The Journal of Physical Chemistry A最新文献

{"title":"Low-Energy Electron and Positron Scattering by Lysine: Cross Sections and Theoretical Insights into Possible DEA Pathways.","authors":"Cesar A do Amaral, Raul V B Morás, Giseli M Moreira, Sergio d'Almeida Sanchez, Alessandra Souza Barbosa","doi":"10.1021/acs.jpca.5c05601","DOIUrl":"https://doi.org/10.1021/acs.jpca.5c05601","url":null,"abstract":"<p><p>We report a theoretical investigation of low-energy electron and positron scattering by the lysine molecule. The calculations were performed using the Schwinger multichannel method with different levels of approximation for each projectile. The static-exchange (SE) and static-exchange plus polarization (SEP) approximations were used for electrons, while the static plus polarization (SP) approximation was used for positrons. Our results for electron scattering show a π* resonance centered at 3.95 eV for SE and 2.73 eV for SEP in the integral cross section, as well as a large structure around 11.0 eV for SE and 9.0 eV for SEP, which may be associated with overlapping σ* resonances. For comparison purposes, since there are no theoretical or experimental cross sections available in the literature, a semiempirical relation was employed to estimate the value of the π* resonance. We also compared the results obtained for electron and positron scattering, showing similar behavior at very low energy due to the dipole interaction and approximately the same order of magnitude from 2 to 6 eV. Differential cross sections for both projectiles also exhibit the same dominant wave pattern. To investigate the connection between the resonance and the dissociative electron attachment (DEA), we calculated threshold energies for hydrogen loss from different sites in the molecule, identifying a low-energy channel (1.85 eV) consistent with previous DEA studies on similar systems. Furthermore, excited electronic states of lysine were obtained by using time-dependent density functional theory (TDDFT), providing additional insight into possible Feshbach-type DEA pathways. These results represent the first theoretical study of scattering processes involving electrons and positrons with lysine and offer a foundation for future experimental and computational investigations.</p>","PeriodicalId":59,"journal":{"name":"The Journal of Physical Chemistry A","volume":" ","pages":""},"PeriodicalIF":2.8,"publicationDate":"2025-10-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145205187","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":"A Class of PAH Polymerization Reactions Featured by Radical Growth from Reactants to Products.","authors":"Bingjie Chen, Peng Liu, Hong Wang, Vasilios Samaras, Huajie Lyu, Jiwen Guan, Linghong Chen, Chenghang Zheng, Zhandong Wang, Xingcai Lu, Xiang Gao, Heinz Pitsch, William L Roberts","doi":"10.1021/acs.jpca.5c05055","DOIUrl":"https://doi.org/10.1021/acs.jpca.5c05055","url":null,"abstract":"<p><p>Polycyclic aromatic hydrocarbons (PAHs) are ubiquitous organic molecules and fundamental building blocks of carbonaceous nanoparticles in material synthesis, flames, and extraterrestrial environments, yet their formation reactions remain elusive. Here, we propose a unique PAH growth reaction of ethynyl-substituted aryl radical addition to ethynyl-substituted peri-condensed aromatic hydrocarbons (AEPAH mechanism) by exploring the exemplary reactions of the 2-ethynyl-phenyl radical with phenylacetylene, 1-ethynylnaphthalene, and 9-ethynylphenanthrene. Instead of stable molecules and small radicals as reaction intermediates in conventional mechanisms, the AEPAH mechanism synthesizes PAH radicals, which further grow to large PAHs and incipient carbonaceous nanoparticles. High-level quantum chemistry calculation, particle composition analysis by matrix-assisted laser desorption/ionization mass spectrometry, and product analysis of the elementary reaction by gas chromatography-mass spectrometry and synchrotron radiation photoionization mass spectrometry evidenced the AEPAH mechanism as a direct and efficient PAH growth reaction class under the temperature range of 800-1500 K. The unraveled AEPAH mechanism may help understand the evolution of organic and prebiotic molecules on Earth and in deep space.