Rational design of boron-dipyrromethene (BODIPY) reporter dyes for cucurbit[7]uril

• Mohammad A. Alnajjar,
• Jürgen Bartelmeß,
• Robert Hein,
• Pichandi Ashokkumar,
• Mohamed Nilam,
• Werner M. Nau,
• Knut Rurack and
• Andreas Hennig

Beilstein J. Org. Chem. 2018, 14, 1961–1971, doi:10.3762/bjoc.14.171

• combination of properties has enabled numerous applications in the life sciences, for example, for protein binding [5][6], stabilization [7], immobilisation [8], isolation [9], self-assembly [10][11], and regulation [12], or for drug solubilisation and delivery [13][14][15]. The combination of CBs with

A pyridinium/anilinium [2]catenane that operates as an acid–base driven optical switch

• Sarah J. Vella and
• Stephen J. Loeb

Beilstein J. Org. Chem. 2018, 14, 1908–1916, doi:10.3762/bjoc.14.165

• (Figure 2) was synthesized using a one-step, self-assembly procedure from two bis(pyridinium)ethane axles, two terphenyl spacers and two DB24C8 crown ethers, a [2]catenane with different recognition sites requires a stepwise approach involving the incorporation of each recognition site independently

Strong binding and fluorescence sensing of bisphosphonates by guanidinium-modified calix[5]arene

• Jie Gao,
• Zhe Zheng,
• Lin Shi,
• Si-Qi Wu,
• Hongwei Sun and
• Dong-Sheng Guo

Beilstein J. Org. Chem. 2018, 14, 1840–1845, doi:10.3762/bjoc.14.157

• to their facial modification, Prof. Böhmer demonstrated calixarenes as having “(almost) unlimited possibilities” [17]. We have focused on molecular recognition and self-assembly of water-soluble calixarene derivatives for a long time [18][19][20][21][22][23][24], directed by exploring biomedical

Host–guest complexes of conformationally flexible C-hexyl-2-bromoresorcinarene and aromatic N-oxides: solid-state, solution and computational studies

• Rakesh Puttreddy,
• Ngong Kodiah Beyeh,
• S. Maryamdokht Taimoory,
• Daniel Meister,
• John F. Trant and
• Kari Rissanen

Beilstein J. Org. Chem. 2018, 14, 1723–1733, doi:10.3762/bjoc.14.146

• various upper-rim substituents, differing lower-rim alkyl chain length, specific guests, and selective solvents, have made resorcinarenes an attractive platform for H–G applications. Through careful rational supramolecular design via self-assembly processes, our lab and others have combined simple 1:1 H–G

Design, synthesis and structure of novel G-2 melamine-based dendrimers incorporating 4-(n-octyloxy)aniline as a peripheral unit

• Cristina Morar,
• Pedro Lameiras,
• Attila Bende,
• Gabriel Katona,
• Emese Gál and
• Mircea Darabantu

Beilstein J. Org. Chem. 2018, 14, 1704–1722, doi:10.3762/bjoc.14.145

• to self-organise in solution and to self-assembly in the solid state. Keywords: amination; dendrimers; melamines; nano-aggregates; 4-(n-octyloxy)aniline; Introduction N-Substituted melamine (2,4,6-triamino-1,3,5-triazine)-based dendrimers are a class of macromolecules reported as early as 2000 by E

• frameworks) [35]. All the above information prompted us towards an ab initio exploration of 4-(n-octyloxy)aniline (seen as the n-octyl ether derivative of 4-aminophenol) as starting material towards new melamine-based dendrimers as synthesis (feasibility and limits), structure and self-assembly propensity

• propensity for self-assembly as nano-aggregates. Indeed, covalent dendrimers 5–7a generated nanospheres with much smaller average diameter (259–732 nm, Figure 9) than the ionic 7b–9 (992–1454 nm, Figure 10). Moreover, according to the literature [71], the last ones appeared to be among the greatest

