A Simple Generic Model of Elastin-Like Polypeptides with Proline Isomerization.

A generic model of elastin-like polypeptides (ELP) is derived that includes proline isomerization (ProI). As a case study, conformational transition of a -[valine-proline-glycine-valine-glycine]- sequence is investigated in aqueous ethanol mixtures. While the non-bonded interactions are based on the Lennard-Jones (LJ) parameters, the effect of ProI is incorporated by tuning the intramolecular 3- and 4-body interactions known from the underlying all-atom simulations into the generic model. One of the key advantages of such a minimalistic model is that it readily decouples the effects of geometry and the monomer-solvent interactions due to the presence of ProI, thus gives a clearer microscopic picture that is otherwise rather nontrivial within the all-atom setups. These results are consistent with the available all-atom and experimental data. The model derived here may pave the way to investigate large scale self-assembly of ELPs or biomimetic polymers in general.

Chilling alcohol on the computer: isothermal compressibility and the formation of hydrogen-bond clusters in liquid propan-1-ol.

Molecular dynamics simulations have been performed to compute the isothermal compressibility [Formula: see text] of liquid propan-1-ol in the temperature range [Formula: see text] K. A change in behaviour, from normal (high T) to anomalous (low T), has been identified for [Formula: see text] at [Formula: see text] K. The average number of hydrogen bonds (H-bond) per molecule turns to saturation in the same temperature interval, suggesting the formation of a relatively rigid network. Indeed, simulation results show a strong tendency to form H-bond clusters with distinct boundaries, with the average largest size and width of the size distribution growing upon decreasing temperature, in agreement with previous theoretical and experimental studies. These results also emphasise a connection between the behaviour of [Formula: see text] and the formation of nanometric structures.

Stabilizing α-Helicity of a Polypeptide in Aqueous Urea: Dipole Orientation or Hydrogen Bonding?

We propose a mechanism for α-helix folding of polyalanine in aqueous urea that reconciles experimental and simulation studies. Over 15 µs long, all-atom simulations reveal that, upon dehydrating the protein's first solvation shell, a delicate balance between localized urea-residue dipole interactions and hydrogen bonds dictates polypeptide solvation properties and structure. Our work clarifies the experimentally observed tendency of these alanine-rich systems to form secondary structures at low and intermediate urea concentrations. Moreover, it is consistent with the commonly accepted hydrogen-bond-induced helix unfolding, dominant at high urea concentrations. These results establish a structure-property relationship highlighting the importance of microscopic dipole-dipole orientations/interactions for the operational understanding of macroscopic protein solvation.

Water Harvesting by Thermoresponsive Ionic Liquids: A Molecular Dynamics Study of the Water Absorption Kinetics and of the Role of Nanostructuring.

Ionic liquids (ILs) whose water solutions are thermoresponsive provide an appealing route to harvest water from the atmosphere at an energy cost that can be accessed by solar heating. IL/water solutions that present a lower critical solution temperature (LCST), i.e., demix upon increasing temperature, represent the most promising choice for this task since they could absorb vapor during the night when its saturation is highest and release liquid water during the day. The kinetics of water absorption at the surface and the role of nanostructuring in this process have been investigated by atomistic molecular dynamics simulations for the ionic liquid tetrabutyl phosphonium 2,4-dimethylbenzenesulfonate whose LCST in water occurs at Tc = 36 °C for solutions of 50-50 wt % composition. The simulation results show that water molecules are readily adsorbed on the IL and migrate along the surface to form thick three-dimensional islands. On a slightly longer time scale, ions crawl on these islands, covering water and recreating the original surface whose free energy is particularly low. At a high deposition rate, this mechanism allows the fast incorporation of large amounts of water, producing subsurface water pockets that eventually merge into the populations of water-rich and IL-rich domains in the nanostructured bulk. Simulation results suggest that strong nanostructuring could ease the separation of water and water-contaminated IL phases even before macroscopic demixing.

