Browsing by Subject "KINETICS"

Sort by: Order: Results:

Now showing items 1-20 of 36
  • Kneis, David; Hiltunen, Teppo; Hess, Stefanie (2019)
    Horizontal gene transfer is an essential component of bacterial evolution. Quantitative information on transfer rates is particularly useful to better understand and possibly predict the spread of antimicrobial resistance. A variety of methods has been proposed to estimate the rates of plasmid-mediated gene transfer all of which require substantial labor input or financial resources. A cheap but reliable method with high-throughput capabilities is yet to be developed in order to better capture the variability of plasmid transfer rates, e.g. among strains or in response to environmental cues. We explored a new approach to the culture-based estimation of plasmid transfer rates in liquid media allowing for a large number of parallel experiments. It deviates from established approaches in the fact that it exploits data on the absence/presence of transconjugant cells in the wells of a well plate observed over time. Specifically, the binary observations are compared to the probability of transconjugant detection as predicted by a dynamic model. The bulk transfer rate is found as the best-fit value of a designated model parameter. The feasibility of the approach is demonstrated on mating experiments where the RP4 plasmid is transfered from Serratia marcescens to several Escherichia coil recipients. The methods uncertainty is explored via split sampling and virtual experiments.
  • Barmaki, Samineh; Jokinen, Ville; Obermaier, Daniela; Blokhina, Daria; Korhonen, Matti; Ras, Robin H. A.; Vuola, Jyrki; Franssila, Sami; Kankuri, Esko (2018)
    Physiological oxygen levels within the tissue microenvironment are usually lower than 14%, in stem cell niches these levels can be as low as 0-1%. In cell cultures, such low oxygen levels are usually mimicked by altering the global culture environment either by O-2 removal (vacuum or oxygen absorption) or by N-2 supplementation for O-2 replacement. To generate a targeted cellular hypoxic microenvironment under ambient atmospheric conditions, we characterised the ability of the dissolved oxygen-depleting sodium sulfite to generate an in-liquid oxygen sink. We utilised a microfluidic design to place the cultured cells in the vertical oxygen gradient and to physically separate the cells from the liquid. We demonstrate generation of a chemical in-liquid oxygen sink that modifies the surrounding O-2 concentrations. O-2 level control in the sink-generated hypoxia gradient is achievable by varying the thickness of the polydimethylsiloxane membrane. We show that intracellular hypoxia and hypoxia response element-dependent signalling is instigated in cells exposed to the microfluidic in-liquid O-2 sink-generated hypoxia gradient. Moreover, we show that microfluidic flow controls site-specific microenvironmental kinetics of the chemical O-2 sink reaction, which enables generation of intermittent hypoxia/re-oxygenation cycles. The microfluidic O-2 sink chip targets hypoxia to the cell culture microenvironment exposed to the microfluidic channel architecture solely by depleting O-2 while other sites in the same culture well remain unaffected. Thus, responses of both hypoxic and bystander cells can be characterised. Moreover, control of microfluidic flow enables generation of intermittent hypoxia or hypoxia/re-oxygenation cycles. (C) 2018 Published by Elsevier Ltd on behalf of Acta Materialia Inc.
  • Berndt, Torsten; Scholz, Wiebke; Mentler, Bernhard; Fischer, Lukas; Herrmann, Hartmut; Kulmala, Markku; Hansel, Armin (2018)
    Hydrocarbons are emitted into the Earth's atmosphere in very large quantities by human and biogenic activities. Their atmospheric oxidation processes almost exclusively yield RO2 radicals as reactive intermediates whose atmospheric fate is not yet fully unraveled. Herein, we show that gas-phase reactions of two RO2 radicals produce accretion products composed of the carbon backbone of both reactants. The rates for accretion product formation are very high for RO2 radicals bearing functional groups, competing with those of the corresponding reactions with NO and HO2. This pathway, which has not yet been considered in the modelling of atmospheric processes, can be important, or even dominant, for the fate of RO2 radicals in all areas of the atmosphere. Moreover, the vapor pressure of the formed accretion products can be remarkably low, characterizing them as an effective source for the secondary organic aerosol.
