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.

J. Tuček, P. Błoński, J. Ugolotti, A. K. Swain, T. Enoki, R. Zbořil: Emerging chemical strategies for imprinting magnetism in graphene and related 2D materials for spintronic and biomedical applications, CHEMICAL SOCIETY REVIEWS, Article in press, 2018.
DOI: 10.1039/c7cs00288b, IF = 38.618

Abstract: Graphene, a single two-dimensional sheet of carbon atoms with an arrangement mimicking the honeycomb hexagonal architecture, has captured immense interest of the scientific community since its isolation in 2004. Besides its extraordinarily high electrical conductivity and surface area, graphene shows a long spin lifetime and limited hyperfine interactions, which favors its potential exploitation in spintronic and biomedical applications, provided it can be made magnetic. However, pristine graphene is diamagnetic in nature due to solely sp2 hybridization. Thus, various attempts have been proposed to imprint magnetic features into graphene. The present review focuses on a systematic classification and physicochemical description of approaches leading to equip graphene with magnetic properties. These include introduction of point and line defects into graphene lattices, spatial confinement and edge engineering, doping of graphene lattice with foreign atoms, and sp3 functionalization. Each magnetism-imprinting strategy is discussed in detail including identification of roles of various internal and external parameters in the induced magnetic regimes, with assessment of their robustness. Moreover, emergence of magnetism in graphene analogues and related 2D materials such as transition metal dichalcogenides, metal halides, metal dinitrides, MXenes, hexagonal boron nitride, and other organic compounds is also reviewed. Since the magnetic features of graphene can be readily masked by the presence of magnetic residues from synthesis itself or sample handling, the issue of magnetic impurities and correct data interpretations is also addressed. Finally, current problems and challenges in magnetism of graphene and related 2D materials and future potential applications are also highlighted.

D. Li, P. Jing, L. Sun, Y. An, X. Shan, X. Lu, D. Zhou, D. Han, D. Shen, Y. Zhai, S. Qu, R. Zbořil, A. L. Rogach, "Near-Infrared Excitation/Emission and Multi-Photon-Induced Fluorescence of Carbon Dots," ADVANCED MATERIALS, vol. 30, iss. 13, no. 1705913, 2018
DOI: 10.1002/adma.201705913, IF = 19.791

Abstract: Carbon dots (CDs) have significant potential for use in various fields including biomedicine, bioimaging, and optoelectronics. However, inefficient excitation and emission of CDs in both near‐infrared (NIR‐I and NIR‐II) windows remains an issue. Solving this problem would yield significant improvement in the tissue‐penetration depth for in vivo bioimaging with CDs. Here, an NIR absorption band and enhanced NIR fluorescence are both realized through the surface engineering of CDs, exploiting electron‐acceptor groups, namely molecules or polymers rich in sulfoxide/carbonyl groups. These groups, which are bound to the outer layers and the edges of the CDs, influence the optical bandgap and promote electron transitions under NIR excitation. NIR‐imaging information encryption and in vivo NIR fluorescence imaging of the stomach of a living mouse using CDs modified with poly(vinylpyrrolidone) in aqueous solution are demonstrated. In addition, excitation by a 1400 nm femtosecond laser yields simultaneous two‐photon‐induced NIR emission and three‐photon‐induced red emission of CDs in dimethyl sulfoxide. This study represents the realization of both NIR‐I excitation and emission as well as two‐photon‐ and three‐photon‐induced fluorescence of CDs excited in an NIR‐II window, and provides a rational design approach for construction and clinical applications of CD‐based NIR imaging agents.

