TOP RCPTM journal publications 2018

(registered by Web of Science, ordered by IF)

J. Šponer, G. Bussi, M. Krepl, P. Banáš, S. Bottaro, R. A. Cunha, A. Gil-Ley, G. Pinamonti, S. Poblete, P. Jurečka, N. G. Walter, M. Otyepka: RNA Structural Dynamics As Captured by Molecular Simulations: A Comprehensive Overview, CHEMICAL REVIEWS, Article in press, 2018.
DOI: 10.1021/acs.chemrev.7b00427, IF = 47.928

Abstract: With both catalytic and genetic functions, ribonucleic acid (RNA) is perhaps the most pluripotent chemical species in molecular biology, and its functions are intimately linked to its structure and dynamics. Computer simulations, and in particular atomistic molecular dynamics (MD), allow structural dynamics of biomolecular systems to be investigated with unprecedented temporal and spatial resolution. We here provide a comprehensive overview of the fast-developing field of MD simulations of RNA molecules. We begin with an in-depth, evaluatory coverage of the most fundamental methodological challenges that set the basis for the future development of the field, in particular, the current developments and inherent physical limitations of the atomistic force fields and the recent advances in a broad spectrum of enhanced sampling methods. We also survey the closely related field of coarse-grained modeling of RNA systems. After dealing with the methodological aspects, we provide an exhaustive overview of the available RNA simulation literature, ranging from studies of the smallest RNA oligonucleotides to investigations of the entire ribosome. Our review encompasses tetranucleotides, tetraloops, a number of small RNA motifs, A-helix RNA, kissing-loop complexes, the TAR RNA element, the decoding center and other important regions of the ribosome, as well as assorted others systems. Extended sections are devoted to RNA–ion interactions, ribozymes, riboswitches, and protein/RNA complexes. Our overview is written for as broad of an audience as possible, aiming to provide a much-needed interdisciplinary bridge between computation and experiment, together with a perspective on the future of the field.

A. Panáček, L. Kvítek, M. Smékalová, R. Večeřová, M. Kolář, M. Röderová, F. Dyčka, M. Šebela, R. Prucek, O. Tomanec, R. Zbořil: Bacterial resistance to silver nanoparticles and how to overcome it, NATURE NANOTECHNOLOGY, vol. 13, iss. 1, pp. 65–71, 2018.
DOI: 10.1038/s41565-017-0013-y, IF = 38.986

Abstract: Silver nanoparticles have already been successfully applied in various biomedical and antimicrobial technologies and products used in everyday life. Although bacterial resistance to antibiotics has been extensively discussed in the literature, the possible development of resistance to silver nanoparticles has not been fully explored. We report that the Gram-negative bacteria Escherichia coli 013, Pseudomonas aeruginosa CCM 3955 and E. coli CCM 3954 can develop resistance to silver nanoparticles after repeated exposure. The resistance stems from the production of the adhesive flagellum protein flagellin, which triggers the aggregation of the nanoparticles. This resistance evolves without any genetic changes; only phenotypic change is needed to reduce the nanoparticles’ colloidal stability and thus eliminate their antibacterial activity. The resistance mechanism cannot be overcome by additional stabilization of silver nanoparticles using surfactants or polymers. It is, however, strongly suppressed by inhibiting flagellin production with pomegranate rind extract.

D. Li, P. Jing, L. Sun, Y. An, X. Shan, X. Lu, D. Zhou, D. Han, D. Shen, Y. Zhai, S. Qu, R. Zbořil, and A. L. Rogach, "Near-Infrared Excitation/Emission and Multi-Photon-Induced Fluorescence of Carbon Dots," ADVANCED MATERIALS, Article in press.
DOI: 10.1002/adma.201705913, IF = 19.791

K. Jayaramulu, D. P. Dubal, B. Nagar, V. Ranc, O. Tomanec, M. Petr, K. K. R. Datta, R. Zboril, P. Gómez-Romero, and R. A. Fischer, "Ultrathin Hierarchical Porous Carbon Nanosheets for High-Performance Supercapacitors and Redox Electrolyte Energy Storage," ADVANCED MATERIALS, Article in press, 2018.
DOI: 10.1002/adma.201705789, IF = 19.791

