Pub Date : 2026-02-11DOI: 10.1007/s00894-025-06578-3
Muhammad Khalid Shabir, Muhammad Naveed Anjum, Muhammad Jawwad Saif, Khurshid Ayub, Basit Niaz
Context
Efficient hole-transport materials and robust blue emitters remain bottlenecks in organic optoelectronics. We computationally designed and screened π-extended benzazaphosphole derivatives (1–9) to clarify how donor/acceptor substitution and conjugation control charge transport, emission, and nonlinear optical (NLO) response.
Methods
The series exhibits narrowed frontier orbital gaps (≈2–3 eV) consistent with intra-molecular charge transfer, blue shifted S1 → S0 fluorescence with substantial oscillator strengths and a systematic preference for hole transport (λh < λe across the set). Stand out candidates include: 6, with an exceptional static first-order hyperpolarizability βtot ≈ 7.7 × 103 a.u., and 7, which shows low hole reorganization energy (λh ≈ 0.13 eV) together with balanced photophysics. Computed energy level alignment indicates compatibility with representative fullerene ETMs and common HTMs, supporting integration into OLED/OSC stacks. Collectively, 6–8 emerge as priority targets for experimental validation as blue emissive HTMs with strong NLO potential.
{"title":"Theoretical insights into charge transport and photophysical properties of conjugated azaphosphole scaffolds","authors":"Muhammad Khalid Shabir, Muhammad Naveed Anjum, Muhammad Jawwad Saif, Khurshid Ayub, Basit Niaz","doi":"10.1007/s00894-025-06578-3","DOIUrl":"10.1007/s00894-025-06578-3","url":null,"abstract":"<div><h3>Context</h3><p>Efficient hole-transport materials and robust blue emitters remain bottlenecks in organic optoelectronics. We computationally designed and screened π-extended benzazaphosphole derivatives (<b>1–9</b>) to clarify how donor/acceptor substitution and conjugation control charge transport, emission, and nonlinear optical (NLO) response.</p><h3>Methods</h3><p>The series exhibits narrowed frontier orbital gaps (≈2–3 eV) consistent with intra-molecular charge transfer, blue shifted S<sub>1</sub> → S<sub>0</sub> fluorescence with substantial oscillator strengths and a systematic preference for hole transport (<i>λh</i><b> < </b><i>λe</i> across the set). Stand out candidates include: <b>6</b>, with an exceptional static first-order hyperpolarizability <i>β</i><sub>tot</sub> ≈ 7.7 × 10<sup>3</sup> a.u., and <b>7</b>, which shows low hole reorganization energy (<i>λh</i> ≈ 0.13 eV) together with balanced photophysics. Computed energy level alignment indicates compatibility with representative fullerene ETMs and common HTMs, supporting integration into OLED/OSC stacks. Collectively, <b>6–8</b> emerge as priority targets for experimental validation as blue emissive HTMs with strong NLO potential.</p></div>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":"32 3","pages":""},"PeriodicalIF":2.5,"publicationDate":"2026-02-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1007/s00894-025-06578-3.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146155611","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}
Pub Date : 2026-02-10DOI: 10.1007/s00894-026-06641-7
Fatma Genç, Fatma Kandemirli
Context
The electronic distribution, aromatic properties, spectroscopic properties, and thermodynamic behaviors of the niclosamide compound, which has antiviral, antiparasitic, and anticancer potential properties, were interpreted in different environments.
Methods
All quantum chemical calculations were performed using density functional theory (DFT) with the B3LYP functional and 6-311++G(2d,2p) basis set with Gaussian 09 software in various phases. Thermodynamic parameters such as heat capacity, enthalpy, entropy, and Gibbs free energy of the nucleosamide molecule were calculated in various phases in the temperature range of 200–1000 K. Molecular surface analyses were performed to investigate the reactivity properties. The aromaticity of the benzene rings of the nucleosamide molecule was evaluated in various phases using HOMA indices. Orbital composition analysis with Mulliken partition was performed to determine the percentage contribution of atomic orbitals to HOMO and LUMO. Additionally, UV-Vis absorption spectra were examined in various phases to investigate the effects of solvent and environment on electronic transitions.
