Chemical systems, chemical contiguity and the emergence of life

• Terrence P. Kee and
• Pierre-Alain Monnard

Beilstein J. Org. Chem. 2017, 13, 1551–1563, doi:10.3762/bjoc.13.155

• acids with a hydrocarbon chain length of 8–12 carbon atoms), where they can drive the formation of proton [75] or electron gradients [16]. In the case of photo-induced electron transport over membranes, the differentiated permeability of small anionic solutes with high charge density, such as potassium

Derivatives of the triaminoguanidinium ion, 5. Acylation of triaminoguanidines leading to symmetrical tris(acylamino)guanidines and mesoionic 1,2,4-triazolium-3-aminides

• Jan Szabo,
• Julian Greiner and
• Gerhard Maas

Beilstein J. Org. Chem. 2017, 13, 579–588, doi:10.3762/bjoc.13.57

• contrast, the δ(C-5) values vary strongly with the substituent attached to this carbon atom. Whereas the values for 7a–c reflect the different interaction of the phenyl, 3,4,5-trimethoxyphenyl and 4-nitrophenyl substituents with the positive charge density at C-5 through mesomeric and inductive effects

Regiochemistry of cyclocondensation reactions in the synthesis of polyazaheterocycles

• Patrick T. Campos,
• Leticia V. Rodrigues,
• Andrei L. Belladona,
• Caroline R. Bender,
• Juliana S. Bitencurt,
• Fernanda A. Rosa,
• Davi F. Back,
• Helio G. Bonacorso,
• Nilo Zanatta,
• Clarissa P. Frizzo and
• Marcos A. P. Martins

Beilstein J. Org. Chem. 2017, 13, 257–266, doi:10.3762/bjoc.13.29

• charge density data were determined and the results showed that the C(6) (β-carbon) of 1 had the largest LUMO coefficient (Table 2), thus indicating its soft electrophilic character. The carbonyl group C(2) had a lower value than C(6) and a significantly higher value than the ester carbonyl C(5). This is

• by the nitrogen atoms (sp2) of the ring (Table 3). These HOMO coefficients designate the first and second nucleophilic attack, respectively. The order of charge density values for the selected carbon atoms in 1 was as follows: C(5) > C(2) > C(4) > C(6). On the other hand, the charge density values

• between the HOMO/LUMO energies of electrophiles and nucleophiles (Table 2 and Table 3), and the reactions were controlled by frontier molecular orbitals rather than by charge density. Analogous calculations using the PM3 method for cyclocondensation reactions were performed by Saiz et al. [14] for the

Selective and eco-friendly procedures for the synthesis of benzimidazole derivatives. The role of the Er(OTf)₃ catalyst in the reaction selectivity

• Natividad Herrera Cano,
• Jorge G. Uranga,
• Mónica Nardi,
• Antonio Procopio,
• Daniel A. Wunderlin and
• Ana N. Santiago

Beilstein J. Org. Chem. 2016, 12, 2410–2419, doi:10.3762/bjoc.12.235

• , which is frequently associated with these reactions. Theoretical calculations helped to understand the different reactivity established for these reactions. Thus, we found that the charge density on the oxygen of the carbonyl group has a significant impact on the reaction pathway. For instance, electron

• procedure with short reaction time (2–5 min), affording single products in excellent yields (75–99%). This convenient and eco-friendly methodology offers numerous benefits with respect to other protocols reported for similar compounds. Keywords: catalysis; charge density; condensation; erbium(III

• molecular descriptor based on the electronic properties of the carbonyl group. These properties could determinate the affinity between the aldehyde and the catalyst. Geometries were optimized for all aldehydes and electrostatic potential (ESP) population analyses were done to obtain the charge density on

Useful access to enantiomerically pure protected inositols from carbohydrates: the aldohexos-5-uloses route

• Felicia D’Andrea,
• Giorgio Catelani,
• Lorenzo Guazzelli and
• Venerando Pistarà

Beilstein J. Org. Chem. 2016, 12, 2343–2350, doi:10.3762/bjoc.12.227

• -withdrawing substituents in positions 4 and 6 diminishes the negative charge density on the 5-oxygen atom and decreases in this way the overall energy of the transition state, thereby favouring the intramolecular reaction. These kind of inductive effects in cyclic system has been reported before [43][44]. The