</p>","PeriodicalId":59,"journal":{"name":"The Journal of Physical Chemistry A","volume":" ","pages":""},"PeriodicalIF":2.8,"publicationDate":"2025-10-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145205219","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":"Benchmarking the Calculated Resonance Raman Spectrum of a Diarylethene-Based Molecular Switch Using the Gradient Approximation.","authors":"Emmaline R Lorenzo, Christopher G Elles","doi":"10.1021/acs.jpca.5c04021","DOIUrl":"https://doi.org/10.1021/acs.jpca.5c04021","url":null,"abstract":"<p><p>Resonance Raman spectroscopy provides important insight into the initial nuclear motions of a molecule following optical excitation. The vibrational frequencies in the spectrum represent the ground-state structure, but the intensities of the Raman bands reflect the dynamics after excitation to an electronically excited state. Calculations are often necessary to assign vibrations in the experimental spectrum in order to correctly identify the excited-state dynamics, but there is a risk of misassignment when using calculations that do not include resonance-enhancement effects. Off-resonance calculations typically give frequencies that are accurate within 10-20 cm^-1 but may not correctly represent the relative Raman scattering intensities of an experimental resonance Raman spectrum. Two approaches for including resonance-enhancement effects in the Raman spectrum are the Franck-Condon method and the gradient approximation method. This contribution examines both methods for obtaining resonance Raman intensities for a diarylethene-based molecular switch with 129 normal modes. Comparing experimental spectra measured both on- and off-resonance with simulated spectra using off-resonance, Franck-Condon, and gradient approximation methods highlights the need to include resonance-enhancement effects in the calculations in order to make accurate mode assignments. The gradient approximation gives good agreement with the experimental resonance Raman spectrum while avoiding potential complications and the computational cost of finding the optimized geometry and normal modes of the excited state. The vibrational assignments reveal key stretching motions involved in the initial excited-state dynamics of the molecular switch.</p>","PeriodicalId":59,"journal":{"name":"The Journal of Physical Chemistry A","volume":" ","pages":""},"PeriodicalIF":2.8,"publicationDate":"2025-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145205121","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":"Dielectric Anisotropy Mitigated by Hydrogen Bonding Governs the Driving Force of Charge Transport within Quinone Pairs in Photosynthetic Reaction Centers.","authors":"Muhammet Erkan Köse, Roshan Khatri, Barry D Dunietz","doi":"10.1021/acs.jpca.5c04134","DOIUrl":"https://doi.org/10.1021/acs.jpca.5c04134","url":null,"abstract":"<p><p>In a bacterial photosynthetic reaction center (bRC) and photosystem II (PSII), the charge transport (CT) is between the primary semiquinone (<i>Q</i>_A) and the secondary quinone (<i>Q</i>_B). The doubly reduced form of <i>Q</i>_B is converted upon protonation to a labile quinol that leaves the binding site. Despite the chemical and structural similarities of the quinone pairs in the two reaction centers (RCs), the free energy change affecting the quinone CT differs significantly due to asymmetries in their electrostatic environment, molecular conformation, and nonbonding interactions with nearby cofactors and protein residues. This study aims to quantify the energetic contributions of these factors to the driving force for the CT between the quinones, resolve the key nonbonded interactions with nearby units, and explain differences in the energetics between the RCs. Toward this goal, we use a screened range-separated hybrid functional, which correctly accounts for polarizable environment. In particular, dielectric anisotropy is found to be the largest contributor to the free energy change of CT in both RCs. Hydrogen-bonding interactions around quinones are identified, and their stabilization is evaluated by accounting for the effective dielectric constant of the surrounding environment. By resolving the free energy contributions, we identify the particular hydrogen-bonding networks affecting the quinones and which determine the reduction midpoint potential differences. In both RCs, the quinones appear to form hydrogen bonds with three protein residue units, of which histidines bear the strongest bond. In considering the forward transport process, we find for both RCs that the anionic <i>Q</i>_A is hydrogen-bonded with all nearby protein residues, while the labile <i>Q</i>_B in the neutral states appears to exclude the nearby serine residues from such interactions. The calculated free energy change for CT agrees remarkably well with experimental findings.