{"title":"Investigation of quantum chemical studies of niclosamide in different solvents using DFT calculations","authors":"Fatma Genç, Fatma Kandemirli","doi":"10.1007/s00894-026-06641-7","DOIUrl":"10.1007/s00894-026-06641-7","url":null,"abstract":"<div><h3>Context</h3><p>The electronic distribution, aromatic properties, spectroscopic properties, and thermodynamic behaviors of the niclosamide compound, which has antiviral, antiparasitic, and anticancer potential properties, were interpreted in different environments.</p><h3>Methods</h3><p>All quantum chemical calculations were performed using density functional theory (DFT) with the B3LYP functional and 6-311++G(2d,2p) basis set with Gaussian 09 software in various phases. Thermodynamic parameters such as heat capacity, enthalpy, entropy, and Gibbs free energy of the nucleosamide molecule were calculated in various phases in the temperature range of 200–1000 K. Molecular surface analyses were performed to investigate the reactivity properties. The aromaticity of the benzene rings of the nucleosamide molecule was evaluated in various phases using HOMA indices. Orbital composition analysis with Mulliken partition was performed to determine the percentage contribution of atomic orbitals to HOMO and LUMO. Additionally, UV-Vis absorption spectra were examined in various phases to investigate the effects of solvent and environment on electronic transitions.</p></div>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":"32 3","pages":""},"PeriodicalIF":2.5,"publicationDate":"2026-02-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146155458","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}
Elucidating the role of the hydrophobic groove in mineralocorticoid receptor (MR)–spironolactone interactions is important for structure-based drug design, receptor modulation, and the development of more selective MR antagonists. Despite the clinical importance of spironolactone, the contribution of the hydrophobic groove, particularly residues M807, F829, M845, C849, and M852, remains underexplored. Here, we demonstrate through molecular dynamic simulations that these hydrophobic residues, together with polar residue N770, stabilize the thioacetyl moiety of spironolactone. Binding free energy calculations of the hydrophobic groove, both with the complete binding site and with the groove alone, demonstrate the impact of the groove’s hydrophobicity along with the polar residues N770, Q776, and R817. Simulation results, supported by statistical analysis, highlight the groove’s structural and energetic significance. Site-directed mutagenesis targeting residues F829, M845, and C849 further clarifies their role in the binding mechanism, offering insights for rational drug design and biomarker development.
Methods
The crystal structure of the MR–spironolactone complex (PDB ID: 3VHU) was retrieved and mutated using COOT. Mutant complexes were constructed and subjected to 1 μs molecular dynamics simulations using GROMACS. Binding free energies were calculated via MM/PBSA. Residue–ligand interactions were analyzed from MD trajectories using LigPlot + and GROMACS tools. Statistical significance of residue contributions was assessed using ANOVA, comparing polar and hydrophobic residue mutations across simulated complexes.
{"title":"Intriguing the significance of hydrophobic groove by the inhibitory mechanism of mineralocorticoid receptor bound with spironolactone through mutations using long-range molecular dynamics simulations in conjunction with statistical analysis","authors":"Seshan Gunalan, Kanagasabai Somarathinam, Sekar Kanagaraj, Jaimohan S.M., Gugan Kothandan","doi":"10.1007/s00894-026-06639-1","DOIUrl":"10.1007/s00894-026-06639-1","url":null,"abstract":"<div><h3>Context</h3><p>Elucidating the role of the hydrophobic groove in mineralocorticoid receptor (MR)–spironolactone interactions is important for structure-based drug design, receptor modulation, and the development of more selective MR antagonists. Despite the clinical importance of spironolactone, the contribution of the hydrophobic groove, particularly residues M807, F829, M845, C849, and M852, remains underexplored. Here, we demonstrate through molecular dynamic simulations that these hydrophobic residues, together with polar residue N770, stabilize the thioacetyl moiety of spironolactone. Binding free energy calculations of the hydrophobic groove, both with the complete binding site and with the groove alone, demonstrate the impact of the groove’s hydrophobicity along with the polar residues N770, Q776, and R817. Simulation results, supported by statistical analysis, highlight the groove’s structural and energetic significance. Site-directed mutagenesis targeting residues F829, M845, and C849 further clarifies their role in the binding mechanism, offering insights for rational drug design and biomarker development.</p><h3>Methods</h3><p>The crystal structure of the MR–spironolactone complex (PDB ID: 3VHU) was retrieved and mutated using COOT. Mutant complexes were constructed and subjected to 1 μs molecular dynamics simulations using GROMACS. Binding free energies were calculated via MM/PBSA. Residue–ligand interactions were analyzed from MD trajectories using LigPlot + and GROMACS tools. Statistical significance of residue contributions was assessed using ANOVA, comparing polar and hydrophobic residue mutations across simulated complexes.</p></div>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":"32 3","pages":""},"PeriodicalIF":2.5,"publicationDate":"2026-02-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146148630","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}
Pub Date : 2026-02-10DOI: 10.1007/s00894-026-06649-z
Xu Xu, Yuanmin Wang, Wenjuan Yao
Context
The successful synthesis of MA2Z4 (M = Mo, W, Nb; A = Si, Ge; Z = P, As) material has recently attracted the interest of researchers. However, they are usually non-magnetic in nature. Based on this, we investigated the geometrical structures, electronic properties and magnetic properties of pure MoSi2P4 monolayers and MoSi2P4 monolayers adsorbed 3d transition metal elements by first principles. Our results show that pure MoSi2P4 is non-magnetic with a bandgap of 0.60 eV. After adsorbing the transition metal, the electronic structure of all the systems is changed, showing semiconducting or semi-metallic properties. Among these systems, Co, Cr, Fe, Mn, Ti, and V adsorption systems produced magnetic moments ranging from 1.09 μB to 4.38 μB, and all the remaining systems were calculated to be n-type doped except for the Co adsorption system, which was p-type doped. We have also calculated the magnetic anisotropy properties of all systems. Among them, the Co system exhibits the largest absolute value of 3.02 meV/f.u., which shows perpendicular magnetic anisotropy. Our calculations indicate the potential value of monolayer MoSi2P4 in the application of spintronic devices.