K. Jayaramulu, D. P. Dubal, B. Nagar, V. Ranc, O. Tomanec, M. Petr, K. K. R. Datta, R. Zboril, P. Gómez-Romero, R. A. Fischer, "Ultrathin Hierarchical Porous Carbon Nanosheets for High-Performance Supercapacitors and Redox Electrolyte Energy Storage," ADVANCED MATERIALS, vol. 30, iss. 15, no. 1705789, 2018.
DOI: 10.1002/adma.201705789, IF = 19.791

Abstract: The design of advanced high‐energy‐density supercapacitors requires the design of unique materials that combine hierarchical nanoporous structures with high surface area to facilitate ion transport and excellent electrolyte permeability. Here, shape‐controlled 2D nanoporous carbon sheets (NPSs) with graphitic wall structure through the pyrolysis of metal–organic frameworks (MOFs) are developed. As a proof‐of‐concept application, the obtained NPSs are used as the electrode material for a supercapacitor. The carbon‐sheet‐based symmetric cell shows an ultrahigh Brunauer–Emmett–Teller (BET)‐area‐normalized capacitance of 21.4 µF cm−2 (233 F g−1), exceeding other carbon‐based supercapacitors. The addition of potassium iodide as redox‐active species in a sulfuric acid (supporting electrolyte) leads to the ground‐breaking enhancement in the energy density up to 90 Wh kg−1, which is higher than commercial aqueous rechargeable batteries, maintaining its superior power density. Thus, the new material provides a double profits strategy such as battery‐level energy and capacitor‐level power density.

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, vol. 12, iss. 1, pp. 464–473, 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-effe ct 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. Nejedlý, I. Císařová, H. Vázquez, M. Moro-Lagares, J. Berger, J. Vacek, I. G. Stará, I. Starý, P. Jelínek: Large Converse Piezoelectric Effect Measured on a Single Molecule on a Metallic Surface, JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, vol. 140, iss. 3, pp. 940–946, 2018, 2018.
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

Abstract:

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 (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.

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, vol. 6, iss. 14, pp. 6096–6106, 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.

R. Szabla, H. Kruse, P. Stadlbauer, J. Šponer, A. L. Sobolewski: Sequential electron transfer governs the UV-induced self-repair of DNA photolesions, CHEMICAL SCIENCE vol. 9, iss. 12, pp. 3131-3140, 2018.
DOI: 10.1039/c8sc00024g, IF = 8.668

Abstract: Cyclobutane pyrimidine dimers (CpDs) are among the most common DNA lesions occurring due to the interaction with ultraviolet light. While photolyases have been well known as external factors repairing CpDs, the intrinsic self-repairing capabilities of the GAT T DNA sequence were discovered only recently and are still largely obscure. Here, we elucidate the mechanistic details of this self-repair process by means of MD simulations and QM/MM computations involving the algebraic diagrammatic construction to the second order [ADC(2)] method. We show that local UV-excitation of guanine may be followed by up to three subsequent electron transfers, which may eventually enable efficient CpD ring opening when the negative charge resides on the T T dimer. Consequently, the molecular mechanism of GAT T self-repair can be envisaged as sequential electron transfer (SET) occurring downhill along the slope of the S1 potential energy surface. Even though the general features of the SET mechanism are retained in both of the studied stacked conformers, our optimizations of different S1/S0 state crossings revealed minor differences which could influence their self-repair efficiencies. We expect that such assessment of the availability and efficiency of the SET process in other DNA oligomers could hint towards other sequences exhibiting similar photochemical properties. Such explorations will be particularly fascinating in the context of the origins of biomolecules on Earth, owing to the lack of external repairing factors in the Archean age.

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.

H. Ahn, A. Goswami, F. Riboni, S. Kment, A. Naldoni, S. Mohajernia, R. Zboril, P. Schmuki: Hematite Photoanode with Complex Nanoarchitecture Providing Tunable Gradient Doping and Low Onset Potential for Photoelectrochemical Water Splitting, CHEMSUSCHEM, Article in press, 2018.
DOI: 10.1002/cssc.201800256, IF = 7.226

Abstract: Over the past years, α‐Fe2O3 (hematite) has re‐emerged as a promising photoanode material in photoelectrochemical (PEC) water splitting. In spite of considerable success in obtaining relatively high solar conversion efficiency, the main drawbacks hindering practical application of hematite are its intrinsically hampered charge transport and sluggish oxygen evolution reaction (OER) kinetics on the photoelectrode surface. In the present work, we report a strategy that synergistically addresses both of these critical limitations. Our approach is based on three key features that are applied simultaneously: i) a careful nanostructuring of the hematite photoanode in the form of nanorods, ii) doping of hematite by Sn4+ ions using a controlled gradient, and iii) surface decoration of hematite by a new class of layered double hydroxide (LDH) OER co‐catalysts based on Zn–Co LDH. All three interconnected forms of functionalization result in an extraordinary cathodic shift of the photocurrent onset potential by more than 300 mV and a PEC performance that reaches a photocurrent density of 2.00 mA cm−2 at 1.50 V vs. the reversible hydrogen electrode.