Synthesis of diamido-bridged bis-pillar[5]arenes and tris-pillar[5]arenes for construction of unique [1]rotaxanes and bis-[1]rotaxanes

• Ying Han,
• Li-Ming Xu,
• Cui-Yun Nie,
• Shuo Jiang,
• Jing Sun and
• Chao-Guo Yan

Beilstein J. Org. Chem. 2018, 14, 1660–1667, doi:10.3762/bjoc.14.142

• ; pillar[5]arene; [1]rotaxane; self-assembly; Introduction The construction and dynamic motion of the mechanically interlocked molecules (MIMs) have attracted significant research interests due to their intrinsic self-assembled nature and potential applications in various aspects [1][2][3][4]. Pseudo[1

• ]arenes. On the basis of 1H NMR and 2D NOESY spectra, we successfully concluded that the chains longer than diaminopropylene threaded into the one or two cavities of the pillar[5]arenes to form the unique [1]rotaxane and bis-[1]rotaxanes. This work not only provided a fundamental self-assembly of the

A conformationally adaptive macrocycle: conformational complexity and host–guest chemistry of zorb[4]arene

• Liu-Pan Yang,
• Song-Bo Lu,
• Arto Valkonen,
• Fangfang Pan,
• Kari Rissanen and
• Wei Jiang

Beilstein J. Org. Chem. 2018, 14, 1570–1577, doi:10.3762/bjoc.14.134

• ] and remote electronic substituents on the guests [34]. In addition, different alkyl side chains on oxatub[4]arenes lead to different macroscopic self-assembly behaviors [36]. Zorb[4]arene was first synthesized, reported and so named by the Georghiou group in 2005. The derivatives per-O-methoxy- and

• per-O-ethoxyzorb[4]arene were shown to be effective tetramethylammonium ion receptors [38]. The per-O-n-butoxyzorb[4]arene (ZB4, Scheme 1a) was only recently further studied by us with respect to its rich conformational properties and the consequence on macroscopic self-assembly [37]. In the present

Recent applications of chiral calixarenes in asymmetric catalysis

• Mustafa Durmaz,
• Erkan Halay and
• Selahattin Bozkurt

Beilstein J. Org. Chem. 2018, 14, 1389–1412, doi:10.3762/bjoc.14.117

• upper and/or lower rims of the molecular skeleton, they have been widely used for construction of artificial host molecules and found applications in various fields like molecular recognition, sensing, self-assembly, catalysis, nanoscience, drug delivery and separation science [7][8][9][10][11][12][13

An overview of recent advances in duplex DNA recognition by small molecules

• Sayantan Bhaduri,
• Nihar Ranjan and
• Dev P. Arya

Beilstein J. Org. Chem. 2018, 14, 1051–1086, doi:10.3762/bjoc.14.93

• study their solution-phase self-association characteristics and DNA molecular-recognition properties [17]. The authors showed a measurable difference in solution-phase self-assembly character with enhanced DNA association characteristics by replacing the formamide head group in thiazotropsin A with

Pyrene–nucleobase conjugates: synthesis, oligonucleotide binding and confocal bioimaging studies

• Artur Jabłoński,
• Yannic Fritz,
• Hans-Achim Wagenknecht,
• Rafał Czerwieniec,
• Tytus Bernaś,
• Damian Trzybiński,
• Krzysztof Woźniak and
• Konrad Kowalski

Beilstein J. Org. Chem. 2017, 13, 2521–2534, doi:10.3762/bjoc.13.249

• compounds. The conjugates bearing a carbonyl function represent weak emitters as compared to compounds with a hydroxy function in the linker. The self-assembly properties of pyrene nucleobases were investigated in respect to their binding to single and double strand oligonucleotides in water and in buffer

• derivative 5 binds to the double-stranded (dA)10–T10 template with a self-assembly ratio of 112%. Such a high value of a self-assembly ratio can be rationalized by a triple-helix-like binding, intercalation, or a mixture of both. Remarkably, compound 5 also shows dual staining pattern in living HeLa cells

