The Journal of Chemical Physics最新文献

{"title":"Interactions of adsorbing cosolutes with hydrophobic hydration shells","authors":"Swaminath Bharadwaj, Madhusmita Tripathy, Nico F. A. van der Vegt","doi":"10.1063/5.0207075","DOIUrl":"https://doi.org/10.1063/5.0207075","url":null,"abstract":"The analysis of water density fluctuations in the hydration shell of nonpolar solutes provides insights into water-mediated interactions, especially hydrophobic interactions. These fluctuations are sensitive to small perturbations due to changes in thermodynamic conditions, such as temperature and pressure, but also to the presence of cosolutes, such as salts or small organic molecules. Herein, we investigate the effect of two classes of adsorbing cosolutes, using urea and methanol as representatives, on the fluctuations in energy and solvent density within the solvation shell of a model extended hydrophobic solute. We focus on the interactions of the cosolutes with the hydrophobic hydration shell, rather than with the solute itself, which though important remain largely unexplored. We calculate and analyze the interfacial partial molar energy of the cosolute, using a methodology based on the small system method. This approach provides correlated solvent density and energy fluctuations and allows us to decompose them into contributions due to interactions between the different components present in the solvation shell of the solute. The results show that adsorbed urea molecules interact more favorably with water than nonadsorbed urea molecules, which leads to the attenuation of interfacial density fluctuations and thus to the stabilization of the solvation shell. By contrast, the adsorbed methanol molecules interact preferably with other methanol molecules in the solvation shell, leading to a nano-phase segregated structure, which enhances interfacial fluctuations.","PeriodicalId":501648,"journal":{"name":"The Journal of Chemical Physics","volume":"171 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-04-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140837369","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Interoperable workflows by exchanging grid-based data between quantum-chemical program packages","authors":"Kevin Focke, Matteo De Santis, Mario Wolter, Jessica A. Martinez B, Valérie Vallet, André Severo Pereira Gomes, Małgorzata Olejniczak, Christoph R. Jacob","doi":"10.1063/5.0201701","DOIUrl":"https://doi.org/10.1063/5.0201701","url":null,"abstract":"Quantum-chemical subsystem and embedding methods require complex workflows that may involve multiple quantum-chemical program packages. Moreover, such workflows require the exchange of voluminous data that go beyond simple quantities, such as molecular structures and energies. Here, we describe our approach for addressing this interoperability challenge by exchanging electron densities and embedding potentials as grid-based data. We describe the approach that we have implemented to this end in a dedicated code, PyEmbed, currently part of a Python scripting framework. We discuss how it has facilitated the development of quantum-chemical subsystem and embedding methods and highlight several applications that have been enabled by PyEmbed, including wave-function theory (WFT) in density-functional theory (DFT) embedding schemes mixing non-relativistic and relativistic electronic structure methods, real-time time-dependent DFT-in-DFT approaches, the density-based many-body expansion, and workflows including real-space data analysis and visualization. Our approach demonstrates, in particular, the merits of exchanging (complex) grid-based data and, in general, the potential of modular software development in quantum chemistry, which hinges upon libraries that facilitate interoperability.","PeriodicalId":501648,"journal":{"name":"The Journal of Chemical Physics","volume":"30 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-04-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140837191","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Ultrafast photochemistry and electron-diffraction spectra in n → (3s) Rydberg excited cyclobutanone resolved at the multireference perturbative level","authors":"V. K. Jaiswal, F. Montorsi, F. Aleotti, F. Segatta, Daniel Keefer, Shaul Mukamel, A. Nenov, I. Conti, M. Garavelli","doi":"10.1063/5.0203624","DOIUrl":"https://doi.org/10.1063/5.0203624","url":null,"abstract":"We study the ultrafast time evolution of cyclobutanone excited to the singlet n → Rydberg state through non-adiabatic surface-hopping simulationsperformed at extended multi-state complete active space second-order perturbation (XMS-CASPT2) level of theory. These dynamics predict relaxation to the ground-state with a timescale of 822 ± 45 fs with minimal involvement of the triplets. The major relaxation path to the ground-state involves a three-state degeneracy region and leads to a variety of fragmented photoproducts. We simulate the resulting time-resolved electron-diffraction spectra, which track the relaxation of the excited state and the formation of various photoproducts