scholarly journals Density functional theory based molecular dynamics study of solution composition effects on the solvation shell of metal ions

2020 ◽  
Vol 22 (28) ◽  
pp. 16301-16313
Author(s):  
Xiangwen Wang ◽  
Dimitrios Toroz ◽  
Seonmyeong Kim ◽  
Simon L. Clegg ◽  
Gun-Sik Park ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Metal Ions ◽  
Density Functional ◽  
Pure Water ◽  
Earth Metal ◽  
Electrolyte Solutions ◽  
Solvation Shell ◽  
Functional Theory ◽  
Composition Effects ◽  
Alkaline Earth Metal Ions

We present an ab initio molecular dynamics study of the alkali metal ions Li+, Na+, K+ and Cs+, and of the alkaline earth metal ions Mg2+ and Ca2+ in both pure water and electrolyte solutions containing the counterions Cl− and SO42−.

Selective complexation of alkaline earth metal ions with nanotubular cyclopeptides: DFT theoretical study

RSC Advances ◽  
2015 ◽  
Vol 5 (3) ◽  
pp. 2305-2317 ◽  
Author(s):  
Fereshte Shahangi ◽  
Alireza Najafi Chermahini ◽  
Hossein Farrokhpour ◽  
Abbas Teimouri
Keyword(s):  
Density Functional Theory ◽  
Metal Ions ◽  
Cyclic Peptides ◽  
Density Functional ◽  
Alkaline Earth ◽  
Theoretical Study ◽  
Earth Metal ◽  
Alkaline Earth Metal ◽  
Functional Theory ◽  
Alkaline Earth Metal Ions

The interaction of alkaline earth metal cations including Be2+, Mg2+, Ca2+, Sr2+ and Ba2+ with cyclic peptides containing 3 or 4 (S) alanine molecules (CyAla3 and CyAla4) was investigated by density functional theory (DFT-CAM-B3LYP and DFT-B3LYP).

Solution chemistry effects on the solvation shell of metal ions

2020 ◽  
Author(s):  
Xiangwen Wang ◽  
Dimitrios Toroz ◽  
Seonmyeong Kim ◽  
Simon Clegg ◽  
Gun-Sik Park ◽  
...  
Keyword(s):  
Metal Ions ◽  
Pure Water ◽  
Solvation Shell ◽  
Solution Chemistry ◽  
Chemical Characteristics ◽  
Velocity Autocorrelation Function ◽  
Ionic Solvation ◽  
General Terms ◽  
Alkaline Earth Metal Ions ◽  
Wide Range

<div> <p>As natural aqueous solutions are far from being pure water, being rich in ions, the properties of solvated ions are of relevance for a wide range of systems, including biological and geochemical environments. We conducted ab initio and classical MD simulations of the alkaline earth metal ions Mg<sup>2+</sup> and Ca<sup>2+</sup> and of the alkali metal ions Li<sup>+</sup>, Na<sup>+</sup>, K<sup>+</sup> and Cs<sup>+</sup> in pure water and electrolyte solutions containing the counterions Cl<sup>–</sup> and SO<sub>4</sub><sup>2–</sup>. Through a detailed analysis of these simulations, this study reports on the effect of solution chemistry (composition and concentration of the solution) to the ion–water structural properties and interaction strength, and to the dynamics, hydrogen bond network, and low-frequency dynamics of the ionic solvation shell. Except for the ion–water radial distribution function, which is weakly dependent on the counter-ions and concentrations, we found that all other properties can be significantly influenced by the chemical characteristics of the solution. Calculation of the velocity autocorrelation function of magnesium ions, for example, shows that chlorine ions located in the second coordination shell of Mg<sup>2+</sup> weaken the Mg(H<sub>2</sub>O)<sub>6</sub><sup>2+</sup> hydration ‘cage’ of the cation. The result reported in this study suggest that ionic solvation shell can be significantly influenced by the interactions between other ions present in solution ions, especially those of opposite charge. In more general terms, the chemical characteristics of the solution, including the balance between ion-solvent and ion-ion interactions, could result in significant differences in behavior and function of the ionic solvation shell.</p> </div>

scholarly journals Hydration interactions beyond the first solvation shell in aqueous phenolate solution

