Physical Chemistry Chemical Physics最新文献

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Molecular-scale corrugation and wall chemistry regulate amphiphilic self-assembly in nanotubes
IF 3.3 3区 化学
Physical Chemistry Chemical Physics Pub Date : 2026-11-10 DOI: 10.1039/d6cp03597c
Noriyoshi Arai,Takahiro Yokoyama,Arash Nikoubashman
{"title":"Molecular-scale corrugation and wall chemistry regulate amphiphilic self-assembly in nanotubes","authors":"Noriyoshi Arai,Takahiro Yokoyama,Arash Nikoubashman","doi":"10.1039/d6cp03597c","DOIUrl":"https://doi.org/10.1039/d6cp03597c","url":null,"abstract":"The organisation of amphiphilic molecules in nanopores depends on both the wall chemistry and channel geometry at the molecular scale. To understand their combined effects, we performed dissipative particle dynamics simulations of five amphiphilic systems in sinusoidally corrugated nanotubes, varying wall chemistry, corrugation amplitude and period, as well as amphiphile concentration and architecture. To accelerate the simulations, we developed a smooth corrugated-wall potential based on a closed-form local-linear projection and validated it against frozen-particle walls. Hydrophobic walls drove direct tail adsorption, whereas hydrophilic walls shifted tail-rich domains towards the tube interior. For equal-interaction reference walls, increasing the corrugation amplitude relative to the molecular radius of gyration generally enhanced axial localisation beyond the geometric variation inherent to the sinusoidal channel, while the effect of corrugation period was weaker and architecture-specific. Flexible amphiphiles readily adsorbed to and followed the corrugated hydrophobic walls, whereas stiff molecules remained in aggregates with persistent internal structure. In binary mixtures of long and short amphiphiles, both components remained within common aggregates, but exhibited distinct preferences for radial wall association and axial localisation. Increasing amphiphile concentration progressively reduced chemistry- and architecture-selective localisation, as favourable regions became filled and crowding drove the system towards more space-filling distributions.","PeriodicalId":99,"journal":{"name":"Physical Chemistry Chemical Physics","volume":"19 1","pages":""},"PeriodicalIF":3.3,"publicationDate":"2026-11-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149374914","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Structural and electronic analysis of β-MoC doped with transition metals based on electronic structure calculations
IF 3.3 3区 化学
Physical Chemistry Chemical Physics Pub Date : 2026-11-10 DOI: 10.1039/d6cp02199a
Yutong Yu,Ángel Morales-García,Francesc Viñes,Lisheng Zhong,Francesc Illas
{"title":"Structural and electronic analysis of β-MoC doped with transition metals based on electronic structure calculations","authors":"Yutong Yu,Ángel Morales-García,Francesc Viñes,Lisheng Zhong,Francesc Illas","doi":"10.1039/d6cp02199a","DOIUrl":"https://doi.org/10.1039/d6cp02199a","url":null,"abstract":"A systematic density functional study (DFT) is carried out to assess the stability of orthorhombic molybdenum carbide (β-Mo2C) doped with 3d, 4d, and 5d transition metal (TM) elements. The doping energy trends are rationalized from electronic descriptors such as the work function (ϕ), d-band center (εd), first ionization energy (IE1) and projected density of states (PDOS). From an energetic point of view, a low ϕ of the doped system and a low IE1 of the doping TM favor doping. On the contrary, a high first ionization energy of the doping TM results in unfavorable β-Mo2C doping. The density of states analysis is consistent with the doping energy trends. In particular, the TM atoms in the middle of the transition series enhance the stability through the strong hybridization of metal d orbitals and C 2p orbitals. This promotes the electron delocalization of the d orbitals of TMs around the Fermi level, favoring the thermodynamic stability of the doped β-Mo2C. This comprehensive study can help experimentalists identify plausible doped transition metal carbide systems beyond the β-Mo2C case study presented here by analyzing the key electronic aspects of doping elements.","PeriodicalId":99,"journal":{"name":"Physical Chemistry Chemical Physics","volume":"10 1","pages":""},"PeriodicalIF":3.3,"publicationDate":"2026-11-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149374921","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Dimethylformamide formation via water bridge assisted C−N coupling between dimethylamine and CO₂ in water microdroplets
IF 3.3 3区 化学
Physical Chemistry Chemical Physics Pub Date : 2026-11-10 DOI: 10.1039/d6cp02513g
Pengju Wu,Yan Xu,Zhiheng Ma,Tianze Xu,Tianyang Liu,Yu Jing
