Journal of Chemical Theory and Computation最新文献

Second-Order Complete Active Space Perturbation Theory (CASPT2) and N-Electron Valence State Perturbation Theory (NEVPT2) Based on Adaptive Sampling Configuration Interaction Self-Consistent Field (ASCI-SCF). 基于自适应采样组态相互作用自一致场的二阶完全主动空间微扰理论（CASPT2）和n电子价态微扰理论（NEVPT2）。

IF 5.5 1区化学

Journal of Chemical Theory and Computation Pub Date : 2025-05-19 DOI: 10.1021/acs.jctc.5c00190

Kyeong Su Min,Jae Woo Park

引用次数: 0

Computing Bulk Phase IR Spectra from Finite Cluster Data via Equivariant Neural Networks. 用等变神经网络从有限簇数据计算体相红外光谱。

IF 5.5 1区化学

Journal of Chemical Theory and Computation Pub Date : 2025-05-17 DOI: 10.1021/acs.jctc.5c00420

Aman Jindal,Philipp Schienbein,Banshi Das,Dominik Marx

引用次数: 0

Computing Excited States of Molecules Using Normalizing Flows. 用归一化流计算分子激发态。

IF 5.7 1区化学

Journal of Chemical Theory and Computation Pub Date : 2025-05-15 DOI: 10.1021/acs.jctc.5c00590

Yahya Saleh, Álvaro Fernández Corral, Emil Vogt, Armin Iske, Jochen Küpper, Andrey Yachmenev

{"title":"Computing Excited States of Molecules Using Normalizing Flows.","authors":"Yahya Saleh, Álvaro Fernández Corral, Emil Vogt, Armin Iske, Jochen Küpper, Andrey Yachmenev","doi":"10.1021/acs.jctc.5c00590","DOIUrl":"https://doi.org/10.1021/acs.jctc.5c00590","url":null,"abstract":"Calculations of highly excited and delocalized molecular vibrational states are computationally challenging tasks, which strongly depend on the choice of coordinates for describing vibrational motions. We introduce a new method that leverages normalizing flows, i.e, parametrized invertible functions, to learn optimal vibrational coordinates that satisfy the variational principle. This approach produces coordinates tailored to the vibrational problem at hand, significantly increasing the accuracy and enhancing the basis set convergence of the calculated energy spectrum. The efficiency of the method is demonstrated in calculations of the 100 lowest excited vibrational states of H2S, H2CO, and HCN/HNC. The method effectively captures the essential vibrational behavior of molecules by enhancing the separability of the Hamiltonian and hence allows for an effective assignment of approximate quantum numbers. We demonstrate that the optimized coordinates are transferable across different levels of basis set truncation, enabling a cost-efficient protocol for computing vibrational spectra of high-dimensional systems.","PeriodicalId":45,"journal":{"name":"Journal of Chemical Theory and Computation","volume":" ","pages":""},"PeriodicalIF":5.7,"publicationDate":"2025-05-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144074921","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

Kinetics and Mechanism of Phase Separation in Ternary Lipid Mixtures Containing APP C99: Atomistic vs Coarse-Grained MD Simulations. 含APP C99的三元脂质混合物相分离动力学和机理：原子与粗粒度MD模拟。

IF 5.7 1区化学

Journal of Chemical Theory and Computation Pub Date : 2025-05-15 DOI: 10.1021/acs.jctc.5c00016

George A Pantelopulos, Sangram Prusty, Asanga Bandara, John E Straub

{"title":"Kinetics and Mechanism of Phase Separation in Ternary Lipid Mixtures Containing APP C99: Atomistic vs Coarse-Grained MD Simulations.","authors":"George A Pantelopulos, Sangram Prusty, Asanga Bandara, John E Straub","doi":"10.1021/acs.jctc.5c00016","DOIUrl":"https://doi.org/10.1021/acs.jctc.5c00016","url":null,"abstract":"The phase separation of lipid bilayers, composed of mixtures of saturated and unsaturated lipids and cholesterol, is a topic of fundamental importance in membrane biophysics and cell biology. The formation of lipid domains, including liquid-disordered domains enriched in unsaturated lipids and liquid-ordered domains enriched in saturated lipids and cholesterol, is believed to be essential to the function of many membrane proteins. Experiment, theory, and simulation have been used to develop a general understanding of the thermodynamic driving forces underlying phase separation in ternary and quaternary lipid mixtures. However, the kinetics of early events in lipid phase separation in the presence of transmembrane proteins remain relatively understudied. Using large-scale all-atom and coarse-grained simulations, we explore the kinetics and phase separation of ternary lipid mixtures of saturated lipid, unsaturated lipid, and cholesterol in the presence of transmembrane proteins. Order parameters employed in the Cahn-Hilliard theory provide insight into the kinetics and mechanism of lipid phase separation. We observe three distinct time regimes in the phase separation process: a shorter exponential time phase, followed by a power-law phase, and then a longer plateau phase. Comparison of lipid, protein, and lipid-protein dynamics between all-atom and coarse-grained models identifies both quantitative and qualitative differences and similarities in the phase separation kinetics. Moreover, timescaling of the dynamics of the AA and CG simulations yields a similar kinetic mechanism of phase separation. The findings of this study elucidate fundamental aspects of membrane biophysics and contribute to ongoing efforts to define the role of lipid rafts in the structure and function of the cellular membrane.","PeriodicalId":45,"journal":{"name":"Journal of Chemical Theory and Computation","volume":" ","pages":""},"PeriodicalIF":5.7,"publicationDate":"2025-05-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144074924","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