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

• temperature can be attributed to the high interaction of carbon dioxide with the framework. Both hyper-cross-linked polymers have hydroxy groups which are polar in nature. On the other hand CO2 molecules have a quadrupole moment, which renders a positive charge density over the carbon atom. So the polar

Scope and mechanism of the highly stereoselective metal-mediated domino aldol reactions of enolates with aldehydes

• M. Emin Cinar,
• Bernward Engelen,
• Martin Panthöfer,
• Hans-Jörg Deiseroth,
• Jens Schlirf and
• Michael Schmittel

Beilstein J. Org. Chem. 2016, 12, 813–824, doi:10.3762/bjoc.12.80

• radius of the B3+ ion is very small (25 pm). In the case of tin(II), a high yield of 6a (up to 90%) was observed but formation of 5a was not detected which indicates a hindrance for the second aldol addition. Presumably due to the low charge density of the Sn2+ ions the second carbonyl function is not

Creating molecular macrocycles for anion recognition

• Amar H. Flood

Beilstein J. Org. Chem. 2016, 12, 611–627, doi:10.3762/bjoc.12.60

• ) and iodide (K ≈ 104 M−1) too large. The binding constants reflect this order. As suggested by Jonathan Sessler in conversations, the bromide is better size-matched but its charge density is just a little less than chloride such that the affinity for chloride is a little higher in dichloromethane. The

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

• this mechanism, synthetic polycarbonates arising from organocatalytic ring-opening polymerization of cholesterol monomers were reported to create self-assemblies possessing high interior charge density and wide spectrum antimicrobial activity [6]. Interestingly, the causative vector of human gastritis

Mechanism, kinetics and selectivity of selenocyclization of 5-alkenylhydantoins: an experimental and computational study

• Biljana M. Šmit,
• Radoslav Z. Pavlović,
• Dejan A. Milenković and
• Zoran S. Marković

Beilstein J. Org. Chem. 2015, 11, 1865–1875, doi:10.3762/bjoc.11.200

• used. Full geometry optimizations, without any symmetry constraints, and frequency calculations were performed for all species in acetonitrile as solvent (dielectric constant = 35.688) using the SMD solvation model [44]. SMD is a continuum solvation model based on the quantum mechanical charge density

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

• electrostatic interaction between the oxidised TTF units within the polymer backbone. The degree to which these polymer oxidation potentials shift is in the order 37 < 35 < 39, which roughly follows the expected charge density of the doped polymer backbone. The chronocoulometry experiment during bulk

Impact of multivalent charge presentation on peptide–nanoparticle aggregation

• Daniel Schöne,
• Boris Schade,
• Christoph Böttcher and
• Beate Koksch

Beilstein J. Org. Chem. 2015, 11, 792–803, doi:10.3762/bjoc.11.89

• and even the binding constant of R2A3 is slightly higher. Therefore it can be assumed that the fiber formation increases the binding constant significantly (Table 1). Compared to coiled-coil oligomers the α-helical peptide fiber has a highly ordered structure and the charge density is well localized

• size of the peptide and finally the charge density plays an important role for its aggregation efficiency. Furthermore, we could show that the quaternary structure of the peptide has important consequences for the formed nanoparticle assemblies, as well as for the thermodynamics of aggregation. First

Multivalent dendritic polyglycerolamine with arginine and histidine end groups for efficient siRNA transfection

• Fatemeh Sheikhi Mehrabadi,
• Hanxiang Zeng,
• Mark Johnson,
• Cathleen Schlesener,
• Zhibin Guan and
• Rainer Haag

Beilstein J. Org. Chem. 2015, 11, 763–772, doi:10.3762/bjoc.11.86

• interactions of these polymers with the cell membrane and depends on multiple factors such as molecular weight, the nature of the polymer surface, and its charge density [30]. The results of the in vitro MTT assays on the NIH 3T3 cell line for cytotoxicity evaluation of AAdPG polyplexes are shown in Figure 3

Fluoride-driven ‘turn on’ ESPT in the binding with a novel benzimidazole-based sensor

• Kai Liu,
• Xiaojun Zhao,
• Qingxiang Liu,
• Jianzhong Huo,
• Bolin Zhu and
• Shihua Diao

