Determination of pKa Values via ab initio Molecular Dynamics and its Application to Transition Metal-Based Water Oxidation Catalysts

Variations in proton transfer pathways and energetics on pristine and defect-rich quartz surfaces in water: Insights into the bimodal acidities of quartz

HYPOTHESIS

Understanding the mechanisms of proton transfer on quartz surfaces in water is critical for a range of processes in geochemical, environmental, and materials sciences. The wide range of surface acidities (>9 pKa units) found on the ubiquitous mineral quartz is caused by the structural variations of surface silanol groups. Molecular scale simulations provide essential tools for elucidating the origin of site-specific surface acidities.

SIMULATIONS

We used density-functional tight-binding-based molecular dynamics combined with rare-event metadynamics simulations to probe the mechanisms of deprotonation reactions from ten representative surface silanol groups found on both pristine and defect-rich quartz (101) surfaces with Si vacancies.

FINDINGS

The results show that deprotonation is a highly dynamic process where both the surface hydroxyls and bridging oxygen atoms serve as the proton acceptors, in addition to water. Deprotonation of embedded silanols through intrasurface proton transfer exhibited lower pKa values with less H-bond participation and higher energy barriers, suggesting a new mechanism to explain the bimodal acidity observed on quartz surface. Defect sites, recently shown to comprise a significant portion of the quartz (101) surface, diversify the coordination and local H-bonding environments of the surface silanols, changing both the deprotonation pathways and energetics, leading to a wider range of pKa values (2.4 to 11.5) than that observed on pristine quartz surface (10.4 and 12.1).

Comprehensive Insights into the Family of Atomically Thin 2D-Materials for Diverse Photocatalytic Applications

2D materials with their fascinating physiochemical, structural, and electronic properties have attracted researchers and have been used for a variety of applications such as electrocatalysis, photocatalysis, energy storage, magnetoresistance, and sensing. In recent times, 2D materials have gained great momentum in the spectrum of photocatalytic applications such as pollutant degradation, water splitting, CO2 reduction, NH3 production, microbial disinfection, and heavy metal reduction, thanks to their superior properties including visible light responsive band gap, improved charge separation and electron mobility, suppressed charge recombination and high surface reactive sites, and thus enhance the photocatalytic properties rationally as compared to 3D and other low-dimensional materials. In this context, this review spot-lights the family of various 2D materials, their properties and their 2D structure-induced photocatalytic mechanisms while giving an overview on their synthesis methods along with a detailed discussion on their diverse photocatalytic applications. Furthermore, the challenges and the future opportunities are also presented related to the future developments and advancements of 2D materials for the large-scale real-time photocatalytic applications.

Closer Look at Inverse Electron Demand Diels–Alder and Nucleophilic Addition Reactions on s-Tetrazines Using Enhanced Sampling Methods

Inverse electron demand [4+2] Diels–Alder (iEDDA) reactions as well as unprecedented nucleophilic (azaphilic) additions of R-substituted silyl-enol ethers (where R is Phenyl, Methyl, and Hydrogen) to 1,2,4,5-tetrazine (s-tetrazine) catalyzed by \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$\hbox {BF}_{3}$$\end{document}BF3 have recently been discovered (Simon et al. in Org Lett 23(7):2426–2430, 2021), where static calculations were employed for calculation of activation energies. In order to have a more realistic dynamic description of these reactions in explicit solution at ambient conditions, in this work we use a semiempirical tight-binding method combined with enhanced sampling techniques to calculate free energy surfaces (FESs) of the iEDDA and azaphilic addition reactions. Relevant products of not only s-tetrazine but also its derivatives such as \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$\hbox {BF}_{3}$$\end{document}BF3-mediated s-tetrazine adducts are investigated. We reconstruct the FESs of the iEDDA and azaphilic addition reactions using metadynamics and blue moon ensemble, and compare the ability of different collective variables (CVs) including bond distances, Social PeRmutation INvarianT (SPRINT) coordinates, and path-CV to describe the reaction pathway. We find that when a bulky Phenyl is used as a substituent at the dienophile the azaphilic addition is preferred over the iEDDA reaction. In addition, we also investigate the effect of \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$\hbox {BF}_{3}$$\end{document}BF3 in the diene and steric hindrance in the dienophile on the competition between the iEDDA and azaphilic addition reactions, providing chemical insight for reaction design.

Connecting Gas-Phase Computational Chemistry to Condensed Phase Kinetic Modeling: The State-of-the-Art

In recent decades, quantum chemical calculations (QCC) have increased in accuracy, not only providing the ranking of chemical reactivities and energy barriers (e.g., for optimal selectivities) but also delivering more reliable equilibrium and (intrinsic/chemical) rate coefficients. This increased reliability of kinetic parameters is relevant to support the predictive character of kinetic modeling studies that are addressing actual concentration changes during chemical processes, taking into account competitive reactions and mixing heterogeneities. In the present contribution, guidelines are formulated on how to bridge the fields of computational chemistry and chemical kinetics. It is explained how condensed phase systems can be described based on conventional gas phase computational chemistry calculations. Case studies are included on polymerization kinetics, considering free and controlled radical polymerization, ionic polymerization, and polymer degradation. It is also illustrated how QCC can be directly linked to material properties.

