Number of sites-based solver for determining coverages from steady-state mean-field micro-kinetic models.

Kinetic models parameterized by ab-initio calculations have led to significant improvements in understanding chemical reactions in heterogeneous catalysis. These studies have been facilitated by implementations which determine steady-state coverages and rates of mean-field micro-kinetic models. As implemented in the open-source kinetic modeling program, CatMAP, the conventional solution strategy is to use a root-finding algorithm to determine the coverage of all intermediates through the steady-state expressions, constraining all coverages to be non-negative and to properly sum to unity. Though intuitive, this root-finding strategy causes issues with convergence to solution due to these imposed constraints. In this work, we avoid explicitly imposing these constraints, solving the mean-field steady-state micro-kinetic model in the space of number of sites instead of solving it in the space of coverages. We transform the constrained root-finding problem to an unconstrained least-squares minimization problem, leading to significantly improved convergence in solving micro-kinetic models and thus enabling the efficient study of more complex catalytic reactions.

On the Thermodynamic Equivalence of Grand Canonical, Infinite-Size, and Capacitor-Based Models in First-Principle Electrochemistry.

First principles-based computational and theoretical methods are constantly evolving trying to overcome the many obstacles towards a comprehensive understanding of electrochemical processes on an atomistic level. One of the major challenges has been the determination of reaction energetics under a constant potential. Here, a theoretical framework was proposed applying standard electronic structure methods and extrapolating to the infinite-cell size limit where reactions do not alter the potential. Today, electronically grand canonical modifications to electronic structure methods, holding the potential constant by varying the number of electrons in a finite simulation cell, become increasingly popular. In this perspective, we show that these two schemes are thermodynamically equivalent. Further, we link these methods to capacitive models of the interface, in the limit that the capacitance of the charging components (whether continuum or atomistic) are equal and invariant along the reaction pathway. We benchmark the three approaches with an example of alkali cation adsorption on Pt(111) showing that all three approaches converge in the cases of Li, Na and K. For Cs, however, strong deviation from the ideal conditions leads to a spread in the respective results. We discuss the latter by highlighting the cases of broken equivalence and assumptions among the approaches.

Characterization of adsorption sites on IrO2via temperature programmed O2 desorption simulations.

This study presents simulations of temperature-programmed desorption (TPD) profiles using desorption energy data from density functional theory (DFT) calculations. We apply this method to investigate the desorption of oxygen (O2) from IrO2(110) to gain insight into the kinetics of oxygen coupling and desorption, important elementary steps in the oxygen evolution reaction (OER). Initially, we confirm the thermodynamically stable adsorption site for oxygen in the pristine IrO2(110) as IrCUS, even with a high oxygen coverage. We successfully simulate TPD for O2 desorption, achieving good agreement with experimental TPD data for different initial oxygen exposures when including more than one adsorption site. We identify a new adsorption site, related to the formation of steps on IrO2(110)(IrCUS-step-0.5), that is essential for reproducing the experimental TPD. Our findings suggest that the observed TPD peaks are the result of different adsorption sites on the surface, rather than solely a lateral interactions effect. This work provides insight into the behavior of oxygen adsorption on IrO2, with implications for understanding surface reactivity and catalytic processes involving this material.

Benchmarking water adsorption on metal surfaces with ab initio molecular dynamics.

Solid-water interfaces are ubiquitous in nature and technology. In particular, technologies evolving in the green transition, such as electrocatalysis, heavily rely on the junction of an electrolyte and an electrode as a central part of the device. For the understanding of atomic-scale processes taking place at the electrolyte-electrode interface, density functional theory (DFT) has become the de facto standard. The validation of DFT's ability to simulate the interfacial solid/water interaction is crucial, and ideal simulation setups need to be identified in order to prevent avoidable systematic errors. Here, we develop a rigorous sampling protocol for benchmarking the adsorption/desorption energetics of water on metallic surfaces against experimental temperature programmed desorption, single crystal adsorption calorimetry, and thermal energy atom scattering. We screened DFT's quality on a series of transition metal surfaces, applying three of the most common exchange-correlation approximations: PBE-D3, RPBE-D3, and BEEF-vdW. We find that all three xc-functionals reflect the pseudo-zeroth order desorption of water rooted in the combination of attractive adsorbate-adsorbate interactions and their saturation at low and intermediate coverages, respectively. However, both RPBE-D3 and BEEF-vdW lead to more accurate water adsorption strengths, while PBE-D3 clearly overbinds near-surface water. We relate the variations in binding strength to specific variations in water-metal and water-water interactions, highlighting the structural consequences inherent in an uninformed choice of simulation parameters. Our study gives atomistic insight into water's complex adsorption equilibrium. Furthermore, it represents a guideline for future DFT-based simulations of solvated solid interfaces by providing an assessment of systematic errors in specific setups.

