Jennifer L. Bjorklund, Logan J. Augustine, Ali Abbaspour Tamijani, Thomas P. Trainor, Anne M. Chaka and Sara E. Mason*,
{"title":"Modeling Pb(II) Adsorption on Mineral Surfaces: Bridging Density Functional Theory and Experiment with Thermodynamic Insights","authors":"Jennifer L. Bjorklund, Logan J. Augustine, Ali Abbaspour Tamijani, Thomas P. Trainor, Anne M. Chaka and Sara E. Mason*, ","doi":"10.1021/acs.jpca.5c0039010.1021/acs.jpca.5c00390","DOIUrl":"https://doi.org/10.1021/acs.jpca.5c00390https://doi.org/10.1021/acs.jpca.5c00390","url":null,"abstract":"<p >Despite decades of work on aqueous lead (Pb) adsorption on α-Fe<sub>2</sub>O<sub>3</sub> (hematite) and α-Al<sub>2</sub>O<sub>3</sub> (alumina), gaps between measurements and modeling obscure molecular-level understanding. Achieving well-matched geometries between theory and experiment for mineral-water interfaces is a hurdle, as surface functional group type and distribution must be accounted for in determining mechanisms. Additionally, computational methods that can describe the substrate are often not appropriate to capture aqueous effects. Progress requires focusing on well-studied and relevant systems, such as key facets (001), (012), and (110) of hematite and alumina, and ubiquitous contaminants such as aqueous Pb. In the past, bulk-parameterized bond-valence principles were used to rationalize Pb(II) adsorption trends. These approaches can break down at surfaces, where flexible bonding environments and adsorption-induced surface relaxations play a critical role. Here, we adapt and apply a density functional theory (DFT) and thermodynamics framework, integrating DFT-calculated energies with experimental data and electrochemical principles, to predict Pb(II) adsorption. Our model results capture trends across the full set of surfaces and predict that inner-sphere Pb(II) sorption on (001) alumina varies from unfavorable to weakly favorable across a range of pH conditions. This aligns with experimental insights that Pb(II) interacts at that surface through outer-sphere interactions. Extending to Fe(II) adsorption, we demonstrate a coverage-dependent site preference, potentially explaining disorder in overlayers grown by the oxidative adsorption of Fe(II) on hematite (001).</p>","PeriodicalId":59,"journal":{"name":"The Journal of Physical Chemistry A","volume":"129 11","pages":"2754–2767 2754–2767"},"PeriodicalIF":2.7,"publicationDate":"2025-03-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143654491","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Sebastian V Pios, Maxim F Gelin, Wolfgang Domcke, Lipeng Chen
{"title":"Imaging the Photochemistry of the Hydrogen-Bonded Heptazine-Water Complex with Femtosecond Time-Resolved Spectroscopy: A Computational Study.","authors":"Sebastian V Pios, Maxim F Gelin, Wolfgang Domcke, Lipeng Chen","doi":"10.1021/acs.jpca.4c08085","DOIUrl":"10.1021/acs.jpca.4c08085","url":null,"abstract":"<p><p>Graphitic carbon nitride (g-CN) has attracted vast interest as a promising inexpensive metal-free photocatalyst for water splitting with solar photons. The heptazine (Hz) molecule is the building block of graphitic carbon nitride. The photochemistry of the Hz molecule and derivatives thereof in protic environments has been the subject of several recent experimental and computational studies. In the present work, the hydrogen-bonded Hz···H<sub>2</sub>O complex was adopted as a model system for the exploration of photoinduced electron and proton transfer processes in this complex with quasi-classical nonadiabatic trajectory simulations, using the ab initio ADC(2) electronic-structure method and a computationally efficient surface-hopping algorithm. The population of the optically excited bright <sup>1</sup>ππ* state of the Hz chromophore relaxes through three <sup>1</sup><i>n</i>π* states and a low-lying charge-transfer state, which drives proton transfer from H<sub>2</sub>O to Hz, to the long-lived optically dark S<sub>1</sub>(ππ*) state of Hz. The imaging of this ultrafast and complex dynamics with femtosecond time-resolved transient absorption (TA) pump-probe (PP) spectroscopy and two-dimensional (2D) electronic spectroscopy (ES) was computationally explored in the framework of the quasi-classical doorway-window approximation. By comparison of the spectra of the Hz···H<sub>2</sub>O complex with those of the free Hz molecule, the effects of the hydrogen bond on the ultrafast internal conversion dynamics can be identified in the spectroscopic signals. Albeit the TA PP and 2D ES spectroscopies are primarily sensitive to electronic excited-state dynamics and less so to proton transfer dynamics, they nevertheless can provide mechanistic insights which can contribute to the acceleration of the optimization of photocatalysts for water splitting.</p>","PeriodicalId":59,"journal":{"name":"The Journal of Physical Chemistry A","volume":" ","pages":"2217-2226"},"PeriodicalIF":2.7,"publicationDate":"2025-03-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143466576","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Quantitative Kinetics of the Hydrogen Shift Reaction of Methylthiomethyl Peroxy Radical (CH<sub>3</sub>SCH<sub>2</sub>OO) in the Atmosphere.","authors":"Yu Xia, Weijun Zhang, Xiaofeng Tang, Bo Long","doi":"10.1021/acs.jpca.4c06818","DOIUrl":"10.1021/acs.jpca.4c06818","url":null,"abstract":"<p><p>Hydrogen shift processes of peroxy radicals are paramount to understanding atmospheric chemical oxidations of volatile organic compounds. However, quantifying these processes using experimental and theoretical methods is also very difficult. Here, we chose methylthiomethyl peroxy radical (CH<sub>3</sub>SCH<sub>2</sub>OO) as a typical reaction to investigate the hydrogen shift in CH<sub>3</sub>SCH<sub>2</sub>OO using a dual-level (DL) strategy. In the DL strategy, GMMQ.L3//CCSD(T)-F12a/cc-pVTZ-F12 is used as a high-level method to calculate the rate constant using transition state theory. Here, GMMQ.L3 is a newly developed composite method for single-point energy calculations that approximates CCSDTQ/CBS accuracy (coupled cluster theory with single, double, triple, and connected quadruple excitations at the complete basis set limit). Additionally, MN15/MG3S is used as a low level to do multistructural canonical variational transition state theory with large curvature tunneling (MS-CVT/LCT) calculations. The calculated rate constants of 0.05-0.08 s<sup>-1</sup> agree well with the corresponding experimental values and the previous MC-TST results for the hydrogen shift of CH<sub>3</sub>SCH<sub>2</sub>OO at 293-298 K. The calculated results unravel that the zero-point vibrational energies depend strongly on the basis set in the CCSD(T)-F12 calculations. We find the large effects of the enthalpy of activation at 0 K, tunneling, and multistructural torsional anharmonicity on the calculated rate constant of the hydrogen shift of CH<sub>3</sub>SCH<sub>2</sub>OO. The current study provides a valuable reference case for the quantitative kinetic calculations of the peroxy radical isomerization reaction in the atmosphere.</p>","PeriodicalId":59,"journal":{"name":"The Journal of Physical Chemistry A","volume":" ","pages":"2275-2285"},"PeriodicalIF":2.7,"publicationDate":"2025-03-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143481738","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Crystalline Organic Compounds as Effective Nuclei in Contact Efflorescence of Ammonium Sulfate.","authors":"Kyle A McMillan, Ryan D Davis, Margaret A Tolbert","doi":"10.1021/acs.jpca.4c07566","DOIUrl":"10.1021/acs.jpca.4c07566","url":null,"abstract":"<p><p>Contact nucleation is believed to play a role in liquid-to-solid phase transitions in the atmosphere including ice nucleation and salt efflorescence. Here contact efflorescence of optically levitated ammonium sulfate droplets by collisions with organic particles is probed using a long working-distance optical trap. Two highly viscous water-soluble organic compounds (<i>d</i>-(+)-raffinose and citric acid), and two insoluble highly surface-active organic compounds (stearic acid and <i>cis</i>-pinonic acid) were probed for their ability to induce efflorescence