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Search for "induced-fit" in Full Text gives 20 result(s) in Beilstein Journal of Organic Chemistry.
Beyond symmetric self-assembly and effective molarity: unlocking functional enzyme mimics with robust organic cages
- Keith G. Andrews
Beilstein J. Org. Chem. 2025, 21, 421–443, doi:10.3762/bjoc.21.30
- that might permit tuning of several consecutive catalytic steps [395], induced-fit binding, product release, allostery [396][397], or signaling. For the acyl transfer reaction, cage 1 is an inferior catalyst compared to cage 2, which we have postulated is due to the larger equilibrium cage height
Graphical Abstract
Figure 1: Catalytic rate enhancements from a reduction in the Gibbs free energy transition barrier can be fra...
Figure 2: Typical catalysis modes using macrocycle cavities performing (non-specific) hydrophobic substrate b...
Figure 3: (A) Cram’s serine protease model system [87,88]. The macrocycle showed strong substrate binding (organizat...
Figure 4: (A) Self-assembling capsules can perform hydrophobic catalysis [116,117]. (B) Resorcin[4]arene building bloc...
Figure 5: (A) Metal-organic cages and key modes in catalysis. (B) Charged metals or ligands can result in +/−...
Figure 6: (A) Frameworks (MOFs, COFs) can be catalysts. (B) Example of a 2D-COF, assembled by dynamic covalen...
Figure 7: (A) Examples of dynamic covalent chemistry used to synthesize organic cages. (B) Organic cages are ...
Figure 8: (A) Design and development of soluble, functionalized, robust organic cages. (B) Examples of modula...
Figure 9: (A) There are 13 metastable conformers (symmetry-corrected) for cage 1 due to permutations of amide...
Switchable molecular tweezers: design and applications
- Pablo Msellem,
- Maksym Dekthiarenko,
- Nihal Hadj Seyd and
- Guillaume Vives
Beilstein J. Org. Chem. 2024, 20, 504–539, doi:10.3762/bjoc.20.45
- the tweezers to selectively bind aromatic guests within a cavity, utilizing an induced fit mechanism. Subsequently, with the emergence and advancement of supramolecular chemistry, the field of molecular tweezers experienced rapid expansion, witnessing the development of rigid clips by Klärner [2] and
Graphical Abstract
Figure 1: Principle of switchable molecular tweezers.
Figure 2: Principle of pH-switchable molecular tweezers 1 [19].
Figure 3: a) pH-Switchable tweezers 2 substituted with alkyl chains as switchable lipids. b) Schematic depict...
Figure 4: Modification of spectral properties of 3 by controlled induction of Pt–Pt interactions.
Figure 5: Conformational switching of di(hydroxyphenyl)pyrimidine-based tweezer 4 upon alkylation or fluoride...
Figure 6: Hydrazone-based pH-responsive tweezers 5 for mesogenic modulation.
Figure 7: pH-Switchable molecular tweezers 6 bearing acridinium moieties.
Figure 8: a) Terpyridine and pyridine-hydrazone-pyridine analogs molecular tweezers and b) extended pyridine ...
Figure 9: Terpyridine-based molecular tweezers with M–salphen arms and their field of application. Figure 9 was adapt...
Figure 10: a) Terpyridine-based molecular tweezers for diphosphate recognition [48]; b) bishelicene chiroptical te...
Figure 11: Terpyridine-based molecular tweezers with allosteric cooperative binding.
Figure 12: Terpyridine-based molecular tweezers presenting closed by default conformation.
Figure 13: Pyridine-pyrimidine-pyridine-based molecular tweezers.
Figure 14: Coordination-responsive molecular tweezers based on nitrogen-containing ligands.
Figure 15: Molecular tweezers exploiting the remote bipyridine or pyridine binding to trigger the conformation...
Figure 16: Bipyridine-based molecular tweezers exploiting the direct s-trans to s-cis-switching for a) anion b...
Figure 17: a) Podand-based molecular tweezers [66,67]. b) Application of tweezers 32 for the catalytic allosteric reg...
Figure 18: Anion-triggered molecular tweezers based on calix[4]pyrrole.
Figure 19: Anion-triggered molecular tweezers.
Figure 20: a) Principle of the weak link approach (WLA) developed by Mirkin and its application to b) symmetri...
Figure 21: Molecular tweezers as allosteric catalyst in asymmetric epoxide opening [80].
Figure 22: Allosteric regulation of catalytic activity in ring-opening polymerization with double tweezers 41.
Figure 23: a) Conformational switching of 42 by intramolecular –S–S– bridge formation. b) Shift of conformatio...
Figure 24: a) Redox-active glycoluril-TTF tweezers 44. b) Mechanism of stepwise oxidation of said tweezers wit...
Figure 25: Mechanism of formation of the mixed-valence dimers of tweezers 45.
Figure 26: Mechanism of carbohydrate liberation upon redox-mediated conformation switching of 46.
Figure 27: a) The encapsulation properties of 47 as well as the DCTNF release process from its host–guest comp...
Figure 28: Redox-active bipyridinium-based tweezers. a) With a ferrocenyl hinge 49, b) with a propyl hinge 50 ...
Figure 29: Redox-active calix[4]arene porphyrin molecular tweezers.
Figure 30: a) Mechanism of the three orthogonal stimuli. b) Cubic scheme showing the eight different states of ...
Figure 31: Redox-controlled molecular gripper based on a diquinone resorcin[4]arene.
Figure 32: a) Shinkai's butterfly tweezers and their different host–guest properties depending on the isomer. ...
Figure 33: Cyclam-tethered tweezers and their different host–guest complexes depending on their configuration.
Figure 34: Azobenzene-based catalytic tweezers.
Figure 35: Photoswitchable PIEZO channel mimic.
Figure 36: Stilbene-based porphyrin tweezers for fullerene recognition.
Figure 37: Stiff-stilbene-based tweezers with urea or thiourea functional units for a) anion binding, b) anion...
Figure 38: Feringa’s photoswitchable organocatalyst (a) and different catalyzed reactions with that system (b)....
Figure 39: a) Irie and Takeshita’s thioindigo-based molecular tweezers. b) Family of hemithioindigo-based mole...
Figure 40: Dithienylethylene crown ether-bearing molecular tweezers reported by Irie and co-workers.
Inclusion complexes of the steroid hormones 17β-estradiol and progesterone with β- and γ-cyclodextrin hosts: syntheses, X-ray structures, thermal analyses and API solubility enhancements
- Alexios I. Vicatos,
- Zakiena Hoossen and
- Mino R. Caira
Beilstein J. Org. Chem. 2022, 18, 1749–1762, doi:10.3762/bjoc.18.184
- host–guest complexation, as a consequence of a mutual-induced fit of host and guest molecules [39]. With reference to γ-CD·PRO, the asymmetric unit (ASU) comprises three pairs of glucose rings that generate three complete γ-CD molecules when rotation of these units around the four-fold axis parallel to
Graphical Abstract
Figure 1: Chemical structures of 17β-estradiol (top) and progesterone (bottom).