  • Rimpelä, Anna-Kaisa; Reunanen, Saku; Hagström, Marja; Kidron, Heidi; Urtti, Arto (2018)
    Pharmacokinetics in the posterior eye segment has therapeutic implications due to the importance of retinal diseases in ophthalmology. In principle, drug binding to the components of the vitreous, such as proteins, collagen, or glycosaminoglycans, could prolong ocular drug retention and modify levels of pharmacologically active free drug in the posterior eye segment. Since drug binding in the vitreous has been investigated only sparsely, we studied vitreal drug binding of 35 clinical small molecule drugs. Isolated homogenized porcine vitreous and the drugs were placed in a two compartment dialysis system that was used to separate the bound and unbound drug. Free drug concentrations and binding percentages were quantitated using LC-MS/MS. Drug binding levels varied between 21 and 74% in the fresh vitreous and 0 and 64% in the frozen vitreous. The vitreal binding percentages did not correlate with those in plasma. Our data-based pharmacokinetic simulations suggest that vitreal binding of small molecule drugs has only a modest influence on the AUC of free drug or drug half-life in the vitreous. Therefore, it is likely that vitreal binding is not a major reason for interindividual variability in ocular drug responses or drug-drug interactions.
  • Heikkinen, Noora; Kärkkäinen, Olli; Laukkanen, Eila; Kekkonen, Virve; Kaarre, Outi; Kivimäki, Petri; Könönen, Mervi; Velagapudi, Vidya; Nandania, Jatin; Lehto, Soili M.; Niskanen, Eini; Vanninen, Ritva; Tolmunen, Tommi (2019)
    Our aim was to analyze metabolite profile changes in serum associated with moderate-to-heavy consumption of alcohol in young adults and to evaluate whether these changes are connected to reduced brain gray matter volumes. These study population consisted of young adults with a 10-year history of moderate-to-heavy alcohol consumption (n = 35) and light-drinking controls (n = 27). We used the targeted liquid chromatography mass spectrometry method to measure concentrations of metabolites in serum, and 3.0 T magnetic resonance imaging to assess brain gray matter volumes. Alterations in amino acid and energy metabolism were observed in the moderate-to-heavy drinking young adults when compared to the controls. After correction for multiple testing, the group of moderate-to-heavy drinking young adults had increased serum concentrations of 1-methylhistamine (p = 0.001, d = 0.82) when compared to the controls. Furthermore, concentrations of 1-methylhistamine (r = 0.48, p = 0.004) and creatine (r = 0.52, p = 0.001) were negatively correlated with the brain gray matter volumes in the females. Overall, our results show association between moderate-to-heavy use of alcohol and altered metabolite profile in young adults as well as suggesting that some of these changes could be associated with the reduced brain gray matter volume. (C) 2018 Elsevier Inc. All rights reserved.
  • Hasan, Galib; Salo, Vili-Taneli; Valiev, Rashid; Kubecka, Jakub; Kurten, Theo (2020)
    Organic peroxy radicals (RO2) are key intermediates in the chemistry of the atmosphere. One of the main sink reactions of RO2 is the recombination reaction RO2 + R'O-2, which has three main channels (all with O-2 as a coproduct): (1) R-H=O + R'OH, (2) RO + R'O, and (3) ROOR'. The RO + R'O "alkoxy" channel promotes radical and oxidant recycling, while the ROOR' "dimer" channel leads to low-volatility products relevant to aerosol processes. The ROOR' channel has only recently been discovered to play a role in the gas phase. Recent computational studies indicate that all of these channels first go through an intermediate complex( 1)(RO center dot center dot center dot O-3(2)center dot center dot center dot OR'). Here, O-3(2) is very weakly bound and will likely evaporate from the system, giving a triplet cluster of two alkoxy radicals: (3)(RO center dot center dot center dot OR'). In this study, we systematically investigate the three reaction channels for an atmospherically representative set of RO + R'O radicals formed in the corresponding RO2+ R'O-2 reaction. First, we systematically sample the possible conformations of the RO center dot center dot center dot OR' clusters on the triplet potential energy surface. Next, we compute energetic parameters and attempt to estimate reaction rate coefficients for the three channels: evaporation/dissociation to RO + R'O, a hydrogen shift leading to the formation of R'(-H)=O + ROH, and "spin-flip" (intersystem crossing) leading to, or at least allowing, the formation of ROOR' dimers. While large uncertainties in the computed energetics prevent a quantitative comparison of reaction rates, all three channels were found to be very fast (with typical rates greater than 10 6 s(-1)). This qualitatively demonstrates that the computationally proposed novel RO2 + R'O-2 reaction mechanism is compatible with experimental data showing non-negligible branching ratios for all three channels, at least for sufficiently complex RO2.
