Search

Cyclic peptide diversity has been broadened by elaborating the A3-macrocyclization to include various di-amino carboxylate components with different Ne-amine substituents. Triple-bond reduction provided new cyclic peptide macrocycles with Z-olefin and completely saturated structures. Moreover, cyclic azasulfurylpeptides were prepared by exchanging the propargylglycine (Pra) component for an amino sulfamide surrogate. Examination of such diversity-oriented methods on potent cyclic azapeptide modulators of the cluster of differentiation 36 receptor (CD36) identified the importance of the triple bond as well as the Ne-allyl lysine and azaPra residues for high CD36 binding affinity. Cyclic azapeptides which engaged CD36 effectively reduced pro-inflammatory nitric oxide and downstream cytokine and chemokine production in macrophages stimulated with a Toll-like receptor-2 agonist. Studying the triple bond and amine components in the multiple-component A3-macrocyclization has given a diverse array of macrocycles and pertinent information to guide the development of ideal CD36 modulators with biomedical potential for curbing macrophage-driven inflammation.

Here, we report a method for the one-pot ribosomal synthesis of macrocyclic depsipeptides. This method is based on a Ser-Pro-Cys-Gly (SPCG) motif discovered by in vitro selection of peptides for the function of self-acylation in the presence of a thioester acyl donor, which forms an O-acyl isopeptide bond via intramolecular S-to-O acyl transfer. Ribosomal synthesis of linear peptides containing the SPCG motif and a backbone "acyl donor" thioester at a downstream position results in spontaneous conversion to the corresponding cyclic depsipeptides (CDPs) in a nearly independent manner of ring size and sequence context. Mutational analysis of the SPCG motif revealed that the P and G residues are dispensable to some extent, but the arrangement of residues in SXCX is crucial for efficient acyl transfer, e.g., CPSG is much less efficient. Finally, one-pot ribosomal synthesis of macrocyclic depsipeptides with various ring sizes and sequences has been demonstrated. This synthetic method can facilitate the ribosomal construction of highly diverse CDP libraries for the discovery of de novo bioactive CDPs.

A Series of new tacrine analogs were designed, synthesized, characterized by respective spectral data and evaluated for cholinesterase inhibitory activity to be useful in Alzheimer’s disease. Most of the synthesized compounds showed good in vitro inhibitory activities toward acetyl cholinesterase (AChE) and butyrylcholinesterase (BuChE) enzymes. Among the compounds, 6i, 6o and 6r with increased saturated carboxylic ring size attached to the pyridine moiety and having 3,4-dihydroxy, 3,4,5-trimethoxy substituents on the aromatic ring attached at the stereogenic center have shown equal potency to that of tacrine with IC50values 0.65 ± 0.06, 1.32 ± 0.02 and 0.85 ± 0.05, 1.65 ± 0.12 and 0.92 ± 0.03, 1.91 ± 0.12 μM against AChE and BuChE, respectively. Standard drug tacrine exhibited IC50 values of 0.47 ± 0.02 and 0.65 ± 0.08, while Donepezil showed IC50 0.71 ± 0.06 and 0.31 ± 0.04 μM against AChE and BuChE, respectively. Docking studies of all the molecules disclosed close hydrogen bond interactions with the binding site.

Bioactive flax cyclic octa- and nona-peptides containing single methionine (Met) and its oxidized forms were treated under mild alkaline conditions to perform regio-selective epimerization. Cyclic peptide epimerization at the Met α-proton in a single chemical step has not been reported previously. The epimerization rate varies among Met oxidation states and ring size. These d-amino isomers along with the developed Met alkylation strategy will enable an approach to novel chemical functionalization of biomolecules. The amino acid configurations were confirmed by Marfey derivatizations, and cytotoxicity studies show the difference among the isomers. These d-amino analogs can act as a potential biomarker in plant protein processing and biomedical applications.

The currently limited portfolio of volatile organoselenium compounds used for atomic layer deposition (ALD) has been extended by designing and preparing a series of four-, five- and six-membered cyclic silylselenides. Their fundamental properties were tailored by alternating the ring size, the number of embedded Se atoms and the used peripheral alkyl chains. In contrast to former preparations based on formation of sodium or lithium selenides, the newly developed synthetic method utilizes a direct and easy reaction of elemental selenium with chlorosilanes. Novel 2,2,4,4-tetraisopropyl-1,3,2,4-diselenadisiletane, which features good trade-off between chemical/thermal stability and reactivity, has been successfully used for gas-to-solid phase reaction with MoCl5 affording MoSe2. A thorough characterization of the as-deposited 2D MoSe2 flakes revealed its out-of-plane orientation and high purity. Hence, the developed four-membered cyclic silylselenide turned out to be well-suited Se-precursor for ALD of MoSe2. Pro depozici atomárních vrstev byla navržena a připravena série čtyř-, pěti- a šestičlenných cyklických silylselenidů. Nově vyvinutá metoda syntézy využila přímou a jednoduchou reakci selenu s chlorsilany. Vyvinuté čtyřčlenné cyklické silylselenidy se ukázaly jako vhodné prekurzory pro ALD sloučeniny MoSe2.

