Journal of Chemical Physics最新文献_第3页

Quantum information reveals that orbital-wise correlation is essentially classical in natural orbitals. 量子信息表明，在自然轨道中，轨道相关本质上是经典的。

IF 3.1 2区化学

Journal of Chemical Physics Pub Date : 2024-12-28 DOI: 10.1063/5.0220306

Davide Materia, Leonardo Ratini, Celestino Angeli, Leonardo Guidoni

{"title":"Quantum information reveals that orbital-wise correlation is essentially classical in natural orbitals.","authors":"Davide Materia, Leonardo Ratini, Celestino Angeli, Leonardo Guidoni","doi":"10.1063/5.0220306","DOIUrl":"https://doi.org/10.1063/5.0220306","url":null,"abstract":"The intersection of quantum chemistry and quantum computing has led to significant advancements in understanding the potential of using quantum devices for the efficient calculation of molecular energies. Simultaneously, this intersection enhances the comprehension of quantum chemical properties through the use of quantum computing and quantum information tools. This paper tackles a key question in this relationship: Is the nature of the orbital-wise electron correlations in wavefunctions of realistic prototypical cases classical or quantum? We address this question with a detailed investigation of molecular wavefunctions in terms of Shannon and von Neumann entropies, common tools of classical and quantum information theory. Our analysis reveals a notable distinction between classical and quantum mutual information in molecular systems when analyzed with Hartree-Fock canonical orbitals. However, this difference decreases dramatically, by ∼100-fold, when natural orbitals are used as reference. This finding suggests that orbital correlations, when viewed through the appropriate basis, are predominantly classical. Consequently, our study underscores the importance of using natural orbitals to accurately assess molecular orbital correlations and to avoid their overestimation.","PeriodicalId":15313,"journal":{"name":"Journal of Chemical Physics","volume":"161 24","pages":""},"PeriodicalIF":3.1,"publicationDate":"2024-12-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142894780","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

Desertion of anomalous magnetic transition and emergence of metallic state in Cu doped Eu2Ru2O7 pyrochlore. Cu掺杂Eu2Ru2O7焦绿石中异常磁跃迁的消失和金属态的出现。

IF 3.1 2区化学

Journal of Chemical Physics Pub Date : 2024-12-28 DOI: 10.1063/5.0238254

Soma Chatterjee, I Das

引用次数: 0

Friction and adhesion: From fundamentals to applications. 摩擦和附着力：从基础到应用。

IF 3.1 2区化学

Journal of Chemical Physics Pub Date : 2024-12-28 DOI: 10.1063/5.0252422

Daniel Bonn, Ali Dhinojwala, Bo Persson, Kathryn Wahl, Mischa Bonn

引用次数: 0

Local field effects of quadrupole contributions on sum frequency generation spectroscopy. 四极贡献对和频产生谱的局域场效应。

IF 3.1 2区化学

Journal of Chemical Physics Pub Date : 2024-12-28 DOI: 10.1063/5.0235557

Tomonori Hirano, Akihiro Morita

引用次数: 0

Physically interpretable performance metrics for clustering. 用于集群的物理可解释的性能指标。

IF 3.1 2区化学

Journal of Chemical Physics Pub Date : 2024-12-28 DOI: 10.1063/5.0241122

Kinjal Mondal, Jeffery B Klauda

{"title":"Physically interpretable performance metrics for clustering.","authors":"Kinjal Mondal, Jeffery B Klauda","doi":"10.1063/5.0241122","DOIUrl":"https://doi.org/10.1063/5.0241122","url":null,"abstract":"Clustering is a type of machine learning technique, which is used to group huge amounts of data based on their similarity into separate groups or clusters. Clustering is a very important task that is nowadays used to analyze the huge and diverse amount of data coming out of molecular dynamics (MD) simulations. Typically, the data from the MD simulations in terms of their various frames in the trajectory are clustered into different groups and a representative element from each group is studied separately. Now, a very important question coming in this process is: what is the quality of the clusters that are obtained? There are several performance metrics that are available in the literature such as the silhouette index and the Davies-Bouldin Index that are often used to analyze the quality of clustering. However, most of these metrics focus on the overlap or the similarity of the clusters in the reduced dimension that is used for clustering and do not focus on the physically important properties or the parameters of the system. To address this issue, we have developed two physically interpretable scoring metrics that focus on the physical parameters of the system that we are analyzing. We have used and tested our algorithm on three different systems: (1) Ising model, (2) peptide folding and unfolding of WT HP35, (3) a protein-ligand trajectory of an enzyme and substrate, and (4) a protein-ligand dissociated trajectory. We show that the scoring metrics provide us clusters that match with our physical intuition about the systems.","PeriodicalId":15313,"journal":{"name":"Journal of Chemical Physics","volume":"161 24","pages":""},"PeriodicalIF":3.1,"publicationDate":"2024-12-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142894826","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

