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The surface of aqueous solutions of simple salts was not the main focus of scientific attention for a long while. Considerable interest in studying such systems has only emerged in the past two decades, following the pioneering finding that large halide ions, such as I-, exhibit considerable surface aflinity. Since then, a number of issues have been clarified; however, there are still several unresolved points (e.g., the effect of various salts on lateral water diffusion at the surface) in this respect. Computer simulation studies of the field have largely benefited from the appearance of intrinsic surface analysis methods, by which the particles staying right at the boundary of the two phases can be unambiguously identified. Considering complex ions instead of simple ones opens a number of interesting questions, both from the theoretical point of view and from that of the applications. Besides reviewing the state-of-the-art of intrinsic surface analysis methods as well as the most important advances and open questions concerning the surface of simple ionic solutions, we focus on two such systems in this Perspective, namely, the surface of aqueous mixtures of room temperature ionic liquids and that of ionic surfactants. In the case of the former systems, for which computer simulation studies have still scarcely been reported, we summarize the theoretical advances that could trigger such investigations, which might well be of importance also from the point of view of industrial applications. Computer simulation methods are, on the other hand, widely used in studies of the surface of surfactant solutions. Here we review the most important theoretical advances and issues to be addressed and discuss two areas of applications, namely, the inclusion of information gathered from such simulations in large scale atmospheric models and the better understanding of the airborne transmission of viruses, such as SARS-CoV-2.

Determining stability constants of uranyl complexes with the principal functional groups in siderophores and identifying stability series is of great importance to predict which siderophore classes preferentially bind to UVI and, hence, impact uranium speciation in the environment. It also helps to develop resins for scavenging UVI from aqueous solutions. Here, we apply a recently developed computational approach to calculate log β values for a set of geochemically relevant uranium organometallic complexes using Density Functional Theory (DFT). We determined the stability series for catecholate, hydroxamate, α-hydroxycarboxylate, α-aminocarboxylate, hydroxy-phenyloxazolonate, and α-hydroxyimidazole with the uranyl cation. In this work, the stability constants (log β110) of α-hydroxyimidazolate and hydroxy-phenyloxazolonate are calculated for the first time. Our approach employed the B3LYP density functional approximation, aug-cc-pVDZ basis set for ligand atoms, MDF60 ECP for UVI, and the IEFPCM solvation model. DFT calculated log β110 were corrected using a previously established fitting equation. We find that the siderophore functional groups stability decreases in the order: α-hydroxycarboxylate bound via the α-hydroxy and carboxylate groups (log β110 = 17.08), α-hydroxyimidazolate (log β110 = 16.55), catecholate (log β110 = 16.43), hydroxamate (log β110 = 9.00), hydroxy-phenyloxazolonate (log β110 = 8.43), α-hydroxycarboxylate bound via the carboxylate group (log β110 = 7.51) and α-aminocarboxylate (log β110 = 4.73). We confirm that the stability for the binding mode of the functional groups decrease in the order: bidentate, monodentate via ligand O atoms, and monodentate via ligand N atoms. The stability series strongly suggests that α-hydroxyimidazolate is an important functional group that needs to be included when assessing uranyl mobility and removal from aqueous solutions.

Understanding the complexity of fragmentation processes is essential for regulating intercellular communication in mechanistic biology and developing novel bottom-up approaches in a large range of multiphase flow processes. In this context, self-fragmentation proceeds without any external mechanical energy input allowing one to create efficiently micro- and nanodroplets. Here we examine self-fragmentation in emulsion nanodroplets stabilized by solid particles with different surface features. Mesoscopic modelling and accelerated dynamics simulations allow us to overcome the limitations of atomistic simulations and offer detailed insight into the interplay between the evolution of the droplet shape and the particle finite-sized effects at the interface. We show that finite-sized nanoparticles play an active role in the necking breakup, behaving like nano-scale razors, and affect strongly the thermodynamic properties of the system. The role played by the particles during self-fragmentation might be of relevance to multifunctional biomaterial design and tuning of signaling pathways in mechanistic biology., Comment: 7 pages, 5 figures

Simulations can be used to accelerate the characterization and discovery of materials. Here we Review how electronic-structure methods such as density functional theory work, what properties they can be used to predict and how they can be used to design materials., The accuracy and efficiency of electronic-structure methods to understand, predict and design the properties of materials has driven a new paradigm in research. Simulations can greatly accelerate the identification, characterization and optimization of materials, with this acceleration driven by continuous progress in theory, algorithms and hardware, and by adaptation of concepts and tools from computer science. Nevertheless, the capability to identify and characterize materials relies on the predictive accuracy of the underlying physical descriptions, and on the ability to capture the complexity of realistic systems. We provide here an overview of electronic-structure methods, of their application to the prediction of materials properties, and of the different strategies employed towards the broader goals of materials design and discovery.

