Journal of Computational Chemistry最新文献

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Tuning Aromaticity, Stability and Radicaloid Character of Periacenes by Chemical BN Doping 通过化学掺杂 BN 调整紫苏烯的芳香性、稳定性和类辐射特性
IF 3.4 3区 化学
Journal of Computational Chemistry Pub Date : 2025-01-20 DOI: 10.1002/jcc.70039
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,&nbsp;Julio C. V. Chagas,&nbsp;Luiz F. A. Ferrão,&nbsp;Adelia J. A. Aquino,&nbsp;Reed Nieman,&nbsp;Hans Lischka,&nbsp;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}
引用次数: 0
Scaled and Weighted Laplacian Matrices as Functional Descriptors for GPCR Ligands 尺度加权拉普拉斯矩阵作为GPCR配体的功能描述符
IF 3.4 3区 化学
Journal of Computational Chemistry Pub Date : 2025-01-17 DOI: 10.1002/jcc.70015
Guillermo Goode-Romero, Laura Dominguez
{"title":"Scaled and Weighted Laplacian Matrices as Functional Descriptors for GPCR Ligands","authors":"Guillermo Goode-Romero,&nbsp;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}
引用次数: 0
Suitability of Available Interatomic Potentials for Sn to Model Its 2D Allotropes Sn的可用原子间电位对其二维同素异形体的适用性
IF 3.4 3区 化学
Journal of Computational Chemistry Pub Date : 2025-01-13 DOI: 10.1002/jcc.70032
Marcin Maździarz
{"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}
引用次数: 0
A Theoretical Study on Crossings Among Electronically Excited States and Laser Cooling of Group VIA (S, Se, and Te) Hydrides VIA (S, Se, Te)组氢化物电子激发态交叉和激光冷却的理论研究
IF 3.4 3区 化学
Journal of Computational Chemistry Pub Date : 2025-01-13 DOI: 10.1002/jcc.70019
Donghui Li, Faiza Fayyaz, Wensheng Bian
{"title":"A Theoretical Study on Crossings Among Electronically Excited States and Laser Cooling of Group VIA (S, Se, and Te) Hydrides","authors":"Donghui Li,&nbsp;Faiza Fayyaz,&nbsp;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}
引用次数: 0
Linear or Cyclic? Theoretical Investigation of Astrophysically Relevant Magnesium-Bearing MgCnH Carbon Chains and Related Isomers 线性的还是循环的?天体物理相关含镁MgCnH碳链及其异构体的理论研究
IF 3.4 3区 化学
Journal of Computational Chemistry Pub Date : 2025-01-13 DOI: 10.1002/jcc.70031
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,&nbsp;Ricardo R. Oliveira,&nbsp;Thiago M. Cardozo,&nbsp;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}
引用次数: 0
Assessment of DFT Functionals for Structural Determination of Lanthanide(III) Complexes Using Ligand Field Splitting 用配体场分裂分析镧系(III)配合物结构的DFT泛函评价
IF 3.4 3区 化学
Journal of Computational Chemistry Pub Date : 2025-01-13 DOI: 10.1002/jcc.70034
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,&nbsp;Renaldo T. Moura Jr,&nbsp;Ricardo L. Longo,&nbsp;Oscar L. Malta,&nbsp;Hermi F. Brito,&nbsp;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}
引用次数: 0
Filling the Gap in LogP $$ LogP $$ and pK a $$ {pK}_a $$ Evaluation for Saturated Fluorine-Containing Derivatives With Machine Learning 填补的差距LogP pKa评价饱和含氟衍生物和机器学习
IF 3.4 3区 化学
Journal of Computational Chemistry Pub Date : 2025-01-13 DOI: 10.1002/jcc.70002
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,&nbsp;Petro Pavliuk,&nbsp;Dmytro Krasnienkov,&nbsp;Oleksandr Liashuk,&nbsp;Kostiantyn Melnykov,&nbsp;Oleksandr O. Grygorenko","doi":"10.1002/jcc.70002","DOIUrl":"10.1002/jcc.70002","url":null,"abstract":"&lt;div&gt;\u0000 \u0000 &lt;p&gt;Lipophilicity and acidity/basicity are fundamental physical properties that profoundly affect the compound's pharmacological activity, bioavailability, metabolism, and toxicity. Predicting lipophilicity, measured by &lt;span&gt;&lt;/span&gt;&lt;math&gt;\u0000 &lt;semantics&gt;\u0000 &lt;mrow&gt;\u0000 &lt;mtext&gt;LogP&lt;/mtext&gt;\u0000 &lt;/mrow&gt;\u0000 &lt;annotation&gt;$$ LogP $$&lt;/annotation&gt;\u0000 &lt;/semantics&gt;&lt;/math&gt; (1-octanol–water distribution coefficient logarithm), and acidity/basicity, measured by &lt;span&gt;&lt;/span&gt;&lt;math&gt;\u0000 &lt;semantics&gt;\u0000 &lt;mrow&gt;\u0000 &lt;msub&gt;\u0000 &lt;mi&gt;pK&lt;/mi&gt;\u0000 &lt;mi&gt;a&lt;/mi&gt;\u0000 &lt;/msub&gt;\u0000 &lt;/mrow&gt;\u0000 &lt;annotation&gt;$$ {pK}_a $$&lt;/annotation&gt;\u0000 &lt;/semantics&gt;&lt;/math&gt; (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 &lt;span&gt;&lt;/span&gt;&lt;math&gt;\u0000 &lt;semantics&gt;\u0000 &lt;mrow&gt;\u0000 &lt;mtext&gt;LogP&lt;/mtext&gt;\u0000 &lt;/mrow&gt;\u0000 &lt;annotation&gt;$$ LogP $$&lt;/annotation&gt;\u0000 &lt;/semantics&gt;&lt;/math&gt; and &lt;span&gt;&lt;/span&gt;&lt;math&gt;\u0000 &lt;semantics&gt;\u0000 &lt;mrow&gt;\u0000 &lt;msub&gt;\u0000 &lt;mi&gt;pK&lt;/mi&gt;\u0000 &lt;mi&gt;a&lt;/mi&gt;\u0000 &lt;/msub&gt;\u0000 &lt;/mrow&gt;\u0000 &lt;annotation&gt;$$ {pK}_a $$&lt;/annotation&gt;\u0000 &lt;/semantics&gt;&lt;/math&gt; 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 &lt;span&gt;&lt;/span&gt;&lt;math&gt;\u0000 &lt;semantics&gt;\u0000 &lt;mrow&gt;\u0000 &lt;mtext&gt;LogP&lt;/mtext&gt;\u0000 &lt;/mrow&gt;\u0000 &lt;annotation&gt;$$ LogP $$&lt;/annotation&gt;\u0000 &lt;/semantics&gt;&lt;/math&gt; and &lt;span&gt;&lt;/span&gt;&lt;math&gt;\u0000 &lt;semantics&gt;\u0000 &lt;mrow&gt;\u0000 &lt;msub&gt;\u0000 &lt;mi&gt;pK&lt;/mi&gt;\u0000 &lt;mi&gt;a&lt;/mi&gt;\u0000 &lt;/msub&gt;\u0000 &lt;/mrow&gt;\u0000 &lt;annotation&gt;$$ {pK}_a $$&lt;/annotation&gt;\u0000 &lt;/semantics&gt;&lt;/math&gt; 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.&lt;/p&gt;\u0000 &lt;/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}
引用次数: 0
Coherent Excitation of the CH Stretching Vibrations in C2H4+: The Role of the Derivative Coupling Studied by the Quantum Ehrenfest Method C2H4+中CH拉伸振动的相干激发:量子Ehrenfest方法研究的导数耦合的作用
IF 3.4 3区 化学
Journal of Computational Chemistry Pub Date : 2025-01-11 DOI: 10.1002/jcc.70028
Thierry Tran, Graham A. Worth, Michael A. Robb
{"title":"Coherent Excitation of the CH Stretching Vibrations in C2H4+: The Role of the Derivative Coupling Studied by the Quantum Ehrenfest Method","authors":"Thierry Tran,&nbsp;Graham A. Worth,&nbsp;Michael A. Robb","doi":"10.1002/jcc.70028","DOIUrl":"10.1002/jcc.70028","url":null,"abstract":"<p>We report nonadiabatic dynamics computations on C<sub>2</sub>H<sub>4</sub><sup>+</sup> initiated on a coherent superposition of the five lowest cationic states, employing the Quantum Ehrenfest method. In addition to the totally symmetric carbon–carbon double bond stretch and carbon-hydrogen stretches, we see that the three non-totally symmetric modes become stimulated; torsion and three different C<span></span>H stretching patterns. Thus, a coherent superposition of states, of the type involved in an attochemistry experiment, leads to the stimulation of specific non-totally symmetric motions. The computations were also performed on the specific combination of the A and C states. In each case normal mode 9 (cis-asymmetric H<sub>2</sub>CCH<sub>2</sub> stretch), out of the set of non-totally-symmetric normal modes, dominates. Thus, we can steer the nuclear motion along specific non-totally symmetric normal modes using a defined coherent superposition.</p>","PeriodicalId":188,"journal":{"name":"Journal of Computational Chemistry","volume":"46 2","pages":""},"PeriodicalIF":3.4,"publicationDate":"2025-01-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/jcc.70028","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142961949","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
A Cost-Effective Computational Strategy for the Electronic Layout Characterization of a Second Generation Light-Driven Molecular Rotary Motor in Solution 一种具有成本效益的计算策略用于第二代光驱动分子旋转电机的电子布局表征
IF 3.4 3区 化学
Journal of Computational Chemistry Pub Date : 2025-01-11 DOI: 10.1002/jcc.70023
Raoul Carfora, Federico Coppola, Paola Cimino, Alessio Petrone, Nadia Rega
{"title":"A Cost-Effective Computational Strategy for the Electronic Layout Characterization of a Second Generation Light-Driven Molecular Rotary Motor in Solution","authors":"Raoul Carfora,&nbsp;Federico Coppola,&nbsp;Paola Cimino,&nbsp;Alessio Petrone,&nbsp;Nadia Rega","doi":"10.1002/jcc.70023","DOIUrl":"10.1002/jcc.70023","url":null,"abstract":"<p>Light-driven molecular rotary motors are nanometric machines able to convert light into unidirectional motions. Several types of molecular motors have been developed to better respond to light stimuli, opening new avenues for developing smart materials ranging from nanomedicine to robotics. They have great importance in the scientific research across various disciplines, but a detailed comprehension of the underlying ultrafast photophysics immediately after photo-excitation, that is, Franck–Condon region characterization, is not fully achieved yet. For this aim, it is first required to rely