Theories for Electrolyte Effects in CO2 Electroreduction.

Electrochemical CO2 reduction (eCO2R) enables the conversion of waste CO2 to high-value fuels and commodity chemicals powered by renewable electricity, thereby offering a viable strategy for reaching the goal of net-zero carbon emissions. Research in the past few decades has focused both on the optimization of the catalyst (electrode) and the electrolyte environment. Surface-area normalized current densities show that the latter can affect the CO2 reduction activity by up to a few orders of magnitude.In this Account, we review theories of the mechanisms behind the effects of the electrolyte (cations, anions, and the electrolyte pH) on eCO2R. As summarized in the conspectus graphic, the electrolyte influences eCO2R activity via a field (ε) effect on dipolar (µ) reaction intermediates, changing the proton donor for the multi-step proton-electron transfer reaction, specifically adsorbed anions on the catalyst surface to block active sites, and tuning the local environment by homogeneous reactions. To be specific, alkali metal cations (M+) can stabilize reaction intermediates via electrostatic interactions with dipolar intermediates or buffer the interfacial pH via hydrolysis reactions, thereby promoting the eCO2R activity with the following trend in hydrated size (corresponding to the local field strength ε)/hydrolysis ability: Cs+ > K+ > Na+ > Li+. The effect of the electrolyte pH can give a change in eCO2R activity of up to several orders of magnitude, arising from linearly shifting the absolute interfacial field via the relationship USHE = URHE - (2.3kBT)pH, homogeneous reactions between OH- and desorbed intermediates, or changing the proton donor from hydronium to water along with increasing pH. Anions have been suggested to affect the eCO2R reaction process by solution-phase reactions (e.g., buffer reactions to tune local pH), acting as proton donors or as a surface poison.So far, the existing models of electrolyte effects have been used to rationalize various experimentally observed trends, having yet to demonstrate general predictive capabilities. The major challenges in our understanding of the electrolyte effect in eCO2R are (i) the long time scale associated with a dynamic ab initio picture of the catalyst|electrolyte interface and (ii) the overall activity determined by the length-scale interplay of intrinsic microkinetics, homogeneous reactions, and mass transport limitations. New developments in ab initio dynamic models and coupling the effects of mass transport can provide a more accurate view of the structure and intrinsic functions of the electrode-electrolyte interface and the corresponding reaction energetics toward comprehensive and predictive models for electrolyte design.

Solvation of furfural at metal-water interfaces: Implications for aqueous phase hydrogenation reactions.

Metal-water interfaces are central to understanding aqueous-phase heterogeneous catalytic processes. However, the explicit modeling of the interface is still challenging as it necessitates extensive sampling of the interfaces' degrees of freedom. Herein, we use ab initio molecular dynamics (AIMD) simulations to study the adsorption of furfural, a platform biomass chemical on several catalytically relevant metal-water interfaces (Pt, Rh, Pd, Cu, and Au) at low coverages. We find that furfural adsorption is destabilized on all the metal-water interfaces compared to the metal-gas interfaces considered in this work. This destabilization is a result of the energetic penalty associated with the displacement of water molecules near the surface upon adsorption of furfural, further evidenced by a linear correlation between solvation energy and the change in surface water coverage. To predict solvation energies without the need for computationally expensive AIMD simulations, we demonstrate OH binding energy as a good descriptor to estimate the solvation energies of furfural. Using microkinetic modeling, we further explain the origin of the activity for furfural hydrogenation on intrinsically strong-binding metals under aqueous conditions, i.e., the endothermic solvation energies for furfural adsorption prevent surface poisoning. Our work sheds light on the development of active aqueous-phase catalytic systems via rationally tuning the solvation energies of reaction intermediates.

Limits to scaling relations between adsorption energies?