Accurate Prediction of Open-Circuit Voltages of Lithium-Ion Batteries via Delta Learning. 基于Delta学习的锂离子电池开路电压精确预测。

IF 5.5 1区化学

Journal of Chemical Theory and Computation Pub Date : 2025-05-15 DOI: 10.1021/acs.jctc.5c00168

Wai Yuet Chiu,Chongzhi Zhang,Rongzhi Gao,Ziyang Hu,GuanHua Chen

{"title":"Accurate Prediction of Open-Circuit Voltages of Lithium-Ion Batteries via Delta Learning.","authors":"Wai Yuet Chiu,Chongzhi Zhang,Rongzhi Gao,Ziyang Hu,GuanHua Chen","doi":"10.1021/acs.jctc.5c00168","DOIUrl":"https://doi.org/10.1021/acs.jctc.5c00168","url":null,"abstract":"Accurate prediction of lithium-ion battery capacity before material synthesis is crucial for accelerating battery material discovery. The capacity can be theoretically determined by integrating open-circuit voltage vs state of charge (OCV-SoC) curves of electrode materials. OCV-SoC curves are traditionally computed using first-principles methods, either through geometry optimization (GO) with density functional theory (DFT) or molecular dynamics (MD) simulations of lithiation/delithiation processes using DFT or force fields. While MD simulations incorporate temperature effects that GO lacks, even DFT-based MD simulated OCV-SoC curves show systematic deviations from experimental results due to inherent approximations in DFT functionals. In this study, we performed MD simulations on 43 cathode materials to obtain their OCV-SoC curves. Initial results showed only moderate agreement with experimental data, yielding a coefficient of determination (R2) of 0.249 and a mean absolute error (MAE) of 1.561 V. Considering the scarcity of data, we implemented a delta learning approach to calibrate the MD results without substantial computational overhead, achieving an improved R2 of 0.933 and an MAE of 0.131 V on the testing set. This calibration method significantly enhanced the accuracy of energy density predictions, reducing the MAE from 106.0 to 10.7 Wh/kg. We also developed an automated delta learning platform to make this approach accessible to researchers without machine learning expertise.","PeriodicalId":45,"journal":{"name":"Journal of Chemical Theory and Computation","volume":"5 1","pages":""},"PeriodicalIF":5.5,"publicationDate":"2025-05-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144065890","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

Correction to "Approximate Hamiltonians from a Linear Vibronic Coupling Model for Solution-Phase Spin Dynamics". 修正“溶液-相自旋动力学线性振动耦合模型的近似哈密顿量”。

IF 5.7 1区化学

Journal of Chemical Theory and Computation Pub Date : 2025-05-15 DOI: 10.1021/acs.jctc.5c00683

Toby R C Thompson, Jakob K Staab, Nicholas F Chilton

引用次数: 0

HDXRank: A Deep Learning Framework for Ranking Protein Complex Predictions with Hydrogen-Deuterium Exchange Data. HDXRank：基于氢-氘交换数据的蛋白质复合物预测排序的深度学习框架。

IF 5.5 1区化学

Journal of Chemical Theory and Computation Pub Date : 2025-05-14 DOI: 10.1021/acs.jctc.5c00175

Liyao Wang,Andrejs Tučs,Songting Ding,Koji Tsuda,Adnan Sljoka

{"title":"HDXRank: A Deep Learning Framework for Ranking Protein Complex Predictions with Hydrogen-Deuterium Exchange Data.","authors":"Liyao Wang,Andrejs Tučs,Songting Ding,Koji Tsuda,Adnan Sljoka","doi":"10.1021/acs.jctc.5c00175","DOIUrl":"https://doi.org/10.1021/acs.jctc.5c00175","url":null,"abstract":"Accurate modeling of protein-protein complex structures is essential for understanding biological mechanisms. Hydrogen-deuterium exchange (HDX) experiments provide valuable insights into binding interfaces. Incorporating HDX data into protein complex modeling workflows offers a promising approach to improve prediction accuracy. Here, we developed HDXRank, a graph neural network (GNN)-based framework for candidate structure ranking utilizing alignment with HDX experimental data. Trained on a newly curated HDX data set, HDXRank captures nuanced local structural features critical for accurate HDX profile prediction. This versatile framework can be integrated with a variety of protein complex modeling tools, transforming the HDX profile alignment into a model quality metric. HDXRank demonstrates effectiveness at ranking models generated by rigid docking or AlphaFold, successfully prioritizing functionally relevant models and improving prediction quality across all tested protein targets. These findings underscore HDXRank's potential to become a pivotal tool for understanding molecular recognition in complex biological systems.","PeriodicalId":45,"journal":{"name":"Journal of Chemical Theory and Computation","volume":"28 1","pages":""},"PeriodicalIF":5.5,"publicationDate":"2025-05-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143982492","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

