2012
Georgakilas, V.; Otyepka, M.; Bourlinos, A. B.; Chandra, V.; Kim, N.; Kemp, C. K.; Hobza, P.; Zboril, R.; Kim, K. S.: Functionalization of Graphene: Covalent and Non-Covalent Approaches, Derivatives and Applications, Chem. Rev., 2012, 112(11), 6156-6214. IF 40,20. Link
Abstract: Graphene, the two-dimensional sp2-hybridized carbon, is currently, without any doubt, the most intensively studied material. This single-atom-thick sheet of carbon atoms arrayed in a honeycomb pattern is the world’s thinnest, strongest, and stiffest material, as well as being an excellent conductor of both heat and electricity. It is no wonder that this two-dimensional material is considered, from the application viewpoint, to be even more promising than other nanostructured carbon allotropes, that is, 1-dimensional nanotubes and 0-dimensional fullerenes.
This comprehensive review represents the first complex work covering all modes and methods of graphene functionalization including their classification. The complementary discussion of both experimental and theoretical aspects of graphene functionalization and interaction is presented. The functionalization modes related to chemistry of graphene derivatives (GO, graphane, fluorographene) represent a significant part of the review, which thus considerably exceeds the chemistry of pristine graphene.
Hobza, P: Calculations on Noncovalent Interactions and Databases of Benchmark Interaction Energies, Accounts Chem. Res., 2012, 45, 663-672. IF 21,64. Link
Abstract: Although covalent interactions determine the primary structure of a molecule, the noncovalent interactions are responsible for the tertiary and quaternary structure of a molecule and create the fascinating world of the 3D architectures of biomacromolecules. For example, the double helical structure of DNA is of fundamental importance for the function of DNA: it allows it to store and transfer genetic information. To fulfill this role, the structure is rigid to maintain the double helix with a proper positioning of the complementary base, and floppy to allow for its opening. Very strong covalent interactions cannot fulfill both of these criteria, but noncovalent interactions, which are about 2 orders of magnitude weaker, can. This Account highlights the recent advances in the field of the design of novel wave function theory (WFT) methods applicable to noncovalent complexes ranging in size from less than 100 atoms, for which highly accurate ab initio methods are available, up to extended ones (several thousands atoms), which are the domain of semiempirical QM (SQM) methods.
Accurate interaction energies for noncovalent complexes are generated by the coupled-cluster technique, taking single- and double-electron excitations iteratively and triple-electron excitation perturbatively with a complete basis set description (CCSD(T)/CBS). The procedure provides interaction energies with high accuracy (error less than 1 kcal/mol). Because the method is computationally demanding, its application is limited to complexes smaller than 30 atoms. But researchers would also like to use computational methods to determine these interaction energies accurately for larger biological and nanoscale structures. Standard QM methods such as MP2, MP3, CCSD, or DFT fail to describe various types of noncovalent systems (H-bonded, stacked, dispersion-controlled, etc.) with comparable accuracy. Therefore, novel methods are needed that have been parametrized toward noncovalent interactions, and existing benchmark data sets represent an important tool for the development of new methods providing reliable characteristics of noncovalent clusters.
Our laboratory developed the first suitable data set of CCSD(T)/CBS interaction energies and geometries of various noncovalent complexes, called S22. Since its publication in 2006, it has frequently been applied in parametrization and/or verification of various wave function and density functional techniques. During the intense use of this data set, several inconsistencies emerged, such as the insufficient accuracy of the CCSD(T) correction term or its unbalanced character, which has triggered the introduction of a new, broader, and more accurate data set called the S66 data set. It contains not only 66 CCSD(T)/CBS interaction energies determined in the equilibrium geometries but also 1056 interaction energies calculated at the same level for nonequilibrium geometries. The S22 and S66 data sets have been used for the verification of various WFT methods, and the lowest RMSE (S66, in kcal/mol) was found for the recently introduced SCS-MI-CCSD/CBS (0.08), MP2.5/CBS (0.16), MP2.X/6-31G* (0.27), and SCS-MI-MP2/CBS (0.38) methods. Because of their computational economy, the MP2.5 and MP2.X/6-31G* methods can be recommended for highly accurate calculations of large complexes with up to 100 atoms.
The evaluation of SQM methods was based only on the S22 data set, and because some of these methods have been parametrized toward the same data set, the respective results should be taken with caution. For really extended complexes such as protein–ligand systems, only the SMQ methods are applicable. After adding the corrections to the dispersion energy and H-bonding, several methods exhibit surprisingly low RMSE (even below 0.5 kcal/mol). Among the various SMQ methods, the PM6-DH2 can be recommended because of its computational efficiency and it can be used for optimization (which is not the case for other SQM methods). The PM6-DH2 is the base of our novel scoring function used in in silico drug design.
Petr, J.; Maier, V.: Analysis of microorganisms by capillary electrophoresis. Trac-Trends in Anal Chemistry, 2012, 31, 9–22. IF 6,27. Link
Abstract: Microorganisms are well known for their positive, as well as negative, effects on health, which mean that there is a great need for methods of discovery, identification and determination of microorganisms. In the past decade, capillary electrophoresis (CE) began to be an interesting tool for analysis of microorganisms, interestingly sometimes with similar dimensions for the separation capillary and the microorganisms. This review focuses on the use of CE in the analysis of microorganisms. First, it looks at the origin of microbial surface charge and then describes key points in the analysis of microbes by capillary zone electrophoresis [first approaches using poly(ethylene oxide), covalent modification of the inner capillary wall, reversed electroosmotic flow, advances in detection, and on-line preconcentration] and capillary isoelectric focusing.
Zeleny, T; Ruckenbauer, M; Aquino, AJA; Muller, T; Lankas, F; Drsata, T; Hase, WL; Nachtigallova, D; Lischka, H: Strikingly Different Effects of Hydrogen Bonding on the Photodynamics of Individual Nucleobases in DNA: Comparison of Guanine and Cytosine, J. Am. Chem. Soc., 2012, 134, 13662-13669. IF 9,91. Link
Abstract: Ab initio surface hopping dynamics calculations were performed to study the photophysical behavior of cytosine and guanine embedded in DNA using a quantum mechanical/molecular mechanics (QM/MM) approach. It was found that the decay rates of photo excited cytosine and guanine were affected in a completely different way by the hydrogen bonding to the DNA environment. In case of cytosine, the geometrical restrictions exerted by the hydrogen bonds did not influence the relaxation time of cytosine significantly due to the generally small cytosine ring puckering required to access the crossing region between excited and ground state. On the contrary, the presence of hydrogen bonds significantly altered the photodynamics of guanine. The analysis of the dynamics indicates that the major contribution to the lifetime changes comes from the interstrand hydrogen bonds. These bonds considerably restricted the out-of-plane motions of the NH2 group of guanine which are necessary for the ultrafast decay to the ground state. As a result, only a negligible amount of trajectories decayed into the ground state for guanine embedded in DNA within the simulation time of 0.5 ps, while for comparison, the isolated guanine relaxed to the ground state with a lifetime of about 0.22 ps. These examples show that, in addition to phenomena related to electronic interactions between nucleobases, there also exist relatively simple mechanisms in DNA by which the lifetime of a nucleobase is significantly enhanced as compared to the gas phase.
Bakandritsos, A; Papagiannopoulos, A; Anagnostou, EN; Avgoustakis, K; Zboril, R; Pispas, S; Tucek, J; Ryukhtin, V; Bouropoulos, N; Kolokithas-Ntoukas, A; Steriotis, TA; Keiderling, U; Winnefeld, F: Merging High Doxorubicin Loading with Pronounced Magnetic Response and Bio-repellent Properties in Hybrid Drug Nanocarriers, Small, 2012, 8, 2381-2393. IF 8,35. Link
Abstract: Hybrid magnetic drug nanocarriers are prepared via a self-assembly process of poly(methacrylic acid)-graft-poly(ethyleneglycol methacrylate) (p(MAA-g-EGMA)) on growing iron oxide nanocrystallites. The nanocarriers successfully merge together bio-repellent properties, pronounced magnetic response, and high loading capacity for the potent anticancer drug doxorubicin (adriamicin), in a manner not observed before in such hybrid colloids. High magnetic responses are accomplished by engineering the size of the magnetic nanocrystallites (∼13.5 nm) following an aqueous single-ferrous precursor route, and through adjustment of the number of cores in each colloidal assembly. Complementing conventional magnetometry, the magnetic response of the nanocarriers is evaluated by magnetophoretic experiments providing insight into their internal organization and on their response to magnetic manipulation. The structural organization of the graft-copolymer, locked on the surface of the nanocrystallites, is further probed by small-angle neutron scattering on single-core colloids. Analysis showed that the MAA segments selectively populate the area around the magnetic nanocrystallites, while the poly(ethylene glycol)-grafted chains are arranged as protrusions, pointing towards the aqueous environment. These nanocarriers are screened at various pHs and in highly salted media by light scattering and electrokinetic measurements. According to the results, their stability is dramatically enhanced, as compared to uncoated nanocrystallites, owing to the presence of the external protective PEG canopy. The nanocarriers are also endowed with bio-repellent properties, as evidenced by stability assays using human blood plasma as the medium.
Bao, X; Guo, PH; Liu, W; Tucek, J; Zhang, WX; Leng, JD; Chen, XM; Gural’skiy, I; Salmon, L; Bousseksou, A; Tong, ML: Remarkably high-temperature spin transition exhibited by new 2D metal-organic frameworks, Chem. Sci., 2012, 3, 1629-1633. IF 7,53. Link
Abstract:Highly stable two-dimensional metal–organic frameworks, 2∞[FeII(L)2] (HL = 3-(2-pyridyl)-5-(3-pyridyl)-1,2,4-triazole (1) and 3-(3-methyl-2-pyridyl)-5-(3-pyridyl)-1,2,4-triazole (2), display well defined two-step spin crossover properties at remarkably high temperatures, namely, Tc1 = 329 K, Tc2 = 501 K for 1 and Tc1 = 351 K, Tc2 = 520 K for 2, which are the highest critical temperatures reported so far.
Berka, K; Hanak, O; Sehnal, D; Banas, P; Navratilova, V; Jaiswal, D; Ionescu, CM; Varekova, RS; Koca, J; Otyepka, M: MOLEonline 2.0: interactive web-based analysis of biomacromolecular channels, Nucleic Acids Res., 2012, 40, W222-W227. IF 8,03. Link
Abstract: Biomolecular channels play important roles in many biological systems, e.g. enzymes, ribosomes and ion channels. This article introduces a web-based interactive MOLEonline 2.0 application for the analysis of access/egress paths to interior molecular voids. MOLEonline 2.0 enables platform-independent, easy-to-use and interactive analyses of (bio)macromolecular channels, tunnels and pores. Results are presented in a clear manner, making their interpretation easy. For each channel, MOLEonline displays a 3D graphical representation of the channel, its profile accompanied by a list of lining residues and also its basic physicochemical properties. The users can tune advanced parameters when performing a channel search to direct the search according to their needs. The MOLEonline 2.0 application is freely available via the Internet at http://ncbr.muni.cz/mole or http://mole.upol.cz.
Marsalek, B; Jancula, D; Marsalkova, E; Mashlan, M; Safarova, K; Tucek, J; Zboril, R: Multimodal Action and Selective Toxicity of Zerovalent Iron Nanoparticles against Cyanobacteria, Environ. Sci. Technol., 2012, 46, 2316-2323. IF 5,23. Link
Abstract: Cyanobacteria pose a serious threat to water resources around the world. This is compounded by the fact that they are extremely resilient, having evolved numerous protective mechanisms to ensure their dominant position in their ecosystem. We show that treatment with nanoparticles of zerovalent iron (nZVI) is an effective and environmentally benign method for destroying and preventing the formation of cyanobacterial water blooms. The nanoparticles have multiple modes of action, including the removal of bioavailable phosphorus, the destruction of cyanobacterial cells, and the immobilization of microcystins, preventing their release into the water column. Ecotoxicological experiments showed that nZVI is a highly selective agent, having an EC50 of 50 mg/L against cyanobacteria; this is 20–100 times lower than its EC50 for algae, daphnids, water plants, and fishes. The primary product of nZVI treatment is nontoxic and highly aggregated Fe(OH)3, which promotes flocculation and gradual settling of the decomposed cyanobacterial biomass.
