The Journal of Physical Chemistry A最新文献

{"title":"Dissociative Photoionization of 2-Thiouracil and 4-Thiouracil: A Molecular Dynamics Study.","authors":"Bonasree Roy, Evgenii Titov, Matthew S Robinson, Markus Gühr, Peter Saalfrank","doi":"10.1021/acs.jpca.5c03342","DOIUrl":"https://doi.org/10.1021/acs.jpca.5c03342","url":null,"abstract":"<p><p>Thionated nucleobases have drawn considerable attention due to their role in medical treatment and biology, which triggered studies of their photophysics and photochemistry using various experimental and theoretical techniques. In particular, vacuum ultraviolet (VUV)-induced dissociative photoionization of 2-thiouracil (2-TU) has been recently studied using synchrotron radiation [Robinson et al., <i>Molecules</i> <b>2023</b>, 28, 2354]. Here, using molecular dynamics simulations at the semiempirical OM2 level, we study the fragmentation dynamics of the cations of 2-TU and its isomer, 4-thiouracil (4-TU). Considering various VUV photon energies, we calculate energy-resolved mass spectra and breakdown diagrams for 2-TU and 4-TU. Remarkably, we find that the major fragments are different between the two compounds: 69 amu (C₃NH₃O⁺) for 2-TU and 85 amu (C₃NH₃S⁺) for 4-TU. Our simulations provide direct mechanistic insight into this observation and the fragmentation processes of thionated uracils in general.</p>","PeriodicalId":59,"journal":{"name":"The Journal of Physical Chemistry A","volume":" ","pages":""},"PeriodicalIF":2.8,"publicationDate":"2025-07-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144751798","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":"Significantly Large Negative Ion Formation in Grazing Scattering of Neutral Deuterium and Tritium Atoms from a CsI(100) Surface.","authors":"Yiqing Wang, Hu Zhou, He Wang, Yuan Li, Zheyan Tu, Lixun Song, Gang Wu, Yali Du, Zebin Li, Qiang Wu, Xin Zhang, Zewen Zong, Dong Feng, Yu Liu, Jianglei Luan, Lei Song, Kaiwen Chang, Yudi Cong, Zhengqi Liu, Guangyi Wang, Yongtao Zhao, Hongfei Zhang, Ximeng Chen","doi":"10.1021/acs.jpca.5c03433","DOIUrl":"10.1021/acs.jpca.5c03433","url":null,"abstract":"<p><p>We present the theoretical evidence of the formation of significantly large fractions of negative ions during grazing scattering of deuterium (D) and tritium (T) atoms from a CsI(100) surface. The negative ion conversion efficiency increases to an impressive ≥50%, and the maximum value even reaches 86% and 82% within projectile velocity ranges of <i>v</i> ∈ [0.15,0.43] a.u. and <i>v</i> ∈ [0.15,0.35] a.u., respectively, for D and T atom incidence. A detailed electron-capture energy defect calculation reveals that these results are obtained primarily because the large anion and cation polarizations of 6.43 and 3.34 ų lead to a large Mott-Littleton polarization interaction, which reduces the energy defect of the valence band electron capture to below 2.4 eV near the surface anion sites and drastically increases the electron-capture probability. The destruction of negative ions is not due to the electron loss to the unoccupied conduction band or neutral exciton states, but results from the affinity electron detachment via Coulomb barrier tunneling to the vacuum level during the interaction with the surface anion sites along their trajectories. Our results indicate that the collision system presented here can pave the way for the design of intense, directional and stable D^- and T^- ion beam sources for fusion DT fuel injection, the production of high-energy neutral beams to heat large fusion plasmas using D^- ions as precursors and the design of high intensity D-D or D-T neutron generators which are widely used in neutron logging.