Simulation optimization of spherical non-polar guest recognition by deep-cavity cavitands

An Affordable Topography-Based Protocol for Assigning a Residue's Character on a Hydropathy (PARCH) Scale

The hydropathy of proteins or quantitative assessment of protein-water interactions has been a topic of interest for decades. Most hydropathy scales use a residue-based or atom-based approach to assign fixed numerical values to the 20 amino acids and categorize them as hydrophilic, hydroneutral, or hydrophobic. These scales overlook the protein's nanoscale topography, such as bumps, crevices, cavities, clefts, pockets, and channels, in calculating the hydropathy of the residues. Some recent studies have included protein topography in determining hydrophobic patches on protein surfaces, but these methods do not provide a hydropathy scale. To overcome the limitations in the existing methods, we have developed a Protocol for Assigning a Residue's Character on the Hydropathy (PARCH) scale that adopts a holistic approach to assigning the hydropathy of a residue. The parch scale evaluates the collective response of the water molecules in the protein's first hydration shell to increasing temperatures. We performed the parch analysis of a set of well-studied proteins that include the following─enzymes, immune proteins, and integral membrane proteins, as well as fungal and virus capsid proteins. Since the parch scale evaluates every residue based on its location, a residue may have very different parch values inside a crevice versus a surface bump. Thus, a residue can have a range of parch values (or hydropathies) dictated by the local geometry. The parch scale calculations are computationally inexpensive and can compare hydropathies of different proteins. The parch analysis can affordably and reliably aid in designing nanostructured surfaces, identifying hydrophilic and hydrophobic patches, and drug discovery.

Cavitand Complexes in Aqueous Solution: Collaborative Experimental and Computational Studies of the Wetting, Assembly, and Function of Nanoscopic Bowls in Water

Water is the dominant liquid on Earth. Despite this, the main focus of supramolecular chemistry research has been on binding and assembly events in organic solvents. This arose because it is more straightforward to synthesize organic-media-soluble hosts and because of the relative simplicity of organic solvents compared to water. Nature, however, relies on water as a solvent, and spurred by this fact, supramolecular chemists have recently been making forays into the aqueous domain to understand water-mediated non-covalent interactions. These studies can benefit from the substantial understanding of the hydrophobic effect and electrostatic interactions developed by physical chemists. Nearly 20 years ago, the Gibb group first synthesized a class of water-soluble host molecules, the deep-cavity cavitands, that possess non-polar pockets that readily bind non-polar moieties in aqueous solution and are capable of assembling into a wide range of complexes with distinct stoichiometries. As such, these amphipathic host species are ideal platforms for studying the role of negatively curved features on guest complexation and the structural requirements for guided assembly processes driven by the hydrophobic effect. Here we review the collaborative experimental and computational investigations between Gibb and Ashbaugh over the past 10 years exploring questions including the following: How does water wet/solvate the non-polar surfaces of non-polar pockets? How does this wetting control the binding of non-polar guests? How does wetting affect the binding of anionic species? How does the nature and size of a guest size impact the assembly of cavitand hosts into multimeric capsular complexes? What are the conformational motifs of guests packed within the confines of capsular complexes? How might the electrostatic environment engendered by hosts impact the properties and reactivity of internalized guests?

Molecular Dynamics Simulations of Water-Mediated Cholesterol Capture within an Open-Ended Single-Walled Carbon Nanotube

The excess concentration of cholesterol in the bloodstream can be brought down to a safer level by utilizing a potential cholesterol-binding agent such as a carbon nanotube (CNT). Here, we have probed solvent-mediated interactions between cholesterol and CNT by performing molecular dynamics simulations and potential-of-mean force (PMF) calculations. Simulations predict favorable interactions between water-mediated cholesterol and CNT owing to strong mutual interactions between them, whereas water plays an opposing role in the association. The breakdown of PMF into its enthalpic and entropic contributions indicates that contrary to traditional entropy-driven hydrophobic association, the cholesterol encapsulation within a CNT is primarily driven by enthalpy.

Water-mediated curvature change in graphene by single-walled carbon nanotubes

Novel nanostructured materials possessing new architectural segments can be synthesized using various combinations of graphene and carbon nanotubes (CNT) that can result in the generation of enhanced physico-chemical properties within the hybrids. Comprehending the various physical processes involved in the creation of these new segments is crucial for designing an optimized nanomaterial for a specific purpose. In this paper we report induced folding in a graphene sheet resulting from the physical interactions between water-mediated graphene and a CNT. Owing to robust binding interactions between the CNT and a compatible graphene sheet, the latter forms a second domed layer around the former culminating in a structure equivalent to a double-walled CNT. The induced curvature change in graphene by CNT was found to have a strong dependence upon their relative physical dimensions. For example, CNT possessing extremely small diameters are unable to induce any significant curvature changes in longer graphene sheets. The potential-of-mean force (PMF) between our reference graphene and CNT in water suggests a favorable binding interaction of -14.5 kcal mol-1. The breakdown of the PMF into direct graphene-nanotube interactions and water-mediated interactions reveals a huge reduction in the strongly attractive binding interactions between graphene and CNT by the water molecules.