The copolymerization of an ε-substituted ε-lactone, menthide (MI), and a range of nonsubstituted lactones (6-, 7-, 8-, and 9-membered rings) was investigated in order to determine the factors that affect the sequencing of the MI copolymers. Analysis by quantitative 13C NMR spectroscopy showed the copolymerization of MI with a nonsubstituted lactone of ring size 7 or less produced a randomly sequenced copolymer, as a consequence of the smaller lactone polymerizing first and undergoing rapid transesterification as MI was incorporated. Conversely, copolymerization with larger ring lactones (ring size 8 and above) produced block-like copolymers as a consequence of MI polymerizing initially, which does not undergo rapid transesterification side reactions during the incorporation of the second monomer. Terpolymerizations of a small ring lactone, macrolactone, and menthide demonstrated methods of producing lactone terpolymers with different final sequences, depending on when the small ring lactone was injected into the reaction mixture.\ud \ud

DAMASCENOLIDETM [1, 4-(4-methylpent-3-en-1-yl)furan-2(5H)-one], which has a citrus-like odor, is an important aroma component of roses. We have previously reported on the synthesis and odor evaluation of 24 analogs of 1 as part of our new aroma compound developing project. To accumulate more information on structure–odor relationships, 10 more promising analogs such as dimethylated and cyclopropanated analogs were synthesized and subjected to odor evaluation. As a result, it was found that dimethylation of the furanone ring affected the odor. It was also found that cyclopropanation of 1 affected the odor, whereas cyclopropanation of the double bond isomer of 1 did not significantly affect the odor. The effects on the odor caused by ring size expansion and replacement of the side chain were also investigated.

This is the peer reviewed version of the following article: Mothe, S. R.; Tan, J. S. J.; Chennamaneni, L. R.; Aidil, F.; Su, Y.; Kang, H. C.; Lim, F. C. H.; Thoniyot, P., A systematic investigation of the ring size effects on the free radical ring-opening polymerization (rROP) of cyclic ketene acetal (CKA) using both experimental and theoretical approach. Journal of Polymer Science DOI: 10.1002/pol.20200210., which has been published in final form at https://doi.org/10.1002/pol.20200210. This article may be used for non-commercial purposes in accordance with Wiley Terms and Conditions for Use of Self-Archived Versions.

Planar chiral zigzag-type [8]- and [12]cyclophenylene (CP) belts have been synthesized in good yields with high ee values of 98% and 83%, respectively, by the rhodium-catalyzed enantioselective intramolecular sequential cyclotrimerizations of the corresponding cyclic polyynes. The observed high enantioselectivity arises from the regioselective formation of a rhodacycle intermediate from an unsymmetric triyne unit. The X-ray crystal structural analysis of the racemic planar chiral zigzag-type [8]CP belt revealed that the uneven molecules mesh with each other to form a one-dimensional columnar packing structure, in which one column contains single enantiomers, giving two types of chiral columns [(S)- and (R)-form columns] arranged alternately. The ring strain of the zigzag-type [8]CP belt was smaller than that of the armchair-type [8]CPP belt despite its smaller ring size, due to the presence of the strain-relieving m-terphenyl moieties. The effect of the number of the benzene rings of the zigzag-type CP belts on absorption and emission peaks was small due to interruption of π-conjugation at the m-phenylene moieties. However, the bending effect on the absolute fluorescence quantum yield as well as absorption and emission peaks was significant. Concerning chiroptical properties, the modest anisotropy dissymmetry factors of ECD and CPL were observed in the [8]CP belt.

Scaffolds of thiophene and benzothiophene are the important class of bioactive compounds found abundant in nature. The Diels-Alder reactions of 2-(1'-cycloalkenyl)thiophenes and 2-(1'-cycloalkenyl)benzo[b]thiophenes having the alkene groups present in five-, six-, seven-, eight-, and twelve-membered rings with substituted N-phenylmaleimides are characterized. The size of the cycloalkene rings plays a critical role in dictating the product distributions of expected and isomerized Diels-Alder adducts. 2D NMR studies indicate that the isolated isomers for 2-(1'-cycloalkenyl)thiophenes having five-, six-, and seven-membered rings are aromatized benzothiophene products, whereas eight- and twelve-membered rings are un-rearranged adducts. In addition, the product of subsequent ene-reaction with the N-phenylmaleimide is isolated for the five- and six-membered ring cases. Interestingly, in the 2-(1'-cycloalkenyl)benzo[b]thiophene having five-, six-, seven-, eight-, and twelve-membered rings, the un-rearranged dibenzothiophene Diels-Alder adduct is isolated in every instance. Molecular mechanics and density functional theory (M06-2X and PBE0-D3) calculations are performed to understand the differential reactivity of the various dienes for both the initial Diels-Alder reaction and a possible, subsequent ene reaction.

The de novo design of new peptide assemblies that expands the repertoire of biomaterial nanostructures has been of a tremendous challenge. Hence, it is evident that a successful research achievement in this area would increase the understanding of molecular interactions in supramolecules and create novel scaffolds exploitable in biotechnology and synthetic biology. The manipulation of cyclic peptide self-assembly is particularly intriguing for this purpose. Herein, we report that a novel type of cyclic peptides, referred to as chiral tether constrained cyclic peptides (CCP), shows promising self-assembly properties. CCPs are the first example of a controllable assembly of all-L-α-cyclic peptides with different ring sizes. A noteworthy feature of the CCP system is good tolerance of different secondary structures, ring size, and peptide sequence. Based on this system, a variety of nanostructures could be constructed, which display different physical properties, rendering it an excellent platform for molecular interaction studies. Further, demonstrate potential applications of these peptide assemblies in bioimaging and energy storage.

