Multiscale Molecular Simulation of Nanostructured Systems

2008/2009Computational materials science based on multiscale approach is very promising in the domain of nanoscience. It gives the modeler a route from the atomistic description of the system to a trust-worthy estimate of the properties of a material, obtained from the underlying molecules in a quantifiable manner. In this thesis we discuss general guidelines for its implementation in the field of nanomaterials and propose an alternative pathway to link effectively atomistic to mesoscopic scale and this, in turn, to the macroscopic scale. As proofs of concept for the reliability of the proposed approach, we consider several systems of industrial interest, ranging from polymeric nanocomposite materials, to epoxy resins, block copolymers, and gels for biomedical applications. In this context, we ascertain that multiscale molecular modelling can play a crucial role in the design of new materials whose properties are influenced by the structure at nanoscale. The results suggest that the combination of simulations at multiple scales can unleash the power of modeling and yield important insights.Le tecniche computazionali fondate su un approccio multiscala costituiscono uno strumento molto promettente nel campo della nanoscienza e dei nanomateriali. Esse forniscono al modellatore un percorso quantitativo che parte dalla descrizione atomistica fino alle proprietà finali del materiale. In questo lavoro di tesi sono discusse le linee guida per l’implementazione della modellistica multiscala nel settore dei nanomateriali ed è proposta una strategia alternativa alle soluzioni attualmente esistenti per collegare la scala atomistica alla mesoscala e, successivamente, la mesoscala alla scala macroscopica. Per dimostrare la validità del metodo proposto, sono stati presi in esame differenti sistemi di interesse industriale, i quali comprendono materiali nanocompositi polimerici, resine epossidiche, copolimeri a blocchi, e gel per applicazioni biomediche. In questo contesto, si è evidenziato come la modellistica multiscala possa svolgere un ruolo cruciale nella progettazione di nuovi materiali le cui proprietà sono influenzate dalla struttura a scala nanometrica. I risultati suggeriscono che la combinazione di simulazioni su scale multiple amplifica sinergicamente la potenza della modellazione e può fornire importanti intuizioni.XXII Ciclo197

Molecular Features for Probing Small Amphiphilic Molecules with Self-Assembled Monolayer Protected Nanoparticles

The sensing of small molecules poses the challenge to develop devices able to discriminate between compounds that may be structurally very similar. Here, attention has been paid to the use of self-assembled monolayer (SAM)-protected gold nanoparticles since they enable a modular approach to tune single-molecule affinity and selectivity simply by changing functional moieties (i.e. covering ligands), alongside with multivalent molecular recognition. To date, the discovery of monolayers suitable for a specific molecular target relies on trial-and-error approaches, with ligand chemistry being the main criteria used to modulate selectivity and sensitivity. By using molecular dynamics, we showcase that either individual molecular characteristics and/or collective features such as ligand flexibility, monolayer organization, ligand local ordering, and interfacial solvent properties can also be exploited conveniently. The knowledge of the molecular mechanisms that drive the recognition of small molecules on SAM covered nanoparticles will critically expand our ability to manipulate and control such supramolecular systems

Chiral recognition at self-assembled multivalent (SAMul) nanoscale interfaces – enantioselectivity in polyanion binding

Self-assembled multivalent (SAMul) ligands based on palmitic acid functionalised with cationic L/D-lysine bind polyanionic heparin or DNA with no chiral preference. Inserting a glycine spacer unit switches on chiral discrimination – a rare example of controlled chiral recognition at a SAMul nanoscale interface

Highly grafted polystyrene/polyvinylpyridine polymer gold nanoparticles in a good solvent: effects of chain length and composition

