J. Kou, C. Lu, J. Wang, Y. Chen, Z. Xu, R. S. Varma: Selectivity Enhancement in Heterogeneous Photocatalytic Transformations, CHEMICAL REVIEWS, Article ASAP, 2017.
DOI: 10.1021/acs.chemrev.6b00396, IF = 54.301
Abstract: Photocatalysis has been invariably considered as an unselective process (especially in water) for a fairly long period of time, and the investigation on selective photocatalysis has been largely neglected. In recent years, the field of selective photocatalysis is developing rapidly and now extended to several newer applications. This review focuses on the overall strategies which can improve the selectivity of photocatalysis encompassing a wide variety of photocatalysts, and modifications thereof, as well as the related vital processes of industrial significance such as reduction and oxidation of organics, inorganics, and CO2 transformation. Comprehensive and successful strategies for enhancing the selectivity in photocatalysis are abridged to reinvigorate and stimulate future investigations. In addition, nonsemiconductor type photocatalysts, such as Ti–Si molecular sieves and carbon quantum dots (CQDs), are also briefly appraised in view of their special role in special selective photocatalysis, namely epoxidation reactions, among others. In the end, a summary and outlook on the challenges and future directions in the research field are included in the comprehensive review.
J. C. Colmenares, R. S. Varma, V. Nair: Selective photocatalysis of lignin-inspired chemicals by integrating hybrid nanocatalysis in microfluidic reactors, CHEMICAL SOCIETY REVIEWS vol. 46, iss. 22, pp. 6675-6686, 2017.
DOI: 10.1039/c7cs00257b, IF = 40.443
Abstract: This tutorial review assesses the available and possible strategies for attaining higher selectivity and yield of value-added chemicals from lignin using nanocatalysts embedded in a photomicroreactor. The design of the photomicroreactor, the choice of photocatalysts and the techniques for assembling the catalysts in such confined spaces are crucial elements. Lignin, a predominant industrial byproduct and pollutant, has been recognized today as a rich reservoir for aromatic chemicals and a prominent resource. The conventional batch photocatalytic studies on lignin, often using dissolved lignin under alkaline conditions, often generates a wide range of valuable organic chemicals which find applications in the pharmaceutical, food processing, cosmetic and fine chemical industries. The role of photocatalysis in such lignin depolymerizations is questionable as the dissolution procedure initiates fragmentation of lignin prior to light exposure. The complexity of the lignin structure also impedes necessary and decisive information to understand the reaction mechanism during such reactions in batch photoreactors. Considering these facts, photocatalysis studies on lignin entail a thoughtful reevaluation and focus on understanding the role of photocatalysis in the product generation and authenticating the implicated reaction mechanisms. The development of a photocatalytic system for lignin depolymerization in a continuous microreactor is a superior approach for the generation of valuable products emanating from lignin depolymerization and the successful execution of such strategies can pave the way for the commercialization of bio-based chemicals.
S. Kment, F. Riboni, S. Pausova, L. Wang, L. Wang, H. Han, Z. Hubicka, J. Krysa, P. Schmuki, R. Zboril: Photoanodes based on TiO2 and α-Fe2O3 for solar water splitting – superior role of 1D nanoarchitectures and of combined heterostructures, CHEMICAL SOCIETY REVIEWS, vol. 46, iss. 12, pp. 3716–3769, 2017.
DOI: 10.1039/c6cs00015k, IF = 40.443
Abstract: Solar driven photoelectrochemical water splitting (PEC-WS) using semiconductor photoelectrodes represents a promising approach for a sustainable and environmentally friendly production of renewable energy vectors and fuel sources, such as dihydrogen (H2). In this context, titanium dioxide (TiO2) and iron oxide (hematite, α-Fe2O3) are among the most investigated candidates as photoanode materials, mainly owing to their resistance to photocorrosion, non-toxicity, natural abundance, and low production cost. Major drawbacks are, however, an inherently low electrical conductivity and a limited hole diffusion length that significantly affect the performance of TiO2 and α-Fe2O3 in PEC devices. To this regard, one-dimensional (1D) nanostructuring is typically applied as it provides several superior features such as a significant enlargement of the material surface area, extended contact between the semiconductor and the electrolyte and, most remarkably, preferential electrical transport that overall suppress charge carrier recombination and improve TiO2 and α-Fe2O3 photoelectrocatalytic properties. The present review describes various synthetic methods and modifying concepts of 1D-photoanodes (nanotubes, nanorods, nanofibers, nanowires) based on titania, hematite, and on α-Fe2O3/TiO2 heterostructures, for PEC applications. Various routes towards modification and enhancement of PEC activity of 1D photoanodes are discussed including doping, decoration with co-catalysts and heterojunction engineering. Finally, the challenges related to the optimization of charge transfer kinetics in both oxides are highlighted.
The Pierre Auger Collaboration: Observation of a large-scale anisotropy in the arrival directions of cosmic rays above 8 × 1018eV, SCIENCE vol. 357, iss. 6357, pp. 1266-1270, 2017.
DOI: 10.1126/science.aan4338, IF = 37.205
Abstract: Cosmic rays are atomic nuclei arriving from outer space that reach the highest energies observed in nature. Clues to their origin come from studying the distribution of their arrival directions. Using 3 × 104 cosmic rays with energies above 8 × 1018 electron volts, recorded with the Pierre Auger Observatory from a total exposure of 76,800 km2 sr year, we determined the existence of anisotropy in arrival directions. The anisotropy, detected at more than a 5.2σ level of significance, can be described by a dipole with an amplitude of 
percent toward right ascension αd = 100 ± 10 degrees and declination δd = 
degrees. That direction indicates an extragalactic origin for these ultrahigh-energy particles.
A. Naldoni, V. M. Shalaev and M. L. Brongersma: Applying plasmonics to a sustainable future, SCIENCE, vol. 356, iss. 6341, 2017.
DOI: 10.1126/science.aan5802, IF = 37.205
Abstract: Chemistry is fundamental for powering our society. A flurry of very promising experiments demonstrate that plasmonics may have a transformative impact on the way we will drive, manipulate, enhance, and monitor chemical processes in the future. Plasmonics offers the ultimate spatial and temporal control over light and photochemistry, with the help of metallic nanostructures capable of concentrating electromagnetic energy into nanoscale volumes. Surface plasmons (SPs) are charge-density oscillations at the surface of a conducting material and decay by reemission of a photon or through the creation of highly energetic (“hot”) electrons and holes. The subsequent equilibration of hot carriers with lattice phonons can lead to appreciable local heating.
ATLAS Collaboration: Evidence for light-by-light scattering in heavy-ion collisions with the ATLAS detector at the LHC, NATURE PHYSICS, 2017.
DOI: 10.1038/nphys4208, IF = 22.806
Abstract: Light-by-light scattering (γγ 
γγ) is a quantum-mechanical process that is forbidden in the classical theory of electrodynamics. This reaction is accessible at the Large Hadron Collider thanks to the large electromagnetic field strengths generated by ultra-relativistic colliding lead ions. Using 480 μb−1 of lead–lead collision data recorded at a centre-of-mass energy per nucleon pair of 5.02 TeV by the ATLAS detector, here we report evidence for light-by-light scattering. A total of 13 candidate events were observed with an expected background of 2.6 ± 0.7 events. After background subtraction and analysis corrections, the fiducial cross-section of the process Pb + Pb (γγ) Pb(∗) + Pb(∗)γγ, for photon transverse energy ET > 3 GeV, photon absolute pseudorapidity |η| < 2.4, diphoton invariant mass greater than 6 GeV, diphoton transverse momentum lower than 2 GeV and diphoton acoplanarity below 0.01, is measured to be 70 ± 24 (stat.) ± 17 (syst.) nb, which is in agreement with the standard model predictions.
K. Jayaramulu, F. Geyer, M. Petr, R. Zboril, D. Vollmer, R. A. Fischer: Shape Controlled Hierarchical Porous Hydrophobic/Oleophilic Metal-Organic Nanofibrous Gel Composites for Oil Adsorption, ADVANCED MATERIALS, vol. 29, iss. 12, no. 1605307, 2017.
DOI: 10.1002/adma.201605307, IF = 19.791
Abstract: A versatile and facile synthetic route toward a ultralight hierarchical poroushybrid composed of metal-organic gels and fluorinated graphene oxide is reported. The composite gels show excellent absorbency of oil and various organic solvents due to their prominent meso/macropores, notable hydrophobicity, and superoleophilicity.
K. Holá, M. Sudolská, S. Kalytchuk, D. Nachtigallová, A. L. Rogach, M. Otyepka, R. Zbořil: Graphitic Nitrogen Triggers Red Fluorescence in Carbon Dots, ACS NANO, vol. 11, iss. 12, pp. 12402–12410, 2017.
DOI: 10.1021/acsnano.7b06399, IF = 13.942
Abstract: Carbon dots (CDs) are a stable and highly biocompatible fluorescent material offering great application potential in cell labeling, optical imaging, LED diodes, and optoelectronic technologies. Because their emission wavelengths provide the best tissue penetration, red-emitting CDs are of particular interest for applications in biomedical technologies. Current synthetic strategies enabling red-shifted emission include increasing the CD particle size (sp2 domain) by a proper synthetic strategy and tuning the surface chemistry of CDs with suitable functional groups (e.g., carboxyl). Here we present an elegant route for preparing full-color CDs with well-controllable fluorescence at blue, green, yellow, or red wavelengths. The two-step procedure involves the synthesis of a full-color-emitting mixture of CDs from citric acid and urea in formamide followed by separation of the individual fluorescent fractions by column chromatography based on differences in CD charge. Red-emitting CDs, which had the most negative charge, were separated as the last fraction. The trend in the separation, surface charge, and red-shift of photoluminescence was caused by increasing amount of graphitic nitrogen in the CD structure, as was clearly proved by XPS, FT-IR, Raman spectroscopy, and DFT calculations. Importantly, graphitic nitrogen generates midgap states within the HOMO–LUMO gap of the undoped systems, resulting in significantly red-shifted light absorption that in turn gives rise to fluorescence at the low-energy end of the visible spectrum. The presented findings identify graphitic nitrogen as another crucial factor that can red-shift the CD photoluminescence.
