Journal of Computational Chemistry最新文献

{"title":"A Closer Look at the FeS Heme Bonds in Azotobacter vinelandii Bacterioferritin: QM/MM and Local Mode Analysis","authors":"Marek Freindorf,&nbsp;Elfi Kraka","doi":"10.1002/jcc.70012","DOIUrl":"10.1002/jcc.70012","url":null,"abstract":"<p>Using the QM/MM methodology and a local mode analysis, we investigated a character and a strength of FeS bonds of heme groups in oxidized and reduced forms of Bacterioferritin from <i>Azotobacter vinelandii</i>. The strength of the FeS bonds was correlated with a bond length, an energy density at a bond critical point, and a charge difference of the F and S atoms. Changing the oxidation state from ferrous to ferric generally makes the FeS bonds weaker, longer, more covalent, and more polar. We also investigated the SFeS bond bending and found that the stronger FeS bond, generally makes the SFeS bond bending stiffer, which could play a key role in the balance between ferric and ferrous oxidation states and related biological activities.</p>","PeriodicalId":188,"journal":{"name":"Journal of Computational Chemistry","volume":"46 1","pages":""},"PeriodicalIF":3.4,"publicationDate":"2025-01-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/jcc.70012","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142917200","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}

{"title":"Examining the Impact of Local Constraint Violations on Energy Computations in DFT","authors":"Vaibhav Khanna,&nbsp;Bikash Kanungo,&nbsp;Vikram Gavini,&nbsp;Ambuj Tewari,&nbsp;Paul M. Zimmerman","doi":"10.1002/jcc.70005","DOIUrl":"10.1002/jcc.70005","url":null,"abstract":"<p>This work examines the impact of locally imposed constraints in Density Functional Theory (DFT). Using a metric referred to as the extent of violation index (EVI), we quantify how well exchange-correlation functionals adhere to local constraints. Applying EVIs to a diverse set of molecules for GGA functionals reveals constraint violations, particularly for semi-empirical functionals. We leverage EVIs to explore potential connections between these violations and errors in chemical properties. While no correlation is observed for atomization energies, a significant statistical correlation emerges between EVIs and total energies. Similarly, the analysis of reaction energies suggests weak positive correlations for specific constraints. However, definitive conclusions about error cancellation mechanisms cannot be made at this time. These observations revealed by EVIs may be useful for consideration when designing future generations of semilocal functionals.</p>","PeriodicalId":188,"journal":{"name":"Journal of Computational Chemistry","volume":"46 1","pages":""},"PeriodicalIF":3.4,"publicationDate":"2025-01-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/jcc.70005","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142911933","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}

{"title":"Machine Learning Prediction of Physicochemical Properties in Lithium-Ion Battery Electrolytes With Active Learning Applied to Graph Neural Networks","authors":"Debojyoti Das,&nbsp;Debdutta Chakraborty","doi":"10.1002/jcc.70009","DOIUrl":"10.1002/jcc.70009","url":null,"abstract":"<div>\u0000 \u0000 <p>Accurate prediction of physicochemical properties, such as electronic energy, enthalpy, free energy, and average vibrational frequencies, is critical for optimizing lithium-ion battery (LIB) performance. Traditional methods like density functional theory (DFT) are computationally expensive and inefficient for large-scale screening. In this study, we apply active learning on top of graph neural networks (GNNs) to efficiently predict these properties. By focusing on uncertain data points, active learning reduces training data size while maintaining high accuracy. Applied to the LIBE and MPcules datasets, the model achieved an R-squared (<i>R</i>²) values of 0.9977 with a mean absolute error (MAE) of 9.66 Ha for electronic energy and an <i>R</i>² values of 0.957 with an MAE of 13.94 cm⁻¹ for average vibrational frequencies. SHapley Additive exPlanations (SHAP) provided insights into key features influencing predictions, such as atomic number and spin multiplicity. This approach enhances both predictive accuracy and model interpretability, offering a scalable solution for LIB electrolyte discovery.</p>\u0000 </div>","PeriodicalId":188,"journal":{"name":"Journal of Computational Chemistry","volume":"46 1","pages":""},"PeriodicalIF":3.4,"publicationDate":"2024-12-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142887022","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}

