Folding‐Induced Modulation of Excited‐State Dynamics in an Oligophenylene–Ethynylene‐Tethered Spiral Perylene Bisimide Aggregate

The excited‐state photophysical behavior of a spiral perylene bisimide (PBI) folda‐octamer ( F8 ) tethered to an oligophenylene–ethynylene scaffold is comprehensively investigated. Solvent‐dependent UV/Vis and fluorescence studies reveal that the degree of folding in this foldamer is extremely sensitive to the solvent, thus giving rise to an extended conformation in CHCl₃ and a folded helical aggregate in methylcyclohexane (MCH). The exciton‐deactivation dynamics are largely governed by the supramolecular structure of F8 . Femtosecond transient absorption (TA) in the near‐infrared region indicates a photoinduced electron‐transfer process from the backbone to the PBI core in the extended conformation, whereas excitation power‐ and polarization‐dependent TA measurements combined with computational modeling showed that excitation energy transfer between the unit PBI chromophores is the major deactivation pathway in the folded counterpart.     

Perylene Bisimide Dimer Aggregates: Fundamental Insights into Self‐Assembly by NMR and UV/Vis Spectroscopy

A novel perylene bisimide (PBI) dye bearing one solubilizing dialkoxybenzyl and one bulky 2,5‐di‐tert‐butylphenyl substituent was synthesized and its aggregation behavior was analyzed by NMR and UV/Vis spectroscopy in various chloroform/methylcyclohexane (MCH) solvent mixtures. In the presence of no less than 10 vol % chloroform, exclusive self‐assembly of this PBI dye into π‐stacked dimers was unambiguously confirmed by means of both concentration‐dependent ¹H NMR and UV/Vis spectroscopic experiments. Based on ROESY NMR, a well‐defined π‐stacked dimer structure was determined and further corroborated by molecular modeling studies. By varying the solvent composition of chloroform and MCH, the solvent effects on the Gibbs free energy of PBI dimerization were elucidated and showed a pronounced nonlinearity between lower and higher MCH contents. This observation could be related to a further growth process of dimers into larger aggregates that occurs in the absence of chloroform, which is required to solvate the aromatic π surfaces. With the help of a single‐crystal structure analysis for a related PBI dye, a structural model could be derived for the extended aggregates that are still composed of defined π–π‐stacked PBI dimer entities.     

Chemical Stimulus‐responsive Folding and Unfolding of a Dendrimeric Assembly

A dendrimeric trimer undergoes folding and unfolding in response to a chemical stimulus. The trimer of interest contains a central dendrimer with a butadiyne‐linked zinc porphyrin dimer ((ZnP)₂) core, in addition to two terminal dendrimers with zinc porphyrin (ZnP) cores. The obtained absorption spectra indicate that the unfolded form is the exclusive conformer in chloroform, while the addition of 1,4‐diazabicyclo[2.2.2]octane (DABCO) in chloroform leads to transformation from the unfolded to the folded structure containing two DABCO units per trimer; the folded structure originates from the cross‐linking of (ZnP)₂ and ZnP with DABCO. Moreover, the addition of excess DABCO promotes the generation of the unfolded structure containing four DABCO units.     

Helical Folding Competing with Unfolded Aggregation in Phenylene Ethynylene Foldamers

The folding and aggregation behavior of a pair of oligo(phenylene ethynylene) (OPE) foldamers are investigated by means of UV/Vis absorption and circular dichroism spectroscopy. With identical OPE backbones, two foldamers, 1 with alkyl side groups and 2 with triethylene glycol side chains, manifest similar helical conformations in solutions in n‐hexane and methanol, respectively. However, disparate and competing folding and aggregation processes are observed in alternative solvents. In cyclohexane, oligomer 1 initially adopts the helical conformation, but the self‐aggregation of unfolded chains, as a minor component, gradually drives the folding–unfolding transition eventually to the unfolded aggregate state completely. In contrast, in aqueous solution (CH₃OH/H₂O) both folded and unfolded oligomer 2 appear to undergo self‐association; aggregates of the folded chains are thermodynamically more stable. In solutions with a high H₂O content, self‐aggregation among unfolded oligomers is kinetically favored; these oligomers very slowly transform into aggregates of helical structures with greater thermodynamic stability. The folded–unfolded conformational switch thus takes place with the free (nonaggregated) molecules, and the very slow folding transition is due to the low concentration of molecularly dispersed oligomers.     

