Journal of Molecular Modeling最新文献

{"title":"DFT studies on the mechanism of one-pot α,γ-difunctionalization of β-ketoesters: regio-, chemo-, and stereoselectivity promoted by DBU/MeOH.","authors":"Ratiba Hadjadj Aoul, Abdelghani Adda, Hadjira Habib Zahmani, Moussa Sehailia, Stéphane Humbel","doi":"10.1007/s00894-025-06509-2","DOIUrl":"https://doi.org/10.1007/s00894-025-06509-2","url":null,"abstract":"<p><strong>Context: </strong>1,3-Dicarbonyl derivatives, such as β-ketoesters, are inexpensive and readily available building blocks widely applied in organic synthesis for the preparation of bioactive molecules. Nevertheless, the mechanistic origins of their regio-, chemo-, and stereoselectivity in multicomponent transformations remain insufficiently understood. Here, the α,γ-difunctionalization of cyclic β-ketoesters with benzaldehyde, allyl bromide, DBU, and methanol was investigated via density functional theory (DFT) to elucidate these selectivities. The reaction follows a five-step mechanism comprising deprotonation, alkylation, γ-deprotonation, aldol condensation, and dehydration. Energetic analysis revealed that the initial deprotonation is kinetically favored through a bimolecular pathway ( <math> <msup><mrow><mi>Δ</mi> <mi>G</mi></mrow> <mo>#</mo></msup> </math> = 8.35 kcal/mol), whereas alkylation occurs stereoselectively via the Si face and aldol condensation via the Re face. Methanol cooperates with DBU by stabilizing enolates through hydrogen bonding and lowering activation barriers. These insights rationalize the observed experimental selectivity and provide a theoretical framework for the rational design of new selective multicomponent reactions in organic synthesis.</p><p><strong>Methods: </strong>All quantum chemical calculations were performed via Gaussian 16 at the B3LYP/6-31G(d,p) level of theory, with Grimme's D3 dispersion correction. Transition states were confirmed by harmonic frequency analysis and connected to their reactants and products via intrinsic reaction coordinate (IRC) calculations. Solvent effects (THF) were modeled using the IEFPCM approach. Conceptual DFT descriptors were computed at the B3LYP/6-311++G(d,p) level to assess the electronic properties. Natural bond orbital (NBO) analysis was conducted with NBO. The topological features of the electron density were examined using Multiwfn (version 3.8) through QTAIM and IGMH analyses, and the molecular structures were visualized using VMD.</p>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":"31 10","pages":"285"},"PeriodicalIF":2.5,"publicationDate":"2025-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145197859","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}

{"title":"Tuning the photophysical properties of triphenylamine pyrazine-based dyes: role of π-spacers in DSSCs with iodine and copper-based redox shuttle.","authors":"Asha, Sumit Sahil Malhotra, Sunita Srivastava, Manoj Kumar Gangwar, Ranjan Kumar Mohapatra, Manoj Kumar Gupta, Azaj Ansari","doi":"10.1007/s00894-025-06507-4","DOIUrl":"https://doi.org/10.1007/s00894-025-06507-4","url":null,"abstract":"<p><strong>Context: </strong>A series of donor-π-acceptor dyes were designed based on the structure of the experimentally reported TPP dye, which incorporates Triphenylamine (TPA) as the donor, Pyrazine as the π-bridge, and a carboxylic acid group as the acceptor. To enhance the photovoltaic performance of dye-sensitized solar cells, five new dyes (TPP1-TPP5) were modelled by introducing different alterations to the π-conjugated bridge. Density functional theory (DFT) and time-dependent DFT (TDDFT) calculations were carried out to examine how the alteration in the π-spacer influences the optical, electronic, and photovoltaic performance. All dyes displayed negative Gibbs free energy values for electron injection into TiO₂, confirming the thermodynamic favourability of the charge transfer process. Short-circuit current density (J_SC) was found as the highest for TPP3 and TPP4, outperforming the other TPP dyes with 1.40 mA cm^-2 and 1.87 mA cm^-2. Furthermore, with the lowest dye regeneration of ΔG_reg = 0.46 eV and a comparable open circuit voltage (V_oc) of 1.17 eV, TPA4 demonstrated higher regeneration kinetics. Natural bond order analysis was conducted to assess the bond strength and examine the molecular orbitals associated with the donor, π-spacer and acceptor unit. All the modelled dyes found strong non-linear optical characteristics having the linear polarizability (α) amplitudes greater than the first-order total polarizability (β_total) relative to the experimental dye. Light harvesting efficiency of the modelled dye TPP4 was found the maximum (89%) among the studied dyes. These findings show that π-spacer alteration is an effective strategy for improving overall dye performance in DSSCs.