The catalytic reaction in SARS-CoV-2 main protease is activated by a proton transfer (PT) from Cys145 to His41. The same PT reaction is likely also required for the covalent binding of some classes of inhibitors. Here we use a hybrid quantum/classical approach to investigate the PT thermodynamics in the apo state and in the presence of a covalent inhibitor, N3. We show that in the apo state a neutral catalytic dyad is favored whereas in the presence of N3 the PT reaction becomes thermodynamically favorable. We also show that a few key sites (including a water molecule) are able to significantly enhance or reduce the thermodynamic feasibility of the PT reaction. The approach presented is a general and cost-effective procedure to identify the enzyme regions that control the activation of the catalytic reaction. It is also useful to guide the screening and design of potential covalent inhibitors., Graphical Abstract

The ionization state of titratable amino acids strongly affects proteins structure and functioning in a large number of biological processes. It is therefore essential to be able to characterize the pK(a) of ionizable groups inside proteins and to understand its microscopic determinants in order to gain insights into many functional properties of proteins. A big effort has been devoted to the development of theoretical approaches for the prediction of deprotonation free energies, yet the accurate theoretical/computational calculation of pK(a) values is recognized as a current challenge. A methodology based on a hybrid quantum/classical approach is here proposed for the computation of deprotonation free energies. The method is applied to calculate the pK(a) of formic acid, methylammonium, and methanethiol, providing results in good agreement with the corresponding experimental estimates. The pK(a) is also calculated for aspartic acid and lysine as single residues in solution and for three aspartic/glutamic acids inside a wellcharacterized protein: hen egg white lysozyme. While for small molecules the method is able to deal with multiple protonation states of all titratable groups, this becomes computationally very expensive for proteins. The calculated pK(a) values for the single amino acids (except for the zwitterionic aspartic acid) and inside the protein display a systematic shift with respect to the experimental values that suggests that the fine balance between hydrophobic and polar interactions might be not accurately reproduced by the usual classical force-fields, thus affecting the computation of deprotonation free energies. The calculated pK(a) shifts inside the protein are in good agreement with the corresponding experimental ones (within 1 pK(a) unit), well reproducing the pK(a) changes due to the protein environment even in the case of large pK(a) shifts.

The generation of surface free energy parameters calculated from contact angle data is a burdensome and time-consuming process. To facilitate these calculations, computational algorithms using three different programming languages—MATLAB, C and Python—were developed and validated by surface properties determination of PO and CPO. The results indicated that the surface free energy parameters calculated using the three algorithms were consistent. The unknowns were obtained directly from within the C and Python programs, however, indirectly from within MATLAB function. In addition, the assembly statements of the C function were longer than those of the other two. The obtained results were also compared with those from an IGC analysis. It showed that the γ S D values determined using the contact angle methods were consistent, although lower than those obtained by IGC analysis. Compared to γ S D , the γ S S P component contributed less to γ S T . The lower γ S D and γ S S P values for CPO which added up to a lower γ S T value, could reduce filler particle/particle interactions, allowing a better dispersion in a polymer matrix.

The self-assembly of bio-inspired supramolecular polymers can be unravelled using molecular dynamics simulations combined with experiments., In bionanotechnology, the field of creating functional materials consisting of bio-inspired molecules, the function and shape of a nanostructure only appear through the assembly of many small molecules together. The large number of building blocks required to define a nanostructure combined with the many degrees of freedom in packing small molecules has long precluded molecular simulations, but recent advances in computational hardware as well as software have made classical simulations available to this strongly expanding field. Here, we review the state of the art in simulations of self-assembling bio-inspired supramolecular systems. We will first discuss progress in force fields, simulation protocols and enhanced sampling techniques using recent examples. Secondly, we will focus on efforts to enable the comparison of experimentally accessible observables and computational results. Experimental quantities that can be measured by microscopy, spectroscopy and scattering can be linked to simulation output either directly or indirectly, via quantum mechanical or semi-empirical techniques. Overall, we aim to provide an overview of the various computational approaches to understand not only the molecular architecture of nanostructures, but also the mechanism of their formation.

The correlation between oxidation state and Lewis acidity is well established for hexaquairon complexes in the +II and +III oxidation state, in which the higher oxidation state leads to a lower pK(a) for the bound H2O ligand. This article addresses the Lewis acidity of the oxoiron(IV) complex [Fe-IV(O)(TMC)(OH2)](2+) (1-OH2; TMC=1,4,8,11-tetramethylcyclam) by determining the pK(a) of the H2O ligand. We establish that 1-OH2 has a pK(a) of 6.9 +/- 0.5, a value that falls in between those found for [Fe-III(OH2)(6)](3+) and [Fe-II(OH2)(6)](2+). This intermediate value can be readily rationalized by the presence of the highly basic oxide ligand that mitigates the Lewis acidity of the iron(IV) center. Although the oxo ligand occupies only one position in 1-OH2, anti to all four methyl groups that protrude from the same face of the nonplanar TMC ligand, its conjugate base 1-OH exists as a mixture of syn and anti tautomers, which are related by proton transfer between the oxo and the hydroxo ligands.

