Theoretical Chemistry Accounts最新文献

{"title":"Energy calculations for sodium vs. potassium on a prokaryotic voltage-gated sodium channel: a quantum-chemical study","authors":"Juan Ferrer, Emilio San-Fabián","doi":"10.1007/s00214-024-03132-x","DOIUrl":"https://doi.org/10.1007/s00214-024-03132-x","url":null,"abstract":"<p>The selectivity of the sodium channel has been the subject of numerous experimental and theoretical studies. In this work, this problem is approached from a theoretical point of view based on a model built from the Selective Filter (SF) of the open structure of the voltage-activated channel of the bacterium <i>Magnetococcus marinus</i>. This approach has allowed us to calculate the interaction energies of the system (cation-water-SF-fragment), both for the sodium cation and the potassium cation. The results have highlighted the importance of differential dehydration of cations, as well as the environment where it occurs. Semi-empirical and <i>ab initio</i> methods have been applied to analyze and quantify the interaction energies when the cations are in the SF of the sodium channel, with the DFT (<i>ab initio</i>) methods giving us the key to the distribution of the interaction energies and therefore how dehydration occurs.\u0000</p>","PeriodicalId":23045,"journal":{"name":"Theoretical Chemistry Accounts","volume":null,"pages":null},"PeriodicalIF":1.7,"publicationDate":"2024-06-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141508472","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"On the Spin-Coupled description of the pi system of the cyclopentadienyl anion","authors":"André G. H. Barbosa","doi":"10.1007/s00214-024-03130-z","DOIUrl":"https://doi.org/10.1007/s00214-024-03130-z","url":null,"abstract":"<p>It is well-known that the Spin-Coupled (SC) description of the cyclopentadienyl anion is problematic. A converged six electrons in six orbitals SC calculation on this anion break the D_5h electron density spatial symmetry by approximately localizing two of the six pi singly-occupied orbitals over one carbon. A complete active space valence bond (CASVB) calculation for the same six pi electrons in six orbitals does not break symmetry, yielding five equivalent pi orbitals over the five carbons and one pi orbital with high amplitude along the C₅ molecular rotation axis. A Spin-Coupled calculation comprising six electrons in five orbitals, SC(6,5), yields five equivalent non-orthogonal pi orbitals over the carbons with “1.2” (6/5) electron occupancy each. In this paper, these different solutions are contrasted with one generated by the present author in which five spatially different but equivalent configurations of a perfect-pairing symmetry broken solution are put together in a multi-configuration Spin-Coupled calculation of six electrons in 30 orbitals. It is concluded that, in spite of the computational complexity of this calculation, its result is qualitatively more akin to a valence bond-like description of the resonant pi system of the cyclopentadienyl anion.</p>","PeriodicalId":23045,"journal":{"name":"Theoretical Chemistry Accounts","volume":null,"pages":null},"PeriodicalIF":1.7,"publicationDate":"2024-06-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141508473","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Transformation to a geminal basis and stationary conditions for the exact wave function therein","authors":"Lasse Kragh Sørensen","doi":"10.1007/s00214-024-03131-y","DOIUrl":"https://doi.org/10.1007/s00214-024-03131-y","url":null,"abstract":"<p>We show the transformation from a one-particle basis to a geminal basis, transformations between different geminal bases demonstrate the Lie algebra of a geminal basis. From the basis transformations, we express both the wave function and Hamiltonian in the geminal basis. The necessary and sufficient conditions of the exact wave function expanded in a geminal basis are shown to be a Brillouin theorem of geminals. The variational optimization of the geminals in the antisymmetrized geminal power (AGP), antisymmetrized product of geminals (APG) and the full geminal product (FGP) wave function ansätze are discussed. We show that using a geminal replacement operator to describe geminal rotations introduce both primary and secondary rotations. The secondary rotations rotate two geminals in the reference at the same time due to the composite boson nature of geminals. Due to the completeness of the FGP, where all possible geminal combinations are present, the FGP is exact. The number of parameters in the FGP scale exponentially with the number of particles, like the full configuration interaction (FCI). Truncation in the FGP expansion can give compact representations of the wave function since the reference function in the FGP can be either the AGP or APG wave function.