Frozen-Pair-Type pCCD-Based Methods and Their Double Ionization Variants to Predict Properties of Prototypical BN-Doped Light Emitters. 基于冷冻对型pccd的方法及其双电离变体预测原型bn掺杂光源的性能。

IF 5.5 1区化学

Journal of Chemical Theory and Computation Pub Date : 2025-05-14 DOI: 10.1021/acs.jctc.5c00057

Ram Dhari Pandey,Matheus Morato F de Moraes,Katharina Boguslawski,Pawel Tecmer

{"title":"Frozen-Pair-Type pCCD-Based Methods and Their Double Ionization Variants to Predict Properties of Prototypical BN-Doped Light Emitters.","authors":"Ram Dhari Pandey,Matheus Morato F de Moraes,Katharina Boguslawski,Pawel Tecmer","doi":"10.1021/acs.jctc.5c00057","DOIUrl":"https://doi.org/10.1021/acs.jctc.5c00057","url":null,"abstract":"Novel, robust, computationally efficient, and reliable theoretical methods are indispensable for the large-scale modeling of desired molecular properties. One such example is the orbital optimized pair coupled-cluster doubles (oo-pCCD) ansatz and its various CC extensions, which range from closed-shell ground- and excited-state models to open-shell variants. Specifically, the ionization-potential equation-of-motion frozen-pair (IP-EOM-fp)CC methods proved to be competitive with standard CC-type methods for modeling the ionization potentials of organic electronics. In this work, we extend the existing IP-EOM-pCCD-based methods to their double ionization potential (DIP) variants, resulting in various DIP-EOM-fpCC models, including up to double excitations. These methods open the way to reach open-shell singlet, triplet, and quintet states using various pCCD reference functions. Their accuracy is tested for the singlet-triplet gaps of the ortho-, meta-, and para-benzynes. Then, the most accurate models are applied to study the effects of boron and nitrogen doping on designing prototypical naphthalene-based donors and acceptors. Our results demonstrate consistent and reliable outcomes with standard methods and available experimental data. Most importantly, fpCC-type methods show slightly better performance than DIP-EOM-CCSD for strongly-correlated cases and similar performance for systems dominated by dynamical correlation when determining singlet-triplet gaps.","PeriodicalId":45,"journal":{"name":"Journal of Chemical Theory and Computation","volume":"36 1","pages":""},"PeriodicalIF":5.5,"publicationDate":"2025-05-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143945369","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

Molecular Polarizability under Vibrational Strong Coupling. 振动强耦合下的分子极化率。

IF 5.7 1区化学

Journal of Chemical Theory and Computation Pub Date : 2025-05-14 DOI: 10.1021/acs.jctc.5c00461

Thomas Schnappinger, Markus Kowalewski

{"title":"Molecular Polarizability under Vibrational Strong Coupling.","authors":"Thomas Schnappinger, Markus Kowalewski","doi":"10.1021/acs.jctc.5c00461","DOIUrl":"https://doi.org/10.1021/acs.jctc.5c00461","url":null,"abstract":"Polaritonic chemistry offers the possibility of modifying molecular properties and even influencing chemical reactivity through strong coupling between vibrational transitions and confined light modes in optical cavities. Despite considerable theoretical progress, and due to the complexity of the coupled light-matter system, the fundamental mechanism of how and if collective strong coupling can induce local changes in individual molecules is still unclear. We derive an analytical formulation of static polarizabilities within linear-response theory for molecules under strong coupling using the cavity Born-Oppenheimer Hartree-Fock ansatz. This ab-initio method consistently describes vibrational strong coupling and electron-photon interactions even for ensembles of molecules. For different types of molecular ensembles, we observed local changes in the polarizabilities and dipole moments that are induced by collective strong coupling. Furthermore, we used the polarizabilities to calculate vibro-polaritonic Raman spectra in the harmonic approximation. This allows us to comprehensively compare the effect of vibrational strong coupling on IR and Raman spectra on an equal footing.","PeriodicalId":45,"journal":{"name":"Journal of Chemical Theory and Computation","volume":" ","pages":""},"PeriodicalIF":5.7,"publicationDate":"2025-05-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144074925","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

Decomposition Analysis for Visualization of Noncovalent Interactions Based on the Fragment Molecular Orbital Method. 基于片段分子轨道法的非共价相互作用可视化分解分析。

IF 5.7 1区化学

Journal of Chemical Theory and Computation Pub Date : 2025-05-13 Epub Date: 2025-02-19 DOI: 10.1021/acs.jctc.4c01654

Dmitri G Fedorov, Diego Inostroza, Bastien Courbiere, Fréderic Guegan, Julia Contreras-García, Seiji Mori

引用次数: 0