AmberTools.

AmberTools is a free and open-source collection of programs used to set up, run, and analyze molecular simulations. The newer features contained within AmberTools23 are briefly described in this Application note.

JAX-ReaxFF: A Gradient-Based Framework for Fast Optimization of Reactive Force Fields.

The reactive force field (ReaxFF) model bridges the gap between traditional classical models and quantum mechanical (QM) models by incorporating dynamic bonding and polarizability. To achieve realistic simulations using ReaxFF, model parameters must be optimized against high fidelity training data which typically come from QM calculations. Existing parameter optimization methods for ReaxFF consist of black box techniques using genetic algorithms or Monte Carlo methods. Due to the stochastic behavior of these methods, the optimization process oftentimes requires millions of error evaluations for complex parameter fitting tasks, thereby significantly hampering the rapid development of high quality parameter sets. Rapid optimization of the parameters is essential for developing and refining Reax force fields because producing a force field which exhibits empirical accuracy in terms of dynamics typically requires multiple refinements to the training data as well as to the parameters under optimization. In this work, we present JAX-ReaxFF, a novel software tool that leverages modern machine learning infrastructure to enable fast optimization of ReaxFF parameters. By calculating gradients of the loss function using the JAX library, JAX-ReaxFF utilizes highly effective local optimization methods that are initiated from multiple guesses in the high dimensional optimization space to obtain high quality results. Leveraging the architectural portability of the JAX framework, JAX-ReaxFF can execute efficiently on multicore CPUs, graphics processing units (GPUs), or even tensor processing units (TPUs). As a result of using the gradient information and modern hardware accelerators, we are able to decrease ReaxFF parameter optimization time from days to mere minutes. Furthermore, the JAX-ReaxFF framework can also serve as a sandbox environment for domain scientists to explore customizing the ReaxFF functional form for more accurate modeling.

A Polarizable Cationic Dummy Metal Ion Model.

A novel locally polarizable multisite model based on the original cation dummy atom (CDA) model is described for molecular dynamics simulations of ions in condensed phases. Polarization effects are introduced by the electronegativity equalization model (EEM) method where charges on the metal ion and its dummy atoms can fluctuate to respond to the environment. This model includes explicit polarization and ion-induced interactions and can be coupled with nonpolarizable or polarizable water models, making it more transferable to simpler force fields. This approach allows us to enhance the original fixed charge CDA model where the charge distribution cannot adapt to the local solvent structure. To illustrate the new CDApol model, we examined properties of the Zn2+, Al3+, and Zr4+ ions in aqueous solution. The polarizable model and Lennard-Jones parameters were refined for octahedrally coordinated Zn2+, Al3+, and Zr4+ CDAs to reproduce thermodynamic and geometrical properties. Using this locally polarizable model, we were able to obtain the experimental hydration free energy, ion-oxygen distance, and coordination number coupled with the standard 12-6 Lennard-Jones model. This model can be used in myriad additional applications where local polarization and charge transfer is important.

ReaxFF/AMBER-A Framework for Hybrid Reactive/Nonreactive Force Field Molecular Dynamics Simulations.

Combined quantum mechanical/molecular mechanical (QM/MM) models using semiempirical and ab initio methods have been extensively reported on over the past few decades. These methods have been shown to be capable of providing unique insights into a range of problems, but they are still limited to relatively short time scales, especially QM/MM models using ab initio methods. An intermediate approach between a QM based model and classical mechanics could help fill this time-scale gap and facilitate the study of a range of interesting problems. Reactive force fields represent the intermediate approach explored in this paper. A widely used reactive model is ReaxFF, which has largely been applied to materials science problems and is generally used as a stand-alone (i.e., the full system is modeled using ReaxFF). We report a hybrid ReaxFF/AMBER molecular dynamics (MD) tool, which introduces ReaxFF capabilities to capture bond breaking and formation within the AMBER MD software package. This tool enables us to study local reactive events in large systems at a fraction of the computational costs of QM/MM models. We describe the implementation of ReaxFF/AMBER, validate this implementation using a benzene molecule solvated in water, and compare its performance against a range of similar approaches. To illustrate the predictive capabilities of ReaxFF/AMBER, we carried out a Claisen rearrangement study in aqueous solution. In a first for ReaxFF, we were able to use AMBER's potential of mean force (PMF) capabilities to perform a PMF study on this organic reaction. The ability to capture local reaction events in large systems using combined ReaxFF/AMBER opens up a range of problems that can be tackled using this model to address both chemical and biological processes.

Surface Curvature and Aminated Side-Chain Partitioning Affect Structure of Poly(oxonorbornenes) Attached to Planar Surfaces and Nanoparticles of Gold.

