Supramolecular Scale Research Articles

Molecular dynamics study of structural properties of [formula omitted]-sheet assemblies formed by synthetic de novo oligopeptides

We study, by means of molecular dynamics (MD) simulations with explicit water, the structure and stability of β -sheet tapes, ribbons and double ribbons formed by rationally designed oligopeptides P 11 -I and P 11 -II in aqueous solutions. Two different methods for the treatment of the electrostatic interactions were considered: a smoothly shifted spherical cutoff approach under spherical harmonic conditions, and the particle mesh Ewald technique. We investigate the transfer of chirality from single l-aminoacids to the molecular scale of oligopeptides and from the latter to the supramolecular scale of peptide clusters. Furthermore, we obtain structural data for the representative conformations of these clusters, as well as study various average properties of their geometry.

A study of the effect of formalin preservation on normal and cancerous breast tissues using small angle X-ray scattering (SAXS)

Small angle X-ray scattering (SAXS) has the ability to provide information on a molecular and supra-molecular scale from biological tissue specimens. It has been postulated that this information will be useful in providing histopathological diagnoses for certain diseases of the breast. In this category, we include cancer, a major health problem for a number of populations around the world. So far studies in our group have been made using flash-frozen tissue samples. This limits the range and ease of use of the technique. If we were able to obtain the same information from preserved tissues then a more extensive use of SAXS diagnosis would be possible. Here we report on the first investigations into this possibility. In the research reported in this paper, 84 human breast biopsies including cancer and normal tissues were obtained from human patients. Small angle scatter data were collected at station 2.1 of the SRS at the Daresbury Laboratory, UK using a beam size of 0.25 mm 2 at the sample and a wavelength of 1.54 Å. The sample to detector distance was 2000 mm. The results verify that there is a quantifiable difference between the scatter curves from flash-frozen cancer and normal breast tissue in the range of scatter vector Q between 0.4 and 0.7 nm −1. After preserving the tissues in formalin, the difference between the normal and cancerous tissues is less marked. The preservation of the tissue in formalin can essentially mask the effects that disease would have on the tissue supra-molecular structure rendering the preserved specimens of less useful for this histopathology technique.

Multiscale approach to investigate the radiochemical degradation of epoxy resins under high‐energy electron‐beam irradiation

AbstractA multiscale investigation of the degradation mechanism of two epoxy systems exposed to electron‐beam irradiation under a helium atmosphere was carried out with a variety of analytical methods, including high‐resolution solution‐ and solid‐state NMR spectroscopy, NMR relaxometry, infrared spectroscopy, sterical exclusion chromatography, and differential scanning calorimetry. As a first step, we studied a linear phenoxy polymer, poly(2‐hydroxyether of bisphenol A), which provided a basis for the investigation of the degradation of a more complex, insoluble epoxy–amine network, diglycidyl ether of bisphenol A/triethylene tetramine. Among different structural modifications, the main degradation process was shown to produce in both cases a chain scission. For the phenoxy resin, the hydroxypropylidene moiety was identified as the fragile site leading to the formation of two phenolic chain ends and acetone and isopropyl alcohol as low‐molecular‐weight products. All methods, ranging from molecular to supramolecular scales, were shown to correlate both qualitatively and quantitatively. Experimental results obtained with diglycidyl ether of bisphenol A/triethylene tetramine evidenced a different degradation scheme occurring at the ethylene amine part and producing a dangling vinyl amine as the major degradation product. A selective increase in the molecular mobility at this site was confirmed by a two‐dimensional, local‐field wide‐line separation experiment. © 2005 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 44: 865–887, 2006

Biomaterials for Regenerative Medicine

AbstractThe following article is based on a presentation given by Samuel I. Stupp of Northwestern University as part of Symposium X—Frontiers of Materials Research on April 13, 2004, at the Materials Research Society Spring Meeting in San Francisco. Materials designed at the molecular and supramolecular scales to interact with cells, biomolecules, and pharmaceuticals will have a profound impact on technologies targeting the regeneration of body parts. Materials science is a great partner to stem cell biology, genomics, and proteomics in crafting the scaffolds that will effectively regenerate tissues lost to trauma, disease, or genetic defects. The repair of humans should be minimally invasive, and thus the best scaffolds would be liquids programmed to create materials inside our bodies. In this regard, self-assembling materials will play a key role in future technologies. This article illustrates how molecules are designed to assemble into cell scaffolds for human repair and provides examples relevant to brain damage, fractures of the skeleton, spinal cord injuries leading to paralysis, and diabetes.

