Spin system assignment of homo-o-phenylene ethynylene oligomers

We previously reported the synthesis and solution characterization of short o-phenylene ethynylene (oPE) foldamers. Proton correlation techniques are not adequate for NMR assignment in these compounds as the ethynylene linkers interrupt proton connectivity. In order to facilitate structural characterization and more fully harness the power of NMR, it is necessary to know the sequence of spin systems along the molecular backbone. For example, spin system assignment is required to unambiguously assign NOE correlations for structural determination of folded forms in solution. Therefore, we developed a method to assign the aromatic spin systems in these compounds using HMBC experiments. This has been performed for tetrameric (Es4), pentameric (Es5), and hexameric (Es6) oligomers and is expected to prove useful for this class of foldamers in general. The proton assignments obtained by this technique have been useful toward confirming the previous hypotheses of helical folding in oPE systems.     

Backbone-rigidified oligo(m-phenylene ethynylenes)

Oligo(m-phenylene ethynylenes) (oligo(m-PE)) with backbones rigidified by intramolecular hydrogen bonds were found to fold into well-defined conformations. The localized intramolecular hydrogen bond involves a donor and an acceptor from two adjacent benzene rings, respectively, which enforces globally folded conformations on these oligomers. Oligomers with two to seven residues have been synthesized and characterized. The persistence of the intramolecular hydrogen bonds and the corresponding curved conformations were established by ab initio and molecular mechanics calculations, 1D and 2D (1)H NMR spectroscopy, and UV spectroscopy. Pentamer 5, hexamer 6, and heptamer 7 adopt well-defined helical conformations. Such a backbone-based conformational programming should lead to molecules whose conformations are resilient toward structural variation of the side groups. These m-PE oligomers have provided a new approach for achieving folded unnatural oligomers under conditions that are otherwise unfavorable for previously described, solvent-driven folding of m-PE foldamers. Stably folded structures based on the design principle described here can be developed and may find important applications.     

Hydrogen bonding-induced aromatic oligoamide foldamers as spherand analogues to accelerate the hydrolysis of nitro-substituted anisole in aqueous media

Four intramolecular hydrogen bonding-driven aromatic amide foldamers 2-5 have been designed and synthesized in which a 2-methoxy-3-nitrobenzamide unit was incorporated at the end of the backbone. Kinetic studies in dioxane-water (4:1, v/v) at 60-90 degrees C have revealed that the folded backbone of the oligomers was, like the rigidified spherand, able to complex Li+, Na+, and K+ and, consequently, accelerated the hydrolysis of the nitro-appended anisole unit of the foldamers. Generally, longer foldamers displayed an increased accelerating effect, and LiOH displayed the highest reactivity probably due to the most efficient complexation by the folded oligomers. Addition of excessive potassium chloride substantially reduced the complexing interaction, and the hydrolysis of the longer oligomers became slower than that of the shorter ones due to an increased steric effect. The results indicate that, even in a hot aqueous medium of high polarity, intramolecular hydrogen bonding is still able to induce structurally matched oligomers to generate a preorganized rigidified conformation.     

Phenylene Ethynylene‐Tethered Perylene Bisimide Folda‐Dimer and Folda‐Trimer: Investigations on Folding Features in Ground and Excited States