Boosting cation mobility in sol-gel derived organic-inorganic hybrid solid electrolytes through physical conditioning. 通过物理调节提高溶胶-凝胶衍生的有机-无机杂化固体电解质中的阳离子迁移率。

IF 3.1 2区化学

Journal of Chemical Physics Pub Date : 2024-12-28 DOI: 10.1063/5.0237949

Vazrik Keshishian, Guangyu Wang, John Kieffer

{"title":"Boosting cation mobility in sol-gel derived organic-inorganic hybrid solid electrolytes through physical conditioning.","authors":"Vazrik Keshishian, Guangyu Wang, John Kieffer","doi":"10.1063/5.0237949","DOIUrl":"https://doi.org/10.1063/5.0237949","url":null,"abstract":"Organic-inorganic hybrid materials are explored for application as solid electrolytes for lithium-ion batteries. The material consists of a porous silica network, of which the pores are infiltrated by poly(ethylene oxide) and lithium perchlorate. The synthesis involves two steps: First, the inorganic backbone is created by the acid-catalyzed sol-gel synthesis of tetraethyl orthosilicate to ensure continuity of the backbone in three dimensions. In the second step, the polymer and salt are imbued into the porous backbone via solvent exchange. During drying, the cylindrical disk-shaped specimens shrink mainly in the radial direction, which results in spatially non-uniform structural developments. While this inhomogeneity is not discernible in the material's chemical compositional or thermal properties, it is manifest in its ionic conductivity and adiabatic elastic modulus. The ionic conductivity in the center of the specimens is projected to be between one and two orders of magnitude higher than the measured average across the sample diameter. The process that yields a structure with enhanced ionic mobility during post-synthesis physical conditioning is inferred from careful analysis and numerical interpretation of measurable quantities, and the implications for the design of nanostructured hybrid electrolytes with high ionic conductivity are discussed.","PeriodicalId":15313,"journal":{"name":"Journal of Chemical Physics","volume":"161 24","pages":""},"PeriodicalIF":3.1,"publicationDate":"2024-12-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142948882","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

Decomposition of friction coefficients to analyze hydration effects on a C60(OH)n. 分解摩擦系数，分析水化对C60(OH)n的影响。

IF 3.1 2区化学

Journal of Chemical Physics Pub Date : 2024-12-28 DOI: 10.1063/5.0241914

Tomoya Iwashita, Yuki Uematsu, Masahide Terazima, Ryo Akiyama

引用次数: 0

Tunneling barriers in an extended Marcus theory of electron transfer: Incorporating effects of the bridging medium. 扩展马库斯电子传递理论中的隧穿势垒：结合桥接介质的影响。

IF 3.1 2区化学

Journal of Chemical Physics Pub Date : 2024-12-28 DOI: 10.1063/5.0235076

Ravinder Kumar, Ravindra Venkatramani

引用次数: 0

Geometric variations in nucleosomal DNA dictate higher-order chromatin structure and enhancer-promoter communication. 核小体DNA的几何变异决定了高阶染色质结构和增强子-启动子通讯。

IF 3.1 2区化学

Journal of Chemical Physics Pub Date : 2024-12-28 DOI: 10.1063/5.0240991

Stefjord Todolli, Ekaterina V Nizovtseva, Nicolas Clauvelin, Ondrej Maxian, Vasily M Studitsky, Wilma K Olson

