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At least 397 records · Page 22

Density Matrix Implementation of the Fermi–Löwdin Orbital Self-Interaction Correction Method

The Fermi–Löwdin orbital self-interaction correction (FLOSIC) method effectively provides a transformation from canonical orbitals to localized Fermi–Löwdin orbitals which are used to remove the self-interaction error in the Perdew–Zunger (PZ) framework. This transformation is solely determined by a set of points in space, called Fermi–Löwdin descriptors (FODs), and the occupied canonical orbitals or the density matrix. In this work, we provide a detailed workflow for the implementation of the FLOSIC method for removal of self-interaction error in DFT calculations in an orbital-by-orbital basis that takes advantage of the unitary invariant nature of the FLOSIC method. In this way, it is possible to cast the self-consistent energy minimization at fixed FODs in the same manner than standard Kohn–Sham with one additional term in the Kohn–Sham Hamiltonian that introduces the PZ self-interaction correction. Each energy minimization iteration is divided in two substeps, one for the density matrix and one for the FODs. Expressions for the effective Kohn–Sham matrix and FOD gradients are provided such that its implementation is suitable for most electronic structure codes. Here, we analyze the convergence characteristics of the algorithm and present applications for the evaluation of NMR shielding constants and real-time time-dependent DFT simulations based on the Liouville–von Neumann equation to calculate excitation energies.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Inferring the Energetics of CO 2 –Aniline Adduct Formation from Vibrational Spectroscopy

Control of atmospheric CO 2 is an important contemporary scientific and engineering challenge. Towards this goal, the reaction of CO 2 with amines to form carbamate bonds is an established method for CO 2 capture. However, controllable reversal of this reaction remains difficult and requires tuning the energetics of the carbamate bond. Through IR spectroscopy, we show that a characteristic frequency observed upon carbamate formation varies as a function of the substituent’s Hammett parameter for a family of para- substituted anilines. We present computational evidence that the vibrational frequency of the adducted CO 2 serves as a predictor of the energy of formation of the carbamate. Electron donating groups typically enhance the driving force of carbamate formation by transferring more charge to the adducted CO 2 and thus increasing the occupancy of the anti-bonding orbital in the carbon-oxygen bonds. Increased occupancy of the anti-bonding orbital within adducted CO 2 indicates a weaker bond, leading to a red shift in the characteristic carbamate frequency. As a result, our work serves the large field of CO 2 capture research where spectroscopic observables, such as IR frequencies, are more easily obtainable and can stand in as a descriptor of driving forces.

Amines↗

Comparison of Machine Learning Approaches for Prediction of the Equivalent Alkane Carbon Number for Microemulsions Based on Molecular Properties

The chemical properties of oils are vital in the design of microemulsion systems. The hydrophilic–lipophilic difference equation used to predict microemulsions’ phase behavior expresses the oils’ physiochemical properties as the equivalent alkane carbon number (EACN). The experimental determination of EACN requires knowledge of the temperature dependence of the microemulsion system and the effects of different surfactant concentrations. Thus, the experimental determination is time-intensive and tedious, requiring days to months for proper separations. Furthermore, the experiments require high purity of chemicals because microemulsions are sensitive to impurities. Our work focuses on the quick and reliable predictions of the EACN with machine learning (ML) models. Due to the immaturity of ML chemical predictions, we compare three graph neural networks (GNNs) and a gradient-boosted tree algorithm, known as XGBoost. The GNNs use the molecular structures represented as simplified molecular-input line-entry system (SMILES) codes for the initial input, which allows us to assess whether geometry optimization is necessary for reliable results. The XGBoost model also begins with the SMILES representations of the molecules but uses molecular descriptors instead of geometry optimizations. As a result, the best model tested (crystal graph convolutional neural network with Merck molecular force field-94) has an error of 1.15 EACN units of the true EACN for unknown data with the errors skewed toward zero and an R² score of 0.9

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Is the Local Ion Density Sufficient to Drive NaCl Nucleation from the Melt and Aqueous Solution?