In this work, we have elucidated in detail the folding properties of two perylene bisimide (PBI) foldamers composed of two and three PBI units, respectively, attached to a phenylene ethynylene backbone. The folding behaviors of these new PBI folda‐dimer and trimer have been studied by solvent‐dependent UV/Vis absorption and 1D and 2D NMR spectroscopy, revealing facile folding of both systems in tetrahydrofuran (THF). In CHCl₃ the dimer exists in extended (unfolded) conformation, whereas partially folded conformations are observed in the trimer. Temperature‐dependent ¹H NMR spectroscopic studies in [D₈]THF revealed intramolecular dynamic processes for both PBI foldamers due to, on the one hand, hindered rotation around C?N imide bonds and, on the other hand, backbone flapping; the latter process being energetically more demanding as it was observed only at elevated temperature. The structural features of folded conformations of the dimer and trimer have been elucidated by different 2D‐NMR spectroscopy (e.g., ROESY and DOSY) in [D₈]THF. The energetics of folding processes for the PBI dimer and trimer have been assessed by calculations applying various methods, particularly the semiempirical PM6‐DH2 and the more sophisticated B97D approach, in which relevant dispersion corrections are included. These calculations corroborate the results of NMR spectroscopic studies. Folding features in the excited states of these PBI foldamers have been characterized by using time‐resolved fluorescence and transient absorption spectroscopy in THF and CHCl₃, exhibiting similar solvent‐dependent behavior as observed for the ground state. Interestingly, photoinduced electron transfer (PET) process from electron‐donating backbone to electron‐deficient PBI core for extended, but not for folded, conformations was observed, which can be explained by a fast relaxation of excited PBI stacks in the folded conformation into fluorescent excimer states.     

Helical Folding of Conjugated Oligo(phenyleneethynylene): Chain‐Length Dependence,Solvent Effects,and Intermolecular Assembly

As a representative folding system that features a conjugated backbone, a series of monodispersed (o‐phenyleneethynylene)‐alt‐(p‐phenyleneethynylene) (PE) oligomers of varied chain length and different side chains were studied. Molecules with the same backbone but different side‐chain structures were shown to exhibit similar helical conformations in respectively suitable solvents. Specifically, oligomers with dodecyloxy side chains folded into the helical structure in apolar aliphatic solvents, whereas an analogous oligomer with tri(ethylene glycol) (Tg) side chains adopted the same conformation in polar solvents. The fact that the oligomers with the same backbone manifested a similar folded conformation independent of side chains and the nature of the solvent confirmed the concept that the driving force for folding was the intramolecular aromatic stacking and solvophobic interactions. Although all were capable of inducing folding, different solvents were shown to bestow slightly varied folding stability. The chain‐length dependence study revealed a nonlinear correlation between the folding stability with backbone chain length. A critical size of approximately 10 PE units was identified for the system, beyond which folding occurred. This observation corroborated the helical nature of the folded structure. Remarkably, based on the absorption and emission spectra, the effective conjugation length of the system extended more effectively under the folded state than under random conformations. Moreover, as evidenced by the optical spectra and dynamic light‐scattering studies, intermolecular association took place among the helical oligomers with Tg side chains in aqueous solution. The demonstrated ability of such a conjugated foldamer in self‐assembling into hierarchical supramolecular structures promises application potential for the system.     

N,N'-linked oligoureas as foldamers: chain length requirements for helix formation in protic solvent investigated by circular dichroism, NMR spectroscopy, and molecular dynamics

N,N'-linked oligoureas with proteinogenic side chains are peptide backbone mimetics belonging to the gamma-peptide lineage. In pyridine, heptamer 4 adopts a stable helical fold reminiscent of the 2.6(14) helical structure proposed for gamma-peptide foldamers. In the present study, we have used a combination of CD and NMR spectroscopies to correlate far-UV chiroptical properties and conformational preferences of oligoureas as a function of chain length from tetramer to nonamer. Both the intensity of the CD spectra and NMR chemical shift differences between alphaCH2 diastereotopic protons experienced a marked increase for oligomers between four and seven residues. No major change in CD spectra occurred between seven and nine residues, thus suggesting that seven residues could be the minimum length required for stabilizing a dominant conformation. Unexpectedly, in-depth NMR conformational investigation of heptamer 4 in CD3OH revealed that the 2.5 helix probably coexists with partially (un)folded conformations and that Z-E urea isomerization occurs, to some degree, along the backbone. Removing unfavorable electrostatic interactions at the amino terminal end of 4 and adding one H-bond acceptor by acylation with alkyl isocyanate (4 --> 7) was found to reinforce the 2.5 helical population. The stability of the 2.5 helical fold in MeOH is further discussed in light of unrestrained molecular dynamics (MD) simulation. Taken together, these new data provide additional insight into the folding propensity of oligoureas in protic solvent and should be of practical value for the design of helical bioactive oligoureas.     