The coatings of initially homogeneous poly(styrene) − poly(methyl methacrylate) − tetrahydrofuran system have been studied. The average concentrations of the polymers, solvent, change in coating thickness with time have been calculated from the gravimetric weight loss data. Doubling the poly(styrene) mass fraction does, not change the mass transfer mechanism within these coatings. However, doubling the poly(methyl methacrylate) mass fraction changes the mass transfer mechanism very significantly, which leads to very slow diffusion process within these coatings. The average concentration profiles show Fickian diffusion in these coatings for reasonably long duration of total drying time.

The solid surface characterization using contact angle measurement is complicated and time-consuming. In this work, two computational algorithms in MATLAB and C were developed and validated by the surface properties determination of talc filler (TCF) and colored talc filler (CTCF). The results indicated that, the surface free energy parameters calculated using the two algorithms for both samples were consistent. As compared to the MATLAB function, the assembly statements of C function were longer, although the unknowns can be directly obtained using this toolbox. The γ S D values determined by the Owens-Wendt-Kaelble (OWK), van Oss-Chaudhury-Good (vOCG) and Wu methods were consistent and contributed a major part of the γ S T . Compared to γ S D , the γ S SP component contributed less to γ S T , implying a lower polarity for both samples. The lower γ S D and γ S SP for CTCF added up to a lower γ S T value, which could reduce filler particle-particle interactions. The mechanical properties study of acrylonitrile-butadiene-styrene (ABS) matrix filled with the two fillers showed that the incorporation of them played mainly a reinforcing role, and a better performance for CTCF was observed.

Macroscopic models of nucleation provide powerful tools for understanding activated phase transition processes. These models do not provide atomistic insights and can thus sometimes lack material-specific descriptions. Here, we provide a comprehensive framework for constructing a continuum picture from an atomistic simulation of homogeneous nucleation. We use this framework to determine the equilibrium shape of the solid nucleus that forms inside bulk liquid for a Lennard-Jones potential. From this shape, we then extract the anisotropy of the solid-liquid interfacial free energy, by performing a reverse Wulff construction in the space of spherical harmonic expansions. We find that the shape of the nucleus is nearly spherical and that its anisotropy can be perfectly described using classical models. Published under license by AIP Publishing.

New density functional theory (DFT) computations are reported concerning the mechanism of the Suzuki-Miyaura cross-coupling reaction of aryl halides and aryl boronic acids catalyzed by palladium phosphine complexes. The calculations are aimed at refining the understanding of the overall catalytic mechanism using state of the art theoretical approaches (including, for the first time, an attempt to describe the Gibbs energy of the reactant base in a realistic way). New experimental results (Thomas and Denmark, Science, 2016, 352, 329-332) concerning pre-transmetallation intermediates with a Pd-O-B linkage provide an invaluable benchmark to test the accuracy of the calculations. The calculations show that bottlenecks to catalysis associated with oxidative addition, X-to-O substitution at Pd, and transmetallation can lie close in energy. ispartof: FARADAY DISCUSSIONS vol:220 issue:0 pages:425-442 ispartof: location:England status: published

Controlled double-deck packing is an appealing means to expand upon conventional 2D self-assembly which is critical in crystal engineering, yet it is rare and poorly understood. Herein, we report the first systematic study of double-deck assembly in a series of alkylated aminoquinone derivatives at the liquid-solid interface. The competition between the fraction of alkyl chains adsorbed on the surface and the optimal conformation of the alkyl chains near the head group leads to a stepwise structural transformation ranging from complete double-deck packing to complete monolayer packing. Alkyl chains on the bottom or top layer of the double-deck assemblies were selectively visualized by carefully tuning the scanning tunneling microscopy settings. A method to easily identify mirror image domains was discovered based on the coincidence of domain boundaries with a graphite main axis. The effect of molecular symmetry and metal complexation on the formation of the double-deck assembly was also explored. Based on 2D crystal engineering principles, this bottom-up double-deck assembly can potentially provide an essential toehold for constructing precise 3D hierarchical structures. ispartof: NANOSCALE vol:10 issue:31 pages:14993-15002 ispartof: location:England status: published

Conformational fluctuations and rotational tumbling of proteins can be experimentally accessed with nuclear spin relaxation experiments. However, interpretation of molecular dynamics from the experimental data is often complicated, especially for molecules with anisotropic shape. Here, we apply classical molecular dynamics simulations to interpret the conformational fluctuations and rotational tumbling of proteins with arbitrarily anisotropic shape. The direct calculation of spin relaxation times from simulation data did not reproduce the experimental data. This was successfully corrected by scaling the overall rotational diffusion coefficients around the protein inertia axes with a constant factor. The achieved good agreement with experiments allowed the interpretation of the internal and overall dynamics of proteins with significantly anisotropic shape. The overall rotational diffusion was found to be Brownian, having only a short subdiffusive region below 0.12 ns. The presented methodology can be applied to interpret rotational dynamics and conformation fluctuations of proteins with arbitrary anisotropic shape. However, a water model with more realistic dynamical properties is probably required for intrinsically disordered proteins.

