Journal of Computational Chemistry最新文献_第6页

A machine learning potential construction based on radial distribution function sampling 基于径向分布函数采样的机器学习潜能构建。

IF 3.4 3区化学

Journal of Computational Chemistry Pub Date : 2024-09-03 DOI: 10.1002/jcc.27497

Natsuki Watanabe, Yuta Hori, Hiroki Sugisawa, Tomonori Ida, Mitsuo Shoji, Yasuteru Shigeta

{"title":"A machine learning potential construction based on radial distribution function sampling","authors":"Natsuki Watanabe, Yuta Hori, Hiroki Sugisawa, Tomonori Ida, Mitsuo Shoji, Yasuteru Shigeta","doi":"10.1002/jcc.27497","DOIUrl":"10.1002/jcc.27497","url":null,"abstract":"Sampling reference data is crucial in machine learning potential (MLP) construction. Inadequate coverage of local configurations in reference data may lead to unphysical behaviors in MLP-based molecular dynamics (MLP-MD) simulations. To address this problem, this study proposes a new on-the-fly reference data sampling method called radial distribution function (RDF)-based data sampling for MLP construction. This method detects and extracts anomalous structures from the trajectories of MLP-MD simulations by focusing on the shapes of RDFs. The detected structures are added to the reference data to improve the accuracy of the MLP. This method allows us to realize a reasonable MLP construction for liquid water with minimal additional data. We prepare data from an H2O molecular cluster system and verify whether the constructed MLPs are practical for bulk water systems. MLP-MD simulations without RDF-based data sampling show unphysical behaviors, such as atomic collisions. In contrast, after applying this method, we obtain MLP-MD trajectories with features, such as RDF shapes and angle distributions, that are comparable to those of ab initio MD simulations. Our simulation results demonstrate that the RDF-based data sampling approach is useful for constructing MLPs that are robust to extrapolations from molecular cluster systems to bulk systems without any specialized know-how.","PeriodicalId":188,"journal":{"name":"Journal of Computational Chemistry","volume":"45 32","pages":"2949-2958"},"PeriodicalIF":3.4,"publicationDate":"2024-09-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/jcc.27497","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142118557","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"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

Quantum chemical investigation of electronic transitions of mitorubrin azaphilones mitorubrin azaphilones 电子跃迁的量子化学研究。

IF 3.4 3区化学

Journal of Computational Chemistry Pub Date : 2024-09-03 DOI: 10.1002/jcc.27498

Muhammad Saalim, Benjamin R. Clark, Peter R. Taylor

引用次数: 0

Enhancing protein-ligand binding affinity prediction through sequential fusion of graph and convolutional neural networks 通过图和卷积神经网络的连续融合增强蛋白质配体结合亲和力预测。

IF 3.4 3区化学

Journal of Computational Chemistry Pub Date : 2024-09-02 DOI: 10.1002/jcc.27499

Yimin Yang, Ruiqin Zhang, Zijing Lin

{"title":"Enhancing protein-ligand binding affinity prediction through sequential fusion of graph and convolutional neural networks","authors":"Yimin Yang, Ruiqin Zhang, Zijing Lin","doi":"10.1002/jcc.27499","DOIUrl":"10.1002/jcc.27499","url":null,"abstract":"Predicting protein-ligand binding affinity is a crucial and challenging task in structure-based drug discovery. With the accumulation of complex structures and binding affinity data, various machine-learning scoring functions, particularly those based on deep learning, have been developed for this task, exhibiting superiority over their traditional counterparts. A fusion model sequentially connecting a graph neural network (GNN) and a convolutional neural network (CNN) to predict protein-ligand binding affinity is proposed in this work. In this model, the intermediate outputs of the GNN layers, as supplementary descriptors of atomic chemical environments at different levels, are concatenated with the input features of CNN. The model demonstrates a noticeable improvement in performance on CASF-2016 benchmark compared to its constituent CNN models. The generalization ability of the model is evaluated by setting a series of thresholds for ligand extended-connectivity fingerprint similarity or protein sequence similarity between the training and test sets. Masking experiment reveals that model can capture key interaction regions. Furthermore, the fusion model is applied to a virtual screening task for a novel target, PI5P4Kα. The fusion strategy significantly improves the ability of the constituent CNN model to identify active compounds. This work offers a novel approach to enhancing the accuracy of deep learning models in predicting binding affinity through fusion strategies.","PeriodicalId":188,"journal":{"name":"Journal of Computational Chemistry","volume":"45 32","pages":"2929-2940"},"PeriodicalIF":3.4,"publicationDate":"2024-09-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142118558","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"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

