Reliable computational design of biological-inorganic materials to the large nanometer scale using Interface-FF

LUNAR: Automated Input Generation and Analysis for Reactive LAMMPS Simulations

Generating simulation-ready molecular models for the LAMMPS molecular dynamics (MD) simulation software package is a difficult task and impedes the more widespread and efficient use of MD in materials design and development. Fixed-bond force fields generally require manual assignment of atom types, bonded interactions, charges, and simulation domain sizes. A new LAMMPS pre- and postprocessing toolkit (LUNAR) is presented that efficiently builds molecular systems for LAMMPS. LUNAR automatically assigns atom types, generates bonded interactions, assigns charges, and provides initial configuration methods to generate large molecular systems. LUNAR can also incorporate chemical reactivity into simulations by facilitating the use of the REACTER protocol. Additionally, LUNAR provides postprocessing for free volume calculations, cure characterization calculations, and property predictions from LAMMPS thermodynamic outputs. LUNAR has been validated via building and simulation of pure epoxy and cyanate ester polymer systems with a comparison of the corresponding predicted structures and properties to benchmark values, including experimental results from the literature. LUNAR provides the tools for the computationally driven development of next-generation composite materials in the Integrated Computational Materials Engineering (ICME) and Materials Genome Initiative (MGI) frameworks. LUNAR is written in Python with the usage of NumPy and can be used via a graphical user interface, a command line interface, or an integrated design environment. LUNAR is freely available via GitHub.

Micromechanical Dilution of PLA/PETG-Glass/Iron Nanocomposites: A More Efficient Molecular Dynamics Approach

Polylactic acid (PLA) and poly(ethylene terephthalate glycol) (PETG) are popular thermoplastics used in additive manufacturing applications. The mechanical properties of PLA and PETG can be significantly improved by introducing fillers, such as glass and iron nanoparticles (NPs), into the polymer matrix. Molecular dynamics (MD) simulations with the reactive INTERFACE force field were used to predict the mechanical responses of neat PLA/PETG and PLA-glass/iron and PETG-glass/iron nanocomposites with relatively high loadings of glass/iron NPs. We found that the iron and glass NPs significantly increased the elastic moduli of the PLA matrix, while the PETG matrix exhibited modest increases in elastic moduli. This difference in reinforcement ability may be due to the slightly greater attraction between the glass/iron NP and PLA matrix. The NASA Multiscale Analysis Tool was used to predict the mechanical response across a range of volume percent glass/iron filler by using only the neat and highly loaded MD predictions as input. This provides a faster and more efficient approach than creating multiple MD models per volume percent per polymer/filler combination. To validate the micromechanics predictions, experimental samples incorporating hollow glass microspheres (MS) and carbonyl iron particles (CIP) into PLA/PETG were developed and tested for elastic modulus. The CIP produced a larger reinforcement in elastic modulus than the MS, with similar increases in elastic modulus between PLA/CIP and PETG/CIP at 7.77 vol % CIP. The micromechanics-based mechanical predictions compare excellently with the experimental values, validating the integrated micromechanical/MD simulation-based approach.

Structure-based screening of sp2 hybridized small donor bridges as donor: acceptor switches for optical and photovoltaic applications: DFT way

CONTEXT

This research aims to investigate the potential of pyrazine-based small donor moieties as donor-acceptor switches for optical and photovoltaic applications. The designed organic dyes have a high light harvesting efficiency (LHE) and can potentially generate significant electrical energy.

METHODS

The study focuses on understanding the structural and electronic properties of these dyes through the analysis of dihedral angles, bond lengths, and energies of frontier molecular orbitals The UV-Vis spectroscopy parameters of the designed organic dyes revealed their absorption characteristics, including transition energies, wavelengths (λmax), and oscillator strengths (f). The photovoltaic properties of the developed organic dyes show a range of values: a range of 0.95-0.99 for LHE and a range of 1.77-33.02 W for maximum power output (Pmax) with the highest value for dye DDP5. For their stabilization energies, their natural bond orbitals had values ranging from 0.56 to 128.48 kcal/mol, their E(j)E(i) values from 0.22 to 1.29 a.u, and their Fi,j values from 0.024 to 0.213 kcal/mol. Out of all dyes, the DDP5 produced highest push-pull effect and can be good choice for further studies. The design of these novel organic materials for effective and economical solar energy conversion will be aided by evaluating the potential of 5,10-diphenyl-5,10-dihydrophenazine as a donor moiety and determining the structure-property correlations controlling the photovoltaic performance of the compounds.

