Journal of Molecular Modeling最新文献

{"title":"Geometric and electronic structures of FeBn−/0/+ clusters (n = 1–3): insights from advanced computational methods","authors":"Hoang Lin Nguyen,&nbsp;Quoc Tri Tran,&nbsp;Kim Tai Dang,&nbsp;Van Tan Tran","doi":"10.1007/s00894-025-06428-2","DOIUrl":"10.1007/s00894-025-06428-2","url":null,"abstract":"<div><h3>Context</h3><p>Boron-doped iron clusters are extensively studied for their potential in materials science. Despite several quantum calculations with DFT and MRCI methods, a comprehensive understanding of the geometric and electronic structures of small FeB_<i>n</i>^−/0/+ clusters (<i>n</i> = 1–3) is still lacking. This work provides new insights into ground and low-lying excited states, detachment energies, and ionization energies of these clusters using DFT and multireference CASPT2, RASPT2, and DMRG-CASPT2 computational methods. Key findings reveal ³Σ⁻, ⁴Σ⁻, and ³Σ⁻ as ground states for FeB^−/0/+, and cyclic-FeB₂^−/0/+ isomers (⁴B₂, ³B₂, ⁴B₁) as the most stable for FeB₂^−/0/+ clusters. For FeB₃ clusters, anionic species have a tetrahedral geometry, while neutral and cationic species favor rhombic structures. Detachment energies of the anionic ground states increase progressively from FeB⁻ to cyclic-FeB₂⁻, and further to the tetrahedral-FeB₃⁻ isomer, which correlates with the number of boron atoms bonded to the iron atom. The vibrational progression in transitions within tetrahedral-FeB₃^−/0 is more prominent than in FeB^−/0 clusters and cyclic-FeB₂^−/0 isomers. The ionization energies of neutral ground states rise from FeB clusters to rhombic-FeB₃ and cyclic-FeB₂ isomers.</p><h3>Methods</h3><p>The geometry optimization and vibrational frequency calculations for the electronic states of FeB₂^−/0/+ and FeB₃^−/0/+ clusters were conducted using density functional theory (DFT) with the BP86 and MN15 functionals and the def2-QZVP basis set, implemented in ORCA 5.0. Franck–Condon factor simulations were performed using the ezSpectra suite, based on DFT-derived geometries and vibrational normal modes. Multireference RASPT2 and CASPT2 calculations utilized OpenMolcas, while DMRG-CASPT2 calculations employed ChemPS2 interfaced to OpenMolcas. The aug-cc-pwCVQZ-DK basis set was applied to iron, and aug-cc-pVQZ-DK to boron. The 1 s, 2 s, and 2p orbitals of iron and the 1 s orbital of boron were frozen in the second-order perturbation calculations. IPEA and imaginary shift parameters were set to 0.25 and 0.10, respectively. To achieve high accuracy, the DMRG-CASPT2 active spaces were expanded to 22 orbitals for FeB^−/0/+ and FeB₂^−/0/+, and 23 orbitals for FeB₃^−/0/+.</p></div>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":"31 7","pages":""},"PeriodicalIF":2.5,"publicationDate":"2025-06-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144482806","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":"Molecular dynamics simulation of crude oil detachment using ScCO2 and miscible agents on SiO2 surfaces","authors":"Congying Lu,&nbsp;Yue Zhao,&nbsp;Zhenyu Yuan,&nbsp;Xinyi Xu,&nbsp;Limin Li,&nbsp;Qinghe Gao,&nbsp;Wei Ding","doi":"10.1007/s00894-025-06421-9","DOIUrl":"10.1007/s00894-025-06421-9","url":null,"abstract":"<div><h3>Context</h3><p>Carbon capture, utilization, and storage technology has garnered increasing attention across various industries. To further elucidate the mechanism of CO₂ enhanced oil recovery, an amphiphilic surfactant was designed based on β-cyclodextrin. The mechanism of oil detachment from SiO₂ was investigated through molecular dynamics simulations. Density distribution curves and diffusion coefficients of oil phase and CO₂ indicated improved miscibility following the addition of surfactants. Subsequent analysis of desorption efficiency for oil phase revealed that the enhanced miscibility between CO₂ and oil molecules facilitated desorption from solid surfaces. The C2-OAC7 system exhibited superior desorption effects due to lower energy levels associated with CO₂ + surfactant and oil interactions. The addition of surfactants promoted mutual dissolution of CO₂ and oil primarily through increased cavity space in β-cyclodextrin, enhancing van der Waals forces between CO₂-philic/oil-philic groups with CO₂ and octane respectively. This study provides valuable data references and theoretical foundations for structural design and action mechanisms of miscible surfactants.