Design and Piezoelectric Energy Harvesting Properties of a Ferroelectric Cyclophosphazene Salt.

Cyclophosphazenes offer a robust and easily modifiable platform for a diverse range of functional systems that have found applications in a wide variety of areas. Herein, for the first time, it reports an organophosphazene-based supramolecular ferroelectric [(PhCH2 NH)6 P3 N3 Me]I, [PMe]I. The compound crystallizes in the polar space group Pc and its thin-film sample exhibits remnant polarization of 5 µC cm-2 . Vector piezoresponse force microscopy (PFM) measurements indicated the presence of multiaxial polarization. Subsequently, flexible composites of [PMe]I are fabricated for piezoelectric energy harvesting applications using thermoplastic polyurethane (TPU) as the matrix. The highest open-circuit voltages of 13.7 V and the maximum power density of 34.60 µW cm-2 are recorded for the poled 20 wt.% [PMe]I/TPU device. To understand the molecular origins of the high performance of [PMe]I-based mechanical energy harvesting devices, piezoelectric charge tensor values are obtained from DFT calculations of the single crystal structure. These indicate that the mechanical stress-induced distortions in the [PMe]I crystals are facilitated by the high flexibility of the layered supramolecular assembly.

Molecular Engineering of Ordered Piezoelectric Sulfonic Acid-Containing Assemblies.

Sulfonic acid-containing bioorganic monomers with wide molecular designability and abundant hydrogen bonding sites hold great potential to design diverse functional biocrystals but have so far not been explored for piezoelectric energy harvesting applications due to the lack of strategies to break the centrosymmetry of their assemblies. Here, a significant molecular packing transformation from centrosymmetric into non-centrosymmetric conformation by the addition of an amide terminus in the sulfonic acid-containing bioorganic molecule is demonstrated, allowing a high electromechanical response. The amide-functionalized molecule self-assembles into a polar supramolecular parallel ß-sheet-like structure with a high longitudinal piezoelectric coefficient d11 = 15.9 pm V-1 that produces the maximal open-circuit voltage of >1 V and the maximal power of 18 nW in nanogenerator devices pioneered. By contrast, molecules containing an amino or a cyclohexyl terminus assemble into highly symmetric 3D hydrogen bonding diamondoid-like networks or 2D double layer structures that show tunable morphologies, thermostability, and mechanical properties but non-piezoelectricity. This work not only presents a facile approach to achieving symmetry transformation of bioorganic assemblies but also demonstrates the terminal group and the property correlation for tailor-made design of high-performance piezoelectric biomaterials.

Guest Molecule-Mediated Energy Harvesting in a Conformationally Sensitive Peptide-Metal Organic Framework.

The apparent piezoelectricity of biological materials is not yet fully understood at the molecular level. In particular, dynamic noncovalent interactions, such as host-guest binding, are not included in the classical piezoelectric model, which limits the rational design of eco-friendly piezoelectric supramolecular materials. Here, inspired by the conformation-dependent mechanoresponse of the Piezo channel proteins, we show that guest-host interactions can amplify the electromechanical response of a conformationally mobile peptide metal-organic framework (MOF) based on the endogenous carnosine dipeptide, demonstrating a new type of adaptive piezoelectric supramolecular material. Density functional theory (DFT) predictions validated by piezoresponse force microscopy (PFM) measurements show that directional alignment of the guest molecules in the host carnosine-zinc peptide MOF channel determines the macroscopic electromechanical properties. We produce stable, robust 1.4 V open-circuit voltage under applied force of 25 N with a frequency of 0.1 Hz. Our findings demonstrate that the regulation of host-guest interactions could serve as an efficient method for engineering sustainable peptide-based power generators.

Self-Assembled Cationic ß-Cyclodextrin Nanostructures for siRNA Delivery.