We report a series of palladium(II)-catalyzed, intramolecular alkene hydrofunctionalization reactions with carbon, nitrogen, and oxygen nucleophiles to form five- and six-membered carbo- and heterocycles. In these reactions, the presence of a proximal bidentate directing group controls the cyclization pathway, dictating the ring size that is generated, even in cases that are disfavored based on Baldwin's rules and in cases where there is an inherent preference for an alternative pathway. DFT studies shed light on the origins of pathway selectivity in these processes.

The syntheses of six bis(imino)-5,6,7,8-tetrahydrocycloheptapyridine-iron(ii) chloride complexes, [2-{(Ar)NCMe}-9-{N(Ar)}C10H10N]FeCl2 (Ar = 2-(C5H9)-6-MeC6H3Fe1, 2-(C6H11)-6-MeC6H3Fe2, 2-(C8H15)-6-MeC6H3Fe3, 2-(C5H9)-4,6-Me2C6H2Fe4, 2-(C6H11)-4,6-Me2C6H2Fe5, 2-(C8H15)-4,6-Me2C6H3Fe6), are reported in which the ring size of the ortho-cycloalkyl group has been varied as has the type of para-substituent. The molecular structures of Fe3 and Fe6 reveal square pyramidal geometries at iron while the ortho-cyclooctyl rings adopt boat-chair conformations. On treatment with either methylaluminoxane (MAO) or modified methylaluminoxane (MMAO), all six complexes showed optimal activities at 80 °C [up to 1.9 × 107 g of PE per mol Fe per h for Fe5/MMAO] for ethylene polymerization forming linear polyethylene (Tm's > 126 °C). Notably, the catalytic activities showed a marked correlation with the ring size of the ortho-cycloalkyl substituent: cyclohexyl (Fe2 and Fe5) > cyclooctyl (Fe3 and Fe6) > cyclopentyl (Fe1 and Fe4) for either para-substituent, H or Me. Furthermore, this family of iron catalysts exhibited remarkable thermostability by remaining highly active even at temperatures as high as 100 °C (1.1 × 107 g of PE per mol Fe per h); the wide variation in polymer molecular weights (Mw: 2.4-166 kg mol-1), influenced through choice of precatalyst and co-catalyst as well as by temperature and pressure, further highlights the versatility of these catalysts.

Macrocyclic analogues of the linear hexapeptide, angiotensin IV (AngIV) have proved to be potent inhibitors of insulin-regulated aminopeptidase (IRAP, oxytocinase, EC 3.4.11.3). Along with higher affinity, macrocycles may also offer better metabolic stability, membrane permeability and selectivity, however predicting the outcome of particular cycle modifications is challenging. Here we describe the development of a series of macrocyclic IRAP inhibitors with either disulphide, olefin metathesis or lactam bridges and variations of ring size and other functionality. The binding mode of these compounds is proposed based on molecular dynamics analysis. Estimation of binding affinities (ΔG) and relative binding free energies (ΔΔG) with the linear interaction energy (LIE) method and free energy perturbation (FEP) method showed good general agreement with the observed inhibitory potency. Experimental and calculated data highlight the cumulative importance of an intact N-terminal peptide, the specific nature of the macrocycle, the phenolic oxygen and the C-terminal functionality.

A series of imidazolinium salts, their six-, seven- and eight-membered homologues, and the related formamidinium salts were prepared, and their pKa values were determined in DMSO at 25 °C using the bracketing indicator method. The effect of each type of structural variation on the acidity of each salt was considered, particularly noting the importance of ring size and the effect of the steric and electronic nature of the N-aryl substituents. The effect of a cyclic structure was also probed through comparing the cyclic systems with the corresponding formamidinium salts, noting the importance of conformational flexibility in the latter cases. Along with allowing choice of appropriate bases for deprotonation of these species, it is anticipated that the data presented will aid in the understanding of the nucleophilicity, and potentially catalytic efficacy, of the corresponding carbenes.

Herein, we report a novel stepwise addition-controlled ring size method, to access tetrahydropyrimidines through an operationally simple [3 + 3] cycloaddition of vinylethylene carbonates with triazinanes. Interestingly, we could also use this method for a [3 + 3] oxidative cycloaddition, which allows the facile synthesis of polysubstituted terphenyls under mild conditions. Mechanistic studies suggest that vinylethylene carbonates could generate α,β-unsaturated aldehydes as 3-carbon synthons for cycloaddition via a combination process of Pd-catalyzed decarboxylation and β-H elimination.

2H-Chromene is an important structural motif present in many biologically active compounds, natural products and showed many other properties. Deep Eutectic Solvent (DES) an environmentally benign and alternative to the conventional organic volatile solvents has been utilized first time for the synthesis of the 2H-chromene derivatives in moderated to excellent yields. The DES is recycled for 5 times for the synthesis of 2H-chromene derivatives. Based on the stability of ring size, we justified the regio-selectivity on the formation of cyclization product. Based on the control experiments, we ruled out the free radical mechanism and propose the ACM mechanistic path to construct chromene skeleton.

[Image: see text] As more macrocycle structures are utilized to drug intracellular targets, new platforms are needed to facilitate the discovery of cell permeable compounds in this unique chemical space. Herein, a method is disclosed that allows for the efficient synthesis and permeability evaluation of novel organo-peptide macrocycle libraries. Thoughtful library design allows for the collection of crude permeability data using supercritical fluid chromatography mass spectrometry (SFC-MS) (EPSA) by mass-encoding the stereochemistry, ring size, and organic linker of the desired macrocycles. Library synthesis was aided via the development of a new on-resin N-arylation reaction. Further insights on the permeation of these organo-peptide macrocycles will be discussed, such as the permeability enhancement when utilizing a 2-substituted phenethyl linker versus a 3-substituted phenethyl linker. Lastly, selected macrocycles were scaled up and tested in the MDCK-II permeability assay, and the results of this assay reiterated the permeability trends from the crude SFC-MS data.

