J Phys Chem A [JOURNAL]
Sun
200 papers
Nonstatistical Unimolecular Decay of the Singly Fluorinated Criegee Intermediate FCHOO.
Karlsson E, Walsh LR, Qian Y … +2 more , Nguyen TL, Lester MI
J Phys Chem A · 2026 May · PMID 42065861 · Publisher ↗
The fluorinated Criegee intermediate, FCHOO, is produced from the ozonolysis of hydrofluoroolefins (HFOs) which are next-generation refrigerants. Unimolecular decay of -FCHOO proceeds via a 1,3 ring closure pathway to fl...
The fluorinated Criegee intermediate, FCHOO, is produced from the ozonolysis of hydrofluoroolefins (HFOs) which are next-generation refrigerants. Unimolecular decay of -FCHOO proceeds via a 1,3 ring closure pathway to fluorodioxirane and subsequent rearrangement and/or dissociation to many products including hydroxyl (OH) radicals that are detected experimentally. Vibrational activation of jet-cooled FCHOO with two quanta of CH stretch (17.70 kcal mol) leads to unimolecular decay via quantum mechanical tunneling at an energy slightly below the transition state barrier of 18.03 ± 0.25 kcal mol, determined utilizing the high accuracy composite HEAT-345(Q) method. The observed unimolecular decay rate of (5.4 ± 1.6) × 10 s is an order of magnitude slower than that predicted by statistical unimolecular reaction theory with quantum mechanical tunneling. The nonstatistical behavior originates from excitation of a CH stretch vibration that is orthogonal to the heavy atom motions along the reaction coordinate and slow intramolecular vibrational energy redistribution due to the sparse density of states.
Effects of Magnetic Ordering on Hole Polaron Transport in Hematite: The Critical Role of Superexchange Interactions.
Lyu S
J Phys Chem A · 2026 May · PMID 42060726 · Publisher ↗
Within the class of technologically important transition metal oxide quantum materials, strong electronic correlations in magnetic oxide semiconductors arise from partially filled shells. For magnetic oxide semiconducto...
Within the class of technologically important transition metal oxide quantum materials, strong electronic correlations in magnetic oxide semiconductors arise from partially filled shells. For magnetic oxide semiconductors, superexchange interactions fundamentally determine the magnetic ordering and can greatly affect the electronic structures and physical properties. The formation of self-trapped small hole polarons is known to hinder the transport properties and, thus, the device applications. Many strategies (e.g., temperature, doping, etc.) have been proposed to enhance hole polaron transport in magnetic oxide semiconductors. However, the slow mobilities of the hole polarons continue to limit the device performance. As a potential alternative approach, the feasibility of magnetic-field control and how the effect of superexchange interactions on the transport properties of small hole polarons remains to be clarified. In the prototypical magnetic oxide semiconductor α-FeO, we computationally studied the superexchange interactions, - hybridizations, formation energies, and hopping barriers of hole polarons. Two types of magnetic ordering are contrasted: antiferromagnetic and ferromagnetic. We found that ferromagnetic ordering leads to higher formation energy, smaller diffusion barrier, and isotropic diffusion of the hole polaron due to the weakened superexchange strength. This comparative study provides insights into the interplay between exchange interactions and hole polaron transport and demonstrates the capability for enhancing the transport properties of small hole polarons in magnetic oxide semiconductors through magnetic-field control.
Infrared Detection and High-Resolution Spectroscopic Study of Very Heavy Carbon Subchalcogenides: Tricarbon Telluride, CTe, and Carbon Subtelluride, TeCTe.
Dudek JB, Burger S, Salomon T … +4 more , Bonah L, Schlemmer S, Gauss J, Thorwirth S
J Phys Chem A · 2026 May · PMID 42060366 · Publisher ↗
Carbon subchalcogenides with tellurium have been studied spectroscopically for the first time in the form of tricarbon telluride, CTe, and carbon subtelluride, TeCTe. Guided by high-level quantum-chemical calculations pe...