Bourlinos, A. B.; Zboril, R.; Petr, J.; Bakandritsos A.; Krysmann, M.; Giannelis, E. P.: Luminescent Surface Quaternized Carbon Dots. Chem. Mater., 2012, 24 (1), 6-8. IF 7,29. Link
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Magro, M.; Sinigaglia, G.; Nodari, L.; Tucek, J.; Polakova, K.; Marusak, Z.; Cardillo, S.; Saliulo, G.; Russo, U.; Stevanato, R.; Zboril, R.; Vianello, F.: Charge binding of rhodamine derivative to OH- stabilized nanomaghemite: Universal nanocarrier for construction of magnetofluorescent biosensors, Acta Biomaterialia, 2012, 8. 2068-2076. IF 4,87. Link
Abstract: Superparamagnetic nanoparticles (20–40 nm) of maghemite, γ-Fe2O3, with well-defined stoichiometric structure, are synthesized by the borohydride reduction of ferric chloride at an elevated temperature (100 °C) followed by thermal treatment of the reaction product. Prepared maghemite nanoparticles reveal excellent colloidal stability for a long time without the necessity for any additional surface modification. These colloidal features are due to surface stabilizing OH– groups, which act as charge barriers preventing a particle aggregation and enabling a reversible binding of various oppositely charged organic substances. Such binding with rhodamine B isothiocyanate results in the fluorescent magnetic nanocarrier providing, at the same time, a spacer arm for covalent immobilization of other biosubstances including enzymes. In this work, we exploit this general applicability of the developed nanocarrier for covalent immobilization of glucose oxidase. This is the first reported example of magnetically drivable fluorescent nanocatalyst. The immobilized enzyme creates a 3–5 nm thick layer on the nanoparticle surface as proved by high-resolution transmission electron microscopy. This layer corresponds to 10 enzyme molecules, which are bound to the nanoparticle surface as found by the fluorimetric determination of flavin adenine dinucleotide. The developed magnetic fluorescent nanocatalyst, showing a rate constant of 32.7 s–1 toward glucose oxidation, can be used as a biosensor in various biochemical, biotechnological, and food chemistry applications. The presence of the nanocatalyst can be simply monitored by its fluorescence; moreover, it can be easily separated from the solution by an external magnetic field and repeatedly used without a loss of catalytic efficiency.
Filip, J.; Bosi, F.; Novak, M.; Skogby, H.; Tucek, J.; Cuda, J.; Wildner, M.: Iron redox reactions in the tourmaline structure: High-temperature treatment of Fe3+-rich schorl, Geochimica et Cosmochimica Acta, 2012, 86, 239-256. IF 4,26. Link
Abstract: We present a detailed study of thermally-driven oxidation and reduction of Fe in the structure of schorl (as the most wide-spread tourmaline), Fe2+-bearing olenite and fluor-schorl. The principal Fe3+-rich tourmaline investigated in this study is a natural schorl sample from a unique occurrence in peralkaline rocks near Cancrinite Hill, east of Bancroft, southern Ontario. Tourmaline samples were thermally-treated in air and hydrogen at temperatures of 700, 800 and 900 °C to oxidize or reduce the structural Fe. High-temperature changes were continuously monitored using 57 Fe Mössbauer and infrared spectroscopy. Proportions of Fe2+ and Fe3+ vary as a function of the heat treatment. An increase in Fe3+ up to 100% after heating in air at 700 °C was observed, whereas only small changes in the Fe3+ / Fetot ratio after heating under hydrogen at 700 °C was revealed. Partial deprotonation/protonation represents charge compensation for the oxidation/reduction of Fe at the Y and Z sites.
Critical samples of Cancrinite Hill tourmaline were investigated in detail by means of 57Fe Mössbauer and infrared spectroscopy, single-crystal X-ray difraction, electron microprobe and magnetometry. The optimized structural formulae are:
X(Na0.93K0.02□0.05)Y()Z()BB3T(Si5.88Al0.12)O27V(OH)3W(O0.12OH0.88) – untreated tourmaline (schorl);
X(Na0.93K0.02□0.05)Y()Z()BB3T(Si5.88Al0.12)O27V(OH)3W(OH) – tourmaline reduced in hydrogen (schorl);
X(Na0.93K0.02□0.05)Y()Z()BB3T(Si5.90Al0.10)O27V(O1.05OH1.95)W(O0.70OH0.30) – tourmaline oxidized in air (H+-rich “buergerite”).
There is evident disorder of Al over the Y, Z and T sites as well as disorder of Fe2+ over the Y and Z sites, and ordering of Fe3+ at the Y site and Mg at the Z site. The fully oxidized tourmaline shows disorder of Fe3+ and Mg over the Y and Z sites. The occurrence of “extra” Fe2+ in the Z site of the reduced tourmaline relative to the untreated sample demonstrates the intra-crystalline cation-exchange driven by elevated temperature. Increased disorder of Fe cations over the edge-shared YO6 and ZO6 octahedra enhances the antiferromagnetic exchange interactions in the tourmaline structure, which are stronger in reduced samples than in oxidized and untreated ones. This suggests that OH groups at the W site could mediate Y–Z inter-site exchange interactions.
Complete oxidation of Fe within the tourmaline structure is possible. However, significant reduction of Fe cannot occur because an excess of H+ may not be incorporated within the tourmaline structure. Further reduction of Fe3+ will not occur until the breakdown of the tourmaline structure above its temperature of reductive decomposition, where metallic Fe immediately appears as a separate phase (α-Fe) together with cristobalite and Na–Al–Fe-borosilicate glass. The scarcity of Fe3+ – rich tourmalines in nature and the separate existence of “buergerite” as the only tourmaline with almost all Fe as Fe3+ support its specific origin, such as from an HT-LP, high fO2 overprint.
Banas, P.; Mladek, A.; Otyepka, M.; Zgarbova, M.; Jurecka, P.; Svozil, D.; Lankas, F.; Sponer, J.: Can we accurately describe the structure of adenine tracts in B-DNA? Reference quantum-chemical computations reveal overstabilization of stacking by molecular mechanics, J. Chem. Theory Comput, 2012, 8(7), 2448-2460. IF 5,22. Link
Abstract: Sequence-dependent local variations of helical parameters, structure, and flexibility are crucial for molecular recognition processes involving B-DNA. A-tracts, i.e., stretches of several consecutive adenines in one strand that are in phase with the DNA helical repeat, mediate signifi cant DNA bending. During the past few decades, there have been intense efforts to understand the sequence dependence of helical parameters in DNA. Molecular dynamics (MD) simulations can provide valuable insights into the molecular mechanism behind the relationship between sequence and structure. However, although recent improvements in empirical force fields have helped to capture many sequence-dependent B-DNA properties, several problems remain, such as underestimation of the helical twist and suspected underestimation of the propeller twist in A-tracts. Here, we employ reference quantum mechanical (QM) calculations, explicit solvent MD, and bioinformatics to analyze the underestimation of propeller twisting of A-tracts in simulations. Although we did not identify a straightforward explanation, we discovered two imbalances in the empirical force fields. The first was overestimation of stacking interactions accompanied by underestimation of base-pairing energy, which we attribute to anisotropic polarizabilities that are not re flected by the isotropic force fi elds. This may lead to overstacking with potentially important consequences for MD simulations of nucleic acids. The second observed imbalance was steric clash between A(N1) and T(N3) nitrogens of AT base pairs in force- fi eld descriptions, resulting in overestimation of the AT pair stretch in MD simulations. We also substantially extend the available set of benchmark estimated CCSD(T)/CBS data for B-DNA base stacking and provide a code that allows the generation of diverse base-stacking geometries suitable for QM computations with prede fi ned intra- and interbase pair parameters.
Krepl, M.; Zgarbova, M.; Stadlbauer, P.; Otyepka, M.; Banas, P.; Koca, J.; Cheatham, T.E.; Jurecka, P.; Sponer, J.*: Reference simulations of noncanonical nucleic acids with different chi variants of the AMBER force field: quadruplex DNA, quadruplex RNA and Z-DNA, J. Chem. Theory Comput., 2012, 8(7), 2506-2520. IF 5,22. Link
Abstract: Refinement of empirical force fields for nucleic acids requires their extensive testing using as wide range of systéme as possible. However, finding unambiguous reference data is not easy. In this paper, we analyze four systems that we suggest should be included in standard portfolio of molecules to test nucleic acids force fields, namely, parallel and antiparallel stranded DNA guanine quadruplex stems, RNA quadruplex stem, and Z-DNA. We highlight parameters that should be monitored to assess the force field performance. The work is primarily based on 8.4 μ s of 100 − 250 ns trajectories analyzed in detail followed by 9.6 μ s of additional selected backup trajectories that were monitored to verify that the results of the initial analyses are correct. Four versions of the Cornell et al. AMBER force fi eld are tested, including an entirely new parm χ OL4 variant with χ dihedral speci fi cally reparametrized for DNA molecules containing syn-nucleotides. We test also different water models and ion conditions. While improvement for DNA quadruplexes is visible, the force fi elds still do not fully reproduce the intricate Z-DNA backbone conformation.
Paloncýová, M.; Berka, K.; Otyepka, M,: Convergence of Free Energy Profile of Coumarin in Lipid Bilayer. J. Chem. Theory Comput., 2012, 8 (4), 1200-1211. IF 5,22. Link
Abstract: Atomistic molecular dynamics (MD) simulations of druglike molecules embedded in lipid bilayers are of considerable interest as models for drug penetration and positioning in biological membranes. Here we analyze partitioning of coumarin in dioleoylphosphatidylcholine (DOPC) bilayer, based on both multiple, unbiased 3 μ s MD simulations (total length) and free energy profiles along the bilayer normal calculated by biased MD simulations (∼7 μ s in total). The convergences in time of free energy profiles calculated by both umbrella sampling and z-constraint techniques are thoroughly analyzed. Two sets of starting structures are also considered, one from unbiased MD simulation and the other from “pulling” coumarin along the bilayer normal. The structures obtained by pulling simulation contain water defects on the lipid bilayer surface, while those acquired from unbiased simulation have no membrane defects. The free energy profiles converge more rapidly when starting frames from unbiased simulations are used. In addition, z-constraint simulation leads to more rapid convergence than umbrella sampling, due to quicker relaxation of membrane defects. Furthermore, we show that the choice of RESP, PRODRG, or Mulliken charges considerably affects the resulting free energy profile of our model drug along the bilayer normal. We recommend using z-constraint biased MD simulations based on starting geometries acquired from unbiased MD simulations for efficient calculation of convergent free energy profiles of druglike molecules along bilayer normals. The calculation of free energy profile should start with an unbiased simulation, though the polar molecules might need a slow pulling afterward. Results obtained with the recommended simulation protocol agree well with available experimental data for two coumarin derivatives.
Kolář, M.; Hobza, P.: On Extension of the Current Biomolecular Empirical Force Field for the Description of Halogen Bonds. J. Chem. Theory. Comput., 2012, 8 (4), 1325-1333. IF 5,22. Link
Abstract: Until recently, the description of halogen bonding by standard molecular mechanics has been poor, owing to the lack of the so-called σ hole localized at the halogen. This region of positive electrostatic potential located on top of a halogen atom explains the counterintuitive attraction of halogenated compounds interacting with Lewis bases. In molecular mechanics, the σ hole is modeled by a massless point charge attached to the halogen atom and referred to as an explicit σ hole (ESH). Here, we introduce and compare three methods of ESH construction, which differ in the complexity of the input needed. The molecular mechanical dissociation curves of three model complexes containing bromine are compared with accurate CCSD(T)/CBS data. Furthermore, the performance of the Amber force field enhanced by the ESH on geometry characteristics is tested on the casein kinase 2 protein complex with seven brominated inhibitors. It is shown how various schemes depend on the selection of the ESH parameters and to what extent the energies and geometries are reliable. The charge of 0.2e placed 1.5 Å from the bromine atomic center is suggested as a universal model for the ESH.
