Computational Predictions of Metal-Macrocycle Stability Constants Require Accurate Treatments of Local Solvent and pH Effects

2021 ◽  
Author(s):  
Brian Gentry ◽  
Tae Hoon Choi ◽  
William Belfield ◽  
John Keith
Keyword(s):  
Density Functional ◽  
Rational Design ◽  
Divalent Cations ◽  
Binding Constants ◽  
Binding Energies ◽  
Average Error ◽  
Ph Effects ◽  
Computationally Efficient ◽  
Metal Interactions ◽  
Solvent Phase

Rational design of molecular chelating agents requires a detailed understanding of physicochemical ligand-metal interactions in solvent phase. Computational quantum chemistry methods should be able to provide this, but computational reports have shown poor accuracy when determining absolute binding constants for many chelating molecules. To understand why, we compare and benchmark static- and dynamics-based computational procedures for a range of monovalent and divalent cations binding to a conventional cryptand molecule: 2.2.2-cryptand ([2.2.2]). The benchmarking comparison shows that dynamics simulations using standard OPLS-AA classical potentials can reasonably predict binding constants for monovalent cations, but these procedures fail for divalent cations. We also consider computationally efficient static procedure using Kohn-Sham density functional theory (DFT) and cluster-continuum modeling that accounts for local microsolvation and pH effects. This approach accurately predicts binding energies for monovalent and divalent cations with an average error of 3.2 kcal mol−1 compared to experiment. This static procedure thus should be useful for future molecular screening efforts, and high absolute errors in the literature may be due to inadequate modeling of local solvent and pH effects.

Computational Predictions of Metal-Macrocycle Stability Constants Require Accurate Treatments of Local Solvent and pH Effects

2021 ◽  
Author(s):  
Brian Gentry ◽  
Tae Hoon Choi ◽  
William Belfield ◽  
John Keith
Keyword(s):  
Density Functional ◽  
Rational Design ◽  
Divalent Cations ◽  
Binding Constants ◽  
Binding Energies ◽  
Average Error ◽  
Ph Effects ◽  
Computationally Efficient ◽  
Metal Interactions ◽  
Solvent Phase

Rational design of molecular chelating agents requires a detailed understanding of physicochemical ligand-metal interactions in solvent phase. Computational quantum chemistry methods should be able to provide this, but computational reports have shown poor accuracy when determining absolute binding constants for many chelating molecules. To understand why, we compare and benchmark static- and dynamics-based computational procedures for a range of monovalent and divalent cations binding to a conventional cryptand molecule: 2.2.2-cryptand ([2.2.2]). The benchmarking comparison shows that dynamics simulations using standard OPLS-AA classical potentials can reasonably predict binding constants for monovalent cations, but these procedures fail for divalent cations. We also consider computationally efficient static procedure using Kohn-Sham density functional theory (DFT) and cluster-continuum modeling that accounts for local microsolvation and pH effects. This approach accurately predicts binding energies for monovalent and divalent cations with an average error of 3.2 kcal mol−1 compared to experiment. This static procedure thus should be useful for future molecular screening efforts, and high absolute errors in the literature may be due to inadequate modeling of local solvent and pH effects.

Computational predictions of metal-macrocycle stability constants require accurate treatments of local solvent and pH effects

2021 ◽  
Author(s):  
Brian Gentry ◽  
Tae Hoon Choi ◽  
William S. Belfield ◽  
John A. Keith
Keyword(s):  
Quantum Chemistry ◽  
Rational Design ◽  
Chelating Agents ◽  
Ph Effects ◽  
Detailed Understanding ◽  
Metal Interactions ◽  
Solvent Phase ◽  
Computational Quantum Chemistry ◽  
Computational Predictions ◽  
Computational Quantum

Rational design of molecular chelating agents requires a detailed understanding of physicochemical ligand-metal interactions in solvent phase. Computational quantum chemistry methods should be able to provide this, but computational reports...

scholarly journals Plasmon Character Index: An Accurate and Efficient Metric for Identifying and Quantifying Plasmons in Molecules