in the ground state.","PeriodicalId":501648,"journal":{"name":"The Journal of Chemical Physics","volume":"38 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-04-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140837354","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Formation of the oxyl’s potential energy surface by the spectral kinetics of a vibrational mode","authors":"James Stewart, Paul Zayka, Christen Courter, Tanja Cuk","doi":"10.1063/5.0202441","DOIUrl":"https://doi.org/10.1063/5.0202441","url":null,"abstract":"One of the most reactive intermediates for oxidative reactions is the oxyl radical, an electron-deficient oxygen atom. The discovery of a new vibration upon photoexcitation of the oxygen evolution catalysis detected the oxyl radical at the SrTiO3 surface. The vibration was assigned to a motion of the sub-surface oxygen underneath the titanium oxyl (Ti–O●−) created upon hole transfer to (or electron extraction from) a hydroxylated surface site. Evidence for such an interfacial mode is derived from its spectral shape, which exhibited a Fano resonance—a coupling of a sharp normal mode to continuum excitations. Here, this Fano resonance is utilized to derive precise formation kinetics of the oxyl radical and its associated potential energy surface (PES). From the Fano lineshape, the formation kinetics are obtained from the anti-resonance (the kinetics of the coupling factor), the resonance (the kinetics of the coupled continuum excitations), and the frequency integrated spectrum (the kinetics of the normal mode’s cross-section). All three perspectives yield logistic function growth with a half-rise of 2.3 ± 0.3 ps and a time constant of 0.48 ± 0.09 ps. A non-equilibrium transient associated with photoexcitation is separated from the rise of the equilibrated PES. The logistic function characterizes the oxyl coverage at the very initial stages (t ∼ 0) to have an exponential growth rate that quickly decreases toward zero as a limiting coverage is reached. Such time-dependent reaction kinetics identify a dynamic activation barrier associated with the formation of a PES and quantify it for oxyl radical coverage.","PeriodicalId":501648,"journal":{"name":"The Journal of Chemical Physics","volume":"21 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-04-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140837193","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"First-principles design of heavy-atom-free singlet oxygen photosensitizers for photodynamic therapy","authors":"Arun K. Pal, Ayan Datta","doi":"10.1063/5.0196557","DOIUrl":"https://doi.org/10.1063/5.0196557","url":null,"abstract":"In photodynamic therapy (PDT) treatment, heavy-atom-free photosensitizers (PSs) are a great source of singlet oxygen photosensitizer. Reactive oxygen species (ROS) are produced by an energy transfer from the lowest energy triplet excited state to the molecular oxygen of cancer cells. To clarify the photophysical characteristics in the excited states of a few experimentally identified thionated (>C=S) molecules and their oxygenated congeners (>C=O), a quantum chemical study is conducted. This study illustrates the properties of the excited states in oxygen congeners that render them unsuitable for PDT treatment. Concurrently, a hierarchy is presented based on the utility of the lowest-energy triplet excitons of thionated compounds. Their non-radiative decay rates are calculated for reverse-ISC and inter-system crossover (ISC) processes. In addition, the vibronic importance of C=O and C=S bonds is clarified by the computation of the Huang–Rhys factor, effective vibrational mode, and reorganization energy inside the Marcus–Levich–Jörtner system. ROS generation in thionated PSs exceeds their oxygen congeners as kf ≪ kISC, where radiative decay rate is designated as kf. As a result, the current work offers a calculated strategy for analyzing the effectiveness of thionated photosensitizers in PDT.","PeriodicalId":501648,"journal":{"name":"The Journal of Chemical Physics","volume":"60 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-04-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140810585","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Structural dynamics of the heme pocket and intersubunit coupling in the dimeric hemoglobin from Scapharca inaequivalvis.","authors":"Xiang Gao, M. Mizuno, H. Ishikawa, Srinivasan Muniyappan, H. Ihee, Y. Mizutani","doi":"10.1063/5.0203594","DOIUrl":"https://doi.org/10.1063/5.0203594","url":null,"abstract":"Cooperativity is essential for the proper functioning of numerous proteins by allosteric interactions. Hemoglobin from Scapharca inaequivalvis (HbI) is a homodimeric protein that can serve as a minimal unit for studying cooperativity. We investigated the structural changes in HbI after carbon monoxide dissociation using time-resolved resonance Raman spectroscopy and observed structural rearrangements in the Fe-proximal histidine bond, the position of the heme in the pocket, and the hydrogen bonds between heme and interfacial water upon ligand dissociation. Some of the