Modeling the Partial Atomic Charges in Inorganometallic Molecules and Solids and Charge Redistribution in Lithium-Ion Cathodes

Deciphering the N1-substituent effects on biodegradation of sulfonamides: Novel insights revealed from molecular biology and computational chemistry approaches

Elucidating biodegradation mechanisms and predicting pollutant reactivities are essential for advancing the application of biodegradation engineering to address the challenge of thousands of emerging contaminants. Molecular biology and computational chemistry are powerful tools for this purpose, enabling the investigation of biochemical reactions at both the gene and atomic levels. This study employs the biodegradation of ten sulfonamide antibiotics as a case study to demonstrate the integration of genomics and quantum chemistry approaches in exploring the biodegradation behavior of emerging contaminants. The isolated functional strain, Paenarthrobacter sp., could completely degrade all ten model sulfonamides under aerobic conditions. These compounds share a 4-aminobenzenesulfonamide core but differ in N1-substituent rings. Despite structural variations, all sulfonamides follow a consistent degradation pathway, yielding aminated heterocycles as end products. This pathway involves key steps such as dehydrogenation activation, ipso-hydroxylation, and the cleavage of S-N and S-C bonds, with the latter being particularly influenced by the N1-substituents. Heterocyclic structures affect biodegradation rates by altering the electronic density at the C3 and N1 atoms of sulfonamides. Substituents with higher electron-donating potential and lower Gibbs free energy barriers for S-C and C-N bond cleavage significantly enhance biodegradation efficiency. This work not only deciphers the universal biodegradation mechanism of sulfonamides but also offers theoretical insights for predicting the biodegradation behavior and pattern of emerging contaminants. These findings contribute to the effective removal of emerging contaminants from aquatic environments, advancing the practical application of biotreatment technologies.

High-Throughput Screening of 1D Chalcogenide Cathode Materials Beyond VS4 for Rechargeable Magnesium-Ion Batteries

Owing to their high theoretical specific capacity and abundance of anodes, rechargeable Mg-ion batteries (rMIBs) have emerged as a supplement for post-Li generation. However, the strong Coulomb interactions on Mg2+ cations lead to inefficient storage and transport in the cathode, which severely restricts the actual performance of rMIBs. Herein, a virtual screening of the 1D material database (C1DB) is proposed to identify novel rMIB chalcogenide cathodes with large voids for relieving the Coulomb forces. By referring to the representative VS4 material, three potential 1D chalcogenide materials (SiS2, GeS2, and SiSe2) with optimized Coulomb interactions are ultimately screened out for rMIB cathodes. In addition, further theoretical analyses on geometry, electronic structures, and atomic charges reveal the significant roles of the large specific pore volume, low bond covalency, and mildly oxidizing anion element in optimizing rMIB cathode materials. Overall, this work may inspire future experimental and theoretical investigations, potentially accelerating breakthroughs of rMIB and other similar metal-ion batteries.

Predicting Magnetic Barriers in Lanthanide Complexes with Electrostatic Potential Charges

Single-molecule magnets (SMMs) with slow relaxation of magnetization and blocking temperatures above that of liquid nitrogen are essential for practical applications in high-density data storage devices and quantum computers. A rapid and accurate prediction of the effective magnetic relaxation barrier (Ueff) is needed to accelerate the discovery of high-performance SMMs. Using density functional theory and multireference calculations, we explored correlations between Ueff, partial atomic charges, and the anisotropic barrier for a series of sandwich-type lanthanide complexes containing cyclooctatetraene, substituted cyclopentadiene, phospholyl, boratabenzene, or borane ligands. Our results show a correlation between the electrostatic potential charge of the lanthanide ion in the complex and Ueff. Systematic ligand modifications show that reducing ligand nucleophilicity and incorporating soft bases enhance magnetic anisotropy and Ueff values. This work identifies a correlation to predict Ueff values and optimization of ligand coordination environments in lanthanide-based SMMs.

Alkyl groups in organic molecules are NOT inductively electron-releasing

It is commonly stated that alkyl groups exert an inductive electron-releasing effect when compared to hydrogen. This information has been given in numerous organic chemistry textbooks over the last 75 years. The evidence for this position is weak, and does not withstand scrutiny, and there is some evidence for the contrary position. We provide a significant body of computational data that clearly show that alkyl groups exert an inductive electron-withdrawing (-I) effect when compared to hydrogen. This revised position is not in conflict with experimental data, since alkyl group inductive effects are small and are likely to be masked by hyperconjugation/polarizability effects (particularly in charged species), and also by solvent effects.

