Journal of Chemical Theory and Computation最新文献_第9页

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 5.5 1区化学

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

Francesco Ambrosio, Alessandro Landi, Andrea Peluso, Amedeo Capobianco

引用次数: 0

DFT-Based Permutationally Invariant Polynomial Potentials Capture the Twists and Turns of C14H30 基于 DFT 的排列不变多项式势能捕捉 C14H30 的曲折变化

IF 5.5 1区化学

Journal of Chemical Theory and Computation Pub Date : 2024-10-21 DOI: 10.1021/acs.jctc.4c00932

Chen Qu, Paul L. Houston, Thomas Allison, Barry I. Schneider, Joel M. Bowman

{"title":"DFT-Based Permutationally Invariant Polynomial Potentials Capture the Twists and Turns of C14H30","authors":"Chen Qu, Paul L. Houston, Thomas Allison, Barry I. Schneider, Joel M. Bowman","doi":"10.1021/acs.jctc.4c00932","DOIUrl":"https://doi.org/10.1021/acs.jctc.4c00932","url":null,"abstract":"Hydrocarbons are ubiquitous as fuels, solvents, lubricants, and as the principal components of plastics and fibers, yet our ability to predict their dynamical properties is limited to force-field mechanics. Here, we report two machine-learned potential energy surfaces (PESs) for the linear 44-atom hydrocarbon C14H30 using an extensive data set of roughly 250,000 density functional theory (DFT) (B3LYP) energies for a large variety of configurations, obtained using MM3 direct-dynamics calculations at 500, 1000, and 2500 K. The surfaces, based on Permutationally Invariant Polynomials (PIPs) and using both a many-body expansion approach and a fragmented-basis approach, produce precise fits for energies and forces and also produce excellent out-of-sample agreement with direct DFT calculations for torsional and dihedral angle potentials. Going beyond precision, the PESs are used in molecular dynamics calculations that demonstrate the robustness of the PESs for a large range of conformations. The many-body PIPs PES, although more compute intensive than the fragmented-basis one, is directly transferable for other linear hydrocarbons.","PeriodicalId":45,"journal":{"name":"Journal of Chemical Theory and Computation","volume":null,"pages":null},"PeriodicalIF":5.5,"publicationDate":"2024-10-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142452106","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

Efficient Parametrization of Transferable Atomic Cluster Expansion for Water 水的可转移原子团簇扩展的高效参数化

IF 5.5 1区化学

Journal of Chemical Theory and Computation Pub Date : 2024-10-21 DOI: 10.1021/acs.jctc.4c00802

Eslam Ibrahim, Yury Lysogorskiy, Ralf Drautz

{"title":"Efficient Parametrization of Transferable Atomic Cluster Expansion for Water","authors":"Eslam Ibrahim, Yury Lysogorskiy, Ralf Drautz","doi":"10.1021/acs.jctc.4c00802","DOIUrl":"https://doi.org/10.1021/acs.jctc.4c00802","url":null,"abstract":"We present a highly accurate and transferable parametrization of water using the atomic cluster expansion (ACE). To efficiently sample liquid water, we propose a novel approach that involves sampling static calculations of various ice phases and utilizing the active learning (AL) feature of the ACE-based D-optimality algorithm to select relevant liquid water configurations, bypassing computationally intensive ab initio molecular dynamics simulations. Our results demonstrate that the ACE descriptors enable a potential initially fitted solely on ice structures, which is later upfitted with few configurations of liquid, identified with AL to provide an excellent description of liquid water. The developed potential exhibits remarkable agreement with first-principles reference, accurately capturing various properties of liquid water, including structural characteristics such as pair correlation functions, covalent bonding profiles, and hydrogen bonding profiles, as well as dynamic properties like the vibrational density of states, diffusion coefficient, and thermodynamic properties such as the melting point of the ice Ih. Our research introduces a new and efficient sampling technique for machine learning potentials in water simulations while also presenting a transferable interatomic potential for water that reveals the accuracy of first-principles reference. This advancement not only enhances our understanding of the relationship between ice and liquid water at the atomic level but also opens up new avenues for studying complex aqueous systems.","PeriodicalId":45,"journal":{"name":"Journal of Chemical Theory and Computation","volume":null,"pages":null},"PeriodicalIF":5.5,"publicationDate":"2024-10-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142452081","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