In this work, the structural features of spherical gold nanoparticles (NPs) decorated with highly grafted poly(styrene) (PS), poly(vinylpyridine) (PVP) and PS\u2013PVP diblock copolymer brushes immersed in a good solvent are investigated by means of Dissipative Particle Dynamics (DPD) simulations as a function of grafted chain length and of homopolymer and copolymer chain composition. For NPs grafted either by PS or PVP homopolymer brushes (selected as a proof of concept), good agreement between the Daoud\u2013Cotton theory, experimental evidence, and our DPD simulations is observed in the scaling behavior of single chain properties, especially for longer grafted chains, and in brush thickness prediction. On the other hand, for grafted chain lengths comparable to NP dimensions parabolic-like profiles of the end-monomer distributions are obtained. Furthermore, a region of high concentration of polymer segments is observed in the monomer density distribution for long homopolymers. In the case of copolymer-decorated NPs, the repulsion between PS and PVP blocks is found to substantially influence the radius of gyration and the shape of the end-monomer distribution of the relevant polymer shell. Moreover, for diblock chains, the un-swollen region is observed to be thinner (and, correspondingly, the swollen layer thicker) than that of a NP modified with a homopolymer of the same length. Finally, the lateral segregation of PS and PVP blocks is evidenced by our calculations and a detailed analysis of the corona behavior is reported, thus revealing the key parameters in controlling the surface properties and the response of diblock copolymer modified nanoparticles

Probing multiscale factors affecting the reactivity of nanoparticle-bound molecules

I. K. M., W. E., E. J. H, S. S. and E. R. K. are grateful for funding from the Leverhulme Trust [RPG-2015-042], the Engineering and Physical Sciences Research Council [EP/K016342/1], the University of St Andrews, and the EPSRC Centre for Doctoral Training in Critical Resource Catalysis (CRITICAT) [Ph.D. studentship to SS: EP/L016419/1]. D. M. and P.P thank the Italian Ministry of University Research (MIUR) for funding [RBSI14PBC6].The structures and physicochemical properties of surface-stabilizing molecules play a critical role in defining the properties, interactions, and functionality of hybrid nanomaterials such as monolayer-stabilized nanoparticles. Concurrently, the distinct surface-bound interfacial environment imposes very specific conditions on molecular reactivity and behavior in this setting. Our ability to probe hybrid nanoscale systems experimentally remains limited, yet understanding the consequences of surface confinement on molecular reactivity is crucial for enabling predictive nanoparticle synthon approaches for postsynthesis engineering of nanoparticle surface chemistry and construction of devices and materials from nanoparticle components. Here, we have undertaken an integrated experimental and computational study of the reaction kinetics for nanoparticle-bound hydrazones, which provide a prototypical platform for understanding chemical reactivity in a nanoconfined setting. Systematic variation of just one molecular-scale structural parameter—the distance between reactive site and nanoparticle surface—showed that the surface-bound reactivity is influenced by multiscale effects. Nanoparticle-bound reactions were tracked in situ using 19F NMR spectroscopy, allowing direct comparison to the reactions of analogous substrates in bulk solution. The surface-confined reactions proceed more slowly than their solution-phase counterparts, and kinetic inhibition becomes more significant for reactive sites positioned closer to the nanoparticle surface. Molecular dynamics simulations allowed us to identify distinct supramolecular architectures and unexpected dynamic features of the surface-bound molecules that underpin the experimentally observed trends in reactivity. This study allows us to draw general conclusions regarding interlinked structural and dynamical features across several length scales that influence interfacial reactivity in monolayer-confined environments.PostprintPeer reviewe

Patchy and Janus Nanoparticles by Self-Organization of Mixtures of Fluorinated and Hydrogenated Alkanethiolates on the Surface of a Gold Core

The spontaneous self-organization of dissimilar ligands on the surface of metal nanoparticles is a very appealing approach to obtain anisotropic "spherical". systems. In addition to differences in ligand length and end groups, a further thermodynamic driving force to control the self-assembled monolayer organization may become available if the ligands are inherently immiscible, as is the case of hydrogenated (H-) and fluorinated (F-) species. Here, we validate the viability of this approach by combining F-19 NMR experiments and multiscale molecular simulations on large sets of mixed-monolayer-protected gold nanoparticles (NPs). The phase segregation of blends of F- and H-thiolates grafted on the surface of gold NPs allows a straightforward approach to patterned mixed monolayers, with the shapes of the monolayer domains being encoded in the structure of the F/H-thiolate ligands. The results obtained from this comprehensive study offer molecular design rules to achieve a precise control of inorganic nanoparticles protected by specifically patterned monolayers

