Identification of 4-Hydroxyproline at the Xaa Position in Collagen by Mass Spectrometry.

Collagen has a triple helix form, structured by a [-Gly-Xaa-Yaa-] repetition, where Xaa and Yaa are amino acids. This repeating unit can be post-translationally modified by enzymes, where proline is often hydroxylated into hydroxyproline (Hyp). Two Hyp isomers occur in collagen: 4-hydroxyproline (4Hyp, Gly-Xaa-Pro, substrate for 4-prolyl hydroxylase) and 3-hydroxyproline (3Hyp, Gly-Pro-4Hyp, substrate for 3-prolyl hydroxylase). If 4Hyp is lacking at the Yaa position, then Pro at the Xaa position should remain unmodified. Nevertheless, in literature 41 positions have been described where Hyp occurs at the Xaa position (?xHyp) lacking an adjacent 4Hyp. We report four additional positions in liver and colorectal liver metastasis tissue (CRLM). We studied the sequence commonalities between the 45 known positions of ?xHyp. Alanine and glutamine were frequently present adjacent to ?xHyp. We showed that proline, position 584 in COL1A2, had a lower rate of modification in CRLM than in healthy liver. The isomeric identity of ?xHyp, that is, 3- and/or 4Hyp, remains unknown. We present a proof of principle identification of ?xHyp. This identification is based on liquid chromatography retention time differences and mass spectrometry using ETD-HCD fragmentation, complemented by ab initio calculations. Both techniques identify ?xHyp at position 584 in COL1A2 as 4-hydroxyproline (4xHyp).

Organogel Formation Rationalized by Hansen Solubility Parameters: Shift of the Gelation Sphere with the Gelator Structure.

To rationalize how the gelation ability of a low molecular weight gelator is influenced by its molecular structure, we performed extensive solubility tests of a group of thiazole-based gelators and made use of Hansen solubility parameter formalism. We observe that the increase of a linear alkyl chain in these gelators promotes an increase of the radius of the gelation sphere as well as a gradual shift of its center to lower values of the polar (δP) and hydrogen bonding (δH) components. The molecular packing within the fibers and the crystal habit were determined by a combination of X-ray diffraction and molecular modeling. We attribute the gradual and linear shift of the gelation sphere to the fact that all of the studied gelators share the same molecular packing, so that an increasing length of the alkyl chain reduces the proportion of polar groups at the surface, resulting in a gradual increase in the contact between apolar parts of the fiber and the solvent.

Tuning the nature and stability of self-assemblies formed by ester benzene 1,3,5-tricarboxamides: the crucial role played by the substituents.

As the benzene 1,3,5-tricarboxamide (BTA) moiety is commonly used as the central assembling unit for the construction of functionalized supramolecular architectures, strategies to tailor the nature and stability of BTA assemblies are needed. The assembly properties of a library of structurally simple BTAs derived from amino dodecyl esters (ester BTAs, 13 members) have been studied, either in the bulk or in cyclohexane solutions, by means of a series of analytical methods (NMR, DSC, POM, FT-IR, UV-Vis, CD, ITC, high-sensitivity DSC, SANS). Two types of hydrogen-bonded species have been identified and characterized: the expected amide-bonded helical rods (or stacks) that are structurally similar to those formed by BTAs with simple alkyl side chains (alkyl BTAs), and ester-bonded dimers in which the BTAs are connected by means of hydrogen bonds linking the amide N-H and the ester C[double bond, length as m-dash]O. MM/MD calculations coupled with simulations of CD spectra allow for the precise determination of the molecular arrangement and of the hydrogen bond pattern of these dimers. Our study points out the crucial influence of the substituent attached on the amino-ester α-carbon on the relative stability of the rod-like versus dimeric assemblies. By varying this substituent, one can precisely tune the nature of the dominant hydrogen-bonded species (stacks or dimers) in the neat compounds and in cyclohexane over a wide range of temperatures and concentrations. In the neat BTAs, stacks are stable up to 213 °C and dimers above 180 °C whilst in cyclohexane stacks form at c* > 3 × 10-5 M at 20 °C and dimers are stable up to 80 °C at 7 × 10-6 M. Ester BTAs that assemble into stacks form a liquid-crystalline phase and yield gels or viscous solutions in cyclohexane, demonstrating the importance of controlling the structure of these assemblies. Our systematic study of these structurally similar ester BTAs also allows for a better understanding of how a single atom or moiety can impact the nature and stability of BTA aggregates, which is of importance for the future development of functionalized BTA supramolecular polymers.