{"title":"Dimethylformamide formation via water bridge assisted C−N coupling between dimethylamine and CO₂ in water microdroplets","authors":"Pengju Wu,Yan Xu,Zhiheng Ma,Tianze Xu,Tianyang Liu,Yu Jing","doi":"10.1039/d6cp02513g","DOIUrl":"https://doi.org/10.1039/d6cp02513g","url":null,"abstract":"Dimethylformamide (DMF) is a widely used industrial solvent and reagent, traditionally synthesized from carbon monoxide (CO) and dimethylamine (DMA) under harsh and energy-intensive conditions. Although alternative routes for DMF production are of growing interest, a fundamental understanding of how solvent environments actively mediate C-N coupling reactions remains limited. Aqueous microdroplets provide a unique interfacial setting in which strong electric fields and highly structured hydrogen-bonding networks emerge, offering an opportunity to probe reaction mechanisms inaccessible in bulk solution. Here, we demonstrate that DMF can form spontaneously from DMA and CO2 within aqueous microdroplets and use this transformation as a model system to interrogate interfacial water-assisted reactivity. Through a combination of quantum chemical calculations, ab initio molecular dynamics (AIMD) simulations, and mass spectrometry analysis, we show that intense interfacial electric fields promote DMA reduction, while water-mediated hydrogen-bonding networks substantially lower proton-transfer barriers along the reaction pathway. The cooperative interplay between these effects enables C-N coupling and DMF formation under ambient and catalyst-free conditions. This work provides molecular-level insight into how confined aqueous interfaces harness electric fields and water-bridged proton relays to reshape reaction energy landscapes, advancing the fundamental understanding of interfacial aqueous chemistry and highlights microdroplets as a powerful platform for uncovering water-assisted reaction mechanisms.","PeriodicalId":99,"journal":{"name":"Physical Chemistry Chemical Physics","volume":"88 1","pages":""},"PeriodicalIF":3.3,"publicationDate":"2026-11-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149374919","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Unveiling the electrocatalytic performance of h-AlN monolayer for nonaqueous Li–O batteries: a first-principles study
IF 3.3 3区 化学
Physical Chemistry Chemical Physics Pub Date : 2026-11-10 DOI: 10.1039/d6cp03043b
Darshil Chodvadiya,Izabela Zgłobicka,Dominik Kurzydłowski,Prafulla K. Jha,Krzysztof J. Kurzydłowski
{"title":"Unveiling the electrocatalytic performance of h-AlN monolayer for nonaqueous Li–O batteries: a first-principles study","authors":"Darshil Chodvadiya,Izabela Zgłobicka,Dominik Kurzydłowski,Prafulla K. Jha,Krzysztof J. Kurzydłowski","doi":"10.1039/d6cp03043b","DOIUrl":"https://doi.org/10.1039/d6cp03043b","url":null,"abstract":"Although nonaqueous lithium–oxygen (Li–O2) batteries (LOBs) possess an exceptionally high theoretical energy density, their practical application is hindered by sluggish oxygen reduction/evolution reaction (ORR/OER) kinetics, large charge–discharge voltage gaps, and poor reversibility of insulating discharge products. Herein, density functional theory (DFT) calculations were performed to evaluate the h-AlN monolayer as a noble-metal-free bifunctional cathode electrocatalyst for LOBs. The h-AlN monolayer exhibits excellent structural stability, confirmed by formation energy, phonon spectrum, and ab initio molecular dynamics (AIMD) analyses. Initial adsorption analysis reveals that O2 adsorption is thermodynamically preferred over Li adsorption, indicating an O2-initiated discharge mechanism. Subsequent adsorption and reaction-energy analyses demonstrate that the ORR proceeds preferentially through a four-electron pathway, *O2 → *LiO2 → *Li2O2 → *Li3O2 → *Li4O2, with *Li4O2 identified as the preferred surface-bound terminal state along the modelled four-electron pathway. Adsorption of Li–O intermediates introduces electronic states near the Fermi level, narrows the band gap, and enhances interfacial charge transport. Within the modelled surface-pathway thermodynamic framework, Gibbs free-energy calculations yield low discharge and charge overpotentials of 0.178 and 0.104 V, respectively, resulting in a total overpotential of only 0.282 V. Furthermore, dimethyl sulfoxide (DMSO) adsorption and AIMD analyses indicate good electrolyte compatibility over the simulated timescale. Overall, these findings establish h-AlN as a promising bifunctional electrocatalyst for nonaqueous LOBs.","PeriodicalId":99,"journal":{"name":"Physical Chemistry Chemical Physics","volume":"33 1","pages":""},"PeriodicalIF":3.3,"publicationDate":"2026-11-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149374932","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Self-Consistent Optical, Thermal, and Morphological Modeling of Gold Nanorod Reshaping under Nanosecond Laser Irradiation
