From chemical metabolism to life: the origin of the genetic coding process

• Antoine Danchin

Beilstein J. Org. Chem. 2017, 13, 1119–1135, doi:10.3762/bjoc.13.111

• how chemical metabolism that began with amino acids progressively shaped into a coding process involving RNAs. Here I explore the role of building up complementarity rules as the first information-based process that allowed for the genetic code to emerge, after RNAs were substituted to surfaces to

• carry over the basic metabolic pathways that drive the pursuit of life. Keywords: algorithmic complexity; complementarity; phagocytosis: reticulum; Turing Machine; Introduction “Man is the measure of all things” (Protagoras), making it difficult to get around an anthropocentric view of the reality

• number of building blocks). To these operations we must add two essential laws, complementarity and its major consequence, coding (just brought up as key to life). Making cells Compartmentalisation The atom of life is the cell, and a cell generate cells: “omnis cellula e cellula” [10]. The obvious

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

• maxima during the binding process. Receptors R1 and R2 showed a higher selectivity towards AcO− ions in organic and aqueous media owing to its shape complementarity and relatively high basicity compared to other anions. A practical application of the colorimetric responses of R1 and R2 as real time

Computational methods in drug discovery

• Sumudu P. Leelananda and
• Steffen Lindert

Beilstein J. Org. Chem. 2016, 12, 2694–2718, doi:10.3762/bjoc.12.267

• OpenEye Scientific, finds protein–ligand docking poses by using a non-stochastic exhaustive method. It uses filters that take shape complementarity into account and the top scoring poses selected are further optimized [136]. Docking algorithms are discussed in detail in reviews [140][141][142] and

Supramolecular polymer assembly in aqueous solution arising from cyclodextrin host–guest complexation

• Jie Wang,
• Zhiqiang Qiu,
• Yiming Wang,
• Li Li,
• Xuhong Guo,
• Duc-Truc Pham,
• Stephen F. Lincoln and
• Robert K. Prud’homme

Beilstein J. Org. Chem. 2016, 12, 50–72, doi:10.3762/bjoc.12.7

• associative forces including hydrogen bonding, coordinate bonding, electrostatic interactions and hydrophobic interactions is ubiquitous in nature. This is exemplified by the use of DNA and RNA complementarity [1][2] and polypeptide helix formation [3][4] to produce three-dimensional structures and materials

Determination of formation constants and structural characterization of cyclodextrin inclusion complexes with two phenolic isomers: carvacrol and thymol

• Miriana Kfoury,
• David Landy,
• Steven Ruellan,
• Lizette Auezova,
• Hélène Greige-Gerges and
• Sophie Fourmentin

Beilstein J. Org. Chem. 2016, 12, 29–42, doi:10.3762/bjoc.12.5

• recognized by β-CD and its derivatives as compared to α-CD and γ-CD. Our findings could be strengthened by the fact that the vigor of binding is highly influenced by the complementarity between guest and CD cavity. Molecules with aromatic ring structures would fit better within the β-CD cavity. When

• which strengthen its binding to guests. Concerning the influence of the position of the hydroxy group of 1 and 2 on their recognition by CDs, the former allowed the formation of relatively more stable inclusion complexes as demonstrated by higher Kf values. A tight steric complementarity between CD and

Donor–acceptor type co-crystals of arylthio-substituted tetrathiafulvalenes and fullerenes

• Xiaofeng Lu,
• Jibin Sun,
• Shangxi Zhang,
• Longfei Ma,
• Lei Liu,
• Hui Qi,
• Yongliang Shao and
• Xiangfeng Shao

Beilstein J. Org. Chem. 2015, 11, 1043–1051, doi:10.3762/bjoc.11.117

• ) connection of two components through covalent bonds [23][24][25][26][27] or (2) supramolecular assembly between TTFs (as host) and fullerene (as guest) [28][29][30][31][32][33][34][35][36][37][38][39][40][41]. For the formation of the host–guest type supramolecular system, the shape and size complementarity

• -crystals with fullerenes: (1) size and shape complementarity, (2) flexibility, and (3) the ability to introduce an additional interaction with fullerene by peripheral aryls. While the interactions between the TTF framework and fullerenes have been observed in many TTF–fullerene supramolecular systems [38

Self-assembly of heteroleptic dinuclear metallosupramolecular kites from multivalent ligands via social self-sorting

