Search results for "Energy profile"
showing 10 items of 12 documents
Molecular Mechanism of the site-specific self-cleavage of the RNA phosphodiester backbone by a Twister Ribozyme
2017
Published as part of the special collection of articles derived from the 10th Congress on Electronic Structure: Principles and Applications (ESPA-2016). The catalytic activity of some classes of natural RNA, named as ribozymes, has been discovered just in the past decades. In this paper, the cleavage of the RNA phosphodiester backbone has been studied in aqueous solution and in a twister ribozyme from Oryza sativa. The free energy profiles associated with a baseline substrate-assisted mechanism for the reaction in the enzyme and in solution were computed by means of free energy perturbation methods within hybrid QM/MM potentials, describing the chemical system by the M06-2× functional and t…
An ab initio potential energy surface for the C2H2-N2 system
2012
International audience; An ab initio potential energy surface determined at the CCSD(T) level of theory is presented for the van der Waals complex C2H2-N2. Additional calculations performed with the HF- and DFT-SAPT methods compare well with the CCSD(T) results and allow a better understanding of the main features of this interaction potential surface. An expansion of this surface over spherical harmonics has also been performed. The global energy minimum of the complex is obtained for the linear conformation. The T conformations are the least attractive. Such characteristics mainly arise because of the variation, in sign and in absolute value of the electrostatic energy between all these c…
Electronic fluxes during diels-alder reactions involving 1,2-benzoquinones: mechanistic insights from the analysis of electron localization function …
2012
By means of the joint use of electron localization function (ELF) and Thom's catastrophe theory, a theoretical analysis of the energy profile for the hetero-Diels-Alder reaction of 4-methoxy-1,2-benzoquinone 1 and methoxyethylene 2 has been carried out. The 12 different structural stability domains obtained by the bonding evolution theory have been identified as well as the bifurcation catastrophes (fold and cusp) responsible for the changes in the topology of the system. This analysis permits finding a relationship between the ELF topology and the evolution of the bond breaking/forming processes and electron pair rearrangements through the reaction progress in terms of the different ways o…
Results of a literature review on methods for estimating buildings energy demand at district level
2019
Abstract In the framework of distributed energy planning, evaluating reliable energy profiles of different sectors has a prominent role. At the same time, it is a quite challenging task, since the availability of actual energy profiles of buildings at the district level is not widespread. A survey of over 70 studies in scientific literature has been accomplished and a set of criteria has been defined for classifying the selected contributions based on the energy demand data features, source and/or estimation methods, highlighting the ones adopting hourly energy profiles. As final results, tables summarizing the main methods characteristics and a selection of studies providing directly useab…
Nature of the ring-closure process along the rearrangement of octa-1,3,5,7-tetraene to cycloocta-1,3,5-triene from the perspective of the electron lo…
2011
We analyze the behavior of the energy profile of the ring-closure process for the transformation of (3Z,5Z)-octa-1,3,5,7-tetraene 5 to (1Z,3Z,5Z)-cycloocta-1,3,5-triene 6 through a combination of electron localization function (ELF) and catastrophe theory (CT). From this analysis, concepts such as bond breaking/forming processes, formation/annihilation of lone pairs, and other electron pair rearrangements arise naturally through the reaction progress simply in terms of the different ways of pairing up the electrons. A relationship between the topology and the nature of the bond breaking/forming processes along this rearrangement is reported. The different domains of structural stability of …
Theoretical Study on the Diffusion Mechanism of Cd in the Cu-Poor Phase of CuInSe2 Solar Cell Material
2013
We have employed first-principles static and molecular dynamics (MD) calculations with semilocal and screened-exchange hybrid density functionals to study the diffusion of Cd in bulk CuIn5Se8, a copper-poor ordered vacancy compound of CuInSe2. The diffusion mechanism and the underlying kinetics/energetics were investigated by combining ab initio metadynamics simulations and nudged elastic band (NEB) calculations. We found that the migration of Cd occurs via a kick-out of Cu atoms, assisted by the pristine vacancies that are constitutive of this compound, and follows a double-hump energy profile. The rate-limiting step has a barrier of about 1 eV at 0 K but reduces to 0.3 eV at 850 K, pointi…
Unraveling the Reaction Mechanism of Enzymatic C5-Cytosine Methylation of DNA. A Combined Molecular Dynamics and QM/MM Study of Wild Type and Gln119 …
2016
M.HhaI is a DNA methyltransferase from Haemophilus hemolyticus that catalyzes the transfer of a methyl group from S-adenosyl-l-methionine (SAM) to the C5 position of a cytosine. This enzyme is a paradigmatic model for C5 DNA methyltransferases due to its major homology to mammalian enzymes and to the availability of high-resolution structures of the DNA–enzyme complex. In spite of the number of experimental and theoretical analyses carried out for this system, many mechanistic details remain unraveled. We have used full atomistic classical molecular dynamics simulations to explore the protein–SAM–DNA ternary complex, where the target cytosine base is flipped out into the active site for bot…
Improved AMYR program: an algorithm for the theoretical simulation of molecular associations, including geometrical and topological characterization …
1991
Program AMYR, originally written by S. Fraga (University of Alberta, Canada), allows for the calculation of molecular associations using a pair-wise atom-atom potential. The interaction energy is evaluated through a 1/R expansion. Our improved version includes a dispersion energy term in the potential corrected by damping functions, the possibility of carrying out energy minimizations through variable metric methods, as well as the optional calculation of geometrical and topological indices. Program AMYR has been adapted also for high-performance computing and vectorization. An interactive version of the program carries out real-time molecular graphics showing simultaneously the energy prof…
The Grignard Reaction − Unraveling a Chemical Puzzle
2020
More than 100 years since its discovery, the mechanism of the Grignard reaction remains unresolved. Ambiguities arise from the concomitant presence of multiple organomagnesium species and the competing mechanisms involving either nucleophilic addition or the formation of radical intermediates. To shed light on this topic, quantum-chemical calculations and ab initio molecular dynamics simulations are used to study the reaction of CH3MgCl in tetrahydrofuran with acetaldehyde and fluorenone as prototypical reagents. All organomagnesium species coexisting in solution due to the Schlenk equilibrium are found to be competent reagents for the nucleophilic pathway. The range of activation energies …
Managing electrical energy storage systems and shiftable loads with an innovative approach in energy districts
2014
In this work, a power dispatch problem for a system composed of an aggregate of loads and an electrical energy storage system is considered. The approach to solve the optimal dispatch is innovative and shows good performances in limited calculation times. According to the more recent indications coming from the European distributors, the architecture for energy dispatch at distribution level will be hierarchical. The 'Aggregator' is the interface between groups of loads and the energy distributor and sends the individual consumers the desired load profiles, following which the user may gets a discount on the energy bill. On the other hand, the energy tariff may follow a given daily profile …