Development of a Fluctuating Charge Model for Zinc-Containing Metalloproteins

Metalloproteins widely exist in biology and play important roles in various processes. To accurately simulate metalloprotein systems, modeling polarization and charge transfer effects is vital. The fluctuating charge (FQ) model can efficiently generate atomic charges and simulate the charge transfer effect; it has been developed for a wide range of applications, but few models have been specifically tailored for metalloproteins. In this study, we present a fluctuating charge model specifically for zinc-containing metalloproteins based on the extended charge equilibration (EQeq) scheme. Our model was parametrized to reproduce CM5 charges instead of RESP/CHELPG charges because the former is less dependent on the conformation or basis set, does not suffer from unphysical charges for buried atoms, and is still being able to well reproduce the molecular dipoles. During our study, we found that adding the Pauling-bond-order-like term (referred to as the "+C term" in a previous study) between the zinc ion and ligating atoms significantly improves the model's performance. Although our model was trained for four-coordinated zinc sites only, our results indicated it can well describe the atomic charges in diverse zinc sites. Morever, our model was used to generate partial charges for the metal sites in three different zinc-containing metalloproteins (with four-, five-, and six-coordinated metal sites, respectively). These charges exhibited performance comparable to that of the RESP charges in molecular dynamics (MD) simulations. Additional tests indicated our model could also well reproduce the CM5 charges when geometric changes were involved. Those results indicate that our model can efficiently calculate the atomic charges for metal sites and well simulate the charge transfer effect, which marks an important step toward developing versatile polarizable force fields for metalloproteins.

Exploring HCl-HCl interactions: QZVPP calculations, improved Lennard-Jones potential, and second virial coefficient analysis for thermodynamics and industrial applications

In this paper, we present a comprehensive analysis of HCl-HCl interactions, including QZVPP calculations, energy fitting, conformation validation, and the determination of the second virial coefficient B using improved Lennard-Jones (ILJ) potential parameters. To acquire accurate interaction energies, initial QZVPP calculations are performed on approximately 1851 randomly generated HCl-HCl conformations. Then, these energies are used to fit an improved Lennard-Jones potential energy surface, allowing for a robust description of HCl-HCl interactions. The ILJ potential parameters are then used to validate particular HCl dimer conformations, ensuring their stability and consistency with experimental observations. The correlation between calculated and experimental conformations strengthens the validity of the ILJ potential parameters. In addition, the second viral coefficient B is calculated at various temperatures using the ILJ potential. The obtained B values are compared to experimental data, demonstrating close agreement, and validating the ILJ potential's ability to accurately capture the intermolecular interactions and gas-phase behavior of the HCl-HCl system. The results of this study demonstrate the effective implementation of QZVPP calculations, energy fitting, and ILJ potential parameters in validating HCl-HCl conformations and accurately determining the second virial coefficient B. The high degree of concordance between calculated B values and experimental data demonstrates the validity of the ILJ potential and its suitability for modeling HCl-HCl interactions. This research contributes to a greater comprehension of HCl-HCl interactions and their implications for numerous chemical and atmospheric processes. The validated conformations, energy fitting method, and calculated second virial coefficients provide valuable instruments for future research and pave the way for more accurate modeling and simulations of HCl-HCl systems.

Enhanced CO2 capture in partially interpenetrated MOFs: Synergistic effects from functional group, pore size, and steric-hindrance

Excessive CO2 emissions have contributed to global environmental issues, driving the development of CO2 capture adsorbents. Among various candidates, metal-organic frameworks (MOFs) are considered the most promising due to their unique microporous structure. Herein, a series of partially interpenetrated MOFs named UPC-XX were built to investigate the continuous enhancement in CO2 capture performance via synergistic effects from functional group, pore size, and steric-hindrance using theoretical calculations. It's showed that the introduction of functional groups improved the structure polarity and created more adsorption sites, thus, enhanced CO2 capture capacity. The pore size modification augments the exposure of adsorption sites to mitigate the negative impact of pore space and surface area reduction caused by the introduction of functional groups, thereby further increasing the CO2 capture capacity. The steric-hindrance effect optimized the adsorption sites distribution, which hasn't been considered in the previous two regulation strategies, thus, further increased the CO2 capture capacity. The results underscore UPC-MOFs as outstanding adsorbent materials, among the UPC-MOFs, UPC-OSO3-steric exhibited the highest CO2 capture capacity of 12.69 mmol/g with selectivities of 1142.41 (CO2 over N2) and 507.42 (CO2 over CH4) at 1.0 bar, 298 K. And the synergistic effect mechanisms of functional group, structure size, and steric hindrance were elucidated through theoretical calculations analyzing pore characteristics, gas distribution, isosteric heat, and van der Waals/Coulomb interactions.

