Physical Chemistry Chemical Physics最新文献

{"title":"Acetamide: a strange brew of structure, spectroscopy and theory.","authors":"Terri E Field-Theodore, Nicolò Quaresima, Peter R Taylor","doi":"10.1039/d6cp03082c","DOIUrl":"https://doi.org/10.1039/d6cp03082c","url":null,"abstract":"<p><p>The importance of acetamide in prebiotic chemistry and structural biology is well established. Possessing a peptide bond with characteristic resonance, it is expected on chemical grounds to adopt a planar framework (aside from the methyl hydrogens). Spectroscopy supports this assignment, yet high-level quantum chemical calculations predict a non-planar minimum. To investigate this discrepancy, we explore the underlying potential energy surface, focusing on the coupling between two large-amplitude motions: CH₃ rotation and NH₂ inversion. The resulting multidimensional landscape contains symmetry-related, non-planar <i>C</i>₁ minima connected through distinct interconversion pathways. Despite the predicted non-planarity, calculated rotational constants and fundamental vibrational frequencies agree closely with experiment, highlighting the distinction between equilibrium and spectroscopically inferred structures. Systematic comparisons with CCSD(T), MP2, and DFT, reveal that the shallow methyl torsional potential is particularly sensitive to the treatment of electron correlation and the choice of basis set. Fourier analysis further highlights the importance of higher-order terms and phase contributions, providing insight into the longstanding uncertainty surrounding the ground-state <i>A/E</i> splitting. More broadly, these findings emphasize the need to understand coupled large-amplitude motions when interpreting the structure and spectroscopy of flexible molecules of chemical, biological, and astrochemical interest.</p>","PeriodicalId":99,"journal":{"name":"Physical Chemistry Chemical Physics","volume":" ","pages":""},"PeriodicalIF":3.0,"publicationDate":"2026-11-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149339944","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}

{"title":"How laser wavelength and polarization shape the molecular Raman response enhanced by capped Ag nanoparticle chains","authors":"Emmanuel De los Santos Vázquez,Maxime Bayle,Frédéric Pailloux,David Babonneau,Bernard Humbert,Sophie CAMELIO","doi":"10.1039/d6cp02818g","DOIUrl":"https://doi.org/10.1039/d6cp02818g","url":null,"abstract":"Surface-enhanced Raman spectroscopy (SERS) sensors using capped Ag nanoparticle (NP) chains provide long-term stability and reusability. However this conguration distances the molecules from the plasmonic hot spots, thus decreasing the signal enhancement. This paper systematically investigates the SERS response of 2,2'-bipyridine (Bpy) molecules deposited on self-organized Ag NP chains capped with 5 nm-thick Al2O3 or SiOx films, fabricated via ion-beam sputtering. The substrates exhibit optical dichroism with two polarization-dependent localized surface plasmon resonances (LSPRs). SERS spectra, acquired under five excitation wavelengths (458-633 nm) and transverse/longitudinal polarization, reveal two distinct contributions: (i) a continuous background from the Ag NPs and dielectric host, and (ii) Raman peaks from Bpy vibrational modes. While the background intensity and shape depend on both wavelength and polarization, the Bpy peak magnitudes are primarily governed by the excitation wavelength, with a unique molecular fingerprint for each wavelength. Finite-Difference Time-Domain simulations confirm that the Raman signal is amplified by electromagnetic field enhancement driven by both LSPRs, regardless of incident polarization, due to the spatial and directional variability of the local electric field at the capping layer/air interface.","PeriodicalId":99,"journal":{"name":"Physical Chemistry Chemical Physics","volume":"21 1","pages":""},"PeriodicalIF":3.3,"publicationDate":"2026-11-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149360404","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}

{"title":"F-loss dynamics of CH2F2+ in the A2B2/B2A1 and C2A2 states using threshold photoelectron-photoion coincidence imaging","authors":"Xinlang Yang,Ying Liu,Tongpo Yu,Ruilang Fan,Xiaoguo Zhou","doi":"10.1039/d6cp03507h","DOIUrl":"https://doi.org/10.1039/d6cp03507h","url":null,"abstract":"The C–F bond cleavage dynamics of CH2F2+ in the A2B2/B2A1 and C2A2 states have been investigated using threshold photoelectron-photoion coincidence (TPEPICO) velocity map imaging combined with potential energy curve calculations. At the A2B2/B2A1 band (15.026 eV), the time-sliced image of the CH2F+ fragment exhibits a narrow total kinetic energy release (TKER) distribution with an average energy partitioning fT = 0.61, in excellent agreement with the impulsive model, and an anisotropy parameter β = 0.72, indicating a direct, rapid dissociation. This mechanism is fully supported by calculated F-loss potential curves, which show low or negligible adiabatic barriers for C–F rupture on these states. In contrast, at the C2A2 state (15.874 eV), the TKER distribution is significantly broader with fT = 0.36 and β = 0.51, suggesting an indirect process. The calculated bound potential well of the C2A2 state indicates that internal conversion to the lower-lying A2B2/B2A1 states precedes C–F bond cleavage, consistent with the broader vibrational populations observed in the CH2F+ fragment. This combined experimental and theoretical study provides a clear state-selective picture of the F-loss dynamics in CH2F2+, highlighting the distinct dissociation pathways of the excited ionic states.","PeriodicalId":99,"journal":{"name":"Physical Chemistry Chemical Physics","volume":"34 1","pages":""},"PeriodicalIF":3.3,"publicationDate":"2026-11-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149360405","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}