Nucleic acids exist in biological systems as linear and cyclic forms and in most cases the biology of the cyclic form is different from the linear form of exactly the same sequence. Case examples are cyclic nucleotides, second messengers in both prokaryotes and eukaryotes whereby the cyclic forms account for their interesting biological profiles and the actions of the cyclic nucleotides are terminated upon phosphodiesterase hydrolysis into linear forms. For mono and dinucleotides, it has been shown that vast conformational changes that accompany the hydrolysis of the cyclized form allow for discrimination between the cyclized and linear forms. As the ring size increases, it becomes difficult to use conformational or structural differences alone to discriminate between cyclic and linear nucleotides. Here we reveal that for the recently discovered CRISPR/Cas-related cyclic hexaadenosine monophosphate, it is possible to discriminate between the cyclized and linear forms. The structures of c-HexaAMP and linear form are different in acidic media and this structural difference facilitated a simple and practical detection platform for this interesting and new bacterial immunity-related molecule, and we also demonstrate that it is possible to distinguish between linear and cyclized polynucleotides using simple spectroscopic techniques, such as CD and fluorescence-based methods.

Bridging of a [2]pseudorotaxane formed from an unsymmetric mono-crown ether and an ammonium salt has provided two types of [2]rotaxanes, with the axle component positioned within a large (4L) and small (4S) ring, respectively. 1H NMR spectroscopy has revealed that 4L is the kinetically favored [2]rotaxane, whereas 4S is thermodynamically favored at low temperature.

A concise protocol for the synthesis of pyrimidinone/indole functionalized hybrid peptide macrocycles with varying ring size is described. The precursors of the macrocycles were obtained from the post reaction modification of multicomponent reaction products and were cyclized via copper (I) catalyzed [3 + 2] azide-alkyne cycloaddition. The macrocycles showed excellent inhibitory property towards CDK2 protein which is responsible for a variety of cancers and were also showed excellent cytotoxicity against human breast cancer cell line MCF-7.

Four different ionic liquids (ILs) consisting of the bis(trifluoromethanesulfonyl)imide ([NTf2]-) anion, with structurally similar systematically varying cations, are investigated herein through classical molecular dynamics. The following cations were examined: pyrrolidinium ([pyrHH]+), piperidinium ([pipHH]+), N-butyl-pyrrolidinium ([pyrH4]+) and N-butyl-N-methyl-pyrrolidinium ([pyr14]+). The focus herein is on understanding the effect of increased ring size and alkyl chain addition, resulting in three protic ILs and one aprotic IL ([pyr14][NTf2]), on the physicochemical properties of the liquids studied herein. Addition of alkyl groups to the cation appears to cause a distinct weakening of inter-ionic interactions and ordering in comparison to increasing the ring size. The influence of these structural changes, however, is clearer on the ordering of like ions than oppositely charged ions. The protic ILs exhibit important similarities in the spatial arrangement of ions on account of their strong and directed H-bonding interactions. The cation is seen to influence particular conformations of the anion which further explains the more selective ordering in the protic ILs. However, the aggregation of the butyl side chain is also seen to be an important structural determinant in [pyrH4][NTf2] and [pyr14][NTf2]. We analyze the formation of domains in order to quantitatively evaluate the microheterogeneity arising in these systems from the separation of phases according to polarities. Velocity autocorrelation functions are studied in order to characterize the stronger caging effect in the protic ILs and the weakening of the caging effect upon addition of alkyl groups to the cation, these are consistent with the coordination environment within the respective liquids. In conclusion, significant correlations between the structure and properties of these ILs are observed and quantified within this contribution.

A systematic study on the directed Pd-catalyzed (hetero)arylation of 26 substituted cyclic α-amino acids at the C(3)-atom was performed. For the first time, the 7- and 8-membered cyclic amino acids were introduced to C-H activation. 8-Aminoquinoline was used as a directing group. Effects of the ring size and the substituents on the reaction efficacy and stereoselectivity were studied.

Kinetics and thermodynamics of the template synthesis and of the acidic decomposition of the methylboron-capped iron(II) tris-1,2-dioximates—the clathrochelate derivatives of six (nioxime)- and eight (octoxime)-membered alicyclic ligand synthons—were compared. In the case of a macrobicyclic iron(II) tris-nioximate, the plausible pathway of its formation contains a rate-determining stage and includes a reversible formation of an almost trigonal-antiprismatic (TAP) protonated tris-complex, followed by its monodeprotonation and addition of CH3B(OH)2. Thus, the formed TAP intermediate undergoes a multistep rate-determining stage of double cyclization with the elimination of two water molecules accompanied by a structural rearrangement, thus giving an almost trigonal-prismatic (TP) iron(FII) semiclathrochelate. It easily undergoes a cross-linking with CH3B(OH)2, resulting in the elimination of H+ ion and in the formation of a macrobicyclic structure. In contrast, the analogous scheme for its macrobicyclic tris-octoximate analog was found to contain up to three initial stages affecting the overall synthesis reaction rate. The rates of acidic decomposition of the above clathrochelates were found to be also affected by the nature of their ribbed substituents. Therefore, the single crystal XRD experiments were performed in order to explain these results. The difference in the kinetic schemes of a formation of the boron-capped iron(II) tris-nioximates and tris-octoximates is explained by necessity of the substantial changes in a geometry of the latter ligand synthon, caused by its coordination to the iron(II) ion, due to both the higher distortion of the FeN6-coordination polyhedra, and the intramolecular sterical clashes in the molecules of the macrobicyclic iron(II) tris-octoximates.

