Exploring Structure and Dynamics of the Diaquotriamminezinc(II) Complex by QM/MM MD Simulation

Fatmi, M. Qaiser; Hofer, Thomas S.; Randolf, Bernhard R.; Rode, Bernd M.

doi:10.1021/jp710270z

Cited by 25 publications

(41 citation statements)

References 50 publications

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“…2͒, predict 14 water molecules in the second shell region ͑3.5-4.7 Å͒ and nearly within the large range of values obtained from the analysis of the x-ray data, 45-50 7.6-13.2 waters. This number also agrees well with the results from several prior MD and QM/MM simulations 40,44,[51][52][53][54][55] and within the range of values of the conventional MD simulations. However, compared to these prior simulations our second shell maximum is found to be 5%-10% smaller.…”

Section: A the Hydration Shell Structuresupporting

confidence: 90%

“…Both the full AIMD ͑64 waters͒ and the AIMD/MM ͑one hydration shell͒ simulations give very similar results for the structural parameters and both agree fairly well with available experimental data. We note here that the QM/MM simulations ͑QM region Gaussian basis set Hartree-Fock͒ by Fatmi et al 40 observed significant structural changes in the solvent when extending their QM region to incorporate the second hydration shell of Zn 2+ that are not observed in our results. The extension of the QM region was not found to be necessary in our simulation where we found substantial agreement between the full AIMD and the AIMD/MM for the structure and dynamics with only the inclusion of the first shell.…”

Section: A the Hydration Shell Structurecontrasting

confidence: 44%

“…We note that in a "perfect acceptor" structure there would be 12 second shell waters as in the highly structured Al 3+ ion-water system. 21 The high second shell occupation numbers of classical MD simulations 40,44 suggest that these models have more tetrahedral bonding in the second shell than our simulations.…”

Section: A the Hydration Shell Structurementioning

confidence: 68%

“…The 40,42 In addition, these average distances are expected to be slightly larger than the measured values and static structural ab initio optimizations because the first shell peak in the radial distribution function, g Zn-O ͑r͒, is found to be around 2.13 and 2.15 Å for the AIMD and AIMD/MM, respectively ͑vide infra͒. The peak widths, Zn The comparisons between the full AIMD simulation, the AIMD/MM, and the larger particle number AIMD/MM simulation show remarkable agreement.…”

Section: A the Hydration Shell Structurementioning

confidence: 99%

“…18,19,62 In developing such models, relatively simplified idealizations of the full manybody potential, such as point charges and localized polarization, are used to provide computational efficiency. 18,20,40,44,63 In the AIMD and AIMD/MM simulations, electronic structure is available and can be used to guide the development of these models.…”

Section: Electronic Structure Changes In the Hydration Shellsmentioning

confidence: 99%

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Structure and dynamics of the hydration shells of the Zn2+ ion from ab initio molecular dynamics and combined ab initio and classical molecular dynamics simulations

Cauët

Bogatko

Weare

et al. 2010

The Journal of Chemical Physics

103

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Results of ab initio molecular dynamics ͑AIMD͒ simulations ͑density functional theory+ PBE96͒ of the dynamics of waters in the hydration shells surrounding the Zn 2+ ion ͑T Ϸ 300 K, Ϸ 1 gm/ cm 3 ͒ are compared to simulations using a combined quantum and classical molecular dynamics ͓AIMD/molecular mechanical ͑MM͔͒ approach. Both classes of simulations were performed with 64 solvating water molecules ͑ϳ15 ps͒ and used the same methods in the electronic structure calculation ͑plane-wave basis set, time steps, effective mass, etc.͒. In the AIMD/MM calculation, only six waters of hydration were included in the quantum mechanical ͑QM͒ region. The remaining 58 waters were treated with a published flexible water-water interaction potential. No reparametrization of the water-water potential was attempted. Additional AIMD/MM simulations were performed with 256 water molecules. The hydration structures predicted from the AIMD and AIMD/MM simulations are found to agree in detail with each other and with the structural results from x-ray data despite the very limited QM region in the AIMD/MM simulation. To further evaluate the agreement of these parameter-free simulations, predicted extended x-ray absorption fine structure ͑EXAFS͒ spectra were compared directly to the recently obtained EXAFS data and they agree in remarkable detail with the experimental observations. The first hydration shell contains six water molecules in a highly symmetric octahedral structure is ͑maximally located at 2.13-2.15 Å versus 2.072 Å EXAFS experiment͒. The widths of the peak of the simulated EXAFS spectra agree well with the data ͑8.4 Å 2 versus 8.9 Å 2 in experiment͒. Analysis of the H-bond structure of the hydration region shows that the second hydration shell is trigonally bound to the first shell water with a high degree of agreement between the AIMD and AIMD/MM calculations. Beyond the second shell, the bonding pattern returns to the tetrahedral structure of bulk water. The AIMD/MM results emphasize the importance of a quantum description of the first hydration shell to correctly describe the hydration region. In these calculations the full d 10 electronic structure of the valence shell of the Zn 2+ ion is retained. The simulations show substantial and complex charge relocation on both the Zn 2+ ion and the first hydration shell. The dipole moment of the waters in the first hydration shell is 3.4 D ͑3.3 D AIMD/MM͒ versus 2.73 D bulk. Little polarization is found for the waters in the second hydration shell ͑2.8 D͒. No exchanges were seen between the first and the second hydrations shells; however, many water transfers between the second hydration shell and the bulk were observed. For 64 waters, the AIMD and AIMD/MM simulations give nearly identical results for exchange dynamics. However, in the larger particle simulations ͑256 waters͒ there is a significant reduction in the second shell to bulk exchanges.