Computational method
This work uses the Vienna ab initio simulation package (VASP) software package based on density-functional theory (DFT) for structural optimization, static calculations, electronic structure and magnetic properties. The data were processed using the VASPKIT software package.
背景：MA2Z4 （M = Mo， W, Nb; A = Si, Ge; Z = P, As）材料的成功合成引起了研究人员的兴趣。然而，它们本质上通常是非磁性的。在此基础上，利用第一性原理研究了纯MoSi2P4单层膜和吸附三维过渡金属元素的MoSi2P4单层膜的几何结构、电子性能和磁性能。结果表明，纯MoSi2P4具有非磁性，带隙为0.60 eV。在吸附过渡金属后，所有体系的电子结构都发生了变化，表现出半导体或半金属性质。其中Co、Cr、Fe、Mn、Ti和V吸附体系产生的磁矩范围为1.09 ~ 4.38 μB，除Co吸附体系为p型掺杂外，其余体系均为n型掺杂。我们还计算了所有体系的磁各向异性。其中Co系的绝对值最大，为3.02 meV/f.u。，显示出垂直的磁各向异性。我们的计算表明了单层MoSi2P4在自旋电子器件应用中的潜在价值。计算方法：本工作使用基于密度泛函理论（DFT）的Vienna ab initio simulation package （VASP）软件包进行结构优化、静态计算、电子结构和磁性能。使用VASPKIT软件包对数据进行处理。
{"title":"Electronic and magnetic properties of 3 d transition-metal adsorbed monolayer MoSi2P4","authors":"Xu Xu, Yuanmin Wang, Wenjuan Yao","doi":"10.1007/s00894-026-06649-z","DOIUrl":"10.1007/s00894-026-06649-z","url":null,"abstract":"<div><h3>Context</h3><p>The successful synthesis of MA<sub>2</sub>Z<sub>4</sub> (M = Mo, W, Nb; A = Si, Ge; Z = P, As) material has recently attracted the interest of researchers. However, they are usually non-magnetic in nature. Based on this, we investigated the geometrical structures, electronic properties and magnetic properties of pure MoSi<sub>2</sub>P<sub>4</sub> monolayers and MoSi<sub>2</sub>P<sub>4</sub> monolayers adsorbed 3d transition metal elements by first principles. Our results show that pure MoSi<sub>2</sub>P<sub>4</sub> is non-magnetic with a bandgap of 0.60 eV. After adsorbing the transition metal, the electronic structure of all the systems is changed, showing semiconducting or semi-metallic properties. Among these systems, Co, Cr, Fe, Mn, Ti, and V adsorption systems produced magnetic moments ranging from 1.09 μB to 4.38 μB, and all the remaining systems were calculated to be n-type doped except for the Co adsorption system, which was p-type doped. We have also calculated the magnetic anisotropy properties of all systems. Among them, the Co system exhibits the largest absolute value of 3.02 meV/f.u., which shows perpendicular magnetic anisotropy. Our calculations indicate the potential value of monolayer MoSi<sub>2</sub>P<sub>4</sub> in the application of spintronic devices.</p><h3>Computational method</h3><p>This work uses the Vienna ab initio simulation package (VASP) software package based on density-functional theory (DFT) for structural optimization, static calculations, electronic structure and magnetic properties. The data were processed using the VASPKIT software package.</p></div>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":"32 3","pages":""},"PeriodicalIF":2.5,"publicationDate":"2026-02-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146148613","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}
Recent outbreaks of the Zika virus (ZIKV) worldwide have underscored its growing epidemiological significance, leading to its recognition as an international health concern. The steady annual rise in ZIKV cases has transformed it into a major challenge for global public health systems. Despite ongoing efforts, the development of effective therapeutic agents against the virus remains difficult. Among the promising avenues for treatment are natural products, particularly those derived from medicinal and aromatic plants.
