Quantum Mechanical Charge Field Molecular Dynamics Research Articles

A hybrid forces Quantum Mechanical Charge Field Molecular Dynamics of Cs+ ion in aqueous ammonia: A solvation lability, “structure breaking” phenomenon and hydrogen bond properties

AbstractThe dynamics and structure of Cs+ solvation in an aqueous ammonia solution have been investigated using the Quantum Mechanical Charge Field Molecular Dynamics (QMCF‐MD) simulation method. The system contained 18.6% ammonia in aqueous solution at 298.15 K. The QM region was set to a radius of 7.0 Å to include the first and second solvation shells. The Hartree‐Fock (HF) level was applied to calculate the ion‐ligand and ligand–ligand interactions in the QM region using the LANL2DZ‐ECP basis set for the ion and DZP‐Dunning for the ligands. The radial distribution revealed only one solvation shell, indicating a labile solvation structure. The various coordination number of ligands suggests an instant exchange between them. The mean residence times of 1.29 and 0.9 ps were less than in the pure water and liquid ammonia system, indicating higher mobility ligands of the aqueous ammonia system. The preferential factor 0.55 supports the hypothesis that the Cs+ ion prefers to be dissolved in water. As the ligands moves further away from the ion, the observed number of hydrogen bonds increases, revealing the “structure‐breaking” property of the Cs+ ion. The minimum angle ligand‐ion‐ligand tends to be higher near the ion, confirming this phenomenon.

Hybrid Forces Molecular Dynamics on the Lability, Dynamics and “Structure Breaking Effect” of Cs+ in Liquid Ammonia

Abstract The lability, dynamics of the first solvation shell, and structure breaking effect properties of Cs+ in liquid ammonia have been evaluated using Quantum Mechanical Charge Field Molecular Dynamics (QMCF-MD) simulation. The system was conducted in a simulation box containing 593 ammonia molecules with a density of 0.690 g/cm3. The Hartree-Fock level of theory was employed to calculate the interaction of the particles in the QM region using LANL2DZ-ECP and DZP (Dunning) basis set for ion and ligands, respectively. The two solvation regions were observed, and the non-single coordination number confirmed a labile solvation structure. The first solvation shell predominantly by [Cs(NH3)9]+ and the angular distribution function (ADF) confirmed a distorted capped square antiprism geometry. The mean residence time of 1.57 ps and reverse sustainability of 3.1 are more dynamic than the “self-solvation” of ammonia, indicating structure breaking effect by Cs+.

Hydration of Closely Related Manganese and Magnesium Porphyrins in Aqueous Solutions: Ab Initio Quantum Mechanical Charge Field Molecular Dynamics Simulation Study.

To the best of our knowledge, the current study based on ab initio quantum mechanical charge field molecular dynamics (QMCF-MD) is the first to explore the difference in the hydration behavior between Mn(II)- and Mg(II)-associated porphyrins (Mn(II)-POR and Mg(II)-POR) in aqueous solution. The simulation study highlights similar and dissimilar characteristics of the structural, dynamical, and thermodynamical properties of these closely related metals bound to porphyrins in aqueous solution. The structural analysis is based on radial and angular distribution functions, coordination number distributions, and angular-radial distributions. Both hydrated systems demonstrate similar pentacoordinated structures formed via the axial coordination of one water molecule to the metal ion in addition to the four nitrogen atoms of the porphyrin ring. However, in the case of Mn(II)-POR, the formation of a distorted square pyramidal geometry was observed. It was envisaged as a weak coordination of the water molecule to the Mn(II) atom and thus higher atomic fluctuation for all atoms in contrast to that for the hydrated Mg(II)-POR. The dynamical data in terms of the mean residence times, velocity autocorrelation function, free energy, and other parameters revealed the difference in the metal binding effect because the Mn(II) atom was observed to inhibit H-bond formation more than the presence of Mg(II) atoms in the core of the porphyrin. The current study thus highlights the significant differences in the structural and dynamical properties of Mn(II)- and Mg(II)-associated porphyrin systems.

Hydration of iron-porphyrins: ab initio quantum mechanical charge field molecular dynamics simulation study.

