Haut PDF REACTIVITY OF URACIL IN THE GAS PHASE: STATISTICAL & NON-STATISTICAL STUDY

REACTIVITY OF URACIL IN THE GAS PHASE: STATISTICAL & NON-STATISTICAL STUDY

REACTIVITY OF URACIL IN THE GAS PHASE: STATISTICAL & NON-STATISTICAL STUDY

REACTIVITY OF URACIL IN THE GAS PHASE: STATISTICAL & NON-STATISTICAL STUDY Estefania ROSSICH MOLINA a,b , E. MARTINEZ-NUÑEZ c , Jean-Yves SALPIN a,b and R. SPEZIA a,b a- LAMBE, CEA, CNRS, Université Paris Saclay, F-91025, Evry, France b- LAMBE, Université d’Evry, F-91025, Evry, France

2 En savoir plus

STUDYING THE REACTIVITY OF URACIL IN THE GAS PHASE:  STATISTICAL vs. NON-STATISTICAL APPROACH

STUDYING THE REACTIVITY OF URACIL IN THE GAS PHASE: STATISTICAL vs. NON-STATISTICAL APPROACH

STUDYING THE REACTIVITY OF URACIL IN THE GAS PHASE: STATISTICAL vs. NON-STATISTICAL APPROACH E. ROSSICH MOLINA a,b , J.-Y. SALPIN a,b , R. SPEZIA a,b and E. MARTINEZ-NUÑEZ c a- LAMBE, CEA, CNRS, Université Paris Saclay, F-91025, Evry, France b- LAMBE, Université de Evry, F-91025, Evry, France

2 En savoir plus

Unimolecular reactivity upon collision of uracil-Ca<sup>2+</sup> complexes in the gas phase: Comparison with uracil-M<sup>+</sup> (M = H, alkali metals) and uracil-M<sup>2+</sup> (M = Cu, Pb) systems

Unimolecular reactivity upon collision of uracil-Ca<sup>2+</sup> complexes in the gas phase: Comparison with uracil-M<sup>+</sup> (M = H, alkali metals) and uracil-M<sup>2+</sup> (M = Cu, Pb) systems

corresponding Ca 2+ complex likely to be detected in our study, in which the metal dication bridges between the carbonyl oxygen atom and the NH imino group of the O=C-CH=CH-NH moiety (Figure 4). The differences in the collision-induced unimolecular reactivity between [Ca(uracil)] 2+ and [M(uracil)] + ions, where M is an alkali metal are also significant since the only fragmentation observed for uracil-alkali + complexes is the loss of the nucleobase [2]. This likely reflects the fact that the polarization of the electron density of the base is significantly larger in presence of the dication, and therefore some of the bonds of uracil become significantly activated and finally cleaved, whereas the activation induced by the interaction with alkali monocations is rather weak and therefore not sufficient to promote a bond fission. This is actually reflected in the corresponding molecular graphs, which show indeed that the activation or reinforcement of the uracil-moiety bonds are stronger upon Ca 2+ than upon Na + association. As illustrated in Figure 6, the activation of the C=O bond induced by Ca 2+ is significantly larger than the one induced by Na + , mirrored in a much larger decrease of the electron density at the corresponding bond critical point. This also applies for the activation of the C2N3 and the C5C6 bonds or with respect to the reinforcement of the N3C4 and C4C5 linkages. In agreement with the experimental results, the bond between the metal and the basic site of uracil is much weaker for Na + than for Ca 2+ .
En savoir plus

32 En savoir plus

Separation of emitted and photochemical formaldehyde in Mexico City using a statistical analysis and a new pair of gas-phase tracers

Separation of emitted and photochemical formaldehyde in Mexico City using a statistical analysis and a new pair of gas-phase tracers

Fig. 7. Average diurnal contributions of primary, secondary and residual HCHO to ambient HCHO for three time periods: before (left), during (middle), after (right) Easter week. The top row of panels gives contributions in units of ppbv, and lower row of panels in percent contributions to ambient HCHO. Primary HCHO, emitted during early morning hours will help “jump start” photochemistry since formaldehyde pho- tolysis is a major source of prompt radical production in the MCMA (Volkamer et al., 2005a 1 ). The resulting photochem- istry will be enhanced, causing more effective VOC oxida- tion and, therefore, more photochemical HCHO production. Thus, the emitted HCHO fraction and its photochemical pro- duction fraction are not decoupled, and it will require a com- prehensive photochemical modeling study to determine de- gree of coupling.
En savoir plus

