Journal of Chemical Physics最新文献_第3页

Ion-modulated polyelectrolyte complexation of DNA and polyacrylic acid from molecular dynamics simulations. 离子调制的聚电解质络合DNA与聚丙烯酸的分子动力学模拟。

IF 3.1 2区化学

Journal of Chemical Physics Pub Date : 2026-05-07 DOI: 10.1063/5.0324821

Sisem Ektirici, Vagelis Harmandaris, Christos N Likos, Terpsichori S Alexiou

{"title":"Ion-modulated polyelectrolyte complexation of DNA and polyacrylic acid from molecular dynamics simulations.","authors":"Sisem Ektirici, Vagelis Harmandaris, Christos N Likos, Terpsichori S Alexiou","doi":"10.1063/5.0324821","DOIUrl":"https://doi.org/10.1063/5.0324821","url":null,"abstract":"The formation of complexes between like-charged polyelectrolytes challenges conventional electrostatic intuition and highlights the central role of ions in mediating macromolecular organization. Here, we investigate the salt-dependent association of DNA with poly(acrylic acid) (PAA) using atomistic molecular dynamics simulations in NaCl, MgCl2, and CaCl2 solutions. A time-resolved state classification scheme, based on heavy-atom distance and hydrogen-bond formation, was applied to distinguish bound and unbound configurations, enabling quantitative analysis of how ion valency modulates complex stability and structure. The results reveal a clear hierarchy of association strength, with Ca2+ promoting persistent complex formation through direct inner-sphere coordination between DNA phosphates and PAA carboxylates, Mg2+ mediating weaker, transient bridging interactions, and Na+ exhibiting only electrostatic screening action with negligible bridge formation. Structural analysis shows that multivalent ions not only enhance complex stability but also reshape the molecular organization of both macromolecules. Ca2+ induces expansion of DNA and compaction of PAA within a strongly bridged complex characterized by directional alignment and backbone-dominated binding, whereas Mg2+ promotes more transient groove associations and Na+ supports flexible, weakly correlated contacts. Our findings provide molecular-level insight into ion-specific mechanisms underlying polyelectrolyte organization and inform the design of responsive biomaterials and nucleic acid-based assemblies in multivalent ionic environments.","PeriodicalId":15313,"journal":{"name":"Journal of Chemical Physics","volume":"164 17","pages":""},"PeriodicalIF":3.1,"publicationDate":"2026-05-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147838620","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

Quantum metrology of pump-probe spectroscopy. 泵浦探测光谱的量子计量。

IF 3.1 2区化学

Journal of Chemical Physics Pub Date : 2026-05-07 DOI: 10.1063/5.0323961

Frank Schlawin

引用次数: 0

Spin-dependent nonorthogonal generalized Wannier functions and their integration with PAW and Hubbard corrections in linear-scaling DFT. 线性标度DFT中自旋相关非正交广义万尼尔函数及其与PAW和Hubbard校正的积分。

IF 3.1 2区化学

Journal of Chemical Physics Pub Date : 2026-05-07 DOI: 10.1063/5.0323596

Miguel Escobar Azor, David D O'Regan, Ali Safavi, Jacek Dziedzic, Chris-Kriton Skylaris, Nicholas D M Hine

{"title":"Spin-dependent nonorthogonal generalized Wannier functions and their integration with PAW and Hubbard corrections in linear-scaling DFT.","authors":"Miguel Escobar Azor, David D O'Regan, Ali Safavi, Jacek Dziedzic, Chris-Kriton Skylaris, Nicholas D M Hine","doi":"10.1063/5.0323596","DOIUrl":"https://doi.org/10.1063/5.0323596","url":null,"abstract":"We present a spin-dependent extension of the non-orthogonal generalized Wannier function (NGWF) formalism within the framework of linear-scaling density functional theory (LS-DFT) as implemented in the ONETEP code. In traditional LS-DFT representations, both spin channels are constrained to share a common variational basis, which limits the accuracy for systems that are spin-polarized or exhibit magnetic order. Our approach allows NGWFs to vary independently for each spin channel, enabling a more accurate representation of spin-polarization in the electronic density. We demonstrate the efficacy of this method through a series of test cases, including localized magnetic defects in two-dimensional hBN, transition metal complexes, two-dimensional van der Waals magnetic materials, and both bulk and nanocluster ferromagnetic Co. In each scenario, the incorporation of spin-dependent NGWFs results in enhanced accuracy for total energy calculations, improved localization of spin density, and accurate predictions of magnetic ground states. This improvement is particularly notable when combined with DFT+U and DFT+U+J corrections. In this study, we take the opportunity to describe the combination of DFT+U+J and the projector-augmented wave (PAW) formalism within the LS-DFT framework, including how PAW participates in the ionic Pulay force and in the minimum-tracking linear response approach for computing parameters in situ. Our findings demonstrate that spin-dependent NGWFs are a crucial and computationally efficient advancement in the linear-scaling DFT simulation of spin-polarized materials.","PeriodicalId":15313,"journal":{"name":"Journal of Chemical Physics","volume":"164 17","pages":""},"PeriodicalIF":3.1,"publicationDate":"2026-05-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147838658","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