Q. Li, J. P. Froning, M. Pykal, S. Zhang, Z. Wang, M. Vondrák, P. Banáš, K. Čépe, P. Jurečka, J. Šponer, R. Zbořil, M. Dong, M. Otyepka: RNA nanopatterning on graphene, 2D MATERIALS vol. 5, iss. 3, pp. 031006, 2018.
DOI: 10.1088/2053-1583/aabdf7, IF = 6.937

Abstract: Graphene-based materials enable the sensing of diverse biomolecules using experimental approaches based on electrochemistry, spectroscopy, or other methods. Although basic sensing was achieved, it had until now not been possible to understand and control biomolecules' structural and morphological organization on graphene surfaces (i.e. their stacking, folding/unfolding, self-assembly, and nano-patterning). Here we present the insight into structural and morphological organization of biomolecules on graphene in water, using an RNA hairpin as a model system. We show that the key parameters governing the RNA's behavior on the graphene surface are the number of graphene layers, RNA concentration, and temperature. At high concentrations, the RNA forms a film on the graphene surface with entrapped nanobubbles. The density and the size of the bubbles depend on the number of graphene layers. At lower concentrations, unfolded RNA stacks on the graphene and forms molecular clusters on the surface. Such a control over the conformational behavior of interacting biomolecules at graphene/water interfaces would facilitate new applications of graphene derivatives in biotechnology and biomedicine.

G. Cassone, J. Sponer, J. E. Sponer, F. Pietrucci, A. M. Saitta, F. Saija: Synthesis of (d)-erythrose from glycolaldehyde aqueous solutions under electric field, CHEMICAL COMMUNICATIONS vol. 54, iss. 26, pp. 3211-3214, 2018.
DOI: 10.1039/c8cc00045j, IF = 6.319

Abstract: The formation of the first C–C bonds from formaldehyde represents the rate-limiting step of the formose reaction. However, the free-energy surface associated with such a process has never been determined in condensed phase. By means of ab initio molecular dynamics and metadynamics techniques here we report on the free-energy landscape underlying the synthesis of glycolaldehyde from a formaldehyde aqueous solution. Moreover, numerical samples of formaldehyde (both neat and in water solution) and of glycolaldehyde (both neat and in aqueous solution) have been exposed to intense electric fields. The application of electrostatic gradients strongly prevents the formaldehyde umpolung and catalyzes the formation of C–O-bonded polymers in formaldehyde-containing samples. However, when the field is applied on glycolaldehyde aqueous solutions, new C–C bonds are formed and (D)-erythrose is synthesized. This way, a numerical Miller-like experiment led

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.

Z. Chaloupková, A. Balzerová, Z. Medříková, J. Srovnal, M. Hajdúch, K. Čépe, V. Ranc, R. Zbořil: Label-free determination and multiplex analysis of DNA and RNA in tumor tissues, APPLIED MATERIALS TODAY vol. 12, pp. 85-91, 2018.
DOI: 10.1016/j.apmt.2017.12.012, IF = 5.710

Abstract: Determination of the total content of nucleic acids constitutes an important part of medicinal diagnosis. This determination is typically performed using a combination of spectrophotometry and polymerase chain reaction, where multi-step and complex sample pretreatment is generally required. To simplify the analysis, we present a nanosensor for the multiplex determination of DNA and RNA. This nanosensor consists of a magnetic Fe3O4@Ag nanocomposite functionalized by a low molecular selector from the family of alkylating agents, chlorambucil. The sensor allows selective isolation of nucleic acids based on the magnetic properties of integrated Fe3O4 nanoparticles and consecutive determination of their content via magnetically assisted surface-enhanced Raman spectroscopy (MA-SERS). Limits of detection of 3.0 ng L−1 and 3.8 ng L−1 are achieved for DNA and RNA, respectively. The enhanced selectivity of the developed sensor, owing to the presence of the alkylating agent, allows multiplexed analysis of DNA and RNA with low relative errors (<10%) of determination.