meta-Substituted benzamide oligomers that complex mono-, di- and tricarboxylates: folding-induced selectivity and chirality

meta-Substituted arylamide trimer, pentamer and heptamer have been prepared from simple benzene-1,3-diamine, benzene-1,3-dicarboxylic acid, and 3-aminobenzoic acid units. 2D NOESY (1)H NMR experiments reveal that these flexible oligomers form folded conformations to complex di- and tricarboxylate anions of varying sizes and shapes in DMSO of high polarity, which is driven by multiple intermolecular N-H···O=C and C-H···O=C hydrogen-bonds between the amide and aromatic hydrogens of the oligomers and the carboxylate oxygens of the anions. Generally, tricarboxylate anions display an increased binding affinity compared with the dicarboxylate anions and the complexes formed by 1,3-benzenedicarboxylate anion are more stable than those formed by 1,2- or 1,4-benzenedicarboxylate anions. Circular dichroism experiments show that chiral glutamic acid dianion can induce the oligomers to produce chiral bias, leading to the formation of chiral supramolecular complexes.     

A folded,secondary structure in step-growth oligomers from covalently linked,crowded aromatics

This study delineates general methods to create a new class of folded oligomers by covalently attaching overcrowded aromatics to each other. Crucial to observing the secondary structure in these oligomers was the employment of C-shaped linkers. These linkers preorganize the strands to form intramolecular hydrogen bonds. In solution, one- and two-dimensional (1)H NMR data show well-defined columnar conformations. The side chains in these oligomers are critical for the secondary structure to emerge in solution. Using tris(dodecyloxy)phenethyl side chains in combination with tert-butyl side chains in the terminal subunit provides a soluble trimer and prevents intermolecular association above millimolar concentrations. This new folding motif, formed through a synergy between hydrogen bonds and pi-stacking, is so robust that even dimers have secondary structure in solution.     

Oligomers of enantiopure bicyclic gamma/delta-amino acids (BTAa). 1. Synthesis and conformational analysis of 3-aza-6,8-dioxabicyclo

A series of dimeric through pentameric oligomers of a bicyclic gamma/delta-amino acid (BTG) were synthesized using peptide coupling methods in solution with PyBroP or HATU. The analysis of (1)H NMR and CD spectra suggests that these oligomers could have a partially ordered structure in alcohol solutions.     

Bis- and tris-(methylphosphonic) acid derivatives of a 14-membered tetraazamacrocycle containing pyridine: synthesis, protonation and complexation studies

Two N-methylphosphonic acid derivatives of a 14-membered tetraazamacrocycle containing pyridine have been synthesized, H(4)L(1) and H(6)L(2). The protonation constants of these compounds and the stability constants of complexes of both ligands with Ni(2+), Cu(2+) and Zn(2+) were determined by potentiometric methods at 298 K and ionic strength 0.10 mol dm(-3) in NMe(4)NO(3). The high overall basicity of both compounds is ascribed to the presence of the phosphonate arms. (1)H and (31)P NMR spectroscopic titrations were performed to elucidate the sequence of protonation, which were complemented by conformational analysis studies. The complexes of these ligands have stability constants of the order of or higher than those formed with ligands having the same macrocyclic backbone but acetate arms. At pH = 7 the highest pM values were found for solutions containing the compound with three acetate groups, followed immediately by those of H(6)L(2), however, as expected, the increasing pH favours the complexes of ligands containing phosphonate groups. The single-crystal structure of Na(2)[Cu(HL(1))]NO(3)x8H(2)O has shown that the coordination geometry around the copper atom is a distorted square pyramid. Three nitrogen atoms of the macrocyclic backbone and one oxygen atom from one methylphosphonate arm define the basal plane, and the apical coordination is accomplished via the nitrogen atom trans to the pyridine ring of the macrocycle. To achieve this geometric arrangement, the macrocycle adopts a folded conformation. This structure seems consistent with Uv-vis-NIR spectroscopy for the Ni(2+) and the Cu(2+) complexes and with the EPR for the latter.     

