Journal of Molecular Modeling最新文献

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A DFT study of the effect of hydrostatic pressure on the structure and electronic properties of sarcosine crystal 关于静水压力对肌氨酸晶体结构和电子特性影响的 DFT 研究。
IF 2.1 4区 化学
Journal of Molecular Modeling Pub Date : 2024-10-04 DOI: 10.1007/s00894-024-06110-z
Geanso M. de Moura, Mateus R. Lage, Adenilson Santos, Rodrigo Gester, Stanislav R. Stoyanov, Tarciso Andrade-Filho
{"title":"A DFT study of the effect of hydrostatic pressure on the structure and electronic properties of sarcosine crystal","authors":"Geanso M. de Moura,&nbsp;Mateus R. Lage,&nbsp;Adenilson Santos,&nbsp;Rodrigo Gester,&nbsp;Stanislav R. Stoyanov,&nbsp;Tarciso Andrade-Filho","doi":"10.1007/s00894-024-06110-z","DOIUrl":"10.1007/s00894-024-06110-z","url":null,"abstract":"<div><h3>Context</h3><p>We perform density functional theory calculations to study the dependence of the structural and electronic properties of the amino acid sarcosine crystal structure on hydrostatic pressure application. The results are analyzed and compared with the available experimental data. Our findings indicate that the crystal structure and properties of sarcosine calculated using the Grimme dispersion-corrected PBE functional (PBE-D3) best agree with the available experimental results under hydrostatic pressure of up to 3.7 GPa. Critical structural rearrangements, such as unit cell compression, head-to-tail compression, and molecular rotations, are investigated and elucidated in the context of experimental findings. Band gap energy tuning and density of state shifts indicative of band dispersion are presented concerning the structural changes arising from the elevated pressure. The calculated properties indicate that sarcosine holds great promise for application in electronic devices that involve pressure-induced structural changes.</p><h3>Methods</h3><p>Three widely used generalized gradient approximation functionals—PBE, PBEsol, and revPBE—are employed with Grimme’s D3 dispersion correction. The non-local van der Waals density functional vdW-DF is also evaluated. The calculations are performed using the projector-augmented wave method in the Quantum Espresso software suite. The geometry optimization results are visualized using VMD. The Multiwfn and NCIPlot programs are used for wavefunction and intermolecular interaction analyses.</p></div>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":null,"pages":null},"PeriodicalIF":2.1,"publicationDate":"2024-10-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11452461/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142370676","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"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
Design of N-doped C60-σ-B-doped C60 photodetector based on resonant tunneling diode using DFT and NEGF method 利用 DFT 和 NEGF 方法设计基于共振隧道二极管的 N 掺杂 C60-σ-B 掺杂 C60 光探测器。
IF 2.1 4区 化学
Journal of Molecular Modeling Pub Date : 2024-10-04 DOI: 10.1007/s00894-024-06166-x
Majid Malek, Mohammad Danaie
{"title":"Design of N-doped C60-σ-B-doped C60 photodetector based on resonant tunneling diode using DFT and NEGF method","authors":"Majid Malek,&nbsp;Mohammad Danaie","doi":"10.1007/s00894-024-06166-x","DOIUrl":"10.1007/s00894-024-06166-x","url":null,"abstract":"<div><h3>Context</h3><p>Photodetectors utilizing donor/acceptor (D/A) molecules have the capacity to detect light through molecular interactions between a donor and an acceptor molecule. These devices leverage electronic or optical changes within molecules when exposed to light, resulting in observable modifications. The unique properties of photodetectors with D/A molecules make them valuable tools in various fields, including molecular electronics. This paper presents the modeling and simulation of a single-molecule photodetector based on a D/A molecule configuration. The acceptor molecule used is N-doped C60 fullerene, while the donor molecule is B-doped C60 fullerene. Initially, simulations were conducted at zero bias voltage to determine the energy and states of the bipartite molecule. Subsequently, the system’s Hamiltonian was computed based on these results. The self-consistent field method (SCF) and optical self-energy coefficients were employed for modeling. Finally, the current–voltage curve of the device was derived for various input light frequencies. The simulation and modeling results demonstrated that the device exhibited negative differential resistances at bias voltages of 0.33 V, 1.58 V, and − 0.93 V, depending on the input light frequency. Furthermore, the designed device demonstrated the ability to detect and absorb waves with different frequencies. The number of current peaks in the current–voltage curve varied with by altering the number of optical modes.