Computational and Theoretical Chemistry最新文献

{"title":"Size-dependent interactions between graphene quantum dots and multidrug resistance protein (MDR-1)","authors":"Mishael Gill ,&nbsp;Isaac Macwan","doi":"10.1016/j.comptc.2025.115527","DOIUrl":"10.1016/j.comptc.2025.115527","url":null,"abstract":"<div><div>MDR-1, a cellular efflux protein responsible for the transport of drugs and other pharmaceutical therapies, is known to increase resistance to chemotherapeutics in tumor cells. This hyperactivity reduces the efficacy of cancer treatment displaying a need to discover avenues of inhibition or downregulation of MDR-1. A more broadly effective potential substrate is the graphene quantum dot (GQD), which has been identified as a single inhibitor affecting multiple transporters associated with drug resistance. This study analyzed the interactions of three different-sized GQDs with MDR-1 using molecular dynamics to understand the effect of GQD size on the adsorption of MDR-1. Several stability and energy analyses indicated an optimal GQD size of 5 × 6 nm based on the information from the number of salt bridges, Van der Waals energy and the ratio of polar to hydrophobic amino acids pointing out that this GQD size is the optimal modulatory substrate for MDR-1.</div></div>","PeriodicalId":284,"journal":{"name":"Computational and Theoretical Chemistry","volume":"1254 ","pages":"Article 115527"},"PeriodicalIF":3.0,"publicationDate":"2025-10-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145263182","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":"DFT insights into proton–π interactions and their role in enhancing the basicity of benzo[h]quinoline amines","authors":"Hamid Saeidian ,&nbsp;Atefeh Javanmard ,&nbsp;Zohreh Mirjafary ,&nbsp;Morteza Rouhani","doi":"10.1016/j.comptc.2025.115501","DOIUrl":"10.1016/j.comptc.2025.115501","url":null,"abstract":"<div><div>In this study, the nature and strength of intramolecular proton–π (H⁺…π) interactions in a series of benzo [h]quinoline derivatives bearing an aryl group at carbon-6 were investigated using quantum chemical methods. The primary goal was to clarify the role of these interactions in stabilizing conjugate acids and their effects on the aromaticity of the involved rings. Density Functional Theory calculations were performed at the B3LYP/6–311 + G(d,p) level in the gas phase and solvent environments using the CPCM model. Thermodynamic analysis showed that proton affinity and gas-phase basicity significantly increased in the presence of electron-donating substituents on the aryl ring, such as amino group with proton affinity exceeding 1000 kJ/mol for compound <strong>5</strong>. In contrast, electron-withdrawing groups (e.g., nitro group) or heteroaromatic rings with low electron density notably decreased these values. Topological analysis based on the Atoms in Molecules framework confirmed bond critical points between the proton and aromatic carbon atoms, with electron density ρ(r) and potential energy density V(r) values indicating medium to strong H⁺…π interactions (20–26 kJ/mol). The strongest interactions were observed in the conjugate acids [<strong>4</strong> + H]⁺ and [<strong>5</strong> + H]⁺. Aromaticity indices-including HOMA, BI, PLR, PDI, and SA-consistently demonstrated a significant decrease in aromaticity and increased ring distortion upon protonation compared to neutral species. Finally, solvent effects showed that protonation tendency and conjugate acid stability increased in polar solvents such as water, while changes were less pronounced in nonpolar media. Overall, these results provide strong evidence for the presence and importance of intramolecular H⁺…π interactions in aromatic systems, highlighting their crucial role in conjugate acid stabilization, aromaticity reduction, and electronic density redistribution.