</p><h3>Method</h3><p>In this study, Packmol was employed to construct the model, Gromacs was utilized for molecular dynamics simulations, and VMD was adopted for graphical visualization. Initially, the energy minimization of the two systems, namely “CO₂ + Surfactant” and “Oil + SiO₂-OH,” was performed. Subsequently, 1ns NPT simulations were conducted on both systems under specific conditions: 313 K and 105 bar for the “CO₂ + Surfactant” system, and 298 K and 101.325 kPa for the “Oil + SiO₂-OH” system. Finally, a 10ns NPT simulation was carried out. The Berendsen and Parrinello-Rahman methods are used to maintain system pressure. The LINCS algorithm is employed to constrain molecular bond lengths, while the Lennard–Jones potential is applied to define the cutoff radius. Long-range electrostatic interactions are handled using the Particle-Mesh Ewald (PME) summation method.</p></div>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":"31 7","pages":""},"PeriodicalIF":2.5,"publicationDate":"2025-06-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144473669","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":"Investigation of structural, electronic and toxicity profiles of pyrene, benzo[e]pyrene, and their ozonolysis products by using computational methods","authors":"Dhyani Vadgama,&nbsp;Harshil Shah,&nbsp;Satyam Shinde,&nbsp;Rohit Srivastava","doi":"10.1007/s00894-025-06418-4","DOIUrl":"10.1007/s00894-025-06418-4","url":null,"abstract":"<div><h3>Context</h3><p>Polycyclic aromatic hydrocarbons (PAHs) have a substantial impact on the decomposition process of the atmosphere and the hydrosphere and also pose health risks due to toxicity and long-range transport capabilities. Despite extensive experimental and field studies, the detailed molecular-level understanding of their chemical reactivity, transformation pathways and toxicity after ozonolysis remains limited. This study investigates the structural, electronic and toxicological changes occurring to PAH (pyrene and benzo[e]pyrene) upon ozonolysis using a quantum chemical approach. Ozonolysis products of pyrene and benzo[e]pyrene exhibit altered stability and reactivity, which suggests that they are unlikely to participate in subsequent atmospheric reactions. Importantly, the toxicity assessment of these compounds indicates that products are less toxic than parental compounds, except pyrene mono-ozonide and benzo[e]pyrene dialdehyde. By integrating these insights, environmental simulations can better predict the behaviour of PAHs in the atmosphere and their role in ozone decomposition, contributing to the development of a more accurate atmospheric model.</p><h3>Methods</h3><p>Gaussian 09 software is used to carry out Density Functional Theory calculations for investigating electronic and structural properties of PAHs and their ozonolysis products. The B3LYP, M06-2X, ωB97XD, PW6B95 and PBE0 functionals with basis sets 6–311++G(d,p), def2-TZVP and cc-pVTZ are employed to determine the suitable method. Among all, B3LYP/6–311++G(d,p) demonstrates better alignment with experimental data for pyrene. Therefore, B3LYP/6–311++G(d,p) level of theory is used to analyse the HOMO–LUMO, electrostatic potential and frequency of reactants and product molecules. The toxicity profile of these compounds is assessed using the ecological structure activity relationships (ECOSARV2.2) software, which estimates their environmental exposure risk.</p></div>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":"31 7","pages":""},"PeriodicalIF":2.5,"publicationDate":"2025-06-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144473668","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":"Optoelectronic behavior of spirocyclopentadithiophene in lattice aromatics","authors":"Wang-yang Wu,&nbsp;Zong-xiang Zheng,&nbsp;Hao-bo Wan,&nbsp;Jie Mao,&nbsp;Fang-li Wang,&nbsp;Lei Yang,&nbsp;Mohamad Akbar Ali,&nbsp;Ling-hai Xie","doi":"10.1007/s00894-025-06411-x","DOIUrl":"10.1007/s00894-025-06411-x","url":null,"abstract":"<div><h3>Context</h3><p>This study investigates the influence of