</p><h3>Methods</h3><p>The computational work was conducted using the software package of Atomistix ToolKit (ATK-2018.06) and MATLAB code. The calculations were based on the density functional theory (DFT) approach and the self-consistent field method, specifically the non-equilibrium Green function (NEGF). The exchange correlation function was investigated using the generalized gradient approximation (GGA) proposed by Perdew, Burke, and Ernzerhof (PBE). For the calculations, we employed the double-ζ plus polarization (DZP) basis set. Initially, the structures of N doped-C60-σ-B-doped-C60 molecule underwent optimization using the DFT approach implemented in the ATK package. This optimization process allowed us to extract the parameters of the molecule. Subsequently, we utilized the NEGF formalism in MATLAB software to model and simulate photodetector based on the optimized molecule. We calculated important features of the photodetector, such as photocurrent, and compared the performance of the photodetector using photons with energies of 2 and 3 eV.</p></div>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":null,"pages":null},"PeriodicalIF":2.1,"publicationDate":"2024-10-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142370677","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"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
Exploring chemical reactivity through a combined conceptual DFT and ELF topology approach 通过概念 DFT 和 ELF 拓扑相结合的方法探索化学反应性。
IF 2.1 4区 化学
Journal of Molecular Modeling Pub Date : 2024-10-03 DOI: 10.1007/s00894-024-06144-3
Bastien Courbière, Julien Pilmé
{"title":"Exploring chemical reactivity through a combined conceptual DFT and ELF topology approach","authors":"Bastien Courbière,&nbsp;Julien Pilmé","doi":"10.1007/s00894-024-06144-3","DOIUrl":"10.1007/s00894-024-06144-3","url":null,"abstract":"<div><h3>Context</h3><p>In a proof-of-concept study, we explore how a combined approach using the topology of the electron localization function (ELF) and the condensed dual descriptor (DD) function can guide the optimal orientation between reactants and mimic the potential energy surfaces of molecular systems at the beginning of the chemical pathway. The DD has been chosen for its ability to evaluate the regioselectivity of neutral and soft species and to potentially mimic the interaction energy obtained from the mutual interactions between nucleophilic and electrophilic regions of the building blocks under perturbative theory.</p><h3>Method</h3><p>Our method has been illustrated with examples in which the optimal orientation of several systems can be successfully identified. The limitations of the presented model in predicting chemical reactivity are outlined in particular the influence of the selected condensation scheme.</p></div>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":null,"pages":null},"PeriodicalIF":2.1,"publicationDate":"2024-10-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1007/s00894-024-06144-3.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142363929","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"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
Cooperativity and halonium transfer in the ternary NCI···CH3I···−CN halogen-bonded complex: An ab initio gas phase study 三元 NCI-CH3I----CN 卤键络合物中的合作性和卤素转移:一项ab initio气相研究。
IF 2.1 4区 化学
Journal of Molecular Modeling Pub Date : 2024-10-03 DOI: 10.1007/s00894-024-06160-3
Rubén D. Parra
