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The ability to predict cell-permeable candidate molecules has great potential to assist drug discovery projects. Large molecules that lie beyond the Rule of Five (bRo5) are increasingly important as drug candidates and tool molecules for chemical biology. However, such large molecules usually do not cross cell membranes and cannot access intracellular targets or be developed as orally bioavailable drugs. Here, we describe a random forest (RF) machine learning model for the prediction of passive membrane permeation rates developed using a set of over 1000 bRo5 macrocyclic compounds. The model is based on easily calculated chemical features/descriptors as independent variables. Our random forest (RF) model substantially outperforms a multiple linear regression model based on the same features and achieves better performance metrics than previously reported models using the same underlying data. These features include: (1) polar surface area in water, (2) the octanol-water partitioning coefficient, (3) the number of hydrogen-bond donors, (4) the sum of the topological distances between nitrogen atoms, (5) the sum of the topological distances between nitrogen and oxygen atoms, and (6) the multiple molecular path count of order 2. The last three features represent molecular flexibility, the ability of the molecule to adopt different conformations in the aqueous and membrane interior phases, and the molecular “chameleonicity.” Guided by the model, we propose design guidelines for membrane-permeating macrocycles. It is anticipated that this model will be useful in guiding the design of large, bioactive molecules for medicinal chemistry and chemical biology applications.

Metal–phenolic networks (MPNs) are amorphous materials that can be used to engineer functional films and particles. A fundamental understanding of the heat-driven structural reorganization of MPNs can offer opportunities to rationally tune their properties (e.g., size, permeability, wettability, hydrophobicity) for applications such as drug delivery, sensing, and tissue engineering. Herein, we use a combination of single-molecule localization microscopy, theoretical electronic structure calculations, and all-atom molecular dynamics simulations to demonstrate that MPN plasticity is governed by both the inherent flexibility of the metal (FeIII)–phenolic coordination center and the conformational elasticity of the phenolic building blocks (tannic acid, TA) that make up the metal–organic coordination complex. Thermal treatment (heating to 150 °C) of the flexible TA/FeIIInetworks induces a considerable increase in the number of aromatic π–π interactions formed among TA moieties and leads to the formation of hydrophobic domains. In the case of MPN capsules, 15 min of heating induces structural rearrangements that cause the capsules to shrink (from ∼4 to ∼3 μm), resulting in a thicker (3-fold), less porous, and higher protein (e.g., bovine serum albumin) affinity MPN shell. In contrast, when a simple polyphenol such as gallic acid is complexed with FeIIIto form MPNs, rigid materials that are insensitive to temperature changes are obtained, and negligible structural rearrangement is observed upon heating. These findings are expected to facilitate the rational engineering of versatile TA-based MPN materials with tunable physiochemical properties for diverse applications.

Surface chemistry is a major factor that determines the wettability of materials, and devising broadly applicable coating strategies that afford tunable and selective surface properties required for next-generation materials remains a challenge. Herein, we report fluorinated metal–organic coatings that display water-wetting and oil-repelling characteristics, a wetting phenomenon different from responsive wetting induced by external stimuli. We demonstrate this selective wettability with a library of metal–organic coatings using catechol-based coordination and silanization (both fluorinated and fluorine-free), enabling sensing through interfacial reconfigurations in both gaseous and liquid environments, and establish a correlation between the coating wettability and polarity of the liquids. This selective wetting performance is substrate-independent, spontaneous, durable, and reversible and occurs over a range of polar and nonpolar liquids (60 studied). These results provide insight into advanced liquid–solid interactions and a pathway toward tuning interfacial affinities and realizing robust, selective superwettability according to the surrounding conditions.

The evolution of life on earth eventually leads to the emergence of species with increased complexity and diversity. Similarly, evolutionary chemical space exploration in the laboratory is a key step to pursue the structural and functional diversity of supramolecular systems. Here, we present a powerful tool that enables rapid peptide diversification and employ it to expand the chemical space for supramolecular functions. Central to this strategy is the exploitation of palladium-catalyzed Suzuki–Miyaura cross-coupling reactions to direct combinatorial synthesis of peptide arrays in microtiter plates under an open atmosphere. Taking advantage of this in situlibrary design, our results unambiguously deliver a fertile platform for creating a set of intriguing peptide functions including green fluorescent protein-like peptide emitters with chemically encoded emission colors, hierarchical self-assembly into nano-objects, and macroscopic hydrogels. This work also offers opportunities for quickly surveying the diversified peptide arrays and thereby identifying the structural factors that modulate peptide properties.

