Search results for "Computation"
showing 10 items of 7362 documents
Ab initiostudy of the mechanism of the atmospheric reaction: NO2+ O3→ NO3+ O2
2003
The atmospheric reaction NO2 + O3 --> NO3 + O2 (1) has been investigated theoretically by using the MP2, G2, G2Q, QCISD, QCISD(T), CCSD(T), CASSCF, and CASPT2 methods with various basis sets. The results show that the reaction pathway can be divided in two different parts at the MP2 level of theory. At this level, the mechanism proceeds along two transition states (TS1 and TS2) separated by an intermediate, designated as A. However, when the single-reference higher correlated QCISD methodology has been employed, the minimum A and the transition state TS2 are not found on the hypersurface of potential energy, which confirms a direct reaction mechanism. Single-reference high correlated and mu…
Understanding the mechanism of polar Diels–Alder reactions
2009
A good correlation between the activation energy and the polar character of Diels-Alder reactions measured as the charge transfer at the transition state structure has been found. This electronic parameter controls the reaction rate to an even greater extent than other recognized structural features. The proposed polar mechanism, which is characterized by the electrophilic/nucleophilic interactions at the transition state structure, can be easily predicted by analyzing the electrophilicity/nucleophilicity indices defined within the conceptual density functional theory. Due to the significance of the polarity of the reaction, Diels-Alder reactions should be classified as non-polar (N), polar…
Oxygen Incorporation Reaction into Mixed Conducting Perovskites: a Mechanistic Analysis for (La,Sr)MnO3 Based on DFT Calculations
2009
Based on DFT calculations of intermediates and transition states, several hypothetical mechanisms for oxygen incorporation into mixed conducting La1-xSrxMnO3{plus minus}d perovskites are discussed. In the most probable mechanism, the rate-determining step comprises the encounter of a highly mobile surface oxygen vacancy and a molecular oxygen adsorbate. Starting from these results, the variation of reaction rates for different materials is explored.
Understanding the Participation of Quadricyclane as Nucleophile in Polar [2σ + 2σ + 2π] Cycloadditions toward Electrophilic π Molecules
2008
The formal [2sigma + 2sigma + 2pi] cycloaddition of quadricyclane, 1, with dimethyl azodicarboxylate, 2, in water has been studied using DFT methods at the B3LYP/6-31G** and MPWB1K/6-31G** levels. In the gas phase, the reaction of 1 with 2 has a two-stage mechanism with a large polar character and an activation barrier of 23.2 kcal/mol. Inclusion of water through a combined discrete-continuum model changes the mechanism to a two-step model where the first nucleophilic attack of 1 to 2 is the rate-limiting step with an activation barrier of 14.7 kcal/mol. Analysis of the electronic structure of the transition state structures points out the large zwitterionic character of these species. A DF…
Approach Matters : The Kinetics of Interfacial Inverse-Electron Demand Diels-Alder Reactions
2017
Rapid and quantitative click functionalization of surfaces remains an interesting challenge in surface chemistry. In this regard, inverse electron demand Diels Alder (IEDDA) reactions represent a promising metal-free candidate. Herein, we reveal quantitative surface functionalization within 15 min. Furthermore, we report the comprehensive effects of substrate stereochemistry, surrounding microenvironment and substrate order on the reaction kinetics as obtained via a combination of XPS and surface-bound mass spectrometry (DART-MS).
Coadsorption of NRR and HER Intermediates Determines the Performance of Ru-N4 toward Electrocatalytic N2 Reduction
2021
Efficiency of the electrochemical N2 reduction reaction (NRR) to ammonia is seriously limited by the competing hydrogen evolution reaction (HER) but our current atomic-scale insight on the factors controlling HER/NRR competition are unknown. Herein we unveil the elementary mechanism, thermodynamics, and kinetics determining the HER/NRR selectivity on the state-of-the-art NRR electrocatalyst, Ru-N4 using constant potential density functional theory calculations (DFT). The calculations show that NRR and HER intermediates coadsorb on the catalyst where HER is greatly suppressed by the NRR intermediates. The first reaction step leading to either *NNH or *H determines the selectivity towards NRR…
A statistical analysis of the three-fold evolution of genomic compression through frame overlaps in prokaryotes
2007
Abstract Background Among microbial genomes, genetic information is frequently compressed, exploiting redundancies in the genetic code in order to store information in overlapping genes. We investigate the length, phase and orientation properties of overlap in 58 prokaryotic species evaluating neutral and selective mechanisms of evolution. Results Using a variety of statistical null models we find patterns of compressive coding that can not be explained purely in terms of the selective processes favoring genome minimization or translational coupling. The distribution of overlap lengths follows a fat-tailed distribution, in which a significant proportion of overlaps are in excess of 100 base…
Equilibrium real gas computations using Marquina's scheme
2003
Marquina's approximate Riemann solver for the compressible Euler equations for gas dynamics is generalized to an arbitrary equilibrium equation of state. Applications of this solver to some test problems in one and two space dimensions show the desired accuracy and robustness
Monitoring Stemness in Long-Term hESC Cultures by Real-Time PCR
2009
Human embryonic stem cells (hESC) involve long-term cultures that must remain undifferentiated. The real-time PCR (RT-PCR) technique allows the relative quantification of target genes, including undifferentiation and differentiation markers when referred to a housekeeping control with the addition of a calibrator that serves as an internal control to compare different lots of reactions during the time. The main aspects will include a minimal number of cells to be analyzed, genes to be tested, and how to choose the appropriate calibrator sample and the reference gene. In this chapter, we present how to apply the RT-PCR technique, protocols for its performance, experimental set-up and softwar…
Evolution-guided evaluation of the inverted terminal repeats of the synthetic transposon Sleeping Beauty.
2018
Abstract Sleeping Beauty (SB) is a synthetic Tc1/mariner transposon that is widely used for genetic engineering in vertebrates, including humans. Its sequence was derived from a consensus of sequences found in fish species including the Atlantic salmon (Salmo salar). One of the functional components of SB, the transposase enzyme, has been subject to extensive mutagenesis yielding hyperactive protein variants for advanced applications. The second functional component, the transposon inverted terminal repeats (ITRs), has so far not been extensively modified, mainly due to a lack of natural sequence information. Importantly, as genome sequences become available, they can provide a rich source …