Journal of Computational Chemistry最新文献

{"title":"Dual-Branch Graph Neural Network for Predicting Molecular Odors and Discovering the Relationship Between Functional Groups and Odors","authors":"Yongquan Jiang,&nbsp;Xin Xie,&nbsp;Yan Yang,&nbsp;Yuerui Liu,&nbsp;Kuanping Gong,&nbsp;Tianrui Li","doi":"10.1002/jcc.70069","DOIUrl":"https://doi.org/10.1002/jcc.70069","url":null,"abstract":"<div>\u0000 \u0000 <p>Prediction of molecular odors is crucial for synthetic chemistry and the perfume industry. This paper presents a dual-branch graph neural network model for predicting molecular odors, named ScentGraphX, which combines transfer learning with graph attention mechanisms to address limitations of existing models. The ScentGraphX model captures atomic, chemical bond, and structural features of molecules through a feature encoder and a subgraph encoder. Experimental results show that the ScentGraphX model exhibits superior performance on a dataset comprising 4967 molecules, accurately predicting multi-label odor descriptors of molecules. Comparative analysis demonstrates that the ScentGraphX model excels in precision, recall, <i>F</i>1, and AUCROC evaluation metrics, validating its effectiveness in the field of molecular odor prediction. Moreover, interpretability analysis of the model reveals the impact of various chemical functional groups on odor characteristics, and ablation studies confirm the indispensability of each module in ScentGraphX.</p>\u0000 </div>","PeriodicalId":188,"journal":{"name":"Journal of Computational Chemistry","volume":"46 6","pages":""},"PeriodicalIF":3.4,"publicationDate":"2025-02-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143490053","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":"Infrared Spectrum and UV-Triggered Transformations of Matrix-Isolated Meta-Fluorothiophenol Supported by Ground and Excited State Theoretical Calculations","authors":"A. J. Lopes Jesus,&nbsp;J. R. Lucena Jr.,&nbsp;G. P. Rodrigues,&nbsp;G. Ogruc Ildiz,&nbsp;S. A. do Monte,&nbsp;E. Ventura,&nbsp;R. Fausto","doi":"10.1002/jcc.70045","DOIUrl":"https://doi.org/10.1002/jcc.70045","url":null,"abstract":"<div>\u0000 \u0000 <p>The infrared (IR) spectrum of <i>meta</i>-fluorothiophenol (mFTP) isolated in a low-temperature N₂ matrix was recorded and interpreted with the aid of B3LYP vibrational frequency calculations for both <i>cis</i> and <i>trans</i> conformers. Then, photochemical transformations in the matrix-isolated compound were triggered through UV–Vis laser irradiations and their outcomes were monitored by IR spectroscopy. Upon excitation at λ = 285 nm, thiol-to-thione phototautomerization was identified as the sole reaction pathway, leading to the formation of three thione isomers. Among them, the <i>ortho</i>-isomer where the hydrogen atom reattaches to the fluorine-substituted side of the aromatic ring was identified as the predominant photoproduct. Identification of the photoproducts was confirmed by comparing the emerging experimental spectra with the IR absorptions predicted for the candidate structures. The photoreaction was found to be reversible, as irradiation at λ = 405 nm partially restored the reactant. The experimental results were complemented with the application of multireference/multiconfigurational (CASSCF, CASPT2, MR-CIS) and TD-DFT (TD-M062X, ωB97XD, and τ-HCTHhyb) methods to investigate the excited state properties of mFTP, including the simulation of its UV photoabsorption spectra. A comparative analysis of the results obtained by the different methods was performed. This combined experimental and theoretical approach provided valuable insights into the photochemical behavior and electronic structure of fluorinated thiophenols.