DFT-Based Permutationally Invariant Polynomial Potentials Capture the Twists and Turns of C14H30 基于 DFT 的排列不变多项式势能捕捉 C14H30 的曲折变化

IF 5.7 1区化学

Journal of Chemical Theory and Computation Pub Date : 2024-10-21 DOI: 10.1021/acs.jctc.4c0093210.1021/acs.jctc.4c00932

Chen Qu*, Paul L. Houston, Thomas Allison, Barry I. Schneider and Joel M. Bowman*,

{"title":"DFT-Based Permutationally Invariant Polynomial Potentials Capture the Twists and Turns of C14H30","authors":"Chen Qu*, Paul L. Houston, Thomas Allison, Barry I. Schneider and Joel M. Bowman*, ","doi":"10.1021/acs.jctc.4c0093210.1021/acs.jctc.4c00932","DOIUrl":"https://doi.org/10.1021/acs.jctc.4c00932https://doi.org/10.1021/acs.jctc.4c00932","url":null,"abstract":"Hydrocarbons are ubiquitous as fuels, solvents, lubricants, and as the principal components of plastics and fibers, yet our ability to predict their dynamical properties is limited to force-field mechanics. Here, we report two machine-learned potential energy surfaces (PESs) for the linear 44-atom hydrocarbon C14H30 using an extensive data set of roughly 250,000 density functional theory (DFT) (B3LYP) energies for a large variety of configurations, obtained using MM3 direct-dynamics calculations at 500, 1000, and 2500 K. The surfaces, based on Permutationally Invariant Polynomials (PIPs) and using both a many-body expansion approach and a fragmented-basis approach, produce precise fits for energies and forces and also produce excellent out-of-sample agreement with direct DFT calculations for torsional and dihedral angle potentials. Going beyond precision, the PESs are used in molecular dynamics calculations that demonstrate the robustness of the PESs for a large range of conformations. The many-body PIPs PES, although more compute intensive than the fragmented-basis one, is directly transferable for other linear hydrocarbons.","PeriodicalId":45,"journal":{"name":"Journal of Chemical Theory and Computation","volume":null,"pages":null},"PeriodicalIF":5.7,"publicationDate":"2024-10-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://pubs.acs.org/doi/epdf/10.1021/acs.jctc.4c00932","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142609049","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

Robust Computation and Analysis of Vibrational Spectra of Layered Framework Materials Including Host–Guest Interactions 包括主客体相互作用在内的层状框架材料振动光谱的稳健计算与分析

IF 5.5 1区化学

Journal of Chemical Theory and Computation Pub Date : 2024-10-20 DOI: 10.1021/acs.jctc.4c01021

Ekin Esme Bas, Karen Marlenne Garcia Alvarez, Andreas Schneemann, Thomas Heine, Dorothea Golze