Finite-size excess-entropy scaling for simple liquids.

Explicit and implicit size effects in computer simulations result from considering systems with a fixed number of particles and periodic boundary conditions, respectively. We investigate these effects in the relation D*(L) = A(L) exp(α(L)s2(L)) between reduced self-diffusion coefficient D*(L) and two-body excess entropy s2(L) for prototypical simple-liquid systems of linear size L. To this aim, we introduce and validate a finite-size two-body excess entropy integral equation. Our analytical arguments and simulation results show that s2(L) exhibits a linear scaling with 1/L. Since D*(L) displays a similar behavior, we show that the parameters A(L) and α(L) are also linearly proportional to 1/L. By extrapolating to the thermodynamic limit, we report the coefficients A∞ = 0.048 ± 0.001 and α∞ = 1.000 ± 0.013 that agree well with the universal values available in the literature [M. Dzugutov, Nature 381, 137-139 (1996)]. Finally, we find a power law relation between the scaling coefficients for D*(L) and s2(L), suggesting a constant viscosity-to-entropy ratio.

Thermoresponsive Ionic Liquid/Water Mixtures: From Nanostructuring to Phase Separation.

The thermodynamics, structures, and applications of thermoresponsive systems, consisting primarily of water solutions of organic salts, are reviewed. The focus is on organic salts of low melting temperatures, belonging to the ionic liquid (IL) family. The thermo-responsiveness is represented by a temperature driven transition between a homogeneous liquid state and a biphasic state, comprising an IL-rich phase and a solvent-rich phase, divided by a relatively sharp interface. Demixing occurs either with decreasing temperatures, developing from an upper critical solution temperature (UCST), or, less often, with increasing temperatures, arising from a lower critical solution temperature (LCST). In the former case, the enthalpy and entropy of mixing are both positive, and enthalpy prevails at low T. In the latter case, the enthalpy and entropy of mixing are both negative, and entropy drives the demixing with increasing T. Experiments and computer simulations highlight the contiguity of these phase separations with the nanoscale inhomogeneity (nanostructuring), displayed by several ILs and IL solutions. Current applications in extraction, separation, and catalysis are briefly reviewed. Moreover, future applications in forward osmosis desalination, low-enthalpy thermal storage, and water harvesting from the atmosphere are discussed in more detail.

Finite-size scaling and thermodynamics of model supercooled liquids: long-range concentration fluctuations and the role of attractive interactions.

We compute partial structure factors, Kirkwood-Buff integrals (KBIs) and chemical potentials of model supercooled liquids with and without attractive interactions. We aim at investigating whether relatively small differences in the tail of the radial distribution functions result in contrasting thermodynamic properties. Our results suggest that the attractive potential favours the nucleation of long-range structures. Indeed, upon decreasing temperature, Bathia-Thornton structure factors display anomalous behaviour in the k→0 limit. KBIs extrapolated to the thermodynamic limit confirm this picture, and excess coordination numbers identify the anomaly with long-range concentration fluctuations. By contrast, the purely repulsive system remains perfectly miscible for the same temperature interval and only reveals qualitatively similar concentration fluctuations in the crystalline state. Furthermore, differences in both isothermal compressibilities and chemical potentials show that thermodynamics is not entirely governed by the short-range repulsive part of the interaction potential, emphasising the nonperturbative role of attractive interactions. Finally, at higher density, where both systems display nearly identical dynamical properties and repulsive interactions become dominant, the anomaly disappears, and both systems also exhibit similar thermodynamic properties.

Connecting density fluctuations and Kirkwood-Buff integrals for finite-size systems.