Rezac, J., Hobza, P.: Advanced Corrections of Hydrogen Bonding and Dispersion for Semiempirical Quantum Mechanical Methods. J. Chem. Theory Comput., 2012, 8 (1), 141-151. IF 5,22. Link
Abstract: Semiempirical quantum mechanical methods with corrections for noncovalent interactions, namely dispersion and hydrogen bonds, reach an accuracy comparable to much more expensive methods while being applicable to very large systems (up to 10 000 atoms). These corrections have been successfully applied in computer-assisted drug design, where they significantly improve the correlation with the experimental data. Despite these successes, there are still several unresolved issues that limit the applicability of these methods. We introduce a new generation of both hydrogen-bonding and dispersion corrections that address these problems, make the method more robust, and improve its accuracy. The hydrogen-bonding correction has been completely redesigned and for the first time can be used for geometry optimization and molecular-dynamics simulations without any limitations, as it and its derivatives have a smooth potential energy surface. The form of this correction is simpler than its predecessors, while the accuracy has been improved. For the dispersion correction, we adopt the latest developments in DFT-D, using the D3 formalism by Grimme. The new corrections have been parametrized on a large set of benchmark data including nonequilibrium geometries, the S66x8 data set. As a result, the newly developed D3H4 correction can accurately describe a wider range of interactions. We have parametrized this correction for the PM6, RM1, OM3, PM3, AM1, and SCC-DFTB methods.
Maier, V; Ranc, V; Svidrnoch, M; Petr, J; Sevcik, J; Tesarova, E; Armstrong, DW: Study on the use of boromycin as a chiral selector in capillary electrophoresis. J. Chromatogr. A, 2012, 1237, 128-132. IF 4,53. Link
Abstract: The first application of boromycin as achiralselector in capillaryelectrophoresis is described. Given boromycin’s insolubility in water, a non-aqueous background electrolyte based on methanol was used for enantiomeric discrimination of selected chiral primary amines (α-methylbenzylamine, R,S-tryptophanol, R,S-norepinephrine, R,S-octopamine, R,S-p-hydroxynorephedrine and R,S-2-amino-1-phenylethanol). A basic study of experimental conditions including the influence of boromycin concentration, the composition and concentration of background electrolyte and also the influence of different organic solvents was performed. The best separation condition was 75 mM Tris/50 mM boric acid in methanol, 9.0, with a positive separation voltage. The enantiomeric separation of the primary amines was achieved within 14 min with resolution values greater than 1.5 for the majority of the studied analytes.
Bourlinos, A.B.; Bakandritsos, A; Kouloumpis, A; Gournis, D; Krysmann, ; Giannelis, E.P; Polakova, K; Safarova, K; Hola, K; Zboril, R: Gd(III)-doped carbon dots as a dual fluorescent-MRI probe. J. MATER. CHEM., 2012, 22, 23327-23330. IF 5,97. Link
Abstract:We describe the synthesis of Gd(III)-doped carbon dots as dual fluorescence-MRI probes for biomedical applications. The derived Gd(III)-doped carbon dots show uniform particle size (3–4 nm) and gadolinium distribution and form stable dispersions in water. More importantly, they exhibit bright fluorescence, strong T1-weighted MRI contrast and low cytotoxicity.
Frydrych, J; Machala, L; Tucek, J; Siskova, K; Filip, J; Pechousek, J; Safarova, K; Vondracek, M; Hwa Seo, J; Schneeweiss, O; Grätzel, M; Sivula, K; Zboril, R: Facile fabrication of tin-doped hematite photoelectrodes – effect of doping on magnetic properties and performance for light-induced water splitting.J. MATER. CHEM., 2012, 22, 23232-23239. IF 5,97. Link
Abstract: We present a new, easily scalable method for the deposition of nanocrystalline hematite photoelectrodes based on the spin-coating of a mixed solution containing tin(II) and iron(III) chlorides followed by thermal treatment. Our facile approach does not require any additional film-forming organic species and allows simple control of the photoelectrochemical performance of the electrode by adjusting the degree of tin doping. When annealed at 650 °C a strong increase in the water oxidation photocurrent is observed with increasing tin concentration. The maximum performance (0.45 mA cm−2 at 1.43 V vs. RHE) was found at the highest possible tin loading (20 : 100, Sn : Fe). The contrasting performance of electrodes annealed at 650 °C and 800 °C suggests different activation processes for dopant diffusion and activation. The doping of tin into the crystal structure of hematite thin films is directly evidenced by X-ray photoelectron spectroscopy and indirectly by changes in the intrinsic magnetic parameters (Morin temperature, Néel temperature) of the hematite films. The magnetization measurements thus represent a potential technique to quantify doping amounts in hematite.
Markova, Z; Bourlinos, A.B; Safarova, K; Polakova, K; Tucek, J; Medrik, I; Siskova, K; Petr, J; Krysmann, M; Gianellis, E.P; Zboril, R: Synthesis and properties of core–shell fluorescent hybrids with distinct morphologies based on carbon dots. J. MATER. CHEM., 2012, 22, 16219-16223. IF 5,97. Link
Abstract: Fluorescent core–shell nanohybrids with the shells derived from carbon dots and cores differing in the chemical nature and morphology were synthesized. Hybrid nanoparticles combine fluorescence with other functionalities such as magnetic response on a single platform. These hybrids can be used in various bioapplications as demonstrated with labeling of stem cells.
Markova, Z; Siskova, K; Filip, J; Safarova, K; Prucek, R; Panacek, A; Kolar, M; Zboril, R: Chitosan-based synthesis of magnetically-driven nanocomposites with biogenic magnetite core, controlled silver size, and high antimicrobial activity. GREEN CHEM, 2012, 14, 2550. IF 6,32. Link
Abstract: We report a new procedure, exploiting “green” chemistry, resulting in biocompatible magnetically-driven nanocomposites with high antibacterial and antifungal activities against ten tested bacterial strains and four Candida species. The nanocomposites consist of silver nanoparticles (NPs), biogenic magnetite NPs isolated from magnetotactic bacteria, and an environmentally friendly polymer – chitosan. These hybrids were prepared using an acidified chitosan suspension to cover biogenic magnetite NPs by a cross-linking method, followed by employing the NH2 groups of chitosan for the reduction of silver salt in an alkaline medium. Thus, in the procedure, chitosan acts as (i) a biocompatible matrix surrounding the magnetite NPs, (ii) a reducing agent for the silver ions, and (iii) a linker between magnetic and silver NPs. The size of the resulting silver NPs and the total amount of silver involved in the nanocomposites can be simply controlled by the initial concentration of the silver salt used in the reaction mixture. The as-prepared nanocomposites reveal increased bactericidal and antifungal activity when compared to previously reported magnetic silver NPs systems which were not prepared by green synthetic routes. The use of biogenic magnetite with an uniform shape and size, the absence of any other reducing agent during synthesis, the simple control of silver NPs size and loading, the biocompatible character of chitosan matrix, and a high antimicrobial effect predetermine the developed nanocomposites for targeted applications in biomedicine.
Maity, D; Zoppellaro, G; Sedenkova, V; Tucek, J; Safarova, K; Polakova, T; Tomankova, K; Diwoky, C; Stollberger, R; Machala, L; Zboril, R: Surface design of core–shell superparamagnetic iron oxide nanoparticles drives record relaxivity values in functional MRI contrast agents. CHEM COMMUN, 2012, 48, 11398-11400. IF 6,17. Link
Abstract: Core–shell hydrophilic superparamagnetic iron oxide (SPIO) nanoparticles, surface functionalized with either terephthalic acid or 2-amino terephthalic acid, showed large negative MRI contrast ability, validating the advantage of using low molecular weight and π-conjugated canopies for engineering functional nanostructures with superior performances.
Bourlinos, A.B; Safarova, K; Siskova, K; Zboril, R: The production of chemically converted graphenes from graphite fluoride. Carbon, 2012, 50, 1422-1444. IF 5,38. Link
Abstract: The liquid-phase extraction of graphene fluoride by exfoliation of graphite fluoride in dimethylformamide and subsequent reduction with triethylsilane or zinc particles yields the corresponding chemically converted graphene, namely reduced graphene fluoride. The formation of either graphene fluoride (fluorographene) or graphene monolayers in the course of the reaction was demonstrated by several microscopy techniques. Fluorine elimination after reduction was verified by elemental analysis and infrared/Raman spectroscopy.
Zboril, R; Andrle, M; Oplustil, F; Machala, L; Tucek, J; Filip, J; Marusak, Z; Sharma, VK: Treatment of chemical warfare agents by zero-valent iron nanoparticles and ferrate(VI)/(III) composite. J. Hazard. Mater., 2012, 2011-2012, 126-130. IF 4,17. Link
Abstract: Nanoscale zero-valentiron (nZVI) particles and a composite containing a mixture of ferrate(VI) and ferrate(III) were prepared by thermal procedures. The phase compositions, valence states of iron, and particle sizes of iron-bearing compounds were determined by combination of X-ray powder diffraction, Mössbauer spectroscopy and scanning electron microscopy. The applicability of these environmentally friendly iron based materials in treatment of chemicalwarfareagents (CWAs) has been tested with three representative compounds, sulfur mustard (bis(2-chlorethyl) sulfide, HD), soman ((3,3′-imethylbutan-2-yl)-methylphosphonofluoridate, GD), and O-ethyl S-[2-(diisopropylamino)ethyl] methylphosphonothiolate (VX). Zero-valentiron, even in the nanodimensional state, had a sluggish reactivity with CWAs, which was also observed in low degrees of CWAs degradation. On the contrary, ferrate(VI)/(III) composite exhibited a high reactivity and complete degradations of CWAs were accomplished. Under the studied conditions, the estimated first-order rate constants (∼10−2s−1) with the ferrate(VI)/(III) composite were several orders of magnitude higher than those of spontaneous hydrolysis of CWAs (10−8–10−6 s−1). The results demonstrated that the oxidative technology based on application of ferrate(VI) is very promising to decontaminate CWAs.
Otyepka, M; Berka, K; Anzenbacher, P: Is There a Relationship Between the Substrate Preferences and Structural Flexibility of Cytochromes P450? Curr. Drug Metab., 2012, 13(2), 130-42. IF 5,11. Link
Abstract: In the last decades, the structural flexibility of cytochromes P450 has been extensively studied by spectroscopic and in silico methods. Here, both approaches are reviewed and compared. Comparison of both methods indicates that the individual cytochromes P450 differ significantly in the flexibilities of their substrate-binding active sites. This finding probably accounts for the large number of isoforms of these enzymes (there are fifty-seven known cytochrome P450 genes in the human genome) and their functional versatility. On the other hand, most of the known cytochrome P450s have a set of common structural features, with an overall structure consisting of a relatively flexible domain (the distal side), a more rigid domain (the heme-binding core) and a domain on the proximal side of the hemoprotein with intermediate flexibility. Substrate access and product egress channels of CYP enzymes are also important structural elements as the majority of these channels are located in the flexible distal side; the location, flexibility, and function of these channels are discussed.
