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Yes / Peptide-enabled nanoparticle (NP) synthesis routes can create and/or assemble functional nanomaterials under environmentally friendly conditions, with properties dictated by complex interactions at the biotic/abiotic interface. Manipulation of this interface through sequence modification can provide the capability for material properties to be tailored to create enhanced materials for energy, catalysis, and sensing applications. Fully realizing the potential of these materials requires a comprehensive understanding of sequence-dependent structure/function relationships that is presently lacking. In this work, the atomic-scale structures of a series of peptide-capped Au NPs are determined using a combination of atomic pair distribution function analysis of high-energy X-ray diffraction data and advanced molecular dynamics (MD) simulations. The Au NPs produced with different peptide sequences exhibit varying degrees of catalytic activity for the exemplar reaction 4-nitrophenol reduction. The experimentally derived atomic-scale NP configurations reveal sequence-dependent differences in structural order at the NP surface. Replica exchange with solute-tempering MD simulations are then used to predict the morphology of the peptide overlayer on these Au NPs and identify factors determining the structure/catalytic properties relationship. We show that the amount of exposed Au surface, the underlying surface structural disorder, and the interaction strength of the peptide with the Au surface all influence catalytic performance. A simplified computational prediction of catalytic performance is developed that can potentially serve as a screening tool for future studies. Our approach provides a platform for broadening the analysis of catalytic peptide-enabled metallic NP systems, potentially allowing for the development of rational design rules for property enhancemen / Air Force Office for Scientific Research (Grant #FA9550-12-1-0226, RRN; AFOSR LRIR) and DOE-BES grant DE-SC0006877, fellowship support from the National Research Council Research Associateship

Yes / A reliable description of ion pair interactions for biological systems, particularly those involving polyatomic ions such as carboxylate and divalent ions such as Ca2+, using biomolecular force-fields is essential for making useful predictions for a range of protein functions. In particular, the interaction of divalent ions with the double carboxylate group present in γ-carboxyglutamic acid (Gla), relevant to the function of many proteins, is relatively understudied using biomolecular force-fields. Using force-field based metadynamics simulations to predict the free energy of binding between Ca2+ and the carboxylate group in liquid water, we show that a widely-used biomolecular force-field, CHARMM22*, substantially over-estimates the binding strength between Ca2+ and the side-chains of both glutamic acid (Glu) and Gla, compared with experimental data obtained for the analogous systems of aqueous calcium–acetate and calcium–malonate. To correct for this, we propose and test a range of modifications to the σ value of the heteroatomic Lennard–Jones interaction between Ca2+ and the oxygen of the carboxylate group. Our revised parameter set can recover the same three association modes of this aqueous ion pair as the standard parameter set, and yields free energies of binding for the carboxylate–Ca2+ interaction in good agreement with experimental data. The revised parameter set recovers other structural properties of the ion pair in agreement with the standard CHARMM22* parameter set.

No / The vitrification solutions used in the cryopreservation of biological samples aim to minimize the deleterious formation of ice by dehydrating cells and promoting the formation of the glassy state of water. They contain a mixture of different cryoprotective agents (CPAs) in water, typically polyhydroxylated alcohols and/or dimethyl sulfoxide (DMSO), which can damage cell membranes. Molecular dynamics simulations have been used to investigate the behavior of pure DPPC, pure DOPC, and mixed DOPC-β-sitosterol bilayers solvated in a vitrification solution containing glycerol, ethylene glycol, and DMSO at concentrations that approximate the widely used plant vitrification solution 2. As in the case of solutions containing a single CPA, the vitrification solution causes the bilayer to thin and become disordered, and pores form in the case of some bilayers. Importantly, the degree of thinning is, however, substantially reduced compared to solutions of DMSO containing the same total CPA concentration. The reduction in the damage done to the bilayers is a result of the ability of the polyhydroxylated species (especially glycerol) to form hydrogen bonds to the lipid and sterol molecules of the bilayer. A decrease in the amount of DMSO in the vitrification solution with a corresponding increase in the amount of glycerol or ethylene glycol diminishes further its damaging effect due to increased hydrogen bonding of the polyol species to the bilayer headgroups. These findings rationalize, to our knowledge for the first time, the synergistic effects of combining different CPAs, and form the basis for the optimization of vitrification solutions. / Australian Research Council linkage grant No. LP0884027; Alcoa Australia Ltd.; BHP Billiton Worsley Alumina Pty. Ltd.

