EQeq+C: An Empirical Bond-Order-Corrected Extended Charge Equilibration Method

Martin-Noble, Geoffrey C.; Reilley, David J.; Rivas, L.M.; Smith, Matthew D.; Schrier, Joshua

doi:10.1021/acs.jctc.5b00037

Cited by 21 publications

(28 citation statements)

References 67 publications

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“…Afterward, Martin-Noble et al found that the EQeq method failed to predict the partial charges of TMs with high oxidation states in the amine-templated metal oxide (ATMO) complexes. 880 They then added a correction term into the EQeq scheme on the basis of the relationship between the bond order and bond distance proposed by Pauling (see eq 123 , where n means the bond order, r means the bond distance, with r 0 and b as two parameters; this relationship was also used in the bond valence sum (BVS) model 881 and CM5 charge correction 723 ). The new method was termed as the EQeq+C method.…”

Section: Classical Modeling Of Metal Ions: the Polarizable Modelmentioning

confidence: 99%

Metal Ion Modeling Using Classical Mechanics

2017

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Metal ions play significant roles in numerous fields including chemistry, geochemistry, biochemistry, and materials science. With computational tools increasingly becoming important in chemical research, methods have emerged to effectively face the challenge of modeling metal ions in the gas, aqueous, and solid phases. Herein, we review both quantum and classical modeling strategies for metal ion-containing systems that have been developed over the past few decades. This Review focuses on classical metal ion modeling based on unpolarized models (including the nonbonded, bonded, cationic dummy atom, and combined models), polarizable models (e.g., the fluctuating charge, Drude oscillator, and the induced dipole models), the angular overlap model, and valence bond-based models. Quantum mechanical studies of metal ion-containing systems at the semiempirical, ab initio, and density functional levels of theory are reviewed as well with a particular focus on how these methods inform classical modeling efforts. Finally, conclusions and future prospects and directions are offered that will further enhance the classical modeling of metal ion-containing systems.

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Section: Classical Modeling Of Metal Ions: the Polarizable Modelmentioning

confidence: 99%

Metal Ion Modeling Using Classical Mechanics

2017

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“…Whereas the determination of atomic charge by theoretical methods is not unified, attempts to find a robust method for its determination have been made from time-to-time. For instance, Stasyuk and coworkers [104], as well as several others [195], have recently proposed new models for evaluating charges that could be utilized for arriving at a fundamental understanding of some chemical systems, including endohedral fullerenes. Evidently, atomic charge is certainly a valuable property [196] that will continue to play a crucial role in the understanding systems in diverse areas of science.…”

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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“…The electrostatic potential inside the MOF is typically modelled by assigning a point charge to each MOF atom; point charges are assigned on the molecular model for the adsorbate as well (as is the case for CO 2 [31]), thereby completing the description of the electrostatic interaction of the adsorbate with the MOF. Quick/cheap charge equilibration [Qeq [175]] methods and its variants [EEM[176], , PQeq[177], SQE[178], SCQeq[179], EQeq[180], MEPO-Qeq[181], FCQeq[182], I-Qeq[182], , EQeq+C[183], and SQE-MEPO[184]] are commonly used to assign point charges to atoms of a MOF. However, point charges derived from the electronic density obtained from a first principles calculation on the particular MOF are generally considered more reliable [32].…”

Section: Computation-ready Crystal Structuresmentioning

confidence: 99%

The role of molecular modelling and simulation in the discovery and deployment of metal-organic frameworks for gas storage and separation

Sturluson

Huynh

Kaija

et al. 2019

Molecular Simulation

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Metal-organic frameworks (MOFs) are highly tuneable, extended-network, crystalline, nanoporous materials with applications in gas storage, separations, and sensing. We review how molecular models and simulations of gas adsorption in MOFs have informed the discovery of performant MOFs for methane, hydrogen, and oxygen storage, xenon, carbon dioxide, and chemical warfare agent capture, and xylene enrichment. Particularly, we highlight how large, open databases of MOF crystal structures, post-processed to enable molecular simulations, are a platform for computational materials discovery. We discuss how to orient research efforts to routinise the computational discovery of MOFs for adsorption-based engineering applications.

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EQeq+C: An Empirical Bond-Order-Corrected Extended Charge Equilibration Method

Cited by 21 publications

References 67 publications

Metal Ion Modeling Using Classical Mechanics

Metal Ion Modeling Using Classical Mechanics

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

The role of molecular modelling and simulation in the discovery and deployment of metal-organic frameworks for gas storage and separation

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