Exploration of Pull-Push Effect for Novel Photovoltaic Dyes with A-π-D Design: A DFT/TD-DFT Investigation

The π-rich versus π-poor units in 4,6-di(thiophen-2-yl)pyrimidine (DTB) alternating the π-backbone of solar cells dyes have been extended with a push-pull technique to lower their HOMO-LUMO energy gap and to increase Intramolecular Charge Transfer (ICT). Density functional theory was used to optimize the ground state molecular geometries of newly designed dyes (DTB1-DTB6). Time Dependent DFT (TD-DFT) was used to simulate the Uv-vis spectral values at the maximum absorbance values ranging between 481-535 nm. These values were red shifted from DTB value of experimental (333 nm) and theoretical (346 nm). however, their computed absorbance and fluorescence spectra revealed a bathochromic shift of them upon an increasing the solvent polarity. Different DFT functionals such as (B3LYP, CAM-B3LYP, B97XD, and APFD) were employed to choose their proper use Uv-visible analysis to reveal an unexpected coherence at the B3LYP level with experimental values. As a result, the B3LYP with most diffused basis sets of 6-31G + (d,p) were used for further calculations. The parameters of Global Chemical reactivities revealed that all the dyes had a softer nature with their softness value range of 0.27-0.41. their Ionization Potentials (IP) ranged between 6.21-8.10 eV to comply that the new dyes had good electron donating potentials. With a good electron injection potential of -1.47-1.74 eV, aluminum can be the best electrode, while Au is excellent towards a hole injection operation which had the potential range of 1.79-3.68 eV. For Natural Bond Orbital (NBO) assessment, (N14)LP → (F16-F28)π* with stabilization energy of 42.55 kcal/mol was noted for DTB4. Their Second order hyperpolarizability [Formula: see text] values as their Nonlinear Optical (NLO) response ranged between 59.16-232.11 debye-angstrom^-1 which were almost 6 times higher than the reference DTB (8.47D). The NLO attributes has also shown that a dyes with its small bandgap was related with higher hyperpolarizability values. Because of the decreased reorganization frequencies, newly discovered derivatives with electron transfer qualities might be comparable to or equivalent to those of commonly used electron transmission materials.

Prediction of the Interfacial Properties of High-Performance Polymers and Flattened CNT-Reinforced Composites Using Molecular Dynamics

The next generation of ultrahigh-strength composites for structural components of vehicles for manned missions to deep space will likely incorporate flattened carbon nanotubes (flCNTs). With a wide range of high-performance polymers to choose from as the matrix component, efficient and accurate computational modeling can be used to efficiently downselect compatible resins and provide critical physical insight into the flCNT/polymer interface. In this study, molecular dynamics simulation is used to predict the interaction energy, frictional sliding resistance, and mechanical binding of flCNT/polymer interfaces for epoxy, bismaleimide (BMI), and benzoxazine high-performance resins. The results indicate that BMI has a stronger interfacial interaction and transverse tension binding with flCNT interfaces, while benzoxazine demonstrates the strongest levels of interfacial friction resistance.