Earth-abundant photocatalyst for H 2 generation from NH 3 with light-emitting diode illumination

Catalysts based on platinum group metals have been a major focus of the chemical industry for decades. We show that plasmonic photocatalysis can transform a thermally unreactive, earth-abundant transition metal into a catalytically active site under illumination. Fe active sites in a Cu-Fe antenna-reactor complex achieve efficiencies very similar to Ru for the photocatalytic decomposition of ammonia under ultrafast pulsed illumination. When illuminated with light-emitting diodes rather than lasers, the photocatalytic efficiencies remain comparable, even when the scale of reaction increases by nearly three orders of magnitude. This result demonstrates the potential for highly efficient, electrically driven production of hydrogen from an ammonia carrier with earth-abundant transition metals.

Theoretical Investigation of Regiodivergent Addition of Anilines and Phenolates to p-Benzoquinone Ring

Two different products were obtained by the regiodivergent reaction of benzoquinone derivatives with phenolates and anilines: 3-aryloxybenzoquinone and 2-phenylamino-3-bromobenzoquinone. Calculated density functional theory free energies of reaction values corroborate the experimental observation of the formation of the substitution product in the reaction with phenolates in acetonitrile and the product of addition/oxidation for the reaction with aniline in water. Calculated charges and Fukui functions are similar for C2 and C3 atoms, indicating an equal possibility to suffer a nucleophilic attack. The calculated energy barriers for nucleophilic attack steps indicated that the first steps of the substitution with phenolates and addition/oxidation with anilines are faster, which justifies the formation of the respective products. The natural bond order analysis for the transition states revealed that there is a strong interaction between lone pairs of N and O atoms and the π_C2C3 ^* for the O → C2 and N → C3 attacks and a weak interaction for the O → C3 and N → C2 attacks, which also agrees with experimental observations.

The adsorption of NO2, SO2, and O3 molecules on the Al-doped stanene nanotube: a DFT study

Adsorption of pollutant gas molecules (NO₂, SO₂, and O₃) on the surface of the Al-doped stanene nanotube was investigated within the first principle calculations of density functional theory (DFT). Adsorption mechanisms were studied by analyzing optimized structures, band structures, projected density of states (PDOS), charge density difference (CDD), molecular orbitals, and band theory. Investigation of charge transfer by Mulliken population showed that NO₂ accumulated while SO₂ and O₃ depleted charge density on the Al-doped nanotube. The differences in band structures before and after adsorption implied that the electronic characteristics of Al-doped nanotube changed dramatically in case of NO₂ adsorption, which converted Al-doped nanotube to a semiconductor material. High adsorption energy and the significant overlap between PDOS spectra indicated that the adsorption process was chemisorption for NO₂, SO₂, and O₃ on the doped nanotube with the obtained order of O₃ > SO₂ > NO₂. The results showed that the adsorption of NO₂, SO₂, and O₃ occurred on the Al-doped stanene nanotube, and that all the three gas molecules could be detected by Al-doped stanene nanotube with various detection strengths.

Benchmarking various types of partial atomic charges for classical all-atom simulations of metal-organic frameworks

The density derived electrostatic and chemical (DDEC) approach for calculating the charges of atoms in a metal-organic framework (MOF) is considered to be the most accurate (yet computationally costly) one among many charge-assignment methods. Here, we conducted a comparative study on five different types of atomic partial charges (namely CM5, Mulliken, Qeq, EQeq and PACMOF) prepared for a subset of MOFs with affordable computational costs and benchmarked them with respect to the DDEC charges, which is particularly relevant because currently most databases lack MOFs with pre-calculated DDEC charges. To find a suitable charge type alternative to the DDEC approach, we statistically ranked the five charge types based on two metrics, the relative standard deviation of charges and relative dipole moment difference, based on which we provide general guidance as well as suggestions for specific MOFs according to bond polarity analyses. Finally, we recommend a possible and more accurate parametrization scheme for future studies.

Li8MnO6: A Novel Cathode Material with Only Anionic Redox

In Li-excess transition metal-oxide cathode materials, anionic oxygen redox can offer high capacity and high voltages, although peroxo and superoxo species may cause oxygen loss, poor cycling performance, and capacity fading. Previous work showed that undesirable formation of peroxide and superoxide bonds was controlled to some extent by Mn substitution, and the present work uses density functional calculations to examine the reasons for this by studying the anionic redox mechanism in Li₈MnO₆. This material is obtained by substituting Mn for Sn in Li₈SnO₆ or for Zr in Li₈ZrO₆, and we also compare this to previous work on those materials. The calculations predict that Li₈MnO₆ is stable at room temperature (with a band gap of 3.19 eV as calculated by HSE06 and 1.82 eV as calculated with the less reliable PBE+U), and they elucidate the chemical and structural effects involved in the inhibition of oxygen release in this cathode. Throughout the whole delithiation process, only O^2- ions are oxidized. The directional Mn-O bonds formed from unfilled 3d orbitals effectively inhibit the formation of O-O bonds, and the layered structure is maintained even after removing 3 Li per Li₈MnO₆ formula unit. The calculated average voltage for removal of 3 Li is 3.69 V by HSE06, and the corresponding capacity is 389 mAh/g. The high voltage of oxygen anionic redox and the high capacity result in a high energy density of 1436 Wh/kg. The Li-ion diffusion barrier for the dominant interlayer diffusion path along the c axis is 0.57 eV by PBE+U. These results help us to understand the oxygen redox mechanism in a new lithium-rich Li₈MnO₆ cathode material and contribute to the design of high-energy density lithium-ion battery cathode materials with favorable electrochemical properties based on anionic oxygen redox.