</p>\u0000 </div>","PeriodicalId":188,"journal":{"name":"Journal of Computational Chemistry","volume":"46 6","pages":""},"PeriodicalIF":3.4,"publicationDate":"2025-02-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143481340","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":"Extending Chemoinformatics Techniques With JMolecular Energy: A Robust CDK-Based Force Field Library","authors":"Rami M. Abdallah","doi":"10.1002/jcc.70071","DOIUrl":"https://doi.org/10.1002/jcc.70071","url":null,"abstract":"<div>\u0000 \u0000 <p>Computational chemistry plays a crucial role in drug design and development, where accurate modeling of molecular interactions is vital in rational drug design. Among the available methods, force fields such as MMFF94 are extensively used to calculate molecular potential energies, especially for small organic molecules. However, current implementations of MMFF94 are primarily available in commercial software or as closed-source modules. Open-source packages often offer limited functionality and lack extensibility. This paper introduces JMolecular Energy (JME), a novel, open-source Java library designed to implement MMFF94 with a robust and extendable API (Application Programming Interface) that allows for access to individual energy components. Leveraging the Chemistry Development Kit (CDK), JME provides a modular framework for potential energy calculation and facilitates functionalities previously absent in CDK, such as 3D conformation energy minimization. Additionally, JME establishes a framework for tailoring force field energy terms for various applications and facilitates the integration of custom-built force fields.</p>\u0000 </div>","PeriodicalId":188,"journal":{"name":"Journal of Computational Chemistry","volume":"46 6","pages":""},"PeriodicalIF":3.4,"publicationDate":"2025-02-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143489919","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":"Increase Docking Score Screening Power by Simple Fusion With CNNscore","authors":"Huicong Liang,&nbsp;Aowei Xie,&nbsp;Ning Hou,&nbsp;Fengjiao Wei,&nbsp;Ting Gao,&nbsp;Jiajie Li,&nbsp;Xinru Gao,&nbsp;Chuanqin Shi,&nbsp;Gaokeng Xiao,&nbsp;Ximing Xu","doi":"10.1002/jcc.70060","DOIUrl":"https://doi.org/10.1002/jcc.70060","url":null,"abstract":"<div>\u0000 \u0000 <p>Scoring functions (SFs) of molecular docking is a vital component of structure-based virtual screening (SBVS). Traditional SFs yield their inherent shortage for idealized approximations and simplifications predicting the binding affinity. Complementarily, SFs based on deep learning (DL) have emerged as powerful tools for capturing intricate features within protein-ligand (PL) interactions. We here present a docking-score fusion strategy that integrates pose scores derived from GNINA's convolutional neural network (CNN) with traditional docking scores. Extensive validation on diverse datasets has shown that by means of multiplying Watvina docking score by CNNscore demonstrates state-of-the-art screening power. Furthermore, in a reverse practice, our docking-score fusion technique was incorporated into the virtual screening (VS) workflow aimed at identifying inhibitors of the challenging target TYK2. Two promising hits with IC₅₀ 9.99 μM and 13.76 μM in vitro were identified from nearly 12 billion molecules.</p>\u0000 </div>","PeriodicalId":188,"journal":{"name":"Journal of Computational Chemistry","volume":"46 6","pages":""},"PeriodicalIF":3.4,"publicationDate":"2025-02-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143456150","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":"Mechanistic Study of LIDT Reduction in KH2PO4 With Yi Predicted by Density Functional Theory","authors":"Xu Lu,&nbsp;Wei Hong,&nbsp;Tingyu Liu,&nbsp;Huifang Li,&nbsp;Jianghai Wang","doi":"10.1002/jcc.70065","DOIUrl":"https://doi.org/10.1002/jcc.70065","url":null,"abstract":"<div>\u0000 \u0000 <p>The defect