Journal of Computational Chemistry最新文献

{"title":"Substituent Effect on the Nucleophilic Aromatic Substitution of Thiophenes With Pyrrolidine: Theoretical Mechanistic and Reactivity Study","authors":"Jean-Thomas Pouzens,&nbsp;Salma Souissi,&nbsp;Benjamin Ludwig,&nbsp;Guillaume Le Breton,&nbsp;Francesca Ingrosso,&nbsp;Sahbi Ayachi,&nbsp;Jean-Cyrille Hierso,&nbsp;Taoufik Boubaker,&nbsp;Paul Fleurat-Lessard","doi":"10.1002/jcc.70169","DOIUrl":"https://doi.org/10.1002/jcc.70169","url":null,"abstract":"<p>Aromatic nucleophilic substitution (S_NAr) is a widely employed synthetic method for modifying thiophene derivatives. Herein, we computationally investigate the reaction mechanism of 2-methoxy-3-<i>X</i>-5-nitrothiophenes with pyrrolidine (where <i>X</i> = NO₂, CN, SO₂CH₃, COCH₃, CO₂CH₃, CONH₂ or H). This S_NAr reaction follows a stepwise pathway: initially, pyrrolidine adds to the <i>C2</i> position of the 2-methoxy thiophene partner. Then, the release of methanol is triggered by a proton transfer from the newly formed ammonium intermediate to the methoxy group. With excess pyrrolidine, this proton transfer is catalyzed by an additional pyrrolidine molecule. We establish linear correlations between the experimental electrophilicity and the Gibbs free energy barrier, Parr electrophilicity (ω), and molecular softness (S). Local reactivity descriptors for the <i>C2</i> position are generally non-informative, except for the population of the C<span></span>O bond basin, the <i>C2</i> population of the ELF_LUMO function, and the condensed electrophilicity index ω⁺(<i>C2</i>). This theoretical approach provides a robust method to further predict electrophilicity parameters in versatile thiophene derivatives chemistry.</p>","PeriodicalId":188,"journal":{"name":"Journal of Computational Chemistry","volume":"46 19","pages":""},"PeriodicalIF":3.4,"publicationDate":"2025-07-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/jcc.70169","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144615036","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":"Adapted DFTB3 Repulsive Potentials Reach DFT Accuracy for Hydride Transfer Reactions in Enzymes","authors":"José Luís Velázquez-Libera,&nbsp;Rodrigo Recabarren,&nbsp;David Adrian Saez,&nbsp;Carlos Castillo,&nbsp;J. Javier Ruiz-Pernía,&nbsp;Iñaki Tuñón,&nbsp;Esteban Vöhringer-Martinez","doi":"10.1002/jcc.70174","DOIUrl":"https://doi.org/10.1002/jcc.70174","url":null,"abstract":"<div>\u0000 \u0000 <p>Enzymatic hydride transfer reactions play a crucial role in numerous metabolic pathways, yet their accurate computational modeling remains challenging due to the trade-off between accuracy and computational efficiency. Ideally, molecular dynamics simulations should sample all enzyme configurations along the reaction path using post-Hartree-Fock or DFT QM/MM electrostatic embedding methods, but these are computationally expensive. Here, we introduce a simple approach to improve the third-order density functional tight binding (DFTB3) semi-empirical method to model hydride transfer reactions in enzymes. We identified deficiencies in DFTB3's description of the potential energy surface for the hydride transfer step in Crotonyl-CoA Carboxylase/Reductase (Ccr) and developed a systematic methodology to address these limitations. Our approach involves modifying DFTB3's repulsive potential functions using linear combinations of harmonic functions, guided by analysis of C-H and C-C distance distributions along the reaction path. The optimized DFTB3 Hamiltonian significantly improved the description of the hydride transfer reaction in Ccr, reproducing the reference DFT activation barrier within 0.1 kcal/mol. We also addressed the transferability of our method by applying it to another hydride transfer reaction bearing the 1,4-dihydropyridine motif but exhibiting distinct structural features of the reactant, as well as the hydride transfer reaction in Dihydrofolate Reductase (DHFR). In both cases, our adapted DFTB3 Hamiltonian correctly reproduced the DFT reference and experimentally observed activation barriers. The low computational cost and transferability of our method will enable more accurate and efficient QM/MM molecular dynamics simulations of hydride transfer reactions, potentially accelerating research in enzyme engineering and drug design.