Metal Release Mechanism and Electrochemical Properties of Lix(Ni1/3Mn1/3Co1/3)O2

Complex metal oxides (CMOs) are used broadly in applications including electroreactive forms found in lithium-ion battery technology. Computational chemistry can provide unique information about how the properties of CMO cathode materials change in response to changes in stoichiometry, for example, changes of the lithium (Li) content during the charge–discharge cycle of the battery. However, this is difficult to measure experimentally due to the small cross-sectional area of the cations. Outside of operational conditions, the Li content can influence the transformations of the CMO when exposed to the environment. For example, metal release from CMOs in aqueous settings has been identified as a cross-cutting mechanism important to CMO degradation. Computational studies investigating metal release from CMOs show that the thermodynamics depend on the oxidation states of lattice cations, which is expected to vary with the lithium content. In this work, computational studies track changes in metal release trends as a function of Li content in Lix(Ni1/3Mn1/3Co1/3)O2 (NMC). The resulting dataset is used to construct a random forest tree (RFT) machine learning (ML) model. A modeling challenge in delithiation studies is the large configurational space to sample. Through investigating multiple configurations at each lithium fraction, we find structural features associated with favorable energies to chemically guide the identification of relevant structures and adequately predict voltage values.

Constrained DFT for Molecular Junctions

We have explored the use of constrained density functional theory (cDFT) for molecular junctions based on benzenediamine. By elongating the junction, we observe that the energy gap between the ionization potential and the electronic affinity increases with the stretching distance. This is consistent with the trend expected from the electrostatic screening. A more detailed analysis shows how this influences the charge distribution of both the individual metal layers and the molecular atoms. Overall, our work shows that constrained DFT is a powerful tool for studying screening effects in molecular junctions.

ab initio study of Mn-based systems for oxidative degradation

Organic contaminants can be removed from water/wastewater by oxidative degradation using oxidants such as manganese oxides and/or aqueous manganese ions. The Mn species show a wide range of activity, which is related to the oxidation state of Mn. Here, we use ab initio molecular dynamics simulations to address Mn oxidation states in these systems. We first develop a correlation between Mn partial atomic charge and the oxidation state based on results of 31 simulations on known Mn aqueous complexes. The results collapse to a master curve; the dependence of partial atomic charge on oxidation state weakens with increasing oxidation state, which concurs with a previously proposed feedback effect. This correlation is then used to address oxidation states in Mn systems used as oxidants. Simulations of MnO₂ polymorphs immersed in water give average oxidation states (AOS) in excellent agreement with experimental results, in that β-MnO₂ has the highest AOS, α-MnO₂ has an intermediate AOS, and δ-MnO₂ has the lowest AOS. Furthermore, the oxidation state varies substantially with the atom's environment, and these structures include Mn(III) and Mn(V) species that are expected to be active. In regard to the MnO₄^-/HSO₃^-/O₂ system that has been shown to be a highly effective oxidant, we propose a novel Mn complex that could give rise to the oxidative activity, where Mn(III) is stabilized by sulfite and dissolved O₂ ligands. Our simulations also show that the O₂ would be activated to O₂^2- in this complex under acidic conditions, and could lead to the formation of OH radicals that serve as oxidants.

Development of Density-Functional Tight-Binding Parameters for the Molecular Dynamics Simulation of Zirconia, Yttria, and Yttria-Stabilized Zirconia