Figure 2: The PXRD patterns of the β-CD·PRO complex produced via kneading (2:1), an isostructural β-CD comple...
Figure 3: The PXRD patterns of the γ-CD·PRO complex produced via kneading (3:2), an isostructural γ-CD comple...
Figure 4: (a) The crystal morphology of β-CD·BES recorded with polarised light. (b) The crystal morphology of...
Figure 5: (a) A representative DSC curve (n = 2) of β-CD·BES, with the respective TGA curve (n = 3); (b) a re...
Figure 6: Stereoscopic views of the host molecule and water oxygen atoms in the ASUs of (a) β-CD·BES and (b) ...
Figure 7: A stereoscopic view down the c-axis displaying the packing arrangement for β-CD·BES.
Figure 8: A stereoscopic view down the c-axis displaying the packing arrangement for β-CD·PRO.
Figure 9: A stereoscopic view of the host atoms and water oxygen atoms in the ASU of γ-CD·PRO.
Figure 10: The host atoms and water oxygen atoms of the ASU viewed down the c-axis, showing that the water mol...
Figure 11: The distinct packing arrangement of the repeat unit of the host molecules in γ-CD·PRO. The four-fol...
Figure 12: A stereoscopic view of γ-CD·PRO viewed down the c-axis, which displays the infinite channel packing...
Beyond ribose and phosphate: Selected nucleic acid modifications for structure–function investigations and therapeutic applications
- Christopher Liczner,
- Kieran Duke,
- Gabrielle Juneau,
- Martin Egli and
- Christopher J. Wilds
Beilstein J. Org. Chem. 2021, 17, 908–931, doi:10.3762/bjoc.17.76
Graphical Abstract
Figure 1: Structures of the chemically modified oligonucleotides (A) N3' → P5' phosphoramidate linkage, (B) a...
Scheme 1: Synthesis of a N3' → P5' phosphoramidate linkage by solid-phase synthesis. (a) dichloroacetic acid;...
Figure 2: Crystal structures of (A) N3' → P5' phosphoramidate DNA (PDB ID 363D) [71] and (B) amide (AM1) RNA in c...
Scheme 2: Synthesis of a phosphorodithioate linkage by solid-phase synthesis. (a) detritylation; (b) tetrazol...
Figure 3: Close-up view of a key interaction between the PS2-modified antithrombin RNA aptamer and thrombin i...
Scheme 3: Synthesis of the (S)-GNA thymine phosphoramidite from (S)-glycidyl 4,4'-dimethoxytrityl ether. (a) ...
Figure 4: Surface models of the crystal structures of RNA dodecamers with single (A) (S)-GNA-T (PDB ID 5V1L) [54]...
Figure 5: Structures of 2'-O-alkyl modifications. (A) 2'-O-methoxy RNA (2'-OMe RNA), (B) 2'-O-(2-methoxyethyl...
Scheme 4: Synthesis of the 2'-OMe uridine from 3',5'-O-(tetraisopropyldisiloxane-1,3-diyl)uridine. (a) Benzoy...
Scheme 5: Synthesis of the 2'-O-MOE uridine from uridine. (a) (PhO)2CO, NaHCO3, DMA, 100 °C; (b) Al(OCH2CH2OCH...
Figure 6: Structure of 2'-O-(2-methoxyethyl)-RNA (MOE-RNA). (A) View into the minor groove of an A-form DNA d...
Figure 7: Structures of locked nucleic acids (LNA)/bridged nucleic acids (BNA) modifications. (A) LNA/BNA, (B...
Scheme 6: Synthesis of the uridine LNA phosphoramidite. (a) i) NaH, BnBr, DMF, ii) acetic anhydride, pyridine...
Scheme 7: Synthesis of the 2'-fluoroarabinothymidine. (a) 30% HBr in acetic acid; (b) 2,4-bis-O-(trimethylsil...
Figure 8: Sugar puckers of arabinose (ANA) and arabinofluoro (FANA) nucleic acids compared with the puckers o...
Figure 9: Structures of C4'-modified nucleic acids. (A) 4'-methoxy, (B) 4'-(2-methoxyethoxy), (C) 2',4'-diflu...
Scheme 8: Synthesis of the 4'-F-rU phosphoramidite. (a) AgF, I2, dichloromethane, tetrahydrofuran; (b) NH3, m...
Scheme 9: Synthesis of the thymine FHNA phosphoramidite. (a) thymine, 1,8-diazabicyclo[5.4.0]undec-7-ene, ace...
Scheme 10: Synthesis of the thymine Ara-FHNA phosphoramidite. (a) i) trifluoromethanesulfonic anhydride, pyrid...
Figure 10: Crystal structures of (A) FHNA and (B) Ara-FHNA in modified A-form DNA decamers (PDB IDs 3Q61 and 3...
Bacterial terpene biosynthesis: challenges and opportunities for pathway engineering
- Eric J. N. Helfrich,
- Geng-Min Lin,
- Christopher A. Voigt and
- Jon Clardy
Beilstein J. Org. Chem. 2019, 15, 2889–2906, doi:10.3762/bjoc.15.283
- diphosphate (FPP, 9) or geranylgeranyl diphosphate (GGPP, 10, Figure 5a) [11][53]. Upon binding of the precursor, the TC undergoes conformational changes to seal the hydrophobic binding pocket [54]. This induced-fit mechanism locks the acyclic precursor into a defined, preorganized conformation that positions
Graphical Abstract
Figure 1: Examples of bioactive terpenoids.
Figure 2: Repetitive electrophilic and nucleophilic functionalities in terpene and type II PKS-derived polyke...
Figure 3: Abundance and distribution of bacterial terpene biosynthetic gene clusters as determined by genome ...
Figure 4: Terpenoid biosynthesis. Terpenoid biosynthesis is divided into two phases, 1) terpene scaffold gene...
Figure 5: Mechanisms for type I, type II, and type II/type I tandem terpene cyclases. a) Tail-to-head class I...
Figure 6: Functional TC characterization. a) Different terpenes were produced when hedycaryol (18) synthase a...
Figure 7: Selected examples of terpene modification by bacterial CYPs. a) Hydroxylation [89]. b) Carboxylation, h...
Figure 8: Off-target effects observed during heterologous expression of terpenoid BGCs. Unexpected oxidation ...
Figure 9: TC promiscuity and engineering. a) Spata-13,17-diene (39) synthase (SpS) can take C15 and C25 oligo...
Figure 10: Substrate promiscuity and engineering of CYPs. a) Selected examples from using a CYP library to oxi...
Figure 11: Engineering of terpenoid pathways. a) Metabolic network of terpenoid biosynthesis. Toxic intermedia...
