{"title":"VaporFit: An Open-Source Software for Accurate Atmospheric Correction of FTIR Spectra","authors":"Przemysław Pastwa, Piotr Bruździak","doi":"10.1039/d5cp01007a","DOIUrl":"https://doi.org/10.1039/d5cp01007a","url":null,"abstract":"This paper introduces VaporFit, an open-source software for automated atmospheric interference correction in Fourier-transform infrared (FTIR) spectroscopy, based on a refined correction algorithm. It significantly improves the accuracy and reproducibility of chemical and biological FTIR analysis by effectively removing variable contributions from water vapor and carbon dioxide that often obscure spectral features. Unlike traditional methods relying on subtraction of a single reference spectrum, which struggle with atmospheric variability, VaporFit employs a multispectral least-squares approach to automatically optimize subtraction coefficients based on multiple atmospheric measurements recorded throughout the experiment. The software provides a user-friendly graphical interface (GUI) and built-in tools, including objective smoothness metrics and a Principal Component Analysis (PCA) module, to facilitate parameter selection and intuitively evaluate correction quality. Furthermore, we offer practical recommendations for data acquisition strategies tailored for effective atmospheric correction. VaporFit, the user guide, and sample data sets are freely available at https://zenodo.org/records/15411176 and https://github.com/piobruzdpg/VaporFit/releases/tag/v1.0.","PeriodicalId":99,"journal":{"name":"Physical Chemistry Chemical Physics","volume":"6 1","pages":""},"PeriodicalIF":3.3,"publicationDate":"2025-05-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144177152","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":"A machine learning-driven prediction of Hammett constants using quantum chemical and structural descriptors","authors":"Vaneet Saini, Ranjeet Kumar","doi":"10.1039/d5cp01184a","DOIUrl":"https://doi.org/10.1039/d5cp01184a","url":null,"abstract":"Understanding and predicting chemical reaction behavior is a fundamental challenge in chemistry. The Hammett equation, introduced in 1935, has been a cornerstone in modelling structure-activity relationships, particularly in physical organic chemistry. This study leverages machine learning (ML) to predict Hammett constants (σm and σp) for a diverse set of benzoic acid derivatives. We developed an open-source dataset of over 900 molecules, including meta-, para-, and symmetrically substituted variants, and employed various ML models to predict Hammett constants. Quantum chemical descriptors, combined with Mordred-based electronic, steric, and topological descriptors, were used to train models such as Extra Trees (ET) and Artificial Neural Networks (ANNs). The ANN model achieved the highest accuracy, with a test R2 of 0.935 and an RMSE of 0.084, outperforming other models and a previously developed graph neural networks. Feature importance analysis revealed key descriptors, including NBO charges and HOMO energies, driving the predictions. Applicability domain (AD) analysis identified outliers and compounds outside the AD, ensuring model reliability. This work highlights the potential of ML in predicting Hammett constants, offering a robust tool for chemical reactivity analysis and molecular design.","PeriodicalId":99,"journal":{"name":"Physical Chemistry Chemical Physics","volume":"10 1","pages":""},"PeriodicalIF":3.3,"publicationDate":"2025-05-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144177311","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}
Emiliano De Santis, Thomas Mandl, Jocky C. K. Kung, Khon Huynh, Steven Daly, Lorenza A. D’Alessandro, Luke MacAleese, Charlotte Uetrecht, Erik Marklund, Carl Caleman
{"title":"Structural stability of chromophore-grafted Ubiquitin mutants in vacuum.","authors":"Emiliano De Santis, Thomas Mandl, Jocky C. K. Kung, Khon Huynh, Steven Daly, Lorenza A. D’Alessandro, Luke MacAleese, Charlotte Uetrecht, Erik Marklund, Carl Caleman","doi":"10.1039/d5cp01297j","DOIUrl":"https://doi.org/10.1039/d5cp01297j","url":null,"abstract":"Structural biology is witnessing a transformative era with gas-phase techniques such as native mass spectrometry (MS), ion mobility, and single-particle imaging (SPI) emerging as critical tools for studying biomolecular assemblies like protein capsids in their native states. SPI with X-ray free- electron lasers has the potential to allow for capturing atomic-resolution structures of proteins without crystallization. However, determining particle orientation during exposure remains a major challenge, compounded by the heterogeneity of the protein complexes. Gas-phase Förster resonance energy transfer (FRET) offers a promising solution to assess alignment-induced structural perturbations, providing insights into the stability of the tertiary structure under various activation methods. This study employs molecular dynamics (MD) simulations to explore chromophore integration’s effect on ubiquitin’s structure and alignment properties in vacuum. Ubiquitin serves as an ideal model due to its small size, well-characterized properties, and computational simplicity. By investigating chromophores placement, we identified optimal sites for monitoring gas-phase denaturation and unfolding processes, advancing SPI applications and a broader understanding of protein stability in the gas-phase.","PeriodicalId":99,"journal":{"name":"Physical Chemistry Chemical Physics","volume":"41 1","pages":""},"PeriodicalIF":3.3,"publicationDate":"2025-05-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144177151","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}
