The Journal of Physical Chemistry A最新文献

{"title":"Zn₅B₃^-: A Coaxial Double-Ring Molecular Rotor with Multifold Aromaticity.","authors":"Ya-Xuan Cheng, Li-Xia Bai, Jin-Chang Guo","doi":"10.1021/acs.jpca.5c05591","DOIUrl":"https://doi.org/10.1021/acs.jpca.5c05591","url":null,"abstract":"<p><p>The first coaxial double-ring C_s Zn₅B₃^- anion with dynamic fluxionality has been designed, consisting of a B₃ triangle and a pentagonal Zn₅ ring below. It is a true global minimum (GM) structure on the potential energy surfaces based on the extensive density functional theory (DFT) isomeric searches and high-level CCSD(T) calculations. Born-Oppenheimer molecular dynamics (BOMD) simulations reveal that the Zn₅B₃^- cluster is dynamically fluxional: the B₃ triangle can rotate freely on the Zn₅ ring around the central axis at 500 K. Bonding analyses indicate that the double-ring Zn₅B₃^- cluster possesses 2π/6σ/6σ/6σ 4-fold aromaticity, conforming to the (4<i>n</i> + 2) Hückel rule, facilitating its structural fluxionality. The unique double-ring structure, interesting dynamic fluxionality, and novel 4-fold aromaticity make the Zn₅B₃^- cluster a highly promising candidate for boron-based molecular rotors.</p>","PeriodicalId":59,"journal":{"name":"The Journal of Physical Chemistry A","volume":" ","pages":""},"PeriodicalIF":2.8,"publicationDate":"2025-10-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145342141","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":"The Influence of Intramolecular C═C Number on the ESIPT Reactions of HBTM Derivatives: A Theoretical Study.","authors":"Zhiqiang Chen, Yang Yu, Xiaofei Tan, Jiaxin Wang, Siyu Xu, Yi Wang","doi":"10.1021/acs.jpca.5c05993","DOIUrl":"https://doi.org/10.1021/acs.jpca.5c05993","url":null,"abstract":"<p><p>In the work, theoretical calculations were utilized to explore how the count of intramolecular double bonds influences the excited-state intramolecular proton transfer (ESIPT) reaction in HBTM derivatives. Three derivatives, namely, HBTM-1 (HBTM: 4-methyl-2-benzothiazolyl-6-pyrimidine vinylphenol), HBTM-2, and HBTM-3, were designed, and their geometric structures in the S₀ and S₁ states were optimized in DMSO solvent using density functional theory (DFT) and time-dependent density functional theory (TD-DFT) methods. The results show that as the number of intramolecular C═C double bonds increases, the strength of intramolecular hydrogen bonds gradually weakens, accompanied by an increase in the energy barrier of the ESIPT reaction, making the process more difficult. Additionally, analyses of frontier molecular orbitals and Sr reveal a negative correlation between the count of double bonds and the intramolecular charge transfer effect. It was also found that a rise in the number of double bonds results in a redshift of the fluorescence emission wavelength and an increase in the Stokes shift. These findings not only provide a theoretical basis for the molecular design of fluorescent derivatives based on the HBTM scaffold but also offer new insights into the fine-tuning of the ESIPT process.</p>","PeriodicalId":59,"journal":{"name":"The Journal of Physical Chemistry A","volume":" ","pages":""},"PeriodicalIF":2.8,"publicationDate":"2025-10-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145342140","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":"Molecular Structure of a Model <i>S</i>-Alkylthiolanium Ionic Liquid Based on NMR Measurements and DFT Predictions for Its Enantiomeric C-H···I^- Hydrogen Bonded Units Achieved in an Unusual Use of QST2 and IRC Methods.","authors":"Ryszard B Nazarski, Gerhard Hägele","doi":"10.1021/acs.jpca.5c05146","DOIUrl":"https://doi.org/10.1021/acs.jpca.5c05146","url":null,"abstract":"<p><p>Using atypical input geometries that led to asymmetric transition state (TS) structures, it was possible to construct the raw geometries of a majority of both units of the title ionic liquid <b>1a</b> of type A/B in the D₂O solution, mainly in a combination of QST2 and IRC methods. Their refinement in all-electron DFT-B3LYP calculations using a locally dense basis sets (LDBS) approach led to 34 complete pairs A/B as binary sets of enantiomeric forms of type A and B, which, according to time-averaged NMR spectra and calculated Gibbs free energy (Δ<i>G</i>) data, exist in a fast symmetrical two-site exchange A ⇌ B. The availability of these structurally diverse structures, in which iodine ion (I^-) occupies various spatial positions, stabilized by weak C-H···I^- hydrogen bonds confirmed by QTAIM analysis, made it possible to test selected DFT methods to calculate the δ_H, δ_C, and ^<i>n</i><i>J</i>_HH data against their experimental values. A modified joint two-nucleus approach (¹H/¹³C) with factor <i>m</i>_H = 6 was also used. The efficiency of these predictions for an ensemble of all pairs A/B, which is the multicomponent molecular structure of <b>1a</b> at the theoretical level used, was analyzed in light of their populations arising from consideration of Δ<i>G</i> data.