14 En savoir plus

Theoretical and numerical study of collision and coalescence - Statistical modeling approaches in gas-droplet turbulent flows

Theoretical and numerical study of collision and coalescence - Statistical modeling approaches in gas-droplet turbulent flows

3 back coupling is subject to many studies (see for example [35], [125]), but is not considered within this work. After appointing the physical interaction phenomena that are taken into account (fluid- particle and particle-particle interaction), the question arises how to simulate two-phase flows in general, and which of these methods are best suitable to investigate the underlying physics as well as to model the influence of fluid turbulence and droplet coalescence. There are two main goals of this work. First, to perform numerical simulations which can be considered as exact, in order to serve as reference for comparison with model predictions and to study the physical mechanisms of fluid-coalescence interaction. Chapters 3 and 5 are concerned with this type of simulation. These simulations are a kind of ’numerical experiment’. Second, to validate and support the development of statistical modeling ap- proaches in comparison with the performed ’numerical experiments’. This subject is treated in chapters 4 and 6. These modeling approaches can be used in industrial-size simulations. On a microscopic length scale (∼ 10 −3 m) full direct numerical simulations of two-phase flows are possible. Such simulation are for example volume of fluids (VOF) [5], [64] or level- set methods [55], [128]. These simulations comprise only a few droplets, but all the physics are resolved on all scales: flow around and inside the droplets, deformation of the droplets, heat, mass and momentum transfer. This means to solve both the Navier-Stokes equations and the continuum mechanic equations. With this approach, however, it is not possible to measure the necessary dispersed-phase statistics that are needed for development of the above mentioned modeling approaches.
En savoir plus

270 En savoir plus

Alkylation of uracil and thymine in the gas phase through interaction with alkylmercury compounds

Alkylation of uracil and thymine in the gas phase through interaction with alkylmercury compounds

rather than exothermic with respect to the entrance channel. It should be remembered however that both mechanisms, as mentioned above, imply activation barriers clearly higher in energy than the entrance channel, and therefore the formation of protonated uracil in any of its forms, should be clearly a minority. The fact that protonated uracil is the most intense fragment ion observed experimentally with n-BuHgCl (Figure 1b) may reflect the fact that experiments are carried out under a multiple collision regime, leading to the increase of the internal energy of the precursor ions, which would allow these high activation barriers to be overpassed. Furthermore, we already demonstrated by using statistical kinetic theories that the products which are thermochemically favored are not necessarily kinetically favored [83].
En savoir plus

39 En savoir plus

Experimental and computational study of the gas-phase interactions between lead(II) ions and two pyrimidic nucleobases: Uracil and thymine

Experimental and computational study of the gas-phase interactions between lead(II) ions and two pyrimidic nucleobases: Uracil and thymine

and the present paper reports the first results obtained with two nucleobases : thymine and uracil (scheme 1). <Scheme 1> This work has been done by combining mass spectrometry experiments and theoretical calculations. From the experimental point of view, the development of electrospray ionization techniques has opened up the possibility of producing organometallic complexes in the gas phase from aqueous solutions [15], and therefore of gaining direct information on the intrinsic reactivity of organic molecules when interacting with metal dications. However, in order to obtain a complete picture of the reactivity patterns one needs to have not only experimental information on the products distribution but also postulate appropriate reaction mechanisms. This was presently achieved by combining mass spectrometry experiments with theoretical DFT calculations by making use of two density functionals methods: B3LYP and G96LYP.
En savoir plus

41 En savoir plus

Interactions of Dimethyltin(IV) with Uracil As Studied in the Gas Phase

Interactions of Dimethyltin(IV) with Uracil As Studied in the Gas Phase

As discussed previously (vide supra), the prominent dominant peak in the MS/MS spectrum is detected at m/z 231. The corresponding loss has been assigned to the two methyl moieties which can be also viewed as the elimination of an ethane molecule. According to our computational study, the interaction between deprotonated uracil and the dimethyltin dichloride preserves the integrity of the dimethyltin moiety, the methyl groups being attached to the metal. Hence, all the complexes could be candidate for this fragmentation. Reasonably, the most stable complex is the most probable that may lead to [Sn(Ura-H)] + by rupture of the Sn-C bonds. The activation barrier of the corresponding transition state is estimated at about 225 kJ/mol at the CCSD(T)/6- 31+G(d,p)//M11L/6-31+G(d,p) level of theory (see Figure 6b). It is worth noting that the resulting fragment ion is similar to the complex obtained in the case of lead interaction with uracil. 43 Considering that both [Pb(Ura-H)] + and [Sn(Ura-H)] + complexes present the same experimental fragmentation patterns, we may reasonable assume that the associates potential energy surfaces would be similar.
En savoir plus

