Predicting Adsorption Affinities of Small Molecules on Carbon Nanotubes Using Molecular Dynamics Simulation

Abstract

Computational techniques have the potential to accelerate the design and optimization of nanomaterials for applications such as drug delivery and contaminant removal; however, the success of such techniques requires reliable models of nanomaterial surfaces as well as accurate descriptions of their interactions with relevant solutes. In the present work, we evaluate the ability of selected models of naked and hydroxylated carbon nanotubes to predict adsorption equilibrium constants for about 30 small aromatic compounds with a variety of functional groups. The equilibrium constants determined using molecular dynamics coupled with free-energy calculation techniques are directly compared to those derived from experimental measurements. The calculations are highly predictive of the relative adsorption affinities of the compounds, with excellent correlation (r ≥ 0.9) between calculated and measured values of the logarithm of the adsorption equilibrium constant. Moreover, the agreement in absolute terms is also reasonable, with average errors of less than one decade. We also explore possible effects of surface loading, although we demonstrate that they are negligible for the experimental conditions considered. Given the degree of reliability demonstrated, we move on to employing the in silico techniques in the design of nanomaterials, using the optimization of adsorption affinity for the herbacide atrazine as an example. Our simulations suggest that, compared to other modifications of graphenic carbon, polyvinylpyrrolidone conjugation gives the highest affinity for atrazine-substantially greater than that of graphenic carbon alone-and may be useful as a nanomaterial for delivery or sequestration of atrazine.

Biological and environmental surface interactions of nanomaterials: characterization, modeling, and prediction

“…Comer et al calculated the binding energy profile of the binding of a few organic molecules, that were used in BSAI studies (described in the next section), onto graphenic surfaces. Subsequently, equilibrium binding coefficients were calculated and compared to experimental results (Figure (b)) . Such comparisons provide solid grounds for the deduction of exact chemical composition and spatial arrangements of the surface ligands.…”

“…(d) Comparison of the logarithm of the adsorption equilibrium constant measured in experiment and the same quantity calculated in simulation for all 29 adsorbates. The full names of the chemicals can be found in the referenced publication . (Reprinted with permission from Ref .…”

Understanding Noncovalent Interactions of Small Molecules with Carbon Nanotubes

“…Alternatively,c lassical molecular dynamics simulations with atomistic models and explicit solvent have arisen as ap romising approach to elucidating interactionsb etween commonn anomaterials and organic molecules. [42] In this work, we report on an in-depth investigation of the supramoleculara ssembly of small-molecule derivativesw ith insoluble carbon-based nanotubes governed by noncovalent interactions through ac ombined experimental andc omputational quantitative approach. [40] Likewise, Ulissi et al [41] have reported the free energies of adsorption of more than 50 compoundso nag raphenic surface; these show ag ood correlation with the predictions of structure-activity models.…”

Interaction processes of ciprofloxacin with graphene oxide and reduced graphene oxide in the presence of montmorillonite in simulated gastrointestinal fluids

“…Given its hydrophobicity and sp 2 carbon atom structure, graphene can interact with aromatic organic chemicals through hydrophobic and π–π interactions. Owing to its excellent interaction properties, graphene offers several opportunities and innovative solutions in various applications, such as contaminant removal and drug delivery 5–7 . However, graphene nanomaterials could be released into aquatic environments during the manufacture, use, and disposal of graphene-enabled products 8, 9 .…”