The novel RNA virus, severe acute respiratory syndrome coronavirus II (SARS-CoV-2), is currently the leading cause of mortality in 2020, having led to over 1.6 million deaths and infecting over 75 million people worldwide by December 2020. While vaccination has started and several clinical trials for a number of vaccines are currently underway, there is a pressing need for a cure for those already infected with the virus. Of particular interest in the design of anti-SARS-CoV-2 therapeutics is the human protein angiotensin converting enzyme II (ACE2) to which this virus adheres before entry into the host cell. The SARS-CoV-2 virion binds to cell-surface bound ACE2 via interactions of the spike protein (s-protein) on the viral surface with ACE2. In this paper, we use all-atom molecular dynamics simulations and binding enthalpy calculations to determine the effect that a bound ACE2 active site inhibitor (MLN-4760) would have on the binding affinity of SARS-CoV-2 s-protein with ACE2. Our analysis indicates that the binding enthalpy could be reduced for s-protein adherence to the active site inhibitor-bound ACE2 protein by as much as 1.48-fold as an upper limit. This weakening of binding strength was observed to be due to the destabilization of the interactions between ACE2 residues Glu-35, Glu-37, Tyr-83, Lys-353, and Arg-393 and the SARS-CoV-2 s-protein receptor binding domain (RBD). The conformational changes were shown to lead to weakening of ACE2 interactions with SARS-CoV-2 s-protein, therefore reducing s-protein binding strength. Further, we observed increased conformational lability of the N-terminal helix and a conformational shift of a significant portion of the ACE2 motifs involved in s-protein binding, which may affect the kinetics of the s-protein binding when the small molecule inhibitor is bound to the ACE2 active site. These observations suggest potential new ways for interfering with the SARS-CoV-2 adhesion by modulating ACE2 conformation through distal active site inhibitor binding.

The orientation-specific immobilization of antibodies onto nanoparticles, to preserve antibody–antigen recognition, is a key challenge in developing targeted nanomedicines. Herein, we report the targeting ability of metal–phenolic network (MPN)-coated gold nanoparticles with surface-physisorbed antibodies against respective antigens. The MPN coatings were self-assembled from metal ions (FeIII, CoII, CuII, NiII, or ZnII) cross-linked with tannic acid. Upon physisorption of antibodies, all particle systems exhibited enhanced association with target antigens, with CoIIsystems demonstrating more than 2-fold greater association. These systems contained more metal atoms distributed in a way to specifically interact with antibodies, which were investigated by molecular dynamics simulations. A model antibody fragment crystallizable (Fc) region in solution with CoII-tannic acid complexes revealed that the solvent-exposed CoIIcan directly coordinate to the histidine-rich portion of the Fc region. This one-pot interaction suggests anchoring of the antibody Fc region to the MPN on nanoparticles, allowing for enhanced targeting.

Biofouling is a multibillion dollar problem in the modern world, stimulating a large research effort in developing antifouling surface coatings. Existing theories that attempt to explain underlying molecular mechanisms of biofilm formation and its attenuation are not consistent with experiments and focus on different aspects of the interactions. To address this knowledge gap, we report a computational molecular dynamics study in which we assess how chemistry and surface density of commonly used antifouling surface ligands affect the interfacial properties relevant to biofouling. We compare the hydration behavior and chain dynamics of poly(ethylene glycol) (PEG) and poly(2-oxazoline) (POX) modified silica surfaces as a function of chemical composition and grafting density. We show that PEG systems exhibit greater chain dynamics, while POX systems show superior hydropathicity and hydration behavior. The observed structure–property relations for the PEG- and POX-modified surfaces provide an improved understanding of the effects of molecular features on antifouling properties and highlight the importance of ligand mobility and interfacial water structure and dynamics for antifouling efficacy. The findings can be exploited in the rational design of biofouling-resistant surfaces for industrial and biomedical applications.

In this study we use density functional theory (DFT) to investigate the properties and H adsorption characteristics of structural isomers of the magnesium-doped aluminum cluster, Al12Mg. Our results show that the exohedral structure (exo-MgAl12) is significantly lower in energy (1.59 eV) than the endohedral structure (endo-Al12Mg); however, the exohedral structure shows significant structural distortion. Our calculations demonstrate that H binds favorably to both exohedral and endohedral structures. Generally, binding energies for H to both clusters range from ∼2.3 to 2.5 eV with atop positions slightly favored, except for addition directly to the exohedral Mg atom, where the binding energy drops to 1.92 eV. We include a DFT molecular dynamics study of the endo-Al12Mg and endo-Al12MgH clusters which revealed the isomerization to the respective exostructures at finite temperatures (100−600 K). Interestingly, hydrogen adsorption appears to enhance the isomerization.