intramolecular π-π stacking interactions on the optoelectronic properties of spirocyclopentadithiophene (spiro-CPDT)-based latticed molecules (GS-CPDT, HGS-CPDT1, and HGS-CPDT2) to optimize their charge transport characteristics. Density functional theory was employed to analyze molecular geometries, frontier molecular orbitals, adiabatic ionization potentials (<i>IP</i>_<i>a</i>), electron affinities (<i>EA</i>_<i>a</i>), and reorganization energies (<i>λ</i>). Crystal structure modeling using the Dreiding force field and computational evaluation of electronic coupling parameters (<i>V</i>_<i>e</i>, <i>V</i>_<i>h</i>) and charge-transfer rate constants (<i>k</i>_<i>e</i>, <i>k</i>_<i>h</i>) were performed to assess intramolecular π-π stacking effects. Results reveal that lattice-induced π-stacking configurations significantly reduce reorganization energies (<i>λ</i>_<i>e</i> = 0.223 eV, <i>λ</i>_<i>h</i> = 0.343 eV) while enhancing charge-transfer rate constants (~ 10¹¹ s⁻¹), demonstrating improved charge transport efficiency compared to conventional spiro-CPDT systems. These findings establish fundamental structure–property relationships for spiro-aromatic hydrocarbons, offering critical theoretical guidance for designing organic electronic materials with tailored charge transport capabilities.</p><h3>Methods</h3><p>The molecular energy, molecular structure, molecular orbitals, and other properties of all molecules designed in this paper were calculated using functional B3LYP and basis set 6-31G(d). Based on these calculations, tasks such as optimizing the ground state geometry of the molecules, calculating electrostatic potential, and optoelectronic properties were carried out. The weak interactions of molecules were investigated using Multiwfn 3.8 and VMD. Finally, the molecular crystal structure was predicted using the Metamorph module in Materials Studio 2020, and the dimer of the studied molecule was obtained.</p></div>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":"31 7","pages":""},"PeriodicalIF":2.5,"publicationDate":"2025-06-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144473670","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":"Evaluation of thermochemical characteristics of salts with pentazenium cation","authors":"D. V. Khakimov,&nbsp;A. A. Voronin","doi":"10.1007/s00894-025-06420-w","DOIUrl":"10.1007/s00894-025-06420-w","url":null,"abstract":"<div><h3>Context</h3><p>Using quantum-chemical and crystal modeling, the solid-state enthalpies of three hypothetical high-energy salts with the pentazenium cation N₅⁺ were estimated: nitrate NO₃⁻, dinitramide N(NO₂)₂⁻, and azide N₃⁻, yielding the cationic contribution of pentazenium. Supplementing the lattice energy mixing method with an additive approach to determining the enthalpies of salts, values are given for salts with the perchlorate anion N₅⁺ClO₄⁻; four salts with the halogen anions N₅⁺I⁻, N₅⁺Br⁻, N₅⁺Cl⁻, and N₅⁺F⁻; and two experimentally existing structures: pentazenium tetrafluoroborate N₅⁺BF₄⁻ and pentazenium hexafluorophosphate N₅⁺PF₆⁻. Calculations of salt structures were performed using a wide range of density functional theory (DFT) methods with varying functionals and bases, as well as composite methods for calculating the enthalpies of gas phase formation, to show the low variability of the final result and the universality of the approach. The calculations of the explosive characteristics of salts with oxygen–nitrogen anions showed that their detonation velocity is in the range of 7.1–7.6 km s⁻¹. Of the three salts considered, the azide salt has the lowest density equal to 1.1 g cm⁻³, while the nitrate and dinitramide are at the level of 1.6 g cm⁻³ and 1.7 g cm⁻³, respectively. The heat of detonation of pentazenium salts is about 800–850 cal g⁻¹.</p><h3>Methods</h3><p>In this work, broad set of DFT calculations were conducted through the software Gaussian 09: B3LYP/6-31G(d,p), B3LYP/aug-cc-PVDZ + GD2, M052X/aug-cc-pVTZ, and M062X/6–311 +  + G(d,p). For crystal structure optimization, the atom–atom potential methods with PMC program (Packing of Molecules in Crystal) were used. Charges for molecular electrostatic potential were fitted by FitMEP, and enthalpies of formation in gas phase were assessed by CBS-4 M, G3B3, G4, and W1BD.