Fulvalene-Based Polycyclic Aromatic Hydrocarbon Ladder-Type Structures: Synthesis and Properties.

Polycyclic aromatic hydrocarbons (PAHs) have found strong interest for their electronic properties and as model systems for graphene. While PAHs have been studied intensively as single units, here PAHs were constructed in ladder-type arrangements using cross-conjugated fulvalene and dithiafulvalene motifs as connecting units and moving forward a convenient synthetic approach for dimerizing (thio)ketones into olefins by the action of Lawesson's reagent. Some of the PAHs can also be regarded as "super-extended" tetrathiafulvalenes (TTFs) with some of the largest cores ever explored, being multi-redox systems that exhibit both reversible oxidations and reductions. Concomitant absorption redshifts were observed when expanding the ladder-type structures from one to two to three indenofluorene units, and optical and electrochemical HOMO-LUMO gaps were found to correlate linearly. Various conformations (and solid-state packing arrangements) were studied by X-ray crystallography and computations.

Synthesis of radiaannulene oligomers to model the elusive carbon allotrope 6,6,12-graphyne.

Graphyne allotropes of carbon are fascinating materials, and their electronic properties are predicted to rival those of the "wonder material" graphene. One allotrope of graphyne, having rectangular symmetry rather than hexagonal, stands out as particularly attractive, namely 6,6,12-graphyne. It is currently an insurmountable challenge, however, to design and execute a synthesis of this material. Herein, we present synthesis and electronic properties of molecules that serve as model compounds. These oligomers, so-called radiaannulenes, are prepared by iterative acetylenic coupling reactions. Systematic optical and redox studies indicate the effective conjugation length of the radiaannulene oligomers is nearly met by the length of the trimer. The HOMO-LUMO gap suggested by the series of oligomers is still, however, higher than that expected for 6,6,12-graphyne from theory, which predicts two nonequivalent distorted Dirac cones (no band gap). Thus, the radiaannulene oligomers present a suitable length in one dimension of a sheet, but should be expanded in the second dimension to provide a unique representation of 6,6,12-graphyne.

Structure and Dynamics of a Promiscuous Xanthan Lyase from Paenibacillus nanensis and the Design of Variants with Increased Stability and Activity.

We have characterized the structure and dynamics of the carbohydrate-modifying enzyme Paenibacillus nanensis xanthan lyase (PXL) involved in the degradation of xanthan by X-ray crystallography, small-angle X-ray scattering, and hydrogen/deuterium exchange mass spectrometry. Unlike other xanthan lyases, PXL is specific for both unmodified mannose and pyruvylated mannose, which we find is correlated with structural differences in the substrate binding groove. The structure of the full-length enzyme reveals two additional C-terminal modules, one of which belongs to a new non-catalytic carbohydrate binding module family. Ca2+ are critical for the activity and conformation of PXL, and we show that their removal by chelating agents results in localized destabilization/unfolding of particularly the C-terminal modules. We use the structure and the revealed impact of Ca2+ coordination on conformational dynamics to guide the engineering of PXL variants with increased activity and stability in a chelating environment, thus expanding the possibilities for industrial applications of PXL.

Complexation of Fullerenes by Subphthalocyanine Dimers.

Tweezer-like molecules comprised of two boron subphthalocyanine (SubPc) units were prepared by Sonogashira couplings and investigated using NMR spectroscopy for their ability to bind fullerenes (C60 and C70). The preorganization of the tweezers provided association constants of ca. 103 M-1 in toluene- d8, while a SubPc monomer did not show any association. Nevertheless, the SubPc monomer crystallized with the fullerenes as 2:1 complexes, supporting the favorable tweezer-like design for complexation, which was further corroborated by computations.

Synthesis and Properties of Subphthalocyanine-Tetracyanobutadiene-Ferrocene Triads.