Kirkwood-Buff integrals (KBIs) connect the microscopic structure and thermodynamic properties of liquid solutions. KBIs are defined in the grand canonical ensemble and evaluated by assuming the thermodynamic limit (TL). In order to reconcile analytical and numerical approaches, finite-size KBIs have been proposed in the literature, resulting in two strategies to obtain their TL values from computer simulations. (i) The spatial block analysis method in which the simulation box is divided into subdomains of volume V to compute density fluctuations. (ii) A direct integration method where a corrected radial distribution function and a kernel that accounts for the geometry of the integration subvolumes are combined to obtain KBI as a function of V. In this work, we propose a method that connects both strategies into a single framework. We start from the definition of finite-size KBI, including the integration subdomain and an asymptotic correction to the radial distribution function, and solve them in Fourier space where periodic boundary conditions are trivially introduced. The limit q → 0, equivalent to the value of the KBI in the TL, is obtained via the spatial block-analysis method. When compared to the latter, our approach gives nearly identical results for all values of V. Moreover, all finite-size effect contributions (ensemble, finite-integration domains, and periodic boundary conditions) are easily identifiable in the calculation. This feature allows us to analyze finite-size effects independently and extrapolates the results of a single simulation to different box sizes. To validate our approach, we investigate prototypical systems, including SPC/E water and aqueous urea mixtures.

From adaptive resolution to molecular dynamics of open systems.

ABSTRACT: We provide an overview of the Adaptive Resolution Simulation method (AdResS) based on discussing its basic principles and presenting its current numerical and theoretical developments. Examples of applications to systems of interest to soft matter, chemical physics, and condensed matter illustrate the method's advantages and limitations in its practical use and thus settle the challenge for further future numerical and theoretical developments.

Role of pH in the synthesis and growth of gold nanoparticles using L-asparagine: a combined experimental and simulation study.

The use of biomolecules as capping and reducing agents in the synthesis of metallic nanoparticles constitutes a promising framework to achieve desired functional properties with minimal toxicity. The system's complexity and the large number of variables involved represent a challenge for theoretical and experimental investigations aiming at devising precise synthesis protocols. In this work, we use L-asparagine (Asn), an amino acid building block of large biomolecular systems, to synthesise gold nanoparticles (AuNPs) in aqueous solution at controlled pH. The use of Asn offers a primary system that allows us to understand the role of biomolecules in synthesising metallic nanoparticles. Our results indicate that AuNPs synthesised in acidic (pH 6) and basic (pH 9) environments exhibit somewhat different morphologies. We investigate these AuNPs via Raman scattering experiments and classical molecular dynamics simulations of zwitterionic and anionic Asn states adsorbing on (111)-, (100)-, (110)-, and (311)-oriented gold surfaces. A combined analysis suggests that the underlying mechanism controlling AuNPs geometry correlates with amine's preferential adsorption over ammonium groups, enhanced upon increasing pH. Our simulations reveal that Asn (both zwitterionic and anionic) adsorption on gold (111) is essentially different from adsorption on more open surfaces. Water molecules strongly interact with the gold face-centred-cubic lattice and create traps, on the more open surfaces, that prevent the Asn from diffusing. These results indicate that pH is a relevant parameter in green-synthesis protocols with the capability to control the nanoparticle's geometry, and pave the way to computational studies exploring the effect of water monolayers on the adsorption of small molecules on wet gold surfaces.

Investigating the Conformational Ensembles of Intrinsically Disordered Proteins with a Simple Physics-Based Model.

