Can one determine the density of an individual synthetic macromolecule?

Dendronized polymers (DPs) are large and compact main-chain linear polymers with a cylindrical shape and cross-sectional diameters of up to ∼15 nm. They are therefore considered molecular objects, and it was of interest whether given their experimentally accessible, well-defined dimensions, the density of individual DPs could be determined. We present measurements on individual, deposited DP chains, providing molecular dimensions from scanning and transmission electron microscopy and mass-per-length values from quantitative scanning transmission electron microscopy. These results are compared with density values obtained from small-angle X-ray scattering on annealed bulk specimen and with classical envelope density measurements, obtained using hydrostatic weighing or a density gradient column. The samples investigated comprise a series of DPs with side groups of dendritic generations g = 1-8. The key findings are a very large spread of the density values over all samples and methods, and a consistent increase of densities with g over all methods. While this work highlights the advantages and limitations of the applied methods, it does not provide a conclusive answer to the question of which method(s) to use for the determination of densities of individual molecular objects. We are nevertheless confident that these first attempts to answer this challenging question will stimulate more research into this important aspect of polymer and soft matter science.

3D Conformations of Thick Synthetic Polymer Chains Observed by Cryogenic Electron Microscopy

The backbone conformations of individual, unperturbed synthetic macromolecules have so far not been observed directly in spite of their fundamental importance to polymer physics. Here we report the dilute solution conformations of two types of linear dendronized polymers, obtained by cryogenic transmission electron stereography and tomography. The three-dimensional trajectories show that the wormlike chain model fails to adequately describe the scaling of these thick macromolecules already beyond a few nanometers in chain length, in spite of large apparent persistence lengths and long before a signature of self-avoidance appears. This insight is essential for understanding the limitations of polymer physical models, and it motivated us to discuss the advantages and disadvantages of this approach in comparison to the commonly applied scattering techniques.

Close contacts at the interface: Experimental-computational synergies for solving complexity problems

The study of material science has been long devoted to the disentanglement of bulk structures which mainly entails finding the inner structure of materials. That structure is accountable for a major portion of materials’ properties. Yet, as our knowledge of these “backbones” enlarged so did the interest for the materials’ boundaries properties which means the properties at the frontier with the surrounding environment that is called interface. The interface is thus to be understood as the sum of the material’s surface plus the surrounding environment be it in solid, liquid or gas phase. The study of phenomena at this interface requires both the use of experimental and theoretical techniques and, above all, a wise combination of them in order to shed light over the most intimate details at atomic, molecular and mesostructure levels. Here, we report several cases to be used as proof of concept of the results achieved when studying interface phenomena by combining a myriad of experimental and theoretical tools to overcome the usual limitation regardind  atomic detail, size and time scales and systems of complex composition. Real world examples of the combined experimental-theoretical work and new tools, software, is offered to the readers.

Exploring the Loading Capacity of Generation Six to Eight Dendronized Polymers in Aqueous Solution

Aspects of size, structural (im)perfection, inner density, and guest molecule loading capacity of dendronized polymers (DPs) of high generation (6≤g≤8) in aqueous solution are studied using electron paramagnetic resonance spectroscopy on amphiphilic, spin-labeled guest molecules. The results show that the interior of the charged DPs is strongly polar, especially in comparison to their lower generation (1-4) analogues. This is a direct sign that large amounts of water penetrate the DP surface, reflecting the structural (im)perfections of these high-generation DPs and much lower segmental densities than theoretically achievable. Images obtained with atomic force microscopy reveal that the high-generation DPs do not aggregate and give further insights into the structural imperfections. Electron paramagnetic resonance spectroscopic data further show that despite their structural imperfections, these DPs can bind and release large numbers of amphiphilic molecules. It is concluded that attention should be paid to their synthesis, for which a protocol needs to be developed that avoids the relatively large amount of defects generated in the direct conversion of a generation g=4 DP to a generation g=6 DP, which had to be used here.

Solvatochromism of dye-labeled dendronized polymers of generation numbers 1-4: comparison to dendrimers

Two series of dendronized polymers (DPs) of generations g = 1-4 with different levels of dendritic substitution (low and high) and a solvatochromic probe at g = 1 level are used to study their swelling behavior in a collection of solvents largely differing in polarity as indicated by the Kamlet-Taft parameters. This is done by measuring the UV-Vis spectra of all samples in all solvents and determining the longest wavelength absorptions (λmax). The λmax values fall into a range defined by the extreme situations, when the solvatochromic probe is either fully surrounded by solvent or completely shielded against it. The former situation is achieved in a model compound and the latter situation is believed to be reached when in a poor solvent the dendritic shell around the backbone is fully collapsed. We observe that solvent penetration into the interior of the DPs decreases with increasing g and does so faster for the more highly dendritically substituted series than for the less highly substituted one. Interestingly, the swelling of the more highly substituted DP series already at the g = 4 level has decreased to approximately 20% of that at the g = 1 level which supports an earlier proposal that high g DPs can be viewed as nano-sized molecular objects. Furthermore, when comparing these two DP series with a g = 1-6 series of dendrimers investigated by Fréchet et al. it becomes evident that even the less substituted series of DPs is much less responsive to solvent changes as assessed by the solvatochromic probe than the dendrimers, suggesting the branches around the (polymeric) core in DPs to be more densely packed compared to those in dendrimers, thus, establishing a key difference between these two dendritic macromolecules.

