Previous Density Functional Theory Research Articles

Effects of uniaxial strain on structural, electronic, and optical properties of LiNbO3: Ab-initio calculations

The semiconductor LiNbO3 has recently attracted a great deal of interest in the material science community. In this study, the effect of uniaxial strain Ɛc on the structural and optoelectronic properties of the material is studied by the first-principles full-potential linearized augmented plane wave method. The results are obtained in a density functional theory (DFT) framework, using a generalized gradient approximation (GGA-PBE) based on total energy minimization, as implemented in the WIEN2k code. The research results show that the unstrained LiNbO3 is an indirect band gap semiconductor with energy of 3.544 eV, which improves the results of some previous DFT calculations, but is still lower than the experimental data. It is found that the strain between −8% and +8% will affect the value of the LiNbO3 band gap. In fact, the results show that the electronic properties are closely related to the external compressive and tensile stress (CTS), causing the electronic band gap of LiNbO3 to increase and decrease, indeed the gap energy goes from 3.119 eV for 8% to 3.746 eV for −8%. The optical coefficients in the in both x-z directions are studied. For unstrained LiNbO3 they are similar but significantly distinct. The applied uniaxial strain increases the anisotropy significantly, and the difference between the xx and zz directions becomes much larger. It has also been found that strain can cause considerable changes in the optical band gap of the material. In addition, the absorption capacity and optical conductivity is improved under tensile stress, which is more efficient and more suitable for optical applications in the visible and ultraviolet spectrum.

Rotational g factors and Lorentz forces of molecules and solids from density functional perturbation theory

Applied magnetic fields can couple to atomic displacements via generalized Lorentz forces, which are commonly expressed as gyromagnetic $g$ factors. We develop an efficient first-principles methodology based on density-functional perturbation theory to calculate this effect in both molecules and solids to linear order in the applied field. Our methodology is based on two linear-response quantities: the macroscopic polarization response to an atomic displacement (i.e., Born effective charge tensor), and the antisymmetric part of its first real-space moment (the symmetric part corresponding to the dynamical quadrupole tensor). The latter quantity is calculated via an analytical expansion of the current induced by a long-wavelength phonon perturbation, and compared to numerical derivatives of finite-wavevector calculations. We validate our methodology in finite systems by computing the gyromagnetic $g$ factor of several simple molecules, demonstrating excellent agreement with experiment and previous density-functional theory and quantum chemistry calculations. In addition, we demonstrate the utility of our method in extended systems by computing the energy splitting of the low-frequency transverse-optical phonon mode of cubic SrTiO$_3$ in the presence of a magnetic field.

A combined first principles study of the structural, magnetic, and phonon properties of monolayer CrI3.

The first magnetic 2D material discovered, monolayer (ML) CrI3, is particularly fascinating due to its ground state ferromagnetism. However, because ML materials are difficult to probe experimentally, much remains unresolved about ML CrI3's structural, electronic, and magnetic properties. Here, we leverage Density Functional Theory (DFT) and high-accuracy Diffusion Monte Carlo (DMC) simulations to predict lattice parameters, magnetic moments, and spin-phonon and spin-lattice coupling of ML CrI3. We exploit a recently developed surrogate Hessian DMC line search technique to determine CrI3's ML geometry with DMC accuracy, yielding lattice parameters in good agreement with recently published STM measurements-an accomplishment given the ∼10% variability in previous DFT-derived estimates depending upon the functional. Strikingly, we find that previous DFT predictions of ML CrI3's magnetic spin moments are correct on average across a unit cell but miss critical local spatial fluctuations in the spin density revealed by more accurate DMC. DMC predicts that magnetic moments in ML CrI3 are 3.62 μB per chromium and -0.145 μB per iodine, both larger than previous DFT predictions. The large disparate moments together with the large spin-orbit coupling of CrI3's I-p orbital suggest a ligand superexchange-dominated magnetic anisotropy in ML CrI3, corroborating recent observations of magnons in its 2D limit. We also find that ML CrI3 exhibits a substantial spin-phonon coupling of ∼3.32 cm-1. Our work, thus, establishes many of ML CrI3's key properties, while also continuing to demonstrate the pivotal role that DMC can assume in the study of magnetic and other 2D materials.