Carbon subchalcogenides with tellurium have been studied spectroscopically for the first time in the form of tricarbon telluride, CTe, and carbon subtelluride, TeCTe. Guided by high-level quantum-chemical calculations performed at the CCSD(T) level of theory using effective-core potentials (to account for scalar-relativistic effects) together with large basis sets, CTe and TeCTe have been detected at 5 μm wavelengths using high-resolution infrared spectroscopy of laser ablation products from carbon-tellurium targets seeded in a free-jet expansion with a large excess of helium. Because of the rich isotopic composition of tellurium and its high atomic mass, the vibrational bands observed show relatively compact and complex structures, despite the simple linear geometrical arrangements of the carriers. For CTe, the spectroscopic pattern found in its ν band enables the identification of five tellurium isotopologues. Owing to an extremely high line density and a poorly resolved spectrum, the analysis of the ν fundamental of TeCTe is very complicated, but plausible assignments of the rotational-vibrational structure of the five major isotopic species have been obtained by comparison with results from CCSD(T) calculations.
Size-Specific Fragmentation and Intracluster Reactions of Methanol Clusters in Superfluid Helium Nanodroplets.
Singha S, Mani D
J Phys Chem A · 2026 May · PMID 42057432 · Publisher ↗
In this work, methanol clusters containing up to ten molecules were formed inside superfluid helium nanodroplets. The fragmentation dynamics following electron ionization of droplets doped with these clusters were system...
In this work, methanol clusters containing up to ten molecules were formed inside superfluid helium nanodroplets. The fragmentation dynamics following electron ionization of droplets doped with these clusters were systematically investigated. The mass spectrum is dominated by the protonated (CHOH)H fragments, consistent with the previous molecular beam studies. However, in helium droplets, intact cluster cations (CHOH), and deprotonated cations (CHOH)CHO are also observed. An investigation of the pressure dependence of relevant signals in the mass spectra led to the determination of the parent cluster(s) for each of the observed mass fragments. This approach provided comprehensive insight into the size-dependent fragment pathways of methanol clusters. Notably, the deprotonated dimethyl ether CHOCH fragment, dimethyl ether molecular radical CHOCH, and protonated dimethyl ether (CHOCH)H fragment are found to originate exclusively from methanol dimers and trimers. Furthermore, we demonstrate that beyond a certain size, (CHOH) clusters forming (CHOH)H, (CHOH)CHO, and (CHOH) species are hosted by droplets of different mean sizes. We also observe weak helium-ion adduct fragments, HeCHO, HeCHO, and HeCHO. The pressure dependence of these fragments shows that they originate from droplets containing methanol monomers, dimers, and trimers.
Prediction of E-Beam-Lithography Performance of PAGs Using Quantum Chemistry Calculations.
Sun K, Ge Z, Cao K
J Phys Chem A · 2026 May · PMID 42055544 · Publisher ↗
Photoacid generators (PAGs) are critical components in electron-beam lithography (EBL), initiating acid-catalyzed reactions through ionization and dissociation within the resist. Yet, identifying structural motifs that e...
Photoacid generators (PAGs) are critical components in electron-beam lithography (EBL), initiating acid-catalyzed reactions through ionization and dissociation within the resist. Yet, identifying structural motifs that enhance PAG performance remains challenging. Here, using density functional theory calculations and the Binary-Encounter-Bethe model, we systematically evaluate the ionization cross sections and vertical electron affinities of a widely employed PAG─triphenyl sulfonium 4-(methacryloxy)-2,3,5,6-tetrafluorobenzenesulfonate─and its isomers across incident electron energies of 30-100 keV, and 10-50 eV. We further examine how distinct functional groups and their substitution patterns govern these electronic properties. Key results demonstrate that carbon-carbon double bonds promote ionization more effectively than carbonyl groups; hydroxyl substitution position and number exert negligible influence on ionization cross sections; while fluorine substitution markedly modulates electron affinity without significantly altering ionization. This work establishes structure-property guidelines that can inform the rational design of next-generation PAGs for high-resolution EBL.
Multispectroscopic Investigation of the Organosilyl Ether -Butoxytrimethylsilane.
Berggötz FEL, Heikura EJ, Hans A … +4 more , Kargin D, Ehresmann A, Pietschnig R, Schnell M
J Phys Chem A · 2026 May · PMID 42051171 · Full text
In a multispectroscopic approach, we investigated the tailored chiral organosilicon compound -butoxytrimethylsilane in the gas phase and report its racemic and enantiopure synthesis. We characterized the structural and c...
