Expected and unexpected intramolecular cationic cyclizations

Cationic cyclizations of N-phenacyl-4-aryl-1,2,3,6-tetrahydropyridines and related compounds were studied, and structures I products formed were elucidated using NMR spectroscopy.Institute for Drug Research, Ltd. H-1045 Budapest, Berlini-u 47-49, Hungary. Published in Khimiya Geterotsiklicheskikh Soedinenii, No. 10, pp. 1367–1372, October, 1995. Original article submitted August 24, 1995.     

On the reactions of trifluorovinylsilanes with aromatic ketones - Expected and some unexpected results

The reactions of aromatic ketones with trialkyl(trifluorovinyl)silanes in the presence of fluoride ions were studied. The conditions for the selective addition of trialkyl(trifluorovinyl)silanes to the carbonyl function of aromatic ketones in the presence of cesium fluoride and absence of any solvents to form the trifluorovinyl containing “silylated” alcohols have been worked out. The analogous reactions in common organic solvents are not terminated on the stage of “silylated” alcohols formation; consecutive reactions lead to fluorinated olefins and acids under the influence of fluoride ions.     

Expected and unexpected photochemical reactions of acyl iodides

Photolysis of acyl iodides RCOI (R = Me, Me₂CH, Ph) under UV irradiation in toluene environment for 20–55 h proved to be a simple and efficient method of preparation of symmetrical α-diketones RCOCOR. In contrast, the photolysis under the same conditions of acyl iodides RCOI [R = Me(CH₂)₃, Me₃C] did not lead to the formation of the corresponding diacyls, and the reaction products were unexpected 1,1-bis(4-methylphenyl)pentane and a mixture of isomeric 3- and 4-methyl(tert-butyl)benzenes respectively. The most probable mechanism of their formation is the primary photochemical acylation of toluene in the aromatic ring followed by the photochemical reduction of the arising butyl 4-methylphenyl ketone in the case of the valeroyl iodide or the photochemical Norrish type I cleavage of isomeric 3- and 4-methylphenyl (tert-butyl) ketones in event of the pivaloyl iodide. In the photolysis of acetyl iodide (R = Me) in benzene or toluene alongside the diacetyl formation polyarylation process was observed of acylated and iodinated into the aromatic ring solvents with the formation of polymeric products with semiconductor and paramagnetic properties.     

De novo design of strand-swapped beta-hairpin hydrogels

De novo designed peptides, capable of undergoing a thermally triggered beta-strand-swapped self-assembly event leading to hydrogel formation were prepared. Strand-swapping peptide 1 (SSP1) incorporates an exchangeable beta-strand domain composed of eight residues appended to a nonexchangeable beta-hairpin domain. CD shows that, at pH 9 and temperatures less than 35 degrees C, this peptide adopts a random coil conformation, rendering it soluble in aqueous solution. On heating to 37 degrees C or greater, SSP1 adopts a beta-hairpin that displays an exchangeable beta-strand region. The exchangeable strand domain participates in swapping with the exchangeable domain of another peptide, affording a strand-swapped dimer. These dimers further assemble into fibrils that define the hydrogel. A second peptide (SSP2) containing an exchangeable strand composed of only four residues was also studied. Microscopy and scattering data show that the length of the exchangeable domain directly influences the fibril nanostructure and can be used as a design element to construct either twisted (SSP1) or nontwisted (SSP2) fibril morphologies. CD, FTIR, and WAXS confirm that both peptides adopt beta-sheet secondary structure when assembled into fibrils. Fibril dimensions, as measured by TEM, AFM, and SANS indicate a fibril diameter of 6.4 nm, a height of 6.0 nm, and a pitch of 50.4 nm for the twisted SSP1 fibrils. The nontwisted SSP2 fibrils are 6.2 nm in diameter and 2.5 nm in height. Oscillatory rheology, used to measure bulk hydrogel rigidity, showed that the gel composed of the nontwisted fibrils is more mechanically rigid (517 Pa at 6 rad/s) than the gel composed of twisted fibrils (367 Pa at 6 rad/s). This work demonstrates that beta-strand-swapping can be used to fabricate biomaterials with tunable fibril nanostructure and bulk hydrogel rheological properties.     

