Mesoscopic Modeling of Bio-Compatible PLGA Polymers with Coarse-Grained Molecular Dynamics Simulations.

A challenging topic in materials engineering is the development of numerical models that can accurately predict material properties with atomistic accuracy, matching the scale and level of detail achieved by experiments. In this regard, coarse-grained (CG) molecular dynamics (MD) simulations are a popular method for achieving this goal. Despite the efforts of the scientific community, a reliable CG model with quasi-atomistic accuracy has not yet been fully achieved for the design and prototyping of materials, especially polymers.

Anisotropic Electrostatic Interactions in Coarse-Grained Water Models to Enhance the Accuracy and Speed-Up Factor of Mesoscopic Simulations.

Water models with realistic physical-chemical properties are essential to study a variety of biomedical processes or engineering technologies involving molecules or nanomaterials. Atomistic models of water are constrained by the feasible computational capacity, but calibrated coarse-grained (CG) ones can go beyond these limits. Here, we compare three popular atomistic water models with their corresponding CG model built using finite-size particles such as ellipsoids.

Peptoids as a Chiral Stationary Phase for Liquid Chromatography: Insights from Molecular Dynamics Simulations.

Peptoids are peptide regioisomers with attractive structural tunability in terms of sequence and three-dimensional arrangement. Peptoids are foreseen to have a great potential for many diverse applications, including their utilization as a chiral stationary phase in chromatography. To achieve chiral recognition, a chiral side chain is required to allow specific interactions with a given enantiomer from a racemic mixture.

Moltemplate: A Tool for Coarse-Grained Modeling of Complex Biological Matter and Soft Condensed Matter Physics.

Coarse-grained models have long been considered indispensable tools in the investigation of biomolecular dynamics and assembly. However, the process of simulating such models is arduous because unconventional force fields and particle attributes are often needed, and some systems are not in thermal equilibrium. Although modern molecular dynamics programs are highly adaptable, software designed for preparing all-atom simulations typically makes restrictive assumptions about the nature of the particles and the forces acting on them.

Design Rules to Maximize Charge-Carrier Mobility along Conjugated Polymer Chains.

The emergence of polymeric materials displaying high charge-carrier mobility values despite poor interchain structural order has spawned a renewal of interest in the identification of structure-property relationships pertaining to the transport of charges along conjugated polymer chains and the subsequent design of optimized architectures. Here, we present the results of intrachain charge transport simulations obtained by applying a robust surface hopping algorithm to a phenomenological Hamiltonian parametrized against first-principles simulations. Conformational effects are shown to provide a clear signature in the temperature-dependent charge-carrier mobility that complies with recent experimental observations.

MOLC. A reversible coarse grained approach using anisotropic beads for the modelling of organic functional materials.

We describe the development and implementation of a coarse grained (CG) modelling approach where complex organic molecules, and particularly the π-conjugated ones often employed in organic electronics, are modelled in terms of connected sets of attractive-repulsive biaxial Gay-Berne ellipsoidal beads. The CG model is aimed at reproducing realistically large scale morphologies (e.g.

3D to 2D reorganization of silver-thiol nanostructures, triggered by solvent vapor annealing.

Metal-organic composites are of great interest for a wide range of applications. The control of their structure remains a challenge, one of the problems being a complex interplay of covalent and supramolecular interactions. This paper describes the self-assembly, thermal stability and phase transitions of ordered structures of silver atoms and thiol molecules spanning from the molecular to the mesoscopic scale.

Pentacene Crystal Growth on Silica and Layer-Dependent Step-Edge Barrier from Atomistic Simulations.

Understanding and controlling the growth of organic crystals deposited from the vapor phase is important for fundamental materials science and necessary for applications in pharmaceutical and organic electronics industries. Here, this process is studied for the paradigmatic case of pentacene on silica by means of a specifically tailored computational approach inspired by the experimental vapor deposition process. This scheme is able to reproduce the early stages of the thin-film formation, characterized by a quasi layer-by-layer growth, thus showcasing its potential as a tool complementary to experimental techniques for investigating organic crystals.

Predicting the Conditions for Homeotropic Anchoring of Liquid Crystals at a Soft Surface. 4-n-Pentyl-4'-cyanobiphenyl on Alkylsilane Self-Assembled Monolayers.

We have studied, using atomistic molecular dynamics simulations, the alignment of the nematic liquid-crystal 4-n-pentyl-4'-cyanobiphenyl (5CB) on self-assembled monolayers (SAMs) formed from octadecyl- and/or hexyltrichlorosilane (OTS and HTS) attached to glassy silica. We find a planar alignment on OTS at full coverage and an intermediate situation at partial OTS coverage because of the penetration of 5CB molecules into the monolayer, which also removes the tilt of the OTS SAM. Binary mixtures of HTS and OTS SAMs instead induce homeotropic (i.

Surface-Induced Phase of Tyrian Purple (6,6'-Dibromoindigo): Thin Film Formation and Stability.

The appearance of surface-induced phases of molecular crystals is a frequently observed phenomenon in organic electronics. However, despite their fundamental importance, the origin of such phases is not yet fully resolved. The organic molecule 6,6'-dibromoindigo (Tyrian purple) forms two polymorphs within thin films.

Direct On-Surface Patterning of a Crystalline Laminar Covalent Organic Framework Synthesized at Room Temperature.

We report herein an efficient, fast, and simple synthesis of an imine-based covalent organic framework (COF) at room temperature (hereafter, RT-COF-1). RT-COF-1 shows a layered hexagonal structure exhibiting channels, is robust, and is porous to N2 and CO2 . The room-temperature synthesis has enabled us to fabricate and position low-cost micro- and submicropatterns of RT-COF-1 on several surfaces, including solid SiO2 substrates and flexible acetate paper, by using lithographically controlled wetting and conventional ink-jet printing.

