Pub Date : 2024-10-22Epub Date: 2024-10-07DOI: 10.1021/acs.jctc.4c01003
Inkoo Kim, Daun Jeong, Leah P Weisburn, Alexandra Alexiu, Troy Van Voorhis, Young Min Rhee, Won-Joon Son, Hyung-Jin Kim, Jinkyu Yim, Sungmin Kim, Yeonchoo Cho, Inkook Jang, Seungmin Lee, Dae Sin Kim
Modern graphics processing units (GPUs) provide an unprecedented level of computing power. In this study, we present a high-performance, multi-GPU implementation of the analytical nuclear gradient for Kohn-Sham time-dependent density functional theory (TDDFT), employing the Tamm-Dancoff approximation (TDA) and Gaussian-type atomic orbitals as basis functions. We discuss GPU-efficient algorithms for the derivatives of electron repulsion integrals and exchange-correlation functionals within the range-separated scheme. As an illustrative example, we calculate the TDA-TDDFT gradient of the S1 state of a full-scale green fluorescent protein with explicit water solvent molecules, totaling 4353 atoms, at the ωB97X/def2-SVP level of theory. Our algorithm demonstrates favorable parallel efficiencies on a high-speed distributed system equipped with 256 Nvidia A100 GPUs, achieving >70% with up to 64 GPUs and 31% with 256 GPUs, effectively leveraging the capabilities of modern high-performance computing systems.
{"title":"Very-Large-Scale GPU-Accelerated Nuclear Gradient of Time-Dependent Density Functional Theory with Tamm-Dancoff Approximation and Range-Separated Hybrid Functionals.","authors":"Inkoo Kim, Daun Jeong, Leah P Weisburn, Alexandra Alexiu, Troy Van Voorhis, Young Min Rhee, Won-Joon Son, Hyung-Jin Kim, Jinkyu Yim, Sungmin Kim, Yeonchoo Cho, Inkook Jang, Seungmin Lee, Dae Sin Kim","doi":"10.1021/acs.jctc.4c01003","DOIUrl":"10.1021/acs.jctc.4c01003","url":null,"abstract":"<p><p>Modern graphics processing units (GPUs) provide an unprecedented level of computing power. In this study, we present a high-performance, multi-GPU implementation of the analytical nuclear gradient for Kohn-Sham time-dependent density functional theory (TDDFT), employing the Tamm-Dancoff approximation (TDA) and Gaussian-type atomic orbitals as basis functions. We discuss GPU-efficient algorithms for the derivatives of electron repulsion integrals and exchange-correlation functionals within the range-separated scheme. As an illustrative example, we calculate the TDA-TDDFT gradient of the S<sub>1</sub> state of a full-scale green fluorescent protein with explicit water solvent molecules, totaling 4353 atoms, at the ωB97X/def2-SVP level of theory. Our algorithm demonstrates favorable parallel efficiencies on a high-speed distributed system equipped with 256 Nvidia A100 GPUs, achieving >70% with up to 64 GPUs and 31% with 256 GPUs, effectively leveraging the capabilities of modern high-performance computing systems.</p>","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":"142379412","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}
Pub Date : 2024-10-22Epub Date: 2024-10-03DOI: 10.1021/acs.jctc.4c00868
Timothy D Loose, Patrick G Sahrmann, Thomas S Qu, Gregory A Voth
The Martini 3.0 coarse-grained force field, which was parametrized to better capture transferability in top-down coarse-grained models, is analyzed to assess its accuracy in representing thermodynamic and structural properties with respect to the underlying atomistic representation of the system. These results are compared to those obtained following the principles of statistical mechanics that start from the same underlying atomistic system. To this end, the potentials of mean force for lateral association in Martini 3.0 binary lipid bilayers are decomposed into their entropic and enthalpic components and compared to those of corresponding atomistic bilayers that have been projected onto equivalent coarse-grained mappings but evolved under the fully atomistic forces. This is accomplished by applying the reversible work theorem to lateral pair correlation functions between coarse-grained lipid beads taken at a range of different temperatures. The entropy-enthalpy decompositions provide a metric by which the underlying statistical mechanical properties of Martini can be investigated. Overall, Martini 3.0 is found to fail to properly partition entropy and enthalpy for the PMFs compared to the mapped all-atom results, despite changes made to the force field from the Martini 2.0 version. This outcome points to the fact that the development of more accurate top-down coarse-grained models such as Martini will likely necessitate temperature-dependent terms in the corresponding CG force-field; although necessary, this may not be sufficient to improve Martini. In addition to the entropy-enthalpy decompositions, Martini 3.0 produces an incorrect undulation spectrum, in particular at intermediate length scales of biophysical pertinence.
