Electronic structure at coarse-grained resolutions from supervised machine learning.

Computational studies aimed at understanding conformationally dependent electronic structure in soft materials require a combination of classical and quantum-mechanical simulations, for which the sampling of conformational space can be particularly demanding. Coarse-grained (CG) models provide a means of accessing relevant time scales, but CG configurations must be back-mapped into atomistic representations to perform quantum-chemical calculations, which is computationally intensive and inconsistent with the spatial resolution of the CG models. A machine learning approach, denoted as artificial neural network electronic coarse graining (ANN-ECG), is presented here in which the conformationally dependent electronic structure of a molecule is mapped directly to CG pseudo-atom configurations. By averaging over decimated degrees of freedom, ANN-ECG accelerates simulations by eliminating backmapping and repeated quantum-chemical calculations. The approach is accurate, consistent with the CG spatial resolution, and can be used to identify computationally optimal CG resolutions.

Free energy of metal-organic framework self-assembly.

Metal-organic frameworks (MOFs) represent an important class of materials. Careful selection of building blocks allows for tailoring of the properties of the resulting framework. The self-assembly process, however, is not understood, and without detailed knowledge of the underlying molecular mechanism, it is difficult to anticipate whether a particular design can be realized, or whether the material adopts a metastable, kinetically arrested state. We present a detailed examination of early-stage self-assembly pathways of the MOF-5. Enhanced sampling techniques are used to model a self-assembly in an explicit solvent (dimethylformamide, DMF). We identify several free energy barriers encountered during the assembly of the final MOF, which arise from structural rearrangements preceding MOF formation and from disrupted MOF-solvent interactions as formation proceeds. In all cases considered here, MOFs exhibit favorable entropic gains during the assembly. More generally, the strategy presented provides a step toward the experimental design characterizing the formation of ordered frameworks and possible sources of polymorphism.

Tenfold increase in the photostability of an azobenzene guest in vapor-deposited glass mixtures.

Improvements to the photostability of organic glasses for use in electronic applications have generally relied on the modification of the chemical structure. We show here that the photostability of a guest molecule can also be significantly improved-without chemical modification-by using physical vapor deposition to pack molecules more densely. Photoisomerization of the substituted azobenzene, 4,4'-diphenyl azobenzene, was studied in a vapor-deposited glass matrix of celecoxib. We directly measure photoisomerization of trans- to cis-states via Ultraviolet-visible (UV-Vis) spectroscopy and show that the rate of photoisomerization depends upon the substrate temperature used during co-deposition of the glass. Photostability correlates reasonably with the density of the glass, where the optimum glass is about tenfold more photostable than the liquid-cooled glass. Molecular simulations, which mimic photoisomerization, also demonstrate that photoreaction of a guest molecule can be suppressed in vapor-deposited glasses. From the simulations, we estimate that the region that is disrupted by a single photoisomerization event encompasses approximately 5 molecules.

Author Correction: Dynamic actuation of glassy polymersomes through isomerization of a single azobenzene unit at the block copolymer interface.

In the version of this Article originally published, multiple changes to the "Results and discussion" section were required. In paragraph 1, "(Supplementary Fig. 1)" should have read "(Fig. 1e-j and Supplementary Fig. 1)"; in the first sentence of paragraph 3, "(R6G)" should have read "(R6G, Fig. 2i)"; in paragraph 6 in the sentence beginning "Temporal release of hydrophilic...", Supplementary Fig. 4 should have been cited after "360 nm"; in paragraph 9, in the sentence beginning "To test this...", "Fig. 4e" should have read "Fig. 4a"; in paragraph 10, in the sentence beginning "When the irradiation...", "(Fig. 4a-d)" should have read "(Fig. 4d,e)"; in paragraph 11, in the sentence beginning "Pristine PLA", "P1" should have read "P2"; and in the penultimate paragraph, in the sentence beginning "Moreover, a control PEG-PLA...", "block copolymer" should have been followed by (P5); Fig. 4g should have been Fig. 4c; "hydrophobic azobenzene small molecules" should have been followed by (12); and Fig. 4f should have been Fig. 4b. Finally, Supplementary Videos 1 and 2 were missing from the Article. All of these corrections have been made to the online versions.

Dynamic actuation of glassy polymersomes through isomerization of a single azobenzene unit at the block copolymer interface.