Ionic charge transport is a ubiquitous language of communication in biological systems. As such, bioengineering is in constant need of innovative, soft, and biocompatible materials that facilitate ionic conduction. Low molecular weight gelators (LMWGs) are complex self-assembled materials that have received increasing attention in recent years. Beyond their biocompatible, self-healing, and stimuli responsive facets, LMWGs can be viewed as a “solid” electrolyte solution. In this work, we investigate 3,4-ethylenedioxythiophene (EDOT) as a capping group for a small peptide library, which we use as a system to understand the relationship between modes of assembly and charge transport in supramolecular gels. Through a combination of techniques including small-angle neutron scattering (SANS), NMR-based Van’t Hoff analysis, atomic force microscopy (AFM), rheology, four-point probe, and electrochemical impedance spectroscopy (EIS), we found that modifications to the peptide sequence result in distinct assembly pathways, thermodynamic parameters, mechanical properties, and ionic conductivities. Four-point probe conductivity measurements and electrochemical impedance spectroscopy suggest that ionic conductivity is approximately doubled by programmable gel assemblies with hollow cylinder morphologies relative to gels containing solid fibers or a control electrolyte. More broadly, it is hoped this work will serve as a platform for those working on charge transport of aqueous soft materials in general.

All-atom molecular dynamics simulations and experimental characterization have been used to examine the structure and dynamics of novel evaporation-suppressing films where the addition of a water-soluble polymer to an ethylene glycol monooctadecyl ether monolayer leads to improved water evaporation resistance. Simulations and Langmuir trough experiments demonstrate the surface activity of poly(vinyl pyrrolidone) (PVP). Subsequent MD simulations performed on the thin films supported by the PVP sublayer show that, at low surface pressures, the polymer tends to concentrate at the film/water interface. The simulated atomic concentration profiles, hydrogen bonding patterns, and mobility analyses of the water-polymer-monolayer interfaces reveal that the presence of PVP increases the atomic density near the monolayer film, improves the film stability, and reduces the mobility of interfacial waters. These observations explain the molecular basis of the improved efficacy of these monolayer/polymer systems for evaporation protection of water and can be used to guide future development of organic thin films for other applications.

Monolayer-protected metal nanoparticles (MPMNs) are a newly discovered class of nanoparticles with an ordered, striped domain structure that can be readily manipulated by altering the ratio of the hydrophobic to hydrophilic ligands. This property makes them uniquely suited to systematic studies of the role of nanostructuring on biomolecule adsorption, a phenomenon of paramount importance in biomaterials design. In this work, we examine the interaction of the simple, globular protein cytochrome C (Cyt C) with MPMN surfaces using experimental protein assays and computational molecular dynamics simulations. Experimental assays revealed that adsorption of Cyt C generally increased with increasing surface polar ligand content, indicative of the dominance of hydrophilic interactions in Cyt C-MPMN binding. Protein−surface adsorption enthalpies calculated from computational simulations employing rigid-backbone coarse-grained Cyt C and MPMN models indicate a monotonic increase in adsorption enthalpy with respect to MPMN surface polarity. These results are in qualitative agreement with experimental results and suggest that Cyt C does not undergo significant structural disruption upon adsorption to MPMN surfaces. Coarse-grained and atomistic simulations furthermore elucidated the important role of lysine in facilitating Cyt C adsorption to MPMN surfaces. The amphipathic character of the lysine side chain enables it to form close contacts with both polar and nonpolar surface ligands simultaneously, rendering it especially important for interactions with surfaces composed of adjacent nanoscale chemical domains. The importance of these structural characteristics of lysine suggests that proteins may be engineered to specifically interact with nanomaterials by targeted incorporation of unnatural amino acids possessing dual affinity to differing chemical motifs.

Understanding the self-organization and structural transformations of molecular ensembles is important to explore the complexity of biological systems. Here, we illustrate the crucial role of cosolvents and solvation effects in thermodynamic and kinetic control over peptide association into ultrathin Janus nanosheets, elongated nanobelts, and amyloid-like fibrils. We gained further insight into the solvation-directed self-assembly (SDSA) by investigating residue-specific peptide solvation using molecular dynamics modeling. We proposed the preferential solvation of the aromatic and alkyl domains on the peptide backbone and protofibril surface, which results in volume exclusion effects and restricts the peptide association between hydrophobic walls. We explored the SDSA phenomenon in a library of cosolvents (protic and aprotic), where less polar cosolvents were found to exert a stronger influence on the energetic balance at play during peptide propagation. By tailoring cosolvent polarity, we were able to achieve precise control of the peptide nanostructures with 1D/2D shape selection. We also illustrated the complexity of the SDSA system with pathway-dependent peptide aggregation, where two self-assembly states (i.e., thermodynamic equilibrium state and kinetically trapped state) from different sample preparation methods were obtained.