Current understanding and biotechnological application of the bacterial diterpene synthase CotB2
- Ronja Driller,
- Daniel Garbe,
- Norbert Mehlmer,
- Monika Fuchs,
- Keren Raz,
- Dan Thomas Major,
- Thomas Brück and
- Bernhard Loll
Beilstein J. Org. Chem. 2019, 15, 2355–2368, doi:10.3762/bjoc.15.228
- [11]. Structural information on selina-4(15),7(11)-diene synthase (SdS), revealed that upon substrate binding by an induced fit mechanism, R178 changes its side chain conformation thereby approaching and interacting with the diphosphate function of the substrate analogue and forming a salt bridge to
- the neighboring D181 [60]. Moreover, a conformational change of the kink of the α-helix G1 moves the catalytically important G182 (effector) towards the active site. Initiated by this induced fit mechanism, the active site is being closed and the Michaelis complex is formed. In CotB2, R177 represents
Graphical Abstract
Figure 1: CotB1 synthesizes geranylgeranyl diphosphate (GGDP) 3 from the substrates dimethylallyl diphosphate...
Figure 2: The bacterial diterpene synthase CotB2wt·Mg2+3·F-Dola in the closed, active conformation (PDB-ID 6G...
Figure 3: Conformational changes of CotB2 upon ligand binding. Superposition of CotB2’s open (teal), pre-cata...
Figure 4: View into the active site of CotB2wt·Mg2+3·F-Dola [37] superimposed with CotB2wt·Mg2+B·GGSDP [36]. (A) The ...
Figure 5: View into the active site of CotB2wt·Mg2+3·F-Dola [37]. Identical view as in Figure 4. (A) The bound F-Dola rea...
Figure 6: The WXXXXXRY motif in protein sequences of diterpene TPS from different bacteria. Highlighted is th...
Scheme 1: Overview of the altered product portfolio as a result of introduced point mutations in the active s...
Scheme 2: Catalytic mechanism of CotB2, derived from isotope labeling experiments [34,35], density functional theory...
Figure 7: (A) The inner surface of the active site is shown in gray. The bound F-Dola reaction intermediate i...
Scheme 3: Variants of CotB2 open the route to a novel product portfolio with altered cyclic carbon skeletons,...
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
- an induced fit mechanism) and, as a consequence, they can form better defined complexes. We think that RSAs can serve similar purposes as CSAs and their adaptability features and possibilities of additional modifications of their lower rims can be highly beneficial for applications in modulation of
Graphical Abstract
Figure 1: Structures of the compounds used in this study and labelling scheme for NMR spectra.
Figure 2: Spectra of complexes [1(LysOMe)2], [1(ArgOMe)2], [1(HisOMe)2]: 1H NMR (a–g) and ROESY (h–j) in meth...
Figure 3: CD (a) and UV (b) spectra of complexes [1(LysOMe)2], [1(PheOMe)2], [1(ValOMe)2], [1(ArgOMe)2], and [...
Figure 4: DOSY spectra of 1 (a), [1(LysOMe)2] (b), [1(ArgOMe)2] (c), [1(HisOMe)2] (d) and [LysOMe + 1(LysOMe)2...
Figure 5: 1H NMR spectra of 1 (a), LysOMe (b), 1H NMR and DOSY spectra of [1(LysOMe)2] (insets show the shape...
Figure 6: 1H NMR spectra of (R)-2 (a); [1((R)-2] (b); [1 + 1((R)-2] (c) (insets show the shape of signals f, ...
Figure 7: 1H NMR and DOSY spectra of (R)-2 (a); [1(R)-2] (b) (inset show the shape signals f, DMSO-d6, 298K, ...
New standards for collecting and fitting steady state kinetic data
- Kenneth A. Johnson
Beilstein J. Org. Chem. 2019, 15, 16–29, doi:10.3762/bjoc.15.2
- kcat/Km. Keywords: computer simulation; data fitting; enzyme catalysis; induced-fit; Michaelis constant; specificity constant; Review When Henri, Michaelis and Menten derived the equation for steady state enzyme turnover, they chose to define the rate in terms of Vmax and the substrate dissociation
- dependent on conformational changes in the loop domain after substrate binding. The concept of induced-fit, where the substrate induces a change in enzyme structure to align catalytic residues, was first proposed in somewhat vague terms by Koshland [18] in an attempt to understand how an enzyme can exclude
- a smaller substrate than the preferred one. The induced-fit model proposes a two-step binding pathway in which the substrate first binds to an open form of the enzyme and then the enzyme closes leading to tighter binding and organization of catalytic residues. For decades debate raged as to whether
Graphical Abstract
Figure 1: Michaelis–Menten plot. The rate of product formation is plotted versus substrate concentration and ...
Figure 2: Fitting data to derive kcat and Km. A) Synthetic data were fit to a straight line and then the obse...
Figure 3: Fitting steady state data by simulation. A) Synthetic data from Figure 2A were fit globally to derive estima...
Figure 4: Fitting full progress curve data by simulation. A) Synthetic data were generated and then were fit ...
Figure 5: Optimal spacing of data points. Different scenarios for computing the distribution of data points f...
Figure 6: Free energy profiles. Free energy profiles are shown for a three step model with different rate con...
Figure 7: Free energy profile for DNA polymerization. Free energy profiles for a correct base pair (solid blu...
What contributes to an effective mannose recognition domain?
- Christoph P. Sager,
- Deniz Eriş,
- Martin Smieško,
- Rachel Hevey and
- Beat Ernst
Beilstein J. Org. Chem. 2017, 13, 2584–2595, doi:10.3762/bjoc.13.255
- from induced-fit binding, which also correlates to facilitated ligand dissociation: due to increased water exposure, the residence time of flexible ligand–lectin complexes is shortened [51]. A comparison of the apo crystal structures of BDCA-2 (A) and LecB (G) (PDB codes: 3WBP [73] and 1OUX
Graphical Abstract
Figure 1: CRDs of the analyzed crystal structures, with mannose pyranosyl units similarly aligned in each str...
Figure 2: A) The solvent exposed binding site of E-selectin interacting with sLex (PDB: 1G1T) [53]. B) The buried...
Figure 3: Dynamic mannose–receptor interactions (20 ns MD simulations), grouped according to the nature of th...
Figure 4: Desolvation of hydroxy groups. A) The desolvation cost of a single hydroxy group associated with th...
Figure 5: Model view of the binding site interactions of DC-SIGN (E) and BC2L-A (H) with water. A) The solven...
Figure 6: Thermodynamic fingerprints of sLex bound to E-selectin and n-heptyl α-D-mannoside bound to FimHLD (I...
Figure 7: Schematic overview of the conformational changes of FimH (I). FimH crystal structures, which corres...
Figure 8: Comparison of the holo (white) and apo (green, magenta) binding sites of LecB (G) and BDCA-2 (A), r...