• investigated towards application as fluorescent cell imaging bioprobes so far. Furthermore, self-assembly studies of pyrene–nucleobases on oligonucleotide templates have not been reported as well. The work presented herein addresses these two problems. Accordingly, in this contribution we report on the

Synthesis and supramolecular properties of regioisomers of mononaphthylallyl derivatives of γ-cyclodextrin

• Markéta Bláhová,
• Sergey K. Filippov,
• Lubomír Kováčik,
• Jiří Horský,
• Simona Hybelbauerová,
• Zdenka Syrová,
• Tomáš Křížek and
• Jindřich Jindřich

Beilstein J. Org. Chem. 2017, 13, 2509–2520, doi:10.3762/bjoc.13.248

• larger than 1 μm, exceeding the limit of the instrument used. To assess the influence of filtration on the self-assembly of naphthylallyl regioisomers, samples were then passed through 0.22 μm pores. The volume-weighted DLS distribution function of the 2-O- and 3-O-samples show a dominant presence of 2.5

Remarkable functions of sn-3 hydroxy and phosphocholine groups in 1,2-diacyl-sn-glycerolipids to induce clockwise (+)-helicity around the 1,2-diacyl moiety: Evidence from conformation analysis by ¹H NMR spectroscopy

• Yoshihiro Nishida,
• Mengfei Yuan,
• Kazuo Fukuda,
• Kaito Fujisawa,
• Hirofumi Dohi and
• Hirotaka Uzawa

Beilstein J. Org. Chem. 2017, 13, 1999–2009, doi:10.3762/bjoc.13.196

• ] examined the effect of self-assembly using 1,2-dihexanoyl (C6) homologs of glycerophospholipids. They added these acyl homologs into D2O at concentrations less than or greater than the critical micellar concentration. In their 1H NMR spectroscopy analysis, the tg conformer is almost absent under the self

β-Cyclodextrin- and adamantyl-substituted poly(acrylate) self-assembling aqueous networks designed for controlled complexation and release of small molecules

• Liang Yan,
• Duc-Truc Pham,
• Philip Clements,
• Stephen F. Lincoln,
• Jie Wang,
• Xuhong Guo and
• Christopher J. Easton

Beilstein J. Org. Chem. 2017, 13, 1879–1892, doi:10.3762/bjoc.13.183

• viscosity of the network as shown by ITC, 1H NMR and UV–vis spectroscopy, and rheological studies. Such networks potentially form a basis for the design of controlled drug release systems. Keywords: controlled release; cyclodextrin; network; poly(acrylate); self-assembly; Introduction The formation of

• and the PAAADen, PAAADhn or PAAADddn strands. The adamantyl group is selected as the guest substituent as it is strongly complexed by β-CD [48], β-CD oligomers [3][4] and β-CD-substituted polymers [10][14][16], and drives the self-assembly of aqueous chitosan [1][5][9], hyaluronic acid [8][9] and poly

• profiles for MO and EO overlap which probably reflects a combination of the abilities of MO, EO and the β-CD–MO and β-CD–EO complexes to pass through the pores of the dialysis membrane. Conclusion The self-assembly of the β-CDen and ADen, ADhn and ADddn substituted poly(acrylate) networks, PAAβ-CDen

Mechanochemical synthesis of thioureas, ureas and guanidines

• Vjekoslav Štrukil

Beilstein J. Org. Chem. 2017, 13, 1828–1849, doi:10.3762/bjoc.13.178

• laboratory, where all the steps from synthesis to structural characterization are carried out without using bulk solvents. The systematic PXRD analyses of 49 thioureas revealed that thioureas, on a supramolecular level, organize into three types of self-assembly motifs based on N–H···S hydrogen bonds

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

• for the determination of environmental conditions conducive to the self-assembly of several cellular-like components, such as bilayer membranes [15] and simple energy systems [16], or dynamic processes, such as growth and division [17][18] and potential evolution [19]. However, the experimental set