A series of boron subphthalocyanine-tetracyanobutadiene-ferrocene (SubPc-TCBD-Fc) triads was synthesized by subjecting SubPcs with a ferrocenylethynyl substituent at either the axial or peripheral position to a [2 + 2] cycloaddition reaction with tetracyanoethylene followed by retroelectrocyclization. The ferrocenylethynyl unit was introduced at the axial position (at the boron atom) by a simple aluminum chloride-mediated alkynylation reaction, while functionalization at the SubPc periphery was accomplished by a Sonogashira coupling reaction. The conversion of one alkyne unit into a TCBD unit in combination with the location of the resulting TCBD-Fc moiety was found to have a strong influence on the optical and redox properties, which is ascribed to very different ground-state interactions between the individual donor/acceptor systems. The first electrochemical oxidation could thus be anodically shifted by as much as 0.4 V from the strongest donor molecule (with most unperturbed ferrocene character) to the poorest donor molecule (with strongly perturbed ferrocene character). Six redox states could be reached reversibly for the SubPc-TCBD-Fc triads, -3, -2, -1, 0, + 1, + 2, and for one compound the formation of a tetraanion persistent at the time scale of slow scan voltammetry was observed.

Thieno-Fused Subporphyrazines: A New Class of Light Harvesters.

Boron subphthalocyanines comprised of three isoindole units bridged by aza-linkages are attractive light harvesters on account of their intense low-energy absorptions. Herein, we present a class of related compounds, in which one or two isoindole units are substituted for thieno[3,4-c]pyrrole units - thieno-fused subporphyrazines. Such changes have remarkable consequences for the optical properties, as was revealed by combined experimental and theoretical studies. Thus, we find that the lowest-energy absorptions cover a much broader region with a significantly redshifted end-absorption and without compromising the absorption intensities. Thieno-fused subporphyrazines also underwent more readily oxidation and reduction, indicating an increased HOMO energy and decreased LUMO energy. In addition, they were found to readily co-crystallize with Buckminsterfullerene, C60 . Altogether, these findings render this new class of chromophores attractive candidates for light-harvesting applications.

Aromaticity-Controlled Energy Storage Capacity of the Dihydroazulene-Vinylheptafulvene Photochromic System.

Photochemical conversion of molecules into high-energy isomers that, after a stimulus, return to the original isomer presents a closed-cycle of light-harvesting, energy storage, and release. One challenge is to achieve a sufficiently high energy storage capacity. Here, we present efforts to tune the dihydroazulene/vinylheptafulvene (DHA/VHF) couple through loss/gain of aromaticity. Two derivatives were prepared, one with aromatic stabilization of DHA and the second of VHF. The consequences for the switching properties were elucidated. For the first type, sigmatropic rearrangements of DHA occurred upon irradiation. Formation of a VHF complex could be induced by a Lewis acid, but addition of H2 O resulted in immediate regeneration of DHA. For the second type, the VHF was too stable to convert into DHA. Calculations support the results and provide new targets. We predict that by removing one of the two CN groups at C-1 of the aromatic DHA, the heat storage capacity will be further increased, as will the life-time of the VHF. Calculations also reveal that a CN group at the fulvene ring retards the back-reaction, and we show synthetically that it can be introduced regioselectively.

Synthesis and Single-Molecule Conductances of Neutral and Cationic Indenofluorene-Extended Tetrathiafulvalenes: Kondo Effect Molecules.

Development of molecules that can switch between redox states with paired and unpaired electrons is important for molecular electronics and spintronics. In this work, a selection of redox-active indenofluorene-extended tetrathiafulvalenes (IF-TTFs) with thioacetate end groups was prepared from a readily obtainable dibromo-functionalized IF-TTF building block using palladium-catalyzed cross-coupling reactions, such as the Suzuki reaction. The end groups served as electrode anchoring groups for single-molecule conductance studies, and the molecules were subjected to mechanically controlled break-junction measurements with gold contacts and to low-bias charge transport measurements in gated three-terminal electromigration junctions. The neutral molecules showed clear conductance signatures, and somewhat surprisingly, we found that a meta-meta anchoring configuration gave a higher conductance than a para-meta configuration. We explain this behavior by "through-space" coupling between the gold electrode and the phenyl on which the anchoring group is attached. Upon charging the molecule in a gated junction, we found reproducibly a Kondo effect (zero-bias conductance) attributed to a net spin. Ready generation of radical cations was supported by cyclic voltammetry measurements, revealing stepwise formation of radical cation and dication species in solution. The first oxidation event was accompanied by association reactions as the appearance of the first oxidation peak was strongly concentration dependent.