</p>","PeriodicalId":23045,"journal":{"name":"Theoretical Chemistry Accounts","volume":null,"pages":null},"PeriodicalIF":1.7,"publicationDate":"2024-06-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141508524","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Structure and properties of 4a,5,7a, 8-tetrahydro-4H-imidazolo [4,5-b] [1, 2, 5] oxadiazolo [3,4-e] pyrazine-6 (7H)-ketone based energetic derivatives","authors":"Mengjie Bo, Zikai Gao, Zhihui Gu, Peng Ma, Congming Ma","doi":"10.1007/s00214-024-03127-8","DOIUrl":"https://doi.org/10.1007/s00214-024-03127-8","url":null,"abstract":"<p>During the research process, it was found that compounds with the \"565\" ring structure exhibited excellent detonation performance, which led to further investigation. TIOP (4a,5,7a, 8-tetrahydro-4H-imidazolo [4,5-b][1,2,5] oxadiazolo [3,4-e] pyrazine-6 (7H) -ketone) energetic compound has been designed. This article uses TIOP as the precursor and designs 54 \"TIOP-based energetic derivatives\" by introducing energetic groups such as –ONO₂, –NHNH₂, and –NH₂. Among these energetic compounds, their maximum density, maximum detonation velocity, and maximum detonation pressure can reach 2.09 g/cm (D6), 10.07 km/s (D4), and 46.58 GPa (D7). Comprehensive analysis shows that energetic compounds A7, D4, D7, and F7 can reach a good equilibrium among high energy and low sensitivity, and can be further studied as potential High Energy Density Compounds. Using Gaussian16 software and the Multiwfn 3.8 software package, the B3LYP method in density functional theory was used to optimize the structure of 54 derivatives, calculate their heat of formation, and further analyze the intermolecular interactions.</p>","PeriodicalId":23045,"journal":{"name":"Theoretical Chemistry Accounts","volume":null,"pages":null},"PeriodicalIF":1.7,"publicationDate":"2024-06-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141508523","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Molecular design and energetic properties of 4H, 8H difurazano [3,4-b; 3′, 4′-e] pyrazine derivatives","authors":"Zikai Gao, Zhihui Gu, Mengjie Bao, Jiani Xu, Tingting Xiao, Jun Chen, Peng Ma, Congming Ma","doi":"10.1007/s00214-024-03128-7","DOIUrl":"https://doi.org/10.1007/s00214-024-03128-7","url":null,"abstract":"<p>Forty-five “4H, 8H difurazano[3,4-b;3′,4′-e] pyrazine (DFP) based energetic derivatives” were designed, and their heat of formation, stability, detonation performance, and impact sensitivity properties were comprehensively studied using density functional theory. The changes in these properties caused by changes in the type and quantity of substituents were analyzed. The results showed that the density range of DFP based energetic derivatives was 1.62–2.02 g/cm, the detonation velocity range was 7.02–9.18 km/s, and the detonation pressure range was 20.99–38.72 GPa. The introduction of –NH₂ and –NHNH₂ groups can effectively reduce the chemical reactivity of the compounds, while the introduction of –NHNH₂ groups can efficiently improve the heat of formation and detonation performance of the compounds and reduce the sensitivity of the derivatives. Compounds <b>B8</b> (4H, 8H bis ([1,2,5] oxadiazolo) [3,4-b:3′,4′-e] pyrizine-4,8-diyl nitrate), <b>C8</b> (8-(trinitromethyl)-4H, 8H bis ([1,2,5] oxadiazolo) [3,4-b:3′,4′-e] pyrizin-4-yl nitrate), <b>E4</b> (<i>N</i>-(8-hydrazine-4H, 8H bis ([1,2,5] oxadiazolo) [3,4-b:3′,4′-e] pyrizin-4-yl) nitrate, <b>E8</b> (8-(nitroamino)-4H, 8H bis([1,2,5] oxadiazolo) [3,4-b:3′,4′-e] pyrizin-4-yl nitrate) can be used as candidates for high-energy density materials.</p>","PeriodicalId":23045,"journal":{"name":"Theoretical Chemistry Accounts","volume":null,"pages":null},"PeriodicalIF":1.7,"publicationDate":"2024-06-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141508525","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Computational screening of matrix metalloproteinase 3 inhibitors to counteract skin aging from phytochemicals of Nelumbo nucifera Gaertn","authors":"Amisha Bisht, Disha Tewari, Kalpana Rawat, Shilpi Rawat, Mohammad Ali Abdullah Almoyad, Shadma Wahab, Sanjay Kumar, Subhash Chandra","doi":"10.1007/s00214-024-03125-w","DOIUrl":"https://doi.org/10.1007/s00214-024-03125-w","url":null,"abstract":"<p>Human matrix metalloproteinase 3 (MMP3), also known as Stromelysin-1, is involved in various cellular processes, including skin aging, making it an attractive drug target against skin aging. This study aims to apply different ML algorithms to develop a prediction model for the MMP3 inhibitor dataset (ChEMBL283) from the ChEMBL database. ML experiments were performed using the Python programming language. Seven machine learning algorithms, namely neural network, decision tree, Xgboost, CatBoost, random forest, LightGBM, and extra trees, were applied to classify molecules as active or inactive (coded 1 or 0) using AutoML. ML models underwent an evaluation process that included ROC plots, a confusion matrix, and a set of statistical measures. These evaluations demonstrated the exceptional predictive capability of the Extra Trees algorithm, achieving a remarkable accuracy rate of 85.8%. The most effective ML model identified 79 active MMP3 inhibitory phytochemicals in <i>Nelumbo nucifera</i>. Molecular docking confirmed the strong binding of seven phytochemicals to MMP3, suggesting their potential as inhibitors. Following Lipinski's rule, three compounds—liensinin, isoliensinin, and isovitex—showed promise in molecular dynamics studies (100 ns) and MM-PBSA analysis (last 30 ns). They exhibited the lowest binding free energies, namely − 112.684 kJ/mol, − 194.871 kJ/mol, and − 101.551 kJ/mol, respectively, compared to the HQQ-MMP3 complex (− 95.410 kJ/mol), suggesting their potential as candidates for MMP3 inhibition. The study highlights the effectiveness of ML and the relative accuracy of MD simulations in screening phytochemicals for dermatological research and provides innovative opportunities for designing MMP3 inhibitors in the future.