upon contact. While three of the organics showed minimal effectiveness as contact nuclei, <i>cis</i>-pinonic acid showed a remarkable ability to initiate contact efflorescence of ammonium sulfate, occurring near ammonium sulfate's deliquescence relative humidity. Further analysis of <i>cis</i>-pinonic acid using bright-field microscopy in an electrodynamic balance provided evidence that the <i>cis</i>-pinonic acid particles are crystalline under the laboratory conditions. We suggest that the close lattice match between crystalline ammonium sulfate and crystalline <i>cis</i>-pinonic acid may account for the observed effectiveness in initiating contact efflorescence of ammonium sulfate. In contrast, tests of contact nucleation between <i>cis</i>-pinonic acid and sodium chloride, a pair with a poor lattice match, did not result in efflorescence. These findings suggest that crystalline organic compounds in the atmosphere could act as effective nuclei for contact efflorescence of atmospherically relevant salts, provided they share a compatible lattice structure.</p>","PeriodicalId":59,"journal":{"name":"The Journal of Physical Chemistry A","volume":" ","pages":"2296-2307"},"PeriodicalIF":2.7,"publicationDate":"2025-03-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143490335","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Accelerating Global Optimization of Cerium Oxide Nanocluster Structures with High-Dimensional Neural Network Potential.","authors":"Jinyuan Shi, Qinghua Ren, Yi Gao","doi":"10.1021/acs.jpca.4c07840","DOIUrl":"10.1021/acs.jpca.4c07840","url":null,"abstract":"<p><p>CeO<sub>2</sub>, characterized by its unique 4f electronic structure and high oxygen storage capacity, is widely recognized as an important catalyst and support material in energy and catalytic applications. Despite its importance, the complexity of CeO<sub>2</sub> nanoclusters poses challenges for structural characterization. Herein, we present a machine learning approach to accelerate the global optimization of cerium oxide nanocluster structures using a high-dimensional neural network potential (HDNNP). Our methodology integrates active learning to construct a versatile HDNNP that enables the exploration of the vast configurational space of small to medium cerium oxide clusters (Ce<sub><i>n</i></sub>O<sub>2<i>n</i>+<i>x</i></sub>, <i>n</i> = 2-18, <i>x</i> = -1, 0, +1). The HDNNP, refined through iterative active learning, achieves an accuracy comparable to first-principles calculations. Results indicate that the configuration of the lowest energy structures varies across different intervals. At <i>n</i> = 9 and <i>n</i> = 14, there is a transition from compact structures to multilayered ordered structures, and subsequently to pyramidal structures. When <i>n</i> > 14, almost all structures are derived from the pyramidal structure as the core grows continuously. In addition, the electronic structures of the lowest-energy clusters are analyzed. Our findings provide insights into the size-dependent stability and electronic behavior of cerium oxide nanoclusters.</p>","PeriodicalId":59,"journal":{"name":"The Journal of Physical Chemistry A","volume":" ","pages":"2190-2199"},"PeriodicalIF":2.7,"publicationDate":"2025-03-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143497557","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Mingyu Xu, Greeshma C Jose, Mouyang Cheng, Cheng Peng, Jose L Gonzalez Jimenez, Wenli Bi, Mingda Li, Weiwei Xie
{"title":"Continuous Evolution of Eu<sup>2+</sup>/Eu<sup>3+</sup> Mixed Valency Driven by Pressure and Temperature.","authors":"Mingyu Xu, Greeshma C Jose, Mouyang Cheng, Cheng Peng, Jose L Gonzalez Jimenez, Wenli Bi, Mingda Li, Weiwei Xie","doi":"10.1021/acs.jpca.4c08660","DOIUrl":"10.1021/acs.jpca.4c08660","url":null,"abstract":"<p><p>Continuous mixed valency involving Eu<sup>2+</sup> and Eu<sup>3+</sup> in Eu<sub>4</sub>Bi<sub>6</sub>Se<sub>13</sub> can be induced under applied pressure or at reduced temperatures. The monoclinic structure of Eu<sub>4</sub>Bi<sub>6</sub>Se<sub>13</sub>, crystallizing in the <i>P</i>2<sub>1</sub>/<i>m</i> space group (No. 11), features linear chains of Eu atoms aligned along the <i>b</i>-axis. Magnetic susceptibility measurements, conducted both parallel and perpendicular to the <i>b</i>-axis and analyzed using Curie-Weiss theory, alongside high-pressure partial fluorescence yield (PFY) data from X-ray absorption spectroscopy (XAS), indicate the material's propensity to adopt a mixed-valent state. Within this state, the trivalent Eu<sup>3+</sup> configuration becomes increasingly favored as the pressure rises or the temperature decreases.