Interaction and reaction of the hydroxyl ion with β-d-galactose and its hydrated complex: an ab initio molecular dynamics study

Abstract

The interaction of OH(-) with the sugar β-D-galactose is studied computationally, with Ab Initio Molecular Dynamics (AIMD) as the prime tool. The main findings are: (1) the OH(-) abstracts a proton from the sugar in a barrier-less process, yielding H(2)O and a Deprotonated beta-d-Galactose anion, (Dep-beta-D-G)(-). (2) This reaction can be reversed when two additional H(2)O molecules are present in the sugar. (3) At 500 K, a ring-opening reaction occurs in (Dep-beta-D-G)(-) within a timescale of 10 ps. The (neutral) sugar itself is stable over this timescale, and well beyond. This indicates that OH(-) can catalyze the degradation of β-d-galactose. Implications of this process are briefly discussed.

Experimental and Theoretical Study of Aqueous cis-Pinonic Acid Photolysis

“…However, it should be adequate for qualitatively testing the effect of solvent molecules on photochemistry. Indeed, past studies demonstrated that already one water molecule can have a large effect on the photolysis dynamics. − It would certainly be of great interest to model the hydrated PA system by a larger cluster, but this is currently not computationally feasible. A comparison of the results of calculations for PA hydrated with zero, one and five molecules should provide a trend for the effect of the solvent, a strategy that proved to be useful in previous studies.…”

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.…”