{"title":"Robust Computation and Analysis of Vibrational Spectra of Layered Framework Materials Including Host–Guest Interactions","authors":"Ekin Esme Bas, Karen Marlenne Garcia Alvarez, Andreas Schneemann, Thomas Heine, Dorothea Golze","doi":"10.1021/acs.jctc.4c01021","DOIUrl":"https://doi.org/10.1021/acs.jctc.4c01021","url":null,"abstract":"Layered framework materials, a rapidly advancing class of porous materials, are composed of molecular components stitched together via covalent bonds and are usually synthesized through wet-chemical methods. Computational infrared (IR) and Raman spectra are among the most important characterization tools for this material class. Besides the a priori known spectra of the molecular building blocks and the solvent, they allow for in situ monitoring of the framework formation during synthesis. Therefore, they need to capture the additional peaks from host–guest interactions and the bands from emerging bonds between the molecular building blocks, verifying the successful synthesis of the desired material. In this work, we propose a robust computational framework based on ab initio molecular dynamics (AIMD), where we compute IR and Raman spectra from the time-correlation functions of dipole moments and polarizability tensors, respectively. As a case study, we apply our methodology to a covalent organic framework (COF) material, COF-1, and present its AIMD-computed IR and Raman spectra with and without 1,4-dioxane solvent molecules in its pores. To determine robust settings, we meticulously validate our model and explore how stacking disorder and different methods for computing dipole moments and polarizabilities affect IR and Raman intensities. Using our robust computational protocol, we achieve excellent agreement with experimental data. Furthermore, we illustrate how the computed spectra can be dissected into individual contributions from the solvent molecules, the molecular building blocks of COF-1, and the bonds connecting them.","PeriodicalId":45,"journal":{"name":"Journal of Chemical Theory and Computation","volume":null,"pages":null},"PeriodicalIF":5.5,"publicationDate":"2024-10-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142452080","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

Robust Computation and Analysis of Vibrational Spectra of Layered Framework Materials Including Host–Guest Interactions 包括主客体相互作用在内的层状框架材料振动光谱的稳健计算与分析

IF 5.7 1区化学

Journal of Chemical Theory and Computation Pub Date : 2024-10-20 DOI: 10.1021/acs.jctc.4c0102110.1021/acs.jctc.4c01021

Ekin Esme Bas*, Karen Marlenne Garcia Alvarez, Andreas Schneemann, Thomas Heine and Dorothea Golze*,

{"title":"Robust Computation and Analysis of Vibrational Spectra of Layered Framework Materials Including Host–Guest Interactions","authors":"Ekin Esme Bas*, Karen Marlenne Garcia Alvarez, Andreas Schneemann, Thomas Heine and Dorothea Golze*, ","doi":"10.1021/acs.jctc.4c0102110.1021/acs.jctc.4c01021","DOIUrl":"https://doi.org/10.1021/acs.jctc.4c01021https://doi.org/10.1021/acs.jctc.4c01021","url":null,"abstract":"Layered framework materials, a rapidly advancing class of porous materials, are composed of molecular components stitched together via covalent bonds and are usually synthesized through wet-chemical methods. Computational infrared (IR) and Raman spectra are among the most important characterization tools for this material class. Besides the a priori known spectra of the molecular building blocks and the solvent, they allow for in situ monitoring of the framework formation during synthesis. Therefore, they need to capture the additional peaks from host–guest interactions and the bands from emerging bonds between the molecular building blocks, verifying the successful synthesis of the desired material. In this work, we propose a robust computational framework based on ab initio molecular dynamics (AIMD), where we compute IR and Raman spectra from the time-correlation functions of dipole moments and polarizability tensors, respectively. As a case study, we apply our methodology to a covalent organic framework (COF) material, COF-1, and present its AIMD-computed IR and Raman spectra with and without 1,4-dioxane solvent molecules in its pores. To determine robust settings, we meticulously validate our model and explore how stacking disorder and different methods for computing dipole moments and polarizabilities affect IR and Raman intensities. Using our robust computational protocol, we achieve excellent agreement with experimental data. Furthermore, we illustrate how the computed spectra can be dissected into individual contributions from the solvent molecules, the molecular building blocks of COF-1, and the bonds connecting them.","PeriodicalId":45,"journal":{"name":"Journal of Chemical Theory and Computation","volume":null,"pages":null},"PeriodicalIF":5.7,"publicationDate":"2024-10-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://pubs.acs.org/doi/epdf/10.1021/acs.jctc.4c01021","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142608126","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

Simulation of Spin Chains with Off-Diagonal Coupling Using the Inchworm Method 使用 Inchworm 方法模拟具有非对角耦合的自旋链

IF 5.5 1区化学

Journal of Chemical Theory and Computation Pub Date : 2024-10-18 DOI: 10.1021/acs.jctc.4c00864

