Experimental and theoretical insights in the alkene–arene intramolecular π-stacking interaction

• Valeria Corne,
• Ariel M. Sarotti,
• Carmen Ramirez de Arellano,
• Rolando A. Spanevello and
• Alejandra G. Suárez

Beilstein J. Org. Chem. 2016, 12, 1616–1623, doi:10.3762/bjoc.12.158

• , Universidad de Valencia, Valencia 46100, Spain 10.3762/bjoc.12.158 Abstract Chiral acrylic esters derived from biomass were developed as models to have a better insight in the aryl–vinyl π-stacking interactions. Quantum chemical calculations, NMR studies and experimental evidences demonstrated the presence

• affected by the electron density of the aromatic counterpart. Keywords: acrylic esters; asymmetric synthesis; biomass; conformational equilibrium; π-stacking interaction; Introduction Noncovalent interactions have demonstrated to have relevant importance in chemistry and biology [1][2][3][4]. Considering

• all noncovalent interactions, π-stacking is perhaps the less well understood, although its application in materials sciences, enzyme design and template-directed synthesis have had a dramatic growth, mainly for arene–arene interactions [1][2][3][4][5][6][7][8]. In particular, the use of π–π overlap as

Creating molecular macrocycles for anion recognition

• Amar H. Flood

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

• triazole nitrogens but not past the pyridine with the steric protection provided by a CH group (see the red arrows in Figure 4c for the overlay of the two ligands). The ruthenium complex showed intermolecular π stacking of ligands on neighboring complexes in the solid state; yet terpyridine analogs did not

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

• grateful for his time and advice. While on the academic interview circuit, I was fortunate to have Steven Wheeler (a postdoctoral researcher with Professor Ken Houk at the time) in the audience at one interview. He was developing computational methods to evaluate π-stacking interactions, and was intrigued

• explained by through-space interactions [15]. Steven, who is now an associate professor at Texas A&M University, is changing the way we understand π stacking, XH/π, and ion/π interactions in organic systems [16][17][18][19][20]. During my postdoctoral studies, I remained fascinated with gels and was

• structures, such as ribbons, fibers, and sheets. This self-aggregation is driven by noncovalent interactions, including hydrogen bonding, π stacking, van der Waals interactions, and halogen bonding. Physical interactions amongst these larger structures lead to gel formation. Because noncovalent interactions

Urethane tetrathiafulvalene derivatives: synthesis, self-assembly and electrochemical properties

• Xiang Sun,
• Guoqiao Lai,
• Zhifang Li,
• Yuwen Ma,
• Xiao Yuan,
• Yongjia Shen and
• Chengyun Wang

Beilstein J. Org. Chem. 2015, 11, 2343–2349, doi:10.3762/bjoc.11.255

• driving forces for self-assembly of TTF derivatives were mainly hydrogen bond interactions and π–π stacking interactions. The electronic conductivity of the T1 and T2 films was tested by a four-probe method. Keywords: hydrogen bond; nanoribbon; self-assembly; tetrathiafulvalene; urethane; Introduction

• nanomaterials is generally accepted to be the self-assembly of supermolecules, which is constructed through weak noncovalent interactions such as π–π stacking, van der Waals interactions, charge transfer and H-bonding interactions [3][4][5][6]. Generally speaking, H-bonding interactions are the key

• units and urethane groups (Figure 1). The combination of the urethane group (forming hydrogen bonds) and the TTF unit (forming π–π stacking) may promote the formation of nanostructures. To the best of our knowledge, urethane groups have been rarely introduced into the molecular structure of TTF

Supramolecular chemistry: from aromatic foldamers to solution-phase supramolecular organic frameworks

• Zhan-Ting Li

Beilstein J. Org. Chem. 2015, 11, 2057–2071, doi:10.3762/bjoc.11.222

• : applications for molecular recognition and self-assembly Donor–acceptor interaction and π-stacking for folding. In January 2001, I returned to SIOC again. When I left SIOC for Urbana in 2000, I had built a small research group with two graduates. Thanks to the persistence of Professor Xi-Kui Jiang [19][20