Full-dimensional coupled-channel statistical approach to atom-triatom systems and applications to H/D + O3 reaction 原子-三原子系统的全维耦合通道统计方法及其在 H/D + O3 反应中的应用。

IF 3.4 3区化学

Journal of Computational Chemistry Pub Date : 2024-09-02 DOI: 10.1002/jcc.27500

Dongzheng Yang, Hua Guo

引用次数: 0

Ichor: A Python library for computational chemistry data management and machine learning force field development Ichor：用于计算化学数据管理和机器学习力场开发的 Python 库

IF 3.4 3区化学

Journal of Computational Chemistry Pub Date : 2024-08-31 DOI: 10.1002/jcc.27477

Yulian T. Manchev, Matthew J. Burn, Paul L. A. Popelier

{"title":"Ichor: A Python library for computational chemistry data management and machine learning force field development","authors":"Yulian T. Manchev, Matthew J. Burn, Paul L. A. Popelier","doi":"10.1002/jcc.27477","DOIUrl":"10.1002/jcc.27477","url":null,"abstract":"We present ichor, an open-source Python library that simplifies data management in computational chemistry and streamlines machine learning force field development. Ichor implements many easily extensible file management tools, in addition to a lazy file reading system, allowing efficient management of hundreds of thousands of computational chemistry files. Data from calculations can be readily stored into databases for easy sharing and post-processing. Raw data can be directly processed by ichor to create machine learning-ready datasets. In addition to powerful data-related capabilities, ichor provides interfaces to popular workload management software employed by High Performance Computing clusters, making for effortless submission of thousands of separate calculations with only a single line of Python code. Furthermore, a simple-to-use command line interface has been implemented through a series of menu systems to further increase accessibility and efficiency of common important ichor tasks. Finally, ichor implements general tools for visualization and analysis of datasets and tools for measuring machine-learning model quality both on test set data and in simulations. With the current functionalities, ichor can serve as an end-to-end data procurement, data management, and analysis solution for machine-learning force-field development.","PeriodicalId":188,"journal":{"name":"Journal of Computational Chemistry","volume":"45 32","pages":"2912-2928"},"PeriodicalIF":3.4,"publicationDate":"2024-08-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/jcc.27477","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142101602","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"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

Delocalization-ratio analysis of 3-center bonding in position-space for closo-boranes and related systems: Approaching the styx picture and beyond 闭硼烷及相关体系位置空间中 3 心键的脱焦比分析：接近样式图及其他

IF 3.4 3区化学

Journal of Computational Chemistry Pub Date : 2024-08-30 DOI: 10.1002/jcc.27486

Frank R. Wagner

{"title":"Delocalization-ratio analysis of 3-center bonding in position-space for closo-boranes and related systems: Approaching the styx picture and beyond","authors":"Frank R. Wagner","doi":"10.1002/jcc.27486","DOIUrl":"10.1002/jcc.27486","url":null,"abstract":"Closo-boron hydrides BnHn2− (n = 5–12) are a conceptually well understood class of compounds. For these and a few related prototype compounds, both the local and the global picture of 3-center bonding are extracted from position-space quantities based on the electron density and the pair density. For this purpose, three-center delocalization indices between quantum theory of atoms in molecules (QTAIM) atoms in position space are used to develop a consistent set of local bond and triangle, and global cluster delocalization ratios (DRs), which are quantitatively compared with conceptual Γ values derived from the styx code for each cluster. Combination of the cluster DRs with associated effective numbers of skeletal electron sharing (SES) for selected cluster surface edges, triangles, or the whole cluster yields effective styx type values describing the trend and even the size of the conceptual styx codes for closo-boranes BnHn2− and related systems with increasing cluster size n reasonably well. For nonuniform cluster topologies, the different vertex degrees are shown to cause systematic 3-center wise bond delocalization effects for the associated edges and triangles of different average vertex degrees. Extension of DR analysis beyond the styx type triangular cluster-surface bonding corresponds to a triangulation of multicentric bonding. The cluster-wise results keep indicating consistency with the mixed 2- and 3-center bonding approach. The successfully established chemical meaning of the local edge, triangle, and global cluster DRs and their associated SES values constitutes the basis for systematic investigations of mixed 2- and 3-center bonding scenarios in particular in intermetallic and related (endohedral) cluster compounds in the future.","PeriodicalId":188,"journal":{"name":"Journal of Computational Chemistry","volume":"45 32","pages":"2862-2877"},"PeriodicalIF":3.4,"publicationDate":"2024-08-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/jcc.27486","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142101603","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"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