  • Suetake, Mizuki; Nakano, Yuriko; Furuki, Genki; Ikehara, Ryohei; Komiya, Tatsuki; Kurihara, Eitaro; Morooka, Kazuya; Yamasaki, Shinya; Ohnuki, Toshihiko; Horie, Kenji; Takehara, Mami; Law, Gareth T.W.; Bower, William; Grambow, Bernd; Ewing, Rodney C.; Utsunomiya, Satoshi (2019)
    To understand the chemical durability of highly radioactive cesium-rich microparticles (CsMPs) released from the Fukushima Daiichi Nuclear Power Plant in March 2011, we have, for the first time, performed systematic dissolution experiments with CsMPs isolated from Fukushima soils (one sample with 108 Bq and one sample with 57.8 Bq of Cs-137) using three types of solutions: simulated lung fluid, ultrapure water, and artificial sea water, at 25 and 37 degrees C for 1-63 days. The Cs-137 was released rapidly within three days and then steady-state dissolution was achieved for each solution type. The steady-state Cs-137 release rate at 25 degrees C was determined to be 4.7 x 10(3), 1.3 x 10(3), and 1.3 x 10(3) Bq . m(-2)s(-1) for simulated lung fluid, ultrapure water, and artificial sea water, respectively. This indicates that the simulated lung fluid promotes the dissolution of CsMPs. The dissolution of CsMPs is similar to that of Si-based glass and is affected by the surface moisture conditions. In addition, the Cs release from the CsMPs is constrained by the rate-limiting dissolution of silicate matrix. Based on our results, CsMPs with similar to 2 Bq, which can be potentially inhaled and deposited in the alveolar region, are completely dissolved after >35 years. Further, CsMPs could remain in the environment for several decades; as such, CsMPs are important factors contributing to the long-term impacts of radioactive Cs in the environment. (C) 2019 Elsevier Ltd. All rights reserved.
  • Heilkkinen, Emma M.; Auriola, Seppo; Ranta, Veli-Pekka; Demarais, Nicholas J.; Grey, Angus C.; del Amo, Eva M.; Toropainen, Elisa; Vellonen, Kati-Sisko; Urtti, Arto; Ruponen, Marika (2019)
    Lens is the avascular tissue in the eye between the aqueous humor and vitreous. Drug binding to the lens might affect ocular pharmacokinetics, and the binding may also have a pharmacological role in drug-induced cataract and cataract treatment. Drug distribution in the lens has been studied in vitro with many compounds; however, the experimental methods vary, no detailed information on distribution between the lens sublayers exist, and the partition coefficients are reported rarely. Therefore, our objectives were to clarify drug localization in the lens layers and establish partition coefficients for a wide range of molecules. Furthermore, we aimed to illustrate the effect of lenticular drug binding on overall ocular drug pharmacokinetics. We studied the distribution of 16 drugs and three fluorescent dyes in whole porcine lenses in vitro with imaging mass spectrometry and fluorescence microscopy techniques. Furthermore, we determined lens/buffer partition coefficients with the same experimental setup for 28 drugs with mass spectrometry. Finally, the effect of lenticular binding of drugs on aqueous humor drug exposure was explored with pharmacokinetic simulations. After 4 h, the drugs and the dyes distributed only to the outermost lens layers (capsule and cortex). The lens/buffer partition coefficients for the drugs were low, ranging from 0.05 to 0.8. On the basis of the pharmacokinetic simulations, a high lens-aqueous humor partition coefficient increases drug exposure in the lens but does not significantly alter the pharmacokinetics in the aqueous humor. To conclude, the lens seems to act mainly as a physical barrier for drug distribution in the eye, and drug binding to the lens affects mainly the drug pharmacokinetics in the lens.