{"title":"Stimuli-responsive 2D assemblies of nitrogen-functionalized tris-stilbene derivatives.","authors":"Jan Patrick Calupitan, Juba Salhi, Jonathan Long, Nicolas Fabre, David Kreher, Imad Arfaoui, Florence Volatron","doi":"10.1039/d6cp00741d","DOIUrl":"https://doi.org/10.1039/d6cp00741d","url":null,"abstract":"<p><p>1,3,5-Tris[(<i>E</i>)-2-(3,5-didodecyloxyphenyl)-ethynyl]-benzene (TSB) and its derivatives are valuable molecules due to their ability to self-assemble on solid substrates and to act as templates for the organization of functional molecules or nano-objects. Although TSB has been extensively studied as a supramolecular seed, the description of new derivatives bearing functional groups remains scarce and investigations into their responsiveness to various stimuli are still limited. In this work, we report the preparation of a new TSB derivative functionalized with pyridine groups on the peripheral rings. Its responsiveness to different stimuli, such as temperature and chemical activation, is studied and compared with that of a TSB derivative based on a central triazine core. The latter undergoes a hexagonal-to-rhombic lattice structural change under annealing, but no structural change occurs with acidic treatment, whereas the TSB derivative with pyridine groups on the peripheral rings shows inertness under annealing and hexagonal-to-rhombic lattice structural rearrangement in the presence of acetic acid. We observe in both cases the emergence of a network with a very large-scale periodicity after the application of stimuli, and notice that molecular functionalization plays a crucial role in the responsiveness of the system.</p>","PeriodicalId":99,"journal":{"name":"Physical Chemistry Chemical Physics","volume":" ","pages":""},"PeriodicalIF":3.0,"publicationDate":"2026-11-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149339945","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}

{"title":"From probability redistribution to vibrational spectra: a vibrational-FELDS study of liquid water.","authors":"Nobuhiro Miura","doi":"10.1039/d6cp03071h","DOIUrl":"https://doi.org/10.1039/d6cp03071h","url":null,"abstract":"<p><p>Vibrational spectra are commonly interpreted in terms of vibrational frequencies, peak positions, and empirical spectral assignments. However, the relationship between intermolecular interactions, molecular structure, vibrational dynamics, and spectroscopic observables often remains indirect. In the present study, we propose and demonstrate vibrational free-energy-landscape-derived spectroscopic dynamics (Vibrational-FELDS), a framework that connects molecular probability distributions, free-energy landscapes, molecular structure, vibrational dynamics, and vibrational spectra within a unified theoretical description. Using molecular dynamics simulations of a charge-free intramolecular reference and liquid water based on the flexible q-TIP4P/F model, probability distributions were constructed for the symmetric stretching, antisymmetric stretching, and bending observation coordinates. The corresponding vibrational free-energy landscapes were obtained through the Boltzmann relation. Comparison between reference and liquid water revealed that intermolecular interactions redistribute probability primarily along the symmetric stretching coordinate, resulting in characteristic deformations of the vibrational free-energy landscape. The deformation of the free-energy landscape produced corresponding shifts in equilibrium coordinates and reductions in effective force constants. Structural information and characteristic vibrational frequencies were derived directly from the free-energy minima and their local curvatures. Infrared intensities were evaluated independently from the coordinate dependence of the molecular dipole moment, thereby separating vibrational dynamics from spectroscopic sensitivity. The resulting IR-FELDS spectrum exhibited a dominant stretching band accompanied by a shoulder arising from the antisymmetric stretching contribution. These spectral features emerged naturally from probability redistribution, free-energy-landscape deformation, vibrational dynamics, and observation sensitivity. A central result of Vibrational-FELDS is that molecular dynamics and spectroscopic visibility are treated as distinct quantities. The free-energy landscape determines the underlying vibrational motion, whereas spectral intensity is governed by the sensitivity of the observable. Vibrational spectra are therefore interpreted as observable manifestations of free-energy-landscape-derived dynamics rather than as primary quantities. The present results establish the sequence intermolecular interactions → <i>P</i>(<i>q</i>) → <i>F</i>(<i>q</i>) → structure → vibration → sensitivity → <i>S</i>(<i>ν</i>). Within this sequence, the spectrum is an observational representation of free-energy-landscape-derived dynamics, not a fitted reproduction of the experimental band shape.</p>","PeriodicalId":99,"journal":{"name":"Physical Chemistry Chemical Physics","volume":" ","pages":""},"PeriodicalIF":3.0,"publicationDate":"2026-11-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149356977","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}