{"title":"Cooperativity and halonium transfer in the ternary NCI···CH3I···−CN halogen-bonded complex: An ab initio gas phase study","authors":"Rubén D. Parra","doi":"10.1007/s00894-024-06160-3","DOIUrl":"10.1007/s00894-024-06160-3","url":null,"abstract":"<div><h3>Context</h3><p>The strength and nature of the two halogen bonds in the NCI···CH<sub>3</sub>I···<sup>−</sup>CN halogen-bonded ternary complex are studied in the gas phase via ab initio calculations. Different indicators of halogen bond strength were employed to examine the interactions including geometries, complexation energies, Natural Bond Order (NBO) Wiberg bond indices, and Atoms in Molecules (AIM)-based charge density topological properties. The results show that the halogen bond is strong and partly covalent in nature when CH<sub>3</sub>I donates the halogen bond, but weak and noncovalent in nature when CH<sub>3</sub>I accepts the halogen bond. Significant halogen bond cooperativity emerges in the ternary complex relative to the corresponding heterodimer complexes, NCI···CH<sub>3</sub>I and CH<sub>3</sub>I···<sup>−</sup>CN, respectively. For example, the CCSD(T) complexation energy of the ternary complex (-18.27 kcal/mol) is about twice the sum of the complexation energies of the component dimers (-9.54 kcal/mol). The halonium transfer reaction that converts the ternary complex into an equivalent one was also investigated. The electronic barrier for the halonium transfer was calculated to be 6.70 kcal/mol at the CCSD(T) level. Although the MP2 level underestimates and the MP3 overestimates the barrier, their calculated MP2.5 average barrier (6.44 kcal/mol) is close to that of the more robust CCSD(T) level. Insights on the halonium ion transfer reaction was obtained by examining the reaction energy and force profiles along the intrinsic reaction coordinate, IRC. The corresponding evolution of other properties such as bond lengths, Wiberg bond indices, and Mulliken charges provides specific insight on the extent of structural rearrangements and electronic redistribution throughout the entire IRC space.</p><h3>Methods</h3><p>The MP2 method was used for geometry optimizations. Energy calculations were performed using the CCSD(T) method. The aug-cc-pVTZ basis set was employed for all atoms other than iodine for which the aug-cc-pVTZ-PP basis set was used instead.</p></div>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":null,"pages":null},"PeriodicalIF":2.1,"publicationDate":"2024-10-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1007/s00894-024-06160-3.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142363928","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"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
Why are information-theoretic descriptors powerful predictors of atomic and molecular polarizabilities 为什么信息论描述符可以有力地预测原子和分子极化率?
IF 2.1 4区 化学
Journal of Molecular Modeling Pub Date : 2024-10-03 DOI: 10.1007/s00894-024-06162-1
Yilin Zhao, Dongbo Zhao, Shubin Liu, Chunying Rong, Paul W. Ayers
{"title":"Why are information-theoretic descriptors powerful predictors of atomic and molecular polarizabilities","authors":"Yilin Zhao,&nbsp;Dongbo Zhao,&nbsp;Shubin Liu,&nbsp;Chunying Rong,&nbsp;Paul W. Ayers","doi":"10.1007/s00894-024-06162-1","DOIUrl":"10.1007/s00894-024-06162-1","url":null,"abstract":"<div><h3>\u0000 <b>Context</b>\u0000 </h3><p>We rationalize the excellent performance of information-theoretic descriptors for predicting atomic and molecular polarizabilities. It seems that descriptors which capture information about the change in valence-shell structure, especially the relative Fisher information measures, are particularly useful. Using this, we can rationalize why the <i>G</i>3 form of the relative Fisher information, which measures the deviation of effective nuclear charge between an atom-in-a-molecule and the reference pro-atom, is especially effective as a predictor of molecular polarizability.</p><h3>\u0000 <b>Methods</b>\u0000 </h3><p>There are no methods used in this paper, which relies on mathematical derivation and analysis.</p></div>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":null,"pages":null},"PeriodicalIF":2.1,"publicationDate":"2024-10-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1007/s00894-024-06162-1.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142363930","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"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
Influence of polypropylene fibers on the tensile mechanical properties of calcium silicate hydrate: molecular simulation 聚丙烯纤维对硅酸钙水合物拉伸机械性能的影响:分子模拟。
IF 2.1 4区 化学