  • Kiiski, Iiro; Ollikainen, Elisa; Artes, Sanna; Järvinen, Päivi; Jokinen, Ville; Sikanen, Tiina (2021)
  • Kosonen, Jukka; Kulmala, Juha-Pekka; Mueller, Erich; Avela, Janne (2017)
    Anti-pronation orthoses, like medially posted insoles (MPI), have traditionally been used to treat various of lower limb problems. Yet, we know surprisingly little about their effects on overall foot motion and lower limb mechanics across walking and running, which represent highly different loading conditions. To address this issue, multi-segment foot and lower limb mechanics was examined among 11 over-pronating men with normal (NORM) and MPI insoles during walking (self-selected speed 1.70 +/- 0.19 m/s vs 1.72 +/- 0.20 m/s, respectively) and running (4.04 +/- 0.17 m/s vs 4.10 +/- 0.13 m/s, respectively). The kinematic results showed that MPI reduced the peak forefoot eversion movement in respect to both hindfoot and tibia across walking and running when compared to NORM (p <0.05-0.01). No differences were found in hindfoot eversion between conditions. The kinetic results showed no insole effects in walking, but during running MPI shifted center of pressure medially under the foot (p <0.01) leading to an increase in frontal plane moments at the hip (p <0.05) and knee (p <0.05) joints and a reduction at the ankle joint (p <0.05). These findings indicate that MPI primarily controlled the forefoot motion across walking and running. While kinetic response to MPI was more pronounced in running than walking, kinematic effects were essentially similar across both modes. This suggests that despite higher loads placed upon lower limb during running, there is no need to have a stiffer insoles to achieve similar reduction in the forefoot motion than in walking. (C) 2017 Elsevier Ltd. All rights reserved.
  • Nocera, Irene; Bonelli, Francesca; Vitale, Valentina; Meucci, Valentina; Conte, Giuseppe; Jose-Cunilleras, Eduard; Gracia-Calvo, Luis Alfonso; Sgorbini, Micaela (2021)
    Simple Summary Procalcitonin (PCT) increased in the case of systemic inflammatory response syndrome (SIRS), especially due to bacterial infection. The correlation between SIRS score and plasma PCT levels in horses have not been evaluated, and no studies investigated plasma PCT concentration over time. In the present study, PCT and SIRS score were evaluated in colic horses at admission to the hospital and at 24, 48, 72 and 96 h. Statistically differences were detected between healthy vs. all colic horses and between healthy vs. SIRS positive or SIRS negative horses. No correlation was observed between SIRS score and PCT. This suggests a role of plasmatic PCT as good biomarker for colic. Colic horses show systemic inflammatory response syndrome (SIRS) clinical signs. Procalcitonin (PCT) showed increased circulating levels in sick horses. This study compares plasma PCT concentrations in healthy vs. SIRS negative/positive colic horses over time, and evaluates PCT and SIRS score potential correlation, to verify the usefulness of PCT for the evaluation of SIRS severity. Ninety-one horses were included; 43/91 were healthy, on basis of physical examination, blood work and SIRS score (score = 0), while 48/91 were sick colic horses, classified as SIRS-negative (score < 2) and positive (score >= 2). Moreover, a 0-6 point-scale SIRS score was calculated (assessing mucous membrane color and blood lactate concentration). PCT was evaluated at admission, and at 24, 48, 72 and 96 h, using a commercial kit for equine species. We verified by the ANOVA test PCT differences between healthy vs. colic horses, healthy vs. SIRS-negative or SIRS-positive colic horses, at all sampling times, and the correlation between the SIRS score at admission with the SIRS score. Statistically significant differences were detected between healthy vs. all colic horses and between healthy vs. SIRS-positive or negative horses at all sampling times. No correlation was observed between the SIRS score at admission and PCT values. PCT was statistically higher in colic horses compared to the healthy ones, suggesting a role as a biomarker for colic.