Methods
These substances act as reservoirs of beneficial chemical compounds that can contribute to developing effective therapies. This work used computer methods to examine 26 bioactive molecules derived from plants as potential Zika inhibitors. Baicalin, epicatechin gallate, epigallocatechin gallate, isoquercetin, and sophoroflavenone are plant-derived bioactive molecules that have demonstrated significant stability at the active site of the receptor examined (PDB code: 5TFR). They provided intense binding energies and were also stabilized at the active site of the target receptor by standard hydrogen bonds. These results were validated by molecular dynamics simulation at 500 ns. The molecules chosen to meet essential therapeutic criteria, such as those of Lipinski, have good ADMET characteristics and are not toxic. As a result, they have excellent pharmacokinetic properties and appreciable bioavailability. The findings of this research strongly suggest that these five molecules could be potential inhibitors of anti-Zika action in the future.
{"title":"Computational investigation of medicinal plants’ active ingredient effects as a potential Zika virus treatment: molecular docking, molecular dynamics simulations, ADMET screening, and DFT","authors":"Farid Elbamtari, Etibaria Belghalia, Khadija Zaki, Marwa Alaqarbeh, Abdelkrim Guendouzi, M’barek Choukrad, Abdelouahid Sbai, Mohammed Bouachrine, Tahar Lakhlifi","doi":"10.1007/s00894-025-06558-7","DOIUrl":"10.1007/s00894-025-06558-7","url":null,"abstract":"<div><h3>Context</h3><p>Recent outbreaks of the Zika virus (ZIKV) worldwide have underscored its growing epidemiological significance, leading to its recognition as an international health concern. The steady annual rise in ZIKV cases has transformed it into a major challenge for global public health systems. Despite ongoing efforts, the development of effective therapeutic agents against the virus remains difficult. Among the promising avenues for treatment are natural products, particularly those derived from medicinal and aromatic plants.</p><h3>Methods</h3><p>These substances act as reservoirs of beneficial chemical compounds that can contribute to developing effective therapies. This work used computer methods to examine 26 bioactive molecules derived from plants as potential Zika inhibitors. Baicalin, epicatechin gallate, epigallocatechin gallate, isoquercetin, and sophoroflavenone are plant-derived bioactive molecules that have demonstrated significant stability at the active site of the receptor examined (PDB code: 5TFR). They provided intense binding energies and were also stabilized at the active site of the target receptor by standard hydrogen bonds. These results were validated by molecular dynamics simulation at 500 ns. The molecules chosen to meet essential therapeutic criteria, such as those of Lipinski, have good ADMET characteristics and are not toxic. As a result, they have excellent pharmacokinetic properties and appreciable bioavailability. The findings of this research strongly suggest that these five molecules could be potential inhibitors of anti-Zika action in the future.</p></div>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":"32 3","pages":""},"PeriodicalIF":2.5,"publicationDate":"2026-02-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146111786","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}
Pub Date : 2026-02-04DOI: 10.1007/s00894-026-06637-3
Moses Udoisoh, Temitope Esther Olajide
Context
Chirality-induced spin selectivity (CISS) represents a remarkable quantum phenomenon whereby electron transmission through chiral molecules, such as DNA, becomes intrinsically spin-polarized even in the absence of magnetic fields. Despite extensive experimental verification of static CISS effects, achieving dynamic control over spin polarization remains an open challenge. Terahertz (THz) radiation offers a promising route to externally modulate molecular electronic structure on sub-picosecond timescales. In this study, we develop a theoretical model that unifies THz-driven Floquet dynamics with the spin–orbit coupling inherent to chiral DNA, thereby introducing the concept of Floquet–CISS, a light-induced regime of topologically controlled spin transport in biological helices.
Method
An effective low-energy Hamiltonian incorporating kinetic motion along the DNA helix, spin–orbit coupling, and the interaction with circularly polarized THz fields was formulated and solved using Floquet theory. The resulting quasi-energy spectra, Berry curvature, and spin polarization were numerically evaluated using plane-wave expansion and LAPACK-based diagonalization. The simulations reveal that THz fields dynamically reshape the Berry curvature, induce tunable spin-split Floquet bands, and produce helicity-dependent spin polarization exceeding 60%. These effects arise entirely from light-matter coupling without magnetic components, establishing DNA as a bio-topological spin filter capable of ultrafast, reversible spin control. The Floquet–CISS mechanism provides a theoretical blueprint for THz-programmable molecular spintronics and paves the way toward optically reconfigurable bio-quantum devices.
