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At least 541 records · Page 30

Atom Equivalent Energies for the Rapid Estimation of the Heat of Formation of Explosive Molecules from Density Functional Tight Binding Theory

Atom equivalent energies have been derived from which the gas-phase heat of formation of explosive molecules can be estimated from fast, semiempirical density functional tight binding total energy calculations. The root-mean-square deviation and maximum deviation of the heats of formation from the experimental values for the set of 45 energetic molecules compiled by Byrd and Rice [ J. Phys. Chem. A, 2006, 110, 1005–1013] are 10.4 and 25.5 kcal/mol, respectively, using 4 atom equivalent energies and 7.4 and 15.0 kcal/mol, respectively, using 7 atom equivalent energies. These errors are around a factor of 2–3 larger than those obtained from density functional theory calculations but are smaller than those obtained from other semiempirical electronic structure methods. Heats of formation calculated with density functional tight binding theory using the 4 and 7 atom equivalent energies, the Byrd and Rice scheme, and the atom pair contribution method for a new set of 531 energetic molecules that contain only carbon, hydrogen, nitrogen, and oxygen are provided.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Density Functionals for Hydrogen Storage: Defining the H2Bind275 Test Set with Ab Initio Benchmarks and Assessment of 55 Functionals

Efficient and high-capacity storage materials are indispensable for a hydrogen-based economy. In silico tools can accelerate the process of discovery of new adsorbent materials with optimal hydrogen adsorption enthalpies. Density functional theory is well-poised to become a very useful tool for enabling high-throughput screening of potential materials. In this work, we have identified density functional approximations that provide good performance for hydrogen binding applications following a two-pronged approach. First, we have compiled a data set (H2Bind275) that comprehensively represents the hydrogen binding problem capturing the chemical and mechanistic diversity in the binding sites encountered in hydrogen storage materials. We have also computed reference interaction energies for this data set using coupled-cluster theory. Second, we have assessed the performance of 55 density functional approximations for predicting H 2 interaction energies and have identified two hybrid density functionals (ωB97X-V and ωB97M-V), two double hybrid density functionals (DSD-PBEPBE-D3(BJ) and PBE0-DH), and one semilocal density functional (B97M-V) as the best performing ones. We have recommended the addition of empirical dispersion corrections to systematically underbinding density functionals such as revPBE, BLYP, and B3LYP for improvements in performance at negligible additional cost. We have also recommended the usage of the def2-TZVPP basis set as it represents a good compromise between accuracy and cost, limiting the finite basis set errors to less than 1 kJ/mol.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Characterizing Defect Dynamics in Silicon Carbide Using Symmetry-Adapted Collective Variables and Machine Learning Interatomic Potentials

Silicon carbide (SiC) divacancies are attractive candidates for spin-defect qubits possessing long coherence times and optical addressability. The high activation barriers associated with SiC defect formation and motion pose challenges for their study by first-principles molecular dynamics. In this work, we develop and deploy machine learning interatomic potentials (MLIPs) to accelerate defect dynamics simulations while retaining ab initio accuracy. We employ an active learning strategy comprising symmetry-adapted collective variable discovery and enhanced sampling to compile configurationally diverse training data, calculation of energies and forces using density functional theory (DFT), and training of an E(3)-equivariant MLIP based on the Allegro model. Here, the trained MLIP reproduces DFT-level accuracy in defect transition activation free energy barriers, enables the efficient and stable simulation of multidefect 216-atom supercells, and permits an analysis of the temperature dependence of defect thermodynamic stability and formation/annihilation kinetics to propose an optimal annealing temperature to maximally stabilize VV divacancies.