We have investigated the role of ring sizes and substituents in NHC ligands in some (NHC)Au(I) complexes in the hydration of internal alkynes. Despite the fact that using (NHC)Au(I) complexes in the hydration of diarylacetylenes leads to Markovnikov-type products, the precise tuning of ligands allows changing the regioselectivity in arylalkylacetylene hydration to the anti-Markovnikov-type.

International audience; Nature offers a huge diversity of glycosidic derivatives. Among numerous structural modulations, the nature of the ring size of hexosides may induce significant differences on both biological and physicochemical properties of the glycoconjugate of interest. On this assumption, we expect that small disaccharides bearing either a furanosyl entity or a pyranosyl residue would give a specific signature, even in the gas phase. On the basis of the scope of mass spectrometry, two analytical techniques to register those signatures were considered, i.e., the ion mobility (IM) and the infrared multiple photon dissociation (IRMPD), in order to build up cross-linked databases. d-Galactose occurs in natural products in both tautomeric forms and presents all possible regioisomers when linked to d-mannose. Consequently, the four reducing Galf-Manp disaccharides as well as the four Galp-Manp counterparts were first synthesized according to a highly convergent approach, and IM-MS and IRMPD-MS data were second collected. Both techniques used afforded signatures, specific to the nature of the connectivity between the two glycosyl entities.

Our earlier report described that a cyclic hemoglobin (Hb) monomer with two β subunits of a Hb molecule (α₂β₂) bound through a flexible polyethylene glycol (PEG) chain undergoes reversible supramolecular ring-opening polymerization (S-ROP) to produce a supramolecular Hb polymer with a Hb–PEG alternating structure. In this work, we polymerized cyclic Hb monomers with different ring sizes (2, 5, 10, or 20 kDa PEG) to evaluate the thermodynamics of S-ROP equilibrium. Quantification of the produced supramolecular Hb polymers and the remaining cyclic Hb monomers in the equilibrium state revealed a negligibly small enthalpy change in S-ROP (ΔHp ≤ 1 kJ·mol⁻¹) and a markedly positive entropy change increasing with the ring size (ΔSp = 26.8–33.2 J·mol⁻¹·K⁻¹). The results suggest an entropy-driven mechanism in S-ROP: a cyclic Hb monomer with the larger ring size prefers to form a supramolecular Hb polymer. The S-ROP used for this study has the potential to construct submicrometer-sized Hb–PEG alternating polymers having structural regularity., This document is the Accepted Manuscript version of a Published Work that appeared in final form in Biomacromolecules, copyright © American Chemical Society after peer review and technical editing by the publisher. To access the final edited and published work see https://doi.org/10.1021/acs.biomac.1c00061.

Enhancing the performance of polymer micelles by purposeful regulation of their structures is a challenging topic that receives widespread attention. In this study, we systematically conduct a comparative study between cyclic grafted copolymers with rigid and flexible rings in the self-assembly behavior via dissipative particle dynamics (DPD) simulation. With a focus on the possible stacking ways of rigid rings, we propose the energy-driven packing mechanism of cyclic grafted copolymers with rigid rings. For cyclic grafted copolymers with large ring size (14 and 21-membered rings), rigid rings present a novel channel-layer-combination layout, which is determined by the balance between the potential energy of micelles (Emicelle) and the interaction energy between water and micelles (Eint). Based on this mechanism, we further regulate a series of complex self-assembling structures, including curved rod-like, T-shape, annular and helical micelles. Compared with flexible copolymers, cyclic grafted copolymers with rigid rings provide a larger and loose hydrophobic core and higher structural stability with micelles due to the unique packing way of rigid rings. Therefore, their micelles have a great potential as drug nanocarriers. They possess a better drug loading capacity and disassemble more quickly than flexible counterparts under acidic tumor microenvironment. Furthermore, the endocytosis kinetics of rigid micelles is faster than the flexible counterparts for the adsorption and wrapping process. This study may provide a reasonable idea of structural design for polymer micelles to enhance their performance in biomedical applications.

Nature offers a huge diversity of glycosidic derivatives. Amongst numerous structural modulations, the nature of the ring size of hexosides may induce significant differences on both biological and physicochemical properties of the glycoconjugate of interest. On this assumption, we expect that small disaccharides bearing either a furanosyl entity or a pyranosyl residue would give a specific signature, even in the gas phase. On the basis of the scope of mass spectrometry, two analytical techniques to register those signatures were considered, i.e. the ion-mobility (IM) and the infra-red multiple photon dissociation (IRMPD), in order to build up cross-linked databases. D-Galactose occurs in natural products in both tautomeric forms and presents all possible regioisomers when linked to D-mannose. Consequently, the four reducing Galf-Manp disaccharides as well as the four Galp-Manp counterparts were firstly synthesized according to a highly convergent approach, and IM-MS and IRMPD-MS data were secondly collected. Both techniques used afforded signatures, specific to the nature of the connectivity between the two glycosyl entities.