为了更好地捕捉自上而下粗粒度模型的可转移性,对马丁尼 3.0 粗粒度力场进行了参数化分析,以评估其相对于系统的基本原子表征在表示热力学和结构特性方面的准确性。将这些结果与根据统计力学原理(从相同的基础原子系统出发)获得的结果进行比较。为此,我们将 Martini 3.0 二元脂质双分子层横向联合的平均力势分解为熵和焓两部分,并与投影到等效粗粒度映射上但在完全原子力作用下演化的相应原子双分子层的平均力势进行比较。这是通过将可逆功定理应用于在一系列不同温度下提取的粗粒度脂珠之间的侧对相关函数来实现的。熵焓分解提供了一种度量方法,通过它可以研究 Martini 的基本统计机械特性。总体而言,尽管力场与 Martini 2.0 版本相比有所变化,但与映射的全原子结果相比,Martini 3.0 未能正确分配 PMF 的熵和焓。这一结果表明,要开发更精确的自上而下粗粒度模型(如马提尼模型),可能需要在相应的 CG 力场中加入温度相关项;尽管这是必要的,但这可能不足以改善马提尼模型。除了熵焓分解之外,Martini 3.0 还产生了不正确的起伏谱,尤其是在与生物物理相关的中等长度尺度上。
{"title":"Changing Your Martini Can Still Give You a Hangover.","authors":"Timothy D Loose, Patrick G Sahrmann, Thomas S Qu, Gregory A Voth","doi":"10.1021/acs.jctc.4c00868","DOIUrl":"10.1021/acs.jctc.4c00868","url":null,"abstract":"<p><p>The Martini 3.0 coarse-grained force field, which was parametrized to better capture transferability in top-down coarse-grained models, is analyzed to assess its accuracy in representing thermodynamic and structural properties with respect to the underlying atomistic representation of the system. These results are compared to those obtained following the principles of statistical mechanics that start from the same underlying atomistic system. To this end, the potentials of mean force for lateral association in Martini 3.0 binary lipid bilayers are decomposed into their entropic and enthalpic components and compared to those of corresponding atomistic bilayers that have been projected onto equivalent coarse-grained mappings but evolved under the fully atomistic forces. This is accomplished by applying the reversible work theorem to lateral pair correlation functions between coarse-grained lipid beads taken at a range of different temperatures. The entropy-enthalpy decompositions provide a metric by which the underlying statistical mechanical properties of Martini can be investigated. Overall, Martini 3.0 is found to fail to properly partition entropy and enthalpy for the PMFs compared to the mapped all-atom results, despite changes made to the force field from the Martini 2.0 version. This outcome points to the fact that the development of more accurate top-down coarse-grained models such as Martini will likely necessitate temperature-dependent terms in the corresponding CG force-field; although necessary, this may not be sufficient to improve Martini. In addition to the entropy-enthalpy decompositions, Martini 3.0 produces an incorrect undulation spectrum, in particular at intermediate length scales of biophysical pertinence.</p>","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":"142363441","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}
Pub Date : 2024-10-22Epub Date: 2024-10-04DOI: 10.1021/acs.jctc.4c00751
Maximilian F X Dorfner, Dominik Brey, Irene Burghardt, Frank Ortmann
The excited-state dynamics of organic molecules, molecular aggregates, and donor-acceptor clusters is typically governed by the interplay of electronic excitations and, due to their flexibility and soft bonding, by the interaction with their vibrations. This interaction in these systems can be characterized by a few relevant electronic states that are coupled to numerous vibrational normal modes, encompassing a vast configurational space of the molecules. The full quantum simulation of these type of systems has been long dominated by the multiconfiguration time-dependent Hartree (MCTDH) approach and its multilayer variants, which are considered the gold standard in the presence of electron-vibration coupling with a large number of modes. Recently, also the matrix product state ansatz (MPS) with appropriate time-evolution schemes has been applied to these types of Hamiltonians. In this article, we provide a numerical comparison of excited-state dynamics between the MCTDH and MPS approaches for two electron-vibration coupled systems. Notably, we consider two models for exciton dissociation at a P3HT:PCBM heterojunction, comprising two electronic states and 100 vibrational modes, and 26 electronic states and 113 vibrational modes, respectively. While both methods agree very well for the first model, more pronounced deviations are found for the second model. We trace back the divergence between the methods to the different way entanglement is treated.
