Amyloid‐Like Fibrillogenesis through Supramolecular Helix‐Mediated Self‐Assembly of Tetrapeptides Containing Non‐Coded α‐Aminoisobutyric Acid (Aib) and 3‐Aminobenzoic Acid (m‐ABA)

Single‐crystal X‐ray diffraction studies of two terminally protected tetrapeptides Boc‐Ile‐Aib‐Val‐m‐ABA‐OMe ( I ) and Boc‐Ile‐Aib‐Phe‐m‐ABA‐OMe ( II ) (Aib=α‐aminoisobutyric acid; m‐ABA=meta‐aminobenzoic acid) reveal that they form continuous H‐bonded helices through the association of double‐bend (type III and I) building blocks. NMR Studies support the existence of the double‐bend (type III and I) structures of the peptides in solution also. Field emission scanning electron‐microscopic (FE‐SEM) and high‐resolution transmission electron‐microscopic (HR‐TEM) images of the peptides exhibit amyloid‐like fibrils in the solid state. The Congo red‐stained fibrils of peptide I and II , observed between crossed polarizers, show green‐gold birefringence, a characteristic of amyloid fibrils.     

Incorporation of an Allene Unit into α‐Pinene via β‐Elimination

The two double‐bond isomers 3‐iodo‐2,6,6‐trimethylbicyclo[3.1.1]hept‐2‐ene ( 6b ) and 3‐iodo‐4,6,6‐trimethylbicyclo[3.1.1]hept‐2‐ene ( 11 ) were synthesized by reacting 2,6,6‐trimethylbicyclo[3.1.1]heptan‐3‐one ( 9 ) with hydrazine, followed by treatment with I₂ in the presence of Et₃N. Treatment of 11 with t‐BuOK as base in diglyme at 220° resulted in the formation of 9 and 6,6‐dimethyl‐4‐methylidenebicyclo[3.1.1]hept‐2‐ene ( 12 ). For the formation of 9 , the cyclic allene 7 is proposed as an intermediate. Treatment of the second isomer, 6b , with t‐BuOK at 170° gave rise to the diene 12 and the dimerization product 17 . The underlying mechanism of this transformation is discussed. On the basis of density‐functional‐theory (DFT) calculations on the allene 7 and the alkyne 15 , the formation of the latter as the intermediate was excluded.     

Synthesis,and Helix or Hairpin‐Turn Secondary Structures of ‘Mixed’ α/β‐Peptides Consisting of Residues with Proteinogenic Side Chains and of 2‐Amino‐2‐methylpropanoic Acid (Aib)

Twelve peptides, 1 – 12 , have been synthesized, which consist of alternating sequences of α‐ and β‐amino acid residues carrying either proteinogenic side chains or geminal dimethyl groups (Aib). Two peptides, 13 and 14 , containing 2‐methyl‐3‐aminobutanoic acid residues or a ‘random mix’ of α‐, β²‐, and β³‐amino acid moieties were also prepared. The new compounds were fully characterized by CD (Figs. 1 and 2), and ¹H‐ and ¹³C‐NMR spectroscopy, and high‐resolution mass spectrometry (HR‐MS). In two cases, 3 and 14 , we discovered novel types of turn structures with nine‐ and ten‐membered H‐bonded rings forming the actual turns. In two other cases, 8 and 11 , we found 14/15‐helices, which had been previously disclosed in mixed α/β‐peptides containing unusual β‐amino acids with non‐proteinogenic side chains. The helices are formed by peptides containing the amino acid moiety Aib in every other position, and their backbones are primarily not held together by H‐bonds, but by the intrinsic conformations of the containing amino acid building blocks. The structures offer new possibilities of mimicking peptide–protein and protein–protein interactions (PPI).     

CuI/amino acid‐catalyzed coupling and cyclization of β‐bromo‐α,β‐unsaturated amides with terminal alkynes leading to (3Z)‐3‐alkylidenepyrrol‐1‐ones

β‐Bromo‐α,β‐unsaturated amides are coupled and cyclized with terminal alkynes in DMF at 110 °C in the presence of a catalytic amount of CuI and amino acid along with a base to give the corresponding (3Z)‐3‐alkylidenepyrrol‐1‐ones in moderate to good yields. Copyright © 2013 John Wiley & Sons, Ltd.     

