Atomic charges for modeling metal–organic frameworks: Why and how

Hamad, Said; Balestra, Salvador R. G.; Bueno-Pérez, Rocío; Calero, Sofı́a; Ruiz‐Salvador, A. Rabdel

doi:10.1016/j.jssc.2014.08.004

Cited by 50 publications

(63 citation statements)

References 122 publications

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“…Comparison to the semi-empirical EQeq method showed large differences to the charges calculated by the DDEC method, leading to possible inaccuracies in adsorption modelling. Hamad et al found that simulations with different charges led to difference in thermal expansion results, thus showing that the choice of framework point charges can also affect modelling of structural properties of MOFs (Hamad et al 2015).…”

Section: Introductionmentioning

confidence: 99%

The effect of atomic point charges on adsorption isotherms of CO2 and water in metal organic frameworks

et al. 2019

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The interactions between metal-organic frameworks (MOFs) and adsorbates have been increasingly predicted and studied by computer simulations, particularly by Grand-Canonical Monte Carlo (GCMC), as this method enables comparing the results with experimental data and also provides a degree of molecular level detail that is difficult to obtain in experiments. The assignment of atomic point charges to each atom of the framework is essential for modelling Coulombic interactions between the MOF and the adsorbate. Such interactions are important in adsorption of polar gases like water or carbon dioxide, both of which are central in carbon capture processes. The aim of this work is to systematically investigate the effect of varying atomic point charges on adsorption isotherm predictions, identify the underlying trends, and based on this knowledge to improve existing models in order to increase the accuracy of gas adsorption prediction in MOFs. Adsorption isotherms for CO 2 and water in several MOFs were generated with GCMC, using the same computational parameters for each material except framework point charge sets that were obtained through a wide range of computational approaches. We carried out this work for 6 widely studied MOFs; IRMOF-1, MIL-47, UiO-66, CuBTC, Co-MOF-74 and SIFSIX-2-Cu-I. We included both MOFs with and without open metal sites (OMS), specifically to investigate whether this property affects the predicted adsorption behaviour. Our results show that point charges obtained from quantum mechanical calculations on fully periodic structures are generally more consistent and reliable than those obtained from either cluster-based QM calculations or semi-empirical approaches. Furthermore, adsorption in MOFs that contain OMS is much more sensitive to the point charge values, with particularly large variability being observed for water adsorption in such MOFs. This suggests that particular care must be taken when simulating adsorption of polar molecules in MOFs with open metal sites to ensure that accurate results are obtained.

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Section: Introductionmentioning

confidence: 99%

The effect of atomic point charges on adsorption isotherms of CO2 and water in metal organic frameworks

et al. 2019

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“…Ionescu and coworkers [190] argued that partial atomic charges are a well-established concept and are very useful in understanding and modeling the chemical reactivity behavior of molecules, ranging from simple compounds, to crystals, to large drug-like molecules, to biomacromolecular complexes with hundreds of thousands of atoms. Hamad et al [191] found that knowledge of atomic charges on specific systems is important, and that they are useful in gaining insight into metal-organic frameworks (MOFs). The strategy, which is applicable to other porous materials, paves the way for large-scale computational screening of MOFs for specific applications as well as contributing to a better understanding of the structure-property relationships for MOFs, eventually assisting in their development and application [192].…”

Section: Is the Concept Of Atomic Charge Meaningful?mentioning

confidence: 99%

Halogen Bonding: A Halogen-Centered Noncovalent Interaction Yet to Be Understood

2019

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In addition to the underlying basic concepts and early recognition of halogen bonding, this paper reviews the conflicting views that consistently appear in the area of noncovalent interactions and the ability of covalently bonded halogen atoms in molecules to participate in noncovalent interactions that contribute to packing in the solid-state. It may be relatively straightforward to identify Type-II halogen bonding between atoms using the conceptual framework of σ-hole theory, especially when the interaction is linear and is formed between the axial positive region (σ-hole) on the halogen in one monomer and a negative site on a second interacting monomer. A σ-hole is an electron density deficient region on the halogen atom X opposite to the R–X covalent bond, where R is the remainder part of the molecule. However, it is not trivial to do so when secondary interactions are involved as the directionality of the interaction is significantly affected. We show, by providing some specific examples, that halogen bonds do not always follow the strict Type-II topology, and the occurrence of Type-I and -III halogen-centered contacts in crystals is very difficult to predict. In many instances, Type-I halogen-centered contacts appear simultaneously with Type-II halogen bonds. We employed the Independent Gradient Model, a recently proposed electron density approach for probing strong and weak interactions in molecular domains, to show that this is a very useful tool in unraveling the chemistry of halogen-assisted noncovalent interactions, especially in the weak bonding regime. Wherever possible, we have attempted to connect some of these results with those reported previously. Though useful for studying interactions of reasonable strength, IUPAC’s proposed “less than the sum of the van der Waals radii” criterion should not always be assumed as a necessary and sufficient feature to reveal weakly bound interactions, since in many crystals the attractive interaction happens to occur between the midpoint of a bond, or the junction region, and a positive or negative site.

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“…Since the definition of partial atomic charges is not strict, various models of partial atomic charges can, however, differ significantly in the reliability of their predictions. Therefore, an evaluation of the performance of a partial atomic charge model for a given problem is necessary before using it for making reliable predictions [23][24][25][26][27][28].…”

Section: Introductionmentioning

confidence: 99%

A Test of Various Partial Atomic Charge Models for Computations on Diheteroaryl Ketones and Thioketones

Matczak

2016

Computation

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Abstract:The effective use of partial atomic charge models is essential for such purposes in molecular computations as a simplified representation of global charge distribution in a molecule and predicting its conformational behavior. In this work, ten of the most popular models of partial atomic charge are taken into consideration, and these models operate on the molecular wave functions/electron densities of five diheteroaryl ketones and their thiocarbonyl analogs. The ten models are tested in order to assess their usefulness in achieving the aforementioned purposes for the compounds in title. Therefore, the following criteria are used in the test: (1) how accurately these models reproduce the molecular dipole moments of the conformers of the investigated compounds; (2) whether these models are able to correctly determine the preferred conformer as well as the ordering of higher-energy conformers for each compound. The results of the test indicate that the Merz-Kollman-Singh (MKS) and Hu-Lu-Yang (HLY) models approximate the magnitude of the molecular dipole moments with the greatest accuracy. The natural partial atomic charges perform best in determining the conformational behavior of the investigated compounds. These findings may constitute important support for the effective computations of electrostatic effects occurring within and between the molecules of the compounds in question as well as similar compounds.

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Atomic charges for modeling metal–organic frameworks: Why and how

Cited by 50 publications

References 122 publications

The effect of atomic point charges on adsorption isotherms of CO2 and water in metal organic frameworks

The effect of atomic point charges on adsorption isotherms of CO2 and water in metal organic frameworks

Halogen Bonding: A Halogen-Centered Noncovalent Interaction Yet to Be Understood

A Test of Various Partial Atomic Charge Models for Computations on Diheteroaryl Ketones and Thioketones

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