Intrinsically disordered proteins (IDPs) play an important role in an array of biological processes but present a number of fundamental challenges for computational modeling. Recently, simple polymer models have regained popularity for interpreting the experimental characterization of IDPs. Homopolymer theory provides a strong foundation for understanding generic features of phenomena ranging from single-chain conformational dynamics to the properties of entangled polymer melts, but is difficult to extend to the copolymer context. This challenge is magnified for proteins due to the variety of competing interactions and large deviations in side-chain properties. In this work, we apply a simple physics-based coarse-grained model for describing largely disordered conformational ensembles of peptides, based on the premise that sampling sterically forbidden conformations can compromise the faithful description of both static and dynamical properties. The Hamiltonian of the employed model can be easily adjusted to investigate the impact of distinct interactions and sequence specificity on the randomness of the resulting conformational ensemble. In particular, starting with a bead-spring-like model and then adding more detailed interactions one by one, we construct a hierarchical set of models and perform a detailed comparison of their properties. Our analysis clarifies the role of generic attractions, electrostatics, and side-chain sterics, while providing a foundation for developing efficient models for IDPs that retain an accurate description of the hierarchy of conformational dynamics, which is nontrivially influenced by interactions with surrounding proteins and solvent molecules.

Why Do Elastin-Like Polypeptides Possibly Have Different Solvation Behaviors in Water-Ethanol and Water-Urea Mixtures?

The solvent quality determines the collapsed or the expanded state of a polymer. For example, a polymer dissolved in a poor solvent collapses, whereas in a good solvent it opens up. While this standard understanding is generally valid, there are examples when a polymer collapses even in a mixture of two good solvents. This phenomenon, commonly known as co-non-solvency, is usually associated with a wide range of synthetic (smart) polymers. Moreover, recent experiments have shown that some biopolymers, such as elastin-like polypeptides (ELPs) that exhibit lower critical solution behavior T l in pure water, show co-non-solvency behavior in aqueous ethanol mixtures. In this study, we investigate the phase behavior of elastin-like polypeptides (ELPs) in aqueous binary mixtures using molecular dynamics simulations of all-atom and complementary explicit solvent generic models. The model is parameterized by mapping the solvation free energy obtained from the all-atom simulations onto the generic interaction parameters. For this purpose, we derive segment-based (monomer level) generic parameters for four different peptides, namely proline (P), valine (V), glycine (G), and alanine (A), where the first three constitute the basic building blocks of ELPs. Here, we compare the conformational behavior of two ELP sequences, namely -(VPGGG)- and -(VPGVG)-, in aqueous ethanol and -urea mixtures. Consistent with recent experiments, we find that ELPs show co-non-solvency in aqueous ethanol mixtures. Ethanol molecules have preferential binding with all ELP residues, with an interaction contrast of 6-8 k B T, and thus driving the coil-to-globule transition. On the contrary, ELP conformations show a weak variation in aqueous urea mixtures. Our simulations suggest that the glycine residues dictate the overall behavior of ELPs in aqueous urea, where urea molecules have a rather weak preferential binding with glycine as observed from the all atom simulations, i.e., less than k B T. This weak interaction dilutes the overall effect of other neighboring residues and thus ELPs exhibit a different conformational behavior in aqueous urea in comparison to aqueous ethanol mixtures. While the validation of the latter findings will require a more detailed experimental investigation, the results presented here may provide a new twist to the present understanding of cosolvent interactions with peptides and proteins.

Open-boundary Hamiltonian adaptive resolution. From grand canonical to non-equilibrium molecular dynamics simulations.

We propose an open-boundary molecular dynamics method in which an atomistic system is in contact with an infinite particle reservoir at constant temperature, volume, and chemical potential. In practice, following the Hamiltonian adaptive resolution strategy, the system is partitioned into a domain of interest and a reservoir of non-interacting, ideal gas particles. An external potential, applied only in the interfacial region, balances the excess chemical potential of the system. To ensure that the size of the reservoir is infinite, we introduce a particle insertion/deletion algorithm to control the density in the ideal gas region. We show that it is possible to study non-equilibrium phenomena with this open-boundary molecular dynamics method. To this aim, we consider a prototypical confined liquid under the influence of an external constant density gradient. The resulting pressure-driven flow across the atomistic system exhibits a velocity profile consistent with the corresponding solution of the Navier-Stokes equation. This method conserves, on average, linear momentum and closely resembles experimental conditions. Moreover, it can be used to study various direct and indirect out-of-equilibrium conditions in complex molecular systems.