</p>\u0000 </div>","PeriodicalId":188,"journal":{"name":"Journal of Computational Chemistry","volume":"46 19","pages":""},"PeriodicalIF":3.4,"publicationDate":"2025-07-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144624407","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":"MSCMLCIDTI: Drug–Target Interaction Prediction Based on Multiscale Feature Extraction and Deep Interactive Attention Fusion Mechanisms","authors":"Jia Peng,&nbsp;Xiaoyu Liu,&nbsp;Yuxuan Liao,&nbsp;Lei Wang,&nbsp;Xianyou Zhu","doi":"10.1002/jcc.70170","DOIUrl":"https://doi.org/10.1002/jcc.70170","url":null,"abstract":"<div>\u0000 \u0000 <p>Drug–target interaction prediction serves as a crucial component in accelerating drug discovery. To overcome current limitations in deep learning approaches, specifically the inadequate representation of local features and insufficient modeling of drug and target information interactions, we propose a multiscale feature extraction coupled multilayer cross-interaction network (MSCMLCIDTI). The model uses multiscale convolutional blocks to extract structural fingerprints of drug compounds and amino acid sequences at different scales for multigranularity pattern recognition across spatial domains, followed by gated attention to obtain multidimensional features. This multidimensional feature extraction enhances the model's capability to identify critical binding sites between pharmacological compounds and their biological targets. Furthermore, we implement a deep cross-interaction mechanism utilizing multilayer attention-based interactions to model complex relationships between distinct drug substructures and protein fragments. This design empowers accurate identification of sophisticated interaction signatures in pharmaceutical target complexes. Comprehensive validation across four open-access benchmark datasets reveals our framework's superior predictive accuracy compared to existing leading-edge models.</p>\u0000 </div>","PeriodicalId":188,"journal":{"name":"Journal of Computational Chemistry","volume":"46 19","pages":""},"PeriodicalIF":3.4,"publicationDate":"2025-07-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144624406","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":"Orbital Interactions in Hydrogen Bonds: A Perspective From the Chemical Bond Overlap Model","authors":"Rodolfo A. Santos,&nbsp;Carlos V. Santos- Jr.,&nbsp;Eduardo C. Aguiar,&nbsp;Albano N. Carneiro Neto,&nbsp;Renaldo T. Moura Jr.","doi":"10.1002/jcc.70166","DOIUrl":"https://doi.org/10.1002/jcc.70166","url":null,"abstract":"&lt;p&gt;Hydrogen bonds are essential chemical interactions that occur in various systems, playing a critical role in determining molecular structures, dynamics, and reactivity. While quantum chemical methods such as Quantum Theory of Atoms in Molecules (QTAIM) and Natural Bond Orbital (NBO) analyses have traditionally been used to explore these interactions, this work introduces the Chemical Bond Overlap (OP) Model and its topological (TOP) descriptors as a complementary approach for analyzing orbital overlap contributions in hydrogen bonds. The study reports a systematic investigation of a series of hydrogen-bonded systems (a total of 25 systems), demonstrating how electron-donating and electron-withdrawing substituents influence bond characteristics. The results reveal that OP/TOP effectively captures the effects of electronic perturbations, offering insights into the &lt;span&gt;&lt;/span&gt;&lt;math&gt;\u0000 &lt;semantics&gt;\u0000 &lt;mrow&gt;\u0000 &lt;mi&gt;n&lt;/mi&gt;\u0000 &lt;/mrow&gt;\u0000 &lt;annotation&gt;$$ n $$&lt;/annotation&gt;\u0000 &lt;/semantics&gt;&lt;/math&gt;(X) &lt;span&gt;&lt;/span&gt;&lt;math&gt;\u0000 &lt;semantics&gt;\u0000 &lt;mrow&gt;\u0000 &lt;mo&gt;→&lt;/mo&gt;\u0000 &lt;/mrow&gt;\u0000 &lt;annotation&gt;$$ to $$&lt;/annotation&gt;\u0000 &lt;/semantics&gt;&lt;/math&gt; &lt;span&gt;&lt;/span&gt;&lt;math&gt;\u0000 &lt;semantics&gt;\u0000 &lt;mrow&gt;\u0000 &lt;msup&gt;\u0000 &lt;mrow&gt;\u0000 &lt;mi&gt;σ&lt;/mi&gt;\u0000 &lt;/mrow&gt;\u0000 &lt;mrow&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;msup&gt;\u0000 &lt;mrow&gt;\u0000 &lt;mtext&gt;X&lt;/mtext&gt;\u0000 &lt;/mrow&gt;\u0000 &lt;mrow&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;mtext&gt;H&lt;/mtext&gt;\u0000 &lt;mo&gt;)&lt;/mo&gt;\u0000 &lt;/mrow&gt;\u0000 &lt;annotation&gt;$$ {sigma}^{ast}left({mathrm{X}}^{prime }-mathrm{H}right) $$&lt;/annotation&gt;\u0000 &lt;/semantics&gt;&lt;/math&gt; interactions and serving as a complementary approach to QTAIM, NBO, and local vibrational modes theory (LVM). Notably, for nonconventional &lt;span&gt;&lt;/span&gt;&lt;math&gt;\u0000 &lt;semantics&gt;\u0000 &lt;mrow&gt;\u0000 &lt;msub&gt;\u0000 &lt;mrow&gt;\u0000 &lt;mo&gt;(&lt;/mo&gt;\u0000 &lt;msub&gt;\u0000 &lt;mrow&gt;\u0000 &lt;mtext&gt;CH&lt;/mtext&gt;\u0000 &lt;/mrow&gt;\u0000 &lt;mrow&gt;\u0000 &lt;mn&gt;3&lt;/mn&gt;\u0000 &lt;/mrow&gt;\u0000 &lt;/msub&gt;\u0000 &lt;mo&gt;)&lt;/mo&gt;\u0000 &lt;/mrow&gt;\u0000 &lt;mrow&gt;\u0000 &lt;mn&gt;3&lt;/mn&gt;\u0000 &lt;/mrow","PeriodicalId":188,"journal":{"name":"Journal of Computational Chemistry","volume":"46 19","pages":""},"PeriodicalIF":3.4,"publicationDate":"2025-07-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/jcc.70166","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144589525","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":"Anti-Symmetric Molecular Graph Learning Approach With Residual Adaptive Network Based Fuzzy Inference System for Lethal Dose Forecasting Problem","authors":"Linh Nguyen Thi My,&nbsp;Tham Vo","doi":"10.1002/jcc.70176","DOIUrl":"https://doi.org/10.1002/jcc.70176","url":null,"abstract":"<div>\u0000 \u0000 <p>In recent times, graph neural networks (GNNs) have become essential tools in molecular graph learning, due to its ability to model intricate structural dependencies. Despite their success, recent research has shown that GNNs still face significant limitations, in capturing long-range dependencies and global structural information. One of the central issues is the over-squashing problem, where information from distant nodes is excessively compressed into fixed-size node representations. This leads to poor information propagation; as a result, ultimately degrading the model's performance—particularly in complex tasks such as lethal dose forecasting, where both local chemical substructures and global molecular topology play vital roles. To overcome these limitations, we propose a novel anti-symmetric fuzzy-enhanced graph learning (ASFGL) model. Generally, our model integrates two key components: an anti-symmetric transformation module and a residual adaptive neuro-fuzzy inference system (ANFIS). The anti-symmetric transformation is designed based on stable graph ordinary differential equations (ODE); thus, ensuring a non-dissipative and stable propagation of information across multiple graph layers. This mechanism effectively mitigates the over-squashing issue, therefore, allows our model to better capture long-range dependencies in a stable manner. Complementarily, the ANFIS module employs bell-shaped membership functions to support robust and interpretable learning; as a result, enabling adaptive rule-based reasoning that refines the molecular representations learned from the graph structure. By combining these modules, the ASFGL model bridges local message passing and global structural awareness, yielding expressive molecular embeddings well-designed for toxicity prediction problems. We evaluate our proposed ASFGL model on different benchmark molecular datasets, where it consistently outperforms state-of-the-art GNN-based architectures in terms of MAE/RMSE evaluation metrics, particularly in scenarios requiring deep representation learning over large interactions. These results highlight the efficacy of integrating anti-symmetric dynamics and fuzzy inference systems in advancing molecular property prediction and overcoming foundational challenges in GNN design.