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no / Exploring nucleation processes by molecular simulation can provide a mechanistic understanding at the atomic level and also enables kinetic and thermodynamic quantities to be estimated. However, whilst the potential for modeling crystal nucleation and growth processes is immense, there are specific technical challenges to modeling [that need to be tackled]. In general, rare events, such as nucleation cannot be simulated using a direct ¿brute force¿ molecular dynamics approach. In recent years, the limited time and length scales that are accessible by conventional molecular dynamics simulations have inspired a number of advances to tackle problems that were hitherto considered outside the scope of molecular simulation. While general insights and features could be explored from efficient generic models, The newer methods have paved the way to realistic crystal nucleation scenarios. The association of single ions in solvent environments, the mechanisms of motif formation in solvents, the nucleation process itself, ripening reactions, role of additives, as well as the self-organization of nanocrystals can now all be investigated at the molecular level. The insights gained should complement experiments and enhance our fundamental understanding of the processes involved and facilitate the rational design of new materials.

Dans ce travail, l’existence et les mécanismes fondamentaux sous-jacents à l’augmentation de la solubilité du CO2 dans les matériaux hybrides. De nombreux supports solide et solvants physiques sont testés. Les adsorbants hybrides synthétisés sont par la suite évalués en mesurant les isothermes d’adsorption du CO2. Généralement, tous les adsorbants hybrides montrent une augmentation de la solubilité du CO2 en comparaison avec le solvant physique. Les résultats obtenus mettent en évidence, certaines conditions à remplir pour l'obtention d'un adsorbant hybride efficace. On montre notamment que le support solide doit posséder une structure mésoporeuse avec une forte surface spécifique. De plus, on identifie une taille optimale du solvant permettant d'obtenir une solubilité améliorée. Parmi tous les candidats testés, le N-méthyl-2-pyrrolidone confiné dans un support mésoporeux de MCM-41 s’est avéré être l’adsorbant hybride dont les performances d'adsorption sont les plus importantes. Des simulations de Monte Carlo dans l'ensemble grand canonique sont ensuite effectuées, afin d'interpréter le comportement de la solubilité du CO2 dans un système modèle d’adsorbant hybride à base de MCM-41. Les mécanismes microscopiques sous-jacents à l’augmentation de la solubilité sont notamment clairement identifiés. La présence des molécules de solvant favorise l'adsorption des molécules de CO2 dans le pore, engendrant une augmentation de la solubilité dans l’adsorbant hybride par rapport à celle de l’adsorbant natif ainsi qu’à celle du solvant macroscopique. De plus, pour évaluer l’efficacité de captage du CO2 de ces adsorbants hybrides, l'effet des interactions entre les adsorbats et le solide ainsi que l’impact de la taille de la molécule du solvant sur la solubilité du CO2 sont étudiés. Nous avons constaté qu’un système hybride idéal doit présenter une faible interaction entre le solvant et le solide et une forte affinité entre le solvant et le CO2. De plus, on identifie l'existence d'une taille optimale de solvant permettant de maximiser la solubilité du CO2 dans le système hybride. D’après les résultats de la simulation, la couche de solvant crée des pseudo-micropores dans le solide mésoporeux MCM-41, et permet à plus de molécules de CO2 d’être absorbés sous l'influence d'un confinement et d'une interaction surfacique plus importants. / In this work, we investigate the existence and the fundamentals mechanisms underlying the apparition of enhanced CO2 solubility in hybrid materials. A number of prospective solid supports and physical solvents are chosen and the synthesized hybrid adsorbents are subsequently evaluated by measuring CO2 adsorption isotherms. Generally, all the hybrid adsorbents show an enhancement of CO2 solubility compared with the bulk physical solvent. According to further investigation, we have obtained certain requisites for a good solid support, of which structure should be mesoporous with large surface area. In addition, there is an optimized solvent's size to achieve an enhanced solubility. As a result, among the candidates, the N-methyl-2-pyrrolidone confined in MCM-41 adsorbent is proven to be the most suitable hybrid adsorbent for an effective CO2-removal application. In order to gain a deeper insight, Grand Canonical Monte Carlo simulations are then performed to interpret the CO2 solubility behavior in a modeled system of hybrid MCM-41 adsorbent. As a result, the microscopic mechanisms underlying the apparition of enhanced solubility are then clearly identified. In fact, the presence of solvent molecules favors the layering of CO2 molecule within the pores thereby the CO2 solubility in hybrid adsorbent markedly increases in comparison with the one found in the raw adsorbent as well as in the bulk solvent. In addition, to fully evaluate the efficiency of hybrid adsorbents in capturing CO2, the sorbent-solid interactions along with the solvent molecular size impact on CO2 solubility are further investigated in this study. We found that an ideal hybrid system should possess a weak solvent-solid interaction but a strong solvent-CO2 affinity. Furthermore, an optimal solvent size is obtained for the enhanced CO2 solubility in the hybrid system. According to the simulation results, the solvent layer builds pseudo-micropores inside the mesoporous MCM-41, enabling more CO2 molecules to be absorbed under greater influence of spatial confinement and surface interaction.