The ab initio quantum mechanical charge field molecular dynamics (QMCF-MD) simulation approach was successfully applied to Fe2+-P and Fe3+-P in water to evaluate their structural, dynamical and energetic properties. Based on the structural data, it was found that Fe2+-P accommodates one water molecule in the first coordination sphere of the Fe2+ ion including the four nitrogen atoms of the porphyrin system coordinating with central metal species. On the other hand, two water molecules were coordinated to Fe3+-P, thus forming a hexa-coordinated species. Comparison of dynamical properties such as the vibrational power spectrum and ligand mean residence times to other metal-free porphyrin systems demonstrate the ions' influence on the hydration structure, enabling a characterisation of the strong interaction of the ions which greatly reduces the hydrogen bonding potential of the complex. The association of water molecules with the metal ions in both solutes was quantified by computing the free energy of binding obtained via the potential of mean force. This further confirmed the strong association of water to the metal ions which was conversely weak as inferred from the energetic data for the Fe2+-P system.

Palladium(ii) in liquid ammonia: an investigation of structural and dynamical properties by applying quantum mechanical charge field molecular dynamics (QMCF-MD).

The structural and dynamical properties of Pd2+ in liquid ammonia have been investigated via quantum mechanical charge field molecular dynamics. Similar to the case of aqueous Pd2+, a six-fold coordination polyhedron in the form of a tetrahedrally elongated octahedron is observed with two ligands in axial positions forming an extended first shell. To highlight the difference in solvation between the aqueous and ammonia case a selection based on the angular-radial distribution with respect to the well-known square planar motif was applied also providing a detailed understanding of ligand exchange between the extended first and second shells. All structural properties resulting from this investigation compare well with the available solid-state data of various N-containing complexes. From the dynamical perspective, Pd2+ in liquid ammonia forms a more flexible complex with a higher rate of ligand exchange than that of its aqueous counterpart.

Structure and dynamics of Ni2+ in liquid ammonia: A quantum mechanical charge field molecular dynamics (QMCF-MD) study

An investigation of structural and dynamical properties of Ni2+ in liquid ammonia has been carried out via Quantum Mechanical Charge Field Molecular Dynamics. By extending the quantum mechanical region to include first and second solvation shell, a more realistic representation of the system was achieved yielding improved results on present computational facilities. The structural results obtained from the 16ps trajectory agree well with experimental investigations for various nitrogen-containing Ni2+ systems. Detailed analysis of mean residence time and vibrational properties highlights a rather flexible structure of the first and second shells compared to Ni2+ in aqueous solution.

Revisiting structure and dynamics of Ag+ in 18.6% aqueous ammonia: An ab initio quantum mechanical charge field simulation

Structures and dynamics of Ag+ in 18.6% aqueous ammonia have been studied using Quantum Mechanical Charge Field Molecular Dynamics (QMCF-MD) simulation at the Hartree–Fock (HF) level theory employing LANL2DZ ECP basis set for Ag+ and Dunning DZP for solvent molecules. Structural properties are in excellent agreement with previous QM/MM and experiments studies. [Ag(NH3)2(H2O)3]+ was found as dominant species during simulation time. For 20ps of simulation time, a labile first solvation shell was observed with both fast ammonia and water ligands exchanges. QMCF-MD framework describes first solvation shell more labile than conventional QM/MM MD simulation.

Thulium(III) and ytterbium(III) in aqueous solution ab initio quantum mechanical charge field molecular dynamics studies

Hydration properties of trivalent thulium and ytterbium ions in aqueous solution are investigated via quantum mechanical charge field molecular dynamics (QMCF-MD) simulations. The QMCF-MD formalism is a special type of QM/MM simulation, where the chemically most relevant part of the system – in this case the ion with its first and second hydration shells – is treated by quantum mechanics. The mean ionO distances and the average coordination numbers of the first hydration shells are compared with experimental EXAFS data. Mean ligand residence times, vibrational frequencies and force constants were evaluated to characterise the dynamics of the systems.

The lanthanoid hydration properties beyond the ‘Gadolinium Break’: Dysprosium (III) and holmium (III), an ab initio quantum mechanical molecular dynamics study

A theoretical study of dysprosium(III) and holmium(III) in aqueous solution based on a quantum mechanical charge field-molecular dynamics (QMCF-MD) simulation is presented. The obtained structural and dynamical data were found to be in good agreement with several experimental and theoretical data. It is shown that the coordination number is constantly switching between eight and nine adopting square antiprismatic and tricapped trigonal prismatic configurations, thus supporting the interpretation of experimental data.

The hydration properties of Gd(III) and Tb(III): An ab initio quantum mechanical molecular dynamics study

The quantum mechanical charge-field molecular dynamics (QMCF-MD) simulation method was employed to study the hydration properties of gadolinium(III) and terbium(III). Slight differences of the solvation shells’ structural and dynamical properties were discovered. While the LnO radial distribution functions are in excellent agreement with recent experiments, average coordination numbers of 8.5 (Gd) and 8.4 (Tb) were found. Vivid ligand exchange dynamics along with rapid intrashell rearrangements were observed, underlined by mean residence times in the picosecond range, which is characteristic for trivalent lanthanoides according to quantum mechanical simulations. Vibrational analysis yielded ion-water force constants below 100Nm−1.

