Journal of Computational Chemistry最新文献

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Choose Your Level Wisely: Assessing Density Functionals and Dispersion Corrections for Metal Carbonyl Compounds 明智地选择你的水平:评估密度功能和分散校正的金属羰基化合物。
IF 4.8 3区 化学
Journal of Computational Chemistry Pub Date : 2025-10-10 DOI: 10.1002/jcc.70245
Vinícius Glitz, Vinícius Capriles Port, Ebbe Nordlander, Rosely Aparecida Peralta, Giovanni Finoto Caramori
{"title":"Choose Your Level Wisely: Assessing Density Functionals and Dispersion Corrections for Metal Carbonyl Compounds","authors":"Vinícius Glitz,&nbsp;Vinícius Capriles Port,&nbsp;Ebbe Nordlander,&nbsp;Rosely Aparecida Peralta,&nbsp;Giovanni Finoto Caramori","doi":"10.1002/jcc.70245","DOIUrl":"10.1002/jcc.70245","url":null,"abstract":"<p>Understanding the structure of metal-ligand complexes is essential for catalyst design, materials development, and biochemical modeling. Metal carbonyls are especially relevant due to their diverse structures and electronic features. Here, we benchmarked seventeen density functionals (B3LYP, BP86, CAM–B3LYP, M06, M06L, PBE, PBE0, r<sup>2</sup>SCAN, r<sup>2</sup>SCAN–3c, revPBE, revTPSS, RPBE, TPSS, TPSS0, TPSSh, <span></span><math>\u0000 <semantics>\u0000 <mrow>\u0000 <mi>ω</mi>\u0000 </mrow>\u0000 <annotation>$$ omega $$</annotation>\u0000 </semantics></math>B97, and <span></span><math>\u0000 <semantics>\u0000 <mrow>\u0000 <mi>ω</mi>\u0000 </mrow>\u0000 <annotation>$$ omega $$</annotation>\u0000 </semantics></math>B97X) combined with three dispersion schemes (D3zero, D3BJ, D4) and also tested calculations without dispersion correction, totaling fifty-four approaches. Their ability to reproduce geometries, structural parameters, and CO stretching frequencies was assessed for thirty-four Mn(I) and Re(I) carbonyls obtained from the CCDC. Relative electronic energies were further compared using DLPNO-CCSD(T) calculations, alongside evaluation of computational cost. Our results highlight that hybrid meta-GGA and meta-GGA functionals, particularly TPSSh(D3zero) and r<sup>2</sup>SCAN(D3BJ, D4), offer the best balance between accuracy and efficiency, providing reliable structures, vibration properties, and energetics consistent with high-level DLPNO-CCSD(T) references.</p>","PeriodicalId":188,"journal":{"name":"Journal of Computational Chemistry","volume":"46 27","pages":""},"PeriodicalIF":4.8,"publicationDate":"2025-10-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/jcc.70245","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145254510","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
Addressing Long-Standing Challenges in Computational Enzymology With Large QM-Cluster Models of the [Ni, Fe]-Hydrogenase Proton Transfer 用[Ni, Fe]-氢化酶质子转移的大qm -簇模型解决计算酶学中长期存在的挑战。
IF 4.8 3区 化学
Journal of Computational Chemistry Pub Date : 2025-10-09 DOI: 10.1002/jcc.70234
Tejaskumar A. Suhagia, Qianyi Cheng, Thomas J. Summers, Makenzie C. Griffing, Nathan J. DeYonker
{"title":"Addressing Long-Standing Challenges in Computational Enzymology With Large QM-Cluster Models of the [Ni, Fe]-Hydrogenase Proton Transfer","authors":"Tejaskumar A. Suhagia,&nbsp;Qianyi Cheng,&nbsp;Thomas J. Summers,&nbsp;Makenzie C. Griffing,&nbsp;Nathan J. DeYonker","doi":"10.1002/jcc.70234","DOIUrl":"10.1002/jcc.70234","url":null,"abstract":"<div>\u0000 \u0000 <p>Hydrogenase enzymes play a crucial role in generating energy for microorganisms by catalyzing the reversible oxidation of molecular hydrogen to protons. This catalytic mechanism has been well studied using computational models of varying complexity, ranging from smaller QM-cluster models of the enzyme active site to QM/MM models that capture the full enzyme structure. However, differences among studies have produced conflicting predictions for the energetics of certain reaction