Switchable supramolecular helices for asymmetric stereodivergent catalysis.

Despite recent developments on the design of dynamic catalysts, none of them have been exploited for the in-situ control of multiple stereogenic centers in a single molecular scaffold. We report herein that it is possible to obtain in majority any amongst the four possible stereoisomers of an amino alcohol by means of a switchable asymmetric catalyst built on supramolecular helices. Hydrogen-bonded assemblies between a benzene-1,3,5-tricarboxamide (BTA) achiral phosphine ligand coordinated to copper and a chiral BTA comonomer are engaged in a copper-hydride catalyzed hydrosilylation and hydroamination cascade process. The nature of the product stereoisomer is related to the handedness of the helices and can thus be directed in a predictable way by changing the nature of the major enantiomer of the BTA comonomer present in the assemblies. The strategy allows all stereoisomers to be obtained one-pot with similar selectivities by conducting the cascade reaction in a concomitant manner, i.e. without inverting the handedness of the helices, or sequentially, i.e. by switching the handedness of the supramolecular helices between the hydrosilylation and hydroamination steps. Supramolecular helical catalysts appear as a unique and versatile platform to control the configuration of molecules or polymers embedding several stereogenic centers.

Beta sheets with a twist: the conformation of helical polyisocyanopeptides determined by using vibrational circular dichroism.

Detailed information on the architecture of polyisocyanopeptides based on vibrational circular dichroism (VCD) spectroscopy in combination with DFT calculations is presented. It is demonstrated that the screw sense of the helical polyisocyanides can be determined directly from the C=N-stretch vibrational region of the VCD spectrum. Analysis of the VCD signals associated with the amide I and amide II modes provides detailed information on the peptide side-chain arrangement in the polymer and indicates the presence of a helical ß-sheet architecture, in which the dihedral angles are slightly different to those of natural ß-sheet helices.

Memory Effect by Melt Crystallization Observed in Polymorphs of a Benzothieno-Benzothiophene Derivative.

This work provides a comprehensive illustration of a crystalline melt memory effect recorded for three solvates of the 2,7-bis(2-(2-methoxyethoxy)ethoxy)benzo[b]benzo[4,5] thieno[2,3-d]thiophene (OEG-BTBT) molecule with dichloromethane (DCM) molecules. Combined optical microscopy and X-ray diffraction measurements at different temperatures are used to get an overview of the structural and morphological properties like melting points, isotropic transition temperatures, induction times, and crystallization kinetics of the three forms. An outstanding observation is made upon annealing the three polymorphs at temperatures well above their respective melting points as well as above the optical clearance temperature. After cooling back to room temperature, recrystallization results in the formation of the initial phase present before the annealing process. This melt memory effect is observed for all three solvates. These observations can be correlated to the strong interaction between the DCM molecules and the oligoethylene glycol side chains, even in the molten state. This conclusion rationalizes the experimental observation made upon solvent vapor annealing of the crystalline sample with DCM, which unambiguously transformed the system into a disordered state.

Polymorph screening at surfaces of a benzothienobenzothiophene derivative: discovering new solvate forms.