</div></div>","PeriodicalId":284,"journal":{"name":"Computational and Theoretical Chemistry","volume":"1254 ","pages":"Article 115501"},"PeriodicalIF":3.0,"publicationDate":"2025-10-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145263179","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":"Study on the sensitivity of transition metal-modified WO3 materials toward triethylamine and H2S gases in food safety by density functional theory","authors":"Jianguo Hu ,&nbsp;Jingyan Gao ,&nbsp;Yu Cai ,&nbsp;Binghua Wang","doi":"10.1016/j.comptc.2025.115524","DOIUrl":"10.1016/j.comptc.2025.115524","url":null,"abstract":"<div><div>The corrupt triethylamine gas and H₂S gas in food safety pose a threat to food and human health. The development of efficient gas sensing materials can sensitively monitor these gases to ensure the safe development of the food industry. In this study, the sensitivity mechanism of transition metal Me (Me = Co, Fe, Mn, Ni) modified WO₃-based sensors was systematically investigated based on density functional theory (DFT). By calculating the adsorption energy, electronic structure and charge transfer characteristics of gas molecules on the modified WO₃ surface, it is found that the introduction of transition metal Me significantly enhances the chemical adsorption capacity of WO₃ for triethylamine and H₂S, and has higher charge transfer ability for H₂S and TEA. The analysis of electron density of states shows that the synergistic effect of Me metal and WO₃ interface reduces the valence band of WO₃–002 composite material and transforms into conductor. There are free electrons near Me atom, forming metal‑oxygen bonds with surrounding O atoms, which is more conducive to the migration of electrons. This change is more conducive to the adsorption of gas molecules and improves the selectivity of gas recognition. The transition metal modification strategy can effectively optimize the performance of WO₃-based sensors. This study provides a new idea for the design of food safety rapid detection devices.</div></div>","PeriodicalId":284,"journal":{"name":"Computational and Theoretical Chemistry","volume":"1254 ","pages":"Article 115524"},"PeriodicalIF":3.0,"publicationDate":"2025-10-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145263180","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":"Computational prediction of supramolecular assembly based on pentacopper(II) 12-MC-4 metallamacrocycles with 3-hydroxy-4-pyridinone moieties","authors":"Grigory Yu. Zhigulin,&nbsp;Marina A. Katkova,&nbsp;Sergey Yu. Ketkov","doi":"10.1016/j.comptc.2025.115523","DOIUrl":"10.1016/j.comptc.2025.115523","url":null,"abstract":"<div><div>DFT calculations predict an association of the copper(II)-containing β-alaninehydroxamic 12-metallacrown-4 (12-MC-4) and cuprate derivatives of the 3-hydroxy-4-pyridinones (3,4-HPs) in molecular ensembles. Noncovalent interactions forming the ensembles are analyzed with QTAIM and RDG approaches. Among the crucial contacts revealed are hydrogen bonds of the NH₂⋯OC(O) type and apical Cu<img>O interactions. Differences between the coordination environments of the central Cu²⁺ ion in 12-MC-4 and cuprates are displayed by ELF. Possible patterns of an ensemble arrangement in a crystal phase are suggested. On the basis of spatial structures formed by the NH₂⋯OC(O) and Cu<img>O interactions and computed dipole moments, the patterns are predicted to be of 1D and 2D packing. Energy changes on formation of corresponding molecular ensembles from separate 12-MC-4 and cuprate species in the polar medium of methanol are 0.7 and −19.2 kcal/mol by PBE0/DGDZVP. The PBE0 results are compared with TPSSH calculations employing the same basis set.</div></div>","PeriodicalId":284,"journal":{"name":"Computational and Theoretical Chemistry","volume":"1254 ","pages":"Article 115523"},"PeriodicalIF":3.0,"publicationDate":"2025-10-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145263178","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":"Theoretical study on the dissociation of HCl-(H2O)1–30 and HNO3-(H2O)1–30 clusters","authors":"Christian Tshikala Mukeba ,&nbsp;Okuma Emile Kasende ,&nbsp;Mireille K. Bilonda ,&nbsp;Hoeil Chung ,&nbsp;Jules Tshishimbi Muya","doi":"10.1016/j.comptc.2025.115518","DOIUrl":"10.1016/j.comptc.2025.115518","url":null,"abstract":"<div><div>HCl-(H₂O)_n and HNO₃-(H₂O)_n clusters are HCl complexes and HNO₃ complexes constituted by small assemblies of n water molecules forming hydrogen bond network with HCl and HNO₃, respectively. Herein, a comparative study on HCl-(H₂O)_n and HNO₃-(H₂O)_n (<em>n</em> ≤ 29) is performed at the B3LYP-D3, ωB97XD, M06-2x, and MP2 levels with the 6–31 + G(d,p) basis set, focusing on hydrogen bonding interactions, relative stabilities, cooperativity energies, NBO charge transfer and vibration of H₃O⁺. The results show that water clusters tend to stabilize more HNO₃ than HCl based on computed binding energies and cooperativity energies. At least four and five water molecules are required for a total dissociation of HCl and HNO₃, respectively. Comparison between endohedral and exohedral clusters HCl-(H₂O)_n and HNO₃-(H₂O)_n (<em>n</em> = 19–20, 27–29) shows that chloride and nitrate are more stabilized inside the cage, unlike H₃O⁺ which prefers laying on the cluster surface. The third overtones of O<img>H mode of H₃O⁺ in HCl-water and HNO₃-water large clusters are found to be in good agreement with experiments laying around 9000–7700 cm⁻¹.