A. Bakandritsos, M. Pykal, P. Blonski, P. Jakubec, D. D. Chronopoulos, K. Polakova, V. Georgakilas, K. Čépe, O. Tomanec, V. Ranc, A. B. Bourlinos, R. Zboril, M. Otyepka: Cyanographene and Graphene Acid - Emerging Derivatives Enabling High-Yield and Selective Functionalization of Graphene, ACS NANO, vol. 11, iss. 3, pp. 2982–2991, 2017.
DOI: 10.1021/acsnano.6b08449, IF = 13.942
Abstract: Efficient and selective methods for covalent derivatization of graphene are needed because they enable tuning of graphene’s surface and electronic properties, thus expanding its application potential. However, existing approaches based mainly on chemistry of graphene and graphene oxide achieve only limited level of functionalization due to chemical inertness of the surface and non-selective simultaneous attachment of different functional groups, respectively. Here we present a conceptually different route based on synthesis of cyanographene via the controllable substitution and defluorination of fluorographene. The highly conductive and hydrophilic cyanographene allows exploiting the complex chemistry of –CN groups towards a broad scale of graphene derivatives with very high functionalization degree. The consequent hydrolysis of cyanographene results in graphene acid, a 2D carboxylic acid with pKa of 5.2, showing excellent biocompatibility, conductivity and dispersibility in water and 3D supramolecular assemblies after drying. Further, the carboxyl groups enable simple, tailored and widely accessible 2D chemistry onto graphene, as demonstrated via the covalent conjugation with a diamine, an aminothiol and an aminoalcohol. The developed methodology represents the most controllable, universal and easy to use approach towards a broad set of 2D materials through consequent chemistries on cyanographene and on the prepared carboxy-, amino-, sulphydryl-, and hydroxy- graphenes.
S. Kalytchuk, K. Poláková, Y. Wang, J. P. Froning, K. Cepe, A. L. Rogach, R. Zbořil: Carbon Dot Nanothermometry: Intracellular Photoluminescence Lifetime Thermal Sensing, ACS NANO, vol. 11, iss. 2, pp. 1432–1442, 2017.
DOI: 10.1021/acsnano.6b06670, IF = 13.942
Abstract: Nanoscale biocompatible photoluminescence (PL) thermometers that can be used to accurately and reliably monitor intracellular temperatures have many potential applications in biology and medicine. Ideally, such nanothermometers should be functional at physiological pH across a wide range of ionic strengths, probe concentrations, and local environments. Here, we show that water-soluble N,S-co-doped carbon dots (CDs) exhibit temperature-dependent photoluminescence lifetimes and can serve as highly sensitive and reliable intracellular nanothermometers. PL intensity measurements indicate that these CDs have many advantages over alternative semiconductor- and CD-based nanoscale temperature sensors. Importantly, their PL lifetimes remain constant over wide ranges of pH values (5–12), CD concentrations (1.5 × 10–5 to 0.5 mg/mL), and environmental ionic strengths (up to 0.7 mol·L–1 NaCl). Moreover, they are biocompatible and nontoxic, as demonstrated by cell viability and flow cytometry analyses using NIH/3T3 and HeLa cell lines. N,S-CD thermal sensors also exhibit good water dispersibility, superior photo- and thermostability, extraordinary environment and concentration independence, high storage stability, and reusability–their PL decay curves at temperatures between 15 and 45 °C remained unchanged over seven sequential experiments. In vitro PL lifetime-based temperature sensing performed with human cervical cancer HeLa cells demonstrated the great potential of these nanosensors in biomedicine. Overall, N,S-doped CDs exhibit excitation-independent emission with strongly temperature-dependent monoexponential decay, making them suitable for both in vitro and in vivo luminescence lifetime thermometry.
D. Sigwalt, M. Šekutor, L. Cao, P. Y. Zavalij, J. Hostaš, H. Ajani, P. Hobza, K. Mlinarić-Majerski, R. Glaser, L. Isaacs: Unraveling the Structure–Affinity Relationship between Cucurbit[n]urils (n = 7, 8) and Cationic Diamondoids, JOURNAL OF THE AMERICAN CHEMICAL SOCIETY vol. 139, iss. 8, pp. 3249-3258, 2017.
DOI: 10.1021/jacs.7b00056, IF = 13.858
Abstract: We report the measurement of the binding constants (Ka) for cucurbit[n]uril (n = 7, 8) toward four series of guests based on 2,6-disubstituted adamantanes, 4,9-disubstituted diamantanes, 1,6-disubstituted diamantanes, and 1-substituted adamantane ammonium ions by direct and competitive 1H NMR spectroscopy. Compared to the affinity of CB[7]·Diam(NMe3)2, the adamantane diammonium ion complexes (e.g., CB[7]·2,6-Ad(NH3)2 and CB[7]·2,6-Ad(NMe3)2) are less effective at realizing the potential 1000-fold enhancement in affinity due to ion–dipole interactions at the second ureidyl C═O portal. Comparative crystallographic investigation of CB[7]·Diam(NMe3)2, CB[7]·DiamNMe3, and CB[7]·1-AdNMe3 revealed that the preferred geometry positions the +NMe3 groups ≈0.32 Å above the C═O portal; the observed 0.80 Å spacing observed for CB[7]·Diam(NMe3)2 reflects the simultaneous geometrical constraints of CH2···O═C close contacts at both portals. Remarkably, the CB[8]·IsoDiam(NHMe2)2 complex displays femtomolar binding affinity, placing it firmly alongside the CB[7]·Diam(NMe3)2 complex. Primary or quaternary ammonium ion looping strategies lead to larger increases in binding affinity for CB[8] than for CB[7], which we attribute to the larger size of the carbonyl portals of CB[8]; this suggests routes to develop CB[8] as the tightest binding host in the CB[n] family. We report that alkyl group fluorination (e.g., CB[7]·1-AdNH2Et versus CB[7]·1-AdNH2CH2CF3) does not result in the expected increase in Ka value. Finally, we discuss the role of solvation in nonempirical quantum mechanical computational methodology, which is used to estimate the relative changes in Gibbs binding free energies.
M. Di Donato, M. M. Lerch, A. Lapini, A. D. Laurent, A. Iagatti, L. Bussotti, S. P. Ihrig, M. Medved’, D. Jacquemin, W. Szymański, W. J. Buma, P. Foggi, B. L. Feringa: Shedding Light on the Photoisomerization Pathway of Donor–Acceptor Stenhouse Adducts, JOURNAL OF THE AMERICAN CHEMICAL SOCIETY vol. 139, iss. 44, pp. 15596-15599, 2017.
DOI: 10.1021/jacs.7b09081, IF = 13.858
Abstract: Donor–acceptor Stenhouse adducts (DASAs) are negative photochromes that hold great promise for a variety of applications. Key to optimizing their switching properties is a detailed understanding of the photoswitching mechanism, which, as yet, is absent. Here we characterize the actinic step of DASA-photoswitching and its key intermediate, which was studied using a combination of ultrafast visible and IR pump–probe spectroscopies and TD-DFT calculations. Comparison of the time-resolved IR spectra with DFT computations allowed to unambiguously identify the structure of the intermediate, confirming that light absorption induces a sequential reaction path in which a Z–E photoisomerization of C2–C3 is followed by a rotation around C3–C4 and a subsequent thermal cyclization step. First and second-generation DASAs share a common photoisomerization mechanism in chlorinated solvents with notable differences in kinetics and lifetimes of the excited states. The photogenerated intermediate of the second-generation DASA was photo-accumulated at low temperature and probed with time-resolved spectroscopy, demonstrating the photoreversibility of the isomerization process. Taken together, these results provide a detailed picture of the DASA isomerization pathway on a molecular level.
P. Blonski, J. Tucek, Z. Sofer, V. Mazánek, M. Petr, M. Pumera, M. Otyepka, R. Zboril: Doping with Graphitic Nitrogen Triggers Ferromagnetism in Graphene, JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, vol. 139, iss. 8, pp. 3171–3180, 2017.
DOI: 10.1021/jacs.6b12934, IF = 13.858
Abstract: Nitrogen doping opens possibilities for tailoring the electronic properties and band gap of graphene towards its applications, e.g., in spintronics and optoelectronics. One major obstacle is development of magnetically active N-doped graphene with spin-polarized conductive behavior. However, the effect of nitrogen on the magnetic properties of graphene has so far only been addressed theoretically and triggering of magnetism through N-doping has not yet been proved experimentally, except for systems containing a high amount of oxygen and thus decreased conductivity. Here, we report the first example of ferromagnetic graphene achieved by controlled doping with graphitic, pyridinic, and chemisorbed nitrogen. The magnetic properties were found to depend strongly on both the nitrogen concentration and type of structural N-motifs generated in the host lattice. Graphenes doped below 5 at.% of nitrogen were nonmagnetic; however, once doped at 5.1 at.% of nitrogen, N-doped graphene exhib-ited transition to a ferromagnetic state at ~69 K and displayed a saturation magnetization reaching 1.09 emu/g. Theoretical calculations were used to elucidate the effects of individual chemical forms of nitrogen on magnetic properties. Results showed that magnetic ef-fects were triggered by graphitic nitrogen, whereas pyridinic and chemisorbed nitrogen contributed much less to the overall ferromagnetic ground state. Calcula-tions further proved the existence of exchange coupling among the paramagnetic centers mediated by the con-duction electrons.
A. Fihri, C. Len, R. S. Varma, A. Solhy: Hydroxyapatite: A review of syntheses, structure and applications in heterogeneous catalysis, COORDINATION CHEMISTRY REVIEWS vol. 347, pp. 48-76, 2017.