Polymorphism of dioctyl-terthiophene within thin films: The role of the first monolayer.

The origins of specific polymorphic phases within thin films are still not well understood. The polymorphism of the molecule dioctyl-terthiophene is investigated during the presence of a silicon-oxide surface during the crystallisation process. It is found that a monolayer of molecules forms two-dimensional crystals on the surface.

Multiscale modeling of the electrostatic impact of self-assembled monolayers used as gate dielectric treatment in organic thin-film transistors.

This study sheds light on the microscopic mechanisms by which self-assembled monolayers (SAMs) determine the onset voltage in organic thin-film transistors (OTFTs). Experiments and modeling are combined to investigate the self-assembly and electrostatic interaction processes in prototypical OTFT structures (SiO2/SAM/pentacene), where alkylated and fluoroalkylated silane SAMs are compared. The results highlight the coverage-dependent impact of the SAM on the density of semiconductor states and enable the rationalization and the control of the OTFT characteristics.

Time-resolved, in situ DRIFTS/EDE/MS studies on alumina-supported rhodium catalysts: effects of ceriation and zirconiation on rhodium-CO interactions.

The effects of ceria and zirconia on the structure-function properties of supported rhodium catalysts (1.6 and 4 wt % Rh/γ-Al2O3) during CO exposure are described. Ceria and zirconia are introduced through two preparation methods: 1) ceria is deposited on γ-Al2O3 from [Ce(acac)3] and rhodium metal is subsequently added, and 2) through the controlled surface modification (CSM) technique, which involves the decomposition of [M(acac)x] (M=Ce, x=3; M=Zr, x=4) on Rh/γ-Al2O3.

Charge dissociation at interfaces between discotic liquid crystals: the surprising role of column mismatch.

The semiconducting and self-assembling properties of columnar discotic liquid crystals have stimulated intense research toward their application in organic solar cells, although with a rather disappointing outcome to date in terms of efficiencies. These failures call for a rational strategy to choose those molecular design features (e.g.

Supramolecular organization of functional organic materials in the bulk and at organic/organic interfaces: a modeling and computer simulation approach.

The molecular organization of functional organic materials is one of the research areas where the combination of theoretical modeling and experimental determinations is most fruitful. Here we present a brief summary of the simulation approaches used to investigate the inner structure of organic materials with semiconducting behavior, paying special attention to applications in organic photovoltaics and clarifying the often obscure jargon hindering the access of newcomers to the literature of the field. Special attention is paid to the choice of the computational "engine" (Monte Carlo or Molecular Dynamics) used to generate equilibrium configurations of the molecular system under investigation and, more importantly, to the choice of the chemical details in describing the molecular interactions.

Predicting the anchoring of liquid crystals at a solid surface: 5-cyanobiphenyl on cristobalite and glassy silica surfaces of increasing roughness.

We employ atomistic molecular dynamics simulations to predict the alignment and anchoring strength of a typical nematic liquid crystal, 4-n-pentyl-4'-cyano biphenyl (5CB), on different forms of silica. In particular, we study a thin (~20 nm) film of 5CB supported on surfaces of crystalline (cristobalite) and amorphous silica of different roughness. We find that the orientational order at the surface and the anchoring strength depend on the morphology of the silica surface and its roughness.

Development and testing of a compact basis set for use in effective core potential calculations on rhodium complexes.

We present a set of effective core potential (ECP) basis sets for rhodium atoms which are of reasonable size for use in electronic structure calculations. In these ECP basis sets, the Los Alamos ECP is used to simulate the effect of the core electrons while an optimized set of Gaussian functions, which includes polarization and diffuse functions, is used to describe the valence electrons. These basis sets were optimized to reproduce the ionization energy and electron affinity of atomic rhodium.

X-ray absorption spectroscopy of hemes and hemeproteins in solution: multiple scattering analysis.

A full quantitative analysis of Fe K-edge X-ray absorption spectra has been performed for hemes in two porphynato complexes, that is, iron(III) tetraphenylporphyrin chloride (Fe(III)TPPCl) and iron(III) tetraphenylporphyrin bis(imidazole) (Fe(III)TPP(Imid)2), in two protein complexes whose X-ray structure is known at atomic resolution (1.0 A), that is, ferrous deoxy-myoglobin (Fe(II)Mb) and ferric aquo-myoglobin (Fe(III)MbH2O), and in ferric cyano-myoglobin (Fe(III)MbCN), whose X-ray structure is known at lower resolution (1.4 A).

Detection of second hydration shells in ionic solutions by XANES: computed spectra for Ni2+ in water based on molecular dynamics.

A general procedure to compute X-ray absorption near-edge structure (XANES) spectra within multiple-scattering theory starting from molecular dynamics (MD) structural data has been developed and applied to the study of a Ni(2+) aqueous solution. This method allows one to perform a quantitative analysis of the XANES spectra of disordered systems using a proper description of the thermal and structural fluctuations. The XANES spectrum of Ni(2+) in aqueous solution has been calculated using the structural information obtained from the MD simulations without carrying out any minimization in the structural parameter space.

Quantitative analysis of XANES spectra of disordered systems based on molecular dynamics.

A general procedure which computes X-ray absorption near-edge structure (XANES) spectra starting from the individual configurations obtained from molecular dynamics (MD) simulations has been developed. This method allows one to perform a quantitative analysis of the XANES spectra of disordered systems and to estimate the effect of disorder on the low-energy region of the X-ray absorption spectra. As a test case, a Ni2+ aqueous solution has been investigated.