Expected and unexpected effects of amino acid substitutions on polypeptide-directed crystal growth

Nature's use of biomineralization polypeptides to control and modulate the growth of biogenic minerals is an important process that, if properly understood, could have significant implications for designing and creating new inorganic-based materials. Although the sequences for a number of biomineralization proteins exist, very little is known about the participation of specific amino acids in the mineral modulation process. In this letter, we investigate the impact of global Asp --> Asn and Glu --> Gln substitutions on two mollusk shell nacre polypeptides, AP7N and n16N. We find that these global substitutions, which remove all anionic Ca(II) binding sites, abolish the expected in vitro mineralization activities associated with each native polypeptide. In addition, the ability of substituted peptides to form complexes with both Ca(II) and Ca(II) metal ion analogs is also abolished. However, some unexpected effects were noted. First, the Asp --> Asn, Glu --> Gln substituted n16N polypeptide is observed to self-assemble and form biofilms or coatings that appear to mineralize in vitro. Second, both polypeptides are structurally affected by these substitutions, with Asp --> Asn substituted AP7N transforming to an alpha helix and Asp --> Asn, Glu --> Gln substituted n16N transforming to a more unfolded random-coil-like structure. We find that the participation of Asp and Glu residues is crucial to the inherent mineralization activities and conformations of AP7N and n16N polypeptides. Surprisingly, we find that the replacement of anionic residues within biomineralization polypeptides such as n16N still permits mineral modulation, but in a different form that now involves peptide self-association and biofilm formation.     

Expected and unexpected reactions in ring‐opening (co)polymerization

This review covers most of the authors' work on ring‐opening polymerization and copolymerization of heterocyclic monomers during the time of their cooperation since 1985. The mechanistic aspects of anionic ring opening polymerization of cyclic carbonates with a variety of functional groups are described first. By sequential polymerization of first styrene, methyl methacrylate or suitable heterocyclic monomers and then secondly a cyclic carbonate, the site transformation is highlighted. The influence of the chemical nature of macroinitiators with identical active sites on the course of polymerization of cyclic carbonates was studied for poly(ethylene oxide), poly(tetrahydrofuran), and poly(dimethylsiloxane) macroinitiators. For the copolymerization of cyclic carbonates with lactones and lactide the dependence of the polymer microstructure on the polymerization conditions is discussed on the basis of the copolymerization mechanism. The copolymerization of cyclic carbonates with ε‐caprolactam and with tetramethylene urea results in an alternating copolymer, i. e. a poly(ester urethane) and an [m, n]‐polyurethane, respectively, the key step being the insertion of the lactam or the cyclic urea into the carbonate chain. The cationic ring opening polymerization of cyclic six and seven membered carbamates leading to [4]‐ and [5]‐polyurethane with uniform microstructure is reported with respect to kinetic, mechanistic, and thermodynamic aspects. This new access to [n]‐polyurethanes by a chain growth reaction allows the synthesis of well defined polymer architectures with polyurethane sequences. Sequential polymerization of tetrahydrofuran and the cyclic carbamate with mono‐ and bifunctional initiators leads to the respective A–B and B–A–B block copolymers. Site transformation from the oxonium to the immonium active species is the key step in the polymerization mechanism. Finally, mechanistic aspects of the ring‐opening polymerization of cyclic ester‐amides are presented.     