DOI: 10.1016/j.ccr.2017.06.009, IF = 13.324
Abstract: The synthesis of hydroxyapatite (HAP) and its applications in heterogeneous catalysis are abridged in view of its demonstrated prowess and utility in chemical, material and industrial industry. This overview documents the strengths and weaknesses of the synthetic routes that have been applied to the synthesis of hydroxyapatite with description of salient structural properties of hydroxyapatite responsible for its reactivity. The significant applications of hydroxyapatite both, as an inorganic support and as a catalyst are described with an emphasis on its performance, stability and reusability. Several newer findings as well as the current challenges pertaining to the use of hydoxyapetite are summarized.
K. Jayaramulu, J. Masa, O. Tomanec, D. Peeters, V. Ranc, A. Schneemann, R. Zboril, W. Schuhmann, R. A. Fischer: Nanoporous Nitrogen-Doped Graphene Oxide/Nickel Sulfide Composite Sheets Derived from a Metal-Organic Framework as an Efficient Electrocatalyst for Hydrogen and Oxygen Evolution, ADVANCED FUNCTIONAL MATERIALS, vol. 27, iss. 33, no. 1700451, 2017.
DOI: 10.1002/adfm.201700451, IF = 12.124
Abstract: Engineering of controlled hybrid nanocomposites creates one of the most exciting applications in the fields of energy materials and environmental science. The rational design and in situ synthesis of hierarchical porous nanocomposite sheets of nitrogen-doped graphene oxide (NGO) and nickel sulfide (Ni7S6) derived from a hybrid of a well-known nickel-based metal-organic framework (NiMOF-74) using thiourea as a sulfur source are reported here. The nanoporous NGO/MOF composite is prepared through a solvothermal process in which Ni(II) metal centers of the MOF structure are chelated with nitrogen and oxygen functional groups of NGO. NGO/Ni7S6 exhibits bifunctional activity, capable of catalyzing both the hydrogen evolution reaction (HER) and the oxygen evolution reaction (OER) with excellent stability in alkaline electrolytes, due to its high surface area, high pore volume, and tailored reaction interface enabling the availability of active nickel sites, mass transport, and gas release. Depending on the nitrogen doping level, the properties of graphene oxide can be tuned toward, e.g., enhanced stability of the composite compared to commonly used RuO2 under OER conditions. Hence, this work opens the door for the development of effective OER/HER electrocatalysts based on hierarchical porous graphene oxide composites with metal chalcogenides, which may replace expensive commercial catalysts such as RuO2 and IrO2.
N. Diarra dit Konté, M. Krepl, F. F. Damberger, N. Ripin, O. Duss, J. Šponer, F. H. Allain: Aromatic side-chain conformational switch on the surface of the RNA Recognition Motif enables RNA discrimination, NATURE COMMUNICATIONS vol. 8, iss. 1, 2017.
DOI: 10.1038/s41467-017-00631-3, IF = 12.124
Abstract: The cyclooxygenase-2 is a pro-inflammatory and cancer marker, whose mRNA stability and translation is regulated by the CUG-binding protein 2 interacting with AU-rich sequences in the 3′ untranslated region. Here, we present the solution NMR structure of CUG-binding protein 2 RRM3 in complex with 5′-UUUAA-3′ originating from the COX-2 3′-UTR. We show that RRM3 uses the same binding surface and protein moieties to interact with AU- and UG-rich RNA motifs, binding with low and high affinity, respectively. Using NMR spectroscopy, isothermal titration calorimetry and molecular dynamics simulations, we demonstrate that distinct sub-states characterized by different aromatic side-chain conformations at the RNA-binding surface allow for high- or low-affinity binding with functional implications. This study highlights a mechanism for RNA discrimination possibly common to multiple RRMs as several prominent members display a similar rearrangement of aromatic residues upon binding their targets.
C. Jia, W. Zuo, D. Yang, Y. Chen, L. Cao, R. Custelcean, J. Hostaš, P. Hobza, R. Glaser, Y. Wang, X. Yang, B. Wu: Selective binding of choline by a phosphate-coordination-based triple helicate featuring an aromatic box, NATURE COMMUNICATIONS vol. 8, iss. 1, 2017.
DOI: 10.1038/s41467-017-00915-8, IF = 12.124
Abstract: In nature, proteins have evolved sophisticated cavities tailored for capturing target guests selectively among competitors of similar size, shape, and charge. The fundamental principles guiding the molecular recognition, such as self-assembly and complementarity, have inspired the development of biomimetic receptors. In the current work, we report a self-assembled triple anion helicate (host 2) featuring a cavity resembling that of the choline-binding protein ChoX, as revealed by crystal and density functional theory (DFT)-optimized structures, which binds choline in a unique dual-site-binding mode. This similarity in structure leads to a similarly high selectivity of host 2 for choline over its derivatives, as demonstrated by the NMR and fluorescence competition experiments. Furthermore, host 2 is able to act as a fluorescence displacement sensor for discriminating choline, acetylcholine, L-carnitine, and glycine betaine effectively.
H. Huang, J. Raith, S. V. Kershaw, S. Kalytchuk, O. Tomanec, L. Jing, A. S. Susha, R. Zboril, A. L. Rogach: Growth mechanism of strongly emitting CH3NH3PbBr3 perovskite nanocrystals with a tunable bandgap, NATURE COMMUNICATIONS vol. 8, no. 996, 2017.
DOI: 10.1038/s41467-017-00929-2, IF = 12.124
Abstract: Metal halide perovskite nanocrystals are promising materials for a diverse range of applications, such as light-emitting devices and photodetectors. We demonstrate the bandgap tunability of strongly emitting CH3NH3PbBr3 nanocrystals synthesized at both room and elevated (60 °C) temperature through the variation of the precursor and ligand concentrations. We discuss in detail the role of two ligands, oleylamine and oleic acid, in terms of the coordination of the lead precursors and the nanocrystal surface. The growth mechanism of nanocrystals is elucidated by combining the experimental results with the principles of nucleation/growth models. The proposed formation mechanism of perovskite nanocrystals will be helpful for further studies in this field and can be used as a guide to improve the synthetic methods in the future.
J. Onoda, M. Ondráček, P. Jelínek, Y. Sugimoto: Electronegativity determination of individual surface atoms by atomic force microscopy, NATURE COMMUNICATIONS vol. 8, pp. 15155, 2017.
DOI: 10.1038/ncomms15155, IF = 12.124
Abstract: Electronegativity is a fundamental concept in chemistry. Despite its importance, the experimental determination has been limited only to ensemble-averaged techniques. Here, we report a methodology to evaluate the electronegativity of individual surface atoms by atomic force microscopy. By measuring bond energies on the surface atoms using different tips, we find characteristic linear relations between the bond energies of different chemical species. We show that the linear relation can be rationalized by Pauling’s equation for polar covalent bonds. This opens the possibility to characterize the electronegativity of individual surface atoms. Moreover, we demonstrate that the method is sensitive to variation of the electronegativity of given atomic species on a surface due to different chemical environments. Our findings open up ways of analysing surface chemical reactivity at the atomic scale.
J. Tuček, K. Holá, A. B. Bourlinos, P. Błoński, A. Bakandritsos, J. Ugolotti, M. Dubecký, F. Karlický, V. Ranc, K. Čépe, M. Otyepka, R. Zbořil: Room temperature organic magnets derived from sp3 functionalized graphene, NATURE COMMUNICATIONS vol. 8, pp. 14525, 2017.
DOI: 10.1038/ncomms14525, IF = 12.124
Abstract: Materials based on metallic elements that have d orbitals and exhibit room temperature magnetism have been known for centuries and applied in a huge range of technologies. Development of room temperature carbon magnets containing exclusively sp orbitals is viewed as great challenge in chemistry, physics, spintronics and materials science. Here we describe a series of room temperature organic magnets prepared by a simple and controllable route based on the substitution of fluorine atoms in fluorographene with hydroxyl groups. Depending on the chemical composition (an F/OH ratio) and sp3 coverage, these new graphene derivatives show room temperature antiferromagnetic ordering, which has never been observed for any sp-based materials. Such 2D magnets undergo a transition to a ferromagnetic state at low temperatures, showing an extraordinarily high magnetic moment. The developed theoretical model addresses the origin of the room temperature magnetism in terms of sp2-conjugated diradical motifs embedded in an sp3 matrix and superexchange interactions via –OH functionalization.
Z. Sofer, J. Luxa, D. Bouša, D. Sedmidubský, P. Lazar, T. Hartman, H. Hardtdegen, M. Pumera: The Covalent Functionalization of Layered Black Phosphorus by Nucleophilic Reagents, ANGEWANDTE CHEMIE INTERNATIONAL EDITION vol. 56, iss. 33, pp. 9891-9896, 2017.
DOI: 10.1002/anie.201705722, IF = 11.994
Abstract: Layered black phosphorus has been attracting great attention due to its interesting material properties which lead to a plethora of proposed applications. Several approaches are demonstrated here for covalent chemical modifications of layered black phosphorus in order to form P−C and P-O-C bonds. Nucleophilic reagents are highly effective for chemical modification of black phosphorus. Further derivatization approaches investigated were based on radical reactions. These reagents are not as effective as nucleophilic reagents for the surface covalent modification of black phosphorus. The influence of covalent modification on the electronic structure of black phosphorus was investigated using ab initio calculations. Covalent modification exerts a strong effect on the electronic structure including the change of band-gap width and spin polarization.
J. Luxa, P. Vosecký, V. Mazánek, D. Sedmidubský, M. Pumera, P. Lazar, Z. Sofer: Layered Transition-Metal Ditellurides in Electrocatalytic Applications—Contrasting Properties, ACS CATALYSIS vol. 7, iss. 9, pp. 5706-5716, 2017.