Beilstein J. Org. Chem. 2015, 11, 563–567, doi:10.3762/bjoc.11.61

• basicity and surface charge density such as AcO− and H2PO4−. Fluorescence spectral changes were driven by original hydrogen bonding interaction between BIP and F−, and the subsequent ESPT which resulted in the ‘turn-on’ of fluorescence. The strategy for the design of simple sensors to detect the important

IR and electrochemical synthesis and characterization of thin films of PEDOT grown on platinum single crystal electrodes in [EMMIM]Tf₂N ionic liquid

• Andrea P. Sandoval,
• Marco F. Suárez-Herrera and
• Juan M. Feliu

Beilstein J. Org. Chem. 2015, 11, 348–357, doi:10.3762/bjoc.11.40

• synthesized applying a charge density of 1.2 mC cm−2 during a chronopotentiometry. Insert graph: Current density vs scan rate of PEDOT on Pt(111). a) Cyclic voltammograms of PEDOT on Pt(111) in [EMMIM]Tf2N. The total charge densities used for the galvanostatic synthesis were 1.2, 3.0, 4.3 and 6.2 mC cm−2

• of PEDOT thin films synthesized on a) Pt(111), b) Pt(100) and c) Pt(110) with a charge density of 1.2 mC cm−2. The film thickness is approximately 10 nm. In situ FTIR spectra of a PEDOT thin film synthesized with a charge density of 0.6 mC cm−2 on Pt(111). 250 interferograms were recorded per

• spectrum. The reference potential was −0.90 V. a) p-Polarized spectrum at 0.80 V. b) s-Polarized spectrum at 0.80 V. c) ATR spectrum of 0.1 M [EMMIM]Tf2N in acetonitrile, obtained as the average of 100 interferograms. a) In situ FTIR spectra of a PEDOT thin film synthesized with a charge density of 0.6 mC

Molecular ordering at electrified interfaces: Template and potential effects

• Thanh Hai Phan and
• Klaus Wandelt

Beilstein J. Org. Chem. 2014, 10, 2243–2254, doi:10.3762/bjoc.10.233

• . In this respect electrochemical deposition has the additional advantage that these electrostatic interactions can be “tuned” by the electrochemical potential in two ways. On the one hand the mere charge density at the electrode surface itself determines the electrostatic forces between adsorbed ions

• cations and the negatively charged chloride layer underneath, with the additional remark that the anion density, and thus the negative charge density, on the chloride precovered Cu(111) surface is higher than on Cl/Cu(100). This manifests itself in the fact, that the respective coverages are consistently

Molecular recognition of AT-DNA sequences by the induced CD pattern of dibenzotetraaza[14]annulene (DBTAA)–adenine derivatives

• Marijana Radić Stojković,
• Marko Škugor,
• Łukasz Dudek,
• Jarosław Grolik,
• Julita Eilmes and
• Ivo Piantanida

Beilstein J. Org. Chem. 2014, 10, 2175–2185, doi:10.3762/bjoc.10.225

• ]). Namely, parameters such as the groove width and depth, steric obstructions like the amino groups of guanine, H-bonding patterns, as well as polynucleotide charge density and the curvature of the ds-helix backbone all differ significantly across the double stranded examples mentioned above (Table S1

• the charge density and the curvature of the DNA backbone, which can influence interactions of the positively charged arm of AP3/AP3am with the phosphate backbone and AP3/AP3am-adenine with thymines of the DNA. The GC-DNA and AU-RNA minor grooves are not suitable for an aromatic dimer binding. In the

Cyclization–endoperoxidation cascade reactions of dienes mediated by a pyrylium photoredox catalyst

• Nathan J. Gesmundo and
• David A. Nicewicz

Beilstein J. Org. Chem. 2014, 10, 1272–1281, doi:10.3762/bjoc.10.128

• -substituted diene 2h also gave none of the desired adduct, which we attributed to lack of charge density on the alkene [28][29]. We next investigated the endoperoxidation cascade by replacing the isoprenyl substituent with a variety of other alkenes. A pendant styrene afforded the desired endoperoxide adduct

One-pot three-component synthesis and photophysical characteristics of novel triene merocyanines

• Christian Muschelknautz,
• Robin Visse,
• Jan Nordmann and
• Thomas J. J. Müller