The geometry of a molecule plays a significant role in determining its physical and chemical properties. Despite its importance, there are relatively few studies on ring puckering and conformations, often focused on small cycloalkanes, 5- and 6-membered carbohydrate rings, and specific macrocycle families. We lack a general understanding of the puckering preferences of medium-sized rings and macrocycles. To address this, we provide an extensive conformational analysis of a diverse set of rings. We used Cremer-Pople puckering coordinates to study the trends of the ring conformation across a set of 140 000 diverse small molecules, including small rings, macrocycles, and cyclic peptides. By standardizing using key atoms, we show that the ring conformations can be classified into relatively few conformational clusters, based on their canonical forms. The number of such canonical clusters increases slowly with ring size. Ring puckering motions, especially pseudo-rotations, are generally restricted and differ between clusters. More importantly, we propose models to map puckering preferences to torsion space, which allows us to understand the inter-related changes in torsion angles during pseudo-rotation and other puckering motions. Beyond ring puckers, our models also explain the change in substituent orientation upon puckering. We also present a novel knowledge-based sampling method using the puckering preferences and coupled substituent motion to generate ring conformations efficiently. In summary, this work provides an improved understanding of general ring puckering preferences, which will in turn accelerate the identification of low-energy ring conformations for applications from polymeric materials to drug binding.

In this study, linear melt rheology of a single-tail tadpole-shaped polystyrene, ST-30/80, having ring and linear sizes of MR ∼ 30 kg mol^−1 and ML ∼ 80 kg mol^−1, respectively, was examined, and the effect of the ring size on rheological properties of tadpole polymers was discussed by comparing with the data of the previously reported tadpole samples having MR ∼ 60 kg mol^−1. ST-30/80 exhibits an entanglement plateau and shows a clearly slower terminal relaxation than that of its component ring and linear polymers. When the zero-shear viscosity η0 for ST-30/80 is plotted against the molecular weight of a linear tail chain, the data point lies on the single curve of η0 for 4- and 6-arm star polymers and the single-tail tadpoles with MR ∼ 60 kg mol^−1. These results suggest that the tadpole molecule in this study spontaneously forms a characteristic entanglement network, i.e., the intermolecular ring–linear threading, in the same manner as the previous tadpole samples, even though the size of the ring part is just slightly larger than the entanglement molecular weight (i.e., MR ∼ 1.8Me).

The cyclic dimeric peptide 1229U91 (GR231118) has an unusual structure and displays potent, insurmountable antagonism of the Y1 receptor. To probe the structural basis for this activity, we have prepared ring size variants and heterodimeric compounds, identifying the specific residues underpinning the mechanism of 1229U91 binding. The homodimeric structure was shown to be dispensible, with analogues lacking key pharmacophoric residues in one dimer arm retaining high antagonist affinity. Compounds 11d-h also showed enhanced Y1R selectivity over Y4R compared to 1229U91.

In this research, we have implemented two-dimensional quantitative structure-activity relationship (2D-QSAR) modeling using two different datasets, namely, acetylcholinesterase (AChE) and butyrylcholinesterase (BuChE) enzyme inhibitors. A third dataset has been derived based on their selectivity and used for the development of partial least squares (PLS) based regression models. The developed models were extensively validated using various internal and external validation parameters. The features appearing in the model against AChE enzyme suggest that a small ring size, higher number of −CH2- groups, higher number of secondary aromatic amines and higher number of aromatic ketone groups may contribute to the inhibitory activity. The features obtained from the model against BuChE enzyme suggest that the sum of topological distances between two nitrogen atoms, higher number of fragments X-C(=X)-X, higher number of secondary aromatic amides, fragment R--CR-X may be more favorable for inhibition. The features obtained from selectivity based model suggest that the number of aromatic ethers, unsaturation content relative to the molecular size and molecular shape may be more specific for the inhibition of the AChE enzyme in comparison to the BuChE enzyme. Moreover, we have implemented the molecular docking studies using the most and least active molecules from the datasets in order to identify the binding pattern between ligand and target enzyme. The obtained information is then correlated with the essential structural features associated with the 2D-QSAR models.

We report a series of palladium(II)-catalyzed, intramolecular alkene hydrofunctionalization reactions with carbon, nitrogen, and oxygen nucleophiles to form five- and six-membered carbo- and heterocycles. In these reactions, the presence of a proximal bidentate directing group controls the cyclization pathway, dictating the ring size that is generated, even in cases that are disfavored based on Baldwin’s rules and in cases where there is an inherent preference for an alternative pathway. DFT studies shed light on the origins of pathway selectivity in these processes.

Antimicrobial peptides are widely studied as an alternative to traditional antibiotics. However, they are difficult to develop, as multiple factors influence their potency and selectivity toward bacterial cells. In this paper, we investigate three simplified model peptides that bear crown ethers, and the effects of simple structural modifications (peptide length and crown ether ring size) on their secondary structures and their permeabilizing activity on living cells and model membranes made with egg yolk phosphatidylcholine or 1-palmitoyl-2-oleoylphosphatidylglycerol. Circular dichroism studies show that the peptide length and the crown ether ring size do influence the conformation, but no trend could be determined from the results. Permeabilization studies with model membranes and with red blood cells demonstrated that from 13 residues to 16 residues, there is a gradual increase in activity as the peptides get longer. However, the shortest tested analogs, with 12 residues, also exhibited an increase in activity caused by the removal of one amino acid that was bearing a crown ether. Permeabilization assays showed that larger ring size analogs showed higher hemolytic activities. Altogether, the results reported help design new and more selective antimicrobial peptides.

tert-Butyl 2,5-diaryl-3-oxopent-4-ynoates, obtained from arylacetylenes and the acid chloride of tert-butyl 2-phenylmalonate, represent strongly enolized β-ketoesters. Their C≡C bonds were activated by Ag(I) salts so that de-tert-butylating π-cyclizations occurred. The latter followed a 6-endo-dig mode giving 3,6-diaryl-4-hydroxy-2-pyrones, or a 5-exo-dig mode giving (Z)-configured 2-aryl-4-(arylmethylidene)tetronic acids (“pulvinones”). Perfectly selective pyrone formations were induced by AgSbF6 in methanol and equally selective pulvinone formations by Ag2CO3 and DABCO in acetonitrile.