Quantum-sized metallic clusters protected by biological ligands represent a new class of luminescent materials; yet the understanding of structural information and photoluminescence origin of these ultrasmall clusters remains a challenge. Herein we systematically study the surface ligand dynamics and ligand–metal core interactions of peptide-protected gold nanoclusters (AuNCs) with combined experimental characterizations and theoretical molecular simulations. We show that the peptide sequence plays an important role in determining the surface peptide structuring, interfacial water dynamics and ligand–Au core interaction, which can be tailored by controlling peptide acetylation, constituent amino acid electron donating/withdrawing capacity, aromaticity/hydrophobicity and by adjusting environmental pH. Specifically, emission enhancement is achieved through increasing the electron density of surface ligands in proximity to the Au core, discouraging photoinduced quenching, and by reducing the amount of surface-bound water molecules. These findings provide key design principles for understanding the surface dynamics of peptide-protected nanoparticles and maximizing the photoluminescence of metallic clusters through the exploitation of biologically relevant ligand properties.

Hydrophilic surface chemistries can strongly bind water to produce surfaces that are highly resistant to protein adsorption and fouling. The interfacial bound water and its distinct properties have intrigued researchers for decades, yet the relationship between the water three-dimensional structure and function in antifouling coatings remains elusive. Here, we use hydrophilic, epoxy organosilane modified silica nanoparticles to demonstrate cheap, robust, and practically applied coatings that we discover have broad-ranging, ultralow fouling properties when challenged by various proteins, bacteria, and fungal spores. To understand their excellent antifouling properties, frequency modulation–atomic force microscopy is used to directly observe the interfacial water structure at subatomic resolution, which we validate using all-atom molecular dynamic simulations that strikingly predict similar structures of water layers on the original and ultralow fouling surfaces. The convergence of experimental and modeling data reveals that suitably spaced, flexible chains with hydrophilic groups interact with water molecules to produce a connective, quasi-stablelayer, consisting of dynamic interfacial water, that provides a basis for antifouling performance of ultrathin, hydrophilic surface chemistries.

Nanostructured materials have potential as platforms for analytical assays and catalytic reactions. Herein, we report the synthesis of electrocatalytically active cobalt phosphate nanostructures (CPNs) using a simple, low-cost, and scalable preparation method. The electrocatalytic properties of CPNs toward the electrooxidation of glucose (Glu) were studied by cyclic voltammetry and chronoamperometry in relevant biological electrolytes, such as phosphate-buffered saline (PBS), at physiological pH (7.4). Using CPNs, Glu detection could be achieved over a wide range of biologically relevant concentrations, from 1 to 30 mM Glu in PBS, with a sensitivity of 7.90 nA/mM cm2and a limit of detection of 0.3 mM, thus fulfilling the necessary requirements for human blood Glu detection. In addition, CPNs showed a high structural and functional stability over time at physiological pH. The CPN-coated electrodes could also be used for Glu detection in the presence of interfering agents (e.g., ascorbic acid and dopamine) and in human serum. Density functional theory calculations were performed to evaluate the interaction of Glu with different faceted cobalt phosphate surfaces; the results revealed that specific surface presentations of under-coordinated cobalt led to the strongest interaction with Glu, suggesting that enhanced detection of Glu by CPNs can be achieved by lowering the surface coordination of cobalt. Our results highlight the potential use of phosphate-based nanostructures as catalysts for electrochemical sensing of biochemical analytes.

Peptide self-assembly represents a powerful bottom-up approach to the fabrication of nanomaterials. β3-Peptides are non-natural peptides composed entirely of β-amino acids, which have an extra methylene in the backbone, and we reported fibers derived from the self-assembly of β3-peptides that adopt 14-helical structures. β3-Peptide assemblies represent a class of stable nanomaterials that can be used to generate bio- and magneto-responsive materials with proteolytic stability. However, the three-dimensional structure of many of these materials remains unknown. To develop structure-based criteria for the design of β3-peptide-based biomaterials with tailored function, we investigated the structure of a tri-β3-peptide nanoassembly by molecular dynamics simulations and X-ray fiber diffraction analysis. Diffraction data was collected from aligned fibrils formed by Ac-β3[LIA] in water and used to inform and validate the model structure. Models with 3-fold radial symmetry resulted in stable fibers with a triple-helical coiled-coil motif and measurable helical pitch and periodicity. The fiber models revealed a hydrophobic core and twist along the fiber axis arising from a maximization of contacts between hydrophobic groups of adjacent tripeptides on the solvent-exposed fiber surface. These atomic structures of macroscale fibers derived from β3-peptide-based materials provide valuable insight into the effects of the geometric placement of the side chains and the influence of solvent on the core fiber structure which is perpetuated in the superstructure morphology.

