Oxygen reduction reaction mechanism on nitrogen-doped graphene:A density functional theory study

Nitrogen-doped graphene (N-graphene) was reported to exhibit a good activity experimentally as an electrocatalyst of oxygen reduction reaction (ORR) on the cathode of fuel cells under the condition of electropotential of similar to 0.04 V (vs. NNE) and pH of 14. This material is promising to replace or partially replace the conventionally used Pt. In order to understand the experimental results. ORR catalyzed by N-graphene is studied using density functional theory (DFT) calculations under experimental conditions taking the solvent, surface adsorbates, and coverages into consideration. Two mechanisms, i.e., dissociative and associative mechanisms, over different N-doping configurations are investigated. The results show that N-graphene surface is covered by O with 1/6 monolayer, which is used for reactions in this work. The transition state of each elementary step was identified using four different approaches, which give rise to a similar chemistry. A full energy profile including all the reaction barriers shows that the associative mechanism is more energetically favored than the dissociative one and the removal of O species from the surface is the rate-determining step. (C) 2011 Elsevier Inc. All rights reserved.

Acrolein hydrogenation on Pt(211) and Au(211) surfaces:a density functional theory study

Partial hydrogenation of acrolein, the simplest alpha, beta-unsaturated aldehyde, is not only a model system to understand the selectivity in heterogeneous catalysis, but also technologically an important reaction. In this work, the reaction on Pt(211) and Au(211) surfaces is thoroughly investigated using density functional theory calculations. The formation routes of three partial hydrogenation products, namely propenol, propanal and enol, on both metals are studied. It is found that the pathway to produce enol is kinetically favoured on Pt while on Au the route of forming propenol is preferred. Our calculations also show that the propanal formation follows an indirect pathway on Pt(211). An energy decomposition method to analyze the barrier is utilized to understand the selectivities at Pt(211) and Au(211), which reveals that the interaction energies between the reactants involved in the transition states play a key role in determining the selectivity difference.

A density functional theory study of CO oxidation on Ru(0001) at low coverage

We have performed ab initio density functional theory calculations with the generalized gradient approximation to investigate CO oxidation on Ru(0001). Several reaction pathways and transition states are identified. A much higher reaction barrier compared to that on Pt(111) is determined, confirming that the Ru is very inactive for CO oxidation under UHV conditions. The origin of the reaction barrier was analyzed. It is found that in the transition state the chemisorbed O atom sits in an unfavorable bonding site and a significant competition for bonding with the same substrate atoms occurs between the CO and the chemisorbed O, resulting in the high barrier. Ab initio molecular dynamics calculations show that the activation of the chemisorbed O atom from the initial hcp hollow site (the most stable site) to the bridge site is the crucial step for the reaction. The CO oxidation on Ru(0001) via the Eley-Rideal mechanism has also been investigated. A comparison with previous theoretical work has been made. (C) 2000 American Institute of Physics. [S0021-9606(00)31223-5].

Insight into CO Activation over Cu(100) under Electrochemical Conditions

The reduction of CO₂ on copper electrodes has attracted great attentions in the last decades, since it provides a sustainable approach for energy restore. During the CO₂ reduction process, the electron transfer to CO_ads is experimentally suggested to be the crucial step. In this work, we examine two possible pathways in CO activation, i.e. to generate COH_ads and CHO_ads, respectively, by performing the state-of-the-art constrained ab initio molecular dynamics simulations on the charged Cu(100) electrode under aqueous conditions, which is close to the realistic electrochemical condition. The free energy profile in the formation of COH_ads via the coupled proton and electron transfer is plotted. Furthermore, by Bader charge analyses, a linear relationship between C-O bond distance and the negative charge in CO fragment is unveiled. The formation of CHO_ads is identified to be a surface catalytic reaction, which requires the adsorption of H atom on the surface first. By comparing these two pathways, we demonstrate that kinetically the formation of COH_ads is more favored than that of CHO_ads, while CHO_ads is thermodynamically more stable. This work reveals that CO activation via COH_ads intermediate is an important pathway in electrocatalysis, which could provide some insights into CO₂ electroreduction over Cu electrodes.

Molecular Modeling on Inhibitor Complexes and Active-Site Dynamics of Cytochrome P450 C17, a Target for Prostate Cancer Therapy

A molecular model for the P450 enzyme cytochrome P450 C17 (CYP17) is presented based on sequence alignments of multiple template structures and homology modeling. This enzyme plays a central role in the biosynthesis of testosterone and is emerging as a major target in prostate cancer, with the recently developed inhibitor abiraterone currently in advanced clinical trials. The model is described in detail, together with its validation, by providing structural explanations to available site-directed mutagenesis data. The CYP17 molecule in this model is in the form of a triangular prism, with an edge of similar to 55 angstrom and a thickness of similar to 37 angstrom. It is predominantly helical, comprising 13 alpha helices interspersed by six 3(10) helices and 11 beta-sheets. Multinanosecond molecular dynamics simulations in explicit solvent have been carried out, and principal components analysis has been used to reveal the details of dynamics around the active site. Coarse-grained methods have also been used to verify low-frequency motions, which have been correlated with active-site gating. The work also describes the results of docking synthetic inhibitors, including the drug abiraterone and the natural substrate pregnenolone, in the CYP17 active site together with molecular dynamics simulations on the complexes. (C) 2010 Elsevier Ltd. All rights reserved.

