Journal of Chemical Theory and Computation最新文献_第8页

Minimum Tracking Linear Response Hubbard and Hund Corrected Density Functional Theory in CP2K. CP2K 中的最小跟踪线性响应哈伯德和 Hund 校正密度泛函理论。

IF 5.7 1区化学

Journal of Chemical Theory and Computation Pub Date : 2024-10-22 Epub Date: 2024-10-03 DOI: 10.1021/acs.jctc.4c00964

Ziwei Chai, Rutong Si, Mingyang Chen, Gilberto Teobaldi, David D O'Regan, Li-Min Liu

{"title":"Minimum Tracking Linear Response Hubbard and Hund Corrected Density Functional Theory in CP2K.","authors":"Ziwei Chai, Rutong Si, Mingyang Chen, Gilberto Teobaldi, David D O'Regan, Li-Min Liu","doi":"10.1021/acs.jctc.4c00964","DOIUrl":"10.1021/acs.jctc.4c00964","url":null,"abstract":"We present the implementation of the Hubbard (U) and Hund (J) corrected Density Functional Theory (DFT + U + J) functionality in the Quickstep program, which is part of the CP2K suite. The tensorial and Löwdin subspace representations are implemented and compared. Full analytical DFT + U + J forces are implemented and benchmarked for the tensorial and Löwdin representations. We also present the implementation of the recently proposed minimum-tracking linear-response method that enables the U and J parameters to be calculated on first-principles basis without reference to the Kohn-Sham eigensystem. These implementations are benchmarked against recent results for different materials properties including DFT + U band gap opening in NiO, the relative stability of various polaron distributions in TiO2, the dependence of the calculated TiO2 band gap on +J corrections, and, finally, the role of the +U and +J corrections for the computed properties of a series of the hexahydrated transition metals. Our implementation provides results consistent with those already reported in the literature from comparable methods. We conclude the contribution with tests on the influence of the Löwdin orthonormalization on the occupancies, calculated parameters, and derived properties.","PeriodicalId":45,"journal":{"name":"Journal of Chemical Theory and Computation","volume":null,"pages":null},"PeriodicalIF":5.7,"publicationDate":"2024-10-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142363442","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"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 Chemical Insights into DNA Nucleobase Oxidation: Bridging Theory and Experiment DNA 核碱基氧化的量子化学启示：理论与实验的桥梁

IF 5.7 1区化学

Journal of Chemical Theory and Computation Pub Date : 2024-10-22 DOI: 10.1021/acs.jctc.4c0104510.1021/acs.jctc.4c01045

Francesco Ambrosio, Alessandro Landi, Andrea Peluso and Amedeo Capobianco*,

引用次数: 0

Quantum Molecular Charge-Transfer Model for Multistep Auger-Meitner Decay Cascade Dynamics. 多步奥格-迈特纳衰变级联动力学的量子分子电荷转移模型。

IF 5.7 1区化学

Journal of Chemical Theory and Computation Pub Date : 2024-10-22 Epub Date: 2024-10-11 DOI: 10.1021/acs.jctc.4c00778

Adam E A Fouda, Stephen H Southworth, Phay J Ho

{"title":"Quantum Molecular Charge-Transfer Model for Multistep Auger-Meitner Decay Cascade Dynamics.","authors":"Adam E A Fouda, Stephen H Southworth, Phay J Ho","doi":"10.1021/acs.jctc.4c00778","DOIUrl":"10.1021/acs.jctc.4c00778","url":null,"abstract":"The fragmentation of molecular cations following inner-shell decay processes in molecules containing heavy elements underpins the X-ray damage effects observed in X-ray scattering measurements of biological and chemical materials, as well as in medical applications involving Auger electron-emitting radionuclides. Traditionally, these processes are modeled using simulations that describe the electronic structure at an atomic level, thereby omitting molecular bonding effects. This work addresses the gap by introducing a novel approach that couples Auger-Meitner decay to nuclear dynamics across multiple decay steps, by developing a decay spawning dynamics algorithm and applying it to potential energy surfaces characterized with ab initio molecular dynamics simulations. We showcase the approach on a model decay cascade following K-shell ionization of IBr and subsequent Kβ fluorescence decay. We examine two competing channels that undergo two decay steps, resulting in ion pairs with a total 3+ charge state. This approach provides a continuous description of the electron transfer dynamics occurring during the multistep decay cascade and molecular fragmentation, revealing the combined inner-shell decay and charge transfer time scale to be approximately 75 fs. Our computed kinetic energies of ion fragments show good agreement with experimental data.","PeriodicalId":45,"journal":{"name":"Journal of Chemical Theory and Computation","volume":null,"pages":null},"PeriodicalIF":5.7,"publicationDate":"2024-10-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142405714","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"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