Cationic amphiphilic polymers are often used to coat nanoparticles as they increase chemical stability in solution and exhibit membrane disruption activities. Among these, poly(oxonorbornenes) (PONs) are tunable membrane disruptors. They can be constructed with either one amine-terminated side chain and one hydrophobic alkyl side chain (PON-50) or two amine-terminated side chains (PON-100) on each repeat unit and can then be conjugated to gold nanoparticles using O-(2-carboxyethyl)-O'-(2-mercaptoethyl) heptaethylene glycol (HEG) spacers. While the amine content and membrane disruption activity of PONs can be controlled, the detailed structural properties of PONs conjugated to gold nanoparticles remain less understood. To address this, we performed molecular dynamics simulations of PON-50 and PON-100 to determine the nonbonded energies of PON structures as a function of amine composition. We found increasing energetic stabilization with decreasing amine composition. These results were consistent with experimental observations obtained with X-ray photoelectron spectroscopy (XPS) in which PON-100 was found to have the lowest conjugation efficiency to gold surfaces out of a range of PON amination ratios. Computationally obtained energetics suggest that replacing the aliphatic amine groups with aromatic amine groups can reverse this behavior and lead to more stable PON structures with increasing amine content. We also found that the curvature of the gold nanoparticle surface affects interactions between the surface and the amine groups of PON-50. Increasing curvature decreased these interactions, resulting in a smaller effective footprint of the HEG-PON-50 structure.

Ionic Environment Affects Bacterial Lipopolysaccharide Packing and Function.

The interaction of lipopolysaccharides (LPS) with metal cations strongly affects the stability and function of the Gram-negative bacterial outer membrane. The sensitivity of deep rough (Re) LPS packing and function to the ionic environment, as affected by cation valency and ionic radius, has been determined using molecular dynamics simulations and Langmuir balance experiments. The degree of LPS aggregation within the LPS models in the presence of different cations is assessed by measuring the effective mean molecular area (Âm) of each LPS molecule projected onto the interfacial plane at the end of the equilibration. These results are compared to the LPS mean molecular area from experimental measurements in which the LPS monolayers are assembled at the air-water interface using a Langmuir film balance. We found that packing of the LPS arrays is sensitive to the ionic radius and ion valency of the cations present in solution during LPS array packing. Using enhanced sampling of the free energy for the intercalation of oligo(allylamine HCl) (OAH) into deep rough Salmonella enterica LPS bilayers, we obtained the affinity of the core section of LPS to OAH as a function of the nature of the metal cations present in solution. We found that packing of the solvated LPS bilayer models is sensitive to ionic radius and ion valency of the neutralizing cations. This further suggests that ion bridging and steric barriers rather than charge shielding are important factors in mitigating ligand intercalation under conditions with low ionic concentrations.

Using an environmentally-relevant panel of Gram-negative bacteria to assess the toxicity of polyallylamine hydrochloride-wrapped gold nanoparticles.

We aim to establish the effect of environmental diversity in evaluating nanotoxicity to bacteria. We assessed the toxicity of 4 nm polyallylamine hydrochloride-wrapped gold nanoparticles to a panel of bacteria from diverse environmental niches. The bacteria experienced a range of toxicities as evidenced by the different minimum bactericidal concentrations determined; the sensitivities of the bacteria was A. vinelandii = P. aeruginosa > S. oneidensis MR-4 > A. baylyi > S. oneidensis MR-1. Interactions between gold nanoparticles and molecular components of the cell wall were investigated by TEM, flow cytometry, and computational modeling. Binding results showed a general trend that bacteria with smooth LPS bind more PAH AuNPs than bacteria with rough LPS. Computational models reveal that PAH migrates to phosphate groups in the core of the LPS structure. Overall, our results demonstrate that simple interactions between nanoparticles and the bacterial cell wall cannot fully account for observed trends in toxicity, which points to the importance of establishing more comprehensive approaches for modeling environmental nanotoxicity.

ReaxFF Reactive Force-Field Study of Molybdenum Disulfide (MoS2).

Two-dimensional layers of molybdenum disulfide, MoS2, have been recognized as promising materials for nanoelectronics due to their exceptional electronic and optical properties. Here we develop a new ReaxFF reactive potential that can accurately describe the thermodynamic and structural properties of MoS2 sheets, guided by extensive density functional theory simulations. This potential is then applied to the formation energies of five different types of vacancies, various vacancy migration barriers, and the transition barrier between the semiconducting 2H and metallic 1T phases. The energetics of ripplocations, a recently observed defect in van der Waals layers, is examined, and the interplay between these defects and sulfur vacancies is studied. As strain engineering of MoS2 sheets is an effective way to manipulate the sheets' electronic and optical properties, the new ReaxFF description can provide valuable insights into morphological changes that occur under various loading conditions and defect distributions, thus allowing one to tailor the electronic properties of these 2D crystals.

Atomistic-Scale Simulations of Defect Formation in Graphene under Noble Gas Ion Irradiation.

Despite the frequent use of noble gas ion irradiation of graphene, the atomistic-scale details, including the effects of dose, energy, and ion bombardment species on defect formation, and the associated dynamic processes involved in the irradiations and subsequent relaxation have not yet been thoroughly studied. Here, we simulated the irradiation of graphene with noble gas ions and the subsequent effects of annealing. Lattice defects, including nanopores, were generated after the annealing of the irradiated graphene, which was the result of structural relaxation that allowed the vacancy-type defects to coalesce into a larger defect. Larger nanopores were generated by irradiation with a series of heavier noble gas ions, due to a larger collision cross section that led to more detrimental effects in the graphene, and by a higher ion dose that increased the chance of displacing the carbon atoms from graphene. Overall trends in the evolution of defects with respect to a dose, as well as the defect characteristics, were in good agreement with experimental results. Additionally, the statistics in the defect types generated by different irradiating ions suggested that the most frequently observed defect types were Stone-Thrower-Wales (STW) defects for He(+) irradiation and monovacancy (MV) defects for all other ion irradiations.