Ab initio diffusional potential energy surface for CO chemisorption on Pd{110} at high coverage:Coupled translation and rotation

The ground state potential energy surface for CO chemisorption across Pd{110} has been calculated using density functional theory with gradient corrections at monolayer coverage. The most stable site corresponds well with the experimental adsorption heat, and it is found that the strength of binding to sites is in the following order: pseudo-short-bridge>atop>long-bridge>hollow. Pathways and transition states for CO surface diffusion, involving a correlation between translation and orientation, are proposed and discussed. (C) 1997 American Institute of Physics.

On the structure and dynamics of ionic liquids

The structure and dynamics of the ionic liquid 1-ethyl-3-methylimidazolium nitrate is studied by molecular dynamics simulations. We find long-range spatial correlations between the ions and a three-dimensional local structure that reflects the asymmetry of the cations. The main contribution to the configurational energy comes from the electrostatic interactions which leads to charge-ordering effects. Radial screening and threedimensional distribution of charge are also analyzed. The motion of a single ion is studied via velocity and reorientational correlation functions. It is found that ions "rattle" in a long-lived cage, while the orientational structure relaxes on a time scale longer than 200 ps. As in a supercooled liquid, the mean square displacements reveal a subdiffusive dynamics. In addition, the presence of dynamic heterogeneities can be detected by analyzing the non-Gaussian behavior of the van Hove correlation function and the spatial arrangement of the most mobile ions. The short-time collective dynamics is also studied through the electric current time correlation function.

Correlated electron-ion dynamics: the excitation of atomic motion by energetic electrons

Correlated electron-ion dynamics (CEID) is an extension of molecular dynamics that allows us to introduce in a correct manner the exchange of energy between electrons and ions. The formalism is based on a systematic approximation: small amplitude moment expansion. This formalism is extended here to include the explicit quantum spread of the ions and a generalization of the Hartree-Fock approximation for incoherent sums of Slater determinants. We demonstrate that the resultant dynamical equations reproduce analytically the selection rules for inelastic electron-phonon scattering from perturbation theory, which control the mutually driven excitations of the two interacting subsystems. We then use CEID to make direct numerical simulations of inelastic current-voltage spectroscopy in atomic wires, and to exhibit the crossover from ionic cooling to heating as a function of the relative degree of excitation of the electronic and ionic subsystems.

Salt-bridge dynamics control substrate-induced conformational change in the membrane transporter GlpT.

Active transport of substrates across cytoplasmic membranes is of great physiological, medical and pharmaceutical importance. The glycerol-3-phosphate (G3P) transporter (GlpT) of the E. coli inner membrane is a secondary active antiporter from the ubiquitous major facilitator superfamily that couples the import of G3P to the efflux of inorganic phosphate (Pi) down its concentration gradient. Integrating information from a novel combination of structural, molecular dynamics simulations and biochemical studies, we identify the residues involved directly in binding of substrate to the inward-facing conformation of GlpT, thus defining the structural basis for the substrate-specificity of this transporter. The substrate binding mechanism involves protonation of a histidine residue at the binding site. Furthermore, our data suggest that the formation and breaking of inter- and intradomain salt bridges control the conformational change of the transporter that accompanies substrate translocation across the membrane. The mechanism we propose may be a paradigm for organophosphate:phosphate antiporters.

Correlated electron-ion dynamics in metallic systems

In this paper we briefly discuss the problem of simulating non-adiabatic processes in systems that are usefully modelled using molecular dynamics. In particular we address the problems associated with metals, and describe two methods that can be applied: the Ehrenfest approximation and correlated electron-ion dynamics (CEID). The Ehrenfest approximation is used to successfully describe the friction force experienced by an energetic particle passing through a crystal, but is unable to describe the heating of a wire by an electric current. CEID restores the proper heating.

Liquid Structure and Dynamics of Aqueous Isopropanol over gamma-Alumina

The liquid structures of thin films of aqueous solutions of 0, 7, 19, 50, and 100 mol % isopropanol above O/Al-terminated gamma-alumina surfaces have been investigated by means of classical molecular dynamics simulations. The structuring effect of the oxide oil the liquid mixtures is strong and heavily dependent on the local structure of the oxide. Two distinct re-ions are found oil the oxide Surface characterized by the degree of coordination of Al atoms. Above octahedral Al atoms, water and isopropanol molecules adsorb via the oxygen atoms to maximize the electrostatic interaction, whereas above tetrahedral Al sites the solvent molecules adsorb via hydrogen atoms with the oxygen atoms away front the surface. More mobility is found in the second layer compared with the first; however, its structure is still influenced significantly by the orientation of molecules in the first adsorbed layer. Qualitatively, the displacement of water from the surface by the adsorption of isopropanol occurs with 2.6 Water molecules lost for every alcohol molecule present based on the effective surface areas of the two species calculated from the pure simulations.