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
- backbone movements as a result of ligand binding by an induced fit mechanism [174]. Two approaches that can be taken to account target flexibility are induced fit docking methods and ensemble-based screening methods. In induced fit docking the target protein structures are modeled as flexible, not rigid
- . They are able to accommodate induced fit that is caused by the ligand molecule binding to it. Schrodinger has introduced induced fit docking protocols through Glide [174]. RosettaLigand also accounts for target flexibility and shows success in predicting target–ligand poses. All residue side chain
- flexibility of the ligand binding pocket and target backbone flexibility are taken into account by RosettaLigand. This method uses a Monte-Carlo-based minimization algorithm and the Rosetta full-atom energy function [175]. Ensemble-based docking is an alternative method to induced fit docking. With ensemble
Graphical Abstract
Figure 1: Schematic representation of a computer-aided drug discovery (CADD) pipeline. CADD methods are broad...
Figure 2: FDA approved drugs Saquinavir and Amprenavir for the treatment of HIV infections. (a) The structure...
Figure 3: (a) The crystal structure showing the binding of Dorzolamide (orange) to carbonic anhydrase II (pur...
Figure 4: The best ligand binding site identified by SiteHound in HIV-1 protease. The ligand binding pocket i...
Figure 5: Binding mode prediction. The known inhibitor Dorzolamide is docked into Carbonic anhydrase II cryst...
Figure 6: The molecular structure of Raltegravir. Raltegravir is an FDA approved drug used in the treatment o...
Figure 7: An example alchemical thermodynamic cycle for a protein–ligand binding free energy calculation. The...
Figure 8: Schematic diagram showing the steps involved in QSAR. Known drug molecule activity and descriptor d...
Figure 9: A few drugs discovered with the help of ligand-based drug discovery tools. (a) Zolmitriptan: used a...
Is conformation a fundamental descriptor in QSAR? A case for halogenated anesthetics
- Maria C. Guimarães,
- Mariene H. Duarte,
- Josué M. Silla and
- Matheus P. Freitas
Beilstein J. Org. Chem. 2016, 12, 760–768, doi:10.3762/bjoc.12.76
- stable minima (ruled by intramolecular interactions) do not necessarily coincide with the bioconformation (ruled by enzyme induced fit). Consequently, a QSAR model based on two-dimensional chemical structures was built and exhibited satisfactory modeling/prediction capability and interpretability, then
- bioconformation is ruled by enzyme induced-fit; consequently, optimized and bioactive geometries are probably different to each other and, to obtain insight on the action mechanism of a drug and substituent effects, MD´s should not be generated over geometries optimized in a receptor-free environment. Efforts
Graphical Abstract
Figure 1: Optimized structures of isoflurane at the ωB97X-D/6-311++g(d,p) level (gas phase and explicit water...
Figure 2: Superimposed chemical structures used to generate the MIA descriptors with atoms colored according ...
Figure 3: Plot of actual vs predicted pMAC obtained from the MIA-QSAR model.
Figure 4: PCA plots for the mean-centered data of the 25 anesthetic haloethers.
A journey in bioinspired supramolecular chemistry: from molecular tweezers to small molecules that target myotonic dystrophy
- Steven C. Zimmerman
Beilstein J. Org. Chem. 2016, 12, 125–138, doi:10.3762/bjoc.12.14
- expanded as in molecular tweezer (clip) 17 (Figure 6), but interestingly, this compound is not active whereas the 1,8-substituted naphthalene is, providing a clip that works by an induced fit mechanism (structure not shown) [28]. The Nolte group went well beyond the simple molecular clip architecture with
Graphical Abstract
Figure 1: Photographs of Howard E. Zimmerman (July 5, 1926–February 12, 2012) (left) and Jane Zimmerman (née ...
Figure 2: (a) Schematic double helix fully saturated with intercalator (in purple) according to the neighbor ...
Figure 3: Bismethidium molecular tweezer 3 proposed as a graduate student at Columbia University, which was q...
Figure 4: Adenine 8 recognition by carboxylic acid containing tweezer 9 and a component analysis showing “com...
Figure 5: The first determination of the cost of freezing single bond rotations in a host–guest complex.
Figure 6: Glycouril-based molecular clip 16 and 17 developed by Nolte, an example of Harmata’s chiral Kagan-e...
Figure 7: Macrocyclic diacridines and dinaphthalene and the intercalation complexes they may form with one ch...
Figure 8: (a) Hairpin structure of CUGexp seen in (CUG)12. (b) U–U or T–T mismatches with no inter-strand hyd...
Figure 9: (a) CTG trinucleotide repeat expansion in DMPK gene produces expanded transcripts, one which CUGexp...
Inclusion complexes of 2-methoxyestradiol with dimethylated and permethylated β-cyclodextrins: models for cyclodextrin–steroid interaction
- Mino R. Caira,
- Susan A. Bourne,
- Halima Samsodien and
- Vincent J. Smith
Beilstein J. Org. Chem. 2015, 11, 2616–2630, doi:10.3762/bjoc.11.281
- structures to be described are the first for crystalline CD inclusion complexes of a representative bioactive steroid and as such, their molecular structures shed some light on the nature of cyclodextrin-steroid interactions, including the phenomenon of ‘mutually induced fit’ accompanying complexation. This
- induced fit’ of host and guest [1][26]. Enhancement of the solubility of 2ME by selected CDs One of the objectives of our study of the anticancer agent 2ME was to investigate methods of improving its aqueous solubility (So = 0.005 mg/cm3 at 25 °C [9]) which might in turn enhance its poor bioavailability
- four independent 1:1 host–guest units in the crystal display a variety of host distortions as well as guest conformational variation, reflecting a mutually induced fit accompanying complexation. The phenomenon of mutually induced fit was highlighted previously by Mavridis et al. for per-derivatised CDs
Graphical Abstract
Figure 1: Chemical structures of 2-methoxyestradiol (top) and the derivatised CDs DIMEB and TRIMEB (bottom).
Figure 2: The mode of inclusion of 2ME in the DIMEB cavity (a), space-filling side view of the complex with t...
Figure 3: Stereoview of the asymmetric unit in the crystal of the inclusion complex TRIMEB•2ME, with the host...
Figure 4: Space-filling images of complex unit A (as representative of units A and B) (a) and complex unit C ...
Figure 5: Inclination of the mean plane of the included 2ME molecule relative to the O4-heptagon of the host ...
Figure 6: Overlay of the steroid nucleus of 2ME (blue) in its own crystal with the refined models (grey) of t...
Figure 7: The TRIMEB·2ME complex unit D with two distinct (guest)O19-H···O(host) hydrogen bonds highlighted. ...
Figure 8: Dissolution profiles in water at 37 °C for untreated 2ME and various β-CD-containing preparations o...
Glycoluril–tetrathiafulvalene molecular clips: on the influence of electronic and spatial properties for binding neutral accepting guests
- Yoann Cotelle,
- Marie Hardouin-Lerouge,
- Stéphanie Legoupy,
- Olivier Alévêque,
- Eric Levillain and
- Piétrick Hudhomme
Beilstein J. Org. Chem. 2015, 11, 1023–1036, doi:10.3762/bjoc.11.115
- through an induced-fit mechanism with a recognition process on the basis of the size rather than the acceptor strength. We can suppose that the presence of stronger π-donor TTF sidewalls in clip 3 favorize donor–acceptor interactions and consequently the binding properties towards m-DNB. We have also
Graphical Abstract
Figure 1: Structures of molecular clips 1–4.