</p>","PeriodicalId":59,"journal":{"name":"The Journal of Physical Chemistry A","volume":" ","pages":""},"PeriodicalIF":2.8,"publicationDate":"2025-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145197426","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":"Two-Photon Absorption and Dynamics of Excited States in Bromochalcone Derivatives.","authors":"Nathan B Marucci, João V P Valverde, Gabriel de O Campos, Eli S A Ducas, Pablo J Gonçalves, Leonardo De Boni, Cleber R Mendonça","doi":"10.1021/acs.jpca.5c02748","DOIUrl":"https://doi.org/10.1021/acs.jpca.5c02748","url":null,"abstract":"<p><p>Two-photon absorption (2PA) in organic compounds has gained significant interest due to its applications in nonlinear optics, including two-photon fluorescence microscopy, photodynamic therapy, and laser microfabrication. This study investigates the two-photon absorption cross section (2PACS) and the excited-state dynamics of 4'-bromochalcone derivatives using a combination of experimental and computational approaches. Quantum chemical calculations employing density functional theory (DFT) and time-dependent DFT (TD-DFT) were performed to analyze the electronic properties of the molecules. Experimental characterization involved linear optical measurements (UV-vis absorption and fluorescence spectroscopy), femtosecond transient absorption spectroscopy (TAS), and open-aperture (AO) Z-scan measurements to determine the degenerate 2PACS (D-2PACS). Our results reveal that resonant donor substituents, such as the dimethylamino group, enhance nonlinear absorption, especially in the lower-energy band. Furthermore, TAS revealed an intriguing dynamic associated with the formation of a twisted intramolecular charge transfer (TICT) state, which was corroborated by anisotropy and solvatochromism measurements as well as by computational simulations. These findings provide insights into the relationship between the molecular structure and nonlinear optical properties, contributing to the development of optimized materials for photonic applications.</p>","PeriodicalId":59,"journal":{"name":"The Journal of Physical Chemistry A","volume":" ","pages":""},"PeriodicalIF":2.8,"publicationDate":"2025-09-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145197385","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":"Selenium-Substituted Nonfused Ring Acceptors: Theoretical Insights into Optoelectronic Properties via Noncovalent Interaction Engineering.","authors":"Zhao Liu, Lei Wang, Shubin Lei, Zhifei Sun, Huanhuan Gao, Haiyang Song","doi":"10.1021/acs.jpca.5c04350","DOIUrl":"https://doi.org/10.1021/acs.jpca.5c04350","url":null,"abstract":"<p><p>Selenium (Se) substitution critically modulates the acceptor electronic structures and optoelectronic properties. This study systematically modifies the high-performance nonfused ring electron acceptor (NFREA) 2BTh-2F through π-bridge S-to-Se substitutions. Using density functional theory (DFT) and time-dependent DFT (TD-DFT), we designed nine novel acceptors (Z1-Z9) and characterized their electronic/optoelectronic properties. Complementary atoms in molecules (AIM) topological analysis and reduced density gradient (RDG) analysis reveal enhanced Se···O noncovalent interactions (NCIs), though molecular planarity remains governed by steric constraints from three-dimensional (3D) side chains. Crucially, Se substitution optimizes the electrostatic potential (ESP) distribution, frontier molecular orbital (FMO) energy levels, and excited-state properties. Z5, a symmetrical Se-substituted derivative of the outer thiophene on the π-bridge, established itself as the most promising NFREA candidate due to its minimum band gap, maximum open-circuit voltage and fill factor, and minimum energy loss. These findings underscore rational substitution strategies for NFREA design and provide critical guidelines for the development of high-performance organic solar cells.