Dimers of anthrathiophene and anthradithiophene derivatives: synthesis and characterization

Synthesis, isolation, and characterization of derivatives of an anthrathiophene dimer (TOTBAT) and of anthradithiophene oligomers (ADTO), possessing octylthiophene units on their backbone, are described. These semiconductors are prepared through oxidative copper(II) chloride coupling. The spectroscopic properties and stability of these newly synthesized semiconductors were evaluated and supported by quantum-chemical calculations.     

Solution structure of quinoline- and pyridine-derived oligoamide foldamers

The unambiguous elucidation of a new folded structure in solution may prove to be a very challenging task. The NMR protocols developed for solving the solution structures of alpha-peptides have been applied to aliphatic beta- and gamma-peptides but are not directly applicable to aromatic oligomers. In particular, the string of spin systems in an aromatic sequence cannot be reconstituted solely from correlations between protons. For aromatic oligomers, it is shown that the assignment of a large part of the 13C NMR spectrum through HMBC and HSQC experiments allows to unambiguously assign proton NMR spectra and in turn to interpret NOE correlations. This has been implemented both with quinoline- and pyridine-derived oligoamide foldamers, and should be applicable to a wide range of oligomers including various combinations of monomers. The NOE correlations allow the unambiguous solution structure elucidation of helical conformations of oligoamides derived from pyridine and quinoline monomers showing that, in these series, the solution structures correspond very well to the structures observed in the solid state.     

Synthesis of α,ω-arylamine functionalized poly(dimethylsiloxane)s

This research has focused on the development of telechelic, aromatic amine functional, poly(dimethylsiloxane) oligomers without any aliphatic components in the polymer backbone. The intent is to produce flexible oligomers with enhanced thermal stability for incorporation into materials which will be processed at elevated temperatures. The poly(dimethylsiloxane)s have been synthesized using living polymerization of hexamethylcyclotrisiloxane with protected aniline derivatives as initiators and termination reagents for the reactions. Low molecular weight oligomers prepared using the living polymerization method can be easily converted to a range of higher, controlled molecular weight materials in redistribution reactions. A basic tetramethylammonium siloxanolate catalyst in conjunction with octamethylcyclotetrasiloxane has been used for the equilibration procedure. © 1993 John Wiley & Sons, Inc.     

Probing the effect of temperature on the backbone dynamics of the human alpha-lactalbumin molten globule

Molten globules are compact, partially folded proteins postulated to be general intermediates in protein folding. Human alpha-lactalbumin (alpha-LA) is a two-domain Ca(2+)-binding protein that partially unfolds at low pH to form a molten globule. NMR spectra of molten globules are characterized by broadened resonances due to conformational fluctuations on microsecond to millisecond time scales. These species are often studied at high temperature where NMR resonances are observed to sharpen. The effect of higher temperatures on fast time-scale backbone dynamics of molten globules has not been investigated previously. Here, 1D (15)N direct-detection and 2D indirect-detection (1)H-(15)N heteronuclear NOE experiments have been used to probe fast time-scale dynamics at low and high temperatures for three disulfide-bond variants of human alpha-LA that form molten globules. Disulfide bonds are found to have a significant effect on backbone dynamics within the beta-domain of the molten globule; within the alpha-domain, dynamics are not significantly influenced by these bonds. At 20 degrees C, backbone mobility is significantly decreased in both domains of the molten globule compared to the mobility at 40-50 degrees C. Heteronuclear NOE values determined at 20 degrees C for the alpha-domain are closely similar to those observed for native alpha-LA, indicating that the alpha-LA molten globule has even more native-like character than suggested by studies conducted at higher temperature. Our results highlight the importance of considering the temperature dependence of the molten globule ensemble when making comparisons between experimental data obtained under different conditions.     