steps. This work focuses on characterizing one step—a cysteine–histidine proton transfer of <i>Desulfovibrio fructosovorans</i> [Ni, Fe]-hydrogenase—using a series of QM-cluster models to explore how model design influences predicted reaction thermodynamics. The Residue Interaction Network-based ResidUe Selector (RINRUS) toolkit was used to systematically create QM-cluster models based on either inter-residue distances or contact metrics from the active site [Ni, Fe] cluster. It is shown that QM-cluster models can achieve reaction energy predictions comparable to QM/MM and “big-QM” models when active site models are designed based on inter-residue contact interactions and with careful consideration of charged residues. Distance-based residue selection, a common strategy for QM-cluster model design, is not as effective compared to the RINRUS rules-based residue ranking approach from inter-residue contact counts. Large differences between previously reported QM and QM/MM reaction energies are resolved with RINRUS-based models, even at a modest level of electronic structure theory (B3LYP with modified LANL2DZ(d) basis sets/effective core potentials on metal atoms and 6-31G(d′)/6-31G on nonmetal atoms). Overall, this [Ni, Fe]-hydrogenase case study underscores the need for careful model design when studying complex biological systems and demonstrates how RINRUS can provide a framework towards addressing this challenge.</p>\u0000 </div>","PeriodicalId":188,"journal":{"name":"Journal of Computational Chemistry","volume":"46 27","pages":""},"PeriodicalIF":4.8,"publicationDate":"2025-10-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145246855","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
Non-Adiabatic Effect in Perovskites: Model and Ab Initio Hamiltonian for Spectral/Ferroelectric Properties 钙钛矿中的非绝热效应:光谱/铁电性质的模型和从头算哈密顿量。
IF 4.8 3区 化学
Journal of Computational Chemistry Pub Date : 2025-10-09 DOI: 10.1002/jcc.70239
Mantu Kumar Sah, Satrajit Adhikari
{"title":"Non-Adiabatic Effect in Perovskites: Model and Ab Initio Hamiltonian for Spectral/Ferroelectric Properties","authors":"Mantu Kumar Sah,&nbsp;Satrajit Adhikari","doi":"10.1002/jcc.70239","DOIUrl":"10.1002/jcc.70239","url":null,"abstract":"&lt;div&gt;\u0000 \u0000 &lt;p&gt;This review presents a comprehensive analysis of Jahn-Teller (JT) and pseudo-Jahn-Teller (PJT) effects in perovskite systems, emphasizing their roles on phase transitions through vibronic coupling. A combined theoretical and computational approach has been applied to focus on roto-vibrational features in dielectric spectra of &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;mtext&gt;LaMnO&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;/mrow&gt;\u0000 &lt;annotation&gt;$$ {mathrm{LaMnO}}_3 $$&lt;/annotation&gt;\u0000 &lt;/semantics&gt;&lt;/math&gt; as well as the origin of ferroelectric behavior in &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;mtext&gt;BaTiO&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;/mrow&gt;\u0000 &lt;annotation&gt;$$ {mathrm{BaTiO}}_3 $$&lt;/annotation&gt;\u0000 &lt;/semantics&gt;&lt;/math&gt;. The centrifugal stabilization of JT-active excited states in &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;mtext&gt;LaMnO&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;/mrow&gt;\u0000 &lt;annotation&gt;$$ {mathrm{LaMnO}}_3 $$&lt;/annotation&gt;\u0000 &lt;/semantics&gt;&lt;/math&gt; and strong PJT coupling in &lt;span&gt;&lt;/span&gt;&lt;math&gt;\u0000 &lt;semantics&gt;\u0000 &lt;mrow&gt;\u0000 &lt;msubsup&gt;\u0000 &lt;mrow&gt;\u0000 &lt;mtext&gt;TiO&lt;/mtext&gt;\u0000 &lt;/mrow&gt;\u0000 &lt;mrow&gt;\u0000 &lt;mn&gt;6&lt;/mn&gt;\u0000 &lt;/mrow&gt;\u0000 &lt;mrow&gt;\u0000 &lt;mn&gt;8&lt;/mn&gt;\u0000 &lt;mo&gt;−&lt;/mo&gt;\u0000 &lt;/mrow&gt;\u0000 &lt;/msubsup&gt;\u0000 &lt;/mrow&gt;\u0000 &lt;annotation&gt;$$ {mathrm{TiO}}_6^{8-} $$&lt;/annotation&gt;\u0000 &lt;/semantics&gt;&lt;/math&gt; clusters of &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;mtext&gt;BaTiO&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;/mrow&gt;\u0000 &lt;annotation&gt;$$ {mathrm{BaTiO}}_3 $$&lt;/annotation&gt;\u0000 &lt;/semantics&gt;&lt;/math&gt; are crucial for exploring observed spectral and structural phenomena. The construction of diabatic Hamiltonians from ab initio adiabatic potential energy surfaces (PESs) and non-adiabatic coupling terms (NACT","PeriodicalId":188,"journal":{"name":"Journal of Computational Chemistry","volume":"46 27","pages":""},"PeriodicalIF":4.8,"publicationDate":"2025-10-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145247167","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
Optimization of Stillinger Weber Potential Parameters for Monolayer ZnS 单层ZnS的Stillinger Weber电位参数优化。
IF 4.8 3区 化学
Journal of Computational Chemistry Pub Date : 2025-10-07 DOI: 10.1002/jcc.70241
Hidayat Ullah Khan, F. Inam, Altaf Karim, Arshad Saleem Bhatti
{"title":"Optimization of Stillinger Weber Potential Parameters for Monolayer ZnS","authors":"Hidayat Ullah Khan,&nbsp;F. Inam,&nbsp;Altaf Karim,&nbsp;Arshad Saleem Bhatti","doi":"10.1002/jcc.70241","DOIUrl":"10.1002/jcc.70241","url":null,"abstract":"&lt;div&gt;\u0000 \u0000 &lt;p&gt;We optimize a Stillinger–Weber (SW) interatomic potential for ZnS monolayers to enable reliable large-scale molecular dynamics across planar, disordered, and curved morphologies. Using force matching algorithm (POTFIT) incorporating referenced density-functional-theory (SIESTA/PBE) forces gathered from diverse finite-temperature trajectories of monolayer ZnS, we refit the parameters due to by Zhou et al. (optimized for bulk phases), yielding comparable cohesive energies and lattice constants for wurtzite, zinc-blende, and 2D phases. For the monolayer, the phonon dispersion closely tracks DFT, notably correcting the optical branches. Moreover, the curvature-law fit &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;msub&gt;\u0000 &lt;mi&gt;E&lt;/mi&gt;\u0000 &lt;mtext&gt;strain&lt;/mtext&gt;\u0000 &lt;/msub&gt;\u0000 &lt;mo&gt;∝&lt;/mo&gt;\u0000 &lt;mn&gt;1&lt;/mn&gt;\u0000 &lt;mo&gt;/&lt;/mo&gt;\u0000 &lt;msup&gt;\u0000 &lt;mi&gt;D&lt;/mi&gt;\u0000 &lt;mn&gt;2&lt;/mn&gt;\u0000 &lt;/msup&gt;\u0000 &lt;/mrow&gt;\u0000 &lt;annotation&gt;$$ Big({E}_{mathrm{strain}}propto 1/{D}^2 $$&lt;/annotation&gt;\u0000 &lt;/semantics&gt;&lt;/math&gt;) to nanotube data extrapolates to negligible strain in the flat limit (&lt;span&gt;&lt;/span&gt;&lt;math&gt;\u0000 &lt;semantics&gt;\u0000 &lt;mrow&gt;\u0000 &lt;mi&gt;D&lt;/mi&gt;\u0000 &lt;mo&gt;→&lt;/mo&gt;\u0000 &lt;mo&gt;∞&lt;/mo&gt;\u0000 &lt;/mrow&gt;\u0000 &lt;annotation&gt;$$ Dto infty $$&lt;/annotation&gt;\u0000 &lt;/semantics&gt;&lt;/math&gt;), reinforcing the reliability of the optimized parameters for planar geometries. The optimized SW parameters demonstrate transferability, yielding an improved bonding network in 2D disordered geometries and thermally stable single-walled ZnS tubes. Quantitatively, curved-structure tests then yield an effective bending modulus &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;mn&gt;35&lt;/mn&gt;\u0000 &lt;mspace&gt;&lt;/mspace&gt;\u0000 &lt;mi&gt;eV&lt;/mi&gt;\u0000 &lt;/mrow&gt;\u0000 &lt;annotation&gt;$$ approx 35 mathrm{eV} $$&lt;/annotation&gt;\u0000 &lt;/semantics&gt;&lt;/math&gt; and thermal shape fluctuations scaling as &lt;span&gt;&lt;/span&gt;&lt;math&gt;\u0000 &lt;semantics&gt;\u0000 &lt;mrow&gt;\u0000 &lt;mtext&gt;RMSD&lt;/mtext&gt;\u0000 &lt;mo&gt;∝&lt;/mo&gt;\u0000 &lt;mn&gt;1&lt;/mn&gt;\u0000 &lt;mo&gt;/&lt;/mo&gt;\u0000 &lt;mi&gt;D&lt;/mi&gt;\u0000 &lt;/mrow&gt;\u0000 &lt;annotation&gt;$$ mathrm{RMSD}propto 