{"title":"Terahertz-induced Berry curvature control of spin-selective transport in chiral DNA molecules","authors":"Moses Udoisoh, Temitope Esther Olajide","doi":"10.1007/s00894-026-06637-3","DOIUrl":"10.1007/s00894-026-06637-3","url":null,"abstract":"<div><h3>Context</h3><p>Chirality-induced spin selectivity (CISS) represents a remarkable quantum phenomenon whereby electron transmission through chiral molecules, such as DNA, becomes intrinsically spin-polarized even in the absence of magnetic fields. Despite extensive experimental verification of static CISS effects, achieving <i>dynamic</i> control over spin polarization remains an open challenge. Terahertz (THz) radiation offers a promising route to externally modulate molecular electronic structure on sub-picosecond timescales. In this study, we develop a theoretical model that unifies THz-driven Floquet dynamics with the spin–orbit coupling inherent to chiral DNA, thereby introducing the concept of Floquet–CISS, a light-induced regime of topologically controlled spin transport in biological helices.</p><h3>Method</h3><p>An effective low-energy Hamiltonian incorporating kinetic motion along the DNA helix, spin–orbit coupling, and the interaction with circularly polarized THz fields was formulated and solved using Floquet theory. The resulting quasi-energy spectra, Berry curvature, and spin polarization were numerically evaluated using plane-wave expansion and LAPACK-based diagonalization. The simulations reveal that THz fields dynamically reshape the Berry curvature, induce tunable spin-split Floquet bands, and produce helicity-dependent spin polarization exceeding 60%. These effects arise entirely from light-matter coupling without magnetic components, establishing DNA as a bio-topological spin filter capable of ultrafast, reversible spin control. The Floquet–CISS mechanism provides a theoretical blueprint for THz-programmable molecular spintronics and paves the way toward optically reconfigurable bio-quantum devices.\u0000</p></div>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":"32 3","pages":""},"PeriodicalIF":2.5,"publicationDate":"2026-02-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146111807","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}
Pub Date : 2026-02-03DOI: 10.1007/s00894-026-06630-w
Mahesh Kumar Gupta, Santosh Kumar Rai, Vinay Panwar, R. P. Mahapatra, Abhishek Tevatia
Context
In the present work, the investigation of polycrystalline nanomaterials has been extended to a specific nanoalloy of copper and tantalum having a 9:1 atomic concentration. The study aims to analyze the influence of temperature and average grain size (AGS) on the mechanical behavior of the polycrystalline Cu-Ta nanoalloy. The results indicate that the critical grain size of polycrystalline 9Cu-Ta is smaller than that of pure Cu. The critical grain size of polycrystalline Cu (6.86 nm) is reduced to 3.89 nm with the addition of approximately 10% Ta atoms. This reduction is attributed to the combined effects of dislocation slip and subgrain strengthening mechanisms. Furthermore, the investigation highlights the variation of mechanical properties with increasing temperature and the influence of temperature on the critical grain size. The analysis also reveals the existence of distinct plastic deformation mechanisms corresponding to the critical grain size in the polycrystalline Cu-Ta nanoalloy.
Methods
Molecular dynamic simulation has been carried out under a fixed strain rate of 1.0 × 1010 s−1 for specifically analyzing the effect of temperature and average grain size (AGS) of the polycrystalline nanoalloy using embedded atom method potential (EAM). The polycrystalline structures with different grain sizes were generated using the Voronoi construction method. Simulations were carried out to evaluate the effect of temperature and grain size on the deformation behavior. The obtained data were analyzed to determine the critical grain size, variation in mechanical properties, and the associated deformation mechanisms of the polycrystalline 9Cu-Ta alloy.