Computational Prediction of All Lanthanide Aqua Ion Acidity Constants

The protonation state of lanthanide-ligand complexes, or lanthanide-containing porous materials, with many Brønsted acid sites can change due to proton loss/gain reactions with water or other heteroatom-containing compounds. Consequently, variations in the protonation state of lanthanide-containing species affect their molecular structure and desired properties. Lanthanide(III) aqua ions undergo hydrolysis and form hydroxides; they are the best characterized lanthanide-containing species with multiple Brønsted acid sites. We employed constrained ab initio molecular dynamics simulations and electronic structure calculations to determine all acidity constants of the lanthanide(III) aqua ions solely from computation. The first, second, and third acidity constants of lanthanide(III) aqua ions were predicted, on average, within 1.2, 2.5, and 4.7 absolute pK_a units from experiment, respectively. A table includes our predicted pK_a values alongside most experimentally measured pK_a values known to date. The approach presented is particularly suitable to determine the Brønsted acidity of lanthanide-containing systems with multiple acidic sites, including those whose measured acidity constants cannot be linked to specific acid sites.

Predicting lanthanide coordination structures in solution with molecular simulation

The chemical and physical properties of lanthanide coordination complexes can significantly change with small variations in their molecular structure. Further, in solution, coordination structures (e.g., lanthanide-ligand complexes) are dynamic. Resolving solution structures, computationally or experimentally, is challenging because structures in solution have limited spatial restrictions and are responsive to chemical or physical changes in their surroundings. To determine structures of lanthanide-ligand complexes in solution, a molecular simulation approach is presented in this chapter, which concurrently considers chemical reactions and molecular dynamics. Lanthanide ion, ligand, solvent, and anion molecules are explicitly included to identify, in atomic resolution, lanthanide coordination structures in solution. The computational protocol described is applicable to determining the molecular structure of lanthanide-ligand complexes, particularly with ligands known to bind lanthanides but whose structures have not been resolved, as well as with ligands not previously known to bind lanthanide ions. The approach in this chapter is also relevant to elucidating lanthanide coordination in more intricate structures, such as in the active site of enzymes.

Quantum-Chemical ab initio Study of Side Chain pKa of Linear and Cyclic Lysine Dipeptides

Cyclic dipeptides show interesting biological activities such as antitumor, antiviral and so on. In biological systems, the bioavailability of drugs is determined by several parameters such as pKa values. In this study, we used DFT and thermodynamics cycle to determine pKa value of side chain of lysine in linear and cyclic dipeptides. All considered dipeptides were optimized using B3LYP and RMSD tool was used to compare the optimized structures. The calculated pKa values were compared with the available experimental data. Our results show that pKa of side chain of lysine increases for cyclic dipeptides compared to the linear ones. To justify the reason of increasing of pKa of cyclic dipeptides, we used NBO and AIM analyses. The analyses showed that a hydrogen bond in cyclic lysine dipeptides is responsible for increasing of pKa.

Nuclear quantum effects on autoionization of water isotopologs studied by ab initio path integral molecular dynamics

In this study, we investigate the nuclear quantum effects (NQEs) on the acidity constant (pK_A) of liquid water isotopologs under the ambient condition by path integral molecular dynamics (PIMD) simulations. We compared simulations using a fully explicit solvent model with a classical polarizable force field, density functional tight binding, and ab initio density functional theory, which correspond to empirical, semiempirical, and ab initio PIMD simulations, respectively. The centroid variable with respect to the proton coordination number of a water molecule was restrained to compute the gradient of the free energy, which measures the reversible work of the proton abstraction for the quantum mechanical system. The free energy curve obtained by thermodynamic integration was used to compute the pK_A value based on probabilistic determination. This technique not only reproduces the pK_A value of liquid D₂O experimentally measured (14.86) but also allows for a theoretical prediction of the pK_A values of liquid T₂O and aqueous HDO and HTO, which are unknown due to their scarcity. It is also shown that the NQEs on the free energy curve can result in a downshift of 4.5 ± 0.9 pK_A units in the case of liquid water, which indicates that the NQEs plays an indispensable role in the absolute determination of pK_A. The results of this study can help inform further extensions into the calculation of the acidity constants of isotope substituted species with high accuracy.

Accurate and rapid prediction of pKa of transition metal complexes: semiempirical quantum chemistry with a data-augmented approach

Data-augmented high-throughput QM approach to compute pK_a of transition metal hydride complexes with hDFT accuracy and low cost.

How accurate are approximate quantum chemical methods at modelling solute-solvent interactions in solvated clusters?

In this paper, the performance of a wide range of DFT methods is assessed for the calculation of interaction energies of thermal clusters of a solute in water. Three different charge states (neutral, proton transfer transition state and zwitterion) of glycine were solvated by 1 to 40 water molecules as sampled from molecular dynamics simulations. While some ab initio composite methods that employ insufficiently large basis sets incurred significant errors even for a cluster containing only 5 water molecules relative to the W1X-2 benchmark, the DLPNO-CCSD(T)/CBS and DSD-PBEP86 (triple zeta basis set) levels of theory predicted very accurate interaction energies. These levels of theory were used to benchmark the performance of 16 density functionals from different rungs of Jacob's Ladder. Of the Rung 4 functionals examined, the ωB97M-V and ωB97X-V functionals stood out for predicting absolute interaction energies in 40-water clusters with mean absolute deviations (MAD) ∼4 kJ mol-1. The B3LYP-D3(BJ) functional performed exceptionally well with a MAD ∼1.7 kJ mol-1 and is the overall best performing method. Calculations of relative interaction energies allow for cancellation of systematic errors, including basis set truncation and superposition errors, and the ωB97M-V and B3LYP-D3(BJ) double zeta basis set calculations yielded relative interaction energies that are within ∼3 kJ mol-1 of the benchmark. The ONIOM approximation provides another strategy for accelerating the calculation of accurate absolute interaction energies provided that the calculations have converged with respect to the size of the "high-level-layer".