Solar Thermal Energy Storage in a Photochromic Macrocycle.

The conversion and efficient storage of solar energy is recognized to hold significant potential with regard to future energy solutions. Molecular solar thermal batteries based on photochromic systems exemplify one possible technology able to harness and apply this potential. Herein is described the synthesis of a macrocycle based on a dimer of the dihydroazulene/vinylheptafulvene (DHA/VHF) photo/thermal couple. By taking advantage of conformational strain, this DHA-DHA macrocycle presents an improved ability to absorb and store incident light energy in chemical bonds (VHF-VHF). A stepwise energy release over two sequential ring-closing reactions (VHF→DHA) combines the advantages of an initially fast discharge, hypothetically addressing immediate energy consumption needs, followed by a slow process for consistent, long-term use. This exemplifies another step forward in the molecular engineering and design of functional organic materials towards solar thermal energy storage and release.

Multistate Switches: Ruthenium Alkynyl-Dihydroazulene/Vinylheptafulvene Conjugates.

Multimode molecular switches incorporating distinct and independently addressable functional components have potential applications as advanced switches and logic gates for molecular electronics and memory storage devices. Herein, we describe the synthesis and characterization of four switches based on the dihydroazulene/vinylheptafulvene (DHA/VHF) photo/thermoswitch pair functionalized with the ruthenium-based Cp*(dppe)Ru ([Ru*]) metal complex (dppe=1,2-bis(diphenylphosphino)ethane; Cp*=pentamethylcyclopentadienyl). The [Ru*]-DHA conjugates can potentially exist in six different states accessible by alternation between DHA/VHF, Ru(II) /Ru(III) , and alkynyl/vinylidene, which can be individually stimulated by using light/heat, oxidation/reduction, and acid/base. Access to the full range of states was found to be strongly dependent on the electronic communication between the metal center and the organic photoswitch in these [Ru*]-DHA conjugates. Detailed electrochemical, spectroscopic (UV/Vis, IR, NMR), and X-ray crystallographic studies indeed reveal significant electronic interactions between the two moieties. When in direct conjugation, the ruthenium metal center was found to quench the photochemical ring-opening of DHA, which in one case could be restored by protonation or oxidation, allowing conversion to the VHF state.

Azulenium chemistry: towards new derivatives of photochromic dihydroazulenes.

Here we present the preparation of a selection of azulenium ions by hydride abstraction from photochromic 1,8a-dihydroazulenes (1,8a-DHAs) incorporating two cyano groups at C-1. The reactivity of the electrophilic tropylium ring of these molecules towards lithium triisopropylsilylacetylide was investigated. The position of attack by the nucleophile depended on the substitution pattern of the azulenium cation but was in general found to occur preferentially at positions C-4, C-5, and C-6, and to a minor extent at positions C-7 and C-8. The outcome was a mixture of non-photochromic, regioisomeric DHAs. One of these compounds containing the ethynyl substituent at position C-4 was partly tautomerized to the photochromic 1,8a-dihydroazulene, which was isolated and its switching properties were investigated by UV-Vis absorption spectroscopy. Upon irradiation, it undergoes a ring-opening reaction to form a vinylheptafulvene (VHF), which in turn returns to the original DHA. The half-life of this reaction was significantly smaller than for a derivative with the alkynyl substituent placed at C-7. This fast switching behavior was according to the calculations explained by an enhancement in the stability of the reactive s-cis conformer of the VHF relative to the, still more stable, s-trans conformer, and by a smaller activation energy for this s-cis conformer to undergo ring-closure.