</div></div>","PeriodicalId":284,"journal":{"name":"Computational and Theoretical Chemistry","volume":"1254 ","pages":"Article 115518"},"PeriodicalIF":3.0,"publicationDate":"2025-09-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145263181","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":"Thermal decomposition mechanism of hydrazine dimer in gas phase and solution","authors":"Qian He,&nbsp;Na Shan,&nbsp;Runyu Zhou,&nbsp;Xinyan Yang,&nbsp;Tao Gao","doi":"10.1016/j.comptc.2025.115519","DOIUrl":"10.1016/j.comptc.2025.115519","url":null,"abstract":"<div><div>Hydrazine's high hydrogen content makes it promising for hydrogen storage, but its explosive decomposition poses challenges. This study explores hydrazine's decomposition mechanisms in gas and solution phases using transition state theory, analyzing pathways for N₂, H₂, and NH₃ formation, including complexes N₃H₅ and N₃H₃ observed experimentally. Reaction rate constants were calculated for 200–1000 K, with kinetic curves comparing gas-phase and solution-phase decomposition. Results show that differing surface electrostatic potentials between phases alter surface polarity, leading to product selectivity variations during thermal decomposition. The findings provide insights for hydrazine's safer application in hydrogen storage and production.</div></div>","PeriodicalId":284,"journal":{"name":"Computational and Theoretical Chemistry","volume":"1254 ","pages":"Article 115519"},"PeriodicalIF":3.0,"publicationDate":"2025-09-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145217369","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":"Theoretical investigation of catalytic activity of bimetallic systems based on tin for methane dissociation","authors":"Yulia Polynskaya ,&nbsp;Andrey Knizhnik ,&nbsp;Alexander Sinitsa ,&nbsp;Yegor Kedalo ,&nbsp;Boris Potapkin","doi":"10.1016/j.comptc.2025.115505","DOIUrl":"10.1016/j.comptc.2025.115505","url":null,"abstract":"<div><div>This work presents a comprehensive density functional theory (DFT) investigation of the catalytic performance of tin (Sn)-based bimetallic surfaces for methane dissociation. The study systematically evaluates the effect of incorporation of catalytically active transition (Ni, Cu, Co, Fe) and noble (Au, Pt, Ag) metals into Sn surfaces on the activation energy for C–H bond breaking in CH<span><math><msub><mrow></mrow><mrow><mn>4</mn></mrow></msub></math></span>. Charge redistribution analysis reveals that the interaction between positively charged Sn atoms and negatively charged dopant metals stabilizes reaction intermediates and reduces the activation energy barriers. Among the ten studied alloys, Sn–Co, Sn–Cu, and Sn–Fe exhibit the lowest activation barriers (about 1.6 eV), suggesting their high potential for industrial methane pyrolysis. Moreover, it is demonstrated that for bimetallic systems based on Ni and Fe increase of the dopant metal concentration leads to further reduction of the activation energy. These results identify Sn-based bimetallic catalysts as promising candidates for efficient and sustainable methane conversion, contributing to the advancement of green hydrogen production technologies.</div></div>","PeriodicalId":284,"journal":{"name":"Computational and Theoretical Chemistry","volume":"1254 ","pages":"Article 115505"},"PeriodicalIF":3.0,"publicationDate":"2025-09-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145217370","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":"Halochromism of alizarin yellow R in aqueous solution: A comparative theoretical analysis of neutral, anionic, and dianionic forms","authors":"Victor Kostjukov","doi":"10.1016/j.comptc.2025.115517","DOIUrl":"10.1016/j.comptc.2025.115517","url":null,"abstract":"<div><div>Photochemical transformations of alizarin yellow R with alternate elimination of two protons from the carboxyl and OH groups are modeled in the present work using TD-DFT, and the accompanying shifts of electron densities are estimated from the analysis of NPA charges. It turned out that the carboxyl group, although