Even though nucleation is ubiquitous in different science and engineering problems, investigating nucleation is extremely difficult due to the complicated ranges of time and length scales involved. In this work, we simulate NaCl nucleation in both molten and aqueous environments using enhanced sampling of all-atom molecular dynamics with deep-learning-based estimation of reaction coordinates. By incorporating various structural order parameters and learning the reaction coordinate as a function thereof, we achieve significantly improved sampling relative to traditional ad hoc descriptions of what drives nucleation, particularly in an aqueous medium. Our results reveal a one-step nucleation mechanism in both environments, with reaction coordinate analysis highlighting the importance of local ion density in distinguishing solid and liquid states. However, although fluctuations in the local ion density are necessary to drive nucleation, they are not sufficient. Our analysis shows that near the transition states, descriptors such as enthalpy and local structure become crucial. Furthermore, our protocol proposed here enables robust nucleation analysis and phase sampling and could offer insights into nucleation mechanisms for generic small molecules in different environments.

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Affinity of Nicotinoids to a Model Nicotinic Acetylcholine Receptor (nAChR) Binding Pocket in the Human Brain

The binding affinity of nicotinoids to the binding residues of the a4ß2 variant of the nicotinic acetylcholine receptor (nAChR) was identified as a strong predictor of the nicotinoid’s addictive character. Using ab-iniito calculations for model binding pockets of increasing size comprising of 3, 6, and 14 amino acids (3AA, 6AA, and 14AA) that are derived from the crystal structure, the differences in binding affinity of 6 nicotinoids, namely nicotine (NIC), nornicotine (NOR), anabasine (ANB), anatabine (ANT), myosmine (MYO), and cotinine (COT) were correlated to their previously reported doses required for increases in intracranial self-stimulation (ICSS) thresholds, a metric for their addictive function. By employing the many body decomposition, the differences in the binding affinities of the various nicotinoids could be attributed mainly to the proton exchange energy between the Pyridine and non-Pyridine rings of the nicotinoids and the interactions between them and a handful of proximal amino acids, namely Trp156, Trpß57, Tyr100, and Tyr204. Interactions between the guest nicotinoid and the amino acids of the binding pocket were found to be mainly classical in nature, except for those between the nicotinoid and Trp156. The larger pockets were found to model binding structures more accurately and predicted the addictive character of all nicotinoids while smaller models, which are more computationally feasible, would only predict the addictive character of nicotinoids that are similar to nicotine. Here, the present study identifies the binding affinity of the guest nicotinoid to the host binding pocket as a strong descriptor of the nicotinoid’s addiction potential and as such it can be employed as a fast screening technique for the potential addiction of nicotine analogs.

60 APPLIED LIFE SCIENCES↗

Size and Stoichiometry Effects on the Reactivity of MoCy Nanoparticles Towards Ethylene

Molybdenum carbides are promising catalysts alternative to Pt-group metals for the hydrogenation of unsaturated hydrocarbons. Nanostructuring has been shown to be an efficient way to boost the catalytic activity of these materials with MoCy nanoparticles (NPs) exhibiting a good performance when encapsulated inside zeolites or dispersed on inert supports such as carbon or gold. In this work, we focus on a systematic DFT study of the interaction of MoCy NPs with ethylene (C 2 H 4 ), as a general and simple approach for examining binding and activation of C≡C bonds. Models for 14 NPs, with a Mo/C ratio in the 0.67 to 2.00 range, have been built following a cascade procedure. Several chemical descriptors, including the adsorption energy, structural NPs distortion, C≡C deformation, and C 2 H 4 attachment energy have been analyzed along with a meticulous geometric and electronic characterization of bare NPs and C2H4 binding. The present results show that 1:1 stoichiometric Mo 6 C 6 , Mo 12 C 12 , and Mo 24 C 24 , and the non-stochiometric Mo 4 C 6 , Mo 8 C 12 (MetCar), and Mo 14 C 13 (Nanocube) are excellent systems for the binding and activation of ethylene, exhibiting a much bigger reactivity than a bulk δ-MoC(001) surface with a similar Mo:C ratio. In addition, C 2 H 4 binding on the NPs with a Mo/C < 1.08 is advantageous since, apart from a rather large adsorption energy, implies low energy values for NPs deformation (from 0.00 to 0.31 eV), C≡C distortion (from 0.30 to 0.52 eV), and C 2 H 4 attachment (from -2.12 to -2.58 eV). These theoretical results point to the ideal MoCy size and composition for C 2 H 4 binding, providing a background for further experimental studies aimed at the preparation of MoCy NPs as hydrogenation catalysts.

