Interaction with a Gold Surface Reshapes the Free Energy Landscape of Alanine Dipeptide

The adsorption of the alanine dipeptide onto a gold surface in aqueous conditions was explored by using molecular dynamics simulations. In particular, using Metadynamics, we reconstructed a three-dimensional free energy landscape to investigate the effect of the metal surface on such landscape. The results show that the adsorption process is able to strongly modify the internal free energy surface of the molecule, even changing its qualitative appearance. The new free energy global minimum corresponds to elongated conformations of the biomolecule, arranged in preferred orientations with respect to the surface. Therefore, the surface-induced changes in the relative stability of the local free energy minima and in the free-energy barriers between them show that the entire conformational ensemble and the interconformer dynamics are also affected by the presence of the surface. The alanine dipeptide is the simplest molecule that exhibits the main features shown by larger peptides. Therefore, these findings provide a basis to rationalize, at the atomistic level, the effects of metal surfaces and nanoparticles on the structure and function of peptides and proteins, which is of paramount importance to engineer new systems for applications in bionanotechnology

Benchmarking Common Approximations for Determining the Particle-Size Dependence of Adsorbate-Induced Localized Surface Plasmon Resonance Shifts

Anomalies are investigated that exist between many long-standing theoretical models of the optical behavior of sensors based on changes in the localized surface plasmon resonance upon analyte adsorption. In particular, we focus on single metal nanoparticles which represent the core building-block of many recent sensing devices. Theoretical approaches include the Retarded Mie theory, the Non-Retarded quasi-static-dipole approximation, and two radiative corrections to the Non-Retarded case (radiative damping and radiative damping + depolarization). We find that the most accurate Non-Retarded approximation to the Retarded Mie theory varies strongly on a case by case basis; anyway, for particle radii beyond a few tens of nanometers, none of the considered approximations represents properly the adsorbate induced plasmon shift. We also find that the size-dependent peak shift has a complex dependence on the metal dielectric function. Accordingly, the trend of the adsorbate-induced plasmon peak shift as a function of the particle radius reveals an unexpected nonmonotonic behavior. We eventually identify an interesting range of particle radii over which the adsorbate-induced plasmon shift is unaffected by the particle size. Moreover, we give examples where nanoparticle batches with large size dispersion provide higher sensor reproducibility than monodisperse samples. On the other hand, in light of our findings, single particle measurements are pivotal to disclose the exact structure of the peak shift trend as a function of the particle radius

Wettability of Azobenzene Self-Assembled Monolayers

The wettability properties of azobenzene self-assembled monolayers (SAMs), in the trans and cis forms, are investigated herein by classical Molecular Dynamics simulations of validated assembly structures described with a dedicated force field. The two different methodologies used for the calculation of the contact angle, one based on the Young’s equation and the other on geometrical models, have provided a consistent description of the SAMs wettability in line with available experimental results. Furthermore, we provide an atomistic description of the first layers of water molecules at the solvent–SAM interface, which rationalizes the wettability difference between the <i>cis</i>- and <i>trans</i>-SAMs

Work Function Changes of Azo-Derivatives Adsorbed on a Gold Surface

By employing state-of-the-art computational techniques, we investigate two self-assembled monolayers (SAMs), constituted by azobenzene derivatives chemisorbed on a gold surface (azo-SAMs). We study the structural features and the work function change of the azo-SAMs as a function of the conformation of the molecules (<i>trans</i> or <i>cis</i>), of the unit cell sizes, and of the anchoring site (bridge, hollow, on-top). The data obtained by the theoretical calculations are compared with both experimental and computational data of literature. Concerning the work function change due to the azo-derivative photoisomerization, the results are in agreement with the experimental data, and are qualitatively robust with respect to the structure of the SAM

Exciton Transfer of Azobenzene Derivatives in Self-Assembled Monolayers

Diphenyl-diazene and its derivative bis­[(1,1′)-biphenyl-4-yl]­diazene were found to have innovative technological applications when arranged in self-assembled monolayers (SAMs). This is due to their switching capability after photoisomerization that is preserved also when they are in a close-packed assembly over the metal surface forming SAMs. One of the possible phenomena that may hinder the photoisomerization process is the intermolecular excitonic transfer. Understanding this possibility is therefore of the utmost importance. For doing so, we tackled a quantum mechanical (QM) study that begins from the exploration of the electronic excited state properties of a single molecule, to the intermolecular exciton couplings computed at different theory levels, until the excitonic diffusion dynamics, evaluated both within a frozen SAM portion and as an average along a molecular dynamics (MD) simulation

Quenching of the Photoisomerization of Azobenzene Self-Assembled Monolayers by the Metal Substrate