</p><p><strong>Methods: </strong>Optimization of all species by using Gaussian16 with functional B3LYP and basis set 6-311G (d,p). NBO analysis was performed to explore the interactions between the filled orbitals of one part and the vacant orbitals of another part. TDDFT studies were performed using ORCA4.2 with Zeroth-Order Regular Approximation for accounting relativistic effects to calculate excitation energies.</p>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":"31 10","pages":"284"},"PeriodicalIF":2.5,"publicationDate":"2025-09-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145197825","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}

{"title":"Nitrogen-rich prismane-based cage compounds: impact of pentazole substitution on detonation and explosive performance","authors":"Anjali Sharma,&nbsp;Dhruba Kshetrimayum,&nbsp;Usman Muhammad Aliyu,&nbsp;Mridula Guin","doi":"10.1007/s00894-025-06494-6","DOIUrl":"10.1007/s00894-025-06494-6","url":null,"abstract":"<div><h3>Context</h3><p>This research explores the impact of systematic addition of pentazole group on the explosive properties of prismane-based compounds on hexanitroprismane and hexaminoprismane. Replacing the NO₂ and NH₂ groups with N₅ in prismane cage-based molecules enhances the material’s energy density and stability, leading to more powerful and stable explosives. The structure-property relationship of the designed molecules is studied using DFT approach. These cage-based compounds exhibit potential as high-energy density explosive compounds reaching up to the level of CL20. Systematic addition of pentazole ring in the prismane cage improves stability and heat of formation. Functionalizing prismane with one pentazole ring can improve the HOF by 300 to 400 kJmol⁻¹. The impact of the number of pentazole rings on density is opposite in nature in -NO₂ and -NH₂ containing sets of molecules. The same trend is observed in the values of D, P, and Q of both sets of molecules as the number of pentazole group increased in the prismane. Insertion of a single pentazole ring in prismane for the nitro group substituted molecules has a better impact on improving the impact sensitivity. Pentazole group substitution enhances the energetic properties of prismane-based high energy density compounds, offering a promising avenue for the development of novel, high-performance explosives with tailored detonation characteristics.</p><h3>Methods</h3><p>Density functional theory (DFT) using Gaussian 16 software was used for all quantum chemical calculations. The optimization of the geometry of the designed compounds is performed at two different levels, e.g., B3LYP/6–311 + + G(d,p) and B3PW91/6-31G(d,p). Molecular surface and other properties are visualized using GaussView 6.0 software. The heat of formation (HOF) of the molecules is estimated using isodesmic reactions. The multiwfn program was used for the calculation of molecular surface properties.\u0000</p></div>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":"31 10","pages":""},"PeriodicalIF":2.5,"publicationDate":"2025-09-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145147356","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}

{"title":"First-principles study on the influence of tensile deformation on the optoelectronic properties of the F-HfSe₂ system","authors":"Tong Yuan,&nbsp;Guili Liu,&nbsp;Guoying Zhang","doi":"10.1007/s00894-025-06504-7","DOIUrl":"10.1007/s00894-025-06504-7","url":null,"abstract":"<div><h3>Context</h3><p>Within the framework of first-principles density functional theory, this study investigates the impacts of doping and tensile deformation on the electronic and optical properties of HfSe₂. The research reveals that, after being doped with halogen elements, HfSe₂ undergoes a transition from a semiconductor to a metal, enhancing the electrical conductivity of the X-HfSe₂ systems (where X represents F, Cl, Br, or I). Among them, F-HfSe₂ exhibits the lowest formation energy and is thus selected as the research object for tensile deformation studies. The study demonstrates that, as the tensile strain increases, the energy band values of F-HfSe₂ increase linearly, enabling effective regulation of its band structure. The density of states indicates that the main contributions come from the 6d orbitals of Hf and the 4p orbitals of Se, with the F atoms contributing minimally. F atoms primarily regulate the energy bands through charge transfer processes. Optically, tensile strain enhances the light-absorbing capacity of F-HfSe₂ and induces a redshift, making it applicable in the visible and near-infrared ranges. This is attributed to the bandgap changes caused by tensile deformation. Consequently, F-HfSe₂ holds promise as an ideal material for photodetectors.