Binding mechanism and binding free energy of amino acids and citrate to hydroxyapatite surfaces as a function of crystallographic facet, pH, and electrolytes

Hydroxyapatite (HAP) is the major mineral phase in bone and teeth. The interaction of individual amino acids and citrate ions with different crystallographic HAP surfaces has remained uncertain for decades, creating a knowledge gap to rationally design interactions with peptides, proteins, and drugs. In this contribution, we quantify the binding mechanisms and binding free energies of the 20 end-capped natural amino acids and citrate ions on the basal (001) and prismatic (010)/(020) planes of hydroxyapatite at pH values of 7 and 5 for the first time at the molecular scale. We utilized over 1500 steered molecular dynamics simulations with highly accurate potentials that reproduce surface and hydration energies of (hkl) hydroxyapatite surfaces at different pH values. Charged residues demonstrate a much higher affinity to HAP than charge-neutral species due to the formation of superficial ion pairs and ease of penetration into layers of water molecules on the mineral surface. Binding free energies range from 0 to -60 kJ/mol and were determined with ∼ 10% uncertainty. The highest affinity was found for citrate, followed by Asp(-) and Glu(-), and followed after a gap by Arg(+), Lys(+), as well as by His(+) at pH 5. The (hkl)-specific area density of calcium ions, the protonation state of phosphate ions, and subsurface directional order of the ions in HAP lead to surface-specific binding patterns. Amino acids without ionic side groups exhibit weak binding, between -3 and 0 kJ/mol, due to difficulties to penetrate the first layer of water molecules on the apatite surfaces. We explain recognition processes that remained elusive in experiments, in prior simulations, discuss agreement with available data, and reconcile conflicting interpretations. The findings can serve as useful input for the design of peptides, proteins, and drug molecules for the modification of bone and teeth-related materials, as well as control of apatite mineralization.

Wetting Simulations of High-Performance Polymer Resins on Carbon Surfaces as a Function of Temperature Using Molecular Dynamics

Resin/reinforcement wetting is a key parameter in the manufacturing of carbon nanotube (CNT)-based composite materials. Determining the contact angle between combinations of liquid resin and reinforcement surfaces is a common method for quantifying wettability. As experimental measurement of contact angle can be difficult when screening multiple high-performance resins with CNT materials such as CNT bundles or yarns, computational approaches are necessary to facilitate CNT composite material design. A molecular dynamics simulation method is developed to predict the contact angle of high-performance polymer resins on CNT surfaces dominated by aromatic carbon, aliphatic carbon, or a mixture thereof (amorphous carbon). Several resin systems are simulated and compared. The results indicate that the monomer chain length, chemical groups on the monomer, and simulation temperature have a significant impact on the predicted contact angle values on the CNT surface. Difunctional epoxy and cyanate ester resins show the overall highest levels of wettability, regardless of the aromatic/aliphatic nature of the CNT material surface. Tetrafunctional epoxy demonstrates excellent wettability on aliphatic-dominated surfaces at elevated temperatures. Bismaleimide and benzoxazine resins show intermediate levels of wetting, while typical molecular weights of polyether ether ketone demonstrate poor wetting on the CNT surfaces.

Synergistic Effect of Binary Surfactant Mixtures in Two-Phase and Three-Phase Systems

Cationic alkyltrimethylammonium bromides (C_nTAB, with n = 8, 12, 16, 18) and their mixtures with n-octanol as a nonionic surfactant were chosen as a model system to study the synergistic effect on foamability (two-phase system) and floatability (three-phase system) of quartz in the presence of binary mixtures of ionic/nonionic surfactants. The foam height of one-component solutions and binary mixtures and floatability of quartz particles were characterized as a function of the surfactant concentration and the number of carbons (n) in the alkyl chain of C_nTAB. The experimental results of foamability and floatability measurements in one-component and mixed solutions revealed the synergistic effect, causing a significant enhancement in the foam height and recovery of quartz. In the presence of n-octanol, the height of foam increased remarkably for all C_nTAB solutions studied, and this effect, whose magnitude depended on the C_nTAB hydrophobic tail length, could not be justified by a simple increase in total surfactant concentration. A similar picture was obtained in the case of flotation response. The mechanism of synergistic effect observed in mixed C_nTAB/n-octanol solutions was proposed. The discussion was supported by molecular dynamics simulations, and the probable mechanism responsible for synergism was discussed. In addition, an analysis allowing accurate determination of the concentration regimes, where the synergistic effect can be expected, was given. It was shown that for the two-phase system, the n-octanol molecule preadsorption at the liquid/gas interface causes an increase in C_nTAB adsorption coverage over the level expected from its equilibrium value in the one-component solution. In the case of the three-phase system, the synergistic effect was related to the ionic surfactants serving as an anchor layer for n-octanol, which, in water/n-octanol solution (one-component system), do not adsorb on the surface of quartz.

