DFT:B3LYP ab initio molecular dynamics study of the Zundel and Eigen proton complexes, H5O2+ and H9O4+, in the triplet state in gas phase and solution

Abstract

DFT:B3LYP ab initio molecular dynamics (MD) approach is used to elucidate the properties of the Zundel and Eigen, H5O2+ and H9O4+, proton complexes in the triplet state. The simulation considers the complexes in the gas phase (isolated complexes) and inside the clusters composed of 32, 64, and 128 water molecules, mimicking the behavior of aqueous solutions. MD simulations reveal three distinct periods. For the complex in solutions, the periods are smoothed out. The H5O2+ and H9O4+ complexes in the triplet state undergo structural rearrangements, which eventually result in hydrogen elimination. For the H5O2+, the hydrogen is eliminated from the center of the water cluster, whereas for the H9O4+ it is removed from a near-surface water molecule. The rate of hydrogen elimination decreases with increasing the number of water molecules surrounding the complex.

Mechanism of proton transport in water clusters and the effect of electric fields: A DFT study

“…We obtained the binding energy, which is defined as the energy difference between the optimized dimer and two optimized monomers, of 19.7 kJ/mol which is in good agreement with literature value [30][31][32][33]. In addition, B3LYP was used extensively in previous studies of proton transfer in water environment [34][35][36]. Therefore, the choice of this method seems reasonable for the balance between computing cost and accuracy.…”

Molecular dynamics DFT:B3LYP study of guanosinetriphosphate conversion into guanosinemonophosphate upon Mg2+ chelation of ? and ? phosphate oxygens of the triphosphate tail

“…The initially cool system (0 K) is heated at 10 K steps over 1 ps (this period is not included in the computation), a period traditionally considered to be sufficient for the system to become equilibrated over the sets of quantum and classical parameters in ab initio MD approaches. 26 This slow step-by-step procedure minimizes the risk of breaking thermodynamic equilibrium between different parts of the system (the Mg 21 -GTP subsystem and the water pool (the other subsystem), including different water coordination shells within the cube volume) during its preparation due to further simulation. Subsequent cooling to 0 K occurred in the reverse sequence with the step of À10 K and served the same purpose, to maintain thermodynamic equilibrium between the reaction products and the water pool.…”

Mg spin affects adenosinetriphosphate activity

“…Within the box the water molecules can change their initial positions when the Mg and ATP subsystems begin to approach. The rearrangements in the water environment during the computations, according to previous results [15,30], meet the following limits: R OO  3.60 Å; R OH  2.45 Å;  OHO  45 0 (R OO is the distance between oxygens, R OH is the distance between the oxygen and hydrogen, and  OHO is the angle between two bonds, formed by a hydrogen atom and two oxygen atoms). With these parameters the water molecules can form hydrogen bonds with the ATP on its periphery (up to 12 molecules) and between themselves in the rest water bulk, but the molecules are not allowed to approach each other close.…”