</p><h3>Methods</h3><p>Utilizing the CASTEP module within Materials Studio software under the framework of first-principles density functional theory (DFT), geometric optimizations and optoelectronic structure calculations were performed for both intrinsic HfSe₂ and doped systems. The GGA-PBE functional was chosen for its computational efficiency and the consistency of its calculated band structure trends with more precise HSE methods, despite its tendency to underestimate bandgaps. But rigorous convergence tests were conducted to ensure the precision and reliability of the results. Specifically, a 7 × 7 × 1 K-point grid was selected for Brillouin Zone sampling after repeated testing, and the plane-wave cutoff energy was set at 600 eV. Energy convergence per atom was set at 1.0 × 10⁻⁵ eV, force convergence at 0.03 eV/Å, with stress and displacement limits at 0.05 GPa and 0.01 Å, respectively. A vacuum spacing of 20 Å was implemented to prevent interactions between periodically replicated units.</p></div>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":"31 10","pages":""},"PeriodicalIF":2.5,"publicationDate":"2025-09-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145136012","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}

{"title":"Machine-learned density functional based quantum chemical computations for ethane: performance of DeepMind 21 on potential energy surface and molecular properties","authors":"B. Jijila,&nbsp;S. Susannal Ezhilarasi,&nbsp;V. Nirmala","doi":"10.1007/s00894-025-06451-3","DOIUrl":"10.1007/s00894-025-06451-3","url":null,"abstract":"<div><h3>Context</h3><p>Machine learning (ML) has proven to be a promising method in quantum chemistry calculations. Researchers at Google DeepMind established the superior performance of a machine-learned functional DeepMind 21 (DM21), the neural network-based functionals which emerged as a powerful tool for developing exchange–correlation energy approximation in density functional theory (DFT), to accurately explain the charge delocalization and strong correlation. While many researchers have cited the work of DeepMind, still there remains a paucity of research publications that perform algorithmic computations with DeepMind’s AI model for quantum sciences. To address this lacuna, this paper investigates quantum chemistry algorithmic computations of potential energy surface and analysis properties of ethane molecule (C₂H₆) by employing the machine learning model to predict exchange–correlation potential. This paper utilizes neural density functional, DeepMind 21 to compute the dipole moment, molecular orbitals (HOMO/LUMO), and long-range interactions. Our computations were based on DM21m TensorFlow neural network model-based prediction of exchange–correlation potential, and then using this prediction to compute self-consistent field energies using PySCF Python package with cc-pVDZ Dunning dual basis set. The accuracy of the DM21 functional was rigorously assessed through comparison with conventional DFT methods (B3LYP, PW6B95) and the reference CCSD(T) standard. The findings indicate that the DM21 functional yields result in close agreement with the CCSD(T) benchmark energies and established literature values, confirming its efficacy for PES generation and quantum chemical computation in systems like ethane. This investigation demonstrates the suitability of the deep learning density functional for quantum science computations of ethane molecule for the first time.</p><h3>Methods</h3><p>In this method, the potential energy surfaces and properties (dipole moment, molecular orbitals) are computed using machine-learned density function approximation using pretrained deep learning models provided by DeepMind 21 researchers. By inserting deep learning inference in density functional theory (DFT) with a pretrained neural network, self-consistent field (SCF) energy at different geometries along the coordinate of interest is computed, and hence potential energy surfaces are computed and obtained. For a given specified molecular geometry, the algorithm computes the electron density vector, which is then used as a machine learning feature input for a pretrained DM21 deep learning model to predict the exchange–correlation. This methodology was implemented in a Python source code using frameworks such as PySCF and DM21.</p></div>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":"31 10","pages":""},"PeriodicalIF":2.5,"publicationDate":"2025-09-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145136190","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}