{"title":"Effect of nanoalloying on dynamic thermophysical response of polycrystalline copper-tantalum","authors":"Mahesh Kumar Gupta, Santosh Kumar Rai, Vinay Panwar, R. P. Mahapatra, Abhishek Tevatia","doi":"10.1007/s00894-026-06630-w","DOIUrl":"10.1007/s00894-026-06630-w","url":null,"abstract":"<div><h3>Context</h3><p>In the present work, the investigation of polycrystalline nanomaterials has been extended to a specific nanoalloy of copper and tantalum having a 9:1 atomic concentration. The study aims to analyze the influence of temperature and average grain size (AGS) on the mechanical behavior of the polycrystalline Cu-Ta nanoalloy. The results indicate that the critical grain size of polycrystalline 9Cu-Ta is smaller than that of pure Cu. The critical grain size of polycrystalline Cu (6.86 nm) is reduced to 3.89 nm with the addition of approximately 10% Ta atoms. This reduction is attributed to the combined effects of dislocation slip and subgrain strengthening mechanisms. Furthermore, the investigation highlights the variation of mechanical properties with increasing temperature and the influence of temperature on the critical grain size. The analysis also reveals the existence of distinct plastic deformation mechanisms corresponding to the critical grain size in the polycrystalline Cu-Ta nanoalloy.</p><h3>Methods</h3><p>Molecular dynamic simulation has been carried out under a fixed strain rate of 1.0 × 10<sup>10</sup> s<sup>−1</sup> for specifically analyzing the effect of temperature and average grain size (AGS) of the polycrystalline nanoalloy using embedded atom method potential (EAM). The polycrystalline structures with different grain sizes were generated using the Voronoi construction method. Simulations were carried out to evaluate the effect of temperature and grain size on the deformation behavior. The obtained data were analyzed to determine the critical grain size, variation in mechanical properties, and the associated deformation mechanisms of the polycrystalline 9Cu-Ta alloy.\u0000</p></div>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":"32 3","pages":""},"PeriodicalIF":2.5,"publicationDate":"2026-02-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146099219","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}
Pub Date : 2026-02-03DOI: 10.1007/s00894-025-06626-y
Farooq Afzaal, Rashid Jalil, Ibtsam Riaz, Nawaz Muhammad, G. Murtaza, Maha Naeem, Muhammad Moin, Hafiz Irfan Ali
Context
Double perovskites have emerged as promising candidates for renewable energy technologies due to their structural simplicity and thermodynamic stability. Among them, K2AgRhF6 is the most stable (-2.54 eV/atom), consistent with its highest bulk modulus (64.15 GPa), tolerance factor (0.85), and octahedral factor (0.86). Elastic analysis indicates ductile behavior for K2AgRhF6 (ν = 0.35, B/G = 3.13) and K2AgRhBr6 (ν = 0.28, B/G = 1.99), while K2AgRhCl6 (ν = 0.26, B/G = 1.75) and K2AgRhI6 (ν = 0.13, B/G = 2.37) lie near the brittle-ductile threshold. Band structure calculations reveal semiconducting gaps of 2.56 eV (F), 2.03 eV (Cl), 1.44 eV (Br), and 0.55 eV (I), with K2AgRhBr6 and K2AgRhI6 exhibiting strong optical absorption in the visible spectrum. Thermoelectric analysis yields figures of merit approaching 0.75 at room temperature across the series, highlighting their efficiency in energy conversion. Collectively, these findings position K2AgRhX6 halide double perovskites as robust, lead-free multifunctional materials with integrated structural stability, tunable optoelectronic response, and promising thermoelectric efficiency for next-generation optoelectronic devices.
Method
In this work, density functional theory (DFT) calculations within the WIEN2k framework were used to explore the structural, mechanical, electronic, optical, and thermoelectric properties of halide-based double perovskites K2AgRhX6 (X = F, Cl, Br, I). All compounds crystallize in the cubic Fm3ˉm (225) space group, and their negative formation energies confirm thermodynamic stability.
{"title":"First-principles insights into lead-free K2AgRhX6 (X = F, Cl, Br, I) halide double perovskites as stable platforms for next-generation optoelectronic and energy conversion devices","authors":"Farooq Afzaal, Rashid Jalil, Ibtsam Riaz, Nawaz Muhammad, G. Murtaza, Maha Naeem, Muhammad Moin, Hafiz Irfan Ali","doi":"10.1007/s00894-025-06626-y","DOIUrl":"10.1007/s00894-025-06626-y","url":null,"abstract":"<div><h3>Context</h3><p>Double perovskites have emerged as promising candidates for renewable energy technologies due to their structural simplicity and thermodynamic stability. Among them, K<sub>2</sub>AgRhF<sub>6</sub> is the most stable (-2.54 eV/atom), consistent with its highest bulk modulus (64.15 GPa), tolerance factor (0.85), and octahedral factor (0.86). Elastic analysis indicates ductile behavior for K<sub>2</sub>AgRhF<sub>6</sub> (ν = 0.35, B/G = 3.13) and