on an accurate description at <i>ab initio</i> level of the system in this potential energy region before performing any further step, that is, dynamics. Thus, we present an extensive investigation aimed at accurately describing the electronic structure of low-lying electronic states (electronic layout) of a molecular rotor in the Franck–Condon region, belonging to the class of overcrowded alkenes: 9-(2-methyl-2,3-dihydro-1H-cyclopenta[a]naphthalen-1-ylidene)-9H-fluorene. This system was chosen since its photophysics is very interesting for a more general understanding of similar compounds used as molecular rotors, where low-lying electronic states can be found (whose energetic interplay is crucial in the dynamics) and where the presence of different substituents can tune the HOMO-LUMO gap. For this scope, we employed different theory levels within the time-dependent density functional theory framework, presenting also a careful comparison adopting very accurate post Hartree–Fock methods and characterizing also the different conformations involved in the photocycle. Effects on the electronic layout of different functionals, basis sets, environment descriptions, and the role of the dispersion correction were all analyzed in detail. In particular, a careful treatment of the solvent effects was here considered in depth, showing how the implicit solvent description can be accurate for excited states in the Franck–Condon region by testing both linear-response and state-specific formalisms. As main results, we chose two cost-effective (accurate but relatively cheap) theory levels for the ground and excited state descriptions, and we also verified how choosing these different levels of theory can influence the curvature of the potential via a frequency analysis of the normal modes of vibrations active in the Raman spectrum. This theoretical survey is a crucial step towards a feasible characterization of the early stage of excited states in solution during photoisomerization processes wherein multiple electronic states might be populated upon the light radiation, leading to a future molecular-level interpretation of time-resolved spectroscopies.</p>","PeriodicalId":188,"journal":{"name":"Journal of Computational Chemistry","volume":"46 2","pages":""},"PeriodicalIF":3.4,"publicationDate":"2025-01-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/jcc.70023","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142961537","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
goChem: A Composable Library for Multi-Scale Computational Chemistry Data Analysis goChem:一个可组合的多尺度计算化学数据分析库
IF 3.4 3区 化学
Journal of Computational Chemistry Pub Date : 2025-01-11 DOI: 10.1002/jcc.70004
Moisés Domínguez, Verónica A. Jiménez, Gökcen Savasci, Rocío Araya-Osorio, Janne Pesonen, Raúl Mera-Adasme
{"title":"goChem: A Composable Library for Multi-Scale Computational Chemistry Data Analysis","authors":"Moisés Domínguez,&nbsp;Verónica A. Jiménez,&nbsp;Gökcen Savasci,&nbsp;Rocío Araya-Osorio,&nbsp;Janne Pesonen,&nbsp;Raúl Mera-Adasme","doi":"10.1002/jcc.70004","DOIUrl":"10.1002/jcc.70004","url":null,"abstract":"<div>\u0000 \u0000 <p>Data analysis is a major task for Computational Chemists. The diversity of modeling tools currently available in Computational Chemistry requires the development of flexible analysis tools that can adapt to different systems and output formats. As a contribution to this need, we report the implementation of goChem, a versatile open-source library for multiscale analysis of computational chemistry data. The library, written in and for the Go programming language, allows for easy integration of different levels of theory, in an easy-to-use API, allowing the development of both one-use and complex analysis programs in Go. We describe the library and detail some selected applications that illustrate the capabilities and potential of this tool. The library is available at http://gochem.org.</p>\u0000 </div>","PeriodicalId":188,"journal":{"name":"Journal of Computational Chemistry","volume":"46 2","pages":""},"PeriodicalIF":3.4,"publicationDate":"2025-01-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142961534","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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