In this work, a set of density-functional tight-binding (DFTB) parameters for the Zr-Zr, Zr-O, Y-Y, Y-O, and Zr-Y interactions was developed for bulk and surface simulations of ZrO₂ (zirconia), Y₂O₃ (yttria), and yttria-stabilized zirconia (YSZ) materials. The parameterization lays the ground work for realistic simulations of zirconia-, yttria-, and YSZ-based electrolytes in solid oxide fuel cells and YSZ-based catalysts on long timescales and relevant size scales. The parameterization was validated for the zirconia and yttria polymorphs observed under standard conditions based on density functional theory calculations and experimental data. Additionally, we performed DFTB-based molecular dynamics (MD) simulations to compute structural and vibrational properties of these materials. The results show that the parameters can give a qualitatively correct phase ordering of zirconia, where the tetragonal phase is more stable than the cubic phase at a lower temperature. The lattice parameters are only slightly overestimated by 0.05-0.1 Å (2% error), still within the typical accuracy of first-principles methods. Additionally, the MD results confirm that zirconia and yttria phases are stable against transformations under standard conditions. The parameterization also predicts that vibrational spectra are within the range of 100-1000 cm^-1 for zirconia and 100-800 cm^-1 for yttria, which is in good agreement with predictions both from full quantum mechanics and a recently developed classical force field. To further demonstrate the advantage of the developed DFTB parameters in terms of computational resources, we conducted DFTB/MD simulations of the YSZ4 and YS12 models containing approximately 750 atoms.

Transition-Metal Chemistry of the Heavier Alkaline Earth Atoms Ca, Sr, and Ba

ConspectusAlkaline earth elements beryllium, magnesium, calcium, strontium, and barium with an ns² valence-shell configuration are usually classified as main-group elements that belong to the s-block atoms. For a long time, the elements were considered to be rather chemically uninteresting atomic species due to preconceived ideas about bonding, structure, and reactivity. They typically use the two ns valence electrons in forming ionic salt compounds with the metal in a formal oxidation state of +2. For the heavier alkaline earth atoms, calcium, strontium, and barium, their (n - 1)d atomic orbitals (AOs) are empty but lie close in energy to the valence np orbitals. Earlier theoretical investigations have already suggested that these elements can employ the (n - 1)d AOs to some extent to form polar bonds in divalent species in which the alkaline earth metal centers are sufficiently positively charged. The d orbital involvement increases from Ca to Sr and markedly in Ba. Thus, barium has been termed an honorary transition metal.Recently, molecular complexes of Ca, Sr, and Ba were prepared in the gas phase and in a low-temperature solid neon matrix and were detected by infrared spectroscopy. An analysis of the electronic structures of [Ba(CO)]⁺, [Ba(CO)]^-, saturated coordinated octacarbonyls [M(CO)₈] and [M(CO)₈]⁺, isoelectronic dinitrogen complexes [M(N₂)₈] and [M(N₂)₈]⁺, and the tribenzene complexes [M(Bz)₃] (M = Ca, Sr, Ba) revealed that the metal-ligand bonding can be straightforwardly discussed using the traditional Dewar-Chatt-Duncanson (DCD) model as in classical transition-metal complexes. The metal-ligand bonds can be explained with metal → ligand π back donation from occupied metal (n - 1)d AOs to vacant antibonding π molecular orbitals of the ligands with concomitant σ donation from occupied MOs of the ligands to vacant metal d orbitals of the alkaline earth atoms. In addition, heteronuclear Ca-Fe carbonyl cation complexes were also produced in the gas phase. Bonding analysis of the coordination saturated [CaFe(CO)₁₀]⁺ complex implies that it can be described by the bonding interactions between a [Ca(CO)₆]²⁺ fragment and an [Fe(CO)₄]^- anion fragment in forming a Fe → Ca d-d dative bond. The nature of metal-ligand and metal-metal bonding was quantitatively elucidated by the energy decomposition analysis in conjunction with the natural orbitals for the chemical valence (EDA-NOCV) method, which indicate that the (n - 1)d AOs of the alkaline earth metals are the dominant orbitals participating in the covalent interactions, just as typical transition metals. The results indicate that the heavier alkaline earth elements have a much richer covalent chemistry than previously thought. These findings, along with earlier studies, suggest that the heavier alkaline earth atoms Ca, Sr, and Ba should be classified as transition metals rather than main group atoms in the periodic table of the elements. This interesting structural chemistry, together with some recently reported examples of spectacular reactivity, establishes these elements as exciting and promising research targets in current research.

Cu[Ni(2,3-pyrazinedithiolate)2] Metal-Organic Framework for Electrocatalytic Hydrogen Evolution

The application of metal-organic frameworks (MOFs) as electrocatalysts for small molecule activation has been an emerging topic of research. Previous studies have suggested that two-dimensional (2D) dithiolene-based MOFs are among the most active for the hydrogen evolution reaction (HER). Here, a three-dimensional (3D) dithiolene-based MOF, Cu[Ni(2,3-pyrazinedithiolate)₂] (1), is evaluated as an electrocatalyst for the HER. In pH 1.3 aqueous electrolyte solution, 1 exhibits a catalytic onset at -0.43 V vs the reversible hydrogen electrode (RHE), an overpotential (η_10 mA/cm²) of 0.53 V to reach a current density of 10 mA/cm², and a Tafel slope of 69.0 mV/dec. Interestingly, under controlled potential electrolysis, 1 undergoes an activation process that results in a more active catalyst with a 200 mV reduction in the catalytic onset and η_10 mA/cm². It is proposed that the activation process is a result of the cleavage of Cu-N bonds in the presence of protons and electrons. This hypothesis is supported by various experimental studies and density functional theory calculations.