Journal of Molecular Modeling Pub Date : 2024-10-02 DOI: 10.1007/s00894-024-06164-z
Yu Chen, Xuyang Yin, Ndukeabasi Peter Udoessiet, Jiale Wang, Jiawen Zhu, Shimei Luo
{"title":"Influence of polypropylene fibers on the tensile mechanical properties of calcium silicate hydrate: molecular simulation","authors":"Yu Chen,&nbsp;Xuyang Yin,&nbsp;Ndukeabasi Peter Udoessiet,&nbsp;Jiale Wang,&nbsp;Jiawen Zhu,&nbsp;Shimei Luo","doi":"10.1007/s00894-024-06164-z","DOIUrl":"10.1007/s00894-024-06164-z","url":null,"abstract":"<div><h3>Context</h3><p>This research assesses the influence of polypropylene (PP) fibers, both homopolymer and hydroxylated (PPOH), on the tensile properties of calcium silicate hydrate (C-S–H) composites through molecular dynamics (MD) simulations. Our models explore C-S–H matrices integrated with PP and PPOH fibers at varying polymerization degrees. The results demonstrate that both PP and PPOH fibers significantly influence the tensile strength and Young’s modulus of the composites. Notably, PPOH fibers contribute to more substantial mechanical enhancements than PP, attributed to the increased polarity and enhanced intermolecular interactions from the hydroxyl groups. The study reveals a nonlinear relationship between polymer additive content and mechanical performance, with optimal properties at a polymerization degree of 20. Additionally, stress–strain analysis indicates that PPOH composites exhibit superior ductility and fracture energy, particularly at polymerization degrees of 20, showing enhanced ultimate strain and fracture energy by up to 9.6% and 13.9%, respectively, compared to PP counterparts. These results highlight the crucial role of tailored polymer additive composition and chemical modifications in maximizing the mechanical efficacy of C-S–H-based materials, enhancing their durability and structural performance.</p><h3>Methods</h3><p>All MD simulations were conducted using LAMMPS. The models employed a combination of Clayff and Cvff force fields. During the entire tensile simulation, the system was configured under the NPT ensemble at 300 K.</p></div>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":null,"pages":null},"PeriodicalIF":2.1,"publicationDate":"2024-10-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1007/s00894-024-06164-z.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142360905","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"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
Development of new sustainable pyridinium ionic liquids: From reactivity studies to mechanism-based activity predictions 新型可持续吡啶离子液体的开发:从反应性研究到基于机理的活性预测。
IF 2.1 4区 化学
Journal of Molecular Modeling Pub Date : 2024-10-02 DOI: 10.1007/s00894-024-06157-y
Bakhtiyor Borikhonov, Elyor Berdimurodov, Tursunali Kholikov, W. B. Wan Nik, Konstantin P. Katin, Muslum DEMİR, Frunza Sapaev, Sherzod Turaev, Nigora Jurakulova, Ilyos Eliboev
{"title":"Development of new sustainable pyridinium ionic liquids: From reactivity studies to mechanism-based activity predictions","authors":"Bakhtiyor Borikhonov,&nbsp;Elyor Berdimurodov,&nbsp;Tursunali Kholikov,&nbsp;W. B. Wan Nik,&nbsp;Konstantin P. Katin,&nbsp;Muslum DEMİR,&nbsp;Frunza Sapaev,&nbsp;Sherzod Turaev,&nbsp;Nigora Jurakulova,&nbsp;Ilyos Eliboev","doi":"10.1007/s00894-024-06157-y","DOIUrl":"10.1007/s00894-024-06157-y","url":null,"abstract":"<div><h3>Context</h3><p>This study addresses the development of sustainable pyridinium ionic liquids (ILs) because of their potential applications in agriculture and pharmaceuticals. Pyridinium-based ILs are known for their low melting points, high thermal stability, and moderate solvation properties. We synthesized three novel pyridinium-based ILs: 1-(2-(isopentyloxy)-2-oxoethyl)pyridin-1-ium chloride, 1-(2-(hexyloxy)-2-oxoethyl)pyridin-1-ium chloride, and 1-(2-(benzyloxy)-2-oxoethyl)pyridin-1-ium chloride. The biological activities of these compounds were evaluated through plant growth promotion, herbicidal, and insecticidal assays. Our results show that the benzyloxy derivative significantly enhances wheat and cucumber growth, whereas the isopentyloxy compound has potent herbicidal effects. Computational methods, including DFT calculations and molecular docking, were applied to understand the structure‒activity relationships (SARs) and mechanisms of action.