Artificial β‐Double Helices from Achiral γ‐Peptides

Double helices are not common in polypeptides and proteins except in the peptide antibiotic gramicidin A and analogous l,d ‐peptides. In contrast to natural polypeptides, remarkable β‐double‐helical structures from achiral γ‐peptides built from α,β‐unsaturated γ‐amino acids have been observed. The crystal structures suggest that they adopted parallel β‐double helical structures and these structures are stabilized by the interstrand backbone amide H‐bonds. Furthermore, both NMR spectroscopy and fluorescence studies support the existence of double‐helical conformations in solution. Although a variety of folded architectures featuring distinct H‐bonds have been discovered from the β‐ and γ‐peptide foldamers, this is the first report to show that achiral γ‐peptides can spontaneously intertwine into β‐double helical structures.     

The Energetics of a Three‐State Protein Folding System Probed by High‐Pressure Relaxation Dispersion NMR Spectroscopy

The energetic and volumetric properties of a three‐state protein folding system, comprising a metastable triple mutant of the Fyn SH3 domain, have been investigated using pressure‐dependent ¹⁵N‐relaxation dispersion NMR from 1 to 2500 bar. Changes in partial molar volumes (ΔV) and isothermal compressibilities (Δκ_T) between all the states along the folding pathway have been determined to reasonable accuracy. The partial volume and isothermal compressibility of the folded state are 100 mL mol^?1 and 40 μL mol^?1 bar^?1, respectively, higher than those of the unfolded ensemble. Of particular interest are the findings related to the energetic and volumetric properties of the on‐pathway folding intermediate. While the latter is energetically close to the unfolded state, its volumetric properties are similar to those of the folded protein. The compressibility of the intermediate is larger than that of the folded state reflecting the less rigid nature of the former relative to the latter.     

Synthesis of a soluble conjugated cumulene polymer: poly(biphenyl‐4,4′‐diyl‐1,4‐bis(4‐dodecyloxyphenyl)‐buta‐1,2,3‐triene‐1,4‐diyl)

A conjugated polymer with a butatriene segment in the main chain, poly(biphenyl‐4,4′‐diyl‐1,4‐bis(4‐dodecyloxyphenyl)buta‐1,2,3‐triene‐1,4‐diyl), was synthesized from 1,4‐bis(4‐bromophenyl)‐1,4‐bis(4‐dodecyloxyphenyl)buta‐1,2,3‐triene by dehalogenative polycondensation using Ni(cod)₂. The polymer was well soluble in usual organic solvents such as CHCl₃ and THF. Structural analyses and characterizations were carried out by IR, NMR, UV‐Vis, PL, and Raman spectroscopy, as well as electrical conductivity. It is suggested that π‐conjugation is extended to some degree through biphenylylene and butatrienylene linkages.     

The Effect of Backbone Stereochemistry on the Folding of Acyclic β2, 3‐Aminoxy Peptides

As a new type of foldamer, β‐aminoxy peptides have the ability to adopt novel β N? O turns or β N? O helices in solution. Herein, we describe a new subclass of β‐aminoxy peptide, that is, peptides of acyclic β^{2, 3}‐aminoxy acids (NH₂OCHR₁CHR₂COOH), in which the presence of two chiral centers provides insight into the effect of backbone stereochemistry on the folding of β‐aminoxy peptides. Acyclic β^{2, 3}‐aminoxy peptides with syn and anti configurations have been synthesized and their conformations investigated by NMR, IR, and circular dichroism (CD) spectroscopic, and X‐ray crystallographic analysis. The β N? O turns or β N? O helices, which feature nine‐membered rings with intramolecular hydrogen bonds and have been identified previously in peptides of β³‐ and β^{2, 2}‐aminoxy acids, are also predominantly present in the acyclic β^{2, 3}‐aminoxy peptides with a syn configuration and N? O bonds gauche to the C_α? C_β bonds in both solution and the solid state. In the acyclic β^{2, 3}‐aminoxy peptides with an anti configuration, an extended strand (i.e., non‐hydrogen‐bonded state) is found in the solid state, and several conformations including non‐hydrogen‐bonded and intramolecular hydrogen‐bonded states are present simultaneously in nonpolar solvents. These results suggest that the backbone stereochemistry does affect the folding of the acyclic β^{2, 3}‐aminoxy peptides. Theoretical calculations on the conformations of model acyclic β^{2, 3}‐aminoxy peptides with different backbone stereochemistry were also conducted to elucidate structural characteristics. Our present work may provide useful guidelines for the design and construction of new foldamers with predicable structures.     

