Quantum Mechanical Charge Field Molecular Dynamics Research Articles

Urea in aqueous solution studied by quantum mechanical charge field-molecular dynamics (QMCF-MD)

This work presents a quantum mechanical charge field-molecular dynamics (QMCF-MD) simulation of urea in dilute aqueous solution. Detailed data for structure and dynamics are provided and compared to previous works of other groups. Radial and angular distributions are employed, as well as higher degree spatial investigations, two-dimensional particle mapping, volume maps and the previously proposed SLICE formalism. Information on dynamical properties are presented in the form of hydrogen bond correlation functions and mean lifetime analysis based on weighted Voronoi decomposition. Dihedral and tilt/theta angle distributions substantiate the previous findings of other groups, that urea is far from being planar within aqueous solution. In addition to the analysis of the complete hydration shell, several specific regions of hydration have been identified, for which individual analysis has been performed in terms of hydrogen bond lifetime correlation functions and re-orientational times. A decomposition study based on Laguerre tessellation further investigates the structure and dynamics of the individual hydration layers. It is found that urea does not show properties found in the case of typical structure breaking agents, such as Rb(+) or Cs(+), which is in accordance with spectroscopic data of Rezus and Bakker.

Ab Initio Quantum Mechanical Charge Field Molecular Dynamics Simulation (QMCF-MD) of Bi3+ in Water

The hydration of the Bi(III) ion was determined via an ab initio quantum mechanical charge field molecular dynamics (QMCF-MD) simulation. Ten picosecond sampling was carried out to determine structural and dynamical properties of the Bi(III) ion in aqueous solution. In the first hydration shell, the ion is 9-fold coordinated with a maximum probability of the Bi-O distance at 2.51 Å. In total, 11 exchanges were observed in the first-shell showing associative, dissociative, and interexchange character. As with the dominant existence of 9-fold coordination, the geometry of the Bi(III) ion is in between the tricapped trigonal prism and the capped square antiprism.

Guanidinium in aqueous solution studied by quantum mechanical charge field-molecular dynamics (QMCF-MD)

Structure and dynamics of guanidinium in aqueous solution were examined via a double zeta HF level Quantum Mechanical Charge Field-Molecular Dynamics (QMCF-MD) simulation, as well as two Molecular Mechanics-Molecular Dynamics (MM-MD) simulations, parametrised via the Amber99 parameter set, employing the side chain of arginine as a template. Coulombic parameters were fitted via Mulliken population data of the QM simulation, as well as via the recommended restrained electrostatic potential fit (RESP). Although guanidinium is one of the most weakly hydrated cations yet characterised, its hydration pattern is quite complex and pronounced in the quantum mechanical simulation. The positive charge is mainly located on the central carbon, resulting in strong solute-oxygen coordination. Hydrogen bonds are mainly donated by the amide hydrogens, but are also accepted via the nitrogens to a very low extent. Detailed analysis of structure and dynamics, comparing the applied QM and MM models, provides evidence that the arginine parametrisation leads to highly different results than the quantum mechanical treatment, and that the RESP parametrisation is too polarised.

Carbon dioxide in aqueous environment—A quantum mechanical charge field molecular dynamics study

AbstractStructure and dynamics of a carbon dioxide molecule in water were studied by an ab initio quantum mechanical charge field molecular dynamics (QMCF‐MD) simulation. Radial distribution functions, angular distribution functions, and coordination number distributions as well as dynamical data such as mean ligand residence time and vibrational spectra were utilized for the evaluation of physico–chemical properties of hydrated CO2. These data served for an assessment of hydrogen bonding between solute and solvent molecules. All the results evaluated were compared with available experimental results leading to a good agreement between theoretical and experimental data. The average lifetime of hydrogen bonding between H2 O and CO2 resulted as 0.61 ps, which is higher than the hydrogen bonding lifetime of pure water. The vibrational frequencies were also calculated for all the modes of hydrated CO2 to demonstrate the influence of solvent molecules on the IR spectrum of the solute. © 2010 Wiley Periodicals, Inc. Int J Quantum Chem, 2010