Synthesis of Dendronized Poly(l-Glutamate) via Azide-Alkyne Click Chemistry

Poly(l-glutamate) (PGlu) was modified with a second-generation dendron to obtain the dendronized polyglutamate, P(Glu-D). Synthesized P(Glu-D) exhibited a degree of polymerization (DP_n) of 46 and a 43% degree of dendronization. Perfect agreement was found between the P(Glu-D) expected structure and the results of nuclear magnetic resonance spectroscopy (NMR) and size-exclusion chromatography coupled to a multi-angle light-scattering detector (SEC-MALS) analysis. The PGlu precursor was modified by coupling with a bifunctional building block (N₃-Pr-NH₂) in the presence of 4-(4,6-dimethoxy-1,3,5-triazin-2-yl)-4-methylmorpholinium chloride (DMTMM) coupling reagent. The second-generation polyamide dendron was prepared by a stepwise procedure involving the coupling of propargylamine to the l-lysine carboxyl group, followed by attaching the protected 2,2-bis(methylol)propionic acid (bis-MPA) building block to the l-lysine amino groups. The hydroxyl groups of the resulting second-generation dendron were quantitatively deprotected under mild acidic conditions. The deprotected dendron with an acetylene focal group was coupled to the pendant azide groups of the modified linear copolypeptide, P(Glu-N₃), in a Cu(I) catalyzed azide-alkyne cycloaddition reaction to form a 1,4-disubstituted triazole. The dendronization reaction proceeded quantitatively in 48 hours in aqueous medium as confirmed by ¹H NMR and Fourier transform infrared spectroscopy (FT-IR) spectroscopy.

Solvent effects on the properties of hyperbranched polythiophenes

QM/MM-MD simulations of dendrimers using explicit solvent molecules capture the conformational flexibility and microfluctuations induced by different types of solvents.

Internal organization of macromonomers and dendronized polymers based on thiophene dendrons

The internal organization of macromonomers (MGs) consisting of all-thiophene dendrons of generation g = 2 and 3 attached to a phenyl core, as well as of the dendronized polymers resulting from polymerization of these macromonomers (PG2 and PG3, respectively), has been investigated using theoretical methods. The conformational preferences of the MGs, determined using density functional theory calculations, are characterized by the relative orientation between dendrons and core. We find that the strain of the MGs increases with the generation number and is alleviated by small conformational re-arrangements of the peripheral thiophene rings. The conformations obtained for the MGs have subsequently been used to construct models for the dendronized polymers. Classical molecular dynamics simulations have evidenced that the interpenetration of dendrons belonging to different repeat units is very small for PG2. In contrast, the degree of interpenetration is found to be very high for PG3, which also shows a significant degree of backfolding (i.e. occurrence of peripheral methyl groups approaching the backbone). Consequently, PG2 behaves as a conventional linear flexible polymer bearing bulk pendant groups, whereas PG3 is better characterized as a semirigid homogeneous cylinder. The two polymers are stabilized by π-π stacking interactions, even though these are significantly more abundant for PG3 than for PG2; the average numbers of interactions per repeat unit are 3.0 and 8.8 for PG2 and PG3, respectively. While in these interactions the thiophene rings can adopt either parallel (sandwich) or perpendicular (T-shaped) dispositions, the former scenario turns out to be the most abundant.

Probing the binding mechanism of novel dual NF-κB/AP-1 inhibitors by 3D-QSAR, docking and molecular dynamics simulations

Potent dual NF-κB/AP-1 inhibitors could effectively treat immunoinflammatory diseases. An integrated computational study was carried out to identify the most favourable binding sites, the structural features and the interaction mechanisms.

Dendronized Polymers: Molecular Objects between Conventional Linear Polymers and Colloidal Particles

The term molecular object (MO) is introduced to describe single, shape persistent macromolecules that retain their form and mesoscopic dimensions irrespective of solvent quality and adsorption onto a surface. The concept is illustrated with results concerning homologous series of dendronized polymers (DP). In particular, we discuss imaging experiments quantifying deformation upon adsorption, defect characterization, and atomistic molecular dynamics simulations of DP structure. We argue that MOs such as high generation DP, with their large dimensions and high internal density, provide an opportunity to address fundamental questions regarding the onset of bulk-like behavior in single molecules. Illustrative examples of such questions concern the smallest MO exhibiting a glass transition, glassy behavior or a constant bulk density. The characteristics of DP MO are highlighted by comparison to polymer beads, polymeric micelles, globular proteins, and carbon nanotubes. We discuss future research directions and speculate on possibilities involving multiarmed and toroid DP and the effect of DP on friction and rheology, as well as their utilization for nanoconstruction.

