New approach to instantaneous polarizable electrostatic embedding of the solvent

Kiataki, M.B.; do N. Varella, M.T.; Coutinho, K.

doi:10.1016/j.molliq.2023.122861

Cited by 4 publications

(11 citation statements)

References 76 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…For larger distances, the water molecules cannot distinguish the anion’s electronic states. The drop in dipole moment magnitude for some water molecules lying far from the solute, beyond 7.5 Å (vertical line), is a consequence of the vacuum effect, which was discussed in ref . This artifact stems from the finite size of the system considered in the calculations.…”

Section: Results and Discussionmentioning

confidence: 85%

“…The atomic charges of the solvent molecules and the solute in a modified electronic state were calculated by fitting the QM electrostatic potential with the CHELPG method at the ωB97x/cc-pVTZ level. More comprehensive details of the scPEE-S-QM/MM method can be found elsewhere …”

Section: Methodsmentioning

confidence: 99%

“…Similarly, a representative configuration was selected based on the same procedure, now including the electrostatic embedding surrounding the clusters, i.e., the 500 water molecules described with SPC/E point charges in the calculations of the energies of the π* virtual orbitals. Details on these approaches for choosing a representative cluster and configuration can be found elsewhere. , …”

Section: Methodsmentioning

confidence: 99%

See 2 more Smart Citations

Novel Approach for Predicting Vertical Electron Attachment Energies in Bulk-Solvated Molecules

Kiataki,

Varella,

Coutinho

et al. 2024

J. Chem. Theory Comput.

Self Cite

View full text Add to dashboard Cite

When low-energy electrons interact with molecules, they can give rise to transient anion states commonly known as resonances. These states are formed through vertical electron attachment processes and have the potential to induce various forms of DNA lesions, including base damage, single-and doublestrand breaks, cross-links, and clustered lesions that are challenging to repair. So far, most experimental and theoretical studies have investigated the formation of resonances of (bio)molecules in the gas phase or in microsolvated environments. Since cellular environments are mainly composed of water molecules, it is crucial to understand how bulk water affects the resonances of (bio)molecules. Given the existing gap in studies on resonances of bulk-solvated molecules, we propose a novel theoretical-computational approach to address this void. Our approach combines the multibasis-set (time-dependent-)density functional theory and selfconsistent sequential quantum mechanics/molecular mechanics polarizable electrostatic embedding methods. We apply this combined methodology to predict the vertical electron attachment energies of 1-methyl-5-nitroimidazole (1M5NI), a well-known radiosensitizer model, in bulk water. In addition, we analyze the rapid mutual polarization between the resonances (both shape-and core-excited) of 1M5NI and the surrounding bulk water environment. For comparison, we also studied the isolated and microsolvated 1M5NI. Overall, while the polarization of the environment is clearly sensitive to the solute charge, causing a significant impact on the vertical electron affinity and consequently on the attachment electron energies, it does not have a significant impact on the excitation energies of the anion.

show abstract

Section: Results and Discussionmentioning

confidence: 85%

Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

See 1 more Smart Citation

Novel Approach for Predicting Vertical Electron Attachment Energies in Bulk-Solvated Molecules

Kiataki,

Varella,

Coutinho

et al. 2024

J. Chem. Theory Comput.

Self Cite

View full text Add to dashboard Cite

show abstract

“…An improved approximation called polarizable embedding incorporates the polarization within the MM region; however, while several schemes have been proposed, the resulting improvements have proven to be modest. 57,58 On the other hand, the so-called ME approach computes the QM/MM electrostatic energy by the Coulombic interaction of point charges centered in each atom, i.e., atomic partial charges where q j is the atomic partial charge of the jth QM atom. The ME approach leads to lower quality results, 59 and its primary challenge stems from the difficulty in assigning partial charges that can accurately model the behavior of the electric density.…”

Section: Electrostatic and Mesmentioning

confidence: 99%

“…Here, the MM q i charges are fixed parameters and the electric field generated by them is accounted for the optimization of the electron density ρ( r ). An improved approximation called polarizable embedding incorporates the polarization within the MM region; however, while several schemes have been proposed, the resulting improvements have proven to be modest. , …”