{"title":"Influence of Ligand Complexity on the Spectroscopic Properties of Type 1 Copper Sites: A Theoretical Study","authors":"Umut Ozuguzel,&nbsp;Serzat Safaltin,&nbsp;S. Pamir Alpay,&nbsp;Kenda Alkadry,&nbsp;Reed Nieman,&nbsp;Carol Korzeniewski,&nbsp;Adelia J. A. Aquino","doi":"10.1002/jcc.70013","DOIUrl":"10.1002/jcc.70013","url":null,"abstract":"<div>\u0000 \u0000 <p>Multi-copper oxidases (MCOs) are enzymes of significant interest in biotechnology due to their efficient catalysis of oxygen reduction to water, making them valuable in sustainable energy production and bio-electrochemical applications. This study employs time-dependent density functional theory (TDDFT) to investigate the electronic structure and spectroscopic properties of the Type 1 (T1) copper site in Azurin, which serves as a model for similar sites in MCOs. Four model complexes of varying complexity were derived from the T1 site, including 3 three-coordinate models and 1 four-coordinate model with axial methionine ligation, to explore the impact of molecular branches and axial coordination. Calculations using ωB97X-D3 functional, def2-TZVP basis set, and conductor-like polarizable continuum model (CPCM) solvation model reproduced key experimental spectral features, with increased model complexity improving agreement, particularly for the ~400 cm⁻¹ band splitting in resonance Raman spectra. This work enhances our understanding of T1 copper sites' electronic properties and spectra, bridging the gap between simplified models and complex proteins. The findings contribute to the interpretation of spectroscopic data in blue copper proteins and may inform future studies on similar biological systems.</p>\u0000 </div>","PeriodicalId":188,"journal":{"name":"Journal of Computational Chemistry","volume":"46 1","pages":""},"PeriodicalIF":3.4,"publicationDate":"2024-12-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142886970","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}

{"title":"A Polarizable CASSCF/MM Approach Using the Interface Between OpenMMPol Library and Cfour","authors":"Tommaso Nottoli,&nbsp;Mattia Bondanza,&nbsp;Filippo Lipparini,&nbsp;Benedetta Mennucci","doi":"10.1002/jcc.27550","DOIUrl":"10.1002/jcc.27550","url":null,"abstract":"<p>We present a polarizable embedding quantum mechanics/molecular mechanics (QM/MM) framework for ground- and excited-state Complete Active Space Self-Consistent Field (CASSCF) calculations on molecules within complex environments, such as biological systems. These environments are modeled using the AMOEBA polarizable force field. This approach is implemented by integrating the OpenMMPol library with the CFour quantum chemistry software suite. The implementation supports both single-point energy evaluations and geometry optimizations, facilitated by the availability of analytical gradients. We demonstrate the methodology by applying it to two distinct photoreceptors, exploring the impact of the protein environment on the structural and photophysical properties of their embedded chromophores.</p>","PeriodicalId":188,"journal":{"name":"Journal of Computational Chemistry","volume":"46 1","pages":""},"PeriodicalIF":3.4,"publicationDate":"2024-12-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/jcc.27550","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142879834","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}

{"title":"Comprehensive Analysis of Deuterium Isotope Effects on Ionic H3O+…π Interactions Using Multi-Component Quantum Mechanics Methods","authors":"Taro Udagawa,&nbsp;Yusuke Kanematsu,&nbsp;Takayoshi Ishimoto,&nbsp;Masanori Tachikawa","doi":"10.1002/jcc.70000","DOIUrl":"10.1002/jcc.70000","url":null,"abstract":"<div>\u0000 \u0000 <p>Deuterium isotope effects on interaction energies and geometrical parameters in several H₃O⁺(D₃O⁺)^…ene and H₃O+(D₃O⁺)^…yne complexes, which involve O-H(D)^…π interactions, have been analyzed using the MP2 level of the multi-component molecular orbital method (MC_MP2), which can incorporate the nuclear quantum effects of light nuclei, such as protons and deuterons. The MC_MP2 calculations revealed that D₃O⁺ replacement reduced the interaction energies of the complexes and induced changes in geometrical parameters. In addition, natural energy decomposition analysis (NEDA) revealed a strong correlation between the H/D isotope effects on the H/D^…π distances and on each energy component.</p>\u0000 </div>","PeriodicalId":188,"journal":{"name":"Journal of Computational Chemistry","volume":"46 1","pages":""},"PeriodicalIF":3.4,"publicationDate":"2024-12-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142857880","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}

