A multiscale approach for electronic transport simulation of carbon nanostructures in aqueous solvent.

Theoretical works addressing electronic nano-devices operating in an aqueous environment often neglect solvent effects. In order to assess the role played by the polarization effects on the electronic transport properties of solvated graphene, for example in possible bio-sensing applications, we have used here a combination of polarizable force-field molecular dynamics, hybrid quantum mechanics/molecular mechanics (QM/MM) approach, density functional theory, and non-equilibrium Green's function method. We considered different solvation conditions, the presence of defects in graphene, as well as various choices for the partitions between the quantum and classical regions in QM/MM, in which we explicitly account for polarization effects. Our results show that the polarization effects on graphene lead to changes in the structure of interfacial water molecules which are more pronounced in the vicinity of defects. The presence of water leads to increased scattering due to the long-range charge interactions with graphene. At the same time, changes in the conductance due to polarization or salt concentration are found to be small, paving the way for robust electronic nano-devices operating in aqueous environments.

Atomic and Electronic Structure of Pilus from Geobacter sulfurreducens through QM/MM Calculations: Evidence for Hole Transfer in Aromatic Residues.

Long-range electron transport has been widely and experimentally reported in Geobacter sulfurreducens pilus protein. However, a better understanding of the still undefined molecular arrangement can bring to light the role of key residues in this phenomenon. We propose a theoretical investigation of the electronic structure of aromatic residue groups in the protein through a classical molecular dynamics (MD) simulation, followed by a quantum mechanics/molecular mechanics (QM/MM) electronic study of different frames sampled from MD trajectories, an electrostatic potential and electron density analysis, an analysis of the density of states, and an investigation of hole formation through Dyson orbital calculations. We observe a highest occupied molecular orbital-lowest unoccupied molecular orbital (HOMO-LUMO) energy gap in the ranges of 1.4-2.3 eV and 2.9-3.3 eV and a less intense dipole moment along the aromatic residues in the presence of water in comparison to the system in vacuum. HOMO and LUMO electron densities highlight the occupation of one tyrosine residue in every representation for HOMO and a delocalization along two to three rings for LUMO. The results show how the electronic structure of the aromatic residues is sensitive to the ring arrangement and the surrounding environment. In our study, we observe that slight rearrangements in the fiber geometry can create temporary conditions for hole transfer.

Steric and Electrostatic Effects on the Diffusion of CH4/CH3OH in Copper-Exchanged Zeolites: Insights from Enhanced Sampling Molecular Dynamics and Free Energy Calculations.

Copper-exchanged zeolites have demonstrated high selectivity in methane-to-methanol conversion carried out on copper-oxo centers. Nevertheless, the reaction can only occur if the methane molecules reach the active site while the methanol molecules must leave the material without high energetic cost for the migration. In this context, we have used force field-based molecular dynamics simulations with the potential of mean force method to estimate the energy barrier in cage to cage diffusion of methane and methanol molecules in the chabazite framework type zeolite. The results show considerably higher energy barrier for methanol diffusion. The steric effect of the active site and the electrostatic environment favors the CH3OH diffusion toward nonactive cages where it tends to accumulate due to the strong interactions with the zeolite. The same behavior is observed in the water molecules distribution, which emphasizes the control of the electrostatic potential over the polar molecules migration. For high concentration of polar molecules, the electrostatic effect is shielded and the driving force is reduced for CH3OH diffusion. The results show that if the electrostatic environment can be controlled, the product migration may be facilitated, which can improve the catalytic process.

Thermodynamic and structural aspects of molecular recognition in mannose-binding protein complexes: a theoretical study over HRP-ArtinM association.

The biomolecular recognition of D-mannose-binding lectin from Artocarpus heterophyllus (ArtinM) by Horseradish Peroxidase (HRP) mediated by glycosylation allows their application in a multitude of biological systems. The present work describes the use of molecular dynamics (MD) to assess the Gibbs free energy associated with the formation of a ArtinM-HRP conjugate mediated by a glycosylation molecule. For the enthalpy term, we applied the molecular mechanics Poisson-Boltzmann surface area (MM-PBSA) method and for the vibrational entropy term, we use the quasi-harmonic approximation. Our results show that, even without glycosylation, the binding free energy between ArtinM and HRP is - 196.154 kJmol- 1, an extremely high affinity with low selectivity, originated mainly through the van der Waals energy terms. The binding free energy between ArtinM and the glycosylated HRP (gHRP) was calculated at - 66.156 kJmol- 1, an absolute and considerably lower value, however, originated from electrostatic energy terms, which increases the selectivity of molecular recognition. Our work has shown that the HRP active site region has a high affinity and low selectivity for other biomolecules. The presence of glycosylation plays a role in increasing this selectivity for this region. Thus, we conclude that performing mutagenesis of amino acid residues near the entrance of the catalytic site, can improve the activity of non-glycosylated HRPs. This illustrates new insights that can be applied to carbohydrate-based immunochemistry.

Ab Initio QM/MM Simulation of Ferrocene Homogeneous Electron-Transfer Reaction.

Here, we demonstrate the feasibility of hybrid computational methods to predict the homogeneous electron exchange between the ferrocene and its oxidized (ferrocenium) state. The free energy for ferrocene oxidation was determined from thermodynamic cycles and implicit solvation strategies within density functional theory (DFT) methods leading to no more than 15% of deviation (in the range of 0.1-0.2 eV) when compared to absolute redox free energies obtained experimentally. Reorganization energy, as defined according to the Marcus theory of electron-transfer rate, was obtained by sampling the vertical ionization/electron affinity energies using hybrid quantum/classical (QM/MM) Born-Oppenheimer molecular dynamics trajectories. Calculated reorganization energies show a subtle but noteworthy dependence with the nature and the localization of the compensating countercharge. We concluded that the adopted hybrid computational strategy, to simulate homogeneous redox reactions, was successfully demonstrated and it further permits applications in more complex systems (required in daily life applications), where the electron transfer occurs heterogeneously.

Exploring Coupled Redox and pH Processes with a Force-Field-Based Approach: Applications to Five Different Systems.

Coupled redox and pH-driven processes are at the core of many important biological mechanisms. As the distribution of protonation and redox states in a system is associated with the pH and redox potential of the solution, having efficient computational tools that can simulate under these conditions becomes very important. Such tools have the potential to provide information that complement and drive experiments. In previous publications we have presented the implementation of the constant pH and redox potential molecular dynamics (C(pH,E)MD) method in AMBER and we have shown how multidimensional replica exchange can be used to significantly enhance the convergence efficiency of our simulations. In the current work, after an improvement in our C(pH,E)MD approach that allows a given residue to be simultaneously pH- and redox-active, we have employed our methodologies to study five different systems of interest in the literature. We present results for capped tyrosine dipeptide, two maquette systems containing one pH- and redox-active tyrosine (α3Y and peptide A), and two proteins that contain multiple heme groups (diheme cytochrome c from Rhodobacter sphaeroides and Desulfovibrio vulgaris Hildenborough cytochrome c3). We show that our results can provide new insights into previous theoretical and experimental findings by using a fully force-field-based and GPU-accelerated approach, which allows the simulations to be executed with high computational performance.