The dynamics of exchange reactions A+BC→AB+C have been examined on two types of potential-energy hypersurfaces that differed in the location of the energy barrier along the reaction coordinate. On “surface I” the barrier was in the entry valley of the energy surface, along the approach coordinate. On “surface II” the barrier was in the exit valley of the energy surface, along the retreat coordinate. The classical barrier height was Ec = 7.0 kcal mole−1 on both surfaces, and was displaced from the corner of the energy surface by the same amount; on surface I, r1‡ = 1.20 Å, r2‡ = 0.80 Å; on surface II, r1‡ = 0.80 Å, r2‡ = 1.20 Å (r1 ≡ rAB, r2 ≡ rBC, and the superscript ‡ refers to the location of the crest of the barrier). Three-dimensional (3D) classical trajectory calculations were performed for the mass combination mA = mB = mC at several reagent energies. The reagent energy took the form of translation, vibration or an equilibrium distribution of the two. The main findings were that translation was markedly more effective than vibration in promoting reaction on surface I, and vibration markedly more effective than translation in promoting reaction on surface II. The total reactive cross section with the entire reagent energy vested in translation was symbolized ST, with the reagent energy (but for 1.5 kcal) in vibration, SV, and with an equilibrium distribution over reagent translation and vibration, Seq. On surface I ST ≫ SV: on surface II SV ≫ ST. Close to the threshold for ST on surface I, ST / Seq ∼ 10; close to the threshold for SV, on surface II, SV / Seq ∼ 10. At high reagent energies (2 × threshold) on surface I ST / Seq fell to 2, whereas on surface II SV / Seq increased to extremely large values. Product energy and angular distributions were recorded for two reagent energies. On surface I with low translational energy in the reagents a major part of the available energy appeared as vibration in the molecular product. At higher collision energy this fraction decreased. On surface II with low vibrational energy in the reagents only a small part of the available energy appeared as vibration in the product. At higher vibrational energy this fraction increased. The product angular distribution at low reagent translational energy on surfaces I and II corresponded to backward-peaked scattering of the molecular product. At increased reagent energy on both surfaces the distribution shifted forward (this is a novel phenomenon in the case of increased reagent vibration; surface II).
Approximately half of known human miRNAs are located in the introns of protein coding genes. Some of these intronic miRNAs are only expressed when their host gene is and, as such, their steady state expression levels are highly correlated with those of the host gene's mRNA. Recently host gene expression levels have been used to predict the targets of intronic miRNAs by identifying other mRNAs that they have consistent negative correlation with. This is a potentially powerful approach because it allows a large number of expression profiling studies to be used but needs refinement because mRNAs can be targeted by multiple miRNAs and not all intronic miRNAs are co-expressed with their host genes.Here we introduce InMiR, a new computational method that uses a linear-Gaussian model to predict the targets of intronic miRNAs based on the expression profiles of their host genes across a large number of datasets. Our method recovers nearly twice as many true positives at the same fixed false positive rate as a comparable method that only considers correlations. Through an analysis of 140 Affymetrix datasets from Gene Expression Omnibus, we build a network of 19,926 interactions among 57 intronic miRNAs and 3,864 targets. InMiR can also predict which host genes have expression profiles that are good surrogates for those of their intronic miRNAs. Host genes that InMiR predicts are bad surrogates contain significantly more miRNA target sites in their 3′ UTRs and are significantly more likely to have predicted Pol II and Pol III promoters in their introns.We provide a dataset of 1,935 predicted mRNA targets for 22 intronic miRNAs. These prediction are supported both by sequence features and expression. By combining our results with previous reports, we distinguish three classes of intronic miRNAs: Those that are tightly regulated with their host gene; those that are likely to be expressed from the same promoter but whose host gene is highly regulated by miRNAs; and those likely to have independent promoters.