formation energy, electronic structures, and optical properties of paraelectric phase (PE-KDP) and ferroelectric phase (FE-KDP) crystals with Y interstitial (Y_i) defects have been investigated using density function theory. The band-edge correction and FNV correction accurately determine the defect formation energies of the Y_i defects in different charge states. The presence of transition energy levels in the band gap may indicate that the Y_i defect has a significant impact on the properties of the FE-KDP. The +3 charged Y_i defects are more stable. The electronic properties in the 2p orbital mainly contribute to the defect states in the band gap, which provides the possibility of multiphoton transition of electrons. New transparent absorption bands near 3.47 eV (357 nm) and 5.66 eV (219 nm) were calculated in PE-KDP, and the absorption bands caused by Y_i defects and strong electron–phonon coupling under the FE-KDP structure showed that the light in the wavelength bands near 5.09 eV (244 nm) and 5.79 eV (214 nm) below the phase transition temperature (123 K) damaged the KDP crystal. The distortion of atoms near the defects indicates that Y_i defects may be accompanied by intrinsic defects. The calculated values are highly consistent with the critical absorption observed at 355 nm in the experiment and the new absorption weak at 230 nm produced in the crystal after low-temperature X-ray irradiation, which suggests that the Y defect may be the key factor affecting the laser-induced damage threshold (LIDT) of the KDP crystal.</p>\u0000 </div>","PeriodicalId":188,"journal":{"name":"Journal of Computational Chemistry","volume":"46 6","pages":""},"PeriodicalIF":3.4,"publicationDate":"2025-02-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143455833","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":"First Principles Global Optimization Method From Parallel Tempering Molecular Dynamics","authors":"Gerald Geudtner,&nbsp;Andreas M. Köster","doi":"10.1002/jcc.70057","DOIUrl":"https://doi.org/10.1002/jcc.70057","url":null,"abstract":"<div>\u0000 \u0000 <p>Global optimization techniques are often based on a stochastic method to explore the potential energy surface of the investigated system. The here-described global optimization is based on a temperature-driven potential energy surface exploration via Parallel Tempering Born-Oppenheimer Molecular Dynamics (PT-BOMD) simulations. Additionally, structure selection from the lowest temperature PT-BOMD trajectory for further optimization is performed with a scheme based on the Discrete Cosine Transformation (DCT). This step can be done automatically and therefore removes a human bias. The influence of parameters for the DCT and the length of the PT-BOMD simulations is investigated with regard to their impact on the result of the global optimization.</p>\u0000 </div>","PeriodicalId":188,"journal":{"name":"Journal of Computational Chemistry","volume":"46 6","pages":""},"PeriodicalIF":3.4,"publicationDate":"2025-02-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143455834","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":"CH Bond Activation Mechanism by a High-Valent Dinuclear Copper Complex: Unraveling the Effect of a Base by a Theoretical Study","authors":"Oceane Mangel,&nbsp;Helene Jamet","doi":"10.1002/jcc.70070","DOIUrl":"https://doi.org/10.1002/jcc.70070","url":null,"abstract":"<p>Recently, an electrochemically monooxidized dinuclear copper(II) complex [Cu₂(L)(<i>μ</i>-OH)₂]²⁺ with the dipyridylethane naphthyridine ligand (L) has been shown to activate the recalcitrant aliphatic C_sp³<span></span>H bond of toluene (bond dissociation free energy, BDFE = 87.0 kcal mol⁻¹) at room temperature. The mechanistic pathway turns from stoichiometric to catalytic upon addition of a base (2,6-lutidine), suggesting a modification of the reactive species. Herein, we report theoretical calculations to characterize the reactive species and obtain a detailed understanding of the reactivity. Since different electronic structures are possible for these high valent systems, we perform DFT calculations coupled to CCSD(T) ones using the DLPNO-CCSD(T) scheme. Our results show that the presence of a base will impact the nature of the reactive species but also the type of mechanism involved in the C<span></span>H activation.