Curvature-related processes are of major importance during protein-membrane interactions. The illusive simplicity of membrane reshaping masks a complex molecular process crucial for a wide range of biological functions like fusion, endo- and exocytosis, cell division, cytokinesis, and autophagy. To date, no functional expression of a reaction coordinate capable of biasing molecular dynamics simulations to produce membrane curvature has been reported. This represents a major drawback given that the adequate identification of proper collective variables to enhance sampling is fundamental for restrained dynamics techniques. In this work, we present a closed-form equation of a collective variable that induces bending in lipid bilayers in a controlled manner, allowing for straightforward calculation of free energy landscapes of important curvature-related events, using standard methods such as umbrella sampling and metadynamics. As a direct application of the collective variable, we calculate the bending free energies of a ternary lipid bilayer in the presence and the absence of a Bin/Amphiphysin/Rvs domain with an N-terminal amphipathic helix (N-BAR), a well-known peripheral membrane protein that induces curvature. Fil: Masone, Diego Fernando. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Mendoza. Instituto de Histología y Embriología de Mendoza Dr. Mario H. Burgos. Universidad Nacional de Cuyo. Facultad de Ciencias Médicas. Instituto de Histología y Embriología de Mendoza Dr. Mario H. Burgos; Argentina Fil: Uhart, Marina. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Mendoza. Instituto de Histología y Embriología de Mendoza Dr. Mario H. Burgos. Universidad Nacional de Cuyo. Facultad de Ciencias Médicas. Instituto de Histología y Embriología de Mendoza Dr. Mario H. Burgos; Argentina Fil: Bustos, Diego Martin. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Mendoza. Instituto de Histología y Embriología de Mendoza Dr. Mario H. Burgos. Universidad Nacional de Cuyo. Facultad de Ciencias Médicas. Instituto de Histología y Embriología de Mendoza Dr. Mario H. Burgos; Argentina

Enhanced molecular dynamics simulations of UiO-66 reveal a highly intrinsic dynamic behavior during activation and easy changes in the coordination number., UiO-66 is a showcase example of an extremely stable metal–organic framework, which maintains its structural integrity during activation processes such as linker exchange and dehydration. The framework can even accommodate a substantial number of defects without compromising its stability. These observations point to an intrinsic dynamic flexibility of the framework, related to changes in the coordination number of the zirconium atoms. Herein we follow the dynamics of the framework in situ, by means of enhanced sampling molecular dynamics simulations such as umbrella sampling, during an activation process, where the coordination number of the bridging hydroxyl groups capped in the inorganic Zr6(μ3-O)4(μ3-OH)4 brick is reduced from three to one. Such a reduction in the coordination number occurs during the dehydration process and in other processes where defects are formed. We observe a remarkable fast response of the system upon structural changes of the hydroxyl group. Internal deformation modes are detected, which point to linker decoordination and recoordination. Detached linkers may be stabilized by hydrogen bonds with hydroxyl groups of the inorganic brick, which gives evidence for an intrinsic dynamic acidity even in the absence of protic guest molecules. Our observations yield a major step forward in the understanding on the molecular level of activation processes realized experimentally but that is hard to track on a purely experimental basis.

Mollusk shells, such as clam, mussel, oyster and pearl oyster shells, are potential candidates for commercial calcium carbonate-based fillers. In this work, the surface properties of colored pearl-oyster-shell-derived filler (CMF) were investigated with comparison to those of pearl oyster shell powder (MSP), using an inverse gas chromatography (IGC) method and contact angle measurements. A developed computational model for the interpretation of surface free energy heterogeneity distributions was applied to both samples. The contact angle measurements revealed an amphiphilic nature. The dispersion component of surface free energy for both samples calculated using the Owens–Wendt–Kaelble (OWK), van Oss–Chaudhury–Good (vOCG) and Wu methods were consistent with those determined using the IGC method. The deconvolution of surface energetic sites confirmed their energetic heterogeneity. The CMF displayed lower work of cohesion, which could be beneficial to the fabrication of polymer composites, as typically reduced filler particle-particle interactions would result., National Natural Science Foundation of China (Grant nos. 51606055 and 41373121) and Zhejiang Provincial Natural Science Foundation of China (Grant no. LY14D010009), info:eu-repo/semantics/publishedVersion

Hydrogen bonding (H-bonding) is an important and very general phenomenon. H-bonding is part of the basis of life in DNA, key in controlling the properties of water and ice, and critical to modern applications such as crystal engineering, catalysis applications, pharmaceutical and agrochemical development. H-bonding also plays a significant role for many ionic liquids (IL), determining the secondary structuring and affecting key physical parameters. ILs exhibit a particularly diverse and wide range of traditional as well as non-standard forms of H-bonding, in particular the doubly ionic H-bond is important. Understanding the fundamental nature of the H-bonds that form within ILs is critical, and one way of accessing this information, that cannot be recovered by any other computational method, is through quantum chemical electronic structure calculations. However, an appropriate method and basis set must be employed, and a robust procedure for determining key structures is essential. Modern generalised solvation models have recently been extended to ILs, bringing both advantages and disadvantages. QC can provide a range of information on geometry, IR and Raman spectra, NMR spectra and at a more fundamental level through analysis of the electronic structure.