Linear scaling relations have led to an understanding of trends in catalytic activity and selectivity of many reactions in heterogeneous and electro-catalysis. However, linear scaling between the chemisorption energies of any two small molecule adsorbates is not guaranteed. A prominent example is the lack of scaling between the chemisorption energies of carbon and oxygen on transition metal surfaces. In this work, we show that this lack of scaling originates from different re-normalized adsorbate valence energies of lower-lying oxygen vs higher-lying carbon. We develop a model for chemisorption of small molecule adsorbates within the d-band model by combining a modified form of the Newns-Anderson hybridization energy with an effective orthogonalization term. We develop a general descriptor to a priori determine if two adsorbates are likely to scale with each other.

Covalent Organic Framework (COF) Derived Ni-N-C Catalysts for Electrochemical CO2 Reduction: Unraveling Fundamental Kinetic and Structural Parameters of the Active Sites.

Electrochemical CO2 reduction is a potential approach to convert CO2 into valuable chemicals using electricity as feedstock. Abundant and affordable catalyst materials are needed to upscale this process in a sustainable manner. Nickel-nitrogen-doped carbon (Ni-N-C) is an efficient catalyst for CO2 reduction to CO, and the single-site Ni-Nx motif is believed to be the active site. However, critical metrics for its catalytic activity, such as active site density and intrinsic turnover frequency, so far lack systematic discussion. In this work, we prepared a set of covalent organic framework (COF)-derived Ni-N-C catalysts, for which the Ni-Nx content could be adjusted by the pyrolysis temperature. The combination of high-angle annular dark-field scanning transmission electron microscopy and extended X-ray absorption fine structure evidenced the presence of Ni single-sites, and quantitative X-ray photoemission addressed the relation between active site density and turnover frequency.

How to extract adsorption energies, adsorbate-adsorbate interaction parameters and saturation coverages from temperature programmed desorption experiments.

We present a scheme to extract the adsorption energy, adsorbate interaction parameter and the saturation coverage from temperature programmed desorption (TPD) experiments. We propose that the coverage dependent adsorption energy can be fit using a functional form including the configurational entropy and linear adsorbate-adsorbate interaction terms. As one example of this scheme, we analyze TPD of CO desorption on Au(211) and Au(310) surfaces. We determine that under atmospheric CO pressure, the steps of both facets adsorb between 0.4-0.9 ML coverage of CO*. We compare this result against energies obtained from five density functionals, RPBE, PBE, PBE-D3, RPBE-D3 and BEEF-vdW. We find that the energies and equilibrium coverages from RPBE-D3 and PBE are closest to the values determined from the TPD.

Incremental value of three-dimensional transthoracic echocardiography in the assessment of ruptured aneurysm of anterior mitral leaflet.

The mitral valve aneurysm is a rare complication of infective endocarditis involving mitral or aortic valve. The perforation of the mitral valve aneurysm can lead to significant mitral regurgitation (MR) or thromboembolism, which can cause sudden hemodynamic deterioration. We describe here a case of healed infective endocarditis of the aortic valve with ruptured mitral valve aneurysm that led to severe MR. The aneurysm of the anterior mitral leaflet was diagnosed by two-dimensional transthoracic echocardiography. In this case, three-dimensional transthoracic echocardiography demonstrated the detailed morphology of mitral valve aneurysm which resulted in successful surgical repair of the aneurysm.

A Critical Analysis of Chemical and Electrochemical Oxidation Mechanisms in Li-Ion Batteries.

Electrolyte decomposition limits the lifetime of commercial lithium-ion batteries (LIBs) and slows the adoption of next-generation energy storage technologies. A fundamental understanding of electrolyte degradation is critical to rationally design stable and energy-dense LIBs. To date, most explanations for electrolyte decomposition at LIB positive electrodes have relied on ethylene carbonate (EC) being chemically oxidized by evolved singlet oxygen (1O2) or electrochemically oxidized. In this work, we apply density functional theory to assess the feasibility of these mechanisms. We find that electrochemical oxidation is unfavorable at any potential reached during normal LIB operation, and we predict that previously reported reactions between the EC and 1O2 are kinetically limited at room temperature. Our calculations suggest an alternative mechanism in which EC reacts with superoxide (O2-) and/or peroxide (O22-) anions. This work provides a new perspective on LIB electrolyte decomposition and motivates further studies to understand the reactivity at positive electrodes.

CoeffNet: predicting activation barriers through a chemically-interpretable, equivariant and physically constrained graph neural network.

