The Journal of Physical Chemistry A最新文献

{"title":"Reduced Scaling Correlated Natural Transition Orbitals for Multilevel Coupled Cluster Calculations","authors":"Sarai Dery Folkestad*,&nbsp; and ,&nbsp;Henrik Koch,&nbsp;","doi":"10.1021/acs.jpca.4c0627110.1021/acs.jpca.4c06271","DOIUrl":"https://doi.org/10.1021/acs.jpca.4c06271https://doi.org/10.1021/acs.jpca.4c06271","url":null,"abstract":"<p >Multilevel coupled cluster theory offers reduced scaling computation of intensive properties in systems that are too large for standard coupled cluster calculations. A significant benefit of the multilevel coupled cluster framework is the possibility of calculating intensive properties that are not tightly localized if an appropriate set of active orbitals is used. Correlated natural transition orbitals (CNTOs) are tailored to describe excitation processes. For multilevel coupled cluster singles and doubles (MLCCSD) and singles and perturbative doubles (MLCC2) calculations, the construction of CNTOs generally becomes the computational bottleneck. Here, we demonstrate how CNTOs can be obtained with <i></i><math><mi>O</mi><mrow><mo>(</mo><msup><mrow><mi>N</mi></mrow><mrow><mn>3</mn></mrow></msup><mo>)</mo></mrow></math> operations, eliminating the <i></i><math><mi>O</mi><mrow><mo>(</mo><msup><mrow><mi>N</mi></mrow><mrow><mn>5</mn></mrow></msup><mo>)</mo></mrow></math>-scaling steps involved in the original approach. This reduction in scaling moves the bottleneck of MLCC2 and MLCCSD calculations from the active orbital space preparation to the MLCC2 and MLCCSD equations with <i></i><math><mi>O</mi><mrow><mo>(</mo><msup><mrow><mi>N</mi></mrow><mrow><mn>4</mn></mrow></msup><mo>)</mo></mrow></math>-scaling.</p>","PeriodicalId":59,"journal":{"name":"The Journal of Physical Chemistry A","volume":null,"pages":null},"PeriodicalIF":2.7,"publicationDate":"2024-10-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://pubs.acs.org/doi/epdf/10.1021/acs.jpca.4c06271","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142608739","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":"Infrared Fingerprint and Unimolecular Decay Dynamics of the Hydroperoxyalkyl Intermediate (•QOOH) in Cyclopentane Oxidation.","authors":"Yujie Qian, Tarun Kumar Roy, Dylan S Valente, Emmanuel Moya Cruz, Marisa C Kozlowski, Andrea Della Libera, Stephen J Klippenstein, Marsha I Lester","doi":"10.1021/acs.jpca.4c05677","DOIUrl":"10.1021/acs.jpca.4c05677","url":null,"abstract":"<p><p>A transient carbon-centered hydroperoxyalkyl intermediate (•QOOH) in the oxidation of cyclopentane is identified by IR action spectroscopy with time-resolved unimolecular decay to hydroxyl (OH) radical products that are detected by UV laser-induced fluorescence. Two nearly degenerate •QOOH isomers, β- and γ-QOOH, are generated by H atom abstraction of the cyclopentyl hydroperoxide precursor. Fundamental and first overtone OH stretch transitions and combination bands of •QOOH are observed and compared with anharmonic frequencies computed by second-order vibrational perturbation theory. An OH stretch transition is also observed for a conformer arising from torsion about a low-energy CCOO barrier. Definitive identification of the β-QOOH isomer relies on its significantly lower transition state (TS) barrier to OH products, which results in rapid unimolecular decay and near unity branching to OH products. A benchmarking approach is utilized to compute high-accuracy stationary point energies, most importantly TS barriers, for cyclopentane oxidation (C₅H₉O₂), building on higher level reference calculations for ethane oxidation (C₂H₅O₂). The experimental OH product appearance rates are compared with computed statistical microcanonical rates using RRKM theory, including heavy-atom tunneling, thereby validating the computed TS barrier. The results are extended to thermal unimolecular decay rate constants at temperatures and pressures relevant to cyclopentane combustion via master-equation modeling. The various torsional and ring puckering states of the wells and transition states are explicitly considered in these calculations.</p>","PeriodicalId":59,"journal":{"name":"The Journal of Physical Chemistry A","volume":null,"pages":null},"PeriodicalIF":2.7,"publicationDate":"2024-10-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142453492","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":"High-Resolution Spectroscopy and Structure of Heavy Carbon Subchalcogenides: Tricarbon Selenide, C₃Se.","authors":"Thomas Salomon, Weslley G D P Silva, John B Dudek, Jürgen Gauss, Stephan Schlemmer, Jennifer van Wijngaarden, Sven Thorwirth","doi":"10.1021/acs.jpca.4c05475","DOIUrl":"10.1021/acs.jpca.4c05475","url":null,"abstract":"<p><p>Linear tricarbon selenide, C₃Se, has been studied spectroscopically for the first time using a combination of high-resolution infrared and microwave