The Thermodynamics of Anion Complexation to Nonpolar Pockets

The interactions between nonpolar surfaces and polarizable anions lie in a gray area between the hydrophobic and Hofmeister effects. To assess the affinity of these interactions, NMR and ITC were used to probe the thermodynamics of eight anions binding to four different hosts whose pockets each consist primarily of hydrocarbon. Two classes of host were examined: cavitands and cyclodextrins. For all hosts, anion affinity was found to follow the Hofmeister series, with associations ranging from 1.6-5.7 kcal mol-1. Despite the fact that cavitand hosts 1 and 2 possess intrinsic negative electrostatic fields, it was determined that these more enveloping hosts generally bound anions more strongly. The observation that the four hosts each possess specific anion affinities that cannot be readily explained by their structures, points to the importance of counter cations and the solvation of the "empty" hosts, free guests, and host-guest complexes, in defining the affinity.

Guest Controlled Nonmonotonic Deep Cavity Cavitand Assembly State Switching

Octa-acid (OA) and tetra-endo-methyl octa-acid (TEMOA) are water-soluble, deep-cavity cavitands with nanometer-sized nonpolar pockets that readily bind complementary guests, such as n-alkanes. Experimentally, OA exhibits a progression of 1:1 to 2:2 to 2:1 host/guest complexes (X:Y where X is the number of hosts and Y is the number of guests) with increasing alkane chain length from methane to tetradecane. Differing from OA only by the addition of four methyl groups ringing the portal of the pocket, TEMOA exhibits a nonmonotonic progression of assembly states from 1:1 to 2:2 to 1:1 to 2:1 with increasing guest length. Here we present a systematic molecular simulation study to parse the molecular and thermodynamic determinants that distinguish the succession of assembly stoichiometries observed for these similar hosts. Potentials of mean force between hosts and guests, determined via umbrella sampling, are used to characterize association free energies. These free energies are subsequently used in a reaction network model to predict the equilibrium distributions of assemblies. Our models accurately reproduce the experimentally observed trends, showing that TEMOA's endo-methyl units constrict the opening of the binding pocket, limiting the conformations available to bound guests and disrupting the balance between monomeric complexes and dimeric capsules. The success of our simulations demonstrate their utility at interpreting the impact of even simple chemical modifications on supramolecular assembly and highlight their potential to aid bottom-up design.

Succession of Alkane Conformational Motifs Bound within Hydrophobic Supramolecular Capsular Assemblies

n-Alkane encapsulation experiments within dimeric octa-acid cavitand capsules in water reveal a succession of packing motifs from extended, to helical, to hairpin, to spinning top structures with increasing chain length. Here, we report a molecular simulation study of alkane conformational preferences within these host-guest assemblies to uncover the factors stabilizing distinct conformers. The simulated alkane conformers follow the trends inferred from ¹H NMR experiments, while guest proton chemical shifts evaluated from Gauge Invariant Atomic Orbital calculations provide further evidence our simulations capture guest packing within these assemblies. Analysis of chain length and dihedral distributions indicates that packing under confinement to minimize nonpolar guest and host interior contact with water largely drives the transitions. Mean intramolecular distance maps and transfer free energy differences suggest the extended and helical motifs are members of a larger family of linear guest structures, for which the guest gauche population increases with increasing chain length to accommodate the chains within the complex. Breaks observed between the helical/hairpin and hairpin/spinning top motifs, on the other hand, indicate the hairpin and spinning top conformations are distinct from the linear family. Our results represent the first bridging of empirical and simulation data for flexible guests encapsulated within confined nanospaces, and constitute an effective strategy by which guest packing motifs within artificial or natural compartments can be rationalized and/or predicted a priori.

Xe affinities of water-soluble cryptophanes and the role of confined water

Simulations provide molecular insight on the aqueous binding of Xe to cryptophanes.

Given their relevance to drug design and chemical sensing, host–guest interactions are of broad interest in molecular science. Natural and synthetic host molecules provide vehicles for understanding selective molecular recognition in aqueous solution. Here, cryptophane–Xe host–guest systems are considered in aqueous media as a model molecular system that also has important applications. ¹²⁹Xe–cryptophane systems can be used in the creation of biosensors and powerful contrast agents for magnetic resonance imaging applications. Detailed molecular information on the determinants of Xe affinity is difficult to obtain experimentally. Thus, molecular simulation and free energy perturbation methods were applied to estimate the affinities of Xe for six water-soluble cryptophanes. The calculated affinities correlated well with the previously measured experimental values. The simulations provided molecular insight on the differences in affinities and the roles of conformational fluctuations, solvent, and counter ions on Xe binding to these host molecules. Displacement of confined water from the host interior cavity is a key component of the binding equilibrium, and the average number of water molecules within the host cavity is correlated with the free energy of Xe binding to the different cryptophanes. The findings highlight roles for molecular simulation and design in modulating the relative strengths of host–guest and host–solvent interactions.