36 MATERIALS SCIENCE↗

Identification of Active Metal Carbide and Nitride Catalytic Facets for Hydrodeoxygenation Reactions

The catalytic hydrodeoxygenation (HDO) reaction is of considerable interest for biomass conversion to valuable chemicals and fuels, where one of the critical bottlenecks is the lack of cost-effective and efficient catalysts. To discover cost-efficient catalysts for the HDO reaction, we employed a density functional theory-based hierarchical catalyst design strategy based on catalytic descriptors, reaction energy profiles, and microkinetic modeling (MKM). We focused on the carbide and nitride catalyst space, for which we calculated 121 catalyst surfaces of Mo 2 C, MoC, Mo 2 N, W 2 C, NbC, VC, VN, and NbN catalysts. Based on the computed surface energies, reaction energies of oxygen removal, carbon binding strength, and the surface area of nanoparticles, the likely active facets are the Mo 2 C(111), MoC(011), VN(100), Mo 2 N(001), Mo 2 N(011), and Mo 2 N(100) surfaces. Further, detailed energy profiles were obtained, and MKM was performed for a model reaction (glycolaldehyde + 2H 2 . ethylene + 2H 2 O) on the Mo 2 C(111), VN(100), and MoC(100) surfaces. Based on the computed volcano map obtained from MKM, the predicted active facets for this HDO reaction are the Mo 2 C(111), MoC(011), VN(011), Mo 2 N(001), Mo 2 N(011), and Mo 2 N(100) surfaces. Additionally, none of the carbide and nitride catalyst surfaces are located in the optimal catalytic activity part. Therefore, it is essential to modify the catalyst via adding dopants or alloying to improve the catalytic activity. Catalytic modifications that can destabilize the surface adsorption of O*/H 2 O* and decrease the energy barriers of O-H bond formation are recommended to facilitate the HDO on the carbide and nitride catalysts. These a priori investigations provide guidelines for future low-cost HDO catalyst development.

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Machine Learning Self-Diffusion Prediction for Lennard-Jones Fluids in Pores

Predicting the diffusion coefficient of fluids under nanoconfinement is important for many applications including the extraction of shale gas from kerogen and product turnover in porous catalysts. Due to the large number of important variables, including pore shape and size, fluid temperature and density, and the fluid–wall interaction strength, simulating diffusion coefficients using molecular dynamics (MD) in a systematic study could prove to be prohibitively expensive. Here, we use machine learning models trained on a subset of MD data to predict the self-diffusion coefficients of Lennard-Jones fluids in pores. Our MD data set contains 2280 simulations of ideal slit pore, cylindrical pore, and hexagonal pore geometries. We use the forward feature selection method to determine the most useful features (i.e., descriptors) for developing an artificial neutral network (ANN) model with an emphasis on easily acquired features. Our model shows good predictive ability with a coefficient of determination (i.e., R 2 ) of ~0.99 and a mean squared error of ~2.9 × 10 –5 . Finally, we propose an alteration to our feature set that will allow the ANN model to be applied to nonideal pore geometries.