Exploring metastable states in UO2 using hybrid functionals and dynamical mean field theory

A detailed exploration of the f-atomic orbital occupancy space for UO2 is performed using a first principles approach based on density functional theory (DFT), employing a full hybrid functional within a systematic basis set. Specifically, the PBE0 functional is combined with an occupancy biasing scheme implemented in a wavelet-based algorithm which is adapted to large supercells. The results are compared with previous DFT + U calculations reported in the literature, while dynamical mean field theory is also performed to provide a further base for comparison. This work shows that the computational complexity of the energy landscape of a correlated f-electron oxide is much richer than has previously been demonstrated. The resulting calculations provide evidence of the existence of multiple previously unexplored metastable electronic states of UO2, including those with energies which are lower than previously reported ground states.

Reinvestigating oxygen adsorption on Ag(111) by using strongly constrained and appropriately normed semi-local density functional with the revised Vydrov van Voorhis van der Waals force correction.

While density functional theory (DFT) at the generalized gradient approximation (GGA) level has made great success in catalysis, it fails in some important systems such as the adsorption of the oxygen molecule on the Ag(111) surface. Previous DFT studies at the GGA level revealed theoretical inconsistencies on the adsorption energies and dissociation barriers of O2 on Ag(111) in comparison with the experimental conclusion. In this study, the strongly constrained and appropriately normed-revised Vydrov van Voorhis van der Waals correction functional (SCAN-rVV10) method at the meta-GGA level with the nonlocal van der Waals (vdW) force correction was used to reinvestigate the adsorption properties of O2 on the Ag(111) surface. The SCAN-rVV10 results successfully confirm the experimental observation that both molecular and dissociative adsorptions can exist for oxygen on Ag(111). The calculated adsorption energy for the physisorption state and the relevant dissociation energy barrier are close to the experimental data. It demonstrates that SCAN-rVV10 can outperform functionals at the GGA level for O2/Ag(111). Therefore, our findings suggest that SCAN-rVV10 can be the desired method for systems where the correct description of intermediate-ranged vdW forces is essential, such as the physisorption of small molecules on the solid surface.

Reflection absorption infrared spectroscopy of the surface chemistry of furfural on Pd(111)

The hydrolysis and subsequent acidic dehydration of biomass leads to the production of smaller oxygenates, including furfural, which can undergo subsequent reactions such as hydrogenation to produce value-added products. Palladium has been found to be an active catalyst for this process. As a result, the surface chemistry of furfural is investigated on a Pd(111) single-crystal surface using reflection-absorption infrared spectroscopy as a basis for understanding the catalytic conversion of furfural to value-added products. Following adsorption at 90 K, furfural adopts a flat-lying geometry at low coverages, but converts to a tilted species as the coverage approaches saturation. Heating to ∼175 K forms a tilted η1(O) species that appears to deprotonate on heating to above 200 K to form an intermediate with a tilted furyl ring and a carbonyl group close to parallel to the surface. Further heating to ∼250 K and above caused this species to decarbonylate to form adsorbed carbon monoxide and an infrared invisible furyl intermediate. This can then undergo a ring-opening reaction to produce further CO and form a C3H3 intermediate that can hydrogenate to produce propylene. This reaction sequence is in good agreement with previous density functional theory calculations and with the products observed in temperature-programmed desorption.

Ground State Properties of the Wide Band Gap Semiconductor Beryllium Sulfide (BeS).

We report the results from self-consistent calculations of electronic, transport, and bulk properties of beryllium sulfide (BeS) in the zinc-blende phase, and employed an ab-initio local density approximation (LDA) potential and the linear combination of atomic orbitals (LCAO). We obtained the ground state properties of zb-BeS with the Bagayoko, Zhao, and Williams (BZW) computational method, as enhanced by Ekuma and Franklin (BZW-EF). Our findings include the electronic energy bands, the total (DOS) and partial (pDOS) densities of states, electron and hole effective masses, the equilibrium lattice constant, and the bulk modulus. The calculated band structure clearly shows that zb-BeS has an indirect energy band gap of 5.436 eV, from Γ to a point between Γ and X, for an experimental lattice constant of 4.863 Å. This is in excellent agreement with the experiment, unlike the findings of more than 15 previous density functional theory (DFT) calculations that did not perform the generalized minimization of the energy functional, required by the second DFT theorem, which is inherent to the implementation of our BZW-EF method.