Computer simulations↗

Transformation of an Embedded Five-Membered Ring in Polycyclic Aromatic Hydrocarbons via the Hydrogen-Abstraction–Acetylene-Addition Mechanism: A Theoretical Study

Five-membered rings are constituents of many polycyclic aromatic hydrocarbons (PAHs) and their presence on the edges of large PAHs has been repeatedly observed experimentally. However, modern kinetic combustion models often do not consider the growth of PAHs through the transformation of the five-membered rings. Here, in connection with the above, we carried out a theoretical study of the mechanism of Hydrogen-Abstraction-aCetylene-Addition (HACA) transformation of an embedded five-membered ring on the armchair PAH edge to a six-membered ring, considering cyclopenta[d,e,f]phenanthrene (4,5-methylenephenanthrene) as a prototype system for this process. The potential energy surface for the reactions of cyclopenta[d,e,f]phenanthrenyl radicals produced by direct H abstractions from cyclopenta[d,e,f]phenanthrene with acetylene has been compiled at the G3(MP2,CC)//B3LYP/6-311G(d,p) level of theory including zero-point vibrational energy corrections. The computed energies and molecular parameters were then used to solve the Rice-Ramsperger-Kassel-Marcus Master Equation (RRKM-ME) in order to calculate reaction rate at various pressures and temperatures, which were fitted to modified Arrhenius equation for further kinetic modeling. The results show that the HACA transformation of the embedded five-membered ring to a six-membered ring is possible, albeit slow. The most viable reaction mechanism involves the R2 + C 2 H 2 reaction, where the acetylene molecules adds to a σ-radical in the six-membered ring adjacent to the five-membered ring via a low entrance barrier. The predominant product of R2 + C 2 H 2 is predicted to be 3 ethynyl 4H cyclopenta[def]phenanthrene Pr5 via immediate H elimination from the initial addition complex. Next, Pr5 undergoes H-assisted isomerization to 4aH-pentaleno[4,3,2,1-cdef]phenanthrene Pr4, and the latter adds an H atom eventually forming the 1-pyrenylmethyl radical Pr3: R2 + C 2 H 2 ⇌ 3 ethynyl 4H cyclopenta[def]phenanthrene (Pr5) + H ⇌ 4aH-pentaleno[4,3,2,1-cdef]phenanthrene (Pr4) + H Pr5 + H ⇌ Pr4 + H Pr4 + H → 1-pyrenylmethyl (Pr3) This HACA sequence may be competitive with the methyl radical addition to the R1 radical formed by H abstraction from the CH 2 group in the five-membered ring of cyclopenta[d,e,f]phenanthrene, which provides a pathway to pyrene following two H atom losses. Relative contributions of the two mechanisms of the five- to six-membered ring transformation would strongly depend on the branching ratios of the R1 and R2 radicals produced by the H abstractions and the available concentration of C 2 H 2 vs. CH 3 and hence differ in different flames.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Assessment of Performance of Density Functionals for Predicting Potential Energy Curves in Hydrogen Storage Applications

We report the availability of accurate computational tools for modeling and simulation is vital to accelerate the discovery of materials capable of storing hydrogen (H 2 ) under given parameters of pressure swing and temperature. Previously, we compiled the H2Bind275 data set consisting of equilibrium geometries and assessed the performance of 55 density functionals over this data set (Veccham, S. P.; Head-Gordon, M. J. Chem. Theory Comput. 2020, 16, 4963-4982). As it is crucial for computational tools to accurately model the entire potential energy curve (PEC), in addition to the equilibrium geometry, we extended this data set with 389 new data points to include two compressed and three elongated geometries along 78 PECs for H 2 binding, forming the H2Bind78 × 7 data set. By assessing the performance of 55 density functionals on this significantly larger and more comprehensive H2Bind78 × 7 data set, we identified the best performing density functionals for H 2 binding applications: PBE0-DH, ωB97X-V, ωB97M-V, and DSD-PBEPBE-D3(BJ). The addition of Hartree-Fock exchange improves the performance of density functionals, albeit not uniformly throughout the PEC. We recommend the usage of ωB97X-V and ωB97M-V density functionals as they offer good performance for both geometries and energies. In addition, we also identified B97M-V and B97M-rV as the best semilocal density functionals for predicting H 2 binding energy at its equilibrium geometry.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Confirmation of PNNL Quantitative Infrared Cross-Sections for Isobutane