</p>","PeriodicalId":59,"journal":{"name":"The Journal of Physical Chemistry A","volume":" ","pages":""},"PeriodicalIF":2.8,"publicationDate":"2025-09-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145197455","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":"Roles of Hydration in Protein-Ligand Binding: Passive or Active Participant?","authors":"Kacie A Evans, He Mirabel Sun, Morgan Powers, Carter Lantz, Arthur Laganowsky, Hays Rye, David H Russell","doi":"10.1021/acs.jpca.5c04986","DOIUrl":"https://doi.org/10.1021/acs.jpca.5c04986","url":null,"abstract":"<p><p>Hydration is a critical yet often underappreciated factor that influences protein dynamics in solution, with direct effects on structure, stability, and interactions such as ligand binding. Native mass spectrometry (nMS) enables the analysis of biomolecules in their solution states, which are shaped by cofactors, osmolytes, ligands, and notably, hydration. Here, we employ variable-temperature electrospray ionization to address a central question in molecular biophysics: does hydration act as a passive background solvent or as an active participant in modulating ligand binding? To investigate these effects, temperature-dependent changes in average charge state (<i>Z</i>_avg), ADP equilibrium binding affinities (<i>K</i>_a), and enthalpy-entropy compensation (EEC) for the GroEL single ring mutant (SR1) were collected in both H₂O and D₂O. Temperature-dependent shifts in <i>Z</i>_avg were observed for SR1-ADP complexes in both solvents, indicating protein conformational changes. Differences in nucleotide binding affinities calculated from mole fraction plots determined as a function of concentration between H₂O and D₂O solutions suggest that hydration plays a role in modulating ligand binding. Changes in hydration can modulate protein conformation and ligand binding affinities, typically reflected in shifts in enthalpy (Δ<i>H</i>) and entropy (-<i>T</i>Δ<i>S</i>), while the overall Gibbs free energy (Δ<i>G</i>) remains relatively unchanged. Thermodynamic analysis revealed distinct patterns of EEC in D₂O compared to H₂O, providing insight into how hydration modulates the SR1(ADP)_1-7 interactions. Collectively, these findings support the view that hydration acts as an active participant in ligand binding, with measurable effects on protein conformation, stability, and thermodynamics.</p>","PeriodicalId":59,"journal":{"name":"The Journal of Physical Chemistry A","volume":" ","pages":""},"PeriodicalIF":2.8,"publicationDate":"2025-09-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145197457","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":"General Spin Restricted Open-Shell Configuration Interaction Singles (GS-ROCIS): Implementation of Spin-Orbit Coupling and Zeeman Operators for Calculation of Optical and X-ray Absorption and Magnetic Circular Dichroism Spectra of Magnetically Coupled Transition Metal Systems.","authors":"Tiago Leyser da Costa Gouveia, Lucas Lang, Dimitrios Maganas, Frank Neese","doi":"10.1021/acs.jpca.5c05086","DOIUrl":"https://doi.org/10.1021/acs.jpca.5c05086","url":null,"abstract":"<p><p>In this paper we present the theory and implementation of the spin-orbit coupling and Zeeman operators in the context of quasi-degenerate perturbation theory into the general spin restricted open-shell configuration interaction singles method. The implementation of the mentioned operators allows for the calculation of magnetic circularly polarized dichroism (MCD), L-edge X-ray absorption spectra (XAS) and X-ray magnetic circularly polarized dichroism (XMCD) spectra. The method was tested on calculating the MCD spectra of isostructural complexes [LCr^III(PyA)₃Ni^II]²⁺, [LCr^III(PyA)₃Zn^II]²⁺and [LGa^III(PyA)₃Ni^II]²⁺, with <i>L</i> = 1,4,7-trimethyl-1,4,7-triazacyclonanane and PyA^- is the monoanion of pyridine-2-aldozime, where it correctly predicts the MCD signs of the lower optical transition of [LCr^III(PyA)₃Ni^II]²⁺and [LGa^III(PyA)₃Ni^II]²⁺. The capabilities of the method in computing L-edge XAS and XMCD spectra were tested on the model complexes [Cu(H₂O)₆]²⁺ and [Cu₂(OAc)₄(H₂O)₂], where it correctly calculates the L_2,3-edge absorption and XMCD spectra, as well as on the antiferromagnetically coupled Cu-Fe dimer [(F₈TPP)Fe(μ-O)Cu(TMPA)]⁺, where it correctly predicts the signs of the L₂ and L₃ edges of the Cu XMCD spectrum. To further illustrate the applicability of the method, the more complex L_2,3-edge XAS and XMCD spectra of thiolate Fe complexes were also calculated.