{"title":"Comparison of Matrix Product State and Multiconfiguration Time-Dependent Hartree Methods for Nonadiabatic Dynamics of Exciton Dissociation.","authors":"Maximilian F X Dorfner, Dominik Brey, Irene Burghardt, Frank Ortmann","doi":"10.1021/acs.jctc.4c00751","DOIUrl":"10.1021/acs.jctc.4c00751","url":null,"abstract":"<p><p>The excited-state dynamics of organic molecules, molecular aggregates, and donor-acceptor clusters is typically governed by the interplay of electronic excitations and, due to their flexibility and soft bonding, by the interaction with their vibrations. This interaction in these systems can be characterized by a few relevant electronic states that are coupled to numerous vibrational normal modes, encompassing a vast configurational space of the molecules. The full quantum simulation of these type of systems has been long dominated by the multiconfiguration time-dependent Hartree (MCTDH) approach and its multilayer variants, which are considered the gold standard in the presence of electron-vibration coupling with a large number of modes. Recently, also the matrix product state ansatz (MPS) with appropriate time-evolution schemes has been applied to these types of Hamiltonians. In this article, we provide a numerical comparison of excited-state dynamics between the MCTDH and MPS approaches for two electron-vibration coupled systems. Notably, we consider two models for exciton dissociation at a P3HT:PCBM heterojunction, comprising two electronic states and 100 vibrational modes, and 26 electronic states and 113 vibrational modes, respectively. While both methods agree very well for the first model, more pronounced deviations are found for the second model. We trace back the divergence between the methods to the different way entanglement is treated.</p>","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":"142370217","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}
Pub Date : 2024-10-22Epub Date: 2024-10-07DOI: 10.1021/acs.jctc.4c00900
Silvia Di Grande, Federico Lazzari, Vincenzo Barone
Accurate geometries of small semirigid molecules in the gas phase are available thanks to high-resolution spectroscopy and accurate quantum chemical approaches. These results can be employed for validating cheaper low-level quantum chemical models or correcting the corresponding structures of large molecules. On these grounds, in this work, a large panel of semiexperimental equilibrium structures already available in the literature is used to confirm the average error (1 mÅ for bond lengths and 2 mrad for valence angles) of a version of the Pisa composite schemes (PCS2), which is applicable to molecules containing up to about 20 atoms. Then, the geometries of 30 additional medium-sized systems were optimized at the PCS2 level to cover a more balanced chemical space containing moieties poorly represented in SE compilations. The final database is available on a public domain Web site (https://www.skies-village.it/databases/) and can be employed for correcting structures of larger molecules obtained by hybrid or double-hybrid density functionals in the framework of the templating molecule approach. Several examples show that corrections based on the structures of building blocks taken from this database reduce the error of the B3LYP geometrical parameters of large molecules by nearly an order of magnitude without increasing the computational cost. Furthermore, the results of different density functional theory (DFT) or wave function (e.g., MP2) models can be improved in the same way by simply computing both the whole molecule and suitable building blocks at the chosen level. Then, whenever reference structures of some building blocks containing up to about 20 atoms are not available, they can be purposely optimized at the PCS2 level by employing reasonable computer resources. Therefore, a new DFT-cost tool is now available for the accurate characterization of large molecules by experiment-oriented scientists.