The discovery of new polymorphs opens up unique applications for molecular materials since their physical properties are predominantly influenced by the crystal structure type. The deposition of molecules at surfaces offers great potential in the variation of the crystallization conditions, thereby allowing access to unknown polymorphs. With our surface crystallization approach, four new phases are found for an oligoethylene glycol-benzothienobenzothiophene molecule, and none of these phases could be identified via classical polymorph screening. The corresponding crystal lattices of three of the new phases were obtained via X-ray diffraction (XRD). Based on the volumetric considerations together with X-ray fluorescence and Raman spectroscopy data, the phases are identified as solvates containing one, two or three solvent molecules per molecule. The strong interaction of dichloromethane with the oligoethylene glycol side chains of the molecules may be responsible for the formation of the solvates. Temperature-dependent XRD reveals the low thermal stability of the new phases, contrary to the thermodynamically stable bulk form. Nevertheless, the four solvates are stable under ambient conditions for at least two years. This work illustrates that defined crystallization at surfaces enables access to multiple solvates of a given material through precise and controlled variations in the crystallization kinetics.

Structural Characterization of Dendriplexes In Vacuo: A Joint Ion Mobility/Molecular Dynamics Investigation.

The combination between ion mobility mass spectrometry and molecular dynamics simulations is demonstrated for the first time to afford valuable information on structural changes undergone by dendriplexes containing ds-DNA and low-generation dendrimers when transferred from the solution to the gas phase. Dendriplex ions presenting 1:1 and 2:1 stoichiometries are identified using mass spectrometry experiments, and the collision cross sections (CCS) of the 1:1 ions are measured using drift time ion mobility experiments. Structural predictions using Molecular Dynamics (MD) simulations showed that gas-phase relevant structures, i.e., with a good match between the experimental and theoretical CCS, are generated when the global electrospray process is simulated, including the solvent molecule evaporation, rather than abruptly transferring the ions from the solution to the gas phase. The progressive migration of ammonium groups (either NH4+ from the buffer or protonated amines of the dendrimer) into the minor and major grooves of DNA all along the evaporation processes is shown to compact the DNA structure by electrostatic and hydrogen-bond interactions. The subsequent proton transfer from the ammonium (NH4+ or protonated amino groups) to the DNA phosphate groups allows creation of protonated phosphate/phosphate hydrogen bonds within the compact structures. MD simulations showed major structural differences between the dendriplexes in solution and in the gas phase, not only due to the loss of the solvent but also due to the proton transfers and the huge difference between the solution and gas-phase charge states.

Stabilization of Supramolecular Polymer Phase at High Pressures.

We utilize dynamic light scattering (DLS) and passive microrheology to examine the phase behavior of a supramolecular polymer at very high pressures. The monomer, 2,4-bis(2-ethylhexylureido)toluene (EHUT), self-assembles into supramolecular polymeric structures in the nonpolar solvent cyclohexane by means of hydrogen bonding. By varying the concentration and temperature at atmospheric pressure, the formation of the viscoelastic network (at lower temperatures) and predominantly viscous phases, based on self-assembled tube and filament structures, respectively, has been established. The associated changes in the rheological properties have been attributed to a structural thickness transition. Here, we investigate the effects of pressure variation from atmospheric up to 1 kbar at a given concentration. We construct a temperature-pressure diagram that reveals the predominance of the viscoelastic network phase at high pressures. The transition from the viscoelastic network organization of the tubes to a weaker viscous-dominated structure of the filaments is rationalized by using the Clapeyron equation, which yields an associated volume change of about 8 Å3 per EHUT molecule. This change is further explained by means of Molecular Dynamics simulations of the two phases, which show a decrease in the molecular volume at the filament-tube transition, originating from increased intermolecular contacts in the tube with respect to the filament. These findings offer insights into the role of pressure in stabilizing self-assemblies.

How Spherical Are Gaseous Low Charged Dendrimer Ions: A Molecular Dynamics/Ion Mobility Study?

The globular shape of gaseous ions, resulting from the ionization of large molecules such as polymers and proteins, is a recurring subject that has undergone a renewed interest with the advent of ion mobility spectrometry (IMS), especially in conjunction with theoretical chemistry techniques such as Molecular Dynamics (MD). Globular conformations result from a fine balance between entropy and enthalpy considerations. For multiply charged ions isolated in the gas phase of a mass spectrometer, the Coulombic repulsion between the different charges tends to prevent the ions from adopting a compact, and folded 3D structure. In the present paper, we closely associate data from IMS experiments and MD simulations to unambiguously access the conformations of dendrimer ions in the gas phase with special attention paid to the dendrimer structure, the generation, and the charge state. By doing so, we here combine a set of structural tools able to evaluate the (non)globular shape of ions based on both experimental and theoretical results.