DOI: 10.1021/acscatal.7b02080, IF = 10.614
Abstract: The layered compounds and especially transition-metal dichalcogenides are at the forefront of current research on electrocatalytic materials. Despite the fact that electrocatalytical properties of molybdenum and tungsten disulfides are well-known, their tellurium analogues are significantly less explored. Here we show an effective method for MoTe2 and WTe2 chemical exfoliation based on alkali metal intercalation and subsequent reaction with water. The as-synthesized and exfoliated tellurides were characterized in detail and investigated for potential application in electrocatalysis. The inherent electrochemical activity related to both cation and anion was observed. This is dominantly related to the oxidation tendency of tellurium. The MoTe2 and WTe2 show significantly contrasting properties toward the hydrogen evolution reaction, where MoTe2 shows highly increased HER activity with little dependence on electrochemical treatment, whereas WTe2 shows slightly worse improvement and strong dependence on the electrochemical treatment. In particular, the exfoliated MoTe2 exhibits improved electrocatalytic activity for hydrogen evolution reaction and possesses a huge application potential.
F. Malara, S. Carallo, E. Rotunno, L. Lazzarini, E. Piperopoulos, C. Milone, A. Naldoni: A Flexible Electrode Based on Al-Doped Nickel Hydroxide Wrapped around a Carbon Nanotube Forest for Efficient Oxygen Evolution, ACS CATALYSIS vol. 7, iss. 7, pp. 4786-4795, 2017.
DOI: 10.1021/acscatal.7b01188, IF = 10.614
Abstract: The development of highly active, cheap, and stable electrocatalysts for overall water splitting is strategic for industrial electrolysis processes aiming to achieve sustainable hydrogen production. Here, we report the impressive electrocatalytic activity of the oxygen evolution reaction of Al-doped Ni(OH)2 deposited on a chemically etched carbon nanotube forest (CNT-F) supported on a flexible polymer/CNT nanocomposite. Our monolithic electrode generates a stable current density of 10 mA/cm2 at an overpotential (η) of 0.28 V toward the oxygen evolution reaction in 1 M NaOH and reaches approximately 200 mA/cm2 at 1.7 V versus the reversible hydrogen electrode in 6 M KOH. The CNT-F/NiAl electrode also shows an outstanding activity for the hydrogen evolution reaction under alkaline conditions. When CNT-F/NiAl is used both at the anode and at the cathode, our device can sustain the overall water splitting, reaching 10 mA/cm2 at η = 1.96 V. The high electrocatalytic activity of the CNT-F/NiAl hydroxide is due to the huge surface area of the CNT forest, the high electrical conductivity of the nanocomposite substrate, and the interactions between the NiAl catalyst and the CNTs.
Y. Hou, Y. Liu, R. Gao, Q. Li, H. Guo, A. Goswami, R. Zboril, M. B. Gawande, X. Zou: Ag@CoxP Core–Shell Heterogeneous Nanoparticles as Efficient Oxygen Evolution Reaction Catalysts, ACS CATALYSIS, pp. 7038-7042, 2017.
DOI: 10.1021/acscatal.7b02341, IF = 10.614
Abstract: We present a facile synthetic method that yields Ag@CoxP core–shell-type heterogeneous nanostructures with excellent oxygen evolution reaction (OER) activity. This nanocatalyst can deliver a current density of 10 mA/cm2 at a small overpotential of 310 mV and exhibits high catalytic stability. Additionally, the catalytic activity of Ag@CoxP is 8 times higher than that of the Co2P nanoparticles, owing primarily to the strong electronic interaction between the Ag core and the CoxP shell.
M. Krepl, M. Blatter, A. Cléry, F. F. Damberger, F. H. Allain, J. Sponer: Structural study of the Fox-1 RRM protein hydration reveals a role for key water molecules in RRM-RNA recognition, NUCLEIC ACIDS RESEARCH vol. 45, iss. 13, pp. 8046-8063, 2017.
DOI: 10.1093/nar/gkx418, IF = 10.162
Abstract: The Fox-1 RNA recognition motif (RRM) domain is an important member of the RRM protein family. We report a 1.8 Å X-ray structure of the free Fox-1 containing six distinct monomers. We use this and the nuclear magnetic resonance (NMR) structure of the Fox-1 protein/RNA complex for molecular dynamics (MD) analyses of the structured hydration. The individual monomers of the X-ray structure show diverse hydration patterns, however, MD excellently reproduces the most occupied hydration sites. Simulations of the protein/RNA complex show hydration consistent with the isolated protein complemented by hydration sites specific to the protein/RNA interface. MD predicts intricate hydration sites with water-binding times extending up to hundreds of nanoseconds. We characterize two of them using NMR spectroscopy, RNA binding with switchSENSE and free-energy calculations of mutant proteins. Both hydration sites are experimentally confirmed and their abolishment reduces the binding free-energy. A quantitative agreement between theory and experiment is achieved for the S155A substitution but not for the S122A mutant. The S155 hydration site is evolutionarily conserved within the RRM domains. In conclusion, MD is an effective tool for predicting and interpreting the hydration patterns of protein/RNA complexes. Hydration is not easily detectable in NMR experiments but can affect stability of protein/RNA complexes.
L. Pravda, D. Sehnal, R. Svobodová Vařeková, V. Navrátilová, D. Toušek, K. Berka, M. Otyepka, J. Koča:
ChannelsDB: database of biomacromolecular tunnels and pores. NUCLEIC ACIDS RESEARCH, in press, 2017
DOI: 10.1093/nar/gkx868, IF = 10.162
Abstract:ChannelsDB (http://ncbr.muni.cz/ChannelsDB) is a database providing information about the positions, geometry and physicochemical properties of channels (pores and tunnels) found within biomacromolecular structures deposited in the Protein Data Bank. Channels were deposited from two sources; from literature using manual deposition and from a software tool automatically detecting tunnels leading to the enzymatic active sites and selected cofactors, and transmembrane pores. The database stores information about geometrical features (e.g. length and radius profile along a channel) and physicochemical properties involving polarity, hydrophobicity, hydropathy, charge and mutability. The stored data are interlinked with available UniProt annotation data mapping known mutation effects to channel-lining residues. All structures with channels are displayed in a clear interactive manner, further facilitating data manipulation and interpretation. As such, ChannelsDB provides an invaluable resource for research related to deciphering the biological function of biomacromolecular channels.
M. Figiel, M. Krepl, J. Poznański, A. Gołąb, J. Šponer, M. Nowotny: Coordination between the polymerase and RNase H activity of HIV-1 reverse transcriptase, NUCLEIC ACIDS RESEARCH, vol. 45, iss. 6, pp. 3341-3352, 2017
DOI: 10.1093/nar/gkx004, IF = 10.162
Abstract: Replication of human immunodeficiency virus 1 (HIV-1) involves conversion of its single-stranded RNA genome to double-stranded DNA, which is integrated into the genome of the host. This conversion is catalyzed by reverse transcriptase (RT), which possesses DNA polymerase and RNase H domains. The available crystal structures suggest that at any given time the RNA/DNA substrate interacts with only one active site of the two domains of HIV-1 RT. Unknown is whether a simultaneous interaction of the substrate with polymerase and RNase H active sites is possible. Therefore, the mechanism of the coordination of the two activities is not fully understood. We performed molecular dynamics simulations to obtain a conformation of the complex in which the unwound RNA/DNA substrate simultaneously interacts with the polymerase and RNase H active sites. When the RNA/DNA hybrid was immobilized at the polymerase active site, RNase H cleavage occurred, experimentally verifying that the substrate can simultaneously interact with both active sites. These findings demonstrate the existence of a transient conformation of the HIV-1 RT substrate complex, which is important for modulating and coordinating the enzymatic activities of HIV-1 RT.
G. Zoppellaro, J. Tuček, J. Ugolotti, C. Aparicio, O. Malina, K. Čépe, R. Zbořil: Triggering Two-Step Spin Bistability and Large Hysteresis in Spin Crossover Nanoparticles via Molecular Nanoengineering, CHEMISTRY OF MATERIALS vol. 29, iss. 20, pp. 8875-8883, 2017.
DOI: 10.1021/acs.chemmater.7b03633, IF = 9.466
Abstract: The local entrapment of the spin crossover complex Fe(II)-tris[2-(2′-pyridyl)benzimidazole] into the pluronic polymeric matrix (P123, PEG20–PPG70–PEG20, MW ∼ 5800) yielded the formation of magnetic nanoparticles of ∼26 nm (SCO-Np). Formation of SCO-Np was driven by the emergence of noncovalent interactions between the aromatic −NH group of the benzimidazole moieties present in Fe(II)-tris[2-(2′-pyridyl)benzimidazole] with the aliphatic ether (−O−) groups of the pluronic polymeric matrix. The nanoparticles show spin crossover behavior, two-step spin bistability, and wide magnetic hysteresis, expressed in the temperature range of 170–280 K (ΔTmax = 38 K). The neat SCO molecules, Fe(II)-tris[2-(2′-pyridyl)benzimidazole], on the contrary show only first-order spin transition and negligible hysteresis. The developed matrix-confinement approach of SCO molecules shown in this work yielded an unprecedented and significant improvement of the magnetic cooperativity compared to the neat spin crossover system, despite the decreased dimension of the magnetic domain in the nanosized architecture.
S. Presolski, L. Wang, A. H. Loo, A. Ambrosi, P. Lazar, V. Ranc, M. Otyepka, R. Zboril, O. Tomanec, J. Ugolotti, Z. Sofer, M. Pumera: Functional Nanosheet Synthons by Covalent Modification of Transition-Metal Dichalcogenides, CHEMISTRY OF MATERIALS vol. 29, iss. 5, pp. 2066-2073, 2017.
DOI: 10.1021/acs.chemmater.6b04171, IF = 9.466
Abstract: We report on the facile preparation of versatile MoS2–thiobarbituric acid conjugates, which, in addition to excellent electrochemical behavior, can serve as nanosheet platforms for further functionalization in a multitude of applications. We show that chemically exfoliated MoS2 was extensively modified with up to 50% surface coverage, while maintaining its metallic character, and that the strategy can be extended to MoSe2, WS2, and WSe2. The covalent functionalization endowed the materials not only with good aqueous dispersibility, but also with improved hydrogen evolution reaction (HER) activity, as well as promise in the oxidative detection of DNA nucleobases in solution.
