Local Environments Created by the Ligand Coating of Nanoparticles and Their Implications for Sensing and Surface Reactions.

ConspectusThe ligand shells of colloidal nanoparticles (NPs) can serve different purposes. In general, they provide colloidal stability by introducing steric repulsion between NPs. In the context of biological applications, the ligand shell plays a critical role in targeting, enabling NPs to achieve specific biodistributions. However, there is also another important feature of the ligand shell of NPs, namely, the creation of a local environment differing from the bulk of the solvent in which the NPs are dispersed. It is known that charged ligand shells can attract or repel ions and change the effective charge of a NP through Debye-Hückel screening. Positively charged ions, such as H+ (or H3O+) are attracted to negatively charged surfaces, whereas negatively charged ions, such as Cl- are repelled. The distribution of the ions around charged NP surfaces is a radial function of distance from the center of the NP, which is governed by a balance of electrostatic forces and entropy of ions and ligands. As a result, the ion concentration at the NP surface is different from its bulk equilibrium concentration, i.e., the charged ligand shell around the NPs has formed a distinct local environment. This not only applies to charged ligand shells but also follows a more general principle of induced condensation and depletion. Polar/apolar ligand shells, for example, result in a locally increased concentration of polar/apolar molecules. Similar effects can be seen for biocatalysts like enzymes immobilized in nanoporous host structures, which provide a special environment due to their surface chemistry and geometrical nanoconfinement. The formation of a local environment close to the ligand shell of NPs has profound implications for NP sensing applications. As a result, analyte concentrations close to the ligand shell, which are the ones that are measured, may be very different from the analyte concentrations in bulk. Based on previous work describing this effect, it will be discussed herein how such local environments, created by the choice of used ligands, may allow for tailoring the NPs' sensing properties. In general, the ligand shell around NPs can be attractive/repulsive for molecules with distinct properties and thus forms an environment that can modulate the specific response. Such local environments can also be optimized to modulate chemical reactions close to the NP surface (for example, by size filtering within pores) or to attract specific low abundance proteins. The importance hereby is that this is based on interaction with low selectivity between the ligands and the target molecules.

Regioselective Fluorination of Acenes: Tailoring of Molecular Electronic Levels and Solid-State Properties.

Optoelectronic properties of molecular solids are important for organic electronic devices and are largely determined by the adopted molecular packing motifs. In this study, we analyzed such structure-property relationships for the partially regioselective fluorinated tetracenes 1,2,12-trifluorotetracene, 1,2,10,12-tetrafluorotetracene and 1,2,9,10,11-pentafluorotetracene that were further compared with tetracene and perfluoro-tetracene. Quantum chemical DFT calculations in combination with optical absorption spectroscopy data show that the frontier orbital energies are lowered with the degree of fluorination, while their optical gap is barely affected. However, the crystal structure changes from a herringbone packing motif of tetracene towards a planar stacking motif of the fluorinated tetracene derivatives, which is accompanied by the formation of excimers and leads to strongly red-shifted photoluminescence with larger lifetimes.

Vicinal ketoesters - key intermediates in the total synthesis of natural products.

This review summarizes examples for the application of vicinal ketoesters such as α-ketoesters, mesoxalic esters, and α,ß-diketoesters as key intermediates in the total synthesis of natural products utilizing their electrophilic keto group as reactive site. Suitable key reactions are, e.g., aldol additions, carbonyl ene reactions, Mannich reactions, and additions of organometallic reagents. The vicinal arrangement of carbonyl groups allows the stabilization of reactive conformations by chelation or dipole control.

Click Chemistry in Ultra-high Vacuum - Tetrazine Coupling with Methyl Enol Ether Covalently Linked to Si(001).