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

• dimensionality of charge carrier transport [1] by involving π–π stacking interactions. Varying the substituents of the conjugated backbone allows control over the polymer’s effective conjugation length and electronic properties, whilst also influencing the extent of inter-chain interactions. Two of the most

• the preparation of TTF mixed valance state materials, which showed superconducting properties [25]. Fusing the TTF unit with dithiin rings in bis(ethylenedithio)tetrathiafulvalene (BEDT-TTF) led to the extension of 1D π–π stacking intermolecular interactions in a donor sheet of a mixed valance state

• -acceptor into the conjugated backbone led to a polymer with a narrow optical band gap (Egopt = 1.32 eV in CH2Cl2 solution), with the expected lower value of Egopt = 1.26 eV in the film due to π–π stacking interactions. The value of the HOMO/LUMO levels (−5.13/−3.49 eV) in the film were noticeably different

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

• interactions between molecules having one or more unpaired electrons [3][4], neutral TTF and its derivatives also easily form stacked columnar structures with face-to-face π···π stacking and side-by-side S···S interactions in the crystalline state. Furthermore, weak intermolecular interactions (hydrogen

• bonding, metal coordination, CT interaction, π···π stacking, van der Waals interaction, etc.) play an important role in the formation of the three-dimensional (3D) crystal structures [5]. For the construction of nanostructured objects, π···π, S···S, and other weak intermolecular interactions first

• formed by casting a solution of 48 on a glass surface (Figure 17c). XRD studies on the fiber and the film of 48 revealed that the fiber has a hexagonal alignment, whereas the film has a lamellar structure with lateral order and π···π stacking. It is worth noting that the film of 48 prepared by casting a

Thiazole-induced rigidification in substituted dithieno-tetrathiafulvalene: the effect of planarisation on charge transport properties

• Rupert G. D. Taylor,
• Joseph Cameron,
• Iain A. Wright,
• Neil Thomson,
• Olena Avramchenko,
• Alexander L. Kanibolotsky,
• Anto R. Inigo,
• Tell Tuttle and
• Peter J. Skabara

Beilstein J. Org. Chem. 2015, 11, 1148–1154, doi:10.3762/bjoc.11.129

• resolved but there is a non-resolved peak caused by overlap of the cathodic peaks on the reverse scan. Compound 2 appears to show a first oxidation wave at 0.09 V, however, this is an artefact due to a minor degree of aggregation induced by π–π stacking between some of the molecules. This is followed by

Are D-manno-configured Amadori products ligands of the bacterial lectin FimH?

• Tobias-Elias Gloe,
• Insa Stamer,
• Cornelia Hojnik,
• Tanja M. Wrodnigg and
• Thisbe K. Lindhorst

Beilstein J. Org. Chem. 2015, 11, 1096–1104, doi:10.3762/bjoc.11.123

• ]. Obviously, FimH binds α-D-mannosides such as simple methyl α-D-mannoside (MeMan, 1) but not β-mannosides. Mannosides with an aromatic aglycone, such as p-nitrophenyl α-D-mannoside (pNPMan) and 4-methylumbelliferyl α-D-mannoside (3) show an improved affinity to FimH due to π–π-stacking interactions of the

Synthesis of photoresponsive cholesterol-based azobenzene organogels: dependence on different spacer lengths

• Yuchun Ren,
• Bin Wang and
• Xiuqing Zhang

Beilstein J. Org. Chem. 2015, 11, 1089–1095, doi:10.3762/bjoc.11.122

• ], etc. The driving force for the spontaneous formation of gel could be relatively non-covalent interactions such as π–π stacking [4][5][6][7], hydrogen bonding [7][8][9], dipole–dipole [10], and van der Waals interactions [11][12]. A series of cholesterol-based gelators were reported [13][14][15]. These