Explicit solvent effects on (1 1 0) ruthenium oxide surface wettability: Structural, electronic and mechanical properties of rutile RuO2 by means of spin-polarized DFT-MD

The structural, electronic and mechanical properties of crystalline ruthenium dioxide RuO2 in its rutile structure have been calculated via forefront spin-polarized Density Functional Theory (DFT) and DFT-Molecular Dynamics (DFT-MD) simulations. Notwithstanding RuO2 is known as a highly active catalyst for a wide number of (photo) electrochemical reactions in aqueous/humid environments, the study of the interaction of RuO2 surfaces with water has been confined largely to (static) surface science and water adsorption calculations. Herein, an atomistic understanding of bulk rutile RuO2 and explicit solvent effects on (110)-RuO2 facet are provided. We especially focus on the comprehension of the mechanistic interplay between surface wettability, interfacial water dynamics and surface chemical activity.Analysis and characterization of the interfacial water and H-bond environment reveal how explicit liquid water and its dynamics play a role in the surface reconstruction and in the hydrophobic nature of the (110)-RuO2 facet with a prevailing H-bond acceptor character. Moreover, we provide a dependence of physical and chemical properties, such as surface electric field and work function, from different degrees of surface wettability of the (110)-RuO2 facet. Results on bulk properties of crystalline ruthenium dioxide RuO2 are in good agreement with the nowadays available experimental evidences and previous DFT studies.

First-principles feasibility assessment of a topological insulator at the InAs/GaSb interface

First-principles simulations are conducted to shed light on the question of whether a two-dimensional topological insulator (2DTI) phase may be obtained at the interface between InAs and GaSb. To this end, the InAs/GaSb interface is compared and contrasted with the HgTe/CdTe interface. Density functional theory (DFT) simulations of these interfaces are performed using a machine-learned Hubbard U correction [npj Comput. Mater. 6, 180 (2020)]. For the HgTe/CdTe interface, our simulations show that band crossing is achieved and an inverted gap is obtained at a critical thickness of 5.1 nm of HgTe, in agreement with experiment and previous DFT calculations. In contrast, for InAs/GaSb, the gap narrows with increasing thickness of InAs; however, the gap does not close for interfaces with up to 50 layers (about 15 nm) of each material. When an external electric field is applied across the InAs/GaSb interface, the GaSb-derived valence band maximum is shifted up in energy with respect to the InAs-derived conduction band minimum until eventually the bands cross and an inverted gap opens. Our results show that it may be possible to reach the topological regime at the InAs/GaSb interface under the right conditions. However, it may be challenging to realize these conditions experimentally, which explains the difficulty of experimentally demonstrating an inverted gap in InAs/GaSb.

Unveiling the Active Structure of Single Nickel Atom Catalyst for Electrochemical CO2 Reduction

A single nickel atom embedded in graphene is one of the most representative single-atom catalysts, and it has a high activity and selectivity for electrochemical CO2 reduction (CO2R) to CO. However, the catalytic origin, especially the coordination structure of Ni, remains highly puzzling, as previous density functional theory (DFT) calculations showed that all the possible structures should be inactive and/or nonselective. Here, using ab initio molecular dynamics (AIMD) and a “slow-growth” sampling approach to evaluate the reaction kinetic barriers, we show that the charge capacity (of the site) and hydrogen bonding (with the intermediates), which were neglected/oversimplified in previous DFT calculations, play crucial roles, and including their effects can resolve the catalytic origin. Particularly, a high charge capacity allows the catalytic site to carry more charges than required for the electrochemical step, lowering the electrochemical barrier, and hydrogen bonding promotes the reaction that produces polar intermediates by stabilizing the intermediates and facilitating the H transfer from water, explaining the high selectivity for CO2R over the hydrogen evolution reaction. Consequently, we find that a hybrid coordination environment (with one nitrogen and three carbon atoms) for the Ni-atom is most active and selective for CO2R. Our work not only explains a long-standing puzzle for an important catalyst but also highlights the crucial roles of charge capacity and hydrogen bonding, which can help elucidate the mechanisms of other heterogeneous electrocatalysts in aqueous solution and enable more effective catalyst design [1,2].[1] X. Zhao, Y. Liu, J. Am. Chem. Soc. 2020, DOI: 10.1021/jacs.9b13872[2] D. Kim, J. Shi, Y. Liu, J. Am. Chem. Soc., 2018, 140, 9127-9131