</p>\u0000 </div>","PeriodicalId":188,"journal":{"name":"Journal of Computational Chemistry","volume":"46 19","pages":""},"PeriodicalIF":3.4,"publicationDate":"2025-07-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144598665","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":"Voronota-LT: Efficient, Flexible, and Solvent-Aware Tessellation-Based Analysis of Atomic Interactions","authors":"Kilment Olechnovič,&nbsp;Sergei Grudinin","doi":"10.1002/jcc.70178","DOIUrl":"https://doi.org/10.1002/jcc.70178","url":null,"abstract":"<div>\u0000 \u0000 <p>Understanding molecular interactions is essential in computational chemistry, structural biology, and bioinformatics. Current methods for describing interatomic contacts are often simplistic, neglecting full structural context, or computationally demanding, limiting their practical utility. With rapidly growing structural datasets, there is an urgent need for more descriptive and efficient interaction analysis tools. We present Voronota-LT, a highly efficient method for computing Voronoi tessellation-based atom-atom contact areas within molecular solvent-accessible surfaces. Voronota-LT differs fundamentally from the original Voronota method by directly constructing each interatomic contact surface without precomputing global Voronoi diagrams or Delaunay triangulations. This enables fast, parallelizable computations with linear scalability and a possibility for targeted analysis of molecular interfaces. In addition to its high performance, Voronota-LT comprehensively describes interatomic interactions with full structural context. Voronota-LT software is open-source and available as a standalone command-line application, a web application, a Python library, and a C++ header-only library at https://www.voronota.com/expansion_lt/.</p>\u0000 </div>","PeriodicalId":188,"journal":{"name":"Journal of Computational Chemistry","volume":"46 19","pages":""},"PeriodicalIF":3.4,"publicationDate":"2025-07-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144589532","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 DFT-Based Protocol for Modeling the Structure and Reactivity of Gold(III) Complexes","authors":"Luana P. P. Cunha,&nbsp;Larissa P. N. M. Pinto,&nbsp;Willian T. G. Novato,&nbsp;Hélio F. Dos Santos,&nbsp;Diego F. S. Paschoal","doi":"10.1002/jcc.70179","DOIUrl":"https://doi.org/10.1002/jcc.70179","url":null,"abstract":"<p>In this study, distinct computational protocols were employed to investigate the structure and kinetic properties of the aquation reaction of the [Au(dien-H)Cl]⁺ Au(III) complex. A total of 154 protocols with nonrelativistic Hamiltonians were initially assessed, comprising 31 basis sets for Au, 52 basis sets for ligand atoms, and 71 levels of theory (including HF, MP2, and 69 DFT-functionals). Additionally, seven protocols with relativistic Hamiltonians, using all-electron basis sets for Au, were evaluated. The results indicate that the structure is relatively insensitive to the computational protocol. In contrast, the activation Gibbs free energy (<span></span><math>\u0000 <semantics>\u0000 <mrow>\u0000 <msubsup>\u0000 <mrow>\u0000 <mi>Δ</mi>\u0000 <mi>G</mi>\u0000 </mrow>\u0000 <mi>aq</mi>\u0000 <mo>‡</mo>\u0000 </msubsup>\u0000 </mrow>\u0000 <annotation>$$ {Delta G}_{mathrm{aq}}^{ddagger } $$</annotation>\u0000 </semantics></math>) are highly sensitive to both the level of theory and basis sets choice. Notably, the basis set used for ligand atoms plays a key role in accurately predicting kinetic parameters. Among the tested 397 combinations, the B3LYP/def2-SVP/6-31G(d,p) protocol yielded the overall best agreement with experimental data for the reference complex. However, for bulkier [Au(R-dien-H)Cl]⁺ derivatives, diffuse functions on ligand atoms are essential, making 6-31+G(d) the recommended basis set. When all five Au(III) complexes are considered, the optimal performance is achieved using B3LYP with the Stuttgart-RSC ECP for Au and 6-31+G(d) for ligand atoms. This combination offers a good balance between accuracy and computational cost, making it a practical choice even for larger Au(III) complexes.