In a multispectroscopic approach, we investigated the tailored chiral organosilicon compound -butoxytrimethylsilane in the gas phase and report its racemic and enantiopure synthesis. We characterized the structural and conformational flexibility using chirped-pulse Fourier transform microwave spectroscopy in a supersonic jet and identified three different conformers from the analysis of the rotational spectrum supported by quantum-chemical calculations. For the lowest energy conformer, characteristic splitting patterns are observed, matching the internal rotation of two nonequivalent methyl rotors, which can be attributed to two out of the three methyl groups attached to the silicon atom. Complementary synchrotron-based photoelectron spectroscopy provided the Si 2p core-level binding energies, characterizing the electronic environment of silicon in this chiral organosilicon framework. These results establish a detailed picture of both the structural dynamics and the electronic properties of this flexible silicon-containing molecule, providing a foundation for future studies of structure-property relationships in chiral organosilicon systems.
Construction of Arbitrary-Order Internal Coordinate Transformations to Improve Studies of Large-Amplitude Motions.
Boyer MA, Tabor DP
J Phys Chem A · 2026 May · PMID 42048545 · Full text
Internal coordinates and their derivatives underpin the efficient treatment of geometry optimizations, high-resolution spectroscopic simulation, and the fitting of potential surfaces in quantum chemistry. Existing descri...
Internal coordinates and their derivatives underpin the efficient treatment of geometry optimizations, high-resolution spectroscopic simulation, and the fitting of potential surfaces in quantum chemistry. Existing descriptions of the construction of internal coordinate derivatives generally either lack simplicity or generality. In this paper, we provide a simple framework for evaluating any internal coordinate derivative to any order and an automatic approach to obtain the corresponding inverse transformation. Through further extension to transformations between internal coordinate systems, this approach provides a complete, generic method for handling a wide variety of molecular problems. The utility of this construction is demonstrated by investigations into the behavior of internal coordinate interpolations for studying isomerizations, quantifying the coupling between carbonyl stretches and a complex stretch coordinate in an organometallic system, and analysis of the performance of a machine learned interatomic potential in computing anharmonic frequencies as a function of low-frequency coordinate distortions. This approach is shown to be numerically efficient as well as general, and a reference implementation is provided.
Systematic Evaluation of a Cluster-Continuum-Model Workflow to Compute the Free Energies of Solvation of Ions in Different Solvents.
Lehmann M, Jameel F, Kaupp M
J Phys Chem A · 2026 May · PMID 42047403 · Full text
A partially automatized computational protocol for the construction of embedded microsolvated clusters based on a combination of the quantum cluster growth algorithm, DFT reoptimization, higher-level energy computations,...
A partially automatized computational protocol for the construction of embedded microsolvated clusters based on a combination of the quantum cluster growth algorithm, DFT reoptimization, higher-level energy computations, conformer selection based on free energy, embedding into advanced implicit solvation models like COSMO-RS, and averaging over a range of cluster sizes has been validated and applied to calculate single-ion Gibbs free energies of solvation in different solvents. For aqueous solution, excellent agreement with a widely accepted single-ion scale based on the cluster pair approximation (CPA) is found, to within the error margins of that scale, but without anchoring to one particular ion like the latter. Similar calculations show that the TATB assumption underlying the second widely used single-ion scale is not justified, shifting the TATB scale even further from the CPA scale. Applications of the cluster-continuum method to single-ion values in acetonitrile show that here the CPA-based proton value may be less settled than with water, methanol, or DMSO, and it deserves closer examination. Finally, the solvation of the fluoride ion is compared in a variety of different solvents (water, acetonitrile, methanol, DMSO, diethyl ether, and benzene). While water and methanol provide the most negative solvation free energies, acetonitrile, methanol, and DMSO are not far behind, and even the relatively nonpolar diethyl ether and benzene exhibit appreciable stabilization. This is due to significant charge-assisted C-H···F hydrogen bonds to the highly compact fluoride ion in all of the formally aprotic solvents, involving in some cases more than one proton from a given solvent molecule in a chelate binding mode.
Theoretical Study on the Central Fused-Ring Modification of Nonfullerene Acceptors for Organic Solar Cells.
Zhang CR, Yu F, Fu JL … +5 more , Gong JJ, Zhang ML, Liu XM, Sang CC, Chen HS
J Phys Chem A · 2026 May · PMID 42046497 · Publisher ↗
Molecular structure modification of nonfullerene acceptors (NFAs) is an important approach to modulate optoelectronic properties and to improve power conversion efficiency of organic solar cells (OSCs). Herein, to deeply...
