Journal of Chemical Physics最新文献

{"title":"Time-resolved vacuum-ultraviolet photoelectron spectroscopy of the Ã1Au state of acetylene.","authors":"Weronika O Razmus, Antonio Prlj, Nathan A Seifert, Matteo Bonanomi, Carlo Callegari, Miltcho Danailov, Piero Decleva, Alexander Demidovich, Giovanni De Ninno, Michele Devetta, Davide Faccialà, Raimund Feifel, Luca Giannessi, Tomislav Piteša, Ivan Powis, Lorenzo Raimondi, Katharine L Reid, Primož Rebernik Ribič, Carlo Spezzani, Richard J Squibb, James O F Thompson, Oksana Plekan, Caterina Vozzi, Emily M Warne, Marco Zangrando, Kevin C Prince, Michele Di Fraia, David M P Holland, Russell S Minns, Nađa Došlić, Stephen T Pratt","doi":"10.1063/5.0241392","DOIUrl":"https://doi.org/10.1063/5.0241392","url":null,"abstract":"<p><p>Ultrafast time-resolved photoelectron spectra are reported for the vacuum-ultraviolet (VUV) photoionization of acetylene following excitation to the Ã1Au state via UV absorption at 200 nm. The excitation energy lies above the lowest dissociation threshold to C2H X̃2Σ+ + H, as well as above the threshold for adiabatic dissociation of the Ã1Au state to form C2H (Ã2Π) + H. The time-dependent mass spectra and photoelectron spectra provide insight into the intramolecular decay processes of the Ã1Au state. In addition, photoelectron spectra of the Ã1Au state with VUV light access both the X̃2Πu and Ã2Σg+ states of the ion, as well as the predicted, but previously unobserved, 1 2Πg state, which corresponds to a two-hole, one-particle configuration that lies in close proximity to the Ã2Σg+ state. The 1 2Πg state is split into 2A2 + 2B2 and 2Ag + 2Bg states in the cis and trans configurations, respectively. Electronic structure calculations, along with trajectory calculations, reproduce the principal features of the experimental data and confirm the assignment of the 1 2Πg state.</p>","PeriodicalId":15313,"journal":{"name":"Journal of Chemical Physics","volume":"162 5","pages":""},"PeriodicalIF":3.1,"publicationDate":"2025-02-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143189699","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":"Collective dynamic length increases monotonically in pinned and unpinned glass forming systems.","authors":"Rajsekhar Das, T R Kirkpatrick, D Thirumalai","doi":"10.1063/5.0241501","DOIUrl":"https://doi.org/10.1063/5.0241501","url":null,"abstract":"<p><p>The Random First-Order Transition (RFOT) theory predicts that transport proceeds by the cooperative movement of particles in domains, whose sizes increase as a liquid is compressed above a characteristic volume fraction, ϕd. The rounded dynamical transition around ϕd, which signals a crossover to activated transport, is accompanied by a growing correlation length that is predicted to diverge at the thermodynamic glass transition density (>ϕd). Simulations and imaging experiments probed the single particle dynamics of mobile particles in response to pinning all the particles in a semi-infinite space or randomly pinning (RP) a fraction of particles in a liquid at equilibrium. The extracted dynamic length increases non-monotonically with a peak around ϕd, which not only depends on the pinning method but is also different from ϕd of the actual liquid. This finding is at variance with the results obtained using the small wavelength limit of a four-point structure factor for unpinned systems. To obtain a consistent picture of the growth of the dynamic length, one that is impervious to the use of RP, we introduce a multiparticle structure factor, Smpc(q,t), that probes collective dynamics. The collective dynamical length, calculated from the small wave vector limit of Smpc(q,t), increases monotonically as a function of the volume fraction in a glass-forming binary mixture of charged colloidal particles in both unpinned and pinned systems. This prediction, which also holds in the presence of added monovalent salt, may be validated using imaging experiments.</p>","PeriodicalId":15313,"journal":{"name":"Journal of Chemical Physics","volume":"162 5","pages":""},"PeriodicalIF":3.1,"publicationDate":"2025-02-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143189529","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":"Applicability of the thermodynamic and mechanical route to Young's equation for rigid and flexible solids: A molecular dynamics simulations study of a Lennard-Jones system model.","authors":"Fulu Zhou, Nicodemo Di Pasquale, Paola Carbone","doi":"10.1063/5.0244126","DOIUrl":"https://doi.org/10.1063/5.0244126","url":null,"abstract":"<p><p>The wetting properties of a liquid in contact with a solid are commonly described by Young's equation, which defines the relationship between the angle made by a fluid droplet onto the solid surface and the interfacial properties of the different interfaces involved. When