</p>","PeriodicalId":188,"journal":{"name":"Journal of Computational Chemistry","volume":"46 6","pages":""},"PeriodicalIF":3.4,"publicationDate":"2025-02-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/jcc.70070","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143447021","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":"Structures and Solvation Energies Effects Versus Temperature. An MP2 Investigations in the Framework of Cluster Model","authors":"Awatef Hattab,&nbsp;Alhadji Malloum,&nbsp;Zoubeida Dhaouadi,&nbsp;Nino Russo","doi":"10.1002/jcc.70066","DOIUrl":"https://doi.org/10.1002/jcc.70066","url":null,"abstract":"&lt;p&gt;Structures, relative stabilities, solvation enthalpies, and free energies of the &lt;span&gt;&lt;/span&gt;&lt;math&gt;\u0000 &lt;semantics&gt;\u0000 &lt;mrow&gt;\u0000 &lt;mspace&gt;&lt;/mspace&gt;\u0000 &lt;msup&gt;\u0000 &lt;mfenced&gt;\u0000 &lt;mrow&gt;\u0000 &lt;mi&gt;Be&lt;/mi&gt;\u0000 &lt;msub&gt;\u0000 &lt;mfenced&gt;\u0000 &lt;mrow&gt;\u0000 &lt;msub&gt;\u0000 &lt;mi&gt;H&lt;/mi&gt;\u0000 &lt;mn&gt;2&lt;/mn&gt;\u0000 &lt;/msub&gt;\u0000 &lt;mi&gt;O&lt;/mi&gt;\u0000 &lt;/mrow&gt;\u0000 &lt;/mfenced&gt;\u0000 &lt;mrow&gt;\u0000 &lt;mi&gt;n&lt;/mi&gt;\u0000 &lt;mo&gt;=&lt;/mo&gt;\u0000 &lt;mn&gt;12&lt;/mn&gt;\u0000 &lt;/mrow&gt;\u0000 &lt;/msub&gt;\u0000 &lt;/mrow&gt;\u0000 &lt;/mfenced&gt;\u0000 &lt;mrow&gt;\u0000 &lt;mn&gt;2&lt;/mn&gt;\u0000 &lt;mo&gt;+&lt;/mo&gt;\u0000 &lt;/mrow&gt;\u0000 &lt;/msup&gt;\u0000 &lt;/mrow&gt;\u0000 &lt;annotation&gt;$$ {left[mathrm{Be}{left({mathrm{H}}_2mathrm{O}right)}_{n=12}right]}^{2+} $$&lt;/annotation&gt;\u0000 &lt;/semantics&gt;&lt;/math&gt; cluster in gas and in water phases were investigated in this work using Moller-Plesset perturbation theory (MP2) and considering a temperature range of 40–400 K. The 12 H&lt;sub&gt;2&lt;/sub&gt;O molecules are distributed between the first, second, and third solvation shells. The calculated distances &lt;span&gt;&lt;/span&gt;&lt;math&gt;\u0000 &lt;semantics&gt;\u0000 &lt;mrow&gt;\u0000 &lt;mspace&gt;&lt;/mspace&gt;\u0000 &lt;msup&gt;\u0000 &lt;mi&gt;Be&lt;/mi&gt;\u0000 &lt;mrow&gt;\u0000 &lt;mn&gt;2&lt;/mn&gt;\u0000 &lt;mo&gt;+&lt;/mo&gt;\u0000 &lt;/mrow&gt;\u0000 &lt;/msup&gt;\u0000 &lt;mo&gt;−&lt;/mo&gt;\u0000 &lt;mi&gt;O&lt;/mi&gt;\u0000 &lt;/mrow&gt;\u0000 &lt;annotation&gt;$$ {mathrm{Be}}^{2+}-mathrm{O} $$&lt;/annotation&gt;\u0000 &lt;/semantics&gt;&lt;/math&gt; distances in gas phase are in good agreement with the experimental range which confirms the strong influence of long-distance interactions in cluster stabilization. Structural comparison between gas and water phases shows that the addition of the bulk solvent causes changes in the cation-water bond lengths of few hundredths of angstroms. The obtained solvation free energy of beryllium ion in water at room temperature (298.15 K) results in &lt;i&gt;b&lt;/i&gt; − 575.1 kcal mol&lt;sup&gt;−1&lt;/sup&gt; in very good agreement with the corresponding experimental counterpart. The computed solvation free energies increase as a polynomial function of the temperature while the change in the solvation enthalpies is ","PeriodicalId":188,"journal":{"name":"Journal of Computational Chemistry","volume":"46 