Molecular structure modification of nonfullerene acceptors (NFAs) is an important approach to modulate optoelectronic properties and to improve power conversion efficiency of organic solar cells (OSCs). Herein, to deeply understand the influence of central-fused ring halogenation and extension on photoelectric properties and photovoltaic performances, we selected a series of NFAs with different central fused rings, including CH-6F, CH-20, CH-22, CH-23, CH-45, CH-BQ, CH-iBQ, and CH-BBQ, combined with electron donor PM6. Based on quantum chemical calculations, the geometric structures, electronic structures, excitation properties, and absorption spectra were systematically studied for the PM6 and NFA molecules, as well as the corresponding interface model complexes. Moreover, the rate constants of the electronic processes were discussed. The results indicate that the peripheral halogen substitution on the central fused ring can effectively enhance molecular backbone planarity, shrink dipole moment, lower the HOMO and LUMO energies with widening energy gap, induce blue shift of optical absorption, increase excitation energy and average electrostatic potential (ESP), and shorten excited-state lifetime. Extending conjugation of the central fused ring not only enhances molecular backbone planarity, lowers the HOMO and LUMO energies, and increases the average ESP and charge-transfer excitation energies but also reveals the importance of the fusing style for extending conjugation. This work unravels the trilateral relationship among molecular structures, properties, and photovoltaic performance of NFAs and provides foundations to design more efficient NFAs for OSCs.
Prediction of Molecular Structure of Asphaltenes in Heavy Oils.
Yuan Z, Jiang Z, Yuan S
J Phys Chem A · 2026 May · PMID 42044475 · Publisher ↗
Asphaltene is a crucial component of petroleum. The molecular structure is difficult to determine, posing challenges for its analysis and application. In this study, a program named Prediction of Molecular Structures of...
Asphaltene is a crucial component of petroleum. The molecular structure is difficult to determine, posing challenges for its analysis and application. In this study, a program named Prediction of Molecular Structures of Asphaltenes (PMSA) was developed to predict asphaltene structures with its validity rigorously verified through molecular dynamics simulations. Using the modified Brown-Ladner method, key structural parameters (with corresponding probabilities) were first derived from basic experimental data, including molecular weight, elemental composition, and H NMR spectra. Based on these parameters, 5000 candidate asphaltene structures were constructed by integrating Monte Carlo sampling with a pre-established library of aromatic building blocks. Nonlinear optimization with a least-squares objective function was then employed to screen out 4-6 dominant molecular structures and determine their respective molar fractions in the sample. To validate the predicted structures, asphaltene-toluene systems were established, and analyses of radial distribution functions (RDF) and dihedral angle distributions between aromatic planes were conducted. The results showed that PMSA-generated molecules can form stable π-π stacked aggregates, exhibiting an aggregation free energy of approximately 4-6 kcal/mol, which aligns well with the characteristic structural features of asphaltenes and provides robust theoretical support for the reliability and applicability of the PMSA program.
The Cu L-edge XPS Spectrum of Copper Phthalocyanine: Quantitative Ab Initio Analysis Including Spin-Orbit Coupling and Löwdin Nonorthogonal Determinant Overlaps.
Benbalagh R, Goldsztejn G, Carniato S
J Phys Chem A · 2026 May · PMID 42043334 · Publisher ↗
We present a detailed ab initio investigation of the Cu L-edge X-ray photoelectron spectroscopy (XPS) spectrum in copper phthalocyanine (CuPc). Spin-orbit coupling is treated with the Breit-Pauli Hamiltonian, and transi...
We present a detailed ab initio investigation of the Cu L-edge X-ray photoelectron spectroscopy (XPS) spectrum in copper phthalocyanine (CuPc). Spin-orbit coupling is treated with the Breit-Pauli Hamiltonian, and transition intensities are computed using the Löwdin formalism within the sudden approximation, accounting for nonorthogonality between initial and final-state wave functions. The nonorthogonal Löwdin determinant approach accurately reproduces experimental intensities, while orbital analysis highlights the charge-transfer and orbital-reorganization processes underlying the excitations. These results provide a quantitative and physically transparent interpretation of the Cu L-edge XPS spectrum, clarifying the distinct ligand and metal-centered character of the main and satellite excitations. The main L peak is dominated by a ligand-centered excitation (Ligand (b) → a), whereas the shakeup satellite arises primarily from metal-to-ligand excitations (Metal (Cu 3d) → a).