36 En savoir plus

Gas-Phase reactivity of Pb2+ ions towards adenine, thymine and uracil

Gas-Phase reactivity of Pb2+ ions towards adenine, thymine and uracil

intimate mechanisms associated with these interactions. In this context, we began a study in order to have a better understanding of these mechanisms, by considering in a first step the gas-phase reactivity between Pb 2+ ions and three nucleobases: thymine (T, R=CH 3 ), uracil (U R=H), and adenine (A).

2 En savoir plus

On the gas phase fragmentation of protonated uracil : a statistical perspective

On the gas phase fragmentation of protonated uracil : a statistical perspective

The potential energy surface of protonated uracil has been explored with an automated transition state search procedure, resulting in the finding of 1398 stationary points and 751 reactive channels, which can be categorized into isomerizations between pairs of isomers, unimolecular fragmentations and bimolecular reactions. The use of statistical Rice- Ramsperger-Kassel-Marcus (RRKM) theory and Kinetic Monte Carlo (KMC) simulations allowed us determining the relative abundances of each fragmentation channel as a function of the ion’s internal energy. The KMC/RRKM product abundances are compared with novel mass spectrometry (MS) experiments in the collision energy range 1-6 eV. To facilitate the comparison between theory and experiments, further dynamics simulations are carried out to determine the fraction of collision energy converted into the ion’s internal energy. The KMC simulations show that the major fragmentation channels are isocyanic acid and ammonia losses, in good agreement with experiments. The third predominant channel is water loss according to both theory and experiments, although the abundance obtained in the KMC simulations is very low, suggesting that non-statistical dynamics might play an important role for this channel. Isocyanic acid (HNCOH + ) is also an important product in the KMC
En savoir plus

12 En savoir plus

A simple statistical approach for fragmentation studies of doubly ionized cytosine, thymine and uracil bases

A simple statistical approach for fragmentation studies of doubly ionized cytosine, thymine and uracil bases

Figure 1: cytosine, thymine and uracil molecule 2. Method 2.1. Experimental context The model we have developed is a tool for the interpretation of experiments of multi-coincidence detection of fragments originating from gas phase bio-molecules doubly ionized by collisions with 100 keV protons. The experimental setup has been described in detail elsewhere [18] . In these experiments, coincidence detection relies on very high detection efficiency and very low detection rate. The density of the proton bunches impinging on the gaseous target molecules is kept very low, so that collision products are detected much less often than once per proton pulse cycle (typically, once every 100 pulses). Consequently, when one singly positive charged product (fragment or parent ion) is detected, it is considered to arise from a singly charged parent molecule. As a consequence, when two singly positive charged fragments are detected during one proton cycle, they are considered as a correlated fragment pair A + /B + originating from the same doubly ionized molecule, and not as two uncorrelated fragments issued from two singly charged molecules (low detection rate) or as two correlated fragments emitted from a triply ionized parent with a third ion product that eluded detection (high detection efficiency). Although we attempted to detect negatively charged products by operating the mass spectrometer in inverse mode, only positively charged products have been detected. Then, the correlated fragment pairs come from the following general reaction path:
En savoir plus

11 En savoir plus

Gas-Phase reactivity of Pb2+ ions with adenine, thymine and uracil

Gas-Phase reactivity of Pb2+ ions with adenine, thymine and uracil

• Many studies have shown that in physiological media, Pb(II) ions are determinant in the activity of some RNA-cleaving ribozymes . Moreover, it recently appeared that some ribozymes require the presence of two metal cations. (1,2) It was thus observed that in solution, Pb 2+ cations do not exhibit any particular reactivity with the DNA, whereas they induce the cleavage of the RNA in the presence of Mg 2+ . On the other hand, few is known about the intimate mechanisms associated with these interactions. In this context, we began a study in order to have a better understanding of these mechanisms, by considering in a first step the gas-phase reactivity between Pb 2+ ions and three nucleobases: thymine (T, R=CH
En savoir plus

2 En savoir plus

Application of the gas-phase reactivity of Pb2+ ions to the structural characterization of disaccharides

Application of the gas-phase reactivity of Pb2+ ions to the structural characterization of disaccharides

• Residual intensity of the parent ion set to 25 % by varying the collision energy, all the other parameters being kept constant. • MS/MS spectra repeated 10 times for each disaccharide to check the reproducibility of the intensities. • The results are summarized below (peaks with relative abundances below 3 % are not taken into account). • All the disaccharides present similar positive ion electrospray spectra.

