pH- and concentration-dependent supramolecular self-assembly of a naturally occurring octapeptide

• Goutam Ghosh and
• Gustavo Fernández

Beilstein J. Org. Chem. 2020, 16, 2017–2025, doi:10.3762/bjoc.16.168

• secondary structures, which lead to nanostructured materials [16][17]. Noncovalent interactions, such as hydrogen bonding, van der Waals interactions, hydrophobic interactions, electrostatic interactions, and π–π interactions [18][19][20][21][22] are common driving forces in peptide self-assembly. These

• noncovalent interactions can also be designed to be responsive to various external stimuli, such as heat, pH, light, enzymes, metal ions, and chemical triggers [23][24][25][26][27][28][29][30][31][32][33][34][35][36][37][38][39]. In this regard, a particularly relevant property of peptide assemblies is their

Synthesis, antiinflammatory activity, and molecular docking studies of bisphosphonic esters as potential MMP-8 and MMP-9 inhibitors

• Abimelek Cortes-Pacheco,
• María Adelina Jiménez-Arellanes,
• Francisco José Palacios-Can,
• José Antonio Valcarcel-Gamiño,
• Rodrigo Said Razo-Hernández,
• María del Carmen Juárez-Vázquez,
• Adolfo López-Torres and
• Oscar Abelardo Ramírez-Marroquín

Beilstein J. Org. Chem. 2020, 16, 1277–1287, doi:10.3762/bjoc.16.108

• small molecular volume increases the pharmacokinetic abilities of the compounds. In addition, 3 and 4 have a greater dipole moment compared to 5 and 6. The hydrogen-bond formation and the noncovalent interactions are influenced by the dipole moment. This means that an increased dipole moment can improve

• to a methyl moiety of Val398 and with Leu187, with distances below 3.5 Å. For MMP-9, the ligands were even more exposed to the solvent, although many more noncovalent interactions were seen between the catalytic site and the molecules (Figure 5). Conclusion In this work, we reported the two-step

Understanding the role of active site residues in CotB2 catalysis using a cluster model

• Keren Raz,
• Ronja Driller,
• Thomas Brück,
• Bernhard Loll and
• Dan T. Major

Beilstein J. Org. Chem. 2020, 16, 50–59, doi:10.3762/bjoc.16.7

• potential. Additionally, structural analysis revealed that each cation was stabilized by noncovalent interactions, such as π–cation and dipole–cation interactions. A comparison of the transition state structures in the gas phase vs the active site model is shown in Table 2. These findings suggest that the

Why do thioureas and squaramides slow down the Ireland–Claisen rearrangement?

• Dominika Krištofíková,
• Juraj Filo,
• Mária Mečiarová and
• Radovan Šebesta

Beilstein J. Org. Chem. 2019, 15, 2948–2957, doi:10.3762/bjoc.15.290

• quantum-chemical calculations employing long-range corrected hybrid density ωB97X-D functional [42]. This dispersion-corrected functional displays very balanced overall performances and has demonstrated excellent treatment of noncovalent interactions [43], which are very important in our studied system

Influence of the cis/trans configuration on the supramolecular aggregation of aryltriazoles

• Sara Tejera,
• Giada Caniglia,
• Rosa L. Dorta,
• Andrea Favero,
• Javier González-Platas and
• Jesús T. Vázquez

Beilstein J. Org. Chem. 2019, 15, 2881–2888, doi:10.3762/bjoc.15.282

• diffraction; Introduction Structures self-assembled by noncovalent interactions give rise to supramolecular architectures with specific physical and/or chemical properties. Gels are colloid systems in which the dispersed phase has combined with the dispersion medium to yield a semisolid material. Gels from

A combinatorial approach to improving the performance of azoarene photoswitches

• Joaquin Calbo,
• Aditya R. Thawani,
• Rosina S. L. Gibson,
• Andrew J. P. White and
• Matthew J. Fuchter

Beilstein J. Org. Chem. 2019, 15, 2753–2764, doi:10.3762/bjoc.15.266

• interactions. The energy-minimized structures for the Z-isomer of representative photoswitches are shown in Figure S2 (Supporting Information File 1). The proximity of the ortho-benzene substituents to the heteroaryl ring in the Z-isomer either stabilizes the Z-isomer ground state via noncovalent interactions

• calculations of the noncovalent index (NCI) surfaces indicate that dispersion forces exist between pyrrolidine groups and the heteroaromatic ring (green surfaces in Figure 3). The inclusion of one pyrrolidine (4pzH-Pyr1) promotes weak but stabilizing noncovalent interactions between the ortho group and the

