Electron transfer across α-helical peptides: Potential influence of molecular dynamics

Three hydrophobic leucine-rich peptides Fc18L, Ac18L and 18LAc were prepared. These peptides are equipped with a cystein sulfhydryl group which enables the formation of thin films on gold surfaces. Using these peptides, two types of films of α-helical peptides have been prepared, in which the redox-active peptide Fc18L is diluted by Ac18L (SAM1) or by a mixture of Ac18L and 18LAc (SAM2). In SAM1, the dipole moments of the peptides are aligned in the same direction, whereas in SAM2, they are opposite. Reflection absorption infrared spectroscopy (RAIRS) revealed that the peptides are more vertically oriented in SAM2 compared to those in SAM1. The interaction among the macroscopic helix dipoles gives tighter packing of the peptides in SAM2. Importantly, the electron transfer properties in the two films are significantly different, which is rationalized by differences in the molecular dynamics of the two films.     

Can a consecutive double turn conformation be considered as a peptide based molecular scaffold for supramolecular helix in the solid state?

Helices and sheets are ubiquitous in nature. However, there are also some examples of self-assembling molecules forming supramolecular helices and sheets in unnatural systems. Unlike supramolecular sheets there are a very few examples of peptide sub-units that can be used to construct supramolecular helical architectures using the backbone hydrogen bonding functionalities of peptides. In this report we describe the design and synthesis of two single turn/bend forming peptides (Boc-Phe-Aib-Ile-OMe 1 and Boc-Ala-Leu-Aib-OMe 2) (Aib: α-aminoisobutyric acid) and a series of double-turn forming peptides (Boc-Phe-Aib-Ile-Aib-OMe 3, Boc-Leu-Aib-Gly-Aib-OMe 4 and Boc-γ-Abu-Aib-Leu-Aib-OMe 5) (γ-Abu: γ-aminobutyric acid). It has been found that, in crystals, on self-assembly, single turn/bend forming peptides form either a supramolecular sheet (peptide 1) or a supramolecular helix (peptide 2), unlike self-associating double turn forming peptides, which have only the option of forming supramolecular helical assemblages.     

Solid-phase synthesis of backbone-cyclized β-helical peptides

This paper describes the synthesis and purification of two 22-residue cyclic peptides, cyclo{[(l-Val-d-Val)₄-(l-Val-d-Pro-Gly)]₂-} 3 and cyclo{[(d-Leu-l-Leu)₄-(d-Leu-l-Pro-Gly)]₂-} 4, that were designed to fold into double-stranded antiparallel β-helical structures. Due to intramolecular hydrogen bonding and the conformational constraints imposed by the two reverse-turn segments (d-Pro-Gly and l-Pro-Gly, respectively), the linear precursors to 3 and 4 (lin-3 and lin-4) were expected to adopt preorganized conformations that would bring the N and C termini close together and thereby favor ring closure. Precursors lin-3 and lin-4 were constructed by stepwise Boc solid-phase peptide synthesis using the commercially available alkanesulfonamide ‘safety-catch’ linker and cyclized head-to-tail via the method of cleavage-by-cyclization. The crude cyclic peptides were highly hydrophobic and contained minor impurities that could not be removed solely by reversed-phase HPLC (RP-HPLC); however, two-step purification—first by RP-HPLC with i-PrOH/water gradients, followed by gel-permeation chromatography (GPC) on Sephadex LH-20 with CHCl₃/MeOH—afforded both peptides in pure form (≥95% by ¹H NMR) and in acceptable yield (23%). Subsequent ¹H NMR experiments supported the expected structures of 3 and 4. The successful formation of the 66-membered rings of 3 and 4 is consistent with the notion of conformational preorganization in the linear precursors; furthermore, the protocols for synthesis and purification described should prove useful for preparing additional cyclic β-helical peptides, including longer peptides and peptides having polar residues.     

Self-assembly of a cavitand-based heteronuclear coordination cage

A new self-assembly protocol leading to the formation of heteronuclear coordination cage 10 is reported. Reaction of tetradentate cavitand ligand 1, bearing one ethynylpyridine and three benzonitriles at the apical positions, with Pt(dppp)OTf₂ and Pd(dppp)OTf₂ in a 1:3 ratio yields 10 as the thermodynamic product. Under the same conditions, the self-assembly of 1 with either Pt or Pd metal precursors gives a mixture of isomeric homonuclear cages 8a-c or 9a-c, respectively.     