The Pacific Northwest National Laboratory (PNNL) gas-phase database is a compilation of quantitative experimental (5, 25, 50 °C) infrared spectra of ca. 500 molecules, designed for in situ, standoff or remote sensing of gases and vapors at or near atmospheric pressure. The data are characterized by calibration on both the wavenumber and intensity axes. Recent papers have called into question the PNNL intensity values for isobutane, (2-methylpropane, HC(CH 3 ) 3 ) suggesting discrepancies of 30 to 40%. In this study we re-measure and re-examine the intensity values of isobutane using both similar and alternate methods to those used to generate the original PNNL database spectra. Here, indirect confirmation from literature data of homologous molecules and direct confirmation from new results confirm that for many band integrals across the isobutane spectrum, the original PNNL data are indeed accurate to within the reported 3% experimental uncertainty.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

VUV Photoionization Dynamics and Reactivity of Heterogeneous Water Clusters

This feature focuses on bridging isolated water and bulk water studies. It assembles experiments and theory on water clusters, mainly probed by vacuum ultraviolet (VUV) radiation, and summarizes what the effects are of intermolecular interactions on both the spectroscopy and the VUV-induced processes in water. In particular, it highlights studies of heterogeneous water clusters─those incorporating other molecular species such as naphthalene, methane, formic acid, and glycerol─which serve as model systems to investigate the fundamental roles of water in hydrogen bonding networks, proton transfer, and astrochemical processes. These mixed clusters provide a platform to revisit the stability of protonated water clusters and compile observations of ionization-induced structural rearrangements and fragmentation, especially in systems involving hydroxyl-rich cosolvents. This feature then explores energy transfer mechanisms in molecular clusters, following VUV photoexcitation. It concludes with potential future directions. First, we investigate excited-state dynamics in molecular clusters through direct probing, complementing the synchrotron studies discussed here. Second, exploring gas-phase molecule evaporation from confined spaces and interfaces using advanced spectroscopic techniques sheds light on these ubiquitous, yet currently debated, molecular processes.

Cluster chemistry↗

Tribute to José N. Onuchic

This Festschrift Virtual Special Issue in The Journal of Physical Chemistry B is dedicated to the scientific contributions of Prof. José Nelson Onuchic. It serves as a celebration of his years of service, mentorship, and leadership to the biological physics, theoretical chemistry, and computational biology communities. This collection of more than 60 articles has been compiled from an extensive network of scientists that have, in distinct ways, been impacted by the scientific legacy of Prof. Onuchic. It is a written testament to how his work has influenced many areas related to the physics and chemistry of biological systems. In conclusion, this Festschrift provides a good sample of the areas in that Professor Onuchic has had a direct impact via collaboration, mentorship, and scientific dissemination of his research.

99 GENERAL AND MISCELLANEOUS↗

Benchmarking DFT Accuracy in Predicting O 1s Binding Energies on Metals

X-ray photoelectron spectroscopy (XPS) is a powerful tool for probing the electronic structure and composition of materials, particularly metals and metal oxides of relevance to solar cells and catalysis. Density functional theory (DFT) is often used to support XPS peak assignments, but its reliability for predicting oxygen species is not well established. Here, we compile a large data set of experimental oxygen binding energies and evaluate corresponding DFT predictions. We find that as the binding energies of metal-bound atomic oxygen species increase, especially above ≈530 eV, there is a general decrease in the accuracy of DFTpredicted values. Thus, high-binding-energy atomic oxygen species, such as those proposed as active for selective Ag-catalyzed epoxidation, are less well represented. The chemical nature of the oxygen species also influences accuracy, with molecularly bound species more reliably captured across the entire range of energies. These findings illustrate the limitations of DFT for interpreting XPS spectra and provide a benchmark for improving computational methods.