Understanding the origins of lipid membrane bilayer rearrangement in response to external stimuli is an essential component of cell biology and the bottom-up design of liposomes for biomedical applications. The enzymes phospholipase C and D (PLC and PLD) both cleave the phosphorus–oxygen bonds of phosphate esters in phosphatidylcholine (PC) lipids. The atomic position of this hydrolysis reaction has huge implications for the stability of PC-containing self-assembled structures, such as the cell wall and lipid-based vesicle drug delivery vectors. While PLC converts PC to diacylglycerol (DAG), the interaction of PC with PLD produces phosphatidic acid (PA). Here we present a combination of small-angle scattering data and all-atom molecular dynamics simulations, providing insights into the effects of atomic-scale reorganization on the supramolecular assembly of PC membrane bilayers upon enzyme-mediated incorporation of DAG or PA. We observed that PC liposomes completely disintegrate in the presence of PLC, as conversion of PC to DAG progresses. At lower concentrations, DAG molecules within fluid PC bilayers form hydrogen bonds with backbone carbonyl oxygens in neighboring PC molecules and burrow into the hydrophobic region. This leads initially to membrane thinning followed by a swelling of the lamellar phase with increased DAG. At higher DAG concentrations, localized membrane tension causes a change in lipid phase from lamellar to the hexagonal and micellar cubic phases. Molecular dynamics simulations show that this destabilization is also caused in part by the decreased ability of DAG-containing PC membranes to coordinate sodium ions. Conversely, PLD-treated PC liposomes remain stable up to extremely high conversions to PA. Here, the negatively charged PA headgroup attracts significant amounts of sodium ions from the bulk solution to the membrane surface, leading to a swelling of the coordinated water layer. These findings are a vital step toward a fundamental understanding of the degradation behavior of PC lipid membranes in the presence of these clinically relevant enzymes, and toward the rational design of diagnostic and drug delivery technologies for phospholipase-dysregulation-based diseases.

The apolipoprotein family is structurally defined by amphipathic α-helical regions that interact with lipid surfaces. In the absence of lipid, human apolipoprotein (apo) C-II also forms well-defined amyloid fibrils with cross-β structure. Formation of this β-structure is accompanied by the burial of two charged residues, K30 and D69, that form an ion-pair within the amyloid fibril core. Molecular dynamics (MD) simulations indicate these buried residues form both intra- and intersubunit ion-pair interactions that stabilize the fibril. Mutations of the ion-pair (either K30D or D69K) reduce fibril stability and prevent fibril formation by K30D apoC-II under standard conditions. We investigated whether mixing K30D apoC-II with other mutants would overcome this loss of fibril forming ability. Co-incubation of equimolar mixtures of K30D apoC-II with wild-type, D69K, or double-mutant (K30D/D69K) apoC-II promoted the incorporation of K30D apoC-II into hybrid fibrils with increased stability. MD simulations showed an increase in the number of intersubunit ion-pair interactions accompanied the increased stability of the hybrid fibrils. These results demonstrate the important role of both intra- and intersubunit charge interactions in stabilizing apoC-II amyloid fibrils, a process that may be a key factor in determining the general ability of proteins to form amyloid fibrils.

The organized assembly of particles into superstructures is typically governed by specific molecular interactions or external directing factors associated with the particle building blocks, both of which are particle-dependent. These superstructures are of interest to a variety of fields because of their distinct mechanical, electronic, magnetic and optical properties. Here, we establish a facile route to a diverse range of superstructures based on the polyphenol surface-functionalization of micro- and nanoparticles, nanowires, nanosheets, nanocubes and even cells. This strategy can be used to access a large number of modularly assembled superstructures, including core–satellite, hollow and hierarchically organized supraparticles. Colloidal-probe atomic force microscopy and molecular dynamics simulations provide detailed insights into the role of surface functionalization and how this facilitates superstructure construction. Our work provides a platform for the rapid generation of superstructured assemblies across a wide range of length scales, from nanometres to centimetres.