Electrochemically Modeling a Nonelectrochemical System: Hydrogen Peroxide Direct Synthesis on Palladium Catalysts.

Nonelectrochemical hydrogen peroxide direct synthesis (HPDS) under ambient conditions is an environmentally benign and energy-efficient process that produces a green oxidizer, yet the reaction mechanism of HPDS is still controversial. Inspired by the recently suggested heterolytic mechanism that involves electron and proton transfer at Pd catalysts, we propose a new electrochemical density functional theory (DFT) model that combines the Butler-Volmer equation and constant-potential DFT with hybrid explicit-implicit solvent treatment. Application of this model to Pd surfaces showed that the heterolytic mechanism has a lower barrier for the protonation steps for H2O2 production than for the nonelectrochemical hydrogenation steps, leading to advantageous kinetics for H2O2 production over H2O production, while the conventionally accepted Langmuir-Hinshelwood mechanism fails to explain the experimental kinetics. This work resolves the unanswered discrepancies between previous experimental and DFT results, and we expect that these results will readily help the systematic development of improved catalysts for HPDS.

Machine-learning-accelerated discovery of single-atom catalysts based on bidirectional activation mechanism

Single-atom catalysts (SACs) have provided new impetus to the field of catalysis because of their high activity, high selectivity, and theoretically full utilization of active atoms. However, the ambiguous activation mechanism prevents a clear understanding of the structure-activity relationship and results in a great challenge of rational design of SACs. Herein, by combining density functional theory (DFT) calculations with machine learning (ML), we explore 126 SACs to analyze and develop the structure-activity relationship for the electrocatalytic nitrogen reduction reaction (NRR). We first propose a bidirectional activation mechanism with a new descriptor for catalytic activity, which provides new insights for the rational design of SACs. More importantly, we establish a ML model for predicting the catalytic performance of NRR, validated by both DFT calculations and experimental works. The successful ML prediction in this work helps with the accelerated design and discovery of new catalysts by computational screening with high practical significance. • A bidirectional activation mechanism is proposed for building catalytic theory • A new descriptor of N ie-d is applied for evalulating the catalytic activity for NRR • The developed ML model could predict the catalytic performance of SACs accurately Single-atom catalysts (SACs) have provided a new impetus to the field of catalysis. The key challenges in the development of SACs are to explore the structure-activity relationship and predict the catalytic performance of SACs. Our work addresses these challenges by examining a series of SACs supported on 2D materials via the combination of density functional theory (DFT) calculations and machine learning (ML). The proposed “bidirectional activation mechanism” not only explains some experimental results but also can be extended to other catalytic reactions, laying the foundations for constructing catalytic theory. Moreover, the developed ML model could predict the catalytic activity of SACs for the nitrogen reduction reaction with reliable accuracy, as validated by previous DFT and experimental work. This work provides new insights into catalysis theory and will accelerate the discovery of SACs, hugely influencing the real-world energy field. Singh and co-workers propose a bidirectional activation mechanism with a new descriptor of N ie-d for providing insights into catalysis on the basis of DFT calculations. Their developed ML model with high accuracy could accelerate the design of SACs for NRR.

Revisiting Understanding of Electrochemical CO2 Reduction on Cu(111): Competing Proton-Coupled Electron Transfer Reaction Mechanisms Revealed by Embedded Correlated Wavefunction Theory.