Adsorption↗

TopPICR: A Companion R Package for Top-Down Proteomics Data Analysis

Top-down proteomics is the analysis of proteins in their intact form without proteolysis, thus preserving valuable information about post-translational modifications, isoforms, and proteolytic processing. However, it is still a developing field due to limitations in the instrumentation, difficulties with interpretation of complex mass spectra, and a lack of well-established quantification approaches. TopPIC is one of the popular tools for proteoform identification. Here we extended its capabilities into label-free proteoform quantification by developing a companion R package (TopPICR). Key steps in the TopPICR pipeline include filtering identifications, inferring a minimal set of protein accessions explaining the observed sequences, aligning retention times, recalibrating measured masses, clustering features across datasets, and finally compiling feature intensities using the match-between-runs approach. The output of the pipeline is an MSnSet object which makes downstream data analysis seamlessly compatible with packages from the Bioconductor project. It also provides the capability for visualizing proteoforms within the context of the parent protein sequence. The functionality of TopPICR is demonstrated on top-down LC-MS/MS datasets of 10 human-in-mouse xenografts of luminal and basal breast tumor samples.

59 BASIC BIOLOGICAL SCIENCES↗

Tailoring MoS 2 for Small-Molecule Electroreduction: The Role of Metal Doping and Heterostructures

The electrification of chemical transformations central to sustainable fuel production and waste valorization, such as overall water splitting (OWS), hydrogen evolution reaction (HER), and electrochemical reduction of CO 2 (CO 2 R), presents a powerful opportunity to advance carbon-neutral energy technologies. Transition metal dichalcogenides (TMDs), particularly MoS 2 , have emerged as promising electrocatalyst candidates, owing to their abundance, tunable active sites, and defect-rich structures. This review highlights recent progress in leveraging metal doping and heterostructure engineering of MoS 2 to enhance the electrocatalytic activity and selectivity. By compiling insights from experimental studies and density functional theory (DFT) predictions, we examine how defect creation, electronic structure modification, and interface design contribute to improved charge transport and catalytic efficiency. Particular emphasis is placed on rational design principles, synthetic strategies, and operando characterization methods that provide a pathway to understanding and optimizing MoS 2 -based materials. We also discuss the challenges of stability, mechanistic ambiguity, and scaling while outlining opportunities to bridge theory and experiment. Collectively, this review underscores how defect and heterostructure engineering of MoS 2 can accelerate the development of efficient, sustainable electrocatalysts for both fuel generation and waste-to-value generation.

CO2 reduction↗

Materials Based on Technical Bulk Lignin

Lignin is the second most abundant biopolymer and the main source of aromatic structures on earth. Lignin has long been produced as a byproduct of the pulping process and utilized in low value-added applications like heat. However, lignin has received increased attention in recent years to improve its value through various chemical processes. This Review compiles recent progress in synthesis, properties, and applications of lignin-based materials. The lignin for material applications can often be classified into three categories: technical bulk lignin (TBL), lignin-derived oligomers (LDOs), and lignin-derived phenols (LDPs). Furthermore, this Review focuses on the chemical modifications of TBLs and their applications in novel smart materials like self-healing, stimulus responsive, and shape memory polymers. The conversion of TBL to polymers can be briefly divided into two steps: (1) introduction of polymerizable functional groups into the lignin backbone and (2) polymerization that achieves desired materials. Both lignin functionalization and polymerization approaches are discussed in detail. As such, this work attempts to provide a comprehensive overview that highlights the importance of these approaches for the utilization of the abundant but largely ignored biopolymer.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Process Model-Based Validation of the Intensification of Biomass Fast Pyrolysis in a Fluidized Bed via Autothermal Operation

A model for the fluidized-bed pyrolysis of biomass is extended to enable the simulation of intensified autothermal operation. In this system, partial oxidation of char and pyrolysate species replaces an external heat source to supply the enthalpy of pyrolysis, greatly increasing the throughput of a given fast pyrolysis reactor. Oxidation reactions are compiled from CRECK and other literature sources and extended to cover the species found in pyrolysis products, including a derivation of the catalytic effect of ash on char combustion from experimental studies at Iowa State University (ISU). Results indicate a roughly 3-fold increase in biomass throughput for a given reactor volume at the pilot scale with minimal loss of valuable products, in agreement with published data from the 3 × 10 -2 m 3 reactor operated by ISU. Additionally, a proposal for a 250 ton/day commercial-scale biomass pyrolysis reactor is analyzed, showing that the same size reactor operated by heating the fluidizing gas externally would have only one-tenth the capacity; if operated by heating the sand externally, the sand would need to circulate at an impractical 0.7 bed volume per minute rate to maintain a 250 ton/day biomass throughput.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Developing an Undergraduate Research Laboratory for Experimental Physical Chemistry [Book Chapter]