Section: Theorymentioning

confidence: 99%

Assessment of Embedding Schemes in a Hybrid Machine Learning/Classical Potentials (ML/MM) Approach

Grassano,

Pickering,

Roitberg

et al. 2024

J. Chem. Inf. Model.

View full text Add to dashboard Cite

Machine learning (ML) methods have reached high accuracy levels for the prediction of in vacuo molecular properties. However, the simulation of large systems solely through ML methods (such as those based on neural network potentials) is still a challenge. In this context, one of the most promising frameworks for integrating ML schemes in the simulation of complex molecular systems are the so-called ML/MM methods. These multiscale approaches combine ML methods with classical force fields (MM), in the same spirit as the successful hybrid quantum mechanics−molecular mechanics methods (QM/MM). The key issue for such ML/MM methods is an adequate description of the coupling between the region of the system described by ML and the region described at the MM level. In the context of QM/MM schemes, the main ingredient of the interaction is electrostatic, and the state of the art is the so-called electrostatic-embedding. In this study, we analyze the quality of simpler mechanical embedding-based approaches, specifically focusing on their application within a ML/MM framework utilizing atomic partial charges derived in vacuo. Taking as reference electrostatic embedding calculations performed at a QM(DFT)/MM level, we explore different atomic charges schemes, as well as a polarization correction computed using atomic polarizabilites. Our benchmark data set comprises a set of about 80k small organic structures from the ANI-1x and ANI-2x databases, solvated in water. The results suggest that the minimal basis iterative stockholder (MBIS) atomic charges yield the best agreement with the reference coupling energy. Remarkable enhancements are achieved by including a simple polarization correction.

show abstract

Toward a numerically efficient description of bulk-solvated anionic states

Kiataki,

Coutinho,

Varella

2024

The Journal of Chemical Physics

View full text Add to dashboard Cite

We investigate the vertical electron attachment energy (VAE) of 1-methyl-4-nitroimidazole, a model radiosensitizer, employing quantum mechanics/molecular mechanics (QM/MM) and QM/polarized continuum (QM/PCM) solvation models. We considered the solvent-excluded surface (QM/PCM-SES) and Van der Waals (QM/PCM-VDW) cavities within the PCM framework, the electrostatic embedding QM/MM (EE-QM/MM) model, and the self-consistent sequential QM/MM polarizable electrostatic embedding (scPEE-S-QM/MM) model. Due to slow VAE convergence concerning the number of QM solvent molecules, full QM calculations prove inefficient. Ensemble averages in these calculations do not align with VAEs computed for the representative solute–solvent configuration. QM/MM and QM/PCM calculations show agreement with each other for sufficiently large QM regions, although the QM/PCM-VDW model exhibits artifacts linked to the cavity. QM/MM models demonstrate good agreement between ensemble averages and VAEs calculated with the representative configuration. Notably, the VAE computed with the scPEE-S-QM/MM model achieves faster convergence concerning the number of QM water molecules compared to the EE-QM/MM model, attributed to enhanced efficiency from MM charge polarization in the scPEE-S-QM/MM approach. This emphasizes the importance of QM/classical models with accurate solute–solvent and solvent–solvent mutual polarization for obtaining converged VAEs at a reasonable computational cost. The full-QM approach is very inefficient, while the microsolvation model is inaccurate. Computational savings in QM/MM models result from electrostatic embedding and the representative configuration, with the scPEE-S-QM/MM approach emerging as an efficient tool for describing bulk-solvated anions within the QM/MM framework. Its potential extends to improving transient anion state descriptions in biomolecules and radiosensitizers, especially given the frequent employment of microsolvation models.

show abstract

New approach to instantaneous polarizable electrostatic embedding of the solvent

Cited by 4 publications

References 76 publications

Novel Approach for Predicting Vertical Electron Attachment Energies in Bulk-Solvated Molecules

Novel Approach for Predicting Vertical Electron Attachment Energies in Bulk-Solvated Molecules

Assessment of Embedding Schemes in a Hybrid Machine Learning/Classical Potentials (ML/MM) Approach

Toward a numerically efficient description of bulk-solvated anionic states

Contact Info

Product

Resources

About