Steering a solute between coexisting solvation states: Revisiting nonequilibrium work relations and the calculation of free energy differences.

By analogy with single-molecule pulling experiments, we present a computational framework to obtain free energy differences between complex solvation states. To illustrate our approach, we focus on the calculation of solvation free energies (SFEs). However, the method can be readily extended to cases involving more complex solutes and solvation conditions as well as to the calculation of binding free energies. The main idea is to drag the solute across the simulation box where atomistic and ideal gas representations of the solvent coexist at constant temperature and chemical potential. At finite pulling speeds, the resulting work allows one to extract SFEs via nonequilibrium relations, whereas at infinitely slow pulling speeds, this process becomes equivalent to the thermodynamic integration method. Results for small molecules well agree with literature data and pave the way to systematic studies of arbitrarily large and complex molecules.

Spatially Resolved Thermodynamic Integration: An Efficient Method To Compute Chemical Potentials of Dense Fluids.

Many popular methods for the calculation of chemical potentials rely on the insertion of test particles into the target system. In the case of liquids and liquid mixtures, this procedure increases in difficulty upon increasing density or concentration, and the use of sophisticated enhanced sampling techniques becomes inevitable. In this work, we propose an alternative strategy, spatially resolved thermodynamic integration, or SPARTIAN for short. Here, molecules are described with atomistic resolution in a simulation subregion and as ideal gas particles in a larger reservoir. All molecules are free to diffuse between subdomains adapting their resolution on the fly. To enforce a uniform density profile across the simulation box, a single-molecule external potential is computed, applied, and identified with the difference in chemical potential between the two resolutions. Since the reservoir is represented as an ideal gas bath, this difference exactly amounts to the excess chemical potential of the target system. The present approach surpasses the high density/concentration limitation of particle insertion methods because the ideal gas molecules entering the target system region spontaneously adapt to the local environment. The ideal gas representation contributes negligibly to the computational cost of the simulation, thus allowing one to make use of large reservoirs at minimal expenses. The method has been validated by computing excess chemical potentials for pure Lennard-Jones liquids and mixtures, SPC and SPC/E liquid water, and aqueous solutions of sodium chloride. The reported results well reproduce literature data for these systems.

Concurrent coupling of realistic and ideal models of liquids and solids in Hamiltonian adaptive resolution simulations.

To understand the properties of a complex system it is often illuminating to perform a comparison with a simpler, even idealised one. A prototypical application of this approach is the calculation of free energies and chemical potentials in liquids, which can be decomposed in the sum of ideal and excess contributions. In the same spirit, in computer simulations it is possible to extract useful information on a given system making use of setups where two models, an accurate one and a simpler one, are concurrently employed and directly coupled. Here, we tackle the issue of coupling atomistic or, more in general, interacting models of a system with the corresponding idealised representations: for a liquid, this is the ideal gas, i.e. a collection of non-interacting particles; for a solid, we employ the ideal Einstein crystal, a construct in which particles are decoupled from one another and restrained by a harmonic, exactly integrable potential. We describe in detail the practical and technical aspects of these simulations, and suggest that the concurrent usage and coupling of realistic and ideal models represents a promising strategy to investigate liquids and solids in silico.

Fluctuations, Finite-Size Effects and the Thermodynamic Limit in Computer Simulations: Revisiting the Spatial Block Analysis Method.

