Journal of Chemical Physics最新文献_第10页

Electrostatic interactions in nucleosome and higher-order structures are regulated by protonation state of histone ionizable residue.

IF 3.1 2区化学

Journal of Chemical Physics Pub Date : 2025-03-14 DOI: 10.1063/5.0252788

Houfang Zhang, Wenhan Guo, Wang Xu, Anbang Li, Lijun Jiang, Lin Li, Yunhui Peng

{"title":"Electrostatic interactions in nucleosome and higher-order structures are regulated by protonation state of histone ionizable residue.","authors":"Houfang Zhang, Wenhan Guo, Wang Xu, Anbang Li, Lijun Jiang, Lin Li, Yunhui Peng","doi":"10.1063/5.0252788","DOIUrl":"https://doi.org/10.1063/5.0252788","url":null,"abstract":"The nucleosome serves as the fundamental unit of chromatin organization, with electrostatic interactions acting as the driving forces in the folding of nucleosomes into chromatin. Perturbations around physiological pH conditions can lead to changes in the protonation states of titratable histone residues, impacting nucleosome surface electrostatic potentials and interactions. However, the effects of proton uptake or release of histone ionizable groups on nucleosome-partner protein interactions and higher-order chromatin structures remain largely unexplored. Here, we conducted comprehensive analyses of histone titratable residue pKa values in various nucleosome contexts, utilizing 96 experimentally determined complex structures. We revealed that pH-induced changes in histone residue protonation states modulated nucleosome surface electrostatic potentials and significantly influenced nucleosome-partner protein interactions. Furthermore, we observed that proton uptake or release often accompanied nucleosome-partner protein interactions, facilitating their binding processes. In addition, our findings suggest that alterations in histone protonation can also regulate nucleosome self-association, thereby modulating the organization and dynamics of higher-order chromatin structure. This study advances our understanding of nucleosome-chromatin factor interactions and how chromatin organization is regulated at the molecular level.","PeriodicalId":15313,"journal":{"name":"Journal of Chemical Physics","volume":"162 10","pages":""},"PeriodicalIF":3.1,"publicationDate":"2025-03-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143604958","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

Function domains and the universal matrix functional of multi-state density functional theory.

IF 3.1 2区化学

Journal of Chemical Physics Pub Date : 2025-03-14 DOI: 10.1063/5.0249583

Yangyi Lu, Jiali Gao

{"title":"Function domains and the universal matrix functional of multi-state density functional theory.","authors":"Yangyi Lu, Jiali Gao","doi":"10.1063/5.0249583","DOIUrl":"10.1063/5.0249583","url":null,"abstract":"On the basis of recent advancements in the Hamiltonian matrix density functional for multiple electronic eigenstates, this study delves into the mathematical foundation of the multistate density functional theory (MSDFT). We extend a number of physical concepts at the core of Kohn-Sham DFT, such as density representability, to the matrix density functional. In this work, we establish the existence of the universal matrix functional for many states as a proper generalization of the Lieb universal functional for the ground state. Consequently, the variation principle of MSDFT can be rigorously defined within an appropriate domain of matrix densities, thereby providing a solid framework for DFT of both the ground state and excited states. We further show that the analytical structure of the Hamiltonian matrix functional is considerably constrained by the subspace symmetry and invariance properties, requiring and ensuring that all elements of the Hamiltonian matrix functional are variationally optimized in a coherent manner until the Hamiltonian matrix within the subspace spanned by the lowest eigenstates is obtained. This work solidifies the theoretical foundation to treat multiple electronic states using density functional theory.","PeriodicalId":15313,"journal":{"name":"Journal of Chemical Physics","volume":"162 10","pages":""},"PeriodicalIF":3.1,"publicationDate":"2025-03-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11903056/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143604998","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

Inherent loss of parahydrogen-induced polarization for systems with magnetically equivalent nuclei in magnetic field cycling experiments.

