Fluorescent carbon dots from mono- and polysaccharides: synthesis, properties and applications

• Stephen Hill and
• M. Carmen Galan

Beilstein J. Org. Chem. 2017, 13, 675–693, doi:10.3762/bjoc.13.67

• relevant molecules have become very useful for drug delivery, sensing and catalysis to name just a few applications. As a result, nanomaterials exhibiting novel electronic and optical properties, having controlled size, geometry, surface distribution and functionality have been developed as materials for

• , chemical sensing, biosensing, bioimaging and nanomedicine, due to their unique tuneable photoluminescence (PL) properties, chemical inertness, high water solubility, ease and low cost fabrication and more importantly, low toxicity profiles. The latter makes these fluorescent nanomaterials attractive for a

• traditionally difficult to detect. The team was able to show significant quenching of the CDs via tryptophan oxidation of the exposed residues on the surface of CDs (Scheme 5). Post-oxidation fluorescence is compromised and therefore can be used as a signal for selectively sensing peroxynitrite up to

Posttranslational isoprenylation of tryptophan in bacteria

• Masahiro Okada,
• Tomotoshi Sugita and
• Ikuro Abe

Beilstein J. Org. Chem. 2017, 13, 338–346, doi:10.3762/bjoc.13.37

• the thiol groups of proteins in eukaryotes. In contrast, the Bacillus quorum sensing peptide pheromone, the ComX pheromone, possesses a posttranslationally modified tryptophan residue, and the tryptophan residue is isoprenylated with either a geranyl or farnesyl group at the gamma position to form a

• ; isoprenylation; post-translational modification; quorum sensing; tryptophan; Introduction Posttranslational modification is the chemical modification of proteins after their translation from mRNAs to the corresponding polypeptide chains synthesized by ribosomes. Since a posttranslational modification generates

• tryptophan residue of the quorum sensing pheromone from Bacillus subtilis, the ComX pheromone [13]. Quorum sensing is a specific gene expression system dependent on the cell density [14]. In terms of a competition for survival, the cell population density is one of the largest factors for microorganisms

Spectral and DFT studies of anion bound organic receptors: Time dependent studies and logic gate applications

• Srikala Pangannaya,
• Neethu Padinchare Purayil,
• Shweta Dabhi,
• Venu Mankad,
• Prafulla K. Jha,
• Satyam Shinde and
• Darshak R. Trivedi

Beilstein J. Org. Chem. 2017, 13, 222–238, doi:10.3762/bjoc.13.25

• calculated rate constants reveal a higher order of reactivity for AcO− ions. The 1H NMR titration and TDDFT studies provide full support of the binding mechanism. The Hg2+ and F− ion sensing property of receptor R1 has been utilized to arrive at “AND” and “INHIBIT” molecular logic gate applications

• receptors could further allow their use for detecting cations. This dual ion sensing property is expected to play a role in the study of logical interpretations at the arithmetic level. Results and Discussion UV–vis spectrophotometric studies Receptors R1and R2 vary in the substituent groups attached to the

• anion sensor. As receptor R1 behaved as a dual sensor being sensitive towards fluoride and acetate anions and Hg2+ as cation, we have fabricated logic gate circuits and performed arithmetic calculations at molecular level [48]. The dual ion sensing property of R1 has been extended to develop a logic

Interactions between photoacidic 3-hydroxynaphtho[1,2-b]quinolizinium and cucurbit[7]uril: Influence on acidity in the ground and excited state

• Jonas Becher,
• Daria V. Berdnikova,
• Darinka Dzubiel,
• Heiko Ihmels and
• Phil M. Pithan

Beilstein J. Org. Chem. 2017, 13, 203–212, doi:10.3762/bjoc.13.23

• acidity or basicity. In fact, it was shown that the pKa of organic acids and bases often shifts by orders of magnitude upon association with CB[n] [16][17][18][19][20][21][22][23][24], which may be used, e.g., to modify catalytic activity [6] or for sensing purposes [7]. Notably, the same effect was

Supramolecular frameworks based on [60]fullerene hexakisadducts

• Andreas Kraft,
• Johannes Stangl,
• Ana-Maria Krause,
• Klaus Müller-Buschbaum and
• Florian Beuerle