{"title":"Groupy: An Open-Source Toolkit for Molecular Simulation and Property Calculation","authors":"Ruichen Liu,&nbsp;Li Wang,&nbsp;Xiangwen Zhang,&nbsp;Guozhu Li","doi":"10.1002/jcc.27527","DOIUrl":"10.1002/jcc.27527","url":null,"abstract":"<div>\u0000 \u0000 <p>In this work, an open-source, versatile, and flexible code named Groupy is present for calculating various molecular properties and preparing input files of molecular simulation software such as Gaussian. This code requires only SMILES as input, but can output many new useful data and files in multiple formats. The output information is clear and easy to read. The tips to the users are very detailed and easy to follow when using. Message passing interface (MPI) parallelization is supported to reduce computing time when the properties of a large number of molecules are calculated. Groupy not only supports the calculation of molecular properties using the traditional group contribution method, but also directly outputs the group-contribution-style molecular fingerprints for machine learning. The code has strong extensibility, which can be used as an external library to build other programs. We hope that Groupy brings great convenience to both computational and experimental chemists in their daily research. The code of Groupy can be freely obtained at https://github.com/47-5/Groupy</p>\u0000 </div>","PeriodicalId":188,"journal":{"name":"Journal of Computational Chemistry","volume":"46 1","pages":""},"PeriodicalIF":3.4,"publicationDate":"2024-12-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142825025","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}

{"title":"Tuning Electronic Relaxation of Nanorings Through Their Interlocking","authors":"Laura Alfonso-Hernandez,&nbsp;Victor M. Freixas,&nbsp;Tammie Gibson,&nbsp;Sergei Tretiak,&nbsp;Sebastian Fernandez-Alberti","doi":"10.1002/jcc.27533","DOIUrl":"10.1002/jcc.27533","url":null,"abstract":"<div>\u0000 \u0000 <p>Electronic and vibrational relaxation processes can be optimized and tuned by introducing alternative pathways that channel excess energy more efficiently. An ensemble of interacting molecular systems can help overcome the bottlenecks caused by large energy gaps between intermediate excited states involved in the relaxation process. By employing this strategy, catenanes composed of mechanically interlocked carbon nanostructures show great promise as new materials for achieving higher efficiencies in electronic devices. Herein, we perform nonadiabatic excited state molecular dynamics on different all-benzene catenanes. We observe that catenanes experience faster relaxations than individual units. Coupled catenanes present overlapping energy manifolds that include several electronic excited states spatially localized on the different moieties, increasing the density of states that ultimately improve the efficiency in the energy relaxation. This result suggests the use of catenanes as a viable strategy for tuning the internal conversion rates in a quest for their utilization for new optoelectronic applications.</p>\u0000 </div>","PeriodicalId":188,"journal":{"name":"Journal of Computational Chemistry","volume":"46 1","pages":""},"PeriodicalIF":3.4,"publicationDate":"2024-12-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142825027","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}

{"title":"The Influence of the Solvation on the Bonding of Molecular Complexes of Diatomic Halogens With Nitrogen-Containing Donors and Their Stability With Respect to the Heterolytic Halogen-Halogen Bond Splitting","authors":"Anna V. Pomogaeva,&nbsp;Anna S. Lisovenko,&nbsp;Alexey Y. Timoshkin","doi":"10.1002/jcc.27549","DOIUrl":"10.1002/jcc.27549","url":null,"abstract":"<div>\u0000 \u0000 <p>In the framework of SMD approach a systematic computational study of structural, electronic and thermodynamic properties of molecular complexes of Cl₂, ICl and I₂ with series of N-containing Lewis bases in solvents of different polarity was carried out. Results indicate that molecular complexes of Cl₂ with strong and medium-strong LB undergo spontaneous ionization in the acetonitrile solution. The increase of the solvent polarity can change the nature of interaction in X'X<span></span>LB systems from molecular X'X ← LB donor-acceptor complexes to 3-center 4-electron bound X'<span></span>→X⁺ ← LB in solvents of medium polarity and to the contact ion pairs X'<span></span>→[X<span></span>LB]⁺ in polar solvents. Thus, the controlled generation of cationic [LB∙X]⁺ species is possible by varying the nature of LB, varying the nature of the solvent, and varying the nature of the halogen X. Molecular Cl₂ has the greatest tendency to form ionic species in polar solvents. Spontaneous ionization of molecular nσ complexes of chlorine with strong LB in medium-polar solvents (starting from OEt₂, <i>ε</i> = 4.24) should not be neglected and single point solvation energy computations on gas phase optimized geometries are not reliable for such systems.</p>\u0000 </div>","PeriodicalId":188,"journal":{"name":"Journal of Computational Chemistry","volume":"46 1","pages":""},"PeriodicalIF":3.4,"publicationDate":"2024-12-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142816170","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}

