sensor approaches and device applications is proposed.

Synthetically tuneable biomimetic artificial photosynthetic reaction centres that closely resemble the natural system in purple bacteria.

Porphyrin-based photosynthetic reaction centre (PRC) mimics, ZnPQ-Q2HP-C60 and MP2Q-Q2HP-C60 (M = Zn or 2H), designed to have a similar special-pair electron donor and similar charge-separation distances, redox processes and photochemical reaction rates to those in the natural PRC from purple bacteria, have been synthesised and extensive photochemical studies performed. Mechanisms of electron-transfer reactions are fully investigated using femtosecond and nanosecond transient absorption spectroscopy. In benzonitrile, all models show picosecond-timescale charge-separations and the final singlet charge-separations with the microsecond-timescale. The established lifetimes are long compared to other processes in organic solar cells or other organic light harvesting systems. These rigid, synthetically flexible molecules provide the closest mimics to the natural PRC so far synthesised and present a future direction for the design of light harvesters with controllable absorption, redox, and kinetics properties.

Conformation-Controlled Diplatinum(II)-Ferrocene Dyads to Achieve Long-Lived Charge-Separated States.

Square-planar polypyridyl platinum(II) complexes possess a rich range of structural and spectroscopic properties that are ideal for designing artificial photosynthetic centers. Taking advantage of the directionality in the charge-transfer excitation from the metal to the polypyridyl ligand, we describe here diplatinum(II)-ferrocene dyads, open-butterfly-like dyad 1 and closed-butterfly-like dyad 2, which were designed to understand the conformation and orientation effects to prolong the lifetime of charge-separated state. In contrast to the open-butterfly-like dyad 1, the closed-butterfly-like dyad 2 shows three-times long lifetime of charge separated state upon photoexcitation, demonstrating that the orientation in the rigid structure of dyad 2 is a very important issue to achieve long-lived charge separated state.

Nanofabrication of a Solid-State, Mesoporous Nanoparticle Composite for Efficient Photocatalytic Hydrogen Generation.

Room-temperature self-assembly was used to fabricate a periodic array of uniformly sized Al3+ -doped SiO2 nanoparticles (Al-SiO2 NPs, 20-30 nm). The uniform mesoporous structure was suitable for uniformly incorporating and distributing Pt nanoparticles (PtNPs), which were used as hydrogen-evolution catalysts in artificial photosynthetic systems, without agglomeration during the catalytic reaction. When the surfaces of the Al-SiO2 NPs were covered with an organic photocatalyst (2-phenyl-4-(1-naphthyl)quinolinium ion, QuPh+ -NA), each PtNP was surrounded by multiple QuPh+ -NA ions. The structure allowed the PtNP to receive multiple electrons from QuPh. -NA molecules, which were generated by reduction of the photoexcited state of QuPh+ -NA ions (QuPh. -NA. + ) with ß-dihydronicotinamide adenine dinucleotide (NADH), thereby resulting in efficient photocatalytic H2 evolution.

Increased upconversion performance for thin film solar cells: a trimolecular composition.

Photochemical upconversion based on triplet-triplet annihilation (TTA-UC) is employed to enhance the short-circuit currents generated by two varieties of thin-film solar cells, a hydrogenated amorphous silicon (a-Si:H) solar cell and a dye-sensitized solar cell (DSC). TTA-UC is exploited to harvest transmitted sub-bandgap photons, combine their energies and re-radiate upconverted photons back towards the solar cells. In the present study we employ a dual-emitter TTA-UC system which allows for significantly improved UC quantum yields as compared to the previously used single-emitter TTA systems. In doing so we achieve record photo-current enhancement values for both the a-Si:H device and the DSC, surpassing 10-3 mA cm-2 sun-2 for the first time for a TTA-UC system and marking a record for upconversion-enhanced solar cells in general. We discuss pertinent challenges of the TTA-UC technology which need to be addressed in order to achieve its viable device application.

A priori calculations of the free energy of formation from solution of polymorphic self-assembled monolayers.