Supramolecular structure of humic acids by TEM with improved sample preparation and staining

Understanding the role of the dissolved organic matter in the environment will benefit from the characterization of its components at the supramolecular scale. With its very high spatial resolution the transmission electron microscope (TEM) allows the determination of colloidal size, structure, and shape on aggregated substances as well as single particles. It also allows the determination of the chemical composition if coupled with an X-ray detector. However, TEM preparation artifacts may hamper the relevance of such observations. This study demonstrates the capacity of TEM for the size and shape analysis of humic substances. Three sample preparation techniques (ultramicrotomy sectioning after embedding into a hydrophilic resin, drop deposition, and absorption) were evaluated with the Fluka humic acid (HA). Additionally, several staining agents (cesium hydroxide, lead citrate, uranyl acetate, and ruthenium tetraoxide) were used to increase the humic acid contrast for TEM observations. An improved simple preparation method with selective staining of the HA is proposed which permits the imaging of the humic acid macromolecules. The results show that the Fluka humic acid is composed mainly of fibrils generated by the interconnection of basic molecules of about 20 nm diameter with some isolated larger macromolecules (30-200 nm).

One-component gels based on peptidic dendrimers: dendritic effects on materials properties.

This paper describes the gelation of symmetric dendrimers based on building blocks constructed from L-lysine. These dendrimers form gel-phase materials in nonpolar organic solvents. The thermal properties and concentration dependence of the gelation were investigated, and it was found that there was a clear dendritic effect on the behavior of the soft materials formed, with higher generation dendrimers giving rise to more thermally stable gels. Variable temperature 1H NMR studies indicated that this behavior was probably a consequence of more extensive interdendrimer hydrogen bonding occurring between the peptidic groups in the higher generation dendrimers. The supramolecular aggregates were found to have a fibrillar structure, with the dimensions and alignment of the fibers being dependent on dendritic generation. Circular dichroism measurements confirmed that these fibers possessed chiral organization of the peptidic groups on the supramolecular (nano) scale, assigned as helicity. This paper indicates that dendritic functionalization provides a useful way of tuning gel-phase materials properties, with clear dendritic effects on gel formation being quantified for the first time, hence illustrating the way dendritic functionalization can play a positive role in the formation of highly functional organic materials with desirable properties.

Armed Cyclen Receptors: From Three Dimensional Cation Recognition to Supramolecular Architecture

Abstract The concept and examples of armed cyclens are described and some of their recent applications in molecular recognition and supramolecular chemistry are explained. Armed cyclens are characterized by a parent tetraamine ring and functionalized sidearms. They can act as three-dimensional ligands for octadentate metal complexation. They exhibit comparable logK values for Na+ complexation to bicyclic cryptands, though they have flexible, open-chained structures. Since the resulting octacoordinate metal complexes have quadruple helicated structures, they can work as unique building blocks having C4 symmetry for chiral supramolecular architecture. Cholesterol-armed cyclen typically formed a self-aggregate with the integrated chirality in aqueous solution, in which asymmetrically helicated cyclen complexes were arrayed on a supramolecular scale. The self-aggregate had asymmetrically ordered domains, in which achiral organic anions and racemic metal complexes were nicely accommodated in stereo-controlled fashions. Since the armed cyclens have broad structural variations, they are applicable as specific receptors for cation recognition at the molecular level and also as building blocks for supramolecular architecture.