Scheme 1: Different routes developed for the synthesis of molecular clips 1–4.
Scheme 2: Reaction between diphenylglycoluril with 4,5-bis(bromomethyl)-2-thioxo-1,3-dithiole.
Figure 2: Intramolecular distances between TTF moieties from X-ray analysis for clips 2 and 3 and theoretical...
Figure 3: Cyclic voltammograms of molecular clips 1, 2, 3, 4 and F4-TCNQ at 10−3 M in 0.1 M TBAPF6/CH2Cl2/CH3...
Figure 4: Cyclic voltammograms of molecular clip 2 at different concentrations (left: 10−5 M; middle: 10−4 M;...
Scheme 3: Graphical representation of the stepwise oxidation of molecular clips 1, 2 and 3.
Scheme 4: Electrochemical mechanism used to simulate the CVs of molecular clips 1, 2 and 3.
Figure 5: Chemical oxidation of molecular clip 1 (10−4 M, CH2Cl2) using aliquots of NOSbF6 oxidizing reagent ...
Figure 6: Spectroelectrochemical experiment of molecular clip 1 during the first oxidation step at different ...
Figure 7: Molecular structure of molecular clip 15 and representation of its stepwise oxidation processes pro...
Figure 8: Molecular packing diagram of clips 2 (left) and 3 (right) obtained from X-ray analysis. A molecule ...
Figure 9: Left: Job plot analysis for DNB vs molecular clip 3 ([3 + DNB] = 10−3 M in o-C6H4Cl2 at 800 nm) at ...
Figure 10: UV–visible absorption spectra of F4-TCNQ (CH2Cl2, 10−5 M) upon titration with molecular clip 3 (CH2...
Figure 11: Redox interaction (left) and complexation (right) of F4-TCNQ with molecular clips 3 and 4.
Inclusion of trans-resveratrol in methylated cyclodextrins: synthesis and solid-state structures
- Lee Trollope,
- Dyanne L. Cruickshank,
- Terence Noonan,
- Susan A. Bourne,
- Milena Sorrenti,
- Laura Catenacci and
- Mino R. Caira
Beilstein J. Org. Chem. 2014, 10, 3136–3151, doi:10.3762/bjoc.10.331
- reported above clearly indicate a mutual induced fit when TMA forms an inclusion complex with RSV. This phenomenon of mutual induced fit has recently been cited as a frequent occurrence in biological systems, but a rare one for synthetic host–guest systems [13]. However, its occurrence in CD inclusion
- occurring in two of the three complex crystal structures investigated. Finally, as far as further new insights from the X-ray studies are concerned, we conclude that CD-RSV inclusion in the more flexible hosts TMA and TMB involves a mutual induced fit. The evidence for this is the flexibility displayed by
Graphical Abstract
Figure 1: Chemical structure of trans-resveratrol (1).
Figure 2: DSC traces of RSV (a), TMA (b), TMA–RSV physical mixture (PM) (c), TMA–RSV preparation by kneading ...
Figure 3: TG (red) and DSC (blue) traces for the hydrated TMA·RSV complex (top), and hot stage micrographs sh...
Figure 4: The two symmetry-independent complex units of TMA·RSV·6.25H2O (A and B), with only the major compon...
Figure 5: Representative atomic labelling for the ordered RSV molecule A (blue) present in host A and the two...
Figure 6: Space-filling representations of the two independent complex units A (a) and B (b) of the complex T...
Figure 7: Crystal packing for the complex TMA·RSV·6.25H2O projected down [010].
Figure 8: The components of the disorder model for RSV in its inclusion complex with TMB (s.o.f. = 0.73 for t...
Figure 9: The asymmetric unit in the crystal of TMB·RSV·5.6H2O (a), and the non-H atom and methylglucose ring...
Figure 10: Space-filling model of the inclusion complex TMB·RSV·5.6H2O showing the inclusion of the RSV molecu...
Figure 11: Packing arrangement in the crystal of TMB·RSV·5.6H2O viewed down [010] (a) and [100] (b). Hydrogen ...
Figure 12: Structure of the host–guest complex DMB·RSV·4.0H2O (a), ring and atomic nomenclature for the host m...
Figure 13: Space-filling model of the inclusion complex DMB·RSV·4.0H2O showing the encapsulation of part of th...
Figure 14: Stereoview of two DMB·RSV·4.0H2O complex units related by a unit translation along the crystal a-ax...
Figure 15: Projections of the crystal structure of the complex DMB·RSV·4H2O along [100] (a) and [010] (b). Hyd...
Figure 16: Solubility of RSV as a function of [β-CD] (blue) and [γ-CD] (red) at 25 °C.
Figure 17: Solubility of RSV as a function of the concentrations of TMB (light blue), DMB (red), HP-β-CD (gree...
The chemistry of isoindole natural products
- Klaus Speck and
- Thomas Magauer
Beilstein J. Org. Chem. 2013, 9, 2048–2078, doi:10.3762/bjoc.9.243
- mimicking several aspects of the adenosine moiety, by induced-fit structural changes and the conformational flexibility of the enzyme residues (Figure 3). Together with several related analogues, 26 displays significant cytotoxic and antiproliferative effects [19]. Due to the key role of protein kinases in
Graphical Abstract
Figure 1: a) Structural features and b) selected examples of non-natural congeners.
Scheme 1: Synthesis of isoindole 18.
Scheme 2: Staining amines with 1,4-diketone 19 (R = H).
Figure 2: Representative members of the indolocarbazole alkaloid family.
Figure 3: Staurosporine (26) bound to the adenosine-binding pocket [19] (from pdb1stc).
Figure 4: Structure of imatinib (34) and midostaurin (35).
Scheme 3: Biosynthesis of staurosporine (26).
Scheme 4: Wood’s synthesis of K-252a via the common intermediate 48.
Scheme 5: Synthesis of 26, 27, 49 and 50 diverging from the common intermediate 48.
Figure 5: Selected members of the cytochalasan alkaloid family.
Scheme 6: Biosynthesis of chaetoglobosin A (57) [56].
Scheme 7: Synthesis of cytochalasin D (70) by Thomas [63].
Scheme 8: Synthesis of L-696,474 (78).
Scheme 9: Synthesis of aldehyde 85 (R = TBDPS).
Scheme 10: Synthesis of (+)-aspergillin PZ (79) by Tanis.
Figure 6: Representative Berberis alkaloids.
Scheme 11: Proposed biosynthetic pathway to chilenine (93).
Scheme 12: Synthesis of magallanesine (97) by Danishefsky [84].
Scheme 13: Kurihara’s synthesis of magallanesine (85).
Scheme 14: Proposed biosynthesis of 113, 117 and 125.
Scheme 15: DNA lesion caused by aristolochic acid I (117) [102].
Scheme 16: Snieckus’ synthesis of piperolactam C (131).
Scheme 17: Synthesis of aristolactam BII (104).