Molecular dynamics were used to simulate the dispersion of graphene in aqueous medium in the presence of a novel organic modifier, sodium salt of 6-amino hexanoic acid (Na-AHA), which non-covalently modifies the graphene surfaces. The modifier molecule contains an ionizable carboxylate head group and an aliphatic tail. The extent of dispersion was estimated by calculating the potential of mean force (PMF) as a function of increasing concentration of the modifier using the thermodynamic perturbation method in conjunction with molecular dynamics simulations. With increasing concentration of the modifier, the PMF changed from a short-range strong attraction to a long-range repulsion at higher modifier concentrations. The simulation results clearly show the adsorption of modifier molecules at the graphene–water interface, which in turn causes the graphene surfaces to acquire a negative charge. Further, the development of a negative electric potential at the graphene surfaces induces a long-range electrostatic repulsion between the graphene sheets, clearly pointing to an electrostatic stabilization of Na-AHA modified-graphene in aqueous medium.

Molecular dynamics simulations of fullerene and fullerols [C-60(OH)(n), where n = 2-30] in aqueous solutions have been performed for the purpose of obtaining a detailed understanding of the structural and dynamic properties of these nanoparticles in water. The structures, dynamics and hydration free energies of the solute molecules in water have been analysed. Radial distribution functions, spatial density distribution functions and hydrogen bond analyses are employed to characterize the solvation shells of water around the central solute molecules. We have found that water molecules form two solvation shells around the central solute molecule. Hydrogen bonding in the bulk solvent is unaffected by increasing n. The large decrease in solvation enthalpies of these solute molecules for n > 14 enhances solubilisation. The diffusion constants of solute molecules decrease with increasing n. The solvation free energy of C-60 in water is positive (52.8 kJ/mol), whereas its value for C-60(OH)(30) is highly negative (-427.1 kJ/mol). The effects of surface hydroxylation become more dominant once the fullerols become soluble. Published by AIP Publishing.

International audience; Basalt fibres are claimed to show better high temperature resistance compared to glass fibres, suggesting better prospects to survive an end-of-life composite thermal recycling process while preserving an adequate reinforcing efficiency. It is well known that sizing agents affect impregnation of fibre reinforcements during composite manufacturing, which influences the overall mechanical behaviour of the resulting composites. However, with the exception of some studies about coupling agent effects on the adhesion between basalt fibres and matrix, no information are present in literature on the wetting characteristics of basalt fibres. The main contribution of this study is the analysis of the surface properties and wetting behaviour of basalt fibres with sizing optimised for both thermoset and thermoplastic matrices. Measurements of static contact angles were performed with a tensiometric procedure designed for singles fibres, in order to determine their surface energy and its components. Modifications of surface properties due to chemical treatments and high temperature exposure were also investigated and discussed.

International audience; Elastin-like polypeptides (ELPs) are biodegradable polymers with interesting physico-chemical properties for biomedical and biotechnological applications. We report herein the recombinant expression of three hydrophobic ELP5 (VPGIG)(n) with variable lengths (n = 20, 40, 60) and sub-ambient transition temperatures. These ELPs were purified from the cytoplasmic soluble fraction of Escherichia coli by inverse transition cycling, and their exact molecular weight was confirmed by various mass spectrometry techniques. Transition temperatures of ELP20, ELP40, and ELP60 were measured at 18.6 degrees C, 12.4 degrees C and 11.7 degrees C, respectively.

pH-Sensitive dyes are increasingly applied on polymer substrates for the creation of novel sensor materials. Recently, these dye molecules were modified to form a covalent bond with the polymer host. This had a large influence on the pH-sensitive properties, in particular on the acidity constant (pKa). Obtaining molecular control over the factors that influence the pK(a) value is mandatory for the future intelligent design of sensor materials. Herein, we show that advanced molecular dynamics (MD) methods have reached the level at which the pK(a) values of large solvated dye molecules can be predicted with high accuracy. Two MD methods were used in this work: steered or restrained MD and the insertion/deletion scheme. Both were first calibrated on a set of phenol derivatives and afterwards applied to the dye molecule bromothymol blue. Excellent agreement with experimental values was obtained, which opens perspectives for using these methods for designing dye molecules.