Nanostaircase formation in the solid state from self-assembling synthetic terephthalamides with a common molecular scaffold

The design and construction of nanostructured materials using proper self-assembling molecular building blocks is a real challenge to scientists. Here, we present the formation of a new nano-architecture, i.e., nanostaircase in the solid state by using molecular building blocks, which are amenable to self-assembly in a directed manner to form the specific nanostructure. The molecular building blocks are terephthalamides 1-4, which are bis-terephthalamides of methyl esters of various α-amino acids including l-leucine 1, d-leucine 2, l-isoleucine 3, and α-aminoisobutyric acid (Aib) 4. All terephthalamides presented here, irrespective of their different side chain residues or stereochemistry, self-assemble to form supramolecular nanostaircase structures in crystals. Each terephthalamide contains two good hydrogen-bond donors and two hydrogen-bond acceptors. Two N-H?O hydrogen bonds and C-H?π interactions are responsible for the formation and stabilization of the nanostaircase structures in crystals. The molecular building blocks are packed orthogonally to each other in crystals and this arrangement can help the formation of nanostaircase structure upon self-assembly.     

Dibromomethane as one-carbon source in organic synthesis: a versatile methodology to prepare the cyclic and acyclic α-methylene or α-keto acid derivatives from the corresponding terminal alkenes

Ozonolysis of mono-substituted alkenes A-1 followed by reacting with a preheated mixture of CH₂Br₂-Et₂NH affords α-substituted acroleins A-2 in good yields. Under very mild reaction conditions, these α-substituted acroleins A-2 can be easily converted to α-methylene esters A-4, which could be further converted to the corresponding α-keto esters A-5. This methodology can be also applied to the preparation of α-methylene lactones B-4, α-methylene lactams, and α-keto lactones B-5 with various ring sizes.     

Synthesis and self-assembly of oligomers containing cruciform 9,10-bis(arylethynyl)anthracene unit: formation of supramolecular nanostructures based on rod-length-dependent organization

Conjugated rod-coil molecules, incorporating flexible and rigid blocks, have a strong affinity to self-organize into various supramolecular nanostructures in the bulk state.In this study, we report synthesized oligomers containing cruciform 9,10-bis(arylethynyl)anthracene units and characterized their self-assembly behavior. The molecular structures were characterized with ¹H, ¹³C NMR, and matrix-assisted laser desorption ionization time-of-flight (MALDI-TOF) mass spectroscopy. An investigation of the supramolecular nanostructures of these molecules using differential scanning calorimetry, thermal polarized optical microscopy, and small-angle X-ray scattering revealed that the rod length of coil-rod-coil molecules with identical rod to coil volume ratios dramatically influences self-assembly behavior in the bulk state. Molecules 2 and 3 with relatively longer rod lengths self-assemble into lamellar structures in the solid state, whereas, molecules 1 and 4 self-assemble into two-dimensional (2-D) oblique columnar structures in the liquid crystalline phase, in addition, on heating, molecule 1 transforms from the oblique columnar phase to the nematic phase.     

Application of tri- and tetrasubstituted alkene dipeptide mimetics to conformational studies of cyclic RGD peptides

The first application of a combination of novel ψ[(E)-CXCX]-type alkene dipeptide isosteres to conformation studies of cyclic bioactive peptides was carried out (X=H or Me). For exploration of bioactive conformations of Kessler's cyclic RGD peptides, cyclo(-Arg-Gly-Asp-d-Phe-Val-) 1 and cyclo(-Arg-Gly-Asp-d-Phe-N-MeVal-) 2, d-Phe-ψ[(E)-CXCX]-l-Val-type dipeptide isosteres were utilized having di-, tri- and tetrasubstituted alkenes containing the γ-methylated isosteres that have been reported to be potential type II′ β-turn promoters. All of the (E)-alkene pseudopeptides 3-6 exhibited higher antagonistic potency against α_vβ₃ integrin than 1, although potencies were slightly lower than 2. Detailed structural analysis using ¹H NMR spectroscopy revealed that representative type II′ β/γ backbone arrangements proposed for 1, were not observed in peptides 3-6. Rather on the basis of ¹H NMR data, the conformations of peptides 3-6 were estimated to be more analogous to those of the N-methylated peptide 2.     

Controlled self-assembly of chiral gelator molecules into aligned fibers induced by nematic to smectic B phase transitions

Chiral bisoxalamide 1 shows remarkable gelling capacity of the nematic and smectic B liquid-crystalline phases of heptylcyclohexanecarboxylic acid (HCCA). Chiral nematic-containing left-handed helical fiber bundles are formed if the gelator is present in amounts higher than 0.55 wt %. With lower amounts of 1, no nematic gel forms, however, a nematic to smectic B phase transition triggers instantaneous self-assembly of gelator molecules into aligned fibers. The latter liquid crystalline gel system represents an example of controlled self-assembly induced by a liquid crystalline phase transition.     