Apolipoproteins form amphipathic helical structures that bind lipid surfaces. Paradoxically, lipid-free apolipoproteins display a strong propensity to form cross-β structure and self-associate into disease-related amyloid fibrils. Studies of apolipoprotein C-II (apoC-II) amyloid fibrils suggest that a K30-D69 ion pair accounts for the dual abilities to form helix and cross-β structure. Consistent with this is the observation that a K30D mutation prevents fibril formation under standard fibril forming conditions. However, we found that fibril formation by K30D apoC-II proceeded readily at low pH and a higher salt or protein concentration. Structural analysis demonstrated that K30D apoC-II fibrils at pH 7 have a structure similar to that of the wild-type fibrils but are less stable. Molecular dynamics simulations of the wild-type apoC-II fibril model at pH 7 and 3 showed that the loss of charge on D69 at pH 3 leads to greater separation between residues K30 and D69 within the fibril with a corresponding reduction in β-strand content around residue 30. In contrast, in simulations of the K30D mutant model at pH 7 and 3, residues D30 and D69 moved closer at pH 3, accompanied by an increase in β-strand content around residue 30. The simulations also demonstrated a strong dominance of inter- over intramolecular contacts between ionic residues of apoC-II and suggested a cooperative mechanism for forming favorable interactions between the individual strands under different conditions. These observations demonstrate the important role of the buried K30-D69 ion pair in the stability and solution properties of apoC-II amyloid fibrils.

The structure and bonding in charged and doped aluminum clusters have been investigated using Regional Density Functional Theory (RDFT). The RDFT method provides a measure of the electronic stress tensor from which it is possible to determine bond indices and electronic chemical potential. We find that the distribution of bond indices on the surface of Al12X clusters provides not only an understanding of the internal bonding and stability but also some insight into the regioselectivity observed in reactions of the clusters.

The adsorption of NO2, NO, and atomic N and O on the clean ZnO(101̅0) surface is examined using density functional theory and ab initio molecular dynamics simulations. Adsorption of NO2is also investigated on a defect surface containing an O vacancy. Calculated binding energy values, Bader charges, vibrational frequencies, density of states, planar averaged charge density differences, and electron localization plots are presented. Both the molecular and atomic adsorbates are found to adsorb in multiple minimum-energy sites with NO2and NO preferring to weakly adsorb on surface Zn sites, while O and N chemisorb in highly coordinated surface sites forming an O2and NO surface species, respectively. The presence of atomic O or N on the surface causes significant structural changes to the surface geometry. All adsorbates can induce magnetism on the surface, with the distribution of the magnetic moment being highly dependent on the adsorption geometry. The adsorbates behave as electron acceptors, withdrawing charge from the surface. The calculations also indicate that dissociation of NO2and NO is exothermally unfavorable. Ab initio molecular dynamics simulations show that NO2and NO readily desorb from the surface at 500 or 700 K, while O and N are more stable, remaining on the surface after ∼2 ps at 700 K, poisoning the surface. On the defect surface with an O vacancy, NO2readily dissociates over the vacancy site to yield O and NO. The dissociated O atom fills the vacancy site to re-form the stoichiometric surface, while the NO desorbs from the surface. At a lower NO2coverage, adsorption is stronger, with no spontaneous dissociation observed at 0 K. Ab initio MD simulations, however, show that NO2dissociation is facile at temperatures as low as 248 K, indicating that the barrier to dissociation is low.

We present a simulation methodology to chemically cross-link the surface of fully atomistic models of polymers. We simulated nanoindentation of the cross-linked model surfaces whereby nanoparticles (fullerene in this case) are used to probe different regions of the polymer surface enabling us to characterize the surface hardness of the polymer film and calculate the work of adhesion between polymer and nanoparticle. The cross-linked polyester surfaces are constructed using hexamethylene and isophorone di-isocyanate cross-linkers. Our results indicate that, despite surface cross-linking with hexamethylene di-isocyanate molecules, the polymer top surface still maintains significant softness. The hexamethylene cross-links that protrude from the surface are deformable, resulting in a strong adhesion between the surface and carbon particle. In contrast, isophorone surface cross-linking results in significantly weaker adhesion with carbon, due to the less deformable rigid structure formed at the top layer. In this case, while rigidity is imparted to the polymer top surface, the flexibility of the core region of the polymer is maintained.