Yixiao Sun, Geshuo Wang, Zhenning Cai

引用次数: 0

Assessing the Partial Hessian Approximation in QM/MM-Based Vibrational Analysis 评估基于 QM/MM 的振动分析中的部分 Hessian 近似值

IF 5.5 1区化学

Journal of Chemical Theory and Computation Pub Date : 2024-10-18 DOI: 10.1021/acs.jctc.4c00882

Jonas Vester, Jógvan Magnus Haugaard Olsen

{"title":"Assessing the Partial Hessian Approximation in QM/MM-Based Vibrational Analysis","authors":"Jonas Vester, Jógvan Magnus Haugaard Olsen","doi":"10.1021/acs.jctc.4c00882","DOIUrl":"https://doi.org/10.1021/acs.jctc.4c00882","url":null,"abstract":"The partial Hessian approximation is often used in vibrational analysis of quantum mechanics/molecular mechanics (QM/MM) systems because calculating the full Hessian matrix is computationally impractical. This approach aligns with the core concept of QM/MM, which focuses on the QM subsystem. Thus, using the partial Hessian approximation implies that the main interest is in the local vibrational modes of the QM subsystem. Here, we investigate the accuracy and applicability of the partial Hessian vibrational analysis (PHVA) approach as it is typically used within QM/MM, i.e., only the Hessian belonging to the QM subsystem is computed. We focus on solute–solvent systems with small, rigid solutes. To separate two of the major sources of errors, we perform two separate analyses. First, we study the effects of the partial Hessian approximation on local normal modes, harmonic frequencies, and harmonic IR and Raman intensities by comparing them to those obtained using full Hessians, where both partial and full Hessians are calculated at the QM level. Then, we quantify the errors introduced by QM/MM used with the PHVA by comparing normal modes, frequencies, and intensities obtained using partial Hessians calculated using a QM/MM-type embedding approach to those obtained using partial Hessians calculated at the QM level. Another aspect of the PHVA is the appearance of normal modes resembling the translation and rotation of the QM subsystem. These pseudotranslational and pseudorotational modes should be removed as they are collective vibrations of the atoms in the QM subsystem relative to a frozen MM subsystem and, thus, not well-described. We show that projecting out translation and rotation, usually done for systems in isolation, can adversely affect other normal modes. Instead, the pseudotranslational and pseudorotational modes can be identified and removed.","PeriodicalId":45,"journal":{"name":"Journal of Chemical Theory and Computation","volume":null,"pages":null},"PeriodicalIF":5.5,"publicationDate":"2024-10-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142451499","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

An Efficient RI-MP2 Algorithm for Distributed Many-GPU Architectures 适用于分布式多 GPU 架构的高效 RI-MP2 算法

IF 5.7 1区化学

Journal of Chemical Theory and Computation Pub Date : 2024-10-18 DOI: 10.1021/acs.jctc.4c0081410.1021/acs.jctc.4c00814

