Ab Initio Quantum Mechanical Charge Research Articles

Deciphering Structural and Dynamical Properties of Hydrated Cobalt Porphyrins via Ab Initio Quantum Mechanical Charge Field Molecular Dynamics Simulation.

The present study successfully implemented the ab initio quantum mechanical charge field molecular dynamics (QMCF MD) formalism for the investigation of structural and dynamical properties of hydrated cobalt-porphyrin complexes. Considering the significance of cobalt ions in biological systems (for instance, vitamin B12), which reportedly incorporate cobalt ions in a d6, low spin, +3 state chelated in the corrin ring, an analog of porphyrin, the current study is focused on cobalt in the oxidation states +2 and +3 bound to the parent porphyrin lead structures embedded in an aqueous solution. These cobalt-porphyrin complexes were investigated in terms of their structural and dynamical properties at the quantum chemical level. The structural attributes of these hydrated complexes revealed the contrasting features of the water binding to these solutes, including a detailed evaluation of the associated dynamics. The study also yielded notable findings in regard to the respective electronic configurations vs coordination, which suggested that Co(II)-POR possesses a 5-fold square pyramidal coordination geometry in an aqueous solution containing the metal ion coordinating to four nitrogen atoms of the porphyrin ring and one axial water as the fifth ligand. On the other hand, high-spin Co(III)-POR was hypothesized to be more stable due to the smaller size-to-charge ratio of the cobalt ion, but the high-spin complex demonstrated unstable structural and dynamical behavior. However, the corresponding properties of the hydrated Co(III)LS-POR revealed a stable structure in an aqueous solution, thus suggesting the Co(III) ion to be in a low-spin state when bound to the porphyrin ring. Moreover, the structural and dynamical data were augmented by computing the free energy of water binding to the cobalt ions and the solvent-accessible surface area, which provide further information on thermochemical properties of the metal-water interaction and the hydrogen bonding potential of the porphyrin ring in these hydrated systems.

Can’t we negotiate the importance of electron correlation? HF vs RIMP2 in ab initio quantum mechanical charge field molecular dynamics simulations of Cu+ in pure liquid ammonia

The impact of electron correlation in quantum mechanical charge field molecular dynamics (QMCF MD) simulations of Cu+ in pure liquid ammonia has been investigated by comparing the results obtained at the Hartree–Fock (HF) level and via resolution-of-identity second order Møller–Plesset perturbation theory (RIMP2). To achieve a manageable computational demand, a rigid-body solvent model was employed to describe the NH3 molecules. The solvation structures observed in both cases have similar characteristics in which tetrahedral [Cu(NH3)4]+ dominates with average CuN distances of 2.24 (HF) and 2.12 (RIMP2) Å, respectively. The ligand dynamics in the first solvation shell of the RIMP2 simulation are notably higher than in the HF case and resulted in the formation of an intermediate [Cu(NH3)3]+ complex along the sampling period. Electron correlation effects were found to mainly impact the solvent–solvent hydrogen bonding interaction, thereby providing a more accurate description of the structural properties in terms of the average CuN distances along with greatly enhanced ligand exchange dynamics occurring between the first and second solvation shell.

Cu2+ in liquid ammonia-The impact of solvent flexibility and electron correlation in ab initio quantum mechanical charge field molecular dynamics.

The impact of solvent flexibility and electron correlation on the simulation results of Cu2+ in liquid ammonia has been investigated via an ab initio quantum mechanical charge field molecular dynamics (QMCF MD) simulation approach. To achieve this, three different simulation systems were considered in this study, namely Cu2+ in rigid and flexible ammonia at Hartree-Fock (HF) level of theory, as well as resolution of identity second order Møller-Plesset (MP2) perturbation theory in the rigid body case. In all cases, a stable octahedral [Cu(NH3 )6 ]2+ complex subject to dynamic Jahn-Teller distortions without the occurrence of ligand exchange was observed. The Cu2+ - NH3 distance in the first shell agrees well with the experimental and other theoretical data. In all three cases, the structural data shows that the rigid-body ammonia model in conjunction with the HF level of theory provides accurate data for the first solvation shell, while at the same time, the computational demand and thus the achievable simulation time are much more beneficial. The vibrational analysis of the Cu2+ - NH3 interaction yields similar force constants in the three investigated systems indicating that there is no distinct difference on the dynamical properties of the first solvation shell. In addition to the QMCF MD simulations, a number of natural bond orbital (NBO) analyses were carried out, confirming the strong electrostatic character of the Cu2+ - NH3 interaction.