Hendrychova, T; Berka, K; Navratilova, V; Anzenbacher, P; Otyepka, M: Dynamics and Hydration of the Active Sites of Mammalian Cytochromes P450 Probed by Molecular Dynamics Simulations. Curr. Drug Metab., 2012, 13(2), 177-89. IF 5,11. Link
Abstract: The flexibility, active site volume, solvation, and access path dynamics of six metabolically active mammalian cytochromes P450 (human 2A6, 2C9, 2D6, 2E1, 3A4 and rabbit 2B4) are extensively studied using molecular dynamics (MD) simulations. On average, the enzymes’ overall structures equilibrate on a 50+ ns timescale. The very open CYP2B4 structure closes slowly over the course of the simulation. The volumes of the active sites fluctuate by more than 50% during the MD runs; these fluctuations are mainly due to movements of the main chains, with only a handful of amino acid residues in CYP2B4, CYP2D6, CYP2A6 and CYP2C9 showing significant independent side chain movement. The volume of the active site of CYP2E1 fluctuates heavily, ranging from 220 to 1310 A(3), due to the opening and closing of gates to two adjacent cavities. CYP2E1 has the least hydrated active site of the studied CYPs; this is consistent with its preference for non-polar substrates. The CYP2A6 and CYP2E1 active sites are deeply buried, with access paths that are narrower than the radius of a water molecule. However, waters are still able to access these active sites due to local adaptations of the channel to accommodate their passage. This finding may imply that the access paths of the CYPs never fully open prior to contact with the substrate; instead, the substrate may induce adaptive conformational changes during its passage to the active site. This may also explain why some substrate recognition sites are localized along individual enzymes’ access paths.
Prucek, R.; Ranc, V.; Kvitek, L.; Panacek, A.; Zboril, R.; Kolar, M.: Reproducible discrimination between Gram-positive and Gram-negative bacteria using surface enhanced Raman spectroscopy with infrared excitation, Analyst, 2012, 137(12), 2866-2870. IF 4,23. Link
Abstract: The on time diagnostics of bacterial diseases is one of the essential steps in the foregoing treatment of such pathogens. Here we sought to present an easy to use and robust method for the discrimination between Gram-positive (Enterococcus faecalis and Streptococcus pyogenes) and Gram-negative (Acinetobacter baumannii and Klebsiella pneumoniae) bacterial genera based on surface enhanced Raman scattering (SERS) spectroscopy. The robustness of our approach lies in the novel method for the production of the SER substrate based on silver nanoparticles and their subsequent re-crystallization in solutions containing high concentrations of chloride ions. The method presented here could be an interesting alternative both to commonly used histochemical approaches and commercial SERS substrates.
Svozilik, J.; Hendrych, M.; Torres, J. P.: Bragg reflection waveguide as a source of wavelength-multiplexed polarization-entangled photon Paris, Optics Express, 2012, 20(14), 15015-15023. IF 3,59. Link
Abstract: We put forward a new highly efficient source of paired photons entangled in polarization with an ultra-large bandwidth. The photons are generated by means of a conveniently designed spontaneous parametric down-conversion process in a semiconductor type-II Bragg reflection waveguide. The proposed scheme aims at being a key element of an integrated source of polarization-entangled photon pairs highly suitable for its use in a multi-user quantum-key-distribution system.
Peřina Jr., J.; Haderka, O.; Michálek, V.; Hamar, M.: Absolute detector calibration using twin beams, Optics Letters, 2012, 37(13), 2475-2477. IF 3,40. Link
Abstract: A method for the determination of absolute quantum detection efficiency is suggested based on the measurement of photocount statistics of twin beams. The measured histograms of joint signal–idler photocount statistics allow us to eliminate an additional noise superimposed on an ideal calibration field composed of only photon pairs. This makes the method superior above other approaches presently used. Twin beams are described using a paired variant of quantum superposition of signal and noise.
Trávníček Z., Štarha P., Vančo J., Šilha T., Hošek J., Suchý P., and Pražanová G.: Anti-inflammatory active gold(I) complexes involving 6‑substituted-purine derivatives. J. Med. Chem., 2012, 55 (10), pp 4568–4579. IF 5,25. Link
Abstract: The gold(I) complexes of the general formula [Au(Ln)(PPh3)]·xH2O (1–8; n = 1–8 and x = 0–1.5), where Ln stands for a deprotonated form of the benzyl-substituted derivatives of 6-benzylaminopurine, were prepared, thoroughly characterized (elemental analyses, FT-IR, Raman and multinuclear NMR spectroscopy, ESI+ mass spectrometry, conductivity, DFT calculations), and studied for their in vitro cytotoxicity and in vitro and in vivo anti-inflammatory effects on LPS-activated macrophages (derived from THP-1 cell line) and using the carrageenan-induced hind paw edema model on rats. The obtained results indicate that the representative complexes (1, 3, 6) exhibit a strong ability to reduce the production of pro-inflammatory cytokines TNF-α, IL-1β and HMGB1 without influence on the secretion of anti-inflammatory cytokine IL-1RA in the LPS-activated macrophages. The complexes also significantly influence the formation of edema, caused by the intraplantar application of polysaccharide λ-carrageenan to rats in vivo. All the tested complexes showed similar or better biological effects as compared with Auranofin, but contrary to Auranofin they were found to be less cytotoxic in vitro. The obtained results clearly indicate that the gold(I) complexes behave as very effective anti-inflammatory agents and could prove to be useful for the treatment of difficult to treat inflammatory diseases such as rheumatoid arthritis.
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Most important ATLAS Collaboration papers (2012)
ATLAS Collaboration: Search for tb Resonances in Proton-Proton Collisions at root s=7 TeV with the ATLAS Detector. Physical Review Letters, 2012, 109(8), 081801. IF 7,37. Link
ATLAS Collaboration: Search for Pair Production of a New b ‘ Quark that Decays into a Z Boson and a Bottom Quark with the ATLAS Detector. Physical Review Letters, 2012, 109(7), 071801. IF 7,37. Link
ATLAS Collaboration: Search for Down-Type Fourth Generation Quarks with the ATLAS Detector in Events with One Lepton and Hadronically Decaying W Bosons. Physical Review Letters, 2012, 109(3), 032001. IF 7,37. Link
ATLAS Collaboration: Determination of the Strange-Quark Density of the Proton from ATLAS Measurements of the W -> lv and Z -> ll Cross Sections. Physical Review Letters, 2012, 109(1), 012001. IF 7,37. Link
ATLAS Collaboration: Search for Supersymmetry in Events with Three Leptons and Missing Transverse Momentum in root s=7 TeV pp Collisions with the ATLAS Detector. Physical Review Letters, 2012, 108(26), 261804. IF 7,37. Link
ATLAS Collaboration: Search for Pair Production of a Heavy Up-Type Quark Decaying to a W Boson and a b Quark in the lepton plus jets Channel with the ATLAS Detector. Physical Review Letters, 2012, 108(26), 261802. IF 7,37. Link
ATLAS Collaboration: Search for a Light Higgs Boson Decaying to Long-Lived Weakly Interacting Particles in Proton-Proton Collisions at root s=7 TeV with the ATLAS Detector. Physical Review Letters, 2012, 108(25), 251801. IF 7,37. Link
ATLAS Collaboration: Search for Gluinos in Events with Two Same-Sign Leptons, Jets, and Missing Transverse Momentum with the ATLAS Detector in pp Collisions at root s=7 TeV. Physical Review Letters, 2012, 108(24), 241802. IF 7,37. Link
ATLAS Collaboration: Observation of Spin Correlation in t(t)over-bar Events from pp Collisions at root s=7 TeV Using the ATLAS Detector. Physical Review Letters, 2012, 108(21), 212001. IF 7,37. Link
ATLAS Collaboration: Search for Production of Resonant States in the Photon-Jet Mass Distribution Using pp Collisions at root s=7 TeV Collected by the ATLAS Detector. Physical Review Letters, 2012, 108(21), 211802. IF 7,37. Link
ATLAS Collaboration: Search for Scalar Bottom Quark Pair Production with the ATLAS Detector in pp Collisions at root s=7 TeV. Physical Review Letters, 2012, 108(18), 181802. IF 7,37. Link
ATLAS Collaboration: Observation of a New χb State in Radiative Transitions to Y(1S) and Υ(2S) at ATLAS. Phys. Rev. Lett., 2012, 108 (15), 152001-15017. IF 7,37. Link
ATLAS Collaboration: Search for the Standard Model Higgs Boson in the Diphoton Decay Channel with 4.9 fb -1 of pp Collision Data at √s = 7 TeV with ATLAS. Phys. Rev. Lett, 212, 108(11), 111803-19. IF 7,37. Link
ATLAS Collaboration: Search for the Higgs Boson in the H→WW(*)→l+νl-ν̅ Decay Channel in pp Collisions at √s = 7 TeV with the ATLAS Detector. Phys. Rev. Lett. 2012, 108, 111802-19. IF7,37. Link
ATLAS Collaboration: Search for New Phenomena in tẗ Events with Large Missing Transverse Momentum in Proton-Proton Collisions at √s=7 TeV with the ATLAS Detector. Phys. Rev. Lett., 2012, 108 (4), 041805. IF 7,37. Link
ATLAS Collaboration: Measurement of the ZZ Production Cross Section and Limits on Anomalous Neutral Triple Gauge Couplings in Proton-Proton Collisions at √s=7 TeV with the ATLAS Detector. Phys. Rev. Lett., 2012, 108 (4), 041804. IF 7,37. Link
ATLAS Collaboration: Hunt for new phenomena using large jet multiplicities and missing transverse momentum with ATLAS in 4.7fb(-1) of root s=7 TeV proton-proton collisions”, Journal of High Energy Physics, 2012, 7, 167. IF 5,83. Link
ATLAS Collaboration: Forward-backward correlations and charged-particle azimuthal distributions in pp interactions using the ATLAS detector. Journal of High Energy Physics 7, 019. IF 5,83. Link
ATLAS Collaboration: Measurement of the W boson polarization in top quark decays with the ATLAS detector. Journal of High Energy Physics, 2012, 6, 088. IF 5,83. Link
ATLAS Collaboration: Search for charged Higgs bosons decaying via H-+/- -> tau nu in t(t)over-bar events using pp collision data at root s=7 TeV with the ATLAS detector. Journal of High Energy Physics, 2012, 6, 039. IF 5,83. Link
ATLAS collaboration: Measurement of the cross section for top-quark pair production in pp collisions at √ s = 7 TeV with the ATLAS detector using final states with two high- pT leptons. J. High Energy Phys., 2012, 05, 059. IF 5,83. Link
ATLAS Collaboration: Measurement of inclusive two-particle angular correlations in pp collisions with the ATLAS detector at the LHC. Journal of High Energy Physics, 2012, 5, 157. IF 5,83. Link
ATLAS Collaboration: Jet mass and substructure of inclusive jets in root s=7 TeV pp collisions with the ATLAS experiment. Journal of High Energy Physics, 2012, 5, 128. IF 5,83. Link
ATLAS Collaboration: Search for same-sign top-quark production and fourth-generation down-type quarks in pp collisions at root s=7 TeV with the ATLAS detector. Journal of High Energy Physics, 2012, 4, 069. IF 5,83. Link
ATLAS Collaboration: Search for scalar top quark pair production in natural gauge mediated supersymmetry models with the ATLAS detector in pp collisions at root s=7 TeV. Physics Letters B, 2012, 715(1-3), 44-60. IF 3,96. Link
ATLAS Collaboration: Measurement of the W W cross section in root s=7 TeV pp collisions with the ATLAS detector and limits on anomalous gauge couplings. Physics Letters B, 2012, 712(4-5), 289-308. IF 3,96. Link
ATLAS Collaboration: Search for new particles decaying to ZZ using final states with leptons and jets with the ATLAS detector in root s=7 TeV proton-proton collisions. Physics Letters B, 2012, 712(4-5), 331-350. IF 3,96. Link
ATLAS Collaboration: Search for FCNC single top-quark production at root s=7 TeV with the ATLAS detector. Physics Letters B, 2012, 712(4-5), 351-369. IF 3,96. Link
ATLAS Collaboration: Search for heavy vector-like quarks coupling to light quarks in proton-proton collisions at root s=7 TeV with the ATLAS detector. Physics Letters B, 2012, 712(1-2), 22-39. IF 3,96. Link
ATLAS Collaboration: Search for contact interactions in dilepton events from pp collisions at root s=7 TeV with the ATLAS detector. Physics Letters B, 2012, 712(1-2), 40-58. IF 3,96. Link
ATLAS Collaboration: Search for first generation scalar leptoquarks in pp collisions at root s = 7 TeV with the ATLAS detector (vol 709, pg 158, 2012). Physics Letters B, 2012, 711(5), 442-455. IF 3,96. Link