Indolizines and pyrrolo[1,2-c]pyrimidines decorated with a pyrimidine and a pyridine unit respectively

• Marcel Mirel Popa,
• Emilian Georgescu,
• Mino R. Caira,
• Florentina Georgescu,
• Constantin Draghici,
• Raluca Stan,
• Calin Deleanu and
• Florea Dumitrascu

Beilstein J. Org. Chem. 2015, 11, 1079–1088, doi:10.3762/bjoc.11.121

• π-stacking, with shortest ring centroid-to-centroid distances of 3.743 Å in 6 and 3.766 Å in 8. It was ascertained from a search of the Cambridge Structural Database [34] (CSD) that the crystal of 6 is isostructural with that of 4,4’-bipyrimidine as the trans-rotamer (CSD refcode SACPAN). This is

Mechanical stability of bivalent transition metal complexes analyzed by single-molecule force spectroscopy

• Manuel Gensler,
• Christian Eidamshaus,
• Maurice Taszarek,
• Hans-Ulrich Reissig and
• Jürgen P. Rabe

Beilstein J. Org. Chem. 2015, 11, 817–827, doi:10.3762/bjoc.11.91

• partially due to the fact that the π–π-stacking of pyridines [50] was a competing interaction. The most probable rupture force, used in the KBE model, was due to the coordination complexes. Methods using the whole data set are strongly influenced by the stacking interaction and would have needed heavily

First principle investigation of the linker length effects on the thermodynamics of divalent pseudorotaxanes

• Andreas J. Achazi,
• Doreen Mollenhauer and
• Beate Paulus

Beilstein J. Org. Chem. 2015, 11, 687–692, doi:10.3762/bjoc.11.78

• first principle calculations show clearly that this enhanced binding is due to electronic effects, namely the dispersion interaction of the two linkers. For the shortest linker this interaction results in a nearly ideal π–π stacking. For the two longer linkers ideal packing is not possible due to steric

• dispersive interaction of the linking unit (two phenyl rings and the linker), which in case of the n0 guest fits perfectly on top of the anthracene linker of the DiC8 host. The distance between the linker of the host and the linker of the n0 guest is around 3.7 Å, quite close to an ideal distance for the π–π

• stacking of two benzene rings. The n1 and n2 guest do not perfectly fit with the host (Figure 2). In the n1-case the linker is folded away from the anthracene bridge, and for the n2-case one phenyl ring is twisted away due to steric constraints. The Gibbs energy of association ΔG in the gas phase of the

C-5’-Triazolyl-2’-oxa-3’-aza-4’a-carbanucleosides: Synthesis and biological evaluation

• Roberto Romeo,
• Caterina Carnovale,
• Salvatore V. Giofrè,
• Maria A. Chiacchio,
• Adriana Garozzo,
• Emanuele Amata,
• Giovanni Romeo and
• Ugo Chiacchio

Beilstein J. Org. Chem. 2015, 11, 328–334, doi:10.3762/bjoc.11.38

• , the 1,2,3-triazole motif is exceedingly stable to basic or acidic hydrolysis and interacts strongly with biological targets through hydrogen bonding to nitrogen atoms as well as through dipole–dipole and π-stacking interactions [39]. Recently, a synthetic approach towards 3-hydroxymethyl-5-(1H-1,2,3

Synthesis and characterization of pH responsive D-glucosamine based molecular gelators

• Navneet Goyal,
• Hari P. R. Mangunuru,
• Bargav Parikh,
• Sonu Shrestha and
• Guijun Wang

Beilstein J. Org. Chem. 2014, 10, 3111–3121, doi:10.3762/bjoc.10.328

• referred to as supramolecular gelators or molecular gelators. They can form reversible gels in organic solvents, aqueous mixtures, and water. The gelation process is completely driven by weak intermolecular forces such as hydrogen bonding, π–π stacking, hydrophobic forces, and van der Waals forces. The