• analogues (Figure 3), their twisted arrangements allow for a large array of weak and stabilizing noncovalent interactions between the ortho-groups and the methyl-substituted pyrazole ring (θ ca. 135°), potentially explaining the increase in t1/2 upon systematic introduction of pyrrolidine moieties (Table 1

1,2,3-Triazolium macrocycles in supramolecular chemistry

• Mastaneh Safarnejad Shad,
• Pulikkal Veettil Santhini and
• Wim Dehaen

Beilstein J. Org. Chem. 2019, 15, 2142–2155, doi:10.3762/bjoc.15.211

• polymers etc. [14][15]. Noncovalent interactions play a dynamic role in the binding mechanism of triazoles as macrocyclic receptors. It has been reported that the combined effects of both an electron lone pair on the nitrogen of the heterocycle and the acidic C5–H proton make 1,2,3-triazoles interesting

• in the literature in which they bind to the anionic species by utilizing multiple noncovalent interactions based on electrostatics, including hydrogen bonding (HB), anion–π interactions [30], and on Lewis acidity/basicity [31]. 2.1. Bile acid-based 1,2,3-triazolium macrocycles Bile acid-based

• interactions, compared to monovalent receptor–ligand interactions offer the advantage of multiple and sequential binding within the host–guest systems. These noncovalent interactions which can be controlled in a chemical or physical manner depend on the binding sites in the multivalent assembly [67

An overview of the cycloaddition chemistry of fulvenes and emerging applications

• Ellen Swan,
• Kirsten Platts and
• Anton Blencowe

Beilstein J. Org. Chem. 2019, 15, 2113–2132, doi:10.3762/bjoc.15.209

• the formation of several materials, including dynamic polymers (dynamers) [190], hydrogels [191], and precursors to charge-transfer complexes [181][234][235]. Dynamers, referred to as dynamers, are a class of adaptive polymers formed through reversible covalent bonds or noncovalent interactions

Synthesis and anion binding properties of phthalimide-containing corona[6]arenes

• Meng-Di Gu,
• Yao Lu and
• Mei-Xiang Wang

Beilstein J. Org. Chem. 2019, 15, 1976–1983, doi:10.3762/bjoc.15.193

• noncovalent interactions between anions and the tetrazine rings. Keywords: anion–π interactions; coronarenes; host–guest complexation; N-functionalized phthalimides; O6-corona[3]arene[3]tetrazines; Introduction Synthetic macrocycles [1][2] are always attractive and important because they are unique

• molecular systems to study molecular recognition and the nature of noncovalent interactions. Functional macrocycles also provide essential components for the fabrication or assembly of sophisticated (supra)molecular structures [1][2][3][4], advanced materials [1][2][5][6][7][8][9][10] and machinery systems

• conformational structures to complex anions in the gas phase and in the solid state owing to the anion–π noncovalent interactions between anions and the tetrazine rings. The easy accessibility, cylindroid cavity and diverse functionality would engender phthalimide-containing functionalized O6-corona[3]arene[3

Morphology-tunable and pH-responsive supramolecular self-assemblies based on AB₂-type host–guest-conjugated amphiphilic molecules for controlled drug delivery

• Yang Bai,
• Cai-ping Liu,
• Di Chen,
• Long-hai Zhuo,
• Huai-tian Bu and
• Wei Tian

Beilstein J. Org. Chem. 2019, 15, 1925–1932, doi:10.3762/bjoc.15.188

• based on noncovalent interactions with dynamic nature and reversible property have attracted increasing attention in the fields of biomedicine [1][2][3][4][5][6][7], smart materials [8][9][10], etc. As one common noncovalent interaction [11], host–guest interaction has been used to effectively create

Complexation of chiral amines by resorcin[4]arene sulfonic acids in polar media – circular dichroism and diffusion studies of chirality transfer and solvent dependence

• Bartosz Setner and
• Agnieszka Szumna

Beilstein J. Org. Chem. 2019, 15, 1913–1924, doi:10.3762/bjoc.15.187

• ; supramolecular chemistry; Introduction Despite of the great progress that has been made in supramolecular chemistry in polar and aqueous media, formation of discrete ordered supramolecular associates with precise patterns of noncovalent interactions still presents a challenge [1][2]. Especially self-assembly

• sensitive technique for the detection of noncovalent interactions involving chiral molecules, even if only one component of the interaction pair is chiral. Considering strong interactions with amino acids we think that RSAs, in analogy to CSAs, can also act as modulators of protein crystallizations

Tautomerism as primary signaling mechanism in metal sensing: the case of amide group

• Vera Deneva,
• Georgi Dobrikov,
• Aurelien Crochet,
• Daniela Nedeltcheva,
• Katharina M. Fromm and
• Liudmil Antonov

