Journal of Chemical Physics最新文献_第10页

Time-dependent quantum dynamics of NO(X) + Ar: Rotational excitation pathways and comparison with mixed quantum/classical theory. NO(X) + Ar的时间依赖量子动力学：旋转激发途径和与混合量子/经典理论的比较。

IF 3.7 2区化学

Journal of Chemical Physics Pub Date : 2026-10-07 DOI: 10.1063/5.0355623

Christopher Robertson, Matthew Strutton, Max McCrea, Dulat Bostan, Dmitri Babikov, Matthew L Costen, Mark Brouard, Martin J Paterson

{"title":"Time-dependent quantum dynamics of NO(X) + Ar: Rotational excitation pathways and comparison with mixed quantum/classical theory.","authors":"Christopher Robertson, Matthew Strutton, Max McCrea, Dulat Bostan, Dmitri Babikov, Matthew L Costen, Mark Brouard, Martin J Paterson","doi":"10.1063/5.0355623","DOIUrl":"https://doi.org/10.1063/5.0355623","url":null,"abstract":"We present time-dependent quantum wavepacket simulations of inelastic NO(X) + Ar collisions using the Multi-Configurational Time-Dependent Hartree (MCTDH) method. The computed state-to-state cross sections and opacity functions agree well with time-independent close-coupled calculations. The time-dependent populations and rotational couplings provide a dynamical perspective on the well-known propensity behavior of this near-homonuclear system. In particular, they reveal how the established interplay between parity-conserving Δj = 2 and parity-breaking Δj = 1 coupling pathways develops during the collision to produce the inverse propensity. A particular emphasis is placed on comparison with mixed quantum/classical theory (MQCT), which previously offered a time-resolved, trajectory-based interpretation of the inverted rotational-population pattern. By broadening the time-dependent MQCT rotational populations to reflect the quantum packet's inherent spread in arrival times, we recover the broad sequence of parity-dependent growth seen in MCTDH, although the detailed long-time populations of individual channels differ somewhat between the two methods. Nevertheless, the wavepacket dynamics support the broad mechanistic interpretation obtained from MQCT while providing a rigorous account of the coupling and excitation process.","PeriodicalId":15313,"journal":{"name":"Journal of Chemical Physics","volume":"165 13","pages":""},"PeriodicalIF":3.7,"publicationDate":"2026-10-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149110279","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}

引用次数: 0

Molecular dynamics simulation and QM/MM study of IscB-ωRNA complex. IscB-ωRNA复合物的分子动力学模拟及QM/MM研究。

IF 3.7 2区化学

Journal of Chemical Physics Pub Date : 2026-10-07 DOI: 10.1063/5.0350765

Amina Abula, Ganggang Bai, Jingjing Li, Buyong Ma

{"title":"Molecular dynamics simulation and QM/MM study of IscB-ωRNA complex.","authors":"Amina Abula, Ganggang Bai, Jingjing Li, Buyong Ma","doi":"10.1063/5.0350765","DOIUrl":"https://doi.org/10.1063/5.0350765","url":null,"abstract":"The CRISPR-Cas9 system's gene-editing fidelity relies on the HNH nuclease domain's ability to hydrolyze DNA via metal-ion catalysis. While IscB-ωRNA variants offer advantages for viral delivery due to their small size, their editing efficiency is much lower than that of Cas9. The understanding of how HNH-domain dynamics and metal-ion selection jointly control catalysis is essential for its rational improvement. Here, we employ molecular dynamics (MD) simulations, quantum mechanics/molecular mechanics (QM/MM) simulations, and free energy perturbations (FEP) to study the conformation dynamics of the IscB-ωRNA-target DNA complex and cation binding energy in the core HNH(IscB)-DNA region. Our MD simulations revealed that the IscB-ωRNA-DNA complex is overall stable. However, the core HNH(IscB)-DNA region shifts to a larger separation, consistent with recent findings of coupling between HNH motion and activation in IscB-ωRNA-DNA. However, the HNH domain motion may be decreased by Cas9-like H246D/H270N mutations. QM/MM and FEP studies found that three Cas9 activating ions, Mg2+, Mn2+, and Co2+, also have higher binding energy in the mutated HNH(IscB)-DNA region, suggesting that the catalytic efficiencies of IscB-ωRNA could be subjected to the balance between stabilizing ion binding and domain motions.","PeriodicalId":15313,"journal":{"name":"Journal of Chemical Physics","volume":"165 13","pages":""},"PeriodicalIF":3.7,"publicationDate":"2026-10-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149110338","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}

引用次数: 0

Temperature-dependent UV photodissociation cross sections and rates of CH. 温度依赖的紫外光解截面和CH的速率。