K<sub>2</sub>AgRhBr<sub>6</sub> (ν = 0.28, B/G = 1.99), while K<sub>2</sub>AgRhCl<sub>6</sub> (ν = 0.26, B/G = 1.75) and K<sub>2</sub>AgRhI<sub>6</sub> (ν = 0.13, B/G = 2.37) lie near the brittle-ductile threshold. Band structure calculations reveal semiconducting gaps of 2.56 eV (F), 2.03 eV (Cl), 1.44 eV (Br), and 0.55 eV (I), with K<sub>2</sub>AgRhBr<sub>6</sub> and K<sub>2</sub>AgRhI<sub>6</sub> exhibiting strong optical absorption in the visible spectrum. Thermoelectric analysis yields figures of merit approaching 0.75 at room temperature across the series, highlighting their efficiency in energy conversion. Collectively, these findings position K<sub>2</sub>AgRhX<sub>6</sub> halide double perovskites as robust, lead-free multifunctional materials with integrated structural stability, tunable optoelectronic response, and promising thermoelectric efficiency for next-generation optoelectronic devices.</p><h3>Method</h3><p>In this work, density functional theory (DFT) calculations within the WIEN2k framework were used to explore the structural, mechanical, electronic, optical, and thermoelectric properties of halide-based double perovskites K<sub>2</sub>AgRhX<sub>6</sub> (X = F, Cl, Br, I). All compounds crystallize in the cubic Fm3ˉm (225) space group, and their negative formation energies confirm thermodynamic stability.</p></div>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":"32 3","pages":""},"PeriodicalIF":2.5,"publicationDate":"2026-02-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146099221","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}
Indigo dyes are historically significant and possess a unique π-conjugated core, making them valuable for both traditional pigments and emerging applications in organic electronics. A fundamental challenge is understanding how subtle molecular modifications, particularly substituent effects, quantitatively influence their conjugation extent and resulting color properties. This study systematically investigates the parent indigo and three N, N′-substituted derivatives (phenyl, ethyl, and vinyl) to elucidate the precise relationship between molecular structure, electronic properties, and visible light absorption. Density functional theory (DFT) and Time-dependent DFT (TD-DFT) calculations reveal how substituents modulate the HOMO–LUMO gap and intramolecular interactions, directly correlating with calculated absorption wavelengths (628 to 807 nm) and predicted colors (medium blue to green-cyan) via complementary color theory. These findings provide a quantitative framework for designing indigo-based dyes with targeted optical properties, including near-infrared absorption.
Methods
Density functional theory (DFT) and time-dependent DFT (TD-DFT) calculations were performed. Ground-state geometry optimizations and frequency calculations were carried out using the B3LYP-D3(BJ) functional with the def2TZVP basis set. Excited-state calculations employed the CAM-B3LYP-D3(BJ)/def2TZVP level, with the IEFPCM solvation model simulating aqueous conditions. The Multiwfn 3.8 and VMD 1.9.3 software packages were used for interaction region indicator (IRI) analysis, electrostatic potential (ESP) mapping, electron density difference (EDD) analysis, hole–electron analysis, and color prediction based on absorption spectra.
靛蓝染料具有重要的历史意义，具有独特的π共轭核，使其在传统颜料和有机电子领域的新兴应用中都有价值。一个基本的挑战是理解细微的分子修饰，特别是取代基效应，如何定量地影响它们的共轭程度和所产生的颜色性质。本研究系统地研究了母体靛蓝和三个N， N '取代衍生物（苯基，乙基和乙烯基），以阐明分子结构，电子性质和可见光吸收之间的精确关系。密度泛函理论（DFT）和时间依赖DFT （TD-DFT）计算揭示了取代基如何调节HOMO-LUMO间隙和分子内相互作用，直接与计算的吸收波长（628至807 nm）和通过互补色理论预测的颜色（中蓝至绿青色）相关。这些发现为设计具有目标光学特性（包括近红外吸收）的靛蓝基染料提供了定量框架。方法进行密度泛函理论（DFT）和时变DFT （TD-DFT）计算。利用def2TZVP基集的B3LYP-D3（BJ）泛函进行了基态几何优化和频率计算。激发态计算采用CAM-B3LYP-D3(BJ)/def2TZVP水平，IEFPCM溶剂化模型模拟水溶液条件。采用Multiwfn 3.8和VMD 1.9.3软件包进行相互作用区指示（IRI）分析、静电电位（ESP）作图、电子密度差（EDD）分析、空穴电子分析和基于吸收光谱的颜色预测。
{"title":"Analysis of molecular conjugation influence on color characteristics of indigo compounds","authors":"Zengbo Ke, Jiahao Zhang, Hao Li, Xiaolong Li, Chengfang Qiao, Youying Di","doi":"10.1007/s00894-026-06638-2","DOIUrl":"10.1007/s00894-026-06638-2","url":null,"abstract":"<div><h3>Context</h3><p>Indigo dyes are historically significant and possess a unique π-conjugated core, making them valuable for both traditional pigments and emerging applications in organic electronics. A fundamental challenge is understanding how subtle molecular modifications, particularly substituent effects, quantitatively influence their conjugation extent and resulting color properties. This study systematically investigates the parent indigo and three <i>N</i>, <i>N</i>′-substituted derivatives (phenyl, ethyl, and vinyl) to elucidate the precise relationship between molecular structure, electronic properties, and visible light absorption. Density functional theory (DFT) and Time-dependent DFT (TD-DFT) calculations reveal how substituents modulate the HOMO–LUMO gap and intramolecular interactions, directly correlating with calculated absorption wavelengths (628 to 807 nm) and predicted colors (medium blue to green-cyan) via complementary color theory. These findings provide a quantitative framework for designing indigo-based dyes with targeted optical properties, including near-infrared absorption.