{"title":"Rejuvenation mechanism of cross-linked epoxy resin on aged asphalt: insights from molecular dynamics and rheology","authors":"Zhenghong Xu,&nbsp;Zijia Xiong,&nbsp;Minghui Gong,&nbsp;Jiao Jin,&nbsp;Jinxiang Hong,&nbsp;Jinliang Cheng,&nbsp;Lei Jiang","doi":"10.1007/s00894-025-06493-7","DOIUrl":"10.1007/s00894-025-06493-7","url":null,"abstract":"<div><h3>Context</h3><p>Asphalt recycling represents an advanced, eco-friendly pavement rehabilitation technology where proper rejuvenation of aged asphalt ensures the economic viability of reclaimed asphalt pavement (RAP). In this study, molecular models of raw asphalt and aged asphalt were constructed using Materials Studio. The reaction between the epoxy resin and curing agent was automated via a Perl script, establishing molecular dynamics models of epoxy asphalt and epoxy-aged asphalt containing approximately 30% epoxy resin and achieving a cross-linking rate of 87.5%. Through a dual-method approach—directly analyzing cross-linked epoxy resin’s impact on aged asphalt molecules and comparatively evaluating aging degradation in virgin versus epoxy asphalt—we employed cohesive energy density, free volume fraction, and mean square displacement analyses. Results demonstrate that cross-linked epoxy resin weakens strong polar interactions between aged asphalt molecules, increases molecular free volume and diffusion capacity, and significantly inhibits polar molecule aggregation, thereby collectively enhancing aged asphalt performance. Rheological testing confirms that epoxy resin partially restores the viscoelastic properties of aged asphalt, providing macroscopic validation of molecular simulation results. This multi-scale verification advances fundamental understanding of epoxy-recycled asphalt (ERA) systems and establishes theoretical foundations for optimizing pavement performance in sustainable regeneration applications.</p><h3>Methods</h3><p>To investigate the effect of epoxy polymers on the aging behavior of asphalt, molecular models of virgin asphalt, aged asphalt, epoxy asphalt, and epoxy-aged asphalt were constructed using the Amorphous Cells module of the Materials Studio 2020 software. Molecular dynamics simulations of these four asphalt models were then performed using the Forcite module, with atomic and molecular interactions described by the COMPASS II force field.</p></div>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":"31 10","pages":""},"PeriodicalIF":2.5,"publicationDate":"2025-09-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145136125","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}

{"title":"The pyrolysis of polyimide and epoxy resin by the ReaxFF molecular dynamics simulation","authors":"Yingzhe Du,&nbsp;Jun Li,&nbsp;Ning Wen,&nbsp;Zheng Zhang,&nbsp;Dan Song","doi":"10.1007/s00894-025-06492-8","DOIUrl":"10.1007/s00894-025-06492-8","url":null,"abstract":"<div><h3>Context</h3><p>Polyimide (PI) and epoxy resin will age by hot corrosion and long-term high temperature, losing the heat insulting property and forming tremendous potential dangers. In order to evaluate the thermal properties accurately and detect the potential damage of them, the pyrolysis processes of them were studied. The results show that the main products of PI are CO₂ and CN· at high temperature, and their formation are both associated with the break of C-N bond in the imide rings. With the increase of the temperature, the number of CN· increases, but the number of CO₂ decrease. Among several reaction path of the PI productions, the <i>p1</i> is the lowest activation energy and can form CO₂. The bond dissociation energies of C-N bond in <i>p3</i> and <i>p4</i> are higher than <i>p1</i>. We also investigated the pyrolysis process of the epoxy resin. The results show that the main products of epoxy resin are H₂, CH₂O, H₂O, and CH₄ at 1300 K, and the H₂ is generated by the collision of the hydrogen atoms (<i>p1</i> path), the CH₂O is generated by the partial decomposition of the C₂ or C₃, which can form the epoxy groups on the ends of the epoxy resin.