Search results for "SIMULATION"
showing 10 items of 5095 documents
Diatropicity of tetraazanaphthalenes
2006
Tetraazanaphthalenes are diatropic molecules, whose magnetic response to a magnetic field perpendicular to the molecular plane closely resembles that of naphthalene. The out-of-plane component of the magnetic susceptibility tensor and its strong anisotropy can be used as quantifiers of magnetic aromaticity. Maps showing streamlines and modulus of the current density field provide clear evidence for diatropicity of these systems. They also explain the strong anisotropy of carbon and nitrogen magnetic shielding, which is determined by the big out-of-plane component of the nuclear shielding tensor. The electronic ring currents observed in the map deshield the nuclei of ring hydrogens by enforc…
Computational design of biological catalysts
2008
The purpose of this tutorial review is to illustrate the way to design new and powerful catalysts. The first possibility to get a biological catalyst for a given chemical process is to use existing enzymes that catalyze related reactions. The second possibility is the use of immune systems that recognize stable molecules resembling the transition structure of the target reaction. We finally show how computational techniques are able to provide an enormous quantity of information, providing clues to guide the development of new biological catalysts
Experimental and DFT Studies on Competitive Heterocyclic Rearrangements. 3. A Cascade Isoxazole−1,2,4-Oxadiazole−Oxazole Rearrangement
2008
The thermal rearrangements of 3-acylamino-5-methylisoxazoles 1 have been investigated under basic and neutral conditions and interpreted with the support of computational data. The density functional theory (DFT) study on the competitive routes available for the base-catalyzed thermal rearrangement of isoxazoles 1 showed that the Boulton-Katritzky (BK) rearrangement, producing the less stable 3-acetonyl-1,2,4-oxadiazoles 5, is a much more favored process than either the migration-nucleophilic attack-cyclization (MNAC) or the ring contraction-ring expansion (RCRE). In turn, an increase in reaction temperature will promote the MNAC of oxadiazoles 5, producing the more stable 2-acylaminooxazol…
Natural micro-scale heterogeneity induced solute and nanoparticle retardation in fractured crystalline rock.
2011
Abstract We studied tracer (Tritiated Water (HTO); Tritium replaces one of the stable hydrogen atoms in the H 2 O molecule) and nanoparticle (quantum dots (QD)) transport by means of column migration experiments and comparison to 3D CFD modeling. Concerning the modeling approach, a natural single fracture was scanned using micro computed tomography (μCT) serving as direct input for the model generation. The 3D simulation does not incorporate any chemical processes besides the molecular diffusion coefficient solely reflecting the impact of fracture heterogeneity on mass (solute and nanoparticles) transport. Complex fluid velocity distributions (flow channeling and flowpath heterogeneity) evo…
Predicting Skin Permeability by Means of Computational Approaches: Reliability and Caveats in Pharmaceutical Studies
2019
The skin is the main barrier between the internal body environment and the external one. The characteristics of this barrier and its properties are able to modify and affect drug delivery and chemical toxicity parameters. Therefore, it is not surprising that permeability of many different compounds has been measured through several in vitro and in vivo techniques. Moreover, many different in silico approaches have been used to identify the correlation between the structure of the permeants and their permeability, to reproduce the skin behavior, and to predict the ability of specific chemicals to permeate this barrier. A significant number of issues, like interlaboratory variability, experim…
Micelles, Rods, Liposomes, and Other Supramolecular Surfactant Aggregates: Computational Approaches
2017
Surfactants are an interesting class of compounds characterized by the segregation of polar and apolar domains in the same molecule. This peculiarity makes possible a whole series of microscopic and macroscopic effects. Among their features, their ability to segregate particles (fluids or entire domains) and to reduce the surface/interfacial tension is the utmost important. The interest in the chemistry of surfactants never weakened; instead, waves of increasing interest have occurred every time a new field of application of these molecules has been discovered. All these special characteristics depend largely on the ability of surfactants to self-assemble and constitute supramolecular struc…
Rational design of allosteric modulators of the aromatase enzyme: An unprecedented therapeutic strategy to fight breast cancer.
2019
Estrogens play a key role in cellular proliferation of estrogen-receptor-positive (ER+) breast cancers (BCs). Suppression of estrogen production by competitive inhibitors of the enzyme aromatase (AIs) is currently one of the most effective therapies against ER + BC. Yet, the development of acquired resistance, after prolonged treatments with AIs, represents a clinical major concern. Serendipitous findings indicate that aromatase may be non-competitively inhibited by clinically employed drugs and/or industrial chemicals. Here, by performing in silico screening on two putative allosteric sites, molecular dynamics and free energy simulations, supported by enzymatic and cell-based assays, we id…
Quantitative Analysis of the Interactions of Metal Complexes and Amphiphilic Systems: Calorimetric, Spectroscopic and Theoretical Aspects.
2022
Metals and metal-based compounds have many implications in biological systems. They are involved in cellular functions, employed in the formation of metal-based drugs and present as pollutants in aqueous systems, with toxic effects for living organisms. Amphiphilic molecules also play important roles in the above bio-related fields as models of membranes, nanocarriers for drug delivery and bioremediating agents. Despite the interest in complex systems involving both metal species and surfactant aggregates, there is still insufficient knowledge regarding the quantitative aspects at the basis of their binding interactions, which are crucial for extensive comprehension of their behavior in sol…
Fick diffusion coefficients of liquid mixtures directly obtained from equilibrium molecular dynamics.
2011
A methodology for computing Fick diffusivities directly from equilibrium molecular dynamics (MD) simulations is presented and validated for acetone-methanol and acetone-tetrachloromethane liquid mixtures. Fick diffusivities are obtained from Maxwell-Stefan (MS) diffusivities and the so-called thermodynamic factor. MS diffusivities describe the friction between different components, while the thermodynamic factor is the concentration derivative of the activity describing the deviation from ideal mixing behavior. It is important to note that all mutual diffusion experiments measure Fick diffusion coefficients, while molecular simulation provides MS diffusivities. The required thermodynamic fa…
Partial molar enthalpies and reaction enthalpies from equilibrium molecular dynamics simulation
2014
We present a new molecular simulation technique for determining partial molar enthalpies in mixtures of gases and liquids from single simulations, without relying on particle insertions, deletions, or identity changes. The method can also be applied to systems with chemical reactions. We demonstrate our method for binary mixtures of Weeks-Chandler-Anderson particles by comparing with conventional simulation techniques, as well as for a simple model that mimics a chemical reaction. The method considers small subsystems inside a large reservoir (i.e., the simulation box), and uses the construction of Hill to compute properties in the thermodynamic limit from small-scale fluctuations. Results …