\u0000</p></div>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":"31 7","pages":""},"PeriodicalIF":2.5,"publicationDate":"2025-06-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144473667","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":"Can pristine/modified graphene repair N7-methylated guanine lesions? A DFT study","authors":"Baharul Islam Laskar,&nbsp;Pradeep Kumar Shukla","doi":"10.1007/s00894-025-06419-3","DOIUrl":"10.1007/s00894-025-06419-3","url":null,"abstract":"<div><h3>Context</h3><p>Graphene is considered to be a wonder material with widespread applications. However, its potential for recovering methylated DNA bases has not yet been explored. DNA methylation is implicated in the development of several health issues such as mutation, ageing, cancer and neurodegenerative diseases. The cytotoxic N7-methylated guanine (N7mG) is the most abundantly occurring methylated DNA lesion. Therefore, we have theoretically investigated the reactions of pristine, heteroatom-doped and functionalized graphene with N7mG cation with an intention to understand the efficacy of graphene in repairing this lesion. The epoxide- and thioepoxide-functionalized graphene can effectively restore guanine from the N7mG cation in both gas and aqueous phases. Pristine and BN-codoped graphene are, however, found to be unsuitable for this work. Thus, the present study offers valuable insights into how graphene may help in repairing N7mG and other modified DNA bases.</p><h3>Methods</h3><p>The calculations related to energetics, structural optimizations, natural bond orbitals (NBOs) and DOS were performed using two functionals (M06-2X and wB97X-D) of density functional theory (DFT) in association with 6-31G* and 6-31+G** basis sets, as available in the Gaussian 09 quantum chemistry code. The IEF-PCM was used for the aqueous phase calculations. The CHelpG charges were used for charge transfer analysis.\u0000</p></div>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":"31 7","pages":""},"PeriodicalIF":2.5,"publicationDate":"2025-06-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144473666","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":"Porosity dependence of mechanical properties of titanium nanofoams","authors":"Thi-Thuy Binh Ngo,&nbsp;Van-Thuc Nguyen,&nbsp;Te-Hua Fang","doi":"10.1007/s00894-025-06416-6","DOIUrl":"10.1007/s00894-025-06416-6","url":null,"abstract":"<div><h3>Context</h3><p>This study employs molecular dynamics (MD) simulations to investigate the mechanical properties and deformation mechanisms of titanium (Ti) nanofoam under uniaxial tensile loading. The effects of porosity (ranging from 20 to 50%), strain rate (from 5 × 10⁸ to 5 × 10⁹ s⁻¹), and temperature (from 300 to 900 K) on the tensile response are systematically examined. The results reveal that increasing porosity significantly reduces the ultimate tensile strength (UTS) and elastic modulus, while intensifying localized shear strain and stress concentration. These conditions facilitate the formation of amorphous phases and grain structures, and substantially influence dislocation behavior. Furthermore, higher strain rates are found to enhance strength by increasing both UTS and elastic modulus. In contrast, elevated temperatures induce phase transformations that improve ductility but compromise strength. Overall, this work provides valuable insights into tailoring the mechanical performance of Ti nanofoams, with implications for their use in biomedical, structural, and functional applications.</p><h3>Methods</h3><p>The simulations were performed using the Large-scale Atomic/Molecular Massively Parallel Simulator (LAMMPS) package. The results were analyzed using the Open Visualization Tool (OVITO). Structural analysis was conducted using common neighbor analysis (CNA) and polyhedral template matching (PTM), while dislocation behavior was studied with dislocation analysis (DXA). Surface meshes for volume and surface computations were generated using the construct surface mesh method.