Tracking molecular resonance forms of donor-acceptor push-pull molecules by single-molecule conductance experiments.

The ability of molecules to change colour on account of changes in solvent polarity is known as solvatochromism and used spectroscopically to characterize charge-transfer transitions in donor-acceptor molecules. Here we report that donor-acceptor-substituted molecular wires also exhibit distinct properties in single-molecule electronics under the influence of a bias voltage, but in absence of solvent. Two oligo(phenyleneethynylene) wires with donor-acceptor substitution on the central ring (cruciform-like) exhibit remarkably broad conductance peaks measured by the mechanically controlled break-junction technique with gold contacts, in contrast to the sharp peak of simpler molecules. From a theoretical analysis, we explain this by different degrees of charge delocalization and hence cross-conjugation at the central ring. Thus, small variations in the local environment promote the quinoid resonance form (off), the linearly conjugated (on) or any form in between. This shows how the conductance of donor-acceptor cruciforms is tuned by small changes in the environment.

Interactions between tetrathiafulvalene units in dimeric structures - the influence of cyclic cores.

A selection of cyclic and acyclic acetylenic scaffolds bearing two tetrathiafulvalene (TTF) units was prepared by different metal-catalyzed coupling reactions. The bridge separating the two TTF units was systematically changed from linearly conjugated ethyne, butadiyne and tetraethynylethene (trans-substituted) units to a cross-conjugated tetraethynylethene unit, placed in either acyclic or cyclic arrangements. The cyclic structures correspond to so-called radiaannulenes having both endo- and exocyclic double bonds. Interactions between two redox-active TTF units in these molecules were investigated by cyclic voltammetry, UV-vis-NIR and EPR absorption spectroscopical methods of the electrochemically generated oxidized species. The electron-accepting properties of the acetylenic cores were also investigated electrochemically.

Adenine phosphoribosyltransferase from Sulfolobus solfataricus is an enzyme with unusual kinetic properties and a crystal structure that suggests it evolved from a 6-oxopurine phosphoribosyltransferase.

The adenine phosphoribosyltransferase (APRTase) encoded by the open reading frame SSO2342 of Sulfolobus solfataricus P2 was subjected to crystallographic, kinetic, and ligand binding analyses. The enzyme forms dimers in solution and in the crystals, and binds one molecule of the reactants 5-phosphoribosyl-α-1-pyrophosphate (PRPP) and adenine or the product adenosine monophosphate (AMP) or the inhibitor adenosine diphosphate (ADP) in each active site. The individual subunit adopts an overall structure that resembles a 6-oxopurine phosphoribosyltransferase (PRTase) more than known APRTases implying that APRT functionality in Crenarchaeotae has its evolutionary origin in this family of PRTases. Only the N-terminal two-thirds of the polypeptide chain folds as a traditional type I PRTase with a five-stranded ß-sheet surrounded by helices. The C-terminal third adopts an unusual three-helix bundle structure that together with the nucleobase-binding loop undergoes a conformational change upon binding of adenine and phosphate resulting in a slight contraction of the active site. The inhibitor ADP binds like the product AMP with both the α- and ß-phosphates occupying the 5'-phosphoribosyl binding site. The enzyme shows activity over a wide pH range, and the kinetic and ligand binding properties depend on both pH and the presence/absence of phosphate in the buffers. A slow hydrolysis of PRPP to ribose 5-phosphate and pyrophosphate, catalyzed by the enzyme, may be facilitated by elements in the C-terminal three-helix bundle part of the protein.

Structure of dimeric, recombinant Sulfolobus solfataricus phosphoribosyl diphosphate synthase: a bent dimer defining the adenine specificity of the substrate ATP.

