Molecular Perception for Visualization and Computation: The Proxima Library

Lazzari, Federico; Salvadori, Andrea; Mancini, Giordano; Barone, Vincenzo

doi:10.1021/acs.jcim.0c00076

Cited by 26 publications

(42 citation statements)

References 24 publications

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“…Gaussian distribution functions with HWHM of 900, 550, and 450 cm −1 were used as broadening functions for pure electronic ONIOM/EE-PMM, vibronic PCM, and combined ONIOM/EE-PMM vibronic approaches, respectively. Spatial Distribution Functions plotted as isosurfaces and virtual sites were visualized employing the Caffeine software (Salvadori et al, 2016 ; Lazzari et al, 2020 ).…”

Section: Methodsmentioning

confidence: 99%

CPL Spectra of Camphor Derivatives in Solution by an Integrated QM/MD Approach

2020

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We extend a recently proposed computational strategy for the simulation of absorption spectra of semi-rigid molecular systems in condensed phases to the emission spectra of flexible chromophores. As a case study, we have chosen the CPL spectrum of camphor in methanol solution, which shows a well-defined bisignate shape. The first step of our approach is the quantum mechanical computation of reference spectra including vibrational averaging effects and taking bulk solvent effects into account by means of the polarizable continuum model. In the present case, the large amplitude inversion mode is explicitly treated by a numerical approach, whereas the other small-amplitude vibrational modes are taken into account within the harmonic approximation. Next, the snapshots of classical molecular dynamics computations are clusterized and one representative configuration from each cluster is used to compute a reference spectrum. In the present case, different clusters correspond to the two stable conformers of camphor in the S1 excited electronic state and, for each of them, to different numbers of strong solute-solvent hydrogen bonds. Finally, local fluctuation effects within each cluster are taken into account by means of the perturbed matrix model. The overall procedure leads to good agreement with experiment for absorption and emission spectra together with their chiral counterparts, thus allowing to analyze the role of different effects (stereo-electronic, vibrational, environmental) in tuning the overall experimental spectra.

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Section: Methodsmentioning

confidence: 99%

CPL Spectra of Camphor Derivatives in Solution by an Integrated QM/MD Approach

2020

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“…The calculation of structural properties was carried out with standard procedures, but taking into account proper normalization for NPBCs. The strength of the hydrogen bonds was calculated with a continuous function 34 referred to in the following as F HB . 72…”

Section: Methodsmentioning

confidence: 99%

Molecular Dynamics Simulations Enforcing Nonperiodic Boundary Conditions: New Developments and Application to the Solvent Shifts of Nitroxide Magnetic Parameters

Mancini

Fusè

Lipparini

et al. 2022

J. Chem. Theory Comput.

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Multiscale methods combining quantum mechanics and molecular mechanics (QM/MM) have become the most suitable and effective strategies for the investigation of the spectroscopic properties of medium-to-large size chromophores in condensed phases. In this context, we are developing a novel workflow aimed at improving the generality, reliability, and ease of use of the available computational tools. In this paper, we report our latest developments with specific reference to a general protocol based on atomistic simulations, carried out under nonperiodic boundary conditions (NPBC). In particular, we add to our in house MD engine a new efficient treatment of mean field electrostatic contributions to energy and forces, together with the capability of performing the simulations either in the canonical ( NVT ) or in the isothermal–isobaric ( NPT ) ensemble. Next, we provide convincing evidence that the NBPC approach enhanced by specific tweaks for rigid body propagation, allows for the simulation of solute–solvent systems with a minimum number of degrees of freedom and large integration time step. After its validation, this new approach is applied to the challenging case of solvatochromic effects on the electron paramagnetic resonance (EPR) spectrum of a prototypical nitroxide radical. To this end, we propose and validate also an automated protocol to extract and weight simulation snapshots, making use of a continuous description of the strength of solute–solvent hydrogen bridges. While further developments are being worked on, the effectiveness of our approach, even in its present form, is demonstrated by the accuracy of the results obtained through an unsupervised approach characterized by a strongly reduced computational cost as compared to that of conventional QM/MM models, without any appreciable deterioration of accuracy.

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“…All the simulations were performed employing the Proxima library 29 to build spherical boxes filled with water molecules at the experimental density and, in the case of creatinine aqueous solution, placing a creatinine molecule at the center of the box and deleting all molecules within the sum of covalent radii from any creatinine atom. In order to avoid any convergence issue, MD simulations were performed using large cavities with radii of 20 and 21 Å (containing 1116 and 1170 water molecules) for pure water and creatinine solution, respectively.…”

Section: Theory and Computational Detailsmentioning

confidence: 99%

Development, Validation, and Pilot Application of a Generalized Fluctuating Charge Model for Computational Spectroscopy in Solution

et al. 2022

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A general approach enforcing nonperiodic boundary conditions for the computation of spectroscopic properties in solution has been improved including an effective description of charge-transfer contributions and coordination number adjustment for explicit solvent molecules. Both contributions are obtained from a continuous description of intermolecular hydrogen bonds, which has been employed also for an effective clustering of molecular dynamics trajectories. Fine tuning of the model has been performed for several water clusters, and then its efficiency and reliability have been demonstrated by computing the absorption spectra of different creatinine tautomers in aqueous solution.

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Molecular Perception for Visualization and Computation: The Proxima Library

Cited by 26 publications

References 24 publications

CPL Spectra of Camphor Derivatives in Solution by an Integrated QM/MD Approach

CPL Spectra of Camphor Derivatives in Solution by an Integrated QM/MD Approach

Molecular Dynamics Simulations Enforcing Nonperiodic Boundary Conditions: New Developments and Application to the Solvent Shifts of Nitroxide Magnetic Parameters

Development, Validation, and Pilot Application of a Generalized Fluctuating Charge Model for Computational Spectroscopy in Solution

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