Reactions of Diazomethanes with 5‐Benzylidene‐3‐phenylrhodanine – A Computational Study

It has been shown previously that the reaction of diazomethane with 5‐benzylidene‐3‐phenylrhodanine ( 1 ) in THF at ?20° occurs at the exocyclic C?C bond via cyclopropanation to give 3a and methylation to yield 4 , respectively, whereas the corresponding reaction with phenyldiazomethane in toluene at 0° leads to the cyclopropane derivative 3b exclusively. Surprisingly, under similar conditions, no reaction was observed between 1 and diphenyldiazomethane, but the 2‐diphenylmethylidene derivative 5 was formed in boiling toluene. In the present study, these results have been rationalized by calculations at the DFT B3LYP/6‐31G(d) level using PCM solvent model. In the case of diazomethane, the formation of 3a occurs via initial Michael addition, whereas 4 is formed via [3+2] cycloaddition followed by N₂ elimination and H‐migration. The preferred pathway of the reaction of 1 with phenyldiazomethane is a [3+2] cycloaddition, subsequent N₂ elimination and ring closure of an intermediate zwitterion to give 3b . Finally, the calculations show that the energetically most favorable reaction of 1 with diphenyldiazomethane is the initial formation of diphenylcarbene, which adds to the S‐atom to give a thiocarbonyl ylide, followed by 1,3‐dipolar electrocyclization and S‐elimination.     

The Effect of Fluoro Substitution upon the β‐Hairpin Fold of a β‐Tetrapeptide in Methanol

The importance of β‐peptides lies in their ability to mimic the conformational behavior of α‐peptides, even with a much shorter chain length, and in their resistance to proteases. To investigate the effect of substitution of β‐peptides on their dominant fold, we have carried out a molecular‐dynamics (MD) simulation study of two tetrapeptides, Ac‐(2R,3S)‐β^2,3hVal(αMe)‐(2S)‐β²hPhe‐(R)‐β³hLys‐(2R,3S)‐β^2,3‐Ala(αMe)‐NH₂, differing in the substitution at the C_α of Phe2 (pepF with F, and pepH with H). Three simulations, unrestrained (UNRES), using ³J‐coupling biasing with local elevation in combination with either instantaneous (INS) or time‐averaging (AVE) NOE distance restraining, were carried out for each peptide. In the unrestrained simulations, we find three (pepF) and two (pepH) NOE distance bound violations of maximally 0.22 nm that involve the terminal residues. The restrained simulations match both the NOE distance bounds and ³J‐values derived from experiment. The fluorinated peptide shows a slightly larger conformational variability than the non‐fluorinated one.     

A Computational Study on Water-assisted Ammonolysis of N-Methyl β-Sultam

IntroductionIt is known that the reactivity and mechanisms ofthe reactions ofβ-sultams with nucleophiles are of in-creasing interest due to the following reasons.1,2-Thi-azetidine1,1-dioxides(β-sultams)are the sulfonyl ana-logues ofβ-lactamantibiotics …     

Nanomagnetic‐supported Sulfonic Acid: Simple and Rapid Method for the Synthesis of α,α′‐Bis‐(substituted‐benzylidene) Cycloalkanones

Nanomagnetic‐supported sulfonic acid is found to be a powerful and reusable heterogeneous catalyst for the rapid synthesis of α,α′‐bis‐(substituted‐benzylidene)cycloalkanones under conventional heating and solvent free conditions. High yield, simple work up and easy recovery of the catalyst are the most obvious advantages of this procedure.     

Palladium‐catalyzed carbonylative cyclization of β‐bromo‐α,β‐unsaturated carboxylic acids with 2,2‐dimethylhydrazine leading to 1‐(dimethylamino)‐1H‐pyrrole‐2,5‐diones

β‐Bromo‐α,β‐unsaturated carboxylic acids are carbonylatively cyclized with 2,2‐dimethylhydrazine under carbon monoxide pressure in THF in the presence of a catalytic amount of a palladium catalyst along with a base to give 1‐(dimethylamino)‐1H‐pyrrole‐2,5‐diones. Copyright © 2014 John Wiley & Sons, Ltd.     