The enzyme 5-phosphoribosyl-1-α-diphosphate (PRPP) synthase (EC 2.7.6.1) catalyses the Mg(2+)-dependent transfer of a diphosphoryl group from ATP to the C1 hydroxyl group of ribose 5-phosphate resulting in the production of PRPP and AMP. A nucleotide sequence specifying Sulfolobus solfataricus PRPP synthase was synthesised in vitro with optimised codon usage for expression in Escherichia coli. Following expression of the gene in E. coli PRPP synthase was purified by heat treatment and ammonium sulphate precipitation and the structure of S. solfataricus PRPP synthase was determined at 2.8 Å resolution. A bent dimer oligomerisation was revealed, which seems to be an abundant feature among PRPP synthases for defining the adenine specificity of the substrate ATP. Molecular replacement was used to determine the S. solfataricus PRPP synthase structure with a monomer subunit of Methanocaldococcus jannaschii PRPP synthase as a search model. The two amino acid sequences share 35 % identity. The resulting asymmetric unit consists of three separated dimers. The protein was co-crystallised in the presence of AMP and ribose 5-phosphate, but in the electron density map of the active site only AMP and a sulphate ion were observed. Sulphate ion, reminiscent of the ammonium sulphate precipitation step of the purification, seems to bind tightly and, therefore, presumably occupies and blocks the ribose 5-phosphate binding site. The activity of S. solfataricus PRPP synthase is independent of phosphate ion.

Controlling two-step multimode switching of dihydroazulene photoswitches.

We present the synthesis and switching studies of systems with two photochromic dihydroazulene (DHA) units connected by a phenylene bridge at either para or meta positions, which correspond to a linear or cross-conjugated pathway between the photochromes. According to UV/Vis absorption and NMR spectroscopic measurements, the meta-phenylene-bridged DHA-DHA exhibited sequential light-induced ring openings of the two DHA units to their corresponding vinylheptafulvenes (VHFs). Initially, the VHF-DHA species was generated, and, ultimately, after continued irradiation, the VHF-VHF species. Studies in different solvents and quantum chemical calculations indicate that the excitation of DHA-VHF is no longer a local DHA excitation but a charge-transfer transition that involves the neighboring VHF unit. For the linearly conjugated para-phenylene-bridged dimer, electronic communication between the two units is so efficient that the photoactivity is reduced for both the DHA-DHA and DHA-VHF species, and DHA-DHA, DHA-VHF, and VHF-VHF were all present during irradiation. In all, by changing the bridging unit, we can control the degree of stepwise photoswitching.

Mono- and bis(pyrrolo)tetrathiafulvalene derivatives tethered to C60: synthesis, photophysical studies, and self-assembled monolayers.

A series of mono- (MPTTF) and bis(pyrrolo)tetrathiafulvalene (BPTTF) derivatives tethered to one or two C60 moieties was synthesized and characterized. The synthetic strategy for these dumbbell-shaped compounds was based on a 1,3-dipolar cycloaddition reaction between aldehyde-functionalized MPTTF/BPTTF derivatives, two different tailor-made amino acids, and C60. Electronic communication between the MPTTF/BPTTF units and the C60 moieties was studied by a variety of techniques including cyclic voltammetry and absorption spectroscopy. These solution-based studies indicated no observable electronic communication between the MPTTF/BPTTF units and the C60 moieties. In addition, femtosecond and nanosecond transient absorption spectroscopy revealed, rather surprisingly, that no charge transfer from the MPTTF/BPTTF units to the C60 moieties takes place on excitation of the fullerene moiety. Finally, it was shown that the MPTTF-C60 and C60-BPTTF-C60 dyad and triad molecules formed self-assembled monolayers on a Au(111) surface by anchoring to C60.

Specificities and pH profiles of adenine and hypoxanthine-guanine-xanthine phosphoribosyltransferases (nucleotide synthases) of the thermoacidophile archaeon Sulfolobus solfataricus.

