Journal of Chemical Physics最新文献

Why do histone monomethylation and dimethylation cause a significant difference in binding to LEDGF? 为什么组蛋白单甲基化和二甲基化会导致与LEDGF结合的显著差异？

IF 3.1 2区化学

Journal of Chemical Physics Pub Date : 2025-05-14 DOI: 10.1063/5.0259337

Hinako X Suzuki, Hisashi Okumura, Satoru G Itoh

引用次数: 0

Imaging the photochemistry of cyclobutanone using ultrafast electron diffraction: Experimental results. 用超快电子衍射成像环丁酮的光化学：实验结果。

IF 3.1 2区化学

Journal of Chemical Physics Pub Date : 2025-05-14 DOI: 10.1063/5.0266559

A E Green, Y Liu, F Allum, M Graßl, P Lenzen, M N R Ashfold, S Bhattacharyya, X Cheng, M Centurion, S W Crane, R Forbes, N A Goff, L Huang, B Kaufman, M-F Kling, P L Kramer, H V S Lam, K A Larsen, R Lemons, M-F Lin, A J Orr-Ewing, D Rolles, A Rudenko, S K Saha, J Searles, X Shen, S Weathersby, P M Weber, H Zhao, T J A Wolf

{"title":"Imaging the photochemistry of cyclobutanone using ultrafast electron diffraction: Experimental results.","authors":"A E Green, Y Liu, F Allum, M Graßl, P Lenzen, M N R Ashfold, S Bhattacharyya, X Cheng, M Centurion, S W Crane, R Forbes, N A Goff, L Huang, B Kaufman, M-F Kling, P L Kramer, H V S Lam, K A Larsen, R Lemons, M-F Lin, A J Orr-Ewing, D Rolles, A Rudenko, S K Saha, J Searles, X Shen, S Weathersby, P M Weber, H Zhao, T J A Wolf","doi":"10.1063/5.0266559","DOIUrl":"https://doi.org/10.1063/5.0266559","url":null,"abstract":"We investigated the ultrafast structural dynamics of cyclobutanone following photoexcitation at λ = 200 nm using gas-phase megaelectronvolt ultrafast electron diffraction. Our investigation complements the simulation studies of the same process within this special issue. It provides information about both electronic state population and structural dynamics through well-separable inelastic and elastic electron scattering signatures. We observe the depopulation of the photoexcited S2 state of cyclobutanone with n3s Rydberg character through its inelastic electron scattering signature with a time constant of (0.29 ± 0.2) ps toward the S1 state. The S1 state population undergoes ring-opening via a Norrish Type-I reaction, likely while passing through a conical intersection with S0. The corresponding structural changes can be tracked by elastic electron scattering signatures. These changes appear with a delay of (0.14 ± 0.05) ps with respect to the initial photoexcitation, which is less than the S2 depopulation time constant. This behavior provides evidence for the ballistic nature of the ring-opening once the S1 state is reached. The resulting biradical species react further within (1.2 ± 0.2) ps via two rival fragmentation channels yielding ketene and ethylene, or propene and carbon monoxide. Our study showcases the value of both gas-phase ultrafast diffraction studies as an experimental benchmark for nonadiabatic dynamics simulation methods and the limits in the interpretation of such experimental data without comparison with such simulations.","PeriodicalId":15313,"journal":{"name":"Journal of Chemical Physics","volume":"162 18","pages":""},"PeriodicalIF":3.1,"publicationDate":"2025-05-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143993976","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

apoCHARMM: High-performance molecular dynamics simulations on GPUs for advanced simulation methods. apoCHARMM：基于gpu的高性能分子动力学模拟，用于高级模拟方法。