IF 3.7 2区化学

Journal of Chemical Physics Pub Date : 2026-10-07 DOI: 10.1063/5.0354189

Di Liu, Qinghui Wei, Hans Ågren, Boris F Minaev, Bing Yan

{"title":"Temperature-dependent UV photodissociation cross sections and rates of CH.","authors":"Di Liu, Qinghui Wei, Hans Ågren, Boris F Minaev, Bing Yan","doi":"10.1063/5.0354189","DOIUrl":"https://doi.org/10.1063/5.0354189","url":null,"abstract":"CH+ is an important reactive molecular ion in the interstellar medium with photodissociation properties that are essential for understanding its formation and destruction in UV-irradiated environments. In this work, high-level MRCI+Q calculations were performed for 18 singlet and triplet states correlating with the six lowest dissociation limits. The resulting potential energy curves, transition dipole moment curves, spin-orbit couplings, and electronic angular momentum couplings were employed to calculate the internal partition functions and the rovibrationally resolved photoabsorption and direct photodissociation cross sections. The results show that photoabsorption by CH+ is dominated by the bound-bound X1Σ+-A1Π transition system, whereas photodissociation is primarily controlled by transitions from the ground state to repulsive excited states, with the X1Σ+-E1Σ+ and X1Σ+-C1Σ+ channels providing the dominant contributions. The positions of the principal photodissociation features are generally consistent with those reported in the Leiden database. Using the cross sections evaluated under local thermodynamic equilibrium, we further determined the photodissociation rates of CH+ under the standard interstellar radiation field and blackbody radiation conditions. The calculated rates exhibit a pronounced dependence on molecular temperature. These results provide valuable molecular data for astrochemical modeling of CH+ activity in ultraviolet-irradiated environments.","PeriodicalId":15313,"journal":{"name":"Journal of Chemical Physics","volume":"165 13","pages":""},"PeriodicalIF":3.7,"publicationDate":"2026-10-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149110311","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}

引用次数: 0

Computational x-ray absorption spectroscopy of gold nanoclusters. 金纳米团簇的计算x射线吸收光谱。

IF 3.7 2区化学

Journal of Chemical Physics Pub Date : 2026-10-07 DOI: 10.1063/5.0348763

M Laborenz, S Malola, H Häkkinen

{"title":"Computational x-ray absorption spectroscopy of gold nanoclusters.","authors":"M Laborenz, S Malola, H Häkkinen","doi":"10.1063/5.0348763","DOIUrl":"https://doi.org/10.1063/5.0348763","url":null,"abstract":"Gold nanoclusters (NCs) are tiny molecules with a gold core protected by an organic ligand layer. They possess a wide range of applications, facilitated by their designability at the atomistic level. They are used in catalysis, bioimaging, biosensing, drug delivery, or as optical waveguides. X-ray absorption spectroscopy (XAS) can provide information about orbital specific density of states, oxidation states, core electron binding energies, and the bonding types occurring in molecules and nanoclusters. Interpreting these data at a single atom level needs a detailed and trustworthy approach to simulate the XAS properties of NCs atom by atom. Here, we investigate L-edge x-ray absorption near edge spectroscopy for various ligand-protected gold NCs (Au13, Au22, Au44, Au102, and Au144) protected by chemically diverse ligand molecules and interpret details of their electronic structure. We show that XAS properties of gold atoms inside these clusters are very diverse depending on their chemical environment and symmetry. Our work deepens the understanding of spatial variations of local oxidation states, charge distributions, and chemical bonding environments of gold atoms inside ligand-protected clusters, highlighting the impact of diverse ligand environments.","PeriodicalId":15313,"journal":{"name":"Journal of Chemical Physics","volume":"165 13","pages":""},"PeriodicalIF":3.7,"publicationDate":"2026-10-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149110362","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}

引用次数: 0

Hydrodynamics substantially affects induced structure formation in magnetic fluids. 流体力学实质上影响磁流体中诱导结构的形成。

IF 3.7 2区化学

Journal of Chemical Physics Pub Date : 2026-10-07 DOI: 10.1063/5.0343876

Henning Reinken, Markus Heiber, Takeaki Araki, Andreas M Menzel

引用次数: 0

Polymer-residue accessibility shapes sequence dependence of critical temperatures for phase separation. 聚合物残基可及性决定了相分离临界温度的序列依赖性。

IF 3.7 2区化学

Journal of Chemical Physics Pub Date : 2026-10-07 DOI: 10.1063/5.0348493

J Pedro de Souza, Benjamin Sorkin, Amala Akkiraju, Athanassios Z Panagiotopoulos, Howard A Stone