Embarking on a faculty career in physical chemistry at a primarily undergraduate institution (PUI) is exciting, but also overwhelming. Becoming both an effective teacher and a productive researcher requires a good plan, hard work and support from others who understand what it takes to be successful. The phrase, “building a laboratory,” calls to mind the physical construction of a research instrument, but beginning a career at a PUI involves much more than assembling equipment. Funding for the lab must be secured, students must be recruited and mentored, and the lab must be overseen to keep things running on a daily basis. While many of these tasks would also be part of starting a career at a doctoral level institution, there are many special considerations that must be taken into account when working with undergraduate students because their laboratory experience and chemical knowledge are still within those beautiful but nascent stages. Here, this unique aspect makes building a research program challenging, but also very rewarding. Exposing young minds to the wonders of physical chemistry and building personal relationships through the mentoring process can be immensely gratifying. This chapter is a compilation of holistic advice for building an experimental physical chemistry research laboratory for undergraduates, reflecting a typical experience found in the United States.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Substitution Reactions in the Pyrolysis of Acetone Revealed through a Modeling, Experiment, Theory Paradigm

The development of high-fidelity mechanisms for chemically reactive systems is a challenging process that requires the compilation of rate descriptions for a large and somewhat ill-defined set of reactions. The present unified combination of modeling, experiment, and theory provides a paradigm for improving such mechanism development efforts. Here we combine broadband rotational spectroscopy with detailed chemical modeling based on rate constants obtained from automated ab initio transition state theory-based master equation calculations and high-level thermochemical parametrizations. Broadband rotational spectroscopy offers quantitative and isomer-specific detection by which branching ratios of polar reaction products may be obtained. Using this technique, we observe and characterize products arising from H atom substitution reactions in the flash pyrolysis of acetone (CH 3 C(O)CH 3 ) at a nominal temperature of 1800 K. The major product observed is ketene (CH 2 CO). Minor products identified include acetaldehyde (CH 3 CHO), propyne (CH 3 CCH), propene (CH 2 CHCH 3 ), and water (HDO). Literature mechanisms for the pyrolysis of acetone do not adequately describe the minor products. The inclusion of a variety of substitution reactions, with rate constants and thermochemistry obtained from automated ab initio kinetics predictions and Active Thermochemical Tables analyses, demonstrates an important role for such processes. Furthermore, the pathway to acetaldehyde is shown to be a direct result of substitution of acetone's methyl group by a free H atom, while propene formation arises from OH substitution in the enol form of acetone by a free H atom.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

SimELIT: A Novel GUI-Based Comprehensive Ion Trajectory Simulation Software for Mass Spectrometry

Ion trajectory simulation in mass spectrometry systems from injection to detection is technically challenging but very important for better understanding the ion dynamics in instrument development. Here, in this work, we present SimELIT (Simulator of Eulerian and Lagrangian Ion Trajectories), a novel ion trajectory simulation platform. SimELIT is built upon a suite of multiphysics solvers compiled into OpenFOAM (an open-source numerical solver library particularly used for computational mechanics), with a simple web-based graphical user interface (GUI) allowing users to define the details of OpenFOAM cases and run simulations. SimELIT is a modular program and can provide extensions of physics (e.g., gas flows, electrodynamic fields) and thus enable ion trajectory simulations from the ion source to detector. The current version (SimELIT) provides two numerical solvers for ion trajectory simulations–(1) a Lagrangian particle tracker in vacuum and (2) a Eulerian ion density solver in background gas in the presence of electric fields. Here, we describe the architecture of SimELIT, including its use of Docker and the React Framework, and demonstrate the computation of ion trajectories of multiple m/z values in a static/linear voltage drop in vacuum (across a 1 m long flight tube). Further, the drift motion of ions under 1 Torr pressure conditions in a static background (N 2 ) gas through a 20 V/cm static electric field is shown. The results produced from SimELIT were compared with SIMION and theoretical estimates. In addition, we report the computation of ion trajectories in electrodynamic fields within a planar FAIMS device operating at atmospheric pressure.