C. C. Mayorga-Martinez, Z. Sofer, J. Luxa, Š. Huber, D. Sedmidubský, P. Brázda, L. Palatinus, M. Mikulics, P. Lazar, R. Medlín, M. Pumera: TaS3 Nanofibers: Layered Trichalcogenide for High-Performance Electronic and Sensing Devices, ACS NANO, Artical in press, 2018.
DOI: 10.1021/acsnano.7b06853, IF = 13.942

Abstract: Layered materials, like transition metal dichalcogenides, exhibit broad spectra with outstanding properties with huge application potential, whereas another group of related materials, layered transition metal trichalcogenides, remains unexplored. Here, we show the broad application potential of this interesting structural type of layered tantalum trisulfide prepared in a form of nanofibers. This material shows tailorable attractive electronic properties dependent on the tensile strain applied to it. Structure of this so-called orthorhombic phase of TaS3 grown in a form of long nanofibers has been solved and refined. Taking advantage of these capabilities, we demonstrate a highly specific impedimetric NO gas sensor based on TaS3 nanofibers as well as construction of photodetectors with excellent responsivity and field-effect transistors. Various flexible substrates were used for the construction of a NO gas sensor. Such a device exhibits a low limit of detection of 0.48 ppb, well under the allowed value set by environmental agencies for NOx (50 ppb). Moreover, this NO gas sensor also showed excellent selectivity in the presence of common interferences formed during fuel combustion. TaS3 nanofibers produced in large scale exhibited excellent broad application potential for various types of devices covering nanoelectronic, optoelectronic, and gas-sensing applications.

O. Stetsovych, P. Mutombo, M. Švec, M. Šámal, J. Nejedly, I. Cisarova, H. Vazquez, M. Moro-Lagares, J. Berger, J. Vacek, I. G. Stará, I. Stary, P. Jelinek: Large converse piezoelectric effect measured on a single molecule on a metallic surface, JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, Article in press, 2017.
DOI: 10.1021/jacs.7b08729, IF = 13.858

Abstract: The converse piezoelectric effect is a phenomenon in which the mechanical strain is generated in a material due to an applied electrical field. In this work, we demonstrate the converse piezoelectric effect in single heptahelicene-derived molecules on the Ag(111) surface using atomic force microscopy (AFM) and total energy density functional (DFT) calculations. The force-distance spectroscopy acquired over a wide range of bias voltages reveals a linear shift of the tip-sample distance at which the contact between the molecule and tip apex is established. We demonstrate that this effect is caused by the bias-induced de-formation of the spring-like scaffold of the helical polyaromatic molecules. We attribute this effect to coupling of a soft vibrational mode of the molecular helix with a vertical electric dipole induced by molecule-substrate charge transfer. In addi-tion, we also performed the same spectroscopic measurements on a more rigid o-carborane dithiol molecule on the Ag(111) surface. In this case, we identify a weaker linear electromechanical response, which underpins the importance of the helical scaffold on the observed piezoelectric response.

J. Peng, J. Guo, P. Hapala, D. Cao, R. Ma, B. Cheng, L. Xu, M. Ondráček, P. Jelínek, E. Wang, Y. Jiang: Weakly perturbative imaging of interfacial water with submolecular resolution by atomic force microscopy, NATURE COMMUNICATIONS vol. 9, iss. 1, 2018.
DOI: 10.1038/s41467-017-02635-5, IF = 12.124

Abstract: Scanning probe microscopy has been extensively applied to probe interfacial water in many interdisciplinary fields but the disturbance of the probes on the hydrogen-bonding structure of water has remained an intractable problem. Here, we report submolecular-resolution imaging of the water clusters on a NaCl(001) surface within the nearly noninvasive region by a qPlus-based noncontact atomic force microscopy. Comparison with theoretical simulations reveals that the key lies in probing the weak high-order electrostatic force between the quadrupole-like CO-terminated tip and the polar water molecules at large tip–water distances. This interaction allows the imaging and structural determination of the weakly bonded water clusters and even of their metastable states with negligible disturbance. This work may open an avenue for studying the intrinsic structure and dynamics of ice or water on surfaces, ion hydration, and biological water with atomic precision.

