Journal of Chemical Physics最新文献

{"title":"Impact of iodine-substitution on the symmetry and room-temperature phosphorescence behavior of thienyl diketone skeleton.","authors":"Daiki Shikichi, Takumi Ehara, Mao Komura, Ken Onda, Kiyoshi Miyata, Yosuke Tani","doi":"10.1063/5.0255535","DOIUrl":"https://doi.org/10.1063/5.0255535","url":null,"abstract":"<p><p>Introducing heavy atoms, or replacing atoms with heavier ones, is a routine approach for accelerating spin-flipping photophysical processes. However, predicting its impact on phosphorescence efficiency is not straightforward. Herein, we report an unexpected consequence of bromine-to-iodine substitution in a bromothienyl diketone derivative, TIPS-BrTn, that exhibits outstanding room-temperature phosphorescence (RTP) in cyclohexane solution. Contrary to our expectation, the iodo-congener TIPS-ITn exhibited feeble photoluminescence, which we confirmed as RTP by ultrafast spectroscopy. Further experimental and theoretical studies revealed that, in the T1 state, an excited-state symmetry breaking occurred on TIPS-ITn while TIPS-BrTn preserved the centrosymmetric geometry. We identified the driving force for the symmetry breaking as an intramolecular two-center three-electron bonding interaction between iodine and carbonyl oxygen in the (n,π*) excited state. Consequently, while the direct T1-S0 spin-orbit coupling (SOC) in TIPS-BrTn is symmetry-forbidden and zero, that of TIPS-ITn is non-zero due to the loss of centrosymmetry, thereby accelerating nonradiative T1-S0 decay to diminish the RTP. Importantly, the phosphorescence rate constant is not solely dictated by the direct T1-S0 SOC; instead, it can be rationalized by the intensity borrowing from higher singlet states. Thus, our work highlights the importance of controlling molecular symmetry, which could suppress the direct T1-S0 SOC and lead to a preferential acceleration of radiative decay over nonradiative decay for achieving efficient RTP.</p>","PeriodicalId":15313,"journal":{"name":"Journal of Chemical Physics","volume":"162 12","pages":""},"PeriodicalIF":3.1,"publicationDate":"2025-03-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143730038","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 dynamics of substituted benzoate anions undergoing counterion condensation in lamellar phase dispersions.","authors":"Iain McKenzie, Victoria L Karner, Leanna M Karn, Brian P Mulley, Robert Scheuermann, Ian M Tucker","doi":"10.1063/5.0251148","DOIUrl":"https://doi.org/10.1063/5.0251148","url":null,"abstract":"<p><p>We have studied the interaction of three ortho-substituted benzoate anions (2-ethylbenzoate, 2-chlorobenzoate, and 2-hydroxybenzoate) and three para-substituted benzoate anions (4-ethylbenzoate, 4-chlorobenzoate, and 4-hydroxybenzoate) with lamellar phase dispersions of the di-chain cationic surfactants 2,3-diheptadecyl ester ethoxypropyl-1,1,1-trimethyl-ammonium chloride (DHTAC) and dioctadecyl-dimethyl-ammonium chloride (DODMAC) using avoided level crossing muon spin resonance (ALC-μSR) spectroscopy. Highly polarized spin probes were produced in situ by the addition of muonium to the aromatic anions, and the muon and methylene proton hyperfine coupling constants (hfccs) of these radical anions were determined from the Δ1 and Δ0 resonance fields in the ALC-μSR spectra. The motionally averaged dipolar muon hfccs, |Dμ‖|, were determined from the width and amplitude of the Δ1 and Δ0 resonances and used to estimate the extent of reorientational motion. The results are consistent with the counterions being electrostatically trapped near the oil/water interface of the surfactant bilayer and undergoing large amplitude anisotropic motion. This motion is generally more restricted in DODMAC bilayers compared with DHTAC, which is likely related to the relative flexibility of the headgroups to which the counterions are loosely bound. The motion of the ortho isomers is generally more restricted than the para isomers, while there is no obvious trend regarding the ethyl, chloro, and hydroxy substituents.</p>","PeriodicalId":15313,"journal":{"name":"Journal of Chemical Physics","volume":"162 12","pages":""},"PeriodicalIF":3.1,"publicationDate":"2025-03-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143709978","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":"Active polymer behavior in two dimensions: A comparative analysis of tangential and push-pull models.","authors":"Giulia Janzen, Juan Pablo Miranda, J Martín-Roca, Paolo Malgaretti, Emanuele Locatelli, Chantal Valeriani, D A Matoz Fernandez","doi":"10.1063/5.0243432","DOIUrl":"https://doi.org/10.1063/5.0243432","url":null,"abstract":"<p><p>In this work, we compare the structural and dynamic behavior of active filaments in two dimensions using tangential and push-pull models, including a variant with passive end monomers, to bridge the two frameworks. These models serve as valuable frameworks for understanding self-organization in biological polymers and synthetic materials. At low activity, all models exhibit similar behavior; as activity increases, subtle differences emerge in intermediate regimes, but at high activity, their behaviors converge. Adjusting for differences in mean active force reveals nearly identical behavior across models, even across varying filament configurations and bending rigidities. Our results highlight the importance of force definitions in active polymer simulations and provide insights into phase transitions across varying filament configurations.