IF 3.3 3区 化学
Physical Chemistry Chemical Physics Pub Date : 2026-11-10 DOI: 10.1039/d6cp03771b
W. Alexander Ooijevaar,Gaston David Godoy,Eduardo A. Coronado
{"title":"Self-Consistent Optical, Thermal, and Morphological Modeling of Gold Nanorod Reshaping under Nanosecond Laser Irradiation","authors":"W. Alexander Ooijevaar,Gaston David Godoy,Eduardo A. Coronado","doi":"10.1039/d6cp03771b","DOIUrl":"https://doi.org/10.1039/d6cp03771b","url":null,"abstract":"Wavelength-selective laser reshaping of gold nanorods (GNRs) provides a means of post-synthetically modifying plasmonic ensembles, yet a quantitative description linking the evolution of individual aspect-ratio populations to their time-dependent optical and thermal response remains lacking. Here, we combine extinction spectroscopy, transmission electron microscopy, electromagnetic sim- ulations, photothermal modeling, and surface-diffusion kinetics to establish a population-resolved framework for nanosecond laser reshaping of cetyltrimethylammonium bromide-stabilized (CTAB) GNRs. Sequential irradiation at 880 and 740 nm selectively transforms distinct nanorod subpopula- tions and progressively narrows the longitudinal plasmon band. Rather than describing these changes only through spectral shifts, the experimental extinction spectra are quantitatively reconstructed as weighted combinations of calculated responses for GNRs with different aspect ratios, allowing the redistribution of nanoparticle populations to be determined. A fully self-consistent optical thermal morphological model is used in which the instantaneous aspect ratio updates the absorption cross section, heat generation, temperature, surface dffusivity, and subsequent morphology at every inte- gration step. Electronic con nement reduces the absorption cross section and predicted photothermal temperature relative to bulk-optical descriptions, whereas the low thermal conductivity of the CTAB interfacial layer enhances transient heating by limiting heat dissipation to the aqueous environment. Under the experimental conditions investigated here, resonantly absorbing GNRs reach the melting regime before surface diffusion can produce the observed morphological evolution, while off -resonant populations remain far below the transformation threshold. These results establish a quantitative connection between single-particle optical thermal dynamics and ensemble-level spectral selection and plasmon-linewidth narrowing.","PeriodicalId":99,"journal":{"name":"Physical Chemistry Chemical Physics","volume":"23 1","pages":""},"PeriodicalIF":3.3,"publicationDate":"2026-11-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149374917","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
High-throughput DFT screening of glutathione-triggered drug release from Au, Ag, and Pt nanoclusters: metal-level selectivity and the limits of geometry-level screening
IF 3.3 3区 化学
Physical Chemistry Chemical Physics Pub Date : 2026-11-10 DOI: 10.1039/d6cp02394k
Saurav Mishra,Brijesh Kumar Pandey,Abhay P. Srivastava
{"title":"High-throughput DFT screening of glutathione-triggered drug release from Au, Ag, and Pt nanoclusters: metal-level selectivity and the limits of geometry-level screening","authors":"Saurav Mishra,Brijesh Kumar Pandey,Abhay P. Srivastava","doi":"10.1039/d6cp02394k","DOIUrl":"https://doi.org/10.1039/d6cp02394k","url":null,"abstract":"Glutathione (GSH)-responsive noble-metal nanoclusters exploit the ∼1000-fold intracellular GSH gradient between tumour and healthy tissue for selective drug release, but rational design of drug–metal pairings has lacked systematic binding data across chemical space. We screened 81 anticancer and drug-like molecules on icosahedral Au13, Ag13, and Pt13 nanoclusters (238 complexes) using dispersion-corrected density functional theory, mapping binding energies onto Boltzmann-weighted tumour selectivity indices. Charge and bond-order analysis reveals a mechanistic dichotomy: Au and Ag coordinate drugs through heteroatom σ-donation (N, O, S), whereas Pt forms η2–π complexes through carbon. Pt binds drugs at −61.4 kcal mol−1 on average, far beyond the strongest heteroatom donation in the dataset (≈−44 kcal mol−1), so no thiol competitor can displace π-bound cargo; Pt is therefore unsuitable as a GSH-triggered carrier, a conclusion robust to spin state, cluster charge, cluster size, basis-set superposition error and level of theory. Individual drug rankings are not. A 5.3 kcal mol−1 displacement-energy window defines tumour-selective release, and 32 complexes fall inside it at the screening level, but geometry relaxation, larger clusters, and corrected thiol-binding modes