An automated approach for the parameterization of accurate intermolecular force‐fields: Pyridine as a case study

Cacelli, Ivo; Cimoli, Antonella; Livotto, Paolo Roberto; Prampolini, Giacomo

doi:10.1002/jcc.22937

Cited by 49 publications

(127 citation statements)

References 88 publications

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“…To this aim, an extensive sampling of the QM-PES of the two systems in gas phase is done by means of scanning procedures of internal coordinates. Another equally viable technique would have been to avoid large PES scans (entirely or avoiding just the stiff, high force constant modes) and include instead hessian information from minimum energy conformations and/or gradient and hessian information along selected mode scans [21][22][23][24][25]. The QM information included in the fitting is comparable, and the overall computational cost is smaller for these approaches, but the scanning of QM-PES is inherently parallelizable which may be convenient depending on the kind of available computational resources.…”

Section: Overview Of the Force Field Form And Parameterization Strategymentioning

confidence: 99%

First-principle-based MD description of azobenzene molecular rods

et al. 2012

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Extensive density functional theory (DFT) calculations have been performed to develop a force field for the classical molecular dynamics (MD) simulations of various azobenzene derivatives. Besides azobenzene, we focused on a thiolated azobenzene's molecular rodthat has been previously demonstrated to photoisomerize from trans to cis with high yields on surfaces. The developed force field is an extension of OPLS All Atoms, and key bonding parameters are parameterized to reproduce the potential energy profiles calculated by DFT. For each of the parameterized molecule, we propose three sets of parameters: one best suited for the trans configuration, one for the cis configuration, and finally, a set able to describe both at a satisfactory degree. The quality of the derived parameters is evaluated by comparing with structural and vibrational experimental data. The developed force field opens the way to the classical MD simulations of selfassembled monolayers (SAMs) of azobenzene's molecular rods, as well as to the quantum mechanics/molecular mechanics study of photoisomerization in SAMs.

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Section: Overview Of the Force Field Form And Parameterization Strategymentioning

confidence: 99%

First-principle-based MD description of azobenzene molecular rods

et al. 2012

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“…A more drastic possibility is to abandon the idea of transferability in favor of FFs specific for the system under study. Following this idea, in the past decade several automated protocols have been proposed [16][17][18][19][20][21][22][23][24][25] to obtain FFs purposely tailored for molecule under investigation. In particular, as recently pointed out by Grimme,26 there is a growing attention to novel parameterization strategies, based solely on QM data, capable of yielding very accurate FFs.…”

Section: Introductionmentioning

confidence: 99%

Accuracy of Quantum Mechanically Derived Force-Fields Parameterized from Dispersion-Corrected DFT Data: The Benzene Dimer as a Prototype for Aromatic Interactions

Prampolini

Livotto

Cacelli

2015

J. Chem. Theory Comput.

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135

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A multilevel approach is presented to assess the ability of several popular dispersion corrected density functionals (M06-2X, CAM-B3LYP-D3, BLYP-D3, and B3LYP-D3) to reliably describe two-body interaction potential energy surfaces (IPESs). To this end, the automated Picky procedure ( Cacelli et al. J. Comput. Chem. 2012 , 33 , 1055 ) was exploited, which consists in parametrizing specific intermolecular force fields through an iterative approach, based on the comparison with quantum mechanical data. For each of the tested functionals, the resulting force field was employed in classical Monte Carlo and Molecular Dynamics simulations, performed on systems of up to 1000 molecules in ambient conditions, to calculate a number of condensed phase properties. The comparison of the resulting structural and dynamic properties with experimental data allows us to assess the quality of each IPES and, consequently, even the quality of the DFT functionals. The methodology is tested on the benzene dimer, commonly used as a benchmark molecule, a prototype of aromatic interactions. The best results were obtained with the CAM-B3LYP-D3 functional. Besides assessing the reliability of DFT functionals in describing aromatic IPESs, this work provides a further step toward a robust protocol for the derivation of sound force field parameters from quantum mechanical data. This method can be relevant in all those cases where standard force fields fail in giving accurate predictions.

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“…28 JOYCE -a program to derive all-atom and united-atom FFs for small molecules has been developed by the Barone group. 29,30 Inputs to this program are QM equilibrium geometry, energy, gradient and the hessian matrix. FFs parameters are obtained by minimizing a cost function, which measures the errors between QM energy, gradient and hessian and those calculated from the FFs.…”

Section: Introductionmentioning

confidence: 99%

Developing accurate molecular mechanics force fields for conjugated molecular systems

Troisi

2015

Phys. Chem. Chem. Phys.

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A rapid method to parameterize the intramolecular component of classical force fields for complex conjugated molecules is proposed. The method is based on a procedure of force matching with a reference electronic structure calculation. It is particularly suitable for those applications where molecular dynamics simulations are used to generate structures that are therefore analysed with electronic structure methods, because it is possible to build force fields that are consistent with the electronic structure calculations that follow the classical simulations. Such applications are commonly encountered in organic electronics, spectroscopy of complex systems and photobiology (e.g. photosynthetic systems). We illustrate the method by parameterizing the force fields of a molecule used in molecular semiconductors (2,2-dicyanovinyl-capped S, N-heteropentacene or DCV-SN5), a polymeric semiconductor (thieno[3,2-b]thiophene-diketopyrrolopyrrole TT-DPP) and a chromophore embedded in a protein environment (15,16-Dihydrobiliverdin or DBV) where several hundreds of parameters need to be optimized in parallel.

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An automated approach for the parameterization of accurate intermolecular force‐fields: Pyridine as a case study

Cited by 49 publications

References 88 publications

First-principle-based MD description of azobenzene molecular rods

First-principle-based MD description of azobenzene molecular rods

Accuracy of Quantum Mechanically Derived Force-Fields Parameterized from Dispersion-Corrected DFT Data: The Benzene Dimer as a Prototype for Aromatic Interactions

Developing accurate molecular mechanics force fields for conjugated molecular systems

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