Functionalized cyclodextrin molecules assemble into a wide variety of superstructures in solution, which are of interest for drug delivery and other nanomaterial and biomaterial applications. Here we use a combined simulation and experimental approach to probe the coassembly of siRNA and cationic cyclodextrin (c-CD) derivatives into a highly stable gene delivery nanostructure. The c-CD form supramolecular structures via interdigitation of their aliphatic tails, analogous to the formation of lipid bilayers and micelles. The native conformation of siRNA is preserved by the encapsulating c-CD superstructure in an extensive hydrogen-bonding network between the positively charged side arms of c-CD and the negatively charged siRNA backbone. The stability of the complexation is confirmed using isothermal titration calorimetry, and the experimental/simulation codesign methodology opens new avenues for creation of highly engineerable gene delivery vectors.

Molecular simulations reveal that a short helical loop regulates thermal stability of type I cohesin-dockerin complexes.

The cellulosome provides a fully worked out example of evolved radical nanotechnology. Improved understanding, and first steps toward re-engineering this biological nanomachine, is providing design rules for the formulation of advanced synthetic materials that can harness molecular flexibility and sticking interactions for applications in clean energy, environmental monitoring, and miniaturized devices. Computer simulations provide atomic scale insights into the mechanical stability of the component protein units, flexibility of short peptides that tether the units into scaffolds, and thermodynamic stability of protein-protein and protein-carbohydrate complexes, complementing and in some cases directing experiments. In the present work, a systematic computational study of cohesin-dockerin pairs, the strongly-bound protein complexes that glue the cellulosome nano-architecture in place, reveals that a short alpha-helix in the middle of the smaller dockerin protein becomes disordered at elevated temperatures and weakens cohesin-dockerin binding in mesophilic species. In thermophilic species, a more extensive and more thermally resistant H-bond network ensures the structure remains ordered at elevated temperatures of up to 400 K. The simulations predict that simply grafting the most crucial eight-residue peptide sequence into the mesophilic complex can, for one species and one of two possible binding modes, potentially create a new thermally resistant complex, providing leads for future experiments to re-engineer designer cellulosomes that can withstand elevated temperatures and so provide clean, renewable biocatalysts.

On the distinct binding modes of expansin and carbohydrate-binding module proteins on crystalline and nanofibrous cellulose: implications for cellulose degradation by designer cellulosomes.

Transformation of cellulose into monosaccharides can be achieved by hydrolysis of the cellulose chains, carried out by a special group of enzymes known as cellulases. The enzymatic mechanism of cellulases is well described, but the role of non-enzymatic components of the cellulose-degradation machinery is still poorly understood, and difficult to measure using experiments alone. In this study, we use a comprehensive set of atomistic molecular dynamics simulations to probe the molecular details of binding of the family-3a carbohydrate-binding module (CBM3a) and the bacterial expansin protein (EXLX1) to a range of cellulose substrates. Our results suggest that CBM3a behaves in a similar way on both crystalline and amorphous cellulose, whereas binding of the dual-domain expansin protein depends on the substrate crystallinity, and we relate our computed binding modes to the experimentally measured features of CBM and expansin action on cellulose.

Steered molecular dynamics simulations reveal the role of Ca2+ in regulating mechanostability of cellulose-binding proteins.

The conversion of cellulosic biomass into biofuels requires degradation of the biomass into fermentable sugars. The most efficient natural cellulase system for carrying out this conversion is an extracellular multi-enzymatic complex named the cellulosome. In addition to temperature and pH stability, mechanical stability is important for functioning of cellulosome domains, and experimental techniques such as Single Molecule Force Spectroscopy (SMFS) have been used to measure the mechanical strength of several cellulosomal proteins. Molecular dynamics computer simulations provide complementary atomic-resolution quantitative maps of domain mechanical stability for identification of experimental leads for protein stabilization. In this study, we used multi-scale steered molecular dynamics computer simulations, benchmarked against new SMFS measurements, to measure the intermolecular contacts that confer high mechanical stability to a family 3 Carbohydrate Binding Module protein (CBM3) derived from the archetypal Clostridium thermocellum cellulosome. Our data predicts that electrostatic interactions in the calcium binding pocket modulate the mechanostability of the cellulose-binding module, which provides an additional design rule for the rational re-engineering of designer cellulosomes for biotechnology. Our data offers new molecular insights into the origins of mechanostability in cellulose binding domains and gives leads for synthesis of more robust cellulose-binding protein modules. On the other hand, simulations predict that insertion of a flexible strand can promote alternative unfolding pathways and dramatically reduce the mechanostability of the carbohydrate binding module, which gives routes to rational design of tailormade fingerprint complexes for force spectroscopy experiments.