Minimalist protein design: a beta-hairpin peptide that binds ssDNA

A 28-residue beta-hairpin dimer (WKWK)2 with two Trp and two Lys residues on one face of each beta-sheet was shown to form a complex with single-stranded oligonucleotides at low micromolar concentrations. Each beta-hairpin of the dimer contains a cross-strand Trp-Trp pair in a diagonal orientation which has previously been shown to create a cleft for the intercalation of aromatic guests such as adenine (J. Am. Chem. Soc. 2003, 125, 9580). The beta-hairpin dimer binds 5-residue ssDNA sequences 5'-AAAAA-3', 5'-TTTTT-3', and 5'-CCCCC-3' in water with dissociation constants in the range of 12-30 muM. A weak energetic preference for binding to sequence 5'-AAAAA-3' was observed, which is believed to result from stronger stacking interactions between Trp and the adenine base. The interaction of 5'-AAAAA-3' with the Lys and Trp residues of the peptide was evident by NMR, and a 1:1 association was demonstrated. The recognition of an 11-residue ssDNA sequence occurred with a dissociation constant of 3 muM under near-physiological ionic strength and pH, demonstrating that the beta-hairpin dimer binds ssDNA as strongly as many naturally occurring proteins. The salt dependence of the interaction of the 11-residue oligonucleotide with the peptide dimer indicates that Trp-nucleobase stacking interactions contribute about -4 kcal/mol to recognition, which is much greater than the contribution of nonionic interactions in unstructured peptides containing Trp. Moreover, recognition of the ssDNA demonstrated reduced salt dependence relative to the corresponding duplex, resulting in selectivity for ssDNA under high salt conditions. Peptide (WKWK)2 is a relevant mimic of OB-fold (oligonucleotide/oligosaccharide-binding) proteins which bind ssDNA on the surface of a beta-sheet.     

Use of molecular dynamics in the design and structure determination of a photoinducible beta-hairpin

The study presented here consists of three parts. In the first, the ability of a set of differently substituted diazobenzene-based linkers to act as photoswitchable beta-turn building blocks was assessed. A 12-residue peptide known to form beta-hairpins was taken as the basis for the modeling process. The central (beta-turn) residue pair was successively replaced by six symmetrically ((o,o), (m,m), or (p,p)) substituted (aminomethyl/carboxymethyl or aminoethyl/carboxyethyl) diazobenzene derivatives leading to a set of peptides with a photoswitchable backbone conformation. The folding behavior of each peptide was then investigated by performing molecular dynamics simulations in water (4 ns) and in methanol (10 ns) at room temperature. The simulations suggest that (o,o)- and (m,m)-substituted linkers with a single methylene spacer are significantly better suited to act as photoswitchable beta-turn building blocks than the other linkers examined in this study. The peptide containing the (m,m)-substituted linker was synthesized and characterized by NMR in its cis configuration. In the second part of this study, the structure of this peptide was refined using explicit-solvent simulations and NOE distance restraints, employing a variety of refinement protocols (instantaneous and time-averaged restraining as well as unrestrained simulations). We show that for this type of systems, even short simulations provide a significant improvement in our understanding of their structure if physically meaningful force fields are employed. In the third part, unrestrained explicit-solvent simulations starting from either the NMR model structure (75 ns) or a fully extended structure (25 ns) are shown to converge to a stable beta-hairpin. The resulting ensemble is in good agreement with experimental data, indicating successful structure prediction of the investigated hairpin by classical explicit-solvent molecular dynamics simulations.     

Photocycloadditions of tetrachloro-1,4-benzoquinone (chloranil) onto cyclobutene and cyclopropene. Expected and unexpected products

Solutions of chloranil (CA) in chlorobenzene were irradiated in the presence of cyclobutene and cyclopropene. Cyclobutene gave rise to two conventional 1 : 2 cycloadducts onto the dichloroethene subunits of CA and an α,β-unsaturated α,γ-dichloro-γ-lactone. Heating of the crude product in methanol converted the lactone into an α,β-unsaturated methyl γ-oxocarboxylate (25% yield) and a large amount of the major 1 : 2 cycloadduct, which contains chlorocyclobutane entities, into a cyclopropylcarbinyl chloride derivative (24% yield). An entirely new product type was the result in the case of cyclopropene. After treatment of the crude product with methanol a tetracyclic acetal containing a cyclopentanone and a dihydropyran subunit was isolated in 36% yield. Apparently, CA had taken up two molecules of cyclopropene. One of the resulting cyclopropane entities must have undergone a rearrangement en route to the final product.     