  • Minwegen, Heiko; Döntgen, Malte; Hemken, Christian; Büttgen, Rene Daniel; Leonhard, Kai; Heufer, Karl Alexander (2019)
    Recently the possibility of hot beta-scission pathways gained attention. These reactions give a shortcut during the important fuel consumption phase in combustion processes leading from H-atom abstraction directly to the beta-scission products without fuel radical thermalization. Methyl formate (MF) was shown to be prone to hot beta-scission due to a low beta-scission barrier height. Furthermore, MF as smallest methyl ester can be considered as biodiesel surrogate and it is an important intermediate product during combustion of various ethers. In this work a predominantly ab-initio derived detailed kinetic model of MF combustion is developed including hot beta-scission pathways and compared to a sophisticated literature model based on classical estimation methods. For this, new stoichiometric MF in air ignition delay time measurements in a shock tube and a rapid compression machine over a wide temperature range (790 K-1250 K) and pressures of 10, 20 and 40 bar served as validation targets. The experimental ignition delay times (IDT) show Arrhenius type behavior in both facilities at all conditions. The newly developed quantum-based model catches the pressure dependency and low-temperature reactivity well although overpredicting the IDT at higher temperatures. It was found that hot beta-scission is the major depletion pathway of formate group-centered MF radicals. This, however, does not change the overall reactivity of MF combustion due to the low stability of the alkyl peroxide (RO2) at the formate group. For species with competing thermal beta-scission and RO2 formation, however, hot beta-scission may have a significant impact. (C) 2018 The Combustion Institute. Published by Elsevier Inc. All rights reserved.
  • Hrustic, Enis; Lignell, Risto; Riebesell, Ulf; Thingstad, Tron Frede (2017)
    The balance in microbial net consumption of nitrogen and phosphorus was investigated in samples collected in two mesotrophic coastal environments: the Baltic Sea (Tvarminne field station) and the North Sea (Espegrend field station). For this, we have refined a bioassay based on the response in alkaline phosphatase activity (APA) over a matrix of combinations in nitrogen and phosphorus additions. This assay not only provides information on which element (N or P) is the primary limiting nutrient, but also gives a quantitative estimate for the excess of the secondary limiting element (P+ or N+, respectively), as well as the ratio of balanced net consumption of added N and P over short timescales (days). As expected for a Baltic Sea late springearly summer situation, the Tvarminne assays (n = 5) indicated N limitation with an average P+ = 0.30 +/- 0.10 mu M-P, when incubated for 4 days. For short incubations (1-2 days), the Espegrend assays indicated P limitation, but the shape of the response surface changed with incubation time, resulting in a drift in parameter estimates toward N limitation. Extrapolating back to zero incubation time gave P limitation with N+ approximate to 0.9 mu M-N. The N : P ratio (molar) of nutrient net consumption varied considerably between investigated locations: from 2.3 +/- 0.4 in the Tvarminne samples to 13 +/- 5 and 32 +/- 3 in two samples from Espegrend. Our assays included samples from mesocosm acidification experiments, but statistically significant effects of ocean acidification were not found by this method.