D. D. Chronopoulos, A. Bakandritsos, P. Lazar, M. Pykal, K. Čépe, R. Zbořil, M. Otyepka: High-Yield Alkylation and Arylation of Graphene via Grignard Reaction with Fluorographene, CHEMISTRY OF MATERIALS, vol. 29, iss. 3, pp. 926–930, 2017.
DOI: 10.1021/acs.chemmater.6b05040, IF = 9.466
B. de la Torre, M. Švec, G. Foti, O. Krejčí, P. Hapala, A. Garcia-Lekue, T. Frederiksen, R. Zbořil, A. Arnau, H. Vázquez, P. Jelínek: Submolecular Resolution by Variation of the Inelastic Electron Tunneling Spectroscopy Amplitude and its Relation to the AFM/STM Signal, PHYSICAL REVIEW LETTERS vol. 119, iss. 16, 2017.
DOI: 10.1103/physrevlett.119.166001, IF = 8.462
Abstract: Here we show scanning tunneling microscopy (STM), noncontact atomic force microscopy (AFM), and inelastic electron tunneling spectroscopy (IETS) measurements on an organic molecule with a CO-terminated tip at 5 K. The high-resolution contrast observed simultaneously in all channels unambiguously demonstrates the common imaging mechanism in STM/AFM/IETS, related to the lateral bending of the CO-functionalized tip. The IETS spectroscopy reveals that the submolecular contrast at 5 K consists of both renormalization of vibrational frequency and variation of the amplitude of the IETS signal. This finding is also corroborated by first principles simulations. We extend accordingly the probe-particle AFM/STM/IETS model to include these two main ingredients necessary to reproduce the high-resolution IETS contrast. We also employ the first principles simulations to get more insight into a different response of frustrated translation and rotational modes of the CO tip during imaging.
V. Urbanová, A. Bakandritsos, P. Jakubec, T. Szambó, R. Zbořil: A facile graphene oxide based sensor for electrochemical detection of neonicotinoids, BIOSENSORS AND BIOELECTRONICS vol. 89, pp. 532-537, 2017.
DOI: 10.1016/j.bios.2016.03.039, IF = 7.780
Abstract: The increasing use of neonicotinoids in systematic seed treatment to crops is a serious cause of pollution of water resources and environment. Consequently, food sources can get eventually contaminated. To this end, it is desirable to develop suitable and effective platforms in order to obtain low-cost and sensitive sensors for neonicotinoids detection. In this work, graphene oxide modified electrodes were used as highly efficient electrochemical sensors for detection of two common insecticides – thiamethoxam and imidacloprid. The proposed sensor responded linearly in the concentration range of 10–200 µmol L−1 for both analytes and the detection limits were determined as low as 8.3 µmol L−1 and 7.9 µmol L−1 for thiamethoxam and imidacloprid, respectively. Analytical performance was also evaluated on spiked water and honey samples.
R. Bartali, M. Otyepka, M. Pykal, P. Lazar, V. Micheli, G. Gottardi, N. Laidani: Interaction of the Helium, Hydrogen, Air, Argon, and Nitrogen Bubbles with Graphite Surface in Water, ACS APPLIED MATERIALS & INTERFACES vol. 9, iss. 20, pp. 17517-17525, 2017.
DOI: 10.1021/acsami.6b16493, IF = 7.504
Abstract: The interaction of the confined gas with solid surface immersed in water is a common theme of many important fields such as self-cleaning surface, gas storage, and sensing. For that reason, we investigated the gas-graphite interaction in the water medium. The graphite surface was prepared by mechanical exfoliation of highly oriented pyrolytic graphite (HOPG). The surface chemistry and morphology were studied by X-ray photoelectron spectroscopy, profilometry, and atomic force microscopy. The surface energy of HOPG was estimated by contact angle measurements using the Owens–Wendt method. The interaction of gases (Ar, He, H2, N2, and air) with graphite was studied by a captive bubble method, in which the gas bubble was in contact with the exfoliated graphite surface in water media. The experimental data were corroborated by molecular dynamics simulations and density functional theory calculations. The surface energy of HOPG equaled to 52.8 mJ/m2 and more of 95% of the surface energy was attributed to dispersion interactions. The results on gas–surface interaction indicated that HOPG surface had gasphilic behavior for helium and hydrogen, while gasphobic behavior for argon and nitrogen. The results showed that the variation of the gas contact angle was related to the balance between the gas–surface and gas–gas interaction potentials. For helium and hydrogen the gas–surface interaction was particularly high compared to gas–gas interaction and this promoted the favorable interaction with graphite surface.
A. Goswami, A. K. Rathi, C. Aparicio, O. Tomanec, M. Petr, R. Pocklanova, M. B. Gawande, R. S. Varma, R. Zboril: In-situ Generation of Pd-Pt Core-shell Nanoparticles on Reduced Graphene Oxide (Pd@Pt/rGO) using Microwaves: Applications in Dehalogenation Reactions and Reduction of Olefins, ACS APPLIED MATERIALS & INTERFACES, vol. 9, iss. 3, pp. 2815-2824, 2017.
DOI: 10.1021/acsami.6b13138, IF = 7.504
Abstract: Core-shell nanocatalysts are distinctive class of nanomaterials with varied potential applications in view of their unique structure and composition-dependent physico-chemical properties and promising synergism among the individual components. A one-pot microwave (MW)-assisted approach is described to prepare the reduced graphene oxide (rGO)-supported Pd-Pt core-shell nanoparticles, (Pd@Pt/rGO); spherical core-shell nanomaterials (~95 nm) with Pd core (~80 nm) and 15 nm Pt shell were nicely distributed on the rGO matrix in view of the choice of reductant and reaction conditions. The well-characterized composite nanomaterials, endowed with synergism among its components and rGO support, served as catalysts in aromatic dehalogenation reactions and for the reduction of olefins with high yield (>98%), excellent selectivity (>98%) and recyclability (up to 5 times); both, Pt/rGO and Pd/rGO and even their physical mixtures showed considerably lower conversions (20 and 57%) in dehalogenation of 3-bromoaniline. Similarly, in the reduction of styrene to ethylbenzene, Pt@Pd core-shell nanoparticles (without rGO support) possess considerably lower conversion (60%), compared to Pd@Pt/rGO. The mechanism of dehalogenation reactions with Pd@Pt/rGO catalyst is discussed with the explicit premise that rGO matrix facilitates the adsorption of the reducing agent thus enhancing its local concentration and expediting the decomposition rate. The versatility of the catalyst has been validated via diverse substrate scope for both, the reduction and dehalogenation reactions.
E. Otyepková, P. Lazar, J. Luxa, K. Berka, K. Čépe, Z. Sofer, M. Pumera, M. Otyepka: Surface properties of MoS2 probed by inverse gas chromatography and their impact on electrocatalytic properties, NANOSCALE vol. 9, iss. 48, pp. 19236-19244, 2017.
DOI: 10.1039/c7nr07342a, IF = 7.367
Abstract: Layered transition metal dichalcogenides (TMDs) are at the forefront of materials research. One of the most important applications of these materials is their electrocatalytic activity towards hydrogen evolution, and these materials are suggested to replace scarce platinum. Whilst there are significant efforts towards this goal, there are various reports of electrocatalysis of MoS2 (which is the most commonly tested TMD) with large variations of the reported electrocatalytic effect of the material, with overpotential varying by several hundreds of millivolts. Here, we analyzed surface properties of various bulk as well as single layer MoS2 samples using inverse gas chromatography. All samples displayed significant variations in surface energies and their heterogeneities. The surface energy ranged from 50 to 120 mJ m−2 depending on the sample and surface coverage. We correlated the surface properties and previously reported structural features of MoS2 with their electrochemical activities. We concluded that the observed differences in electrochemistry are caused by the surface properties. This is an important finding with an enormous impact on the whole field of electrocatalysis of layered materials.
J. P. Froning, P. Lazar, M. Pykal, Q. Li, M. Dong, R. Zbořil, M. Otyepka: Direct mapping of chemical oxidation of individual graphene sheets through dynamic force measurements at the nanoscale, NANOSCALE vol. 9, iss. 1, pp. 119-127, 2017.
DOI: 10.1039/c6nr05799c, IF = 7.367
Abstract: Graphene oxide is one of the most studied nanomaterials owing to its huge application potential in many fields, including biomedicine, sensing, drug delivery, optical and optoelectronic technologies. However, a detailed description of the chemical composition and the extent of oxidation in graphene oxide remains a key challenge affecting its applicability and further development of new applications. Here, we report direct monitoring of the chemical oxidation of an individual graphene flake during ultraviolet/ozone treatment through in situ atomic force microscopy based on dynamic force mapping. The results showed that graphene oxidation expanded from the graphene edges to the entire graphene surface. The interaction force mapping results correlated well with X-ray photoelectron spectroscopy data quantifying the degree of chemical oxidation. Density functional theory calculations confirmed the specific interaction forces measured between a silicon tip and graphene oxide. The developed methodology can be used as a simple protocol for evaluating the chemical functionalization of other two-dimensional materials with covalently attached functional groups.
H. Han, F. Riboni, F. Karlický , S. Kment, A. Goswami, P. . Sudhagar, J. Yoo, L. Wang, O. Tomanec, M. Petr, O. Haderka, C. Terashima, A. Fujishima, P. Schmuki, R. Zboril: α-Fe2O3/TiO2 3D Hierarchical Nanostructures for enhanced Photoelectrochemical Water Splitting, NANOSCALE, vol. 9, iss. 1, pp. 134-142, 2017.