techniques. Probing laser ablation products from carbon-selenium targets in a free jet expansion with He, initial spectroscopic detection was accomplished in the infrared at a wavelength of 5 μm in search of the ν₁ vibrational fundamental. Along with the band of the most abundant isotopic species C₃⁸⁰Se found centered at about 2039 cm^-1, the corresponding bands of the C₃⁸²Se, C₃⁷⁸Se, C₃⁷⁶Se, and C₃⁷⁷Se isotopologues were also detected. Pure rotational spectra of the five C₃Se isotopologues in the 8-18 GHz frequency range were observed in a supersonic jet expansion using chirped-pulse microwave spectroscopy of the discharge products of selenophene, c-C₄H₄Se. Spectroscopic analyses were guided by results from high-level quantum-chemical calculations carried out at the coupled-cluster level of theory using large correlation-consistent basis sets. Using the experimentally derived ground-state rotational constants of five isotopologues and calculated zero-point vibrational corrections, an accurate semiexperimental equilibrium carbon-selenium bond length is derived.</p>","PeriodicalId":59,"journal":{"name":"The Journal of Physical Chemistry A","volume":null,"pages":null},"PeriodicalIF":2.7,"publicationDate":"2024-10-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142386330","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":"Dissociation Energies via Embedding Techniques.","authors":"Florian Feyersinger, Peter E Hartmann, Johannes Hoja, Peter Reinholdt, Florian Libisch, Jacob Kongsted, Peter Puschnig, A Daniel Boese","doi":"10.1021/acs.jpca.4c02851","DOIUrl":"10.1021/acs.jpca.4c02851","url":null,"abstract":"<p><p>Due to the large number of interactions, evaluating interaction energies for large or periodic systems results in time-consuming calculations. Prime examples are liquids, adsorbates, and molecular crystals. Thus, there is a high demand for a cheap but still accurate method to determine interaction energies and gradients. One approach to counteract the computational cost is to fragment a large cluster into smaller subsystems, sometimes called many-body expansion, with the fragments being molecules or parts thereof. These subsystems can then be embedded into larger entities, representing the bigger system. In this work, we test several subsystem approaches and explore their limits and behaviors, determined by calculations of trimer interaction energies. The methods presented here encompass mechanical embedding, point charges, polarizable embedding, polarizable density embedding, and density embedding. We evaluate nonembedded fragmentation, QM/MM (quantum mechanics/molecular mechanics), and QM/QM (quantum mechanics/quantum mechanics) embedding theories. Finally, we make use of symmetry-adapted perturbation theory utilizing density functional theory for the monomers to interpret the results. Depending on the strength of the interaction, different embedding methods and schemes prove favorable to accurately describe a system. The embedding approaches presented here are able to decrease the interaction energy errors with respect to full system calculations by a factor of up to 20 in comparison to simple/unembedded approaches, leading to errors below 0.1 kJ/mol.</p>","PeriodicalId":59,"journal":{"name":"The Journal of Physical Chemistry A","volume":null,"pages":null},"PeriodicalIF":2.7,"publicationDate":"2024-10-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11514013/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142453486","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":"Investigation of the Structure and Optical Properties of Polymethine-Based NIR-II Fluorophores Using Many-Body Perturbation Theory: GW-BSE Approaches","authors":"Hengquan Guo,&nbsp;Nguyet N. T. Pham,&nbsp;Jong S. Park* and Seung Geol Lee*,&nbsp;","doi":"10.1021/acs.jpca.4c0611510.1021/acs.jpca.4c06115","DOIUrl":"https://doi.org/10.1021/acs.jpca.4c06115https://doi.org/10.1021/acs.jpca.4c06115","url":null,"abstract":"<p >Fluorescence imaging is a widely used technique for detecting pathophysiological microenvironments and guiding fluorescence-guided therapy owing to its noninvasiveness, high spatiotemporal resolution, ease of operation, and real-time monitoring capabilities. In particular, NIR-II materials are promising for fluorescence imaging applications because they exhibit reduced light scattering and absorption by biological tissues, enabling deeper imaging with improved spatial resolution and contrast compared to visible or first near-infrared imaging. NIR-II materials refer to those that emit in the second near-infrared region of the electromagnetic spectrum, spanning wavelengths from approximately 1000 to 1700 nm. The emission peaks of organic fluorophores within the NIR-II window are of particular interest due to their minimal biotoxicity, in vivo biocompatibility, and biodegradability. In this study, we investigated a new series of NIR-II fluorescent polymethine-based dyes and their NIR-II absorption properties using density functional theory and the GW-BSE approximation. Our calculated maximum absorption peak under the GW-BSE approximation showed good agreement with experimental results, demonstrating the potential of these dyes for NIR-II fluorescence imaging applications.