spectral changes were different from those observed for human adult hemoglobin due to differences in subunit assembly and quaternary changes. The structural rearrangements were similar for the singly and doubly dissociated species but occurred at different rates. The rates of the observed rearrangements indicated that they occurred synchronously with subunit rotation and are influenced by intersubunit coupling, which underlies the positive cooperativity of HbI.","PeriodicalId":501648,"journal":{"name":"The Journal of Chemical Physics","volume":"53 8","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-04-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140652036","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Prediction of the univariant two-phase coexistence line of the tetrahydrofuran hydrate from computer simulation.","authors":"J. Algaba, C. Romero-Guzmán, Miguel J Torrejón, F. J. Blas","doi":"10.1063/5.0206109","DOIUrl":"https://doi.org/10.1063/5.0206109","url":null,"abstract":"In this work, the univariant two-phase coexistence line of the tetrahydrofuran (THF) hydrate is determined from 100 to 1000 bar by molecular dynamics simulations. This study is carried out by putting in contact a THF hydrate phase with a stoichiometric aqueous solution phase. Following the direct coexistence technique, the pressure is fixed, and the coexistence line is determined by analyzing if the hydrate phase grows or melts at different values of temperature. Water is described using the well-known TIP4P/Ice model. We have used two different models of THF based on the transferable parameters for phase equilibria-united atom approach (TraPPE-UA), the original (flexible) TraPPe-UA model and a rigid and planar version of it. Overall, at high pressures, small differences are observed in the results obtained by both models. However, large differences are observed in the computational efforts required by the simulations performed using both models, being the rigid and planar version much faster than the original one. The effect of the unlike dispersive interactions between the water and THF molecules is also analyzed at 250 bar using the rigid and planar THF model. In particular, we modify the Berthelot combining rule via a parameter ξO-THF that controls the unlike water-THF dispersive interactions. We analyze the effect on the dissociation temperature of the hydrate when ξO-THF is modified from 1.0 (original Berthelot combining rule) to 1.4 (modified Berthelot combining rule). We use the optimized value ξO-THF = 1.4 and the rigid THF model in a transferable way to predict the dissociation temperatures at other pressures. We find excellent agreement between computer simulation predictions and experimental data taken from the literature.","PeriodicalId":501648,"journal":{"name":"The Journal of Chemical Physics","volume":"54 5","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-04-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140652031","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Symmetry-breaking charge separation in a null-excitonic 3-dimensional rigid nonconjugated trimer.","authors":"Kangwei Wang, Xingyu Chen, Shaoqian Peng, Guijie Liang, Jingwen Xu, Lei Zhang, Di Wu, Jianlong Xia","doi":"10.1063/5.0195384","DOIUrl":"https://doi.org/10.1063/5.0195384","url":null,"abstract":"Photoinduced symmetry-breaking charge separation (SB-CS) has been extensively observed in various oligomers and aggregates, which holds great potential for robust artificial solar energy conversion systems. It attaches great importance to the precise manipulation of interchromophore electronic coupling in realizing efficient SB-CS. The emerging studies on SB-CS suggested that it could be realized in null-excitonic aggregates, and a long-lived SB-CS state was observed, which offers an advanced platform and has gathered immense attention in the SB-CS field. Here, we unveiled the null-exciton coupling induced ultrafast SB-CS in a rigid polycyclic aromatic hydrocarbon framework, triperyleno[3,3,3]propellane triimides (TPPTI), in which three chromophores were attached through a nonconjugated bridge. Through a combination of theoretical calculations and steady-state absorption results, we demonstrated that this nonconjugated TPPTI possesses negligible exciton coupling. Increased solvent polarity was found to significantly enhance state mixing between local excited and charge transfer states. Using transient absorption spectroscopy, ultrafast SB-CS was observed in highly polar dimethylformamide, facilitated by a selective hole-transfer coupling and a favorable charge separation free energy (ΔGCS). Additionally, the rate ratio between SB-CS and charge recombination was at least high to 1800 in dimethylformamide. This investigation provides profound insights into the role of null-exciton coupling in dominating ultrafast SB-CS in multichromophoric systems.","PeriodicalId":501648,"journal":{"name":"The Journal of Chemical Physics","volume":"53 12","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-04-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140652033","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"NH3 