polarized upon excitation, is almost not involved in the photoinduced charge transfer from the aromatic A ring to the diazo linker and does not affect it. Therefore, the neutral form and the anion have an absorption maximum at the same wavelength (<em>λ</em>_max = 374 nm). On the contrary, the OH group, although also not directly involved in this, significantly affects this process: when a proton is eliminated from it, the path of charge transfer from the A ring through the diazo linker is extended and reaches the second B ring. This leads to a significant shift of the absorption maximum of the dianion (<em>λ</em>_max = 496 nm) relative to the neutral form and the monoanion. Moreover, photoinduced changes in the conformations of all three forms of the dye are local: in contrast to the famous parent unsubstituted azobenzene, alizarin yellow R has a <em>trans</em> conformation in both the ground and excited states.</div></div>","PeriodicalId":284,"journal":{"name":"Computational and Theoretical Chemistry","volume":"1254 ","pages":"Article 115517"},"PeriodicalIF":3.0,"publicationDate":"2025-09-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145217367","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":"Potassium decoration on graphenyldiene monolayer for advanced reversible hydrogen storage","authors":"José A.S. Laranjeira ,&nbsp;Nicolas F. Martins ,&nbsp;Kleuton A.L. Lima ,&nbsp;Bill. D. Aparicio-Huacarpuma ,&nbsp;Luiz A. Ribeiro Junior ,&nbsp;Xihao Chen ,&nbsp;Douglas S. Galvao ,&nbsp;Julio R. Sambrano","doi":"10.1016/j.comptc.2025.115504","DOIUrl":"10.1016/j.comptc.2025.115504","url":null,"abstract":"<div><div>Potassium-decorated graphenyldiene (K@GPD) is investigated as a promising two-dimensional material for reversible hydrogen storage using first-principles density functional theory calculations. Potassium atoms bind strongly to the GPD monolayer, and ab initio molecular dynamics (AIMD) simulations confirm the thermal stability of the functionalized system at 300 K. Hydrogen adsorption energies range from -0.11 to -0.14 eV per H<span><math><msub><mrow></mrow><mrow><mn>2</mn></mrow></msub></math></span>, denoting reversible storage. At full coverage (18 H<span><math><msub><mrow></mrow><mrow><mn>2</mn></mrow></msub></math></span> molecules), the system reaches a storage capacity of 8.82 wt%, exceeding the U.S. DOE target. AIMD simulations reveal spontaneous H<span><math><msub><mrow></mrow><mrow><mn>2</mn></mrow></msub></math></span> desorption at ambient temperature, demonstrating excellent reversibility.</div></div>","PeriodicalId":284,"journal":{"name":"Computational and Theoretical Chemistry","volume":"1254 ","pages":"Article 115504"},"PeriodicalIF":3.0,"publicationDate":"2025-09-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145217371","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":"Enhanced thermal stability in nitrogen-containing gold carbide cages: A DFT study of Au30N20C60 vs. Au30C20C60","authors":"Jing-Jing Guo ,&nbsp;Hong-Man Ma ,&nbsp;Peng-Bo Liu ,&nbsp;Yi-Sha Chen ,&nbsp;Hui-Yan Zhao ,&nbsp;Jing Wang ,&nbsp;Ying Liu","doi":"10.1016/j.comptc.2025.115513","DOIUrl":"10.1016/j.comptc.2025.115513","url":null,"abstract":"<div><div>Two typical deltoidal hexecontahedron-like gold carbide clusters of Au₃₀N₂₀C₆₀ and Au₃₀C₂₀C₆₀ cages have been constructed under BP86/6-31 g(d) for C, N atoms and BP86/def2-TZVPP for Au atoms in this work. No imaginary frequencies have been found in the vibrational frequency analysis for Au₃₀N₂₀C₆₀ and Au₃₀C₂₀C₆₀ cages. The simulated IR and Raman spectrum may also provide theoretical basis for further exploration. Molecular dynamics simulations show that the highest temperature at which Au₃₀N₂₀C₆₀ maintains its original configuration and subunits after 20 <em>ps</em> NVT MD simulations is 1200 K, which is significantly higher than the 900 K observed for Au₃₀C₂₀C₆₀, indicating that the doped N atoms enhance the thermodynamic stability of gold-carbide clusters. The electronic properties of Au₃₀N₂₀C₆₀ has been discussed via density of states, electron density, and adaptive natural density partitioning, which can clearly explain its electronic behavior.</div></div>","PeriodicalId":284,"journal":{"name":"Computational and Theoretical Chemistry","volume":"1254 ","pages":"Article 115513"},"PeriodicalIF":3.0,"publicationDate":"2025-09-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145217366","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}