Partial Charges in Periodic Systems: Improving Electrostatic Potential (ESP) Fitting via Total Dipole Fluctuations and Multiframe Approaches

Gabrieli, Andrea; Sant, Marco; Demontis, Pierfranco; Suffritti, Giuseppe Baldovino

doi:10.1021/acs.jctc.5b00503

Cited by 20 publications

(30 citation statements)

References 127 publications

(263 reference statements)

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“…66 The simulations of large biomolecules is another common example. 14,17 Fig . 104 Thus, it is important for the NACs to simultaneously have good conformational transferability and approximately reproduce the electrostatic potential around the material.…”

Section: Conformational Transferability and Accuracy For Reproducing mentioning

confidence: 99%

“…8 (2) Bader's quantum chemical topology (QCT) has many theoretically desirable properties, but it can lead to non-nuclear attractors that produce undened NACs. [13][14][15][16][17] Including constraints (e.g., RESP 13,14 methods) improves this, but the form of these constraints is exible leading to numerous possible charge values. [13][14][15][16][17] Including constraints (e.g., RESP 13,14 methods) improves this, but the form of these constraints is exible leading to numerous possible charge values.…”

Section: Introductionmentioning

confidence: 99%

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Introducing DDEC6 atomic population analysis: part 1. Charge partitioning theory and methodology

2016

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Net atomic charges (NACs) are widely used in all chemical sciences to concisely summarize key information about the partitioning of electrons among atoms in materials. The objective of this article is to develop an atomic population analysis method that is suitable to be used as a default method in quantum chemistry programs irrespective of the kind of basis sets employed. To address this challenge, we introduce a new atoms-in-materials method with the following nine properties: (1) exactly one electron distribution is assigned to each atom, (2) core electrons are assigned to the correct host atom, (3) NACs are formally independent of the basis set type because they are functionals of the total electron distribution, (4) the assigned atomic electron distributions give an efficiently converging polyatomic multipole expansion, (5) the assigned NACs usually follow Pauling scale electronegativity trends, (6) NACs for a particular element have good transferability among different conformations that are equivalently bonded, (7) the assigned NACs are chemically consistent with the assigned atomic spin moments, (8) the method has predictably rapid and robust convergence to a unique solution, and (9) the computational cost of charge partitioning scales linearly with increasing system size. We study numerous materials as examples: (a) a series of endohedral C 60 complexes, (b) high-pressure compressed sodium chloride crystals with unusual stoichiometries, (c) metal-organic frameworks, (d) large and small molecules, (e) organometallic complexes, (f) various solids, and (g) solid surfaces. Due to non-nuclear attractors, Bader's quantum chemical topology could not assign NACs for some of these materials. We show for the first time that the Iterative Hirshfeld and DDEC3 methods do not always converge to a unique solution independent of the initial guess, and this sometimes causes those methods to assign dramatically different NACs on symmetry-equivalent atoms. By using a fixed number of charge partitioning steps with well-defined reference ion charges, the DDEC6 method avoids this problem by always converging to a unique solution. These characteristics make the DDEC6 method ideally suited for use as a default charge assignment method in quantum chemistry programs. † Electronic supplementary information (ESI) available: Summary of alternative charge partitioning algorithms considered; summary of integration routines; iterative algorithm for computing the Convex functional NACs; ow diagrams for the DDEC6 method; and .xyz les (which can be read using any text editor or the free Jmol visualization program downloadable from http://jmol.sourceforge.net) containing geometries, net atomic charges, atomic dipoles and quadrupoles, tted tail decay exponents, and ASMs. See

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Section: Conformational Transferability and Accuracy For Reproducing mentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Introducing DDEC6 atomic population analysis: part 1. Charge partitioning theory and methodology

2016

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“…The method capabilities were extensively studied in ZIF-8 framework, and subsequently applied to IRMOF-1 and ITQ-29 crystal structures. [275] InfiniCharges [276] is a tool for generating reliable partial charges for molecular simulations in periodic systems using the DM-REPEAT method. The stability of the resulting charges, over a large set of fitting regions, is obtained through the simultaneous fit of multiple electrostatic potential (ESP) configurations together with the total dipole fluctuations (TDF).…”

Section: Point Chargesmentioning

confidence: 99%

Design, Parameterization, and Implementation of Atomic Force Fields for Adsorption in Nanoporous Materials