Two novel α-tocopheroids from the aerial roots of Ficus microcarpa

Two novel α-tocopheroids, namely α-tocospiros A (1) and B (2), together with α-tocopherol (3) were isolated from the aerial roots of Ficus microcarpa. Their structures were elucidated by spectral methods. Under basic conditions, compounds 1 and 2 were obtained from α-tocoquinon-2,3-oxide (6a and 6b) via a highly stereoselective nucleophilic addition reaction. Reaction and biotransformation mechanisms of 1 and 2 are proposed.     

Efficient synthesis of fluorinated α- and β-amino nitriles from fluoroalkylated α,β-unsaturated imines

A simple and efficient synthesis of fluoroalkylated α-amino nitrile (4) derivatives by regioselective 1,2-addition of trimethylsilyl cyanide to fluoroalkylated α,β-unsaturated imines (1) is described. Fluoroalkylated β-amino nitriles (7) are also prepared by regioselective 1,2-addition of α-carbanions derived from acetonitrile to fluoroalkylated α,β-unsaturated imines (1). Fluoroalkylated α-(4) and β-amino nitriles (7) are also prepared through an ‘one pot’ procedure by reaction of enaminophosphonate 2 with BuLi, addition of aldehydes and subsequent addition of either trimethylsilyl cyanide or α-carbanion derived from acetonitrile. Basic hydrolysis of α-(4) and β-amino nitriles (7) gives fluoroalkylated α-(5) and β-amino acids (8).     

Selenium dioxide-mediated synthesis of α-ketoamides from arylglyoxals and secondary amines

A facile and expeditious synthetic approach for the synthesis of α-ketoamides 3 is described. A series of α-ketoamides 3 was synthesized via reaction of selenium dioxide-mediated oxidative amidation between arylglyoxals 1 and secondary amines 2, and accelerated with microwave irradiation. Our findings indicate that constrained amines, such as piperazine and piperidine exhibit higher conversions for this transformation. This reaction was explored by synthesizing a series of α-ketoamides 3 from various arylglyoxals 1 with cyclic and acyclic secondary amines 2.     

Stabilization of β-hairpin structures via inter-strand π-π and hydrogen bond interactions in α-, β-, γ-hybrid peptides

Synthesis and conformational studies of α-, β-, γ-hybrid peptides containing a pyrrole amino acid (Paa, 1) and a furan amino acid (Faa, 2), namely Boc-β-Phe-Faa-d-Pro-Gly-Paa-β-HGly-Faa-OMe (3) and Boc-Paa-β-Phe-Faa-d-Pro-Gly-Paa-β-HGly-Faa-OMe (4), were carried out and they adopt β-hairpin structures stabilized via inter-strand π-π and hydrogen bonding interactions.     

Supramolecular organogelators based on Janus type AT nucleosides

J-AT nucleoside-based organogelators 1a and 1b were designed and synthesized. They were endowed with unparalleled superiority to natural nucleobase analogues 2–6 to gelate aromatic solvents due to their excellent self-assembly properties. The J-AT nucleoside-based organogelators showed a specific self-complementary base pair recognition characteristic. The gel stabilities of 1a and 1b were drastically influenced by adenine analogue 2, hardly affected by thymine analogue 3, uracil analogue 4, cytosine analogue 5, and mildly interrupted by guanine analogue 6.     

Toward a synthesis of the antitumor macrolide peloruside A: a chiral pool approach for the C(1)-C(11) segment

Dihydroxylation of the glucose derived α,β-unsaturated lactones 6 and 13 was found to be on the α-face of the pyranolactone ring exclusively. The resulting dihydroxylated compound from 13 has been used in a synthesis of the lactone 4, which corresponds to C(1)-C(11) of peloruside A.     

A convenient synthesis of pyridine and 2,2′-bipyridine derivatives

α-Chloro-α-acetoxy-β-keto-esters 9 were readily prepared from β-keto-esters 6 in good overall yields. These compounds reacted as α,β-diketo-ester equivalents 2 with amidrazones 1 yielding triazines 3, generally in good yields. Picolinates 10 provided an alternative source of α,β-diketo-ester equivalents 2 when treated with copper(II) acetate. A ‘one-pot’ reaction of the α,β-diketo-ester equivalents 2 with amidrazones 1 in the presence of 2,5-norbornadiene 5 in boiling ethanol yielded the pyridines 4 and 2,2′-bipyridines 4 (R¹=2-pyridyl) directly without the need to isolate the corresponding triazines 3. Triazine 3c reacted with the aza-dienophiles 13 and 17 affording the products 16 and 18, respectively, in good yields.     