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Section: A the Hydration Shell Structuresupporting

confidence: 90%

Section: A the Hydration Shell Structurecontrasting

confidence: 44%

Section: A the Hydration Shell Structurementioning

confidence: 68%

Section: A the Hydration Shell Structurementioning

confidence: 99%

Section: Electronic Structure Changes In the Hydration Shellsmentioning

confidence: 99%

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Structure and dynamics of the hydration shells of the Zn2+ ion from ab initio molecular dynamics and combined ab initio and classical molecular dynamics simulations

Cauët

Bogatko

Weare

et al. 2010

The Journal of Chemical Physics

103

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Empowering Protein Engineering through Recombination of Beneficial Substitutions

Wang,

Li,

et al. 2024

Chemistry A European J

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Directed evolution stands as a seminal technology for generating novel protein functionalities, a cornerstone in biocatalysis, metabolic engineering, and synthetic biology. Today, with the development of various mutagenesis methods and advanced analytical machines, the challenge of diversity generation and high‐throughput screening platforms is largely solved, and one of the remaining challenges is: how to empower the potential of single beneficial substitutions with recombination to achieve the epistatic effect. This review overviews experimental and computer‐assisted recombination methods in protein engineering campaigns. In addition, integrated and machine learning‐guided strategies were highlighted to discuss how these recombination approaches contribute to generating the screening library with better diversity, coverage, and size. A decision tree was finally summarized to guide the further selection of proper recombination strategies in practice, which was beneficial for accelerating protein engineering.

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Quantum mechanical charge field molecular dynamics simulation of the TiO²⁺ ion in aqueous solution

et al. 2007

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Structural and dynamical properties of the TiO(2+) ion in aqueous solution have been investigated by using the new ab initio quantum mechanical charge field (QMCF) molecular dynamics (MD) formalism, which does not require any other potential functions except those for solvent-solvent interactions. Both first and second hydration shell have been treated at Hartree-Fock (HF) quantum mechanical level. A Ti-O bond distance of 1.5 A was observed for the [Ti=O](2+) ion. The first hydration shell of the ion shows a varying coordination number ranging from 5 to 7, five being the dominant one and representing one axial and four equatorial water molecules directly coordinated to Ti, which are located at 2.3 A and 2.1 A, respectively. The flexibility in the coordination number reflects the fast exchange processes, which occur only at the oxo atom, where water ligands are weakly bound through hydrogen bonds. Considering the first shell hydration, the composition of the TiO(2+) hydrate can be characterized as [(H(2)O)(0.7)(H(2)O)(4) (eq)(H(2)O)(ax)](2+). The second shell consists in average of 12 water molecules located at a mean distance of 4.4 A. Several other structural parameters such as radial and angular distribution functions and coordination number distributions were analyzed to fully characterize the hydration structure of the TiO(2+) ion in aqueous solution. For the dynamics of the TiO(2+) ion, different sets of dynamical parameters such as Ti=O, Ti-O(eq), and Ti-O(ax) stretching frequencies and ligands' mean residence times were evaluated. During the simulation time of 15 ps, 3 water exchange processes in the first shell were observed at the oxo atom, corresponding to a mean residence time of 3.6 ps. The ligands' mean residence time for the second shell was determined as 3.5 ps.

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Exploring Structure and Dynamics of the Diaquotriamminezinc(II) Complex by QM/MM MD Simulation

Cited by 25 publications

References 50 publications

Structure and dynamics of the hydration shells of the Zn2+ ion from ab initio molecular dynamics and combined ab initio and classical molecular dynamics simulations

Structure and dynamics of the hydration shells of the Zn2+ ion from ab initio molecular dynamics and combined ab initio and classical molecular dynamics simulations

Empowering Protein Engineering through Recombination of Beneficial Substitutions

Quantum mechanical charge field molecular dynamics simulation of the TiO²⁺ ion in aqueous solution

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Exploring Structure and Dynamics of the Diaquotriamminezinc(II) Complex by QM/MM MD Simulation

Cited by 25 publications

References 50 publications

Structure and dynamics of the hydration shells of the Zn2+ ion from ab initio molecular dynamics and combined ab initio and classical molecular dynamics simulations

Structure and dynamics of the hydration shells of the Zn2+ ion from ab initio molecular dynamics and combined ab initio and classical molecular dynamics simulations

Empowering Protein Engineering through Recombination of Beneficial Substitutions

Quantum mechanical charge field molecular dynamics simulation of the TiO2+ ion in aqueous solution

Contact Info

Product

Resources

About

Quantum mechanical charge field molecular dynamics simulation of the TiO²⁺ ion in aqueous solution