Nature of the Interaction between Natural and Size-Expanded Guanine with Gold Clusters: A Density Functional Theory Study

In this paper, we study the interaction of natural and size-expanded guanine molecules with small gold clusters, to shed light on the nature of the N/O–Au bonds and of the unconventional NH···Au hydrogen bonds, as well as on the dependence of these bonds on the charge state of the systems. Based on density functional theory results, it is found that the nature of the N/O–Au bonds between both guanine and its size-expanded form and three- and four-atom Au clusters is covalent in the neutral systems. In the −1 charged systems, the binding energy decreases by almost 50% with a significant change of geometry. Although the NH site in the spacer ring of size-expanded guanine may supply a new acceptor opportunity for forming an additional NH···Au hydrogen bond, this hardly emerges because of the nonplanarity and the large steric effect. The introduction of a spacer ring in guanine decreases the highest occupied molecular orbital–lowest unoccupied molecular orbital gap and expands the spatial distribution of electron wave functions, which make size-expanded guanine appealing for charge transfer performance. At the same time, it increases the steric hindrance, making the adsorption process more orderly, which is also good in view of molecular electronic devices

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

A Density Functional Theory Study of Cytosine on Au(111)

The adsorption of cytosine on Au(111) is investigated using density functional theory with the nonlocal van der Waals density functional. Test calculations performed on the benzene stacked dimer and on a benzene molecule adsorbed on Au(111) allow us to assess the methodology and reveal the accuracy and predictivity of the van der Waals density funcional relative to experimental outcome. Our results for cytosine on Au(111) indicate that the inclusion of dispersion interactions is crucial for the treatment of this system. In fact, such terms enhance the value of the adsorption energy and also affect the cytosine bonding geometry: in particular, we find that a tilted geometry is always favorable relative to a parallel geometry, which was not found in standard density functional theory investigations. The combined new data for energetics and geometry lead to conclusions that contrast the common opinion that the surface–molecule interaction is negligible in the process of monolayer formation

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

Is the G‑Quadruplex an Effective Nanoconductor for Ions?

We use a stepwise pulling protocol in molecular dynamics simulations to identify how a G-quadruplex selects and conducts Na⁺, K⁺, and NH₄⁺ ions. By estimating the minimum free-energy changes of the ions along the central channel via Jarzynski’s equality, we find that the G-quadruplex selectively binds the ionic species in the following order: K⁺ > Na⁺ > NH₄⁺. This order implies that K⁺ optimally fits the channel. However, the features of the free-energy profiles indicate that the channel conducts Na⁺ best. These findings are in fair agreement with experiments on G-quadruplexes and reveal a profoundly different behavior from the prototype potassium-ion channel KcsA, which selects and conducts the same ionic species. We further show that the channel can also conduct a single file of water molecules and deform to leak water molecules. We propose a range for the conductance of the G-quadruplex

Representative structures of the most populated clusters.

<p>The clustering algorithm was applied during the last 100-NMR and MD-XR trajectories are shown in light and dark colors, respectively. The color code for the different protein segments is the same as in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0074383#pone-0074383-g001" target="_blank">Figure 1</a>.</p

Cartoon representation of the crystallographic and NMR structures.

<p>(A) Crystallographic structure from PDB file 1G8I; (B) NMR structure, the first model that appears in the PDB file 2LCP. Residues 11–174 between H1 and H9 define the protein core (PC). The definitions of the other protein segments are given in the section “Material and Method” and in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0074383#pone-0074383-t001" target="_blank">Table 1</a>.</p

RMSDs of the protein core evaluated with respect to the crystal structure along the MD trajectories.

<p>Gray line: RMSD evaluated along the 250 ns of the MD-XR trajectory. Orange: RMSD evaluated along the 525 ns of the MD-NMR simulation. Smoothed RMSDs signals are reported as black lines.</p

Surface representation of the most representative structures.

<p>The surface representation highlights the shape of the HC and the allocation of the L3 into the crevice. (A) Most representative structure for the MD-XR trajectory; (B) most representative structure for the MD-NMR trajectory.</p