Physical Chemistry Chemical Physics最新文献

VaporFit: An Open-Source Software for Accurate Atmospheric Correction of FTIR Spectra VaporFit：用于FTIR光谱精确大气校正的开源软件

IF 3.3 3区化学

Physical Chemistry Chemical Physics Pub Date : 2025-05-30 DOI: 10.1039/d5cp01007a

Przemysław Pastwa, Piotr Bruździak

{"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}

引用次数: 0

A machine learning-driven prediction of Hammett constants using quantum chemical and structural descriptors 使用量子化学和结构描述符的哈米特常数的机器学习驱动预测

IF 3.3 3区化学

Physical Chemistry Chemical Physics Pub Date : 2025-05-30 DOI: 10.1039/d5cp01184a

Vaneet Saini, Ranjeet Kumar

{"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}

引用次数: 0

Structural stability of chromophore-grafted Ubiquitin mutants in vacuum. 真空中泛素发色团接枝突变体的结构稳定性。

IF 3.3 3区化学

Physical Chemistry Chemical Physics Pub Date : 2025-05-30 DOI: 10.1039/d5cp01297j

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}

引用次数: 0

Correlation Between Domain Size and Charge Transport Properties in Benzothiadiazole–Thiophene Molecules: Insights from Nano-Focus X-Ray Scattering and Fast Scanning Chip Calorimetry 苯并噻唑-噻吩分子的畴大小与电荷输运性质的关系：来自纳米聚焦x射线散射和快速扫描芯片量热法的见解

IF 3.3 3区化学

Physical Chemistry Chemical Physics Pub Date : 2025-05-30 DOI: 10.1039/d5cp00876j

Azaliia Akhkiamova, Ainur F. Abukaev, Mariia V. Gaikovich, Iliya E. Kuznetsov, Alexey Piryazev, Ilya I. Rulev, Alexander V Akkuratov, Denis Anokhin, Dimitri A. Ivanov

引用次数: 0

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 中等光学带隙能量对电子器件用Ce离子掺杂NiFe2O4纳米粒子介电性能影响的研究：掺杂浓度的影响

IF 3.3 3区化学

Physical Chemistry Chemical Physics Pub Date : 2025-05-30 DOI: 10.1039/d5cp00923e

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 Ni1−xCexFe2O4 (x = 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 NiFe2O4 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 x = 0.10 doping concentration of Ce ions. The optical band gap energy decreased with the upsurge in the substitution of Ce ions in NiFe2O4 nanoparticles. The insertion of Ce ions in NiFe2O4 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 NiFe2O4 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 (x = 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}

引用次数: 0

MXenes enhance electrocatalytic water electrolysis of NiFe layered double hydroxides through bifunctional heterostructuring MXenes通过双功能异质结构增强了NiFe层状双氢氧化物的电催化水解

IF 3.3 3区化学

Physical Chemistry Chemical Physics Pub Date : 2025-05-30 DOI: 10.1039/d5cp01202c

Nannan Li, Xiaotong Han, Ho Seok Park, Jin Yong Lee

{"title":"MXenes enhance electrocatalytic water electrolysis of NiFe layered double hydroxides through bifunctional heterostructuring","authors":"Nannan Li, Xiaotong Han, Ho Seok Park, Jin Yong Lee","doi":"10.1039/d5cp01202c","DOIUrl":"https://doi.org/10.1039/d5cp01202c","url":null,"abstract":"Transition metal-based layered double hydroxides (TM-LDHs) are among the most promising catalytic materials for the electrochemical reactions involved in energy conversion and storage technology. We systematically investigate NiFe-LDH-based electrocatalysts toward application in water electrolysis. We start with the highly accurate advanced density functional theory description of NiFe-LDH’s fundamental properties, and demonstrate that coupling spin-polarized p-band or d-band center model with the Gibbs free energy calculations explains NiFe-LDH’s oxygen evolution reaction (OER) mechanism. By involving the related transition states, the reversible oxygen vacancy assisted reaction mechanism has been directly observed and motivated by the high spin transition metal impurity which is further confirmed by time-consuming hybrid functional method. To further facilitate the electrocatalytic activity of NiFe-LDH, we study NiFe-LDH/MXenes heterostructures where the essential semiconductor-to-metallic transition takes place by the additional Ti-3d orbitals and the interfacial non-covalent interaction between the two catalysts. On the basis of calculated results, we propose a link between microscopic properties and macroscopic electrocatalytic kinetics of heterogenous electrocatalysts. Accurately describing the electronic and magnetic structures of electrocatalysts leads us to a step-by-step process for tailoring desired electrocatalytic property, especially for the high spin state contained TM-LDHs. A descriptor based on combination of the calculated d-band center of transition metal and p-band center of oxygen is the key to predicting electrochemical activity and stability of oxides electrocatalyst. From our results, we establish a design strategy for NiFe-LDH-based bifunctional electrocatalyst fabrication.","PeriodicalId":99,"journal":{"name":"Physical Chemistry Chemical Physics","volume":"244 1","pages":""},"PeriodicalIF":3.3,"publicationDate":"2025-05-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144183846","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

Proposing Explainable Descriptors Towards Enhanced N2 Reduction Performance on the Two-Dimensional Bismuthine Nanosheets Modified by P-block Element-based Electrocatalysts p -嵌段元素基电催化剂修饰二维铋纳米片增强N2还原性能的可解释描述符

IF 3.3 3区化学

Physical Chemistry Chemical Physics Pub Date : 2025-05-30 DOI: 10.1039/d5cp01837d

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}

引用次数: 0

Structural dynamics of wild-type p53 DNA-binding domain and hotspot mutants reveal oncogenic conformational shifts 野生型p53 dna结合域和热点突变体的结构动力学揭示了致癌构象的变化

IF 3.3 3区化学

Physical Chemistry Chemical Physics Pub Date : 2025-05-30 DOI: 10.1039/d5cp01257k

Ziqian Zhao, Gang Wang, Xiaoxiao Wu, Zhenyu Qian

{"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}

引用次数: 0

Influence of Molecular Orientation on Photovoltaic Performance in Double Donor with Fullerene and Non-Fullerene Acceptors based Heterojunctions 分子取向对基于富勒烯和非富勒烯受体异质结的双给体光伏性能的影响

IF 3.3 3区化学

Physical Chemistry Chemical Physics Pub Date : 2025-05-30 DOI: 10.1039/d5cp00849b

Susanta Mahapatra, Mohd Shavez

{"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}

引用次数: 0

The Poisson Equation and Polarization Charge Density in the Concentration Gradient of a Diffusing Electrolyte 扩散电解质浓度梯度中的泊松方程和极化电荷密度

IF 3.3 3区化学

Physical Chemistry Chemical Physics Pub Date : 2025-05-29 DOI: 10.1039/d5cp00787a

Gerald S. Manning

引用次数: 0