Beilstein J. Org. Chem. 2017, 13, 1–9, doi:10.3762/bjoc.13.1

• materials with the prospect of applications in gas storage [2][3], catalysis [4][5], luminescence [6][7][8][9] and sensing [10][11][12][13] or optoelectronics [14][15][16]. Owing to a modular approach, building blocks and cross-linking interactions can be varied over a wide range resulting in metal-organic

Chemical probes for competitive profiling of the quorum sensing signal synthase PqsD of Pseudomonas aeruginosa

• Michaela Prothiwa,
• Dávid Szamosvári,
• Sandra Glasmacher and
• Thomas Böttcher

Beilstein J. Org. Chem. 2016, 12, 2784–2792, doi:10.3762/bjoc.12.277

• Michaela Prothiwa David Szamosvari Sandra Glasmacher Thomas Bottcher Department of Chemistry, Konstanz Research School Chemical Biology, University of Konstanz, 78457 Konstanz, Germany 10.3762/bjoc.12.277 Abstract The human pathogen Pseudomonas aeruginosa uses the pqs quorum sensing system to

• coordinate the production of its broad spectrum of virulence factors to facilitate colonization and infection of its host. Hereby, the enzyme PqsD is a virulence related quorum sensing signal synthase that catalyzes the central step in the biosynthesis of the Pseudomonas quinolone signals HHQ and PQS. We

• is coordinated on population level by several layers of hierarchically interconnected quorum sensing systems [6]. Quorum sensing signals are released from the cells and accumulate in a growing bacterial population to a certain threshold by which they start inducing the production of virulence factors

A versatile route to polythiophenes with functional pendant groups using alkyne chemistry

• Xiao Huang,
• Li Yang,
• Rikard Emanuelsson,
• Jonas Bergquist,
• Maria Strømme,
• Martin Sjödin and
• Adolf Gogoll

Beilstein J. Org. Chem. 2016, 12, 2682–2688, doi:10.3762/bjoc.12.265

• ][4][5][6][7][8][9], as well as ion sensing devices [10], biosensors [11], and thermoelectric polymers [12]. Therefore, the chemistry of its building block 3,4-ethylenedioxythiophene (EDOT) and the functionalization of the basic structure have been attracting interest as well [13]. The vast amount of

A direct method for the N-tetraalkylation of azamacrocycles

• Andrew J. Counsell,
• Angus T. Jones,
• Matthew H. Todd and
• Peter J. Rutledge

Beilstein J. Org. Chem. 2016, 12, 2457–2461, doi:10.3762/bjoc.12.239

• , as part of ongoing efforts to develop multi-functionalised cyclam derivatives for fluorescence sensing [25][26][27][28][40][41] and other biomedical applications [14][15][16][42][43]. However, we found the previously reported methods to be at best capricious when it comes to substitution with

• . Utilisation of the N-tetrapropargyl products 3 and 8 to generate ‘click’-triazolylcyclam/cyclen derivatives for fluorescence sensing and other applications is underway and will be reported in due course. Ball-and-stick depiction of the crystal structure obtained for [(3)H2](ClO4)2, generated with X-Seed [51

Hydroxy-functionalized hyper-cross-linked ultra-microporous organic polymers for selective CO₂ capture at room temperature

• Partha Samanta,
• Priyanshu Chandra and
• Sujit K. Ghosh

Beilstein J. Org. Chem. 2016, 12, 1981–1986, doi:10.3762/bjoc.12.185

• surface area, small pore size and low skeletal density [9][10][11][12]. This type of materials has already been used for various purposes of applications such as gas storage, gas separation, catalysis, sensing, clean energy, etc. [13][14][15][16][17][18]. Relatively weaker coordination bonds in MOFs have

From supramolecular chemistry to the nucleosome: studies in biomolecular recognition

• Marcey L. Waters

Beilstein J. Org. Chem. 2016, 12, 1863–1869, doi:10.3762/bjoc.12.175

• highly amenable to structure–function studies, since only a new monomer must be synthesized, rather than an entirely new receptor. With my interest in trimethyllysine provided a significant problem in which DCC seemed to be a promising solution. It turns out that the main tool for sensing protein post