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Trends in Formic Acid Electro-Oxidation on Transition Metals Alloyed with Platinum and Palladium

Direct formic acid fuel cells (DFAFCs) have emerged as a promising power source to meet increased demands for alternative energy sources in the transportation and portable energy storage sectors. Furthermore, these fuel cells utilize formic acid (FA), a nontoxic and carbon-neutral fuel when produced from biomass or via CO 2 reduction. Despite the promise of DFAFCs, the best monometallic catalysts, platinum and palladium, are poisoned by CO through the indirect oxidation pathway and require large overpotentials. By alloying Pt and Pd with other metals, we aim to improve both the activity and selectivity of these catalysts. Here, we present a systematic density functional theory (GGA-PW91) study of FA electro-oxidation (FAO) on the (111) facet of bimetallic Pt (Pt 3 M) or Pd (Pd 3 M) catalysts (M = Au, Ag, Cu, Pt, Pd, Ir, Rh, Ru, or Re) to evaluate the catalytic performance of these surfaces. For each surface, we calculate free energy diagrams and onset potentials of three key reaction mechanisms: direct oxidation of FA via carboxyl (COOH), direct oxidation of FA via formate (HCOO), and the indirect oxidation of FA that first forms CO en route to full oxidation to CO 2 . We then display the trends in the form of phase diagrams that compare the activity of the calculated surfaces against regions of high activity using the free energies of adsorbed CO and OH as descriptors, enabling high-throughput screening and design of improved catalysts, particularly those alloying Pt or Pd with Ir, Ru, or Re.

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Molecular Simulations of CH 4 and CO 2 Diffusion in Rigid Nanoporous Amorphous Materials

Molecular diffusion in nanoporous materials is important in determining the rate of equilibration of various adsorption processes and plays a pivotal role in kinetic separations and membrane-based separations. Because generating realistic structures of amorphous nanoporous materials is difficult, far less is known about diffusion in amorphous nanoporous materials than in their crystalline counterparts. Here, we present molecular dynamics simulations assessing the room-temperature self-diffusion of CH 4 and CO 2 in a wide range of rigid amorphous nanoporous materials, including porous carbons, kerogens, polymers of intrinsic microporosity, and hyper-cross-linked polymers. Our results are the largest collection of molecular diffusivities in amorphous nanoporous materials to date. In each material, the diffusivity increases with the adsorbate concentration at low and moderate adsorbate concentrations, reaching a maximum before decreasing due to steric effects at higher concentrations. The observed diffusivities are much slower than that would be expected based on standard descriptions of Knudsen diffusivity. Here we show that the observed diffusivities are not correlated in a simple way with scalar descriptors of the pore structures such as the pore limiting diameter.

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Unraveling Electronic Trends in O* and OH* Surface Adsorption in the MO 2 Transition-Metal Oxide Series

Understanding the bond strength of O* and OH* intermediates to metal-oxide surfaces is key to predicting the catalytic activity in oxygen-based electrochemistry. Here, we uncover highly non-linear trends in O* and OH* adsorption energies across the 3d, 4d, and 5d series of MO 2 transition-metal (TM) oxide surfaces computed within Hubbard- U corrected density functional theory (DFT + U ). Investigating the electronic structure with crystal orbital Hamiltonian populations (COHP) of the relevant metal–oxygen bonds reveals that the spin-dependent coupling strength between metal-d and oxygen-2p atomic orbitals together with the extent of filling of bonding and anti-bonding orbitals are the primary contributors to the adsorption energy. Importantly, we show that the integrated COHP obtained purely from bulk calculations is a highly accurate descriptor for surface adsorption energetics that captures trends across the group 5–12 TM oxide series within 0.19–0.36 eV. Our results suggest a pathway to prediction of adsorption energies for an arbitrary metal–ligand catalyst system.

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Experimental Investigation of Thermodynamic Stabilization in Boron Imidazolate Frameworks (BIFs) Synthesized by Mechanochemistry

This study experimentally explores the energetics for the formation of boron–imidazolate frameworks (BIFs), which are synthesized by mechanochemistry. The topologically similar frameworks employ the same tetratopic linker based on tetrakis(imidazolyl)boric acid but differ in the monovalent cation metal nodes. This permits assessment of the stabilizing effect of metal nodes in frameworks with sodalite (SOD) and diamondoid (dia) topologies. The enthalpy of formation from endmembers (metal oxide and linker), which define thermodynamic stability of the structures, has been determined by use of acid solution calorimetry. The results show that heavier metal atoms in the node promote greater energetic stabilization of denser structures. Overall, in BIFs the relation between cation descriptors (ionic radius and electronegativity) and thermodynamic stability depends on framework topology. Thermodynamic stability increases with the metallic character of the cation employed as the metal node, independent of the framework topology. In conclusion, the results suggest unifying aspects for thermodynamic stabilization across MOF systems.

