Search results for "reaktiomekanismit"

Scalable Constant pH Molecular Dynamics in GROMACS

2022

Molecular dynamics (MD) computer simulations are used routinely to compute atomistic trajectories of complex systems. Systems are simulated in various ensembles, depending on the experimental conditions one aims to mimic. While constant energy, temperature, volume, and pressure are rather straightforward to model, pH, which is an equally important parameter in experiments, is more difficult to account for in simulations. Although a constant pH algorithm based on the λ-dynamics approach by Brooks and co-workers [Kong, X.; Brooks III, C. L. J. Chem. Phys.1996, 105, 2414–2423] was implemented in a fork of the GROMACS molecular dynamics program, uptake has been rather limited, presumably due to…

Nanoscale etching of III-V semiconductors in acidic hydrogen peroxide solution: GaAs and InP, a striking contrast in surface chemistry

2019

In this study of nanoscale etching for state-of-the-art device technology, the importance of surface chemistry, in particular the nature of the surface oxide, is demonstrated for two III-V materials. Striking differences in etching kinetics were found for GaAs and InP in sulphuric and hydrochloric acidic solutions containing hydrogen peroxide. Under similar conditions, etching of GaAs was much faster, while the dependence of the etch rate on pH, and on H2O2 and acid concentrations also differed markedly for the two semiconductors. Surface analysis techniques provided information on the product layer present after etching: strongly non-stoichiometric porous (hydr)oxides on GaAs and a thin st…

Oxidative Dehydrogenation of Ethanol on Gold : Combination of Kinetic Experiments and Computation Approach to Unravel the Reaction Mechanism

2021

Abstract Selective alcohol dehydrogenation on heterogeneous catalysts is a key industrial reaction for production of aldehydes, ketones, and carboxylic compounds. Design of catalysts with improved activity and selectivity requires understanding of the reaction mechanism and kinetics. Herein, experiments, density functional theory (DFT) and kinetic modelling were combined to elucidate the mechanism and kinetics of ethanol oxidative dehydrogenation to acetaldehyde on gold catalysts. Catalytic experiments clearly emphasized the role of oxygen in this reaction. Ethanol conversion was rather independent on the gold cluster size. Formation of minor products, acetic acid and ethyl acetate was stru…

Experimental and computational investigation on the formation pathway of [RuCl2(CO)2(ERR′)2] (E = S, Se, Te; R, R′ = Me, Ph) from [RuCl2(CO)3]2 and E…

2022

The pathways to the formation of the series of [RuCl2(CO)2(ERR′)2] (E = S, Se, Te; R, R′ = Me, Ph) complexes from [RuCl2(CO)3]2 and ERR′ have been explored experimentally in THF and CH2Cl2, and computationally by PBE0-D3/def2-TZVP calculations. The end-products and some reaction intermediates have been isolated and identified by NMR spectroscopy, and their crystal structures have been determined by X-ray diffraction. The relative stabilities of the [RuCl2(CO)2(ERR′)2] isomers follow the order cct > ccc > tcc > ttt ≈ ctc (the terms c/t refer to cis/trans arrangement of the ligands in the order of Cl, CO, and ERR′). The yields were rather similar in both solvents, but the reactions were signi…

Best Practices in Constant pH MD Simulations: Accuracy and Sampling

2022

Various approaches have been proposed to include the effect of pH in molecular dynamics (MD) simulations. Among these, the λ-dynamics approach proposed by Brooks and co-workers [Kong, X.; Brooks III, C. L. J. Chem. Phys.1996, 105, 2414−2423] can be performed with little computational overhead and hfor each typeence be used to routinely perform MD simulations at microsecond time scales, as shown in the accompanying paper [Aho, N. et al. J. Chem. Theory Comput.2022, DOI: 10.1021/acs.jctc.2c00516]. At such time scales, however, the accuracy of the molecular mechanics force field and the parametrization becomes critical. Here, we address these issues and provide the community with guidelines on…

Detailed modeling of the kraft pulping chemistry : carbohydrate reactions

2020

The article introduces a detailed model for carbohydrate chemistry in kraft pulping. This article is continuation to the modeling work carried out for hot water extraction and chemical pulp bleaching. The model includes galactoglucomannan, xylan, and cellulose acid–base equilibria, in addition to peeling, stopping, and alkaline hydrolysis reactions of the same carbohydrates, as well as hexenuronic acid formation and degradation reactions. The Arrhenius parameters were applied from the literature or regressed against experimental data in the present study. The model is very successful in predicting the experimental data of carbohydrate reactions during kraft pulping. Many features of the pul…

Mukaiyama-Michael reactions with α-substituted acroleins - a useful tool for the synthesis of the pectenotoxins and other natural product targets

2013

Conformational-Dependent Photodissociation of Glycolic Acid in an Argon Matrix

2023

Ultraviolet-induced photodissociation and photo-isomerization of the three most stable conformers (SSC, GAC, and AAT) of glycolic acid are investigated in a low-temperature solid argon matrix using FTIR spectroscopy and employing laser radiation with wavelengths of 212 nm, 226 nm, and 230 nm. The present work broadens the wavelength range of photochemical studies of glycolic acid, thus extending the understanding of the overall photochemistry of the compound. The proposed kinetic model for the photodissociation of glycolic acid proceeds from the lowest energy conformer (SSC). The model suggests that ultraviolet light induces isomerization only between the SSC and GAC conformers and between …

Understanding selective reduction reactions with heterogeneous Pd and Pt : climbing out of the black box

2016

Carboxylate catalyzed isomerization of β,γ‐unsaturated N-acetylcysteamine thioesters

2022

We demonstrate herein the capacity of simple carboxylate salts – tetrametylammonium and tetramethylguanidinium pivalate – to act as catalysts in the isomerization of β,γ-unsaturated thioesters to α,β-unsaturated thioesters. The carboxylate catalysts gave reaction rates comparable to those obtained with DBU, but with fewer side reactions. The reaction exhibits a normal secondary kinetic isotope effect ( k 1H / k 1D = 1.065±0.026) with a β,γ−deuterated substrate. Computational analysis of the mechanism provides a similar value ( k 1H / k 1D = 1.05) with a mechanism where γ-reprotonation of the enolate intermediate is rate determining. peerReviewed