</p>","PeriodicalId":59,"journal":{"name":"The Journal of Physical Chemistry A","volume":" ","pages":"6815-6824"},"PeriodicalIF":2.8,"publicationDate":"2025-07-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144648011","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 Computational Study on the Atmospheric Fate of Carbon-Centered Radicals from the 3-Methyl-2-butene-1-thiol + ^•OH Reaction: Mechanistic Insights and Atmospheric Implications.","authors":"Parandaman Arathala, Avinash Kumar, Rabi A Musah","doi":"10.1021/acs.jpca.5c00743","DOIUrl":"10.1021/acs.jpca.5c00743","url":null,"abstract":"<p><p>The reaction of 3-methyl-2-butene-1-thiol (MBT; (CH₃)₂C═CHCH₂SH) with the OH radical is reported to proceed via the addition to either of the sp² hybridized C atoms, forming the two distinct C-centered radicals: (CH₃)₂C(OH)C^•HCH₂SH (R1) and (CH₃)₂C^•CH(OH)CH₂SH (R2). Understanding the fate of these radicals is important for elucidating MBT's atmospheric transformation mechanisms and the reaction products. Using quantum chemical calculations and kinetic modeling, we show that the unimolecular dissociation as well as isomerization reactions of R1 are kinetically unfavorable due to high energy barriers, and that R1 most likely reacts with atmospheric O₂ to form R1O₂ ((CH₃)₂C(OH)CH(OO^•)CH₂SH). In contrast, R2 can either undergo isomerization to form the sulfur-centered MBT-OH radical or add O₂ to form R2O₂ ((CH₃)₂C(OO^•)CH(OH)CH₂SH). These radicals undergo HO₂ elimination and intramolecular hydrogen atom transfer (HAT) pathways. Specifically, intramolecular HAT from the -SH group to the terminal oxygen atom of R-OO forms S-centered QOOH radicals, with barrier heights of -18.6 and -18.3 kcal mol^-1 for R1O₂ and R2O₂, respectively, calculated relative to those of the R1 + O₂ and R2 + O₂ reactants. Rate coefficients for key pathways, including unimolecular dissociation and O₂ addition followed by subsequent reactions, were calculated and analyzed. The kinetics results suggest that the intramolecular H atom transfer paths of R1O₂ and R2O₂ are significantly faster by ∼3 orders of magnitude compared to their bimolecular reactions with NO/HO₂, respectively. The findings suggest that under low NO concentrations R1O₂ and R2O₂ are capable of undergoing H-shift-driven autoxidation mechanisms. The atmospheric implications are discussed. Results indicate that MBT-derived peroxy radicals contribute to tropospheric chemistry by generating reactive species such as highly oxygenated peroxy radicals, HC(O)CH₂SH, (CH₃)₂C(OH)C(═O)H, CH₃C(O)CH₃, and various S- and C-centered alkyl radicals in the atmosphere.</p>","PeriodicalId":59,"journal":{"name":"The Journal of Physical Chemistry A","volume":" ","pages":"6866-6882"},"PeriodicalIF":2.8,"publicationDate":"2025-07-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144663842","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":"Theoretical Study on the Properties of Small Molecules with the Block Effective Hamiltonian Theory and Multireference Methods.","authors":"Mengyuan Wu, Yixuan An, Xiangling Hou, Feiwu Chen","doi":"10.1021/acs.jpca.5c03714","DOIUrl":"10.1021/acs.jpca.5c03714","url":null,"abstract":"<p><p>The effective Hamiltonian theory is extended from the original three blocks in our previous study to the four blocks and finally to the <i>n</i>-block. The four block and <i>n</i>-block-effective Hamiltonian are derived. The vertical and adiabatic excitation energies of H₂O, NH₂, and CH₂ are calculated with three-block-effective Hamiltonian theory (BEHT3), two types of multireference perturbation theories, and multireference configuration interaction (MRCI). The BEHT3 energies of the ground state and vertical and adiabatic excited states of H₂O, NH₂, and CH₂ converge with the size of model space from below to the corresponding MRCI energies. On the other hand, the BEHT3 excitation energies of these molecules converge with the size of model space from above to the corresponding experimental energies or energies calculated with higher-level theoretical models such as full configuration interaction. The effect of basis set on the electron affinities of F, PH₂, and SH calculated with the complete active space self-consistent field (CASSCF), the second- and third-order Møller-Plesset perturbation theory (MP2, MP3), coupled-cluster with single and double excitations (CCSD), CCSD plus the perturbation correction of triple excitations (CCSD(T)) and BEHT3 are investigated. It is found that the diffuse basis function plays an important role in achieving accurate electron affinity results. Among all theoretical models considered here, the performance of BEHT3 is best.