{"title":"pKa prediction in non-aqueous solvents","authors":"Jonathan W. Zheng,&nbsp;Emad Al Ibrahim,&nbsp;Ivari Kaljurand,&nbsp;Ivo Leito,&nbsp;William H. Green","doi":"10.1002/jcc.27517","DOIUrl":"10.1002/jcc.27517","url":null,"abstract":"&lt;p&gt;Acid dissociation constants (&lt;span&gt;&lt;/span&gt;&lt;math&gt;\u0000 &lt;semantics&gt;\u0000 &lt;mrow&gt;\u0000 &lt;mi&gt;p&lt;/mi&gt;\u0000 &lt;msub&gt;\u0000 &lt;mi&gt;K&lt;/mi&gt;\u0000 &lt;mi&gt;a&lt;/mi&gt;\u0000 &lt;/msub&gt;\u0000 &lt;/mrow&gt;\u0000 &lt;annotation&gt;$$ mathrm{p}{K}_{mathrm{a}} $$&lt;/annotation&gt;\u0000 &lt;/semantics&gt;&lt;/math&gt;) are widely measured and studied, most typically in water. Comparatively few datasets and models for non-aqueous &lt;span&gt;&lt;/span&gt;&lt;math&gt;\u0000 &lt;semantics&gt;\u0000 &lt;mrow&gt;\u0000 &lt;mi&gt;p&lt;/mi&gt;\u0000 &lt;msub&gt;\u0000 &lt;mi&gt;K&lt;/mi&gt;\u0000 &lt;mi&gt;a&lt;/mi&gt;\u0000 &lt;/msub&gt;\u0000 &lt;/mrow&gt;\u0000 &lt;annotation&gt;$$ mathrm{p}{K}_{mathrm{a}} $$&lt;/annotation&gt;\u0000 &lt;/semantics&gt;&lt;/math&gt; values exist. In this work, we demonstrate how the &lt;span&gt;&lt;/span&gt;&lt;math&gt;\u0000 &lt;semantics&gt;\u0000 &lt;mrow&gt;\u0000 &lt;mi&gt;p&lt;/mi&gt;\u0000 &lt;msub&gt;\u0000 &lt;mi&gt;K&lt;/mi&gt;\u0000 &lt;mi&gt;a&lt;/mi&gt;\u0000 &lt;/msub&gt;\u0000 &lt;/mrow&gt;\u0000 &lt;annotation&gt;$$ mathrm{p}{K}_{mathrm{a}} $$&lt;/annotation&gt;\u0000 &lt;/semantics&gt;&lt;/math&gt; in one solvent can be accurately determined using reference data in another solvent, corrected by solvation energy calculations from the COSMO-RS method. We benchmark this approach in 10 different solvents, and find that &lt;span&gt;&lt;/span&gt;&lt;math&gt;\u0000 &lt;semantics&gt;\u0000 &lt;mrow&gt;\u0000 &lt;mi&gt;p&lt;/mi&gt;\u0000 &lt;msub&gt;\u0000 &lt;mi&gt;K&lt;/mi&gt;\u0000 &lt;mi&gt;a&lt;/mi&gt;\u0000 &lt;/msub&gt;\u0000 &lt;/mrow&gt;\u0000 &lt;annotation&gt;$$ mathrm{p}{K}_{mathrm{a}} $$&lt;/annotation&gt;\u0000 &lt;/semantics&gt;&lt;/math&gt; values calculated in six solvents deviate from experimental data on average by less than 1 &lt;span&gt;&lt;/span&gt;&lt;math&gt;\u0000 &lt;semantics&gt;\u0000 &lt;mrow&gt;\u0000 &lt;mi&gt;p&lt;/mi&gt;\u0000 &lt;msub&gt;\u0000 &lt;mi&gt;K&lt;/mi&gt;\u0000 &lt;mi&gt;a&lt;/mi&gt;\u0000 &lt;/msub&gt;\u0000 &lt;/mrow&gt;\u0000 &lt;annotation&gt;$$ mathrm{p}{K}_{mathrm{a}} $$&lt;/annotation&gt;\u0000 &lt;/semantics&gt;&lt;/math&gt; unit. We observe comparable performance on a more diverse test set including amino acids and drug molecules, with higher error for large molecules. The model performance in four other solvents is worse, with one MAE exceeding 3 &lt;span&gt;&lt;/span&gt;&lt;math&gt;\u0000 &lt;semantics&gt;\u0000 &lt;mrow&gt;\u0000 &lt;mi&gt;p&lt;/mi&gt;\u0000 &lt;msub&gt;\u0000 &lt;mi&gt;K&lt;/mi&gt;\u0000 &lt;mi&gt;a&lt;/mi&gt;\u0000 &lt;/msub&gt;\u0000 &lt;/mrow&gt;\u0000 &lt;annotation&gt;$$ mathrm{p}{K}_{mathrm{a}} $$&lt;/annotation&gt;\u0000 &lt;/semantics&gt;&lt;/math&gt; units; we discuss how such errors arise due to both model error and ","PeriodicalId":188,"journal":{"name":"Journal of Computational Chemistry","volume":"46 1","pages":""},"PeriodicalIF":3.4,"publicationDate":"2024-12-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/jcc.27517","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142805037","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}