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AUGUST 2012 -
J. of Chemical Physics 137, 2012, 034304.
(article chosen as a Research Highlight featured on the journal website home page).
Uptake of atmospheric molecules by ice nanoparticles: Pickup cross sections (article here).
Jozef Lengyel, Jaroslav Kočišek, Viktoriya Poterya, Andriy Pysanenko, Pavla Svrčková, Michal Fárník, Dimitrios Zaouris, and Juraj Fedor.
Abstract: Uptake of several atmospheric molecules on free ice nanoparticles was investigated. Typical examples were chosen: water, methane, NOx species (NO, NO2), hydrogen halides (HCl, HBr), and volatile organic compounds (CH3OH, CH3CH2OH). The cross sections for pickup of these molecules on ice nanoparticles (H2O)N with the mean size of math ≈ 260 (diameter ∼2.3 nm) were measured in a molecular beam experiment. These cross sections were determined from the cluster beam velocity decrease due to the momentum transfer during the pickup process. For water molecules molecular dynamics simulations were performed to learn the details of the pickup process. The experimental results for water are in good agreement with the simulations. The pickup cross sections of ice particles of several nanometers in diameter can be more than 3 times larger than the geometrical cross sections of these particles. This can have significant consequences in modelling of atmospheric ice nanoparticles, e.g., their growth.
ARCHIVE 2009-2012......
JULY 2012 -
Inorganic Chemistry, 2012, 51 , 5128-5137.
Measured and Calculated Oxidation Potentials of 1-X-12-Y-CB11Me10– Anions (article here).
Abdul Wahab, Brian Stepp, Christos Douvris, Michal Valášek, Jan Štursa, Jiřı́ Klı́ma, Mari-Carmen Piqueras, Raül Crespo, Jiřı́ Ludvı́k, and Josef Michl.
Abstract: Cyclic voltammetry of 31 icosahedral carborane anions 1-X-12-Y-CB11Me10– at a Pt electrode in liquid SO2 revealed a completely reversible one-electron oxidation even at low scan rates, except for the anions with Y = I, which are oxidized irreversibly up to a scan rate of 5.0 V/s, and the anion with X = COOH and Y = H, whose oxidation is irreversible at scan rates below 1.0 V/s. Relative reversible oxidation potentials agree well with RI-B3LYP/TZVPP,COSMO and significantly less well with RI-BP86/TZVPP,COSMO or RI-HF/TZVPP,COSMO calculated adiabatic electron detachment energies. Correlations with HOMO energies of the anions are nearly as good, even though the oxidized forms are subject to considerable Jahn–Teller distortion. Except for the anion with X = F and Y = Me, the oxidation potentials vary linearly with substituent σp Hammett constants. The slopes (reaction constants) are 0.31 and 0.55 V for positions 1 and 12, respectively.
J. Am. Chem. Soc. 134, 2012, 8655-8661.
Dramatically Enhanced Cleavage of the C–C Bond Using an Electrocatalytically Coupled Reaction (article here).
Qinggang He, Badri Shyam, Kateřina Macounová, Petr Krtil, David Ramaker, and Sanjeev Mukerjee.
Abstract: This paper describes a generalized approach for the selective electrocatalytic C–C bond splitting in aliphatic alcohols at low temperature in aqueous state, with ethanol as an example. We show that selective C–C bond cleavage, leading to carbon dioxide, is possible in high pH aqueous media at low overpotentials. This improved selectivity and activity is achieved using a solution-born co-catalyst based on Pb(IV) acetate, which controls the mode of the ethanol adsorption so as to facilitate direct activation of the C–C bond. The simultaneously formed under-potentially deposited (UPD) Pb and surface lead hydroxide change the functionality of the catalyst surface for efficient promotion of CO oxidation. The resulting catalyst retains an unprecedented ability to sustain the full oxidation reaction pathway on an extended time scale of hours as opposed to minutes without addition of Pb(IV) acetate.
JUNE 2012 -
Analytical Chemistry, 2012, 84 (11), pp 4979-4983.
Real-Time Quantification of Traces of Biogenic Volatile Selenium Compounds in Humid Air by Selected Ion Flow Tube Mass Spectrometry (article here).
Sovová K., Shestivská V., Španěl, P.
Abstract: iological volatilization of selenium, Se, in a contaminated area is an economical and environmentally friendly approach to phytoremediation techniques, but analytical methods for monitoring and studying volatile compounds released in the process of phytovolatilization are currently limited in their performance. Thus, a new method for real time quantification of trace amounts of the vapors of hydrogen selenide (H2Se), methylselenol (CH3SeH), dimethylselenide ((CH3)2Se), and dimethyldiselenide ((CH3)2Se2) present in ambient air adjacent to living plants has been developed. This involves the characterization of the mechanism and kinetics of the reaction of H3O+, NO+, and O2+• reagent ions with molecules of these compounds and then use of the rate constants so obtained to determine their absolute concentrations in air by selected ion flow tube mass spectrometry, SIFT-MS. The results of experiments demonstrating this method on emissions from maize (Zea mays) seedlings cultivated in Se rich medium are also presented.
Biophysical Journal, Vol.102 (9), 2012, 2104–2113.
Dynamics and Size of Cross-Linking-Induced Lipid Nanodomains in Model Membranes (article here).
Štefl M., Šachl R., Humpolíčková J., Cebecauer M., Macháň R., Kolářová M., Johansson L. B.-Å. , Hof. M.