modeling such interfacial systems, several assumptions are usually made to determine this angle of contact, such as a completely rigid solid or the use of the tension at the interface instead of the surface free energy. In this work, we perform molecular dynamics simulations of a Lennard-Jones liquid in contact with a Lennard-Jones crystal and compare the contact angles measured from a droplet simulation with those calculated using Young's equation based on surface free energy or surface stress. We analyze cases where the solid atoms are kept frozen in their positions and where they are allowed to relax and simulate surfaces with different wettability and degrees of softness. Our results show that using either surface free energy or surface stress in Young's equation leads to similar contact angles but different interfacial properties. We find that the approximation of keeping the solid atoms frozen must be done carefully, especially if the liquid can efficiently pack at the interface. Finally, we show that to correctly reproduce the measured contact angles when the solid becomes soft, the quantity to be used in Young's equation is the surface free energy only and that the error committed in using the surface stress becomes larger as the softness of the solid increases.</p>","PeriodicalId":15313,"journal":{"name":"Journal of Chemical Physics","volume":"162 5","pages":""},"PeriodicalIF":3.1,"publicationDate":"2025-02-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143255722","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":"Growth of crystalline thin films of picene on semimetallic Bi(111) surface.","authors":"Shi-Run Fu, Tao Yu, Ting-Ting Zhang, Xiao-Tian Yang, Kai Sun, Min-Long Tao, Ji-Yong Yang, Jun-Zhong Wang","doi":"10.1063/5.0247758","DOIUrl":"https://doi.org/10.1063/5.0247758","url":null,"abstract":"<p><p>We report the scanning tunneling microscopy/spectroscopy (STM/STS) studies on structural and electronic properties of picene films grown on the semimetallic Bi(111) substrate held at different temperatures. Under room-temperature deposition, the picene molecules form a crystalline (001) monolayer with the standing-up orientation, indicating the weak molecule-substrate interaction. When deposited on the Bi(111) substrate held at 150 K, picene molecules form a bulk-like (211̄ monolayer with building blocks of picene trimers. High-resolution STM images reveal that each trimer consists of two tilted molecules and one side-on molecule. Further reducing the deposition temperature to 90 K leads to the formation of nanostripe arrays, in which the side-on molecules adopt the π-π stacking. STS measurements demonstrate that the crystalline (001) monolayer of picene exhibits a larger gap compared with picene crystals, which can be attributed to the decoupling of the upright standing molecules from the semimetallic Bi(111) substrate.</p>","PeriodicalId":15313,"journal":{"name":"Journal of Chemical Physics","volume":"162 5","pages":""},"PeriodicalIF":3.1,"publicationDate":"2025-02-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143189513","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 temperature melting of dense molecular hydrogen from machine-learning interatomic potentials trained on quantum Monte Carlo.","authors":"Shubhang Goswami, Scott Jensen, Yubo Yang, Markus Holzmann, Carlo Pierleoni, David M Ceperley","doi":"10.1063/5.0250686","DOIUrl":"https://doi.org/10.1063/5.0250686","url":null,"abstract":"<p><p>We present results and discuss methods for computing the melting temperature of dense molecular hydrogen using a machine learned model trained on quantum Monte Carlo data. In this newly trained model, we emphasize the importance of accurate total energies in the training. We integrate a two phase method for estimating the melting temperature with estimates from the Clausius-Clapeyron relation to provide a more accurate melting curve from the model. We make detailed predictions of the melting temperature, solid and liquid volumes, latent heat, and internal energy from 50 to 180 GPa for both classical hydrogen and quantum hydrogen. At pressures of roughly 173 GPa and 1635 K, we observe molecular dissociation in the liquid phase. We compare with previous simulations and experimental measurements.