2 En savoir plus

Computational and statistical challenges in high dimensional statistical models

Computational and statistical challenges in high dimensional statistical models

forward argument that 𝑛 info trivialized to zero and therefore when 𝑛 = 1, 𝛽 * is recoverable from 𝑌 = ⟨𝑋, 𝛽 * ⟩ + 𝑊 . This can also be verified by a brute-force method which finds 𝛽 * directly, as 𝛽 * is the only binary 𝑘-sparse vector which can satisfy 𝑌 = ⟨𝑋, 𝛽 * ⟩ + 𝑊 with probability tending to one as 𝑝 goes to infinity (whp). On the other hand, for sparse and binary-valued 𝛽 * , the Basis Pursuit method in the noiseless case [DT10] and the Basis Pursuit Denoising Scheme in the noisy case [GZ17b] have been proven to fail to recover a binary 𝛽 * with 𝑛 = 𝑜(𝑘 log (︀ 𝑝 𝑘 )︀ ) samples. Furthermore, LASSO has been proven to fail to recover a vector with the same sup- port of 𝛽 * , with 𝑛 = 𝑜(𝑘 log 𝑝) samples [Wai09b]. This failure to capture the complexity of the problem accurately enough for small sample sizes also lead to an algorithmic hardness conjecture for the regime 𝑛 = 𝑜(𝑘 log (︀ 𝑝 𝑘 )︀ ) [GZ17a], [GZ17b] which is described in Chapters 3, 4. While this conjecture still stands in the general case, as we show in this Chapter, in the special case where 𝛽 * is rational-valued and the magnitude of the noise 𝑊 is sufficiently small, the statistical computational gap can be closed and 𝛽 * can be recovered even when 𝑛 = 1.
En savoir plus

301 En savoir plus

Application of the gas-phase reactivity of Pb2+ ions to the structural characterization of disaccharides

Application of the gas-phase reactivity of Pb2+ ions to the structural characterization of disaccharides

• Residual intensity of the parent ion set to 25 % by varying the collision energy, all the other parameters being kept constant. • MS/MS spectra repeated 10 times for each disaccharide to check the reproducibility of the intensities. • The results are summarized below (peaks with relative abundances below 3 % are not taken into account). • All the disaccharides present similar positive ion electrospray spectra.

2 En savoir plus

Statistical Analysis of Non-Deterministic Fork-Join Processes

Statistical Analysis of Non-Deterministic Fork-Join Processes

a class of programs that uses a fork-join model of synchronization, together with loops and a choice construct for non-determinism. This is a simple formalism but it is non-trivial in terms of the concurrency features it provides. Most im- portantly, the underlying combinatorial interpretation is already quite involved. In previous work we studied the combinatorial interpretation of three fundamen- tal aspects of concurrency: parallelism (as interleaving) interpreted as (strictly) increasing labelled structures [8], non-determinism as partial labelling [7] and synchronization as non-strict labelling [9]. In this paper, we integrate these vari- ous interpretations into a single unified combinatorial specification based on the symbolic method of [2]. The main interest of this specification of process behav- iors is that we can then obtain, in a systematic way, the generating function for the possible executions of a given program. Because we only study finite objects, the executions are considered of bounded length. At the theoretical level, this is often a suitable starting point for the study of a quantitative problem in analytic combinatorics (cf. e.g. [8]). At a more practical level, the combinatorial speci- fication is also a good source of algorithmic investigations, which is our main concern in the present paper.
En savoir plus

21 En savoir plus

The statistical physics of cities

The statistical physics of cities

The values of scaling exponents are also subject to fitting issues [79]. The data is usually noisy and incomplete and the number of available decades not very large. An important difficulty is that most values of 𝛽 are close to unity: typically for the superlinear quantities considered in Ref. [75] the exponent measured over two decades is in the range 1.07–1.34 with an average 1.19. The relevant question is then the existence of a nonlinear behavior [79]. When comparing a nonlinear fit of the form 𝑎𝑃 Š with a linear fit 𝑎𝑃, the nonlinear fit is always ‘better’, owing to its larger number of parameters (here, two compared to one), and a rigorous statistical analysis is needed to determine which fit is preferable. Deciding whether the best fit is linear also depends crucially on assumptions about the noise, which need to be tested. When this rigorous statistical analysis was performed over 15 different datasets, although the ‘naïve’ fit gave nonlinear behaviour the linear assumption could not be rejected in several cases [79]. This empirical problem is serious and should be addressed in future studies of scaling in cities.
En savoir plus