1/D $$&lt;/annotation&gt;\u0000 &lt;/semantics&gt;&lt;/math&gt;, indicating a practical stability threshold near &lt;span&gt;&lt;/span&gt;&lt;math&gt;\u0000 &lt;semantics&gt;\u0000 &lt;mrow&gt;\u0000 &lt;mi&gt;D&lt;/mi&gt;\u0000 &lt;mo&gt;≈&lt;/mo&gt;\u0000 &lt;mn&gt;38&lt;/mn&gt;\u0000 &lt;mo&gt;−&lt;/mo&gt;\u0000 &lt;/mrow&gt;\u0000 &lt;annotation&gt;$$ Dapprox 38- $$&lt;/annotation&gt;\u0000 &lt;/semantics&gt;&lt;/math&gt;40 Å. Collectively, our optimi","PeriodicalId":188,"journal":{"name":"Journal of Computational Chemistry","volume":"46 27","pages":""},"PeriodicalIF":4.8,"publicationDate":"2025-10-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145235867","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
Extensive TDDFT Benchmark Study of the Resonance Raman Spectra of Lumiflavin 荧光黄素共振拉曼光谱的广泛TDDFT基准研究
IF 4.8 3区 化学
Journal of Computational Chemistry Pub Date : 2025-10-04 DOI: 10.1002/jcc.70229
Prokopis C. Andrikopoulos, Heba Halimeh
{"title":"Extensive TDDFT Benchmark Study of the Resonance Raman Spectra of Lumiflavin","authors":"Prokopis C. Andrikopoulos,&nbsp;Heba Halimeh","doi":"10.1002/jcc.70229","DOIUrl":"10.1002/jcc.70229","url":null,"abstract":"<p>An extensive computational TDDFT resonance Raman study of lumiflavin is presented including 42 DFT functionals, benchmarked against the experimental Evolution Associated Spectra (EAS) of the equilibrated S<sub>1</sub> and T<sub>1</sub> states of FMN published earlier. Initially, off-resonance spectra were computed, yielding adequate agreement, and fine-tuning was achieved with the inclusion of specific frequency scaling factors. Since the experimental EAS were obtained under resonance for the singlet and near-resonance for the triplet state, the subsequent inclusion of resonance effects in the calculations improved the correlation for most functionals. Their evaluation according to specific criteria narrowed down the choice to HCTH, OLYP, and TPSSh. Among the included criteria were the percent error of the 0–0 transitions, the quantification of the increase/decrease in correlation due to the addition of resonance enhancements, and the reproduction of the singlet-triplet peak shifts. Owing to the extensive data set, valuable insights were gained to assist similar studies.</p>","PeriodicalId":188,"journal":{"name":"Journal of Computational Chemistry","volume":"46 26","pages":""},"PeriodicalIF":4.8,"publicationDate":"2025-10-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/jcc.70229","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145215573","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
Rationalizing the DCD Model in Transition Metal Carbonyls: A Conceptual Density Functional Theory Analysis 过渡金属羰基中DCD模型的合理化:一个概念密度泛函理论分析。
IF 4.8 3区 化学
Journal of Computational Chemistry Pub Date : 2025-10-03 DOI: 10.1002/jcc.70242
Shanti Gopal Patra, Chhanda Paul, Nirmal Dutta, Pratim Kumar Chattaraj
{"title":"Rationalizing the DCD Model in Transition Metal Carbonyls: A Conceptual Density Functional Theory Analysis","authors":"Shanti Gopal Patra,&nbsp;Chhanda Paul,&nbsp;Nirmal Dutta,&nbsp;Pratim Kumar Chattaraj","doi":"10.1002/jcc.70242","DOIUrl":"10.1002/jcc.70242","url":null,"abstract":"<div>\u0000 \u0000 <p>The bonding in transition metal carbonyls is discussed through the Dewar-Chatt-Duncanson (DCD) model of <i>σ</i>-donation from the ligand and <i>π</i>-back donation from the metal. However, there are no reports of direct quantification of the donation and back donation. Whenever it comes to the aspect of electron transfer, the fundamental concepts that are important are ionization energy (<i>I</i>), electron affinity (<i>A</i>), electronegativity (<i>χ</i>), hardness (<i>η</i>), and electrophilicity (<i>ω</i>). The global reactivity indices are calculated using conceptual density functional theory (CDFT). It was found that the back bonding and hence the experimental CO stretching frequency provide excellent correlation with <i>I</i>, <i>A</i>, and <i>χ</i> with <i>r</i><sup>2</sup> values of 0.963, 0.903, and 0.965, respectively. While in correlation to <i>η</i>, two categories are developed in correlation to ν<sub>CO</sub>. However, the best correlation is achieved from the local electrophilicity description of the multiphilic descriptor (Δ<i>ω</i><sub><i>M</i></sub>). Finally, the directional approach of the back donation is tackled by the extended transition state-natural orbitals for chemical valence (ETS-NOCV) method, considering CO as one fragment and the rest as the other. A very good correlation to ν<sub>CO</sub> is found with <i>r</i><sup>2</sup> = 0.964. The back-bonding aspect is also explained from the second-order perturbation energy term as obtained from the natural bond orbital analysis. These correlations remain valid upon changing the functional and basis sets. In addition, considering Sc(CO) as the starting complex, hydrogen molecules are added to obtain Sc(CO)(H<sub>2</sub>)<sub>n</sub> (<i>n</i> = 1–5) complexes. In these complexes, the Kubas-type interactions are studied employing ETS-NOCV and quantum theory of atoms in molecules (QTAIM) analyses.</p>\u0000 </div>","PeriodicalId":188,"journal":{"name":"Journal of Computational Chemistry","volume":"46 26","pages":""},"PeriodicalIF":4.8,"publicationDate":"2025-10-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145209102","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
Cyclo[16]Carbon for Sensing and Safe Handling of TNT and TATB: A DFT Investigation 环[16]碳用于TNT和TATB的传感和安全处理:DFT研究。
IF 4.8 3区 化学
Journal of Computational Chemistry Pub Date : 2025-10-03 DOI: 10.1002/jcc.70235
Souvik Santra, Sobitri Sen, Arijit Bag, Sourav Pal
{"title":"Cyclo[16]Carbon for Sensing and Safe Handling of TNT and TATB: A DFT Investigation","authors":"Souvik Santra,&nbsp;Sobitri Sen,&nbsp;Arijit Bag,&nbsp;Sourav Pal","doi":"10.1002/jcc.70235","DOIUrl":"10.1002/jcc.70235","url":null,"abstract":"<div>\u0000 \u0000 <p>The development of advanced materials for the detection and safe handling of energetic compounds such as TATB (1,3,5-triamino-2,4,6-trinitrobenzene) and TNT (2,4,6-trinitrotoluene) is critical for defense, homeland security, and industrial safety. However, current technologies often suffer from limited cost-efficiency, sensitivity, and real-world applicability. While traditional carbon allotropes such as graphene, fullerenes, and carbon nanotubes have been explored for explosive sensing and hazard mitigation, emerging <i>sp</i>-hybridized carbon nanostructures like cyclo[<i>n</i>]carbons remain underexplored. In this article, we present a theoretical investigation of cyclo[16]carbon (C<sub>16</sub>), a novel <i>sp</i>-hybridized carbon ring, for interaction with energetic molecules. TNT was selected as a benchmark explosive due to its widespread use, whereas TATB was chosen for its remarkable insensitivity, allowing us to explore safe handling and adsorption scenarios. Our results reveal the formation of stable hollow-layered and sandwich-type supramolecular complexes with TNT and TATB via non-covalent C…O, C…N, and C…C interactions. Notably, the C<sub>16</sub>–TNT and C<sub>16</sub>–TATB complexes exhibit enhanced thermodynamic stability and reduced electrostatic sensitivity. Binding energy and electronic structure analyses indicate tunable optical properties, supporting the role of C<sub>16</sub> as a metal-free, spectroscopically active sensor. These findings underscore the dual functionality of cyclo[16]carbon in promoting safe handling and detection of high-energy materials, positioning it as a promising platform for passive sensing and hazard mitigation in challenging environments.</p>\u0000 </div>","PeriodicalId":188,"journal":{"name":"Journal of Computational Chemistry","volume":"46 26","pages":""},"PeriodicalIF":4.8,"publicationDate":"2025-10-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145209103","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