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The Surface Chemistry of Methanol on Cu 3 Pd(111): Effects of Metal Alloying and Reaction with Hydrogen

Synchrotron-based ambient-pressure X-ray photoelectron spectroscopy (AP-XPS) was used to study the adsorption and surface chemistry of methanol on a Cu 3 Pd(111) model surface. The composition and morphological properties of the pristine Cu 3 Pd(111) substrate were analyzed using a combination of low-energy electron diffraction (LEED), scanning tunneling microscopy (STM), and low-energy ion scattering (LEIS). The results of ion scattering showed segregation of Pd toward the surface, with a Pd/Cu ratio close to 0.5, a larger value than the ratio of 0.33 expected for a Cu 3 Pd bimetallic structure. The surface of the alloy exhibited a good LEED pattern with three-fold long-range periodicities. In STM, clusters of palladium with hexagonal arrays and Pd- Pd distances of 2.7-2.8 Å were detected. Bonding to copper perturbed the electronic properties of the atoms in the Pd clusters, shifting their 4d states toward higher binding energy with respect to the Fermi level. Further, the valence band spectrum of Cu 3 Pd(111) exhibited a line shape that was very different from those displayed by Cu(111) or Pd(111). At low pressures, the adsorption of methanol on Cu 3 Pd(111) at 300 K mainly produced CH 3 O, CO and CH x species. AP-XPS showed that most Pd atoms in the surface of the Cu 3 Pd(111) alloy interacted with the decomposition products of methanol. No significant changes were observed in the core levels of copper upon the adsorption and dissociation of methanol, suggesting that the molecule mainly interacted with Pd sites of the alloy. Reaction with hydrogen led to fast removal of CH x , C and PdC x species from Cu 3 Pd(111) at moderate (< 450 K) temperatures and prevented a CH x → C transformation. If the stability of adsorbed CH 3 O is used as a descriptor for the hydrogenation of CO 2 to methanol, Cu 3 Pd should be a much better catalyst than monometallic palladium. This may be a consequence of electronic and ensemble effects in the alloy that moderate the reactivity of Pd sites.

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Unraveling Fundamental Activity–Stability Relationships in Rutile Oxides

The oxygen evolution reaction (OER) is a key anodic half-cell reaction that accompanies several critical electrochemical reduction reactions of interest to a variety of applications. Despite steady advances in understanding and qualitatively predicting OER activity and selectivity trends, a comprehensive description or prediction of material aqueous (in)stability and degradation mechanisms remains elusive, even though these processes critically influence device lifetime and economic feasibility. In this work, we investigate the interplay, or lack thereof, between OER activity and material aqueous stability across rutile oxides, with a particular focus on iridium oxide (IrO 2 ). By applying a Born–Haber cycle, we calculate the thermodynamic driving force for metal dissolution as a function of the applied bias and electrolyte conditions. We apply interpretable machine learning techniques, including principal component analysis and symbolic regression, to analyze trends across rutile oxides and find that key thermodynamic descriptors for OER activity and surface stability are only very weakly correlated. Instead, the local atomic environment─especially electronic structure signatures for interactions between the active site and its neighbors─plays a more important role in predicting material stability. Leveraging these insights, we investigate the impact of doping IrO 2 with a range of transition metals and show that the stability of Ir active sites can be tuned largely independently of its predicted OER activity. These insights lay the foundation for material design to improve stability with respect to corrosion, with the ultimate aim to enhance long-term stability without sacrificing catalytic performance in the OER.

evolution reactions↗

Decoherence in Molecular Electron Spin Qubits: Insights from Quantum Many-Body Simulations