Ab initio electronic absorption spectra of para-nitroaniline in different solvents: Intramolecular charge transfer effects 对硝基苯胺在不同溶剂中的 Ab initio 电子吸收光谱：分子内电荷转移效应

IF 3.4 3区化学

Journal of Computational Chemistry Pub Date : 2024-08-30 DOI: 10.1002/jcc.27493

Matheus Máximo-Canadas, Lucas Modesto-Costa, Itamar Borges Jr

{"title":"Ab initio electronic absorption spectra of para-nitroaniline in different solvents: Intramolecular charge transfer effects","authors":"Matheus Máximo-Canadas, Lucas Modesto-Costa, Itamar Borges Jr","doi":"10.1002/jcc.27493","DOIUrl":"10.1002/jcc.27493","url":null,"abstract":"Intramolecular charge transfer (ICT) effects of para-nitroaniline (pNA) in eight solvents (cyclohexane, toluene, acetic acid, dichloroethane, acetone, acetonitrile, dimethylsulfoxide, and water) are investigated extensively. The second-order algebraic diagrammatic construction, ADC(2), ab initio wave function is employed with the COSMO implicit and discrete multiscale solvation methods. We found a decreasing amine group torsion angle with increased solvent polarity and a linear correlation between the polarity and ADC(2) transition energies. The first absorption band involves π → π* transitions with ICT from the amine and the benzene ring to the nitro group, increased by 4%–11% for different solvation models of water compared to the vacuum. A second band of pNA is characterized for the first time. This band is primarily a local excitation on the nitro group, including some ICT from the amine group to the benzene ring that decreases with the solvent polarity. For cyclohexane, the COSMO implicit solvent model shows the best agreement with the experiment, while the explicit model has the best agreement for water.","PeriodicalId":188,"journal":{"name":"Journal of Computational Chemistry","volume":"45 32","pages":"2899-2911"},"PeriodicalIF":3.4,"publicationDate":"2024-08-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142101604","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"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

Photophysical properties of donor (D)–acceptor (A)–donor (D) diketopyrrolopyrrole (A) systems as donors for applications to organic electronic devices 供体（D）-受体（A）-供体（D）二酮吡咯并吡咯（A）系统作为供体应用于有机电子器件的光物理特性

IF 3.4 3区化学

Journal of Computational Chemistry Pub Date : 2024-08-30 DOI: 10.1002/jcc.27492

Nathália M. P. Rosa, Itamar Borges Jr

{"title":"Photophysical properties of donor (D)–acceptor (A)–donor (D) diketopyrrolopyrrole (A) systems as donors for applications to organic electronic devices","authors":"Nathália M. P. Rosa, Itamar Borges Jr","doi":"10.1002/jcc.27492","DOIUrl":"10.1002/jcc.27492","url":null,"abstract":"Fourteen substituted diketopyrrolopyrrole (DPP) molecules in a donor (D)–acceptor (DPP)–donor (D) arrangement were designed. We employed density functional theory, time-dependent DFT, DFT-MRCI and the ab initio wave function second-order algebraic diagrammatic construction (ADC(2)) methods to investigate theoretically these systems. The examined aromatic substituents have one, two, or three hetero- and non-hetero rings. We comprehensively investigated their optical, electronic, and charge transport properties to evaluate potential applications in organic electronic devices. We found that the donor substituents based on one, two, or three aromatic rings bonded to the DPP core can improve the efficiency of an organic solar cell by fine-tuning the highest occupied molecular orbital/lowest unoccupied molecular orbital levels to match acceptors in typical bulk heterojunctions acceptors. Several properties of interest for organic photovoltaic devices were computed. We show that the investigated molecules are promising for applications as donor materials when combined with typical acceptors in bulk heterojunctions because they have appreciable energy conversion efficiencies resulting from their low ionization potentials and high electron affinities. This scenario allows a more effective charge separation and reduces the recombination rates. A comprehensive charge transfer analysis shows that D–A (DDP)–D systems have significant intramolecular charge transfer, further confirming their promise as candidates for donor materials in solar cells. The significant photophysical properties of DPP derivatives, including the high fluorescence emission, also allow these materials to be used in organic light-emitting diodes.","PeriodicalId":188,"journal":{"name":"Journal of Computational Chemistry","volume":"45 32","pages":"2885-2898"},"PeriodicalIF":3.4,"publicationDate":"2024-08-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142101605","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"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