Nature has engineered exquisitely responsive systems where molecular-scale information is transferred across an interface and propagated over long length scales. Such systems rely on multiple interacting, signalling and adaptable molecular and supramolecular networks that are built on dynamic, non-equilibrium structures. Comparable synthetic systems are still in their infancy. Here, we demonstrate that the light-induced actuation of a molecularly thin interfacial layer, assembled from a hydrophilic- azobenzene -hydrophobic diblock copolymer, can result in a reversible, long-lived perturbation of a robust glassy membrane across a range of over 500 chemical bonds. We show that the out-of-equilibrium actuation is caused by the photochemical trans-cis isomerization of the azo group, a single chemical functionality, in the middle of the interfacial layer. The principles proposed here are implemented in water-dispersed nanocapsules, and have implications for on-demand release of embedded cargo molecules.

Anticancer potential of benzothiazolic derivative (E)-2-((2-(benzo[d]thiazol-2-yl)hydrazono)methyl)-4-nitrophenol against melanoma cells.

Malignant melanoma is an important type of cancer worldwide due to its aggressiveness and poor survival rate. Significant efforts to understand the biology of melanoma and approaches to treat the advanced disease are focused on targeted gene inhibitors. Frequently mutated genes, such as NRAS, B-RAF and TP53, significantly exceed the frequency of mutations of other genes, emphasizing their importance for future targeted therapies. Considering the antitumor activity of benzothiazolic derivatives, this study aimed to demonstrate the action of benzothiazolic (E)-2-((2-(benzo[d]thiazol-2-yl)hydrazono)methyl)-4-nitrophenol (AFN01) against three established human melanoma cell lines that recapitulate the molecular landscape of the disease in terms of its genetic alterations and mutations, such as the TP53, NRAS and B-RAF genes. The results presented here indicate that AFN01, as a significant cytostatic and cytotoxic drug due to its induction of DNA fragmentation, causes single and double DNA strand breaks, consequently inhibiting cell proliferation, migration and invasion by promoting apoptosis. Our data suggest that AFN01 might be considered as a future therapeutic option for managing melanoma.

Influence of Molecular Shape on the Thermal Stability and Molecular Orientation of Vapor-Deposited Organic Semiconductors.

High thermal stability and anisotropic molecular orientation enhance the performance of vapor-deposited organic semiconductors, but controlling these properties is a challenge in amorphous materials. To understand the influence of molecular shape on these properties, vapor-deposited glasses of three disk-shaped molecules were prepared. For all three systems, enhanced thermal stability is observed for glasses prepared over a wide range of substrate temperatures and anisotropic molecular orientation is observed at lower substrate temperatures. For two of the disk-shaped molecules, atomistic simulations of thin films were also performed and anisotropic molecular orientation was observed at the equilibrium liquid surface. We find that the structure and thermal stability of these vapor-deposited glasses results from high surface mobility and partial equilibration toward the structure of the equilibrium liquid surface during the deposition process. For the three molecules studied, molecular shape is a dominant factor in determining the anisotropy of vapor-deposited glasses.

Influence of Vapor Deposition on Structural and Charge Transport Properties of Ethylbenzene Films.

Organic glass films formed by physical vapor deposition exhibit enhanced stability relative to those formed by conventional liquid cooling and aging techniques. Recently, experimental and computational evidence has emerged indicating that the average molecular orientation can be tuned by controlling the substrate temperature at which these "stable glasses" are grown. In this work, we present a comprehensive all-atom simulation study of ethylbenzene, a canonical stable-glass former, using a computational film formation procedure that closely mimics the vapor deposition process. Atomistic studies of experimentally formed vapor-deposited glasses have not been performed before, and this study therefore begins by verifying that the model and method utilized here reproduces key structural features observed experimentally. Having established agreement between several simulated and experimental macroscopic observables, simulations are used to examine the substrate temperature dependence of molecular orientation. The results indicate that ethylbenzene glasses are anisotropic, depending upon substrate temperature, and that this dependence can be understood from the orientation present at the surface of the equilibrium liquid. By treating ethylbenzene as a simple model for molecular semiconducting materials, a quantum-chemical analysis is then used to show that the vapor-deposited glasses exhibit decreased energetic disorder and increased magnitude of the mean-squared transfer integral relative to isotropic, liquid-cooled films, an effect that is attributed to the anisotropic ordering of the molecular film. These results suggest a novel structure-function simulation strategy capable of tuning the electronic properties of organic semiconducting glasses prior to experimental deposition, which could have considerable potential for organic electronic materials design.