"Helter-skelter-like" perylene polyisocyanopeptides.

Exciton migration! Spectroscopic analyses and extensive molecular dynamics studies revealed a well-defined 4(1) helix in which the perylene molecules (see figure) form four "helter-skelter-like" overlapping pathways along which excitons and electrons can rapidly migrate.We report on a combined experimental and computational investigation on the synthesis and thorough characterization of the structure of perylene-functionalized polyisocyanides. Spectroscopic analyses and extensive molecular dynamics studies revealed a well defined 4(1) helix in which the perylene molecules form four "helter skelter-like" overlapping pathways along which excitons and electrons can rapidly migrate. The well-defined polymer scaffold stabilized by hydrogen bonding, to which the chromophores are attached, accounts for the precise architectural definition, and molecular stiffness observed for these molecules. Molecular-dynamics studies showed that the chirality present in these polymers is expressed in the formation of stable right-handed helices. The formation of chiral supramolecular structures is further supported by the measured and calculated bisignated Cotton effect. The structural definition of the chromophores aligned in one direction along the backbone is highlighted by the extremely efficient exciton migration rates and charge densities measured with Transient Absorption Spectroscopy.

Molecular modeling simulations of the morphology of polyphenylene dendrimers.

Three polyphenylene dendrimers were studied by molecular modeling techniques with the goal of better defining the notion of shape persistence often associated with these molecules. We show that despite the rigidity of the monomers, a large variety of dendrimer morphologies is accessible, in large part due to the asymmetrical branching pattern of the monomers (they have nodes in meta and para positions with respect to their anchor point). The folding ability of a branch depends on the number and sequence of the meta and para nodes it contains: while some of the branches are always straight, others can fold back, and the amplitude of that folding increases with generation. As a result, the range of accessible morphologies increases with the generation, from a dense-shell model in low generation to a model intermediate between a dense shell and a dense core in high generation. When the typical A2B monomer is replaced by an A4B monomer, the dense packing limit is reached as early as the second generation because of a higher density and the presence of nodes in the ortho position, which are oriented backward.

Chiral supramolecular organization and cooperativity in DNA-templated assemblies of ZnII-chromophore complexes.

Templated cooperative binding induced assembly of chromophores is achieved via interactions between Zn-complexes and the DNA phosphodiester backbone. The chromophores are organized in left-handed (M)-helices via double-zipper assembly with the DNA templates.

Tuning the structure of 1,3,5-benzene tricarboxamide self-assemblies through stereochemistry.

A heterochiral 1,3,5-benzene tricarboxamide (BTA) monomer, derived from valine dodecyl ester, forms long rods in cyclohexane whilst its homochiral analogue assembles into dimers only at the same concentration. This highly original assembly behaviour is related to the destabilization of the dimeric structure containing the two heterochiral monomers as corroborated by a combined experimental and computational study.

The conformation of amine- and amide-terminated poly(propylene imine) dendrimers as investigated by molecular simulation methods.

The parameters that influence the conformation of poly(propylene imine) dendrimers were investigated by molecular simulations using molecular mechanics and simulated annealing methods. Dendrimers with two types of peripheral units able to communicate via hydrogen bonding-amine and amide moieties-were considered in order to study the role that secondary interactions among the end groups have in the spatial organization of the dendritic branches. Radial atomic density profiles and radial atomic probability distributions were used to extract global properties, such as the degree of packing of the branches, the distribution of the monomers throughout the molecular volume, and the extent and characteristics of the surface region. Information was also obtained about the nature, location, and extent of formation of the hydrogen bonds, as well as their evolution with dendrimer generation and their assembly into networks. The analyses were supported by a detailed investigation of the first two generations, with an emphasis on the relationship between hydrogen bonding and the compactness and stability of the molecules; this allowed us to account for the generational evolution of hydrogen bonding that is experimentally observed in several poly(propylene imine) dendrimers.