Co3+ and Ir3+ in pure liquid ammonia: Structure and dynamics from ab initio quantum mechanical charge field molecular dynamics

Abstract The solvation properties of Co3+ and Ir3+ in pure liquid ammonia have been investigated via ab initio quantum mechanical charge field molecular dynamics (QMCF MD) simulations. During the simulation time of 20 ps, octahedral [Co(NH3)6]3+ and [Ir(NH3)6]3+ complexes were formed in the first solvation shell without the occurance of ligand exchange. The respective average first shell ion distance of Co3+ and Ir3+ were found to be 2.07 and 2.18 A, respectively. The solvation properties in the first shells of each system are found in excellent agreement with experimental data. A number of ligands were exchanged between the second solvation shell and the bulk phase in both systems along the simulation. The associated mean residence times of NH3 ligands in the second shell are 3.06 and 2.47 ps for Co3+ and Ir3+, respectively.

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.

The Jahn-Teller effect in mixed aqueous solution: the solvation of Cu2+ in 18.6% aqueous ammonia obtained from ab initio quantum mechanical charge field molecular dynamics

Abstract The solvation structure and dynamics of Cu2+ in 18.6 % aqueous ammonia have been investigated using an ab initio quantum mechanical charge field molecular dynamics (QMCF MD) simulation approach at the Hartree–Fock (HF) level of theory applying the LANL2DZ ECP and Dunning DZP basis sets for Cu2+, ammonia and water, respectively. During a simulation time of 20 ps, only NH3 molecules are observed within the first solvation shell of Cu2+, resulting in the formation of an octahedral [Cu(NH3)6]2+ complex. While no exchange of these ligands with the second solvation shell are observed along the simulation, the monitoring of the associated N-Ntrans distances highlight the dynamics of the associated Jahn-Teller distortions, showing on average 2 elongated axial (2.19 Å) and 4 equatorial Cu–N bonds (2.39 Å). The observed structural properties are found in excellent agreement with experimental studies. In addition, an NBO analysis was carried out, confirming the strong electrostatic character of the Cu2+–NH3 interaction.

Investigation of the preferential solvation and dynamical properties of Cu+ in 18.6% aqueous ammonia solution using ab initio quantum mechanical charge field (QMCF) molecular dynamics and NBO analysis

Structural and dynamical properties of Cu+ in 18.6% aqueous ammonia solution at 298.15 K have been investigated via quantum mechanical charge field molecular dynamics (QMCF MD). The QM region was set to a radius of 6.7 Å to include the first and second solvation shell. 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 Cu+N and Cu+O radial distribution functions showed maximum first shell probabilities at distances of 2.23 and 2.30 Å, respectively. Predominantly, four NH3 molecules were found to form a tetrahedral [Cu(NH3)4]+ complex, although the formation of a short-lived intermediate [Cu(NH3)3H2O]+ complex was also observed. The mean residence times of NH3 and H2O ligands in the first solvation shell were estimated as 14.6 ps and 1.3 ps, respectively, reflecting the strong interaction between Cu+ and ammonia as well as the occurrence of rapid water exchange. The vibrational power spectrum of the Cu+N vibration in the first solvation shell revealed a wave number of 252 cm−1 with a corresponding force constant of 43.0 Nm−1. In addition, an NBO analysis was carried out, confirming the strong electrostatic character of the Cu+NH3 and Cu+H2O interaction, and highlighting that the presence of H2O ligands may destabilize the first solvation shell.

Investigation of rubidium(I) ion solvation in liquid ammonia using QMCF-MD simulation and NBO analysis of first solvation shell structure.