Fracture Mechanics of Cortical Bone Tissue: A Hierarchical Perspective

The performance of bone tissue in the presence of flaws is a highly remarkable one. Bone tissue is the outcome of an adaptive evolutionary process; thus, insight into the mechanisms by which it fails would provide valuable information not only for development of mechanically superior biomimetic materials but also for development of treatment modalities to prevent debilitating bone fractures. Clinically, fractures of skeletal organs occur as a result of aging, disease, overuse, and trauma. Fracture mechanics, a sub-discipline of solid mechanics that investigates the performance of cracked materials, has been employed extensively in characterizing the mechanisms by which bone tissue fractures. At present the fracture mechanisms at the macroscale are better characterized than at the microscale. On the other hand, a mechanistic understanding of damage evolution at the submicroscopic scale is largely limited to postulations with little experimental insight. The challenge of skeletal fragility will be dealt with more efficiently with deeper understanding of the fracture process at each hierarchical size scale. The most recent review on this subject matter was a decade ago, and there have been numerous developments in the fracture mechanics of bone since then. This review recaps the existing literature with an emphasis on the hierarchical nature of the fracture process in bone, entailing the supramolecular, microscopic, and macroscopic scales.

Organic materials for second-harmonic generation: advances in relating structure to function

The relationships between molecular structure and the nonlinear optical phenomenon second-harmonic generation (SHG) are discussed. New-found relationships built up from basic structural axioms that were deduced in the 1970s and 1980s are the particular focus of this article, using structural results from X-ray and neutron-diffraction studies. The molecular and supramolecular manifestations of the SHG effect are borne out, although ways to optimize the effect on the molecular scale feature predominantly, since control of SHG on the supramolecular scale remains difficult given present limitations. The use of a variety of templates to generate head-to-tail oriented host-guest species thereby bypassing such limitations is described. The paper concludes with a look ahead at next generation 'octupolar' SHG-active compounds, the prediction of new series of SHG-active compounds via data-mining computational procedures, and developments in diffraction technology that may enable structural movies of a molecule to be captured during the SHG process. A practical assessment of the viability of organic SHG materials for industrial application is reviewed with a positive outcome, thus indicating a promising future for organic SHG materials.

On the Microscopic Interpretation of Stress and Couple Stress

Exact continuum forms of balance (for mass, linear momentum, and tensor-valued moment of momentum) are established as relations between weighted spatial averages of corpuscular quantities computed at any supra-molecular length scale. Explicit expressions for stress and generalised couple stress in terms of particle interactions are obtained using a theorem due to Noll, and their physical interpretation is discussed for a specific choice of weighting function. Remarks are made on other choices of weighting function, the interpretation of partial stress in mixture theory, a link between couple stress and inhomogeneity, and other forms of moment of momentum balance. Comparison is made with the statistical mechanical viewpoint pioneered by Irving and Kirkwood.

From chiral counterions to twisted membranes.

In membranes, the chirality of the amphiphile constituents is sometimes expressed at a supramolecular scale of nanometers or micrometers. We have recently reported that membranes of nonchiral dicationic n-2-n amphiphiles can also be chirally twisted upon interacting with chiral tartrate counterions. Here, we demonstrate that the mechanism of the chiral induction by counterions involves specific anion-cation recognition and the induction of conformationally labile chirality in the cations. Single-crystal X-ray diffraction shows that the amphiphilic cations exist as a mixture of chiral conformers. (1)H NMR data establish a specific recognition between tartrate and n-2-n cations and show that chiral conformers also exist in solution. Circular dichroism (CD) in the UV-vis shows a sharp conformational change of tartrate ions from anti to gauche when bound to the chiral cationic membranes. This is confirmed by CD in the infrared region which also shows concomitant induced CD bands in the vibrations of the n-2-n amphiphiles. These results represent the first example of the so-called Pfeiffer effect in a membrane. They provide a general framework for designing new tunable membrane systems. Our work also includes the first application of vibrational circular dichroism in the study of chiral conformations of amphiphiles in membranes and demonstrates the very high potential of this technique.