How accurate can Kohn-Sham density functional be for both main-group and transition metal reactions Kohn-Sham 密度函数对主族金属和过渡金属反应的精确度有多高

IF 3.4 3区化学

Journal of Computational Chemistry Pub Date : 2024-08-30 DOI: 10.1002/jcc.27488

Yizhen Wang, Igor Ying Zhang, Xin Xu

{"title":"How accurate can Kohn-Sham density functional be for both main-group and transition metal reactions","authors":"Yizhen Wang, Igor Ying Zhang, Xin Xu","doi":"10.1002/jcc.27488","DOIUrl":"10.1002/jcc.27488","url":null,"abstract":"Achieving chemical accuracy in describing reactions involving both main-group elements and transition metals poses a substantial challenge for density functional approximations (DFAs), primarily due to the significantly different behaviors for electrons moving in the s,p-orbitals or in the d,f-orbitals. MOR41, a representative dataset of transition metal chemistry, has highlighted the PWPB95-D3(BJ) functional, a B2PLYP-type doubly hybrid (bDH) approximation equipped with an empirical dispersion correction, as the leading functional thus far (Dohm et al., J Chem Theory Comput 2018;14: 2596–2608). However, this functional is not among the top bDH methods for main-group chemistry (Goerigk et al., Phys Chem Chem Phys. 2017;19: 32184). Conversely, bDH methods such as DSD-BLYP-D3, proficient in main-group chemistry, often falter for transition metal chemistry. Herein, taking advantage of the home-made Rust-based Electronic-Structure Toolkits, we examine a suite of XYG3-type doubly hybrid (xDH) methods. We confirm that the trade-off in descriptive accuracy between main-group and transition metal systems persists within the realm of perturbation theory (PT2)-based xDH methods. Notably, however, our study ushers in a pivotal advance with the recently proposed renormalized xDH method, R-xDH7-SCC15. This method not only distinguishes itself among the elite methods for main-group chemistry, but also achieves an unprecedented accuracy for the MOR41 dataset, outperforming all other reported DFAs. The efficacy of R-xDH7-SCC15 stems from the successful integration of a renormalized PT2 correlation model (rPT2) and a machine-learning strong-correlation correction (SCC15), marking a significant step forward in the realm of computational chemistry.","PeriodicalId":188,"journal":{"name":"Journal of Computational Chemistry","volume":"45 32","pages":"2878-2884"},"PeriodicalIF":3.4,"publicationDate":"2024-08-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142101637","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"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 algorithm for very high pressure molecular dynamics simulations 超高压分子动力学模拟算法

IF 3.4 3区化学

Journal of Computational Chemistry Pub Date : 2024-08-29 DOI: 10.1002/jcc.27461

Marina Tesi, Roberto Cammi, Giovanni Granucci, Maurizio Persico

{"title":"An algorithm for very high pressure molecular dynamics simulations","authors":"Marina Tesi, Roberto Cammi, Giovanni Granucci, Maurizio Persico","doi":"10.1002/jcc.27461","DOIUrl":"10.1002/jcc.27461","url":null,"abstract":"We describe a method to run simulations of ground or excited state dynamics under extremely high pressures. The method is based on the introduction of a fictitious ideal gas that exerts the required pressure on a molecular sample and is therefore called XP-GAS (eXtreme Pressure by Gas Atoms in a Sphere). The algorithm is most suitable for approximately spherical clusters of molecules described by quantum chemistry methods, Molecular Mechanics or mixed QM/MM approaches. We compare the results obtained by the algorithm here presented and by the XP-PCM approach, based on a continuum description of the environment. As a test case, we study the conformational dynamics of 1,3-butadiene either as an isolated molecule (“naked” butadiene) or embedded in a cluster of argon atoms, under pressures up to 15 GPa. Overall, our results show that the XP-GAS QM/MM simulation method is in good agreement with the XP-PCM QM/Continuum model (Cammi model) in describing the effect of the pressure on static properties as the equilibrium geometry of butadiene in the ground state. Furthermore, the comparison of XP-GAS simulations with naked butadiene and butadiene in argon shows the importance, for XP-GAS and related methods, of a realistic representation of the medium in modelling pressure effects.","PeriodicalId":188,"journal":{"name":"Journal of Computational Chemistry","volume":"45 32","pages":"2848-2861"},"PeriodicalIF":3.4,"publicationDate":"2024-08-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/jcc.27461","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142101638","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"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