Calum Snowdon, and , Giuseppe M. J. Barca*,

{"title":"An Efficient RI-MP2 Algorithm for Distributed Many-GPU Architectures","authors":"Calum Snowdon,  and , Giuseppe M. J. Barca*, ","doi":"10.1021/acs.jctc.4c0081410.1021/acs.jctc.4c00814","DOIUrl":"https://doi.org/10.1021/acs.jctc.4c00814https://doi.org/10.1021/acs.jctc.4c00814","url":null,"abstract":"Second-order Møller–Plesset perturbation theory (MP2) using the Resolution of the Identity approximation (RI-MP2) is a widely used method for computing molecular energies beyond the Hartree–Fock mean-field approximation. However, its high computational cost and lack of efficient algorithms for modern supercomputing architectures limit its applicability to large molecules. In this paper, we present the first distributed-memory many-GPU RI-MP2 algorithm explicitly designed to utilize hundreds of GPU accelerators for every step of the computation. Our novel algorithm achieves near-peak performance on GPU-based supercomputers through the development of a distributed memory algorithm for forming RI-MP2 intermediate tensors with zero internode communication, except for a single <math><mi>O</mi><mrow><mo>(</mo><msup><mi>N</mi><mn>2</mn></msup><mo>)</mo></mrow></math> asynchronous broadcast, and a distributed memory algorithm for the <math><mi>O</mi><mrow><mo>(</mo><msup><mi>N</mi><mn>5</mn></msup><mo>)</mo></mrow></math> energy reduction step, capable of sustaining near-peak performance on clusters with several hundred GPUs. Comparative analysis shows our implementation outperforms state-of-the-art quantum chemistry software by over 3.5 times in speed while achieving an 8-fold reduction in computational power consumption. Benchmarking on the Perlmutter supercomputer, our algorithm achieves 11.8 PFLOP/s (83% of peak performance) performing and the RI-MP2 energy calculation on a 314-water cluster with 7850 primary and 30,144 auxiliary basis functions in 4 min on 180 nodes and 720 A100 GPUs. This performance represents a substantial improvement over traditional CPU-based methods, demonstrating significant time-to-solution and power consumption benefits of leveraging modern GPU-accelerated computing environments for quantum chemistry calculations.","PeriodicalId":45,"journal":{"name":"Journal of Chemical Theory and Computation","volume":null,"pages":null},"PeriodicalIF":5.7,"publicationDate":"2024-10-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142608516","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

Assessing the Partial Hessian Approximation in QM/MM-Based Vibrational Analysis 评估基于 QM/MM 的振动分析中的部分 Hessian 近似值

IF 5.7 1区化学

Journal of Chemical Theory and Computation Pub Date : 2024-10-18 DOI: 10.1021/acs.jctc.4c0088210.1021/acs.jctc.4c00882

Jonas Vester*, and , Jógvan Magnus Haugaard Olsen*,

{"title":"Assessing the Partial Hessian Approximation in QM/MM-Based Vibrational Analysis","authors":"Jonas Vester*,  and , Jógvan Magnus Haugaard Olsen*, ","doi":"10.1021/acs.jctc.4c0088210.1021/acs.jctc.4c00882","DOIUrl":"https://doi.org/10.1021/acs.jctc.4c00882https://doi.org/10.1021/acs.jctc.4c00882","url":null,"abstract":"The partial Hessian approximation is often used in vibrational analysis of quantum mechanics/molecular mechanics (QM/MM) systems because calculating the full Hessian matrix is computationally impractical. This approach aligns with the core concept of QM/MM, which focuses on the QM subsystem. Thus, using the partial Hessian approximation implies that the main interest is in the local vibrational modes of the QM subsystem. Here, we investigate the accuracy and applicability of the partial Hessian vibrational analysis (PHVA) approach as it is typically used within QM/MM, i.e., only the Hessian belonging to the QM subsystem is computed. We focus on solute–solvent systems with small, rigid solutes. To separate two of the major sources of errors, we perform two separate analyses. First, we study the effects of the partial Hessian approximation on local normal modes, harmonic frequencies, and harmonic IR and Raman intensities by comparing them to those obtained using full Hessians, where both partial and full Hessians are calculated at the QM level. Then, we quantify the errors introduced by QM/MM used with the PHVA by comparing normal modes, frequencies, and intensities obtained using partial Hessians calculated using a QM/MM-type embedding approach to those obtained using partial Hessians calculated at the QM level. Another aspect of the PHVA is the appearance of normal modes resembling the translation and rotation of the QM subsystem. These pseudotranslational and pseudorotational modes should be removed as they are collective vibrations of the atoms in the QM subsystem relative to a frozen MM subsystem and, thus, not well-described. We show that projecting out translation and rotation, usually done for systems in isolation, can adversely affect other normal modes. Instead, the pseudotranslational and pseudorotational modes can be identified and removed.","PeriodicalId":45,"journal":{"name":"Journal of Chemical Theory and Computation","volume":null,"pages":null},"PeriodicalIF":5.7,"publicationDate":"2024-10-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://pubs.acs.org/doi/epdf/10.1021/acs.jctc.4c00882","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142608650","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