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Generally adopted design strategies for enhancing the photocatalytic activity are aimed at tuning properties such as the visible light response, the exposed crystal facets, and the nanocrystal shape. Here, we present a different approach for designing efficient photocatalysts displaying a substrate-specific reactivity upon defect engineering. The defective anisotropic brookite TiO2 photocatalyst functionalized with Pt nanocrystals are tested for alcohol photoreforming showing up to an 11-fold increase in methanol oxidation rate, compared to the unreduced one, whilst presenting much lower ethanol or isopropanol specific oxidation rates. We demonstrate that the alcohol oxidation and hydrogen evolution reactions are tightly related, and when the substrate-specific alcohol oxidation ability is increased, the hydrogen evolution is significantly boosted. The reduced anisotropic brookite shows up to twenty-six-fold higher specific photoactivity with respect to anatase and brookite with isotropic nanocrystals, reflecting the different type of defective catalytic sites formed depending on the TiO2 polymorph and its crystal shape. Advanced in-situ characterizations and theoretical investigations reveal that controlled engineering over oxygen vacancies and lattice strain produces large electron polarons hosting the substrate-specific active sites for alcohol photo-oxidation.

Doping of the graphene lattice with transition metal atoms resulting in high magnetic anisotropy energy (MAE) is an important goal of materials research owing to its potential application in spintronics. In this article, by using spin-polarized density functional theory including spin-orbit coupling, we examined magnetic properties of graphene with vacancy defects, both bare and nitrogen-decorated, and doped by Cr, Mn and Fe transition metal single atom (TM-SA) and two different TM atoms simultaneously. [...] The computational findings are supplemented by an atomic-resolution characterization of an incidental Mn impurity bonded to four carbon atoms, whose localized spin matches expectations as measured using core-level electron energy-loss spectroscopy. Conducting TM-doped graphene with robust magnetic features offers prospects for the design of graphene-based spintronic devices., Comment: 31 + 61 pages, 5 + 81 figures

The development of synthetic strategies to engineer \pi-conjugated polymers is of paramount importance in modern chemistry and materials science. Here we introduce a theoretical and experimental synthetic paradigm based on the search for specific vibrational modes through an appropriate tailoring of the \pi-conjugation of the precursors, in order to increase the attempt frequency of a chemical reaction. First, we on-surface design a 1D \pi-conjugated polymer with specific \pi-topology, which is based on bisanthene monomers linked by cumulene bridges that tune specific vibrational modes. In a second step, upon further annealing, such vibrational modes steer the two-fold cyclization reaction between adjacent bisanthene moieties, which gives rise to a long and free-defect pentalene-bridged conjugated ladder polymer featuring a low band gap. In addition, high resolution atomic force microscopy allows us to identify by atomistic insights the resonant form of the polymer, thus confirming the validity of the Glidewell and Lloyd's rules for aromaticity. This on-surface synthetic strategy may stimulate exploiting previously precluded reactions towards novel pi-conjugated polymers with specific structures and properties.

Graphene has demonstrated great promise for technological use, yet control over material growth and understanding of how material imperfections affect the performance of devices are challenges that hamper the development of applications. In this work we reveal new insight into the connections between the performance of the graphene devices as environmental sensors and the microscopic details of the interactions at the sensing surface. Specifically, we monitor changes in the resistance of the chemical-vapour deposition grown graphene devices as exposed to different concentrations of ethanol. We perform thermal surface treatments after the devices are fabricated, use scanning probe microscopy to visualize their effects on the graphene sensing surface down to nanometer scale and correlate them with the measured performance of the device as an ethanol sensor. Our observations are compared to theoretical calculations of charge transfers between molecules and the graphene surface. We find that, although often overlooked, the surface cleanliness after device fabrication is responsible for the device performance and reliability. These results further our understanding of the mechanisms of sensing in graphene-based environmental sensors and pave the way to optimizing such devices, especially for their miniaturization, as with decreasing size of the active zone the potential role of contaminants will rise.

Background: Guanine quadruplexes (GQs) play vital roles in many cellular processes and are of much interest as drug targets. In contrast to the availability of many structural studies, there is still limited knowledge on GQ folding. Scope of review: We review recent molecular dynamics (MD) simulation studies of the folding of GQs, with an emphasis paid to the human telomeric DNA GQ. We explain the basic principles and limitations of all types of MD methods used to study unfolding and folding in a way accessible to non-specialists. We discuss the potential role of G-hairpin, G-triplex and alternative GQ intermediates in the folding process. We argue that, in general, folding of GQs is fundamentally different from funneled folding of small fast-folding proteins, and can be best described by a kinetic partitioning (KP) mechanism. KP is a competition between at least two (but often many) well-separated and structurally different conformational ensembles. Major conclusions: The KP mechanism is the only plausible way to explain experiments reporting long time-scales of GQ folding and the existence of long-lived sub-states. A significant part of the natural partitioning of the free energy landscape of GQs comes from the ability of the GQ-forming sequences to populate a large number of syn-anti patterns in their G-tracts. The extreme complexity of the KP of GQs typically prevents an appropriate description of the folding landscape using just a few order parameters or collective variables. General significance: We reconcile available computational and experimental studies of GQ folding and formulate basic principles characterizing GQ folding landscapes, Comment: \c{opyright} 2016. This manuscript version is made available under the CC-BY-NC-ND 4.0 license http://creativecommons.org/licenses/by-nc-nd/4.0/