International audience; Achieving (bio) macromolecular structural assignment from the interpretation of ion mobility spectrometry (IMS) experiments requires successful comparison with computer modeling. Replica-exchange molecular dynamics simulations with suitable force fields not only offer a convenient framework to locate relevant conformations, especially in the case of multiple-funnel energy landscapes, but they are also well suited to statistical analyses. In the present paper, we discuss two extensions of the method used to improve its efficiency in the context of IMS. Two doubly-protonated polyalanines [RA(4)XA(4)K + 2H](2+) with X=V and D appear as favorable cases for which the calculated collision cross-section distributions naturally agree with the measurements, providing reliable candidate structures. For these compounds, a careful consideration of other order parameters based on the weighted histogram method resolves several otherwise hidden underlying conformational families. In the case of a much larger peptide exhibiting bistability, assignment is more difficult but could be achieved by guiding the sampling with an umbrella potential using the square gyration radius as the biasing coordinate. Applied to triply protonated bradykinine, the two presented methods indicate that different conformations compatible with the measurements are very close in energy.

We present a comparison between Monte Carlo (MC) results for homogeneous vapour-liquid nucleation of Lennard-Jones clusters and previously published values from molecular dynamics (MD) simulations. Both the MC and MD methods sample real cluster configuration distributions. In the MD simulations, the extent of the temperature fluctuation is usually controlled with an artificial thermostat rather than with more realistic carrier gas. In this study, not only a primarily velocity scaling thermostat is considered, but also Nosé-Hoover, Berendsen, and stochastic Langevin thermostat methods are covered. The nucleation rates based on a kinetic scheme and the canonical MC calculation serve as a point of reference since they by definition describe an equilibrated system. The studied temperature range is from T = 0.3 to 0.65 ϵ/k. The kinetic scheme reproduces well the isothermal nucleation rates obtained by Wedekind et al. [J. Chem. Phys. 127, 064501 (2007)] using MD simulations with carrier gas. The nucleation rates obtained by artificially thermostatted MD simulations are consistently lower than the reference nucleation rates based on MC calculations. The discrepancy increases up to several orders of magnitude when the density of the nucleating vapour decreases. At low temperatures, the difference to the MC-based reference nucleation rates in some cases exceeds the maximal nonisothermal effect predicted by classical theory of Feder et al. [Adv. Phys. 15, 111 (1966)].

© 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim Meniscus-guided solution-coating techniques offer a great potential for the realization of high-performance, single-crystalline films of organic semiconductors over large areas. Such techniques rely on the creation of a shallow meniscus and a subsequent one-directional coating. To achieve shallow meniscus fronts, the wetting behavior of the solvents on the substrate is crucial. Literature typically simply employs high surface energy substrates without investigating the exact impact of the surface treatment on film morphology and electrical characteristics. In this work, the zone-casting of (2,7-dioctyl[1]benzothieno[3,2-b][1]benzothiophene) is systematically studied on various surface treatments with widely varying surface energies. A fundamental observation is that, as long as the solution wets the substrate with a low contact angle, the morphology of the coated thin films is independent from the surface treatment. Through a systematic characterization of the wetting envelope of the treated substrate, a predictive rule for the wetting behavior is defined that is more accurate than the quantification of substrate surface energy alone. Furthermore, thin films formed on different surfaces show similar mobilities, but can nevertheless display largely varying threshold voltages. Hence, such films are ideal to study the influence of different surface treatments on the electrical characteristics without interference from morphological effects. ispartof: ADVANCED MATERIALS INTERFACES vol:5 issue:12 status: published

The unusual chemistry of sulfur is illustrated by the tendency for catenation. Sulfur forms a range of open and closed S$_n$ species in the gas phase, which has led to speculation on the composition of sulfur vapours as a function of temperature and pressure for over a century. Unlike elemental gases such as O$_2$ and N$_2$, there is no widely accepted thermodynamic potential for sulfur. Here we combine a first-principles global structure search for the low energy clusters from S$_2$ to S$_8$ with a thermodynamic model for the mixed-allotrope system, including the Gibbs free energy for all gas-phase sulfur on an atomic basis. A strongly pressure-dependent transition from a mixture dominant in S$_2$ to S$_8$ is identified. A universal chemical potential function, $\mu_{\mathrm{S}}(T,P)$, is proposed with wide utility in modelling sulfurisation processes including the formation of metal chalcogenide semiconductors., Comment: 12 pages, 9 figures. Supporting code and data is available at https://github.com/WMD-Bath/sulfur-model [snapshot DOI: 10.5281/zenodo.28536]. Further data will be available from DOI:10.6084/m9.figshare.1513736 and DOI:10.6084/m9.figshare.1513833 following peer-review