</p><h3>Methods</h3><p>The computational techniques involved dispersion-corrected density functional theory (DFT) with the B3LYP functional and the 6-311G** basis set. Grimme’s D3 corrections were included to account for dispersion interactions. The calculations were performed via GAMESS-US software. Quantum descriptors of reactivity, such as ionization potential, electron affinity, chemical potential, and electrophilicity index, were derived from the HOMO and LUMO energies. Molecular docking studies were conducted via the CB-Dock server via AutoDock Vina software to predict binding affinities to cancer-related proteins. Petra/Osiris/Molinspiration (POM) analysis was used to predict the drug likeness and other pharmaceutical properties of the synthesized ILs.</p></div>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":null,"pages":null},"PeriodicalIF":2.1,"publicationDate":"2024-10-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1007/s00894-024-06157-y.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142360904","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"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
Approximate resolutions of the Schrodinger theory applying the WKB approximation for certain diatomic molecular interactions 应用 WKB 近似值对某些二原子分子相互作用的薛定谔理论进行近似解析。
IF 2.1 4区 化学
Journal of Molecular Modeling Pub Date : 2024-09-30 DOI: 10.1007/s00894-024-06143-4
Khalid Reggab
{"title":"Approximate resolutions of the Schrodinger theory applying the WKB approximation for certain diatomic molecular interactions","authors":"Khalid Reggab","doi":"10.1007/s00894-024-06143-4","DOIUrl":"10.1007/s00894-024-06143-4","url":null,"abstract":"<div><h3>Context</h3><p>The Analyzing of energetic bond spectra of diatomic compounds is crucial to understanding their qualities because it allows one to evaluate their attributes. Diatoms compounds' spectral properties and bound energies are presented in this study. These energies are found by solving the Schrodinger equation while making consideration of the employing of the Kratzer Feus potential.</p><h3>Method</h3><p>This study focuses on the calculation of bound states for diatomic molecules using the WKB approximation. The final energy spectrum equation is utilized to compute the bound states of specific diatomic molecules for varying quantum numbers n and l through the utilization of the Mathematica software. The method produced the desired and anticipated results, as shown by a comparison of the eigenvalue results with earlier studies.</p></div>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":null,"pages":null},"PeriodicalIF":2.1,"publicationDate":"2024-09-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142338937","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"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
Tuning optoelectronic properties of indandione-based D-A materials by malononitrile group acceptors: A DFT and TD-DFT approach 通过丙二腈基团受体调谐茚二酮基 D-A 材料的光电特性:DFT 和 TD-DFT 方法。
IF 2.1 4区 化学
Journal of Molecular Modeling Pub Date : 2024-09-30 DOI: 10.1007/s00894-024-06159-w
Pankaj Kumar Kushwaha, Sunil Kumar Srivastava
{"title":"Tuning optoelectronic properties of indandione-based D-A materials by malononitrile group acceptors: A DFT and TD-DFT approach","authors":"Pankaj Kumar Kushwaha,&nbsp;Sunil Kumar Srivastava","doi":"10.1007/s00894-024-06159-w","DOIUrl":"10.1007/s00894-024-06159-w","url":null,"abstract":"<div><h3>Context</h3><p>Indandione-based materials are promising candidates for organic electronics, offering high electron mobility and tunable optoelectronic properties. In this study, we explore the optoelectronic and photovoltaic properties of indandione-based donor–acceptor (D-A) materials, specifically (R1) and (R2), by introducing malononitrile group acceptors into their molecular structure. These strong electron-withdrawing acceptors are designed to enhance charge transfer and overall material performance. The designed molecules (DM1–DM4) exhibit a low optical band gap of approximately 1.77 eV, significantly lower than the reference materials (R1 and R2) at around 2.24 eV in a solvent environment. Among the designed molecules, DM4 stands out with superior photovoltaic parameters, including a narrow optical band gap (1.77 eV), higher electron affinity (3.49 eV), an extended excited state lifetime (10.0 ns) owing to its low electron and hole reorganization energies (<i>λ</i><sub><i>e</i></sub> ~ 0.13 eV and <i>λ</i><sub><i>h</i></sub> ~ 0.24 eV), and improved short-circuit current density (<i>J</i><sub><i>sc</i></sub>) of ~ 15.73 mA/cm<sup>2</sup>. Notably, DM4 achieves a power conversion efficiency (PCE) of ~ 18.5%, making it an excellent candidate for device applications.