Activation barriers of elementary reactions are essential to predict molecular reaction mechanisms and kinetics. However, computing these energy barriers by identifying transition states with electronic structure methods (e.g., density functional theory) can be time-consuming and computationally expensive. In this work, we introduce CoeffNet, an equivariant graph neural network that predicts activation barriers using coefficients of any frontier molecular orbital (such as the highest occupied molecular orbital) of reactant and product complexes as graph node features. We show that using coefficients as features offer several advantages, such as chemical interpretability and physical constraints on the network's behaviour and numerical range. Model outputs are either activation barriers or coefficients of the chosen molecular orbital of the transition state; the latter quantity allows us to interpret the results of the neural network through chemical intuition. We test CoeffNet on a dataset of SN2 reactions as a proof-of-concept and show that the activation barriers are predicted with a mean absolute error of less than 0.025 eV. The highest occupied molecular orbital of the transition state is visualized and the distribution of the orbital densities of the transition states is described for a few prototype SN2 reactions.

Noninvasive cardiac-specific biomarkers for the diagnosis and prevention of vascular stenosis in cardiovascular disorder.

Background: The most frequent lesion in the blood vessels feeding the myocardium is vascular stenosis, a condition that develops slowly but can prove to be deadly in a long run. Non-invasive biomarkers could play a significant role in timely diagnosis, detection and management for vascular stenosis events associated with cardiovascular disorders. Aims: The study aimed to investigate high sensitivity troponin I (hs-TnI), cardiac troponin I (c-TnI) and high sensitivity C-reactive protein (hs-CRP) that may be used solely or in combination in detecting the extent of vascular stenosis in CVD patients. Methodology: 274 patients with dyspnea/orthopnea complaints visiting the cardiologists were enrolled in this study. Angiographic study was conducted on the enrolled patients to examine the extent of stenosis in the five prominent vessels (LDA, LCX, PDA/PLV, RCA, and OM) connected to the myocardium. Samples from all the cases suspected to be having coronary artery stenosis were collected, and subjected to biochemical evaluation of certain cardiac inflammatory biomarkers (c-TnI, hsTn-I and hs-CRP) to check their sensitivity with the level of vascular stenosis. The extent of mild and culprit stenosis was detected during angiographic examination and the same was reported in the form significant (≥50% stenosis in the vessels) and non-significant (<50% stenosis in the vessels) Carotid Stenosis. Ethical Clearance for the study was provided by Dr. Ram Manohar Lohia Institute of Medical Sciences Institutional Ethical Committee. Informed consent was obtained from all the participants enrolled in the study. Results: We observed that 85% of the total population enrolled in this study was suffering from hypertension followed by 62.40% detected with sporadic episodes of chest pain. Most of the subjects (42% of the total population) had stenosis in their LAD followed by 38% who had stenosis in their RCA. Almost 23% patients were reported to have stenosis in their LCX followed by OM (18% patients), PDA/PLV (13%) and only 10% patients had blockage problem in their diagonal. 24% of the subjects were found to have stenosis in a single vessel and hence were categorized in the Single Vessel Disease (SVD) group while 76% were having stenosis in two or more than two arteries (Multiple Vessel Disease). hs-TnI level was found to be correlated with the levels of stenosis and was higher in the MVD group as compared to the SVD group. Conclusion: hs-TnI could be used as a novel marker as it shows prominence in detecting the level of stenosis quite earlier as compared to c-TnI which gets detected only after a long duration in the CVD patients admitted for angiography. hs- CRP gets readily detected as inflammation marker in these patients and hence could be used in combination with hs-TnI to detect the risk of developing coronary artery disease.

Giant intrapericardial lipoma: an unusual cause of dyspnoea.

The pericardial lipomas are rare benign cardiac tumors. The clinical presentation of these cardiac neoplasms varies according to the site of growth. We describe here a case of massive intrapericardial lipoma leading to severe dyspnea, its diagnostic work up and briefly review the existing literature of this uncommon disorder. The patient underwent successful surgical resection of the tumor with complete alleviation of the symptoms.

Pacemaker lead induced inferior vena caval thrombosis leading to portal hypertension.

Inferior vena caval thrombosis is an unusual complication of permanent pacemaker implantation. The clinical presentation due to thrombosis depends on the site of thrombus. We have described here a rare case of pacemaker lead associated thrombosis of inferior vena cava, its diagnostic work up and briefly reviewed the existing literature of this uncommon complication.