Improved Spin-State Energy Differences of Fe(II) Molecular and Crystalline Complexes via the Hubbard U-Corrected Density

We recently showed that the DFT+U approach with a linear-response U yields adiabatic energy differences biased toward high spin [Mariano et al. J. Chem. Theory Comput. 2020, 16, 6755-6762]. Such bias is removed here by employing a density-corrected DFT approach where the PBE functional is evaluated on the Hubbard U-corrected density. The adiabatic energy differences of six Fe(II) molecular complexes computed using this approach, named PBE[U] here, are in excellent agreement with coupled cluster-corrected CASPT2 values for both weak- and strong-field ligands resulting in a mean absolute error (MAE) of 0.44 eV, smaller than that of the recently proposed Hartree-Fock density-corrected DFT (1.22 eV) and any other tested functional, including the best performer TPSSh (0.49 eV). We take advantage of the computational efficiency of this approach and compute the adiabatic energy differences of five molecular crystals using PBE[U] with periodic boundary conditions. The results show, again, an excellent agreement (MAE = 0.07 eV) with experimentally extracted values and a superior performance compared with the best performers M06-L (MAE = 0.08 eV) and TPSSh (MAE = 0.31 eV) computed on molecular fragments.

Fast and Accurate Machine Learning Strategy for Calculating Partial Atomic Charges in Metal-Organic Frameworks

Computational high-throughput screening using molecular simulations is a powerful tool for identifying top-performing metal-organic frameworks (MOFs) for gas storage and separation applications. Accurate partial atomic charges are often required to model the electrostatic interactions between the MOF and the adsorbate, especially when the adsorption involves molecules with dipole or quadrupole moments such as water and CO₂. Although ab initio methods can be used to calculate accurate partial atomic charges, these methods are impractical for screening large material databases because of the high computational cost. We developed a random forest machine learning model to predict the partial atomic charges in MOFs using a small yet meaningful set of features that represent both the elemental properties and the local environment of each atom. The model was trained and tested on a collection of about 320 000 density-derived electrostatic and chemical (DDEC) atomic charges calculated on a subset of the Computation-Ready Experimental Metal-Organic Framework (CoRE MOF-2019) database and separately on charge model 5 (CM5) charges. The model predicts accurate atomic charges for MOFs at a fraction of the computational cost of periodic density functional theory (DFT) and is found to be transferable to other porous molecular crystals and zeolites. A strong correlation is observed between the partial atomic charge and the average electronegativity difference between the central atom and its bonded neighbors.

Determining Partial Atomic Charges for Liquid Water: Assessing Electronic Structure and Charge Models

Partial atomic charges provide an intuitive and efficient way to describe the charge distribution and the resulting intermolecular electrostatic interactions in liquid water. Many charge models exist and it is unclear which model provides the best assignment of partial atomic charges in response to the local molecular environment. In this work, we systematically scrutinize various electronic structure methods and charge models (Mulliken, natural population analysis, CHelpG, RESP, Hirshfeld, Iterative Hirshfeld, and Bader) by evaluating their performance in predicting the dipole moments of isolated water, water clusters, and liquid water as well as charge transfer in the water dimer and liquid water. Although none of the seven charge models is capable of fully capturing the dipole moment increase from isolated water (1.85 D) to liquid water (about 2.9 D), the Iterative Hirshfeld method performs best for liquid water, reproducing its experimental average molecular dipole moment, yielding a reasonable amount of intermolecular charge transfer, and showing modest sensitivity to the local water environment. The performance of the charge model is dependent on the choice of the density functional and the quantum treatment of the environment. The computed molecular dipole moment of water generally increases with the percentage of the exact Hartree-Fock exchange in the functional, whereas the amount of charge transfer between molecules decreases. For liquid water, including two full solvation shells of surrounding water molecules (within about 5.5 Å of the central water) in the quantum chemical calculation converges the charges of the central water molecule. Our final pragmatic quantum chemical charge-assigning protocol for liquid water is the Iterative Hirshfeld method with M06-HF/aug-cc-pVDZ and a quantum region cutoff radius of 5.5 Å.