DOI: 10.1039/c6nr06908h, IF = 7.367
Abstract: We report the fabrication of 3D hierarchical hetero-nanostructures composed of thin α-Fe2O3 nanoflakes branched on TiO2 nanotubes. The novel α-Fe2O3/TiO2 hierarchical nanostructures, synthesized on FTO through a multi-step hydrothermal process, exhibit enhanced performances in photo-electrochemical water splitting and in the photocatalytic degradation of an organic dye, with respect to pure TiO2 nanotubes. An enhanced separation of photogenerated charge carriers is here proposed as main factor for the observed photo-activities: electrons photogenerated in TiO2 are efficiently collected at FTO, while holes are transferred to the α-Fe2O3 nanobranches that serve as charge mediator to the electrolyte. The morphology of α-Fe2O3 that varies from ultra-thin nanoflakes to nanorod/nanofiber structures depending on the Fe precursor concentration was shown to have a significant impact on the photo-induced activity of the α-Fe2O3/TiO2 composites. In particular, it is shown that for an optimized photo-electrochemical structure a combination of critical factors should be achieved such as i) TiO2 light absorption and photo-activation vs. α-Fe2O3-induced shadowing effect and ii) the availability of free TiO2 surface vs. α-Fe2O3-coated surface. Finally, theoretical analysis, based on DFT calculations, confirmed the optical properties experimentally determined for the α-Fe2O3/TiO2 hierarchical nanostructures. We anticipate that this new multi-step hydrothermal process can be a blueprint for the design and development of other hierarchical heterogeneous metal oxide electrodes suitable for photo-electrochemical applications.
Z. Tian, X. Zhang, D. Li, D. Zhou, P. Jing, D. Shen, S. Qu, R. Zboril, A. L. Rogach: Full-Color Inorganic Carbon Dot Phosphors for White-Light-Emitting Diodes, ADVANCED OPTICAL MATERIALS, vol. 5, iss. 19, pp. 1700416, 2017.
DOI: 10.1002/adom.201700416, IF = 6.875
Abstract: Light-emitting carbon dots (CDots) are widely investigated due to their distinct merits. However, it is still a challenge to modulate their bandgap emissions and conquer their aggregation-induced luminescence quenching to achieve full-color highly emissive CDot-based phosphors. Herein, this study proposes an approach toward realization of full-color emissive CDots from two common precursors, citric acid and urea, through employing three different solvents (water, glycerol, and dimethylformamide) and their combinations in a solvothermal synthesis. Employing sodium silicate solution, this study further demonstrates the microwave-assisted method allowing to incorporate CDots into a silica network, which effectively prevents aggregation of CDots and results in strongly luminescent full-color inorganic CDot phosphors with photoluminescence quantum yields of 30–40%. Through deposition of the red- and green-emitting CDot phosphors on blue-emitting InGaN chips, white-light-emitting diodes are fabricated with Commission Internationale de L'Eclairage of (0.34, 0.31) and the color rendering index of 82.4, indicating their promising application for solid-state lighting.
S. Kalytchuk, M. Adam, O. Tomanec, R. Zbořil, N. Gaponik, A. L. Rogach: Sodium Chloride Protected CdHgTe Quantum Dot Based Solid-State Near-Infrared Luminophore for Light-Emitting Devices and Luminescence Thermometry, ACS PHOTONICS, vol. 4, iss. 6, pp. 1459–1465, 2017.
DOI: 10.1021/acsphotonics.7b00222, IF = 6.756
Abstract: Solid-state luminophores operating in the near-infrared (NIR) region may have applications in sensing, communication, and medicine. We report environmentally protected solid-state NIR-emitting luminophores fabricated by embedding CdHgTe colloidal quantum dots (QDs) into a NaCl matrix, with remarkable photo- and thermal stability and a photoluminescence quantum yield of 31% in the solid state, which is among the highest reported for solid-state NIR luminophores so far. We employed this luminophore as a down-conversion layer in a NIR-light-emitting device with a stable emission at 940 nm. Carrier recombination dynamics of the CdHgTe QDs@NaCl powders are examined as a function of temperature using steady-state and transient photoluminescence spectroscopy, and characteristic parameters such as the band gap, the temperature coefficient, the Debye temperature, the activation energy of thermal quenching, and radiative and nonradiative recombination rates are derived. Temperature-dependent changes of the spectral position and the photoluminescence lifetime of CdHgTe QDs@NaCl are shown to serve as a base for two temperature detection schemes, namely, luminescence spectral and luminescence lifetime thermometry, a versatile optical technique for the noninvasive, noncontact estimation of local temperature.
A. Fargašová, A. Balzerová, R. Prucek, M. H. Sedláková, K. Bogdanová, J. Gallo, M. Kolář, V. Ranc, R. Zbořil: Detection of Prosthetic Joint Infection Based on Magnetically Assisted Surface Enhanced Raman Spectroscopy, ANALYTICAL CHEMISTRY, vol. 89, iss. 12, pp. 6598–6607, 2017.
DOI: 10.1021/acs.analchem.7b00759, IF = 6.320
Abstract: Accurate and rapid diagnosis of prosthetic joint infection (PJI) is vital for rational and effective therapeutic management of this condition. Several diagnostic strategies have been developed for discriminating between infected and noninfected cases. However, none of them can reliably diagnose the whole spectrum of clinical presentations of PJI. Here, we report a new method for PJI detection based on magnetically assisted surface enhanced Raman spectroscopy (MA-SERS) using streptavidin-modified magnetic nanoparticles (MNP@Strep) whose surface is functionalized with suitable biotinylated antibodies and then coated with silver nanoparticles by self-assembly. The high efficiency of this approach is demonstrated by the diagnosis of infections caused by two bacterial species commonly associated with PJI, namely, Staphylococcus aureus and Streptococcus pyogenes. The method’s performance was verified with model samples of bacterial lysates and with four real-matrix samples of knee joint fluid spiked with live pathogenic bacterial cells. This procedure is operationally simple, versatile, inexpensive, and quick to perform, making it a potentially attractive alternative to established diagnostic techniques based on Koch’s culturing or colony counting methods.
V. B. Gade, A. K. Rathi, S. B. Bhalekar, J. Tucek, O. Tomanec, R. S. Varma, R. Zboril, S. N. Shelke, M. B. Gawande: Iron-Oxide-Supported Ultrasmall ZnO Nanoparticles: Applications for Transesterification, Amidation, and O-Acylation Reactions, ACS SUSTAINABLE CHEMISTRY & ENGINEERING, vol. 5, iss. 4, pp. 3314–3320, 2017.
DOI: 10.1021/acssuschemeng.6b03167, IF = 5.951
Abstract: An efficient maghemite–ZnO nanocatalyst has been synthesized via a simple coprecipitation method, where ZnO nanoparticles are uniformly decorated on the maghemite core and characterized by XRD, SEM-EDS, ICP-AES, XPS, TEM, HRTEM, and Mössbauer spectroscopy; maghemite nanoparticles are in the typical size range 10–30 nm with ultrasmall (3–5 nm) ZnO nanoparticles. A competent and benign protocol is reported for various organic transformations, namely, transesterification, amidation, and O-acylation reaction in good to excellent yields (75–97%) using magnetically separable and reusable maghemite–ZnO nanocatalyst.
J. Tuček, R. Prucek, J. Kolařík, G. Zoppellaro, M. Petr, J. Filip, V. K. Sharma, R. Zbořil: Zero-Valent Iron Nanoparticles Reduce Arsenites and Arsenates to As(0) Firmly Embedded in Core–Shell Superstructure: Challenging Strategy of Arsenic Treatment under Anoxic Conditions, ACS SUSTAINABLE CHEMISTRY & ENGINEERING, vol. 5, iss. 4, pp. 3027–3038, 2017.
DOI: 10.1021/acssuschemeng.6b02698, IF = 5.951
Abstract: Arsenites and arsenates are carcinogenic to humans and are typically removed from contaminated water using various sorbents. However, these treatment methods result in the secondary release of weakly bound As species and require large amounts of sorbents. Here, we introduce a groundbreaking method involving the use of oxidic-shell-free nanoscale zero-valent iron (OSF-nZVI) to treat arsenite/arsenate-polluted underground water. Under anoxic conditions, OSF-nZVI is capable to reduce As(III)/As(V) species to As(0) (up to 65% of total arsenic content). Thus, reduction synergistically contributes to sorption tuning suitably the chemical nature and isoelectric points of As species, thereby enhancing arsenic removal from an anoxic aqueous environment. More importantly, As species are locked between the Fe(0) core and iron(III) oxide outer shell. For comparison, the removal capability of OSF-nZVI is 2 times lower under oxic conditions, due to the complex redox mechanism resulting in exclusive sorption of As(III)/As(V) species onto the surface of oxidized OSF-nZVI particles. The unique strategy to treat arsenites/arsenates by their reduction to zero-valent arsenic with OSF-nZVI was also demonstrated in experiments with real polluted water. Results suggest that “green” reduction and firm immobilization of toxic As species through OSF-nZVI could provide environmentally friendly tool to treat arsenic-polluted underground water, a main source of highly contaminated drinking water worldwide.
E. Petala, Y. Georgiou, V. Kostas, K. Dimos, M. A. Karakassides, Y. Deligiannakis, C. Aparicio, J. Tuček, R. Zboril: Magnetic Carbon Nanocages: An Advanced Architecture with Surface- and Morphology-Enhanced Removal Capacity for Arsenites, ACS SUSTAINABLE CHEMISTRY & ENGINEERING, vol. 5, iss. 7, pp. 5782–5792, 2017.