</p>","PeriodicalId":59,"journal":{"name":"The Journal of Physical Chemistry A","volume":" ","pages":"7008-7021"},"PeriodicalIF":2.8,"publicationDate":"2025-07-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144673370","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":"","authors":"Johanna G. M. Schrauwen,&nbsp;Herma M. Cuppen*,&nbsp;Sergio Ioppolo and Britta Redlich,&nbsp;","doi":"","DOIUrl":"","url":null,"abstract":"","PeriodicalId":59,"journal":{"name":"The Journal of Physical Chemistry A","volume":"129 30","pages":"XXX-XXX XXX-XXX"},"PeriodicalIF":2.8,"publicationDate":"2025-07-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://pubs.acs.org/doi/pdf/10.1021/acs.jpca.5c03186","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144737866","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A Bottom-up Computational Study of Doped Amorphous Carbon Clusters as Precursors of Carbon Nanodots.","authors":"Francesca D'Ambrosio, Alice Frustaci, Enrico Bodo","doi":"10.1021/acs.jpca.5c03577","DOIUrl":"10.1021/acs.jpca.5c03577","url":null,"abstract":"<p><p>In this work, we present a bottom-up computational study of unsaturated amorphous carbon clusters partially doped with nitrogen and other typical chemical groups. We focus on their structure and electronic properties with the aim of providing possible models of the amorphous portions of the core of carbon nanodots, a class of fluorescent carbon-based nanoparticles whose complex atomistic structure is not yet fully understood. Using the GOAT-EXPLORE algorithm in combination with semiempirical and DFT methods, we generated and optimized a broad ensemble of structural isomers for C_<i>n</i>X clusters of up to 35 atoms of carbon, with X including nitrogen and typical functional groups found in the carbon nanodots (X = OH, NH₂, COOH, and CONH₂). Structural and electronic parameters were evaluated to understand how size, doping, and functionalization impact electronic delocalization, stability, and potential reactivity. Our findings highlight a structural evolution from linear to polycyclic and cage-like motifs with increasing size and demonstrate that functionalization mainly influences local electronic environments without drastically affecting the overall architecture.</p>","PeriodicalId":59,"journal":{"name":"The Journal of Physical Chemistry A","volume":" ","pages":"6825-6836"},"PeriodicalIF":2.8,"publicationDate":"2025-07-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144673367","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":"Femtosecond Time- and Spectrally Resolved Ion Photofragmentation Spectroscopy: Case Studies of Two Alkylbenzene Cations.","authors":"Chen-Yi Chu, Hsin Liu, Po-Yuan Cheng","doi":"10.1021/acs.jpca.5c04149","DOIUrl":"10.1021/acs.jpca.5c04149","url":null,"abstract":"<p><p>Ultrafast photoionization-induced ionic relaxation dynamics in <i>n</i>-propylbenzene and 2,2-dimethylpropylbenzene cations were investigated using time- and spectrally resolved ion photofragmentation spectroscopy with a femtosecond photoionization-photofragmentation (PI-PF) detection scheme. Photoionization was initiated via 1 + 1 REMPI using femtosecond UV pump pulses well below the strong-field ionization regime, and the evolving ionic systems were probed by delayed visible-wavelength probe pulses to induce photofragmentation. Despite substantial ionic fragmentation induced by UV photoionization, the observed parent ion depletion transient signals can be attributed exclusively to the relaxation dynamics of intact parent cations generated at the two-photon level. Highly excited cationic states initially accessed by absorption of additional UV photons within the pump pulse do not contribute to the parent ion depletion transient signals, although their dynamics may appear in fragment ion formation transients. Ultrafast time-resolved photofragmentation spectra, obtained by measuring probe-induced parent ion depletion yield as a function of wavelength at a fixed delay time, reveal prominent ionic resonance absorption in the visible region. The observed time invariance of ion depletion signals across this spectral range indicates the absence of substantial postionization relaxation processes capable of altering the nature or resonance absorption characteristic of the cation. These findings establish alkylbenzene cations as ideal reference systems for benchmarking ultrafast dynamics in more complex ionic systems that do undergo substantial structural or electronic transformations following photoionization.