• processes [50]. In the case of amphiphiles, these phenomena lead to the formation of compartments by self-assembly, which can encapsulate other solutes, e.g., RNA [17][51]. The accumulation ability of porous minerals allows for the amphiphile concentration to surpass their critical vesicle concentration to

• effect self-assembly [51]. Thus, mineral surfaces and porous formations could have been excellent media to foster the emergence of “self-contained”, dispersed chemical systems. Furthermore, mineral surfaces can serve as supports for chemical systems to undergo organization. The polymerization of nucleic

Grip on complexity in chemical reaction networks

• Albert S. Y. Wong and
• Wilhelm T. S. Huck

Beilstein J. Org. Chem. 2017, 13, 1486–1497, doi:10.3762/bjoc.13.147

• oscillation periods enable the construction of more complex systems capable of dynamical self-assembly. In this case, it is a dynamic self-assembly that is exactly out-of-phase with the initial oscillations. Correlating the molecular structure to network behavior This design strategy enables the chemist to

• permission from [75], copyright 2013 American Chemical Society. (c) Self-assembly fibrous structures fueled by molecular gelators. Reprinted with permission from [76], copyright 2010 Wiley-VCH Verlag GmbH & Co. (d) Biocatalytic self-assembly in the presence of chymotrypsin (green) forming hydrogelators that

Framing major prebiotic transitions as stages of protocell development: three challenges for origins-of-life research

• Ben Shirt-Ediss,
• Sara Murillo-Sánchez and
• Kepa Ruiz-Mirazo

Beilstein J. Org. Chem. 2017, 13, 1388–1395, doi:10.3762/bjoc.13.135

• -life simplifications that do not completely erase this aspect at the beginning. The combination of diverse chemical reactions with self-organization and self-assembly processes in heterogeneous, multi-phase conditions could actually be crucial at those first stages: this is the main assumption that

• functional capacities (see [15] for a review). In particular, fatty acid vesicles have become the standard protocell model, not just because of their prebiotic plausibility [27][28], but also because of their remarkable stability as compartments [29][30]; their rapid self-assembly kinetics and amenability to

Biomimetic molecular design tools that learn, evolve, and adapt

• David A Winkler

Beilstein J. Org. Chem. 2017, 13, 1288–1302, doi:10.3762/bjoc.13.125

• designed and synthesized using these self-assembly paradigms. They are being developed to tackle two major and interrelated environmental challenges facing the planet, the rise in CO2 levels in the atmosphere due to burning of fossil fuels, and the storage of hydrogen for zero carbon emission transport

Towards open-ended evolution in self-replicating molecular systems

• Herman Duim and
• Sijbren Otto

Beilstein J. Org. Chem. 2017, 13, 1189–1203, doi:10.3762/bjoc.13.118

• macrocycles of different sizes as depicted in Figure 12b. The design of the peptide chains is such that self-assembly of the chains into parallel β-sheets is promoted, which in turn leads to the formation of stacks of macrocycles as shown in Figure 12c. Growth of these stacks occurs exclusively via the ends

Aggregation behaviour of a single-chain, phenylene-modified bolalipid and its miscibility with classical phospholipids

• Simon Drescher,
• Vasil M. Garamus,
• Christopher J. Garvey,
• Annette Meister and
• Alfred Blume

Beilstein J. Org. Chem. 2017, 13, 995–1007, doi:10.3762/bjoc.13.99

• behaviour; nanofibres; self-assembly; Introduction Bolalipids are amphiphilic molecules consisting of two hydrophilic headgroups attached to both ends of a long hydrocarbon spacer [1]. The hydrophobic spacer is composed of either a single alkyl chain or two chains connected via a glycerol moiety. These

• conformation into phospholipid bilayers is energetically unfavourable as it produces void volume, which can be filled by neither bolalipid nor phospholipid. Consequently, the self-assembly of PC-C32-PC into nanofibres is preferred. To evade these packing problems, we expanded the cross-sectional area of the