</p>","PeriodicalId":188,"journal":{"name":"Journal of Computational Chemistry","volume":"46 19","pages":""},"PeriodicalIF":3.4,"publicationDate":"2025-07-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/jcc.70179","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144589697","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":"Electron Dynamics Induced by Circularly Polarized Laser Pulses in Im-3m H3S in the Superconducting Pressure Regime","authors":"Lizhi Tang,&nbsp;Genwei Hong,&nbsp;Tianlv Xu,&nbsp;Herbert Früchtl,&nbsp;Tanja van Mourik,&nbsp;Steven R. Kirk,&nbsp;Samantha Jenkins","doi":"10.1002/jcc.70173","DOIUrl":"https://doi.org/10.1002/jcc.70173","url":null,"abstract":"<div>\u0000 \u0000 <p>We investigated crystalline <i>Im-3m</i> H₃S at 200 GPa, a pressure regime where H₃S is generally considered to be an exotic superconductor. Simulated circularly polarized 10 femtosecond (fs) laser pulses were applied and we quantified the effects on the electron dynamics during the application of “pump” and candidate “probe” laser pulses to discover optimal “probe” laser pulses. This is undertaken for the first application of Next Generation Quantum Theory of Atoms in Molecules (NG-QTAIM) using the Hessian of the “spin-up” and “spin-down” contributions to the total electronic charge density <i>ρ</i>(<b>r</b>). The optimal “probe” pulse was found to possess a peak electric field <i>E</i> = 10.0 × 10⁻⁴ a.u. compared with the “pump” pulse of <i>E</i> = 200.0 × 10⁻⁴ a.u. Separately considering the spin-up and spin-down contributions doubles the values of the chirality-helicity <i>C</i>_helicity function relative to that of the total charge density contribution for the H-H bonding for the application of the “pump” laser pulse. Within the NG-QTAIM interpretation, a combination of highly responsive and coherent behaviors is associated with superconductivity. These behaviors were discovered from the very high values of the <i>C</i>_helicity function, near-linear scaling of the bond-flexing <i>F</i> and bond-chirality <i>C</i> values with peak <i>E</i>-field and all instances of the H-H bonding possessing <b>R</b> electronic chirality assignments. The “pump” pulse was found to magnify the effects associated with superconductivity within the NG-QTAIM interpretation. Future applications are discussed including chiral spin selective phenomena and exotic high temperature superconductivity where phonons do not play a significant role.</p>\u0000 </div>","PeriodicalId":188,"journal":{"name":"Journal of Computational Chemistry","volume":"46 18","pages":""},"PeriodicalIF":3.4,"publicationDate":"2025-07-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144550927","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":"Bonding Evolution Theory Study of the [3+2] Cycloaddition Reaction Between Benzonitrile Oxide and Ethylenic Derivatives","authors":"Adjieufack Abel Idrice,&nbsp;Champagne Benoît,&nbsp;Andrés Juan,&nbsp;Olivia Mónica,&nbsp;Safont Vicent S.,&nbsp;Liégeois Vincent","doi":"10.1002/jcc.70164","DOIUrl":"https://doi.org/10.1002/jcc.70164","url":null,"abstract":"<div>\u0000 \u0000 <p>Using the framework of the bonding evolution theory (BET), we investigated the molecular mechanism of the [3+2] cycloaddition reaction of benzonitrile oxide (<b>1</b>) with five ethylenic derivatives (2<b>a–e</b>). The global mechanism consists in the concerted attack of one of the O lone pairs of <b>1</b> on one of the atoms of the C–X double or triple bond of <b>2</b> (X = C, O, N), the