Osmolyte mediated modulation of liquid-vapor interfacial water dynamics: A theoretical two-dimensional vibrational sum frequency generation spectroscopic study of aqueous mixtures of trimethylamine N-oxide and urea. 渗透介质介导的液-气界面水动力学调制：三甲胺n -氧化物和尿素水混合物的二维理论振动和频率产生光谱研究。

IF 3.1 2区化学

Journal of Chemical Physics Pub Date : 2026-05-07 DOI: 10.1063/5.0325552

Anjali Negi, Ravi Malik, Amalendu Chandra

{"title":"Osmolyte mediated modulation of liquid-vapor interfacial water dynamics: A theoretical two-dimensional vibrational sum frequency generation spectroscopic study of aqueous mixtures of trimethylamine N-oxide and urea.","authors":"Anjali Negi, Ravi Malik, Amalendu Chandra","doi":"10.1063/5.0325552","DOIUrl":"https://doi.org/10.1063/5.0325552","url":null,"abstract":"Two-dimensional vibrational sum frequency generation (2D-VSFG) spectroscopic calculations and molecular dynamics simulations are employed to investigate the dynamics of interfacial water at the liquid-vapor interface of aqueous urea, trimethylamine N-oxide (TMAO), and ternary aqueous TMAO-urea mixtures. The 2D-VSFG spectra in the hydrogen-bonded OH stretch region reveal a slowing down of spectral diffusion from binary water-urea to binary water-TMAO and to ternary water-TMAO-urea mixtures. Calculations of the slope of the nodal line and frequency-time correlation functions show that the fast sub-picosecond dynamics is weakly dependent on the presence of the osmolytes, whereas the long-time spectral diffusion time scale increases significantly in the presence of TMAO, revealing the existence of a more rigid and heterogeneous interfacial hydrogen-bond network. Analyses of dangling OH dynamics through diagonal peak decay, cross-peak growth, and non-hydrogen-bond correlation functions demonstrate reduced dangling OH populations and hindered hydrogen-bonded to dangling interconversion at increasingly crowded interfaces in the presence of osmolytes. The orientational relaxation and hydrogen-bond lifetime calculations further reveal slower rotational dynamics and longer-lived hydrogen bonds in the interfacial systems containing TMAO. Together, these results establish a unified molecular level picture of osmolyte induced modulation of aqueous interfacial dynamics.","PeriodicalId":15313,"journal":{"name":"Journal of Chemical Physics","volume":"164 17","pages":""},"PeriodicalIF":3.1,"publicationDate":"2026-05-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147838667","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

Rotational memory function of SPC/E water. SPC/E水的旋转记忆功能。

IF 3.1 2区化学

Journal of Chemical Physics Pub Date : 2026-05-07 DOI: 10.1063/5.0323084

Dilipkumar N Asthagiri, Dmitry V Matyushov

引用次数: 0

Photon counting statistics in the presence of spectral diffusion induced by nonequilibrium environmental fluctuations. 由非平衡环境波动引起的光谱扩散存在下的光子计数统计。

IF 3.1 2区化学

Journal of Chemical Physics Pub Date : 2026-05-07 DOI: 10.1063/5.0325248

Xiangji Cai, Yonggang Peng, Yujun Zheng

{"title":"Photon counting statistics in the presence of spectral diffusion induced by nonequilibrium environmental fluctuations.","authors":"Xiangji Cai, Yonggang Peng, Yujun Zheng","doi":"10.1063/5.0325248","DOIUrl":"https://doi.org/10.1063/5.0325248","url":null,"abstract":"We theoretically investigate the statistical properties of photon emission of a driven two-level single-molecule system undergoing spectral diffusion induced by nonequilibrium environmental fluctuations. Within the framework of the generating function method and the stochastic Liouville equation, we analyze the influence of the nonequilibrium characteristics of environmental fluctuations, respectively, governed by nonstationary Ornstein-Uhlenbeck noise and random telegraph noise on the photon counting statistics of the driven single-molecule system. In the slow modulation limit of spectral diffusion, the intensity and statistical fluctuations of photon emission depend on the environmental nonequilibrium characteristics at short time scales, whereas they become independent of the nonequilibrium characteristics of environmental fluctuations in the steady state. In the fast modulation limit of spectral diffusion, neither the line shape nor the Mandel's parameter depends on the environmental nonequilibrium characteristics owing to the rapid relaxation of environmental fluctuations. These findings not only shed light on the role of nonequilibrium environmental fluctuations in shaping the photon emission properties of single-molecule systems but also provide a basis for distinguishing between equilibrium and nonequilibrium characteristics of environmental fluctuations in experimental measurements.","PeriodicalId":15313,"journal":{"name":"Journal of Chemical Physics","volume":"164 17","pages":""},"PeriodicalIF":3.1,"publicationDate":"2026-05-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147838720","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