Modern quantum chemical electronic structure methods typically applied to localized chemical bonding are developed to predict atomic structures and free energies for meso-tetraalkylporphyrin self-assembled monolayer (SAM) polymorph formation from organic solution on highly ordered pyrolytic graphite surfaces. Large polymorph-dependent dispersion-induced substrate-molecule interactions (e.g., -100 kcal mol(-1) to -150 kcal mol(-1) for tetratrisdecylporphyrin) are found to drive SAM formation, opposed nearly completely by large polymorph-dependent dispersion-induced solvent interactions (70-110 kcal mol(-1)) and entropy effects (25-40 kcal mol(-1) at 298 K) favoring dissolution. Dielectric continuum models of the solvent are used, facilitating consideration of many possible SAM polymorphs, along with quantum mechanical/molecular mechanical and dispersion-corrected density functional theory calculations. These predict and interpret newly measured and existing high-resolution scanning tunnelling microscopy images of SAM structure, rationalizing polymorph formation conditions. A wide range of molecular condensed matter properties at room temperature now appear suitable for prediction and analysis using electronic structure calculations.

Amino acid-linked porphyrin-nitroimidazole antibiotics targeting Porphyromonas gingivalis.

The periodontal pathogen Porphyromonas gingivalis requires porphyrin supplementation for growth. Previously, in order to inhibit P. gingivalis growth, we synthesised very effective 'Trojan horse' ester and amide-linked deuterporphyrin-nitroimidazole (DPIX-Nim) adducts that exploited this requirement to transport metronidazole-derived antibiotics with excellent antimicrobial selectivity and recognition by the HA2 porphyrin binding site. Herein, in the context of developing topical agents to target P. gingivalis, l-amino acids are incorporated into adducts as linkers to improve uptake. Ten 13- and 17-propionic amide regioisomers of l-amino acid-linked deuterporphyrin-nitroimidazole adducts were synthesised using a peptide coupling approach. DPIX-Lys regioisomers without attached nitroimidazole were also synthesised as comparison compounds. All the porphyrin adducts bound (Kd50 7 to 20 nM) to a recombinant HA2 receptor with similar binding affinity to haem, except the lysine-proline linked DPIX-Lys(Boc)Pro-Nim adducts (Kd50 300 nM) and the DPIX-Lys(Nim)-Nim adducts (Kd50 200 nM), both of which have large appended groups. DPIX-Lys(Boc)-Nim, DPIX-Lys(OH)-Nim, and DPIX-Pro-Nim adducts were shown to be very effective against P. gingivalis. DPIX-Lys(Boc)Pro-Nim adducts and DPIX-Lys(Nim)-Nim adducts showed weak activity. Importantly, DPIX-Lys(Boc)-Nim adducts were selective for P. gingivalis and, unlike metronidazole, did not kill a range of other anaerobic bacteria isolated from the human gastrointestinal tract.

Nanostructuring of self-assembled porphyrin networks at a solid/liquid interface: local manipulation under global control.

Molecules of (5,10,15,20-tetraundecylporphyrinato)-copper(II) [(TUP)Cu] can self-assemble into four different polymorphs at the interface between highly oriented pyrolytic graphite and 1-octanoic acid. Scanning tunneling microscopy (STM) reveals that it is possible to combine the global control over monolayer structure, provided by the composition and concentration of the supernatant solution, with local control, from nanomanipulation by the STM tip. In the initially formed monolayer, with a polymorph composition governed by the concentration of (TUP)Cu in the supernatant solution, the exchange of molecules physisorbed at the solid/liquid interface with those in the liquid is very limited. By using a nanoshaving procedure at the tip, defects are created in the monolayer, and these serve as local manipulation sites to create domains of higher or lower molecular density, and to incorporate a second molecular species, (TUP)Co into the monolayer of (TUP)Cu.

Percolation Diffusion into Self-Assembled Mesoporous Silica Microfibres.