ATLAS Collaboration: Measurement of the top quark pair production cross-section with ATLAS in the single lepton channel. Physics Letters B, 2012, 711(3-4), 244-263. IF 3,96. Link
ATLAS Collaboration: Search for diphoton events with large missing transverse momentum in 1 fb(-1) of 7 TeV proton-proton collision data with the ATLAS detector ATLAS Collaboration. Physics Letters B, 2012, 710(4-5), 519-537. IF 3,96. Link
ATLAS Collaboration: Search for extra dimensions using diphoton events in 7 TeV proton-proton collisions with the ATLAS detector ATLAS Collaboration. Physics Letters B, 2012, 710(4-5), 538-556. IF 3,96. Link
ATLAS Collaboration: Measurement of the centrality dependence of the charged particle pseudorapidity distribution in lead-lead collisions at root s(NN)=2.76 TeV with the ATLAS detector. Physics Letters B, 2012, 710(3), 363-382. IF 3,96. Link
ATLAS Collaboration: Search for the Standard Model Higgs boson in the decay channel H -> ZZ((*)) -> 4l with 4.8 fb(-1) of pp collision data at root s=7 TeV with ATLAS. Physics Letters B, 2012, 710(3), 383-402. IF 3,96. Link
ATLAS Collaboration: Combined search for the Standard Model Higgs boson using up to 4.9 fb(-1) of pp collision data at root s=7 TeV with the ATLAS detector at the LHC. Physics Letter B, 2012, 710(1), 49-66. IF 3,96. Link
ATLAS Collaboration: Search for squarks and gluinos using final states with jets and missing transverse momentum with the ATLAS detector in root s=7 TeV proton-proton collisions. Physics Letters B, 2012, 710(1), 67-85. IF 3,96. Link
ATLAS Collaboration: Search for strong gravity signatures in same-sign dimuon final states using the ATLAS detector at the LHC. Phys. Lett. B, 2012, 709(4-5), 322-324. IF 3,96. Link
ATLAS Collaboration: Measurement of the W±Z production cross section and limits on anomaloustriple gauge couplings in proton–proton collisions at √s = 7 TeV with the ATLAS detector. Phys. Lett. B, 2012, 709 (4-5), 341-357. IF 3,96. Link
ATLAS Collaboration: Searches for supersymmetry with the ATLAS detector using final states with two leptons and missing transverse momentum in √s = 7 TeV proton–proton collisions. Phys. Lett B, 2012, 709(3), 137-157. IF 3,96. Link
ATLAS Collaboration: Search for first generation scalar leptoquarks in pp collisions at √s = 7 TeV with the ATLAS detector. Phys. Lett B, 2012, 709(3), 158-176. IF 3,96. Link
ATLAS Collaboration: Search for new physics in the dijet mass distribution using 1 fb− 1 of pp collision data at √s = 7 TeV collected by the ATLAS detektor. Phys. Lett B, 2012, 708(1-2), 37-54. IF 3,96. Link
ATLAS Collaboration: Measurement of the cross section for the production of a W boson in association with b-jets in pp collisions at √s = 7 TeV with the ATLAS detektor. Phys. Lett B, 2012, 707 (5), 418-437. IF 3,96. Link
ATLAS Collaboration: Measurements of the electron and muon inclusive cross-sections in proton–proton collisions at √s = 7 TeV with the ATLAS detektor. Phys. Lett B, 2012, 707(), 438-458. IF 3,96. Link
ATLAS Collaboration: Measurement of the top quark pair production cross section in pp collisions at √s = 7 TeV in dilepton final states with ATLAS. Phys. Lett. B, 2012, 707(5), 459-477. IF 3,96. Link
ATLAS Collaboration: Search for displaced vertices arising from decays of new heavy particles in 7 TeV pp collisions at ATLAS. Phys. Lett. B, 2012, 707(5), 478-496. IF 3,96. Link
ATLAS Collaboration: Measurement of the pseudorapidity and transverse momentum dependence OF the elliptic flow of charged particles in lead–lead collisions at at root s(NN) = 2.76 TeV with the ATLAS detektor. Phys. Lett B, 2012, 707(3-4), 330-348. IF 3,96. Link
ATLAS Collaboration: Search for a heavy Standard Model Higgs boson in the channel H → Z Z →l+l−q(q)over-bar using the ATLAS detector. Phys. Lett. B, 2012, 707 (1), 27-45. IF 3,96. Link
ATLAS Collaboration: Measurement of the W→τντ cross section in pp collisions at √s=7 TeV with the ATLAS experiment. Phys. Lett. B, 2012, 706 (4-5), 276-294. IF 3,96. Link
ATLAS Collaboration: Measurement of the cross-section for b-jets produced in association with a Z boson at √s=7 TeV with the ATLAS detector. Phys. Lett. B, 2012, 706 (4-5), 295-313. IF 3,96. Link
ATLAS Collaboration: A measurement of the ratio of the W and Z cross sections with exactly one associated jet in pp collisions at √s = 7 TeV with ATLAS. Phys.Lett.B, 2012, 708(3-5), 221-24. IF 3,96.Link
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Most important Pierre Auger Collaboration papers (2012)
Pierre Auger Collaboration: Measurement of the Proton-Air Cross Section at root s=57 TeV with the Pierre Auger Observatory. Physical Review Letters, 2012, 109(6), 062002. IF 7,37. Link
Piere Auger Collaboration: A search for anisotropy in the arrival directions of ultra high energy cosmic rays recorded at the Pierre Auger Observatory, Journal of Cosmology and Astroparticle Physics, 2012, 4, 040. IF 6,50. Link
Pierre Auger Collaboration: Search for point-like sources of ultra-high energy neutrinos at the Pierre Auger Observatory and improved limit on the diffuse flux of tau neutrinos.Astrophysical Journal Letters, 2012, 755(1), L4. IF 5,53. Link
2011
Prucek, R.; Tuček, J.; Kilianová, M.; Panáček, A.; Kvítek, L.; Filip, J.; Kolář, M.; Tománková, K.; Zbořil, R.: The targeted antibacterial and antifungal properties of magnetic nanocomposite of iron oxide and silver nanoparticles. Biomaterials, 2011, 32 (21), 4704-4713. IF 7,88. Link
Abstract: Two types of magnetic binary nanocomposites, Ag@Fe3O4 and γ-Fe2O3@Ag, were synthesized and characterized and their antibacterial activities were tested. As a magnetic component, Fe3O4 (magnetite) nanoparticles with an average size of about 70 nm and monodisperse γ-Fe2O3 (maghemite) nanoparticles with an average size of 5 nm were used. Nanocomposites were prepared via in situ chemical reduction of silver ions by maltose in the presence of particular magnetic phase and molecules of polyacrylate serving as a spacer among iron oxide and silver nanoparticles. In the case of the Ag@Fe3O4 nanocomposite, silver nanoparticles, caught at the surfaces of Fe3O4 nanocrystals, were around 5 nm in a size. On the contrary, in the case of the γ-Fe2O3@Ag nanocomposite, ultrafine γ-Fe2O3 nanoparticles surrounded silver nanoparticles ranging in a size between 20 and 40 nm. In addition, the molecules of polyacrylate in this nanocomposite type suppress considerably interparticle magnetic interactions as proved by magnetization measurements. Both synthesized nanocomposites exhibited very significant antibacterial and antifungal activities against ten tested bacterial strains (minimum inhibition concentrations (MIC) from 15.6 mg/L to 125 mg/L) and four candida species (MIC from 1.9 mg/L to 31.3 mg/L). Moreover, acute nanocomposite cytotoxicity against mice embryonal fibroblasts was observed at concentrations of higher than 430 mg/L (Ag@Fe3O4) and 292 mg/L (γ-Fe2O3@Ag). With respect to the non-cytotoxic nature of the polyacrylate linker, both kinds of silver nanocomposites are well applicable for a targeted magnetic delivery of silver nanoparticles in medicinal and disinfection applications.
Lemr, K.; Černoch, A.; Soubusta, J.; Kieling, K.; Eisert, J.; Dušek, M.: Experimental Implementation of the Optimal Linear-Optical Controlled Phase Gate. Phys. Rev. Lett., 2011, 106 (1), 013602013602. IF 7,62. Link
Abstract: We report on the first experimental realization of optimal linear-optical controlled phase gates for arbitrary phases. The realized scheme is entirely flexible in that the phase shift can be tuned to any given value. All such controlled phase gates are optimal in the sense that they operate at the maximum possible success probabilities that are achievable within the framework of postselected linear-optical implementations with vacuum ancillas. The quantum gate is implemented by using bulk optical elements and polarization encoding of qubit states. We have experimentally explored the remarkable observation that the optimum success probability is not monotone in the phase.
Dallas, P; Sharma, V. K; Zboril, R.: Silver polymeric nanocomposites as advanced antimicrobial agents: Classification, synthetic paths, applications, and perspectives. Adv. Colloid Interface Sci., 2011, 166 (1-2), 119-135. IF 8,66. Link
Abstract: Utilization of metallic nanoparticles in various biotechnological and medical applications represents one of the most extensively investigated areas of the current materials science. These advanced applications require the appropriate chemical functionalization of the nanoparticles with organic molecules or their incorporation in suitable polymer matrices. The intensified interest in polymer nanocomposites with silver nanoparticles is due to the high antimicrobial effect of nanosilver as well as the unique characteristics of polymers which include their excellent structural uniformity, multivalency, high degree of branching, miscellaneous morphologies and architectures, and highly variable chemical composition. In this review, we explore several aspects of antimicrobial polymer silver nanocomposites, giving special focus to the critical analysis of the reported synthetic routes including their advantages, drawbacks, possible improvements, and real applicability in antibacterial and antifungal therapy. A special attention is given to “green” synthetic routes exploiting the biopolymeric matrix and to the methods allowing preparing magnetically controllable antimicrobial polymers for targeting to an active place. The controversial mechanism of the action of silver against bacteria, fungi and yeasts as well as perspectives and new applications of silver polymeric nanocomposites is also briefly discussed.
Machala, L; Tuček, J and Zboril, R.: Polymorphous Transformations of Nanometric Iron(III) Oxide: A Review. Chem. Mater., 2011, 23 (14), 3255-3272. IF 6,40. Link
Cover designed by the authors of RCPTM; Abstract: There is great interest in iron oxides, especially in nanosized form, for both fundamental and practical reasons. Because of its polymorphism, iron(III) oxide (ferric oxide, Fe2O3) is one of the most interesting and potentially useful phases of the iron oxides. Each of the four different known crystalline Fe2O3 polymorphs (alpha-, beta-, gamma-, and epsilon-Fe2O3) has unique biochemical, magnetic, catalytic, and other properties that make it suitable for specific technical and biomedical applications. High temperature treatment is a key step in most syntheses of iron(III) oxides but often triggers polymorphous transformations that result in the formation of undesired mixtures of Fe2O3 polymorphs. It is therefore important to control the parameters that induce polymorphous transformations when seeking to prepare a given Fe2O3 polymorph as a single phase; identifying and understanding these parameters is a major challenge in the study of the polymorphism of solid compounds. This review discusses the dependence of the mechanism and kinetics of the polymorphous transformations of Fe2O3 on the intrinsic properties of the material (polymorph structure, particle size, particle morphology, surface coating, particle aggregation, incorporation of particles within a matrix) and external parameters of synthetic and/or natural conditions such as temperature, atmosphere, and pressure. The high-temperature and high-pressure induced transformations of Fe2O3 are reviewed in detail. In addition, the question of whether different Fe2O3 polymorphs are formed sequentially or simultaneously during thermal processes is discussed extensively, with reference to the experimental results that have been invoked to support these two different mechanisms. The use of selected analytical tools in studying the polymorphous transformations of Fe2O3 is also discussed, with particular emphasis on in situ approaches. Finally, key objectives for future research in this area are highlighted: (i) the development of more sophisticated kinetic control of the γ-Fe2O3 → ε-Fe2O3 phase transformation; (ii) investigation of particle morphology changes during the polymorphous transformations of Fe2O3; and (iii) the study of high-pressure induced phase transformations of Fe2O3 polymorphs other than α-Fe2O3.