• Christian Benkhäuser and
• Arne Lützen

Beilstein J. Org. Chem. 2015, 11, 693–700, doi:10.3762/bjoc.11.79

• has become an important issue in supramolecular chemistry [1][2][3][4][5]. Such self-sorting can either occur in a social self-discriminating or a narcissistic self-recognition manner (Scheme 1). In general, geometrical size and shape complementarity are used to ensure high-fidelity self-sorting. This

Photocatalytic nucleophilic addition of alcohols to styrenes in Markovnikov and anti-Markovnikov orientation

• Martin Weiser,
• Sergej Hermann,
• Alexander Penner and
• Hans-Achim Wagenknecht

Beilstein J. Org. Chem. 2015, 11, 568–575, doi:10.3762/bjoc.11.62

• derivatives by photocatalysis. The regioselectivity – Markovnikov or anti-Markovnikov – can simply be controlled by the chosen photocatalyst, either Py or 1,7-dicyanoperylene-3,4:9,10-tetracarboxylic acid bisimide (PDI). Results and Discussion Photocatalytic complementarity The photocatalytic complementarity

• give 72% yield over only 1 h, or four high-power LEDs, to give 76% yield over 3 h (Table 2). As control that 1 was not excited directly by sunlight, a sample without PDI was set into sunlight and, as expected, yielded no product. Conclusion The photocatalytic complementarity of the two different routes

Sequence-specific RNA cleavage by PNA conjugates of the metal-free artificial ribonuclease tris(2-aminobenzimidazole)

• Friederike Danneberg,
• Alice Ghidini,
• Plamena Dogandzhiyski,
• Elisabeth Kalden,
• Roger Strömberg and
• Michael W. Göbel

Beilstein J. Org. Chem. 2015, 11, 493–498, doi:10.3762/bjoc.11.55

• complementarity to 15mer PNAs, i.e., the binding sites, are underlined. When 10mer PNAs bind to substrates 15 and 16, the first five ribonucleotides at the 5’ end will remain single stranded. Cleavage of RNA by their corresponding PNA conjugates (150 nM substrate, 750 nM conjugate, 50 mM Tris-HCl, pH 8, 37 °C, 20

Come-back of phenanthridine and phenanthridinium derivatives in the 21st century

• Lidija-Marija Tumir,
• Marijana Radić Stojković and
• Ivo Piantanida

Beilstein J. Org. Chem. 2014, 10, 2930–2954, doi:10.3762/bjoc.10.312

• accompanied with simultaneous phosphorylation [42] (Scheme 19). The particular importance of this economic and highly efficient synthetic method is the complementarity of the starting material, the easy availability of 2-isocyanobiphenyls, which could be converted to variously substituted phenanthridines in

Improving ITC studies of cyclodextrin inclusion compounds by global analysis of conventional and non-conventional experiments

• Eléonore Bertaut and
• David Landy

Beilstein J. Org. Chem. 2014, 10, 2630–2641, doi:10.3762/bjoc.10.275

• , confirming the strong reliability of both approaches and demonstrating the complementarity of the various non-conventional protocols. Conclusion If the titration protocol constitutes the overwhelming majority of the published ITC studies on cyclodextrin complexes, our work clearly demonstrates that non

Autonomous assembly of synthetic oligonucleotides built from an expanded DNA alphabet. Total synthesis of a gene encoding kanamycin resistance

• Kristen K. Merritt,
• Kevin M. Bradley,
• Daniel Hutter,
• Mariko F. Matsuura,
• Diane J. Rowold and
• Steven A. Benner

Beilstein J. Org. Chem. 2014, 10, 2348–2360, doi:10.3762/bjoc.10.245

• low concentrations of oligonucleotide. Adding components of an artificially expanded genetic information system (AEGIS, here S and B) prevent a class of these obstructive structures. Watson–Crick pairing rules follow two rules of complementarity: (a) size complementarity (large purines pair with small

• pyrimidines) and (b) hydrogen-bonding complementarity (hydrogen-bond acceptors, A, pair with hydrogen-bond donors, D). Rearranging donor and acceptor groups on the nucleobases, while not changing the geometry of the Watson–Crick pair, creates an artificially expanded genetic information system (AEGIS). AEGIS

Specific DNA duplex formation at an artificial lipid bilayer: fluorescence microscopy after Sybr Green I staining

• Emma Werz and
• Helmut Rosemeyer

Beilstein J. Org. Chem. 2014, 10, 2307–2321, doi:10.3762/bjoc.10.240

• -glycero-3-phosphocholine (POPC). The bilayer separates two compartments (cis/trans channel) of an optical transparent microfluidic sample carrier with perfusion capabilities. Injection of unlabeled target DNA sequences (6, 8, or 9), differing in sequence and length, leads in the case of complementarity to