DOI: 10.1021/acssuschemeng.7b00394, IF = 5.951
Abstract: Magnetic carbon nanocages (Mag@CNCs) have been synthesized via a green one-step process using pine resin and iron nitrate salt as a carbon and iron source, respectively. In order to produce Mag@CNCs, pristine materials have been carbonized at high temperature under inert atmosphere. The structural, textural, and surface properties of as-synthesized Mag@CNCs were studied employing microscopic, spectroscopic, and surface physicochemical methods. The obtained results showed that the new Mag@CNCs have significant surface area (177 m2 g–1) with both microporosity and mesoporosity. Moreover, the material exhibits a homogeneous distribution of core-shell-type magnetic nanoparticles within the carbon matrix, formed by iron carbide (Fe3C) and metallic iron (α-Fe), with sizes of 20-100 nm, surrounded by few graphitic layers-walls. Most importantly, Mag@CNCs were tested as absorbent for As(III) removal from aqueous solutions, showing a total As(III) uptake capacity of 263.9 mg of per gram of material at pH = 7, a record sorption capacity value among all previously tested iron-based materials and one of highest values among all reported sorbents so far. The adsorbed As(III) are anchored at the surface of Mag@CNCs, as demonstrated by high-resolution transmission electron microscopy and X-ray phtotoelectron spectroscopy measurements. The pH-edge As(III)-adsorption experiments combined with theoretical surface complexation modeling allow a detailed understanding of the interfacial properties of Mag@CNCs, and hence the As(III) uptake mechanism. The analysis revealed that As(III) binds on two types of surface sites of Mag@CNCs, i.e., on carbon-surface species (≡CxOH2) and on Fe-oxide layer (≡FeΟH2) of nanoparticles. This exemplifies that the advanced morphology- and surface-driven synergistic properties of the Mag@CNCs material are crucial for its As(III)-uptake performance.
D. S. Doke, S. B. Umbarkar, M. B. Gawande, R. Zboril, A. V. Biradar: Environmentally Benign Bio-derived Carbon Microspheres-supported Molybdena Nanoparticles as Catalyst for the Epoxidation Reaction, ACS SUSTAINABLE CHEMISTRY & ENGINEERING, vol. 5, iss.1, pp. 904-910, 2017.
DOI: 10.1021/acssuschemeng.6b02229, IF = 5.951
Abstract: A one-pot synthesis of molybdenum oxide nanoparticles (NPs) supported on bio-derived carbon microspheres is reported. The catalyst was synthesized by the low temperature hydrothermal (LTH) method using D-glucose and bagasse as the car-bon source. The carbonization of bagasse resulted in the formation of non-uniform carbon microspheres while glucose re-sulted in uniform carbon spheres. SEM and STEM elemental mapping show the uniform distribution of molybdenum oxide NPs over the carbon microspheres. XPS spectroscopy confirmed that molybdenum was in Mo6+ oxidation state. The 1% MoO3 supported on carbon microspheres derived from D-glucose showed excellent catalytic activity up to 100% olefin con-version with 100% epoxide selectivity using organic tert-Butyl hydroperoxide as an oxidant. The catalyst was successfully used up to five cycles without losing substantial activity and selectivity.
D. D. Chronopoulos, A. Bakandritsos, M. Pykal, R. Zbořil, M. Otyepka: Chemistry, properties, and applications of fluorographene, APPLIED MATERIALS TODAY vol. 9, pp. 60-70, 2017.
DOI: 10.1016/j.apmt.2017.05.004, IF = 5.710
Abstract: Fluorographene, formally a two-dimensional stoichiometric graphene derivative, attracted remarkable attention of the scientific community due to its extraordinary physical and chemical properties. We overview the strategies for the preparation of fluorinated graphene derivatives, based on top-down and bottom-up approaches. The physical and chemical properties of fluorographene, which is considered as one of the thinnest insulators with a wide electronic band gap, are presented. Special attention is paid to the rapidly developing chemistry of fluorographene, which was advanced in the last few years. The unusually high reactivity of fluorographene, which can be chemically considered perfluorinated hydrocarbon, enables facile and scalable access to a wide portfolio of graphene derivatives, such as graphene acid, cyanographene and allyl-graphene. Finally, we summarize the so far reported applications of fluorographene and fluorinated graphenes, spanning from sensing and bioimaging to separation, electronics and energy technologies.
A. B. Bourlinos, V. Georgakilas, V. Mouselimis, A. Kouloumpis, E. Mouzourakis, A. Koutsioukis, M. Antoniou, D. Gournis, M. A. Karakassides, Y. Deligiannakis, V. Urbanova, K. Cepe, A. Bakandritsos, R. Zboril: Fullerol–graphene nanobuds: Novel water dispersible and highly conductive nanocarbon for electrochemical sensing, APPLIED MATERIALS TODAY vol. 9, pp. 71-76, 2017.
DOI: 10.1016/j.apmt.2017.05.006, IF = 5.710
Abstract: The covalent functionalization of graphene enabling to overcome its hydrophobicity and still keeping a high conductivity is a challenging task, particularly for advanced biosensing applications. We present a facile strategy towards water dispersible nanocarbon with excellent conductive and sensing properties. Graphene–fullerol (GFL) covalent hybrid is prepared by impregnation of chemically exfoliated graphene sheets with fullerol clusters followed by thermal treatment. The partial dehydroxylation of fullerol during heating is necessary for exposing the fullerene skeleton to graphene and promoting their covalent bonding. The remaining hydroxyl and ionic groups equip the final product with good dispersibility in water (0.04 mg mL−1). Simultaneously, the GFL hybrid retains a high electrical conductivity of 0.8 × 105 S m−1, which is comparable to that of unmodified graphene. The conductive and hydroxyl-bearing derivative was successfully applied for electrochemical sensing of dopamine, hydroquinone (HQ), and catechol (C) using cyclic voltammetry. GFL modified electrodes exhibited simultaneous HQ and C detection at lower potentials compared to other nanosensors.
S. Kment, H. Krysova, Z. Hubicka, H. Kmentova, L. Kavan, R. Zboril: Very thin thermally stable TiO 2 blocking layers with enhanced electron transfer for solar cells, APPLIED MATERIALS TODAY vol. 9, pp. 122-129, 2017.
DOI: 10.1016/j.apmt.2017.05.008, IF = 5.710
Abstract: Very thin TiO2 blocking layers (BLs) are important components for achieving high solar power conversion efficiencies (PCEs) in the dye-sensitized solar cells, and particularly perovskite solar cells (PSCs). When reasonably thin, TiO2 BLs prevent recombination of photogenerated charges at the conductive fluorine-doped tin oxide (FTO) glass substrate used in these devices. However, all previous attempts to generate efficient TiO2 BLs have been hampered by an insufficient charge transfer rate at quasi-amorphous TiO2 and very low thermal stability, leading to the loss of blocking properties after thermal calcination. In this work, we report the deposition of homogenous very thin (∼30 nm) TiO2 BLs by combining advanced high impulse power magnetron sputtering (HiPIMS) and additional bipolar medium-frequency (MF) magnetron co-sputtering. The as-deposited TiO2 films were shown to provide excellent blocking properties which were preserved even after thermal treatment at 450 °C. Moreover, TiO2 BLs thermally treated at 450 °C show a well-developed rutile structure and 70 times higher photocurrents compared to the as-deposited layers. This work opens possibilities for the utilization of very thin TiO2 layers in solar cell technologies providing a double mode of action: blocking functionality and efficient electron transport.
A. B. Bourlinos, A. K. Rathi, M. B. Gawande, K. Hola, A. Goswami, S. Kalytchuk, M. A. Karakassides, A. Kouloumpis, D. Gournis, Y. Deligiannakis, E. P. Giannelis, R. Zboril: Fe(III)-functionalized carbon dots—Highly efficient photoluminescence redox catalyst for hydrogenations of olefins and decomposition of hydrogen peroxide, APPLIED MATERIALS TODAY vol. 7, pp. 179-184, 2017.
DOI: 10.1016/j.apmt.2017.03.002, IF = 5.710
Abstract: We present the first bottom-up approach to synthesize Fe(III)-functionalized carbon dots (CDs) from molecular precursors without the need of conventional thermal or microwave treatment and additional reagents. Specifically, sonication of xylene in the presence of anhydrous FeCl3 results in oxidative coupling of the aromatic substrate towards Fe(III)-functionalized CDs. The as-prepared CDs are spherical in shape with a size of 3–8 nm, highly dispersible in organic solvents and display wavelength-dependent photoluminescence (PL). The iron ions attached to the surface endow the CDs with superior catalytic activity for olefin hydrogenation with excellent conversion and selectivity (up to 100%). The Fe(III)-CDs are more effective in the hydrogenation of a series of electron donating or withdrawing olefin substrates compared to conventional homogeneous or heterogeneous Fe(III)-based catalysts. The as-prepared heterogeneous nanocatalyst can be used repeatedly without any loss of catalytic activity. Importantly, the stability of the new catalysts can be easily monitored by PL intensity or quantum yield measurements, which certainly opens the doors for real time monitoring in a range of applications. Additionally, to the best of our knowledge, for the first time, the oxidative property of Fe-CDs was also explored in decomposition of hydrogen peroxide in water with the first order rate constant of 0.7 × 10−2 min−1, proving the versatile catalytic properties of such hybrid systems.
J. Martincová, M. Otyepka, P. Lazar: Is Single Layer MoS2
Stable in the Air?, CHEMISTRY - A EUROPEAN JOURNAL vol. 23, iss. 53, pp. 13233-13239, 2017.
DOI: 10.1002/chem.201702860, IF = 5.317
Abstract: Molybdenum disulfide (MoS2) is extensively studied because of its potential applications in catalysis, electronic and optoelectronic devices, and composite nanostructures. However, a recent experimental study indicated that, contrary to current beliefs, MoS2 monolayers lack long-term stability in air. Here, a study is presented on the oxidation of MoS2 monolayers based on density functional theory (DFT) calculations. The results suggest that single-layer MoS2 samples with exposed edge sites are indeed unstable to oxidation, which occurs because of the low energetic barrier to dissociation of oxygen molecules at the Mo-edges of MoS2. After an oxygen molecule dissociates, oxygen atoms replace sulfur atoms, and further oxidation causes the formation of a one-dimensional chain-like structure resembling that of bulk MoO3. This MoO3 structure facilitates the spread of oxidation onto the surface, and the stress associated with the misfit between the MoS2 and MoO3 lattices may cause the experimentally observed cracking of MoS2 flakes.