IF 3.1 2区化学

Journal of Chemical Physics Pub Date : 2025-05-14 DOI: 10.1063/5.0264937

Samarjeet Prasad, Felix Aviat, James E Gonzales, Bernard R Brooks

{"title":"apoCHARMM: High-performance molecular dynamics simulations on GPUs for advanced simulation methods.","authors":"Samarjeet Prasad, Felix Aviat, James E Gonzales, Bernard R Brooks","doi":"10.1063/5.0264937","DOIUrl":"10.1063/5.0264937","url":null,"abstract":"We present apoCHARMM, a high-performance molecular dynamics (MD) engine optimized for graphics processing unit (GPU) architectures, designed to accelerate the simulation of complex molecular systems. The distinctive features of apoCHARMM include single-GPU support for multiple Hamiltonians, computation of a full virial tensor for each Hamiltonian, and full support for orthorhombic periodic systems in both P1 and P21 space groups. Multiple Hamiltonians on a single GPU permit rapid single-GPU multi-dimensional replica exchange methods, multi-state enveloping distribution sampling methods, and several efficient free energy methods where efficiency is gained by eliminating post-processing requirements. The combination of these capabilities enables constant-pH molecular dynamics in explicit solvent with enveloping distribution sampling, where Hamiltonian replica exchange can be performed on a single GPU with minimal host-GPU memory transfers. A full atomic virial tensor allows support for many different pressure, surface tension, and temperature ensembles. Support for orthorhombic P21 systems allows for the simulation of lipid bilayers, where the two leaflets have equalized chemical potentials. apoCHARMM uses CUDA and modern C++ to enable efficient computation of energy, force, restraint, constraint, and integration calculations directly on the GPU. This GPU-exclusive design focus minimizes host-GPU memory transfers, ensuring optimal performance during simulations, with such transfers occurring only during logging or trajectory saving. Benchmark tests demonstrate that apoCHARMM achieves competitive or superior performance when compared to other GPU-based MD engines, positioning it as a versatile and useful tool for the molecular dynamics community.","PeriodicalId":15313,"journal":{"name":"Journal of Chemical Physics","volume":"162 18","pages":""},"PeriodicalIF":3.1,"publicationDate":"2025-05-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12074570/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144020079","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

A perspective marking 20 years of using permutationally invariant polynomials for molecular potentials. 20年来使用排列不变多项式计算分子电位的展望。

IF 3.1 2区化学

Journal of Chemical Physics Pub Date : 2025-05-14 DOI: 10.1063/5.0268420

Joel M Bowman, Chen Qu, Riccardo Conte, Apurba Nandi, Paul L Houston, Qi Yu

{"title":"A perspective marking 20 years of using permutationally invariant polynomials for molecular potentials.","authors":"Joel M Bowman, Chen Qu, Riccardo Conte, Apurba Nandi, Paul L Houston, Qi Yu","doi":"10.1063/5.0268420","DOIUrl":"https://doi.org/10.1063/5.0268420","url":null,"abstract":"This Perspective is focused on permutationally invariant polynomials (PIPs). Since their introduction in 2004 and first use in developing a fully permutationally invariant potential for the highly fluxional cation CH5+, PIPs have found widespread use in developing machine learned potentials (MLPs) for isolated molecules, chemical reactions, clusters, condensed phase, and materials. More than 100 potentials have been reported using PIPs. The popularity of PIPs for MLPs stems from their fundamental property of being invariant with respect to permutations of like atoms; this is a fundamental property of potential energy surfaces. This is achieved using global descriptors and, thus, without using an atom-centered approach (which is manifestly fully permutationally invariant). PIPs have been used directly for linear regression fitting of electronic energies and gradients for complex energy landscapes to chemical reactions with numerous product channels. PIPs have also been used as inputs to neural network and Gaussian process regression methods and in many-body (atom-centered, water monomer, etc.) applications, notably for gold standard potentials for water. Here, we focus on the progress and usage of PIPs since 2018, when the last review of PIPs was done by our group.","PeriodicalId":15313,"journal":{"name":"Journal of Chemical Physics","volume":"162 18","pages":""},"PeriodicalIF":3.1,"publicationDate":"2025-05-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143966156","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