A one-pot multistep cyclization yielding thiadiazoloimidazole derivatives

• Debabrata Samanta,
• Anup Rana,
• Jan W. Bats and
• Michael Schmittel

Beilstein J. Org. Chem. 2014, 10, 2989–2996, doi:10.3762/bjoc.10.317

• by multiple π–π stacking (slighly displaced) at a distance of 3.36−3.40 Å (Figure 1c) while the iminophenyl groups are connected by weak intermolecular C(phenyl)-H···π(phenyl) contacts. Moreover, Figure 1a shows that the structure is planar except for the phenyl ring attached to the N4 atom (C2–N4–C5

• –C6 = 49.0°). The phenyl ring attached to the N3 atom is nearly coplanar (C1–N3–C3–C4 = 2.5°) with the thiadiazole ring allowing additional delocalization. This coplanar arrangement might help for intercalation into biological molecules using e.g., π–π stacking, C–H···π or ion–dipole interactions

• –π stacking. To take the solvent into consideration, the thermochemical analyses were performed in dichloromethane using the COSMO model with gas phase optimized geometries. Originally, DMAP should be hydrogen bonded to both amide protons in complex 8 increasing the nucleophilicity of both N-centers

A comparative study of the interactions of cationic hetarenes with quadruplex-DNA forming oligonucleotide sequences of the insulin-linked polymorphic region (ILPR)

• Darinka Dzubiel,
• Heiko Ihmels,
• Mohamed M. A. Mahmoud and
• Laura Thomas

Beilstein J. Org. Chem. 2014, 10, 2963–2974, doi:10.3762/bjoc.10.314

• terminal π-stacking [20], which is in agreement with the observed binding stoichiometry of 1:1 (Figure 7), the different composition of the loops in ILPR-quadruplex (ACA and TGT in ILPR versus TTA in telomeric quadruplex) may affect the binding affinity of ligands towards the ILPR-DNA. On the other hand

Synthesis and characterization of a new photoinduced switchable β-cyclodextrin dimer

• Florian Hamon,
• Claire Blaszkiewicz,
• Marie Buchotte,
• Estelle Banaszak-Léonard,
• Hervé Bricout,
• Sébastien Tilloy,
• Eric Monflier,
• Christine Cézard,
• Laurent Bouteiller,
• Christophe Len and
• Florence Djedaini-Pilard

Beilstein J. Org. Chem. 2014, 10, 2874–2885, doi:10.3762/bjoc.10.304

• cyclic polymers are aggregated into larger objects stabilized by hydrogen bonds between cyclodextrin moieties and by π-stacking interactions between azobenzene linkers. Finally, according to the computational data, the complexes of AZO-CDim 1 with ADAdim 4 are further stabilized by intramolecular

Solution processable diketopyrrolopyrrole (DPP) cored small molecules with BODIPY end groups as novel donors for organic solar cells

• Diego Cortizo-Lacalle,
• Calvyn T. Howells,
• Upendra K. Pandey,
• Joseph Cameron,
• Neil J. Findlay,
• Anto Regis Inigo,
• Tell Tuttle,
• Peter J. Skabara and
• Ifor D. W. Samuel

Beilstein J. Org. Chem. 2014, 10, 2683–2695, doi:10.3762/bjoc.10.283

• organic field-effect transistors [24][25]. The DPP-based conjugated polymers usually show good electron and hole mobility and promising PCE values in OPVs due to large intermolecular interactions through π–π stacking. Nguyen et al. have investigated the DPP core in small molecules for OPVs with excellent

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

• stacked dimers within the DNA minor groove similar to the crystal structure of close analogue (Figure 4, right). Conversely, the AP5 and AP6 aliphatic linkers are long enough to allow self-folding and easy intramolecular π–π stacking of adenine with DBTAA (Figure 4, upper right). During the binding event