The additive-free tetrazine/enol ether click reaction was performed in ultra-high vacuum (UHV) with an enol ether group covalently linked to a silicon surface: Dimethyl 1,2,4,5-tetrazine-3,6-dicarboxylate molecules were coupled to the enol ether group of a functionalized cyclooctyne which was adsorbed on the silicon (001) surface via the strained triple bond of cyclooctyne. The reaction was observed at a substrate temperature of 380 K by means of X-ray photoelectron spectroscopy (XPS). A moderate energy barrier was deduced for this click reaction in vacuum by means of density functional theory based calculations, in good agreement with the experimental results. This UHV-compatible click reaction thus opens a new, flexible route for synthesizing covalently bound organic architectures.

Combined XPS and DFT investigation of the adsorption modes of methyl enol ether functionalized cyclooctyne on Si(001).

The reaction of methyl enol ether functionalized cyclooctyne on the silicon (001) surface was investigated by means of X-ray photoelectron spectroscopy (XPS) and density functional theory (DFT). Three different groups of final states were identified; all of them bind on Si(001) via the strained triple bond of cyclooctyne but they differ in the configuration of the methyl enol ether group. The majority of molecules adsorbs without additional reaction of the enol ether group; the relative contribution of this configuration to the total coverage depends on substrate temperature and coverage. Further configurations include enol ether groups which reacted on the silicon surface either via ether cleavage or enol ether groups which transformed on the surface into a carbonyl group.

Understanding Substrate Selectivity of Phoslactomycin Polyketide Synthase by Using Reconstituted in Vitro Systems.

Polyketide synthases (PKSs) use simple extender units to synthesize complex natural products. A fundamental question is how different extender units are site-specifically incorporated into the growing polyketide. Here we established phoslactomycin (Pn) PKS, which incorporates malonyl- and ethylmalonyl-CoA, as an in vitro model to study substrate specificity. We combined up to six Pn PKS modules with different termination sites for the controlled release of tetra-, penta- and hexaketides, and challenged these systems with up to seven different extender units in competitive assays to test for the specificity of Pn modules. While malonyl-CoA modules of Pn PKS exclusively accept their natural substrate, the ethylmalonyl-CoA module PnC tolerates different α-substituted derivatives, but discriminates against malonyl-CoA. We show that the ratio of extender transacylation to hydrolysis controls incorporation in PnC, thus explaining site-specific selectivity and promiscuity in the natural context of Pn PKS.

Unilaterally Fluorinated Acenes: Synthesis and Solid-State Properties.

The rapid development of organic electronics is closely related to the availability of molecular materials with specific electronic properties. Here, we introduce a novel synthetic route enabling a unilateral functionalization of acenes along their long side, which is demonstrated by the synthesis of 1,2,10,11,12,14-hexafluoropentacene (1) and the related 1,2,9,10,11-pentafluorotetracene (2). Quantum chemical DFT calculations in combination with optical and X-ray absorption spectroscopy data indicate that the single-molecule properties of 1 are a connecting link between the organic semiconductor model systems pentacene (PEN) and perfluoropentacene (PFP). In contrast, the crystal structure analysis reveals a different packing motif than for the parent molecules. This can be related to distinct F⋅⋅⋅H interactions identified in the corresponding Hirshfeld surface analysis and also affects solid-state properties such as the exciton binding energy and the sublimation enthalpy.

Synthesis of 6,13-difluoropentacene.

6,13-Difluoropentacene was synthesized from 1,4-difluorobenzene. Friedel-Crafts annulation of the latter with phthalic anhydride and subsequent reduction of the anthraquinone gave 1,4-difluoroanthracene. After ortho-lithiation and reaction with phthalic anhydride a carboxylic acid was obtained whose Friedel-Crafts acylation and subsequent reductive removal of the oxygen-functionalities resulted in the formation of the target compound. The HOMO-LUMO gap of 6,13-difluoropentacene was determined via UV-vis spectroscopy and compared to other fluorinated pentacenes.

Controlling an SN 2 Reaction by Electronic and Vibrational Excitation: Tip-Induced Ether Cleavage on Si(001).