Lithium bis(trifluoromethanesulfonyl)imide (LiNTf2) doped ionic liquids (ILs) are investigated herein, as potential electrolytes for lithium-ion batteries, via scaled-charge molecular dynamics simulations. Four model ILs based on the [NTf2]− anion and heterocyclic ammonium cations were studied with varying concentrations, ranging from 0 to 1 M solutions, of the dissolved lithium salt. The pyrrolidinium ([pyrHH]+), piperidinium ([pipHH]+), N-butyl-pyrrolidinium ([pyrH4]+), and N-butyl-N-methyl-pyrrolidinium ([pyr14]+) cations were considered to evaluate the combined effects of increased ring size, as well as the introduction of apolar groups on the nitrogen atom of the cations, on the liquid structure properties of the electrolytes. Among the investigated ILs, [pyr14][NTf2] is the only aprotic IL allowing for a comparison of protic and aprotic ILs. The lithium coordination shell is seen to be quite different in the various IL-based systems; networks of lithium ions bridged by [NTf2]− ions have interesting ...

Recently, a number of fentanyl analogs have been implicated in overdose deaths in Europe and in the US. So far, little is known of the molecular behavior of the structurally related subgroup; the alicyclic fentanyls. In this study, reference standards of cyclopropyl, cyclobutyl, cyclopentyl, cyclohexyl, and 2,2,3,3-tetramethylcyclopropyl fentanyl (TMCPF) at a final concentration of 5 µM were incubated with cryopreserved human hepatocytes (1 × 106 cells/mL) for 0, 1, 3 and 5 h. The metabolites formed were identified by liquid chromatography–quadrupole time-of-flight mass spectrometry analysis. The most abundant biotransformation found was N-dealkylation (formation of normetabolites) and oxidation of the alicyclic rings. As ring size increased, the significance of N-dealkylation decreased in favor of alicyclic ring oxidation. An example of this was cyclopropyl fentanyl, with a three-carbon ring, whose normetabolite covered 82% of the total metabolic peak area and no oxidation of the alicyclic ring was observed. In contrast, TMCPF, with a seven-carbon ring structure, rendered as much as 85% of its metabolites oxidized on the alicyclic ring. Other biotransformations found included oxidation of the piperidine ethyl moiety and/or the phenethyl substructure, glucuronidation as well as amide hydrolysis to form metabolites identical to despropionyl fentanyl. Taken together, this study provides a base for understanding the metabolism of a number of structurally related fentanyl analogs formed upon intake. Electronic supplementary material The online version of this article (10.1007/s00204-018-2330-9) contains supplementary material, which is available to authorized users.

Nanocluster models were investigated to explore the diversity of metallacycle intermediates for ethylene dimerization over NiMCM-41 at B3LYP/6-311+G* and M06/Def2-TZVP. The thermodynamic favorability of the formation of matallacycle with respect to the ring size of silica varied in the sequence of 6T

Monomers possessing two functionalities suitable for polymerization are often designed and utilized in syntheses directed to the formation of cross-linked macromolecules. In this review, we give an account of recent developments related to the use of such monomers in cyclopolymerization processes, in order to form linear, soluble macromolecules. These processes can be activated by means of radical, ionic, or transition-metal mediated chain-growth polymerization mechanisms, to achieve cyclic moieties of variable ring size which are embedded within the polymer backbone, driving and tuning peculiar physical properties of the resulting macromolecules. The two functionalities are covalently linked by a "tether", which can be appropriately designed in order to "imprint" elements of chemical information into the polymer backbone during the synthesis and, in some cases, be removed by postpolymerization reactions. The two functionalities can possess identical or even very different reactivities toward the polymerization mechanism involved; in the latter case, consequences and outcomes related to the sequence-controlled, precision synthesis of macromolecules have been demonstrated. Recent advances in new initiating systems and polymerization catalysts enabled the precision syntheses of polymers with regulated cyclic structures by highly regio- and/or stereoselective cyclopolymerization. Cyclopolymerizations involving double cyclization, ring-opening, or isomerization have been also developed, generating unique repeating structures, which can hardly be obtained by conventional polymerization methods.

The one-pot synthesis and modification of cyclic peptides through a self-cleaving on-resin protocol is described. We apply Dawson's MeDbz linker to achieve direct intramolecular peptide cyclization by thioesterification followed by S → N acyl shift. This native chemical ligation approach requires no activating additive and allows direct modification of the crude cyclic peptides in one-pot. The strategy was applied to synthesize 5 cyclic peptide natural products of varying ring size. Finally, one-pot modifications include desulfurization, fluorophore conjugation, and intramolecular disulfide formation.