Revisiting the assembly of amino ester-based benzene-1,3,5-tricarboxamides: chiral rods in solution.

Some benzene-1,3,5-tricarboxamide (BTA) monomers derived from (l) α-amino esters self-assemble into long rods at millimolar concentrations, and display a strong chiral amplification effect. These rods are in competition with dimeric species.

A dynamic supramolecular polymer with stimuli-responsive handedness for in situ probing of enzymatic ATP hydrolysis.

Design of artificial systems, which can respond to fluctuations in concentration of adenosine phosphates (APs), can be useful in understanding various biological processes. Helical assemblies of chromophores, which dynamically respond to such changes, can provide real-time chiroptical readout of various chemical transformations. Towards this concept, here we present a supramolecular helix of achiral chromophores, which shows chiral APs responsive tunable handedness along with dynamically switchable helicity. This system, composing of naphthalenediimides with phosphate recognition unit, shows opposite handedness on binding with ATP compared with ADP or AMP, which is comprehensively analysed with molecular dynamic simulations. Such differential signalling along with stimuli-dependent fast stereomutations have been capitalized to probe the reaction kinetics of enzymatic ATP hydrolysis. Detailed chiroptical analyses provide mechanistic insights into the enzymatic hydrolysis and various intermediate steps. Thus, a unique dynamic helical assembly to monitor the real-time reaction processes via its stimuli-responsive chiroptical signalling is conceptualized.

Conformational plasticity of hydrogen bonded bis-urea supramolecular polymers.

We report a detailed structural investigation of supramolecular polymers formed by hydrogen bonded self-assembly of bis-urea monomers. The careful exploration of the energy landscape by molecular mechanics/molecular dynamics (MM/MD) simulations has allowed us to identify three distinct self-assembled structures of similar stabilities. These structures have been compared to X-ray crystal data. We observe that a slight change in the molecular structure can favor a particular structure over the others. Detailed analysis shows that hydrogen bonds stabilize all three structures to a similar extent. Therefore, it is the interactions among the lateral substituents, and with the filament environment, that are the decisive factors in the competition between the possible self-assembled structures. This study constitutes a clear reminder that the conformation of a supramolecular polymer is a sensitive function of the molecular structure and may significantly differ from the solid-state conformation of a model compound.

Expression of chirality in molecular layers at surfaces: insights from modelling.

This tutorial review illustrates how modelling can be used to understand the structure and properties of chiral surfaces formed by adsorption of molecular layers. The two major theoretical approaches for such modelling (Density Functional Theory and classical force-field methods) are briefly described and compared. A few examples of their use are given, focussing on: (i) the expression of chirality at the local and global scale in layers of chiral molecules, (ii) the appearance of chirality in layers of achiral molecules on achiral surfaces, and (iii) the molecular organisation in layers formed from racemic mixtures.

Microscopic morphology of chlorinated polyethylene-based nanocomposites synthesized from poly(epsilon-caprolactone)/clay masterbatches.

Chlorinated polyethylene (CPE) nanocomposites were synthesized by melt blending clay-rich/poly(epsilon-caprolactone) (PCL) masterbatches to CPE matrices. The masterbatches were prepared following two synthetic routes: either PCL is melt-blended to the clay or it is grafted to the clay platelets by in situ polymerization. The microscopic morphology of the nanocomposites was characterized by X-ray diffraction, atomic force microscopy, transmission electron microscopy, and modulated temperature differential scanning calorimetry. When using free PCL, intercalated composites are formed, with clay aggregates that can have micrometric dimensions and a morphology similar to that of the talc particles used as fillers in commercial CPE. PCL crystallizes as long lamellae dispersed in the polymer matrix. When using grafted PCL, the nanocomposite is intercalated/exfoliated, and the clay stacks are small and homogeneously dispersed. PCL crystallizes as lamellae and smaller crystals, which are localized along the clay layers. Thanks to the grafting of PCL to the clay platelets, these crystalline domains are thought to form a network with the clay sheets, which is responsible for the large improvement of the mechanical properties of these materials.