</p>","PeriodicalId":15313,"journal":{"name":"Journal of Chemical Physics","volume":"162 11","pages":""},"PeriodicalIF":3.1,"publicationDate":"2025-03-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143657280","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":"Effect of structural bending on the photophysical properties of perylene bisimide.","authors":"Hikaru Sotome, Masahiro Higashi, Yuki Tanaka, Hiroshi Shinokubo, Yasuhiro Kobori, Norihito Fukui","doi":"10.1063/5.0255756","DOIUrl":"https://doi.org/10.1063/5.0255756","url":null,"abstract":"<p><p>The effect of nonplanarity on the electronic properties of π-systems has been difficult to study systematically because of the limited availability of suitable model compounds. Our group recently synthesized a series of end-to-end bent perylene bisimide (PBI) cyclophanes, whose degree of bending is adjustable by modifying the internal alkyl tethers. Herein, we subjected these bent PBI derivatives to theoretical calculations and time-resolved spectroscopy. The current study has offered rational explanations for several unique photophysical characteristics of bent PBIs: (1) the redshifts of the S0-S1 transitions, (2) the decrease in extinction coefficients, (3) the broadening of spectral shapes, and (4) the suppression of nonradiative decay processes. Furthermore, the investigation of the S1 states and radical anions has revealed that structural bending also substantially alters the energy levels of upper molecular orbitals such as LUMO+2.</p>","PeriodicalId":15313,"journal":{"name":"Journal of Chemical Physics","volume":"162 11","pages":""},"PeriodicalIF":3.1,"publicationDate":"2025-03-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143657333","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":"SHARC-VQE: Simplified Hamiltonian approach with refinement and correction enabled variational quantum eigensolver for molecular simulation.","authors":"Harshdeep Singh, Sonjoy Majumder, Sabyashachi Mishra","doi":"10.1063/5.0249447","DOIUrl":"https://doi.org/10.1063/5.0249447","url":null,"abstract":"<p><p>Quantum computing is finding increasingly more applications in quantum chemistry, particularly to simulate electronic structure and molecular properties of simple systems. The transformation of a molecular Hamiltonian from the fermionic space to the qubit space results in a series of Pauli strings. Calculating the energy then involves evaluating the expectation values of each of these strings, which presents a significant bottleneck for applying variational quantum eigensolvers (VQEs) in quantum chemistry. Unlike fermionic Hamiltonians, the terms in a qubit Hamiltonian are additive. This work leverages this property to introduce a novel method for extracting information from the partial qubit Hamiltonian, thereby enhancing the efficiency of VQEs. This work introduces the SHARC-VQE (Simplified Hamiltonian Approximation, Refinement, and Correction-VQE) method, where the full molecular Hamiltonian is partitioned into two parts based on the ease of quantum execution. The easy-to-execute part constitutes the partial Hamiltonian, and the remaining part, while more complex to execute, is generally less significant. The latter is approximated by a refined operator and added up as a correction into the partial Hamiltonian. SHARC-VQE significantly reduces computational costs for molecular simulations. The cost of a single energy measurement can be reduced from O(N4ϵ2) to O(1ϵ2) for a system of N qubits and accuracy ϵ, while the overall cost of VQE can be reduced from O(N7ϵ2) to O(N3ϵ2). Furthermore, measurement outcomes using SHARC-VQE are less prone to errors induced by noise from quantum circuits, reducing the errors from 20%-40% to 5%-10% without any additional error correction or mitigation technique. In addition, the SHARC-VQE is demonstrated as an initialization technique, where the simplified partial Hamiltonian is used to identify an optimal starting point for a complex problem. Overall, this method improves the efficiency of VQEs and enhances the accuracy and reliability of quantum simulations by mitigating noise and overcoming computational challenges.