2021 ◽  
Author(s):  
James Langford ◽  
Xi Xu ◽  
Yang Yang
Keyword(s):  
Density Functional Theory ◽  
Density Functional ◽  
Rational Design ◽  
Charge Carriers ◽  
Time Dependent ◽  
Classical Electrodynamics ◽  
Computationally Efficient ◽  
Functional Theory ◽  
Solar Energy Harvesting ◽  
Dependent Density

Plasmons, which are collective and coherent oscillations of charge carriers driven by an external field, play an important role in applications such as solar energy harvesting, sensing, and catalysis. Plasmons can be found in bulk and nanomaterials, and in recent years, plasmons have also been identified in molecules and these molecules have been utilized to build plasmonic devices. As molecular plasmons can no longer be described by classical electrodynamics, a description using quantum mechanics is necessary. Many methods have been developed to identify and quantify molecular plasmons based on the properties of plasmonic excitations. However, there is not currently a method that is widely accepted, connects to collectivity and coherence, and is computationally practical. Here we develop a metric to accurately and efficiently identify and quantify plasmons in molecules. A number, which we call plasmon character index (PCI), can be calculated for each electronic excited state and describes the plasmonicity of the excitation. PCI is developed from the collective and coherent excitation picture in orbitals and shows excellent agreement with the predictions from scaled time-dependent density functional theory but is vastly more computationally efficient. Therefore, PCI can be a useful tool in identifying and quantifying plasmons and will inform the rational design of plasmonic molecules and small nanomaterials.

scholarly journals Accuracy and Reproducibility of Host-Guest Interactions in Zeolites

2020 ◽  
Author(s):  
Daniel Schwalbe-Koda ◽  
Rafael Gomez-Bombarelli
Keyword(s):  
Density Functional ◽  
Single Point ◽  
Cost Effective ◽  
Binding Energies ◽  
Binding Affinities ◽  
Computationally Efficient ◽  
Zeolite Framework ◽  
Functional Theory ◽  
Organic Structure ◽  
Dynamics Simulations

Molecular modeling plays an important role in the discovery of organic structure-directing agents (OSDAs) for zeolites. By quantifying the intensity of host-guest interactions, it is possible to select cost-effective molecules that maximize binding towards a given zeolite framework. Over the last decades, a variety of methods and levels of theory have been used to calculate these binding energies. Nevertheless, no benchmark examining these calculation strategies has been reported. In this work, we compare binding affinities from density functional theory (DFT) and force field calculations for 272 zeolite-OSDA pairs obtained from static and time-averaged simulations. We show that binding energies from the frozen pose method correlate best with DFT time-averaged energies. They are also less sensitive to the choice of initial lattice parameters and optimization algorithms, as well as less computationally expensive. Furthermore, we demonstrate that a broader exploration of the conformation space from molecular dynamics simulations does not provide significant improvements in binding energy trends over single-point calculations. The code and benchmark data are open-sourced and together with the reported results, provide robust, reproducible, and computationally-efficient guidelines to calculating binding energies in zeolite-OSDA pairs.

scholarly journals Accuracy and Reproducibility of Host-Guest Interactions in Zeolites

2020 ◽  
Author(s):  
Daniel Schwalbe-Koda ◽  
Rafael Gomez-Bombarelli
Keyword(s):  
Density Functional ◽  
Single Point ◽  
Cost Effective ◽  
Binding Energies ◽  
Binding Affinities ◽  
Computationally Efficient ◽  
Zeolite Framework ◽  
Functional Theory ◽  
Organic Structure ◽  
Dynamics Simulations

Molecular modeling plays an important role in the discovery of organic structure-directing agents (OSDAs) for zeolites. By quantifying the intensity of host-guest interactions, it is possible to select cost-effective molecules that maximize binding towards a given zeolite framework. Over the last decades, a variety of methods and levels of theory have been used to calculate these binding energies. Nevertheless, no benchmark examining these calculation strategies has been reported. In this work, we compare binding affinities from density functional theory (DFT) and force field calculations for 272 zeolite-OSDA pairs obtained from static and time-averaged simulations. We show that binding energies from the frozen pose method correlate best with DFT time-averaged energies. They are also less sensitive to the choice of initial lattice parameters and optimization algorithms, as well as less computationally expensive. Furthermore, we demonstrate that a broader exploration of the conformation space from molecular dynamics simulations does not provide significant improvements in binding energy trends over single-point calculations. The code and benchmark data are open-sourced and together with the reported results, provide robust, reproducible, and computationally-efficient guidelines to calculating binding energies in zeolite-OSDA pairs.