</p>","PeriodicalId":59,"journal":{"name":"The Journal of Physical Chemistry A","volume":" ","pages":"6845-6865"},"PeriodicalIF":2.8,"publicationDate":"2025-07-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144681682","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":"Highly Accurate Expectation Values Using High-Order Relativistic Coupled Cluster Theory.","authors":"Gabriele Fabbro, Jan Brandejs, Trond Saue","doi":"10.1021/acs.jpca.5c02844","DOIUrl":"10.1021/acs.jpca.5c02844","url":null,"abstract":"<p><p>This work presents the automatic generation of analytic first derivatives of the energy for general coupled-cluster models using the tenpi toolchain. We report the first implementation of expectation values for CCSDT and CCSDTQ methods within the DIRAC program package for relativistic molecular calculations. As pivotal calculations, we focus on the electric field gradient (EFG) evaluated at the lithium nucleus in LiX (X = H, F, Cl) compounds, enabling the extraction of the nuclear electric quadrupole moment <i>Q</i>(⁷Li), and at the aluminum nucleus in AlY (Y = H, F, Cl, Br) compounds, for the determination of <i>Q</i>(²⁷Al). These high-order methods are applied to compute corrections for triple and quadruple excitations for the EFG, a crucial quantity for determining nuclear quadrupole moments. We obtain <i>Q</i>(²⁷Al) = 0.146598 ± 0.000001 b, in excellent agreement with the recommended value, and <i>Q</i>(⁷Li) = -0.038624 ± 0.000292 b, which is smaller than the currently recommended value, and suggests the need for further investigation.</p>","PeriodicalId":59,"journal":{"name":"The Journal of Physical Chemistry A","volume":" ","pages":"6942-6958"},"PeriodicalIF":2.8,"publicationDate":"2025-07-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144612050","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":"DIALECT, a Software Package for Exciton Spectra and Dynamics in Large Molecular Assemblies from Weak to Strong Light-Matter Coupling Regimes.","authors":"Richard Einsele, Xincheng Miao, Luca Nils Philipp, Roland Mitrić","doi":"10.1021/acs.jpca.5c03307","DOIUrl":"10.1021/acs.jpca.5c03307","url":null,"abstract":"<p><p>The software package DIALECT is introduced, which provides the capability of calculating excited-state properties and nonadiabatic dynamics of large molecular systems and can be applied to simulate energy and charge-transfer processes in molecular materials. To this end, we employ the FMO-LC-TDDFTB methodology, which combines the use of the fragment molecular orbital approach with the density-functional tight-binding method and an excitonic Hamiltonian including local and charge-transfer excitations. In this work, we present the features and capabilities of the DIALECT software package in simulating the excited state dynamics of molecules and molecular aggregates using exemplary trajectory surface hopping as well as decoherence corrected Ehrenfest dynamics calculations in the framework of LC-TDDFTB and FMO-LC-TDDFTB. In addition, the capability of simulating the polaritonic excited state properties is highlighted by the calculation of the polariton dispersion of an aggregate of naphthalene molecules. The development of the DIALECT program will facilitate the investigation of exciton and charge transport in large and complex molecular systems, such as biological aggregates, nanomaterials and other complex organic molecular systems.</p>","PeriodicalId":59,"journal":{"name":"The Journal of Physical Chemistry A","volume":" ","pages":"6994-7007"},"PeriodicalIF":2.8,"publicationDate":"2025-07-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144647940","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":"","authors":"Nicoló Antonini,&nbsp;Enrico Ronca,&nbsp;Loriano Storchi* and Leonardo Belpassi*,&nbsp;","doi":"","DOIUrl":"","url":null,"abstract":"","PeriodicalId":59,"journal":{"name":"The Journal of Physical Chemistry A","volume":"129 30","pages":"XXX-XXX XXX-XXX"},"PeriodicalIF":2.8,"publicationDate":"2025-07-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://pubs.acs.org/doi/pdf/10.1021/acs.jpca.5c02772","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144737812","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}