The length but not the sequence of peptide linker modules exerts the primary influence on the conformations of protein domains in cellulosome multi-enzyme complexes.

Cellulosomes are large multi-protein catalysts produced by various anaerobic microorganisms to efficiently degrade plant cell-wall polysaccharides down into simple sugars. X-ray and physicochemical structural characterisations show that cellulosomes are composed of numerous protein domains that are connected by unstructured polypeptide segments, yet the properties and possible roles of these 'linker' peptides are largely unknown. We have performed coarse-grained and all-atom molecular dynamics computer simulations of a number of cellulosomal linkers of different lengths and compositions. Our data demonstrates that the effective stiffness of the linker peptides, as quantified by the equilibrium fluctuations in the end-to-end distances, depends primarily on the length of the linker and less so on the specific amino acid sequence. The presence of excluded volume - provided by the domains that are connected - dampens the motion of the linker residues and reduces the effective stiffness of the linkers. Simultaneously, the presence of the linkers alters the conformations of the protein domains that are connected. We demonstrate that short, stiff linkers induce significant rearrangements in the folded domains of the mini-cellulosome composed of endoglucanase Cel8A in complex with scaffoldin ScafT (Cel8A-ScafT) of Clostridium thermocellum as well as in a two-cohesin system derived from the scaffoldin ScaB of Acetivibrio cellulolyticus. We give experimentally testable predictions on structural changes in protein domains that depend on the length of linkers.

Coupled protein-ligand dynamics in truncated hemoglobin N from atomistic simulations and transition networks.

BACKGROUND: The nature of ligand motion in proteins is difficult to characterize directly using experiment. Specifically, it is unclear to what degree these motions are coupled. METHODS: All-atom simulations are used to sample ligand motion in truncated Hemoglobin N. A transition network analysis including ligand- and protein-degrees of freedom is used to analyze the microscopic dynamics. RESULTS: Clustering of two different subsets of MD trajectories highlights the importance of a diverse and exhaustive description to define the macrostates for a ligand-migration network. Monte Carlo simulations on the transition matrices from one particular clustering are able to faithfully capture the atomistic simulations. Contrary to clustering by ligand positions only, including a protein degree of freedom yields considerably improved coarse grained dynamics. Analysis with and without imposing detailed balance agree closely which suggests that the underlying atomistic simulations are converged with respect to sampling transitions between neighboring sites. CONCLUSIONS: Protein and ligand dynamics are not independent from each other and ligand migration through globular proteins is not passive diffusion. GENERAL SIGNIFICANCE: Transition network analysis is a powerful tool to analyze and characterize the microscopic dynamics in complex systems. This article is part of a Special Issue entitled Recent developments of molecular dynamics.

Solvation of fluoro-acetonitrile in water by 2D-IR spectroscopy: A combined experimental-computational study.

The solvent dynamics around fluorinated acetonitrile is characterized by 2-dimensional infrared spectroscopy and atomistic simulations. The lineshape of the linear infrared spectrum is better captured by semiempirical (density functional tight binding) mixed quantum mechanical/molecular mechanics simulations, whereas force field simulations with multipolar interactions yield lineshapes that are significantly too narrow. For the solvent dynamics, a relatively slow time scale of 2 ps is found from the experiments and supported by the mixed quantum mechanical/molecular mechanics simulations. With multipolar force fields fitted to the available thermodynamical data, the time scale is considerably faster--on the 0.5 ps time scale. The simulations provide evidence for a well established CF-HOH hydrogen bond (population of 25%) which is found from the radial distribution function g(r) from both, force field and quantum mechanics/molecular mechanics simulations.