scholarly journals Benchmarking binding energy calculations for organic structure-directing agents in pure-silica zeolites

2021 ◽  
Author(s):  
Daniel Schwalbe-Koda ◽  
Rafael Gomez-Bombarelli
Keyword(s):  
Binding Energy ◽  
Density Functional ◽  
Single Point ◽  
Cost Effective ◽  
Binding Energies ◽  
Computationally Efficient ◽  
Organic Structure ◽  
Pure Silica ◽  
Structure Directing Agents ◽  
Dynamics Simulations

Molecular modeling plays an important role in the discovery of organic structure-directing agents (OSDAs) for zeolites. By quantifying the intensity of host-guest interactions, it is possible to select cost-effective molecules that maximize binding towards a given zeolite framework. Over the last decades, a variety of methods and levels of theory have been used to calculate these binding energies. Nevertheless, there is no consensus on the best calculation strategy for high-throughput virtual screening undertakings. In this work, we compare binding affinities from density functional theory (DFT) and force field calculations for 272 zeolite-OSDA pairs obtained from static and time-averaged simulations. Enabled by automation software, we show that binding energies from the frozen pose method correlate best with DFT time-averaged energies. They are also less sensitive to the choice of initial lattice parameters and optimization algorithms, as well as less computationally expensive. Furthermore, we demonstrate that a broader exploration of the conformation space from molecular dynamics simulations does not provide significant improvements in binding energy trends over single-point calculations. The code and benchmark data are open-sourced and provide robust and computationally-efficient guidelines to calculating binding energies in zeolite-OSDA pairs.

In the Quest for a Stable Triplet State in Small Polyaromatic Hydrocarbons : An In-Silico Tool for Rational Design and Prediction

2019 ◽  
Author(s):  
Madhumita Rano ◽  
Sumanta K Ghosh ◽  
Debashree Ghosh
Keyword(s):  
Triplet State ◽  
Small Molecules ◽  
In Silico ◽  
Qualitative Agreement ◽  
Rational Design ◽  
Polyaromatic Hydrocarbons ◽  
Spin Hamiltonian ◽  
Spin Frustration ◽  
Computationally Efficient ◽  
High Level

<div>Combining the roles of spin frustration and geometry of odd and even numbered rings in polyaromatic hydrocarbons (PAHs), we design small molecules that show exceedingly small singlet-triplet gaps and stable triplet ground states. Furthermore, a computationally efficient protocol with a model spin Hamiltonian is shown to be capable of qualitative agreement with respect to high level multireference calculations and therefore, can be used for fast molecular discovery and screening.</div>

High-Entropy Alloys as Catalysts for the CO2 and CO Reduction Reactions

2019 ◽  
Author(s):  
Jack Pedersen ◽  
Thomas Batchelor ◽  
Alexander Bagger ◽  
Jan Rossmeisl
Keyword(s):  
Density Functional ◽  
Rational Design ◽  
Hydrogen Adsorption ◽  
Co Adsorption ◽  
Reduction Reaction ◽  
Supervised Machine Learning ◽  
High Entropy Alloys ◽  
High Entropy ◽  
Co Reduction ◽  
Disordered Alloy

Using the high-entropy alloys (HEAs) CoCuGaNiZn and AgAuCuPdPt as starting points we provide a framework for tuning the composition of disordered multi-metallic alloys to control the selectivity and activity of the reduction of carbon dioxide (CO2) to highly reduced compounds. By combining density functional theory (DFT) with supervised machine learning we predicted the CO and hydrogen (H) adsorption energies of all surface sites on the (111) surface of the two HEAs. This allowed an optimization for the HEA compositions with increased likelihood for sites with weak hydrogen adsorption{to suppress the formation of molecular hydrogen (H2) and with strong CO adsorption to favor the reduction of CO. This led to the discovery of several disordered alloy catalyst candidates for which selectivity towards highly reduced carbon compounds is expected, as well as insights into the rational design of disordered alloy catalysts for the CO2 and CO reduction reaction.