Navigating Homogeneous Graph Paths Through Amyloidogenic and Non-Amyloidogenic Hexapeptides 通过淀粉样蛋白和非淀粉样蛋白六肽导航均匀图路径
IF 4.8 3区 化学
Journal of Computational Chemistry Pub Date : 2025-10-03 DOI: 10.1002/jcc.70238
László Keresztes, Evelin Szögi, Bálint Varga, Viktor Farkas, András Perczel, Vince Grolmusz
{"title":"Navigating Homogeneous Graph Paths Through Amyloidogenic and Non-Amyloidogenic Hexapeptides","authors":"László Keresztes,&nbsp;Evelin Szögi,&nbsp;Bálint Varga,&nbsp;Viktor Farkas,&nbsp;András Perczel,&nbsp;Vince Grolmusz","doi":"10.1002/jcc.70238","DOIUrl":"10.1002/jcc.70238","url":null,"abstract":"<p>Hexapeptides are increasingly applied as model systems for studying the amyloidogenic properties of oligo- and polypeptides. It is possible to construct 64 million different hexapeptides from the twenty proteinogenic amino acid residues. Today's experimental amyloid databases contain only a fraction of these annotated hexapeptides. For labeling all the possible hexapeptides as “amyloidogenic” or “non-amyloidogenic” there exist several computational predictors with good accuracy. It may be of interest to define and study a simple graph structure on the 64 million hexapeptides as nodes, when two hexapeptides are connected by an edge if they differ by only a single residue. For example, in this graph, HIKKLM is connected to AIKKLM, or HIKKNM, or HIKKLC, but it is not connected with an edge to VVKKLM or HIKNPM. In the present contribution, we consider our previously published artificial intelligence-based tool, the Budapest Amyloid Predictor (BAP for short), and demonstrate a spectacular property of this predictor in the graph defined above. We show that for any two hexapeptides predicted to be “amyloidogenic” by the BAP predictor, there exists an easily constructible path of length at most six that passes through neighboring hexapeptides all predicted to be “amyloidogenic” by BAP. For example, the predicted amyloidogenic ILVWIW and FWLCYL hexapeptides can be connected through the length-6 path ILVWIW-IWVWIW-IWVCIW-IWVCIL-FWVCIL-FWLCIL-FWLCYL in such a way that the neighbors differ in exactly one residue, and all hexapeptides on the path are predicted to be amyloidogenic by BAP. The symmetric statement also holds true for non-amyloidogenic predicted hexapeptides: For any such pair, there exists a path of length at most six, traversing only predicted non-amyloidogenic hexapeptides. It is noted that the mentioned property of the Budapest Amyloid Predictor https://pitgroup.org/bap is not proprietary; it is also true for any linear Support Vector Machine (SVM)-based predictors; therefore, for any future improvements of BAP using the linear SVM prediction technique.</p>","PeriodicalId":188,"journal":{"name":"Journal of Computational Chemistry","volume":"46 26","pages":""},"PeriodicalIF":4.8,"publicationDate":"2025-10-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/jcc.70238","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145209454","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
Correction to “Exploring Lead-Free Ca3BiCl3-Based Perovskite Solar Cells: A Computational Comparison of Charge Transport Layers With DFT and SCAPS-1D” 对“探索无铅ca3bicl3基钙钛矿太阳能电池:DFT和SCAPS-1D电荷传输层的计算比较”的更正。
IF 4.8 3区 化学
Journal of Computational Chemistry Pub Date : 2025-09-29 DOI: 10.1002/jcc.70247
