Conspectus This Account is about templates as construction tools: molecules for making molecules. A template organizes the reactants and provides information to promote formation of a specific ...product, but it is not part of the final product. We have developed many different strategies for using oligopyridines as templates for the synthesis of alkyne-linked π-conjugated metalloporphyrin oligomers. These compounds include some of the largest macrocycles ever synthesized, such as a 50-porphyrin ring with a diameter of 21 nm containing a ring of 750 C–C bonds. Metalloporphyrins are excellent models for exploring template directed synthesis, as they can be functionalized in many different positions and the central metal (typically Zn or Mg) provides a handle for coordination to templates. Classical template-directed macrocyclization reactions have a 1:1 complementarity between the template and the product. This strategy works well for preparing nanorings of 5–7 porphyrin units, but larger templates are laborious to synthesize. Rings of 8 or more porphyrin units are most easily prepared using “nonclassical” strategies, in which several small templates work together to direct the formation of a large ring. In the Vernier approach, a mismatch between the number of binding sites on the template and the building block leads to a mathematical amplification of the length scale: the number of binding sites in the product is the lowest common multiple of those in the template and the building block. For example, a 40-porphyrin ring can be prepared by coupling a linear decamer in the presence of an octadentate template. Linear Vernier templating opens up intriguing possibilities for self-replication. When several small radial oligopyridine templates bind inside a large nanoring they can form complexes with some vacant coordination sites that display correlated motion like the caterpillar tracks of a bulldozer. These caterpillar track complexes can be used in template-directed synthesis and they provide the most convenient route to 8- and 10-porphyrin rings. Russian doll complexes provide another strategy for template-directed synthesis: a number of specifically designed ligands bind to a central nanoring to form a template for constructing a larger concentric nanoring. The same oligopyridine templates that are used to prepare nanorings can also be used to synthesize three-dimensional nanotubes and nanoballs. Again, nonclassical approaches, in which several small templates work together cooperatively, are much simpler than creating a single large template with sufficient binding sites to define the whole geometry of the product. Oligopyridine ligands can also be used as shadow mask templates to control the demetalation of magnesium porphyrin nanorings, because metal centers that are not coordinated by the template can be selectively demetalated with acid. Thus, the template forms a permanent shadow on the porphyrin nanostructure that remains after the template has been removed. Shadow mask templates provide a simple route to heterometalated molecular architectures. The insights emerging from these studies are widely applicable, and there are many opportunities for inventing new ways of using templates to control reactions.
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Pathogenesis of Gram-Negative Bacteremia Holmes, Caitlyn L; Anderson, Mark T; Mobley, Harry L T ...
Clinical microbiology reviews,
06/2021, Volume:
34, Issue:
2
Journal Article
Peer reviewed
Open access
Gram-negative bacteremia is a devastating public health threat, with high mortality in vulnerable populations and significant costs to the global economy. Concerningly, rates of both Gram-negative ...bacteremia and antimicrobial resistance in the causative species are increasing. Gram-negative bacteremia develops in three phases. First, bacteria invade or colonize initial sites of infection. Second, bacteria overcome host barriers, such as immune responses, and disseminate from initial body sites to the bloodstream. Third, bacteria adapt to survive in the blood and blood-filtering organs. To develop new therapies, it is critical to define species-specific and multispecies fitness factors required for bacteremia in model systems that are relevant to human infection. A small subset of species is responsible for the majority of Gram-negative bacteremia cases, including
,
,
, and
The few bacteremia fitness factors identified in these prominent Gram-negative species demonstrate shared and unique pathogenic mechanisms at each phase of bacteremia progression. Capsule production, adhesins, and metabolic flexibility are common mediators, whereas only some species utilize toxins. This review provides an overview of Gram-negative bacteremia, compares animal models for bacteremia, and discusses prevalent Gram-negative bacteremia species.
Carbon allotropes built from rings of two-coordinate atoms, known as cyclo
carbons, have fascinated chemists for many years, but until now they could not be isolated or structurally characterized ...because of their high reactivity. We generated cyclo18carbon (C
) using atom manipulation on bilayer NaCl on Cu(111) at 5 kelvin by eliminating carbon monoxide from a cyclocarbon oxide molecule, C
O
Characterization of cyclo18carbon by high-resolution atomic force microscopy revealed a polyynic structure with defined positions of alternating triple and single bonds. The high reactivity of cyclocarbon and cyclocarbon oxides allows covalent coupling between molecules to be induced by atom manipulation, opening an avenue for the synthesis of other carbon allotropes and carbon-rich materials from the coalescence of cyclocarbon molecules.
Tn-Seq is a high throughput technique for analysis of transposon mutant libraries to determine conditional essentiality of a gene under an experimental condition. A special feature of the Tn-seq data ...is that multiple mutants in a gene provides independent evidence to prioritize that gene as being essential. The existing methods do not account for this feature or rely on a high-density transposon library. Moreover, these methods are unable to accommodate complex designs.
The method proposed here is specifically designed for the analysis of Tn-Seq data. It utilizes two steps to estimate the conditional essentiality for each gene in the genome. First, it collects evidence of conditional essentiality for each insertion by comparing read counts of that insertion between conditions. Second, it combines insertion-level evidence for the corresponding gene. It deals with data from both low- and high-density transposon libraries and accommodates complex designs. Moreover, it is very fast to implement. The performance of the proposed method was tested on simulated data and experimental Tn-Seq data from Serratia marcescens transposon mutant library used to identify genes that contribute to fitness in a murine model of infection.