Figure 7: Representative cularine alkaloids.
Scheme 18: Proposed biosynthesis of 136.
Scheme 19: The syntheses of 136 and 137 reported by Castedo and Suau.
Scheme 20: Synthesis of 136 by Couture.
Figure 8: Representative isoindolinone meroterpenoids.
Scheme 21: Postulated biosynthetic pathway for the formation of 156 (adopted from George) [143].
Scheme 22: Synthesis of stachyflin (156) by Katoh [144].
Figure 9: Selected examples of spirodihydrobenzofuranlactams.
Scheme 23: Synthesis of stachybotrylactam I (157).
Scheme 24: Synthesis of pestalachloride A (193) by Schmalz.
Scheme 25: Proposed mechanism for the BF3-catalyzed metal-free carbonyl–olefin metathesis [149].
Scheme 26: Preparation of the isoindoline core of muironolide A (204).
Scheme 27: Proposed biosynthesis of 208.
Scheme 28: Model for the biosynthesis of 215 and 217.
Scheme 29: Synthesis of lactonamycin (215) and lactonamycin Z (217).
Figure 10: Hetisine alkaloids 225–228.
Scheme 30: Biosynthetic proposal for the formation of the hetisine core [167].
Scheme 31: Synthesis of nominine (225).
Chemical–biological characterization of a cruzain inhibitor reveals a second target and a mammalian off-target
- Jonathan W. Choy,
- Clifford Bryant,
- Claudia M. Calvet,
- Patricia S. Doyle,
- Shamila S. Gunatilleke,
- Siegfried S. F. Leung,
- Kenny K. H. Ang,
- Steven Chen,
- Jiri Gut,
- Juan A. Oses-Prieto,
- Jonathan B. Johnston,
- Michelle R. Arkin,
- Alma L. Burlingame,
- Jack Taunton,
- Matthew P. Jacobson,
- James M. McKerrow,
- Larissa M. Podust and
- Adam R. Renslo
Beilstein J. Org. Chem. 2013, 9, 15–25, doi:10.3762/bjoc.9.3
- from the crystal structure of TcCYP51 to compare predicted binding modes of 4 and (R)-5. The two ligands were docked by using the induced-fit docking protocol with Glide XP [34], and the models were further refined by minimizing the energies of the ligand and surrounding residues (within 5 Å of ligand
Graphical Abstract
Figure 1: Chemical structures of vinylsulfone-based cruzain inhibitors 1–4, known TcCYP51 inhibitor 5, dihydr...
Figure 2: Computational docking models. (A) Predicted binding modes of 4 and (R)-5 bound to TcCYP51. For 4, t...
Figure 3: Synthesis of the additional control compound 6–8, the reduced forms of analogues 1, 3, and 4 respec...
Figure 4: GC/MS analysis of lipid extracts from T. cruzi parasites treated with test compounds. DMSO and K777...
Figure 5: Chemical structures of compound 9, a “clickable” activity-based probe based on 1 and complementary ...
Figure 6: Competitive labeling of host cell (C2C12) proteins. Intact cells were labeled with probe 9 followin...
Figure 7: MS/MS spectrum of the tryptic peptide S264-R281 from mouse cathepsin B, identified in pull-down exp...
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
Graphical Abstract
Scheme 1: Biphenyl-capped (5), naphthalene-capped (6), and naphthalene-appended γ-cyclodextrin (7).
Figure 1: UV–vis spectral changes of 0.2 mM AC upon increasing the concentration of 7 in pH 9 phosphate buffe...
Figure 2: Circular dichroism spectra of 7 (0.2 mM) in the presence of 0, 0.0083, 0.025, 0.048, 0.071, 0.093, ...
Figure 3: Circular dichroism spectra of 6 (0.2 mM) in the presence of 0, 0.0083, 0.025, 0.048, 0.071, 0.093, ...
Figure 4: UV–vis spectra of AC (black dashed line) and 7 (red dashed line) and fluorescence spectra of 7 (0.0...
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
- polymeric hosts features two prominent advantages. On one hand, it simplifies the complex recognition interface to isolated 1:1 complexes between monomeric binding sites and single complementary amino acid residues, while simultaneously allowing for an extensive induced-fit process of the linear polymer on
- slope of the binding curve. Graphical illustration of the potential binding mode on hemoglobin tetramer (represented as electrostatic potential surface, lysines = blue). The RAFT copolymer T20CH15 (tetrazole rings = red) undergoes an extensive induced fit procedure on the protein surface maximizing
Graphical Abstract
Figure 1: Structures of monomers 1–7 and chain transfer agent 8 used in the RAFT polymerizations.
Figure 2: a) Second derivative UV–vis spectra [17-19] observed during a full titration of a stock solution of RAFT c...
Figure 3: Isothermal calorimetric binding curves for selected polymer/protein host–guest pairs. a) Typical bi...
Figure 4: Graphical illustration of the potential binding mode on hemoglobin tetramer (represented as electro...
Molecular recognition of organic ammonium ions in solution using synthetic receptors
- Andreas Späth and
- Burkhard König
Beilstein J. Org. Chem. 2010, 6, No. 32, doi:10.3762/bjoc.6.32
Graphical Abstract
Figure 1: Biologically important amines and quaternary ammonium salts: histamine (1), dopamine (2) and acetyl...
Figure 2: Crown ether 18-crown-6.
Figure 3: Conformations of 18-crown-6 (4) in solvents of different polarity.
Figure 4: Binding topologies of the ammonium ion depending on the crown ring size.
Figure 5: A “pseudorotaxane” structure consisting of 24-crown-8 and a secondary ammonium ion (5); R = Ph.
Figure 6: Typical examples of azacrown ethers, cryptands and related aza macrocycles.
Figure 7: Binding of ammonium to azacrown ethers and cryptands [111-113].
Figure 8: A 19-crown-6-ether with decalino blocking groups (11) and a thiazole-dibenzo-18-crown-6-ether (12).
Figure 9: 1,3-Bis(6-oxopyridazin-1-yl)propane derivatives 13 and 14 by Campayo et al.
Figure 10: Fluorescent azacrown-PET-sensors based on coumarin.
Figure 11: Two different pyridino-cryptands (17 and 18) compared to a pyridino-crown (19); chiral ammonium ion...
Figure 12: Pyridino-18-crown-6 ligand (21), a similar acridino-18-crown-6 ligand (22) and a structurally relat...
Figure 13: Ciral pyridine-azacrown ether receptors 24.
Figure 14: Chiral 15-crown-5 receptors 26 and an analogue 18-crown-6 ligand 27 derived from amino alcohols.
Figure 15: C2-symmetric chiral 18-crown-6 amino alcohol derivatives 28 and related macrocycles.
Figure 16: Macrocycles with diamide-diester groups (30).
Figure 17: C2-symmetric chiral aza-18-crown-6 ethers (31) with phenethylamine residues.
Figure 18: Chiral C-pivot p-methoxy-phenoxy-lariat ethers.
