Automated Parametrization of AMBER Force Field Terms from Vibrational Analysis with a Focus on Functionalizing Dinuclear Zinc(II) Scaffolds

Burger, Steven K.; Lacasse, Mike; Verstraelen, Toon; Drewry, Joel A.; Gunning, Patrick T.; Ayers, Paul W.

doi:10.1021/ct2007742

Cited by 46 publications

(66 citation statements)

References 45 publications

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“…However, the user needs to determine weight factors for the different contributions in the cost function, which is a nontrivial task that has to be repeated for every molecule separately. Another approach was used by the group of Ayers, they proposed an automated procedure for parameterizing Amber‐compatible force fields . This procedure requires input from AMBER force fields and the force constants of the harmonic terms are derived by means of a term‐by‐term projection of the ab initio Hessian.…”

Section: Introductionmentioning

confidence: 99%

QuickFF: A program for a quick and easy derivation of force fields for metal‐organic frameworks from ab initio input

et al. 2015

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QuickFF is an software package to derive accurate force fields for isolated and complex molecular systems in a quick and easy manner. Apart from its general applicability, the program has been designed to generate force fields for metal-organic frameworks in an automated fashion. The force field parameters for the covalent interaction are derived from ab initio data. The mathematical expression of the covalent energy is kept simple to ensure robustness and to avoid fitting deficiencies as much as possible. The user needs to produce an equilibrium structure and a Hessian matrix for one or more building units. Afterwards, a force field is generated for the system using a three-step method implemented in QuickFF. The first two steps of the methodology are designed to minimize correlations among the force field parameters. In the last step the parameters are refined by imposing the force field parameters to reproduce the ab initio Hessian matrix in Cartesian coordinate space as accurate as possible. The method is applied on a set of 1000 organic molecules to show the easiness of the software protocol. To illustrate its application to MOFs, QuickFF is used to determine force fields for MIL-53(Al) and MOF-5. For both materials accurate force fields were already generated in literature but they requested a lot of manual interventions. QuickFF is a tool that can easily be used by anyone with a basic knowledge of performing ab initio calculations. As a result accurate force fields are generated with minimal effort.

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Section: Introductionmentioning

confidence: 99%

QuickFF: A program for a quick and easy derivation of force fields for metal‐organic frameworks from ab initio input

et al. 2015

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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.

138

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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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“…A similar approach was also carried out by the Ayers group aiming to produce an automated procedure for parameterising AMBER-compatible FFs for transition metal complexes. 33 The force constant of the harmonic terms are derived from the knowledge of the ab initio Hessian matrix and the torsion potentials are obtained from relaxed potential energy surface scan. Efforts in the same spirit have been presented for metalloproteins 34 and Metal Organic Frameworks.…”

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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Automated Parametrization of AMBER Force Field Terms from Vibrational Analysis with a Focus on Functionalizing Dinuclear Zinc(II) Scaffolds

Cited by 46 publications

References 45 publications

QuickFF: A program for a quick and easy derivation of force fields for metal‐organic frameworks from ab initio input

QuickFF: A program for a quick and easy derivation of force fields for metal‐organic frameworks from ab initio input

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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