</p><h3>Methods</h3><p>Reactive force field (ReaxFF) molecular dynamics simulations were used to study the pyrolysis of PI and epoxy resin. The initial structures of PI and epoxy resin were constructed using Material Studio software, followed by geometry optimization to achieve the most stable configuration. Pyrolysis simulations were performed using the large-scale atomic/molecular massively parallel simulator (LAMMPS). The simulation employed NPT ensemble (0.1 MPa, 298 K) to adjust the system density to 1.0 g/cm³, and NVT ensemble for pyrolysis Calculations with a time step of 1 fs and total simulation time of 1 ns. Temperature was controlled using the Bersenden method, with key simulation temperatures including 1300 K (epoxy resin) and 2800–3800 K (PI).</p></div>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":"31 10","pages":""},"PeriodicalIF":2.5,"publicationDate":"2025-09-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145136144","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}

{"title":"Discovery of a potent ROR1 inhibitor using μs-scale MD simulations, wt-metadynamics, and absolute binding free energy calculations","authors":"Shradheya R. R. Gupta,&nbsp;Rashmi Rameshwari,&nbsp;Indrakant Kumar Singh","doi":"10.1007/s00894-025-06508-3","DOIUrl":"10.1007/s00894-025-06508-3","url":null,"abstract":"<div><h3>Context</h3><p>Receptor tyrosine kinase-like orphan receptor 1 (ROR1) is a cancer-associated pseudokinase with low expression in normal adult tissues but elevated levels in various malignancies, making it a promising therapeutic target. Among ~ 4 million compounds, CHEMBL3926946 emerged as the most promising candidate, demonstrating a persistent binding pose and a well-defined free energy basin. Well-tempered metadynamics (wt-MetaD) revealed a deep minimum of 26.00 ± 2.44 kcal/mol, indicating a highly stable interaction. CHEMBL3926946 exhibited a favourable Absolute Binding Free Energy Perturbation (ABFEP) of − 16.52 ± 0.37 kcal/mol, significantly outperforming the inhibitor Ponatinib (− 8.67 ± 0.94 kcal/mol), supported by persistent interactions with GLU523 and LEU479. This study highlights CHEMBL3926946 as a robust lead for ROR1-targeted cancer therapy and emphasizes the utility of combining wt-MetaD and ABFEP for reliable hit prioritization.</p><h3>Methods</h3><p>We employed a multilayered in silico pipeline integrating high-throughput virtual screening, long-timescale molecular dynamics (MD), wt-MetaD, and ABFEP. Ligands and protein were prepared using the OPLS2005 force field, and all stages up to wt-MetaD were conducted in Maestro (v12.8.117) using the same force field. A library of ~ 4 million compounds yielded 137 candidates, Further shortlisted via MD. 7 high-confidence molecules underwent 5 independent MD replicates with randomized seeds to ensure statistical robustness. The top 3 compounds were validated by 1 μs (1000 ns) simulations to assess long-term conformational stability and wt-MetaD to reveal deep minimum. ABFEP calculations were performed using the CGenFF force field in NAMD 3.0. We benchmarked ABFEP protocol against experimentally validated ligands, successfully reproducing experimental binding free energies (ΔG), confirming the protocol’s predictive reliability.</p><h3>Graphical Abstract</h3><div><figure><div><div><picture><source><img></source></picture></div></div></figure></div></div>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":"31 10","pages":""},"PeriodicalIF":2.5,"publicationDate":"2025-09-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145136042","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}