Thermal and Structural Behavior of Milk Fat: 3. Influence of Cooling Rate and Droplet Size on Cream Crystallization

Crystallization of triacylglycerols (TG) within milk fat globules of creams is studied with an instrument coupling time-resolved synchrotron X-ray diffraction (XRDT) at both small and wide angles and high-sensitivity differential scanning calorimetry (DSC) at cooling rates of −3 and −1°C/min from 60 to −10°C and compared to that of the anhydrous milk fat (AMF). Simultaneous thermal analysis permits correlation of the formation of the different crystalline species monitored by XRDT to the DSC events. Under the above cooling conditions, milk fat TG sequentially crystallize, within the globules, from about 19°C, in three different lamellar structures with double-chain length (2L) stackings of 47 and 42 Å and a triple-chain length (3L) stacking of 71 Å, all of α type, which are correlated to two or three overlapped exothermic peaks recorded by DSC. Compared to what is observed for AMF, TG crystallization in emulsion (i) favors sub-α formation at low temperature and (ii) induces layer stacking defects in 3L crystals. Subsequent heating at 2°C/min shows numerous structural rearrangements before final melting, confirming that (i) cooling at −1°C/min leads to the formation of unstable crystalline varieties in the dispersed state and (ii) a monotropic transition α→β′ takes place. Similar behavior is observed for cooling at −3°C/min and subsequent heating. An overall comparison of the thermal and structural properties of the crystalline species formed as a function of the cooling rate, between >1000 and 0.15°C/min, and stabilization time at 4°C is given. Depending on the cooling rate, at least five crystalline subcell species are observed at wide angles, α and sub-α, two β′ and one β. At small angles, at least six lamellar stackings are identified, three 3L and three 2L. However, a single subcell packing (e.g., α) might correspond to several longitudinal chain stackings, demonstrating the usefulness of the small-angle XRD technique. Reconstituted emulsions homogenized under different pressures are used to determine the influence of droplet size on crystallization. The decrease of droplet size induces (i) a higher supercooling/supersaturation and (ii) a higher disorder and/or a smaller size of TG crystals within the emulsion droplets. At the supramolecular scale, polarized light microscopy shows that various cooling rates applied in situ using a temperature-controlled stage directly influence crystal sizes and their type of organization within milk fat globules. The faster the cooling rate, the smaller the size of the crystals within the globules.

Thermal and Structural Behavior of Milk Fat3. Influence of Cooling Rate and Droplet Size on Cream Crystallization

Crystallization of triacylglycerols (TG) within milk fat globules of creams is studied with an instrument coupling time-resolved synchrotron X-ray diffraction (XRDT) at both small and wide angles and high-sensitivity differential scanning calorimetry (DSC) at cooling rates of -3 and -1 degrees C/min from 60 to -10 degrees C and compared to that of the anhydrous milk fat (AMF). Simultaneous thermal analysis permits correlation of the formation of the different crystalline species monitored by XRDT to the DSC events. Under the above cooling conditions, milk fat TG sequentially crystallize, within the globules, from about 19 degrees C, in three different lamellar structures with double-chain length (2L) stackings of 47 and 42 A and a triple-chain length (3L) stacking of 71 A, all of alpha type, which are correlated to two or three overlapped exothermic peaks recorded by DSC. Compared to what is observed for AMF, TG crystallization in emulsion (i) favors sub-alpha formation at low temperature and (ii) induces layer stacking defects in 3L crystals. Subsequent heating at 2 degrees C/min shows numerous structural rearrangements before final melting, confirming that (i) cooling at -1 degrees C/min leads to the formation of unstable crystalline varieties in the dispersed state and (ii) a monotropic transition alpha-->beta' takes place. Similar behavior is observed for cooling at -3 degrees C/min and subsequent heating. An overall comparison of the thermal and structural properties of the crystalline species formed as a function of the cooling rate, between >1000 and 0.15 degrees C/min, and stabilization time at 4 degrees C is given. Depending on the cooling rate, at least five crystalline subcell species are observed at wide angles, alpha and sub-alpha, two beta' and one beta. At small angles, at least six lamellar stackings are identified, three 3L and three 2L. However, a single subcell packing (e.g., alpha) might correspond to several longitudinal chain stackings, demonstrating the usefulness of the small-angle XRD technique. Reconstituted emulsions homogenized under different pressures are used to determine the influence of droplet size on crystallization. The decrease of droplet size induces (i) a higher supercooling/supersaturation and (ii) a higher disorder and/or a smaller size of TG crystals within the emulsion droplets. At the supramolecular scale, polarized light microscopy shows that various cooling rates applied in situ using a temperature-controlled stage directly influence crystal sizes and their type of organization within milk fat globules. The faster the cooling rate, the smaller the size of the crystals within the globules.