Abstract: Changes of membrane organization upon cross-linking of its components trigger cell signaling response to various exogenous factors. Cross-linking of raft gangliosides GM1 with cholera toxin (CTxB) was shown to cause microscopic phase separation in model membranes, and the CTxB-GM1 complexes forming a minimal lipid raft unit are the subject of ongoing cell membrane research. Yet, those subdiffraction sized rafts have never been described in terms of size and dynamics. By means of two-color z-scan fluorescence correlation spectroscopy, we show that the nanosized domains are formed in model membranes at lower sphingomyelin (Sph) content than needed for the large-scale phase separation and that the CTxB-GM1 complexes are confined in the domains poorly stabilized with Sph. Förster resonance energy transfer together with Monte Carlo modeling of the donor decay response reveal the domain radius of ∼8 nm, which increases at higher Sph content. We bserved two types of domains behaving differently, which suggests a dual role of the cross-linker: first, local transient condensation of the GM1 molecules compensating for a lack of Sph and second, coalescence of existing nanodomains ending in large-scale phase separation.
MAY 2012 -
Astronomy & Astrophysics, 2012, 541, A125.
Potassium spectra in the 700–7000 cm-1 domain: Transitions involving f-, g-, and h-states (article here).
S. Civiš, M. Ferus, P. Kubelík, P. Jelinek and V. E. Chernov.
Abstract:
Context - The infrared (IR) range is becoming increasingly important to astronomical studies of cool or dust-obscured objects, such as dwarfs, disks, or planets, and in the extended atmospheres of evolved stars. A general drawback of the IR spectral region is the much lower number of atomic lines available (relative to the visible and ultraviolet ranges).
Aims - We attempt to obtain new laboratory spectra to help us identify spectral lines in the IR. This may result in the discovery of new excited atomic levels that are difficult to compute theoretically with high accuracy, hence can be determined solely from IR lines.
Results - Precision laboratory measurements are presented for 38 KI lines in the infrared (including 25 lines not measured previously in the laboratory) range using time-resolved Fourier transform infrared spectroscopy. The 6g, 6h, and 7h levels of KI are observed for the first time, in addition to updated energy values of the other 23 KI levels and the f-values for the transitions involving these levels.
Conclusions - The recorded wave numbers are in good agreement with the data from the available solar spectrum atlases. Nevertheless, we correct their identification for three lines (1343.699, 1548.559, and 1556.986 cm-1).
Catalysis Reviews:Science and Engineering, 2012, 54 (2), 135-223.
Siting and Distribution of Framework Aluminium Atoms in Silicon-Rich Zeolites and Impact on Catalysis (article here).
J. Dědeček, Z. Sobalík, B.Wichterlová.
Abstract:
Siting of Al atoms in the framework T sites, in zeolite rings and channel/cavity system, and the distribution of Al atoms between single Al atoms and close Al atoms in various Al-O-(Si-O)n-Al sequences in Si-rich zeolites represent key parameters controlling properties of counter ion species. Framework Al siting and distribution is not random or controlled by simple rules and depends on the conditions of the zeolite synthesis. Al in Al-O-(Si-O)2-Al in one 6-MR and single Al atoms predominate in Si-rich zeolites and their population can be varied to a large extent. The siting and distribution of framework Al atoms dramatically affect catalytic activity/selectivity both of protonic and transition metal ion-containing zeolite catalysts.
APRIL 2012 -
Chemical Communications, 2012, 48 (34), pp 4094-4096.
Competitive inhibition of a metal-free porphyrin oxygen-reduction catalyst by water (article here).
A.Trojánek, J. Langmaier, S. Záliš, Z. Samec.
Abstract:A stopped-flow method is used to study the effects of water and reactant acid anion TB− = tetrakis(pentafluorophenyl)borate on the homogeneous oxygen reduction catalyzed by the protonated tetraphenylporphyrin. Observed competitive inhibition of the catalyst is linked to the DFT free energy of extraction of O2, water, and TB− from the porphyrin complex.
Nano Letters, 2012, 12 (2), pp 687-693 .
Phonon and Structural Changes in Deformed Bernal Stacked Bilayer Graphene (article here).
Frank, O., Bouša, M., Riaz, I., Jalil, R.,Novoselov, K. S., Tsoukleri, G., Parthenios, J., Kavan, L.,Papagelis, K., Galiotis, C.
Abstract: We present the first Raman spectroscopic study of Bernal bilayer graphene flakes under uniaxial tension. Apart from a purely mechanical behavior in flake regions where both layers are strained evenly, certain effects stem from inhomogeneous stress distribution across the layers. These phenomena such as the removal of inversion symmetry in bilayer graphene may have important implications in the band gap engineering, providing an alternative route to induce the formation of a band gap.
MARCH 2012 -
Chemical Communications, 2012, 48 (28), pp 3433-3435.
The oxidation of natural flavonoid quercetin (article here).
Sokolová, R., Ramešová, Š., Degano I., Hromadová, M., Gál, M., Žabka, J.
Abstract: This study explains the controversies in the literature concerning the number of electrons involved in the oxidation of quercetin. This stems from inappropriate
handling samples, which require strict anaerobic conditions. The redox potential of quercetin strongly depends on the pH and on the presence of dissociation forms in solution.
J. Chem. Theory Comput., 2012, 8 (2), pp 487–497.
Parallel Implementation of Multireference Coupled-Cluster Theories Based on the Reference-Level Parallelism (article here).
Jiří Brabec, Jiří Pittner, Hubertus J. J. van Dam, Edoardo Aprà, and Karol Kowalski.
Abstract: A novel algorithm for implementing a general type of multireference coupled-cluster (MRCC) theory based on the Jeziorski–Monkhorst exponential ansatz [Jeziorski, B.; Monkhorst, H. J. Phys. Rev. A1981, 24, 1668] is introduced. The proposed algorithm utilizes processor groups to calculate the equations for the MRCC amplitudes. In the basic formulation, each processor group constructs the equations related to a specific subset of references. By flexible choice of processor groups and subset of reference-specific sufficiency conditions designated to a given group, one can ensure optimum utilization of available computing resources. The performance of this algorithm is illustrated on the examples of the Brillouin–Wigner and Mukherjee MRCC methods with singles and doubles (BW-MRCCSD and Mk-MRCCSD). A significant improvement in scalability and in reduction of time to solution is reported with respect to recently reported parallel implementation of the BW-MRCCSD formalism [Brabec, J.; van Dam, H. J. J.; Kowalski, K.; Pittner, J. Chem. Phys. Lett.2011, 514, 347].