</p>","PeriodicalId":59,"journal":{"name":"The Journal of Physical Chemistry A","volume":" ","pages":""},"PeriodicalIF":2.8,"publicationDate":"2025-09-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145190422","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":"Comprehensive Quantum Chemical Analysis of the Microwave and Infrared Spectra of Cyclopropenone.","authors":"Kemal Oenen, Subhasish Das, Klaus R Liedl, Guntram Rauhut","doi":"10.1021/acs.jpca.5c05429","DOIUrl":"https://doi.org/10.1021/acs.jpca.5c05429","url":null,"abstract":"<p><p>Rovibrational configuration interaction theory including up to sextuple excitations has been used to study, simulate, and analyze the rotational spectrum and low-lying rovibrational states of cyclopropenone. This molecule has been repeatedly discovered in space, experimentally investigated in the laboratory, and was subject to theoretical studies. However, a comprehensive ab initio study of its microwave spectrum and rovibrational transitions in the far-infrared region has not yet been provided. A line list with about 3 million rovibrational transitions has been generated, covering temperature ranges between 10 and 300 K. Furthermore, this study reports highly accurate geometrical parameters, fundamental vibrational transitions, and spectroscopic constants. All calculations rely on a multidimensional potential energy surface including up to 4-mode coupling terms being obtained from explicitly correlated coupled-cluster theory including core correlation effects and estimates for high-order excitations. The computed results were validated against available experimental data, showing excellent agreement for most properties.</p>","PeriodicalId":59,"journal":{"name":"The Journal of Physical Chemistry A","volume":" ","pages":""},"PeriodicalIF":2.8,"publicationDate":"2025-09-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145197460","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":"Time-Dependent Multiconfigurational Short-Range Density Functional Theory with Generalized Valence Bond Wave Functions.","authors":"Michał Hapka, Hans Jørgen Aa Jensen","doi":"10.1021/acs.jpca.5c04699","DOIUrl":"https://doi.org/10.1021/acs.jpca.5c04699","url":null,"abstract":"<p><p>We present a theory and an efficient implementation of TD-GVB-srDFT, a time-dependent multiconfigurational range-separated density functional theory based on generalized valence bond perfect-pairing (GVB-PP) wave functions. In GVB-srDFT, dynamic correlation effects are incorporated via range-separation of the Coulomb potential, using tailored Kohn-Sham functionals of the density. The present implementation builds on our earlier work on TD-GVB [Hapka et al. <i>J. Chem. Phys.</i> <b>2022</b>, <i>156</i>, 174102], which employs direct Hessian techniques for both wave function optimization and linear response. We benchmark the performance of TD-GVB-srDFT for singlet and triplet excitation energies, as well as indirect spin-spin coupling constants (SSCCs). Compared to the underlying GVB-PP model, the method significantly improves excitation energies and achieves accuracy comparable to the complete active space variant, CAS-srDFT, with mean absolute deviations of 0.2 eV. The use of the generalized Tamm-Dancoff approximation (gTDA) is mandatory for reliable treatment of triplet excitations. For organic molecules, SSCCs computed with GVB-srDFT closely match those from CAS-srDFT and HF-srDFT results, whereas pure GVB-PP performs markedly worse than CASSCF for all coupling terms. Both GVB-srDFT and CAS-srDFT accurately reproduce fluorine-metal couplings in transition metal complexes, provided that gTDA is applied to singlet contributions.</p>","PeriodicalId":59,"journal":{"name":"The Journal of Physical Chemistry A","volume":" ","pages":""},"PeriodicalIF":2.8,"publicationDate":"2025-09-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145190381","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}