Azaliia Akhkiamova, Ainur F. Abukaev, Mariia V. Gaikovich, Iliya E. Kuznetsov, Alexey Piryazev, Ilya I. Rulev, Alexander V Akkuratov, Denis Anokhin, Dimitri A. Ivanov
{"title":"Correlation Between Domain Size and Charge Transport Properties in Benzothiadiazole–Thiophene Molecules: Insights from Nano-Focus X-Ray Scattering and Fast Scanning Chip Calorimetry","authors":"Azaliia Akhkiamova, Ainur F. Abukaev, Mariia V. Gaikovich, Iliya E. Kuznetsov, Alexey Piryazev, Ilya I. Rulev, Alexander V Akkuratov, Denis Anokhin, Dimitri A. Ivanov","doi":"10.1039/d5cp00876j","DOIUrl":"https://doi.org/10.1039/d5cp00876j","url":null,"abstract":"Conjugated compounds including thiophene and benzothiadiazole units are promising candidates for next-generation semiconductor materials. Precise control over morphology and crystal orientation is critical for optimizing device performance. By employing a combination of synchrotron nano-focus X-ray scattering and fast chip calorimetry, a correlation was established between the size of ordered domains formed during isothermal crystallization and charge carrier mobility. These findings highlight the potential of advanced in-situ techniques for fine-tuning the electronic properties of organic semiconductors.","PeriodicalId":99,"journal":{"name":"Physical Chemistry Chemical Physics","volume":"58 1","pages":""},"PeriodicalIF":3.3,"publicationDate":"2025-05-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144177148","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}
Abdulrahman I. Alharthi, Awais Khalid, Pervaiz Ahmad, Arshad Ali, Shahroz Saleem, Muhammad Adnan Munir
{"title":"A study on the role of moderate optical band gap energy in dielectric properties of NiFe2O4 nanoparticles by Ce ion doping for electronic device applications: the effect of doping concentration","authors":"Abdulrahman I. Alharthi, Awais Khalid, Pervaiz Ahmad, Arshad Ali, Shahroz Saleem, Muhammad Adnan Munir","doi":"10.1039/d5cp00923e","DOIUrl":"https://doi.org/10.1039/d5cp00923e","url":null,"abstract":"This research work employs a sol–gel process to prepare Ni<small><sub>1−<em>x</em></sub></small>Ce<small><sub><em>x</em></sub></small>Fe<small><sub>2</sub></small>O<small><sub>4</sub></small> (<em>x</em> = 0.00, 0.05, and 0.10) samples. Ce ion doping was performed to modify the optical band gap for tuning the dielectric properties of NiFe<small><sub>2</sub></small>O<small><sub>4</sub></small> for use in electronic device applications. XRD and Raman spectra confirm the formation and phase purity of synthesized samples. Increasing the concentration of Ce ion content increases the crystallite size in sintered ceramics, and then the crystallite size decreases with <em>x</em> = 0.10 doping concentration of Ce ions. The optical band gap energy decreased with the upsurge in the substitution of Ce ions in NiFe<small><sub>2</sub></small>O<small><sub>4</sub></small> nanoparticles. The insertion of Ce ions in NiFe<small><sub>2</sub></small>O<small><sub>4</sub></small> leads to the development of inter-granular boundaries, causing a decrease in resistivity and a drop in dielectric losses. The obtained spectra showed that the doping concentrations influenced the structural, optical, and dielectric characteristics of NiFe<small><sub>2</sub></small>O<small><sub>4</sub></small> nanoparticles. The dielectric investigation demonstrated frequency-dependent behavior with a consistent decrease in dielectric constant, permittivity, capacitance, resistivity, and impedance with increasing frequency. Tunable dielectric behavior with low dielectric loss in high-frequency and moderate band gap due to desired Ce ion concentration (<em>x</em> = 0.05) regimes makes them potential materials for applications in high-frequency devices, energy storage, and nanoelectronic devices.","PeriodicalId":99,"journal":{"name":"Physical Chemistry Chemical Physics","volume":"36 1","pages":""},"PeriodicalIF":3.3,"publicationDate":"2025-05-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144177212","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}
Zhongti Sun, Dengning Sun, Yangyang Wan, Guoqiang Liu, Ruirui Wang, Hao Shen, Jing Chen, Ying Wang, Xiaokun Du, Tao Ye