A molecular scale analysis of TEMPO-oxidation of native cellulose molecules

The native cellulose, through TEMPO (2,2,6,6-tetramethylpiperidine-1-oxyl radical)-mediated oxidation, can be converted into individual fibers. It has been observed that oxidized fibers disperse completely and individually in water. It is believed that electrostatic repulsive forces might be responsible for such observations. In order to study the TEMPO-oxidation of cellulose molecules, we used Density Functional Theory (DFT) calculations and Flory-Huggins theory combined with molecular dynamics (MD). The surface electrostatic potential in native cellulose and TEMPO-oxidized cellulose were calculated using DFT calculations. We found that TEMPO-oxidized cellulose accommodates a threefold screw conformation where the negatively charged (–COO–) functional groups are pointed away from the surface in all spatial directions. This spatial orientation causes that TEMPO-oxidized cellulose molecules repulse each other due to strong negatively charged surface. At the same time, the spatial orientation increases the hydrophilicity in TEMPO-oxidized cellulose molecules. These observations explain the improved dispersion in water and separability of TEMPO-oxidized cellulose molecules. We obtained large and positive Flory–Huggins interaction parameters for TEMPO-oxidized cellulose molecules indicating their higher dispersion once in water.

Interpretable molecular models for molybdenum disulfide and insight into selective peptide recognition

Molybdenum disulfide (MoS2) is a layered material with outstanding electrical and optical properties. Numerous studies evaluate the performance in sensors, catalysts, batteries, and composites that can benefit from guidance by simulations in all-atom resolution. However, molecular simulations remain difficult due to lack of reliable models. We introduce an interpretable force field for MoS2 with record performance that reproduces structural, interfacial, and mechanical properties in 0.1% to 5% agreement with experiments. The model overcomes structural instability, deviations in interfacial and mechanical properties by several 100%, and empirical fitting protocols in earlier models. It is compatible with several force fields for molecular dynamics simulation, including the interface force field (IFF), CVFF, DREIDING, PCFF, COMPASS, CHARMM, AMBER, and OPLS-AA. The parameters capture polar covalent bonding, X-ray structure, cleavage energy, infrared spectra, bending stability, bulk modulus, Young's modulus, and contact angles with polar and nonpolar solvents. We utilized the models to uncover the binding mechanism of peptides to the MoS2 basal plane. The binding strength of several 7mer and 8mer peptides scales linearly with surface contact and replacement of surface-bound water molecules, and is tunable in a wide range from -86 to -6 kcal mol-1. The binding selectivity is multifactorial, including major contributions by van-der-Waals coordination and charge matching of certain side groups, orientation of hydrophilic side chains towards water, and conformation flexibility. We explain the relative attraction and role of the 20 amino acids using computational and experimental data. The force field can be used to screen and interpret the assembly of MoS2-based nanomaterials and electrolyte interfaces up to a billion atoms with high accuracy, including multiscale simulations from the quantum scale to the microscale.

Poly-sarcosine and Poly(Ethylene-Glycol) Interactions with Proteins Investigated Using Molecular Dynamics Simulations

Nanoparticles coated with hydrophilic polymers often show a reduction in unspecific interactions with the biological environment, which improves their biocompatibility. The molecular determinants of this reduction are not very well understood yet, and their knowledge may help improving nanoparticle design. Here we address, using molecular dynamics simulations, the interactions of human serum albumin, the most abundant serum protein, with two promising hydrophilic polymers used for the coating of therapeutic nanoparticles, poly(ethylene-glycol) and poly-sarcosine. By simulating the protein immersed in a polymer-water mixture, we show that the two polymers have a very similar affinity for the protein surface, both in terms of the amount of polymer adsorbed and also in terms of the type of amino acids mainly involved in the interactions. We further analyze the kinetics of adsorption and how it affects the polymer conformations. Minor differences between the polymers are observed in the thickness of the adsorption layer, that are related to the different degree of flexibility of the two molecules. In comparison poly-alanine, an isomer of poly-sarcosine known to self-aggregate and induce protein aggregation, shows a significantly larger affinity for the protein surface than PEG and PSar, which we show to be related not to a different patterns of interactions with the protein surface, but to the different way the polymer interacts with water.