</p>","PeriodicalId":59,"journal":{"name":"The Journal of Physical Chemistry A","volume":null,"pages":null},"PeriodicalIF":2.7,"publicationDate":"2024-10-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142608839","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":"On the Nature of HOPG-Supported Pt₁Ti₂O₇ and its Decomposition of a Nerve Agent Simulant: A Cluster Model of a Single Atom Catalyst Active Site.","authors":"Michael A Denchy, Benjamin R Bilik, Kathryn Foreman, Linjie Wang, Lucas Hansen, Sandra Albornoz, Francisco Lizano, Kit H Bowen","doi":"10.1021/acs.jpca.4c05779","DOIUrl":"10.1021/acs.jpca.4c05779","url":null,"abstract":"<p><p>Chemical weapons, including hyper lethal nerve agents, are a persistently looming threat across the modern geopolitical landscape. There is a pressing need for the design and development of improved protective materials, which can be substantially aided by the cultivation of a fundamental molecular-level understanding of candidate systems and the corresponding decomposition chemistry. The emergence of the exciting new class of single atom catalyst (SAC) materials has enhanced the prospect of subnanoscale design tailoring in the hopes of optimizing activity and selectivity for a variety of chemical applications. Here, we apply our recently developed experimental technique for modeling the active sites of such SAC materials through the preparation of surface supported size-selected single metal-atom doped metal oxide clusters. The propensity for an SAC cluster model system for Pt₁/TiO₂ materials, Pt₁Ti₂O₇ supported on highly oriented pyrolytic graphite (HOPG), to adsorb and decompose nerve agent simulant dimethyl methylphosphonate (DMMP) was investigated through a combination of temperature-programmed desorption/reaction (TPD/R) and X-ray photoelectron spectroscopy (XPS). XPS measurements of the as-prepared Pt₁Ti₂O₇ clusters supported the successful isolation of single Pt atoms in clusters monodispersed across the HOPG surface. TPD/R experiments showed that the reactivity exhibited by the Pt₁Ti₂O₇ clusters was distinct from that of Ti₂O₇ clusters lacking the single Pt atom. It was found that DMMP decomposed over Pt₁Ti₂O₇ upon heating to as low as room temperature, and higher temperature treatments evolved exclusively H₂O, CO, and H₂, while decomposition over Ti₂O₇ evolved only methanol and formaldehyde at elevated temperatures. This indicated the promotion of C-H and PO-C bond cleavage within DMMP due to the presence of single Pt atoms in the clusters. Further, the Pt₁Ti₂O₇ clusters were found to desorb P-containing decomposition species, preventing active site poisoning; however, a change of reactivity reflecting that of Ti₂O₇ was observed following a single TPD/R cycle. This suggested the encapsulation of active Pt sites by titanium oxide during high temperature treatment and is thus an issue deserving of serious attention in the study of Pt₁/Ti₂O₇ SAC materials.</p>","PeriodicalId":59,"journal":{"name":"The Journal of Physical Chemistry A","volume":null,"pages":null},"PeriodicalIF":2.7,"publicationDate":"2024-10-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142453501","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":"<i>UltraStat</i>: Ultrafast Spectroscopy beyond the Fourier Limit Using Bayesian Inference.","authors":"Elad Harel","doi":"10.1021/acs.jpca.4c04385","DOIUrl":"10.1021/acs.jpca.4c04385","url":null,"abstract":"<p><p>The discrete Fourier transform (dFT) plays a central role in many ultrafast experiments, allowing the recovery of spectroscopic observables from time-domain measurements. In resonant experiments when population relaxation and coherence components of the signal coexist, the dFT is usually preceded by multiexponential fitting to remove the large population term. However, this procedure results in errors in both the recovered decay rates and the line shapes of the coherence spectral components. While other methods such as linear prediction singular value decomposition fit both terms simultaneously, they are limited to specific models that may not represent the true signal. These methods do not allow for systematic noise analysis or error estimation and require <i>a priori</i> knowledge of the signal rank. Here, we describe a general approach to parameter estimation in ultrafast spectroscopy─<i>UltraStat</i>─grounded in Bayesian analysis without the limitations set by Fourier theory. Using simulated, but realistic data, we demonstrate in a statistical sense how <i>UltraStat</i> provides accurate parameter estimation in the presence of many experimental constraints: noise, signal truncation, limited photon budget, and nonuniform sampling. <i>UltraStat</i> provides superior resolution compared to the dFT, up to an order of magnitude in cases where the line shapes are well-approximated. In these cases, we establish that primarily noise, not sampling, limits spectral resolution. Moreover, we show that subsampling may reduce the number of acquired points by 90% compared to the Nyquist-Shannon criteria. <i>UltraStat</i> greatly improves parameter estimation by providing statistically bound spectral and dynamics analysis, pushing the limits of ultrafast science.