</p></div>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":"31 7","pages":""},"PeriodicalIF":2.5,"publicationDate":"2025-06-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144324106","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":"Shedding light on main-group dithiolene chemistry: electronic and geometrical perspectives of tris(dmit) complexes","authors":"Heloisa N. S. Menezes,&nbsp;Henrique C. S. Junior,&nbsp;Glaucio B. Ferreira","doi":"10.1007/s00894-025-06417-5","DOIUrl":"10.1007/s00894-025-06417-5","url":null,"abstract":"<div><h3>Context</h3><p>1,3-Dithiola-2-thiona-4,5-dithiolate is a versatile noninnocent ligand with applications in superconductivity, magnetism, and nonlinear optical materials. This study evaluated the tris(dmit) antimony(V) and tin(IV) complexes via modern computational methods. A local energy decomposition analysis of metal‒sulfur bond formation revealed that the distorted geometry of the tris(dmit) complexes in acetonitrile is the most stable conformation for both systems, whereas other conformations remain energetically accessible. The geometrical stability arises from the ionic and soft acid‒base interactions between the highly oxidized cations and thiolated sulfur atoms. State-averaged complete active-space self-consistent field with N-electron valence second-order perturbation theory correction calculations indicated that while the ground states are dominated by a single configuration, the excited state manifold in both systems shows multiconfigurational character, which is relevant for understanding systems with potentially non-innocent ligands. Finally, similarity-transformed equations of motion coupled-cluster calculations successfully reproduced the experimental UV‒Vis spectra of the two complexes in acetonitrile, highlighting the low-energy ligand-to-metal charge-transfer excitations in the tris(dmit) antimony(V) complex. These findings increase the understanding of the electronic structure and stability of tris(dmit) complexes, which can help in understanding potential applications.</p><h3>Methods</h3><p>The tris(dmit) complexes were computationally investigated via two solvation models: implicit and explicit solvation. All ab initio and DFT wave function calculations were performed via ORCA software version 5.0.3. Model implicit solvation were optimized via the TPSSh/Def2-TZVP level of theory with CPCM used to simulate an acetonitrile medium. AIMD calculations for explicit solvation of the dmit salts were conducted using the GFN2-xTB method with 40 explicit acetonitrile molecules as the solvent at 300 K for a total simulation time of 35.0 ps, a timestep of 0.2 fs and data dumps every 10.0 fs. The final geometries were optimized via an ONIOM approach, with the high-level region set at the R2SCAN-3C method, which included the complexes and the first solvation shell. The low-level region utilized the extended tight-binding (xTB) method to encapsulate the explicitly solvated models, which comprised the remaining solvent molecules. Local energy decomposition (LED) analysis at the DLPNO-CCSD(T)/Def2-TZVP level of theory was utilized to investigate the stability of the complex geometries identified by AIMD. The electronic structures of the complexes were assessed using the SA-CASSCF/NEVPT2/Def2-TZVP method to confirm the multiconfigurational and multireference nature of their electronic structures. Electronic spectra were analyzed using the STEOM-DLPNO-CCSD/Def2-TZVP method, with CPCM used to simulate an acetonitrile medium.</p></div>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":"31 7","pages":""},"PeriodicalIF":2.5,"publicationDate":"2025-06-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144300919","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":"Chiral generation in achiral lower diamondoid triamantane through prochiral halogen substitution","authors":"Aravindhan R,&nbsp;Jianping Hu,&nbsp;Ummal Momeen M","doi":"10.1007/s00894-025-06407-7","DOIUrl":"10.1007/s00894-025-06407-7","url":null,"abstract":"<div><h3>Context</h3><p>Our work demonstrates the chiral and chiroptical behavior of lower diamondoid molecules such as triamantane. Through the halogen substitution prochirality process, chirality was attained from the achiral triamantane molecule. The chiroptical behavior of chiral triamantane obtained from VCD, ROA, and ORD analysis evidences the significant chiral