J. Tuček, P. Błoński, O. Malina, M. Pumera, C. K. Chua, M. Otyepka, and R. Zbořil: Morphology-Dependent Magnetism in Nanographene: Beyond Nanoribbons, ADVANCED FUNCTIONAL MATERIALS, Article in press, 2018.
DOI: 10.1002/adfm.201800592, IF = 12.124


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 vol. 46, iss. D1, pp. D399-D405, 2018.
DOI: 10.1093/nar/gkx868, IF = 10.162

Abstract: 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.

Y. Huang, C. Han, Y. Liu, M. N. Nadagouda, L. Machala, K. E. O’Shea, V. K. Sharma, D. D. Dionysiou: Degradation of atrazine by ZnxCu1−xFe2O4 nanomaterial-catalyzed sulfite under UV–vis light irradiation: Green strategy to generate SO4·−, APPLIED CATALYSIS B: ENVIRONMENTAL vol. 221, pp. 380-392, 2018.
DOI: 10.1016/j.apcatb.2017.09.001, IF = 9.446

Abstract: Degradation of atrazine, a widely-used herbicide, by a novel advanced oxidation process was investigated through photo-catalyzing sulfite, the precursor of sulfate radical (SO4·) in this study, by zinc-copper ferrites (ZnxCu1−xFe2O4) under UV–vis light irradiation. The ZnxCu1−xFe2O4 with different ratios of Zn to Cu was synthesized through a facile sol-gel combustion method, and characterized by X-ray powder diffractometry, scanning electron microscopy, transmission electron microscopy, porosimetry, and UV–vis diffuse reflectance spectroscopy, and by a vibrating sample magnetometer and Mössbauer spectrometer. The Zn0.8Cu0.2Fe2O4 demonstrated the highest photocatalytic ability to activate sulfite for the degradation of atrazine under current experimental conditions. The sulfate radical generated in the UV–vis light/Zn0.8Cu0.2Fe2O4/sulfite system was identified as the main reactive species through radical quenching experiments and measuring two important byproducts (atrazine-desethyl and atrazine-desisopropyl). The XPS spectra of fresh and used catalysts were analyzed to further elucidate the reaction mechanisms. There are two possible approaches to produce SO4·: the oxidation of sulfite by photo-generated holes and the accelerated decomposition of metal-sulfito complexes (Fe(III)-sulfito and Cu(II)-sulfito) on the surface of Zn0.8Cu0.2Fe2O4. Based on the detected byproducts, the transformation pathways of atrazine by UV–vis light/Zn0.8Cu0.2Fe2O4/sulfite were proposed as well. After the complete decomposition of atrazine, the used catalysts could be magnetically recovered using a magnet and no sulfite remained in the system. The results suggest that the UV–vis light/Zn0.8Cu0.2Fe2O4/sulfite system is a “green” advanced oxidation technology for future application in wastewater treatment.

A. Halder, M. Kilianová, B. Yang, E. C. Tyo, S. Seifert, R. Prucek, A. Panáček, P. Suchomel, O. Tomanec, D. J. Gosztola, D. Milde, H. Wang, L. Kvítek, R. Zbořil, S. Vajda: Highly efficient Cu-decorated iron oxide nanocatalyst for low pressure CO 2 conversion, APPLIED CATALYSIS B: ENVIRONMENTAL vol. 225, pp. 128-138, 2017.
DOI: 10.1016/j.apcatb.2017.11.047, IF = 9.446

Abstract: We report a nanoparticulate iron oxide based catalyst for CO2 conversion with high efficiency at low pressures and on the effect of the presence of copper on the catalyst’s restructuring and its catalytic performance. In situ X-ray scattering reveals the restructuring of the catalyst at the nanometer scale. In situ X-ray absorption near edge structure (XANES) shows the evolution of the composition and oxidation state of the iron and copper components under reaction conditions along with the promotional effect of copper on the chemical transformation of the iron component. X-ray diffraction (XRD), XANES and Raman spectroscopy proved that the starting nanocatalyst is composed of iron oxides differing in chemical nature (α-Fe2O3, Fe3O4, FeO(OH)) and dimensionality, while the catalyst after CO2 conversion was identified as a mixture of α-Fe, Fe3C, and traces of Fe5C2. The significant increase of the rate CO2 is turned over in the presence of copper nanoparticles indicates that Cu nanoparticles activate hydrogen, which after spilling over to the neighbouring iron sites, facilitate a more efficient conversion of carbon dioxide.