Expected and unexpected behavior of the orientational order and dynamics induced by azobenzene solutes in a nematic

We have explored the changes in the phase stability, orientational order, and dynamics of the nematic 4-cyano-4'-n-pentylbiphenyl (5CB) doped with either the trans or the cis form of different p-azobenzene derivatives using the ESR spin-probe technique. In particular, we have studied the effects induced by each of the seven nonmesogenic 4-R-phenylazobenzenes (R = H, F, Br, CH3, CF3, On-Bu, Ot-Bu) at 1% and 7% mole fraction on the order parameter and on the shift of the nematic-isotropic transition temperature (TNI), as reported by a nitroxide spin probe, and we have tried to relate them to the solute shape and charge distribution. In all the cases the presence of the azo-derivative causes a depression of T(NI), more pronounced for the cis isomers. The dependence of on the reduced temperature T* = T/T(NI) remains the same as that of pure 5CB in all trans-doped samples at 1% and 7% and decreases only slightly in the cis at 1%. However, we observe different and in some cases large variations (up to 25%) in for the cis at 7%, showing solute effects that go beyond the shift in T(NI). Surprisingly enough, even at the highest concentration, the probe dynamics appears to be essentially independent of the nature, the configuration, and the concentration of the different solutes and very similar to that observed in the pure 5CB.     

Expected and unexpected reactions of 1,3-benzothiazine derivatives, II. Formation of isomeric 5,6-dihydro-1,5-benzothiazocines

A method for the synthesis of medium-sized 1,5-benzothiazocines by ring enlargement of 1,3-benzothiazines has been developed. When N-alkyl-1,3-benzothiazines were reacted with dimethyl acetylenedicarboxylate in acetonitrile at room temperature, regioisomeric 5,6-dihydro-2H-1,5-benzothiazocines and 5,6-dihydro-4H-1,5-benzothiazocines were obtained as novel ring systems. Dimethyl acetylenedicarboxylate could attack either the nitrogen or the sulfur atom of the thiazines. NMR spectroscopic and X-ray crystallographic investigations confirmed the structures of the products.     

Alpha-helix and beta-hairpin Folding from experiment,analytical theory and molecular dynamics simulations

The alpha-helix and beta-hairpin are the minimal secondary structure elements of proteins. Identification of the factors governing the formation of these structures independently of the rest of the protein is important for understanding the determinants and rules driving the folding process to a unique native structure. It has been shown that some alpha-helices and beta-hairpins can fold autonomously into native-like structures, either in aqueous solution or in the presence of an organic co-solvent; possible mechanisms of these processes have been considered in literature. The characteristic times for folding of alpha and beta structures are estimated from experiments, simple analytical theories and more detailed computer models. Our aim is to review recent experimental and theoretical studies of folding of alpha and beta structures focusing much attention on beta-hairpins.     

Minimization and optimization of designed beta-hairpin folds

Minimized beta hairpins have provided additional data on the geometric preferences of Trp interactions in TW-loop-WT motifs. This motif imparts significant fold stability to peptides as short as 8 residues. High-resolution NMR structures of a 16- (KKWTWNPATGKWTWQE, DeltaG(U)(298) >or= +7 kJ/mol) and 12-residue (KTWNPATGKWTE, DeltaG(U)(298) = +5.05 kJ/mol) hairpin reveal a common turn geometry and edge-to-face (EtF) packing motif and a cation-pi interaction between Lys(1) and the Trp residue nearest the C-terminus. The magnitude of a CD exciton couplet (due to the two Trp residues) and the chemical shifts of a Trp Hepsilon3 site (shifted upfield by 2.4 ppm due to the EtF stacking geometry) provided near-identical measures of folding. CD melts of representative peptides with the -TW-loop-WT- motif provided the thermodynamic parameters for folding, which reflect enthalpically driven folding at laboratory temperatures with a small DeltaC(p) for unfolding (+420 J K(-)(1)/mol). In the case of Asx-Pro-Xaa-Thr-Gly-Xaa loops, mutations established that the two most important residues in this class of direction-reversing loops are Asx and Gly: mutation to alanine is destabilizing by about 6 and 2 kJ/mol, respectively. All indicators of structuring are retained in a minimized 8-residue construct (Ac-WNPATGKW-NH(2)) with the fold stability reduced to DeltaG(U)(278) = -0.7 kJ/mol. NMR and CD comparisons indicate that -TWXNGKWT- (X = S, I) sequences also form the same hairpin-stabilizing W/W interaction.     