{"title":"Accurate Geometries of Large Molecules at DFT Cost by Semiexperimental and Coupled Cluster Templating Fragments.","authors":"Silvia Di Grande, Federico Lazzari, Vincenzo Barone","doi":"10.1021/acs.jctc.4c00900","DOIUrl":"10.1021/acs.jctc.4c00900","url":null,"abstract":"<p><p>Accurate geometries of small semirigid molecules in the gas phase are available thanks to high-resolution spectroscopy and accurate quantum chemical approaches. These results can be employed for validating cheaper low-level quantum chemical models or correcting the corresponding structures of large molecules. On these grounds, in this work, a large panel of semiexperimental equilibrium structures already available in the literature is used to confirm the average error (1 mÅ for bond lengths and 2 mrad for valence angles) of a version of the Pisa composite schemes (PCS2), which is applicable to molecules containing up to about 20 atoms. Then, the geometries of 30 additional medium-sized systems were optimized at the PCS2 level to cover a more balanced chemical space containing moieties poorly represented in SE compilations. The final database is available on a public domain Web site (https://www.skies-village.it/databases/) and can be employed for correcting structures of larger molecules obtained by hybrid or double-hybrid density functionals in the framework of the templating molecule approach. Several examples show that corrections based on the structures of building blocks taken from this database reduce the error of the B3LYP geometrical parameters of large molecules by nearly an order of magnitude without increasing the computational cost. Furthermore, the results of different density functional theory (DFT) or wave function (e.g., MP2) models can be improved in the same way by simply computing both the whole molecule and suitable building blocks at the chosen level. Then, whenever reference structures of some building blocks containing up to about 20 atoms are not available, they can be purposely optimized at the PCS2 level by employing reasonable computer resources. Therefore, a new DFT-cost tool is now available for the accurate characterization of large molecules by experiment-oriented scientists.</p>","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":"142379408","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}
Pub Date : 2024-10-22Epub Date: 2024-10-07DOI: 10.1021/acs.jctc.4c00804
Zheng Yu, Nicholas E Jackson
Recent advances in machine-learning-based electronic coarse graining (ECG) methods have demonstrated the potential to enable electronic predictions in soft materials at mesoscopic length scales. However, previous ECG models have yet to confront the issue of chemical transferability. In this study, we develop chemically transferable ECG models for polythiophenes using graph neural networks. Our models are trained on a data set that samples over the conformational space of random polythiophene sequences generated with 15 different monomer chemistries and three different degrees of polymerization. We systematically explore the impact of coarse-grained representation on ECG accuracy, highlighting the significance of preserving the C-β coordinates in thiophene. We also find that integrating unique polymer sequences into training enhances the model performance more efficiently than augmenting conformational sampling for sequences already in the training data set. Moreover, our ECG models, developed initially for one property and one level of quantum chemical theory, can be efficiently transferred to related properties and higher levels of theory with minimal additional data. The chemically transferable ECG model introduced in this work will serve as a foundation model for new classes of chemically transferable ECG predictions across chemical space.
{"title":"Chemically Transferable Electronic Coarse Graining for Polythiophenes.","authors":"Zheng Yu, Nicholas E Jackson","doi":"10.1021/acs.jctc.4c00804","DOIUrl":"10.1021/acs.jctc.4c00804","url":null,"abstract":"<p><p>Recent advances in machine-learning-based electronic coarse graining (ECG) methods have demonstrated the potential to enable electronic predictions in soft materials at mesoscopic length scales. However, previous ECG models have yet to confront the issue of chemical transferability. In this study, we develop chemically transferable ECG models for polythiophenes using graph neural networks. Our models are trained on a data set that samples over the conformational space of random polythiophene sequences generated with 15 different monomer chemistries and three different degrees of polymerization. We systematically explore the impact of coarse-grained representation on ECG accuracy, highlighting the significance of preserving the C-β coordinates in thiophene. We also find that integrating unique polymer sequences into training enhances the model performance more efficiently than augmenting conformational sampling for sequences already in the training data set. Moreover, our ECG models, developed initially for one property and one level of quantum chemical theory, can be efficiently transferred to related properties and higher levels of theory with minimal additional data. The chemically transferable ECG model introduced in this work will serve as a foundation model for new classes of chemically transferable ECG predictions across chemical space.</p>","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":"142379410","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}
Pub Date : 2024-10-22Epub Date: 2024-10-09DOI: 10.1021/acs.jctc.4c00656
Chythra J N, Olgun Guvench, Alexander D MacKerell, Takumi Yamaguchi, Sairam S Mallajosyula
We present a revised version of the Drude polarizable carbohydrate force field (FF), focusing on refining the ring and exocyclic torsional parameters for hexopyranose monosaccharides. This refinement addresses the previously observed discrepancies between calculated and experimental NMR 3J coupling values, particularly in describing ring dynamics and exocyclic rotamer populations within major hexose monosaccharides and their anomers. Specifically, α-MAN, β-MAN, α-GLC, β-GLC, α-GAL, β-GAL, α-ALT, β-ALT, α-IDO, and β-IDO were targeted for optimization. The optimization process involved potential energy scans (PES) of the ring and exocyclic dihedral angles computed using quantum mechanical (QM) methods. The target data for the reoptimization included PES of the inner ring dihedrals (C1-C2-C3-C4, C2-C3-C4-C5, C5-O5-C1-C2, C4-C5-O5-C1, O5-C1-C2-C3, C3-C4-C5-O5) and the exocyclic torsions, other than the pseudo ring dihedrals (O1-C1-O5-C5, O2-C2-C1-O5, and O4-C4-C5-O5) and hydroxyl torsions used in the previous parametrization efforts. These parameters, in conjunction with previously developed Drude parameters for hexopyranose monosaccharides, were validated against experimental observations, including NMR data and conformational energetics, in aqueous environments. The resulting polarizable model is shown to be in good agreement with a range of QM data, experimental NMR data, and conformational energetics of monosaccharides in aqueous solutions. This offers a significant improvement of the Drude carbohydrate force field, wherein the refinement enhances the accuracy of accessing the conformational dynamics of carbohydrates in biomolecular simulations.