{"title":"Polymer-residue accessibility shapes sequence dependence of critical temperatures for phase separation.","authors":"J Pedro de Souza, Benjamin Sorkin, Amala Akkiraju, Athanassios Z Panagiotopoulos, Howard A Stone","doi":"10.1063/5.0348493","DOIUrl":"https://doi.org/10.1063/5.0348493","url":null,"abstract":"Biological polymers, such as intrinsically disordered proteins, play a central role in cellular biology, including mediating phase separation and controlling activity of biological condensates. The physical properties and functions of biopolymers are determined by their residue sequence. Recently, significant computational and theoretical efforts have been devoted to characterizing the combinatorially complex sequence dependence of biopolymer phase diagrams. Here, we quantitatively show that monomer accessibility is central to determining the strength of pair interactions. We formulate an analytical perturbative approach, phenomenologically precluding two polymers' centers of mass from overlapping within a correlation hole. This theory yields the correction to the strength of mean-field interactions in terms of a residue-accessibility parameter (RAP), which accounts for the limited availability of inner monomers to interactions. RAP rationalizes the variations in critical temperatures found in extensive Monte Carlo simulations for thousands of two-letter polymer solutions of varying lengths and sequences. RAP may thus be effective for deciphering the polymer-sequence dependence of phase diagrams given any polymer length, set of monomer types, and polymer mixtures.","PeriodicalId":15313,"journal":{"name":"Journal of Chemical Physics","volume":"165 13","pages":""},"PeriodicalIF":3.7,"publicationDate":"2026-10-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149110387","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}

引用次数: 0

Periodic-boundary-aware normalized persistent homology for glass-forming liquids: A simulation methodology. 玻璃形成液体的周期性边界感知归一化持久同调：一种模拟方法。

IF 3.7 2区化学

Journal of Chemical Physics Pub Date : 2026-10-07 DOI: 10.1063/5.0349045

Zhenpeng Li

{"title":"Periodic-boundary-aware normalized persistent homology for glass-forming liquids: A simulation methodology.","authors":"Zhenpeng Li","doi":"10.1063/5.0349045","DOIUrl":"https://doi.org/10.1063/5.0349045","url":null,"abstract":"Persistent homology provides multiscale structural descriptors for disordered particle systems, but state-to-state comparisons require consistent treatment of characteristic length scales, periodic boundaries, and statistical uncertainty. We define a lift-consistent local H1 observable under periodic boundary conditions (PBCs), normalize its longest finite persistence lifetime by the PBC mean nearest-neighbor distance, and compare states using the ratio RA/B of state-averaged dimensionless lifetimes. Confidence intervals for R are obtained by nonparametric bootstrap for independent configurations and circular moving-block bootstrap for serially dependent trajectories. For the public N = 44 glass-forming benchmark, R0.32/1.0 = 0.914 53 with a 95% confidence interval [0.905 17, 0.923 97], resolving a residual difference below unity. The local-PBC observable is unchanged over the validated range 2.0 ≤ α ≤ 3.4. Comparison with the raw local lifetime shows that normalization increases the departure from unity by 0.021 60, so it is interpreted as dimensionless local-length rescaling rather than correction of a specific contraction mechanism. A filled-disk/ring calibration resolves a prescribed H1 contrast. For DFTB SiO2 trajectories, the pressure ratios are 0.517 88, 0.377 01, and 0.728 00, with all 95% confidence intervals excluding unity. The framework, therefore, supports statistically consistent local-topology comparisons across thermodynamic states while treating periodic winding and sampling dependence explicitly.","PeriodicalId":15313,"journal":{"name":"Journal of Chemical Physics","volume":"165 13","pages":""},"PeriodicalIF":3.7,"publicationDate":"2026-10-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149110394","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}

引用次数: 0

Fast temperature up steps as a test of the Tool-Narayanaswamy formalism. 快速升温步骤作为对工具-纳拉亚纳斯瓦米形式主义的测试。

IF 3.7 2区化学

Journal of Chemical Physics Pub Date : 2026-09-28 DOI: 10.1063/5.0352723

Armand Rykner, François Ladieu, Marceau Hénot

{"title":"Fast temperature up steps as a test of the Tool-Narayanaswamy formalism.","authors":"Armand Rykner, François Ladieu, Marceau Hénot","doi":"10.1063/5.0352723","DOIUrl":"https://doi.org/10.1063/5.0352723","url":null,"abstract":"We investigated the aging dynamics of a glass-forming liquid triethyl-2-acetylcitrate, following fast temperature up steps with amplitudes ranging from 0.3 to 13.6 K. The initial states were either at equilibrium or prepared at increasing levels of out-of-equilibrium through a prior down step experiment. Our goal was to test the predictive power of the Tool-Narayanaswamy (TN) formalism, which assumes that the non-linear re-equilibration of a liquid can be linked to its linear response to a small perturbation. We determined the TN parameters for steps with small-to-moderate amplitude (≤3.3 K) and crucially took advantage of down step aging experiments below the glass transition temperature to constrain the determination of the equilibrium relaxation time. We tested the TN predictions and found very good agreement for differences in fictive temperature characterizing the distance from equilibrium as high as 10 K. For larger steps, however, the prediction progressively fails to capture the aging dynamics. This likely indicates that the re-equilibration mechanism is no longer related to the equilibrium dynamics. Finally, we discuss the possibility of obtaining a general criterion for the limit of validity of the TN formalism, which we compare to other systems from the literature.","PeriodicalId":15313,"journal":{"name":"Journal of Chemical Physics","volume":"165 12","pages":""},"PeriodicalIF":3.7,"publicationDate":"2026-09-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149074899","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}