Unraveling the allosteric mechanism and mechanical stability of partial and complete loss-of-function mutations in p53 DNA-binding domain. 揭示p53 dna结合域部分和完全功能丧失突变的变构机制和机械稳定性。

IF 3.1 2区化学

Journal of Chemical Physics Pub Date : 2026-05-07 DOI: 10.1063/5.0328162

Han Zhou, Tao Zhou, Shiwei Yan

{"title":"Unraveling the allosteric mechanism and mechanical stability of partial and complete loss-of-function mutations in p53 DNA-binding domain.","authors":"Han Zhou, Tao Zhou, Shiwei Yan","doi":"10.1063/5.0328162","DOIUrl":"https://doi.org/10.1063/5.0328162","url":null,"abstract":"Mutations in functional proteins are the core cause of protein misfolding and dysfunction. Different mutation types exert distinct effects on protein structure and function, thus determining the specificity and diversity of targeted therapeutic strategies. In this study, we took the tumor suppressor protein p53 as a model to investigate the impacts of different mutation types on protein structure and function. Mutations in the p53 protein primarily occur in its DNA-binding domain (p53-DBD), and such mutations are classified into hotspot mutations (causing complete loss-of-function) and non-hotspot mutations (inducing partial loss-of-function). However, the allosteric mechanisms underlying non-hotspot mutations remain elusive. We conducted all-atom molecular dynamics simulations for the three systems: p53-WT, non-hotspot p53-E180R, and hotspot p53-R248W dimer-DNA complexes. Our results demonstrate that both mutations weaken intramolecular interactions in p53-DBD and enhance its structural flexibility. In particular, E180R perturbs dimer interface interactions, impairing dimer stability and cooperative DNA binding; R248W disrupts interactions between the L3/L1 loops and DNA, leading to the loss of DNA-binding capacity. These allosteric effects agree with available experimental data. Steered molecular dynamics simulations further confirm that both mutations accelerate p53 dimer dissociation. We also reveal for the first time the mechanical stability features of intermolecular interactions within p53 dimers. These findings provide atomic-level insights into p53 mutation-associated allostery and offer a basis for distinguishing mutation subtypes in prognosis prediction and targeted therapeutic strategy design.","PeriodicalId":15313,"journal":{"name":"Journal of Chemical Physics","volume":"164 17","pages":""},"PeriodicalIF":3.1,"publicationDate":"2026-05-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147838727","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

Benchmark assessment of collinear, mixed-reference, and spin-adapted variants of spin-flip time-dependent density functional theory, for closed- and open-shell molecules. 闭合壳和开壳分子的自旋翻转时相关密度泛函理论共线、混合参考和自旋适应变体的基准评估。

IF 3.1 2区化学

Journal of Chemical Physics Pub Date : 2026-05-07 DOI: 10.1063/5.0327478

Avik Kumar Ojha, John M Herbert

{"title":"Benchmark assessment of collinear, mixed-reference, and spin-adapted variants of spin-flip time-dependent density functional theory, for closed- and open-shell molecules.","authors":"Avik Kumar Ojha, John M Herbert","doi":"10.1063/5.0327478","DOIUrl":"https://doi.org/10.1063/5.0327478","url":null,"abstract":"Spin-flip methods provide access to certain electronic states having multireference character while retaining single-reference cost. However, conventional spin-flip time-dependent density functional theory (SF-TDDFT) often suffers from severe spin contamination that may cause inaccurate state ordering or engender ambiguous state character. For singlet excited states, this is largely rectified by a \"mixed-reference\" formulation (MRSF-TDDFT), while a spin-adapted formalism (SA-SF-TDDFT) addresses spin contamination in a general way for arbitrary multiplicities. Here, we revisit SA-SF-TDDFT and demonstrate that it significantly improves the agreement with reference data compared to other variants and also relative to conventional (spin-conserving) linear response TDDFT. Overall, SA-SF-TDDFT proves to be the most accurate among these methods, for excitation energies of both closed-shell molecules and doublet radicals as well as for singlet-triplet gaps. However, SF methods exhibit a notable limitation in the case of linear and quasi-linear doublet radicals, due to degeneracies in the high-spin quartet reference state.","PeriodicalId":15313,"journal":{"name":"Journal of Chemical Physics","volume":"164 17","pages":""},"PeriodicalIF":3.1,"publicationDate":"2026-05-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147838293","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

Beyond photon shot noise: Chemical limits in spectrophotometric precision. 超越光子噪声：分光光度法精度的化学限制。

IF 3.1 2区化学

Journal of Chemical Physics Pub Date : 2026-05-07 DOI: 10.1063/5.0324892

Georg Engelhardt, Dahai He, JunYan Luo

引用次数: 0

Fluctuation-induced acceleration of inter-ligand exciton transfer in bis(dipyrrinato)Zn(II) complex. 波动诱导的双吡啶酸锌（II）配合物中配体间激子转移的加速。

IF 3.1 2区化学

Journal of Chemical Physics Pub Date : 2026-05-07 DOI: 10.1063/5.0329790

Hiroki Uratani, Hirofumi Sato

引用次数: 0