Hydrogen bond formation of formamide and N-methylformamide in aqueous solution studied by quantum mechanical charge field-molecular dynamics (QMCF-MD)

The formation of hydrogen-bonds of formamide and "cis"-N-methylformamide in aqueous solution was examined using double zeta HF level Quantum Mechanical Charge Field-Molecular Dynamics (QMCF-MD) simulations. Basic attributes such as structure and dynamics of the solvates and hydrogen-bonds were studied in particular by means of coordination number distributions, mean residence times and radial distribution functions, on which spatial restrictions in the form of planes and cones were applied. Advanced methods of analysis gave detailed information about the sterical environment and the dynamic behavior of strong and weak hydrogen-bonds formed by the residues. The comparison of both molecules over a sampling period of 12 ps provided information on the influence of methylation of the amide function on molecular and hydration properties.

STRUCTURE OF IRIDIUM(III) HYDRATION BASED ON AB INITIO QUANTUM MECHANICAL CHARGE FIELD MOLECULAR DYNAMICS SIMULATIONS

Structural properties of Iridium(III) hydration have been studied based on an ab initio Quantum Mechanical Charge Field (QMCF) Molecular Dynamics (MD) Simulations. The most chemical-relevant region was treated by ab initio calculation at Hartree-Fock level. For the remaining region was calculated by Molecular Mechanics method. LANL2DZ ECP and DZP Dunning basis sets were applied to Ir3+ ion and water, respectively. The average distance of Ir-O in the first hydration shell is 2.03 Å. The QMCF MD Simulation can detect only one complex structure with coordination number of 6 in the first hydration shell. Bond angle analysis shows that Ir3+ ion hydration in the first hydration shell has octahedral structure.

Structure and Dynamics of the Chromate Ion in Aqueous Solution. An ab Initio QMCF-MD Simulation

An ab initio quantum-mechanical charge-field molecular-dynamics (QMCF-MD) simulation of the chromate ion in aqueous solution at ambient temperature was performed to study the structure and dynamics of this ion and its hydration shell. In contrast to conventional quantum-mechanical molecular-mechanics molecular-dynamics (QM/MM-MD) simulations, the QMCF-MD approach offers the possibility of investigating composite systems with the accuracy of a QM/MM method but without the time-consuming construction of solute-solvent potential functions. The data of the simulation give a clear picture of the first hydration shell of the chromate anion, which consists of 14 water molecules. The mean distance between the oxygen atoms of the chromate and the hydrogen atoms of water is 1.82 A. Each chromate oxygen atom is in average coordinated to 2.6 water molecules. The first-shell mean ligand residence time was evalulated as 2.2 ps; the vibrational frequency of the nu(OH) mode was found to be 185 cm(-1). Several structural parameters such as the radial distribution functions, angular distribution functions, and coordination number distributions enable a full characterization of the embedding of the chromate ion in the solvent water. The dynamics of the hydration structure are described by mean residence times of the water molecules in the first hydration shell, distance plots, and velocity autocorrelation functions.

A Quantum Mechanical Charge Field Molecular Dynamics Study of Fe2+ and Fe3+ Ions in Aqueous Solutions

Ab initio quantum mechanical charge field molecular dynamics (QMCF-MD) simulations have been performed for aqueous solutions of Fe(2+) and Fe(3+) ions at the Hartree-Fock level of theory to describe and compare their structural and dynamical behavior. The structural features of both hydrated ions are characterized by radial distribution functions that give the maximum probability of the ion-O distance for Fe(2+) and Fe(3+) ions at 2.15 and 2.03 A, respectively. The angular distribution functions of both ions prove the octahedral arrangement of six water ligands, whereas the second shells of these ions differ. Both ions show influence on the water molecules beyond the second shells. The structure-forming abilities of both ions are visible from the ligand mean residence times and ion-O stretching frequencies evaluated for both ions. The substantially improved data obtained from these QMCF-MD simulations show better correlation with available experimental results than the conventional quantum mechanics/molecular mechanics molecular dynamics (QM/MM MD) approaches with one hydration shell treated by quantum mechanics.