  • Heß, Stefanie; Hiltunen, Teppo; Berendonk, Thomas U.; Kneis, David (2020)
    The horizontal transfer of plasmids is a key mechanism behind the spread of antibiotic resistance in bacteria. So far, transfer rate constants were measured for a variety of plasmids, donors and recipients. The employed strains typically had a long history in laboratories. Existing data are, therefore, not necessarily representative for real-world environments. Moreover, information on the inter-strain variability of plasmid transfer rates is scarce. Using a high-throughput approach, we studied the uptake of RP4 by various Escherichia coli recipients using Serratia marcescens as the donor. The recipient strains were isolated from human-borne sewage and river sediments. The rate constants of plasmid transfer generally followed a log-normal distribution with considerable variance. The rate constants for good and poor recipients (95 and 5% quantile) differed by more than three orders of magnitude. Specifically, the inter-strain variability of the rate constant was large in comparison to alterations induced by low-level antibiotic exposure. We did not find evidence for diverging efficiencies of plasmid uptake between E. coli recipients of different origin. On average, strains isolated from river bottom sediments were equally efficient in the acquisition of RP4 as isolates extracted from sewage. We conclude that E. coli strains persisting in the aquatic environment and those of direct human origin share a similar intrinsic potential for the conjugative uptake of certain plasmids. In view of the large inter-strain variability, we propose to work towards probabilistic modeling of the environmental spread of antibiotic resistance.
  • Valiev, Rashid; Hasan, Galib; Salo, Vili-Taneli; Kubecka, Jakub; Kurten, Theo (2019)
    High molecular weight "ROOR" dimers, likely formed in the gas phase through self- and cross-reactions of complex peroxy radicals (RO2), have been suggested to play a key role in forming ultrafine aerosol particles in the atmosphere. However, the molecular-level reaction mechanism producing these dimers remains unknown. Using multireference quantum chemical methods, we explore one potentially competitive pathway for ROOR' production, involving the initial formation of triplet alkoxy radical (RO) pairs, followed by extremely rapid intersystem crossings (ISC) to the singlet surface, permitting subsequent recombination to ROOR'. Using CH3OO + CH3OO as a model system, we show that the initial steps of this reaction mechanism are likely to be very fast, as the transition states for both the formation and the decomposition of the CH3O4CH3 tetroxide intermediate are far below the reactants in energy. Next, we compute ISC rates for seven different atmospherically relevant (3)(RO center dot center dot center dot R'O) complexes. The ISC rates vary significantly depending on the conformation of the complex and also exhibit strong stereoselectivity. Furthermore, the fastest ISC process is usually not between the lowest-energy triplet and singlet states but between the triplet ground state and an exited singlet state. For each studied (RO center dot center dot center dot R'O) system, at least one low-energy conformer with an ISC rate above 10(8) s(-1) can be found. This demonstrates that gas-phase dimer formation in the atmosphere very likely involves ISCs originating in relativistic quantum mechanics.
  • de Oliveira, Paulo F. M.; Michalchuk, Adam A. L.; Marquardt, Julien; Feiler, Torvid; Prinz, Carsten; Torresi, Roberto M.; Camargo, Pedro H. C.; Emmerling, Franziska (2020)
    Control over the bottom up synthesis of metal nanoparticles (NP) depends on many experimental factors, including the choice of stabilising and reducing agents. By selectively manipulating these species, it is possible to control NP characteristics through solution-phase synthesis strategies. It is not known, however, whether NPs produced from mechanochemical syntheses are governed by the same rules. Using the Au NPs mechanosynthesis as a model system, we investigate how a series of common reducing agents affect both the reduction kinetics and size of Au NPs. It is shown that the relative effects of reducing agents on mechanochemical NP synthesis differ significantly from their role in analogous solution-phase reactions. Hence, strategies developed for control over NP growth in solution are not directly transferrable to environmentally benign mechanochemical approaches. This work demonstrates a clear need for dedicated, systematic studies on NP mechanosynthesis.