</p><h3>Method</h3><p>A comprehensive computational investigation was carried out on indandione-based D-A materials with malononitrile group acceptors (DM1–DM4) using density functional theory (DFT) and time-dependent DFT (TD-DFT) methods, as implemented in Gaussian 16 software. We examined the electronic and optical properties of the proposed molecules through frontier molecular orbital (FMO) analysis, UV–Vis absorption spectra, density of states (DOS), exciton binding energy (<i>E</i><sub><i>b</i></sub>), and transition density matrix (TDM) analysis, utilizing GaussView 6.0 and Multiwfn 3.8 software. The photovoltaic parameters and power conversion efficiency (PCE) were evaluated using the Scharber and Alharbi models.</p></div>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":null,"pages":null},"PeriodicalIF":2.1,"publicationDate":"2024-09-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142338945","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"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
Transition from synchronous to asynchronous mechanisms in 1,3-dipolar cycloadditions: a polarizability perspective 1,3-二极环加成反应中从同步到异步机制的转变:极化性视角。
IF 2.1 4区 化学
Journal of Molecular Modeling Pub Date : 2024-09-30 DOI: 10.1007/s00894-024-06161-2
César Barrales-Martínez, Rocío Durán, Pablo Jaque
{"title":"Transition from synchronous to asynchronous mechanisms in 1,3-dipolar cycloadditions: a polarizability perspective","authors":"César Barrales-Martínez,&nbsp;Rocío Durán,&nbsp;Pablo Jaque","doi":"10.1007/s00894-024-06161-2","DOIUrl":"10.1007/s00894-024-06161-2","url":null,"abstract":"<div><h3>Context</h3><p>This study investigates the energetic and polarizability characteristics of three 1,3-dipolar cycloaddition reactions between diazene oxide and substituted ethylenes, focusing on the transition from synchronous to asynchronous mechanisms. Synchronicity analysis, using the reaction force constant, indicates that the bond evolution process becomes increasingly decoupled as the number of cyano groups increases. Polarizability analysis reveals that isotropic polarizability reaches its maximum near the transition state in all cases, while anisotropy of polarizability shifts from the transition state toward the product direction as asynchronicity increases. The larger the shift, the more asynchronous the mechanism, as reflected by the weight of the transition region. A detailed examination of the parallel and perpendicular polarizability components to the newly formed sigma bonds shows that the evolution of the parallel component is closely aligned with the energetic changes along the reaction coordinate, particularly in the synchronous reaction. We have also identified a relationship between the displacement in the maximum state of the parallel component from the transition state and the synchronicity of the mechanism. The larger the displacement, the more asynchronous the mechanism. These findings suggest that asynchronous 1,3-dipolar cycloaddition mechanisms are characterized by a decoupling of isotropic and anisotropic polarizabilities and a shift in the maximum polarizability state of the parallel component toward the product direction.</p><h3>Methods</h3><p>Density functional theory calculations were performed at the B3LYP/6–311 +  + G(d,p)//B3LYP/6-31G(d,p) level of theory. The polarizability was calculated at each point of the reaction path, obtained using the intrinsic reaction coordinate method, as implemented in Gaussian 16.</p></div>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":null,"pages":null},"PeriodicalIF":2.1,"publicationDate":"2024-09-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142338944","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"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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