Porous Aromatic Framework Nanosheets Anchored with Lewis Pairs for Efficient and Recyclable Heterogeneous Catalysis

Lewis pairs (LPs) with outstanding performance for nonmetal-mediated catalysis reactions have high fundamental interest and remarkable application prospects. However, their solubility characteristics lead to instability and deactivation upon recycling. Here, the layered porous aromatic framework (PAF-6), featuring two kinds of Lewis base sites (NPiperazine and NTriazine), is exfoliated into few-layer nanosheets to form the LP entity with the Lewis acid. After comparison with various porous networks and verification by density functional theory (DFT) calculations, the NTriazine atom in the specific spatial environment is determined to preferably coordinate with the electron-deficient boron compound in a sterically hindered pattern. LP-bare porous product displays high catalytic activity for the hydrogenation of both olefin and imine compounds, and demonstrates ≈100% activity after 10 successful cycles in hydrogenation reactions. Considering the natural advantage of porous organic frameworks to construct LP groups opens up novel prospects for preparing other nonmetallic heterogeneous catalysts for efficient and recyclable catalysis.

Calculating and Characterizing the Charge Distributions in Solids

Accurate estimation of the partial atomic charges on metal centers is useful for understanding electronic and catalytic properties of materials. However, different methods of calculating these charges may give quite different results; this issue has been more widely studied for molecules than for solids. Here we study the charges on the metal centers of a test set of 18 solids containing transition metals by using density functional theory with several density functionals (PBE, PBE+U, TPSS, revTPSS, HLE17, revM06-L, B3LYP, B3LYP*, and other exchange-modified B3LYP functionals) and four charge models (Bader, Hirshfeld, CM5, and DDEC6). The test set contains 12 systems with nonmagnetic metal centers (eight metal oxides (MO₂), two metal sulfides (MS₂), and two metal selenides (MSe₂)) and six ferromagnetic transition metal complexes. Our study shows that, among the four types of charges, Bader charges are the highest and Hirshfeld charges are the lowest for all the systems, regardless of the functional being used. The CM5 charges are bigger than DDEC6 charges for MX₂ with M = Ti or Mo and X = S or Se, but for the other 14 cases they are lower. We found that the most of the systems are sensitive to the Hubbard U parameters in PBE+U and to the percentage X of Hartree-Fock exchange in exchange-modified B3LYP; as we increase U or X, the charges on the metal atoms in MX₂ increase steadily. Testing different density functionals shows charges calculated with higher Hubbard U parameters in PBE+U are comparable to B3LYP (with 20% Hartree-Fock exchange). Among four meta-GGA functionals studied, the charges with HLE17 have the closest agreement with B3LYP. The variation of charges with choice of charge model is greater than the variation with choice of density functional.

Theoretical Study on the Electronic Structure of Heavy Alkali-Metal Suboxides

On the metal-rich side of the phase diagrams of the Rb-O, Cs-O, and Rb-Cs-O systems, one can find a variety of stoichiometries: for example, Rb₉O₂, Rb₆O, Cs₄O, Cs₇O, Cs₁₁O₃, RbCs₁₁O₃, and Rb₇Cs₁₁O₃. They may be termed heavy alkali-metal suboxides. The application of the standard electron-counting scheme to these compounds suggests the presence of surplus electrons. This motivated us to carry out a theoretical study using the first-principles density functional theory (DFT) method. The structures of these compounds are based on either a formally cationic Rb₉O₂ or Cs₁₁O₃ cluster. The analyses of the partial charge density just below the Fermi level and the electron localization function (ELF) have revealed that there exist surplus electrons in interstitial regions of all the investigated suboxides so that the excess positive charge of the cluster can be compensated. Density of states (DOS) calculations suggest that all of the compounds are metallic. Therefore, the suboxides listed above may be regarded as a new family of metallic electrides, where coreless electrons reside in interstitial spaces and provide a conduction channel. Except for the phases of Rb₉O₂ and Cs₁₁O₃, the suboxide structures include both the cationic clusters and alkali-metal matrix. Several charge analyses indicate that the interstitial surplus-electron density can be assigned to the alkali-metal atoms in the metal matrix, leading to the possibility of the presence of negatively charged alkali-metal atoms, namely Rb^- (rubidide) and Cs^- (caeside) ions, a.k.a. alkalides. In Rb₆O, Rb^-, Rb⁰, and Rb⁺ are found to coexist in the same crystal structure. Similarly, in Cs₇O, one can find the three types of Cs atoms. However, in Cs₄O, no Cs⁰ state is identified. In the Rb-Cs-O ternary suboxides, Rb takes a negatively charged anion state or neutral state, while all of the Cs atoms are found to be cationic because they get involved in the Cs₁₁O₃ cluster and all the Rb atoms exist in interstitial sites. Orbital interactions between the clusters are analyzed to understand how the condensation of the clusters into the solid happens and how the electride nature ensues. These clusters are found to have some superatomic character.

A DFT study of structure and electrochemical properties of diiron-hydrogenase models with benzenedithiolato and benzenediselenato ligands

The chalcogen atom substitution in the Fe₂(bdt)(CO)₆ complex results in higher and lower proton affinities of iron and chalcogen atoms, respectively.