{"title":"Refinement of the Drude Polarizable Force Field for Hexose Monosaccharides: Capturing Ring Conformational Dynamics with Enhanced Accuracy.","authors":"Chythra J N, Olgun Guvench, Alexander D MacKerell, Takumi Yamaguchi, Sairam S Mallajosyula","doi":"10.1021/acs.jctc.4c00656","DOIUrl":"10.1021/acs.jctc.4c00656","url":null,"abstract":"<p><p>We present a revised version of the Drude polarizable carbohydrate force field (FF), focusing on refining the ring and exocyclic torsional parameters for hexopyranose monosaccharides. This refinement addresses the previously observed discrepancies between calculated and experimental NMR <sup>3</sup><i>J</i> coupling values, particularly in describing ring dynamics and exocyclic rotamer populations within major hexose monosaccharides and their anomers. Specifically, α-MAN, β-MAN, α-GLC, β-GLC, α-GAL, β-GAL, α-ALT, β-ALT, α-IDO, and β-IDO were targeted for optimization. The optimization process involved potential energy scans (PES) of the ring and exocyclic dihedral angles computed using quantum mechanical (QM) methods. The target data for the reoptimization included PES of the inner ring dihedrals (C1-C2-C3-C4, C2-C3-C4-C5, C5-O5-C1-C2, C4-C5-O5-C1, O5-C1-C2-C3, C3-C4-C5-O5) and the exocyclic torsions, other than the pseudo ring dihedrals (O1-C1-O5-C5, O2-C2-C1-O5, and O4-C4-C5-O5) and hydroxyl torsions used in the previous parametrization efforts. These parameters, in conjunction with previously developed Drude parameters for hexopyranose monosaccharides, were validated against experimental observations, including NMR data and conformational energetics, in aqueous environments. The resulting polarizable model is shown to be in good agreement with a range of QM data, experimental NMR data, and conformational energetics of monosaccharides in aqueous solutions. This offers a significant improvement of the Drude carbohydrate force field, wherein the refinement enhances the accuracy of accessing the conformational dynamics of carbohydrates in biomolecular simulations.</p>","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":"142386399","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}
Pub Date : 2024-10-22Epub Date: 2024-10-03DOI: 10.1021/acs.jctc.4c00964
Ziwei Chai, Rutong Si, Mingyang Chen, Gilberto Teobaldi, David D O'Regan, Li-Min Liu
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.
我们介绍了在 CP2K 套件的 Quickstep 程序中实现哈伯德(U)和亨德(J)校正密度泛函理论(DFT + U + J)功能的情况。实现并比较了张量子空间和 Löwdin 子空间表示法。针对张量表示法和 Löwdin 表示法,实现了全分析 DFT + U + J 力,并进行了基准测试。我们还介绍了最近提出的最小跟踪线性响应方法的实现,该方法可以在第一原理基础上计算 U 和 J 参数,而无需参考 Kohn-Sham 特征系统。这些实现方法以不同材料性质的最新结果为基准,包括氧化镍中的 DFT + U 带隙开度、二氧化钛中各种极子分布的相对稳定性、计算出的二氧化钛带隙对 +J 修正的依赖性,以及 +U 和 +J 修正对一系列六水过渡金属计算性质的作用。我们的实施结果与文献中已报道的同类方法的结果一致。最后,我们检验了洛文正则化对占位、计算参数和推导性质的影响。
{"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":"<p><p>We present the implementation of the Hubbard (<i>U</i>) and Hund (<i>J</i>) corrected Density Functional Theory (DFT + <i>U</i> + <i>J</i>) 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 + <i>U</i> + <i>J</i> 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 <i>U</i> and <i>J</i> 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 + <i>U</i> band gap opening in NiO, the relative stability of various polaron distributions in TiO<sub>2</sub>, the dependence of the calculated TiO<sub>2</sub> band gap on +<i>J</i> corrections, and, finally, the role of the +<i>U</i> and +<i>J</i> 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.</p>","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}
Pub Date : 2024-10-22Epub Date: 2024-10-07DOI: 10.1021/acs.jctc.4c00850
Tomasz K Piskorz, Bernadette Lee, Shaoqi Zhan, Fernanda Duarte
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).