  • Valiev, Rashid R.; Kurten, Theo (2020)
    Peroxyl radicals (ROO.) are key intermediates in atmospheric chemistry, with relatively long lifetimes compared to most other radical species. In this study, we use multireference quantum chemical methods to investigate whether photolysis can compete with well-established ROO. sink reactions. We assume that the photolysis channel is always ROO. + h nu => RO + O(P-3). Our results show that the maximal value of the cross-section for this channel is sigma = 1.3 x 10(-18) cm(2) at 240 nm for five atmospherically representative peroxyl radicals: CH3OO., C(O)HCH2OO., CH3CH2OO., HC(O)OO. and CH3C(O)OO.. These values agree with experiments to within a factor of 2. The rate constant of photolysis in the troposphere is around 10(-5) s(-1) for all five ROO.. As the lifetime of peroxyl radicals in the troposphere is typically less than 100 s, photolysis is thus not a competitive process. Furthermore, we investigate whether or not electronic excitation to the first excited state (D-1) by infrared radiation can facilitate various H-shift reactions, leading, for example, in the case of CH3OO. to formation of O.H and CH2O or HOO. and CH2 products. While the activation barriers for H-shifts in the D-1 state may be lower than in the ground state (D-0), we find that H-shifts are unlikely to be competitive with decay back to the D-0 state through internal conversion, as this has a rate of the order of 10(13) s(-1) for all studied systems.
  • Pessi, Jenni; Svanbäck, Sami; Lassila, Ilkka; Haeggstrom, Edward; Yliruusi, Jouko (2017)
    We introduce a system with a lyophilic matrix to aid dissolution studies of powders and particulate systems. This lyophilic matrix method (LM method) is based on the ability to discriminate between non-dissolved particles and the dissolved species. In the LM method the test substance is embedded in a thin lyophilic core-shell matrix. This permits rapid contact with the dissolution medium while minimizing dispersion of non-dissolved particles without presenting a substantial diffusion barrier. The method produces realistic dissolution and release results for particulate systems, especially those featuring nanoscale particles. By minimizing method-induced effects on the dissolution profile of nanopowders, the LM method overcomes shortcomings associated with current dissolution tests. (C) 2017 Elsevier B.V. All rights reserved.
  • Nilsson, Sofia; Henschel, Henning; Scotti, Gianmario; Haapala, Markus; Kiriazis, Alexandros; Boije af Gennäs, Gustav; Kotiaho, Tapio; Yli-Kauhaluoma, Jari (2019)
    We have identified the most likely reaction mechanism for oxidizing heptafulvenes to the corresponding tropones by experimental and theoretical investigations. The experimental studies were done by coupling a three-dimensional printed miniaturized reactor with an integrated electrospray ionization needle to a mass spectrometer. Using the experimentally observed ions as a basis, nine alternative reaction pathways were investigated with density functional theory calculations. The lowest energy reaction pathway starts with the formation of an epoxide that is opened upon the addition of a second equivalent of the oxidizing species meta-chloroperoxybenzoic acid. The adduct formed then undergoes a Criegee-like rearrangement to yield a positively charged hemiketal, which on deprotonation dissociates into acetone resembles a Hock-like rearrangement. and tropone. Overall, the reaction mechanism resembles a Hock-like rearrangement.
  • Hooda, Sonu; Avchachov, Konstantin; Khan, S. A.; Djurabekova, Flyura; Satpati, B.; Nordlund, Kai; Bernstorff, Sigrid; Ahlawat, Sarita; Kanjilal, D.; Kabiraj, D. (2017)
    The formation of nanoscale voids in amorphous-germanium (a-Ge), and their size and shape evolution under ultra-fast thermal spikes within an ion track of swift heavy ion, is meticulously expatiated using experimental and theoretical approaches. Two step energetic ion irradiation processes were used to fabricate novel and distinct embedded nanovoids within bulk Ge. The 'bow-tie' shape of voids formed in a single ion track tends to attain a spherical shape as the ion tracks overlap at a fluence of about 1 x 10(12) ions cm(-2). The void assumes a prolate spheroid shape with major axis along the ion trajectory at sufficiently high ion fluences. Small angle x-ray scattering can provide complementary information about the primary stage of void formation hence this technique is applied for monitoring simultaneously their formation and growth dynamics. The results are supported by the investigation of cross-sectional transmission and scanning electron micrographs. The multi-time-scale theoretical approach corroborates the experimental findings and relates the bow-tie shape void formation to density variations as a result of melting and resolidification of Ge within the region of thermal spike generated along an ion track, plus non-isotropic stresses generated towards the end of the thermal spike.