Surface-Plasmon-Induced Ammonia Decomposition on Copper: Excited-State Reaction Pathways Revealed by Embedded Correlated Wavefunction Theory

Ammonia is a promising hydrogen storage medium; however, its decomposition via conventional thermal catalysis requires a significant amount of thermal energy input in order to overcome the reaction barriers. Here, we use embedded correlated wavefunction (ECW) theory to quantify reaction pathways and energetics for ammonia decomposition (N-H bond dissociation and N₂ and H₂ associative desorption) on copper (Cu) nanoparticles using a Cu (111) surface model. We predict that surface plasmon excitations will be able to facilitate ammonia decomposition by substantially reducing the effective barriers along excited-state pathways. We estimate the reductions in reaction barriers for breaking the first N-H bond and for recombinative desorption of surface-bound nitrogen and hydrogen atoms to be approximately 1.7, 0.8, and 0.5 eV, respectively. Further, by using the experimental N₂ desorption barrier as a reference, we compare the accuracy of various theoretical methods, including plane-wave Kohn-Sham density functional theory calculations with commonly used exchange-correlation functionals, embedded complete active space second-order perturbation theory, and embedded multiconfiguration pair-density functional theory. This work offers further confirmation that the ECW theoretical framework is the most robust for treating highly correlated local electronic structures of solids.

The interplay and strength of the π⋯HF, C⋯HF, F⋯HF and F⋯HC hydrogen bonds upon the formation of multimolecular complexes based on C2H2⋯HF and C2H4⋯HF small dimers

The conception of this theoretical research was idealized aiming to unveil the intermolecular structures of complexes formed by acetylene or ethylene and hydrofluoric acid. At light of computational calculations by using the B3LYP/6-311++G(d,p) method, the geometries of the C₂H₂⋯(HF), C₂H₂⋯2(HF), C₂H₂⋯4(HF), C₂H₄⋯(HF), C₂H₄⋯2(HF) and C₂H₄⋯4(HF) hydrogen-bonded complexes were fully optimized. Moreover, the Post-Hartree-Fock calculations MP2/6-311++G(d,p), MP2/aug-cc-pVTZ, MP4(SDQ)/6-311++G(d,p) and CCSD/6-311++G(d,p) also were also used. The infrared spectra were analyzed in order to identify the new vibrational modes and frequencies of the proton donors shifted to red region. Through the modeling of charge-fluxes on the basis of the Quantum Theory of Atoms In Molecules (QTAIM) and, by contradicting the expectation of the hydrofluorination mechanisms of acetylene or ethylene, C⋯HF was recognized as a new type of hydrogen bond instead of the already well known π⋯H. The calculations of the Natural Bonding Orbital (NBO) and Charges derived from the Electrostatic Potential Grid-based (ChElPG) were also applied to interpret the shifting frequencies as well as measuring of the punctual charge-transfer after the formation of the complexes. Finally, the determination of the stabilization energy was carried out through the arguments of the Fock matrix in NBO basis and through the supermolecule approach. Also it is worthwhile to notice that some algebraic formulations were used for determining the electronic cooperative effect (CE).

A charge polarization model for the metal-specific activity of superoxide dismutases

The pathogenicity of Staphylococcus aureus is enhanced by having two superoxide dismutases (SODs): a Mn-specific SOD and another that can use either Mn or Fe. Using 94 GHz electron-nuclear double resonance (ENDOR) and electron double resonance detected (ELDOR)-NMR we show that, despite their different metal-specificities, their structural and electronic similarities extend down to their active-site ¹H- and ¹⁴N-Mn(ii) hyperfine interactions. However these interactions, and hence the positions of these nuclei, are different in the inactive Mn-reconstituted Escherichia coli Fe-specific SOD. Density functional theory modelling attributes this to a different angular position of the E. coli H171 ligand. This likely disrupts the Mn-H171-E170' triad causing a shift in charge and in metal redox potential, leading to the loss of activity. This is supported by the correlated differences in the Mn(ii) zero-field interactions of the three SOD types and suggests that the triad is important for determining metal specific activity.

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

We introduce a new atomic population analysis method that performs exceptionally well across an extremely broad range of periodic and non-periodic material types.

Introducing DDEC6 atomic population analysis: part 2. Computed results for a wide range of periodic and nonperiodic materials

DDEC6 atomic population analysis gives excellent performance for small and large molecules, porous solids, dense solids, solid surfaces, organometallic complexes, nanoclusters, and magnetic materials.

Exploring the possibilities of two-dimensional transition metal carbides as anode materials for sodium batteries

MXenes are predicted to be a family of promising Na anode materials with desirable electrochemical properties using density functional theory.