Unraveling Hydrophobic Interactions at the Molecular Scale Using Force Spectroscopy and Molecular Dynamics Simulations

Interactions between hydrophobic moieties steer ubiquitous processes in aqueous media, including the self-organization of biologic matter. Recent decades have seen tremendous progress in understanding these for macroscopic hydrophobic interfaces. Yet, it is still a challenge to experimentally measure hydrophobic interactions (HIs) at the single-molecule scale and thus to compare with theory. Here, we present a combined experimental-simulation approach to directly measure and quantify the sequence dependence and additivity of HIs in peptide systems at the single-molecule scale. We combine dynamic single-molecule force spectroscopy on model peptides with fully atomistic, both equilibrium and nonequilibrium, molecular dynamics (MD) simulations of the same systems. Specifically, we mutate a flexible (GS)₅ peptide scaffold with increasing numbers of hydrophobic leucine monomers and measure the peptides' desorption from hydrophobic self-assembled monolayer surfaces. Based on the analysis of nonequilibrium work-trajectories, we measure an interaction free energy that scales linearly with 3.0-3.4 k_BT per leucine. In good agreement, simulations indicate a similar trend with 2.1 k_BT per leucine, while also providing a detailed molecular view into HIs. This approach potentially provides a roadmap for directly extracting qualitative and quantitative single-molecule interactions at solid/liquid interfaces in a wide range of fields, including interactions at biointerfaces and adhesive interactions in industrial applications.

Ligand structure and mechanical properties of single-nanoparticle-thick membranes

The high mechanical stiffness of single-nanoparticle-thick membranes is believed to result from the local structure of ligand coatings that mediate interactions between nanoparticles. These ligand structures are not directly observable experimentally. We use molecular dynamics simulations to observe variations in ligand structure and simultaneously measure variations in membrane mechanical properties. We have shown previously that ligand end group has a large impact on ligand structure and membrane mechanical properties. Here we introduce and apply quantitative molecular structure measures to these membranes and extend analysis to multiple nanoparticle core sizes and ligand lengths. Simulations of nanoparticle membranes with a nanoparticle core diameter of 4 or 6 nm, a ligand length of 11 or 17 methylenes, and either carboxyl (COOH) or methyl (CH(3)) ligand end groups are presented. In carboxyl-terminated ligand systems, structure and interactions are dominated by an end-to-end orientation of ligands. In methyl-terminated ligand systems large ordered ligand structures form, but nanoparticle interactions are dominated by disordered, partially interdigitated ligands. Core size and ligand length also affect both ligand arrangement within the membrane and the membrane's macroscopic mechanical response, but are secondary to the role of the ligand end group. Moreover, the particular end group (COOH or CH(3)) alters the nature of how ligand length, in turn, affects the membrane properties. The effect of core size does not depend on the ligand end group, with larger cores always leading to stiffer membranes. Asymmetry in the stress and ligand density is observed in membranes during preparation at a water-vapor interface, with the stress asymmetry persisting in all membranes after drying.

Temperature effects on nanostructure and mechanical properties of single-nanoparticle thick membranes

The properties of mechanically stable single-nanoparticle (NP)-thick membranes have largely been studied at room temperature. How these membranes soften as nanoparticle ligands disorder with increasing temperature is unknown. Molecular dynamics simulations are used to probe the temperature dependence of the mechanical and nanostructural properties of nanoparticle membranes made of 6 nm diameter Au nanoparticles coated with dodecanethiol ligands and terminated with either methyl (CH₃) or carboxyl (COOH) terminal groups. For methyl-terminated ligands, interactions along the alkane chain provide mechanical stiffness, with a Young's modulus of 1.7 GPa at 300 K. For carboxyl-terminated chains, end-group interactions are significant, producing stiffer membranes at all temperatures, with a Young's modulus of 3.8 GPa at 300 K. For both end-group types, membrane stiffness is reduced to zero at about 400 K. Ligand structure and mechanical properties of membranes at 300 K that have been annealed at 400 K are comparable to samples that do not undergo thermal annealing.

Phthalocyaninato complexes with peripheral alkylthio chains: disk-like adsorbate species for the vertical anchoring of ligands on gold surfaces

Thin metalorganic films were prepared on gold by self-assembly of thioether-functionalised phthalocyaninato complexes from solution. The phthalocyaninato ligands used contain eight peripheral, β-positioned, alkylthio substituents SR (1a: R = n-C(8)H(17), 1b: R = n-C(12)H(25)), which serve as headgroups for surface binding and promote lateral assembly, while the disk-like phthalocyaninato core offers the scope for the attachment of axial ligands to the adsorbed molecules. This process was mimicked by coordination of pyridine (Py) to [Zn(1a)] and [Zn(1b)], respectively. The crystal structures of the products [Zn(1a)(Py)] and [Zn(1b)(Py)] were determined. The crystal structures of 4,5-bis(octylthio)phthalodinitrile and 4,5-bis(dodecylthio)phthalodinitrile were also determined. The films fabricated from [Mn(1a)Cl] and [Mn(1b)Cl] on gold were characterised by XPS, ToF-SIMS and NEXAFS spectroscopy, which revealed the presence of well-defined and homogeneous self-assembled monolayers (SAMs), whose constituents are bound to the substrate by thioether-gold linkages. The orientation of the macrocycles is predominantly parallel to the surface. Strong electronic interaction of the manganese(III) centre with the substrate leads to Cl loss upon adsorption and its reduction to Mn(II).

Steric and chain length effects in the (√(3)×√(3))R30° structures of alkanethiol self-assembled monolayers on Au(111)

The translational and orientational potential energy surfaces (PESs) of n-alkanethiols with up to four carbon atoms are studied for (√(3)×√(3))R30° self-assembled monolayers (SAMs). The PESs indicate that methanethiol may form SAM structures that are not accessible for long-chain thiols. The tilt of the thiol molecules is determined by a compromise between the preferred binding geometry at the sulfur atom and the steric requirements of the alkane chains. The Au-S bond lengths, offset from the bridge position (brg), and the Au-S-C bond angles result in tilt angles of the S-C bond in the range of 55-60°. As DFT/generalized gradient approximation systematically underestimates chain-chain interactions, the binding energies are corrected by comparison to MP2 interaction energies of alkane dimers in SAM-like configurations. The resulting thiol binding energies increase by approximately 1 kcal mol(-1) per CH(2) group, which results in a substantial stabilization of long-chain SAMs due to chain-chain interactions. Furthermore, as the chain length increases, the accessible range of backbone tilt angles is constrained due to steric effects. The combination of these two effects may explain why SAM structures with long-chain thiols exhibit higher order in experiments. For each thiol two favorable SAM structures are found with the sulfur head group at the fcc-brg and hcp-brg positions, respectively. These domains may coexist in thermal equilibrium. In combination with the symmetry of the gold (111) surface, this raises the possibility of up to six different domains on single-crystal terraces. Reconstructions by an adatom or vacancy of ethanethiol SAMs with (√(3)×√(3))R30° lattice are also studied using PES scans. The results indicate that adsorption of thiols next to a vacancy is favorable and may lead to point defects inside SAMs.