</p>","PeriodicalId":59,"journal":{"name":"The Journal of Physical Chemistry A","volume":" ","pages":""},"PeriodicalIF":2.8,"publicationDate":"2025-10-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145342137","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":"Revisiting the Conformational Equilibrium of 1,1,2-Trifluoroethane and 1,1,2,2-Tetrafluoroethane: An NBO Study.","authors":"Matheus P Freitas","doi":"10.1021/acs.jpca.5c06020","DOIUrl":"https://doi.org/10.1021/acs.jpca.5c06020","url":null,"abstract":"<p><p>Organofluorine compounds are key to pharmaceutical, agrochemical, and high-performance material applications, where C-F bond conformations influence critical properties such as solubility, lipophilicity, and biological activity. While the conformational behavior of 1,2-difluoroethane and its characteristic <i>gauche</i> effect is well understood, the structural preferences of 1,1,2-trifluoroethane and 1,1,2,2-tetrafluoroethane have remained less explored, particularly in light of hyperconjugation theory. In this quantum-chemical study, the conformational equilibria of these two model fluoroalkanes were investigated using density functional theory and Natural Bond Orbital (NBO) analysis, with complementary NMR coupling constant calculations. The results reveal that Lewis-type interactions govern conformational stability, favoring the <i>anti-gauche</i> conformer in 1,1,2-trifluoroethane and the <i>double antigauche</i> conformer in 1,1,2,2-tetrafluoroethane. Nevertheless, electron delocalization plays an essential role in ensuring that staggered conformations remain energy minima, as fully localized electronic structures would yield only a single conformer for each compound. These findings refine our understanding of hyperconjugative and electrostatic effects in fluorinated ethanes and provide a more nuanced framework for predicting conformational preferences in difluoromethyl-containing systems.</p>","PeriodicalId":59,"journal":{"name":"The Journal of Physical Chemistry A","volume":" ","pages":""},"PeriodicalIF":2.8,"publicationDate":"2025-10-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145342139","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":"Basis Set Effect on Linear Response Density Functional Theory Calculations on Periodic Systems.","authors":"Emmanuel Forson, Taylor Parsons, Marco Caricato","doi":"10.1021/acs.jpca.5c04251","DOIUrl":"https://doi.org/10.1021/acs.jpca.5c04251","url":null,"abstract":"<p><p>In this work, we present an investigation of the role of basis set size on linear response (LR) calculations of electronic properties of extended systems using density functional theory with periodic boundary conditions (DFT-PBC) and Gaussian-type atomic orbital (GTO) bases. We report the results of electric dipole-electric dipole polarizability, optical rotation, and electronic excitation energies (computed as poles of the LR function) on a series of one-dimensional (1D) and three-dimensional (3D) periodic systems. The basis sets employed are based on the Dunning series: cc-pVXZ, with X ranging from double-ζ to quintuple-ζ, and include the bases augmented with diffuse functions: aug-cc-pVXZ. The calculations are possible thanks to an extension of the coupled-perturbed Kohn-Sham code in the GAUSSIAN software to work with a different number of orbitals at each <i>k</i> point in reciprocal space, as orbitals with small overlap eigenvalues are projected out during the orthonormalization procedure of the basis set before the self-consistent field procedure used to evaluate the energy. The results on the test systems indicate that large basis sets, including diffuse functions, are necessary to reach quantitative agreement with experimental data and the complete basis set limit for LR properties even at DFT-PBC level.</p>","PeriodicalId":59,"journal":{"name":"The Journal of Physical Chemistry A","volume":" ","pages":""},"PeriodicalIF":2.8,"publicationDate":"2025-10-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145342133","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":"Modeling Structural and Optical Properties of 6,6,12-Graphyne Oligomer Fragments.","authors":"Andreas Erbs Hillers-Bendtsen, Frederik Ørsted Kjeldal, Nicolai Machholdt Høyer, Kurt V Mikkelsen","doi":"10.1021/acs.jpca.5c01540","DOIUrl":"https://doi.org/10.1021/acs.jpca.5c01540","url":null,"abstract":"<p><p>This study investigates the structural and optical properties of 6,6,12-graphyne by analyzing five different radiaannulene oligomer fragments of the two-dimensional (2D) sheet in vacuum, cyclohexane, dichloromethane, and toluene. These properties are examined using various density functional theory (DFT) methods in combination with different basis sets. Solvent effects are incorporated using the integral equation formalism polarizable continuum model (IEF-PCM). The findings indicate that structural properties are primarily influenced by the inclusion of exact Hartree-Fock exchange in the chosen DFT method and the presence of polarization functions in the applied basis sets. For optical properties, all five molecules absorb light across the visible spectrum through both one- and two-photon processes. Notably, the inclusion of range correction in the selected method significantly alters the optical characteristics making alignment with experiment and CC2 (Coupled Cluster with Singles and approximate Doubles) calculations better. The presence of a solvent is found to enhance both infrared and ultraviolet-visible (UV-vis) absorption, while enforcing a planar geometry on the systems has minimal impact on the observed properties. Finally, comparisons with experimental spectra confirm that the calculations accurately reproduce key features and trends in the experimental data.