Electrostatic binding of polyanions using self-assembled multivalent (SAMul) ligand displays-structure-activity effects on DNA/heparin binding

This paper reports that modifying the ligands in self-assembled multivalent (SAMul) displays has an impact on apparent binding selectivity towards two nanoscale biological polyanions-heparin and DNA. For the nanostructures assayed here, spermidine ligands are optimal for heparin binding but spermine ligands are preferred for DNA. Probing subtle differences in such nanoscale binding interfaces is a significant challenge, and as such, several experimental binding assays-competition assays and isothermal calorimetry-are employed to confirm differences in affinity and provide thermodynamic insights. Given the dynamic nature and hierarchical binding processes involved in SAMul systems, we employed multiscale modelling to propose reasons for the origins of polyanion selectivity differences. The modelling results, when expressed in thermodynamic terms and compared with the experimental data, suggest that DNA is a shape-persistent polyanion, and selectivity originates only from ligand preferences, whereas heparin is more flexible and adaptive, and as such, actively reinforces ligand preferences. As such, this study suggests that inherent differences between polyanions may underpin subtle binding selectivity differences, and that even simple electrostatic interfaces such as these can have a degree of tunability, which has implications for biological control and regulation on the nanoscale

Emergence of highly-ordered hierarchical nanoscale aggregates on electrostatic binding of self-assembled multivalent (SAMul) cationic micelles with polyanionic heparin

We report three surfactants, with cationic N,N-di-(3-aminopropyl)-N-methylamine (DAPMA) head groups and aliphatic chains connected via an amide linkage, and investigate their ability to self-assemble and bind polyanionic heparin – a process of potential clinical importance in coagulation control. Modifying the hydrophobic chain length tunes the self-assembly event, with C16-DAPMA having the lowest critical micelle concentration and also being the optimal heparin binder. Remarkably highly structured hierarchical nanoscale aggregates are formed on binding between the spherical cationic micelles and linear polyanionic heparin. C14-DAPMA and C16-DAPMA yield organized polycrystalline assemblies as observed by transmission electron microscopy (TEM), predicted in solution by mesoscale simulations and characterized by small-angle X-ray scattering (SAXS). This confirms that the micelles remain intact during the hierarchical assembly process and become packed in a face-centered cubic manner. The nanoscale assembly formed by C16-DAPMA showed the highest degree of order. Importantly, these studies indicate the impact of hydrophobic modification on self-assembly and heparin binding, demonstrate remarkably high stability of these self-assembled micelles even when forming strong electrostatic interactions with heparin, and provide structural insights into nanoscale hierarchical electrostatic assemblies

Spotting local environments in self-assembled monolayer-protected gold nanoparticles

Organic-inorganic (O-I) nanomaterials are versatile platforms for an incredible high number of applications, ranging from heterogeneous catalysis, molecular sensing, cell targeting, imaging, cancer diagnosis and therapy, just to name a few. Much of their potential stems from the unique control of organic environments around inorganic sites within a single O-I nanomaterial, which allows for new properties inaccessible using purely organic or inorganic materials. Structural and mechanistic characterization plays a key role in understanding and rationally designing such hybrid nanoconstructs. Here, we introduce a general methodology to identify and classify local (supra)molecular environments in an archetypal class of O-I nanomaterials, i.e. self-assembled monolayer-protected gold nanoparticles (SAM-AuNPs). By using an atomistic machine-learning guided workflow based on the Smooth Overlap of Atomic Positions (SOAP) descriptor, we analyze a collection of chemically different SAM-AuNPs, and detect and compare local environments in a way that is agnostic and automated, i.e. with no need of a-priori information and minimal user intervention. In addition, the computational results coupled with experimental electron spin resonance measurements prove that is possible to have more than one local environment inside SAMs, being thickness of the organic shell and solvation primary factors in determining number and nature of multiple co-existing environments. These indications are extended to complex mixed hydrophilic-hydrophobic SAMs. This work demonstrates that it is possible to spot out and compare local molecular environments in SAM-AuNPs exploiting atomistic machine-learning approaches, establishes ground rules to control them, and holds the potential for rational design of O-I nanomaterials instructed from data