FEBRUARY 2012 -
J. Am. Chem. Soc. 134, 2012, 2691-2705.
Single-step versus Stepwise Two-electron Reduction of Polyarylpyridiniums: Insights from the Steric Switching of the Redox Potential Compression.
J. Fortage, C. Peltier, Ch. Perruchot, Y. Takemoto, Y. Teki, F. Bedioui, V. Marvaud, G. Dupeyre, L. Pospíšil, C. Adamo, M. Hromadová, I. Ciofini, Ph. Lainé.
Abstract: Contrary to 4,4′-dipyridinium (i.e., archetypal methyl viologen), which is reduced by two single-electron transfers (stepwise reduction), the 4,1′-dipyridinium isomer (so-called “head-to-tail” isomer) undergoes two electron transfers at apparently the same potential (single-step reduction). A combined theoretical and experimental study has been undertaken to establish that the latter electrochemical behavior, also observed for other polyarylpyridinium electrophores, is due to potential compression originating in a large structural rearrangement. (read more)
J. Phys. Chem. C 116 (5), 2012, 3379-3786 .
Electron Transfer Triggers Fast Dimer/Monomer Switching of Pyridinium and Quinolinium Cations (article here).
F. Teplý, M. Čížková, P. Slavíček, V. Kolivoška, J. Tarábek, M. Hromadová, L. Pospíšil.
Abstract: N-Heteroaromatic cations with quaternary pyridine-type nitrogen atoms have a rich application potential due to their bioactivity, fluorescence, and redox properties. Reactivityof radicals formed by reduction of such compounds is of key importance. We report the electron transfer mechanism of four novel compounds containing pyridinium, quinolinium, and benzothiazolium moiety. The reduction of pyridinium and quinolinium derivatives by one electron yields radicals that very rapidly form σ-dimers. Dimers can be converted to parent cations by oxidation, which proceeds at considerably higher potentials. Hence the dimerization can be reversibly switched by application of the appropriate electrode potential. In contrast, in benzothiazolium derivative the electron transfer yields a stable radical in which the follow-up dimerization reaction is completely blocked. Analysis of experimental data as well as theoretical models led to the identification of dimerization sites in reduced pyridinium and quinolinium species. We show the advantage of using the combination of electrochemical impedance data and simulation of cyclic voltammograms for estimation of kinetic parameters of the heterogeneous electron transfer rates and the coupled chemical reactions.
JANUARY 2012 -
Nano Letters, 11 (12), 2011, 5501–5506.
Graphene Nanoplatelets Outperforming Platinum as the Electrocatalyst in Co-Bipyridine-Mediated Dye-Sensitized Solar Cells (article here).
Kavan, L; Yum, JH; Gratzel, M.
Abstract: Graphene nanoplatelets (GNP) in the form of thin semitransparent films on F-doped SnO2 (FTO) exhibit high electrocatalytic activity for the Co(bpy)33+/2+ redox couple in acetonitrile electrolyte solution. The GNP film is superior to the traditional electrocatalyst, that is, platinum, both in charge-transfer resistance (exchange current) and in electrochemical stability under prolonged potential cycling. The good electrochemical performance of GNP is readily applicable for dye-sensitized solar cells with Y123-sensitized TiO2 photoanodes and Co(bpy)33+/2+ as the redox shuttle. The dye-sensitized solar cell with GNP cathode is superior to that with the Pt-FTO cathode particularly in fill factor and in power conversion efficiency at higher illumination intensity.
Biochimica et Biophysica Acta, 1818, 2012, 609–616.
Structure, dynamics, and hydration of POPC/POPS bilayers suspended in NaCl, KCl, and CsCl solutions
P.Jurkiewicz, L. Cwiklik, A.Vojtíšková, P.Jungwirth, M. Hof
Abstract: Effects of alkali metal chlorides on the properties of mixed negatively charged lipid bilayers are experimentally measured and numerically simulated. Addition of 20 mol% of negatively charged phosphatidylserine to zwitterionic phosphatidylcholine strengthens adsorption of monovalent cations revealing their specificity, in the following order: Cs+ K+ Na+. Time-resolved fluorescence solvent relaxation shows significant decrease both in mobility and hydration of the lipid carbonyls probed by Laurdan upon addition of the cations. The experimental findings are supported by molecular dynamics simulations, which show deep penetration of the cations down to the glycerol level of the lipid bilayer where they pair with oxygen atoms of carbonyl groups (with pairing with sn-2 carbonyl being about twice stronger than pairing with the sn-1 one). Moreover, the cations bridge neighboring lipids forming clusters of up to 4 lipid molecules, which decreases the area per lipid, thickens the membrane, causes rising of lipid headgroups, and hinders lipid dynamics. All these effects follow the same Hofmeister ordering as the cationic adsorption to the bilayer.
DECEMBER 2011 -
ACS NANO, 5 (11), 2011, 9171-9178.
Graphene Nanoplatelet Cathode for Co(III)/(II) Mediated Dye-Sensitized Solar Cells (article here).
Kavan, L; Yum, JH; Nazeeruddin, MK; Gratzel, M.
Abstract: Graphene nanoplatelets (GNP) in the form of thin semitransparent film on F-doped SnO2(FTO) exhibit high electrocatalytic activity for Co(L)2; where L is 6-(1H-pyrazol-1-yl)-2,2'-bipyridine.
The exchange current densities for the Co2+/3+(L)2 redox reaction scaled linearly with the GNP film's optical absorbance, and they were by 1-2 orders of magnitude larger than those for the l3-/l- couple on the same electrode.
The electrocatalytic activity of GNP films with optical the Co2+/3+(L)2 redox reaction. Dye-sensitized solar cells with Y123 dye adsorbed on TiO2 photoanode achieved energy conversion efficiencies between 8 and 10% for both GNP and Pt-based cathodes. However, the cell with GNP cathode is superior to that with Pt-FTO cathode particularly in fill factors and in the efficiency at higher illumination intensities.