</p>","PeriodicalId":59,"journal":{"name":"The Journal of Physical Chemistry A","volume":" ","pages":""},"PeriodicalIF":2.8,"publicationDate":"2025-10-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145342136","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 Mechanistic Study on the Synthesis Reaction of Glycerol Sulfite─A Key Intermediate for Novel Electrolyte Additives.","authors":"Honghua Xu, Weiya Zhang, Yiwen Shen, Lu Yu, Qiang Wang","doi":"10.1021/acs.jpca.5c04978","DOIUrl":"https://doi.org/10.1021/acs.jpca.5c04978","url":null,"abstract":"<p><p>Using SO₂ as a sulfinic-acid building block to synthesize valuable sulfur-based electrolyte additives is an important issue in the field of green and sustainable chemistry. Glycerol sulfite, as a key intermediate for the design and synthesis of sulfite-based electrolyte additives, clarifying its synthesis mechanism is of great significance for the design and synthesis of sulfite-based additives. Herein, the reaction mechanisms of synthesizing glycerol sulfite were explored by density functional theory (DFT) calculations, based on an analysis of glycerol sulfite's structures and properties. The results show that the reaction of SOCl₂ with glycerol proceeds through two steps and removes two molecules of HCl, generating glycerol sulfite. The first step of removing HCl is the rate-determining step, with an activation energy barrier of 36.97 kcal/mol. Based on this, we proposed an innovative green synthetic strategy for the atom-economical synthesis of glycerol sulfite by the direct reaction of SO₂ with glycerol. The reaction of the SO₂ with glycerol involves three steps and removes one molecule of H₂O to form glycerol sulfite. The formation of the S-O bond in the second step is the rate-determining step. The activation energy barrier was reduced to 29.75 kcal/mol, which is better than the reaction of SOCl₂ with glycerol to form glycerol sulfite. Further exploration of the three-molecule synergistic reaction of 2-cyanopyridine, SO₂, and glycerol revealed that glycerol sulfite was generated through four steps. The second step, where the cyano group of 2-cyanopyridine was transformed into an imide group, was identified as the rate-determining step, with an activation energy barrier as low as 25.51 kcal/mol, which was better than the reactions of SOCl₂ with glycerol and SO₂ with glycerol to form glycerol sulfite. These results provide a new avenue for the design and synthesis of sulfur-based electrolyte additives.</p>","PeriodicalId":59,"journal":{"name":"The Journal of Physical Chemistry A","volume":" ","pages":""},"PeriodicalIF":2.8,"publicationDate":"2025-10-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145342132","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":"Evaluation of Density Functionals for Si-O-C-H Molecule Thermochemistry.","authors":"Ingeborg-Helene Svenum, Francesca Lønstad Bleken, Stefan Andersson","doi":"10.1021/acs.jpca.5c04844","DOIUrl":"https://doi.org/10.1021/acs.jpca.5c04844","url":null,"abstract":"<p><p>The energies and vibrational frequencies of molecular species with Si-O-C-H compositions have been calculated at the CCSD(T) level (coupled cluster with single and double excitations and a perturbative treatment of triple excitations). The CCSD(T) results compare well with experimental data where the difference in enthalpy of formation is typically only about 1-2 kJ/mol in most cases. In addition, the same molecules have been calculated with density functional theory (DFT) calculations using nine commonly used density functionals and two different basis sets. The performance of the DFT calculations is compared with the CCSD(T) benchmark values in terms of enthalpy of formation, reaction energy, vibrational frequencies, and zero-point energies. The results show that the M06-2X functional provides the lowest mean absolute error (MAE) in terms of the enthalpy of formation, whereas, for the vibrational frequencies and zero-point energies, the SCAN functional gives the lowest MAE values. The results were also grouped according to the types of bonds that are present in the molecules. Moreover, an elaborate set of possible reactions within the molecular species in the Si-O-C-H system is included to evaluate the performance of the different DFT functionals with respect to the relative stability of species within the same reaction system. In this case, the B2GP-PLYP functional shows the smallest errors. PW6B95 is the functional that most consistently performs well for the studied properties of the included molecules. The coupled cluster data sets provide new benchmark data, several of which are not previously available for silicon chemistry.