Rezac, J.; Riley, K. E.; Hobza, P.: Extensions of the S66 Data Set: More Accurate Interaction Energies and Angular-Displaced Nonequilibrium Geometries. J. Chem. Theory Comput., 2011, 7 (11), 3466-3470. IF 5,14. Link
Abstract: We present two extensions of the recently published S66 data set [Řezáč, Riley, Hobza; DOI: 10.1021/ct2002946]. Interaction energies for the equilibrium geometry complexes have been recalculated using a triple-ζ basis set for the CCSD(T) term in the CCSD(T)/CBS scheme. This allows for the extrapolation of this term to the complete basis set limit, improving accuracy by almost 1 order of magnitude compared to the scheme previously used for the S66 set. Now, we estimate the largest error in the set to be about 1%. Validation of several methods against the new data indicates the exceptional robustness and accuracy of the SCS-MI-CCSD method. The second extension improves the coverage of nonequilibrium geometries. We introduce a new data set, S66a8, that samples intermolecular angular degrees of freedom in the S66 complexes. For each of the 66 complexes, eight displaced geometries have been constructed, systematically sampling possible rotations of the monomers. Interaction energies in this set are calculated at the CCSD(T)/CBS level consistently with the earlier introduced S66x8 data set that samples the intermolecular distance.
Granatier, J; Lazar, P; Otyepka, M; Hobza, P.: The Nature of the Binding of Au, Ag, and Pd to Benzene, Coronene, and Graphene: From Benchmark CCSD(T) Calculations to Plane-Wave DFT Calculations. J. Chem. Theory Comput., 2011, 7 (11), 3743-3755. IF 5,14. Link
Abstract: The adsorption of Ag, Au, and Pd atoms on benzene, coronene, and graphene has been studied using post Hartree–Fock wave function theory (CCSD(T), MP2) and density functional theory (M06-2X, DFT-D3, PBE, vdW-DF) methods. The CCSD(T) benchmark binding energies for benzene–M (M = Pd, Au, Ag) complexes are 19.7, 4.2, and 2.3 kcal/mol, respectively. We found that the nature of binding of the three metals is different: While silver binds predominantly through dispersion interactions, the binding of palladium has a covalent character, and the binding of gold involves a subtle combination of charge transfer and dispersion interactions as well as relativistic effects. We demonstrate that the CCSD(T) benchmark binding energies for benzene–M complexes can be reproduced in plane-wave density functional theory calculations by including a fraction of the exact exchange and a nonempirical van der Waals correction (EE+vdW). Applying the EE+vdW method, we obtained binding energies for the graphene–M (M = Pd, Au, Ag) complexes of 17.4, 5.6, and 4.3 kcal/mol, respectively. The trends in binding energies found for the benzene–M complexes correspond to those in coronene and graphene complexes. DFT methods that use empirical corrections to account for the effects of vdW interactions significantly overestimate binding energies in some of the studied systems.
Karlicky, F; Otyepka, M.: First Step in the Reaction of Zerovalent Iron with Water. J. Chem. Theory Comput., 2011, 7 (9), 2876-2885. IF 5,14. Link
Abstract: Here we present a comprehensive quantum chemical study of the simplest model system for the reactions of nanoscale zerovalent iron, i.e., the gas-phase reaction of an iron atom with water, to identify a theoretical method that provides reasonably accurate geometries and thermochemical data for selected iron compounds along the reaction path (Fe, FeO, HFeOH, Fe(OH)2). The energies of selected stationary points on the ground electronic potential energy surface were systematically studied using HF and post-HF methods (MP2, MP3, MP4, CCSD, CCSD(T), CASSCF, MRCI) and selected DFT functionals (B3LYP, B97-1, BPW91, M06, M06-HF, M06-L, M06-2X and MPW1K) using various basis sets up to the complete basis set. Scalar relativistic effects were modeled using the Douglas–Kroll–Hess Hamiltonian up to the fourth order, and the effects of valence plus outer-core electronic correlation were also evaluated. The calculations showed that (i) dynamic electron correlation is crucial for accurate modeling of the reactions in question, (ii) the PES around the stationary points along the reaction path is rather flat, (iii) the single-point energies calculated at the CCSD(T)/CBS level are in reasonably good agreement with experimental measurements, (iv) it is difficult to interpret DFT energies in the absence of benchmarking against experimental data or results obtained at a level of theory that is known to accurately reproduce experimental results, (v) relativistic effects are relatively modest in this system but should be included if chemical accuracy is desired, and (vi) careful analysis of the multireference character of the system and potential spin contamination is important. The CCSD(T)-3s3p-DKH2/CBS method can be considered the gold standard for this reaction because calculations at this level are in good agreement with experimental atomic excitation energies and thermochemical data. The gas-phase activation energy of the reaction between Fe and H2O is 23.6 kcal/mol including the ZPVE correction (ΔG‡298K = 29.2 kcal/mol), and HFeOH is a stable intermediate lying −31.2 kcal/mol below the reactants (ΔG298K = −25.4 kcal/mol).
Zgarbova, M; Otyepka, M; Sponer, J; Mladek, A; Banas, P; Cheatham, TE; Jurecka, P.: Refinement of the Cornell et al. Nucleic Acids Force Field Based on Reference Quantum Chemical Calculations of Glycosidic Torsion Profiles. J. Chem. Theory Comput., 2011, 7 (9), 2886-2902. IF 5,14. Link
Abstract: We report a reparameterization of the glycosidic torsion χ of the Cornell et al. AMBER force field for RNA, χOL. The parameters remove destabilization of the anti region found in the ff99 force field and thus prevent formation of spurious ladder-like structural distortions in RNA simulations. They also improve the description of the syn region and the syn–anti balance as well as enhance MD simulations of various RNA structures. Although χOL can be combined with both ff99 and ff99bsc0, we recommend the latter. We do not recommend using χOL for B-DNA because it does not improve upon ff99bsc0 for canonical structures. However, it might be useful in simulations of DNA molecules containing syn nucleotides. Our parametrization is based on high-level QM calculations and differs from conventional parametrization approaches in that it incorporates some previously neglected solvation-related effects (which appear to be essential for obtaining correct anti/high-anti balance). Our χOL force field is compared with several previous glycosidic torsion parametrizations.
Sklenovsky, P; Florova, P; Banas, P; Reblova, K; Lankas, F; Otyepka, M; Sponer, J.: Understanding RNA Flexibility Using Explicit Solvent Simulations: The Ribosomal and Group I Intron Reverse Kink-Turn Motifs. J. Chem. Theory Comput., 2011, 7 (9), 2963-2980. IF 5,14. Link
Abstract: Reverse kink-turn is a recurrent elbow-like RNA building block occurring in the ribosome and in the group I intron. Its sequence signature almost matches that of the conventional kink-turn. However, the reverse and conventional kink-turns have opposite directions of bending. The reverse kink-turn lacks basically any tertiary interaction between its stems. We report unrestrained, explicit solvent molecular dynamics simulations of ribosomal and intron reverse kink-turns (54 simulations with 7.4 μs of data in total) with different variants (ff94, ff99, ff99bsc0, ff99χOL, and ff99bsc0χOL) of the Cornell et al. force field. We test several ion conditions and two water models. The simulations characterize the directional intrinsic flexibility of reverse kink-turns pertinent to their folded functional geometries. The reverse kink-turns are the most flexible RNA motifs studied so far by explicit solvent simulations which are capable at the present simulation time scale to spontaneously and reversibly sample a wide range of geometries from tightly kinked ones through flexible intermediates up to extended, unkinked structures. A possible biochemical role of the flexibility is discussed. Among the tested force fields, the latest χOL variant is essential to obtaining stable trajectories while all force field versions lacking the χ correction are prone to a swift degradation toward senseless ladder-like structures of stems, characterized by high-anti glycosidic torsions. The type of explicit water model affects the simulations considerably more than concentration and the type of ions.
Rezac, J; Riley, K. E.; Hobza, P.: S66: A Well-balanced Database of Benchmark Interaction Energies Relevant to Biomolecular Structures. J. Chem. Theory Comput., 2011, 7 (8), 2427-2438. IF 5,14. Link
Abstract: With numerous new quantum chemistry methods being developed in recent years and the promise of even more new methods to be developed in the near future, it is clearly critical that highly accurate, well-balanced, reference data for many different atomic and molecular properties be available for the parametrization and validation of these methods. One area of research that is of particular importance in many areas of chemistry, biology, and material science is the study of noncovalent interactions. Because these interactions are often strongly influenced by correlation effects, it is necessary to use computationally expensive high-order wave function methods to describe them accurately. Here, we present a large new database of interaction energies calculated using an accurate CCSD(T)/CBS scheme. Data are presented for 66 molecular complexes, at their reference equilibrium geometries and at 8 points systematically exploring their dissociation curves; in total, the database contains 594 points: 66 at equilibrium geometries, and 528 in dissociation curves. The data set is designed to cover the most common types of noncovalent interactions in biomolecules, while keeping a balanced representation of dispersion and electrostatic contributions. The data set is therefore well suited for testing and development of methods applicable to bioorganic systems. In addition to the benchmark CCSD(T) results, we also provide decompositions of the interaction energies by means of DFT-SAPT calculations. The data set was used to test several correlated QM methods, including those parametrized specifically for noncovalent interactions. Among these, the SCS-MI-CCSD method outperforms all other tested methods, with a root-mean-square error of 0.08 kcal/mol for the S66 data set.
Filip, J; Yngard, RA; Siskova, K; Marusak, Z; Ettler, V; Sajdl, P; Sharma, VK; Zboril, R.: Mechanisms and Efficiency of the Simultaneous Removal of Metals and Cyanides by Using Ferrate(VI): Crucial Roles of Nanocrystalline Iron(III) Oxyhydroxides and Metal Carbonates. Chem-Eur. J., 2011, 17 (36), 10097-10105. IF 5,48. Link
Abstract: The reaction of potassium ferrate(VI), K(2)FeO(4), with weak-acid dissociable cyanides–namely, K(2)[Zn(CN)(4)], K(2)[Cd(CN)(4)], K(2)[Ni(CN)(4)], and K(3)[Cu(CN)(4)]–results in the formation of iron(III) oxyhydroxide nanoparticles that differ in size, crystal structure, and surface area. During cyanide oxidation and the simultaneous reduction of iron(VI), zinc(II), copper(II), and cadmium(II), metallic ions are almost completely removed from solution due to their coprecipitation with the iron(III) oxyhydroxides including 2-line ferrihydrite, 7-line ferrihydrite, and/or goethite. Based on the results of XRD, Mössbauer and IR spectroscopies, as well as TEM, X-ray photoelectron emission spectroscopy, and Brunauer-Emmett-Teller measurements, we suggest three scavenging mechanisms for the removal of metals including their incorporation into the ferrihydrite crystal structure, the formation of a separate phase, and their adsorption onto the precipitate surface. Zn and Cu are preferentially and almost completely incorporated into the crystal structure of the iron(III) oxyhydroxides; the formation of the Cd-bearing, X-ray amorphous phase, together with Cd carbonate is the principal mechanism of Cd removal. Interestingly, Ni remains predominantly in solution due to the key role of nickel(II) carbonate, which exhibits a solubility product constant several orders of magnitude higher than the carbonates of the other metals. Traces of Ni, identified in the iron(III) precipitate, are exclusively adsorbed onto the large surface area of nanoparticles. We discuss the relationship between the crystal structure of iron(III) oxyhydroxides and the mechanism of metal removal, as well as the linear relationship observed between the rate constant and the surface area of precipitates.