Improved Accuracy in Semi-Experimental Structure Determination by Resolving Problems Associated with Rotation of Principal Inertial Axes of Isotopologues: Structures of 1,3-Oxazole (-CHNO).
Esselman BJ, Zdanovskaia MA, Atwood MG … +8 more , Adkins TK, Kobayashi M, Tsunekawa S, Kobayashi K, Sahoo NP, Stanton JF, Woods RC, McMahon RJ
J Phys Chem A · 2026 May · PMID 42031557 · Full text
The rotational spectrum of the normal isotopologue of 1,3-oxazole (-CHNO) was observed from 43 to 750 GHz. Over 3900 transitions for the ground vibrational state are measured, assigned, and least-squares fit to sextic ce...
The rotational spectrum of the normal isotopologue of 1,3-oxazole (-CHNO) was observed from 43 to 750 GHz. Over 3900 transitions for the ground vibrational state are measured, assigned, and least-squares fit to sextic centrifugally distorted-rotor Hamiltonians. The measured frequencies and resulting spectroscopic constants from this extended spectral range, combined with previous measurements of the nuclear quadrupole coupling constants, will facilitate astronomical searches for oxazole across the majority of the range of modern radiotelescopes. Spectra for a set of 30 oxazole isotopologues, which include multiple isotopic substitutions of each atom, are used to determine the first semi-experimental equilibrium () structure and semi-experimental substitution structure (), each using CCSD(T) computed values for the vibration-rotation interaction and electron-mass corrections. The large number of isotopologues, including 21 isotopologues observed for the first time, and the redundant substitutions of each atom provide sufficient spectroscopic information to determine the structure with the expected high level of accuracy and precision (0.0001 or 0.0002 Å in bond distances and 0.013 to 0.025° in bond angles). In the course of this study, we analyzed a known issue for some structure determinations of near-oblate asymmetric tops in which inclusion of individual isotopologues degrades the structure determination. We demonstrate that this problem primarily arises from the difference in the values of the computed vibration-rotation interaction corrections as evaluated at the computed geometry vs the geometry of the "real" molecule. Our solution to this problem substantially improves the structure of oxazole and likely can be generalized to many other molecules.
The Importance of Contributions of Conformations to the Radiative Efficiency Value of a Compound Compared to the Lowest Energy Conformer using Quantum Chemistry.
Farris S, Duarte A, Stever M … +6 more , Gruszka E, Hussen M, Lesenfants MA, Passement S, Liszka D, Blowers P
J Phys Chem A · 2026 May · PMID 42030485 · Publisher ↗
Accurate prediction of the radiative efficiency (RE) is essential in assessing the climate impact of fluorinated compounds. This study investigates the role of molecular conformers in determining the RE of perfluorobutyl...
Accurate prediction of the radiative efficiency (RE) is essential in assessing the climate impact of fluorinated compounds. This study investigates the role of molecular conformers in determining the RE of perfluorobutylbutylmethylamine (PFBBM) using quantum chemical methods and thermodynamic modeling. By evaluating the complete ensemble of possible conformers and applying a Boltzmann distribution of those conformers from Gibbs free energy calculations, we found that relying solely on the lowest-energy conformer can underestimate the RE of a compound. Our results emphasize the importance of incorporating various conformations of molecules in climate modeling and regulatory assessments of greenhouse gas and global warming potentials (GWPs) when using quantum chemical methods.
A Benchmark and Basis-Set Extrapolation Study of Hyperfine Coupling Constants from the Random Phase Approximation and σ-Functionals.
Graf D, Liu L, Siekmann F … +2 more , Drontschenko V, Ochsenfeld C
J Phys Chem A · 2026 May · PMID 42024854 · Full text
Hyperfine coupling constants (HFCCs) provide an important link between theory and experiment; however, their accurate computation at a reasonable computational cost remains challenging. In this work, we present the theor...
