In silico design, building and gas adsorption of nano-porous graphene scaffolds

Functionalized Amorphous Carbon Materials via Reactive Molecular Dynamics Simulations

We derive a database of atomistic structural models of amorphous carbon materials endowed with exohedral functional groups. We start from phases previously derived using the DynReaxMas method for reactive molecular dynamics simulations, which exhibit atomistic and medium-length-scale features in excellent agreement with available experimental data. Given a generic input structure/phase, we develop postprocessing simulation algorithms mimicking experimental preparation protocols aimed at: (1) "curing" the phase to decrease the defect concentration; (2) automatically selecting the most reactive carbon atoms via interaction with a probe molecular species, and (3) stabilizing the phase by saturating the valence of carbon atoms with single-bond functional groups. Although we focus on oxygen-bearing functionalities, they can be replaced with other monovalent groups, such as -H, -COOH, -CHO, so that the protocol is quite general. We finally classify reactive sites in terms of their location within the structural framework and coordination environment (edges, tunnels, rings, aromatic carbons becoming aliphatic) and try to single out descriptors that correlate with tendency to functionalization.

GeomBD3: Brownian Dynamics Simulation Software for Biological and Engineered Systems

GeomBD3 is a robust Brownian dynamics simulation package designed to easily handle natural or engineered systems in diverse environments and arrangements. The software package described herein allows users to design, execute, and analyze BD simulations. The simulations use all-atom, rigid molecular models that diffuse according to overdamped Langevin dynamics and interact through electrostatic, Lennard-Jones, and ligand desolvation potentials. The program automatically calculates molecular association rates, surface residence times, and association statistics for any number of user-defined association criteria. Users can also extract molecular association pathways, diffusion coefficients, intermolecular interaction energies, intermolecular contact probability maps, and more using the provided supplementary analysis scripts. We detail the use of the package from start to finish and apply it to a protein-ligand system and a large nucleic acid biosensor. GeomBD3 provides a versatile tool for researchers from various disciplines that can aid in rational design of engineered systems or play an explanatory role as a complement to experiments. GeomBD version 3 is available on our website at http://chemcha-gpu0.ucr.edu/geombd3/ and KBbox at https://kbbox.h-its.org/toolbox/methods/molecular-simulation/geombd/.

Covalent organic functionalization of graphene nanosheets and reduced graphene oxide via 1,3-dipolar cycloaddition of azomethine ylide

Organic functionalization of graphene is successfully performed via 1,3-dipolar cycloaddition of azomethine ylide in the liquid phase. The comparison between 1-methyl-2-pyrrolidinone and N,N-dimethylformamide as dispersant solvents, and between sonication and homogenization as dispersion techniques, proves N,N-dimethylformamide and homogenization as the most effective choice. The functionalization of graphene nanosheets and reduced graphene oxide is confirmed using different techniques. Among them, energy-dispersive X-ray spectroscopy allows to map the pyrrolidine ring of the azomethine ylide on the surface of functionalized graphene, while micro-Raman spectroscopy detects new features arising from the functionalization, which are described in agreement with the power spectrum obtained from ab initio molecular dynamics simulation. Moreover, X-ray photoemission spectroscopy of functionalized graphene allows the quantitative elemental analysis and the estimation of the surface coverage, showing a higher degree of functionalization for reduced graphene oxide. This more reactive behavior originates from the localization of partial charges on its surface due to the presence of oxygen defects, as shown by the simulation of the electrostatic features. Functionalization of graphene using 1,3-dipolar cycloaddition is shown to be a significant step towards the controlled synthesis of graphene-based complex structures and devices at the nanoscale.

Diverse Phases of Carbonaceous Materials from Stochastic Simulations

Amorphous carbon systems are emerging to have unparalleled properties at multiple length scales, making them the preferred choice for creating advanced materials in many sectors, but the lack of long-range order makes it difficult to establish structure/property relationships. We propose an original computational approach to predict the morphology of carbonaceous materials for arbitrary densities that we apply here to graphitic phases at low densities from 1.15 to 0.16 g/cm³, including glassy carbon. This approach, dynamic reactive massaging of the potential energy surface (DynReaxMas), uses the ReaxFF reactive force field in a simulation protocol that combines potential energy surface (PES) transformations with global optimization within a multidescriptor representation. DynReaxMas enables the simulation of materials synthesis at temperatures close to experiment to correctly capture the interplay of activated vs entropic processes and the resulting phase morphology. We then show that DynReaxMas efficiently and semiautomatically produces atomistic configurations that span wide relevant regions of the PES at modest computational costs. Indeed, we find a variety of distinct phases at the same density, and we illustrate the evolution of competing phases as a function of density ranging from uniform vs bimodal distributions of pore sizes at higher and intermediate density (1.15 g/cm³ and 0.50 g/cm³) to agglomerated vs sparse morphologies, further partitioned into boxed vs hollow fibrillar morphologies, at lower density (0.16 g/cm³). Our observations of diverse phases at the same density agree with experiment. Some of our identified phases provide descriptors consistent with available experimental data on local density, pore sizes, and HRTEM images, showing that DynReaxMas provides a systematic classification of the complex field of amorphous carbonaceous materials that can provide 3D structures to interpret experimental observations.