Lithium(I) in liquid ammonia: A quantum mechanical charge field (QMCF) molecular dynamics simulation study

The solvation of Li(I) in liquid ammonia has been investigated by an ab initio quantum mechanical charge-field molecular dynamics (QMCF-MD) simulation. Being the first simulation of a metal cation in liquid ammonia employing this methodology, the work yields a wide range of accurate structural and dynamical data. Li(I) is tetrahedrally coordinated by four ammonia molecules in the first solvation shell at a distance of 2.075Å. Two ligand exchange attempts have been observed within 12ps of simulation time. The second solvation shell shows a more labile structure with numerous successful exchanges. The results are in excellent agreement with experiments.

The hydration properties of Eu(II) and Eu(III): An ab initio quantum mechanical molecular dynamics study

A comparison of the hydration characteristics of di- and trivalent europium ions in aqueous solution is presented. The established quantum mechanical charge-field molecular dynamics (QMCF-MD) approach yielded two 30ps simulations. Significant differences among the two species were found in the Eu–O radial distribution functions, both in good agreement with experiments. The first shell coordination numbers of 8.1 and 8.9 were observed for Eu(II) and Eu(III), respectively. The mean residence time of first shell ligands differ by more than one order of magnitude, the divalent ion's hydration shell being more flexible, which is underlined by a weak ion-water bond strength.

Ionized [formula omitted] and [formula omitted] in aqueous environment: Ab initio QMCF-MD studies

Ab initio quantum mechanical charge field molecular dynamics (QMCF-MD) simulations were performed for CO2+ and SO2+ in water at the restricted open-shell Hartree–Fock (ROHF) level of theory employing Dunning DZP basis sets for solute and solvent molecules. Simulation data of these hydrated ionic species were compared to their corresponding neutral precursors, CO2 and SO2 illustrating contrasting structures and dynamical behavior. Hydrated CO2+ is subject to weaker hydration than CO2 whereas SO2+ associates with water molecules via stronger H-bonds than SO2, CO2+ and CO2 molecules. Ionization of both gases also leads to a different relative influence on the hydration behavior in aqueous environment reflected by COwat and SOwat mean distances of ∼3.1Å and ∼2.7Å in hydrated CO2+ and SO2+, respectively. In a cloudy atmosphere hydrated CO2+ and SO2+ can produce other oxidized species, which are thought to be partly implicated in earth’s temperature activity.

Characteristics of selenate in aqueous solution – An ab initio QMCF-MD study

An ab initio quantum mechanical charge field molecular dynamics (QMCF-MD) study of the selenate ion in water was performed at the Hartree Fock/6-31G (d,p) level of theory. The intramolecular geometry, structure and dynamics of the hydration shell and the vibrational frequency modes calculated via velocity autocorrelation functions are presented. The resulting bond distances as well as angles and vibrational frequencies are in good agreement with experimental data. The structure and dynamics reveal the hydrogen bonding network between the ion and neighboring water molecules and exchange processes in the hydration sphere characterize the ion as a structure-forming anion.

Ab initio quantum mechanical simulations confirm the formation of all postulated species in ionic dissociation

A single sodium chloride molecule in aqueous solution was simulated by the ab initio quantum mechanical charge field-molecular dynamics (QMCF-MD) approach. During a series of simulations the solvated molecule (CIP), dissociated solvated ions and - most noticeably - a solvent separated ion pair (SSIP) were observed and the structural and dynamical characteristics of these systems were investigated. In addition to a detailed structural analysis of the observed species, vibrational spectra and charge distributions were calculated to elucidate the mechanism of the NaCl dissociation.