N-Acylation of 4-alkylidene-β-lactams: unexpected results

This paper describes the different reactivity of E- and Z-4-alkylidene-β-lactams in acylation reactions under basic conditions. The E isomer is readily acylated, whereas the Z reacted sluggishly rearranging to the corresponding oxazin-6-one. The N-acylation of Z isomers was successfully obtained with oxalyl- or malonyl chlorides in benzene at reflux.     

Expected and unexpected etherification of 2-per(poly)fluoroethyl 4-substitutedphenol with β-haloethanol

Under different reaction conditions, the expected and unexpected reaction products (of which X-ray crystallographic structure was presented) of etherification of 2-per(poly)fluoroethyl 4-substituted phenol with β-haloethanol can be obtained respectively.     

Expected and unexpected photoreactions of 9-(10-)substituted anthracene derivatives in cucurbit[n]uril hosts

By arranging substrates in a “reaction ready” state through noncovalent interactions, supramolecular nanoreactors/catalysts show high selectivity and/or rate acceleration features. Herein, we report the host–guest complexation of 9-(10-)substituted anthracene derivatives (G1–G3) with cucurbit[n]uril (CB[n], n = 8, 10), and the photoreactions of these derivatives in the presence of CB[n] hosts. Both CB[10] and CB[8] showed no obvious effects on the photoreaction of 9,10-disubstituted derivative G1. For G2 and G3, CB[10] operated as either a nanoreactor or catalyst (10%) for the photodimerization of two compounds with high selectivity and high yield. However, although CB[8] formed a 1 : 2 complex with G2, as also observed with CB[10], the photosolvolysis product (9-anthracenemethanol) was obtained quantitatively after photoirradiation of the CB[8]·2G2 complex. This unexpected photosolvolysis was rationalized by a plausible catalytic cycle in which anthracene acts as a photoremovable protecting group (PPG) and the carbonium ion intermediate is stabilized by CB[8].

The photodimerization of 9-substituted anthracene derivative was tremendously promoted by a catalytic amount of cucurbit[10]uril (CB[10]) in water. While CB[8] exclusively induced the photosolvolysis of the anthracene derivative.     

Theoretical characterization of alpha-helix and beta-hairpin folding kinetics

By means of the conformational free energy surface and corresponding diffusion coefficients, as obtained by long time scale atomistic molecular dynamics simulations (mus time scale), we model the folding kinetics of alpha-helix and beta-hairpin peptides as a diffusive process over the free energy surface. The two model systems studied in this paper (the alpha-helical temporin L and the beta-hairpin prion protein H1 peptide) exhibit a funnel-like almost barrierless free energy profile, leading to nonexponential folding kinetics matching rather well the available experimental data. Moreover, using the free energy profile provided by Mu?oz et al. [Mu?oz et al. Nature 1997, 390: 196-199], this model was also applied to reproduce the two-state folding kinetics of the C-terminal beta-hairpin of protein GB1, yielding an exponential folding kinetics with a time constant (approximately 5 micros) in excellent agreement with the experimentally observed one (approximately 6 micros). Finally, the folding kinetics obtained by solving the diffusion equation, considering either a one-dimensional or a two-dimensional free energy surface, are also compared in order to understand the relevance of the possible kinetic coupling between conformational degrees of freedom in the folding process.