Biophysical Journal, 101 (11), 2011, L60-L62.
Limitations of Electronic Energy Transfer in the Determination of Lipid Nanodomain Sizes.
R. Šachl, J. Humpolíčková, M. Štefl, L. B.-Å. Johansson, M. Hof.
Abstract: Even though superresolution microscopy indicates that size of plasma membrane rafts is <20 nm, those structures have never been observed. Förster resonance energy transfer (FRET) is therefore still the most powerful optical method for characterization of such domains. In this letter we investigate relation between nanodomain affinity of a donor-acceptor (D/A) pair and the detectable nanodomain size/area. We show that probes with high affinity to the liquid-ordered (Lo) phase are required for detecting domain sizes of a few nanometers, and/or domains that occupy a few percent of the bilayer area. A combination of donors and acceptors that prefer different phases is the more favorable approach. For instance, a D/A pair with the distribution constant of donors KD = 5 and acceptors KA = 0.01 can resolve a broad spectrum of nanodomain sizes. On the other hand, currently available donors and acceptors that prefer the same phase, either the liquid-disordered (Ld) or Lo phase, are not so convenient for determining domain sizes <20 nm. Here the detection limits of FRET experiments employing several commonly used D/A pairs have been investigated (read more).
NOVEMBER 2011 -
Low-Energy Electron Scattering from Molecules, Biomolecules and Surfaces.
Čársky P.; R. Čurík (Eds.).
1st Edition., 2011, 296 p., CRC Press. ISBN-10: 1439839107; ISBN-13: 978-1439839102
Since the turn of the 21st century, the field of electron molecule collisions has undergone a renaissance. The importance of such collisions in applications from radiation chemistry to astrochemistry has flowered, and their role in industrial processes such as plasma technology and lighting are vital to the advancement of next generation devices. Furthermore, the development of the scanning tunneling microscope highlights the role of such collisions in the condensed phase, in surface processing, and in the development of nanotechnology.
Low-Energy Electron Scattering from Molecules, Biomolecules and Surfaces highlights recent progress in the theory and experiment of electron-molecule collisions, providing a detailed review of the current state of knowledge of electron molecule scattering—theoretical and experimental—for the general physicist and chemist interested in solving practical problems.
In few other branches of science is the collaboration between theorists and experimentalists so topical. Covering advancements in practical problems, such as those met in plasma physics, microelectronics, nanolithography, DNA research, atmospheric chemistry, and astrochemistry, this book describes the formal general scattering theory and description of the experimental setup at a level the interested non-expert can appreciate.
Physical Review Letters, 2011, 107 (15).
Observation of Electronic Raman Scattering in Metallic Carbon Nanotubes.
Farhat, H., Berciaud, S., Kalbáč, M., Saito, R at al.
Abstract: We present experimental measurements of the electronic contribution to the Raman spectra of individual metallic single-walled carbon nanotubes (MSWNTs). Photoexcited carriers are inelastically scattered by a continuum of low-energy electron-hole pairs created across the graphenelike linear electronic subbands of the MSWNTs. The optical resonances in MSWNTs give rise to well-defined electronic Raman peaks. This resonant electronic Raman scattering is a unique feature of the electronic structure of these one-dimensional quasimetals.
OCTOBER 2011 -
Acta Biomaterialia, 2011, 7 (12) , Pages 4195-4203.
Raster image correlation spectroscopy as a novel tool to study interactions of macromolecules with nanofiber scaffolds.
S.C.P. Norris, J. Humpolíčková, E. Amler, M. Huranová, M. Buzgo, R. Macháň, D. Lukáš, M. Hof.
Abstract: Dynamic processes such as diffusion and binding/unbinding of acromolecules (e.g. growth factors or nutrients) are crucial parameters for the design and application of effective artificial tissue materials. Here, dynamics of selected macromolecules were studied in two different composite tissue engineering scaffolds containing an electrospun nanofiber mesh (polycaprolactone or hydrophobically plasma modified polyvinylalcohol–chitosan) encapsulated in agarose hydrogels by a conventional approach fluorescence recovery after photobleaching (FRAP) and a novel technique, raster image correlation spectroscopy (RICS). The two approaches are compared, and it is shown that FRAP is unable to determine processes occurring at low molecular concentrations, especially accurately separating binding/unbinding from diffusion, and its results depend on the concentration of the studied molecules. RICS measures processes of single molecules and, because of its multiple adjustable timescales, can distinguish whether diffusion or binding controls molecular movement and separates fast diffusion from slow transient binding. In addition, RICS provides a robust read-out parameter quantifying binding affinity. Finally, the combination of FRAP and RICS helps to characterize diffusion and binding of macromolecules in tested artificial tissues better, and therefore predicts the behavior of biologically active molecules in these materials for medical applications.
SEPTEMBER 2011 -
Langmuir, 2011, 27 (19), 12115–12123.
Mutable Lewis and Brønsted Acidity of Aluminated SBA-15 as Revealed by NMR of Adsorbed Pyridine-15N
Andrey A. Gurinov, Yulia A. Rozhkova, Arnošt Zukal, Jiří Čejka, and Ilya G. Shenderovich.
Abstract: 1H and variable-temperature 15N NMR techniques have been used to study the effect of the gradual alumination of SBA-15 on the structure and adsorption properties of this mesoporous material. The interpretation of experimental spectra suggests that aluminum chlorhydrol most effectively reacts with silica surfaces in the confinement of the cavities of rough mesopore walls, instead of forming a homogeneous aluminum film. This first leads to a gradual filling of the cavities and finally results in aluminum islands on the inner surfaces of mesopores. ( read more)
AUGUST 2011 -
Biophysical Journal, 101 (6), 2011, 1376-1384.