Facile synthesis of carbon-coated silicon nanocomposite with tremella-like porous structure for superior lithium-ion storage. 具有银耳状多孔结构的碳包覆硅纳米复合材料的简单合成。

IF 3.1 2区化学

Journal of Chemical Physics Pub Date : 2025-05-14 DOI: 10.1063/5.0265543

Lihua Ma, Jibin Tian, Xiaozhong Zhou

{"title":"Facile synthesis of carbon-coated silicon nanocomposite with tremella-like porous structure for superior lithium-ion storage.","authors":"Lihua Ma, Jibin Tian, Xiaozhong Zhou","doi":"10.1063/5.0265543","DOIUrl":"https://doi.org/10.1063/5.0265543","url":null,"abstract":"Silicon/carbon (Si/C) composites have been envisaged as one of the most promising anode materials for the next-generation lithium-ion batteries (LIBs) with high energy density, and constructing reasonable and cross-scale structures is crucial adjective for high-performance Si/C electrodes. Herein, a facile synthesis strategy was developed by combining gel coating, carbonization, and molten salt-assisted magnesiothermic reduction (MSA-MR), and a unique tremella-like Si/C composite with internal void structure (IV-Si/C) was successfully prepared. The working mechanisms of both sodium alginate (SA) and molten salt (NaCl) on the successful preparation of the target IV-Si/C nanocomposite were also investigated in detail. It was demonstrated that, α-L-guluronic (G) blocks in SA can be cross-linked with cations to promote the interactions with silicon dioxide (SiO2) particles, boosting uniform distribution of nanosized Si particles in the SA-derived carbon matrix. Meanwhile, NaCl generated from SA not only effectively boosted the crystallization of SiO2 during the high-temperature carbonization process but also can effectively inhibit the formation of inert SiC and strengthen reduction of carbon during the MSA-MR treatment, resulting in successful preparation of the tremella-like Si/C composite with abundant internal voids. Benefitting from its unique structure, when used as an alternative anode material for electrochemical lithium storage, the as-obtained IV-Si/C nanocomposite delivered a high reversible specific capacity of 1899.6 mAh g-1 with an initial Coulomb efficiency of 75.96% and superior rate capability and long-term cycling stability. This facile and low-cost synthesis strategy may shed light on the controllable preparation of functional nanomaterials with unique structures, especially high-performance Si/C anode materials for their large-scale application in LIBs.","PeriodicalId":15313,"journal":{"name":"Journal of Chemical Physics","volume":"162 18","pages":""},"PeriodicalIF":3.1,"publicationDate":"2025-05-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143992883","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 local and global dynamics of atactic polystyrene: A coarse-grained molecular dynamics simulation study. 无规聚苯乙烯的温度依赖局部和全局动力学：粗粒度分子动力学模拟研究。

IF 3.1 2区化学

Journal of Chemical Physics Pub Date : 2025-05-14 DOI: 10.1063/5.0253982

Jiaxian Zhang, Hongxia Guo

{"title":"Temperature-dependent local and global dynamics of atactic polystyrene: A coarse-grained molecular dynamics simulation study.","authors":"Jiaxian Zhang, Hongxia Guo","doi":"10.1063/5.0253982","DOIUrl":"https://doi.org/10.1063/5.0253982","url":null,"abstract":"A systematic coarse-grained (CG) model, as a promising and helpful tool to access the accurate knowledge of the local and global polymer dynamics of real polymers, is required to preserve structural, thermodynamic, and dynamic properties of the underlying atomistic model over a wide temperature range. In the present work, to explore the temperature-dependent local and global dynamic properties of atactic polystyrene (PS) as well as the dynamic consistency of a PS CG model constructed via a structure- and thermodynamics-based CG approach with the united-atom (UA) counterpart, we have investigated and compared the translational and rotational dynamics of the two models in the scale from a single monomer to a global chain in a broad temperature range. The CG model accurately reproduces the time-dependent translational diffusion scaling and the shift from a multistep relaxation to a single-step long-time decay process with increasing span of bond vectors as the UA model. There exists the coupling of the conformational relaxation and diffusion of the PS chains to the local structural α-relaxation. Both diffusion coefficients and relaxation times of the UA and CG models show the same temperature dependence and follow a power-law relationship of mode-coupling theory. These findings advance our understanding of the complex dynamics of atactic PS and give a sounder basis for the further development of CG PS models with the (time-dependent) frictional correction to perform a quantitative study of structural relaxation and dynamical heterogeneity near glass transition temperature.","PeriodicalId":15313,"journal":{"name":"Journal of Chemical Physics","volume":"162 18","pages":""},"PeriodicalIF":3.1,"publicationDate":"2025-05-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144016941","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