</p>","PeriodicalId":15313,"journal":{"name":"Journal of Chemical Physics","volume":"162 11","pages":""},"PeriodicalIF":3.1,"publicationDate":"2025-03-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143657414","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 many faces of vibrational energy relaxation in N2(v) + O(1D) collisions: Dynamics on 1Π and 1Δ potential energy surfaces.","authors":"Qizhen Hong, Massimiliano Bartolomei, Fernando Pirani, Quanhua Sun, Cecilia Coletti","doi":"10.1063/5.0255380","DOIUrl":"https://doi.org/10.1063/5.0255380","url":null,"abstract":"<p><p>Complete datasets of rate coefficients for the vibrational quenching of molecular nitrogen by collision with electronically excited atomic oxygen O(1D) over a wide temperature range are calculated for the first time. Such data are important ingredients in the modeling of non-local thermal equilibrium conditions that characterize the atmosphere, media of astronomical interest, and cold and hot plasmas, where O(1D), also formed when O2 molecules break, represents a significant fraction of the gas mixture. To this end, we developed analytical potential energy surfaces (PESs) for the 1Π and 1Δ electronic states of the N2-O(1D) system to accurately describe the interaction in the long, medium, and first repulsive range of intermolecular distances, the most effective regions in inelastic collisions under a variety of conditions of interest. The derived PESs are used to calculate the vibration-to-translation (V-T) and vibration-to-electronic (V-E) energy transfer rates by mixed quantum-classical dynamics and by the Landau-Zener formulation, respectively. In addition, the datasets are extended to cover the entire N2 vibrational ladder by using the Gaussian process regression. The results show that at low temperatures, where V-E relaxation dominates, N2 vibrational quenching by O(1D) collisions is faster than by O(3P) collisions.</p>","PeriodicalId":15313,"journal":{"name":"Journal of Chemical Physics","volume":"162 11","pages":""},"PeriodicalIF":3.1,"publicationDate":"2025-03-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143657447","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 structure and symmetry of modular state space for complex quantum systems.","authors":"Guohua Tao","doi":"10.1063/5.0245447","DOIUrl":"https://doi.org/10.1063/5.0245447","url":null,"abstract":"<p><p>Understanding the state space structure of complex quantum systems can help to effectively characterize the system properties and explore underlying mechanisms. The structure of the state space could be quite complicated for quantum many-body systems, and the systematic decomposition of the state space is normally involved. Recently, a modular tensor diagram approach was proposed to reorganize the state space hierarchically based on a modular basis. Here, we review the construction of spin eigenfunctions for multiple exciton systems and further develop modular tensor diagrams to exemplify the hierarchical symmetry of the state space. The newly constructed spin eigenfunctions for quadruple excitons, along with the results for triple excitons, are used to demonstrate the effective decomposition of the state space into hierarchical tensorial structures. A universal recursive relation is derived to determine the coefficients of spin eigenfunctions exhibiting transformation symmetry between different classes of elementary modules for an arbitrary number of exciton units. Interestingly, different coupling schemes mapped to quantum many-body interactions lead to different spin adapted basis states, which may correspond to different realistic systems upon the breakdown of spin degeneracy. This work highlights the hierarchical symmetry of the tensorial structure of quantum many-body systems, which may facilitate a better understanding of the structure property relationship toward the object-oriented materials design.</p>","PeriodicalId":15313,"journal":{"name":"Journal of Chemical Physics","volume":"162 11","pages":""},"PeriodicalIF":3.1,"publicationDate":"2025-03-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143657449","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":"Efficient exploration of reaction pathways using reaction databases and active learning.","authors":"Domantas Kuryla, Gábor Csányi, Adri C T van Duin, Angelos Michaelides","doi":"10.1063/5.0235715","DOIUrl":"https://doi.org/10.1063/5.0235715","url":null,"abstract":"<p><p>The fast and accurate simulation of chemical reactions is a major goal of computational chemistry. Recently, the pursuit of this goal has been aided by machine learning interatomic potentials (MLIPs), which provide energies and forces at quantum mechanical accuracy but at a fraction of the cost of the reference quantum mechanical calculations. Assembling the training set of relevant configurations is key to building the MLIP. Here, we demonstrate two approaches to training reactive MLIPs based on reaction pathway information. One approach exploits reaction datasets containing reactant, product, and transition state structures. Using an SN2 reaction dataset, we accurately locate reaction pathways and transition state geometries of up to 170 unseen reactions. In another approach, which does not depend on data availability, we