A comparative analysis of clustering algorithms: O2 migration in truncated hemoglobin I from transition networks.

The ligand migration network for O2-diffusion in truncated Hemoglobin N is analyzed based on three different clustering schemes. For coordinate-based clustering, the conventional k-means and the kinetics-based Markov Clustering (MCL) methods are employed, whereas the locally scaled diffusion map (LSDMap) method is a collective-variable-based approach. It is found that all three methods agree well in their geometrical definition of the most important docking site, and all experimentally known docking sites are recovered by all three methods. Also, for most of the states, their population coincides quite favourably, whereas the kinetics of and between the states differs. One of the major differences between k-means and MCL clustering on the one hand and LSDMap on the other is that the latter finds one large primary cluster containing the Xe1a, IS1, and ENT states. This is related to the fact that the motion within the state occurs on similar time scales, whereas structurally the state is found to be quite diverse. In agreement with previous explicit atomistic simulations, the Xe3 pocket is found to be a highly dynamical site which points to its potential role as a hub in the network. This is also highlighted in the fact that LSDMap cannot identify this state. First passage time distributions from MCL clusterings using a one- (ligand-position) and two-dimensional (ligand-position and protein-structure) descriptor suggest that ligand- and protein-motions are coupled. The benefits and drawbacks of the three methods are discussed in a comparative fashion and highlight that depending on the questions at hand the best-performing method for a particular data set may differ.

Tracking Prenucleation Molecular Clustering of Salicylamide in Organic Solvents.

Crystal nucleation shapes the structure and product size distribution of solid-state pharmaceuticals and is seeded by early-stage molecular self-assemblies formed in host solution. Here, molecular clustering of salicylamide in ethyl acetate, methanol, and acetonitrile was investigated using photon correlation spectroscopy. Cluster size steadily increased over 3 days and with concentration across the range from undersaturated to supersaturated solutions. Solute concentration normalized by solubility provided more sensitive characterization of molecular-level conditions than concentration alone. In saturated solution, cluster size is independent of solvent, while at equal supersaturation, solvent-dependent cluster size increases as methanol < acetonitrile < ethyl acetate, commensurate with increasing nucleation propensity. In ethyl acetate, with largest prenucleation clusters, the driving force required for nucleation is lowest, compared to methanol with smallest clusters and highest driving force. To understand solvent-solute effects, we performed IR spectroscopy supported by molecular simulations. We observe solute-solvent interaction weakening in the same order: methanol < acetonitrile < ethyl acetate, quantifying the weaker solvent-solute interactions that permit the formation of larger prenucleation clusters. Our results support the hypothesis that nucleation is easier in weaker solvents because weak solute-solvent interactions favor growth of large clusters, as opposed to relying solely on ease of desolvation.

Regulating photosalient behavior in dynamic metal-organic crystals.

Dynamic photoactuating crystals have become a sensation due to their potential applications in developing smart medical devices, molecular machines, artificial muscles, flexible electronics actuators, probes and microrobots. Here we report the synthesis of two iso-structural metal-organic crystals, [Zn(4-ohbz)2(4-nvp)2] (1) and [Cd(4-ohbz)2(4-nvp)2] (2) {H4-ohbz = 4-hydroxy benzoic acid; 4-nvp = 4-(1-naphthylvinyl)pyridine} which undergo topochemical [2 + 2] cycloaddition under UV irradiation as well as sunlight to generate a dimerized product of discrete metal-complex [Zn(4-ohbz)2(rctt-4-pncb)] {rctt-4-pncb = 1,3-bis(4'-pyridyl)-2,4-bis(naphthyl)cyclobutane} (1') and one-dimensional coordination polymer (1D CP) [Cd(4-ohbz)2(rctt-4-pncb)] (2') respectively, in a single-crystal-to-single-crystal (SCSC) process. The Zn-based compound demonstrates photosalient behaviour, wherein crystals show jumping, splitting, rolling, and swelling upon UV irradiation. However, the Cd-based crystals do not show such behaviour maintaining the initial supramolecular packing and space group. Thus the photomechanical behaviour can be induced by choosing a suitable metal ion. The above findings are thoroughly validated by quantitative density functional theory (DFT) calculations which show that the Zn-based crystal shifts towards an orthorhombic structure to resolve the anisotropic UV-induced mechanical strain. Furthermore, the mechano-structure-property relationship has been established by complimentary nanoindentation measurements, which are in-line with the DFT-predicted single crystal values.