</p>","PeriodicalId":59,"journal":{"name":"The Journal of Physical Chemistry A","volume":" ","pages":""},"PeriodicalIF":2.8,"publicationDate":"2025-10-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145342134","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":"PySIDT: Subgraph Isomorphic Decision Trees for Molecular Property Prediction.","authors":"Matthew S Johnson, Hao-Wei Pang, Anna C Doner, William H Green, Judit Zádor","doi":"10.1021/acs.jpca.5c04483","DOIUrl":"https://doi.org/10.1021/acs.jpca.5c04483","url":null,"abstract":"<p><p>Accurate molecular property prediction is important across all fields of chemistry. Deep neural networks (DNNs) have become increasingly popular due to their ability to train automatically, avoiding the incredibly tedious process of constructing and extending traditional property estimation schemes. However, DNNs require large amounts of training data, are challenging to interpret, require large amounts of memory to load even during inference, and have severe difficulties incorporating qualitative chemical knowledge, which are often desired for molecular property prediction tasks. Here we present PySIDT (https://github.com/zadorlab/PySIDT), a software for training and running inference on Subgraph Isomorphic Decision Trees (SIDTs). SIDTs are graph-based decision trees made of nodes associated with molecular substructures. Inference is done by descending target molecular structures down the decision tree to nodes with matching subgraph isomorphic substructures and making predictions based on the final (most specific) nodes matched. SIDTs scale down well to dataset sizes much smaller than is feasible for DNNs. As trees of molecular substructures, SIDTs are inherently readable and easy to visualize, making them easy to analyze. They are also straightforward to extend and retrain, facilitate uncertainty estimation, and enable easy integration of expert knowledge. We demonstrate the SIDT approach discussing its application to a diverse range of molecular prediction tasks: rate coefficient estimation, diffusion coefficient estimation, thermochemistry estimation, transition state bond stretch prediction, p<i>K</i>_a prediction, stability of molecular structures, stability of surface structures, and prediction of surface lateral interaction energetics. Additionally, we demonstrate the power of the SIDT algorithms in two direct learning curve vanilla comparisons with the popular DNN-based software Chemprop and the popular gradient boosted trees-based software XGBoost on enthalpy of formation and rate coefficient prediction tasks. In particular, in the enthalpy of formation case, vanilla PySIDT is able to outperform vanilla Chemprop and XGBoost across the full range of training/validation set sizes out to 11,560 data points.</p>","PeriodicalId":59,"journal":{"name":"The Journal of Physical Chemistry A","volume":" ","pages":""},"PeriodicalIF":2.8,"publicationDate":"2025-10-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145342138","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":"First-Principles Molecular Dynamics Simulations of Infrared and Raman Vibrational Spectra of H₅O₂⁺, D₅O₂⁺, DH₄O₂⁺, and D₄HO₂⁺ from 50 to 300 K.","authors":"Oluwaseun Omodemi, Martina Kaledin","doi":"10.1021/acs.jpca.5c05184","DOIUrl":"https://doi.org/10.1021/acs.jpca.5c05184","url":null,"abstract":"<p><p>We report molecular dynamics simulations of infrared (IR) and Raman spectra of H₅O₂⁺ and its deuterium-substituted analogs. We use the well-tested HBB potential and dipole surfaces along with a recently fitted polarizability surface of CCSD(T)/aug-cc-pVTZ quality. The focus of the present work is to provide new insights into the O···O stretch region, located in the [500-700] cm^-1 spectral range, by means of analyzing the spectra over a broad range of temperatures: from 50 to 300 K. Also, rovibrational thermal averaging was performed to untangle the unusually complex spectra of partially deuterated isotopologues DH₄O₂⁺ and D₄HO₂⁺ with H and D minority species in both internal (int) and external (ext) positions. Our findings show that DH₄O₂⁺ (ext) is at least 90% prevalent at the [50-300] Kelvin temperatures, predominantly due to its low zero-point energy (ZPE). Furthermore, contrary to previous reports that the mixed isotopologue D₄HO₂⁺ (int) should be favored over D₄HO₂⁺ (ext) due to its lower ZPE, the present calculations indicate that while the D₄HO₂⁺ (ext) species is \"invisible\" at lower temperatures, it overtakes D₄HO₂⁺ (int) as the dominant species at 84.9 K and higher.</p>","PeriodicalId":59,"journal":{"name":"The Journal of Physical Chemistry A","volume":" ","pages":""},"PeriodicalIF":2.8,"publicationDate":"2025-10-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145342135","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}