Perina, J; Luks, A; Perinova, V; Leonski, W.: Fano zeros in photoelectron spectra of an autoionization system interacting with a neighboring atom. Opt. Express, 2011, 19 (18), 17133-17142. IF 3,75. Link
Abstract: Photoelectron ionization spectra of an autoionization system interacting with a neighboring two-level atom are studied using the method of canonical transformation. Conditions for the occurrence of a Fano zero are exactly derived, together with its frequency. Ionization spectra are typically composed of at most four peaks in this case. Sharp peaks occur not far from the Fano zero due to the confluence of bound-free coherences. Spectral peaks close to the Fano zero are suppressed. Also dynamical zeros appearing once per the Rabi period in conditioned photoelectron ionization spectra are observed.
Nozka, L; Pech, M; Hiklova, H; Mandat, D; Hrabovsky, M; Schovanek, P; Palatka, M.: BRDF profile of Tyvek and its implementation in the Geant4 simulation toolkit. Opt. Express, 2011, 19 (5), 4199-4209. IF 3,75. Link
Abstract: Diffuse and specular characteristics of the Tyvek 1025-BL material are reported with respect to their implementation in the Geant4 Monte Carlo simulation toolkit. This toolkit incorporates the UNIFIED model. Coefficients defined by the UNIFIED model were calculated from the bidirectional reflectance distribution function (BRDF) profiles measured with a scatterometer for several angles of incidence. Results were amended with profile measurements made by a profilometer.
Prucek, R; Panacek, A; Soukupova, J; Novotny, R; Kvitek, L.: Reproducible synthesis of silver colloidal particles tailored for application in near-infrared surface-enhanced Raman spectroscopy. J. Mater. Chem., 2011, 21 (17), 6416-6420. IF 5,10. Link
Abstract: Reproducible synthesis of silver colloidal particles, with diameters of hundreds of nanometres, represents an experimentally rather difficult task although they have revealed a great application potential in e.g. SERS. The newly developed method, based on the reduction of the complex anion [Ag(SO3)2]3−, offers an approach enabling to manage the preparation of silver particles with adjustable average diameters in the interval from 200 nm up to 700 nm due to the choice of the reducing agent and the sulfite concentration. These particles proved their efficiency as substrates for surface enhanced Raman spectroscopy with the excitation in the near infrared region (λ = 1064 nm) and therefore this newly developed method confirmed the expected application potential.
Reischl, RJ; Hartmanova, L; Carrozzo, M; Huszar, M; Fruhauf, P; Lindner, W.: Chemoselective and enantioselective analysis of proteinogenic amino acids utilizing N-derivatization and 1-D enantioselective anion-exchange chromatography in combination with tandem mass spectrometric detection. J. Chromatogr. A, 2011, 1218 (46), 8379-8387. IF 4,19. Link
Abstract: Amino acid analysis in biological samples still poses a challenge to analytical chemists. In higher developed species trace amounts of d-amino acids have to be detected in vast excesses of the corresponding l-enantiomers. This method utilizes an easy-to-carry-out derivatization step on the amino group with an iron ferrocenyl propionate hydroxy succinimide ester followed by one-dimensional enantioselective anion exchange chromatography with cinchona alkaloid based chiral stationary phases (CSPs). MS detection is carried out in the highly sensitive SRM (selected reaction monitoring) mode, which allows a chemoselective differentiation of amino acid derivatives as well as their enantioselective separation in one step. Application of this method allows LOD (limits of detection) in the low μmol L−1 range and baseline enantioseparation for all proteinogenic amino acids except for Pro, Arg and His. The d-enantiomers of isomeric Leu and Ile were separated chromatographically and pose an example for the complementary selectivities of LC and MS. A successful application of this procedure to unprocessed human urine indicated the eligibility to analyse biological samples.
Papouskova, B; Bednar, P; Hron, K; Stavek, J; Balik, J; Myjavcova, R; Bartak, P; Tomankova, E; Lemr, K.: Advanced liquid chromatography/mass spectrometry profiling of anthocyanins in relation to set of red wine varieties certified in Czech Republic. J. Chromatogr. A, 2011, 1218 (42), 7581-7591. IF 4,19. Link
Abstract: Hyphenation of micro-liquid and ultra-performance liquid chromatography with a hybrid (QqTOF) tandem mass spectrometry was studied from the viewpoint of their applicability for monitoring of anthocyanin dyes in various cultivars and different vintages of red wine. After appropriate optimization both techniques proved to be suitable for this task. UHPLC system provided lower LOD and LOQ values as well as higher productivity and precision of retention parameters and peak areas with respect to micro-LC method. On the other hand, micro-LC method offers significant savings of mobile phase, less contamination of ion source of mass spectrometer and makes the nebulization process in electrospray much easier. In combination with principal component analysis (PCA), the method allows to elucidate long-term relations in a complete set of certified red wine cultivars grown in South Moravia (certified in Czech Republic until year 2005). Among the studied varieties Rubinet exhibit a specific anthocyanin profile. Especially interesting is a high content of 3-coumaroylglucoside-5-glucosides of malvidin and peonidin. Those dyes can be used as markers of artificial color enhancement. Principal component analysis applied to data processed with regard to enzymatic activity markedly facilitate classification among varieties. This approach allows resolution of teinturiers, variety Blaufränkish and partial classification of other varieties.
Herchel, R.; Travnicek, Z. and Zboril, R.: Tuning of the Critical Temperature in Iron(II) Spin-Crossover Materials Based on Bridging Polycyanidometallates: Pentacyanidonitrosylferrate(II) and Hexacyanidoplatinate(IV), Inorg. Chem. 2011, 50 (24), 12390–12392. IF 4,33. Link
Abstract: The reactions of iron(II) sulfate, 4-amino-3,5-di-2-pyridyl-4H-1,2,4-triazole (abpt), and pentacyanidonitrosylferrate(II) or hexacyanidoplatinate(IV) resulted in the formation of one-dimensional iron(II) spin-crossover compounds [Fe(abpt)(2)(μ-Fe(CN)(5)(NO))](n) (1) and [Fe(abpt)(2)(μ-Pt(CN)(6))](n) (2) with the spin-transition critical temperature near or above room temperature accompanied by thermochromism. Furthermore, it has been proven that the critical temperature T(c) is influenced by the type of dianionic polycyanidometallate within the series of discussed systems, and it changes in the sequence of [Fe(CN)(5)(NO)](2-) < [Pt(CN)(6))](2-) < [Ni(CN)(4))](2-) ≈ [Pd(CN)(4))](2-) ≈ [Pt(CN)(4))](2-).
Herchel, R; Tucek, J; Travnicek, Z; Petridis, D; Zboril, R.: Crystal Water Molecules as Magnetic Tuners in Molecular Metamagnets Exhibiting Antiferro-Ferro-Paramagnetic Transitions. Inorg. Chem., 2011, 50 (18), 9153-9163. IF 4,33. Link
Abstract: We studied the effects of the number of crystal water molecules on the magnetic behavior of {[Ni(en)2]3[Fe(CN)6]2·xH2O}n (1–3) (where en = ethylenediamine and x = 3, 2, or 0) coordination polymers by 57Fe Mössbauer spectroscopy, single-crystal X-ray diffraction, and magnetization measurements. Magnetic phase diagrams constructed for all three compounds indicate that they behave as metamagnets exhibiting very rare field-induced antiferro–ferro–paramagnetic transitions. The number of crystal water molecules has a major effect on the Néel temperature, critical field, and magnetic hardness of the compounds in the ferromagnetic state. Moreover, the systems behave as molecular magnetic sponges, changing their magnetic properties due to the controllable and reversible dehydration/hydration process.
Novak, M; Skoda, R; Filip, J; Macek, I; Vaculovic, T.: COMPOSITIONAL TRENDS IN TOURMALINE FROM INTRAGRANITIC NYF PEGMATITES OF THE TREBIC PLUTON, CZECH REPUBLIC: AN ELECTRON MICROPROBE, MOSSBAUER AND LA-ICP-MS STUDY. Can. Mineral., 2011, 49 (1), 359-380. IF 1,29. Link
Abstract: Tourmalines (dravite – schorl – uvite – povondraite) from intragranitic pegmatites of the Třebíč Pluton (porphyritic, amphibole–biotite melasyenite to quartz melasyenite – melagranite), in the Czech Republic, were examined using an electron microprobe, Mössbauer spectroscopy and LA–ICP–MS analyses. Pegmatites with the common assemblage Kfs + qtz + pl (An0–13) + Fe-rich phlogopite (0.49 < XMg < 0.70) and accessory allanite-(Ce), ilmenite, tourmaline and titanite, were divided into three types generally related to the NYF (REL–REE) pegmatites: allanite-type, euxenite-type (+ euxenite, aeschynite, pyrochlore, beryl, niobian rutile, zircon), and the most evolved euxenite-type pegmatite, Klučov I (with annite, XMg 0.09), cassiterite, herzenbergite, and abundant graphic intergrowths of quartz + feldspars and quartz + tourmaline). Black tourmaline occurs in several distinct morphological, paragenetic and textural types with very high variability in zoning; however, the morphological types of tourmaline do not differ chemically. They generally show two distinct trends: Fetot/(Fetot + Mg) = 0.243–0.882, 0.657–0.978; Altot = 5.039–6.464, 5.040–7.030 apfu; Ca ≤0.508, ≤0.174 apfu; Mn ≤0.079, ≤0.445, respectively. High concentrations of Ti ≤0.490, ≤0.361 apfu are typical, as well as low F, ≤0.288, 0.046–0.508 apfu, and low vacancy at the X site, 0.152, 0.348 pfu, respectively. Mössbauer spectroscopy revealed~21% of the Fe as Fe3+ for allanite-type, 17 to 26% for euxenite-type, and 22% for tourmaline from the pegmatite Klučov I, respectively, values that are high relative to ordinary granitic pegmatites. Our LA–ICP–MS study revealed highly variable concentrations of the individual trace elements within single grains and within the individual types of pegmatites. Explicit compositional evolution from less to highly evolved pegmatites was revealed only rarely, e.g., increase in Ni, Co, Zn, Ga, Sc and Ce from less to more evolved pegmatites. Two distinct sets of substitutions are dominant: R3+O R2+−1(OH) −1 and □R3+ Na−1R2+−1. In addition, there are minor substitutions, CaR2+ Na−1Al−1, Fe2+ Mg−1 and MnF Fe2+−1(OH) −1, the latter exclusively at Klučov I. They are similar to those from ordinary Li-poor to slightly Li-enriched granitic pegmatites. Tourmalines from allanite-type and euxenite-type pegmatites exhibit less convincing plots, with the dominant substitutions CaR2+3O2 Na−1R3+−3(OH)−2 and Fe2+ Mg−1, and minor Al Fe3+−1. High contents of Ti4+ imply the presence of the component XCa2+YR2+1.5YTi1.5ZR3+5ZMg2+ Si6O18 (BO3)3O3(OH). These substitutions are different from those normally encountered in granitic pegmatites, but show some features of non-pegmatitic Fe3+-enriched tourmalines. Textural relations suggest very late solidus to early subsolidus origin of the tourmaline. Discussions of a tourmaline’s stability in moderately aluminous granitic systems is shifted to the role of tourmaline composition along with the melt’s composition.
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ATLAS Collaboration
There are several areas of interest of the ATLAS collaboration. Without any doubt, the most “hot” area is the search for the Higgs boson – a hypothetical elementary particle predicted by the Standard Model of particle physics that would explain why fundamental particles such as quarks and electrons have mass. The ATLAS collaboration together with the CMS collaboration presented their reports on December 13, 2011:
Based on this plot, Higgs boson masses between 124 GeV and 519 GeV are expected to be excluded at the 95% confidence level. An exclusion of the SM Higgs boson production at the 99% confidence level is achieved in the regions between 133 GeV and 230 GeV and between 260 GeV and 437 GeV. It also means that remaining promising regions will be studied with a maximal effort in the year 2012.