High performance mechano-optoelectronic molecular switch.

Highly-efficient molecular photoswitching occurs ex-situ but not to-date inside electronic devices due to quenching of excited states by background interactions. Here we achieve fully reversible in-situ mechano-optoelectronic switching in self-assembled monolayers (SAMs) of tetraphenylethylene molecules by bending their supporting electrodes to maximize aggregation-induced emission (AIE). We obtain stable, reversible switching across >1600 on/off cycles with large on/off ratio of (3.8 ± 0.1) × 103 and 140 ± 10 ms switching time which is 10-100× faster than other approaches. Multimodal characterization shows mechanically-controlled emission with UV-light enhancing the Coulomb interaction between the electrons and holes resulting in giant enhancement of molecular conductance. The best mechano-optoelectronic switching occurs in the most concave architecture that reduces ambient single-molecule conformational entropy creating artificially-tightened supramolecular assemblies. The performance can be further improved to achieve ultra-high switching ratio on the order of 105 using tetraphenylethylene derivatives with more AIE-active sites. Our results promise new applications from optimized interplay between mechanical force and optics in soft electronics.

Oxygen migration pathways in NO-bound truncated hemoglobin.

Atomistic simulations of dioxygen (O(2)) dynamics and migration in nitric oxide-bound truncated Hemoglobin N (trHbN) of Mycobacterium tuberculosis are reported. From more than 100 ns of simulations the connectivity network involving the metastable states for localization of the O(2) ligand is built and analyzed. It is found that channel I is the primary entrance point for O(2) whereas channel II is predominantly an exit path although access to the protein active site is also possible. For O(2) a new site compared to nitric oxide, from which reaction with the heme group can occur, was found. As this site is close to the heme iron, it could play an important role in the dioxygenation mechanism as O(2) can remain there for hundreds of picoseconds after which it can eventually leave the protein, while NO is localized in Xe2. The present study supports recent experimental work which proposed that O(2) docks in alternative pockets than Xe close to the reactive site. Similar to other proteins, a phenylalanine residue (Phe62) plays the role of a gate along the access route in channel I. The most highly connected site is the Xe3 pocket which is a "hub" and free energy barriers between the different metastable states are ≈1.5 kcal mol(-1) which allows facile O(2) migration within the protein.

Molecular Engineering of Rigid Hydrogels Co-assembled from Collagenous Helical Peptides Based on a Single Triplet Motif.

The potential of ultra-short peptides to self-assemble into well-ordered functional nanostructures makes them promising minimal components for mimicking the basic ingredient of nature and diverse biomaterials. However, selection and modular design of perfect de novo sequences are extremely tricky due to their vast possible combinatorial space. Moreover, a single amino acid substitution can drastically alter the supramolecular packing structure of short peptide assemblies. Here, we report the design of rigid hybrid hydrogels produced by sequence engineering of a new series of ultra-short collagen-mimicking tripeptides. Connecting glycine with different combinations of proline and its post-translational product 4-hydroxyproline, the single triplet motif, displays the natural collagen-helix-like structure. Improved mechanical rigidity is obtained via co-assembly with the non-collagenous hydrogelator, fluorenylmethoxycarbonyl (Fmoc) diphenylalanine. Characterizations of the supramolecular interactions that promote the self-supporting and self-healing properties of the co-assemblies are performed by physicochemical experiments and atomistic models. Our results clearly demonstrate the significance of sequence engineering to design functional peptide motifs with desired physicochemical and electromechanical properties and reveal co-assembly as a promising strategy for the utilization of small, readily accessible biomimetic building blocks to generate hybrid biomolecular assemblies with structural heterogeneity and functionality of natural materials.