Beilstein J. Org. Chem. 2014, 10, 599–612, doi:10.3762/bjoc.10.51

• product. Therefore, the local charge density in 13 is most crucial for the bifurcation and, hence, for the product formation. For scrutinizing this rationale we computed the electrostatic charges on the atoms 1–7 of the allenyl enolate moiety of model zwitterions 16, which only differ by the N-substituent

• -methyl (16a) and an N-tosyl intermediate (16b) clearly shows charge density differences at five distinct atoms (Table 3). All merocyanines 8 and 10 are expectedly deeply colored both in the solid state and in solution. For further investigation of the photophysical properties the absorption spectra were

Recent advances towards azobenzene-based light-driven real-time information-transmitting materials

• Jaume García-Amorós and
• Dolores Velasco

Beilstein J. Org. Chem. 2012, 8, 1003–1017, doi:10.3762/bjoc.8.113

• the pyridine moiety places a positive-charge density over the pyridine nitrogen, which increases susbsequently the push–pull electronic distribution of the azo-dye (compounds 22 and 23). As observed in Figure 22, the relaxation time of these two azocompounds in ethanol is 49 ms and 14 ms, respectively

An efficient and practical entry to 2-amido-dienes and 3-amido-trienes from allenamides through stereoselective 1,3-hydrogen shifts

• Ryuji Hayashi,
• John B. Feltenberger,
• Andrew G. Lohse,
• Mary C. Walton and
• Richard P. Hsung

Beilstein J. Org. Chem. 2011, 7, 410–420, doi:10.3762/bjoc.7.53

• state through increasing negative charge density at the β-carbon. This action would lead to an N-acyl iminium ion-like character with the migrating hydrogen being proton-like with the α-position being favoured. This polarized transition state should also have a lower thermal activation barrier for the

Fluorometric recognition of both dihydrogen phosphate and iodide by a new flexible anthracene linked benzimidazolium-based receptor

• Kumaresh Ghosh and
• Debasis Kar

Beilstein J. Org. Chem. 2011, 7, 254–264, doi:10.3762/bjoc.7.34

• receptor 1 also binds the larger sized iodide ion with 2:1 (guest:host) stoichiometry. By comparison, the change in emission of 1 in the presence of the smaller sized F− is attributed to its greater charge density which causes strong hydrogen bonding followed by deprotonation. Although receptor 1

A new fluorescent chemosensor for fluoride anion based on a pyrrole–isoxazole derivative

• Zhipei Yang,
• Kai Zhang,
• Fangbin Gong,
• Shayu Li,
• Jun Chen,
• Jin Shi Ma,
• Lyubov N. Sobenina,
• Albina I. Mikhaleva,
• Guoqiang Yang and
• Boris A. Trofimov

Beilstein J. Org. Chem. 2011, 7, 46–52, doi:10.3762/bjoc.7.8

• charge density and smaller size, fluoride as strong base can deprotonate the receptor 1 to afford the heterocyclic conjugated anion [22][23], the emission of which is significantly lower than that of its charge neutral species when excited at 340 nm. The deprotonation site could be determined by the 1H

Chromo- and fluorophoric water-soluble polymers and silica particles by nucleophilic substitution reaction of poly(vinyl amine)

• Katja Hofmann,
• Ingolf Kahle,
• Frank Simon and
• Stefan Spange

Beilstein J. Org. Chem. 2010, 6, No. 79, doi:10.3762/bjoc.6.79

• charge-neutral amines (−NH2). In this context, PVAm can be considered as a weak cationic polyelectrolyte. The pH-variation is an excellent tool to control and adjust the net-charge density along the polymer chain or in a layer made from PVAm [16][17]. Full conversion of the amino groups into their

• cationic form leads to a polymer with the highest known charge density along the polymer backbone. Such highly protonated polymers appear to be very interesting compounds for the prevention of bacteria adhesion on surfaces [18]. Non-protonated primary amino groups in the PVAm polymer have a high synthetic

RAFT polymers for protein recognition

• Alan F. Tominey,
• Julia Liese,
• Sun Wei,
• Klaus Kowski,
• Thomas Schrader and
• Arno Kraft

Beilstein J. Org. Chem. 2010, 6, No. 66, doi:10.3762/bjoc.6.66

• . Obviously, the bisphosphonate’s high negative charge density is especially effective for protein surfaces with a high density of basic amino acids such as the DNA-binding histones or for those offering distinct clusters of cationic amino acid residues (e.g. BSA). Interestingly, although in most cases