Y. Meng, Q. Sheng, M. N. Hoque, Y. Chen, S. Wu, J. Tucek, R. Zboril, T. Liu, Z. Ni, M. Tong: Two-Step Spin-Crossover with Three Inequivalent FeII
Sites in a Two-Dimensional Hofmann-Type Coordination Polymer, CHEMISTRY - A EUROPEAN JOURNAL vol. 23, iss. 42, pp. 10034-10037, 2017.
DOI: 10.1002/chem.201702356, IF = 5.317
Abstract: An unprecedented two-step spin-crossover behavior with the sequence of γHS=1↔γHS=3/4↔γHS=1/4 was observed in two-dimensional Hofmann type coordination polymer [Fe(isoq)2{Ag(CN)2}2] (isoq=isoquinoline), which resulted from three crystallographically inequivalent FeII sites with distinct transition temperatures.
P. Lazar, M. Otyepka: Role of the Edge Properties in the Hydrogen Evolution Reaction on MoS2, CHEMISTRY - A EUROPEAN JOURNAL vol. 23, iss. 20, pp. 4863-4869, 2017.
DOI: 10.1002/chem.201605848, IF = 5.317
Abstract: Molybdenum disulfide, in particular its edges, has attracted considerable attention as possible substitute for platinum catalysts in the hydrogen evolution reaction (HER). The complex nature of the reaction complicates its detailed experimental investigations, which are mostly indirect and sample dependent. Therefore, density functional theory calculations were employed to study how the properties of the MoS2 Mo-edge influence the thermodynamics of hydrogen adsorption onto the edge. The effect of the computational model (one-dimensional nanostripe), border symmetry imposed by its length, sulfur saturation of the edge, and dimensionality of the material are discussed. Hydrogen adsorption was found to depend critically on the coverage of extra sulfur at the Mo edge. The bare Mo-edge and fully sulfur-covered Mo-edge are catalytically inactive. The most favorable hydrogen binding towards HER was found for the Mo-edge covered by sulfur monomers. This edge provides hydrogen adsorption free energies positioned around −0.25 eV at up to 50 % hydrogen coverage, close to the experimental values of overpotential needed for the HER reaction.
O. Jankovsky, M. Lojka, J. Luxa, D. Sedmidubsky, O. Tomanec, R. Zboril, M. Pumera, Z. Sofer: Selective bromination of graphene oxide by Hunsdiecker reaction, CHEMISTRY - A EUROPEAN JOURNAL, vol. 23, iss. 43, pp. 10473–10479, 2017.
DOI: 10.1002/chem.201702031, IF = 5.317
Abstract: Halogenated graphenes have been attracting great attention in the recent years. The currently used methods are usually non-specific and halogen groups are randomly distributed over the graphene surface. The selective functionalization based on well known reaction mechanism allowed selective functionalization of graphene sheets. We show the application of Hunsdicker based reaction on the graphene oxide for selective bromination of graphene oxide. The chemical analysis using various spectroscopic methods proved a highly effective functionalization. Bromination can be carried out under mild conditions without any high temperature or high pressure treatment. The chemical modification led to introduction of up to 20 wt.% of bromine covalently bonded to graphene skeleton. Modified graphene was characterized in detail using a broad spectrum of microscopic and spectroscopic methods and no significant contamination by reaction byproducts was detected.
V. Georgakilas, A. Koutsioukis, V. Belessi, R. Zboril: Highly conductive water-based polymer/graphene nanocomposites for printed electronics., CHEMISTRY - A EUROPEAN JOURNAL, vol. 23, iss. 34, pp. 8268-8274, 2017.
DOI: 10.1002/chem.201700997, IF = 5.317
Abstract: The present article describes the preparation and characterization of highly conductive carbon inks based on nanocomposites that combine a polystyrene-acrylic resin or water-soluble polymers with a hydrophilic graphene/carbon nanotube hybrid. The water-based carbon inks show high electrical conductivity and can be effectively used in advanced technologies such as gravure printing for printed electronics. Moreover, the conductivity is shown to be increased with a power law of the nanohybrid volume fraction, with an exponent close to that predicted from the percolation theory, indicating a limited impact of the polymer tunnelling barrier on the electrical conductivity of such nanocomposites.
B. Islam, P. Stadlbauer, A. Gil-Ley, G. Pérez-Hernández, S. Haider, S. Neidle, G. Bussi, P. Banas, M. Otyepka, J. Sponer: Exploring the Dynamics of Propeller Loops in Human Telomeric DNA Quadruplexes Using Atomistic Simulations, JOURNAL OF CHEMICAL THEORY AND COMPUTATION vol. 13, iss. 6, pp. 2458-2480, 2017.
DOI: 10.1021/acs.jctc.7b00226, IF = 5.245
Abstract: We have carried out a series of extended unbiased molecular dynamics (MD) simulations (up to 10 μs long, ∼162 μs in total) complemented by replica-exchange with the collective variable tempering (RECT) approach for several human telomeric DNA G-quadruplex (GQ) topologies with TTA propeller loops. We used different AMBER DNA force-field variants and also processed simulations by Markov State Model (MSM) analysis. The slow conformational transitions in the propeller loops took place on a scale of a few μs, emphasizing the need for long simulations in studies of GQ dynamics. The propeller loops sampled similar ensembles for all GQ topologies and for all force-field dihedral-potential variants. The outcomes of standard and RECT simulations were consistent and captured similar spectrum of loop conformations. However, the most common crystallographic loop conformation was very unstable with all force-field versions. Although the loss of canonical γ-trans state of the first propeller loop nucleotide could be related to the indispensable bsc0 α/γ dihedral potential, even supporting this particular dihedral by a bias was insufficient to populate the experimentally dominant loop conformation. In conclusion, while our simulations were capable of providing a reasonable albeit not converged sampling of the TTA propeller loop conformational space, the force-field description still remained far from satisfactory.
M. Havrila, P. Stadlbauer, B. Islam, M. Otyepka, J. Šponer: Effect of Monovalent Ion Parameters on Molecular Dynamics Simulations of G-Quadruplexes, JOURNAL OF CHEMICAL THEORY AND COMPUTATION vol. 13, iss. 8, pp. 3911-3926, 2017.
DOI: 10.1021/acs.jctc.7b00257, IF = 5.245
Abstract: G-quadruplexes (GQs) are key noncanonical DNA and RNA architectures stabilized by desolvated monovalent cations present in their central channels. We analyze extended atomistic molecular dynamics simulations (∼580 μs in total) of GQs with 11 monovalent cation parametrizations, assessing GQ overall structural stability, dynamics of internal cations, and distortions of the G-tetrad geometries. Majority of simulations were executed with the SPC/E water model; however, test simulations with TIP3P and OPC water models are also reported. The identity and parametrization of ions strongly affect behavior of a tetramolecular d[GGG]4 GQ, which is unstable with several ion parametrizations. The remaining studied RNA and DNA GQs are structurally stable, though the G-tetrad geometries are always deformed by bifurcated H-bonding in a parametrization-specific manner. Thus, basic 10-μs-scale simulations of fully folded GQs can be safely done with a number of cation parametrizations. However, there are parametrization-specific differences and basic force-field errors affecting the quantitative description of ion-tetrad interactions, which may significantly affect studies of the ion-binding processes and description of the GQ folding landscape. Our d[GGG]4 simulations indirectly suggest that such studies will also be sensitive to the water models. During exchanges with bulk water, the Na+ ions move inside the GQs in a concerted manner, while larger relocations of the K+ ions are typically separated. We suggest that the Joung-Cheatham SPC/E K+ parameters represent a safe choice in simulation studies of GQs, though variation of ion parameters can be used for specific simulation goals.
F. Karlický, E. Otyepková, R. Lo, M. Pitoňák, P. Jurečka, M. Pykal, P. Hobza, M. Otyepka: Adsorption of Organic Molecules to van der Waals Materials: Comparison of Fluorographene and Fluorographite with Graphene and Graphite, JOURNAL OF CHEMICAL THEORY AND COMPUTATION vol. 13, iss. 3, pp. 1328-1340, 2017.
DOI: 10.1021/acs.jctc.6b01130, IF = 5.245
Abstract: Understanding strength and nature of noncovalent binding to surfaces imposes significant challenge both for computations and experiments. We explored the adsorption of five small nonpolar organic molecules (acetone, acetonitrile, dichloromethane, ethanol, ethyl acetate) to fluorographene and fluorographite using inverse gas chromatography and theoretical calculations, providing new insights into the strength and nature of adsorption of small organic molecules on these surfaces. The measured adsorption enthalpies on fluorographite range from −7 to −13 kcal/mol and are by 1–2 kcal/mol lower than those measured on graphene/graphite, which indicates higher affinity of organic adsorbates to fluorographene than to graphene. The dispersion-corrected functionals performed well, and the nonlocal vdW DFT functionals (particularly optB86b-vdW) achieved the best agreement with the experimental data. Computations show that the adsorption enthalpies are controlled by the interaction energy, which is dominated by London dispersion forces (∼70%). The calculations also show that bonding to structural features, like edges and steps, as well as defects does not significantly increase the adsorption enthalpies, which explains a low sensitivity of measured adsorption enthalpies to coverage. The adopted Langmuir model for fitting experimental data enabled determination of adsorption entropies. The adsorption on the fluorographene/fluorographite surface resulted in an entropy loss equal to approximately 40% of the gas phase entropy.
J. Šponer, G. Bussi, P. Stadlbauer, P. Kührová, P. Banáš, B. Islam, S. Haider, S. Neidle, M. Otyepka: Folding of guanine quadruplex molecules–funnel-like mechanism or kinetic partitioning? An overview from MD simulation studies, BIOCHIMICA ET BIOPHYSICA ACTA (BBA) - GENERAL SUBJECTS vol. 1861, iss. 5, pp. 1246-1263, 2017.
DOI: 10.1016/j.bbagen.2016.12.008, IF = 4.702
Abstract: 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. This article is part of a Special Issue entitled "G-quadruplex" Guest Editor: Dr. Concetta Giancola and Dr. Daniela Montesarchio.