Oxidized Phosphatidylcholines Facilitate Phospholipid Flip-Flop in Liposomes
Roman Volinsky, Lukasz Cwiklik, Piotr Jurkiewicz, Martin Hof, Pavel Jungwirth, Paavo K.J. Kinnunen.
Abstract: Lipid asymmetry is a ubiquitous property of the lipid bilayers in cellular membranes and its maintenance and loss play important roles in cell physiology, such as blood coagulation and apoptosis. The resulting exposure of phosphatidylserine on the outer surface of the plasma membrane has been suggested to be caused by a specific membrane enzyme, scramblase, which catalyzes phospholipid flip-flop. Despite extensive research the role of scramblase(s) in apoptosis has remained elusive. Here, we show that phospholipid flip-flop is efficiently enhanced in liposomes by oxidatively modified phosphatidylcholines. A combination of fluorescence spectroscopy and molecular dynamics simulations reveal that the mechanistic basis for this property of oxidized phosphatidylcholines is due to major changes imposed by the oxidized phospholipids on the biophysical properties of lipid bilayers, resulting in a fast cross bilayer diffusion of membrane phospholipids and loss of lipid asymmetry, requiring no scramblase protein (article here).
Analytica Chimica Acta, 697, 2011, 23-26.
Spectroelectrochemical determination of the electron consumption
Viliam Kolivoška, Miroslav Gál, Štěpánka Lachmanová, Michal Valášek, Magdaléna Hromadová and Lubomír Pospíšil.
Abstract: Measurements of UV–vis spectra as a function of the consumed charge in an optically transparent thin layer cell (OTTLE) offer a fast, small-volume and reliable method for the determination of the number of electrons n exchanged in the redox reaction. The determination of n is based on the calibration procedure using the ferrocene oxidation and the methyl viologen reduction. Virtues of this method are demonstrated on the determination of n of two oligomers of ‘extended viologens’ with multiple redox centers and correspondingly large n. The described method eliminates problems of side reactions of reactive intermediates with the parent oxidized form, which often impede a reliable estimation of n by the established coulometric method (article here).
JULY 2011 -
Chemistry of Materials, 2011, 23 (10), 2573–2585.
Isomorphous Introduction of Boron in Germanosilicate Zeolites with UTL Topology
Oleksiy V. Shvets, Mariya V. Shamzhy, Pavel S. Yaremov, Zuzana Musilová, Dana
Procházková, and Jiří Čejka.
Abstract: The direct introduction of boron into the framework of germanosilicate zeolites with UTL topology using different organic spiro azo compounds as structure-directing agents (SDAs) was performed. The influence of the SDA's nature, chemical composition and pH of the reaction mixture, and duration of the synthesis on the phase selectivity, limit of isomorphous introduction of boron into the zeolite framework and its location and coordination, and adsorption and acidic properties of prepared borogermanosilicates was investigated in detail. Experimental data provided clear evidence that the properties of the SDAs control the upper limit of the B content in the reaction mixture for successful synthesis of a pure UTL phase ( more information read here).
Inorganic Chemistry, 2011, 50 (13), 6122-6134.
Photoinduced Intramolecular Tryptophan Oxidation and Excited-State Behavior of [Re(L-AA)(CO)3(alpha-diimine)]+ (L = Pyridine or Imidazole, AA = Tryptophan, Tyrosine, Phenylalanine)
Blanco-Rodriguez, A.M. ; Towrie, M.; Sýkora, J. ; Záliš, S.; Vlček, A. Jr.
Abstract: ReI carbonyl-diimine complexes [Re(L-AA)(CO)3(N,N)]+(N,N = bpy, phen) containing an aromatic amino acid (AA), phenylalanine (Phe), tyrosine (Tyr), or tryptophan (Trp), linked to Re by a pyridine-amido or imidazole-amido ligand L have been synthesized and their excited-state properties investigated by nanosecond time-resolved IR (TRIR) and emission spectroscopy (more information read here).
JUNE 2011 -
Trends in Analytical Chemistry, 2011, 30 (7), 945-959.
Direct, rapid quantitative analyses of BVOCs using SIFT-MS and PTR-MS obviating sample collection.
David Smith and Patrik Španěl (article here).
Abstract: The purpose of this short review is to describe the origins and the principles of operation of selected-ion flow-tube mass spectrometry (SIFT-MS) and proton-transfer-reaction mass spectrometry (PTR-MS), and their application to the analysis of biogenic volatile organic compounds (BVOCs) in ambient air, the humid air (headspace) above biological samples, and other samples. We briefly review the ion chemistry that underpins these analytical methods, which allows accurate analyses. We pay attention to the inherently uncomplicated sampling methodologies that allow on-line, real-time analyses, obviating sample collection into bags or onto traps, which can compromise samples.
Whilst these techniques have been applied successfully to the analysis of a wide variety of media, we give just a few examples of data, including for the analysis of BVOCs that are present in tropospheric air and those emitted by plants, in exhaled breath and in the headspace above cell and bacterial cultures (which assist clinical diagnosis and therapeutic monitoring), and the products of combustion. The very wide dynamic ranges of real-time analyses of BVOCs in air achieved by SIFT-MS and PTR-MS – from sub-ppbv to tens of ppmv – ensure that these analytical methods will be applied to many other media, especially when combined with gas-chromatography methods, as recently trialed.
Phys. Chem. Chem. Phys, June 2011, 13, 12123-12137. Photochemistry of hydrogen bonded heterocycles probed by photodissociation experiments and ab initio methods.
Petr Slavíček and Michal Fárník (article here).