Side chain dynamics in unfolded protein states: an NMR based 2H spin relaxation study of delta131delta

NMR relaxation data on disordered proteins can provide insight into both structural and dynamic properties of these molecules. Because of chemical shift degeneracy in correlation spectra, detailed site-specific analyses of side chain dynamics have not been possible. Here, we present new experiments for the measurement of side chain dynamics in methyl-containing residues in unfolded protein states. The pulse schemes are similar to recently proposed methods for measuring deuterium spin relaxation rates in (13)CH(2)D methyl groups in folded proteins.(1) However, because resolution in (1)H-(13)C correlation maps of unfolded proteins is limiting, relaxation data are recorded as a series of (1)H-(15)N spectra. The methodology is illustrated with an application to the study of side chain dynamics in delta131delta, a large disordered fragment of staphylococcal nuclease containing residues 1-3 and 13-140 of the wide-type protein. A good correlation between the order parameters of the symmetry axes of the methyl groups and the backbone (1)H-(15)N bond vectors of the same residue is observed. Simulations establish that such a correlation is only possible if the unfolded state is comprised of an ensemble of structures which are not equiprobable. A motional model, which combines wobbling-in-a-cone and Gaussian axial fluctuations, is proposed to estimate chi(1) torsion angle fluctuations, sigma(chi)()1, of Val and Thr residues on the basis of the backbone and side chain order parameters. Values of sigma(chi)()1 are approximately 10 degrees larger than what has previously been observed in folded proteins. Of interest, the value of sigma(chi)()1 for Val 104 is considerably smaller than for other Val or Thr residues, suggesting that it may be part of a hydrophobic cluster. Notably large (15)N transverse relaxation rates are observed in this region. To our knowledge, this is the first time that side chain dynamics in an unfolded state have been studied in detail by NMR.     

Molecular Bottle Brushes with Positioned Selenols: Extending the Toolbox of Oxidative Single Polymer Chain Folding with Conformation Analysis by Atomic Force Microscopy

A synthesis route to controlled and dynamic single polymer chain folding is reported. Sequence-controlled macromolecules containing precisely located selenol moieties within a polymer chain are synthesized. Oxidation of selenol functionalities lead to diselenide bridges and induces controlled intramolecular crosslinking to generate single chain collapse. The cyclization process is successfully characterized by SEC as well as by ¹H NMR and 2D HSQC NMR spectroscopies. In order to gain insight on the molecular level to reveal the degree of structural control, the folded polymers are transformed into folded molecular brushes that are known to be visualizable as single molecule structures by AFM. The “grafting onto” approach is performed by using triazolinedione−diene reaction to graft the side chain polymers. A series of folded molecular brushes as well as the corresponding linear controls are synthesized. AFM visualization is proving the cyclization of the folded backbone by showing globular objects, where non-folded brushes show typical worm-like structures. © 2019 Wiley Periodicals, Inc. J. Polym. Sci. 2020 , 58, 154–162     