Percolation diffusion into long (11.5 cm) self-assembled, ordered mesoporous microfibres is studied using optical transmission and laser ablation inductive coupled mass spectrometry (LA-ICP-MS). Optical transmission based diffusion studies reveal rapid penetration (<5 s, D > 80 µm²âˆ™s-¹) of Rhodamine B with very little percolation of larger molecules such as zinc tetraphenylporphyrin (ZnTPP) observed under similar loading conditions. The failure of ZnTPP to enter the microfibre was confirmed, in higher resolution, using LA-ICP-MS. In the latter case, LA-ICP-MS was used to determine the diffusion of zinc acetate dihydrate, D~3 × 10-4 nm²âˆ™s-1. The large differences between the molecules are accounted for by proposing ordered solvent and structure assisted accelerated diffusion of the Rhodamine B based on its hydrophilicity relative to the zinc compounds. The broader implications and applications for filtration, molecular sieves and a range of devices and uses are described.

Fabricating Nanoporous Silica Structure on D-Fibres through Room Temperature Self-Assembly.

The room temperature deposition of self-assembling silica nanoparticles onto D-shaped optical fibres ("D-fibre"), drawn from milled preforms fabricated by modified chemical vapour deposition (MCVD), is studied. Vertical dip-and-withdraw produces tapered layers, with one end thicker (surface coverage >0.85) than the other, whilst horizontal dip-and-withdraw produces much more uniform layers over the core region. The propagation of induced fracturing over the core region during drying is overcome using a simple protrusion of the inner cladding. Thick coatings are discernible through thin film interference colouring, but thinner coatings require scanning electron microscopy (SEM) imaging. Here, we show that fluorescence imaging, using Rhodamine B, in this example, can provide some qualitative and speedy assessment of coverage.

A multiscale simulation technique for molecular electronics: design of a directed self-assembled molecular n-bit shift register memory device.

A general method useful in molecular electronics design is developed that integrates modelling on the nano-scale (using quantum-chemical software) and on the micro-scale (using finite-element methods). It is applied to the design of an n-bit shift register memory that could conceivably be built using accessible technologies. To achieve this, the entire complex structure of the device would be built to atomic precision using feedback-controlled lithography to provide atomic-level control of silicon devices, controlled wet-chemical synthesis of molecular insulating pillars above the silicon, and controlled wet-chemical self-assembly of modular molecular devices to these pillars that connect to external metal electrodes (leads). The shift register consists of n connected cells that read data from an input electrode, pass it sequentially between the cells under the control of two external clock electrodes, and deliver it finally to an output device. The proposed cells are trimeric oligoporphyrin units whose internal states are manipulated to provide functionality, covalently connected to other cells via dipeptide linkages. Signals from the clock electrodes are conveyed by oligoporphyrin molecular wires, and µ-oxo porphyrin insulating columns are used as the supporting pillars. The developed multiscale modelling technique is applied to determine the characteristics of this molecular device, with in particular utilization of the inverted region for molecular electron-transfer processes shown to facilitate latching and control using exceptionally low energy costs per logic operation compared to standard CMOS shift register technology.

Tunable self-assembly of triazole-linked porphyrin-polymer conjugates.

The convergence of supramolecular chemistry and polymer science offers many powerful approaches for building functional nanostructures with well-defined dynamic behaviour. Herein we report the efficient "click" synthesis and self-assembly of AB2 - and AB4 -type multitopic porphyrin-polymer conjugates (PPCs). PPCs were prepared using the copper(I)-catalysed azide-alkyne cycloaddition (CuAAC) reaction, and consisted of linear polystyrene, poly(butyl acrylate), or poly(tert-butyl acrylate) arms attached to a zinc(II) porphyrin core via triazole linkages. We exploit the presence of the triazole groups obtained from CuAAC coupling to direct the self-assembly of the PPCs into short oligomers (2-6 units in length) via intermolecular porphyrinatozinc-triazole coordination. By altering the length and grafting density of the polymer arms, we demonstrate that the association constant of the porphyrinatozinc-triazole complex can be systematically tuned over two orders of magnitude. Self-assembly of the PPCs also resulted in a 6 K increase in the glass transition temperature of the bulk material compared to a non-assembling PPC. The modular synthesis and tunable self-assembly of the triazole-linked PPCs thus represents a powerful supramolecular platform for building functional nanostructured materials.