</p>","PeriodicalId":15313,"journal":{"name":"Journal of Chemical Physics","volume":"162 5","pages":""},"PeriodicalIF":3.1,"publicationDate":"2025-02-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143189540","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":"Molecular dynamics investigation of structural, thermal, and dynamic properties of maghemite through thermal cycling.","authors":"Shalmali Sudhindra, Niroj Kumar Sahu, Bruno D'Aguanno","doi":"10.1063/5.0248660","DOIUrl":"https://doi.org/10.1063/5.0248660","url":null,"abstract":"<p><p>We analyzed the thermal, structural, and dynamic properties of maghemite using classical molecular dynamics, focusing on bulk and nanoparticle systems. We explored their behavior when heated to high temperatures (above the melting point) and during cooling, as well as under thermal cycles ending at intermediate temperatures. Our findings show that in the bulk system, both the tetrahedral and octahedral iron sub-lattices undergo a phase transition prior to melting. Cooling the system from above this transition, or from above the melting point, leads to the formation of different metastable maghemite structures. In contrast, this sub-lattice transition is absent in nanoparticles, where melting occurs through an interface-mediated process. At temperatures just above the transition, nanoparticles adopt an ellipsoidal shape, which is retained during cooling. In addition, the specific heat of both bulk and nanoparticle systems at temperatures above the Debye temperature is evaluated and compared with the available experimental data. Overall, our results highlight the complex thermal behavior of maghemite across a range of temperatures, which remains insufficiently explored experimentally. Further experimental investigations could also provide valuable feedback for model refinements.</p>","PeriodicalId":15313,"journal":{"name":"Journal of Chemical Physics","volume":"162 4","pages":""},"PeriodicalIF":3.1,"publicationDate":"2025-01-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143047006","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":"Rationalizing protein-ligand interactions via the effective fragment potential method and structural data from classical molecular dynamics.","authors":"Andres S Urbina, Lyudmila V Slipchenko","doi":"10.1063/5.0247878","DOIUrl":"10.1063/5.0247878","url":null,"abstract":"<p><p>The Effective Fragment Potential (EFP) method, a polarizable quantum mechanics-based force field for describing non-covalent interactions, is utilized to calculate protein-ligand interactions in seven inactive cyclin-dependent kinase 2-ligand complexes, employing structural data from molecular dynamics simulations to assess dynamic and solvent effects. Our results reveal high correlations between experimental binding affinities and EFP interaction energies across all the structural data considered. Using representative structures found by clustering analysis and excluding water molecules yields the highest correlation (R2 of 0.95). In addition, the EFP pairwise interaction energy decomposition analysis identifies critical interactions between the ligands and protein residues and provides insight into their nature. Overall, this study indicates the potential applications of the EFP method in structure-based drug design.</p>","PeriodicalId":15313,"journal":{"name":"Journal of Chemical Physics","volume":"162 4","pages":""},"PeriodicalIF":3.1,"publicationDate":"2025-01-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11774556/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143046140","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":"Nature and stability of the chemical bond in H3C-XHn (XHn = CH3, NH2, OH, F, Cl, Br, I).","authors":"Pascal Vermeeren, F Matthias Bickelhaupt","doi":"10.1063/5.0245218","DOIUrl":"https://doi.org/10.1063/5.0245218","url":null,"abstract":"<p><p>We have quantum chemically analyzed the trends in bond dissociation enthalpy (BDE) of H3C-XHn single bonds (XHn = CH3, NH2, OH, F, Cl, Br, I) along three different dissociation pathways at ZORA-BLYP-D3(BJ)/TZ2P: (i) homolytic dissociation into H3C∙ + ∙XHn, (ii) heterolytic dissociation into H3C+ + -XHn, and (iii) heterolytic dissociation into H3C- + +XHn. The associated BDEs for the three pathways differ not only quantitatively but, in some cases, also in terms of opposite trends along the C-X series. Based on activation strain analyses and quantitative molecular orbital theory, we explain how these differences are caused by the profoundly different electronic structures of, and thus bonding mechanisms between, the resulting fragments in the three different dissociation pathways. We demonstrate that the nature and strength of a chemical bond are only fully defined when considering both (i) the molecule in which the bond exists and (ii) the fragments from which it forms or into which it dissociates.