On the origin of chaotrope-modulated electrocatalytic activity of cytochrome c at electrified aqueous|organic interfaces.

Electrochemical, spectroscopic and computational methods are used to demonstrate that electrified aqueous|organic interfaces are a suitable bio-mimetic platform to study and contrast the accelerated electrocatalytic activity of cytochrome c towards the production of reactive oxygen species (ROS) in the presence of denaturing agents such as guanidinium chloride and urea.

Mapping the deformability of natural and designed cellulosomes in solution.

BACKGROUND: Natural cellulosome multi-enzyme complexes, their components, and engineered 'designer cellulosomes' (DCs) promise an efficient means of breaking down cellulosic substrates into valuable biofuel products. Their broad uptake in biotechnology relies on boosting proximity-based synergy among the resident enzymes, but the modular architecture challenges structure determination and rational design. RESULTS: We used small angle X-ray scattering combined with molecular modeling to study the solution structure of cellulosomal components. These include three dockerin-bearing cellulases with distinct substrate specificities, original scaffoldins from the human gut bacterium Ruminococcus champanellensis (ScaA, ScaH and ScaK) and a trivalent cohesin-bearing designer scaffoldin (Scaf20L), followed by cellulosomal complexes comprising these components, and the nonavalent fully loaded Clostridium thermocellum CipA in complex with Cel8A from the same bacterium. The size analysis of Rg and Dmax values deduced from the scattering curves and corresponding molecular models highlight their variable aspects, depending on composition, size and spatial organization of the objects in solution. CONCLUSIONS: Our data quantifies variability of form and compactness of cellulosomal components in solution and confirms that this native plasticity may well be related to speciation with respect to the substrate that is targeted. By showing that scaffoldins or components display enhanced compactness compared to the free objects, we provide new routes to rationally enhance their stability and performance in their environment of action.

Computational spectroscopy and reaction dynamics.

Physico- and bio-chemical processes on the femto- to picosecond time scale are ideally suited to be investigated with all-atom simulations. They include, amongst others, vibrational relaxation, ligand migration in sterically demanding environments (proteins, ices), or vibrational spectra. By comparing with experimental data, the results can be used to obtain an understanding of the mechanisms underlying the observations. Furthermore, most of these processes are sensitive to the intermolecular interactions. Therefore, detailed refinement of such interaction potentials is possible.

Extended Lifetime of Molecules Adsorbed onto Excipients Drives Nucleation in Heterogeneous Crystallization.

Monte Carlo (MC) and molecular dynamics (MD) computer simulations were used to investigate the role of adsorption during seeded and heterogeneous crystallization. The simulations characterized the range of adsorption energies and configurations encountered during adsorption of individual molecules of active pharmaceutical ingredients (APIs), with varying hydrogen-bonding tendencies, onto seed and heterosurfaces. Specifically, the adsorption of acetaminophen (AAP), carbamazepine (CBMZ), fenofibrate (FF), phenylbutazone (PBZ), clozapine (CPB), and risperidone (RIS) was simulated on selected crystallographic facets of their own crystals as examples of seeded crystallizations and on lactose or microcrystalline cellulose (MCC) substrates as heterosurfaces. The MC screening provided adsorption enthalpies in the range of -59 to -155 kJ mol-1 for these APIs on lactose, generally increasing as the molar mass of the API increased. The corresponding values predicted for adsorption of each API onto its own crystal were in the range of -92 to -201 kJ mol-1. More detailed MD simulations performed in methanol showed adsorption free energies for RIS on MCC in the range of -37 to -50 kJ mol-1 with strong molecule-surface complexation lifetime of tens of nanoseconds on the (010) face of MCC. This extended lifetime is a key feature in understanding the mechanism of heterogeneous crystallization. A well-formed nucleus is generated on the surface starting with a single adsorbed molecule. Individual or small clusters add to the adsorbed species. This addition is facilitated by the extended lifetime of the adsorbed molecule, which is several orders of magnitude greater than the time required for additional molecules to assemble and grow into a stable nucleus attached to the heterosurface.