Controlling chemical reactions beyond thermally activated reaction schemes can open alternative reaction channels, and thus lead to new final products. Herein, we show for tetrahydrofuran (THF) cleavage on Si(001), the surface analogue of an SN 2 reaction, that excitation by electrons from the tip of a scanning tunneling microscope (STM) not only opens new reaction channels, but that different final products can be selectively addressed by the type of excitation: Above a threshold voltage of 2.5 V, direct excitation by electron transfer into the antibonding C-O orbital of the THF molecules induces ether cleavage of the datively bonded intermediate of THF on Si(001). Below the threshold, ether cleavage is induced by multiple excitation of vibrational modes. In both modes of excitation, additional final configurations were observed when compared to the thermally activated reaction. The branching ratios of the final configurations are different for the two different excitation mechanisms, which in turn can be controlled by the applied sample bias.

Dynamics of the peptidoglycan biosynthetic machinery in the stalked budding bacterium Hyphomonas neptunium.

Most commonly studied bacteria grow symmetrically and divide by binary fission, generating two siblings of equal morphology. An exception to this rule are budding bacteria, in which new offspring emerges de novo from a morphologically invariant mother cell. Although this mode of proliferation is widespread in diverse bacterial lineages, the underlying mechanisms are still incompletely understood. Here, we report the first molecular-level analysis of growth and morphogenesis in the stalked budding alphaproteobacterium Hyphomonas neptunium. Peptidoglycan labeling shows that, in this species, buds originate from a stalk-like extension of the mother cell whose terminal segment is gradually remodeled into a new cell compartment. As a first step toward identifying the machinery mediating the budding process, we performed comprehensive mutational and localization studies of predicted peptidoglycan biosynthetic proteins in H. neptunium. These analyses identify factors that localize to distinct zones of dispersed and zonal growth, and they suggest a critical role of the MreB-controlled elongasome in cell morphogenesis. Collectively, our work shows that the mechanism of growth in H. neptunium is distinct from that in related, polarly growing members of the order Rhizobiales, setting the stage for in-depth analyses of the molecular principles regulating the fascinating developmental cycle of this species.

From Acenaphthenes to (+)-Delavatine A: Visible-Light-Induced Ring Closure of Methyl (α-Naphthyl) Acrylates.

Disclosed herein is a visible light mediated cyclization of methyl (α-naphthyl) acrylates and heteroaromatic analogues yielding substituted acenaphthenes and azaacenaphthenes. This highly functional-group-tolerant transformation was put to the test in an enantioselective formal synthesis of delavatine A. Mechanistic details were elucidated by DFT-calculations revealing an unusual intramolecular H-transfer mediated by a primary amine. The generality of this transformation enables a novel synthetic strategy of five membered ring annulation at an advanced stage, allowing reliance upon naphthalene chemistry up to the point of acenaphthene construction.

Antitubercular evaluation of root extract and isolated phytochemicals from Lophira lanceolata against two resistant strains of Mycobacterium tuberculosis.

CONTEXT: The roots of Lophira lanceolata Van Tiegh. Ex Keay (Ochnaceae) have numerous medicinal values in the Central African region. Even though the MeOH extract of the roots has shown antimycobacterial activities, the constituents responsible for this inhibitory activity remain unknown. OBJECTIVE: Phytochemical investigation of the MeOH root extract of L. lanceolata and determination of the antimycobacterial activities of that extract and constituents against the growth of Mycobacterium tuberculosis. MATERIALS AND METHODS: Column chromatography was used to provide bioactive phytoconstituents. Those compounds were elucidated using MS and NMR spectroscopic data. Antimycobacterial screening of the extract (4.882-5000 µg/mL in DMSO during 24 h at 37 °C) and isolated compounds (0.244-250 µg/mL in DMSO during 24 h at 37 °C) was performed by microplate alamar blue assay (MABA) against two mycobacterial strains. RESULTS: The investigation of L. lanceolata MeOH roots extract provided of mixture of unseparated biflavonoids with a newly described one, dihydrolophirone A (1a) associated to lophirone A (1b). The bioactive compounds that effectively inhibited the growth of M. tuberculosis AC45 were found to be compounds 1 and 2. They exhibited MIC values of 31.25 and 15.75 µg/mL, respectively, and their MIC was found to be 62.5 µg/mL against resistant strain AC83. DISCUSSION AND CONCLUSIONS: It is clearly evident from the results obtained that the mycobacterial activity of L. lanceolata could be related mainly to its steroid and flavonoid contents. Therefore, this study suggests the potential of the above-mentioned classes of compounds as promising candidate agents for developing new anti-tuberculosis drugs.