Another very interesting area is the search for supersymmetric particles – there all ATLAS measurements are in a good agreement with the Standard Model predictions. Moreover, all tests of the perturbative quantum chromodynamics were successful.
Finally, we cannot forget for searches of new physics: extra dimensions/missing energy, micro black holes production, axions etc. All of these searches were negative and pushed exclusionary limits higher.
The full installation of the ALFA detector (Absolute Luminosity For Atlas), where the RCPTM team plays the key role in its software and simulation group, was finished and the first measurement of the total cross section at 7 TeV was performed. The results are expected to be published in the first half of the year 2012.
ATLAS Collaboration: Search for Dilepton Resonances in pp Collisions at √s=7 TeV with the ATLAS Detector. Phys. Rev. Lett., 2011, 107 (27), 272002. IF 7,62. Link
ATLAS Collaboration: Search for the Higgs Boson in the H→WW→lνjj Decay Channel in pp Collisions at √s=7 TeV with the ATLAS Detector. Phys. Rev. Lett., 2011, 107 (23), 23181. IF 7,62. Link
ATLAS Collaboration: Search for a Standard Model Higgs Boson in the H→ZZ→ℓ+ℓ-νν̅ Decay Channel with the ATLAS Detector. Phys. Rev. Lett., 2011, 107 (22), 221802. IF 7,62. Link
ATLAS Collaboration: Measurement of the W+W- Cross Section in √s=7 TeV pp Collisions with ATLAS. Phys. Rev. Lett., 2011, 107 (4), 041802. IF 7,62. Link
ATLAS Collaboration: Search for a Heavy Particle Decaying into an Electron and a Muon with the ATLAS Detector in √s=7 TeV pp collisions at the LHC. Phys. Rev. Lett., 2011, 106 (25), 251801. IF 7,62. Link
ATLAS Collaboration: Measurement of Dijet Azimuthal Decorrelations in pp Collisions at √s=7 TeV. Phys. Rev. Lett., 2011, 106 (17), 172002. IF 7,62. Link
ATLAS Collaboration: Search for Supersymmetry Using Final States with One Lepton, Jets, and Missing Transverse Momentum with the ATLAS Detector in √s=7 TeV pp Collisions. Phys. Rev. Lett., 2011, 106 (13), 131802. IF 7,62. Link
ATLAS Collaboration: Measurement of the inclusive isolated prompt photon cross-section in pp collisions at √s=7 TeV using 35 pb-1 of ATLAS data. Phys. Lett. B, 2011, 706 (2-3), 150-167. IF 5,26. Link
ATLAS Collaboration: Measurement of the transverse momentum distribution of Z/γ* bosons in proton-proton collisions at √s=7 TeV with the ATLAS detector. Phys. Lett. B, 2011, 705 (5), 415-434. IF 5,26. Link
ATLAS Collaboration: Search for the Standard Model Higgs boson in the decay channel H → ZZ(*) → 4l with the ATLAS detector. Phys. Lett. B, 2011, 705 (5), 435-451. IF 5,26. Link
ATLAS Collaboration: Search for the Standard Model Higgs boson in the two photon decay channel with the ATLAS detector at the LHC. Phys. Lett. B, 2011, 705 (5), 452-470. IF 5,26. Link
ATLAS Collaboration: Search for new phenomena with the monojet and missing transverse momentum signature using the ATLAS detector in √s = 7 TeV proton-proton collisions. Phys. Lett. B, 2011, 705 (4), 294-312. IF 5,26. Link
ATLAS Collaboration: Search for neutral MSSM Higgs bosons decaying to τ+τ− pairs in proton-proton collisions √s=7 TeV with the ATLAS detector. Phys. Lett. B, 2011, 705 (3), 174-192. IF 5,26. Link
ATLAS Collaboration: Search for a heavy gauge boson decaying to a charged lepton and a neutrino in 1 fb− 1 of pp collisions at √s = 7 TeV using the ATLAS detector. Phys. Lett. B, 2011, 705 (1-2), 28-46. IF 5,26. Link
ATLAS Collaboration: Measurement of the ϒ(1S) production cross-section in pp collisions at √s=7 TeV in ATLAS. Phys. Lett. B, 2011, 705 (1-2), 9-27. IF 5,26. Link
ATLAS Collaboration: Search for heavy long-lived charged particles with the ATLAS detector in pp collisions at √s=7 TeV. Phys. Lett. B, 2011, 703 (4), 428-446. IF 5,26. Link
ATLAS Collaboration: Search for supersymmetry in pp collisions at √s=7 TeV in final states with missing transverse momentum and b-jets. Phys. Lett. B, 2011, 701 (4), 398-416. IF 5,26. Link
ATLAS Collaboration: Search for squarks and gluinos using final states with jets and missing transverse momentum with the ATLAS detector in √s=7 TeV proton-proton collisions. Phys. Lett. B, 2011, 701 (2), 186-203. IF 5,26. Link
ATLAS Collaboration: Search for stable hadronising squarks and gluinos with the ATLAS experiment at the LHC. Phys. Lett. B, 2011, 701 (1), 1-19. IF 5,26. Link
ATLAS Collaboration: Measurement of the W charge asymmetry in the W→μν decay mode in pp collisions at √s=7 TeVwith the ATLAS detector. Phys. Lett. B, 2011, 701 (1), 31-49. IF 5,26. Link
ATLAS Collaboration: Search for high-mass states with one lepton plus missing transverse momentum in proton-proton collisions √s=7 TeV with the ATLAS detector. Phys. Lett. B, 2011, 701 (1), 50-69. IF 5,26. Link
ATLAS Collaboration: Search for high mass dilepton resonances in pp collisions at √s=7 TeV with the ATLAS experiment. Phys. Lett. B, 2011, 700 (3-4), 163-180. IF 5,26. Link
ATLAS Collaboration: Measurement of Wγ and Zγ production in proton-proton collisions √s = 7 TeV with the ATLAS detector. J. High Energy Phys., 2011, 9, 072. IF 6,05. Link
ATLAS Collaboration: Measurement of dijet production with a veto on additional central jet activity in pp collisions √s = 7 TeV using the ATLAS detector. J. High Energy Phys., 2011, 9, 053. IF 6,05. Link
ATLAS Collaboration: A search for new physics in dijet mass and angular distributions in pp collisions at √s = 7 TeV measured with the ATLAS detector. New J. Phys., 2011, 13, 053044. IF 3,85. Link
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Pierre Auger Collaboration
The Pierre Auger Observatory (PAO), built in western-Argentinean pampa, is studying the most energetic and rarest particles in the universe. When these particles strike the atmosphere of the Earth, they produce extensive air showers made of billions of secondary particles. The nature and origin of the particles with extremely high energies remain a puzzle that the PAO is trying to solve.
Publications of results achieved by PAO belong to the most-cited works in the field of astroparticle physics. The studied problems include determination of the energy spectrum of cosmic rays, its distribution across the sky, assessment of its chemical composition, but mainly the most fundamental question – question of its origin. The most energetic particles may come from decay of supermassive dark-matter particles as well as they might by created by gradual acceleration in astrophysical objects. One direction of the study is focused on events caused by high-energy neutrinos (also a subject of one M.Sc. thesis finished in RCPTM in 2011). The observation of such events would substantially contribute to revealing of the nature of the ultra-high-energy particles: if their number exceeds classical expectations, they would signal the decays of massive dark matter.
While members of RCPTM contributed to building and operation of PAO since its commencement, in spring of 2011 RCPTM became an official member of the Pierre Auger Collaboration. In recent months, RCPTM workers focused on several tasks towards trouble-free operation of PAO. The „full-sky cameras“ developed in Olomouc were installed on site and will help to optimize the operation of PAO fluorescence detectors. New methods of spectral reflectivity and shape-evaluation of mirror segments have been developed which also open the way to contribute to another international collaboration – the Cherenkov Telescope Array. And of course, RCPTM workers made their share of routine services at PAO.
Piere Auger Collaboration: The effect of the geomagnetic field on cosmic ray energy estimates and large scale anisotropy searches on data from the Pierre Auger Observatory. J. Cosmol. Astropart. Phys., 2011, 11, 022. IF 6,50. Link
Piere Auger Collaboration: Anisotropy and chemical composition of ultra-high energy cosmic rays using arrival directions measured by the Pierre Auger Observatory. J. Cosmol. Astropart. Phys., 2011, 6, 022. IF 6,50. Link
Piere Auger Collaboration: The Pierre Auger Observatory scaler mode for the study of solar activity modulation of galactic cosmic rays. J. Instrum., 2011, 6, P1003. IF 3,15. Link
2010
Zbořil, R.; Karlický, F.; Bourlinos, A. B.; Steriotis, T. A.; Stubos, A. K.; Georgakilas, V.; Šafářová, K.; Jančík, D.; Trapalis, C.; Otyepka, M.: Graphene Fluoride: A Stable Stoichiometric Graphene Derivative and Its Chemical Conversion to Graphene. Small, 2010, 6 (24), 2885-2891. IF 7,34. Link
Abstract: Stoichoimetric graphene fluoride monolayers are obtained in a single step by the liquid-phase exfoliation of graphite fluoride with sulfolane. Comparative quantum-mechanical calculations reveal that graphene fluoride is the most thermodynamically stable of five studied hypothetical graphene derivatives; graphane, graphene fluoride, bromide, chloride, and iodide. The graphene fluoride is transformed into graphene via graphene iodide, a spontaneously decomposing intermediate. The calculated bandgaps of graphene halides vary from zero for graphene bromide to 3.1 eV for graphene fluoride. It is possible to design the electronic properties of such two-dimensional crystals.
Banas, P; Hollas, D; Zgarbova, M; Jurecka, P; Orozco, M; Cheatham, TE; Sponer, J; Otyepka, M.: Performance of Molecular Mechanics Force Fields for RNA Simulations: Stability of UUCG and GNRA Hairpins. J. Chem. Theory Comput., 2010, 6 (12), 3836-3849. IF 5,14. Link
Abstract: The RNA hairpin loops represent important RNA topologies with indispensable biological functions in RNA folding and tertiary interactions. 5′-UNCG-3′ and 5′-GNRA-3′ RNA tetraloops are the most important classes of RNA hairpin loops. Both tetraloops are highly structured with characteristic signature three-dimensional features and are recurrently seen in functional RNAs and ribonucleoprotein particles. Explicit solvent molecular dynamics (MD) simulation is a computational technique which can efficiently complement the experimental data and provide unique structural dynamics information on the atomic scale. Nevertheless, the outcome of simulations is often compromised by imperfections in the parametrization of simplified pairwise additive empirical potentials referred to also as force fields. We have pointed out in several recent studies that a force field description of single-stranded hairpin segments of nucleic acids may be particularly challenging for the force fields. In this paper, we report a critical assessment of a broad set of MD simulations of UUCG, GAGA, and GAAA tetraloops using various force fields. First, we utilized the three widely used variants of Cornell et al. (AMBER) force fields known as ff94, ff99, and ff99bsc0. Some simulations were also carried out with CHARMM27. The simulations reveal several problems which show that these force fields are not able to retain all characteristic structural features (structural signature) of the studied tetraloops. Then we tested four recent reparameterizations of glycosidic torsion of the Cornell et al. force field (two of them being currently parametrized in our laboratories). We show that at least some of the new versions show an improved description of the tetraloops, mainly in the syn glycosidic torsion region of the UNCG tetraloop. The best performance is achieved in combination with the bsc0 parametrization of the R /γ angles. Another critically important region to properly describe RNA molecules is the anti/high-anti region of the glycosidic torsion, where there are significant differences among the tested force fields. The tetraloop simulations are complemented by simulations of short A-RNA stems, which are especially sensitive to an appropriate description of the anti/high-anti region. While excessive accessibility of the high-anti region converts the A-RNA into a senseless “ladder-like” geometry, excessive penalization of the high-anti region shifts the simulated structures away from typical A-RNA geometry to structures with a visibly underestimated inclination of base pairs with respect to the helical axis.