Polymorphism in porphyrin monolayers: the relation between adsorption configuration and molecular conformation.

Self-assembled monolayers of meso-5,10,15,20-tetrakis(undecyl)porphyrin copper(II) on a graphite/1-octanoic acid interface have been studied by Scanning Tunnelling Microscopy. Four distinct polymorphs were observed, varying in their unit cell size. Arrays of unit cells of the various polymorphs seamlessly connect to each other via shared unit cell vectors. The monolayers are not commensurate, but coincident with the underlying graphite substrate. The seamless transition between the polymorphs is proposed to be the result of an adaptation of the molecular conformations in the polymorphs and at the boundaries, which is enabled by the conformational freedom of the alkyl tails of these molecules.

Gold(III) porphyrins containing two, three, or four ß,ß'-fused quinoxalines. Synthesis, electrochemistry, and effect of structure and acidity on electroreduction mechanism.

Gold(III) porphyrins containing two, three, or four ß,ß'-fused quinoxalines were synthesized and examined as to their electrochemical properties in tetrahydrofuran (THF), pyridine, CH2Cl2, and CH2Cl2 containing added acid in the form of trifluoroacetic acid (TFA). The investigated porphyrins are represented as Au(PQ2)PF6, Au(PQ3)PF6, and Au(PQ4)PF6, where P is the dianion of the 5,10,15,20-tetrakis(3,5-di-tert-butylphenyl)porphyrin and Q is a quinoxaline group fused to a ß,ß'-pyrrolic position of the porphyrin macrocycle. In the absence of added acid, all three gold(III) porphyrins undergo a reversible one-electron oxidation and several reductions. The first reduction is characterized as a Au(III)/Au(II) process which is followed by additional porphyrin- and quinoxaline-centered redox reactions at more negative potentials. However, when 3-5 equivalents of acid are added to the CH2Cl2 solution, the initial Au(III)/Au(II) process is followed by a series of internal electron transfers and protonations, leading ultimately to triply reduced and doubly protonated Au(II)(PQ2H2) in the case of Au(III)(PQ2)(+), quadruply reduced and triply protonated Au(II)(PQ3H3) in the case of Au(III)(PQ3)(+), and Au(II)(PQ4H4) after addition of five electrons and four protons in the case of Au(III)(PQ4)(+). Under these solution conditions, the initial Au(PQ2)PF6 compound is shown to undergo a total of three Au(III)/Au(II) processes while Au(PQ3)PF6 and Au(PQ4)PF6 exhibit four and five metal-centered one-electron reductions, respectively, prior to the occurrence of additional reductions at the conjugated macrocycle and fused quinoxaline rings. Each redox reaction was monitored by cyclic voltammetry and thin-layer spectroelectrochemistry, and an overall mechanism for reduction in nonaqueous media with and without added acid is proposed. The effect of the number of Q groups on half-wave potentials for reduction and UV-visible spectra of the electroreduced species are analyzed using linear free energy relationships.

Dye-Sensitized Solar Cell with Integrated Triplet-Triplet Annihilation Upconversion System.

Photon upconversion (UC) by triplet-triplet annihilation (TTA-UC) is employed in order to enhance the response of solar cells to sub-bandgap light. Here, we present the first report of an integrated photovoltaic device, combining a dye-sensitized solar cell (DSC) and TTA-UC system. The integrated device displays enhanced current under sub-bandgap illumination, resulting in a figure of merit (FoM) under low concentration (3 suns), which is competitive with the best values recorded to date for nonintegrated systems. Thus, we demonstrate both the compatibility of DSC and TTA-UC and a viable method for device integration.