A convenient synthesis of α,α′‐ homo‐ and α,α′‐hetero‐bifunctionalized poly(ε‐caprolactone)s by ring opening polymerization: The potentially valuable precursors for miktoarm star copolymers

Two new ring opening polymerization (ROP) initiators, namely, (3‐allyl‐2‐(allyloxy)phenyl)methanol and (3‐allyl‐2‐(prop‐2‐yn‐1‐yloxy)phenyl)methanol each containing two reactive functionalities viz. allyl, allyloxy and allyl, propargyloxy, respectively, were synthesized from 3‐allylsalicyaldehyde as a starting material. Well defined α‐allyl, α′‐allyloxy and α‐allyl, α′‐propargyloxy bifunctionalized poly(ε‐caprolactone)s with molecular weights in the range 4200–9500 and 3600–10,900 g/mol and molecular weight distributions in the range 1.16–1.18 and 1.15–1.16, respectively, were synthesized by ROP of ε‐caprolactone employing these initiators. The presence of α‐allyl, α′‐allyloxy and α‐allyl, α′‐propargyloxy functionalities on poly(ε‐caprolactone)s was confirmed by FT‐IR, ¹H, ¹³C NMR spectroscopy, and MALDI‐TOF analysis. The kinetic study of ROP of ε‐caprolactone with both the initiators revealed the pseudo first order kinetics with respect to ε‐caprolactone consumption and controlled behavior of polymerization reactions. The usefulness of α‐allyl, α′‐allyloxy functionalities on poly(ε‐caprolactone) was demonstrated by performing the thiol‐ene reaction with poly(ethylene glycol) thiol to obtain (mPEG)₂‐PCL miktoarm star copolymer. α‐Allyl, α′‐propargyloxy functionalities on poly(ε‐caprolactone) were utilized in orthogonal reactions i.e copper catalyzed alkyne‐azide click (CuAAC) with azido functionalized poly(N‐isopropylacrylamide) followed by thiol‐ene reaction with poly(ethylene glycol) thiol to synthesize PCL‐PNIPAAm‐mPEG miktoarm star terpolymer. The preliminary characterization of A₂B and ABC miktoarm star copolymers was carried out by ¹H NMR spectroscopy and gel permeation chromatography (GPC). © 2015 Wiley Periodicals, Inc. J. Polym. Sci., Part A: Polym. Chem. 2016 , 54, 844–860     

A New Route to N‐Aryl 2‐Alkenamides,N‐Allyl N‐Aryl 2‐Alkenamides,and N‐Aryl α,β‐Unsaturated γ‐Lactams from N‐Aryl 3‐(Phenylsulfonyl)propanamides

A series of N‐aryl 2‐alkenamides were produced efficiently by treating N‐aryl 3‐(phenylsulfonyl)‐propanamides with potassium tert‐butoxide in THF at 0°C. With out isolation, it was further treated with an additional equivalent of potassium tert‐butoxide and allyl bromide to give N‐allyl N‐aryl 2‐alkenamides in one pot in good yields. Followed by a ring‐closing metathesis reaction, these N‐allyl N‐aryl 2‐alkenamides were respectively converted into corresponding N‐aryl α,β‐unsaturated γ‐lactams in moderate yields.     

A rare occurrence of a β‐turn in an amyloid βA4 peptide

The fragment β(25–35) of the amyloid β‐peptide, like its parent βA4, has shown neurotrophic and late neurotoxic activities in cultured cells. The 3D structure of this important peptide was examined by ¹H and ¹³C 2D‐NMR and MD simulations in DMSO‐d₆ and water. The NMR parameters of chemical shift, ³J(N,Hα) coupling constants, temperature coefficients of NH chemical shifts and the pattern of intra and inter‐residue NOEs were used to deduce the structures. In DMSO‐d₆, the peptide was found to take up a type I β‐turn around the C‐terminal residues Ile⁸–Gly⁹–Leu¹⁰–Met¹¹, whereas in water at pH 5.5, it adopts a random coil conformation. This is only the second report of a β‐turn in the β‐amyloid class of peptides. The solution structures generated using restrained molecular dynamics were refined by MARDIGRAS to an R factor of 0.33 in the case of DMSO‐d₆ and to 0.56 for water. Copyright © 2002 John Wiley & Sons, Ltd.     