Analytical Evaluation of Ground State Gradients in Quantum Electrodynamics Coupled Cluster Theory. 量子电动力学耦合簇理论中基态梯度的分析评估。

IF 5.7 1区化学

Journal of Chemical Theory and Computation Pub Date : 2024-10-22 Epub Date: 2024-10-11 DOI: 10.1021/acs.jctc.4c00763

Marcus T Lexander, Sara Angelico, Eirik F Kjønstad, Henrik Koch

引用次数: 0

Metallicious: Automated Force-Field Parameterization of Covalently Bound Metals for Supramolecular Structures. Metallicious：超分子结构共价结合金属的自动力场参数化。

IF 5.7 1区化学

Journal of Chemical Theory and Computation Pub Date : 2024-10-22 Epub Date: 2024-10-07 DOI: 10.1021/acs.jctc.4c00850

Tomasz K Piskorz, Bernadette Lee, Shaoqi Zhan, Fernanda Duarte

{"title":"Metallicious: Automated Force-Field Parameterization of Covalently Bound Metals for Supramolecular Structures.","authors":"Tomasz K Piskorz, Bernadette Lee, Shaoqi Zhan, Fernanda Duarte","doi":"10.1021/acs.jctc.4c00850","DOIUrl":"10.1021/acs.jctc.4c00850","url":null,"abstract":"Metal ions play a central, functional, and structural role in many molecular structures, from small catalysts to metal-organic frameworks (MOFs) and proteins. Computational studies of these systems typically employ classical or quantum mechanical approaches or a combination of both. Among classical models, only the covalent metal model reproduces both geometries and charge transfer effects but requires time-consuming parameterization, especially for supramolecular systems containing repetitive units. To streamline this process, we introduce metallicious, a Python tool designed for efficient force-field parameterization of supramolecular structures. Metallicious has been tested on diverse systems including supramolecular cages, knots, and MOFs. Our benchmarks demonstrate that parameters accurately reproduce the reference properties obtained from quantum calculations and crystal structures. Molecular dynamics simulations of the generated structures consistently yield stable simulations in explicit solvent, in contrast to similar simulations performed with nonbonded and cationic dummy models. Overall, metallicious facilitates the atomistic modeling of supramolecular systems, key for understanding their dynamic properties and host-guest interactions. The tool is freely available on GitHub (https://github.com/duartegroup/metallicious).","PeriodicalId":45,"journal":{"name":"Journal of Chemical Theory and Computation","volume":null,"pages":null},"PeriodicalIF":5.7,"publicationDate":"2024-10-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11500408/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142379407","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"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

Active Learning of Boltzmann Samplers and Potential Energies with Quantum Mechanical Accuracy. 主动学习具有量子力学精度的波尔兹曼采样器和势能。

IF 5.7 1区化学

Journal of Chemical Theory and Computation Pub Date : 2024-10-22 Epub Date: 2024-10-06 DOI: 10.1021/acs.jctc.4c00506

Ana Molina-Taborda, Pilar Cossio, Olga Lopez-Acevedo, Marylou Gabrié

引用次数: 0

Quantum Equation-of-Motion Method with Single, Double, and Triple Excitations. 单、双、三激发量子运动方程法

IF 5.7 1区化学

Journal of Chemical Theory and Computation Pub Date : 2024-10-22 Epub Date: 2024-10-07 DOI: 10.1021/acs.jctc.4c01071