6","pages":""},"PeriodicalIF":3.4,"publicationDate":"2025-02-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/jcc.70066","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143446856","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":"Theoretical Insights Into Structures and U–C Bonding in the Uranium Benzyl Derivatives","authors":"Rui-Ying Liu,&nbsp;Qun-Yan Wu,&nbsp;Cong-Zhi Wang,&nbsp;Jian-Hui Lan,&nbsp;Cheng-Peng Li,&nbsp;Wei-Qun Shi","doi":"10.1002/jcc.70051","DOIUrl":"https://doi.org/10.1002/jcc.70051","url":null,"abstract":"<div>\u0000 \u0000 <p>The uranium benzyl derivatives are a class of uranium carbon complex with saturated carbon atom coordination. We investigated the electronic structures of the tetravalent uranium benzyl (Bn) complex U(CH₂Ph)₄ and its derivatives U(2-CH₂(NC₅H₄))₄, U(<i>o</i>-OMeBn)₄, U(<i>m</i>-OMeBn)₄, and the bonding nature between the uranium atom and methylene carbon atom (U–C_me) using scalar-relativistic quantum chemical calculations. The structures of the four uranium benzyl derivatives identify that the electronic structures are not sensitive to <i>meta</i>-OMe substitution, while they are significantly sensitive to the <i>ortho</i>-OMe and pyridine due to the coordination of O and N to the uranium atom. The U–C_me bonds have highly polarized σ-bonding with partial covalency, which are predominantly composed of U 6d and 5f orbitals. Moreover, U 6d orbitals are favored for the U–C_me bonds compared with U 5f orbitals. Furthermore, there are no additional π interactions in the U(<i>o</i>-OMeBn)₄ and the corresponding U–C_me bonds appear the strongest covalent character among the four U(IV) system. The energy decomposition analysis suggests that the electrostatic interaction plays a dominant role between uranium and ligands. Finally, the complexes U(2-CH₂(NC₅H₄))₄ and U(<i>o</i>-OMeBn)₄ are the most thermodynamically accessible among the four complexes based on the binding energies. This study improves our understanding of tetravalent uranium benzyl derivatives bearing uranium-saturated carbon bondings.</p>\u0000 </div>","PeriodicalId":188,"journal":{"name":"Journal of Computational Chemistry","volume":"46 6","pages":""},"PeriodicalIF":3.4,"publicationDate":"2025-02-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143431190","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":"Evaluation of Density-Functional Tight-Binding Methods for Simulation of Protic Molecular Ion Pairs","authors":"Tyler Walker,&nbsp;Van-Quan Vuong,&nbsp;Stephan Irle,&nbsp;Jihong Ma","doi":"10.1002/jcc.70064","DOIUrl":"https://doi.org/10.1002/jcc.70064","url":null,"abstract":"<p>In this work, we benchmark the accuracy of the density-functional tight-binding (DFTB) method, namely the long-range corrected second-order (LC-DFTB2) and third-order (DFTB3) models, for predicting energetics of imidazolium-based ionic liquid (IL) ion pairs. We compare the DFTB models against popular density functionals such as LC-ωPBE and B3LYP, using ab initio domain-based local pair-natural orbital coupled cluster (DLPNO-CC) energies as reference. Calculations were carried out in the gas phase, as well as in aqueous solution using implicit solvent methods. We find that the LC-DFTB2 model shows excellent performance in the gas phase and agrees well with reference energies in implicit solvent, often outperforming DFTB3 predictions for complexation energetics. Our study identifies a range of opportunities for use of the LC-DFTB method and quantifies its sensitivity to protonation states and the types of chemical interactions between ion pairs.</p>","PeriodicalId":188,"journal":{"name":"Journal of Computational Chemistry","volume":"46 5","pages":""},"PeriodicalIF":3.4,"publicationDate":"2025-02-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/jcc.70064","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143396900","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}