Synthesis and self-assembly of dibenzo[jk,mn]naphtho[2,1,8-fgh]thebenidinium derivates

A novel synthetic method toward nitrogen containing positively charged dibenzo[jk,mn]naphtho[2,1,8-fgh]thebenidinium (DBNT, 1) salts was developed. In this method, the undehydrogenated precursor of DBNT, 14-phenyl-14-dibenzo[a,j]acridinium salt (6), was produced directly from the reaction between 14-phenyl-14-dibenzo[a,j]xanthenylium (2) and amine/aniline in reasonable yield. Various DBNT salts with different alkyl and alkylphenyl chains were synthesized in this two-step method. The self-assembly behavior of two alkylated DBNT salts, 1c and 1f, was studied in this work. Due to the different substituents and counterions, compound 1c formed nanoscale wirelike fibers, and helical aggregates were obtained from 1f, in their methanolic solutions.     

A synthesis of a common intermediate to the lactone-pyrrolidinone ring systems in oxazolomycin A and neooxazolomycin

A 5-exo-dig radical cyclisation of the bromoamide 34 derived from the enantiopure α-ethynyl substituted amino alcohol 31 led to a 2:1 mixture of β-C3 and α-C3 methyl epimers of the pyrrolidinone 35a-36a in a combined yield of 73%. Treatment of the homoallylic alcohol 35b, derived from 35a, with OsO₄-TMEDA, gave a single diastereoisomer of the pyrrolidinone triol 37, resulting from selective dihydroxylation from the β-face, i.e. syn to the CH₂OH group of 35b. The pyrrolidinone triol 37 is a potential common precursor, cf. 9, to the spiro β-lactone pyrrolidinone 8 and the γ-lactone pyrrolidinone 10 ring systems in oxazolomycin A (1) and neooxazolomycin 2, respectively. Sequential protection of the 1,2-diol functionality in 37 as the acetonide 39, and the primary alcohol group in 39 as the SEM ether 41a, followed by methylation of the nitrogen centre in 41a, using NaH-MeI, then gave the selectively protected pyrrolidinone 42.     

Fluorescent detection of amidinium-carboxylate and amidinium formation using a 1,8-diphenylnaphthalene-based diamidine: dicarboxylic acid recognition with high fluorescence efficiency

A 1,8-diphenylnaphthalene-based diamidine (1) ‘turn-on’ fluorescent probe for the detection of dicarboxylic acids has been designed and synthesized. The fluorescence spectra of the diamidine 1 with carboxylic acids that showed two different fluorescence bands, which corresponded to the amidinium-carboxylate (λ_em=410–430 nm) and amidinium (λ_em=440–470 nm as a broad band, which consisted from two peaks) formation, were confirmed by DOSY NMR and TD-DFT calculations. The complexation of diamidine 1 with dicarboxylic acids, which have sufficient distances between the two carboxylic groups for binding to the diamidine 1 (dicarboxylic acids 3, 4, and α,ω-dicarboxylic acids 6 (C₆–C₂₀)), showed the formation of 1:1 complexes (i.e., amidinium-carboxylate formation). On the other hand, for the complexation with monocarboxylic acids and dicarboxylic acids having insufficient distances between the two carboxylic groups (benzoic acid 5, acetic acid 7, and α,ω-dicarboxylic acids 6 (C₃–C₅)), formation of the amidinium (1·2H⁺) was observed. Relatively similar binding constants (10⁻⁵) for the complexation of the diamidine 1 with dicarboxylic acids 6, which depend on their chain length (strain), were observed due to the flexibility of the 1,8-diphenylnaphthalene unit. Additionally, for the complexation of the diamidine 1 with dicarboxylic acids, higher fluorescence quantum yields (Φ_fl: up to 80%) were observed when compared to the binding of the diamidine 2 (Φ_fl: up to 35%).     

Synthesis,structure and reactivity of a macrocyclic imine: aza-[13]-macrodiolides

The in situ synthesis and subsequent reactions of macrocylic imine 2 are reported. The imine was trapped with cyanotrimethylsilane to give α-amino nitrile aza-[13]-macrodiolides in a 1:1 ratio of diastereomers. A crystal structure of the syn α-cyano nitrile diastereomer, 7a, provided insights into the lack of selectivity in reactions of 2 relative to macrocyclic alkene 1. Reactions to functionalize the syn diastereomer 7a are also reported.