A Comparative Quantum Mechanical Charge Field Study of Uranyl Mono- and Dicarbonate Species in Aqueous Solution

A theoretical study of the structure and dynamics of the uranyl mono- and dicarbonate species in aqueous solution employing the quantum mechanical charge field-molecular dynamics (QMCF-MD) method is presented. The obtained structural and dynamical data were found to be in good agreement with several experimental data and theoretical investigations available in the literature. The five-fold coordination pattern observed for the equatorially bounded ligands of the uranyl ion was found to deviate from the results of a number of previous studies based on quantum chemical cluster calculations and classical molecular dynamics studies, however. The reason for the different description of the system can be seen on the one hand in the capability of QM/MM-type simulations to take charge transfer, polarization, and many-body effects into account, while the presence of a large number of MM solvent molecules ensures that the simulation system mimics the environment in the bulk of a liquid. In addition to pair, three-body and angular distributions, the use of spatial density data enabled a detailed characterization of the three-dimensional arrangement of ligands in the vicinity of the complex. Further analysis of dynamical data such as hydrogen-bond correlation functions and mean lifetime analysis enabled a detailed characterization of the properties of the complexes in aqueous solution. It could be shown that the bulk-oriented oxygen atoms of the carbonate ions form strong hydrogen bonds with bulk molecules, while the tendency of the oxygen atoms of the uranyl(VI) show decreasing tendency to form hydrogen bonds upon complexation.

Erbium(III) in Aqueous Solution: An Ab Initio Molecular Dynamics Study

Structural and dynamical properties of the erbium(III) ion in water have been obtained by means of ab initio quantum mechanical charge field molecular dynamics (QMCF-MD) simulations for the ground state and an excited state. The quality of the simulations has been monitored by recording UV/vis and Raman spectra of dilute solutions of ErCl3 and Er(NO3)3 in water and by comparison with EXAFS data from literature. Slight deviations between these data can be mainly attributed to relativistic effects, which are not sufficiently considered by the methodological framework. In both simulations, a mixture of coordination numbers eight and nine and a ligand exchange on the picosecond range are observed. The strength of the Er-ligand bond is considerably lower than that of trivalent transition metal ions but higher than that for La(III) and Ce(III) in aqueous solution. The main difference between ground state and excited state is the ligand exchange rate of the first shell. The second hydration shell is stable in both cases but with significantly different properties.

Structure and dynamics of the Th4+-ion in aqueous solution – An ab initio QMCF-MD study

An ab initio quantum mechanical charge-field molecular dynamics simulation of the tetravalent thorium ion in aqueous environment is presented. Including the first and second hydration shell in the quantum mechanical treatment to enhance accuracy, this study yields very good results for a wide range of characteristics, as compared to experimental data. 20ps of simulation time were used to investigate structural and dynamical properties of the hydrate by numerous methods, including radial and angular distribution functions, three-body distribution functions, ligand exchange analysis and vibrational spectra. The hydrate proved stable during the simulation and did not show hydrolysis. The first solvation shell was found to be a very flexible one, with a number of intrashell ligand rearrangements occurring along the simulation. The data of the simulation also indicated the existence of a third hydration layer. Vibrational analysis yielded an average ion–oxygen frequency of 420cm−1, which is in excellent agreement with experimental data.

Dynamics of ligand exchange mechanism at Cu(II) in water: An ab initio quantum mechanical charge field molecular dynamics study with extended quantum mechanical region

Ab initio quantum mechanical charge field molecular dynamics (QMCF-MD) were successfully applied to Cu(II) embedded in water to elucidate structure and to understand dynamics of ligand exchange mechanism. From the simulation studies, it was found that using an extended large quantum mechanical region including two shells of hydration is required for a better description of the dynamics of exchanging water molecules. The structural features characterized by radial distribution function, angular distribution function and other analytical parameters were consistent with experimental data. The major outcome of this study was the dynamics of exchange mechanism and reactions in the first hydration shell that could not be studied so far. The dynamical data such as mean residence time of the first shell water molecules and other relevant data from the simulations are close to the results determined experimentally. Another major characteristic of hydrated Cu(II) is the Jahn-Teller distortion which was also successfully reproduced, leading to the final conclusion that the dominating aqua complex is a 6-coordinated species. The ab initio QMCF-MD formalism proved again its capabilities of unraveling even ambiguous properties of hydrated species that are far difficult to explore by any conventional quantum mechanics/molecular mechanics (QM/MM) approach or experiment.

Combined Ab Initio Computational and Infrared Spectroscopic Study of the cis- and trans-Bis(glycinato)copper(II) Complexes in Aqueous Environment.

The cis- and trans-bis(glycinato)copper(II) complexes in aqueous solution have been investigated by means of a combined theoretical and experimental approach. The conducted quantum mechanical charge field molecular dynamics (QMCF-MD) studies, being the first quantum mechanical simulations of organometallic complexes by this method, yielded accurate structural details of the investigated isomers as well as novel dynamic data, which has successfully been confirmed and extended by subsequent mid-infrared measurements. The spectroscopic results, critically assessed by adjacent multivariate data analysis, indicate an isomeric stability at ambient conditions, vanishing at elevated temperatures.