Ab initio simulation of spin-vibronic spectra of methoxy radical. 甲氧基自由基自旋振动谱的从头算模拟。

IF 3.1 2区化学

Journal of Chemical Physics Pub Date : 2025-05-14 DOI: 10.1063/5.0266367

Ketan Sharma, Oleg A Vasilyev, John F Stanton, Terry A Miller

{"title":"Ab initio simulation of spin-vibronic spectra of methoxy radical.","authors":"Ketan Sharma, Oleg A Vasilyev, John F Stanton, Terry A Miller","doi":"10.1063/5.0266367","DOIUrl":"https://doi.org/10.1063/5.0266367","url":null,"abstract":"Despite the fact that experimental and theoretical work on the spectrum of methoxy has stretched from the microwave to the ultraviolet and proceeded for nearly 50 years, parts of the spectrum have remained a challenge to simulate theoretically and make reliable line-by-line assignments. The spectral complexity arises because the radical has a non-zero electron spin and significant vibronic coupling between the two electronic components of the ground state due to the presence of a conical intersection. This work describes a completely ab initio effort to understand and assign the spin-vibronic levels of the X̃2E state from 0 to above 3000 cm-1, a region that includes the fundamental transitions of the C-H symmetric and asymmetric stretches that have not previously been identified uniquely. A potential energy surface for methoxy was calculated at the equation-of-motion (EOM)-coupled cluster singles, doubles, and triples (CCSDT)/atomic natural orbital (ANO1) level of theory. Subsequently, this potential energy surface was fit to a quartic power series expansion of all nine vibrational normal coordinates (as determined at the minimum of the conical intersection) by the use of a machine-learning-based algorithm. After the addition of spin-orbit coupling, the spin-vibronic problem was solved using both the Krylov-Schur and Lanczos algorithms with the SOCJT3 software to converge eigenvalues up to 3500 cm-1 and their eigenvectors. The latter were used, in conjunction with the calculated dipole moment and its derivatives (calculated using finite differences at the EOM-CCSDT/ANO1 level), to determine spectral intensities for the spin-vibronic spectra. The calculated transition frequencies and intensities were used to simulate and assign the observed transitions of the spin-vibronic spectra of the radical. The credibility of the assignments and their significance is discussed in detail.","PeriodicalId":15313,"journal":{"name":"Journal of Chemical Physics","volume":"162 18","pages":""},"PeriodicalIF":3.1,"publicationDate":"2025-05-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144020599","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

Ab initio phase diagrams of binary alloys in the low solute concentration limit. 低溶质浓度极限下二元合金的从头算相图。

IF 3.1 2区化学

Journal of Chemical Physics Pub Date : 2025-05-14 DOI: 10.1063/5.0264856

Shambhu Bhandari Sharma, Shailesh Mehta, Dario Alfè

引用次数: 0

GPU acceleration of hybrid functional calculations in the SPARC electronic structure code. GPU加速混合泛函计算中的SPARC电子结构代码。

IF 3.1 2区化学

Journal of Chemical Physics Pub Date : 2025-05-14 DOI: 10.1063/5.0260892

Xin Jing, Abhiraj Sharma, John E Pask, Phanish Suryanarayana

引用次数: 0

Overcoming experimental obstacles in two-dimensional spectroscopy of a single molecule. 克服了单分子二维光谱的实验障碍。