Hyperfine coupling constants (HFCCs) provide an important link between theory and experiment; however, their accurate computation at a reasonable computational cost remains challenging. In this work, we present the theory for evaluating HFCCs on the level of the promising σ-functionals developed in the Görling group. We show that the best-performing σ-functional achieves accuracies, relative to coupled-cluster singles doubles and perturbative triples (CCSD(T)) reference values, comparable to those of domain-based local pair-natural orbital coupled-cluster singles doubles (DLPNO-CCSD)─currently among the most accurate methods applicable beyond the few-atoms scale─while being significantly less computationally demanding. We further investigate the influence of the atomic-orbital basis on random phase approximation (RPA), σ-functional, and also CCSD(T) HFCCs, showing that the pcH and pcJ basis-set families developed in the Jensen group are well suited for these methods. The availability of these basis-set families enables systematic complete basis-set (CBS) extrapolations for all HFCC calculations, with different extrapolation schemes producing very similar results. The presented basis-set extrapolated CCSD(T) HFCCs can hence serve as new reference values for future method developments or benchmarks.
Antiaromaticity and π-Electron Behavior of Cyclo[25]carbon Modulated by Odd-Topology Phase Frustration.
Wu Y, Wu J, Quan Y … +2 more , Liu G, Chen D
J Phys Chem A · 2026 May · PMID 42018769 · Publisher ↗
Cyclo[]carbons─molecular rings composed exclusively of sp-hybridized carbon atoms─represent a uniquely demanding frontier in carbon allotrope chemistry owing to their extreme structural sensitivity and unconventional π-e...
Cyclo[]carbons─molecular rings composed exclusively of sp-hybridized carbon atoms─represent a uniquely demanding frontier in carbon allotrope chemistry owing to their extreme structural sensitivity and unconventional π-electron behavior. The recent on-surface synthesis of cyclo[25] carbon (C), the largest odd-membered ring realized to date, provides an unprecedented opportunity to interrogate the fundamental properties of electron-deficient, symmetry-broken carbon nanostructures. Here we combine extensive first-principles calculations─spanning ground-state electronic structure, magnetic response, and thermodynamic stability─to elucidate the bonding and antiaromatic character of C. We show that C adopts a planar -symmetric triplet ground state featuring pronounced bond-length and bond-angle alternation, reflecting a delicate interplay between Peierls distortion and electron delocalization. π-Electron analysis reveals a striking departure from even-membered cyclocarbons: the π subsystem supports simultaneous clockwise and counterclockwise induced ring currents under an external magnetic field. This counterintuitive duality originates from the intrinsic phase discontinuity of odd-membered rings, wherein the π wave function cannot achieve periodic phase closure and undergoes a π phase inversion between the inner and outer regions of the ring. ACID, NICS and ICSS analyses collectively confirm that C is globally antiaromatic, with its unusual current patterns arising from phase-frustrated π conjugation rather than conventional Hückel-type electron counting. NICS analysis of structures sampled from AIMD trajectories confirms the thermally robust weak antiaromaticity of C without aromaticity inversion. Excited-state calculations further show that the dominant absorption features stem from strongly localized π → π* transitions involving mixed contributions from both π and π manifolds. These results identify C as a phase-frustrated, open-shell cyclocarbon with structural and magnetic properties fundamentally distinct from those of even-membered homologues. The insights obtained here provide a basis for understanding antiaromaticity and excited-state behavior in odd-membered sp-carbon rings and may facilitate future studies of larger or functionalized cyclocarbons.
Analyzing Peptide Torsional Dynamics: An Angular-Displacement PCA Pipeline for Short-Horizon Prediction from Molecular Dynamics.
Albrizzi L, Gayoso G, Colbes J … +3 more , Di Lella S, Schaerer CE, Alvarez AC
J Phys Chem A · 2026 May · PMID 42018286 · Full text
Analyzing the conformational dynamics of short peptides from molecular dynamics (MD) simulations remains challenging. The high dimensionality of torsional space and the periodic nature of dihedral angles complicate stati...