Hofmeister Solute Effects on Hydrophobic Adhesion Forces in SFM Experiments

One of the chief problems currently facing surface scientists is determining the relationship between mechanical forces, such as those measured by surface forces apparatus (SFA) or scanning force microscopes (SFM), and chemical driving forces, such as those governing interactions between molecules. Hydrophobic forces are important at both levels, but there is no clear relationship between their manifestation at molecular and supramolecular scales. To help bridge this gap, we have used an SFM to measure detachment forces between untreated silicon nitride SFM tips, which are moderately hydrophobic, and the highly hydrophobic surfaces paraffin and octadecylsilane−mica in the presence of various 2.0 and 3.0 M salt solutions. The salts were chosen for their strong abilities to promote or inhibit hydrophobically driven phenomena, according to their positions in the Hofmeister series. Thus, this is the first systematic assessment of Hofmeister salt effects on supramolecular hydrophobic adhesion in solution-phase chemical terms. NaCl has no effect on hydrophobic adhesion force relative to pure water, which agrees with previous SFM and SFA work but lies in contrast with the effects of NaCl on solution-phase behavior such as aqueous nonpolar compound solubility. Chaotropes such SCN- and guanidinium+, which promote exposure of molecular nonpolar surfaces to water, decrease adhesion force, whereas kosmotropes such as NH4+ and SO42-, which promote sequestration of nonpolar molecular surfaces from water, enhance adhesion force. Our results suggest that solvent structures near molecular and supramolecular hydrophobic surfaces are fundamentally different but that the nonideal effects embodied by the Hofmeister series have similar mechanisms in both length scales. Preferential interactions of solutes with hydrophobic surfaces and potential sources of hydrophobic adhesion, such as cavitation, van der Waals interactions, and solvent ordering, are discussed.

Micellization of Hydrophobically Modified Cyclodextrins: 2. Inclusion of Guest Molecules

The association of guest molecules in aggregates of a modified cyclodextrin, 6I-(cholest-5-en-3α-ylamido)succinylamido-6I-deoxy-per(2,6-di-O-methyl)cyclomaltoheptaose, was investigated for four different sparingly water-soluble molecules and an anionic surfactant (sodium dodecyl sulfate). The binding and spatial proximities were demonstrated for these different guests by NMR (nuclear Overhauser effect pumping). By use of small-angle X-ray and neutron scattering, the microstructure at the supramolecular scale of the modified cyclodextrin micelle, i.e., aggregation number, charge, and volume, in the presence of guest molecules could be defined. From the analysis of the variations in terms of aggregation number and charge induced by the presence of the guest molecule, the cavity of the cyclodextrin was shown to remain available for solubilization and transport. The stability and specificity of the mixed micelle involving target molecules demonstrated here make these hydrophobically modified cyclodextrins goo...