Abstract: In this perspective article, we focus on the photochemistry of five-membered nitrogen containing heterocycles (pyrrole, imidazole and pyrazole) in clusters. These heterocycles represent paradigmatic structures for larger biologically active heterocyclic molecules and complexes. The dimers of the three molecules are also archetypes of different bonding patterns: N–Hπ interaction, N–HN hydrogen bond and double hydrogen bond. We briefly review available data on photochemistry of the title molecules in the gas phase, but primarily we focus on the new reaction channels opened upon the complexation with other heterocycles or solvent molecules. Based on ab initio calculations we discuss various possible reactions in the excited states of the clusters: (1) hydrogen dissociation, (2) hydrogen transfer between the heterocyclic units, (3) molecular ring distortion, and (4) coupled electron–proton transfer. The increasing photostability with complexity of the system can be inferred from experiments with photodissociation in these clusters. A unified view on photoinduced processes in five-membered N-heterocycles is provided. We show that even though different deactivation channels are energetically possible for the complexed heterocycles, in most cases the major result is a fast reconstruction of the ground state. The complexed or solvated heterocycles are thus inherently photostable although the stability can in principle be achieved via different reaction routes.
MAY 2011 -
Journal of Physical Chemistry C, 2011, 115 (22), pp 11156–11162. Oxygen-Isotope Exchange between CO2 and Solid Ti18O2 ( article here).
Svatopluk Civiš, Martin Ferus, Pavel Kubát, Markéta Zukalová, and Ladislav Kavan.
Abstract: The light–induced oxygen-isotope exchange between gaseous CO2 and solid Ti18O2 (anatase) and the spontaneous thermal isotope exchange that takes place between the vacuum-calcined solid Ti18O2 and CO2 were studied by gas-phase high-resolution Fourier transform infrared absorption spectroscopy over a period of several days. The absorption ro-vibrational spectra of all the measured carbon dioxide isotopologues were assigned and served as the quantification of the time-dependent isotope exchange between the oxygen atoms from the Ti18O2 solid and the oxygen related to the gaseous CO2. The C18O2 was formed as the dominating final product with a minor content of C16O18O. The rate of oxygen-isotope exchange is highly sensitive to the conditions of the titania pretreatment; vacuum-annealed Ti18O2 at 450 °C exhibited a very high spontaneous oxygen exchange activity with gaseous C16O2. A mechanism for the 18O/16O exchange process is discussed at the molecular level. The photocatalytic formation of methane, acetylene, and C16O released from the Ti18O2 surface was observed after irradiation by an excimer laser.
Nano Letters, 2011, 11, 1957–1963. Raman Spectroscopy and in Situ Raman Spectroelectrochemistry of Bilayer 12C/13C Graphene (article here).
M.Kalbáč, H. Farhat, J. Kong, P. Janda, L.Kavan, and M.S. Dresselhaus.
Abstract: Bilayer graphene was prepared by the subsequent deposition of a 13C single-layer graphene and a 12C single-layer graphene on top of a SiO2/Si substrate. The bilayer graphene thus prepared was studied using Raman spectroscopy and in situ Raman spectroelectrochemistry. The Raman frequencies of the 13C graphene bands are significantly shifted with respect to those of 12C graphene, which allows us to investigate the single layer components of bilayer graphene individually. It is shown that the bottom layer of the bilayer graphene is significantly doped from the substrate, while the top layer does not exhibit a signature of the doping from the environment. The electrochemical doping has the same effect on the charge carrier concentration at the top and the bottom layer despite the top layer being the only layer in contact with the electrolyte. This is here demonstrated by essentially the same frequency shifts of the G and G ' bands as a function of the electrode potential for both the top and bottom layers. Nevertheless, analysis of the intensity of the Raman modes showed an anomalous bleaching of the Raman intensity of the G mode with increasing electrode potential, which was not observed previously in one-layer graphene.
APRIL 2011 -
J. Am. Chem. Soc. 2011, 133, 6130–6133. Postsynthesis transformation of Three-Dimensional Framework into a Lamellar Zeolite with Modifiable Architecture (article here).
Wieslaw J. Roth, Oleksiy V. Shvets, Mariya Shamzhy, Pavla Chlubná, Martin Kubů, Petr Nachtigall, and Jiří Čejka.
Abstract: Mild treatment of zeolite UTL results in degradation of its structure with preservation of the initially present dense layers connected by D4R “bridges”. The lamellar product obtained through this 3D to 2D zeolite conversion has been structurally modified similar to methodologies applied to layered zeolite precursors, which show the opposite 2D to 3D zeolite transformation.
Chem. Commun., 2011, 47, 5446–5448. Fine tuning of the catalytic effect of a metal-free porphyrin on the homogeneous oxygen reduction (article here).
Antonín Trojánek, Jan Langmaier, Jakub Šebera, Stanislav Záliš, Jean-Michel Barbe, Hubert H. Giraultc and Zdeněk Samec.
Abstract: The catalytic effect of tetraphenylporphyrin on the oxygen reduction with ferrocene in 1,2-dichloroethane can be finely tuned by varying the molar ratio of the acid to the catalyst present in the solution. The mechanism involves binding of molecular oxygen to the protonated free porphyrin base, in competition with ion pairing between the protonated base and the acid anion present.
MARCH 2011 -
ACS Nano, 2011, 5 (3), pp 2231–2239.
Otakar Frank, Marcel Mohr, Janina Maultzsch, Christian Thomsen, Ibtsam Riaz, Rashid Jalil, Kostya S. Novoselov, Georgia Tsoukleri, John Parthenios, Konstantinos Papagelis, Ladislav Kavan, and Costas Galiotis: Raman 2D-Band Splitting in Graphene: Theory and Experiment (article here).
Abstract: We present a systematic experimental and theoretical study of the two-phonon (2D) Raman scattering in graphene under uniaxial tension. The external perturbation unveils that the 2D mode excited with 785 nm has a complex line-shape mainly due to the contribution of two distinct double resonance scattering processes (inner and outer) in the Raman signal. The splitting depends on the direction of the applied strain and the polarization of the incident light. The results give new insight into the nature of the 2D band and have significant implications for the use of graphene as reinforcement in composites since the 2D mode is crucial to assess how effectively graphene uptakes an applied stress or strain.
Coordination Chemistry Reviews 255, 7-8, 2011, 975–989.