Efficient Syntheses of Novel Fluoro-Substituted Pentacenes and Azapentacenes: Molecular and Solid-State Properties.

Non-symmetrical 6,13-disubstituted pentacenes bearing trifluoromethyl and aryl substituents have been synthesized starting from pentacenequinone. Diazapentacenes with a variety of fluorine substituents were prepared either via a Hartwig-Buchwald aryl amination route or by a SNAr strategy. As a result of a non-symmetric substitution pattern containing electron-donating substituents in combination with electron-accepting fluorine substituents, the synthesized compounds feature distinct molecular dipoles. All compounds are analyzed regarding their optoelectronic properties in solution with special focus on the frontier orbital energies as well as their molecular packing in the crystal structures. The analyses of isolated molecules are complemented by thin-film studies to examine their solid-state properties. A precise comparison between these and the molecular properties gave detailed insights into the exciton binding energies of these compounds, which are explained by means of a simple model considering the molecular packing and polarizabilities.

Structure-based engineering of a minimal porin reveals loop-independent channel closure.

Porins, like outer membrane protein G (OmpG) of Escherichia coli, are ideal templates among ion channels for protein and chemical engineering because of their robustness and simple architecture. OmpG shows fast transitions between open and closed states, which were attributed to loop 6 (L6). As flickering limits single-channel-based applications, we pruned L6 by either 8 or 12 amino acids. While the open probabilities of both L6 variants resemble that of native OmpG, their gating frequencies were reduced by 63 and 81%, respectively. Using the 3.2 Å structure of the shorter L6 variant in the open state, we engineered a minimal porin (220 amino acids), where all remaining extramembranous loops were truncated. Unexpectedly, this minimized porin still exhibited gating, but it was 5-fold less frequent than in OmpG. The residual gating of the minimal pore is hence independent of L6 rearrangements and involves narrowing of the ion conductance pathway most probably driven by global stretching-flexing deformations of the membrane-embedded ß-barrel.

Ion-channels: goals for function-oriented synthesis.

Ion channels provide a conductance pathway for the passive transport of ions across membranes. These functional molecules perform key tasks in biological systems such as neuronal signaling, muscular control, and sensing. Recently, function-oriented synthesis researchers began to focus on ion channels with the goal of modifying the function of existing ion channels (ion selectivity, gating) or creating new channels with novel functions. Both approaches, ion channel engineering and de novo design, have involved synthetic chemists, biochemists, structural biologists, and neurochemists. Researchers characterize the function of ion channels by measuring their conductance in samples of biological membranes (patch clamp) or artificial membranes (planar lipid bilayers). At the single molecule level, these measurements require special attention to the purity of the sample, a challenge that synthetic chemists should be aware of. Ideally, researchers study the function of channels while also acquiring structural data (X-ray, NMR) to understand and predict how synthetic modifications alter channel function. Long-term oriented researchers would like to apply synthetic ion channels to single molecule sensing and to implantat these synthetic systems in living organisms as tools or for the treatment of channelopathies. In this Account, we discuss our own work on synthetic ion channels and explain the shift of our research focus from a de novo design of oligo-THFs and oligo-THF-amino acids to ion channel engineering. We introduce details about two biological lead structures for ion channel engineering: the gramicidin ß(6,3) helix as an example of a channel with a narrow ion conductance pathway and the outer membrane porins (OmpF, OmpG) with their open ß-barrel structure. The increase and the reversal of ion selectivity of these systems and the hydrophobic match/mismatch of the channel with the phospholipid bilayer are of particular interest. For engineering ion channels, we need to supplement the single-point attachment of a synthetic modulator with the synthesis of a more challenging two-point attachment. The successful function-oriented synthesis of ion channels will require interdisciplinary efforts that include new electrophysiology techniques, efficient synthesis (peptide/protein/organic), and good structural analysis.