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.     

Arrangement of Proteinogenic α‐Amino Acids on a Cyclic Peptide Comprising Alternate Biphenyl‐Cored ζ‐Amino Acids

Aiming at precisely arranging several proteinogenic α‐amino acids on a folded scaffold, we have developed a cyclic hexapeptide comprising an alternate sequence of biphenyl‐cored ζ‐amino acids and proteinogenic α‐amino acids such as l ‐leucine. The amino acids were connected by typical peptide synthesis, and the resultant linear hexapeptide was intramolecularly cyclized to form a target cyclic peptide. Theoretical analyses and NMR spectroscopy suggested that the cyclic peptide was folded into an unsymmetrical conformation, and the structure was likely to be flexible in CHCl₃. The optical properties including UV/Vis absorption, fluorescence, and circular dichroism (CD) were also evaluated. Furthermore, the cyclic peptide became soluble in water by introducing three carboxylate groups at the periphery of the cyclic skeleton. This α/ζ‐alternating cyclic peptide is therefore expected to serve as a unique scaffold for arranging several functionalities.     

Molecular‐Dynamics and NMR Investigation of the Property Space of the Zwitterionic Antihistamine Cetirizine

The zwitterionic antihistamine cetirizine and its parent drug hydroxyzine as reference compound were examined for their 3D structures and dynamics. After attributing, by NMR spectroscopy, the two basic pK_a values, the most common conformations for each electrical species were determined by molecular‐dynamics simulations and confirmed by NMR measurements. For cetirizine, the results demonstrate that the zwitterion, which is the predominant species at physiological pH, exists as folded conformers able to partly mask polar groups. Extended and folded conformers of similar energy were also found for neutral hydroxyzine, whereas its monocationic species displayed folded conformers stabilized by intramolecular H‐bonds. These findings are in full agreement with previous results on the lipophilicity behavior of cetirizine in isotropic solvent systems and, taken together, could explain the favorable pharmacokinetic properties of the drug.     

Protonation‐Driven Membrane Insertion of a pH‐Low Insertion Peptide

The pH‐low insertion peptide (pHLIP) inserts into membranes and forms a transmembrane (TM) α‐helix in response to slight acidity, and has shown great potential for cancer diagnosis and treatment. As a lead, pHLIP is challenging to optimize because the mechanism of its pH‐dependent membrane interactions is not completely understood. Within pHLIP there are multiple D/E residues which could sense the pH change, the particular role played by each of them in the protonation‐driven insertion process is not clear. The precise location of the TM helix within the pHLIP sequence is also unknown. In this work, solid‐state NMR spectroscopy is used to address these central questions. Tracing backbone conformations revealed that the TM helix spans from A10 to D33 with a break at T19 to P20. Residue‐specific pK_a values of D31, D33, D25, and D14 were determined to be 6.5, 6.3, 6.1, and 5.8, respectively, and define the sequence of protonations which lead to insertion. Furthermore, possible intermediate states which disrupt membranes at pH 6.4 were proposed based on tryptophan fluorescence quenching and NMR data.     