</p><h3>Methods</h3><p>Density functional theory (DFT) and time-dependent DFT (TD-DFT) calculations were performed. Ground-state geometry optimizations and frequency calculations were carried out using the B3LYP-D3(BJ) functional with the def2TZVP basis set. Excited-state calculations employed the CAM-B3LYP-D3(BJ)/def2TZVP level, with the IEFPCM solvation model simulating aqueous conditions. The Multiwfn 3.8 and VMD 1.9.3 software packages were used for interaction region indicator (IRI) analysis, electrostatic potential (ESP) mapping, electron density difference (EDD) analysis, hole–electron analysis, and color prediction based on absorption spectra.</p></div>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":"32 3","pages":""},"PeriodicalIF":2.5,"publicationDate":"2026-02-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146099216","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}
A modified attachment energy model combined with classical molecular dynamics simulations is employed to study the solvent-dependent crystal growth of α-CL-20 in six solvent systems commonly used for the preparation of CL-20: maleic acid, pentaerythritol, glycine, citric acid, polyvinyl alcohol, and butyl carbamate. Surface roughness is quantified via the ratio of solvent-accessible area to geometric cross-sectional area, and electrostatic potential maps and radial distribution functions are used to characterize the polarity and non-bonded interactions at the interfaces. The results show that the interactions between α-CL-20 and solvent are dominated by hydrogen bonding, with some contributions from van der Waals contacts. The calculation results based on modified attachment energy theory show that in all six solvent systems, the growth of the (021) face is substantially inhibited, while the (020), (102), (111), and (002) faces tend to remain as persistent, moderately growing facets. The predicted morphologies in solutions evolve from the prismatic vacuum habit toward nearly polyhedral, spheroidal crystals, which suggest that strong, face-selective hydrogen bonding on rough, polar faces can serve as an effective microscopic mechanism for solvent-based morphology engineering of CL-20.
The Materials Studio software was used to calculate crystal growth, electrostatic potential, and radial distribution functions of α-CL-20. The VISTA software was used to predict morphologies of α-CL-20 in six solutions.
{"title":"Effect of single-solvent systems on the predicted crystal morphology of α-CL-20: a molecular dynamics and modified attachment energy study","authors":"Zhijiang Yue, Zhenfeng Jia, Qingying Duan, Shan Sha, Xianfeng Wei","doi":"10.1007/s00894-026-06643-5","DOIUrl":"10.1007/s00894-026-06643-5","url":null,"abstract":"<p>A modified attachment energy model combined with classical molecular dynamics simulations is employed to study the solvent-dependent crystal growth of α-CL-20 in six solvent systems commonly used for the preparation of CL-20: maleic acid, pentaerythritol, glycine, citric acid, polyvinyl alcohol, and butyl carbamate. Surface roughness is quantified via the ratio of solvent-accessible area to geometric cross-sectional area, and electrostatic potential maps and radial distribution functions are used to characterize the polarity and non-bonded interactions at the interfaces. The results show that the interactions between α-CL-20 and solvent are dominated by hydrogen bonding, with some contributions from van der Waals contacts. The calculation results based on modified attachment energy theory show that in all six solvent systems, the growth of the (021) face is substantially inhibited, while the (020), (102), (111), and (002) faces tend to remain as persistent, moderately growing facets. The predicted morphologies in solutions evolve from the prismatic vacuum habit toward nearly polyhedral, spheroidal crystals, which suggest that strong, face-selective hydrogen bonding on rough, polar faces can serve as an effective microscopic mechanism for solvent-based morphology engineering of CL-20.</p><p>The Materials Studio software was used to calculate crystal growth, electrostatic potential, and radial distribution functions of α-CL-20. The VISTA software was used to predict morphologies of α-CL-20 in six solutions.</p>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":"32 3","pages":""},"PeriodicalIF":2.5,"publicationDate":"2026-02-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146099218","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}
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