A molecular model for drug binding to tandem repeats of telomeric G-quadruplexes.

The extreme 3'-ends of human telomeres consist of 150–250 nucleotides of single-stranded DNA sequence together with associated proteins. Small-molecule ligands can compete with these proteins and induce a conformational change in the DNA to a four-stranded quadruplex arrangement, which is also no longer a substrate for the telomerase enzyme. The modified telomere ends provide signals to the DNA-damage-response system and trigger senescence and apoptosis. Experimental structural data are available on such quadruplex complexes comprising up to four telomeric DNA repeats, but not on longer systems that are more directly relevant to the single-stranded overhang in human cells. The present paper reports on a molecular modelling study that uses Molecular Dynamics simulation methods to build dimer and tetramer quadruplex repeats. These incorporate ligand-binding sites and are models for overhang–ligand complexes.

Comparison of Dynamics of Extracellular Accesses to the β(1) and β(2) Adrenoceptors Binding Sites Uncovers the Potential of Kinetic Basis of Antagonist Selectivity.

From the molecular mechanism of antagonist unbinding in the ß(1) and ß(2) adrenoceptors investigated by steered molecular dynamics, we attempt to provide further possibilities of ligand subtype and subspecies selectivity. We have simulated unbinding of ß(1) -selective Esmolol and ß(2) -selective ICI-118551 from both receptors to the extracellular environment and found distinct molecular features of unbinding. By calculating work profiles, we show different preference in antagonist unbinding pathways between the receptors, in particular, perpendicular to the membrane pathway is favourable in the ß(1) adrenoceptor, whereas the lateral pathway involving helices 5, 6 and 7 is preferable in the ß(2) adrenoceptor. The estimated free energy change of unbinding based on the preferable pathway correlates with the experimental ligand selectivity. We then show that the non-conserved K347 (6.58) appears to facilitate in guiding Esmolol to the extracellular surface via hydrogen bonds in the ß(1) adrenoceptor. In contrast, hydrophobic and aromatic interactions dominate in driving ICI-118551 through the easiest pathway in the ß(2) adrenoceptor. We show how our study can stimulate design of selective antagonists and discuss other possible molecular reasons of ligand selectivity, involving sequential binding of agonists and glycosylation of the receptor extracellular surface. © 2012 John Wiley & Sons A/S.

Conformational Dynamics of the Human Propeller Telomeric DNA Quadruplex on a Microsecond Time Scale

The human telomeric DNA sequence with four repeats can fold into a parallel-stranded propeller-type topology. NMR structures solved under molecular crowding experiments correlate with the crystal structures found with crystal-packing interactions that are effectively equivalent to molecular crowding. This topology has been used for rationalization of ligand design and occurs experimentally in a number of complexes with a diversity of ligands, at least in the crystalline state. While G-quartet stems have been well characterised, the interactions of the TTA loop with the G-quartets are much less defined. To better understand the conformational variability and structural dynamics of the propeller-type topology, we performed molecular dynamics simulations in explicit solvent up to 1.5 µs. The analysis provides a detailed atomistic account of the dynamic nature of the TTA loops highlighting their interactions with the G-quartets including formation of an A:A base pair, triad, pentad and hexad. The results present a threshold in quadruplex simulations, with regards to understanding the flexible nature of the sugar-phosphate backbone in formation of unusual architecture within the topology. Furthermore, this study stresses the importance of simulation time in sampling conformational space for this topology.

Pinning down the solid-state polymorphism of the ionic liquid [bmim][PF6]

The solid-state polymorphism of the ionic liquid 1-butyl-3-methylimidazolium hexafluorophosphate, [bmim][PF6], has been investigated via low-temperature and high-pressure crystallisation experiments. The samples have been characterised by single-crystal X-ray diffraction, optical microscopy and Raman spectroscopy. The solid-state phase behaviour of the compound is confirmed and clarified with respect to previous phase diagrams. The structures of the previously reported gamma-form, which essentially exhibits a G'T cation conformation, as well as those of the elusive beta- and alpha-forms, are reported. Crystals of the beta-phase are twinned and the structure is heavily disordered; the cation conformation in this form is predominantly TT, though significant contributions from other less frequently encountered conformers are also observed at low temperature and high pressure. The cation conformation in the alpha-form is GT; the presence of the G'T conformer at 193 K in this phase can be eliminated on cooling to 100 K. Whilst X-ray structural data are overall in good agreement with previous interpretations based on Raman and NMR studies, they also reveal a more subtle interplay of intermolecular interactions, which give rise to a wider range of conformers than previously considered.