Beilstein J. Org. Chem. 2019, 15, 1898–1906, doi:10.3762/bjoc.15.185

• exchange was especially developed to describe main-group thermochemistry and noncovalent interactions. It shows very good results in predicting the position of the tautomeric equilibria for compounds with intramolecular hydrogen bonds as well as describing the ground and excited state proton transfer

Molecular recognition using tetralactam macrocycles with parallel aromatic sidewalls

• Dong-Hao Li and
• Bradley D. Smith

Beilstein J. Org. Chem. 2019, 15, 1086–1095, doi:10.3762/bjoc.15.105

• between the equatorial sugar hydroxy groups and the receptor NH residues and also in the CH···π interactions with the hydrophobic anthrylene sidewalls. This combination of noncovalent interactions closely mimics the sugar-binding behavior exhibited by lectin proteins. The Davis group has explored more

The phenyl vinyl ether–methanol complex: a model system for quantum chemistry benchmarking

• Dominic Bernhard,
• Fabian Dietrich,
• Mariyam Fatima,
• Cristóbal Pérez,
• Hannes C. Gottschalk,
• Axel Wuttke,
• Ricardo A. Mata,
• Martin A. Suhm,
• Melanie Schnell and
• Markus Gerhards

Beilstein J. Org. Chem. 2018, 14, 1642–1654, doi:10.3762/bjoc.14.140

• -chemical calculations in order to investigate the delicate interplay of noncovalent interactions. The complementary results of vibrational and rotational spectroscopy applied in molecular beam experiments reveal the preference of a hydrogen bond of the methanol towards the ether oxygen (OH∙∙∙O) over the π

• hydrogen bonds; Introduction The balance of different noncovalent interactions is crucial for chemical and biochemical processes as it controls molecular recognition and aggregation [1][2][3][4][5][6]. In order to gain a deeper understanding of these processes, knowledge on exact structural arrangements

Cobalt-catalyzed C–H cyanations: Insights into the reaction mechanism and the role of London dispersion

• Eric Detmar,
• Valentin Müller,
• Daniel Zell,
• Lutz Ackermann and
• Martin Breugst

Beilstein J. Org. Chem. 2018, 14, 1537–1545, doi:10.3762/bjoc.14.130

• chemical transformations. Presumably due to attractive dispersive interactions between two adamantyl groups in the transition state of a [4 + 2] cycloaddition of benzynes (Scheme 1), the seemingly sterically more hindered product is formed preferentially [8]. Similar to other noncovalent interactions [9

• analysis of the intramolecular interactions in these complexes employing the NCIPLOT program [48][49] furthermore confirms these noncovalent interactions. While all plots are shown in Supporting Information File 1, Figure 3 summarizes those for selected intermediates and transition states. For all

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

• calixarene; organocatalyst; supramolecular catalyst; Introduction The catalysis of organic reactions by macrocyclic host compounds is a longstanding proposed application of supramolecular chemistry and utilizes the use of noncovalent interactions in catalytic systems to achieve higher reaction rates, more

• selective catalysts, or a larger numbers of ligands [1]. The formation of noncovalent interactions due to the selective binding of the substrate by the catalyst results in conversion of the reactants into the products and causes an activity and selectivity increase. Especially the use of supramolecules in

• to the noncovalent interactions, aluminum complexes of calixarene diphosphites 118a–e were synthesized via lower-rim functionalization of the p-tert-butylcalix[4]arene core with axially chiral diol ligands 117 (Scheme 37). The asymmetric MPV reduction of various substituted acetophenones were

London dispersion as important factor for the stabilization of (Z)-azobenzenes in the presence of hydrogen bonding

• Andreas H. Heindl,
• Raffael C. Wende and
• Hermann A. Wegner

Beilstein J. Org. Chem. 2018, 14, 1238–1243, doi:10.3762/bjoc.14.106

• noncovalent interactions). Half-lives for the thermal Z→E isomerization of all-meta-alkyl-substituted azobenzenes 1–3 in DMSO and n-octane at 53.2 °C (examples taken from ref. [23], Cy = cyclohexyl, Ad = adamantyl). Isomerization of N-substituted Z-azobenzenes (a). Rotational equilibrium of (Z)-4 allowing

Correlation effects and many-body interactions in water clusters

• Andreas Heßelmann

Beilstein J. Org. Chem. 2018, 14, 979–991, doi:10.3762/bjoc.14.83

• they enable a description of water on a molecular level that often can provide further insights than are accessible from spectroscopic measurements. The basis for such simulations are the so-called force fields that describe both the covalent as well as the noncovalent interactions within the system