A three-atom model has been employed in a first study of the dynamics of the reactions of hot tritium with hydrogen-containing organic molecules, e.g., T + CH4. After exploring many extended-London–Eyring–Polanyi–Sato (LEPS) potential-energy hypersurfaces of the type introduced in Part II, a surface was obtained which was in qualitative accord with experiment in that it predicted predominantly abstraction at the low end of the hot-atom range of energies (taken to be 2 eV). Abstraction (ABS) consists in T + HR → TH + R; displacement (DIS): T + HR → TR + H; fragmentation (FRAG): T + HR → T + H + R. The model was employed in a computer study of the 3-D classical dynamics of abstraction, displacement, and fragmentation in the prototype reaction T + HR and in isotopic variants D + HR, T + DR, and T + HR′ (masses H = 1, D = 2, T = 3, R = 15 and R′ = 31 amu). The quantities calculated were the total reactive cross section as a function of collision energy (2–18 eV), the partial reactive cross section as a function of the initial THR angle α, and the partial reactive cross section as a function of the initial impact parameter b. In addition, product vibrational, rotational, and translational energy distributions, and product angular distributions, were computed. The principal findings were (i) that the abstraction and displacement both constituted direct (as opposed to complex) and concerted (in contrast to sequential) reactions. The outcome of a particular reactive encounter depended on a delicate balance between strong repulsive forces, and, consequently, was no easier to predict for these hot-atom reactions than for thermal ones. (ii) Displacement was favored at intermediate collision energy (4–6 eV) because of the moderating effect that attraction from the heavy R group produced in the speed of T. (iii) At high energies (≳7 eV) a new, stripping, reaction path opened up which made abstraction again dominate displacement; consequently, over all, the mean collision energy for abstraction exceeded that for displacement. This is in accord with recent experiments. (iv) In general, translational energy in the products accounted for the largest part of the collision energy, with a fairly broad energy distribution. (v) At 2–4-eV collision energy the peak of the angular distribution for the molecular product was sideways following abstraction, backwards following displacement; higher collision energy shifted both peaks (especially abstraction) in the forward direction. (vi) Fragmentation accounted for only a few percent of the total reaction at collision energies 25% in excess of that required for formation of T + H + R, but at higher energies (≳7 eV) was comparable in importance to abstraction. (vii) At 2–4-eV collision energy the cross section for abstraction decreased when T was replaced by a mass equivalent to D, H by D, or R by R′. The cross section for displacement also decreased when T was replaced by D, or H by D (providing further evidence of concerted reaction), and increased when R was replaced by R′.
Articles you may be interested inExamination of the Br+HI, Cl+HI, and F+HI hydrogen abstraction reactions by photoelectron spectroscopy of BrHI−, ClHI−, and FHI− J. Chem. Phys. 92, 7205 (1990); 10.1063/1.458208Temperature dependence of the total reaction rates for Cl+HI and Cl+HBr J. Chem. Phys. 67, 3936 (1977); 10.1063/1.435409Energy dependence and isotope effect for the total reaction rate of Cl+HI and Cl+HBrThe dynamics of the thermal (300 0 K) reactions CI+HI->CIH+I and CI+DI->C1D+I have been examined by the classical trajectory method, in 3D. The CI+HI reaction has also been studied at an enhanced (6 kcal mole-I) collision energy. The potential-energy hypersurface was the same as that used earlier O. Chern. Phys. 49,5189 (1968)]. Though it is a highly repulsive energy surface it is able to account for the efficient vibrational excitation of the molecular product for the mass combination characteristic of this reaction. The effect of changing the mass combination from H+LH (heavy+light-heavy; masses mCl+mm) to L+HH (light+heavy-heavy; masses mH+mc12) on the CI+HI surface has been explored using a full 3D set of trajectories at 300 o K. The effect is to markedly reduce the" mixed energy release" responsible for the efficient vibrational excitation on the repulsive surface. Vibrational and rotational excitation in the reaction products is correspondingly diminished, and translational excitation is enhanced. The efficient vibrational and rotational excitation for H+LH (CI+HI), and contrasting behavior for L+HH (H+CI2) have been observed in infrared chemiluminescence experiments. The present findings are therefore in accord with earlier proposals that both these reactions involve predominantly "repulsive" energy release. The computed product angular distribution for the CI+HI reaction at 300 0 K was almost isotropic, in contrast to the exclusively backward-hemisphere scattering for the L+ HH mass combination on the same energy surface. At 6 kcal molel collision energy the computed angular distribution of HCI from the CI+HI reaction showed exclusively sharply-forward scattering, in accord with the results of recent molecular beam experiments O. D. MacDonald and D. R. Herschbach (unpublished)]. Enhanced collision energy gave rise to a small decrease in the computed mean product vibrational excitation, a small increase in mean product rotational excitation and a large increase in product translational excitation. These changes in product energy distribution are in qualitative accord with the findings from infrared chemiluminescence and molecular beam studies at enhanced collision energy. The overall conclusion is that the repulsive LEPS (London, Eyring, Polanyi, Sato) potential-energy hypersurface used here and in our earlier work, provides an acceptable (though not unique) first approximation to the actual interaction potential.
Recombination of Br atoms in Ar was studied by 3D trajectory calculations between 300 and 1500°K. The recombination path via unstable Br–Ar quasidimers was included in the calculations, which yield recombination rate constants in agreement with experiment within a factor of 2, provided that the ArBr Lennard-Jones interaction is of the order of 0.5 kcal/mole.
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