The spatial block analysis (SBA) method has been introduced to efficiently extrapolate thermodynamic quantities from finite-size computer simulations of a large variety of physical systems. In the particular case of simple liquids and liquid mixtures, by subdividing the simulation box into blocks of increasing size and calculating volume-dependent fluctuations of the number of particles, it is possible to extrapolate the bulk isothermal compressibility and Kirkwood-Buff integrals in the thermodynamic limit. Only by explicitly including finite-size effects, ubiquitous in computer simulations, into the SBA method, the extrapolation to the thermodynamic limit can be achieved. In this review, we discuss two of these finite-size effects in the context of the SBA method due to (i) the statistical ensemble and (ii) the finite integration domains used in computer simulations. To illustrate the method, we consider prototypical liquids and liquid mixtures described by truncated and shifted Lennard-Jones (TSLJ) potentials. Furthermore, we show some of the most recent developments of the SBA method, in particular its use to calculate chemical potentials of liquids in a wide range of density/concentration conditions.

Gold Nanoparticle Internal Structure and Symmetry Probed by Unified Small-Angle X-ray Scattering and X-ray Diffraction Coupled with Molecular Dynamics Analysis.

Shape and size are known to determine a nanoparticle's properties. Hardly ever studied in synthesis, the internal crystal structure (i.e., particle defects, crystallinity, and symmetry) is just as critical as shape and size since it directly impacts catalytic efficiency, plasmon resonance, and orients anisotropic growth of metallic nanoparticles. Hence, its control cannot be ignored any longer in today's research and applications in nanotechnology. This study implemented an unprecedented reliable measurement combining these three structural aspects. The unified small-angle X-ray scattering and diffraction measurement (SAXS/XRD) was coupled with molecular dynamics to allow simultaneous determination of nanoparticles' shape, size, and crystallinity at the atomic scale. Symmetry distribution (icosahedra-Ih, decahedra-Dh, and truncated octahedra-TOh) of 2-6 nm colloidal gold nanoparticles synthesized in organic solvents was quantified. Nanoparticle number density showed the predominance of Ih, followed by Dh, and little, if any, TOh. This result contradicts some theoretical predictions and highlights the strong effect of the synthesis environment on structure stability. We foresee that this unified SAXS/XRD analysis, yielding both statistical and quantitative counts of nanoparticles' symmetry distribution, will provide new insights into nanoparticle formation, growth, and assembly.

Role of the environment in the stability of anisotropic gold particles.

Despite the long-lasting interest in the synthesis control of nanoparticles (NPs) in both fundamental and applied nanosciences, the driving mechanisms responsible for their size and shape selectivity in an environment (solution) are not completely understood, and a clear assessment of the respective roles of equilibrium thermodynamics and growth kinetics is still missing. In this study, relying on an efficient atomistic computational approach, we decipher the dependence of energetics, shapes and morphologies of gold NPs on the strength and nature of the metal-environment interaction. We highlight the conditions under which the energy difference between isotropic and elongated gold NPs is reduced, thus prompting their thermodynamic coexistence. The study encompasses both monocrystalline and multi-twinned particles and extends over size ranges particularly representative of the nucleation and early growth stages. Computational results are further rationalized with arguments involving the dependence of facet and edge energies on the metal-environment interactions. We argue that by determining the abundance and diversity of particles nucleated in solution, thermodynamics may constitute an important bias influencing their final shape. The present results provide firm grounds for kinetic simulations of particle growth.

An efficient many-body potential for the interaction of transition and noble metal nano-objects with an environment.

We present a mean-field model for the description of transition or noble metal nano-objects interacting with an environment. It includes a potential given by the second-moment approximation to the tight-binding Hamiltonian for metal-metal interactions, and an additional many-body potential that depends on the local atomic coordination for the metal-environment interaction. The model does not refer to a specific type of chemical conditions, but rather provides trends as a function of a limited number of parameters. The capabilities of the model are highlighted by studying the relative stability of semi-infinite gold surfaces of various orientations and formation energies of a restricted set of single-faceted gold nanoparticles. It is shown that, with only two parameters and in a very efficient way, it is able to generate a great variety of stable structures and shapes, as the nature of the environment varies. It is thus expected to account for formation energies of nano-objects of various dimensionalities (surfaces, thin films, nano-rods, nano-wires, nanoparticles, nanoribbons, etc.) according to the environment.