{"title":"Geometric variations in nucleosomal DNA dictate higher-order chromatin structure and enhancer-promoter communication.","authors":"Stefjord Todolli, Ekaterina V Nizovtseva, Nicolas Clauvelin, Ondrej Maxian, Vasily M Studitsky, Wilma K Olson","doi":"10.1063/5.0240991","DOIUrl":"10.1063/5.0240991","url":null,"abstract":"The dynamic organization of chromatin plays an essential role in the regulation of genetic activity, interconverting between open and compact forms at the global level. The mechanisms underlying these large-scale changes remain a topic of widespread interest. The simulations of nucleosome-decorated DNA reported herein reveal profound effects of the nucleosome itself on overall chromatin properties. Models that capture the long-range communication between proteins on nucleosome-decorated DNA chains incorporate DNA pathways different from those that were previously proposed based on ultracentrifugation and chemical cross-linking data. New quantitative biochemical assays measuring the rates of communication between interacting proteins bound to a promoter and an enhancer at the ends of saturated, precisely positioned, nucleosome-decorated DNA chains reveal a chromatin architecture with a three-nucleosome repeat, a model inconsistent with the two-start configurations deduced from earlier physical studies. Accompanying computations uncover small differences in the twisting of successive base pairs that seemingly give rise to the observed global properties. These data suggest that the novel state of chromatin determined under physiological conditions differs from that deduced under standard physical conditions, likely reflecting the different salt conditions used in the two types of experiments. This novel chromatin state may be important for a number of DNA transactions that occur in the cell nucleus.","PeriodicalId":15313,"journal":{"name":"Journal of Chemical Physics","volume":"161 24","pages":""},"PeriodicalIF":3.1,"publicationDate":"2024-12-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11681976/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142894820","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}

引用次数: 0

Proton diffusion and hydrogen/deuterium exchange in amorphous solid water at temperatures from 114 to 134 K. 温度从114到134 K的非晶固体水中质子扩散和氢/氘交换。

IF 3.1 2区化学

Journal of Chemical Physics Pub Date : 2024-12-28 DOI: 10.1063/5.0233755

Megan K Dunlap, Loni Kringle, Bruce D Kay, Greg A Kimmel

{"title":"Proton diffusion and hydrogen/deuterium exchange in amorphous solid water at temperatures from 114 to 134 K.","authors":"Megan K Dunlap, Loni Kringle, Bruce D Kay, Greg A Kimmel","doi":"10.1063/5.0233755","DOIUrl":"https://doi.org/10.1063/5.0233755","url":null,"abstract":"The reaction coefficient for hydrogen/deuterium (H/D) exchange and the diffusion of hydrated excess protons within amorphous solid water (ASW) are characterized as a function of temperature. For these experiments, water films are deposited on a Pt(111) substrate at 108 K, and reactions with pre-adsorbed hydrogen atoms produce hydrated protons. Upon heating, protons diffuse within the water, and H/D exchange occurs when they encounter D2O probe molecules deposited in the films. The time-dependent concentration of D2O is monitored with infrared spectroscopy, and it indicates the protons diffusion from the substrate and establish an equilibrium distribution prior to significant H/D exchange for temperatures 114 K ≤T≤ 134 K. By controlling the distance between the D2O molecules and the substrate, we probe the distribution of protons within the film. It decays as x-2 for the examined range of x (12-52 nm) due to the electric field that develops between the diffusing protons and their image charges in the metal substrate. This agrees with the theoretical distance scaling for the equilibrated proton concentration in a dielectric near a metal boundary. From the proton concentration and the measured D2O decay rate, a lower bound for the proton diffusion coefficient ranging from 10-20 m2/s at 114 K to 10-18 m2/s at 134 K is estimated. The diffusion coefficient has an activation energy of 0.40 eV, which is comparable to energies reported for molecular translations and rotations of H2O, suggesting they may play a critical role in the proton diffusion mechanism within ASW.","PeriodicalId":15313,"journal":{"name":"Journal of Chemical Physics","volume":"161 24","pages":""},"PeriodicalIF":3.1,"publicationDate":"2024-12-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142894834","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