each dismantle these nominations; the combined uncertainties exceed the window itself, so the window is not resolvable at this level of theory. Machine learning reproduces the metal-level dichotomy but predicts within-carrier release only weakly. Carrier choice, not drug choice, is the reliable design variable, and candidate-level selectivity claims require full geometry optimisation and free-energy corrections.","PeriodicalId":99,"journal":{"name":"Physical Chemistry Chemical Physics","volume":"95 1","pages":""},"PeriodicalIF":3.3,"publicationDate":"2026-11-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149374922","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Sub-5 nm monolayer KNaGaP transistor: a first-principles quantum transport simulation
IF 3.3 3区 化学
Physical Chemistry Chemical Physics Pub Date : 2026-11-10 DOI: 10.1039/d6cp03411j
Daming Wu,Yuhao Pu,Xin Tian,Putian Wang,Le Yang,Tanxiao Wu,Jinxia Tian,Jianning Zhang,Xuemei Zhang,Linqiang Xu,Lianqiang Xu
{"title":"Sub-5 nm monolayer KNaGaP transistor: a first-principles quantum transport simulation","authors":"Daming Wu,Yuhao Pu,Xin Tian,Putian Wang,Le Yang,Tanxiao Wu,Jinxia Tian,Jianning Zhang,Xuemei Zhang,Linqiang Xu,Lianqiang Xu","doi":"10.1039/d6cp03411j","DOIUrl":"https://doi.org/10.1039/d6cp03411j","url":null,"abstract":"Monolayer (ML) K2NaGaP2 emerges as a highly promising two-dimensional (2D) channel material. Its unique quasi-one-dimensional chain-like configuration endows it with a moderate bandgap and ultrahigh carrier mobility, enabling a relatively high ballistic on-state current (Ion) while maintaining a low off-state leakage. Herein, we systematically evaluate the ultimate scaling potential of ML K2NaGaP2 metal-oxide-semiconductor field-effect transistors using first-principles quantum transport simulations. Our results reveal that the Ion, intrinsic delay, and power consumption of the ML K2NaGaP2 device can meet the strict IRDS targets for high-performance (HP) applications and high-density (HD) applications with gate lengths scaled down to 1 and 2 nm, respectively. In addition, the device exhibits an ultra-steep subthreshold swing strictly below the 60 mV dec−1 room-temperature limit due to quantum tunneling effects. Furthermore, comprehensive benchmarking at the 5 nm scale reveals that the ML K2NaGaP2 device achieves the highest Ion among all evaluated 2D candidates and a lower subthreshold swing than materials such as WSi2N4 and MoSi2N4. Additionally, under the HP standard, it achieves the lowest energy-delay product at the 1 nm gate length limit, comprehensively outperforming all evaluated materials including conventional MoS2. This study identifies ML K2NaGaP2 metal-oxide-semiconductor field-effect transistors as viable candidates for logic circuits at the sub-5 nm scale. Their combined electrostatic control and high on-state current make them a realistic alternative to silicon in advanced integrated circuits.","PeriodicalId":99,"journal":{"name":"Physical Chemistry Chemical Physics","volume":"12 1","pages":""},"PeriodicalIF":3.3,"publicationDate":"2026-11-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149374979","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Strain-tunable 2D Type-II PtS2/PtSSe van der Waals heterostructure with high carrier mobility for solar cell application
IF 3.3 3区 化学
Physical Chemistry Chemical Physics Pub Date : 2026-11-10 DOI: 10.1039/d6cp03870k
Xin Zhou,Xi Zhang,Feng Tang,Wenjie He,Ya Nie,Gang Xiang
{"title":"Strain-tunable 2D Type-II PtS2/PtSSe van der Waals heterostructure with high carrier mobility for solar cell application","authors":"Xin Zhou,Xi Zhang,Feng Tang,Wenjie He,Ya Nie,Gang Xiang","doi":"10.1039/d6cp03870k","DOIUrl":"https://doi.org/10.1039/d6cp03870k","url":null,"abstract":"The realization of two-dimensional (2D) van der Waals (vdW) heterostructures (HSs) with high optical absorption, superior carrier mobility, and ideal type-II band alignment is pivotal for photovoltaic applications. Using first-principles calculations, we systematically study 2D Janus PtS2/PtSSe HSs. We find that the S-Se interface (PtS2/SePtS) possesses an intrinsic type-II band alignment that enables efficient carrier separation, unlike the type-I alignment of the S-S interface (PtS2/SPtSe). Due to strong interlayer coupling, the pristine PtS2/SePtS HS demonstrates a maximum optical absorption of 23.96% and anisotropic ultrahigh carrier mobility surpassing 1×104 cm2 V-1 s-1. Furthermore, under -8% compressive strain, the intrinsic type-II band alignment is maintained while the maximum optical absorption increases to 27.62%. Kinetically, this strain significantly amplifies the transport disparity between electrons and holes, thereby facilitating rapid spatial carrier separation. Thermodynamically, the substantial reduction in the donor bandgap and conduction band offset effectively mitigates intrinsic interfacial energy losses, elevating the theoretical power conversion efficiency (PCE) to 15.50%. These findings not only provide insights into the Janus PtS2/SePtS HS but also establish it as a robust platform for high-efficiency solar cells.","PeriodicalId":99,"journal":{"name":"Physical Chemistry Chemical Physics","volume":"1 1","pages":""},"PeriodicalIF":3.3,"publicationDate":"2026-11-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149374915","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Structure–property relations on exchange couplings in distorted halide-bridged Gd() complexes