</p>","PeriodicalId":59,"journal":{"name":"The Journal of Physical Chemistry A","volume":" ","pages":"2371-2377"},"PeriodicalIF":2.7,"publicationDate":"2025-03-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11891896/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143497559","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Jennifer L Bjorklund, Logan J Augustine, Ali Abbaspour Tamijani, Thomas P Trainor, Anne M Chaka, Sara E Mason
{"title":"Modeling Pb(II) Adsorption on Mineral Surfaces: Bridging Density Functional Theory and Experiment with Thermodynamic Insights.","authors":"Jennifer L Bjorklund, Logan J Augustine, Ali Abbaspour Tamijani, Thomas P Trainor, Anne M Chaka, Sara E Mason","doi":"10.1021/acs.jpca.5c00390","DOIUrl":"https://doi.org/10.1021/acs.jpca.5c00390","url":null,"abstract":"<p><p>Despite decades of work on aqueous lead (Pb) adsorption on α-Fe<sub>2</sub>O<sub>3</sub> (hematite) and α-Al<sub>2</sub>O<sub>3</sub> (alumina), gaps between measurements and modeling obscure molecular-level understanding. Achieving well-matched geometries between theory and experiment for mineral-water interfaces is a hurdle, as surface functional group type and distribution must be accounted for in determining mechanisms. Additionally, computational methods that can describe the substrate are often not appropriate to capture aqueous effects. Progress requires focusing on well-studied and relevant systems, such as key facets (001), (012), and (110) of hematite and alumina, and ubiquitous contaminants such as aqueous Pb. In the past, bulk-parameterized bond-valence principles were used to rationalize Pb(II) adsorption trends. These approaches can break down at surfaces, where flexible bonding environments and adsorption-induced surface relaxations play a critical role. Here, we adapt and apply a density functional theory (DFT) and thermodynamics framework, integrating DFT-calculated energies with experimental data and electrochemical principles, to predict Pb(II) adsorption. Our model results capture trends across the full set of surfaces and predict that inner-sphere Pb(II) sorption on (001) alumina varies from unfavorable to weakly favorable across a range of pH conditions. This aligns with experimental insights that Pb(II) interacts at that surface through outer-sphere interactions. Extending to Fe(II) adsorption, we demonstrate a coverage-dependent site preference, potentially explaining disorder in overlayers grown by the oxidative adsorption of Fe(II) on hematite (001).</p>","PeriodicalId":59,"journal":{"name":"The Journal of Physical Chemistry A","volume":" ","pages":""},"PeriodicalIF":2.7,"publicationDate":"2025-03-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143571567","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Vebjørn H Bakkestuen, Vegard Falmår, Maryam Lotfigolian, Markus Penz, Michael Ruggenthaler, Andre Laestadius
{"title":"Quantum-Electrodynamical Density-Functional Theory Exemplified by the Quantum Rabi Model.","authors":"Vebjørn H Bakkestuen, Vegard Falmår, Maryam Lotfigolian, Markus Penz, Michael Ruggenthaler, Andre Laestadius","doi":"10.1021/acs.jpca.4c07690","DOIUrl":"10.1021/acs.jpca.4c07690","url":null,"abstract":"<p><p>The key features of density-functional theory (DFT) within a minimalistic implementation of quantum electrodynamics are demonstrated, thus allowing to study elementary properties of quantum-electrodynamical density-functional theory (QEDFT). We primarily employ the quantum Rabi model that describes a two-level system