A novel synthesis of multicyclic polymers that feature ultradense arrays of cyclic polymer units has been developed by exploiting the cyclopolymerization of α,ω-norbornenyl end-functionalized macromonomers mediated by the Grubbs third-generation catalyst (G3). Owing to the living polymerization nature, the number of cyclic repeating units in these multicyclic polymers was controlled to be between 1 and approximately 70 by varying the initial macromonomer-to-G3 ratio. The ring size was also tuned by choosing the molecular weight of the macromonomer; in this way we successfully prepared multicyclic polymers that possess cyclic repeating units composed of up to about 500 atoms, which by far exceeds those prepared to date by cyclopolymerization. Specifically, cyclopolymerizations of α,ω-norbornenyl end-functionalized poly(l-lactide)s (PLLAs) proceeded homogeneously under highly dilute conditions (∼0.1 mM in CH2Cl2) to give multicyclic polymers that feature cyclic PLLA repeating units on the polynorbornene bac...

This review considers noncovalent bonds between divalent chalcogen centers. In the first part we present X-ray data taken from the solid state structures of dimethyl- and diphenyl-dichalcogenides as well as oligoalkynes kept by alkyl-sulfur, -selenium, and -tellurium groups. Furthermore, we analyzed the solid state structures of medium sized (12-24 ring size) selenium coronands and medium to large rings with alkyne and alkene units between two chalcogen centers. The crystal structures of the cyclic structures revealed columnar stacks with close contacts between neighboring rings via noncovalent interactions between the chalcogen centers. To get larger space within the cavities, rings with diyne units between the chalcogen centers were used. These molecules showed channel-like structures in the solid state. The flexibility of the rings permits inclusion of guest molecules such as five-membered heterocycles and aromatic six-membered rings. In the second part we discuss the results of quantum chemical calculations. To treat properly the noncovalent bonding between chalcogens, we use diffuse augmented split valence basis sets in combination with electron correlation methods. Our model substances were 16 dimers consisting of two Me-X-Me (X = O, S, Se, Te) pairs and dimers of Me-X-Me/Me-X-CN (X = O, S, Se, Te) pairs. The calculations show the anticipated increase of the interaction energy from (Me-O-Me)

Rotaxane is a supramolecule in which ring chains are threaded on an axial chain, showing a fascinating sliding dynamics of ring chains along the axial chain. In this study, we investigated the sliding dynamics of ring chains on a knotted polymer chain in rotaxane, exhibiting a sub-diffusion at the intermediate time range resulting from the intra-strand interaction between the ring chains and the knotted axial chain in the knot crossing region. Meanwhile, the non-monotonous dependence of sliding diffusion coefficient D of ring chains on ring size Nring indicates that there exist two competing effects: one is the friction effect between the ring chains and the axial chain in which the ring chains slide fast along the knotted axial chain for large Nring, and another is the knot effect in which the ring chains move slowly along the knotted axial chain for large Nring because the knot crossing hinders ring chains to pass through for large Nring. Based on the unique sliding sub-diffusion behaviour of the threaded ring chains, we also proposed a new approach to estimate the average knot size of the knotted axial chain, and our estimation about the average knot size is in good agreement with the result according to the Alexander polynomial calculation using the free python package TOPOLY. These results may provide a fundamental view for understanding the dominant factors of the sliding dynamics of ring chains in complex polymer-based rotaxane.

Ring closing metathesis of acyclic trienes that can provide oxacycles or carbocycles has been investigated. It was found that a substituent on one of the alkene units determines the reaction course to provide either oxacycles or carbocyles exclusively irrespective of the ring size of the resulting compounds. Ring closing metathesis of acyclic trienes with Grubbs’ first generation (G-I) catalyst was found to be greately influenced by the presence of an alkyl substituent on one of the alkene units to provide either oxacycles or carbocyles exclusively irrespective of the ring size of the resulting compounds.

The effect of macrocycle ring size on the corrosion inhibition efficiency of dibenzo-12-crown-4 (DB12C4), dibenzo-15-crown-5 (DB15C5), dibenzo-18-crown-6 (DB18C6), dibenzo-21-crown-7 (DB21C7) and dibenzo-24-crown-8 (DB24C8) have been elucidated by mean of density functional calculation at B3LYP/6-31G(d) level of theory in the gas and aqueous environment. The quantum chemical parameters including the frontier orbital energies (EHOMO, ELUMO), ionization potential (I), electron affinity (A), the absolute electronegativity (χ), hardness (η), softness (σ), and the fraction of electron transferred (ΔN) are positively correlated to the corrosion inhibition efficiency (IE%) of the studied crown ethers. The calculation results indicate that DB24C8 exhibits the highest corrosion inhibition efficiency, whereas DB12C4 exhibits the lowest corrosion inhibition efficiency. The results of this study will contribute to design crown ethers potential as corrosion inhibitors.

The complexation of molecular clips containing fragments of diphenylglycoluril and benzocrown ethers with paraquat and its derivatives has been studied both in solution and in the solid state. In this paper we studied the influence of the crown ether ring size and the nature of the substituents at the nitrogen atoms of the paraquat derivatives on the composition and stability of these complexes.

Macrolides are a relatively common structural motif prevalent in Nature. However, the structures of these large ring lactones have been relatively difficult to elucidate via NMR spectroscopy due to the minute amounts of compounds that are sometimes obtainable from natural sources. Thus, GC-MS analysis of individual macrolactones has become the method of choice for the structural identification of these compounds. Here we discuss the mass spectrometric behavior of aliphatic macrolides, evaluating spectra from numerous compounds of various ring size, including derivatives containing methyl branches as well as double bonds. The specific fragmentation of these macrolactones under electron impact conditions allows for the development of a general rule set aimed at the identification of similar compounds by mass spectrometry. In addition, the mass spectra of dimethyl disulfide adducts of unsaturated macrolides are discussed. The mass spectra of almost 50 macrolides are presented.