Structure and dynamics of the UO+2 ion in aqueous solution: an ab initio QMCF-MD study

The quantum mechanical charge field molecular dynamics (QMCF-MD) framework was applied in a simulation of the uranyl(v) ion in aqueous solution. The structure was evaluated on the basis of overall and sectorial radial distribution functions, angular distribution functions, tilt- and Theta-angle distribution functions and coordination number distributions. The cation is strongly coordinated by 4 water ligands at an average distance of 2.51 A, while the oxygen atoms are on average bound to 1.2 water molecules at a distance of 2.9 A. A mean residence time of 2.83 ps was evaluated for the oxygen sites of the uranyl(v) ion. The results are in good agreement with previous experimental and theoretical data on the hydration of similar ions.

Hydrolysis of As(III): A femtosecond process

A Quantum Mechanical Charge Field Molecular Dynamics (QMCF-MD) study of As(III) in aqueous medium was carried out, in order to gain insight into its solvation behavior, both in structural and dynamic aspects. Immediately after the formation of the hydrated As 3 + ion, a two step hydrolysis was observed resulting in the As(OH) 2 + species which seems to be the stable species of As(III) in water.

Germanium(II) in water: An unusual hydration structure results of a QMCF MD simulation

Quantum mechanical charge field (QMCF) molecular dynamics (MD) simulations including first and second hydration shell in the QM region have been performed to describe structural and dynamical properties of Ge(II) in water. The first and second hydration shells were treated by ab initio quantum mechanics at restricted Hartree-Fock (RHF) level. The radial distribution function (RDF) showed the maximum probability of the Ge–O bond length at 2.04 Å, accompanied by an extended first shell located at ∼2.8 Å. A uniquely distorted hydration structure with two tri-pyramidal substructures provides a new basis for the interpretation of the kinetic properties of germanium(II) complexes.

Al(III) Hydration Revisited. An ab Initio Quantum Mechanical Charge Field Molecular Dynamics Study

To assess the novel quantum mechanical charge field (QMCF) molecular dynamics (MD) approach, two simulations of hydrated Al(III) have been carried out, as this system proved to be a well-suited test case for hybrid ab initio/molecular mechanics simulations. Two different population analysis schemes according to Mulliken and Lowdin have been applied to evaluate the atomic charges in the QM region. It is shown that the QMCF MD approach yields a substantially improved description of the system and that, due to the fact that solute-solvent potentials can be renounced, the QMCF MD framework is a more convenient approach to investigate solvated systems compared to conventional ab initio QM/MM MD approaches.

Structure and Dynamics of Sulfate Ion in Aqueous SolutionAn ab initio QMCF MD Simulation and Large Angle X-ray Scattering Study

The hydrated sulfate ion has been characterized in aqueous solution in structural and dynamic aspects using ab initio quantum mechanical charge field (QMCF) molecular dynamics (MD) simulation and large angle X-ray scattering (LAXS) methods. The LAXS data show an average coordination number of the sulfate ion of up to 12 water molecules bound through hydrogen bonding, while the QMCF MD simulation displays a wide range of coordination numbers between 8 and 14 with an average value of approximately 11. The Os...Ow distance cannot be distinguished from the Ow...Ow distance in the LAXS experiment; the weighted mean O...O distance is 2.880(10) A. In the simulation, the Os...Ow and Ow...Ow distances are found to be very similar, namely, 2.86 and 2.84 A, respectively. The S-Os bond and S...Ow distance have been determined by the LAXS experiment as 1.495(6) and 3.61(2) A, respectively, indicating an average nearly tetrahedral S-Os...Ow angle. The approximately 5% deviations of simulation distances (1.47 and 3.82 A) from the experimental ones can probably be ascribed to the neglect of correlation energy in the quantum mechanical method. The mean residence time of water ligands at O atoms, 2.57 ps, is longer than that in pure water, 1.7 ps, characterizing the sulfate ion as a weak structure maker.