Search results for "Diss"
showing 10 items of 2500 documents
A TDDFT-based Study on the Proton-DNA Collision
2019
The interaction of heavy charged particles with DNA is of interest for several areas, from hadrontherapy to aero-space industry. In this paper, a TD-DFT study on the interaction of a 4 keV proton with an isolated DNA base pair was carried out. Ehrenfest dynamics was used to study the evolution of the system during and after the proton impact up to about 193 fs. This time was long enough to observe the dissociation of the target, which occurs between 80-100 fs. The effect of base pair linking to the DNA double helix was emulated by fixing the four O3' atoms responsible for the attachment. The base pair tends to dissociate into its main components, namely the phosphate groups, sugars and nitr…
Asymmetry and Non-Adiabaticity in Fragmentation of Disulfide Bonds upon Electron Capture
2010
Although it has been generally assumed that electron attachment to disulfide derivatives leads to a systematic and significant activation of the S-S bond, we show, by using [CH(3)SSX] (X = CH(3), NH(2), OH, F) derivatives as model compounds, that this is the case only when the X substituents have low electronegativity. Through the use of MP2, QCI and CASPT2 molecular orbital (MO) methods, we elucidate, for the first time, the mechanisms that lead to unimolecular fragmentation of disulfide derivatives after electron attachment. Our theoretical scrutiny indicates that these mechanisms are more intricate than assumed in previous studies. The most stable products, from a thermodynamic viewpoint…
Electrochemical detection of the 2-isobutyl-3-methoxypyrazine model odorant based on odorant-binding proteins: The proof of concept
2014
Abstract We developed an electrochemical assay for the detection of odorant molecules based on a rat odorant-binding protein (rOBP3). We demonstrated that rOBP3 cavity binds 2-methyl-1,4-naphtoquinone (MNQ), an electrochemical probe, as depicted from the decrease of its electrochemical signal, and deduced the dissociation constant, Kd MNQ = 0.5(± 0.2) μM. The amount of MNQ displaced from rOBP3 by 2-isobutyl-3-methoxypyrazine (IBMP), a model odorant molecule, was measured using square-wave voltammetry. The release of MNQ by competition led to an increase of the electrochemical response. In addition, this method allowed determination of the dissociation constant of rOBP3 for IBMP, Kd IBMP =…
Statistics of reversible transitions in two-state trajectories in force-ramp spectroscopy
2014
A possible way to extract information about the reversible dissociation of a molecular adhesion bond from force fluctuations observed in force ramp experiments is discussed. For small loading rates the system undergoes a limited number of unbinding and rebinding transitions observable in the so-called force versus extension (FE) curves. The statistics of these transient fluctuations can be utilized to estimate the parameters for the rebinding rate. This is relevant in the experimentally important situation where the direct observation of the reversed FE-curves is hampered, e.g. due to the presence of soft linkers. I generalize the stochastic theory of the kinetics in two-state models to the…
Autonomous artificial nanomotor powered by sunlight
2006
Light excitation powers the reversible shuttling movement of the ring component of a rotaxane between two stations located at a 1.3-nm distance on its dumbbell-shaped component. The photoinduced shuttling movement, which occurs in solution, is based on a “four-stroke” synchronized sequence of electronic and nuclear processes. At room temperature the deactivation time of the high-energy charge-transfer state obtained by light excitation is ≈10 μs, and the time period required for the ring-displacement process is on the order of 100 μs. The rotaxane behaves as an autonomous linear motor and operates with a quantum efficiency up to ≈12%. The investigated system is a unique example of an artif…
Silicic acid competes for dimethylarsinic acid (DMA) immobilization by the iron hydroxide plaque mineral goethite.
2015
Abstract A surface complexation modeling approach was used to extend the knowledge about processes that affect the availability of dimethylarsinic acid (DMA) in the soil rhizosphere in presence of a strong sorbent, e.g., Fe plaques on rice roots. Published spectroscopic and molecular modeling information suggest for the organoarsenical agent to form bidentate-binuclear inner-sphere surface complexes with Fe hydroxides similar to the inorganic As oxyanions. However, since also the ubiquitous silicic acid oxyanion form the same bidentate binuclear surface complexes, our hypothesis was that it may have an effect on the adsorption of DMA by Fe hydroxides in soil. Our experimental batch equilibr…
An efficient dissipative particle dynamics-based algorithm for simulating electrolyte solutions
2015
We propose an efficient simulation algorithm based on the dissipative particle dynamics (DPD) method for studying electrohydrodynamic phenomena in electrolyte fluids. The fluid flow is mimicked with DPD particles while the evolution of the concentration of the ionic species is described using Brownian pseudo particles. The method is designed especially for systems with high salt concentrations, as explicit treatment of the salt ions becomes computationally expensive. For illustration, we apply the method to electro-osmotic flow over patterned, superhydrophobic surfaces. The results are in good agreement with recent theoretical predictions.
Proteomic identification of FHL1 as the protein mutated in human reducing body myopathy
2007
Reducing body myopathy (RBM) is a rare disorder causing progressive muscular weakness characterized by aggresome-like inclusions in the myofibrils. Identification of genes responsible for RBM by traditional genetic approaches has been impossible due to the frequently sporadic occurrence in affected patients and small family sizes. As an alternative approach to gene identification, we used laser microdissection of intracytoplasmic inclusions identified in patient muscle biopsies, followed by nanoflow liquid chromatography-tandem mass spectrometry and proteomic analysis. The most prominent component of the inclusions was the Xq26.3-encoded four and a half LIM domain 1 (FHL1) protein, expresse…
Effect of protonation and deprotonation on the gas phase reactivity of fluorinated 1,2,4-triazines
2008
Positive and negative electrospray mass spectrometry (MS), in-time and in-space MS n experiments, high-resolution and accurate mass measurements obtained with an Orbitrap, together with density functional theory calculations have been used to study the gas-phase ion chemistry of a series of fluorinated 1,2,4-triazines. As a result of low-energy collision-induced dissociations, occurring in an ion trap and in a triple quadrupole, their protonated and deprotonated molecules show interesting features depending on the nature and structure of the precursor ions. The occurrence of elimination/hydration reactions produced by positive ions in the ion trap is noteworthy. Decompositions of deprotonat…
Thermal and electrochemically assisted Pd-Cl bond cleavage in the d9-d9 Pd2dppm2Cl2 complex by Pd3 dppm3COn+ clusters (n = 2, 1, 0).
2007
A new aspect of reactivity of the cluster [Pd3(dppm)3(micro3-CO)]n+, ([Pd3]n+, n = 2, 1, 0) with the low-valent metal-metal-bonded Pd2(dppm)2Cl2 dimer (Pd2Cl2) was observed using electrochemical techniques. The direct reaction between [Pd3]2+ and Pd2Cl2 in THF at room temperature leads to the known [Pd3(dppm)3(micro3-CO)(Cl)]+ ([Pd3(Cl)]+) adduct and the monocationic species Pd2(dppm)2Cl+ (very likely as Pd2(dppm)2(Cl)(THF)+, [Pd2Cl]+) as unambiguously demonstrated by UV-vis and 31P NMR spectroscopy. In this case, [Pd3]2+ acts as a strong Lewis acid toward the labile Cl- ion, which weakly dissociates from Pd2Cl2 (i.e., dissociative mechanism). Host-guest interactions between [Pd3]2+ and Pd2…