Crossover critical phenomena in complex fluids

It is assumed that near-critical complex fluids, such as polymer and ionic solutions, belong to the same universality class of criticality as simple fluids. However, the range of universal critical behavior in complex fluids is usually so small that it may not be experimentally accessible. In practice, physical properties of complex fluids in the critical region often exhibit some kind of crossover behavior rather than universal asymptotic critical behavior. The character of the crossover reflects an interplay between universality caused by long-range fluctuations and a specific supramolecular structure characterized by an additional nanoscopic or mesoscopic length scale. When the correlation length of the critical fluctuations becomes comparable to this supramolecular length scale, a specific sharp and even nonmonotonic crossover from classical (van der Waals-like) behavior to universal asymptotic behavior is exhibited. In the region far away from the critical point, where the correlation length is still smaller than the characteristic length scale, one can observe classical behavior. Ultimately, in the immediate vicinity of the critical point, the correlation length becomes dominant and one should expect universal asymptotic behavior. Such a crossover has been indeed observed in polymer and ionic solutions.

Tuning bilayer twist using chiral counterions.

From seashells to DNA, chirality is expressed at every level of biological structures. In self-assembled structures it may emerge cooperatively from chirality at the molecular scale. Amphiphilic molecules, for example, can form a variety of aggregates and mesophases that express the chirality of their constituent molecules at a supramolecular scale of micrometres. Quantitative prediction of the large-scale chirality based on that at the molecular scale remains a largely unsolved problem. Furthermore, experimental control over the expression of chirality at the supramolecular level is difficult to achieve: mixing of different enantiomers usually results in phase separation. Here we present an experimental and theoretical description of a system in which chirality can be varied continuously and controllably ('tuned') in micrometre-scale structures. We observe the formation of twisted ribbons consisting of bilayers of gemini surfactants (two surfactant molecules covalently linked at their charged head groups). We find that the degree of twist and the pitch of the ribbons can be tuned by the introduction of opposite-handed chiral counterions in various proportions. This degree of control might be of practical value; for example, in the use of the helical structures as templates for helical crystallization of macromolecules.

On the simulation of complex polymer systems

Correlation of molecular details with macroscopic properties of complex polymer systems requires application of various simulation methods corresponding to various size scales. Two problems related to simulations on the mesoscopic size scale are discussed. The first one concerns the mechanism of molecular rearrangements in coarse-grained molecular simulations and the second one concerns numerical renormalization of properties on the supramolecular scale, where various properties of microphases organized in various ways over a broad size range contribute to macroscopic properties.

Spectroscopic determination of lipid dynamics in membranes

Membranes are highly mobile entities, and motional characteristics on the intramolecular, molecular or supra-molecular length scale can be inferred either directly or indirectly from a variety of spectroscopic techniques. It is, however, of the utmost importance to understand the intrinsic time and distance scales to which the particular measurement technique is sensitive. In this article we briefly survey selected findings from various spectroscopic, diffraction and scattering experiments which contribute to the current knowledge of membrane lipid dynamics. We then explore in more detail some insights into lipid dynamics obtained from NMR spectroscopy and relaxation time determinations.

Modeling Organic Surfaces with Self‐Assembled Monolayers

AbstractThe interfacial properties of organic materials are of critical importance in many applications, especially the control of wettability, adhesion, tribology, and corrosion. The relationships between the microscopic structure of an organic surface and its macroscopic physical properties are, however, only poorly understood. This short review presents a model system that has the case of preparation and the structural definition required to provide a firm understanding of interfacial phenomena. Long‐chain thiols, HS(CH2)nX, adsorb from solution onto gold and form densely packed, oriented monolayers. By varying the terminal functional group, X, of the thiol, organic surfaces can be created having a wide range of structures and properties. More complex systems can be constructed by coadsorbing two or more thiols with different terminal functional groups or with different terminal functional groups or with different chain lengths onto a common gold substrate. By these techniques, controlled degrees of disorder can be introduced into model surfaces. We have used these systems to explore the relationships between the microscopic structure of the monolayers on a molecular and supramolecular scale and their macroscopic properties. Wettability is a macroscopic interfacial property that has proven of particular interest.