{"title":"Proposing Explainable Descriptors Towards Enhanced N2 Reduction Performance on the Two-Dimensional Bismuthine Nanosheets Modified by P-block Element-based Electrocatalysts","authors":"Zhongti Sun, Dengning Sun, Yangyang Wan, Guoqiang Liu, Ruirui Wang, Hao Shen, Jing Chen, Ying Wang, Xiaokun Du, Tao Ye","doi":"10.1039/d5cp01837d","DOIUrl":"https://doi.org/10.1039/d5cp01837d","url":null,"abstract":"P-block element-based electrocatalysts that feature tunable electronic structure to achieve exceptional N2 activation and proton suppression have garnered extensive interests in the electrochemical N2 reduction reaction (NRR). Albeit various reaction mechanisms were proposed to understand and optimize the NRR performance, the method to effectively design and rapidly screen potential candidates was still elusive. Herein, a couple of explicit and interpretable descriptors on the entire p-block element-based electrocatalysts are put forward to predict NRR activity and selectivity via high-throughput theoretical simulations and symbolic regression algorithm, taking two-dimensional (2D) bismuthine doped and adsorbed by p-block elements as an example. The descriptor is merely composed by inherent atomic properties (p orbital electron number, electron affinity, electronegativity, and atomic radius, etc.) combining with algebraic operators, independent on the intricated DFT calculations. Multi-task regression results demonstrate that the doped and adsorbed bismuthine system possess the same descriptor, namely, doped descriptor can primely forecast the NRR performance of adsorbed system, vice versa. Five potential candidates (5/40) with outstanding NRR activity, selectivity and stability are screened. C-doped and Si-doped bismuthine possess the less negative limiting potential of NRR [UL(NRR)] with 0.46 and 0.68 V and positive [UL(NRR)UL(HER)] value of 1.15 and 0.13 V, respectively, superior to the majority of reported p-block element-based electrocatalyst, which are expected to be verified by the experimental research. This work offers a feasible solution for developing promising NRR electrocatalysts and potentially other electrochemical reactions on the basis of explainable descriptor using geometric information and intrinsic atomic quantities.","PeriodicalId":99,"journal":{"name":"Physical Chemistry Chemical Physics","volume":"8 1","pages":""},"PeriodicalIF":3.3,"publicationDate":"2025-05-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144177149","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":"Structural dynamics of wild-type p53 DNA-binding domain and hotspot mutants reveal oncogenic conformational shifts","authors":"Ziqian Zhao, Gang Wang, Xiaoxiao Wu, Zhenyu Qian","doi":"10.1039/d5cp01257k","DOIUrl":"https://doi.org/10.1039/d5cp01257k","url":null,"abstract":"The tumor suppressor protein p53, widely known for the potency and diversity of its functions, acts as a critical barrier to tumorigenesis. Mutations in p53, particularly within its DNA-binding domain (DBD), compromise its tumor suppressing function in over 40% of human tumors. Diverse p53 mutants adopt three major types of oncogenic effects, namely loss-of-function effect, dominant-negative effect and gain-of-function effect. However, the conformational mechanisms by which hotspot mutations (e.g., R175H, R273H/C) drive p53 dysfunction remain elusive. Here, we performed microsecond-level molecular dynamics simulations to dissect the structural dynamics of wild-type p53DBD and three oncogenic mutants. In wild-type p53DBD, multi-state conformational switching of the L1 loop was governed by hydrophobic interactions (A119/V122-P278) and an intra-loop hydrogen bond network. Notably, a previously unidentified β-hairpin conformation within the L1 loop was discovered, suggesting a latent regulatory motif. Mutations at R273 disrupted the H2 α-helix integrity, inducing helix-to-coil transitions that destabilized the DNA-binding interface. In contrast, R175H mutation triggered allosteric flexibility in both L2 and L3 loops, distorting the DNA contact surface through synergistic loop rearrangements. Interaction network analysis further revealed that these mutations remodeled non-local residue couplings, with R273H/C primarily destabilizing local interactions and R175H perturbing long-range communication with the LSH motif. Our findings provide structural insights into wild-type p53’s complex activities and link mutation-specific conformational shifts to p53’s loss/gain-of-function phenotypes, offering new avenues for restoring p53 activity in cancers.","PeriodicalId":99,"journal":{"name":"Physical Chemistry Chemical Physics","volume":"19 1","pages":""},"PeriodicalIF":3.3,"publicationDate":"2025-05-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144177150","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":"Influence of Molecular Orientation on Photovoltaic Performance in Double Donor with Fullerene and Non-Fullerene Acceptors based Heterojunctions","authors":"Susanta Mahapatra, Mohd