Yuhan Zheng, Zhijie Sun, Jie Liu, Yi Fan, Zhenyu Li, Jinlong Yang

{"title":"Quantum Equation-of-Motion Method with Single, Double, and Triple Excitations.","authors":"Yuhan Zheng, Zhijie Sun, Jie Liu, Yi Fan, Zhenyu Li, Jinlong Yang","doi":"10.1021/acs.jctc.4c01071","DOIUrl":"10.1021/acs.jctc.4c01071","url":null,"abstract":"The quantum equation-of-motion (qEOM) method with single and double excitations (qEOM-SD) has been proposed to study electronically excited states, but it fails to handle states dominated by double excitations. In this work, we reformulate the qEOM method within the effective Hamiltonian framework that satisfies the killer condition, and then present an efficient implementation incorporating single, double, and triple excitations. To reduce computational complexity, we employ point-group symmetry and perturbation theory to screen triple excitations, effectively reducing the scaling from No6Nv6 to No5Nv5, where No and Nv are the numbers of occupied and virtual spin orbitals, respectively. Furthermore, we account for the effect of neglected triple excitations by introducing a perturbative correction to the excitation energy. We apply this method to challenging cases where the qEOM-SD method exhibits significant errors, such as the 2 1Δ state of CH+ and the 2 1Σ state of HF. Our new method achieves energy errors below 0.18 eV while incorporating less than 8.2% of triple excitations. Additionally, we extend the operator screening technique to the quantum subspace expansion method for the efficient inclusion of selected triple excitations.","PeriodicalId":45,"journal":{"name":"Journal of Chemical Theory and Computation","volume":null,"pages":null},"PeriodicalIF":5.7,"publicationDate":"2024-10-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142379411","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"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

Response Matching for Generating Materials and Molecules. 生成材料和分子的响应匹配。

IF 5.7 1区化学

Journal of Chemical Theory and Computation Pub Date : 2024-10-22 Epub Date: 2024-10-04 DOI: 10.1021/acs.jctc.4c00998

Bingqing Cheng

{"title":"Response Matching for Generating Materials and Molecules.","authors":"Bingqing Cheng","doi":"10.1021/acs.jctc.4c00998","DOIUrl":"10.1021/acs.jctc.4c00998","url":null,"abstract":"Diffusion models have recently emerged as powerful tools for the generation of new molecular and material structures. The key insight is that the noise in these models is related to the response of the atoms to displacement, and the denoising step is thus analogous to the geometry relaxation of atomistic systems starting from a random structure. Building on this, we present a generative method called Response Matching (RM), which leverages the fact that each stable material or molecule exists at the minimum of its potential energy surface. Any perturbation induces a response in energy and stress, driving the structure back to equilibrium. Matching this response is closely related to score matching in diffusion models. Another important aspect of state-of-the-art diffusion models is the incorporation of physical symmetries such as translation, rotation, and periodicity. RM employs a machine learning interatomic potential and random structure search as the denoising model, inherently respecting these symmetries and exploiting the locality of atomic interactions. RM handles both molecules and bulk materials under the same framework. Its efficiency and generalization are demonstrated on three systems: a small organic molecular data set, stable crystals from the Materials Project, and one-shot learning on a single diamond configuration.","PeriodicalId":45,"journal":{"name":"Journal of Chemical Theory and Computation","volume":null,"pages":null},"PeriodicalIF":5.7,"publicationDate":"2024-10-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11500275/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142370218","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"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

Δ-Machine Learning to Elevate DFT-Based Potentials and a Force Field to the CCSD(T) Level Illustrated for Ethanol. 通过 Δ 机器学习将基于 DFT 的势能和力场提升到 CCSD(T) 水平的乙醇图解。

IF 5.7 1区化学

Journal of Chemical Theory and Computation Pub Date : 2024-10-22 Epub Date: 2024-10-03 DOI: 10.1021/acs.jctc.4c00977

Apurba Nandi, Priyanka Pandey, Paul L Houston, Chen Qu, Qi Yu, Riccardo Conte, Alexandre Tkatchenko, Joel M Bowman