Free-atom-like d states beyond the dilute limit of single-atom alloys.

Through a data-mining and high-throughput density functional theory approach, we identify a diverse range of metallic compounds that are predicted to have transition metals with "free-atom-like" d states that are highly localized in terms of their energetic distribution. Design principles that favor the formation of localized d states are uncovered, among which we note that site isolation is often necessary but that the dilute limit, as in most single-atom alloys, is not a pre-requisite. Additionally, the majority of localized d state transition metals identified from the computational screening study exhibit partial anionic character due to charge transfer from neighboring metal species. Using CO as a representative probe molecule, we show that localized d states for Rh, Ir, Pd, and Pt tend to reduce the binding strength of CO compared to their pure elemental analogues, whereas this does not occur as consistently for the Cu binding sites. These trends are rationalized through the d-band model, which suggests that the significantly reduced d-band width results in an increased orthogonalization energy penalty upon CO chemisorption. With the multitude of inorganic solids that are predicted to have highly localized d states, the results of the screening study are likely to result in new avenues for heterogeneous catalyst design from an electronic structure perspective.

Delineation of anatomy of the ruptured sinus of Valsalva with three-dimensional echocardiography: the advantage of the added dimension.

The rupture of sinus of Valsalva is a rare complication of infective endocarditis. Three-dimensional (3D) echocardiography represents an important adjunctive tool to demonstrate the ruptured sinus of Valsalva with better delineation of its characteristics. We present an adult patient with rupture of right sinus of Valsalva aneurysm due to infective endocarditis of the aortic valve, in whom the two-dimensional (2D) transthoracic echocardiogram erroneously localized the site of rupture into the right atrium. Whereas, 3D transthoracic echocardiogram accurately delineated the site of rupture into the right ventricle and it was confirmed on subsequent cardiac catheterization and angiogram. In addition, 3D echocardiography clearly showed the size and shape of the defect, which helped in successful transcatheter closure of the defect with amplatzer duct occluder device.

Left hemitruncus with tetralogy of fallot and right aortic arch: rare survival beyond the first decade.

Hemitruncus is an uncommon congenital anomaly that has been described in isolation or in association with other congenital cardiac malformations. This report describes a rare case of left hemitruncus with tetralogy of Fallot and a right-sided aortic arch. The patient presented to us in the early second decade. The diagnosis was suspected with echocardiography and confirmed with cardiac catheterization. The patient underwent successful surgical correction of the anomaly.

Computational Screening of Single and Di-Atom Catalysts for Electrochemical CO2 Reduction.

Supported single atom catalysts on defected graphene show great potential for electrochemical reduction of CO2 to CO. In this study, we perform a computational screening of single and di-atom catalysts (MNCs and FeMNC respectively) with M varying from Sc to Zn on nitrogen-doped graphene for CO2 reduction using hybrid-density functional theory and potential dependent micro-kinetic modeling. The formation energy calculations reveal several stable single and di-atom doping site motifs. We consider the kinetics of CO2 using the binding energies of CO2* and COOH* intermediates as the descriptors to analyze the activity of these catalysts. In comparison to (211) transition metal (TM) surfaces, both MNCs and FeMNCs show a variety of binding motifs of the reaction intermediates on different metal dopants. We find four MNCs as CrNC, MnNC, FeNC, and CoNC with high catalytic efficiency for CO2R. Among the different FeMNCs with varying doping geometry and surrounding N-coordination, we have identified 11 candidates having high TOF for CO production and lower selectivity for the hydrogen evolution reaction. FeMnNC shows the highest activity for CO2R. Large CO2* dipole-field interactions in both the MNCs and FeMNCs give rise to deviations in scaling from TM surfaces.

Force-Based Method to Determine the Potential Dependence in Electrochemical Barriers.

Determining ab initio potential-dependent energetics is critical to the investigation of mechanisms for electrochemical reactions. While methodology for evaluating reaction thermodynamics is established, simulation techniques for the corresponding kinetics is still a major challenge owing to a lack of potential control, finite cell size effects, or computational expense. In this work, we develop a model that allows for computing electrochemical activation energies from just a handful of density functional theory (DFT) calculations. The sole input into the model are the atom-centered forces obtained from DFT calculations performed on a homogeneous grid composed of varying field strengths. We show that the activation energies as a function of the potential obtained from our model are consistent for different supercell sizes and proton concentrations for a range of electrochemical reactions.