2020 ◽  
Vol 22 (35) ◽  
pp. 19940-19947
Author(s):  
Roberto Cota ◽  
Ambuj Tiwari ◽  
Bernd Ensing ◽  
Huib J. Bakker ◽  
Sander Woutersen
Keyword(s):  
Molecular Dynamics ◽  
Density Functional Theory ◽  
Molecular Dynamics Simulations ◽  
Vibrational Spectroscopy ◽  
Density Functional ◽  
Solvation Shell ◽  
Water Molecules ◽  
Functional Theory ◽  
Ultrafast Vibrational Spectroscopy ◽  
Dynamics Simulations

We investigate the orientational dynamics of water molecules solvating phenolate ions using ultrafast vibrational spectroscopy and density functional theory-based molecular dynamics simulations.

Activation of Cellulose with Alkaline Earth Metals

2021 ◽  
Author(s):  
Gregory Facas ◽  
Vineet Maliekkal ◽  
Matthew Neurock ◽  
Paul Dauenhauer
Keyword(s):  
Density Functional ◽  
Alkaline Earth ◽  
Earth Metal ◽  
Density Functional Theory Calculations ◽  
Alkaline Earth Metal ◽  
Magnesium Ions ◽  
Functional Theory ◽  
Naturally Occurring ◽  
Alkaline Earth Metal Ions ◽  
And Control

Alkaline earth metal ions accelerate the breaking of cellulose bonds and control the distribution of products in the pyrolysis of lignocellulose to biofuels and chemicals. Here, the activation of cellulose via magnesium ions was measured over a range of temperatures from 370 to 430 ⁰C for 20 to 2000 milliseconds and compared with activation of cellulose via calcium, another naturally-occurring alkaline earth metal in lignocellulose materials. The experimental approach of pulse heated analysis of solid/surface reactions (PHASR) showed that magnesium significantly catalyzes cellulose activation with a second order rate dependence on the catalyst concentration. An experimental barrier of 45.6 ± 2.1 kcal mol-1 and a pre-factor of 1.18 x 1016 (mmol Mg2+ / g CD)-2 * s-1 was obtained for the activation of α-cyclodextrin (CD), a cellulose surrogate, for catalyst concentrations of 0.1 to 0.5 mmol Mg+2 per gram of CD. First principles density functional theory calculations showed that magnesium ions play a dual role in catalyzing the reaction by breaking the hydrogen bonds with hydroxymethyl groups and destabilizing the reacting cellulose chain, thus making it more active. The calculated barrier of 47 kcal mol-1 is in agreement with the experimentally measured barriers and similar to that for calcium ion catalysts (~50 kcal mol-1).

Computational Study: Noncovalent Interaction of Cys-Ala Peptide with Alkaline Earth Metal Ions and its Conformation Changes

2021 ◽  
Vol 874 ◽  
pp. 128-135
Author(s):  
Mutiara Anisa Tresnoningtias ◽  
Andre Sasongko Nurwarrohman ◽  
Ihyar Kurnia ◽  
Christian Rinaldy ◽  
Asy’ari Mukhammad ◽  
...  
Keyword(s):  
Metal Ions ◽  
Density Functional ◽  
Alkaline Earth ◽  
Computational Study ◽  
Earth Metal ◽  
Basis Set ◽  
Alkaline Earth Metal ◽  
Interaction Energies ◽  
Water Solvent ◽  
Alkaline Earth Metal Ions