The computer-aided folding of biomolecules, particularly RNAs, is one of the most difficult challenges in computational structural biology. RNA tetraloops are fundamental RNA motifs playing key roles in RNA folding and RNA-RNA and RNA-protein interactions. Although state-of-the-art Molecular Dynamics (MD) force fields correctly describe the native state of these tetraloops as a stable free-energy basin on the microsecond time scale, enhanced sampling techniques reveal that the native state is not the global free energy minimum, suggesting yet unidentified significant imbalances in the force fields. Here, we tested our ability to fold the RNA tetraloops in various force fields and simulation settings. We employed three different enhanced sampling techniques, namely, temperature replica exchange MD (T-REMD), replica exchange with solute tempering (REST2), and well-tempered metadynamics (WT-MetaD). We aimed to separate problems caused by limited sampling from those due to force-field inaccuracies. We found that none of the contemporary force fields is able to correctly describe folding of the 5'-GAGA-3' tetraloop over a range of simulation conditions. We thus aimed to identify which terms of the force field are responsible for this poor description of TL folding. We showed that at least two different imbalances contribute to this behavior, namely, overstabilization of base-phosphate and/or sugar-phosphate interactions and underestimated stability of the hydrogen bonding interaction in base pairing. The first artifact stabilizes the unfolded ensemble, while the second one destabilizes the folded state. The former problem might be partially alleviated by reparametrization of the van der Waals parameters of the phosphate oxygens suggested by Case et al., while in order to overcome the latter effect we suggest local potentials to better capture hydrogen bonding interactions., Comment: Reprinted with permission from J. Chem. Theory Comput. 2016, 12 (9), pp 4534-4548. Copyright 2016 American Chemical Society

DNA G-hairpins are potential key structures participating in folding of human telomeric guanine quadruplexes (GQ). We examined their properties by standard MD simulations starting from the folded state and long T-REMD starting from the unfolded state, accumulating ~130 {\mu}s of atomistic simulations. Antiparallel G-hairpins should spontaneously form in all stages of the folding to support lateral and diagonal loops, with sub-{\mu}s scale rearrangements between them. We found no clear predisposition for direct folding into specific GQ topologies with specific syn/anti patterns. Our key prediction stemming from the T-REMD is that an ideal unfolded ensemble of the full GQ sequence populates all 4096 syn/anti combinations of its four G-stretches. The simulations can propose idealized folding pathways but we explain that such few-state pathways may be misleading. In the context of the available experimental data, the simulations strongly suggest that the GQ folding could be best understood by the kinetic partitioning mechanism with a set of deep competing minima on the folding landscape, with only a small fraction of molecules directly folding to the native fold. The landscape should further include nonspecific collapse processes where the molecules move via diffusion and consecutive random rare transitions, which could, e.g., structure the propeller loops., Comment: This article has been accepted for publication in Nucleic Acids Research Published by Oxford University Press

The reactivity of iron atoms, clusters and nanoparticles (nZVI) is of increasing interest owing to their important practical applications, ranging from the steel industry to water remediation technologies. Here, we provide an overview of computational methods and models that can be applied to study nZVI reactions and discuss their benefits and limitations. We also report current progress in calculations through recent examples treating the reactivity of nZVI particles. Finally, we consider the potential use of highly accurate methods with favorable scaling (such as quantum Monte Carlo or random phase approximation), which are currently considered too computationally expensive but are expected to become more amenable in the future as computer power increases.

We compare first-principle band gaps and optical absorption spectra of single- and double-layer fluorographene with bulk graphite fluoride. The electronic properties are calculated using the many-body GW approximation and the optical spectra using the Bethe-Salpeter equation (BSE). The inclusion of electron-hole interactions is crucial for predicting low energy excitonic absorption peaks. The position of the first exciton peak is identical in single-, double- and multilayer fluorographene, which may indicate that the onset of the absorption spectra does not differ in these materials.

Reliable theoretical predictions of noncovalent interaction energies, which are important e.g. in drug-design and hydrogen-storage applications, belong to longstanding challenges of contemporary quantum chemistry. In this respect, the fixed-node diffusion Monte Carlo (FN-DMC) is a promising alternative to the commonly used "gold standard" coupled-cluster CCSD(T)/CBS method for its benchmark accuracy and favourable scaling, in contrast to other correlated wave function approaches. This work is focused on the analysis of protocols and possible tradeoffs for FN-DMC estimations of noncovalent interaction energies and proposes an efficient yet accurate computational protocol using simplified explicit correlation terms with a favorable O(N^3) scaling. It achieves an excellent agreement (mean unsigned error ~0.2 kcal/mol) with respect to the CCSD(T)/CBS data on a number of complexes, including benzene/hydrogen,T-shape benzene dimer, stacked adenine-thymine and a set of small noncovalent complexes A24. The high accuracy and reduced computational costs predestinate the reported protocol for practical interaction energy calculations of large noncovalent complexes, where the CCSD(T)/CBS is prohibitively expensive.

DFT calculations of the electronic structure of graphane and stoichiometrically halogenated graphene derivatives (fluorographene and other analogous graphene halides) show (i) localized orbital basis sets can be successfully and effectively used for such 2D materials; (ii) several functionals predict that the band gap of graphane is greater than that of fluorographene, whereas HSE06 gives the opposite trend; (iii) HSE06 functional predicts quite good values of band gaps w.r.t benchmark theoretical and experimental data; (iv) the zero band gap of graphene is opened by hydrogenation and halogenation and strongly depends on the chemical composition of mixed graphene halides; (v) the stability of graphene halides decreases sharply with increasing size of the halogen atom - fluorographene is stable, whereas graphene iodide spontaneously decomposes. In terms of band gap and stability, the C2FBr, and C2HBr derivatives seem to be promising materials, e.g., for (opto)electronics applications, because their band gaps are similar to those of conventional semiconductors, and they are expected to be stable under ambient conditions. The results indicate that other fluorinated compounds (CaHbFc and CaFbYc, Y = Cl, Br, I) are stable insulators.