Structural Insights into the Trp‐Cage Folding Intermediate Formation

The 20 residue long Trp‐cage is the smallest protein known, and thus has been the subject of several in vitro and in silico folding studies. Here, we report the multistate folding scenario of the miniprotein in atomic detail. We detected and characterized different intermediate states by temperature dependent NMR measurements of the ¹⁵N and ¹³C/¹⁵N labeled protein, both at neutral and acidic pH values. We developed a deconvolution technique to characterize the invisible—fully folded, unfolded and intermediate—fast exchanging states. Using nonlinear fitting methods we can obtain both the thermodynamic parameters (ΔH^F–I, T_m^F–I, ΔC_p^F–I and ΔH^I–U, T_m^I–U, ΔC_p^I–U) and the NMR chemical shifts of the conformers of the multistate unfolding process. During the unfolding of Trp‐cage distinct intermediates evolve: a fast‐exchanging intermediate is present under neutral conditions, whereas a slow‐exchanging intermediate‐pair emerges at acidic pH. The fast‐exchanging intermediate has a native‐like structure with a short α‐helix in the G¹¹–G¹⁵ segment, whereas the slow‐exchanging intermediate‐pair presents elevated dynamics, with no detectable native‐like residue contacts in which the G¹¹? P¹² peptide bond has either cis or trans conformation. Heteronuclear relaxation studies combined with MD simulations revealed the source of backbone mobility and the nature of structural rearrangements during these transitions. The ability to detect structural and dynamic information about folding intermediates in vitro provides an excellent opportunity to gain new insights into the energetic aspects of the energy landscape of protein folding. Our new experimental data offer exceptional testing ground for further computational simulations.     

Monitoring Backbone Hydrogen‐Bond Formation in β‐Barrel Membrane Protein Folding

β‐barrel membrane proteins are key components of the outer membrane of bacteria, mitochondria and chloroplasts. Their three‐dimensional structure is defined by a network of backbone hydrogen bonds between adjacent β‐strands. Here, we employ hydrogen–deuterium (H/D) exchange in combination with NMR spectroscopy and mass spectrometry to monitor backbone hydrogen bond formation during folding of the outer membrane protein X (OmpX) from E. coli in detergent micelles. Residue‐specific kinetics of interstrand hydrogen‐bond formation were found to be uniform in the entire β‐barrel and synchronized to formation of the tertiary structure. OmpX folding thus propagates via a long‐lived conformational ensemble state in which all backbone amide protons exchange with the solvent and engage in hydrogen bonds only transiently. Stable formation of the entire OmpX hydrogen bond network occurs downhill of the rate‐limiting transition state and thus appears cooperative on the overall folding time scale.     

A Five‐layer π‐Aromatic Structure Formed through Self‐assembly of a Porphyrin Trimer and Two Aromatic Guests

In this study we synthesized two‐ and four‐armed porphyrins – bearing two carboxyl and four 2‐aminoquinolino functionalities, respectively, at their meso positions – as a complementary hydrogen bonding pair for the self‐assembly of a D₂‐symmetric porphyrin trimer host. Two units of the two‐armed porphyrin and one unit of the four‐armed porphyrin self‐assembled quantitatively into the D₂‐symmetric porphyrin trimer, stabilized through ammidinium‐carboxylate salt bridge formation, in CH₂Cl₂ and CHCl₃. The porphyrin trimer host gradually bound two units of 1,3,5‐trinitrobenzene between the pair of porphyrin units, forming a five‐layer aromatic structure. At temperatures below ?40 °C, the rates of association and dissociation of the complexes were slow on the NMR spectroscopic time scale, allowing the 1 : 1 and 1 : 2 complexes of the trimer host and trinitrobenzene guest(s) to be detected independently when using less than 2 eq of trinitrobenzene. Vis titration experiments revealed the values of K₁ (2.1±0.4×10⁵ M^?1) and K₂ (2.2±0.06×10⁴ M^?1) in CHCl₃ at room temperature.     

Isomerization‐ and Temperature‐Jump‐Induced Dynamics of a Photoswitchable β‐Hairpin

Conformational changes in proteins and peptides can be initiated by diverse processes. This raises the question how the variation of initiation mechanisms is connected to differences in folding or unfolding processes. In this work structural dynamics of a photoswitchable β‐hairpin model peptide were initiated by two different mechanisms: temperature jump (T‐jump) and isomerization of a backbone element. In both experiments the structural changes were followed by time‐resolved IR spectroscopy in the nanosecond to microsecond range. When the photoisomerization of the azobenzene backbone switch initiated the folding reaction, pronounced absorption changes related to folding into the hairpin structure were found with a time constant of about 16 μs. In the T‐jump experiment kinetics with the same time constant were observed. For both initiation processes the reaction dynamics revealed the same strong dependence of the reaction time on temperature. The highly similar transients in the microsecond range show that the peptide dynamics induced by T‐jump and isomerization are both determined by the same mechanism and exclude a downhill‐folding process. Furthermore, the combination of the two techniques allows a detailed model for folding and unfolding to be presented: The isomerization‐induced folding process ends in a transition‐state reaction scheme, in which a high energetic barrier of 48 kJ mol^?1 separates unfolded and folded structures.     