OligArch: A software tool to allow artificially expanded genetic information systems (AEGIS) to guide the autonomous self-assembly of long DNA constructs from multiple DNA single strands

• Kevin M. Bradley and
• Steven A. Benner

Beilstein J. Org. Chem. 2014, 10, 1826–1833, doi:10.3762/bjoc.10.192

• from both the 5’- and 3’-end (the default is four nucleotides) to minimize unwanted complementarity. Remaining spans are then ranked based upon number of AEGIS nucleobases, distribution of AEGIS nucleobases, and presence and size of repeating nucleotide patterns. Once ranked, these spans are compared

• against all other AEGIS spans being used in the current assembly set, with those that might hybridize with an unintended target being excluded. Potential hybridization is defined as any complementarity with a Tm of ≥50% of the minimum span Tm that can be designed. Further, spans that will result in

• intermolecular hybridization, especially at low concentrations of oligonucleotide. Watson–Crick pairing rules follow two rules of complementarity: (a) size complementarity (large purines pair with small pyrimidines) and (b) hydrogen bonding complementarity (hydrogen bond acceptors, A, pair with hydrogen bond

Influence of perylenediimide–pyrene supramolecular interactions on the stability of DNA-based hybrids: Importance of electrostatic complementarity

• Christian B. Winiger,
• Simon M. Langenegger,
• Oleg Khorev and
• Robert Häner

Beilstein J. Org. Chem. 2014, 10, 1589–1595, doi:10.3762/bjoc.10.164

• interaction indicating the importance of electrostatic complementarity for aromatic π–π stacking interactions. Keywords: DNA; hybridization; nucleic acids; perylenediimide; pyrene; Introduction When two aromatic molecules are in close proximity they often have a tendency to interact non-covalently in a face

• ’-dimethyl-PDI. The former is considerably more electron-rich/higher electron density (red) than the latter, which is expected to favour an alternating aromatic π–π stacking arrangement of E and Y due to electrostatic complementarity. We show herein that duplex formation by our chimeric DNA-oligoarenotide

• the hybrid stabilities are as follows: ΔTm/(Y−E) ≈ 7.5 °C, whereas ΔTm/(Y−Y) and ΔTm/(E−E) ≈ 5.5 °C. The results of electrostatic complementarity between an electron-rich pyrene and an electron-poor PDI is highlighted by the fact that duplexes with only pyrene or PDI are considerably less stable

Multivalent scaffolds induce galectin-3 aggregation into nanoparticles

• Candace K. Goodman,
• Mark L. Wolfenden,
• Pratima Nangia-Makker,
• Anna K. Michel,
• Avraham Raz and
• Mary J. Cloninger

Beilstein J. Org. Chem. 2014, 10, 1570–1577, doi:10.3762/bjoc.10.162

• at molar ratios of 9:1 galectin:glycodendrimer were largest while 220:1 and 3:1 ratios produced smaller complexes. The difference in aggregate sizes may relate to the size and shape complementarity between dendrimer and lectin or to the interplay of enthalpic and entropic contributions to aggregate

Why a diaminopyrrolic tripodal receptor binds mannosides in acetonitrile but not in water?

• Diogo Vila-Viçosa,
• Oscar Francesconi and
• Miguel Machuqueiro

Beilstein J. Org. Chem. 2014, 10, 1513–1523, doi:10.3762/bjoc.10.156

• complementarity between molecular mechanics/molecular dynamics (MM/MD) simulations, that correctly samples the conformational space of a system according to a classic potential energy function, and Poisson–Boltzmann/Monte Carlo methods, that can efficiently treat multiple protonation equilibria on rigid

Self-assembly of metallosupramolecular rhombi from chiral concave 9,9’-spirobifluorene-derived bis(pyridine) ligands

• Rainer Hovorka,
• Sophie Hytteballe,
• Torsten Piehler,
• Georg Meyer-Eppler,
• Filip Topić,
• Kari Rissanen,
• Marianne Engeser and
• Arne Lützen

Beilstein J. Org. Chem. 2014, 10, 432–441, doi:10.3762/bjoc.10.40

• -discrimination or a narcissistic self-recognition manner [1][2][3]. Usually, geometrical size and shape complementarity are employed to ensure such self-sorting. However, these factors do not account in self-sorting processes where enantiomers are involved whose shape and size does not vary but only their