Copper (Cu) electrodes, as the most efficacious of CO2 reduction reaction (CO2RR) electrocatalysts, serve as prototypes for determining and validating reaction mechanisms associated with electrochemical CO2 reduction to hydrocarbons. As in situ electrochemical mechanism determination by experiments is still out of reach, such mechanistic analysis typically is conducted using density functional theory (DFT). The semilocal exchange-correlation (XC) approximations most often used to model such catalysis unfortunately engender a basic error: predicting the wrong adsorption site for CO (a key CO2RR intermediate) on the most ubiquitous facet of Cu, namely, Cu(111). This longstanding inconsistency casts lingering doubt on previous DFT predictions of the attendant CO2RR kinetics. Here, we apply embedded correlated wavefunction (ECW) theory, which corrects XC functional error, to study the CO2RR on Cu(111) via both surface hydride (*H) transfer and proton-coupled electron transfer (PCET). We predict that adsorbed CO (*CO) reduces almost equally to two intermediates, namely, hydroxymethylidyne (*COH) and formyl (*CHO) at -0.9 V vs the RHE. In contrast, semilocal DFT approximations predict a strong preference for *COH. With increasing applied potential, the dominance of *COH (formed via potential-independent surface *H transfer) diminishes, switching to the competitive formation of both *CHO and *COH (both formed via potential-dependent PCET). Our results also demonstrate the importance of including explicitly modeled solvent molecules in predicting electron-transfer barriers and reveal the pitfalls of overreliance on simple surface *H transfer models of reduction reactions.

Aluminum Hugoniot from model calculations including semicore electrons based on density functional theory

We present a method to obtain Hugoniot from model calculations based on density functional theory, and apply the method to aluminum Hugoniot. Technological advances have extended the experimental research of high energy density physics, and call for quantitative theoretical analysis. However, direct computation of Hugoniot from density functional theory is very difficult. We propose two step calculations of Hugoniot from density functional theory. The first step is molecular dynamics simulations with an ambient temperature for electrons. The second step is total energy calculations of a crystal with desired high temperatures for electrons and with the ambient temperature for electrons. We treated the semicore 2s and 2p electrons of aluminum as valence electrons only for the total energy calculations of the aluminum crystal. The aluminum Hugoniot from our model calculations is in excellent agreement with available experimental data and the previous density functional theory calculations in the literature.

Dipolar coupling of nanoparticle-molecule assemblies: An efficient approach for studying strong coupling.

Strong light-matter interactions facilitate not only emerging applications in quantum and non-linear optics but also modifications of properties of materials. In particular, the latter possibility has spurred the development of advanced theoretical techniques that can accurately capture both quantum optical and quantum chemical degrees of freedom. These methods are, however, computationally very demanding, which limits their application range. Here, we demonstrate that the optical spectra of nanoparticle-molecule assemblies, including strong coupling effects, can be predicted with good accuracy using a subsystem approach, in which the response functions of different units are coupled only at the dipolar level. We demonstrate this approach by comparison with previous time-dependent density functional theory calculations for fully coupled systems of Al nanoparticles and benzene molecules. While the present study only considers few-particle systems, the approach can be readily extended to much larger systems and to include explicit optical-cavity modes.

R2SCAN-3c: A "Swiss army knife" composite electronic-structure method.

The recently proposed r2SCAN meta-generalized-gradient approximation (mGGA) of Furness and co-workers is used to construct an efficient composite electronic-structure method termed r2SCAN-3c. To this end, the unaltered r2SCAN functional is combined with a tailor-made triple-ζ Gaussian atomic orbital basis set as well as with refitted D4 and geometrical counter-poise corrections for London-dispersion and basis set superposition error. The performance of the new method is evaluated for the GMTKN55 database covering large parts of chemical space with about 1500 data points, as well as additional benchmarks for non-covalent interactions, organometallic reactions, and lattice energies of organic molecules and ices, as well as for the adsorption on polar salt and non-polar coinage-metal surfaces. These comprehensive tests reveal a spectacular performance and robustness of r2SCAN-3c: It by far surpasses its predecessor B97-3c at only twice the cost and provides one of the best results of all semi-local density-functional theory (DFT)/QZ methods ever tested for the GMTKN55 database at one-tenth of the cost. Specifically, for reaction and conformational energies as well as non-covalent interactions, it outperforms prominent hybrid-DFT/QZ approaches at two to three orders of magnitude lower cost. Perhaps, the most relevant remaining issue of r2SCAN-3c is self-interaction error (SIE), owing to its mGGA nature. However, SIE is slightly reduced compared to other (m)GGAs, as is demonstrated in two examples. After all, this remarkably efficient and robust method is chosen as our new group default, replacing previous composite DFT and partially even expensive high-level methods in most standard applications for systems with up to several hundreds of atoms.