scholarly journals Tuning the electronic structure of Ag-Pd alloys to enhance performance for alkaline oxygen reduction

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
José A. Zamora Zeledón ◽  
Michaela Burke Stevens ◽  
G. T. Kasun Kalhara Gunasooriya ◽  
Alessandro Gallo ◽  
Alan T. Landers ◽  
...  
Keyword(s):  
Metal Binding ◽  
Precious Metal ◽  
Metal Content ◽  
Density Functional ◽  
Binding Energies ◽  
Intrinsic Activity ◽  
Energy Technologies ◽  
Highly Active ◽  
Wide Range ◽  
Precious Metal Content

AbstractAlloying is a powerful tool that can improve the electrocatalytic performance and viability of diverse electrochemical renewable energy technologies. Herein, we enhance the activity of Pd-based electrocatalysts via Ag-Pd alloying while simultaneously lowering precious metal content in a broad-range compositional study focusing on highly comparable Ag-Pd thin films synthesized systematically via electron-beam physical vapor co-deposition. Cyclic voltammetry in 0.1 M KOH shows enhancements across a wide range of alloys; even slight alloying with Ag (e.g. Ag0.1Pd0.9) leads to intrinsic activity enhancements up to 5-fold at 0.9 V vs. RHE compared to pure Pd. Based on density functional theory and x-ray absorption, we hypothesize that these enhancements arise mainly from ligand effects that optimize adsorbate–metal binding energies with enhanced Ag-Pd hybridization. This work shows the versatility of coupled experimental-theoretical methods in designing materials with specific and tunable properties and aids the development of highly active electrocatalysts with decreased precious-metal content.

scholarly journals Nanotechnology-based approaches for targeting and delivery of drugs via Hexakis (m-PE) macrocycles

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Samaneh Pasban ◽  
Heidar Raissi
Keyword(s):  
Drug Delivery ◽  
Density Functional ◽  
Water Solution ◽  
Decomposition Analysis ◽  
Binding Energies ◽  
Energy Decomposition Analysis ◽  
Partial Density ◽  
High Propensity ◽  
The Stability ◽  
Novel Applications

AbstractHexakis (m-phenylene ethynylene) (m-PE) macrocycles, with aromatic backbones and multiple hydrogen-bonding side chains, had a very high propensity to self-assemble via H-bond and π–π stacking interactions to form nanotubular structures with defined inner pores. Such stacking of rigid macrocycles is leading to novel applications that enable the researchers to explored mass transport in the sub-nanometer scale. Herein, we performed density functional theory (DFT) calculations to examine the drug delivery performance of the hexakis dimer as a novel carrier for doxorubicin (DOX) agent in the chloroform and water solvents. Based on the DFT results, it is found that the adsorption of DOX on the carrier surface is typically physisorption with the adsorption strength values of − 115.14 and − 83.37 kJ/mol in outside and inside complexes, respectively, and so that the essence of the drug remains intact. The negative values of the binding energies for all complexes indicate the stability of the drug molecule inside and outside the carrier's cavities. The energy decomposition analysis (EDA) has also been performed and shown that the dispersion interaction has an essential role in stabilizing the drug-hexakis dimer complexes. To further explore the electronic properties of dox, the partial density of states (PDOS and TDOS) are calculated. The atom in molecules (AIM) and Becke surface (BS) methods are also analyzed to provide an inside view of the nature and strength of the H-bonding interactions in complexes. The obtained results indicate that in all studied complexes, H-bond formation is the driving force in the stabilization of these structures, and also chloroform solvent is more favorable than the water solution. Overall, our findings offer insightful information on the efficient utilization of hexakis dimer as drug delivery systems to deliver anti-cancer drugs.

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