Gold(I)-catalyzed enantioselective cycloaddition reactions

• Fernando López and
• José L. Mascareñas

Beilstein J. Org. Chem. 2013, 9, 2250–2264, doi:10.3762/bjoc.9.264

• active cyclobutanes [77]. Several chiral phosphoramidite–gold complexes, such as (S,R,R)-Au7, (S,R,R)-Au15 and (R,R,R)-Au16, derived from Siphos, Binol and Vanol, respectively, provided excellent enantioselectivities, displaying useful complementarity in some of the cases. Importantly, the method also

Molecular assembly of amino acid interlinked, topologically symmetric, π-complementary donor–acceptor–donor triads

• M. B. Avinash,
• K. V. Sandeepa and
• T. Govindaraju

Beilstein J. Org. Chem. 2013, 9, 1565–1571, doi:10.3762/bjoc.9.178

• ][2]. The significance of geometric complementarity and chemical functionality can be exemplified by the well-known “lock and key” mechanism of enzymes as well as the prototypal molecular recognition manifested in biochemical processes [1][2][3][4]. It is this elementary yet elegant design strategy

Supramolecular hydrogels formed from poly(viologen) cross-linked with cyclodextrin dimers and their physical properties

• Yoshinori Takashima,
• Yang Yuting,
• Miyuki Otsubo,
• Hiroyasu Yamaguchi and
• Akira Harada

Beilstein J. Org. Chem. 2012, 8, 1594–1600, doi:10.3762/bjoc.8.182

• α-CD unit of the α,α-CD dimer cannot exceed the electric barrier at 30 °C, whereas after heating at 100 °C, the α-CD unit exceeds the barrier to form polyrotaxanes. To confirm complementarity between the CD dimer and VP, we then investigated the formation of supramolecular hydrogels of VP with the α

• and self-healing abilities. The complementarity between α-CD and the decamethylene units plays an important role in the formation of supramolecular hydrogels composed of α,α-CD dimer/VP. VP has an electric barrier between the decamethylene units, which is a unique feature of this supramolecular

Diarylethene-modified nucleotides for switching optical properties in DNA

• Sebastian Barrois and
• Hans-Achim Wagenknecht

Beilstein J. Org. Chem. 2012, 8, 905–914, doi:10.3762/bjoc.8.103

• polymerase-assisted PEX and PCR experiments, an absolutely critical issue regarding the application of single C–C bonds, or ethinyl or phenylene linkers is the question of whether the canonical base-recognition complementarity is effected by the chromophore modification [42][43]. Due to the strongest

Fifty years of oxacalix[3]arenes: A review

• Kevin Cottet,
• Paula M. Marcos and
• Peter J. Cragg

Beilstein J. Org. Chem. 2012, 8, 201–226, doi:10.3762/bjoc.8.22

• complementarity between the arrangement of phenolic groups and the preferred coordination environment of Na+. Removal of the tert-butyl groups through a conventional AlCl3 driven retro-Friedel–Crafts de-tert-butylation reaction, as seen in other calixarenes, is unsuccessful in the case of oxacalixarenes

Ratiometric fluorescent probe for enantioselective detection of D-cysteine in aqueous solution

• Xiao-bo Zhou,
• Wing-Hong Chan,
• Albert W. M. Lee and
• Chi-Chung Yeung

Beilstein J. Org. Chem. 2011, 7, 1508–1515, doi:10.3762/bjoc.7.176

• health [32]. On the basis of multipoint electrostatic interactions and structure complementarity of the host–guest, we have rationally designed and synthesised a bis(spiropyran) as a fluorescence turn-on probe for selective binding of GSH [33]. We have also developed the first spiropyran–metal sensing

• enantioselectivity of 3.35 conferred by the chiral trans-1,2-diaminocyclohexane moiety for recognizing D-cysteine in 1% ACN/HEPES buffered solutions (pH 7.4) (Figure 5). Apparently, owing to the structure complementarity of the host–guest, D-cysteine outperforms its enantiomer in forming a more stable complex with

Supramolecular FRET photocyclodimerization of anthracenecarboxylate with naphthalene-capped γ-cyclodextrin

• Qian Wang,
• Cheng Yang,
• Gaku Fukuhara,
• Tadashi Mori,
• Yu Liu and
• Yoshihisa Inoue

Beilstein J. Org. Chem. 2011, 7, 290–297, doi:10.3762/bjoc.7.38

• non-covalent interactions in the ground state [4][5][6][7][8][9][10][11]. The geometrical and functional complementarity and the subsequent induced fit between chiral host and guest substrate should play a crucial role in determining the stereochemical fate of chiral photoreaction, and therefore the