Effects of Th doping on mechanical properties of U<sub>1–</sub><i><sub>x</sub></i>Th<i><sub>x</sub></i>O<sub>2</sub>: An atomistic simulation

Since thorium (Th) owns high conversion ratio in thermal neutron spectrum, high melting temperature, high thermal conductivity and good corrosion resistance in high-temperature water, it can be doped into UO<sub>2</sub> based fuel to initiate the fission reaction, and improve the physical properties of UO<sub>2</sub>. Owing to the challenging experimental conditions and technologies, molecular dynamics (MD) simulations are conducted to investigate the influences of Th doping on the mechanical properties of U<sub>1–</sub><i><sub>x</sub></i>Th<i><sub>x</sub></i>O<sub>2</sub>. The phase transition from initial fluorite structure to the metastable scrutinyite phase when loading along the [001] direction is observed, which accords well with the previous density functional theory calculations. However, if U<sub>1–</sub><i><sub>x</sub></i>Th<i><sub>x</sub></i>O<sub>2</sub> is loaded along the [111] direction, only brittle fracture is observed. It is found that both the elastic modulus and fracture stress decrease linearly with elevating temperature but the fracture strain increases. As the Th concentration increases from 0 to 0.55, the elastic modulus first decreases and then increases; if the Th concentration is larger than 0.1, the fracture stress increases and the fracture strain decreases monotonically. The cracks are nucleated with an angle of 45º to the loading direction, propagate rapidly, and are characteristic of brittle fracture, which accords well with the classical failure criteria and experimental results for brittle materials. By comparison, the uniaxial tensile loading is also performed for polycrystalline U<sub>1–</sub><i><sub>x</sub></i>Th<i><sub>x</sub></i>O<sub>2</sub>. It is found that the elastic modulus and fracture stress decrease as the temperature increases. However, the elastic modulus is not sensitive to the Th concentration and the fracture increases as the Th concentration increases. The brittle intergranular fracture is observed in each of all polycrystalline samples. The obtained physical parameters are useful for designing the fuels in nuclear reactors.

Improved Peierls-Nabarro model for asymmetric nonplanar 1/2

The 1/2 < 11_0]{111} ordinary dislocations play an important role in the mechanical behaviors of L10 alloys. The core of this kind of dislocations has asymmetric four-fold nonplanar structure spreading onto two equivalent {111} planes, which makes the traditional planar core structure based Peierls-Nabarro (P–N) model inappropriate to describe the dislocation properties. Under this context, an improved Peierls-Nabarro (P–N) model is developed in the present work to investigate the dislocation width, stress field and Peierls stress of the ordinary 1/2 < 11_0]{111} screw dislocation in L10 alloys (TiAl, TiGa and CuAu). This extended P–N model considers the nonplanar core structure with physical information obtained by the density functional theory (DFT) simulations. By the variational method, the corresponding dislocation equation is solved. It is found that the dislocation width of the ordinary 1/2 < 11_0]{111} screw dislocation is as narrow as 0.5b. Compared to the results predicted for the planar core structure or the assumed Volterra dislocation, the long-range stress field induced by the real asymmetric four-fold core presents a clear rotation. When increasing the applied stress, the distribution of the Burgers vector along the four different core folds differs more and more from each other. When the applied stress attains a critical value (i.e., the Peierls stress), the dislocation core turns to be a planar structure and a fully discrete method is used to calculate the Peierls stress. Different from the original P–N model that underestimates the Peierls stress by several orders of magnitude, the Peierls stress predicted by the improved P–N model is well consistent with the previous DFT simulations. Apparently, when the long-range interaction between dislocations is taken into account for discrete dislocation simulations or theoretical analysis and when the Peierls stress is calculated for L10 alloys, the consideration of the asymmetric nonplanar core structure by the improved P–N model is necessary to have more accurate results.