Membrane Permeation versus Amyloidogenicity: A Multitechnique Study of Islet Amyloid Polypeptide Interaction with Model Membranes.

Islet amyloid polypeptide (IAPP) is responsible for cell depletion in the pancreatic islets of Langherans, and for multiple pathological consequences encountered by patients suffering from type 2 Diabetes Mellitus. We have examined the amyloidogenicity and cytotoxic mechanisms of this peptide by investigating model-membrane permeation and structural effects of fragments of the human IAPP and several rat IAPP mutants. In vitro experiments and molecular dynamics simulations reveal distinct physical segregation, membrane permeation, and amyloid aggregation processes that are mediated by two separate regions of the peptide. These observations suggest a "detergent-like" mechanism, where lipids are extracted from the bilayer by the N-terminus of IAPP, and integrated into amyloid aggregates. The amyloidogenic aggregation would kinetically compete with the process of membrane permeation and, therefore, inhibit it. This hypothesis represents a new perspective on the mechanism underlying the membrane disruption by amyloid peptides, and could influence the development of new therapeutic strategies.

Photostability Can Be Significantly Modulated by Molecular Packing in Glasses.

While previous work has demonstrated that molecular packing in organic crystals can strongly influence photochemical stability, efforts to tune photostability in amorphous materials have shown much smaller effects. Here we show that physical vapor deposition can substantially improve the photostability of organic glasses. Disperse Orange 37 (DO37), an azobenzene derivative, is studied as a model system. Photostability is assessed through changes in the density and molecular orientation of glassy thin films during light irradiation. By optimizing the substrate temperature used for deposition, we can increase photostability by a factor of 50 relative to the liquid-cooled glass. Photostability correlates with glass density, with density increases of up to 1.3%. Coarse-grained molecular simulations, which mimic glass preparation and the photoisomerization reaction, also indicate that glasses with higher density have substantially increased photostability. These results provide insights that may assist in the design of organic photovoltaics and light-emission devices with longer lifetimes.

Orientational anisotropy in simulated vapor-deposited molecular glasses.

Enhanced kinetic stability of vapor-deposited glasses has been established for a variety of glass organic formers. Several recent reports indicate that vapor-deposited glasses can be orientationally anisotropic. In this work, we present results of extensive molecular simulations that mimic a number of features of the experimental vapor deposition process. The simulations are performed on a generic coarse-grained model and an all-atom representation of N,N'-bis(3-methylphenyl)-N,N'-diphenylbenzidine (TPD), a small organic molecule whose vapor-deposited glasses exhibit considerable orientational anisotropy. The coarse-grained model adopted here is found to reproduce several key aspects reported in experiments. In particular, the molecular orientation of vapor-deposited glasses is observed to depend on substrate temperature during deposition. For a fixed deposition rate, the molecular orientation in the glasses changes from isotropic, at the glass transition temperature, Tg, to slightly normal to the substrate at temperatures just below Tg. Well below Tg, molecular orientation becomes predominantly parallel to the substrate. The all-atom model is used to confirm some of the equilibrium structural features of TPD interfaces that arise above the glass transition temperature. We discuss a mechanism based on distinct orientations observed at equilibrium near the surface of the film, which get trapped within the film during the non-equilibrium process of vapor deposition.

Sculpting bespoke mountains: Determining free energies with basis expansions.

The intriguing behavior of a wide variety of physical systems, ranging from amorphous solids or glasses to proteins, is a direct manifestation of underlying free energy landscapes riddled with local minima separated by large barriers. Exploring such landscapes has arguably become one of statistical physics's great challenges. A new method is proposed here for uniform sampling of rugged free energy surfaces. The method, which relies on special Green's functions to approximate the Dirac delta function, improves significantly on existing simulation techniques by providing a boundary-agnostic approach that is capable of mapping complex features in multidimensional free energy surfaces. The usefulness of the proposed approach is established in the context of a simple model glass former and model proteins, demonstrating improved convergence and accuracy over existing methods.