{"title":"Rational design of triphenylamine-based sensitizers for DSSCs: a DFT comparison of pyridine and amine donor substituents","authors":"Damián Delgado-Montiel,&nbsp;Norma Flores-Holguín,&nbsp;Jesús Baldenebro-López,&nbsp;Rody Soto-Rojo,&nbsp;Manuel Luque-Roman,&nbsp;Tomás Delgado-Montiel,&nbsp;Daniel Glossman-Mitnik","doi":"10.1007/s00894-025-06498-2","DOIUrl":"10.1007/s00894-025-06498-2","url":null,"abstract":"<div><h3>Context</h3><p>The rational design of metal-free organic sensitizers is critical for developing cost-effective, high-efficiency dye-sensitized solar cells (DSSCs). This study uses density functional theory (DFT) to explore how modifying the triphenylamine (TPA) donor with pyridine rings or amino groups at ortho-, meta-, and para-positions affects the optoelectronic properties of D-π-A sensitizers. Our calculations show that para-position amino substitution (dye N3) yields the most red-shifted absorption (<span>({lambda }_{max})</span>=523, 50 nm beyond reference dyes), the highest theoretical open-circuit voltage (Voc = 1.77 eV, 0.3 eV higher than others), and enhanced charge transfer efficiency. These findings highlight para-position amines as a promising strategy for optimizing DSSC performance and identify N3 as a prime candidate for synthesis and experimental validation.</p><h3>Methods</h3><p>Ground-state geometries, vibrational frequencies, and frontier molecular orbitals were calculated using the M06 functional with the 6-31G(d) basis set, chosen for its accuracy in organic systems. UV–Vis absorption and excited-state properties were predicted via time-dependent DFT (TD-DFT) with the M06-2X functional, optimized for excited-state accuracy, and the 6-31G(d) basis set. Solvation effects in acetonitrile were modeled using the IEF-PCM polarizable continuum model. Calculations were performed with Gaussian 16.</p></div>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":"31 10","pages":""},"PeriodicalIF":2.5,"publicationDate":"2025-09-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145136182","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}

{"title":"Theoretical investigation on sensing of dopamine and tyramine neurotransmitters by the B9N9 nanoring","authors":"Ascharya Kumar Kar,&nbsp;Swetapadma Praharaj,&nbsp;Tarun Yadav,&nbsp;Somenath Garai,&nbsp;Dileep Kumar Gupta,&nbsp;Dibyaranjan Rout","doi":"10.1007/s00894-025-06478-6","DOIUrl":"10.1007/s00894-025-06478-6","url":null,"abstract":"<div><h3>Purpose</h3><p>The investigation concerns the first demonstration of employing the B₉N₉ nanoring as an active material for sensing dopamine and tyramine neurotransmitters.</p><h3>Method</h3><p>The calculations for optimization and vibrational frequencies of B₉N₉ ring, dopamine, and tyramine neurotransmitters have been executed by using density functional theory (DFT) available in the Gaussian09 suite. The standard functional (B3LYP) coupled with the basis set 6-311G(d, p) have been adopted for calculations. Natural bond orbital (NBO) analysis quantified charge transfer, while molecular electrostatic potential (MEP) mapping, electron localization function (ELF), reduced density gradient (RDG) analysis, and quantum theory of atoms in molecules (QTAIM) characterized intermolecular interactions.</p><h3>Results</h3><p>The responsiveness of B₉N₉ ring towards the considered neurotransmitters is characterized thoroughly by the optimized electronic structures, energies, electronic, and other properties using density functional theory (B3LYP/6-311G(d, p)). The interaction of dopamine and tyramine governs through formation of the N-B dative bond in the most favorable configurations. The interaction energies for the most stable configurations of dopamine@B₉N₉ and tyramine@B₉N₉ complexes are found to be −22.11 and −21.49 kcal/mol, respectively, which show a significant interaction of neurotransmitters to nanoring and elucidate the adoption of B₉N₉ ring in sensing applications for these neurotransmitters. The critical conventional electronic parameters, viz., HOMO, LUMO, Fermi energy, work function, and energy gap, are also computed, and the effect of an aqueous medium is investigated on these parameters. The ELF and RGD techniques are used to quantify the electron density distribution and explore the involved interactions. TD-DFT calculations are performed to simulate the UV-Vis spectra. Additionally, a quantum theory of atoms in molecules (QTAIM) analysis is conducted, which shows that dopamine@B₉N₉ and tyramine@B₉N₉ exhibit stronger hydrogen bond interactions, resulting in increased bond strengths.</p><h3>Conclusion</h3><p>B₉N₉ nanoring shows significant interaction with both neurotransmitters and results in the change in the electronic properties helping in detection of both neurotransmitters.</p><h3>Graphical Abstract</h3><div><figure><div><div><picture><source><img></source></picture></div></div></figure></div></div>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":"31 10","pages":""},"PeriodicalIF":2.5,"publicationDate":"2025-09-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145136101","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}