Formation of Periodic γ‐Turns in α/β‐Hybrid Peptides: DFT and NMR Experimental Evidence

Hybrid peptidic oligomers comprising natural and unnatural amino acid residues that can exhibit biomolecular folding and hydrogen‐bonding mimicry have attracted considerable interest in recent years. While a variety of hybrid peptidic helices have been reported in the literature, other secondary structural patterns such as γ‐turns and ribbons have not been well explored so far. The present work reports the design of novel periodic γ‐turns in the oligomers of 1:1 natural‐α/unnatural trans‐β‐norborenene (TNAA) amino acid residues. Through DFT, NMR, and MD studies, it is convincingly shown that, in the mixed conformational pool, the heterogeneous backbone of the hybrid peptides preferentially adopt periodic 8‐membered (pseudo γ‐turn)/7‐membered (inverse γ‐turn) hydrogen bonds in both polar and non‐polar solvent media. It is observed that the stereochemistry and local conformational preference of the β‐amino acid building blocks have a profound influence on accessing the specific secondary fold. These findings may be of significant relevance for the development of molecular scaffolds that facilitate desired positioning of functional side‐chains.     

Numerical Simulation of the Pressure Denaturation of a Helical β‐Peptide Heptamer Solvated in Methanol

The effect of elevated pressure on the conformational behavior of a β‐peptide heptamer ( 1 ) in MeOH solution was considered. The response of the peptide to elevated pressure was probed by means of molecular dynamics (MD) simulations, and described in atomic terms. The most‐striking features of the response are that the region of the ‘unfolded’ state of the peptide accessible at elevated pressure is narrow, and that thermal and pressure denaturation produce similar ‘unfolded’ states in the case of 1 .     

Synthesis and Conformational Studies of a Hybrid Cyclic Peptide Based on cis‐β‐Furanoid Sugar Amino Acid (FSAA) and Ornithine

The conformational control of a 14‐helix nucleating template, cis‐β‐furanoid sugar amino acid (FSAA), over a flexible δ‐amino acid, ornithine is studied in a FSAA‐ornithine cyclic tetrapeptide. Extensive NMR and MD studies reveal that the cyclic peptide adopts a three‐dimentional bowl‐shape cavity, which promotes six‐ and seven‐membered intra‐ and inter‐residue H‐bonding, in polar and non‐polar solvents, respectively.     

The Rearrangement of 2,2‐Diphenyl‐1‐[(E)‐2‐phenylethenyl]cyclopropane to 3,4,4‐Triphenylcyclopent‐1‐ene: a DFT Analysis

A computational study on the rearrangement of 2,2‐diphenyl‐1‐[(E)‐2‐phenylethenyl]cyclopropane ( 1 ) is presented, using density functional theory (DFT), (U)B3LYP with the 6‐31G* basis set (DFT1) and (U)M05‐2X with the 6‐311+G** basis set (DFT2). In agreement with a biradical character of the transition structure (TS) or intermediate, the potential‐energy hypersurface is lowered by the influence of three conjugated Ph groups. Surprisingly, two conformations of the geminal diphenyl group (different twist angles) induce two different minimum‐energy pathways for the rearrangement. Independent of the functional used, the first hypersurface harbors true biradical intermediates, whereas the second energy surface is a flat, slightly ascending slope from the starting material to the TS. The functional (U)M05‐2X with the basis set 6‐311+G** provides realistic energies which seem to be close to experiment. The activation energy for racemization of enantiomers of 1 is lower than that of rearrangement by 2.5 kcal mol^?1, in agreement with experiment.     

Reaction of α,β‐unsaturated ketones using cerium (IV) sulfate tetrahydrate in acetic acid

The reaction of α,β‐unsaturated ketones with cerium (IV) sulfate tetrahydrate [Ce(SO₄)₂·4H₂O, CS] in acetic acid gave the corresponding β‐acetoxy ketones. In the case of 2‐cyclohexen‐1‐one with CS in acetic acid, benzobicyclo[2.2.2]octen‐2‐one was obtained. The reaction mechanism also was proposed. Moreover, we report the aromatization and esterification of (R)‐(?)‐carvone by CS in acetic acid. Copyright © 2007 John Wiley & Sons, Ltd.     

