Multiple minima hypersurfaces studies of aluminosilicate hydration

Abstract

Hydrothermal zeolite synthesis is a complex process that is difficult toanalyze experimentally. In this work, the role of water as solvent on the formation of aluminate and aluminosilicate clusters is described by quantum chemical calculations. The multiple minima hypersurfaces approach was used. It combines quantum chemical Hamiltonians for the calculation of the internal energy with statistical modeling and formulae for the calculation of thermodynamic functions of association. The structures of most probable hydration clusters are proposed and some of their association properties are calculated. Ab initio and semiempirical calculations of the structures and relevant reactions of aluminate and aluminosilicate fragments were reported. The results could be employed for an interpretation of the aluminosilicate synthesis. Calculations demonstrate the importance of considering other than the deepest minimum structures, giving a significant role to consider entropy of association.

Recalibrating the calcium trap in amino acid carboxyl groups via classical molecular dynamics simulations

“…In the systems with biomolecules, two Na 2+ were added as background electrolytes to charge balance the 2e-overall charge of the biomolecule. We created four different starting configurations, to enhance the statistics of the results, and a similarity analysis between the initial configurations was conducted to quantify the differences in ion distributions using the Tanimoto distance [30][31][32] . For the Tanimoto distance, the vectors (configuration A and B, equation ( 1)) were ordered according to the distance to the center of mass (COM) of the biomolecule, whereas the pure systems were created by removing L-Asp from the starting configurations.…”

“…We created four different starting configurations, to enhance the statistics of the results, and a similarity analysis between the initial configurations was conducted to quantify the differences in ion distributions using the Tanimoto distance. [30][31][32] For the Tanimoto distance, the vectors (configuration A and B, eqn (1)) were ordered according to the distance to the center of mass (COM) of the biomolecule, whereas the pure systems were created by removing L-Asp from the starting configurations. The vectors contain, first, the distance between the atom closest to the COM of the biomolecule and the other atoms in the CaCO 3 cluster, followed by the distances between the atom closest to this first atom and the other atoms and so on.…”

Cross-talk between amino acid residues and flavonoid derivatives: insights into their chemical recognition

“…[39][40][41] Initial structures were taken from the AM1 global minimum obtained from Multiple Minima Hypersurfaces (MMH) procedures, 36,37 which has been a successful strategy in the last few years for generating initial configurations for intermolecular interaction studies. [44][45][46][47][48][49][50] All details of the MMH procedure have been provided in ref. 36 and 42. In general, MMH combines the calculation of quantum mechanical energies of several, randomly generated, weakly bound clusters with statistical thermodynamics for the selection of the most relevant configurations.…”

“…36 and 42. In general, MMH combines the calculation of quantum mechanical energies of several, randomly generated, weakly bound clusters with statistical thermodynamics for the selection of the most relevant configurations. 36 MMH has been widely used in the last decade [42][43][44][45][46][47][48] to give a good preliminary starting guess of the most important structures of intermolecular interactions which have to be further refined utilizing ab initio methods. In our case, one hundred randomly arranged flavonoids-amino acid clusters were generated and analyzed by MMH procedures.…”