How and why kinetics, thermodynamics, and chemistry induce the logic of biological evolution

• Addy Pross and
• Robert Pascal

Beilstein J. Org. Chem. 2017, 13, 665–674, doi:10.3762/bjoc.13.66

• in support of that view. Results and Discussion From thermodynamic self-assembly to kinetic self-assembly Organised supramolecular structures are commonly formed when favourable interactions lead to the assembly of different components [18]. The release of chemical binding energy, i.e., the

• elaborate processes, in particular that of increasing complexity, are clearly involved. As an example of a higher degree of complexity, out-of-equilibrium self-assembly can be observed when reactants that have no affinity for self-assembly in themselves, can be converted upon activation into transient

• (Figure 1B). These structures therefore result from dissipative self-assembly for which fascinating examples have been provided in the recent literature [19][20][21]. In biology, one of the most typical examples of this kind of assembly processes can be found in the dynamics of the cytoskeleton. However

Synthesis of 1-indanones with a broad range of biological activity

• Marika Turek,
• Dorota Szczęsna,
• Marek Koprowski and
• Piotr Bałczewski

Beilstein J. Org. Chem. 2017, 13, 451–494, doi:10.3762/bjoc.13.48

• cyclized to the 1-indanone 25. The latter was then converted to biologically active 1-indanone derivatives 26 in three steps (Scheme 9). The authors tested activities of the synthesized compounds 26 for inhibition of cholinesterases (AChE and BuChE) and inhibition of amyloid beta (Aβ) self-assembly. The

A new class of organogelators based on triphenylmethyl derivatives of primary alcohols: hydrophobic interactions alone can mediate gelation

• Wangkhem P. Singh and
• Rajkumar S. Singh

Beilstein J. Org. Chem. 2017, 13, 138–149, doi:10.3762/bjoc.13.17

• LMWGs can immobilize organic solvents (forming organogels) and water or aqueous solvents (forming hydrogels) under different experimental conditions. Gels, so formed are supramolecular in nature as they result from self-assembly of the gelator molecules through secondary interactions like H-bonding, π

• stress of the viscoelastic material. For these gels, similar yield stress values (≈6–7 Pa) were obtained. These values are somewhat on the lower side. FTIR studies FTIR is one of the techniques used to study the influence of non-covalent interactions in the self-assembly of gelator molecules [35]. We

• values and energy minimized molecular size, we propose a possible molecular packing arrangement of TPM-G12 in the self-assembled gel state (Figure 9a). Self-assembly in the gel state will be driven predominantly by hydrophobic interactions between the octyl alkyl chains and triphenylmethyl groups. The

New approaches to organocatalysis based on C–H and C–X bonding for electrophilic substrate activation

• Pavel Nagorny and
• Zhankui Sun

Beilstein J. Org. Chem. 2016, 12, 2834–2848, doi:10.3762/bjoc.12.283

• one molecule of (S)-1,2-dibromohexafluoropropane. The Br−···Br distance (Scheme 13) is about 3.3 Å, which is approximately 20% shorter than the sum of the van der Waals radii. The angle between Br−···Br–C is about 175º. The strong Br−···Br–C halogen bonds are robust enough to drive the self-assembly

Effects of solvent additive on “s-shaped” curves in solution-processed small molecule solar cells

• John A. Love,
• Shu-Hua Chou,
• Ye Huang,
• Guilllermo C. Bazan and
• Thuc-Quyen Nguyen

Beilstein J. Org. Chem. 2016, 12, 2543–2555, doi:10.3762/bjoc.12.249

• -on” orientation adopted by p-SIDT(FBTTh2)2 [40], demonstrating how sensitive molecular self-assembly can be to relatively small molecular design choices. However, consistent with previous reports of related molecules, DIO does seem to improve crystallinity. Atomic force microscopy (AFM) topography