{"title":"Δ-Machine Learning to Elevate DFT-Based Potentials and a Force Field to the CCSD(T) Level Illustrated for Ethanol.","authors":"Apurba Nandi, Priyanka Pandey, Paul L Houston, Chen Qu, Qi Yu, Riccardo Conte, Alexandre Tkatchenko, Joel M Bowman","doi":"10.1021/acs.jctc.4c00977","DOIUrl":"10.1021/acs.jctc.4c00977","url":null,"abstract":"Progress in machine learning has facilitated the development of potentials that offer both the accuracy of first-principles techniques and vast increases in the speed of evaluation. Recently, Δ-machine learning has been used to elevate the quality of a potential energy surface (PES) based on low-level, e.g., density functional theory (DFT) energies and gradients to close to the gold-standard coupled cluster level of accuracy. We have demonstrated the success of this approach for molecules, ranging in size from H3O+ to 15-atom acetyl-acetone and tropolone. These were all done using the B3LYP functional. Here, we investigate the generality of this approach for the PBE, M06, M06-2X, and PBE0 + MBD functionals, using ethanol as the example molecule. Linear regression with permutationally invariant polynomials is used to fit both low-level and correction PESs. These PESs are employed for standard RMSE analysis for training and test data sets, and then general fidelity tests such as energetics of stationary points, normal-mode frequencies, and torsional potentials are examined. We achieve similar improvements in all cases. Interestingly, we obtained significant improvement over DFT gradients where coupled cluster gradients were not used to correct the low-level PES. Finally, we present some results for correcting a recent molecular mechanics force field for ethanol and comment on the possible generality of this approach.","PeriodicalId":45,"journal":{"name":"Journal of Chemical Theory and Computation","volume":null,"pages":null},"PeriodicalIF":5.7,"publicationDate":"2024-10-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11500277/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142363443","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"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

Enhancing Optoelectronic Performance of All-Inorganic Double Perovskites via Halogen Doping: Synergistic Screening Strategies and Multiscale Simulations. 通过掺杂卤素提高全无机双包晶石的光电性能：协同筛选策略与多尺度模拟。

IF 5.7 1区化学

Journal of Chemical Theory and Computation Pub Date : 2024-10-22 Epub Date: 2024-10-11 DOI: 10.1021/acs.jctc.4c01115

Xifeng Fu, Zhi-Ying Zhao, Sai Guo, Zi-Ang Nan, Lingyi Meng, Can-Zhong Lu

{"title":"Enhancing Optoelectronic Performance of All-Inorganic Double Perovskites via Halogen Doping: Synergistic Screening Strategies and Multiscale Simulations.","authors":"Xifeng Fu, Zhi-Ying Zhao, Sai Guo, Zi-Ang Nan, Lingyi Meng, Can-Zhong Lu","doi":"10.1021/acs.jctc.4c01115","DOIUrl":"10.1021/acs.jctc.4c01115","url":null,"abstract":"Designing all-inorganic double perovskites through element mixing is a promising strategy to enhance their optoelectronic performance and structural stability. The complex interplay between multilevel structures and optoelectronic properties in element-mixed double perovskites necessitates further in-depth theoretical exploration. In this study, we employ screening strategies and multiscale simulations combining first-principles methods and device-scale continuum models to identify two novel element-mixed compounds, Rb2AgInCl3I3 and Cs2AgInCl3I3, as promising candidates for photovoltaic applications. These compounds exhibit favorable structural factors and suitable direct band gaps. Theoretical investigations using first-principles methods with the HSE06 functional reveal direct band gaps of 0.98 and 1.26 eV for Rb2AgInCl3I3 and Cs2AgInCl3I3, respectively, with corresponding optical absorption coefficients exceeding 105 cm-1 in the visible light range. Cs2AgInCl3I3 features high charge mobilities of approximately 20 cm2·V-1·s-1 and a notable single-junction spectroscopic limited maximum efficiency (SLME) of 25.54%. Further analysis using the device-scale continuum model simulated the nonradiative recombination effects on power conversion efficiency, integrating quantum-mechanically calculated optoelectronic properties. These theoretical investigations, which bridge composition engineering with multiscale simulations, provide valuable insights into screening novel, lead-free, halogen-mixed double metal perovskite optoelectronic devices, highlighting their potential for high-performance solar energy applications.","PeriodicalId":45,"journal":{"name":"Journal of Chemical Theory and Computation","volume":null,"pages":null},"PeriodicalIF":5.7,"publicationDate":"2024-10-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142405713","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"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