present an efficient active learning procedure that yields an accurate MLIP and converged minimum energy path given only the reaction end point structures, avoiding quantum mechanics driven reaction pathway search at any stage of training set construction. We demonstrate this procedure on an SN2 reaction in the gas phase and with a small number of solvating water molecules, predicting reaction barriers within 20 meV of the reference quantum chemistry method. We then apply the active learning procedure on a more complex reaction involving a nucleophilic aromatic substitution and proton transfer, comparing the results against the reactive ReaxFF force field. Our active learning procedure, in addition to rapidly finding reaction paths for individual reactions, provides an approach to building large reaction path databases for training transferable reactive machine learning potentials.</p>","PeriodicalId":15313,"journal":{"name":"Journal of Chemical Physics","volume":"162 11","pages":""},"PeriodicalIF":3.1,"publicationDate":"2025-03-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143674055","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":"Exploring combined spin-labeling approach for structural studies of mRNA in the human ribosome.","authors":"Mikhail Kolokolov, Alexey Malygin, Dmitri Graifer, Mariya Meschaninova, Mariya Vorobyeva, Matvey Fedin, Olesya Krumkacheva, Elena Bagryanskaya","doi":"10.1063/5.0245722","DOIUrl":"https://doi.org/10.1063/5.0245722","url":null,"abstract":"<p><p>In this study, we investigated the structural variability of mRNA in the human ribosome by comparing two spin-labeling strategies: one involving an mRNA analog bearing two spin labels attached to the ribose-phosphate backbone and the other placing labels at the nucleotide bases. The use of two strategies of spin labeling of mRNAs allowed us to study for the first time the effect of the structure and location of spin labels on the measured interspin distances in human ribosome complexes. Experiments using dipolar EPR spectroscopy, supported by molecular dynamics calculations, demonstrated that labels introduced at nucleotide bases provide a higher resolution between mRNA conformations in the ribosome mRNA channel, compared to labels introduced at the ribose-phosphate backbone. Although ribose-phosphate labeling turned out to be less informative on its own for studying mRNA conformations in the ribosome than the previously used base labeling, it can find application in other complex studies of the structure of RNAs and their complexes.</p>","PeriodicalId":15313,"journal":{"name":"Journal of Chemical Physics","volume":"162 11","pages":""},"PeriodicalIF":3.1,"publicationDate":"2025-03-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143674056","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":"Gas-phase reactivity of protonated oxazolone: Chemical dynamics simulations and graph theory-based analysis reveal the importance of ion-molecule complexes.","authors":"Ariel F Perez Mellor, Thomas Bürgi, Riccardo Spezia","doi":"10.1063/5.0245766","DOIUrl":"https://doi.org/10.1063/5.0245766","url":null,"abstract":"<p><p>This study delves into the fragmentation mechanisms of the oxazolone form (OXA) of protonated cyclo-di-glycine using chemical dynamics simulations at multiple internal energies. While we focus our in-depth analyses on a representative total energy of 178 kcal/mol, we also performed simulations over the 127-187 kcal/mol range. This broader energy sampling reveals how the population of states evolves with increasing internal energy, enabling us to compute rate constants and then effective energy thresholds using a previously introduced three-state model [Perez Mellor et al., J. Chem. Phys. 155, 124103 (2021)]. By transforming molecular geometries into graph representations, we systematically analyze fragmentation processes and identify key intermediates and ion-molecule complexes (IMCs) that play a crucial role in fragmentation dynamics. The study highlights the distinct isomerization landscapes of OXA, driven by IMC formation, which contrasts with the previously reported behavior of cyclic and linear forms [Perez Mellor et al., J. Chem. Phys. 155, 124103 (2021)]. The resulting fragmentation channels are characterized by their unique energetic thresholds and branching ratios and can provide a molecular explanation of what was observed experimentally. Thanks to an accurate analysis of the trajectories using our graph-theory-based tools, it was possible to point out the particular behavior of OXA fragmentation, which is different from other isomers. In particular, the important role of IMCs is shown, which has an impact on populating different isomeric structures.</p>","PeriodicalId":15313,"journal":{"name":"Journal of Chemical Physics","volume":"162 11","pages":""},"PeriodicalIF":3.1,"publicationDate":"2025-03-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143674061","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}