We present a molecular dynamics study of the interaction of fullerene (C 60) with polyester surfaces in water. Three different polyester surfaces are studied, including untreated polyester (Polyester), fluorine-modified polyester (Polyester75F), and hydroxyl-modified polyester (Polyester75OH). Results indicate that in the absence of any surface modification, the fullerene particle is drawn down onto the polyester, even for a significant initial depth of water separating the particle and the surface. However, the addition of hydroxyl or fluorine groups on the surface of the polymer leads to a stronger interaction between water and surface atoms and, when combined with structural features such as rigidity and surface roughness, can reduce adhesion of the C 60particle in water.

The adsorption of H2S on Fe(110) is examined using ab initiomolecular dynamics at 298, 800, 1000, and 1808 K. The stages of the reaction are identified and compared for different temperatures. At 298 K, H2S adsorbs dissociatively, to leave adsorbed S and H atoms on the surface. At higher temperatures, H2S dissociation is followed by H diffusing into the subsurface layers. After complete dissociation at the Fe melting point, the H atoms recombine into molecular hydrogen which desorbs to leave S on the surface. The dissociation mechanism at each temperature is found to be different with the structure and position of the adsorbate on the surface being affected by reconstruction of the surface Fe atoms at higher temperatures.

This study uses classical molecular dynamics to examine how aging (relaxation) of functionalized polyester surfaces effects their adhesion to carbon particles. We show that relaxation leads to significantly increased adhesion compared to the rigid polymers. Functionalization of polyester surfaces followed by aging results in negligible reductions in adhesion to carbon compared to the unmodified polyester and, in some cases, leads to slight increases in interfacial adhesion. These results indicate that for surface modification to be effective, i.e., reduce interfacial adhesion with carbon, the polyester surfaces need to maintain both the rigidity and atomic roughness.

This theoretical study examines the adhesion of amorphous carbon to functionalized polyester surfaces. Several modifications to the polyester surface have been investigated including the addition of hydroxyl, carboxyl, or fluorine substituents at varying surface concentrations. Initially, the polyesters were artificially held rigid, and the surface modification not only imparted chemical changes to the polymer surface but also accentuated its atomic scale roughness. Under this rigid regime, low concentrations of surface modifiers have been shown to lead to the greatest reduction in adhesion with amorphous carbon, and increasing the level of modification does not provide further advantages in the reduction of adhesion, due to saturation. The effects of surface reorganization were also investigated and have been shown to be strongly dependent on the structure of the carbon surface, the chemical type, and surface density of modifiers. The surface modifiers reorganize during relaxation, which leads to significant differences in their effects on adhesion.

We present a methodology for modeling atomically layered nanoporous carbonaceous solids. Our method models carbon atoms interacting on sets of analytically defined surfaces, in conjunction with reverse Monte Carlo techniques (RMC). Our approach allows the construction of large, physically realistic nanoporous models of low-density carbonaceous solids that are both physical and statistically consistent with experimental observations. To demonstrate the flexibility of our approach and to investigate different mesostructures, we have modeled two nanoporous structures of glassy carbon. One model is comprised of multiple surfaces with the same center of symmetry, and the other is based on sets of parallel surfaces. The resulting models contain highly curved graphitic regions that also resemble the glassy carbon microstructure observed in high-resolution electron microscopy.

The Quantum Monte Carlo (QMC) technique[1] offers advantages of good scaling with system size (number of electrons) and an ability to uniformly recover over 90% of the electron correlation energy, compared to the more conventional quantum chemistry approaches. For the water molecule in its ground state, it has been shown[2] that the QMC method gives results that are comparable in accuracy to those obtained by the best available conventional methods, while at the same time using much more modest basis sets than is necessary with these methods. Furthermore, the effect of the orbitals needed for these QMC calculations (which may be obtained from either Hartree?Fock or Density Functional Theory) has been investigated. Both the advantages and disadvantages of the QMC method are discussed.

Atomistic modelling was employed to investigate interactions between the precursors used in preparation of organic/inorganic polymer hybrids. Three molecular systems composed of different kinds of organofunctionalised silanes and an organic polymer in aqueous solution have been simulated, representing various model stages of the hydrolysis reaction during the sol/gel processing. The equilibrium configurations obtained by Molecular Dynamics were analysed in order to elucidate the extent of the hydrogen bonding network and clustering of components within the systems. Diffusion coefficients were obtained to estimate the mobility of the components and the stability of the molecular associations. It has been concluded that the molecular mechanism of the initial stages of the sol/gel process used for preparation of the organic/inorganic hybrids involves clustering of the organofunctionalysed inorganic components as a first step and then progressive hydrolysis as consequent steps. The organic polymer component plays a role of the cluster "wrap" and thus prevents the particles from unlimited growth and precipitation from the solution.