attack of the C–X double or triple bond of <b>2</b> on the C of the C–N triple bond of <b>1</b>, and the conversion of C–N triple bond of <b>1</b> into a double bond and the creation of a lone pair on N. The reaction proceeds through a <i>one-step</i> mechanism, the creation and modification of the electron basins occur at different places along the intrinsic reaction coordinate, as unraveled by the BET study. In the cases of dipolarophiles (<b>2a–c</b>), first the C–N triple bond of <b>1</b> is converted into a double bond with the creation of a lone pair on N. Then, a C–C single bond between the C–N triple bond of <b>1</b> and one of the C atoms of the C–C double or triple bond of <b>2</b> is created. Finally, the O–C single bond is formed. Concerning <b>2e</b>, the <i>meta</i>-path follows the same reaction mechanism as <b>2a–c</b>, while for the <i>ortho</i>-path, the formation of C–N and C–O bonds are synchronous and mediated by the N4 lone pair. A similar observation (but for the two C–O bonds) is found for <b>2d</b> <i>ortho</i>-path while the mechanism for the <i>meta</i>-path is quite different to the other ones due to the formation of an O–O bond. The present work represents a new example showing how the use of BET can provide curly arrows and electron flow representation to unravel molecular mechanisms.</p>\u0000 </div>","PeriodicalId":188,"journal":{"name":"Journal of Computational Chemistry","volume":"46 18","pages":""},"PeriodicalIF":3.4,"publicationDate":"2025-07-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144550928","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":"Accurate Prediction of HOMO–LUMO Gap Using DFT Functional and Application to Next-Generation Organic Telluro[n]Helicenes Materials","authors":"Rahul Kumar,&nbsp;Rahul Kar,&nbsp;Dilip K. Maity","doi":"10.1002/jcc.70175","DOIUrl":"https://doi.org/10.1002/jcc.70175","url":null,"abstract":"<p>The present work purposes and establishes an accurate prediction of HOMO–LUMO energies of thiophene-, selenophene-, and tellurophene-based helicenes using 15 different DFT methodologies. DFT functionals used in this work are PBE, PBE0, B3LYP, B3LYP-D, B3LYP-D3, M06, MN15, HSE06, LC-BLYP, CAM-B3LYP, LC-ωPBE, ωΒ97XD and B2PLYP. DFT HOMO–LUMO gaps are compared with the fundamental gaps calculated at the CCSD(T) level of theory. The LANL2DZ basis set is used for tellurium atoms, and the 6–311++G(d,p) basis set is used for other elements. Statistical error analysis suggests that the HOMO–LUMO energy gaps can be accurately obtained using ωB97XD functional, with geometry optimization performed at the same theoretical level. However, geometry optimization using the B3LYP functional, followed by single-point energy calculation with the ωB97XD functional, provides a more cost-effective method with similar accuracy for energy gap prediction. HOMO–LUMO gaps of telluro[n]helicenes ([n]TeH) are redshifted compared with their S- and Se-analogs. Tellurophene-based helicenes ([n]TeH) systems are easy to oxidize in contrast to their S- and Se-analogs. Dimerization studies have found that substituted [7]TeH^•+ is more stable in dichloromethane than its S- and Se-analogs. The CAM-B3LYP and ωΒ97XD functionals are used in conjunction with the TDDFT procedure to explore the excited states of [n]TeH radical cations. These radical cation systems showed better absorption in the infrared range than S- and Se-systems. Overall, our benchmarking studies lead to an accurate prediction of HOMO–LUMO gaps of [<i>n</i>]TeH. Further, this study demonstrates the potential of Te-based helical structures to create versatile next-generation organic materials.</p>","PeriodicalId":188,"journal":{"name":"Journal of Computational Chemistry","volume":"46 18","pages":""},"PeriodicalIF":3.4,"publicationDate":"2025-07-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/jcc.70175","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144537124","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}