Interactions in dendronized polymers: intramolecular dominates intermolecular

In an attempt to relate atomistic information to the rheological response of a large dendritic object, interand intramolecular hydrogen bonds and p,p-interactions have been characterized in a dendronized polymer (DP) that consists of a polymethylmethacrylate backbone with tree-like branches of generation four (PG4) and contains both amide and aromatic groups. Extensive atomistic molecular dynamics simulations have been carried out on (i) an isolated PG4 chain and (ii) ten dimers formed by two PG4 chains associated with different degrees of interpenetration. Results indicate that the amount of nitrogen atoms involved in hydrogen bonding is ~11% while ~15% of aromatic groups participate in p,pinteractions. Furthermore, in both cases intramolecular interactions clearly dominate over intermolecular ones, while exhibiting markedly different behaviors. Specifically, the amount of intramolecular hydrogen bonds increases when the interpenetration of the two chains decreases, whereas intramolecular p,pinteractions remain practically insensitive to the amount of interpenetration. In contrast, the strength of the corresponding two types of intermolecular interactions decreases with interpenetration. Although the influence of complexation on the density and cross-sectional radius is relatively small, interpenetration affects significantly the molecular length of the DP. These results support the idea of treating DPs as long colloidal molecules.

Structure and enzymatic properties of molecular dendronized polymer-enzyme conjugates and their entrapment inside giant vesicles

Macromolecular hybrid structures were prepared in which two types of enzymes, horseradish peroxidase (HRP) and bovine erythrocytes Cu,Zn-superoxide dismutase (SOD), were linked to a fluorescently labeled, polycationic, dendronized polymer (denpol). Two homologous denpols of first and second generation were used and compared, and the activities of HRP and SOD of the conjugates were measured in aqueous solution separately and in combination. In the latter case the efficiency of the two enzymes in catalyzing a two-step cascade reaction was evaluated. Both enzymes in the two types of conjugates were highly active and comparable to free enzymes, although the efficiency of the enzymes bound to the second-generation denpol was significantly lower (up to a factor of 2) than the efficiency of HRP and SOD linked to the first-generation denpol. Both conjugates were analyzed by atomic force microscopy (AFM), confirming the expected increase in object size compared to free denpols and demonstrating the presence of enzyme molecules localized along the denpol chains. Finally, giant phospholipid vesicles with diameters of up to about 20 μm containing in their aqueous interior pool a first-generation denpol-HRP conjugate were prepared. The HRP of the entrapped conjugate was shown to remain active toward externally added, membrane-permeable substrates, an important prerequisite for the development of vesicular multienzyme reaction systems.

Solvent induced phenomena in a dendronized linear polymer

The properties of a dendronized linear polymer (DP) in dilute solutions depending on solvent quality and temperature are described. The polymer has a contour length of Lc = 1,060 nm. The sample of the fourth generation (PG4) was analyzed in the thermodynamically good solvents dioxane, chloroform, and methanol. The wormlike macromolecule has a persistence length lp = 7 nm in dioxane and a cross-section radius determined by small angle X-ray scattering (SAXS) of Rc (SAXS) = 2.8 nm. The bulk density of PG4 determined by SAXS was compared with solution density. Evidence for substantial swelling of the cross-section was found. Toluene acts as a thermodynamically poor solvent (θ solvent). Above the θ temperature Tθ , a strong temperature dependence of the size and the Young's modulus E was observed. Following Odijk, E/kBT ∼1 was found. Below Tθ , a regime characterized by unswelling of the wormlike chains was observed. The results suggest that DPs can be described as soft colloid filaments, which are subject to commonly observed interactions in colloidal systems. A phase diagram indicates a regime below Tθ in which fluctuations of osmotic pressure inside the filaments result in periodic undulation of the chains. In summary, introducing a dense dendritic shell around the backbone converts conventional polymers into molecular colloids. Figureᅟ

Computer simulation of fifth generation dendronized polymers: impact of charge on internal organization

The internal organization of a fifth-generation dendronized polymer (PG5) has been investigated by atomistic molecular dynamics simulations in a vacuum. This study reveals an exceptional behavior of PG5 within the homologous series of g-generation PGg polymers. Three molecular configurations, which present a heterogeneous distribution of dendrons and an amount of backfolding lower than PG4 and PG6, have been obtained for PG5. The highest stability and closest agreement with available experimental data corresponds to a helical conformation characterized by a pitch of about 30 Å, thickness of 105 Å, and average density of 0.861 g/cm(3). While small angle neutron scattering studies of PG5 in solution show a constant radial density distribution around the backbone, we here in our vacuum studies find a cylindrical volume element of sharply reduced density reminiscent of a pore. This neutral PG5 was compared with its charged deprotected analogue, dePG5 in water, to see in as much the positive charges in the periphery of this macromolecule would affect its conformational behavior. During deprotection of PG5, the tert-butyloxycarbonyl protected amine groups are converted into ammonium, mimicking the experimental situation during a divergent synthesis procedure. The repulsive interactions among the positively charged ammonium groups are responsible for a huge (~30%) reduction of the average density and a small (~1%) increase of elongation of the helical backbone, which results in a structure with a spongy appearance. Also here, we find a reduced dendron density near the backbone which is compensated for by the pore being filled with water.