When a proton attacks cellobiose in the gas phase: ab initio molecular dynamics simulations

Beyond a solvent: the roles of 1-butyl-3-methylimidazolium chloride in the acid-catalysis for cellulose depolymerisation

“…Considering the number of short- and long-range interactions that may be established between the cellulosic chains, one could envisage that such environments could very well be solvating H 3 O + species, and assisting the proton transfer mechanism. 67,68 More importantly, in the cases that H-bonds can be established between [H + ]-donor and [H + ]-acceptor, the H + transfer reactions are very fast and essentially diffusion controlled. Tentatively, the solvation of H 3 O + species by the polymeric environment could stabilise the H + species in the surroundings of the glycosidic bond.…”

“…Tentatively, the solvation of H 3 O + species by the polymeric environment could stabilise the H + species in the surroundings of the glycosidic bond. In this situation, the protonated glycosidic bond would live for a longer time, 68 compared to that in cellobiose solution, being thus conducive to improved reaction kinetics because the protonated species must exist throughout the entire reaction coordinate, which involves conformation changes in order to activate the protonated glycosidic bond towards a heterolytic cleavage, as proposed by computational studies. 22,69 …”

Selenium Substitution-Induced Hydration Changes of Crown Ethers As Tools for Probing Water Interactions with Supramolecular Macrocycles in Aqueous Solutions

“…With respect to dynamics, short-time (20 ps) AIMD simulations were performed to probe the noncovalent interactions of C7 / C7Se with water clusters starting from the lowest-energy structures of C7 / C7Se –(H 2 O) 3,10,20 at BLYP-D3/DZVP level with the Goedecker, Teter, and Hutter (GTH) type pseudopotential. Many AIMD simulations using BLYP potential have been reported to reduce computational costs and offered good qualitative results in depicting the noncovalent interactions of hydrogen bonds. − The hydrogen bonds between C7 / C7Se and water clusters (excluding the hydrogen bonds of water–water molecules) were compared, and we counted the total number of hydrogen bonds in each snapshot in the duration of 20 ps (40 000 snapshots in total). As displayed in Figure b, it is found that Se substitution decreases the hydrogen bond interactions between C7Se and water clusters.…”

Selective reactivity of glycosyl cation stereoisomers: the role of intramolecular hydrogen bonding

“…All AIMD simulations in this study were conducted at the B3LYP-D/6-31+G(d,p) level of theory. 50–57 While our previous study of experimentally isolated galactosyl oxocarbenium ion was the first instance when the B3LYP functional was used to calculate the vibrational spectrum with the Fourier transform of the dipole autocorrelation function for a biomolecule, 21 the more popular 34,58–61 and computationally efficient BLYP functional was insufficiently accurate for these glycosyl cation systems as has been reported in other instances. 62–65 The CP2K suite of programs was used to optimize the initial guess structures of the low energy conformers as well as compute the electronic structure ‘on-the-fly’ with the Quickstep module 66 that employs a hybrid Gaussian and plane wave approach to Kohn–Sham density functional theory for ab initio Born–Oppenheimer molecular dynamics.…”