IF 3.1 2区化学

Journal of Chemical Physics Pub Date : 2025-03-14 DOI: 10.1063/5.0245351

S V Babenko, O G Salnikov, R Z Sagdeev, I V Koptyug

{"title":"Inherent loss of parahydrogen-induced polarization for systems with magnetically equivalent nuclei in magnetic field cycling experiments.","authors":"S V Babenko, O G Salnikov, R Z Sagdeev, I V Koptyug","doi":"10.1063/5.0245351","DOIUrl":"https://doi.org/10.1063/5.0245351","url":null,"abstract":"In the present work, we elucidate the inherent loss of net magnetization (⟨Iz⟩) in parahydrogen-induced polarization (PHIP) experiments with magnetic field cycling (MFC) for spin systems containing magnetically equivalent protons. The effects are shown for propane and diethyl ether as representative examples of potential hyperpolarized MRI contrast agents, but the findings of this work are equally applicable to other multispin systems in the liquid or gas phase. These results are relevant to both adiabatic longitudinal transport after dissociation engenders net alignment (ALTADENA) experiments (where 1H nuclei are polarized) and MFC protocols used to transfer parahydrogen spin order to a heteronucleus such as 13C. The investigated effects should be incorporated for a correct evaluation of both the maximum possible NMR signal enhancement and the pairwise selectivity, which are useful in the context of mechanistic studies in the field of catalytic hydrogenation. Among signal enhancement damping factors in ALTADENA, such as T1 relaxation and insufficient adiabaticity of a field sweep, the inherent loss of net magnetization in spin systems containing magnetically equivalent protons (especially in PHIP systems commonly used for mechanistic studies such as propene or propane) has not been thoroughly considered and needs to be clarified. The maximum possible net magnetization in ALTADENA for diethyl ether and propane was shown to be ∑|⟨Iiz⟩| ≈ 0.56 for diethyl ether and ∑|⟨Iiz⟩| ≈ 0.45 for propane, respectively. The inherent loss of net heteronuclear magnetization of the same order of magnitude with an increase in the number of magnetically equivalent protons was also demonstrated for AmMnX-type spin systems.","PeriodicalId":15313,"journal":{"name":"Journal of Chemical Physics","volume":"162 10","pages":""},"PeriodicalIF":3.1,"publicationDate":"2025-03-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143605010","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

Assessing the performance of coupled-trajectory schemes on full-dimensional two-state linear vibronic coupling models. 评估耦合轨迹方案在全维度二态线性振子耦合模型上的性能。

IF 3.1 2区化学

Journal of Chemical Physics Pub Date : 2025-03-14 DOI: 10.1063/5.0252505

Peter Schürger, Lea M Ibele, David Lauvergnat, Federica Agostini

引用次数: 0

Enhancing reaction efficiency in photochemical organic synthesis by controlling the dynamic effects of excitons.

IF 3.1 2区化学

Journal of Chemical Physics Pub Date : 2025-03-14 DOI: 10.1063/5.0240938

Harunobu Mitsunuma, Ryosuke Matsubara

引用次数: 0

Numerically stable resonating Hartree-Fock.

IF 3.1 2区化学

Journal of Chemical Physics Pub Date : 2025-03-14 DOI: 10.1063/5.0246790

Ericka Roy Miller, Shane M Parker

引用次数: 0

Revealing correlation mechanisms through nonorthogonal multiconfiguration self-consistent field calculations. 通过非正交多配置自洽场计算揭示相关机制

IF 3.1 2区化学

Journal of Chemical Physics Pub Date : 2025-03-14 DOI: 10.1063/5.0253224

Zihui Song, Jonathan S Bersson, Lee M Thompson

{"title":"Revealing correlation mechanisms through nonorthogonal multiconfiguration self-consistent field calculations.","authors":"Zihui Song, Jonathan S Bersson, Lee M Thompson","doi":"10.1063/5.0253224","DOIUrl":"https://doi.org/10.1063/5.0253224","url":null,"abstract":"The presence of spin and spatial symmetry breaking upon variational optimization of mean-field wavefunctions is known to be an indicator of nondynamical electron correlation. However, a single mean-field wavefunction may not have sufficient flexibility to flag the correlated orbital space where there are multiple correlation mechanisms present. In such situations, there are multiple nearly degenerate self-consistent field solutions that describe different correlation mechanisms, but it is often not possible to know a priori when such situations will occur or if sufficient solutions have been obtained. In this work, we examine the role of spin and spatial symmetries of nonorthogonal multiconfigurational self-consistent field (NOMCSCF) calculations in revealing correlation mechanisms. We provide details of the theory for optimization of NOMCSCF wavefunctions with desired symmetries, establish which types of symmetries recover the most correlation energy when the symmetry constraints are relaxed, and discuss how the different-orbitals for different-configuration wavefunctions reveal the different correlation mechanisms present.","PeriodicalId":15313,"journal":{"name":"Journal of Chemical Physics","volume":"162 10","pages":""},"PeriodicalIF":3.1,"publicationDate":"2025-03-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143605093","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

Incorporating multiscale methylation effects into nucleosome-resolution chromatin models for simulating mesoscale fibers.