coupled to a single photon mode and also discuss the Dicke model, where multiple two-level systems couple to the same photon mode. In these settings, the density variables of the system are the polarization and the displacement of the photon field. We give analytical expressions for the constrained-search functional and the exchange-correlation potential and compare them to established results from QEDFT. We further derive a form for the adiabatic connection that is almost explicit in the density variables, up to only a nonexplicit correlation term that gets bounded both analytically and numerically. This allows several key features of DFT to be studied without approximations.</p>","PeriodicalId":59,"journal":{"name":"The Journal of Physical Chemistry A","volume":" ","pages":"2337-2360"},"PeriodicalIF":2.7,"publicationDate":"2025-03-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11891911/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143447499","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Importance of Charge Balance for the Embedding of Zwitterionic Solutes in the Fragment Molecular Orbital Method.","authors":"Dmitri G Fedorov","doi":"10.1021/acs.jpca.4c07218","DOIUrl":"10.1021/acs.jpca.4c07218","url":null,"abstract":"<p><p>Three new schemes of induced solvent charges for the auxiliary polarization formulation of the fragment molecular orbital method are proposed and compared to the original approach. It is found that the charge balance of the solute and solvent embeddings is crucial for maintaining a proper gap between occupied and virtual orbitals of fragments for zwitterionic systems in solution. The original instability is eliminated with the new scheme of fragment-specific solvent charges. The developed stable embedding method is applied to perform MP2/aug-cc-pVTZ calculations of a protein-ligand complex containing 1102 amino acid residues.</p>","PeriodicalId":59,"journal":{"name":"The Journal of Physical Chemistry A","volume":" ","pages":"2325-2336"},"PeriodicalIF":2.7,"publicationDate":"2025-03-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142816712","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Nonlinear Optics Materials Designed by Intramolecular Boron- and Nitrogen-Locking Strategies: Exploring Torsion Angle Descriptors.","authors":"Bo Li, Shichen Lin, Feng Long Gu","doi":"10.1021/acs.jpca.4c07831","DOIUrl":"10.1021/acs.jpca.4c07831","url":null,"abstract":"<p><p>Gaining mechanistic insights into the structure-performance relationship connecting the donor and acceptor is essential to the rational design of high performance nonlinear optics (NLO) materials. Here, intramolecular boron/nitrogen (B/N)-locking strategies in combination with various electron-withdrawing groups, R (R = TXO, DPzS, TTR, DPyS, DTC, DSCZ, DMPS and TXO2), are proposed to address this issue. With the decreasing of torsion angles (θ<sub>1</sub> and θ<sub>2</sub>) between donor (TPA) and acceptor (Py-Ph) units, the first hyperpolarizability (β) values are increased 45-65% and 4-27% by intramolecular B/N-locking strategies, respectively. Intriguingly, we also found some good linear correlations between θ<sub>1</sub>, θ<sub>2</sub>, and lgβ (where the determination coefficient <i>R</i><sup>2</sup> ranges from 0.84 to 1.00). Meanwhile, between θ<sub>1</sub>, θ<sub>2</sub>, and the excited energy (Δ<i>E</i>) of the crucial excited state there have also good correlations, namely, the <i>R</i><sup>2</sup> ranges from 0.80 to 1.00. As a result, given the fact of finding results, one can draw some meaningful insights, namely, intramolecular B/N-locking strategies hold good application perspective for enhancing β, and θ<sub>1</sub> and θ<sub>2</sub> can serve as effective descriptors in designing high-performance NLO materials based on the D-A architecture system.</p>","PeriodicalId":59,"journal":{"name":"The Journal of Physical Chemistry A","volume":" ","pages":"2182-2189"},"PeriodicalIF":2.7,"publicationDate":"2025-03-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143447497","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}