Oligonucleosides with a Nucleobase‐Including Backbone. Part 11

A linear and a convergent synthesis of uridine‐derived backbone‐base‐dedifferentiated (backbone including) oligonucleotide analogues were compared. The Sonogashira cross‐coupling of the alkyne 1 and the iodide 2 gave the dimer 4 that was C‐desilylated and again coupled with 2 to give the trimer 6 (Scheme 1). Repeating this linear sequence led to the pentamer 10 . Coupling yields were satisfactory up to formation of the trimer 6 , but decreased for the coupling to higher oligomers. Similarly, coupling of the alkynes 5, 7 , and 9 with the iodouridine 3 gave, in decreasing yields, the trimer 12 , tetramer 13 , and pentamer 14 , respectively. The dimeric iodouracil 20 was synthesized by coupling the alkyne 17 with the iodide 16 to the dimer 18 , followed by iodination at C(6/I) to 19 and O‐silylation (Scheme 2). The iodinated dimer 23 was prepared by iodinating and O‐silylating the known dimer 21 . Coupling of 20 and 23 with the dimer 5 , trimer 7 , and tetramer 9 gave the tetramers 8 and 13 , the pentamers 10 and 14 , and the hexamer 15 , respectively (Scheme 3). The oligomers up to the pentamer 14 were deprotected to provide the trimer 24 , tetramer 25 , and pentamer 26 (Scheme 4). There was no evidence for the heteropairing of the pentamer 26 and rA₇ , nor for the pairing of rU₅ and rA₇, while a UV melting experiment showed the beginning of a sigmoid curve for the interaction of rU₇ with rA₇. Therefore, the pentamer 26 does not pair more strongly with rA₇ than rU₅.     

A Series of Diamagnetic Pyridine Monoimine Rhenium Complexes with Different Degrees of Metal‐to‐Ligand Charge Transfer: Correlating 13C NMR Chemical Shifts with Bond Lengths in Redox‐Active Ligands

A set of pyridine monoimine (PMI) rhenium(I) tricarbonyl chlorido complexes with substituents of different steric and electronic properties was synthesized and fully characterized. Spectroscopic (NMR and IR) and single‐crystal X‐ray diffraction analyses of these complexes showed that the redox‐active PMI ligands are neutral and that the overall electronic structure is little affected by the choices of the substituent at the ligand backbone. One‐ and two‐electron reduction products were prepared from selected starting compounds and could also be characterized by multiple spectroscopic methods and X‐ray diffraction. The final product of a one‐electron reduction in THF is a diamagnetic metal–metal‐bonded dimer after loss of the chlorido ligand. Bond lengths in and NMR chemical shifts of the PMI ligand backbone indicate partial electron transfer to the ligand. Two‐electron reduction in THF also leads to the loss of the chlorido ligand and a pentacoordinate complex is obtained. The comparison with reported bond lengths and ¹³C NMR chemical shifts of doubly reduced free pyridine monoaldimine ligands indicates that both redox equivalents in the doubly reduced rhenium complex investigated here are located in the PMI ligand. With diamagnetic complexes varying over three formal reduction stages at the PMI ligand we were, for the first time, able to establish correlations of the ¹³C NMR chemical shifts with the relevant bond lengths in redox‐active ligands over a full redox series.     

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.     

Diorganomorpholinometallane von Gallium und Indium – Monomer‐Dimer‐Gleichgewichte in Lösung

Diorganomorpholinometalates of Gallium and Indium – Monomer‐Dimer‐Equilibrium in Solution The reaction of Li[N(CH₂CH₂)₂O] (LiMorpholinate; Li(Morph)) with Me₂GaCl and Me₂InCl gives by salt‐elimination the diorganoamidometalates Me₂M(Morph) ( M = Ga: 1 ; M = In: 2 ), respectively. 1 and 2 were characterized by NMR and vibrational spectroscopy as well as by X‐ray structure determinations. According to this, centrosymmetrical dimers are present in the solid state while a monomer‐dimer equilibrium was assumed for the THF‐solution. Cryoscopic molecular weight determinations confirmed our assumptions.