{"title":"<i>Metallicious</i>: 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":"<p><p>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 <i>metallicious</i>, a Python tool designed for efficient force-field parameterization of supramolecular structures. <i>Metallicious</i> 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, <i>metallicious</i> 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).</p>","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":"142379407","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}
Pub Date : 2024-10-22Epub Date: 2024-10-11DOI: 10.1021/acs.jctc.4c00763
Marcus T Lexander, Sara Angelico, Eirik F Kjønstad, Henrik Koch
Analytical gradients of potential energy surfaces play a central role in quantum chemistry, allowing for molecular geometry optimizations and molecular dynamics simulations. In strong coupling conditions, potential energy surfaces can account for strong interactions between matter and the quantized electromagnetic field. In this paper, we derive expressions for the ground state analytical gradients in quantum electrodynamics coupled cluster theory. We also present a Cholesky-based implementation for the coupled cluster singles and doubles model. We report timings to show the performance of the implementation and present optimized geometries to highlight cavity-induced molecular orientation effects in strong coupling conditions.
{"title":"Analytical Evaluation of Ground State Gradients in Quantum Electrodynamics Coupled Cluster Theory.","authors":"Marcus T Lexander, Sara Angelico, Eirik F Kjønstad, Henrik Koch","doi":"10.1021/acs.jctc.4c00763","DOIUrl":"10.1021/acs.jctc.4c00763","url":null,"abstract":"<p><p>Analytical gradients of potential energy surfaces play a central role in quantum chemistry, allowing for molecular geometry optimizations and molecular dynamics simulations. In strong coupling conditions, potential energy surfaces can account for strong interactions between matter and the quantized electromagnetic field. In this paper, we derive expressions for the ground state analytical gradients in quantum electrodynamics coupled cluster theory. We also present a Cholesky-based implementation for the coupled cluster singles and doubles model. We report timings to show the performance of the implementation and present optimized geometries to highlight cavity-induced molecular orientation effects in strong coupling conditions.</p>","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":"142405712","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}
Pub Date : 2024-10-22Epub Date: 2024-10-11DOI: 10.1021/acs.jctc.4c00778
Adam E A Fouda, Stephen H Southworth, Phay J Ho
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.
在对生物和化学材料进行 X 射线散射测量时,以及在涉及奥杰电子发射放射性核素的医疗应用中,分子阳离子在含有重元素的分子中发生内壳衰变过程后碎裂,这是观察到 X 射线损伤效应的基础。传统上,这些过程都是通过在原子层面描述电子结构的模拟来建模的,因此忽略了分子键效应。这项研究通过开发一种衰变催生动力学算法,并将其应用于以原子分子动力学模拟为特征的势能面,引入了一种将奥杰-迈特纳衰变与多个衰变步骤的核动力学结合起来的新方法,从而弥补了这一空白。我们在 IBr 的 K 壳电离和随后的 Kβ 荧光衰变之后的模型衰变级联上展示了这种方法。我们研究了两个相互竞争的通道,它们经历了两个衰变步骤,产生了总电荷状态为 3+ 的离子对。这种方法连续描述了多步衰变级联和分子破碎过程中发生的电子转移动力学,揭示了内壳衰变和电荷转移的综合时间尺度约为 75 fs。我们计算的离子碎片动能与实验数据显示出良好的一致性。
{"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":"<p><p>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 <i>ab initio</i> molecular dynamics simulations. We showcase the approach on a model decay cascade following K-shell ionization of IBr and subsequent <i>K</i>β 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.</p>","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}