In this study, we aim at investigating the role played by the metal surface as a possible dissipative channel in the photoisomerization process of azobenzene-derivative-based self-assembled monolayers (azo-SAMs). In particular we compare the cases of gold and platinum. We study the excitonic transfer <i>phenomena</i> of two azo-derivatives (both in <i>trans</i> and in <i>cis</i> conformation) chemisorbed on Au{111} and Pt{111} to the metal surfaces. The metal effects are evaluated within the local and nonlocal regimes, showing that nonlocality in the metal response plays an important role and nonlocal accounting quenching rates are one order of magnitude smaller than the corresponding local results. The couplings are stronger for Au{111} than for Pt{111}, but for both cases the energy transfer between the molecule and the metal turns out not to be able to suppress photoisomerization

Structural Properties of Azobenzene Self-Assembled Monolayers by Atomistic Simulations

Azobenzene self-assembled monolayers (SAMs) are examples of optomechanical nanostructures capable of producing mechanical work through the well-known azobenzene photoisomerization process. Experimental studies have provided information on their structural properties, but an atomistic description of the SAMs in both the <i>cis</i> and <i>trans</i> forms is still lacking. In this work, a computational investigation of the SAM structures is conducted by classical molecular dynamics with a dedicated force. Experimental data on the SAM unit cell is used to set up SAM models of different molecular densities. The optimal structures are identified through the comparison with structural data from X-ray photoelectron and near-edge X-ray absorption fine structure spectroscopies. The resulting SAM atomistic models are validated by comparing simulated and experimental scanning tunneling microscopy images

Adsorption Mechanisms of Nucleobases on the Hydrated Au(111) Surface

The solution environment is of fundamental importance in the adsorption of molecules on surfaces, a process that is strongly affected by the capability of the adsorbate to disrupt the hydration layer above the surface. Here we disclose how the presence of interface water influences the adsorption mechanism of DNA nucleobases on a gold surface. By means of metadynamics simulations, we describe the distinctive features of a complex free-energy landscape for each base, which manifests activation barriers for the adsorption process. We characterize the different pathways that allow each nucleobase to overcome the barriers and be adsorbed on the surface, discussing how they influence the kinetics of adsorption of single-stranded DNA oligomers with homogeneous sequences. Our findings offer a rationale as to why experimental data on the adsorption of single-stranded homo-oligonucleotides do not straightforwardly follow the thermodynamics affinity rank

Interaction of Nucleic Acid Bases with the Au(111) Surface

The fate of an individual DNA molecule when it is deposited on a hard inorganic surface in a “dry” environment is unknown, while it is a crucial determinant for nanotechnology applications of nucleic acids. In the absence of experimental approaches that are able to unravel the three-dimensional atomic structure of the target system, here we tackle the first step toward a computational solution of the problem. By using first-principles quantum mechanical calculations of the four nucleobases on the Au(111) surface, we present results for the geometries, energetics, and electronic structure, in view of developing a force field that will enable classical simulations of DNA on Au(111) to investigate the structural modifications of the duplex in these non-native conditions. We fully characterize each system at the individual level. We find that van der Waals interactions are crucial for a correct description of the geometry and energetics. However, the mechanism of adsorption is well beyond pure dispersion interactions. Indeed, we find charge sharing between the substrate and the adsorbate, the formation of hybrid orbitals, and even bonding orbitals. Yet, this molecule–surface association is qualitatively distinct from the thiol adsorption mechanism: we discuss such differences and also the relation to the adsorption mechanism of pure aromatic molecules

Reactivity of the ZnS(101̅0) Surface to Small Organic Ligands by Density Functional Theory

The adsorption process of small organic molecules that represent reactive groups in amino acids (H₂O, H₂S, NH₃, and HCOOH) on the nonpolar ZnS(101̅0) surface was investigated by van der Waals corrected density functional theory calculations. At the accomplished interfaces, the oxygen, sulfur and nitrogen atoms of the adsorbates point toward the zinc atoms of the substrate, realizing electronic hybridization of their <i>p</i> lone pairs with the <i>s</i> and <i>d</i> bands of Zn. This electronic hybridization that involves surface cations is accompanied by H-bond formation that involves surface anions: this concerted mechanism enhances the interface strength and stability. On the basis of our results, we distinguish two classes of adsorption modes: molecular adsorption pertains to H₂O, NH₃, and HCOOH independently of the coverage and to H₂S at low coverage, while concurrent adsorption/dissociation pertains to H₂S at saturation coverage as a compromise between steric repulsion and H-bond-like interactions. Our results shed light on the passivation and modification of ZnS substrates (quantum dots and flat surfaces) in the prospect of technological and biomedical applications