The effect of amino acid backbone length on molecular packing: crystalline tartrates of glycine, β‐alanine, γ‐aminobutyric acid (GABA) and dl‐α‐aminobutyric acid (AABA)

We report a novel 1:1 cocrystal of β‐alanine with dl ‐tartaric acid, C₃H₇NO₂·C₄H₆O₆, (II), and three new molecular salts of dl ‐tartaric acid with β‐alanine {3‐azaniumylpropanoic acid–3‐azaniumylpropanoate dl ‐tartaric acid–dl ‐tartrate, [H(C₃H₇NO₂)₂]⁺·[H(C₄H₅O₆)₂]⁻, (III)}, γ‐aminobutyric acid [3‐carboxypropanaminium dl ‐tartrate, C₄H₁₀NO₂⁺·C₄H₅O₆⁻, (IV)] and dl ‐α‐aminobutyric acid {dl ‐2‐azaniumylbutanoic acid–dl ‐2‐azaniumylbutanoate dl ‐tartaric acid–dl ‐tartrate, [H(C₄H₉NO₂)₂]⁺·[H(C₄H₅O₆)₂]⁻, (V)}. The crystal structures of binary crystals of dl ‐tartaric acid with glycine, (I), β‐alanine, (II) and (III), GABA, (IV), and dl ‐AABA, (V), have similar molecular packing and crystallographic motifs. The shortest amino acid (i.e. glycine) forms a cocrystal, (I), with dl ‐tartaric acid, whereas the larger amino acids form molecular salts, viz. (IV) and (V). β‐Alanine is the only amino acid capable of forming both a cocrystal [i.e. (II)] and a molecular salt [i.e. (III)] with dl ‐tartaric acid. The cocrystals of glycine and β‐alanine with dl ‐tartaric acid, i.e. (I) and (II), respectively, contain chains of amino acid zwitterions, similar to the structure of pure glycine. In the structures of the molecular salts of amino acids, the amino acid cations form isolated dimers [of β‐alanine in (III), GABA in (IV) and dl ‐AABA in (V)], which are linked by strong O—H…O hydrogen bonds. Moreover, the three crystal structures comprise different types of dimeric cations, i.e. (A…A)⁺ in (III) and (V), and A⁺…A⁺ in (IV). Molecular salts (IV) and (V) are the first examples of molecular salts of GABA and dl ‐AABA that contain dimers of amino acid cations. The geometry of each investigated amino acid (except dl ‐AABA) correlates with the melting point of its mixed crystal.     

Base‐Induced Decarboxylation of Polyunsaturated α‐Cyano Acids Derived from Malonic Acid: Synthesis of Sesquiterpene Nitriles and Aldehydes with β‐, φ‐, and ψ‐End Groups

Catalytic base‐induced decarboxylation of polyunsaturated α‐cyano‐β‐methyl acids derived from malonic acid led to the corresponding nitriles 3 (Schemes 2 and 3), 6 (Scheme 5), and 9 (Scheme 6). This decarboxylation occurred with previous deconjugation of the α,β‐alkene moiety of the α‐cyano‐β‐methyl acid, leading to an α‐cyano‐β‐methylene propanoic acid which was easily decarboxylated (see Scheme 2). β‐Methylene intermediates, in some cases, could be isolated; mechanistic pathways are proposed. The nitriles 3, 6 , and 9 were reduced to the sesquiterpene aldehydes 4 (β‐end group), 7 (φ‐end group), and 10 (ψ‐end group), respectively.     

α‐Cyclodextrin Host–Guest Binding: A Computational Study of the Different Driving Forces

Free‐energy differences govern the equilibrium between bound and unbound states of a host and its guest molecules. The understanding of the underlying entropic and enthalpic contributions, and their complex interplay are crucial for the design of new drugs and inhibitors. In this study, molecular dynamics (MD) simulations were performed with inclusion complexes of α‐cyclodextrin (αCD) and three monosubstituted benzene derivatives to investigate host–guest binding. αCD Complexes are an ideal model system, which is experimentally and computationally well‐known. Thermodynamic integration (TI) simulations were carried out under various conditions for the free ligands in solution and bound to αCD. The two possible orientations of the ligand inside the cavity were investigated. Agreement with experimental data was only found for the more stable orientation, where the substituent resides inside the cavity. The better stability of this conformation results from stronger Van der Waals interactions and a favorable antiparallel host–guest dipole–dipole alignment. To estimate the entropic contributions, simulations were performed at three different temperatures (250, 300, and 350 K) and using positional restraints for the host. The system was found to be insensitive to both factors, due to the large and symmetric cavity of αCD, and the nondirectional nature of the host–guest interactions.