The stability and dynamics of a double-stranded DNA (dsDNA) is affected by the preferential occupancy of small monovalent molecular ions. Small metal and molecular ions such as sodium and alkyl ammonium have crucial biological functions in human body, affect the thermodynamic stability of the duplex DNA and exhibit preferential binding. Here, using atomistic molecular dynamics simulations, we investigate the preferential binding of metal ion such as Na+ and molecular ions such as tetramethyl ammonium (TMA(+)) and 2-hydroxy-N,N,N-trimethylethanaminium (CHO+) to double-stranded DNA. The thermodynamic driving force for a particular molecular ion-DNA interaction is determined by decomposing the free energy of binding into its entropic and enthalpic contributions. Our simulations show that each of these molecular ions preferentially binds to the minor groove of the DNA and the extent of binding is highest for CHO+. The ion binding processes are found to be entropically favourable. In addition, the contribution of hydrophobic effects towards the entropic stabilisation (in case of TMA(+)) and the effect of hydrogen bonding contributing to enthalpic stabilisation (in case of CHO+) have also been investigated.

The Polarizable Continuum Model (PCM) can be used in conjunction with Density Functional Theory (DFT) and its time-dependent extension (TDDFT) to simulate the electronic and optical properties of molecules and nanoparticles immersed in a dielectric environment, typically liquid solvents. In this contribution, we develop a methodology to account for solvation effects in real-space (and real-time) (TD)DFT calculations. The boundary elements method is used to calculate the solvent reaction potential in terms of the apparent charges that spread over the Van der Waals solute surface. In a real-space representation this potential may exhibit a Coulomb singularity at grid points that are close to the cavity surface. We propose a simple approach to regularize such singularity by using a set of spherical Gaussian functions to distribute the apparent charges. We have implemented the proposed method in the Octopus code and present results for the electrostatic contribution to the solvation free energies and solvatochromic shifts for a representative set of organic molecules in water., Version submitted to The Journal of Chemical Physics 10 pages, 7 Figures + supplemental material

Halo alcohol dehalogenase HheC catalyzes the highly enantioselective dehalogenation of vicinal halo alcohols to epoxides, as well as the reverse reaction, the enantioselective and beta-regioselective nucleophilic ring opening of epoxides by pseudo-halides such as azide and cyanide. To investigate this latter reaction, we determined X-ray structures of complexes of HheC with the favored and unfavored enantiomers of para-nitrostyrene oxide. The aromatic parts of the two enantiomers bind in a very similar way, but the epoxide ring of the unfavored (S)-enantiomer binds in a nonproductive inverted manner, with the epoxide oxygen and Cbeta atom positions interchanged with respect to those of the favored (R)-enantiomer. The calculated difference in relative Gibbs binding energy is in agreement with the observed loss of a single hydrogen bond in the S bound state with respect to the R bound state. Our results indicate that it is the nonproductive binding of the unfavored (S)-enantiomer, rather than the difference in affinity for the two enantiomers, that allows HheC to catalyze the azide-mediated ring opening of para-nitrostyrene oxide with high enantioselectivity. This work represents a rare opportunity to explain the enantioselectivity of an enzymatic reaction by comparison of crystallographic data on the binding of both the favored and unfavored enantiomers.

N.S. thanks the UJF and the CNRS for financial support and the CECIC (project: liqsim) for computer resources. NWChem calculations made use of the facilities of HECToR, the U.K. national high-performance computing service, which is provided by UoE HPCx Ltd at the University of Edinburgh, Cray Inc., and NAG Ltd and funded by the Office of Science and Technology through EPSRC's High End Computing Programme. Static ab initio and density-functional computations, as well as Car–Parrinello molecular dynamics simulations in aqueous solution are reported for [UO2(OH)(κ2-O2)(H2O)2]− and [UO2(OH)2(κ1-O2H)(H2O)]−. Whereas the κ1-hydroperoxo isomer is found to be more stable than the κ2-peroxo form in the gas phase, the order of stability is reversed in explicit bulk solution. Based on free energies from thermodynamic integration (BLYP functional), the peroxo form is favoured by ca. 32 kJ mol−1 in water. This stabilisation is discussed in terms of the hydration shells about the individual ligands and dipole moments of the complexes in water, and highlights the importance of explicit solute–solvent interactions and bulk solvation for the speciation of uranyl(VI) compounds. Postprint

International audience; Inverse gas chromatography (IGC) is widely used for the characterizationof surfaces. The present work describes a novel IGC tool, therecently developed film cell module, which measures monolithic thinsolid film surface properties, whereas only samples in powder or fiberstate or polymer-coated supports can be studied by classic IGC. Thesurface energy of four different solid supports was measured usingboth classic IGC with columns packed with samples in the powderstate, and IGC with the new film cell module or the sessile drop technique,using samples in the film state. The total surface energy andits dispersive and specific components were measured for glass,polyethylene, polyamide and polytetrafluoroethylene. Similar resultswere obtained for the four materials using the three different techniques.The main conclusion is that the new film cell module forIGC is an attractive alternative to the sessile drop technique as itgives very accurate and reproducible results for surface energy components,with significant savings in time and the possible control ofsample humidity and temperature. This film cell module for IGC extendsthe application field of IGC to any thin solid film and can beused to study the effect of any surface treatment on surface energy.