</p>","PeriodicalId":59,"journal":{"name":"The Journal of Physical Chemistry A","volume":null,"pages":null},"PeriodicalIF":2.7,"publicationDate":"2024-10-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11514019/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142453480","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":"Study on Quantum Dynamics of the Na + Na2 Exchanged Reaction and Lifetime Prediction of Na3 Complex Based on the Neural Network Potential Energy Surface","authors":"Jiapeng Zhang,&nbsp;Bayaer Buren* and Yongqing Li*,&nbsp;","doi":"10.1021/acs.jpca.4c0571210.1021/acs.jpca.4c05712","DOIUrl":"https://doi.org/10.1021/acs.jpca.4c05712https://doi.org/10.1021/acs.jpca.4c05712","url":null,"abstract":"<p >A high-precision global potential energy surface (PES) is constructed for the Na₃ system based on high-level <i>ab initio</i> calculations and the fundamental invariant neural network (FI-NN) method. The root-mean-square error (RMSE) of the PES is 2.88 cm^–1. The state-resolved quantum dynamics of the ground-state Na + Na₂ (<i>v</i> = 0, <i>j</i> = 0) → Na₂ (<i>v</i>′, <i>j</i>′) + Na reaction is studied using the time-dependent wave packet (TDWP) method on the new PES. Analysis of the relevant integral cross sections revealed a complicated energy-transfer mechanism during collisions. Similarly, the characteristics of the differential cross sections indicate that the complex-forming mechanism plays a dominant role in the reaction, providing conditions for a comprehensive exploration of the lifetimes of the complexes. Based on the Rice-Ramsperger-Kassel-Marcus (RRKM) theory, the calculated lifetime of the Na₃ complex is approximately 3.9 ns.</p>","PeriodicalId":59,"journal":{"name":"The Journal of Physical Chemistry A","volume":null,"pages":null},"PeriodicalIF":2.7,"publicationDate":"2024-10-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142609231","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":"Diagrams in Polaritonic Coupled Cluster Theory","authors":"Laurenz Monzel*,&nbsp; and ,&nbsp;Stella Stopkowicz*,&nbsp;","doi":"10.1021/acs.jpca.4c0438910.1021/acs.jpca.4c04389","DOIUrl":"https://doi.org/10.1021/acs.jpca.4c04389https://doi.org/10.1021/acs.jpca.4c04389","url":null,"abstract":"<p >We present a diagrammatic notation to derive the quantum-electrodynamic coupled cluster (QED-CC) equations needed for the description for polaritonic ground and excited states. Our presented notation is a generalization of the existing diagrammatic notation of standard electronic coupled-cluster theory. It is used to derive the QED-CC and QED-EOM-CC equations for the QED-CCSD-1-SD and QED-CCSD-12-SD truncation schemes. Furthermore, we present the diagrams for the CC Λ-equations and reduced density matrices which are needed for the calculation of molecular properties.</p>","PeriodicalId":59,"journal":{"name":"The Journal of Physical Chemistry A","volume":null,"pages":null},"PeriodicalIF":2.7,"publicationDate":"2024-10-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142609228","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":"Electric Field Influence on CO Clathrate Hydrates","authors":"Smita Rai,&nbsp; and ,&nbsp;Dhurba Rai*,&nbsp;","doi":"10.1021/acs.jpca.4c0507410.1021/acs.jpca.4c05074","DOIUrl":"https://doi.org/10.1021/acs.jpca.4c05074https://doi.org/10.1021/acs.jpca.4c05074","url":null,"abstract":"<p >We consider carbon monoxide (CO) confined in the hydrogen-bonded building blocks of sI and sII clathrate hydrates, viz., (5¹², 5¹²6², 5¹²6⁴) cages, within the density functional theory-based calculations. We study their response to the applied electric fields in terms of changes in the geometrical parameters, dipole moment, HOMO–LUMO gap, and vibrational frequency shift. We examine the stability of CO clathrate hydrate building block cages and identify a possible indication of the field-induced release of CO.</p>","PeriodicalId":59,"journal":{"name":"The Journal of Physical Chemistry A","volume":null,"pages":null},"PeriodicalIF":2.7,"publicationDate":"2024-10-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142609232","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}