Kβ X-ray Emission Spectroscopy as a Probe of Cu(I) Sites: Application to the Cu(I) Site in Preprocessed Galactose Oxidase.

Cu(I) active sites in metalloproteins are involved in O2 activation, but their O2 reactivity is difficult to study due to the Cu(I) d10 closed shell which precludes the use of conventional spectroscopic methods. Kβ X-ray emission spectroscopy (XES) is a promising technique for investigating Cu(I) sites as it detects photons emitted by electronic transitions from occupied orbitals. Here, we demonstrate the utility of Kβ XES in probing Cu(I) sites in model complexes and a metalloprotein. Using Cu(I)Cl, emission features from double-ionization (DI) states are identified using varying incident X-ray photon energies, and a reasonable method to correct the data to remove DI contributions is presented. Kβ XES spectra of Cu(I) model complexes, having biologically relevant N/S ligands and different coordination numbers, are compared and analyzed, with the aid of density functional theory (DFT) calculations, to evaluate the sensitivity of the spectral features to the ligand environment. While the low-energy Kβ2,5 emission feature reflects the ionization energy of ligand np valence orbitals, the high-energy Kβ2,5 emission feature corresponds to transitions from molecular orbitals (MOs) having mainly Cu 3d character with the intensities determined by ligand-mediated d-p mixing. A Kβ XES spectrum of the Cu(I) site in preprocessed galactose oxidase (GOpre) supports the 1Tyr/2His structural model that was determined by our previous X-ray absorption spectroscopy and DFT study. The high-energy Kβ2,5 emission feature in the Cu(I)-GOpre data has information about the MO containing mostly Cu 3dx2-y2 character that is the frontier molecular orbital (FMO) for O2 activation, which shows the potential of Kβ XES in probing the Cu(I) FMO associated with small-molecule activation in metalloproteins.

Ion-Exchange Modeling of Monovalent Alkali Cation Adsorption on Montmorillonite

AbstractIon-exchange modeling is one of the most widely used methods to predict ion adsorption data on clay minerals. The model parameters (e.g. number of adsorption sites and the cation adsorption capacity of each site) are optimized normally by curve fitting experimental data, which does not definitively identify the local environment of the adsorption sites. A new approach for constructing an ion-exchange model was pursued, whereby some of the parameters needed were obtained independently, resulting in fewer parameters being based on data-curve fitting. Specifically, a reversed modeling approach was taken in which the number of types of sites used by the model was based on a previous first-principles Density Functional Theory study, and the relative distribution of these sites was based on the clay’s chemical composition. To simplify the ion-exchange reactions involved, montmorillonite was Na-saturated to produce a well-controlled Na-montmorillonite (NaMnt) adsorbent. Ion adsorption data on NaMnt were collected from batch experiments over a wide range of pH, Cs+ concentrations, and in the presence of coexisting cations. Ion-exchange models were developed and optimized to predict these cation adsorption data on NaMnt. The maximum amount of adsorption of monovalent cations on NaMnt was obtained from the plateau of the adsorption envelope data at high pH. The remaining equilibrium constants (pK) were optimized by curve fitting the edges of the adsorption envelope data. The resultant three-site ion-exchange model was able to predict the retention of Li+, Na+, K+, and Cs+ very well as a function of pH. The model was then tested on adsorption envelopes of various combinations of these cations, and on Cs+ adsorption isotherms at three different pH values. The pK values were constant for all assays. The interlayer spacing of NaMnt was also analyzed to investigate its relation with cation adsorption strength. An X-ray diffraction study of the samples showed that the measured d001 values for these cations were consistent with their adsorption pK values. The Cs+ cation showed a strong ability to collapse the interlayer region of montmorillonite. In the presence of multiple competing cations, the broadening and presence of multiple d001 XRD peaks suggested that the cations in the interlayers may be segregated.