{"title":"Colloidal Interaction Energy Barrier Approach to Make Spherical ZrO 2 Suspensions Time-dependent in Ageing -Slow Bonding Effect","authors":"Yee-Kwong Leong","doi":"10.1039/d6cp03246j","DOIUrl":"https://doi.org/10.1039/d6cp03246j","url":null,"abstract":"The spontaneous increase of gel strength of suspension in ageing and stepdown shear stress response in observable timescale was postulated to be due to slow particulate bonding in forming the network. The exploitation of the DLVO energy barrier near the flocculated -disperse state transition point slowed the particulate bonding sufficiently to cause the suspension to display structure rebuilding time-dependent behavior in both modes. This behavior was obtained with homogeneously charged spherical ZrO2 suspension at solids volume fraction of 0.15. In ageing, the yield stress increased by ~ 9-folds over a period of ~100 min. The stepdown shear stress response showed an immediate sharp increase over a short period, followed by a more gradual increase heading towards a steady state. The imposed low shear hastened strong bond formation and the structural recovery process.","PeriodicalId":99,"journal":{"name":"Physical Chemistry Chemical Physics","volume":"64 1","pages":""},"PeriodicalIF":3.3,"publicationDate":"2026-11-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149360070","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}

{"title":"Doping, defect engineering, and hybridization of metal oxides for multifunctional applications.","authors":"Samia Alyami, Ramzi Dhahri, Arwa Alyami, Kenany Brens Elkenany","doi":"10.1039/d6cp03898k","DOIUrl":"https://doi.org/10.1039/d6cp03898k","url":null,"abstract":"<p><p>Metal oxides have attracted sustained interest as versatile functional materials because their structural, optical, electrical, and surface properties can be tailored for a wide range of technological applications. In particular, doping, defect engineering, nanostructuring, and hybridization through heterostructure formation, composite design, and surface decoration provide effective routes for tuning their physicochemical properties and improving their functional performance. This review presents an overview of modified metal oxides and oxide-based hybrid materials, with emphasis on the relationship between their composition, structure, defects, interfaces, and resulting properties. Here, hybridization refers to combining metal oxides with distinct functional components, including carbon materials, metal-organic frameworks, other semiconductors, and metallic nanoparticles. These approaches are distinguished from lattice doping and ion intercalation to clarify their different contributions to material performance. The discussion first considers structural and morphological evolution, optical behavior, and electrical and charge-transport characteristics, providing a foundation for understanding the origin of their enhanced performance. Recent progress in environmental applications is then highlighted, particularly photocatalytic degradation and water treatment, followed by developments in gas and chemical sensing. The review further examines the growing role of modified metal oxides and their hybrids in energy technologies, including rechargeable batteries, supercapacitors, and solar-energy conversion, with particular attention to charge-transfer processes, interfacial effects, defect chemistry, and compositional optimization. Finally, the remaining challenges associated with stability, reproducibility, dopant and defect control, interfacial compatibility, scalability, and practical implementation are discussed, together with emerging opportunities for multifunctional and integrated metal-oxide systems. Overall, this review provides a materials-oriented perspective on how rational control of composition, defects, interfaces, and architecture can advance metal oxides toward more efficient, durable, and scalable technologies.</p>","PeriodicalId":99,"journal":{"name":"Physical Chemistry Chemical Physics","volume":" ","pages":""},"PeriodicalIF":3.0,"publicationDate":"2026-11-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149331761","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}