{"title":"Correction to “Exploring Lead-Free Ca3BiCl3-Based Perovskite Solar Cells: A Computational Comparison of Charge Transport Layers With DFT and SCAPS-1D”","authors":"","doi":"10.1002/jcc.70247","DOIUrl":"10.1002/jcc.70247","url":null,"abstract":"<p>Biswas, B. C., Shimul, A. I., Ghosh, A., Awaad, N. S., and Ibrahium, H. A., “Exploring Lead-Free Ca<sub>3</sub>BiCl<sub>3</sub>-Based Perovskite Solar Cells: A Computational Comparison of Charge Transport Layers With DFT and SCAPS-1D,” <i>Journal of Computational Chemistry</i> 46 (2025): e70231, https://doi.org/10.1002/jcc.70231.</p><p>The acknowledgment section has been changed as below:</p><p>The authors extend their appreciation to the Deanship of Research and Graduate Studies at King Khalid University for funding this work through Large Research Project under grant number RGP2/338/46.</p><p>We apologize for this error.</p>","PeriodicalId":188,"journal":{"name":"Journal of Computational Chemistry","volume":"46 25","pages":""},"PeriodicalIF":4.8,"publicationDate":"2025-09-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/jcc.70247","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145189448","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
Accurate and Cost-Efficient DLPNO-CCSD(T)-Based Feller-Peterson-Dixon Protocols Calibrated on Association Reactions of Li+ Ion With Mixed Organic Carbonates 基于DLPNO - CCSD(T) - Based的Li+离子与混合有机碳酸盐缔合反应校准的Feller - Peterson - Dixon方案准确且具有成本效益
IF 4.8 3区 化学
Journal of Computational Chemistry Pub Date : 2025-09-29 DOI: 10.1002/jcc.70244
Arseniy A. Otlyotov, Andrey D. Moshchenkov, Alexander S. Ryzhako, Luigi Cavallo, Yury Minenkov
{"title":"Accurate and Cost-Efficient DLPNO-CCSD(T)-Based Feller-Peterson-Dixon Protocols Calibrated on Association Reactions of Li+ Ion With Mixed Organic Carbonates","authors":"Arseniy A. Otlyotov,&nbsp;Andrey D. Moshchenkov,&nbsp;Alexander S. Ryzhako,&nbsp;Luigi Cavallo,&nbsp;Yury Minenkov","doi":"10.1002/jcc.70244","DOIUrl":"10.1002/jcc.70244","url":null,"abstract":"<div>\u0000 \u0000 <p>We present a benchmark set LIMIXCARB_RE12 comprising 12 reference DLPNO-CCSD(T<sub>1</sub>)/CPS(6,7)/CBS(cc-pwCVTZ/cc-pwCVQZ)//PBE0-D3(BJ)/def2-TZVP binding energies for the sizeable (up to 69 atoms) clusters of Li<sup>+</sup> ion with mixed cyclic and linear organic carbonates. A number of computationally cheaper DLPNO-CCSD(T)-based Feller-Peterson-Dixon protocols including contributions due to core-valence electron correlation, using more accurate iterative triples correction (T<sub>1</sub>) and tighter-than-default PNO settings are examined with respect to their accuracy and efficiency. Particular splittings of the total binding energy into components allow maintaining high accuracy (deviations less than 0.2 kcal mol<sup>−1</sup>) at significantly reduced computational cost. Much faster convergence of the DLPNO-CCSD(T) binding energies to the reference values is reached if Ahlrichs' def2 basis sets are used instead of their correlation-consistent Dunning counterparts. Evaluation of the DFT approximations against the LIMIXCARB_RE12 reveals double hybrid PWPB95-D4 in conjunction with CBS(def2-TZVPP/def2-QZVPP) extrapolation to be the best performer with mean signed deviation (MSD) of only −0.1 kcal mol<sup>−1</sup> followed by r<sup>2</sup>SCAN-D4/D3(BJ) and r<sup>2</sup>SCAN-3c (MSD &lt; 1 kcal mol<sup>−1</sup>), while hybrid B3LYP and PBE0 functionals complemented with D3(BJ) or D4 dispersion corrections are clearly inferior. The obtained results provide a guide for the accurate calculations of the binding energies of the microsolvated clusters and can be used for the development and validation of the emerging computational methods.</p>\u0000 </div>","PeriodicalId":188,"journal":{"name":"Journal of Computational Chemistry","volume":"46 25","pages":""},"PeriodicalIF":4.8,"publicationDate":"2025-09-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145188596","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
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