Organic chemistry meets polymers, nanoscience, therapeutics and diagnostics

• Vincent M. Rotello

Beilstein J. Org. Chem. 2016, 12, 1638–1646, doi:10.3762/bjoc.12.161

• with great precision. Bringing together these two very disparate skill sets is, however, quite uncommon. This autobiographical review provides some insight into how my program evolved, as well as giving some idea of where we are going. Keywords: organic synthesis, supramolecular, nanoparticle sensing

• to doing the occasional eccentric experiment. Building nanonoses As we were developing our delivery vehicle platforms, we were starting to think about sensing applications. One of the things that we observed in our protein binding work was that our nanoparticles had varying affinities for different

• had two limitations. The second issue we had was lack of choices in emission color – blue and green are easy, yellow is challenging, and getting a red conjugated polymer with a respectable quantum yield is nigh impossible. We had an idea, however, that we could use multi-channel sensing to increase

Discovery of an inhibitor of the production of the Pseudomonas aeruginosa virulence factor pyocyanin in wild-type cells

• Bernardas Morkunas,
• Balint Gal,
• Warren R. J. D. Galloway,
• James T. Hodgkinson,
• Brett M. Ibbeson,
• Yaw Sing Tan,
• Martin Welch and
• David R. Spring

Beilstein J. Org. Chem. 2016, 12, 1428–1433, doi:10.3762/bjoc.12.137

• . aeruginosa infections. Evidence suggests that the active compound reduces the level of pyocyanin production by inhibiting the cell–cell signalling mechanism known as quorum sensing. This could have interesting implications; quorum sensing regulates a range of additional elements associated with the

• pathogenicity of P. aeruginosa and there is a wide range of other potential applications where the inhibition of quorum sensing is desirable. Keywords: antibacterial; antivirulence; Pseudomonas aeruginosa; pyocyanin; quorum sensing; Findings The Gram-negative bacterium Pseudomonas aeruginosa is a clinically

• inhibition of this phenotype by a member of this structural sub-class. Thus, a promising new scaffold for pyocyanin inhibition has been identified. A cell–cell signalling process known as quorum sensing regulates pyocyanin production by P. aeruginosa [8][9][20]. This bacterium uses (at least) three different

Cyclisation mechanisms in the biosynthesis of ribosomally synthesised and post-translationally modified peptides

• Andrew W. Truman

Beilstein J. Org. Chem. 2016, 12, 1250–1268, doi:10.3762/bjoc.12.120

• thiolactone is generated in AIP biosynthesis (Figure 9). Autoinducing peptides are secreted molecules that form part of a quorum-sensing system in Staphylococcus [121]. Heterologous expression in E. coli showed that only AgrD (precursor peptide) and AgrB (peptidase) are required for AIP biosynthesis, although

• candidate enzymes. A number of these cyclisations are found in partially characterised pathways, such as the S–C cross-link in α-amanitin (Figure 8B) that is formed between cysteine and tryptophan residues (the tryptathionine linkage [131]). The ComQXPA quorum sensing (QS) system [132] found in Bacillus

Stimuli-responsive HBPS-g-PDMAEMA and its application as nanocarrier in loading hydrophobic molecules

• Yongsheng Chen,
• Li Wang,
• Haojie Yu,
• Zain-Ul-Abdin,
• Ruoli Sun,
• Guanghui Jing,
• Rongbai Tong and
• Zheng Deng

Beilstein J. Org. Chem. 2016, 12, 939–949, doi:10.3762/bjoc.12.92

• nanocarriers for loading guest molecules is dynamic. It has been widely studied in applications including drug controlled release, smart sensing, catalysis, and modeling. In this paper, a graft copolymer (hyperbranched polystyrene)-g-poly[2-(dimethylamino)ethyl methacrylate] (HBPS-g-PDMAEMA) was synthesized

• -responsive nanocarriers; Introduction Stimuli-responsive polymers have attracted much attention due to their broad applications including drug controlled release [1][2][3][4][5], sensing [6][7] and 4D printing [8][9]. Nanocarriers prepared from amphiphilic stimuli-responsive polymers are promising

Self and directed assembly: people and molecules

• Tony D. James

Beilstein J. Org. Chem. 2016, 12, 391–405, doi:10.3762/bjoc.12.42

• collaborate and in particular we worked together to improve the chiral discriminating systems. In order to improve the chiral systems we designed sensors using a d-PET rather than the normal a-PET fluorescence sensing mechanism. With d-PET systems the fluorophore is the electron donor and the protonated amine