• left – note the stacking of DBTAA and adenine) and AP3 (lower left – note the short linker which does not allow for the stacking of DBTAA and adenine); (right) detail of three molecules packing in crystal by π–π stacking of parallel DBTAA rings with a distance of ca. 3 Å (see [13] and Figure 8 therein

Scalable synthesis of 5,11-diethynylated indeno[1,2-b]fluorene-6,12-diones and exploration of their solid state packing

• Bradley D. Rose,
• Peter J. Santa Maria,
• Aaron G. Fix,
• Chris L. Vonnegut,
• Lev N. Zakharov,
• Sean R. Parkin and
• Michael M. Haley

Beilstein J. Org. Chem. 2014, 10, 2122–2130, doi:10.3762/bjoc.10.219

• structure revealed 1-dimensional π-stacking with a close interplanar distance of 3.30 Å [15]. Due to the inherent insolubility of compounds 3 and 4, however, they needed to be vapor deposited under vacuum. More recently IF-diones 5–7 were reported (along with polymeric and other derivatives) with 5 and 6

• backbone and the solubilizing groups, and π-stacking is observed in all but the largest (8f, SiPh3), but there are significant differences in the nature of the π-stacking of the other nine compounds. The smallest (8a, SiMe3, vol. ~130 Å3) is monoclinic, P21/c, with a unit cell elongated along b. The

• )°, giving a variant of the common herringbone motif, despite the lack of a crystallographic glide plane. In addition to the IF-dione π-stacking, inversion-related phenyl groups on the solubilizing groups are paired by π–π interactions. The stacking in compounds 8c and 8d (Si(n-Pr)3 and Si(iPr)3, vol. ~278

Chiral phosphines in nucleophilic organocatalysis

• Yumei Xiao,
• Zhanhu Sun,
• Hongchao Guo and
• Ohyun Kwon

Beilstein J. Org. Chem. 2014, 10, 2089–2121, doi:10.3762/bjoc.10.218

Supercritical carbon dioxide: a solvent like no other

• Jocelyn Peach and
• Julian Eastoe

Beilstein J. Org. Chem. 2014, 10, 1878–1895, doi:10.3762/bjoc.10.196

• chain, due to poor solvency of styrene in CO2. It was anticipated that π–π stacking between phenyl groups is a main contributor to the viscosity increase, through its provision of a fundamental intermolecular force needed to raise viscosity in a system. The optimum composition of polymers for viscosity

Aryl substitution of pentacenes

• Andreas R. Waterloo,
• Anna-Chiara Sale,
• Dan Lehnherr,
• Frank Hampel and
• Rik R. Tykwinski

Beilstein J. Org. Chem. 2014, 10, 1692–1705, doi:10.3762/bjoc.10.178

• ; pentacene; π-stacking; polycyclic aromatic hydrocarbon; solid-state structure; Introduction Conjugated organic molecules are promising candidates for use in optoelectronic applications including OLEDs [1], photovoltaics [2], and OFETs [3]. Even though there is literally an infinite number of possibilities

• often observed for samples which give solution cast films that result in significant π-stacking between molecules, such as TIPSPc, in which λmax shifts from 643 nm in solution to ca. 705 nm in the solid film [11][35][40]. This same logic also suggests that the minimal difference between the absorption

• characteristics of 3c and 3h results from both a lack of influence from the different silyl groups, as well as the absence of strong π-stacking for both derivatives in the films, even though X-ray crystallographic analysis suggests that strong interactions might be possible for some derivatives in the solid state

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

• Christian B. Winiger Simon M. Langenegger Oleg Khorev Robert Haner Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, CH-3012 Bern, Switzerland 10.3762/bjoc.10.164 Abstract Aromatic π–π stacking interactions are ubiquitous in nature, medicinal chemistry and materials

• 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

• -to-face stacking arrangement. Face-centered, parallel aromatic π–π stacking interactions have been studied and reviewed in great detail [1][2][3][4][5]. These interactions are especially important for polycyclic aromatic hydrocarbons (PAHs) [6][7]. The interaction is the result of solvophobicity, as