IF 3.3 3区 化学
Physical Chemistry Chemical Physics Pub Date : 2026-11-10 DOI: 10.1039/d6cp03565e
Christian F. Pachl,Karin Fink
{"title":"Structure–property relations on exchange couplings in distorted halide-bridged Gd() complexes","authors":"Christian F. Pachl,Karin Fink","doi":"10.1039/d6cp03565e","DOIUrl":"https://doi.org/10.1039/d6cp03565e","url":null,"abstract":"In comparison to transition metals, the connection between the bridging geometry and the magnetic exchange coupling constant J remains vague for Gd(iii)–Gd(iii) magnetic couplings. However, such couplings are an important feature, for example for compounds showing a strong magnetocaloric effect. In this study, a series of Gd2X6 (X = F, Cl, Br, I) was systematically distorted and the magnetic coupling calculated using broken-symmetry DFT. We find an inversely exponential metal–metal distance dependence as well as the dependence on a second structural parameter, either the Gd–X distance or the Gd–X–Gd angle. We compared these structural dependencies with different DFT-features. We furthermore find that the nature of terminal ligands has neglectable influence. Using these results, we showed that such simple model complexes can be used to predict the coupling in experimentally investigated complexes with the same bridge. This lets us conclude that it may be possible to effectively extract reasonable exchange coupling constants and Spin-Hamiltonians for larger Gd(iii)-clusters.","PeriodicalId":99,"journal":{"name":"Physical Chemistry Chemical Physics","volume":"5 1","pages":""},"PeriodicalIF":3.3,"publicationDate":"2026-11-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149374975","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Characterizing ligand-mediated conformational dynamics and state transitions of KRAS-G12C through machine learning and molecular dynamics simulations
IF 3.3 3区 化学
Physical Chemistry Chemical Physics Pub Date : 2026-11-10 DOI: 10.1039/d6cp03730e
Gopal Hema,Kandhan Palanisamy,Muthuramalingam Prakash
{"title":"Characterizing ligand-mediated conformational dynamics and state transitions of KRAS-G12C through machine learning and molecular dynamics simulations","authors":"Gopal Hema,Kandhan Palanisamy,Muthuramalingam Prakash","doi":"10.1039/d6cp03730e","DOIUrl":"https://doi.org/10.1039/d6cp03730e","url":null,"abstract":"KRAS mutations are major drivers of cancer initiation and progression, with KRAS G12C representing an important therapeutic target. In the present study, an integrated computational approach comprising machine learning-based virtual screening, molecular docking, molecular dynamics simulations, and Markov state modeling was utilized to identify potential allosteric inhibitors targeting the switch-II pocket of KRAS G12C. Supervised ML models were trained using a curated ChEMBL dataset, with the Random Forest classifier achieving the highest predictive performance for activity classification. The best-ranked compounds were evaluated using molecular docking. Triplicate 500 ns MD simulations demonstrated that complexes 5 and 115 maintained stable binding, exhibited reduced residue fluctuations, and formed persistent hydrogen-bond interactions. Our analysis demonstrated that the ligands strongly interacted with the key residues and reduced the flexibility of KRAS. Furthermore, MSM and tICA analyses showed that compound 115 stabilizes the coupled dynamics of the switch-I and switch-II regions through interactions with Thr36, Ile37, Glu38, Met68, Gln71, and Tyr72, promoting a highly populated inactive metastable state. Overall, compound 115 represents a promising lead scaffold for KRAS G12C inhibition and provides mechanistic insights for the rational design of next-generation anticancer therapeutics.","PeriodicalId":99,"journal":{"name":"Physical Chemistry Chemical Physics","volume":"19 1","pages":""},"PeriodicalIF":3.3,"publicationDate":"2026-11-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149374933","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
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