Figure 19: Chiral lariat crown ether 34.
Figure 20: Sucrose-based chiral crown ether receptors 36.
Figure 21: Permethylated fructooligosaccharide 37 showing induced-fit chiral recognition.
Figure 22: Biphenanthryl-18-crown-6 derivative 38.
Figure 23: Chiral lariat crown ethers derived from binol by Fuji et al.
Figure 24: Chiral phenolic crown ether 41 with “aryl chiral barriers” and guest amines.
Figure 25: Chiral bis-crown receptor 43 with a meso-ternaphthalene backbone.
Figure 26: Chromogenic pH-dependent bis-crown chemosensor 44 for diamines.
Figure 27: Triamine guests for binding to receptor 44.
Figure 28: Chiral bis-crown phenolphthalein chemosensors 46.
Figure 29: Crown ether amino acid 47.
Figure 30: Luminescent receptor 48 for bis-alkylammonium guests.
Figure 31: Luminescent CEAA (49a), a bis-CEAA receptor for amino acids (49b) and the structure of lysine bindi...
Figure 32: Luminescent CEAA tripeptide for binding small peptides.
Figure 33: Bis crown ether 51a self assembles co-operatively with C60-ammonium ion 51b.
Figure 34: Triptycene-based macrotricyclic dibenzo-[24]-crown-8 ether host 52 and guests.
Figure 35: Copper imido diacetic acid azacrown receptor 53a and the suggested His-Lys binding motif; a copper ...
Figure 36: Urea (54) and thiourea (55) benzo crown receptor for transport and extraction of amino acids.
Figure 37: Crown pyryliums ion receptors 56 for amino acids.
Figure 38: Ditopic sulfonamide bridged crown ether receptor 57.
Figure 39: Luminescent peptide receptor 58.
Figure 40: Luminescent receptor 59 for the detection of D-glucosamine hydrochloride in water/ethanol and lumin...
Figure 41: Guanidinium azacrown receptor 61 for simple amino acids and ditopic receptor 62 with crown ether an...
Figure 42: Chiral bicyclic guanidinium azacrown receptor 63 and similar receptor 64 for the enantioselective t...
Figure 43: Receptors for zwitterionic species based on luminescent CEAAs.
Figure 44: 1,10-Azacrown ethers with sugar podand arms and the anticancer agent busulfan.
Figure 45: Benzo-18-crown-6 modified β-cyclodextrin 69 and β-cyclodextrin functionalized with diaza-18-crown-6...
Figure 46: Receptors for colorimetric detection of primary and secondary ammonium ions.
Figure 47: Porphyrine-crown-receptors 72.
Figure 48: Porphyrin-crown ether conjugate 73 and fullerene-ammonium ion guest 74.
Figure 49: Calix[4]arene (75a), homooxocalix[4]arene (75b) and resorcin[4]arene (75c) compared (R = H, alkyl c...
Figure 50: Calix[4]arene and ammonium ion guest (R = H, alkyl, OAcyl etc.), possible binding sites; A: co-ordi...
Figure 51: Typical guests for studies with calixarenes and related molecules.
Figure 52: Lower rim modified p-tert-butylcalix[5]arenes 82.
Figure 53: The first example of a water soluble calixarene.
Figure 54: Sulfonated water soluble calix[n]arenes that bind ammonium ions.
Figure 55: Displacement assay for acetylcholine (3) with a sulfonato-calix[6]arene (84b).
Figure 56: Amino acid inclusion in p-sulfonatocalix[4]arene (84a).
Figure 57: Calixarene receptor family 86 with upper and lower rim functionalization.
Figure 58: Calix[6]arenes 87 with one carboxylic acid functionality.
Figure 59: Sulfonated calix[n]arenes with mono-substitution at the lower rim systematically studied on their r...
Figure 60: Cyclotetrachromotropylene host (91) and its binding to lysine (81c).
Figure 61: Calixarenes 92 and 93 with phosphonic acids groups.
Figure 62: Calix[4]arene tetraphosphonic acid (94a) and a double bridged analogue (94b).
Figure 63: Calix[4]arene tetraphosphonic acid ester (92c) for surface recognition experiments.
Figure 64: Calixarene receptors 95 with α-aminophosphonate groups.
Figure 65: A bridged homocalix[3]arene 95 and a distally bridged homocalix[4]crown 96.
Figure 66: Homocalix[3]arene ammonium ion receptor 97a and the Reichardt’s dye (97b) for colorimetric assays.
Figure 67: Chromogenic diazo-bridged calix[4]arene 98.
Figure 68: Calixarene receptor 99 by Huang et al.
Figure 69: Calixarenes 100 reported by Parisi et al.
Figure 70: Guest molecules for inclusion in calixarenes 100: DAP × 2 HCl (101a), APA (101b) and Lys-OMe × 2 HC...
Figure 71: Different N-linked peptido-calixarenes open and with glycol chain bridges.
Figure 72: (S)-1,1′-Bi-2-naphthol calixarene derivative 104 published by Kubo et al.
Figure 73: A chiral ammonium-ion receptor 105 based on the calix[4]arene skeleton.
Figure 74: R-/S-phenylalaninol functionalized calix[6]arenes 106a and 106b.
Figure 75: Capped homocalix[3]arene ammonium ion receptor 107.
Figure 76: Two C3 symmetric capped calix[6]arenes 108 and 109.
Figure 77: Phosphorous-containing rigidified calix[6]arene 110.
Figure 78: Calix[6]azacryptand 111.
Figure 79: Further substituted calix[6]azacryptands 112.
Figure 80: Resorcin[4]arene (75c) and the cavitands (113).
Figure 81: Tetrasulfonatomethylcalix[4]resorcinarene (114).
Figure 82: Resorcin[4]arenes (115a/b) and pyrogallo[4]arenes (115c, 116).
Figure 83: Displacement assay for acetylcholine (3) with tetracyanoresorcin[4]arene (117).
Figure 84: Tetramethoxy resorcinarene mono-crown-5 (118).
Figure 85: Components of a resorcinarene based displacement assay for ammonium ions.
Figure 86: Chiral basket resorcin[4]arenas 121.
Figure 87: Resorcinarenes with deeper cavitand structure (122).
Figure 88: Resorcinarene with partially open deeper cavitand structure (123).
Figure 89: Water-stabilized deep cavitands with partially structure (124, 125).
Figure 90: Charged cavitands 126 for tetralkylammonium ions.
Figure 91: Ditopic calix[4]arene receptor 127 capped with glycol chains.
Figure 92: A calix[5]arene dimer for diammonium salt recognition.
Figure 93: Calixarene parts 92c and 129 for the formation molecular capsules.
Figure 94: Encapsulation of a quaternary ammonium cation by two resorcin[4]arene molecules (NMe4+@[75c]2 × Cl−...
Figure 95: Encapsulation of a quaternary ammonium cation by six resorcin[4]arene molecules (NMe3D+@[130]6 × Cl−...
Figure 96: Structure and schematic of cucurbit[6]uril (CB[6], 131a).