The study of the intermolecular interactions is important to explain the phenomenon occurred on the human body. One of the most important processes that can be studied is the interaction of the peptide with metal ions. In this study, a computational approach was harnessed to predict the interaction and the changes in peptide’s conformation between Cys-Ala peptide which is one of the important amino acids in e-cadherin with some of alkaline earth metal ions. Cys-Ala peptide (Ac-CA-NH2) was used as a molecular model in this calculation. All the molecular structure involved in the interaction was optimized by density functional theory DFT/M06-2X, and basis set 6-31G** to obtain minimum energy, the interaction energies, and the changes in its conformation. The results showed that the interaction energy of Ac-CA-NH2 with alkaline earth metal ions from top to bottom based on the Periodic table is getting higher in a row. The interaction energies of Ac-CA-NH2 with Be2+, Mg2+ and Ca2+ ions are -2.393kcal, -17.489 kcal, and -25.938 kcal respectively. These energies were obtained from the interaction of the peptide with ions in a water solvent. The changes in the peptide's bond length and dihedral angle indicate a conformational change in the Cys-Ala peptide, but it still maintains the trans conformation in its peptide bonds. The results and evaluations of this study may be used for further research considerations and may be applied to enzymes or other peptides that have the Cys-Ala residue.

Solution chemistry effects on the solvation shell of metal ions

2020 ◽  
Author(s):  
Xiangwen Wang ◽  
Dimitrios Toroz ◽  
Seonmyeong Kim ◽  
Simon Clegg ◽  
Gun-Sik Park ◽  
...  
Keyword(s):  
Metal Ions ◽  
Pure Water ◽  
Solvation Shell ◽  
Solution Chemistry ◽  
Chemical Characteristics ◽  
Velocity Autocorrelation Function ◽  
Ionic Solvation ◽  
General Terms ◽  
Alkaline Earth Metal Ions ◽  
Wide Range

<div> <p>As natural aqueous solutions are far from being pure water, being rich in ions, the properties of solvated ions are of relevance for a wide range of systems, including biological and geochemical environments. We conducted ab initio and classical MD simulations of the alkaline earth metal ions Mg<sup>2+</sup> and Ca<sup>2+</sup> and of the alkali metal ions Li<sup>+</sup>, Na<sup>+</sup>, K<sup>+</sup> and Cs<sup>+</sup> in pure water and electrolyte solutions containing the counterions Cl<sup>–</sup> and SO<sub>4</sub><sup>2–</sup>. Through a detailed analysis of these simulations, this study reports on the effect of solution chemistry (composition and concentration of the solution) to the ion–water structural properties and interaction strength, and to the dynamics, hydrogen bond network, and low-frequency dynamics of the ionic solvation shell. Except for the ion–water radial distribution function, which is weakly dependent on the counter-ions and concentrations, we found that all other properties can be significantly influenced by the chemical characteristics of the solution. Calculation of the velocity autocorrelation function of magnesium ions, for example, shows that chlorine ions located in the second coordination shell of Mg<sup>2+</sup> weaken the Mg(H<sub>2</sub>O)<sub>6</sub><sup>2+</sup> hydration ‘cage’ of the cation. The result reported in this study suggest that ionic solvation shell can be significantly influenced by the interactions between other ions present in solution ions, especially those of opposite charge. In more general terms, the chemical characteristics of the solution, including the balance between ion-solvent and ion-ion interactions, could result in significant differences in behavior and function of the ionic solvation shell.</p> </div>

scholarly journals Molecular dynamics simulations of alkaline earth metal ions binding to DNA reveal ion size and hydration effects

2020 ◽  
Vol 22 (10) ◽  
pp. 5584-5596 ◽  
Author(s):  
Makenzie Provorse Long ◽  
Serra Alland ◽  
Madison E. Martin ◽  
Christine M. Isborn
Keyword(s):  
Molecular Dynamics ◽  
Metal Ions ◽  
Molecular Dynamics Simulations ◽  
Alkaline Earth ◽  
Earth Metal ◽  
Alkaline Earth Metal ◽  
Size Dependent ◽  
Alkaline Earth Metal Ions ◽  
Dynamics Simulations ◽  
Ion Size

Classical molecular dynamics simulations reveal size-dependent trends of alkaline earth metal ions binding to DNA are due to ion size and hydration behavior.

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