</p>","PeriodicalId":15313,"journal":{"name":"Journal of Chemical Physics","volume":"162 4","pages":""},"PeriodicalIF":3.1,"publicationDate":"2025-01-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143045904","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":"Decoherence and vibrational energy relaxation of the electronically excited PtPOP complex in solution.","authors":"Benedikt O Birgisson, Asmus Ougaard Dohn, Hannes Jónsson, Gianluca Levi","doi":"10.1063/5.0241573","DOIUrl":"https://doi.org/10.1063/5.0241573","url":null,"abstract":"<p><p>Understanding the ultrafast vibrational relaxation following photoexcitation of molecules in a condensed phase is essential to predict the outcome and improve the efficiency of photoinduced molecular processes. Here, the vibrational decoherence and energy relaxation of a binuclear complex, [Pt2(P2O5H2)4]4- (PtPOP), upon electronic excitation in liquid water and acetonitrile are investigated through direct adiabatic dynamics simulations. A quantum mechanics/molecular mechanics (QM/MM) scheme is used where the excited state of the complex is modeled with orbital-optimized density functional calculations while solvent molecules are described using potential energy functions. The decoherence time of the Pt-Pt vibration dominating the photoinduced dynamics is found to be ∼1.6 ps in both solvents. This is in excellent agreement with experimental measurements in water, where intersystem crossing is slow (>10 ps). Pathways for the flow of excess energy are identified by monitoring the power of the solvent on vibrational modes. The latter are obtained as generalized normal modes from the velocity covariances, and the power is computed using QM/MM embedding forces. Excess vibrational energy is found to be predominantly released through short-range repulsive and attractive interactions between the ligand atoms and surrounding solvent molecules, whereas solute-solvent interactions involving the Pt atoms are less important. Since photoexcitation deposits most of the excess energy into Pt-Pt vibrations, energy dissipation to the solvent is inefficient. This study reveals the mechanism behind the exceptionally long vibrational coherence of the photoexcited PtPOP complex in solution and underscores the importance of short-range interactions for accurate simulations of vibrational energy relaxation of solvated molecules.</p>","PeriodicalId":15313,"journal":{"name":"Journal of Chemical Physics","volume":"162 4","pages":""},"PeriodicalIF":3.1,"publicationDate":"2025-01-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143052523","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":"How well do empirical molecular mechanics force fields model the cholesterol condensing effect?","authors":"J Sawdon, T J Piggot, J W Essex","doi":"10.1063/5.0238409","DOIUrl":"https://doi.org/10.1063/5.0238409","url":null,"abstract":"<p><p>Membrane properties are determined in part by lipid composition, and cholesterol plays a large role in determining these properties. Cellular membranes show a diverse range of cholesterol compositions, the effects of which include alterations to cellular biomechanics, lipid raft formation, membrane fusion, signaling pathways, metabolism, pharmaceutical therapeutic efficacy, and disease onset. In addition, cholesterol plays an important role in non-cellular membranes, with its concentration in the skin lipid matrix being implicated in several skin diseases. In phospholipid membranes, cholesterol increases the tail ordering of neighboring lipids, decreasing the membrane lateral area and increasing the thickness. This reduction in the lateral area, known as the cholesterol condensing effect, results from cholesterol-lipid mixtures deviating from ideal mixing. Capturing the cholesterol condensing effect is crucial for molecular dynamics simulations as it directly affects the accuracy of predicted membrane properties, which are essential for understanding membrane function. We present a comparative analysis of cholesterol models across several popular force fields: CHARMM36, Slipids, Lipid17, GROMOS 53A6L, GROMOS-CKP, MARTINI 2, MARTINI 3, and ELBA. The simulations of 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC) and 1,2-dioleoyl-sn-glycero-3-phosphocholine (DOPC) membranes with varying cholesterol concentrations were conducted to calculate the partial-molecular areas of cholesterol and other condensing parameters, which are compared to the experimental data for validation. While all tested force fields predict small negative deviations from ideal mixing in cholesterol-DOPC membranes, only all-atom force fields capture the larger deviations expected in DMPC membranes. United-atom and coarse-grained models under-predict this effect, condensing fewer neighboring lipids by smaller magnitudes, resulting in too small deviations from ideal mixing. These results suggest that all-atom force fields, particularly CHARMM36 or Slipids, should be used for accurate simulations of cholesterol-containing membranes.</p>","PeriodicalId":15313,"journal":{"name":"Journal of Chemical Physics","volume":"162 4","pages":""},"PeriodicalIF":3.1,"publicationDate":"2025-01-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143052560","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}