Dubbeldam

Walton

Vlugt

et al. 2019

Advcd Theory and Sims

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Molecular simulations are an excellent tool to study adsorption and diffusion in nanoporous materials. Examples of nanoporous materials are zeolites, carbon nanotubes, clays, metal-organic frameworks (MOFs), covalent organic frameworks (COFs) and zeolitic imidazolate frameworks (ZIFs). The molecular confinement these materials offer has been exploited in adsorption and catalysis for almost 50 years. Molecular simulations have provided understanding of the underlying shape selectivity, and adsorption and diffusion effects. Much of the reliability of the modeling predictions depends on the accuracy and transferability of the force field. However, flexibility and the chemical and structural diversity of MOFs add significant challenges for engineering force fields that are able to reproduce experimentally observed structural and dynamic properties. Recent developments in design, parameterization, and implementation of force fields for MOFs and zeolites are reviewed.contain silicon and oxygen. They are readily available, very stable, and relatively cheap. The material should have the right combination of high adsorption selectivity, combined with adequate capacity for use in fixed-bed devices. Recently, new classes of nanoporous materials have been designed that have stability, high void volumes, and well defined tailorable cavities of uniform size. Example are metal-organic frameworks (MOFs), [1][2][3][4][5][6][7] covalent organic frameworks (COFs), [8,9] and zeolitic imidazolate frameworks (ZIFs). [10] These novel materials posses almost unlimited structural variety because of the many combinations of building blocks that can be imagined. The building blocks self-assembly during synthesis into crystalline materials that, after evacuation of the structure, can find applications in adsorption separations, air purification, gas storage, chemical sensing, and catalysis. [4,11] The judicious selection of building blocks allows the pore volume and functionality to be tailored in a rational manner. Because of the designprinciple underlying the synthesis, it is important to understand structure-properties relations, such as the mechanisms of gas separation as a function of shape and size of the pore system, in order to create "blueprints to MOF-design." Computer simulation is cost-effective, fast, and allows for rapid identification of important structural parameters affecting adsorption.Most of the published works on molecular simulation studying zeolites have used the Kiselev model. [12] In this model, zeolite atoms are fixed and interactions of guest atoms with silicon atoms is accounted for by an effective interaction only with the surrounding oxygen atoms. Interactions between sorbate molecules and the host are modeled by placing Lennard-Jones sites and partial charges on all framework atoms and sorbate molecules. The Kiselev model is attractive because of its simplicity and computational efficiency. This model has shown significant success, both in using the molecular dynamics method to compute, for example, the diffu...

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“…CHelpG [99] and RESP [100]). New electrostatic potential-based methods for periodic solids include REPEAT [101,102] and DDEC [103,104], while charge equilibration methods can be used for fast, highthroughput calculations, at the expense of accuracy [105]. Determination of atomic charges can be avoided by using full DFT-based electrostatic potential maps of the material [106], but this is computationally expensive.…”

Section: Grand Canonical Monte Carlo (Gcmc) Simulationsmentioning

confidence: 99%

Outlook and challenges for hydrogen storage in nanoporous materials

et al. 2016

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Considerable progress has been made recently in the use of nanoporous materials for hydrogen storage. In this article, the current status of the field and future challenges are discussed, ranging from important open fundamental questions, such as the density and volume of the adsorbed phase and its relationship to overall storage capacity, to the development of new functional materials and complete storage system design. With regard to fundamentals, the use of neutron scattering to study adsorbed H 2 , suitable adsorption isotherm equations, and the accurate computational modelling and simulation of H 2 adsorption are discussed. The new materials covered include flexible metal-organic frameworks, core-shell materials, and porous organic cage compounds. The article concludes with a discussion of the experimental investigation of real adsorptive hydrogen storage tanks, the improvement in the thermal conductivity of storage beds, and new storage system concepts and designs.

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Partial Charges in Periodic Systems: Improving Electrostatic Potential (ESP) Fitting via Total Dipole Fluctuations and Multiframe Approaches

Cited by 20 publications

References 127 publications

Introducing DDEC6 atomic population analysis: part 1. Charge partitioning theory and methodology

Introducing DDEC6 atomic population analysis: part 1. Charge partitioning theory and methodology

Design, Parameterization, and Implementation of Atomic Force Fields for Adsorption in Nanoporous Materials

Outlook and challenges for hydrogen storage in nanoporous materials

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