Prediction of Hydrophobic Reagent for Flotation Process Using Molecular Modeling

The interaction or nonbonded energies of base organic ions and water molecules during the flotation process of minerals have important meanings for organizing hydrophobic and stable collectors. Furthermore, the interaction, cross-term, and valence energies of optimized structures are important for understanding the properties and structures of selective collectors. The simulation of pure scheelite mineral (PSM) surfaces with four different negative ions, using an adsorption locator module is demonstrated. The interaction energies for base organic ions and water molecules were resolved and detected by shaping the best hydrophobic interaction and the most stable suspension over the PSM surface (112) and (101). The adsorption locator results for base organic ions and water molecules on PSM surfaces (112) and (101) using buffer width 0.5 Å and temperature range from 318.15 to 283.15 K confirmed the results obtain from Forcite calculations. The results have demonstrated that the possibilities of using consistent valence force field implemented by Forcite and adsorption locator modules in the selection of flotation reagents are cost saving. Furthermore, hydrophobicity of the main negative ions in soaps were solved by the simulation methods and results are in a good agreement with the experimental methods that proved that mustard soap is more selective on the mineral surfaces than sunflower soap when used as a collector. Increasing the molecular weight of negative ions increases the interaction energy between base collector ions and PSM surfaces (112) and (101) significantly.

Carbon Nanotube Dispersion in Solvents and Polymer Solutions: Mechanisms, Assembly, and Preferences

Debundling and dispersion of carbon nanotubes (CNTs) in polymer solutions play a major role in the preparation of carbon nanofibers due to early effects on interfacial ordering and mechanical properties. A roadblock toward ultrastrong fibers is the difficulty to achieve homogeneous dispersions of CNTs in polyacrylonitrile (PAN) and poly(methyl methacrylate) (PMMA) precursor solutions in solvents such as dimethyl sulfoxide (DMSO), N,N-dimethylacetamide (DMAc), and N,N-dimethylformamide (DMF). In this contribution, molecular dynamics simulations with accurate interatomic potentials for graphitic materials that include virtual π electrons are reported to analyze the interaction of pristine single wall CNTs with the solvents and polymer solutions at 25 °C. The results explain the barriers toward dispersion of SWCNTs and quantify CNT-solvent, polymer-solvent, as well as CNT-polymer interactions in atomic detail. Debundling of CNTs is overall endothermic and unfavorable with dispersion energies of +20 to +30 mJ/m² in the pure solvents, + 20 to +40 mJ/m² in PAN solutions, and +20 to +60 mJ/m² in PMMA solutions. Differences arise due to molecular geometry, polar, van der Waals, and CH-π interactions. Among the pure solvents, DMF restricts CNT dispersion less due to the planar geometry and stronger van der Waals interactions. PAN and PMMA interact favorably with the pure solvents with dissolution energies of -0.7 to -1.1 kcal per mole monomer and -1.5 to -2.2 kcal per mole monomer, respectively. Adsorption of PMMA onto CNTs is stronger than that of PAN in all solvents as the molecular geometry enables more van der Waals contacts between alkyl groups and the CNT surface. Polar side groups in both polymers prefer interactions with the polar solvents. Higher polymer concentrations in solution lead to polymer aggregation via alkyl groups and reduce adsorption onto CNTs. PAN and PMMA solutions in DMSO and dilute solutions in DMF support CNT dispersion more than other combinations whereby the polymers significantly adsorb onto CNTs in DMSO solution. The observations by molecular simulations are consistent with available experimental data and solubility parameters and aid in the design of carbon nanofibers. The methods can be applied to other multiphase graphitic materials.