Luan G. F. dos Santos, Julio C. V. Chagas, Luiz F. A. Ferrão, Adelia J. A. Aquino, Reed Nieman, Hans Lischka, Francisco B. C. Machado
{"title":"Tuning Aromaticity, Stability and Radicaloid Character of Periacenes by Chemical BN Doping","authors":"Luan G. F. dos Santos, Julio C. V. Chagas, Luiz F. A. Ferrão, Adelia J. A. Aquino, Reed Nieman, Hans Lischka, Francisco B. C. Machado","doi":"10.1002/jcc.70039","DOIUrl":"10.1002/jcc.70039","url":null,"abstract":"<div>\u0000 \u0000 <p>In this work, the stability, aromaticity and radical character of pristine and eleven BN-doped armchair 5 and zigzag 5, 6, and 7 periacenes, were chosen for studying the effect of different doping schemes to stabilize the periacene, and to direct the open-shell density into specific regions of the PAH sheets. Ab initio multireference methods and different DFT functionals were used to analyze the singlet triplet (S<span></span>T) energy. Moreover, a range of descriptors were used to characterize the open-shell character and aromaticity of the different doped structures. The overall results provide a good overview of the efficiency of the different doping topologies. In general, because of the closed-shell character of the borazine doping units, the role of the doping is to reduce the strong open-shell character of the pristine periacenes. Substitutions along the zigzag edges has a significant effect while doping along the armchair edges is not significant.</p>\u0000 </div>","PeriodicalId":188,"journal":{"name":"Journal of Computational Chemistry","volume":"46 3","pages":""},"PeriodicalIF":3.4,"publicationDate":"2025-01-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142991618","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":"Scaled and Weighted Laplacian Matrices as Functional Descriptors for GPCR Ligands","authors":"Guillermo Goode-Romero, Laura Dominguez","doi":"10.1002/jcc.70015","DOIUrl":"10.1002/jcc.70015","url":null,"abstract":"<div>\u0000 \u0000 <p>The G protein-coupled receptor (GPCR) pharmacology accounts for a significant field in research, clinical studies, and therapeutics. Computer-aided drug discovery is an evolving suite of techniques and methodologies that facilitate accelerated progress in drug discovery and repositioning. However, the structure–activity relationships of molecules targeting GPCRs are highly challenging in many cases since slight structural modifications can lead to drastic changes in biological functionality. Numerous molecular descriptors have been described, many of which successfully characterize the structural and physicochemical features of drug sets. Nonetheless, elucidating the structure–functionality relationships over extensive sets of drugs with multiple structural variations and known biological activity remains challenging in various biological systems. This work presents novel topological descriptors using Laplacian matrices, weighted, and scaled by atomic mass and partial charges. We tested these descriptors on three sets of GPCR ligands: muscarinic, β-adrenergic, and δ-opioid receptor ligands, evaluating their potential as functional descriptors of these receptors.</p>\u0000 </div>","PeriodicalId":188,"journal":{"name":"Journal of Computational Chemistry","volume":"46 3","pages":""},"PeriodicalIF":3.4,"publicationDate":"2025-01-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142987851","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":"Suitability of Available Interatomic Potentials for Sn to Model Its 2D Allotropes","authors":"Marcin Maździarz","doi":"10.1002/jcc.70032","DOIUrl":"10.1002/jcc.70032","url":null,"abstract":"<div>\u0000 \u0000 <p>The suitability of a range of interatomic potentials for elemental tin was evaluated in order to identify an appropriate potential for modeling the stanene (2D tin) allotropes. Structural and mechanical features of the flat (F), low-buckled (LB), high-buckled (HB), full dumbbell (FD), trigonal dumbbell (TD), honeycomb dumbbell (HD), and large honeycomb dumbbell (LHD) monolayer tin (stanene) phases, were gained by means of the density functional theory (DFT) and molecular statics (MS) calculations with ten different Tersoff, modified embedded atom method (MEAM), and machine-learning-based (ML-IAP) interatomic potentials. A systematic quantitative comparison and discussion of the results is reported.