Analyzing the conformational dynamics of short peptides from molecular dynamics (MD) simulations remains challenging. The high dimensionality of torsional space and the periodic nature of dihedral angles complicate statistical analysis and dimensionality reduction. This work presents an integrated computational workflow that combines all-atom MD simulations with a multistage analytical framework to characterize torsional reorganization patterns. Our approach introduces an angular-displacement representation χ that resolves periodic discontinuities by focusing on frame-to-frame torsional changes rather than absolute configurations. This transformation yields variables suitable for linear analysis and acts as a high-pass filter, emphasizing rapid reorganization events over slow conformational drift. We analyze these transformed coordinates using spatiotemporal principal component analysis (PCA) to identify collective torsional patterns. To evaluate how different coordinate choices preserve dynamical information, we quantitatively compare raw dihedral angles, sine-cosine embedding, and the displacement representation χ using the VAMP score. This comparison reveals their complementary nature: sine-cosine coordinates capture slow conformational variability, while χ highlights rapid torsional reorganizations. Subspace convergence analysis confirms the stability of the reduced PCA representation within the simulation time scale. We apply the methodology to the DENV-2 peptide (CGYGLC) as a representative short system. Our approach identifies hierarchical patterns of torsional flexibility─characterized by a flexible central core and region-specific dynamics─and reconstructs short-term structural evolution with angular errors below 25% and RMSD values of 1.0-2.1 Å. The main contributions are (i) a geometry-aware angular-displacement representation that respects the periodic nature of torsional variables; (ii) a spectral characterization of the displacement transformation; (iii) a quantitative comparison of observable representations using the VAMP score; and (iv) a demonstration of short-horizon structural prediction from reduced dynamical subspaces. The workflow provides a computationally efficient framework for analyzing torsional reorganization dynamics in peptide simulations.
Unlocking the Potential of Phosphate-Based Weakly Coordinating Anions as Electrolyte Components for Calcium-Ion Batteries.
Vishnubhotla VSSB, Faizan M, Yadav AK … +2 more , Pooja, Pawar R
J Phys Chem A · 2026 May · PMID 42017687 · Publisher ↗
Development of calcium-ion batteries (CIBs) is strongly hindered by the limited availability of electrolytes that enable reversible plating and stripping of Ca ions while maintaining interfacial and electrochemical stabi...
Development of calcium-ion batteries (CIBs) is strongly hindered by the limited availability of electrolytes that enable reversible plating and stripping of Ca ions while maintaining interfacial and electrochemical stability. Motivated by this need for chemically distinct and less fluorinated weakly coordinating anions, we present a density functional theory (DFT) evaluation of hexacoordinated phosphate/phosphorate anions as prospective electrolyte components for CIBs. Surface electrostatic analysis indicates diffuse negative potential distributions consistent with weakly coordinating anion (WCA)-like behavior, broadly comparable to fluorinated alkoxy borate and aluminate anions. Their electrochemical viability was further assessed using frontier molecular orbital (HOMO/LUMO) descriptors, binding energies, and oxidation/reduction limits to estimate electrochemical stability windows (ESW) in representative solvents. Across the series, oxygen-rich chelating frameworks generally exhibit weaker Ca-anion association and enhanced oxidative robustness, which is consistent with the calculated ESW values. Overall, the phosphate-based anions fall within the performance window of previously investigated WCA families, supporting their potential as a chemically distinct class of electrolyte additives for CIBs. Among the anions examined, TOP and TCP show higher ESW, with TOP in ethylene carbonate (EC) emerging as the best combination under the descriptors considered, making it a viable electrolyte component.
Bond-Length Alternation as a Structural Coordinate for Electronic Regime Crossover in Indophenines.
Faleiro Berbigier J, Seferos DS
J Phys Chem A · 2026 May · PMID 42013374 · Publisher ↗
The emergence of diradical character in conjugated π-systems is often described qualitatively in terms of quinoidal distortion, yet simple quantitative structural descriptors that link molecular geometry to electronic gr...
The emergence of diradical character in conjugated π-systems is often described qualitatively in terms of quinoidal distortion, yet simple quantitative structural descriptors that link molecular geometry to electronic ground-state regime remain scarce. Here, we show that bond-length alternation (BLA) serves as a compact geometric descriptor that correlates with the electronic regime crossover in donor-acceptor indophenine derivatives. Broken-symmetry density functional calculations show that progressive reduction of BLA is accompanied by a transition from a closed-shell electronic structure to weak diradicaloid character and, for the smallest-BLA members, approach to a near-degenerate frontier orbital manifold. This crossover is consistently reflected by a rapid reduction of the singlet-triplet separation (Δ), accompanied by increased fractional frontier natural occupations and enhanced spin polarization in the broken-symmetry solutions (⟨S⟩), all converging within a narrow BLA window. Frontier natural orbitals exhibit a progressive loss of classical bonding-antibonding complementarity and the emergence of a quasi-degenerate symmetry-related frontier pair. These results identify BLA as a practical structural parameter for classifying electronic regimes within this indophenine family and suggest that related quinoidal π-frameworks may exhibit similar structure-electronic correlations.