adsorption and competition with H2O on a hydroxylated aluminosilicate surface.","authors":"Giada Franceschi, Andrea Conti, Luca Lezuo, R. Abart, F. Mittendorfer, M. Schmid, Ulrike Diebold","doi":"10.1063/5.0202573","DOIUrl":"https://doi.org/10.1063/5.0202573","url":null,"abstract":"The interaction between ammonia (NH3) and (alumino)silicates is of fundamental and applied importance, yet the specifics of NH3 adsorption on silicate surfaces remain largely unexplored, mainly because of experimental challenges related to their electrically insulating nature. An example of this knowledge gap is evident in the context of ice nucleation on silicate dust, wherein the role of NH3 for ice nucleation remains debated. This study explores the fundamentals of the interaction between NH3 and microcline feldspar (KAlSi3O8), a common aluminosilicate with outstanding ice nucleation abilities. Atomically resolved non-contact atomic force microscopy, x-ray photoelectron spectroscopy, and density functional theory-based calculations elucidate the adsorption geometry of NH3 on the lowest-energy surface of microcline, the (001) facet, and its interplay with surface hydroxyls and molecular water. NH3 and H2O are found to adsorb molecularly in the same adsorption sites, creating H-bonds with the proximate surface silanol (Si-OH) and aluminol (Al-OH) groups. Despite the closely matched adsorption energies of the two molecules, NH3 readily yields to replacement by H2O, challenging the notion that ice nucleation on microcline proceeds via the creation of an ordered H2O layer atop pre-adsorbed NH3 molecules.","PeriodicalId":501648,"journal":{"name":"The Journal of Chemical Physics","volume":"53 3","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-04-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140652136","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Probing the electronic structure and ground state symmetry of gas phase C60+ via VUV photoionization and comparison with theory.","authors":"H. R. Hrodmarsson, M. Rapacioli, F. Spiegelman, Gustavo A Garcia, J. Bouwman, L. Nahon, H. Linnartz","doi":"10.1063/5.0203004","DOIUrl":"https://doi.org/10.1063/5.0203004","url":null,"abstract":"Recently, some of us reviewed and studied the photoionization dynamics of C60 that are of great interest to the astrochemical community as four of the diffuse interstellar bands (DIBs) have been assigned to electronic transitions in the C60+ cation. Our previous analysis of the threshold photoelectron spectrum (TPES) of C60 [Hrodmarsson et al., Phys. Chem. Chem. Phys. 22, 13880-13892 (2020)] appeared to give indication of D3d ground state symmetry, in contrast to theoretical predictions of D5d symmetry. Here, we revisit our original measurements taking account of a previous theoretical spectrum presented in the work of Manini et al., Phys. Rev. Lett. 91(19), 196402 (2003), obtained within a vibronic model parametrized on density functional theory/local-density approximation electronic structure involving all hg Jahn-Teller active modes, which couple to the 2Hu components of the ground state of the C60+ cation. By reanalyzing our measured TPES of the ground state of the C60 Buckminsterfullerene, we find a striking resemblance to the theoretical spectrum calculated in the work of Manini et al., Phys. Rev. Lett. 91(19), 196402 (2003), and we provide assignments for many of the hg modes. In order to obtain deeper insights into the temperature effects and possible anharmonicity effects, we provide complementary modeling of the photoelectron spectrum via classical molecular dynamics (MD) involving density functional based tight binding (DFTB) computations of the electronic structure for both C60 and C60+. The validity of the DFTB modeling is first checked vs the IR spectra of both species which are well established from IR spectroscopic studies. To aid the interpretation of our measured TPES and the comparisons to the ab initio spectrum we showcase the complementarity of utilizing MD calculations to predict the PES evolution at high temperatures expected in our experiment. The comparison with the theoretical spectrum presented in the work of Manini et al., Phys. Rev. Lett. 91(19), 196402 (2003), furthermore, provides further evidence for a D5d symmetric ground state of the C60+ cation in the gas phase, in complement to IR spectroscopy in frozen noble gas matrices. This not only allows us to assign the first adiabatic ionization transition and thus determine the ionization energy of C60 with greater accuracy than has been achieved at 7.598 ± 0.005 eV, but we also assign the two lowest excited states (2E1u and 2E2u) which are visible in our TPES. Finally, we discuss the energetics of additional DIBs that could be assigned to C60+ in the future.","PeriodicalId":501648,"journal":{"name":"The Journal of Chemical Physics","volume":"53 4","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-04-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140652135","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}