24 En savoir plus

Statistical study of blood cell populations by very wide-field bimodal phase/ fluorescence imaging

Statistical study of blood cell populations by very wide-field bimodal phase/ fluorescence imaging

Granulocytes are the most common WBC type (40 to 75%), they are roughly 12 µm in diameter and their nucleus has a characteristic multi-lobe or irregular-shape. As illustrated on a bi-lobes nucleus in Figure 7, our system’s resolution was sufficient to distinguish the morphological features of granulocytes. Lymphocytes account for 20 to 40 % of WBC, are regular and round-shaped cells of 7 µm diameter with a nucleus occupying almost the entire cell. Monocytes represent 2 to 10% of WBC, are large 15-20 µm cells with a granular horse shoe shaped nucleus. As illustrated in Figure 7, lymphocytes and monocytes could be differentiated. The size difference of the nuclei of two sub- types were discernable, and the fluorescence signal of monocytes were more diffuse.
En savoir plus

8 En savoir plus

Statistical Study of the Corrosion Behavior of Al2CuMg Intermetallics in AA2024-T351 by SKPFM

Statistical Study of the Corrosion Behavior of Al2CuMg Intermetallics in AA2024-T351 by SKPFM

when an S-phase particle is attacked, its chemical composition changes 共the copper content increases while the aluminum and mag- nesium contents decrease 兲 until its copper content reaches about 60–70 atom %, corresponding to the formation of a probable Cu 2 O-rich oxide film on the surface of the particle. This copper enrichment of the S-phase particle parallels a decrease of its poten- tial relative to the matrix down to around −410 mV. Then, the SKPFM potential and the chemical composition of the particle do not evolve any longer while the dissolution depth continues to in- crease. Figure 12 shows that corroded S-phase particles have a po- rous structure arising from heterogeneous dissolution with preferen- tial removal of aluminum and magnesium, leading to copper enrichment. 34,35 It can be assumed that, subsequent to the formation of the pores in the particle, settling of the structure occurs, which would explain the increase of the dissolution depth while neither the chemical composition nor the SKPFM potential continue to change. Furthermore, due to the copper enrichment, the particle becomes nobler. Oxygen reduction increases on the particle mainly at the particle/matrix interface favoring the dissolution of the surrounding matrix, as observed. When the dissolution of the matrix is so strong that there is no longer any mechanical cohesion with the particle, the particle falls out; the potential measured on this site is then that of the matrix 共Fig. 5兲. As a conclusion, when an S-particle is corroded, particle dealloying is observed as well as the formation of a groove around the perimeter of the particle due to increased oxygen reduc- tion on the particle and subsequent alkalinization at the interface particle/matrix.
En savoir plus

9 En savoir plus

Physico-statistical modelling of the primary phase of an unprotected loss of flow

Physico-statistical modelling of the primary phase of an unprotected loss of flow

Hyatt Re ge n cy C hicago, C hicago, IL, USA, August 30 -Se pte mbe r 4, 2015 The Unprotected Loss of Flow accident is assumed to be initiated by the primary pump rundown. Shutdown systems are supposed to fail and the transient starts at nominal power. As a consequence, the sodium flow rate is highly and progressively reduced and the core temperature increases. The sum of the reactivity feedback effects due to the core heating-up being negative, the fuel power starts to decrease. Then, depending on the flow rate decrease and on the power evolution, sodium boiling may occur. But on the contrary to cores presenting a positive void effect, with this new core design, boiling does not cause a primary power excursion. Depending on the power conditions when boiling occurs, the two-phase core flow may stabilize in the upper part of the subassemblies (SAs). However, in case of high power transient, boiling conditions may become unstable. A flow excursion transient would then lead to the downwards progression of the boiling front within the core, possibly inducing the fuel pins dry-out and the degradation of SAs. The primary phase finally ends with the first hexcan failure in the core.
En savoir plus

14 En savoir plus

Show all 10000 documents...