Radka Baková, Majed Chergui, Chantal Daniel, Antonín Vlček Jr., Stanislav Záliš: Relativistic effects in spectroscopy and photophysics of heavy-metal complexes illustrated by spin–orbit calculations of [Re(imidazole)(CO)3(phen)]+ (article here).
Abstract: Spin–orbit coupling (SOC) is an essential factor in photophysics of heavy ransition metal complexes. By enabling efficient population of the lowest triplet state and its strong emission, it gives rise to a very interesting photophysical behavior and underlies photonic applications such as organic light emitting diodes (OLED) or luminescent imaging agents. SOC affects excited-state characters, relaxation dynamics, radiative and nonradiative decay pathways, as well as lifetimes and reactivity. We present a new photophysical model based on mixed-spin states, illustrated by relativistic spin–orbit TDDFT and MS-CASPT2 calculations of [Re(imidazole)(CO)3(1,10-phenanthroline)]+. An excited-state scheme is constructed from spin–orbit (SO) states characterized by their energies, double-group symmetries, parentages in terms of contributing spin-free singlets and triplets, and oscillator strengths of corresponding transitions from the ground state. Some of the predictions of the relativistic SO model on the number and nature of the optically populated and intermediate excited states are qualitatively different from the spin-free model. The relativistic excited-state model accounts well for electronic absorption and emission spectra of ReI carbonyl diimines, as well as their complex photophysical behavior. Then, we discuss the SO aspects of photophysics of heavy metal complexes from a broader perspective. Qualitative SO models as well as previous relativistic excited-state calculations are briefly reviewed together with experimental manifestations of SOC in polypyridine and cyclometallated complexes of second- and third row d6 metals. It is shown that the relativistic SO model can provide a comprehensive and unifying photophysical picture.
FEBRUARY 2011 -
Chemistry of Materials, 2011, 23 (2), 200-207 .
Petrykin V. , Macounova K. , Franc J. , Shlyakhtin O., Klementova M., Mukerjee S., Krtil P.: Zn-Doped RuO2 electrocatalyts for Selective Oxygen Evolution: Relationship between Local Structure and Electrocatalytic Behavior in Chloride Containing Media
Abstract: Nanocrystalline electrocatalytically active materials of chemical composition
Ru1-xZnxO2 (0< x < 0.3) were synthesized by freeze-drying technique. The diffraction patterns of the prepared samples corresponded to single-phase rutile type oxides. Local structure of the Ru1-xZnxO2 based on refinement of Ru K and Zn K edge EXAFS functions shows clustering of the Zn ions in the blocks with ilmenite structure intergrowing with Ru-rich rutile blocks. Ru1- ZnxO2 oxides are selective catalysts for anodic oxygen evolution. The selectivity toward oxygen evolution in the presence of chlorides is affected by the actual Zn content and can be ascribed to structural hindrance of the formation of the surface peroxo group based active sites for chlorine evolution. The selectivity toward oxygen evolution in presence of chlorides is accompanied by the drop of the total activity, which gets more pronounced with
increasing Zn content (article here).
Phys. Chem. Chem. Phys., 2011, 13, 4365–4371.
Lubomír Pospıíšil, Magdaléna Hromadová, Nicolangelo Fanelli, Michal Valášek, Viliam Kolivoška and Miroslav Gál: Extended viologen as a source of electric oscillations.
Abstract: A long organic molecule 1 with five bipyridinium functions separated by benzene rings (extended viologen) undergoes a reversible multi-step electron transfer. Here we show that this decacation accepts electrons at the heterogeneous interface with the occurrence of the periodically changing electric reduction currents. According to the applied bias voltage the observed current–time dependence changes from chaotic through periodic and irregular to sinusoidal and finally to monotonous. A careful choice of the controlling parameters yields the sustained periodic sinusoidal urrents lasting for a prolonged time. Oscillations stem from a mutual interplay of the heterogeneous supply of electrons and the homogeneous redox reactions (disproportionation) between the transient redox forms. In difference to many other electrochemical oscillating systems the described oscillations do not require any additional external impedance. The principle of these oscillatory currents may serve as a model of a truly ‘molecular oscillator’ (article here).
JANUARY 2011 -
Mass Spectrometry Reviews, 2011, Vol. 30 (2), pages 236–267.
Patrik Španěl, David Smith: Progress in SIFT-MS: Breath analysis and other applications.
Abstract: The development of selected ion flow tube mass spectrometry, SIFT-MS, is described from its inception as the modified very large SIFT instruments used to demonstrate the feasibility of SIFT-MS as an analytical technique, towards the smaller but bulky transportable instruments and finally to the current smallest Profile 3 instruments that have been located in various places, including hospitals and schools to obtain on-line breath analyses. The essential physics and engineering principles are discussed, which must be appreciated to design and construct a SIFT-MS instrument. The versatility and sensitivity of the Profile 3 instrument is illustrated by typical mass spectra obtained using the three precursor ions H3O+, NO+ and equation image, and the need to account for differential ionic diffusion and mass discrimination in the analytical algorithms is emphasized to obtain accurate trace gas analyses. The performance of the Profile 3 instrument is illustrated by the results of several pilot studies, including (i) on-line real time quantification of several breath metabolites for cohorts of healthy adults and children, which have provided representative concentration/population distributions, and the comparative analyses of breath exhaled via the mouth and nose that identify systemic and orally-generated compounds, (ii) the enhancement of breath metabolites by drug ingestion, (iii) the identification of HCN as a marker of Pseudomonas colonization of the airways and (iv) emission of volatile compounds from urine, especially ketone bodies, and from skin. Some very recent developments are discussed, including the quantification of carbon dioxide in breath and the combination of SIFT-MS with GC and ATD, and their significance. Finally, prospects for future SIFT-MS developments are alluded to (article here).
Anal. Chem., 2011, 83 (3), pp 1069–1077.