</p>\u0000 </div>","PeriodicalId":188,"journal":{"name":"Journal of Computational Chemistry","volume":"46 2","pages":""},"PeriodicalIF":3.4,"publicationDate":"2025-01-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142968045","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 Theoretical Study on Crossings Among Electronically Excited States and Laser Cooling of Group VIA (S, Se, and Te) Hydrides","authors":"Donghui Li, Faiza Fayyaz, Wensheng Bian","doi":"10.1002/jcc.70019","DOIUrl":"10.1002/jcc.70019","url":null,"abstract":"<div>\u0000 \u0000 <p>Various electronically excited states and the feasibility of direct laser cooling of SH, SeH, and TeH are investigated using the highly accurate ab initio and dynamical methods. For the detailed calculations of the seven low-lying Λ-S states of SH, we utilized the internally contracted multireference configuration interaction approach, considering the spin-orbit coupling (SOC) effects. Our calculated spectroscopic constants are in very good agreement with the available experimental results. It is found that, from SH to TeH, the crossing points among the A<sup>2</sup>Σ<sup>+</sup> and three electronically excited states gradually shift downward toward the ground vibrational level of the A<sup>2</sup>Σ<sup>+</sup> state. This is consistent with our previous findings in other molecular systems and makes the laser cooling of TeH unfeasible. Our calculations indicate that the three crossing points, respectively, between the A<sup>2</sup>Σ<sup>+</sup> and a<sup>4</sup>Σ<sup>−</sup>, A<sup>2</sup>Σ<sup>+</sup> and B<sup>2</sup>Σ<sup>−</sup>, and A<sup>2</sup>Σ<sup>+</sup> and b<sup>4</sup>Π states of SH, all lie above the <i>v'</i> = 1 vibrational level of the A<sup>2</sup>Σ<sup>+</sup> state, as a result of which the crossings involving electronic states of higher energy would not hinder its laser cooling. Based upon our study on various excited states, we have constructed a viable laser-cooling scheme for SH, utilizing three laser beams and leveraging the A<sup>2</sup>Σ<sup>+</sup> → X<sup>2</sup>Π transition. This transition possesses a very large vibrational branching ratio <i>R</i><sub>00</sub> (0.9558), an abundant number of scattered photons (9.30 × 10<sup>3</sup>), and a short radiative lifetime (787 ns). Our work underscores the important role of excited-state crossings in molecular laser cooling and demonstrates that SH emerges as a very good candidate for ultracold molecules.</p>\u0000 </div>","PeriodicalId":188,"journal":{"name":"Journal of Computational Chemistry","volume":"46 2","pages":""},"PeriodicalIF":3.4,"publicationDate":"2025-01-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142967955","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}
A. Karolyna M. S. Gomes, Ricardo R. Oliveira, Thiago M. Cardozo, Felipe Fantuzzi
{"title":"Linear or Cyclic? Theoretical Investigation of Astrophysically Relevant Magnesium-Bearing MgCnH Carbon Chains and Related Isomers","authors":"A. Karolyna M. S. Gomes, Ricardo R. Oliveira, Thiago M. Cardozo, Felipe Fantuzzi","doi":"10.1002/jcc.70031","DOIUrl":"10.1002/jcc.70031","url":null,"abstract":"<p>Magnesium-containing molecules, including MgC<sub>2</sub>H, MgC<sub>4</sub>H, and MgC<sub>6</sub>H, have been detected in the interstellar medium, largely facilitated by their high dipole moments. However, despite great efforts, MgC<sub>2<i>m</i> + 1</sub>H species remain elusive. Given the challenges in obtaining experimental data for these molecules, theoretical studies play a crucial role in guiding their detection. In this work, we present a theoretical analysis of MgC<sub><i>n</i></sub>H isomers (<i>n</i> = 4–7) using density functional theory and coupled-cluster methods to identify low-lying isomers and characterize their structural and electronic properties. Our findings reveal that across the entire series investigated, the global minimum geometry is linear for even values of <i>n</i>, whereas for odd values, a cyclic geometry is favored. Additionally, our calculations highlight the enhanced stability of anionic MgC<sub><i>n</i></sub>H<sup>−</sup> systems, providing insights that could aid future astronomical detections in the interstellar medium.</p>","PeriodicalId":188,"journal":{"name":"Journal of Computational Chemistry","volume":"46 2","pages":""},"PeriodicalIF":3.4,"publicationDate":"2025-01-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/jcc.70031","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142968043","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}
Lucca Blois, Renaldo T. Moura Jr, Ricardo L. Longo, Oscar L. Malta, Hermi F. Brito, Albano N. Carneiro Neto