Shavez","doi":"10.1039/d5cp00849b","DOIUrl":"https://doi.org/10.1039/d5cp00849b","url":null,"abstract":"Benzodithiophene (BDT) and fullerene (C60)/non-fullerene (Y6) are donor and acceptor molecules, respectively, and are often used as organic photovoltaic (OPV) devices. In the present study, we employed density functional theory (DFT) and time-dependent DFT (TD-DFT) methodologies to explore various system orientations, focusing on structural characteristics, optoelectronic properties, and charge transfer dynamics. Our results reveal that systems with face-on-configurations exhibit deeper highest-occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO) energies. Non-fullerene based complexes (A4 to A6) exhibit greater negative ΔGCT values compared to the fullerene-based systems (A1 to A3). Systems with a face-on orientation molecule show higher charge transfer rates than those with an edge-on orientation. Notably, A1 and A4 have the faster charge transfer rate among fullerene and non-fullerene-based systems. Thus, these results suggest that the face-on-orientation alignment of C60 and Y6 with α and β BDT units can significantly enhance the efficiency and stability of OPVs.","PeriodicalId":99,"journal":{"name":"Physical Chemistry Chemical Physics","volume":"9 1","pages":""},"PeriodicalIF":3.3,"publicationDate":"2025-05-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144177153","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":"The Poisson Equation and Polarization Charge Density in the Concentration Gradient of a Diffusing Electrolyte","authors":"Gerald S. Manning","doi":"10.1039/d5cp00787a","DOIUrl":"https://doi.org/10.1039/d5cp00787a","url":null,"abstract":"The effect of a polarizable medium on the Poisson equation of electrostatics is usually expressed by multiplying the vacuum permittivity with a dimensionless factor called the dielectric constant. A more fundamental form of the Poisson equation, however, supplements the free charge density with a polarization charge. In the concentration gradient of a diffusing electrolyte the electroneutrality principle requires zero free charge density. The source of the electric field of a diffusing electrolyte is the charge density due to polarization of the ion distribution. The polarization charge density is proportional to the difference between the mobilities of the constituent ions and to the divergence of the gradient of the logarithm of electrolyte concentration.","PeriodicalId":99,"journal":{"name":"Physical Chemistry Chemical Physics","volume":"36 1","pages":""},"PeriodicalIF":3.3,"publicationDate":"2025-05-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144165247","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}
Selma Rabhi, Asif Nawaz Khan, Oualid Chinoune, Rania CHARIF, Nabil Bouri, Samah Al-Qaisi, Shima Sadaf, Amal Ali Baqais, MIR WAQAS ALAM
{"title":"Insight into NaSiCl3: A Lead-Free Perovskite for the Next Generation Revealed by DFT and SCAPS-1D","authors":"Selma Rabhi, Asif Nawaz Khan, Oualid Chinoune, Rania CHARIF, Nabil Bouri, Samah Al-Qaisi, Shima Sadaf, Amal Ali Baqais, MIR WAQAS ALAM","doi":"10.1039/d5cp01747e","DOIUrl":"https://doi.org/10.1039/d5cp01747e","url":null,"abstract":"This study theoretically explores the potential of lead-free NaSiCl3, a chloride-based perovskite, as a photovoltaic absorber. Using density functional theory (DFT) calculations via WIEN2k and CASTEP, alongside SCAPS-1D simulations, we assess the material’s suitability from both atomic and device perspectives. The results confirm that NaSiCl3 is structurally, thermodynamically, dynamically (via phonon dispersion), and mechanically stable. Detailed electronic, optical, and thermoelectric analyses further support its promise for optoelectronic applications. NaSiCl3 exhibits an indirect bandgap of 0.869 eV (PBE-GGA+TB-mBJ) and 1.307 eV (HSE06), with the latter aligning well with optimal values for efficient solar energy harvesting. The broad absorption range across the infrared and visible spectrum, combined with favorable optical constants, highlights its potential as a solar absorber. Furthermore, thermoelectric evaluations reveal strong performance at elevated temperatures, expanding its utility in high-temperature optoelectronic devices. Based on these DFT insights, a planar n-i-p perovskite solar cell incorporating NaSiCl3 was modeled in SCAPS-1D. Among the eight tested architectures, the FTO/SnS/NaSiCl3/Zn3P2/Ni configuration yielded a maximum power conversion efficiency of 27.11%. These findings not only establish NaSiCl3 as a highly promising, lead-free perovskite for next-generation solar cells but also provide a strong theoretical basis to guide future experimental synthesis and device fabrication.","PeriodicalId":99,"journal":{"name":"Physical Chemistry Chemical Physics","volume":"5 1","pages":""},"PeriodicalIF":3.3,"publicationDate":"2025-05-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144165252","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}