{"title":"Fatty alcohol bilayers mimic phospholipid membranes for rapid prediction of membrane permeability of small drug-like molecules.","authors":"Huong Thi Lan Nguyen, Nur Afiqah Ahmad, Jan Kazimierz Marzinek, Peter John Bond, Junming Ho","doi":"10.1039/d6cp02889f","DOIUrl":"https://doi.org/10.1039/d6cp02889f","url":null,"abstract":"<p><p>Passive membrane permeation is an important consideration in drug development. However, permeability coefficients obtained from atomistic molecular dynamics (MD) simulations are much too costly for routine use in the drug discovery pipeline. In this paper, we demonstrate that fatty alcohols such as dodecanol bilayers can reproduce key transmembrane free energy features that govern passive permeation in phospholipid bilayers for a wide range of hydrophilic, hydrophobic and amphiphilic solutes with molecular weights up to 400 Da. The dodecanol bilayers remain stable over the simulation timescales required for potentials of mean force calculations. The strong correlation between permeability coefficients (log <i>P</i>_m) and the transmembrane permeation barrier was exploited to develop a regression model that can potentially reduce computational cost by about 300-fold relative to a POPC umbrella sampling simulation. This regression model uses the dodecanol transmembrane barrier as input and is demonstrated to efficiently recover phospholipid MD-predicted log <i>P</i>_m values with an average prediction error of approximately 0.39 log units across 41 diverse solutes. For compounds with available experimental data, we showed that the regression model can generally reproduce experimental log <i>P</i>_m values to within 1 to 2 log units. We further compared this method with alternative approaches based on an anisotropic implicit solvent model (PerMM) and Martini coarse-grained simulations. Our findings suggest complementary strategies to accelerate computational prediction of phospholipid membrane permeability using atomic-resolution MD simulations.</p>","PeriodicalId":99,"journal":{"name":"Physical Chemistry Chemical Physics","volume":" ","pages":""},"PeriodicalIF":3.0,"publicationDate":"2026-11-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149331762","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}

{"title":"Data-Driven Structure-Spectrum Mapping of a Heterogeneous miRNA Ensemble","authors":"Monika Michaelis,Laura Thiessen,Beatriz Santos-Carballal,Lucio Colombi Ciacchi,Massimo Delle Piane","doi":"10.1039/d6cp02631a","DOIUrl":"https://doi.org/10.1039/d6cp02631a","url":null,"abstract":"Short regulatory RNAs populate heterogeneous conformational ensembles in which recurrent local motifs can be difficult to resolve from ensemble-averaged observables. Here, we combine synchrotron circular dichroism (CD), enhanced-sampling molecular dynamics, CD back-calculation, and descriptor-based clustering to map hsa-miR-145 conformations onto their spectral signatures. The hsa-miR-145 duplex provides a reference in which compact A-form-like states produce helical CD profiles, whereas loss of hybridization attenuates and broadens the spectra. In contrast, hsa-miR-145-5p remains highly heterogeneous and lacks persistent self-pairing. Cross-validation across nucleobase geometry, torsional, and spectral descriptors identifies recurrent compact-bend conformations stabilized by local non-Watson-Crick stacking. These conformers are associated with computed helical-like CD signatures, while other recurrent geometries are spectroscopically flat. The results show that local noncanonical stacking can generate CD-active conformational families in a flexible miRNA strand without canonical pairing.","PeriodicalId":99,"journal":{"name":"Physical Chemistry Chemical Physics","volume":"5 1","pages":""},"PeriodicalIF":3.3,"publicationDate":"2026-11-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149359956","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}

{"title":"Hydroxyl group substitution influences the recognition of non-canonical DNA structures by natural flavonoids.","authors":"Manikul Islam Sk, Sagar Bag, Aman Ahmad Siddiqui, Souvik Ghosal, Mangal Deep Burman, Sudipta Bhowmik","doi":"10.1039/d6cp03316d","DOIUrl":"https://doi.org/10.1039/d6cp03316d","url":null,"abstract":"<p><p>Non-canonical DNA structures, especially G-quadruplexes (GQ) and i-motifs, have been identified as significant biological targets for cancer therapy because of their critical roles in telomere maintenance, gene regulation, and oncogene activation. Natural small molecules, particularly flavonoids, have attracted considerable attention for their ability to recognize and modulate these DNA constructions. This review examines how the number, position, and orientation of hydroxyl (-OH) groups influence the interaction of these flavonoids with G-quadruplexes and i-motifs. Evidence from recent experimental and computational studies indicates that hydroxyl substitution influences molecular planarity, hydrogen-bond formation, π-π stacking, thermodynamic stability, and binding selectivity. In flavonoids, hydroxyl groups at specific positions, particularly in combination with molecular planarity, enhance recognition and stabilization of non-canonical DNA structures, whereas unfavourable substitutions may introduce steric hindrance and reduce binding affinity. This review further discusses the implications of hydroxyl-mediated interactions for drug design, emphasizing their potential to regulate oncogene promoters and telomeric DNA. Current challenges, including limited bioavailability, rapid metabolism, and insufficient physiological stability, are also highlighted, together with emerging strategies such as structural optimization, nanocarrier-based delivery, and biosensor development. Overall, understanding the role of hydroxyl group substitution provides valuable insights for the rational design of selective natural-product-based ligands targeting non-canonical DNA structures and supports the development of next-generation anticancer therapeutics.</p>","PeriodicalId":99,"journal":{"name":"Physical Chemistry Chemical Physics","volume":" ","pages":""},"PeriodicalIF":3.0,"publicationDate":"2026-11-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149331763","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}