{"title":"Assessment of DFT Functionals for Structural Determination of Lanthanide(III) Complexes Using Ligand Field Splitting","authors":"Lucca Blois, Renaldo T. Moura Jr, Ricardo L. Longo, Oscar L. Malta, Hermi F. Brito, Albano N. Carneiro Neto","doi":"10.1002/jcc.70034","DOIUrl":"10.1002/jcc.70034","url":null,"abstract":"<div>\u0000 \u0000 <p>Lanthanide (Ln<sup>3+</sup>) tetrakis complexes, C[Ln(L)<sub>4</sub>], are important for applications due to their high quantum yields, solubility, and stability. Their luminescent properties depend on the structure, particularly the coordination polyhedron, the assessment of computational methods for calculating their structures is paramount. Usually, this assessment uses the RMSD of distances in the [Ln(L)<sub>4</sub>]<sup>−</sup> complex or {LnO<sub>8</sub>} polyhedron between crystallographic and calculated structures. However, since ligand field (LF) splitting is highly geometry-dependent, the RMSD between experimental LF splitting and Stark levels (RMSD-LF) offers a more accurate measure for evaluating quantum methods. LF energy eigenvalues were calculated using the simple overlap model (SOM), with geometries optimized by various density functionals. M06 and M06-L functionals, with def2-SVP/MWB52(Eu)/CPCM, demonstrate the best balance in best accuracy and low computational cost, making them suitable for modeling C[Eu(L)<sub>4</sub>] complexes.</p>\u0000 </div>","PeriodicalId":188,"journal":{"name":"Journal of Computational Chemistry","volume":"46 2","pages":""},"PeriodicalIF":3.4,"publicationDate":"2025-01-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142968044","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}
Oleksandr Gurbych, Petro Pavliuk, Dmytro Krasnienkov, Oleksandr Liashuk, Kostiantyn Melnykov, Oleksandr O. Grygorenko
{"title":"Filling the Gap in \u0000 \u0000 \u0000 LogP\u0000 \u0000 $$ LogP $$\u0000 and \u0000 \u0000 \u0000 \u0000 pK\u0000 a\u0000 \u0000 \u0000 $$ {pK}_a $$\u0000 Evaluation for Saturated Fluorine-Containing Derivatives With Machine Learning","authors":"Oleksandr Gurbych, Petro Pavliuk, Dmytro Krasnienkov, Oleksandr Liashuk, Kostiantyn Melnykov, Oleksandr O. Grygorenko","doi":"10.1002/jcc.70002","DOIUrl":"10.1002/jcc.70002","url":null,"abstract":"<div>\u0000 \u0000 <p>Lipophilicity and acidity/basicity are fundamental physical properties that profoundly affect the compound's pharmacological activity, bioavailability, metabolism, and toxicity. Predicting lipophilicity, measured by <span></span><math>\u0000 <semantics>\u0000 <mrow>\u0000 <mtext>LogP</mtext>\u0000 </mrow>\u0000 <annotation>$$ LogP $$</annotation>\u0000 </semantics></math> (1-octanol–water distribution coefficient logarithm), and acidity/basicity, measured by <span></span><math>\u0000 <semantics>\u0000 <mrow>\u0000 <msub>\u0000 <mi>pK</mi>\u0000 <mi>a</mi>\u0000 </msub>\u0000 </mrow>\u0000 <annotation>$$ {pK}_a $$</annotation>\u0000 </semantics></math> (negative of acid ionization constant logarithm), is essential for early drug discovery success. However, the limited availability of experimental data and poor accuracy of standard <span></span><math>\u0000 <semantics>\u0000 <mrow>\u0000 <mtext>LogP</mtext>\u0000 </mrow>\u0000 <annotation>$$ LogP $$</annotation>\u0000 </semantics></math> and <span></span><math>\u0000 <semantics>\u0000 <mrow>\u0000 <msub>\u0000 <mi>pK</mi>\u0000 <mi>a</mi>\u0000 </msub>\u0000 </mrow>\u0000 <annotation>$$ {pK}_a $$</annotation>\u0000 </semantics></math> assessment methods for saturated fluorine-containing derivatives pose a significant challenge to achieving satisfactory results for this compound class. To overcome this challenge, we compiled a unique dataset of saturated fluorinated and corresponding non-fluorinated derivatives with <span></span><math>\u0000 <semantics>\u0000 <mrow>\u0000 <mtext>LogP</mtext>\u0000 </mrow>\u0000 <annotation>$$ LogP $$</annotation>\u0000 </semantics></math> and <span></span><math>\u0000 <semantics>\u0000 <mrow>\u0000 <msub>\u0000 <mi>pK</mi>\u0000 <mi>a</mi>\u0000 </msub>\u0000 </mrow>\u0000 <annotation>$$ {pK}_a $$</annotation>\u0000 </semantics></math> experimental values. Aiming to create an optimal approach to acidity/basicity and lipophilicity prediction, we evaluated, trained from scratch, or fine-tuned more than 40 machine learning models, including linear, tree-based, and neural networks. The study was supplemented with a substructure mask explanation (SME), which confirmed the critical role of the fluorinated substituents on both physicochemical properties studied and testified to the consistency of the developed models. The results were open-sourced as a GitHub repository, pip, conda packages, and a KNIME node, allowing the public to perform the targeted molecular design of the proposed class of compounds.</p>\u0000 </di","PeriodicalId":188,"journal":{"name":"Journal of Computational Chemistry","volume":"46 2","pages":""},"PeriodicalIF":3.4,"publicationDate":"2025-01-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142968011","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}