Two open reading frames in the genome of Sulfolobus solfataricus (SSO2342 [corrected] and SSO2424) were cloned and expressed in E. coli. The protein products were purified and their enzymatic activity characterized. Although SSO2342 [corrected] was annotated as a gene (gpT-1) encoding a 6-oxopurine phosphoribosyltransferase (PRTase), the protein product turned out to be a PRTase highly specific for adenine and we suggest that the reading frame should be renamed apT. The other reading frame SSO2424 (gpT-2) proved to be a true 6-oxopurine PRTase active with hypoxanthine, xanthine and guanine as substrates, and we suggest that the gene should be renamed gpT. Both enzymes exhibited unusual profiles of activity versus pH. The adenine PRTase showed the highest activity at pH 7.5-8.5, but had a distinct peak of activity also at pH 4.5. The 6-oxo PRTase showed maximal activity with hypoxanthine and guanine around pH 4.5, while maximal activity with xanthine was observed at pH 7.5. We discuss likely reasons why SSO2342 [corrected] in S. solfataricus and similar open reading frames in other Crenarchaeota could not be identified as genes encoding APRTase.

Arylethynyl derivatives of the dihydroazulene/vinylheptafulvene photo/thermoswitch: tuning the switching event.

A selection of dihydroazulene (DHA) photoswitches incorporating an arylethynyl-substituent in the seven-membered ring was prepared by palladium-catalyzed Sonogashira cross-coupling reactions employing a suitable bromo-functionalized DHA. Shielding of the alkyne bridge and separating the aryl and DHA units, by sterically demanding groups, was required to obtain stable compounds. The DHAs underwent a light-induced ring-opening to vinylheptafulvenes (VHFs) which were thermally converted to a mixture of two DHA regioisomers, one of which was the original one. The influence of the aryl groups on the DHA and VHF absorptions and on their interconversion was investigated in detail. The rates of the switching events were finely tuned by the donor or acceptor strength of the aryl group. The thermal ring closure was found to proceed most readily in the presence of an electron-donating group on the seven-membered ring. The rate constant was found to follow a Hammett linear free energy correlation, which signals that stabilization of a positive charge in the seven-membered ring plays a crucial role in the ring-closure reaction. In view of these findings, it was possible to control the switching event by protonation/deprotonation of an anilino-substituted DHA. Also, the light-induced ring opening reaction was strongly controlled by acid/base. In addition to the mesomeric effects exerted by an arylethynyl group, the inductive effects exerted by different groups on the thermal ring closure were elucidated. Although the alkyne bridge transmits the electronic character of the aryl group, the ring-closure is retarded for all the ethynylated compounds relative to the parent unsubstituted compound. Along with our synthesis of suitable arylalkynes, we discovered an interesting byproduct in a Sonogashira cross-coupling reaction involving a nitrophenyl group, namely a diaryl azoxy compound. Its structure was confirmed by X-ray crystallographic analysis.

Dihydro-beta-agarofuran sesquiterpenes and pentacyclic triterpenoids from the root bark of Osyris lanceolata.

Three new dihydro-beta-agarofuran polyesters, 1alpha,9beta-difuranoyloxy-2-oxodihydro-beta-agarofuran (1), 1alpha,9beta-difuranoyloxy-2-oxo-3-enedihydro-beta-agarofuran (2), and 1alpha,9beta-difuranoyloxydihydro-beta-agarofuran (3), have been isolated from the CHCl(3) extract of the root bark of Osyris lanceolata, together with two known pentacylic triterpenoids, 4 and 5. Compounds 1-5 did not scavenge the DPPH radical within 30 min of reaction time. All five compounds displayed antifungal activity against Candida albicans. Compounds 1, 3, 4, and 5 showed antibacterial activity against the Gram-positive Bacillus subtilis and Staphylococcus aureus and Gram-negative Escherichia coli and Pseudomonas aeruginosa, with 4 and 5 being the most active. Compound 2 displayed weak antibacterial activity only against Escherichia coli.