IF 3.1 2区化学

Journal of Chemical Physics Pub Date : 2025-03-07 DOI: 10.1063/5.0242199

Zilong Li, Stephanie Portillo-Ledesma, Moshe Janani, Tamar Schlick

{"title":"Incorporating multiscale methylation effects into nucleosome-resolution chromatin models for simulating mesoscale fibers.","authors":"Zilong Li, Stephanie Portillo-Ledesma, Moshe Janani, Tamar Schlick","doi":"10.1063/5.0242199","DOIUrl":"10.1063/5.0242199","url":null,"abstract":"Histone modifications play a crucial role in regulating chromatin architecture and gene expression. Here we develop a multiscale model for incorporating methylation in our nucleosome-resolution physics-based chromatin model to investigate the mechanisms by which H3K9 and H3K27 trimethylation (H3K9me3 and H3K27me3) influence chromatin structure and gene regulation. We apply three types of energy terms for this purpose: short-range potentials are derived from all-atom molecular dynamics simulations of wildtype and methylated chromatosomes, which revealed subtle local changes; medium-range potentials are derived by incorporating contacts between HP1 and nucleosomes modified by H3K9me3, to incorporate experimental results of enhanced contacts for short chromatin fibers (12 nucleosomes); for long-range interactions we identify H3K9me3- and H3K27me3-associated contacts based on Hi-C maps with a machine learning approach. These combined multiscale effects can model methylation as a first approximation in our mesoscale chromatin model, and applications to gene systems offer new insights into the epigenetic regulation of genomes mediated by H3K9me3 and H3K27me3.","PeriodicalId":15313,"journal":{"name":"Journal of Chemical Physics","volume":"162 9","pages":""},"PeriodicalIF":3.1,"publicationDate":"2025-03-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11888786/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143567312","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

Enhanced photoisomerization with hybrid metallodielectric cavities based on mode interference.

IF 3.1 2区化学

Journal of Chemical Physics Pub Date : 2025-03-07 DOI: 10.1063/5.0252988

Anael Ben-Asher, Thomas Schnappinger, Markus Kowalewski, Johannes Feist

{"title":"Enhanced photoisomerization with hybrid metallodielectric cavities based on mode interference.","authors":"Anael Ben-Asher, Thomas Schnappinger, Markus Kowalewski, Johannes Feist","doi":"10.1063/5.0252988","DOIUrl":"https://doi.org/10.1063/5.0252988","url":null,"abstract":"The ability to control chemical reactions by coupling organic molecules to confined light in a cavity has recently attracted much attention. While most previous studies have focused on single-mode photonic or plasmonic cavities, here we investigate the effect of hybrid metallodielectric cavities on photoisomerization reactions. Hybrid cavities, which support both photonic and plasmonic modes, offer unique opportunities that arise from the interplay between these two distinct types of modes. In particular, we demonstrate that interference in the spectral density due to a narrow photonic mode and a broad plasmonic mode that are coupled to each other enables hybrid cavities to provide an energy-selective Purcell effect. This effect enhances electronic relaxation only to the desired molecular geometry, providing the ability to increase the yield of photoisomerization reactions. As a test case, we study the asymmetric proton transfer reaction in the electronically excited state of 3-aminoacrolein. Our results, which are robust for a range of realistic cavity parameters, highlight the advantages of hybrid cavities in cavity-induced photochemical processes.","PeriodicalId":15313,"journal":{"name":"Journal of Chemical Physics","volume":"162 9","pages":""},"PeriodicalIF":3.1,"publicationDate":"2025-03-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143567310","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

Enhancing half-integer quadrupolar solid-state NMR signals via steady states: A double frequency sweep-based approach.

IF 3.1 2区化学

Journal of Chemical Physics Pub Date : 2025-03-07 DOI: 10.1063/5.0249863

Y T Angel Wong, Mattia Negroni, Arno P M Kentgens

{"title":"Enhancing half-integer quadrupolar solid-state NMR signals via steady states: A double frequency sweep-based approach.","authors":"Y T Angel Wong, Mattia Negroni, Arno P M Kentgens","doi":"10.1063/5.0249863","DOIUrl":"https://doi.org/10.1063/5.0249863","url":null,"abstract":"We introduce a novel signal enhancement technique, termed steadyDFS, for quadrupolar solid-state nuclear magnetic resonance spectroscopy. It can substantially increase the performance of double frequency sweeps (DFSs) for all half-integer quadrupolar spins (I = 3/2, 5/2, 7/2, and 9/2). In steadyDFS, the DFS and readout pulse are repeated multiple times with a repetition time of TR,DFS to generate a steady state that provides substantial sensitivity enhancement. Using a series of simulations, we show that steadyDFS can outperform conventional DFS methods, and enhancements per unit time of ∼5 to 21 can be achieved depending on the value of I. The sensitivity of steadyDFS is robust toward changes in repetition times and quadrupolar relaxation rates of the system. Moreover, steadyDFS is highly modular and can be combined with quadrupolar Carr-Purcell-Meiboom-Gill (QCPMG) detection. Using 39K (I = 3/2), 17O (I = 5/2), and 49Ti (I = 7/2) as representative challenging nuclei, we show that enhancements up to 46× can be realized experimentally via steadyDFS-QCPMG, translating to a 20× enhancement per unit time. We applied steadyDFS-QCPMG to protonated and deprotonated samples, as well as to samples with a diverse range of transverse relaxation times (i.e., T2/T2*), where steadyDFS-QCPMG can provide an enhancement per unit time of at least 7. For samples that are not amendable to QCPMG, we explored the use of steady-state free precession (SSFP). Although SSFP is fundamentally incompatible with steadyDFS, we show that beneficial results can be obtained when DFSs are combined with SSFP in an interruptive manner.","PeriodicalId":15313,"journal":{"name":"Journal of Chemical Physics","volume":"162 9","pages":""},"PeriodicalIF":3.1,"publicationDate":"2025-03-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143567311","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