MoBioTools: A Toolkit to Setup QM/MM Calculations

Cárdenas, Gustavo; Lucia-Tamudo, Jesús; Mateo-delaFuente, Henar; Palmisano, Vito F.; Anguita-Ortiz, Nuria; Ruano, Lorena; Pérez-Barcia, Álvaro; Díaz‐Tendero, Sergio; Mandado, Marcos; Nogueira, Juan J.

doi:10.26434/chemrxiv-2022-cncp2

Cited by 9 publications

(9 citation statements)

References 88 publications

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“…To apply the QM/MM-EDA scheme explained above, three different electronic structure calculations are required; one for the complex (pollutant + solvated membrane), one for the solvated membrane, and another one for the pollutant molecule. The Gaussian input files for these calculations have been automatically generated with the MoBioTools package [ 40 , 41 ]. Both the pollutant and membrane input files include the full complex basis set in order to avoid the basis set superposition error in the QM region.…”

Section: Methodsmentioning

confidence: 99%

On the Permeation of Polychlorinated Dibenzodioxins and Dibenzofurans through Lipid Membranes: Classical MD and Hybrid QM/MM-EDA Analysis

et al. 2022

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The permeation of dioxin-like pollutants, namely, chlorinated dibenzodioxins and dibenzofurans, through lipid membranes has been simulated using classic molecular dynamics (CMD) combined with the umbrella sampling approach. The most toxic forms of chlorinated dibenzodioxin and dibenzofuran, 2,3,7,8-tetrachloro-p-dibenzodioxin (TCDD) and 2,3,7,8-tetrachlorodibenzofuran (TCDF), and a dioleyl-phosphatidylcholine (DOPC) lipid membrane of 50 Å wide have been chosen for our study. The free energy profile shows the penetration process is largely favoured thermodynamically (ΔG ≈ −12 kcal/mol), with a progressively decrease of the free energy until reaching the energy minima at distances of 8 Å and 9.5 Å from the centre of the membrane for, respectively, TCDD and TCDF. At the centre of the membrane, both molecules display subtle local maxima with free energy differences of 0.5 and 1 kcal/mol with respect to the energy minima for TCDD and TCDF, respectively. Furthermore, the intermolecular interactions between the molecules and the lipid membrane have been characterized at the minima and the local maxima using hybrid quantum mechanics/molecular mechanics energy decomposition analysis (QM/MM-EDA). Total interaction energies of −17.5 and −16.5 kcal/mol have been found at the energy minima for TCDD and TCDF, respectively. In both cases, the dispersion forces govern the molecule-membrane interactions, no significant changes have been found at the local maxima, in agreement with the classical free energy profile. The small differences found in the results obtained for TCDD and TCDF point out that the adsorption and diffusion processes through the cell membrane are not related to the different toxicity shown by these pollutants.

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Section: Methodsmentioning

confidence: 99%

On the Permeation of Polychlorinated Dibenzodioxins and Dibenzofurans through Lipid Membranes: Classical MD and Hybrid QM/MM-EDA Analysis

et al. 2022

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“…Then, the QM/MM calculations were performed with Gaussian16, using the M062X functional and the cc-pVDZ basis set, later increasing the basis set to a cc-pVTZ for the whole system. − The QM region was defined with the solute at its center and the number of closest water molecules was increased from 10 to 240, with the remaining solvent molecules included as point charges assigned by the TIP3P model. The MoBioTools toolkit () was used for the definition of each region. To perform the EDA, three single point QM/MM calculations were carried out for each system without periodic boundary conditions but including the whole environment in the MM layer, corresponding to the full system (QM region and MM point charges) and the fragments on which to compute the interaction energy.…”

Section: Computational Detailsmentioning

confidence: 99%

Effect of the QM Size, Basis Set, and Polarization on QM/MM Interaction Energy Decomposition Analysis

Pérez-Barcia

Cárdenas

Nogueira

et al. 2023

J. Chem. Inf. Model.

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Herein, an Energy Decomposition Analysis (EDA) scheme extended to the framework of QM/MM calculations in the context of electrostatic embeddings (QM/MM-EDA) including atomic charges and dipoles is applied to assess the effect of the QM region size on the convergence of the different interaction energy components, namely, electrostatic, Pauli, and polarization, for cationic, anionic, and neutral systems interacting with a strong polar environment (water). Significant improvements are found when the bulk solvent environment is described by a MM potential in the EDA scheme as compared to pure QM calculations that neglect bulk solvation. The predominant electrostatic interaction requires sizable QM regions. The results reported here show that it is necessary to include a surprisingly large number of water molecules in the QM region to obtain converged values for this energy term, contrary to most cluster models often employed in the literature. Both the improvement of the QM wave function by means of a larger basis set and the introduction of polarization into the MM region through a polarizable force field do not translate to a faster convergence with the QM region size, but they lead to better results for the different interaction energy components. The results obtained in this work provide insight into the effect of each energy component on the convergence of the solute−solvent interaction energy with the QM region size. This information can be used to improve the MM FFs and embedding schemes employed in QM/MM calculations of solvated systems.

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“…[57][58][59][60][61] The QM region was defined with the solute at its centre and the number of closest water molecules was increased from 10 to 240, with the remaining solvent molecules included as point charges assigned by the TIP3P model. The MoBioTools toolkit 62,63 was used for the definition of each region. To perform the EDA, three single point QM/MM calculations were carried out for each system, corresponding to the full system (QM region and MM point charges) and the fragments on which to compute the interaction energy.…”

Section: Computational Detailsmentioning

confidence: 99%

Effect of the QM Size, Basis Set and Polarisation on QM/MM Energy Decomposition Analysis

Mandado

Nogueira

Cárdenas

et al. 2022

Preprint

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Herein, an Energy Decomposition Analysis (EDA) scheme extended to the framework of QM/MM calculations in the context of electrostatic and polarisable embeddings (QM/MM-EDA) is applied to assess the effect of the QM region size on the convergence of the different interaction energy components, nameyl, electrostatic, Pauli and polarisation, for cationic, anionic and neutral systems interacting with a strong polar environment (water). Significant improvements are found when the bulk solvent environment is described by a MM potential in the EDA scheme as compared to pure QM calculations that neglect bulk solvation. The predominant electrostatic interaction requires for sizeable QM regions. The results reported here show that it is necessary to include a surprisingly large number of water molecules in the QM region to obtain converged values for this energy term, contrary to most cluster models often employed in the literature. Both the improvement of the QM wavefunction by means of a larger basis set and the introduction of polarisation into the MM region through a polarisable embedding do not translate to a faster convergence with the QM region size, but lead to better results for the different interaction energy components.

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MoBioTools: A Toolkit to Setup QM/MM Calculations

Cited by 9 publications

References 88 publications

On the Permeation of Polychlorinated Dibenzodioxins and Dibenzofurans through Lipid Membranes: Classical MD and Hybrid QM/MM-EDA Analysis

On the Permeation of Polychlorinated Dibenzodioxins and Dibenzofurans through Lipid Membranes: Classical MD and Hybrid QM/MM-EDA Analysis

Effect of the QM Size, Basis Set, and Polarization on QM/MM Interaction Energy Decomposition Analysis

Effect of the QM Size, Basis Set and Polarisation on QM/MM Energy Decomposition Analysis

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