Uracil (U) can be found in DNA as a mismatch paired either to adenine (A) or to guanine (G). Removal of U from DNA is performed by a class of enzymes known as uracil–DNA–glycosylases (UDG). Recent studies suggest that recognition of U–A and U–G mismatches by UDG takes place via an extra-helical mechanism. In this work, we use molecular dynamics simulations to analyze the structure, dynamics and open base pair kinetics of U–A base pairs relative to their natural T–A counterpart in 12 dodecamers. Our results show that the presence of U does not alter the local conformation of B-DNA. Breathing dynamics and base pair closing kinetics are only weakly dependent on the presence of U versus T, with open T–A and U–A pairs lifetimes in the nanosecond timescale. Additionally, we observed spontaneous base flipping in U–A pairs. We analyze the structure and dynamics for this event and compare the results to available crystallographic data of open base pair conformations. Our results are in agreement with both structural and kinetic data derived from NMR imino proton exchange measurements, providing the first detailed description at the molecular level of elusive events such as spontaneous base pair opening and flipping in mismatched U–A sequences in DNA. Based on these results, we propose that base pair flipping can occur spontaneously at room temperature via a 3-step mechanism with an open base pair intermediate. Implications for the molecular basis of U recognition by UDG are discussed.

We study the thermodynamic and structural properties of a five-site tetrahedral molecular model by means of different Monte Carlo simulation techniques, and the reference interaction site model (RISM) theory of molecular fluids. Simulations and theory signal the onset, at sufficiently low temperatures, of two different tetrahedral molecular arrangements, with a more open topology progressively giving place to a fully bonded one, as the temperature decreases. The RISM theory reproduces the splitting of the static structure factor at low temperatures, a feature intimately related to the onset of the tetrahedral ordering. Less accurate predictions are obtained for the liquid-vapor coexistence and the short-range correlations.

In recent experimental work on spherical colloidal particles decorated with two hydrophobic poles separated by an electrically charged middle band (triblock Janus particles)-when particles are confined by gravity at the bottom of the sample holder-self-assembly into a Kagome two dimensional lattice has been documented [Qian Chen, Sung Chul Bae and Steve Granick, Nature, 2011, 469, 381]. Here, we assess the ability of a simple two-patch effective potential to reproduce the experimental findings. The model parameters are selected to match the experimental values, with a short-range attraction mimicking hydrophobic interactions and a patch width that allows for a maximum of two contacts per patch. We show that the effective potential is able to reproduce the observed crystallisation pathway in the Kagome structure. On the basis of free energy calculations, we also show that the Kagome lattice is stable at low temperature and low pressure, but that it transforms into a hexagonal lattice with alternating attractive and repulsive bands on increasing pressure.

The potential of mean force (PMF) of a phospholipid in a bilayer is a key thermodynamic property that describes the energetic cost of localized lipid defects. We have calculated the PMF by umbrella sampling using molecular dynamics simulations. The profile has a deep minimum at the equilibrium position in the bilayer and steeply rises for displacements both deeper into the bilayer and moving away from the bilayer. As the lipid loses contact with the bilayer, the profile abruptly flattens without a significant barrier. The calculated free energy difference of 80 kJ/mol between the minimum of the PMF and the value in water agrees well with the free energy difference calculated from the experimentally measured critical micelle concentration. Significant water/lipid defects form when a lipid is forced into the bilayer interior, in the form of a small water pore that spans the membrane. The energy required to form such a water pore is also found to be 80 kJ/mol. On the basis of this energy, we estimate the lipid flip-flop rate and permeability rate of sodium ions. The resulting rates are in good agreement with experimental measurements, suggesting lipid flip-flop and basal permeability of ions are pore mediated.

Understanding the binding and insertion of peptides in lipid bilayers is a prerequisite for understanding phenomena such as antimicrobial activity and membrane-protein folding. We describe molecular dynamics simulations of the antimicrobial peptide alamethicin in lipid/water and octane/water environments, taking into account an external electric field to mimic the membrane potential. At cis-positive potentials, alamethicin does not insert into a phospholipid bilayer in 10ns of simulation, due to the slow dynamics of the peptide and lipids. However, in octane N-terminal insertion occurs at field strengths from 0.33V/nm and higher, in simulations of up to 100ns duration. Insertion of alamethicin occurs in two steps, corresponding to desolvation of the Gln7 side chain, and the backbone of Aib10 and Gly11. The proline induced helix kink angle does not change significantly during insertion. Polyalanine and alamethicin form stable helices both when inserted in octane and at the water/octane interface, where they partition in the same location. In water, both polyalanine and alamethicin partially unfold in multiple simulations. We present a detailed analysis of the insertion of alamethicin into the octane slab and the influence of the external field on the peptide structure. Our findings give new insight into the mechanism of channel formation by alamethicin and the structure and dynamics of membrane-associated helices.