Expected and unexpected results from combined beta-hairpin design elements

A model beta-hairpin dodecapeptide [EFGWVpGKWTIK] was designed by including a favorable D-ProGly Type II' beta-turn sequence and a Trp-zip interaction, while also incorporating a beta-strand unfavorable glycine residue in the N-terminal strand. This peptide is highly folded and monomeric in aqueous solution as determined by combined analysis with circular dichroism and 1H NMR spectroscopy. A peptide representing the folded conformation of the model beta-hairpin [cyclic(EFGWVpGKWTIKpG)] and a linear peptide representing the unfolded conformation [EFGWVPGKWTIK] yield unexpected relative deviations between the CD and 1H NMR spectroscopic results that are attributed to variations in the packing interactions of the aromatic side chains. Mutational analysis of the model beta-hairpin indicates that the Trp-zip interaction favors folding and stability relative to an alternate hydrophobic cluster between Trp and Tyr residues [EFGYVpGKWTIK]. The significance of select diagonal interactions in the model beta-hairpin was tested by rearranging the cross-strand hydrophobic interactions to provide a folded peptide [EWFGIpGKTYWK] displaying evidence of an unusual backbone conformation at the hydrophobic cluster. This unusual conformation does not appear to be a result of the glycine residue in the beta-strand, as replacement with a serine results in a peptide [EWFSIpGKTYWK] with a similar and seemingly characteristic CD spectrum. However, an alternate arrangement of hydrophobic residues with a Trp-zip interaction in a similar position to the parent beta-hairpin [EGFWVpGKWITK] results in a folded beta-hairpin conformation. The differences between side chain packing of these peptides precludes meaningful thermodynamic analysis and illustrates the caution necessary when interpreting beta-hairpin folding thermodynamics that are driven, at least in part, by aromatic cross strand interactions.     

Synthesis and morphological characterization of poly(ϵ-caprolactone) and poly(2-methyloxazoline) substituted phenyl rings and phenylene oligomers

Poly(ϵ-caprolactone) (PCL) and poly(2-methyloxazoline) (POx) substituted phenyl rings (macromonomers) and the corresponding substituted polyphenylene oligomers have been synthesized in various chemical structures. Macromonomers were synthesized by ring opening polymerization. Poly(phenylene) oligomers were then synthesized by cross-coupling of the macromonomers in Ni-catalyzed polycondensation reactions. The macromonomers and oligomers have been characterized by ¹H-NMR, IR, GPC, and DSC. The effect of side chain chemistry and architecture on the resulting morphology in thin films has been investigated by atomic force micro-scopy and wide angle X-ray scattering. Polyphenylene oligomers showed layered morphologies in thin films. The orientation of the layers depended on the chemistry of the side chains and the backbone architecture. Linear oligomers containing statistically distributed segments having POx or PCL side chains showed layers perpendicular to the underlying substrate. Attachment of polystyrene end block to PCL chain together with the meta-connectivity of the backbone resulted in layers parallel to the substrate. Our results also indicate that substitution of polymeric chains to phenyl rings can induce ordered structures of macromonomers. © 2007 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 45: 2091–2104, 2007     

Controlling chain conformation in conjugated polymers using defect inclusion strategies

The Horner method was used to synthesize random copolymers of poly(2-methoxy-5-(2'-ethylhexyloxy)-p-phenylene vinylene) (MEH-PPV) that incorporated different backbone-directing monomers. Single-molecule polarization absorption studies of these new polymers demonstrate that defects that preserve the linear backbone of PPV-type polymers assume the highly anisotropic configurations found in defect-free MEH-PPV. Rigid defects that are bent lower the anisotropy of the single chain, and saturated defects that provide rotational freedom for the chain backbone allow for a wide variety of possible configurations. Molecular dynamics simulations of model defect PPV oligomers in solution demonstrate that defect-free and linearly defected oligomers remain extended while the bent and saturated defects tend toward more folded, compact structures.     

Intrastrand foldamer crosslinking by reductive amination

A series of m‐phenylene ethynylene (mPE) foldamers were crosslinked in their helical conformation using a reductive amination‐based strategy. This was accomplished by placing aldehyde moieties in the backbone of the oligomer at specific residues, which allowed a diamine crosslinker to covalently link the helical loops together. Three different foldamers with crosslinks placed at different locations in the backbone were synthesized and characterized by mass spectrometry, ¹H NMR, and gel permeation chromatography. The effect of the crosslinking on the stability of the folded state was evaluated through solvent denaturation studies. These studies show a reduction in the oligomer's ability to unfold of up to 30% relative to an unmodified mPE oligomer of the same length in solvents that promote unfolding. © 2010 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 48: 927–935, 2010