Total synthesis of isoquinocyclinone.

The total synthesis of the heptacyclic natural product isoquinocyclinone has been achieved. A Hauser annulation was used to assemble the anthraquinone core structure. The unique 2,4,5,6-tetrahydropyrrolo[2,3-b]pyrrole substructure was prepared by alkyne addition to a lactone intermediate and subsequent Ni(0) -mediated cyanide addition, the conversion of an O,O- into an N,O-acetal, and final intramolecular N-alkylation.

Complex surface chemistry of an otherwise inert solvent molecule: tetrahydrofuran on Si(001).

The reaction of tetrahydrofuran (THF), an otherwise inert solvent molecule, on Si(001) was experimentally studied in ultra-high vacuum. Using scanning tunneling microscopy (STM) and photoelectron spectroscopy at variable temperature, we could both isolate a datively bound intermediate state of THF on Si(001), as well as the final configuration that bridges two dimer rows of the Si(001) surface after ether cleavage. The latter configuration implies splitting of the OC bond, which is typically kinetically suppressed. THF thus exhibits a hitherto unknown reactivity on Si(001).

Total synthesis of the postulated structure of fulicineroside.

A total synthesis of the proposed structures of fulicineroside and its aglycone fulicinerine is reported. The tetrasubstituted dibenzofuran substructure was accessible either through a Pd-mediated ortho-metalation or by an Ir-catalyzed meta-borylation. The synthesis of the ß,ß,α-linked trisaccharide consisting of D-olivose, L-rhodinose, and L-rhamnose was challenged by the unprecedented ß-linked rhodinose. A Pd-catalyzed ß-selective glycosylation of a 4-epi-rhodinose and a subsequent Mitsunobu inversion provided selectively the ß-linked L-rhodinose-L-rhamnose disaccharide. Comparison with the reported data for the natural product and the aglycone suggests a misassignment of the structure of the natural product.

Fluorotrifluoromethyl Group Installation: Tetrasubstituted Tertiary Stereocenters Containing C-F and C-CF3 Bonds via Copper-Mediated Allylic Substitution.

Tetrasubstituted tertiary centers containing a fluorotrifluoromethyl (FTF) motif were obtained from secondary 3-fluoro-3-trifluoromethyl allylic phosphates by a copper(I)-mediated allylic substitution reaction using Grignard reagents. The reaction features a broad substrate scope, high γ-regioselectivity, and excellent (E)-stereoselectivity. Two examples of chirality transfer from enantiopure secondary fluorine-substituted allylic phosphates to the corresponding scalemic products indicate the stereoselective potential of the method to install FTF stereocenters.

Shape control in 2D molecular nanosheets by tuning anisotropic intermolecular interactions and assembly kinetics.

Since molecular materials often decompose upon exposure to radiation, lithographic patterning techniques established for inorganic materials are usually not applicable for the fabrication of organic nanostructures. Instead, molecular self-organisation must be utilised to achieve bottom-up growth of desired structures. Here, we demonstrate control over the mesoscopic shape of 2D molecular nanosheets without affecting their nanoscopic molecular packing motif, using molecules that do not form lateral covalent bonds. We show that anisotropic attractive Coulomb forces between partially fluorinated pentacenes lead to the growth of distinctly elongated nanosheets and that the direction of elongation differs between nanosheets that were grown and ones that were fabricated by partial desorption of a complete molecular monolayer. Using kinetic Monte Carlo simulations, we show that lateral intermolecular interactions alone are sufficient to rationalise the different kinetics of structure formation during nanosheet growth and desorption, without inclusion of interactions between the molecules and the supporting MoS2 substrate. By comparison of the behaviour of differently fluorinated molecules, experimentally and computationally, we can identify properties of molecules with regard to interactions and molecular packing motifs that are required for an effective utilisation of the observed effect.