We describe a new, efficient method for identifying conditionally essential genes in Tn-Seq experiments with high detection sensitivity and specificity. It is implemented as TnseqDiff function in R package Tnseq and can be installed from the Comprehensive R Archive Network, CRAN.
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What is Cooperativity Hunter, Christopher A; Anderson, Harry L
Angewandte Chemie (International ed.),
September 28, 2009, Volume:
48, Issue:
41
Journal Article
Peer reviewed
The lamprey holds the clue to the link between supramolecular self‐assembly and allosteric ligand binding. Chelate cooperativity in self‐assembled structures results in denaturation behavior that is ...indistinguishable from allosteric ligand binding. The chelate effect is the most common origin of positive cooperativity, yet its significance has been widely overlooked.
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Two photons are better than one: This principle applies to a wide range of applications, ranging from engineering to physiology. Recent advances in our understanding of the phenomenon of two-photon ...absorption (see picture) and in the design of two-photon dyes are rapidly increasing the scope of this field.Two-photon absorption has important advantages over conventional one-photon absorption, which has led to applications in microscopy, microfabrication, three-dimensional data storage, optical power limiting, up-converted lasing, photodynamic therapy, and for the localized release of bio-active species. These applications have generated a demand for new dyes with high two-photon absorption cross-sections. This Review introduces the theory of two-photon absorption, surveys the wide range of potential applications, and highlights emerging structure-property correlations that can serve as guidelines for the development of efficient two-photon dyes.
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7.
Insulated Molecular Wires Frampton, Michael J.; Anderson, Harry L.
Angewandte Chemie (International ed.),
01/2007, Volume:
46, Issue:
7
Journal Article
Peer reviewed
An astonishing assortment of structures have been described as “insulated molecular wires” (IMWs), thus illustrating the diversity of approaches to molecular‐scale insulation. These systems ...demonstrate the scope of encapsulation in the molecular engineering of optoelectronic materials and organic semiconductors. This Review surveys the synthesis and structural characterization of IMWs, and highlights emerging structure–property relationships to determine how insulation can enhance the behavior of a molecular wire. We focus mainly on three IMW architectures: polyrotaxanes, polymer‐wrapped π systems, and dendronized polymers, and compare the properties of these systems with those of conjugated polymers threaded through mesoporous frameworks and zeolites. Encapsulation of molecular wires can enhance properties as diverse as luminescence, electrical transport, and chemical stability, which points to applications in electroluminescent displays, sensors, and the photochemical generation of hydrogen.
Plastic nanoelectronics! Threading a molecular organic semiconductor inside an insulating sheath (see example) provides control of properties such as luminescence, electrical transport, and chemical stability. Applications in electroluminescent displays, sensors, and hydrogen generators are now within reach.
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Cyclo18carbon (C18, a molecular carbon allotrope) can be synthesized by dehalogenation of a bromocyclocarbon precursor, C18Br6, in 64% yield, by atomic manipulation on a sodium chloride bilayer on ...Cu(111) at 5 K, and imaged by high-resolution atomic force microscopy. This method of generating C18 gives a higher yield than that reported previously from the cyclocarbon oxide C24O6. The experimental images of C18 were compared with simulated images for four theoretical model geometries, including possible bond-angle alternation: D 18h cumulene, D 9h polyyne, D 9h cumulene, and C 9h polyyne. Cumulenic structures, with (D 9h ) and without (D 18h ) bond-angle alternation, can be excluded. Polyynic structures, with (C 9h ) and without (D 9h ) bond-angle alternation, both show a good agreement with the experiment and are challenging to differentiate.
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Aromatic and antiaromatic molecules-which have delocalized circuits of 4n + 2 or 4n electrons, respectively-exhibit ring currents around their perimeters. The direction of the ring current in an ...aromatic molecule is such as to generate a magnetic field that opposes the external field inside the ring (a 'diatropic' current), while the ring current in an antiaromatic molecule flows in the reverse direction ('paratropic'). Similar persistent currents occur in metal or semiconductor rings, when the phase coherence of the electronic wavefunction is preserved around the ring. Persistent currents in non-molecular rings switch direction as a function of the magnetic flux passing through the ring, so that they can be changed from diatropic ('aromatic') to paratropic ('antiaromatic') simply by changing the external magnetic field. As in molecular systems, the direction of the persistent current also depends on the number of electrons. The relationship between ring currents in molecular and non-molecular rings is poorly understood, partly because they are studied in different size regimes: the largest aromatic molecules have diameters of about one nanometre, whereas persistent currents are observed in microfabricated rings with diameters of 20-1,000 nanometres. Understanding the connection between aromaticity and quantum-coherence effects in mesoscopic rings provides a motivation for investigating ring currents in molecules of an intermediate size. Here we show, using nuclear magnetic resonance spectroscopy and density functional theory, that a six-porphyrin nanoring template complex, with a diameter of 2.4 nanometres, is antiaromatic in its 4+ oxidation state (80 π electrons) and aromatic in its 6+ oxidation state (78 π electrons). The antiaromatic state has a huge paramagnetic susceptibility, despite having no unpaired electrons. This work demonstrates that a global ring current can be promoted in a macrocycle by adjusting its oxidation state to suppress the local ring currents of its components.The discovery of ring currents around a molecule with a circumference of 7.5 nanometres, at room temperature, shows that quantum coherence can persist in surprisingly large molecular frameworks.
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![Synthesis of Cyclo[18]carbo...](http://api.summon.serialssolutions.com/2.0.0/image/issn/XR4PS5YY4K/0002-7863_1943-2984_1520-5126/small "Synthesis of Cyclo[18]carbon via Debromination of C18Br6")