Rb(I) ion solvation in liquid ammonia has been studied by an ab initio quantum mechanical charge field molecular dynamics simulation, and the first solvation shell structure has been analyzed using natural bond orbital. The simulation was performed for an ion and 593 ammonia molecules in a box with a length of 29.03Å corresponding to a liquid ammonia density of 0.69g/mL at 235.16K. The quantum mechanical calculation was carried out for atomic interactions in the radius of 6.4Å from the ion using LANL2DZ ECP and DZP (Dunning) basis sets for Rb(I) ion and ammonia respectively. The trajectories of the simulation were analyzed in terms of radial, angular, and coordination number distribution functions, vibration, and mean residence time (MRT). Two solvation shell regions are observed for the Rb(I)-N as well as the Rb(I)-H. The maximum distance of Rb(I)-N in the first solvation shell is in accordance with experimental data where a coordination number of 8 is favorable. A non-single coordination number of the first and second shell indicates dynamic solvation structure. It is confirmed by frequent exchange ligand processes observed within a simulation time of 15ps. The low stabilization energy of donor acceptor ion-ligand interaction with a small Wiberg bond index affirms that the Rb(I)-NH3 interaction is weak electrostatically.

Revisiting structure and dynamics of preferential solvation of K(I) ion in aqueous ammonia using QMCF-MD simulation

Structure and dynamics of preferential solvation of K(I) ion in aqueous ammonia have been reinvestigated using ab initio quantum mechanical charge field (QMCF) molecular dynamics (MD) simulation. The average coordination number of the first solvation consists of 2 ammonia and 4 waters. The mean residence time is less than 2 ps confirming the rapid mobility of ligands. The distance evolution data shows the frequent of ligand exchanges. The second solvation shell shows a more labile structure. The NBO analysis of the first shell structure emphasizes that interaction of K(I)-H2O is stronger than K(I)-NH3. The Wiberg bond confirms a weak electrostatic of ion-ligand interaction.

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.

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.

Hydration of the cyanide ion: an ab initio quantum mechanical charge field molecular dynamics study.

This paper presents an ab initio quantum mechanical charge field molecular dynamics simulation study of the cyanide anion (CN(-)) in aqueous solution where hydrogen bond formation plays a dominant role in the hydration process. Preferential orientation of water hydrogens compared to oxygen atoms was quantified in terms of radial, angular as well as coordination number distributions. All structural results indicate that the water hydrogens are attracted towards CN(-) atoms, thus contributing to the formation of the hydration layer. Moreover, a clear picture of the local arrangement of water molecules around the ellipsoidal CN(-) ion is provided via angular-radial distribution and spatial distribution functions. Apart from the structural analysis, the evaluation of water dynamics in terms of ligand mean residence times and H-bond correlation functions indicates the weak structure making capacity of the CN(-) ion. The similar values of H-bond lifetimes obtained for the NHwat and CHwat bonds indicate an isokinetic behaviour of these H-bonds, since there is a very small difference in the magnitude of the lifetimes. On the other hand, the H-bond lifetimes between water molecules of the hydration shell, and between solute and solvent evidence the slightly stable hydration of the CN(-). Overall, the H-bonding dominates in the hydration process of the cyanide anion enabling it to become soluble in the aqueous environment associated to chemical and biological processes.

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.

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.

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.

The Stability of Bisulfite and Sulfonate Ions in Aqueous Solution Characterized by Hydration Structure and Dynamics

The aqueous solutions of bisulfite (SO(3)H(-)) and sulfonate (HSO(3)(-)) were simulated by the ab initio quantum mechanical charge field molecular dynamics (QMCF MD) formalism. All superimposed trajectories for the atomic coordinates of solutes with three-dimensional alignment here illustrated the reactivities of the ions. Power spectra were evaluated on the basis of the velocity autocorrelation functions (VACFs) with the normal-mode analysis, presenting a higher frequency of the symmetric SO(3) deformation (δ(s)(SO(3))) than the asymmetric SO(3) deformation (δ(as)(SO(3))) modes for the sulfonate ion. The different influence of solvent on the frequency of the O-H and S-H stretching suggests a higher stability of hydrated sulfonate ion. The bisulfite shows a slightly stronger molecular hydration shell than the sulfonate ion with the average number of ion-solvent hydrogen bonds (H-bonds) of 5.3 and 5.0, respectively. Extra water molecules within the molecular hydration shell are found for bisulfite (1.2) and for sulfonate (1.6). The mean residence times for the water ligands classify each ion as a structure maker, while the S-H bond within the sulfonate ion displays a hydrophobic behavior. No tautomerization was observed within the simulation period.

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.