97 MATHEMATICS AND COMPUTING↗

Reply to Comment by Peterie Et Al. on “Accelerated Fill‐Up of the Arbuckle Group Aquifer and Links to U.S. Midcontinent Seismicity”

Abstract Peterie et al. question one observation in our paper: associating pressure increases to injection volumes at distances of up to 25 km from an injection well. In this reply, we show that the comment misunderstands our analysis and the evidence that led to this conclusion. We also show that gauge‐depth‐corrected pressures, used by the authors to produce statewide pressure maps, are discrepant with the static fluid level data, provided in our original compilation and analysis. The discrepancies are a result of the pressure correction method employed, which naïvely substitutes formation pressure for bottomhole pressure to calculate wellbore fluid density. Their linearly interpolated pressure maps, based on sparse data, contain interpolation and extrapolation artifacts that contradict injection trends in the state, the Theis solution, and the superposition principle. We reiterate that pressure and static fluid level increases in Class I wells existed prior to 2013, most notably in central Kansas, where recent earthquakes are cited in the comment as evidence of a pressure plume emanating from the Kansas‐Oklahoma border, 90 km away. We show that the space‐time pattern of seismicity in this area is inconsistent with a northward propagating pressure plume and, instead, seismicity appears to be centered on and near a cluster of high‐rate injection wells, two of which are among the highest rate wells in the state. These observations, along with recent M4 + earthquakes during continued decreases in wastewater injection in southern Kansas and northern Oklahoma, question the usefulness of the comment for understanding and managing societally significant earthquakes.

Ansari, Esmail↗

A data-driven global soil heterotrophic respiration dataset and the drivers of its inter-annual variability

Soil heterotrophic respiration (SHR), one of the primary carbon fluxes from terrestrial ecosystems to the atmosphere, is important for carbon-climate feedbacks because of its sensitivity to available litter and soil carbon, climatic conditions, and nutrient availability. However, until recently limited SHR data were available, and most published global SHR estimates have either a short time span, coarse spatial resolution, or reply on overly-simple model formulations. To better understand and quantify the global distribution of SHR and its sensitivity to climate variability, we produced a new global SHR dataset using Random Forest algorithms, up-scaling 455 point data from the Global Soil Respiration Database (SRDB 4.0) with gridded fields of climatic, edaphic and productivity as explanatory variables. We estimated a global total SHR of 46.8 Pg C yr-1 over 1985-2013 (95% confidence interval: 38.6-56.3 Pg C yr-1), with a significant increasing trend of 0.03 Pg C yr-2 during this period. We found that the choice of soil moisture datasets contributes more to the difference among these data-driven SHR members rather than that of productivity, temperature and precipitation data sources. We also analyzed the influence of climatic variables on the inter-annual variability (IAV) of our SHR product. Water availability was the dominant driver of IAV at global scales, although the inferred sensitivity depends on the choice of the soil moisture gridded dataset. At the ecosystem scale, temperature strongly controls the IAV of SHR in tropical forests, while water availability dominates in extra-tropical forest and semi-arid regions. Our machine-learning gridded SHR dataset and outputs from process-based land surface models (TRENDYv6) show agreement for a strong association between water variability and SHR IAV at the global scale, but the two approaches lead to different temporal trend globally and different controlling variables for IAV at the ecosystem scale. Our study provides evidence for the pervasive and important role of water availability in driving SHR, indicating both a direct effect limiting decomposition rates and an indirect effect through the amount of fresh organic matter made available to SHR from productivity. In consideration of potential limitations and uncertainties remaining in our data-driven SHR datasets, we call for a more scientifically designed observation network for SHR, more observation data compilation, and increased use of deep learning methods making maximum use of observation data in hand. This will benefit process-based models, and improve our understanding of SHR response to future anomalous environmental conditions.

Yao, Yitong↗