Quantum states are described by wave functions whose phases cannot be directly measured, but which play a vital role in quantum effects such as interference and entanglement. The loss of the relative phase information, termed decoherence, arises from the interactions between a quantum system and its environment. Decoherence is perhaps the biggest obstacle on the path to reliable quantum computing. Here we show that decoherence occurs even in an isolated molecule although not all phase information is lost via a theoretical study of a central electron spin qubit interacting with nearby nuclear spins in prototypical magnetic molecules. The residual coherence, which is molecule-dependent, provides a microscopic rationalization for the nuclear spin diffusion barrier proposed to explain experiments. The contribution of nearby molecules to the decoherence has a non-trivial dependence on separation, peaking at intermediate distances. Molecules that are far away only affect the long-time behavior. Because the residual coherence is simple to calculate and correlates well with the coherence time, it can be used as a descriptor for coherence in magnetic molecules. This work will help establish design principles for enhancing coherence in molecular spin qubits and serve to motivate further theoretical work

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Hydrogen in Nanocatalysis

Hydrogen is ubiquitous in catalysis. It is involved in many important reactions such as water splitting, N 2 reduction, CO 2 reduction, and alkane activation. In this Perspective, we focus on the hydrogen atom and follow its electron as it interacts with a catalyst or behaves as part of a catalyst from a computational point of view. In this work, we present recent examples in both nanocluster and solid catalysts to elucidate the parameters governing the strength of the hydrogen–surface interactions based on site geometry and electronic structure. We further show the interesting behavior of hydride in nanometal and oxides for catalysis. Overall, the key take-home messages are: (1) the in-the-middle electronegativity and small size of hydrogen give it great versatility in interacting with active sites on nanoparticles and solid surfaces; (2) the strength of hydrogen binding to an active site on a surface is an important descriptor of the chemical and catalytic properties of the surface; (3) the energetics of the hydrogen binding is closely related to the electronic structure of the catalyst; (4) hydrides in nanoclusters and oxides and on surfaces offer unique reactivity for reduction reactions.

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Screening of Therapeutic Agents for COVID-19 Using Machine Learning and Ensemble Docking Studies

The current pandemic demands a search for therapeutic agents against the novel coronavirus SARS-CoV-2. In this work, we present an efficient computational strategy that combines machine learning (ML)-based models and high-fidelity ensemble docking studies to enable rapid screening of possible therapeutic ligands. Targeting the binding affinity of molecules for either the isolated SARS-CoV-2 S-protein at its host receptor region or the S-protein:human ACE2 interface complex, we screen ligands from drug and biomolecule data sets that can potentially limit and/or disrupt the host-virus interactions. Top scoring one hundred eighty-seven ligands (with 75 approved by the Food and Drug Administration) are further validated by all atom docking studies. Important molecular descriptors ( 2 χ n , topological surface area, and ring count) and promising chemical fragments (oxolane, hydroxy, and imidazole) are identified to guide future experiments. Overall, this work expands our knowledge of small-molecule treatment against COVID-19 and provides a general screening pathway (combining quick ML models with expensive high-fidelity simulations) for targeting several chemical/biochemical problems.

60 APPLIED LIFE SCIENCES↗

Latent Representation Learning for Structural Characterization of Catalysts

Supervised machine learning-enabled mapping of the X-ray absorption near edge structure (XANES) spectra to local structural descriptors offers new methods for understanding the structure and function of working nanocatalysts. We briefly summarize a status of XANES analysis approaches by supervised machine learning methods. We present an example of an autoencoder-based, unsupervised machine learning approach for latent representation learning of XANES spectra. This new approach produces a lower-dimensional latent representation, which retains a spectrum–structure relationship that can be eventually mapped to physicochemical properties. Furthermore, the latent space of the autoencoder also provides a pathway to interpret the information content “hidden” in the X-ray absorption coefficient. Our approach (that we named latent space analysis of spectra, or LSAS) is demonstrated for the supported Pd nanoparticle catalyst studied during the formation of Pd hydride. By employing the low-dimensional representation of Pd K-edge XANES, the LSAS method was able to isolate the key factors responsible for the observed spectral changes.

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