Martin Civiš, Svatopluk Civiš, Kristyna Sovová, Kseniya Dryahina, Patrik Šaněl, and
Martin Kyncl: Laser Ablation of FOX-7: Proposed Mechanism of Decomposition
Abstract: A novel high-energy explosive material, FOX-7 (1,1-diamino-2,2-dinitroethylene), was studied using a combination of laser-induced breakdown spectroscopy (LIBS) and selected ion flow tube mass spectrometry (SIFT-MS). The LIBS technique uses short laser pulses (an ArF excimer laser) as the energy source to convert small quantities of a sample into plasma and to induce the emission of its molecular fragments or atoms. SIFT-MS is a novel method for absolute quantification based on chemical ionization using three reagent ions, with the ability to determine concentrations of trace gases and vapors of volatile organic compounds in real time. SIFT-MS was used to study the release of NO, NO2, HCN, HONO, HCHO, CH3CH2OH, and C2H2 after laser ablation of the explosive compound FOX-7 in solid crystalline form. The radiation emitted after excitation was analyzed using a time-resolved UV−vis spectrometer with an ICCD detector. The electronic bands of CN (388 nm), OH (308.4 nm), and NO (237.1 nm) radicals and the atomic lines of C, N, and H were identified (article here).
DECEMBER 2010 -
J.Phys.Chem. B, 114, 2010, pp. pp 15773–15779.
J. Mosinger, K. Lang, J. Hostomský, J. Franc, J. Sýkora, M. Hof and P.Kubát:
Singlet Oxygen Imaging in Polymeric Nanofibers by Delayed Fluorescence.
Abstract: Polymeric nanofiber materials loaded with photosensitizers exhibit significant antibacterial activity due to their generation of cytotoxic singlet oxygen O2(1Δg). A time-gated fluorescence imaging technique as used to monitor the photosensitized processes in polystyrene (PS) and gelatin (GE) nanofibers loaded with 0.1 wt % tetraphenylporphyrin (TPP) photosensitizer. The fluorescence decay of TPP at the periphery of the PS nanofibers was single exponential. Increased fluorescence quenching was observed in the domains with higher TPP loading, located in the center of the nanofibers, and added a shorter lifetime component to the kinetics. The domains exhibiting singlet oxygen activity within the nanofibers were visualized and analyzed by singlet oxygen-sensitized delayed fluorescence imaging (SODF). Whereas O2(1Δg) was produced in PS nanofibers, its production in GE nanofibers was limited. These results were confirmed by time-resolved phosphorescence measurements at 1270 nm (article here).
Our publication J. Chem. Phys.,2010, 133, 194106 is on "Top 20 Most Downloaded Articles" of the Journal of Chemical Physics (November 2010):
J. Chem. Phys., 2010, 133, 194106 (10 pages).
Libor Veis and Jiří Pittner: Quantum computing applied to calculations of molecular energies: CH2 benchmark
Abstract: Quantum computers are appealing for their ability to solve some tasks much faster than their classical counterparts. It was shown in [ Aspuru-Guzik et al., Science 309, 1704 (2005) ] that they, if available, would be able to perform the full configuration interaction (FCI) energy calculations with a polynomial scaling. This is in contrast to conventional computers where FCI scales exponentially. We have developed a code for simulation of quantum computers and implemented our version of the quantum FCI algorithm. We provide a detailed description of this algorithm and the results of the assessment of its performance on the four lowest lying electronic states of CH2 molecule. This molecule was chosen as a benchmark, since its two lowest lying 1A1 states exhibit a multireference character at the equilibrium geometry. It has been shown that with a suitably chosen initial state of the quantum register, one is able to achieve the probability amplification regime of the iterative phase estimation algorithm even in this case (article here).
NOVEMBER 2010 -
Journal of Catalysis 276, 2010, 327-334 (article here).
ACS Nano, 2010, 4 (10), pp 6055–6063. (article here).
OCTOBER 2010 -
Chem. Eur.J. 2010, 16, 11753 – 11759 (article here).
Organometallics, 2010, 29 (17), pp 3780–3789 (abstract).
SEPTEMBER 2010 -
Journal of Physical Chemistry C, 2010, 114, 32, 13685-13694 (article here).
Chemistry of Materials, 2010, 22, 13, 4045-4055 (article here).
AUGUST 2010 -
Book: Recent Progress in Coupled Cluster Methods. Theory and Applications.
1st Edition., 2010, XXI, 650 p., Springer. ISBN: 978-90-481-2884-6
(read more about this book).
Anal. Chem. 2010, 82, 5819-5829. (article here).
JULY 2010 -
Angew. Chem. Int. Ed. 2010, 49, 4813-4815. (article here).
Chem. Eur. J. 2010, 16, 7773 – 7780. (article here).
JUNE 2010 -
Coordination Chemistry Reviews, 2010, 254, 1383–1396. (article here).
Journal of Catalysis, 2010, 272 (2), 262-274. (article here).
MAY 2010 -
BBA - Biomembranes, Vol.1798, 7, 2010, 1377-1391. (artile here).
Chem. Mater., 2010, 22 (11), pp 3482–3495. (article here).
APRIL 2010 -
Phys. Chem. Chem. Phys., 2010, 12, 5240-5247 (article here).
Zeolites and Catalysis: Synthesis, Reactions and Applications
Jiří Čejka (Editor), Avelino Corma (Editor), Stacey Zones (Editor). Wiley, ISBN:
978-3-527-32514-6, 918 pages, April 2010. (more info about book...).
MARCH 2010 -
Angew. Chem. Int. Ed. 2010, 49, 2937 –2940 (article here).
Phys. Chem. Chem. Phys., 2010, 12 (13), 3145-3155 (article here).
FEBRUARY 2010 -
J.Am.Chem. Soc., 2010,132(8), 2655–2662 (article here).
JANUARY 2010 -
Phys. Chem. Chem. Phys., 20100, 12, 1550-1556 (article here).
DECEMBER 2009 -
CARBON, 2009, 48 (1), 153-162 (article here).
NOVEMBER 2009 -
Biophysical Journal, 2009, 97 ( 9), 2623-2629 (article here).
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