• ) who as it happens had employed Susumu Arimori after he left my group at the end of 2001 as a Post-Doctoral Research Fellow. The two weeks on the road also allowed Steve and me to discuss research. Steve is interested in chiral catalysis and I am interested in chiral sensing so a collaborative project

• International Conference on Molecular Machines and Sensor (ICMMS). Therefore, we Jianzhang Zhao and Tony James (with Steven Bull and John Fossey) applied for funding to host a Thematic Workshop during 2008 on “Catalysis and Sensing for our Environment” (CASE) in Bath. We were very lucky in obtaining the funding

Art, auto-mechanics, and supramolecular chemistry. A merging of hobbies and career

• Eric V. Anslyn

Beilstein J. Org. Chem. 2016, 12, 362–376, doi:10.3762/bjoc.12.40

• that propels the automobile. The expanded version of a 1953 in-line six-cylinder bottom-end from an Mk VII Jaguar owner’s manual is a powerful image that accentuates the idea of emergent properties. As described below, the field of differential sensing, in which our group works extensively, takes the

• for sensing purposes. The impetus for doing so was driven by an attempt to have a higher impact with our work, but, admittedly, was also due to serendipity. Several events moved our group’s research toward sensing applications. One was having a synthesis to create 9 as an RNA hydrolysis catalyst

• fluorophores bound in the cavity of cyclodextrins to measure Keq values, our idea was to instead exploit the displacement as the sensing modality. Thus, the idea of an indicator-displacement assay (IDA) was born [58][59]. As with so many “new” ideas in chemistry, the approach had actually been used before, by

My maize and blue brick road to physical organic chemistry in materials

• Anne J. McNeil

Beilstein J. Org. Chem. 2016, 12, 229–238, doi:10.3762/bjoc.12.24

• providing a portable and potentially inexpensive method for sensing. Considering how naïve my understanding of gelation was at the time, I am still surprised that my proposal idea worked almost exactly as described. Molecular gels form through the self-assembly of small molecules into supramolecular

• for sensing in real time. Increased NO concentrations led to gels within a minute, but these concentrations were outside the useful range for breath analysis. Nevertheless, these initial studies laid the foundation for our next effort, which was focused on developing a more sophisticated approach to

• were interested in applying our new gelators in sensing platforms. Because analyte-mediated sensors rely on a chemical transformation to take place prior to gel formation, the reaction rate should be fast, or ideally instantaneous. While most of our sensors were designed with this criterion in mind, we

Bright molecules for sensing, computing and imaging: a tale of two once-troubled cities

• A. Prasanna de Silva

Beilstein J. Org. Chem. 2015, 11, 2774–2784, doi:10.3762/bjoc.11.298

• electron transfer) sensing/switching as a design tool, b) the construction of a market-leading blood electrolyte analyzer and c) the invention of molecular logic-based computation as an experimental field, are delineated. Efforts to extend the philosophy of these approaches into issues of small object

• identification, nanometric mapping, animal visual perception and visual art are also outlined. Keywords: blood electrolyte analyzer; luminescent PET sensing/switching; molecular logic-based computation; photoinduced electron transfer; small molecular edge detection; Review Prologue Colombo, Sri Lanka: A civil

• compete for the deactivation of the same excited state, it was equally clear that a luminescence signal could be switched ‘on’ by chemical command. Therefore, we were fortunate to be able to introduce a general design tool of luminescent PET sensing/switching [11][12][13][14][15], which even handled

Recent advances in metathesis-derived polymers containing transition metals in the side chain

• Ileana Dragutan,
• Valerian Dragutan,
• Bogdan C. Simionescu,
• Albert Demonceau and
• Helmut Fischer

Beilstein J. Org. Chem. 2015, 11, 2747–2762, doi:10.3762/bjoc.11.296

• confer an optimal set of capabilities that recommend them for diverse emerging application areas, e.g., as electro-optical and magnetic devices, for energy storage, nanomaterials, sensing, catalytic and drug-delivery systems [6][12][13][14]. Numerous synthetic routes have been explored to achieve the