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).

L. Pogány, B. Brachňaková, J. Moncol, J. Pavlik, I. Nemec, Z. Trávníček, M. Mazúr, L. Bučinský, L. Suchánek, I. Šalitroš: Impact of Substituent Variation on the Presence of Thermal Spin Crossover in a Series of Mononuclear Iron(III) Schiff Base Complexes with Terminal Pseudohalido Co-ligands, CHEMISTRY - A EUROPEAN JOURNAL vol. 24, iss. 20, pp. 5191-5203, 2018.
DOI: 10.1002/chem.201704546, IF = 5.317

Abstract: A series of novel iron(III) complexes of the general formula [Fe(L)X] (where L is a dianion of pentadentate Schiff base ligand N,N′‐bis({2‐hydroxy‐3,5‐dimethylphenyl}phenyl)methylidene‐1,6‐diamino‐3‐azapentane=H2L1 for 1 and 2; N,N′‐bis({2‐hydroxy‐3‐ethoxyphenyl}methylidene)‐1,6‐diamino‐3‐azapentane=H2L2 for 3 and 3⋅C3H6O) and X is terminal pseudohalido ligand (X=N3 for 1, X=NCS for 2, and X=NCSe for 3 and 3⋅C3H6O) were synthesized and thoroughly characterized. Magnetic measurements revealed the above room temperature spin crossover for isomorphic complexes 1 and 2 (T1/2=441 K and T1/2=435 K, respectively), whereas the solvent‐free complex 3 showed a half complete spin crossover (T1/2=250 K), which was detected by variable temperature crystallography as well. On the other hand, solvated complex 3⋅C3H6O exhibited permanent high spin state behaviour and either recrystallization or in situ thermal desolvation converts 3⋅C3H6O to solvent‐free and spin‐crossover‐active form 3. Magnetic properties of all the reported complexes were also supported by EPR spectroscopy experiments and in addition, DFT and ab initio calculations were employed for the evaluation of the g‐factor and zero field splitting parameters.

M. Paloncýová, M. Langer, M. Otyepka: Structural Dynamics of Carbon Dots in Water and N,N-Dimethylformamide Probed by All-Atom Molecular Dynamics Simulations, JOURNAL OF CHEMICAL THEORY AND COMPUTATION vol. 14, iss. 4, pp. 2076-2083, 2018.
DOI: 10.1021/acs.jctc.7b01149, IF = 5.245

Abstract: Carbon dots (CDs), one of the youngest members of the carbon nanostructure family, are now widely experimentally studied for their tunable fluorescence properties, bleaching resistance, and biocompatibility. Their interaction with biomolecular systems has also been explored experimentally. However, many atomistic details still remain unresolved. Molecular dynamics (MD) simulations enabling atomistic and femtosecond resolutions simultaneously are a well-established tool of computational chemistry which can provide useful insights into investigated systems. Here we present a full procedure for performing MD simulations of CDs. We developed a builder for generating CDs of a desired size and with various oxygen-containing surface functional groups. Further, we analyzed the behavior of various CDs differing in size, surface functional groups, and degrees of functionalization by MD simulations. These simulations showed that surface functionalized CDs are stable in a water environment through the formation of an extensive hydrogen bonding network. We also analyzed the internal dynamics of individual layers of CDs and evaluated the role of surface functional groups on CD stability. We observed that carboxyl groups interconnected the neighboring layers and decreased the rate of internal rotations. Further, we monitored changes in the CD shape caused by an excess of charged carboxyl groups or carbonyl groups. In addition to simulations in water, we analyzed the behavior of CDs in the organic solvent DMF, which decreased the stability of pure CDs but increased the level of interlayer hydrogen bonding. We believe that the developed protocol, builder, and parameters will facilitate future studies addressing various aspects of structural features of CDs and nanocomposites containing CDs.

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.