D. P. Dubal, J. Kolleboyina , R. Zboril, R. A. Fischer, P. Gomez-Romero: Unveiling BiVO4 Nanorods as a Novel Anode Material for High Performance Lithium Ion Capacitor: Beyond intercalation strategy, JOURNAL OF MATERIALS CHEMISTRY A, 2018.
DOI: 10.1039/c8ta00549d, IF = 8.867

Abstract: Energy storage is increasingly demanded in many new niches of applications from wearables to unmanned autonomous vehicles. However, current energy storage systems are unable to fulfill the power requirements (high energy at high power) needed for these novel applications. Recently, Li-ion capacitors (LICs) have been spotted as hybrid device with the potential to display high energy and high power. Nevertheless, it is still a great challenge to achieve high performance LICs due to the unmatched kinetic property and capacity between anode and cathode materials. Herein, we are presenting our first seminal report on the use of BiVO4 nanorods as a new anode material for LICs coupled with a partially reduced graphene oxide (PRGO) cathode. The BiVO4 nanorods show an excellent reversible capacity of 877 mAh/g (ultrahigh volumetric capacity of 4560 mAh/cm3) at 1.1 A/g with a great capacity retention (in half-cell design), which is highest value reported so far for metal vanadates. Later on, a LIC was constructed with BiVO4 as an anode and PRGO as a cathode electrode delivering high energy density of 152 Wh/kg and a maximum power density of 9.6 kW/kg compared to that for hard carbon and intercalation (such as Li4Ti5O12, Li3VO4) based anode materials. Additionally, BiVO4//PRGO LIC exhibits good cyclability of 81 % over 6000 cycles. Thus, this investigation opens up new opportunities to develop different LIC systems.

H. Han, S. Kment, F. Karlicky, L. Wang, A. Naldoni, P. Schmuki, and R. Zboril,: Sb-doped SnO2 Nanorods Underlayer Effect to the α-Fe2O3 Nanorods Sheathed with TiO2 for Enhanced Photoelectrochemical Water Splitting, SMALL, Article in press, 2018.
DOI: 10.1002/smll.201703860, IF = 8.643

M. Medveď, G. Zoppellaro, J. Ugolotti, D. Matochová, P. Lazar, T. Pospíšil, A. Bakandritsos, J. Tuček, R. Zbořil, M. Otyepka: Reactivity of fluorographene is triggered by point defects: beyond the perfect 2D world, NANOSCALE vol. 10, iss. 10, pp. 4696-4707, 2018.
DOI: 10.1039/c7nr09426d, IF = 7.367

Abstract: Preparation of graphene derivatives using fluorographene (FG) as a precursor has become a key strategy for the large-scale synthesis of new 2-D materials (e.g. graphene acid, cyanographene, allyl-graphene) with tailored physicochemical properties. However, to gain full control over the derivatization process, it is essential to understand the reaction mechanisms and accompanying processes that affect the composition and structure of the final products. Despite the strength of C–F bonds and high chemical stability of perfluorinated hydrocarbons, FG is surprisingly susceptible to reactions under ambient conditions. There is clear evidence that nucleophilic substitution on FG is accompanied by spontaneous defluorination, and solvent-induced defluorination can occur even in the absence of any nucleophilic agent. Here, we show that distributed radical centers (fluorine vacancies) on the FG surface need to be taken into account in order to rationalize the defluorination mechanism. Depending on the environment, these radical centers can react as electron acceptors, electrophilic sites and/or cause homolytic bond cleavages. We also propose a new radical mechanism of FG defluorination in the presence of N,N′-dimethylformamide (DMF) solvent. Spin-trap experiments as well as 19F NMR measurements unambiguously confirmed formation of N,N′-dimethylformyl radicals and also showed that N,N′-dimethylcarbamoyl fluoride plays a key role in the proposed mechanism. These findings imply that point defects in 2D materials should be considered as key factor determining their chemical properties and reactivity.