Figure 97: Cyclohexanocucurbit[6]uril (CB′[6], 132) and the guest molecule spermine (133).
Figure 98: α,α,δ,δ-Tetramethylcucurbit[6]uril (134).
Figure 99: Structure of the cucurbituril-phthalhydrazide analogue 135.
Figure 100: Organic cavities for the displacement assay for amine differentiation.
Figure 101: Displacement assay methodology for diammonium- and related guests involving cucurbiturils and some ...
Figure 102: Nor-seco-Cucurbituril (±)-bis-ns-CB[6] (140) and guest molecules.
Figure 103: The cucurbit[6]uril based complexes 141 for chiral discrimination.
Figure 104: Cucurbit[7]uril (131c) and its ferrocene guests (142) opposed.
Figure 105: Cucurbit[7]uril (131c) guest inclusion and representative guests.
Figure 106: Cucurbit[7]uril (131c) binding to succinylcholine (145) and different bis-ammonium and bis-phosphon...
Figure 107: Paraquat-cucurbit[8]uril complex 149.
Figure 108: Gluconuril-based ammonium receptors 150.
Figure 109: Examples of clefts (151a), tweezers (151b, 151c, 151d) and clips (151e).
Figure 110: Kemp’s triacid (152a), on example of Rebek’s receptors (152b) and guests.
Figure 111: Amino acid receptor (154) by Rebek et al.
Figure 112: Hexagonal lattice designed hosts by Bell et al.
Figure 113: Bell’s amidinium receptor (156) and the amidinium ion (157).
Figure 114: Aromatic phosphonic acids.
Figure 115: Xylene phosphonates 159 and 160a/b for recognition of amines and amino alcohols.
Figure 116: Bisphosphonate recognition motif 161 for a colorimetric assay with alizarin complexone (163) for ca...
Figure 117: Bisphosphonate/phosphate clip 164 and bisphosphonate cleft 165.
Figure 118: N-Methylpyrazine 166a, N-methylnicotinamide iodide (166b) and NAD+ (166c).
Figure 119: Bisphosphate cavitands.
Figure 120: Bisphosphonate 167 of Schrader and Finocchiaro.
Figure 121: Tweezer 168 for noradrenaline (80b).
Figure 122: Different tripods and heparin (170).
Figure 123: Squaramide based receptors 172.
Figure 124: Cage like NH4+ receptor 173 of Kim et al.
Figure 125: Ammonium receptors 174 of Chin et al.
Figure 126: 2-Oxazolin-based ammonium receptors 175a–d and 176 by Ahn et al.
Figure 127: Racemic guest molecules 177.
Figure 128: Tripods based on a imidazole containing macrocycle (178) and the guest molecules employed in the st...
Figure 129: Ammonium ion receptor 180.
Figure 130: Tetraoxa[3.3.3.3]paracyclophanes 181 and a cyclophanic tetraester (182).
Figure 131: Peptidic bridged paraquat-cyclophane.
Figure 132: Shape-selective noradrenaline host.
Figure 133: Receptor 185 for binding of noradrenaline on surface layers from Schrader et al.
Figure 134: Tetraphosphonate receptor for binding of noradrenaline.
Figure 135: Tetraphosphonate 187 of Schrader and Finocchiaro.
Figure 136: Zinc-Porphyrin ammonium-ion receptors 188 and 189 of Mizutani et al.
Figure 137: Zinc porphyrin receptor 190.
Figure 138: Zinc porphyrin receptors 191 capable of amino acid binding.
Figure 139: Zinc-porphyrins with amino acid side chains for stereoinduction.
Figure 140: Bis-zinc-bis-porphyrin based on Tröger’s base 193.
Figure 141: BINAP-zinc-prophyrin derivative 194 and it’s guests.
Figure 142: Bisaryl-linked-zinc-porphyrin receptors.
Figure 143: Bis-zinc-porphyrin 199 for diamine recognition and guests.
Figure 144: Bis-zinc-porphyrin crown ether 201.
Figure 145: Bis-zinc-porphyrin 202 for stereodiscrimination (L = large substituent; S = small substituent).
Figure 146: Bis-zinc-porphyrin[3]rotaxane and its copper complex and guests.
Figure 147: Dien-bipyridyl ligand 206 for co-ordination of two metal atoms.
Figure 148: The ligand and corresponding tetradentate co-complex 207 serving as enantioselective receptor for a...
Figure 149: Bis(oxazoline)–copper(II) complex 208 for the recognition of amino acids in aqueous solution.
Figure 150: Zinc-salen-complexes 209 for the recognition tertiary amines.
Figure 151: Bis(oxazoline)–copper(II) 211 for the recognition of amino acids in aqueous solution.
Figure 152: Zn(II)-complex of a C2 terpyridine crown ether.
Figure 153: Displacement assay and receptor for aspartate over glutamate.
Figure 154: Chiral complex 214 for a colorimetric displacement assay for amino acids.
Figure 155: Metal complex receptor 215 with tripeptide side arms.
Figure 156: A sandwich complex 216 and its displaceable dye 217.
Figure 157: Lanthanide complexes 218–220 for amino acid recognition.
Figure 158: Nonactin (221), valinomycin (222) and vancomycin (223).
Figure 159: Monesin (224a) and a chiral analogue for enantiodiscrimination of ammonium guests (224b).
Figure 160: Chiral podands (226) compared to pentaglyme-dimethylether (225) and 18-crown-6 (4).
Figure 161: Lasalocid A (228).
Figure 162: Lasalocid derivatives (230) of Sessler et al.
Figure 163: The Coporphyrin I tetraanion (231).
Figure 164: Linear and cyclic peptides for ammonium ion recognition.
Figure 165: Cyclic and bicyclic depsipeptides for ammonium ion recognition.
Figure 166: α-Cyclodextrin (136a) and novocaine (236).
Figure 167: Helical diol receptor 237 by Reetz and Sostmann.
Figure 168: Ammonium binding spherand by Cram et al. (238a) and the cyclic[6]metaphenylacetylene 238b in compar...
Figure 169: Receptor for peptide backbone and ammonium binding (239).
Figure 170: Anion sensor principle with 3-hydroxy-2-naphthanilide of Jiang et al.
Figure 171: 7-bromo-3-hydroxy-N-(2-hydroxyphenyl)naphthalene 2-carboxamide (241) and its amine binding.
Figure 172: Naturally occurring catechins with affinity to quaternary ammonium ions.
Figure 173: Spiropyran (244) and merocyanine form (244a) of the amino acid receptors of Fuji et al.
Figure 174: Coumarin aldehyde (245) and its iminium species with amino acid bound (245a) by Glass et al.
Figure 175: Coumarin aldehyde appended with boronic acid.
Figure 176: Quinolone aldehyde dimers by Glass et al.
Figure 177: Chromogenic ammonium ion receptors with trifluoroacetophenone recognition motifs.
Figure 178: Chromogenic ammonium ion receptor with trifluoroacetophenone recognition motif bound on different m...