activity for all halogen substitutions ranging from fluorine to iodine for both S and R enantiomers. These chiral and chiroptical characteristics of the triamantane enantiomers can be tuned well through various halogen substitutions. The absolute configurations for chiral triamantane molecules are identified through the Cahn-Ingold-Prelog rule together with VCD analysis. The optical rotatory dispersion (ORD) of chiral triamantane molecules is dominant for chlorine, bromine, and iodine substitutions. Chiral triamantane molecules with various halogen substitutions also find a prominent role in pharmacology through their anisotropic charge distribution and binding abilities, tunable lipophilicity, nominal synthetic accessibility, and good bioavailability score.</p><h3>Methods</h3><p>The absolute configurations for chiral triamantane molecules are identified through the Cahn-Ingold-Prelog rule. To study the chiroptical behavior of chiral triamantane molecules, wB97XD and M06-2X DFT functionals are employed, and for the initial guesses, 6-311G(d,p) and MidiX basis sets are used.</p></div>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":"31 7","pages":""},"PeriodicalIF":2.5,"publicationDate":"2025-06-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144293079","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":"Novel push–pull dyes with cyclic ring spacers (titanol, chromol, ferrol, nickelol, and zinkol): a DFT study for optoelectronic optimization in DSSCs","authors":"Mourad Zouaoui-Rabah,&nbsp;Abdelkader M. Elhorri,&nbsp;Madani Hedidi,&nbsp;Hicham Mahdjoub–Araibi,&nbsp;Laib Assia,&nbsp;Mahammed Zenati","doi":"10.1007/s00894-025-06414-8","DOIUrl":"10.1007/s00894-025-06414-8","url":null,"abstract":"<div><h3>Context</h3><p>This computational investigation delves into the strategic design of bimetallic Zn/M organometallic D–π–A dyes for dye-sensitized solar cells (DSSCs), with a focus on how transition metals (Ti, Cr, Fe, Ni) modulate optoelectronic behavior and photovoltaic performance. Employing density functional theory (DFT) and time-dependent DFT (TD–DFT) simulations, four dyes (Dye1–Dye4) were systematically evaluated for their light-harvesting efficiency (LHE), charge transfer kinetics, and stability under vacuum and tetrahydrofuran (THF) solvation. The results underscore distinct metal-dependent trade-offs: the chromium-based dye (Dye2) demonstrates outstanding visible-light absorption (λ_max = 570 nm) with a high LHE (85%) and oscillator strength (<i>f</i> = 0.830), whereas the nickel-based dye (Dye4) exhibits redshifted absorption (λ_max = 609 nm) and an extended excited-state lifetime (<i>τ</i> = 1.55 ns), advantageous for charge separation. Titanium (Dye1) and iron (Dye3) variants emerge as economical alternatives, offering moderate efficiency and stability. THF solvation induces pronounced bathochromic shifts (+ 138 nm for Dye1) and thermodynamically favorable interactions (ΔG_solv &lt;  − 61 kcal·mol⁻¹), enhancing light absorption and stability. Critical metrics such as electron injection energy (ΔG_inj), open-circuit voltage (V_oc), and regeneration energy (ΔG_reg) emphasize the need to harmonize optical performance with charge management. The study advocates co-sensitization of Dye2 and Dye4 to synergistically broaden spectral response and boost power conversion efficiency. These findings pave the way for sustainable DSSCs leveraging earth-abundant metals, aligning with global initiatives for green energy innovation.</p><h3>Method</h3><p>All calculations were performed with Gaussian 16. Ground state geometries were optimized by DFT with the B3LYP functional. The LanL2DZ basis set was used for transition metals, while 6–31 +  + G(d,p) was used for non-metallic atoms. The solvation models studied are the CPCM (Conductor Polarizable Continuum) model and the SMD (Solvation Model Density) model. Excited state properties have been calculated using TD-DFT with the CAM-B3LYP functional to evaluate electronic transitions.</p></div>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":"31 7","pages":""},"PeriodicalIF":2.5,"publicationDate":"2025-06-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144293080","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}