Explicit Hydration of the Beryllium Trifluoride Anion with One to Three Water Molecules: BeF(HO).
Autry KR, Tschumper GS
J Phys Chem A · 2026 May · PMID 42013373 · Full text
This work investigates the microhydration of the beryllium trifluoride anion (BeF) with up to three water molecules (BeF(HO) where = 1-3). Full geometry optimizations and harmonic vibrational frequencies were computed o...
This work investigates the microhydration of the beryllium trifluoride anion (BeF) with up to three water molecules (BeF(HO) where = 1-3). Full geometry optimizations and harmonic vibrational frequencies were computed on various BeF(HO) stationary points using density functional theory methods (B3LYP-D3BJ, B3LYP, ωB97XD, and M06-2X) as well as the CCSD(T) and MP2 ab initio methods with a triple-ζ correlation-consistent basis set augmented with diffuse functions on all non-hydrogen atoms (haTZ). One BeF(HO), five BeF(HO) and 11 BeF(HO) minima were identified, most of which have not been reported in the literature to date. Two of the new BeF(HO) configurations have lower electronic energies than the previously reported trihydrate structure by nearly 1 kcal mol, but the previous structure has the lowest energy when harmonic zero-point vibrational energies are included. For the mono- and dihydrates, the water molecule(s) prefer to bind directly to the beryllium trifluoride anion via double ionic hydrogen bonds (DIHBs) to form planar structures with C symmetry. With the introduction of a third water molecule, the hydration pattern associated with the lowest-energy structure (with C symmetry) changes from solely DIHBs to a hydrogen-bonded network that also includes water-water interactions. The CCSD(T)/haTZ electronic dissociation energies for the BeF(HO) global minima are 16.0, 30.1, and 43.6 kcal mol for = 1, 2, and 3, respectively, and these values decrease by about 5% when a counterpoise procedure is applied. The CCSD(T)/haTZ harmonic OH stretching frequencies of HO decrease appreciably when donating hydrogen bonds to BeF and/or HO molecules. The magnitude of these shifts is strongly dependent on the hydration motif. For the symmetric structures exhibiting only DIHB contacts, the largest shifts at this level of theory are -168 cm for = 1 (C), -138 cm for = 2 (C), and -122 cm for = 3 (D). In contrast, the C trihydrate global minimum also has hydrogen bonding between the water molecules, and the largest shift exceeds 200 cm. The magnitude can even exceed 300 cm in structures with an H atom that does not participate in hydrogen bonding.
Computational Analysis of Structural and Photophysical Properties of a 1,8-Naphthalimide Derivative in Aqueous Solution.
Watanabe N, Sumita M, Izawa H … +2 more , Yagi K, Matsui T
J Phys Chem A · 2026 May · PMID 42012861 · Publisher ↗
-[2-(Trimethylammonium)ethyl]-1,8-naphthalimide (TENI) is a promising, versatile anion sensor that can detect the electronegativity of a target anion depending on the fluorescence intensity. In TENI, an emission from a l...
-[2-(Trimethylammonium)ethyl]-1,8-naphthalimide (TENI) is a promising, versatile anion sensor that can detect the electronegativity of a target anion depending on the fluorescence intensity. In TENI, an emission from a lower-energy state than the first excited state of a single TENI is observed experimentally, and its character has remained unknown. Here, we have investigated the origin of the lower-energy peaks in the fluorescence spectrum of TENI using molecular dynamics (MD) simulations and time-dependent density functional theory (TD-DFT) calculations with three functionals. The computation reveals that TENIs form a structural ensemble in solution, and that stacked TENI dimers exhibit red-shifted fluorescence compared to a single TENI. The formation of excimer results in the longer-wavelength fluorescence that can be corroborated by changes in frontier orbital energies due to the intermolecular interaction. Our work will provide valuable knowledge for the development of new anion sensors.
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