B. Hudcová, V. Veselská, J. Filip, S. Číhalová, M. Komárek: Highly effective Zn(II) and Pb(II) removal from aqueous solutions using Mg-Fe layered double hydroxides: Comprehensive adsorption modeling coupled with solid state analyses, JOURNAL OF CLEANER PRODUCTION vol. 171, pp. 944-953, 2018.
DOI: 10.1016/j.jclepro.2017.10.104, IF = 5.715

Abstract: Comprehensive mechanistic and modeling approaches are needed to effectively evaluate sorption of metal ions from aqueous solutions. However, such a complex study using layered double hydroxides has not yet been presented. Therefore, adsorption modeling was performed coupled with solid state analyses describing the mode of zinc and lead removal by magnesium-iron layered double hydroxides, and an excellent removal efficiency for both metal ions was observed. The maximal adsorbed concentration, as established by the Langmuir model, increased with the increasing magnesium/iron molar ratio. The pH-dependent sorption was fitted by the diffuse layer model, which described the formation of monodentate inner-sphere complexes, indicating strong binding between metal ions and the layered double hydroxides surface. Based on the solid state analyses of materials with high surface concentrations of zinc (1.44 mmol g−1) and lead (1.65 mmol g−1), respectively, the whole sorption mechanism was also influenced by other processes, i.e., precipitation (lead) and surface accumulation/precipitation/isomorphic substitution (zinc). Transmission electron microscopy-based elemental mapping showed a heterogeneous distribution of zinc and lead on the surface of particles. Low-temperature Mössbauer spectra were nearly identical for the studied materials before/after zinc and lead sorption indicating no structural changes in incorporated iron. Generally, we suggest that these layered double hydroxides are highly effective sorbents for metal ions from aqueous solutions. Furthermore, we propose a comprehensive mechanistic/modeling approach as a powerful tool for describing the mechanism of metal ions binding on layered double hydroxides in contaminated waters.

A. V.C., A. Goswami, H. Sopha, D. Nandan, M. B. Gawande, K. Cepe, S. Ng, R. Zboril, J. M. Macak: Pt nanoparticles decorated TiO 2 nanotubes for the reduction of olefins, APPLIED MATERIALS TODAY vol. 10, pp. 86-92, 2018.
DOI: 10.1016/j.apmt.2017.12.006, IF = 5.710

Abstract: High surface area TiO2 nanotubes (TNTs) were used as a catalyst support for well dispersed, stable and ultra-small (3–5 nm) Pt nanoparticles (Pt@TNTs) for the reduction of olefins. Pt@TNT catalyst was synthesized by a simple soaking of anodized TNTs in the chloroplatinic (H2PtCl6) acid solution. Various techniques such as XRD, SEM, TEM, and XPS were used to characterize the materials and its catalytic property for the olefin reduction has been described along with a proposed mechanism. The Pt@TNT catalyst showed moderate to high catalytic conversions of styrene and its derivative to ethyl benzene-based products using hydrazine hydrate as a reducing agent. An excellent catalytic activity along with high product selectivity was achieved using low amount (10 mg) of Pt@TNT catalyst containing ∼2.2 wt.% Pt and short reaction time (45 min).

M. Zgarbová, P. Jurečka, J. Šponer, M. Otyepka: A- to B-DNA Transition in AMBER Force Fields and Its Coupling to Sugar Pucker, JOURNAL OF CHEMICAL THEORY AND COMPUTATION vol. 14, iss. 1, pp. 319-328, 2018.
DOI: 10.1021/acs.jctc.7b00926, IF = 5.245

Abstract: The A/B transition is a basic element of DNA conformational change. Because of its involvement in the sensing of the ionic conditions by DNA and in specific protein–DNA interactions, this transition is important for biological functions of DNA. Therefore, accurate modeling of the A/B equilibrium by means of empirical force fields is of utmost interest. In this work, we examine the A/B equilibrium in three AMBER force fields, including the recent bsc1 and OL15 modifications, using much longer MD simulations than attempted before. Special attention is paid to the coupling of the A/B equilibrium with the south/north (S/N) transition of the sugar pucker. We found that none of the tested force fields provided a satisfactory description of the A/B equilibrium because the B-form was predicted to be much too stable and the A-form was predicted to be almost absent even in concentrated trifluoroethanol solutions. Based on comparison with NMR data for duplexes and single nucleosides, we hypothesize that this problem arose from the incorrect description of the S/N equilibrium of sugar pucker, where the south conformation is much too stable, thus stabilizing the B-form. Because neither the A/B equilibrium in duplexes nor the S/N equilibrium in nucleosides was described accurately, further refinements of the AMBER DNA force fields are needed.