• electrochemistry, sensing, catalysis, nanomaterials, etc. [37][38][39][40]. Not surprisingly, therefore, attention of researchers has turned first on metallopolymers containing ferrocene [33][34][41][42][43]. Review Iron-containing polymers Following the first successful application of Mo–alkylidene catalysts by

• used to prepare modified Pt electrodes with high stability and good qualitative sensing of ATP2− anions. It was supposed that the triethylene glycol domains in the block copolymers favor the amidoferrocene–ATP interactions by encapsulation. Astruc assumed that during the recognition process different H

Smart molecules for imaging, sensing and health (SMITH)

• Bradley D. Smith

Beilstein J. Org. Chem. 2015, 11, 2540–2548, doi:10.3762/bjoc.11.274

• -authored a book chapter entitled “Applications of Synthetic Receptors for Biomolecules [45].” The chapter grouped the most common applications into four general groups; Separations, Imaging and Sensing, Catalysis, and Pharmaceutical Activity – important topics that will continue to attract the attention of

Conformational equilibrium in supramolecular chemistry: Dibutyltriuret case

• Karina Mroczyńska,
• Małgorzata Kaczorowska,
• Erkki Kolehmainen,
• Ireneusz Grubecki,
• Marek Pietrzak and
• Borys Ośmiałowski

Beilstein J. Org. Chem. 2015, 11, 2105–2116, doi:10.3762/bjoc.11.227

• studied by MS [44] while its interaction preferences with anions in solution are not known. On the other hand the tris-urea derivatives with a spacer between NHCONH groups were used in several supramolecular complexes including those with encapsulated anions [45][46], sensing nerve agents [47] or in self

Synthesis, antimicrobial and cytotoxicity evaluation of new cholesterol congeners

• Mohamed Ramadan El Sayed Aly,
• Hosam Ali Saad and
• Shams Hashim Abdel-Hafez

Beilstein J. Org. Chem. 2015, 11, 1922–1932, doi:10.3762/bjoc.11.208

• their immunostimulant activities [21]. Finally, the ability of cholesterol derivatives to self-assembly and gelation as supramolecular gels was reviewed [22]. They are beneficially applicable in materials science, reaction media, sensing and responsive materials, energy supply, biomedicine, and tissue

Polythiophene and oligothiophene systems modified by TTF electroactive units for organic electronics

• Alexander L. Kanibolotsky,
• Neil J. Findlay and
• Peter J. Skabara

Beilstein J. Org. Chem. 2015, 11, 1749–1766, doi:10.3762/bjoc.11.191

• trapping by the TTF unit. This hole trapping was explained to be the reason for a negative Seebeck coefficient of the non-doped polymer 13e and was used for sensing trinitrotoluene (TNT) using the drain-source current-increase response to TTF-TNT complexation in an OFET fabricated from 13e with 5% of PQT12

Star-shaped tetrathiafulvalene oligomers towards the construction of conducting supramolecular assembly

• Masahiko Iyoda and
• Masashi Hasegawa

Beilstein J. Org. Chem. 2015, 11, 1596–1613, doi:10.3762/bjoc.11.175

• hand, the conductivities of the corresponding neutral nanoobjects are determined by pulse-radiolysis or flash-photolysis time-resolved microwave conductivity techniques [48][49]. Current-sensing atomic force microscopy (CS-AFM) and combination of scanning tunneling microscopy and spectroscopy (STM/STS

A novel and widespread class of ketosynthase is responsible for the head-to-head condensation of two acyl moieties in bacterial pyrone biosynthesis

• Darko Kresovic,
• Florence Schempp,
• Zakaria Cheikh-Ali and
• Helge B. Bode

Beilstein J. Org. Chem. 2015, 11, 1412–1417, doi:10.3762/bjoc.11.152

• , 60438 Frankfurt am Main, Germany 10.3762/bjoc.11.152 Abstract The biosynthesis of photopyrones, novel quorum sensing signals in Photorhabdus, has been studied by heterologous expression of the photopyrone synthase PpyS catalyzing the head-to-head condensation of two acyl moieties. The biochemical

• sensing; Introduction Chemical compounds containing an α-pyrone moiety are widespread in nature [1][2] and show a high diversity in their biological activity. Members of this class of compounds have been identified with antimicrobial, cytotoxic [3] and antitumor activities [4], as HIV protease inhibitors