Journal of Chemical Physics最新文献

{"title":"Least popular vibrational entropy model provides the best accuracy and robustness.","authors":"Julia A Velmiskina, Vadim I Malyshev, Igor S Gerasimov, Michael G Medvedev","doi":"10.1063/5.0255622","DOIUrl":"https://doi.org/10.1063/5.0255622","url":null,"abstract":"<p><p>Vibrational contributions into free energies usually amount to several kcal/mol and can significantly affect computational predictions. However, they are generally estimated incorrectly for chemical systems in solutions because the usual (employed in ∼99% of cases) models of vibrational entropies are extremely sensitive to errors in low-lying frequencies (below 300 cm-1), and these low-lying frequencies involve solvent molecules that are usually neglected (computed implicitly) in quantum chemical calculations. We find that only one vibrational entropy approximation-the one proposed by Truhlar in 2011-which is used in only ∼2% of cases, is stable in the low-lying frequency region and does not exhibit this problem. Accordingly, this approximation shows the best accuracy and robustness on a diverse set of experimental complexation energies and can be somewhat improved even further.</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":"143730043","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":"Excited-state structural characterization of a series of nanosecond-lived [Fe(terpy)2]2+ derivatives using x-ray solution scattering.","authors":"Bianca L Hansen, Verena Markmann, Mátyás Pápai, Philipp Lenzen, Morten Lunn Haubro, Antal Mikeházi, Zoltán Németh, Andor Vancza, Matteo Levantino, Serhane Zerdane, Diana Bregenholt Zederkof, Dmitry Khakhulin, Asmus Ougaard Dohn, Martin Meedom Nielsen, Kristoffer Haldrup, György Vankó","doi":"10.1063/5.0237705","DOIUrl":"https://doi.org/10.1063/5.0237705","url":null,"abstract":"<p><p>[ F e ( t e r p y ) 2 ] 2 + (terpy = 2,2':6',2″-terpyridine) is a transition metal complex where the spin state is photoswitchable and where the properties of the metal-centered quintet excited state (5MC) can be tuned by substituting different electron withdrawing or electron donating groups on the 4' position of the terpyridine. To better understand the physics determining the photoswitching performance, a deeper insight into the positions of the relevant potential energy surfaces and the molecular structure of the 5MC state is needed. We present a structural investigation based on Time Resolved x-ray Solution Scattering (TR-XSS) by which we determine the average dFe-N bond-length elongation following population of the 5MC state as well as the lifetime of this state in a series of seven modified [Fe(terpy)2]2+ systems in aqueous solution following photo-excitation. The analysis of the TR-XSS data is supported by Density Functional Theory (DFT) and Molecular Dynamics calculations. The quintet state lifetime is determined to vary by more than a factor of 10 (from 1.5 to 16 ns) based on the electron withdrawing/donating properties of the substituting group. Both the DFT calculations and the structural analysis of the experimental data show that the main photo-induced change in metal-ligand bond lengths ΔdFe-N is ∼0.2 Å for all systems.</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":"143752798","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":"Spectro-temporal symmetry in action-detected optical spectroscopy: Highlighting excited-state dynamics in large systems.","authors":"K Charvátová, P Malý","doi":"10.1063/5.0255316","DOIUrl":"https://doi.org/10.1063/5.0255316","url":null,"abstract":"<p><p>Multidimensional optical spectroscopy observes transient excitation dynamics through time evolution of spectral correlations. Its action-detected variants offer several advantages over the coherent detection and are thus becoming increasingly widespread. Nevertheless, a drawback of action-detected spectra is the presence of a stationary background of the so-called incoherent mixing of excitations from independent states that resembles a product of ground-state absorption spectra and obscures the excited-state signal. This issue is especially problematic in fluorescence-detected two-dimensional electronic spectroscopy (F-2DES) and fluorescence-detected pump-probe spectroscopy (F-PP) of extended systems, where large incoherent mixing arises from efficient exciton-exciton annihilation. In this work, we demonstrate on the example of F-2DES and F-PP an inherent spectro-temporal symmetry of action-detected spectra, which allows general, system-independent subtraction of any stationary signals including incoherent mixing. We derive the expressions for spectra with normal and reversed time ordering of the pulses, relating these to the symmetry of the system response. As we show both analytically and numerically, the difference signal constructed from spectra with normal and reversed pulse ordering is free of incoherent mixing and highlights the excited-state dynamics. We further verify the approach on the experimental F-PP spectra of a molecular squaraine heterodimer and the F-2DES spectra of the photosynthetic antenna light-harvesting complex 2 of purple bacteria. The approach is generally applicable to action-detected 2DES and pump-probe spectroscopy without experimental modifications and is independent of the studied system, enabling their application to large systems such as molecular complexes.</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":"143752867","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":"Multiphase-field approach to grain boundary- and triple junction-induced barrierless premelting of polycrystals and size-effect.","authors":"Newton, Anup Basak","doi":"10.1063/5.0254024","DOIUrl":"https://doi.org/10.1063/5.0254024","url":null,"abstract":"<p><p>Grain boundaries (GBs) and their triple junctions (TJs) induced barrierless premelting of the polycrystalline solids and length scales effect are studied using a thermodynamically and physically consistent Ginzburg-Landau type multiphase-field approach at the nanoscale. Distinct dry GB and TJ energies and GB widths are considered in contrast to the earlier phase-field studies, which assumed identical properties for the dry GBs and TJs and are far from reality. The strong effects of the intrinsic length scales, including the dry GB widths and grain size, on the temperatures of barrierless transformations between the solid, premelt (an intermediate stationary state between solid and melt with a degree of disorder) and melt, their nucleation induced by the GB network, kinetics, and complex microstructures evolution are explored, which was still missing in the literature. The thermodynamic processes involved in the melting of polycrystalline solids, which include the jump-like (discontinuous) appearance of premelt or melt pockets in the TJ regions, followed by premelting and melting of the connected GBs, curvature-driven shrinking of the grains surrounded by the melt pools and their jump-like melting at critical temperatures, all occurring at temperatures below the bulk melting point, are revealed. The reverse transformation (solidification) of the molten GB network and the bistability regime, where the temperatures for solid → premelt and premelt → solid transformations differ and yield thermal hysteresis, are studied. The role of the disjoining potential on the jump-like GB premelting and stability of the thermodynamic states is explored.</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":"143752865","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":"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":"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}

{"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":"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}