引用次数: 0

Rotation of NH3+ and H3O+ ions in superfluid helium droplets. 超流氦滴中NH3+和h30 +离子的旋转。

IF 3.7 2区化学

Journal of Chemical Physics Pub Date : 2026-09-28 DOI: 10.1063/5.0348985

Amandeep Singh, Arisa Iguchi, Boris G Sartakov, Susumu Kuma, Andrey F Vilesov

{"title":"Rotation of NH3+ and H3O+ ions in superfluid helium droplets.","authors":"Amandeep Singh, Arisa Iguchi, Boris G Sartakov, Susumu Kuma, Andrey F Vilesov","doi":"10.1063/5.0348985","DOIUrl":"https://doi.org/10.1063/5.0348985","url":null,"abstract":"Infrared spectra of small molecules embedded in helium nanodroplets exhibit well-resolved rotational structure owing to the superfluid nature of the droplets and the weak interactions between the dopant molecules and surrounding helium atoms. In this work, we investigated the ν3 stretching bands of the light cationic rotors NH3+ and H3O+ in helium nanodroplets. The ν3 band of NH3+ displays a well-resolved rotational structure, whereas that of H3O+ is only partially resolved. The rotational constants associated with rotation about the C3 symmetry axis remain close to their gas-phase values. In contrast, the rotational constants corresponding to tumbling motion are reduced in helium to ∼60% of their free-molecule values. A substantially larger reduction was reported previously for the CH3+ ion. This difference is attributed to differences in the electronic structures of the ions, which govern their interactions with helium atoms. In addition, the NH3+ spectrum exhibits anomalies in both line positions and intensities, suggesting that the rotational dynamics of ions in superfluid helium may not be adequately described by the conventional free-molecule rotational Hamiltonian.","PeriodicalId":15313,"journal":{"name":"Journal of Chemical Physics","volume":"165 12","pages":""},"PeriodicalIF":3.7,"publicationDate":"2026-09-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149069808","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}

引用次数: 0

Reactivity of ambident nucleophiles in magnetic fields: A combined conceptual DFT and current-DFT study. 环境亲核试剂在磁场中的反应性：概念DFT和电流DFT的结合研究。

IF 3.7 2区化学

Journal of Chemical Physics Pub Date : 2026-09-28 DOI: 10.1063/5.0351445

Bang C Huynh, Meilani Wibowo-Teale, Andrew M Wibowo-Teale, Frank De Proft, Paul Geerlings

{"title":"Reactivity of ambident nucleophiles in magnetic fields: A combined conceptual DFT and current-DFT study.","authors":"Bang C Huynh, Meilani Wibowo-Teale, Andrew M Wibowo-Teale, Frank De Proft, Paul Geerlings","doi":"10.1063/5.0351445","DOIUrl":"https://doi.org/10.1063/5.0351445","url":null,"abstract":"The influence of strong external magnetic fields (up to 0.30 B0) on the electronic structure and reactivity of ambident nucleophiles is investigated using the nitrite and thiocyanate anions as prototypical examples. To capture magnetic-field-induced changes in reactivity, current-density-functional theory (current-DFT) calculations are interpreted through conceptual density-functional theory (conceptual DFT) descriptors, namely global hardness and local softness via Fukui functions, focusing on the evolution of the electronic structure and associated properties with increasing field strength in different orientations. By extending our previous adiabatic treatment of molecules to include higher-spin states, in analogy with an earlier study on atoms, and by considering the symmetry properties of relevant quantum-chemical quantities within full magnetic groups using the qsym2 framework, we uncover substantial magnetic-field-induced modulations of both molecular polarity and the shape of the Fukui function. Despite these modulations, the ambident nucleophilicity of both (NO2)- and SCN- is largely preserved, as is the preference for attack by soft electrophiles at the sulfur end of SCN-. At higher field strengths, however, the Fukui functions become increasingly diffuse, reflecting the growing importance of external magnetic interactions relative to internal electrostatic forces. The resulting redistribution of local reactivity not only predicts reaction pathways with unexpected geometries but also raises the possibility that regioselectivity may become progressively less well-defined in the strong-field regime.","PeriodicalId":15313,"journal":{"name":"Journal of Chemical Physics","volume":"165 12","pages":""},"PeriodicalIF":3.7,"publicationDate":"2026-09-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149069771","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}

引用次数: 0