The results of molecular dynamics simulations of three lignin-water systems are presented. Static and dynamic properties of each system are compared to a benchmark system consisting entirely of water molecules. The significantly reduced mobility of water molecules local to lignin hydroxyl regions is attributed to hydrogen bond formation, while the slightly reduced mobility of water molecules in the vicinity of lignin methoxyl groups results from a hydrophobic effect that causes water molecules to structure themselves around these groups. The average diffusion of water in each system correlates with the number of methoxyl groups present in the system. As the number of methoxyls in the system increases, so too does the average diffusion constant of water in that system. The bulky methoxyl groups obstruct water from accessing lignin hydroxyl regions where hydrogen bond formation is anticipated and the hydrogen-bonded water lowers the average diffusion constant.

An improved method for the modelling of carbon structures based on a hybrid reverse Monte Carlo (HRMC) method is presented. This algorithm incorporates an accurate environment dependent interaction potential (EDIP) in conjunction with the commonly used constraints derived from experimental data. In this work, we compare this new method with other modelling results for a small system of 2.9 g/cc amorphous carbon. We find that the new approach greatly improves the structural description, alleviating the common problem in standard reverse Monte Carlo method (RMC) of generating structures with a high proportion of unphysical small rings. The advantage of our method is that larger systems can now be modelled, allowing the incorporation of mesoscopic scale features.

In this work, a methodology has been developed for construction of atomistic models of crosslinked polymer networks. The methodology has been applied to low molecular weight water soluble epoxy resins crosslinked with different curing agents that are being considered for use as a primer coating on steel. The simulations allowed the crosslink density and the amount of free crosslinking sites in the coatings to be predicted. Shrinkage of the resin upon curing was reproduced by the simulation. In addition, the barrier properties of the model coatings were estimated. The interface between an inorganic substrate and cured epoxy resin has been constructed and the strength and molecular mechanisms of adhesion have been revealed. The developed methodology has a potential to significantly impact on the design and development of new coatings with improved barrier and adhesion properties.

Ultrasmall peptide-protected gold nanoclusters are a promising class of bioresponsive material exhibiting pH-sensitive photoluminescence. We present a theoretical insight into the effect peptide-ligand environment has on pH-responsive fluorescence, with the aim of enhancing the rational design of gold nanoclusters for bioapplications. Employing a hybrid quantum/classical computational methodology, we systematically calculate deprotonation free energies of N-terminal cysteine amine groups in proximity to the inherently fluorescent core of Au25(Peptide)18nanoclusters. We find that subtle changes in hexapeptide sequence alter the electrostatic environment and significantly shift the conventional N-terminal amine pKaexpected for amino acids free-in-solution. Our findings provide an insight into how the deprotonation equilibrium of N-terminal amine and side chain carboxyl groups cooperatively respond to solution pH changes, explaining the experimentally observed, yet elusive, pH-responsive fluorescence of peptide-functionalized Au25clusters.

Short-chain alcohols (i.e., ethanol) can induce membrane interdigitation in saturated-chain phosphatidylcholines (PCs). In this process, alcohol molecules intercalate between phosphate heads, increasing lateral separation and favoring hydrophobic interactions between opposing acyl chains, which interpenetrate forming an interdigitated phase. Unraveling mechanisms underlying the interactions between ethanol and model lipid membranes has implications for cell biology, biochemistry, and for the formulation of lipid-based nanocarriers. However, investigations of ethanol–lipid membrane systems have been carried out in deionized water, which limits their applicability. Here, using a combination of small- and wide-angle X-ray scattering, small-angle neutron scattering, and all-atom molecular dynamics simulations, we analyzed the effect of varying CaCl2and NaCl concentrations on ethanol-induced interdigitation. We observed that while ethanol addition leads to the interdigitation of bulk phase 1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC) bilayers in the presence of CaCl2and NaCl regardless of the salt concentration, the ethanol-induced interdigitation of vesicular DPPC depends on the choice of cation and its concentration. These findings unravel a key role for cations in the ethanol-induced interdigitation of lipid membranes in either bulk phase or vesicular form.

The theoretical background, methodology and some applications of atomistic simulation of interfaces in materials are described in this paper. Interfaces between crystalline solids and polymers as well as between two polymers can be simulated using the methods described. Applications include various interfaces in a multilayered coated metal system. The methodology enables such properties as the work of adhesion, interfacial stability, degree of curing in polymers and permeability to small molecules to be predicted. In addition, interfacial structure and molecular mechanisms of adhesion and barrier performance of coatings can be revealed.