Position-dependent impact of hexafluoroleucine and trifluoroisoleucine on protease digestion

• Susanne Huhmann,
• Anne-Katrin Stegemann,
• Kristin Folmert,
• Damian Klemczak,
• Johann Moschner,
• Michelle Kube and
• Beate Koksch

Beilstein J. Org. Chem. 2017, 13, 2869–2882, doi:10.3762/bjoc.13.279

• hydrophobic than their hydrocarbon analogues [44][45]. Furthermore, fluorine substitution has been shown to polarize neighboring C–H bonds (here the γ-hydrogens) that could affect noncovalent interactions [9][11]. Since the amino acids used here (Figure 1a) differ in their degree of fluorination, spatial

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

• it via noncovalent interactions. Figure 2 shows three different channels in a minimal replicating system. Building blocks A and B can react via the bimolecular reaction pathway, to form the template molecule T. In the second pathway – binary complex formation – A and B bind together reversibly to

Conformational study of L-methionine and L-cysteine derivatives through quantum chemical calculations and ³J_HH coupling constant analyses

• Weslley G. D. P. Silva,
• Carolyne B. Braga and
• Roberto Rittner

Beilstein J. Org. Chem. 2017, 13, 925–937, doi:10.3762/bjoc.13.94

• atoms in molecules (QTAIM) and noncovalent interactions (NCI) methodologies, the conformational preferences for the compounds are not dictated by intramolecular hydrogen bonding, but by a joint contribution of hyperconjugative and steric effects. Keywords: amino acid derivatives; conformational

• insights about the main conformers and the operating effects in the compounds, both in isolated phase and in various aprotic solvents, 1H NMR spectroscopy and quantum chemical calculations, including natural bond orbitals (NBO), quantum theory of atoms in molecules (QTAIM), and noncovalent interactions

• ), assumed as the reference level, and as the ωB97X-D DFT functional has been recognized to reliably treat noncovalent interactions as well as to present good proximity with spectroscopic results [22][23][24], it was used in all subsequent calculations. These calculations were only performed for the

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

• classic aliphatic, hydrophobic interactions, based on the electrostatic component of aromatic interactions. In the late 1980’s and early 1990’s, much work was also done defining the factors that stabilize monomeric α-helices, including the role of noncovalent interactions such as salt bridges, as

• relatively isolated positions for evaluating noncovalent interactions, making them a superb model system. Chad and I set out on this course, which led to the publication of more than a dozen papers on a wide range of aromatic interactions in aqueous solution (Figure 4) [16][17][18][19][20][21][22][23][24][25

• -Sanders Model for π–π stacking from 1990 [4]. (d) Kool’s nonpolar isostere of thymidine from 1995 [5].(e) Gellman’s model for π–π stacking in aqueous solution [6]. (a) Model β-hairpin for investigation of aromatic interactions. (b) Examples of noncovalent interactions studied, from weakest to strongest

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

• 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

• conformational dynamics, we further carried out a detailed computational study at the M06-2X level of theory [22] for the three acrylates 6a–c. This meta-GGA functional, developed by Truhlar [23] has been shown to be one of the approaches of choice to model noncovalent interactions [9]. After a complete

Supramolecular chemistry at the interface of biology, materials and medicine

• Eric V. Anslyn and
• Steven C. Zimmerman

Beilstein J. Org. Chem. 2016, 12, 1101–1102, doi:10.3762/bjoc.12.105

• their own unique perspective and subarea. There is an enormous amount still to learn about the fundamental nature of noncovalent interactions and particularly how to design and synthesize molecules that complex other molecules or are able to assemble spontaneously into three-dimensional structures. Thus

Dynamic behavior of rearranging carbocations – implications for terpene biosynthesis

• Stephanie R. Hare and
• Dean J. Tantillo

Beilstein J. Org. Chem. 2016, 12, 377–390, doi:10.3762/bjoc.12.41

• a factor of 2–3 for the bornyl cation, based on the preliminary calculations described) if the secondary carbocation engages in noncovalent interactions with electron rich groups (e.g., C–H···X hydrogen bonds [81]), thereby increasing the probability of trapping these species by deprotonation or

• the absence of specifically oriented noncovalent interactions with groups in terpene synthase active sites. Molecular dynamics calculations using the full bornyl diphosphate synthase enzyme were also carried out (here using a combination of DFT and molecular mechanics) [21][22]. These simulations

• structures in the vicinity of transition states, tend to have short lifetimes, on the order of the period of a single-bond stretching vibration. • These lifetimes can be increased via noncovalent interactions with electron-rich groups. Abietadiene – navigating past forks in the road Pathways to abietadiene