</p>","PeriodicalId":23045,"journal":{"name":"Theoretical Chemistry Accounts","volume":null,"pages":null},"PeriodicalIF":1.7,"publicationDate":"2024-06-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141254721","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"DFT and machine learning for predicting hydrogen adsorption energies on rocksalt complex oxides","authors":"Adrian Domínguez-Castro","doi":"10.1007/s00214-024-03124-x","DOIUrl":"https://doi.org/10.1007/s00214-024-03124-x","url":null,"abstract":"<p>The prediction of hydrogen adsorption energies on complex oxides by integrating DFT calculations and machine learning is considered. In particular, 14 descriptors for electronic and geometric properties evaluation are adapted within a 336 hydrogen adsorption energy dataset created. Supervised learning techniques were explored to establish an accurate predictive model. With the deep neural network results, a MAE of about 0.06 eV is achieved. This research highlights the synergistic potential of DFT and machine learning for accelerating the exploration of materials for catalysis.</p>","PeriodicalId":23045,"journal":{"name":"Theoretical Chemistry Accounts","volume":null,"pages":null},"PeriodicalIF":1.7,"publicationDate":"2024-06-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141254717","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Improving the stability of 2-phenyl-1,3-dimethyl imidazolium cations under alkaline conditions through various substitution strategies","authors":"Tiancheng Xiang, Hongyan Si","doi":"10.1007/s00214-024-03126-9","DOIUrl":"https://doi.org/10.1007/s00214-024-03126-9","url":null,"abstract":"<p>The effects of various substituents at different substitution positions on the stability of imidazolium cations were investigated by studying the degradation reactions of several substituted 2-phenyl-1,3-dimethyl imidazolium cations (PDMIm⁺). The results of density functional theory calculations revealed that the stability of the imidazolium cation could be significantly enhanced by substitutions near the C2 position. These substitution positions included the ortho positions of the phenyl group and the N1/N3 and C4/C5 positions on the imidazole ring of PDMIm⁺. Moreover, the ethyl group was the most effective substituent among the ones discussed. The calculations also revealed that double alkyl substituents at ortho positions could more effectively improve the stability of imidazolium cations in the degradation reactions.</p>","PeriodicalId":23045,"journal":{"name":"Theoretical Chemistry Accounts","volume":null,"pages":null},"PeriodicalIF":1.7,"publicationDate":"2024-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141194941","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Topological analysis of the electron density in the chromium–manganese chalcogenide clusters, [E2CrMn2(CO)9]−2 (E = S, Se, Te)","authors":"Nadia Ezzat Al-kirbasee, Ahlam Hassan, M. Al-Ibadi, E. Abood, Siti Syaida Sirat","doi":"10.1007/s00214-024-03129-6","DOIUrl":"https://doi.org/10.1007/s00214-024-03129-6","url":null,"abstract":"","PeriodicalId":23045,"journal":{"name":"Theoretical Chemistry Accounts","volume":null,"pages":null},"PeriodicalIF":1.7,"publicationDate":"2024-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141399029","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A computational study into the mechanism and selectivities of the reaction of 1, 1-diaryl-2-isopropylidene-3-methylenecyclopropane (DIMCP) with C, N-diarylnitrone","authors":"Emmanuel Komla Oyetey, Caroline R. Kwawu, Albert Aniagyei, Gabriel Amankwah, Richmond Arhin, Evans Adei","doi":"10.1007/s00214-024-03121-0","DOIUrl":"https://doi.org/10.1007/s00214-024-03121-0","url":null,"abstract":"<p>The site- and regioselectivities of the [3 + 2] cycloaddition (32CA) reactions of C, N-diarylnitrone [<b>B2</b>] with 1, 1-diaryl-2-isopropylidene-3-methylenecyclopropane (DIMCP) [<b>B1</b>] and subsequent rearrangement have been studied using unrestricted density functional theory (UDFT) at the UB3LYP/6-311G (d, p) level of theory. 1, 1-Diaryl-2-isopropylidene-3-methylenecyclopropane possesses two exocyclic olefinic bonds (reactive centers): one unsubstituted and the other dimethyl-substituted. The preferred pathway with the lowest activation barrier occurs by the addition of <b>B2</b> across the unsubstituted exocyclic bond of <b>B1</b> to afford two regioisomeric products <b>P4A</b> and intermediate <b>INT1A</b>, where the generated <b>INT1A</b> proceeds through rearrangement to afford the experimentally observed products <b>P2A</b> and <b>P3A</b>. The rearrangement process was triggered by the concerted homolytic cleavage of the isoxazolidine N–O bond and the cyclopropane C–C (Ar¹)₂ bond. Electron-donating groups (EDGs) at the para position of Ar¹ and Ar² substituted on <b>B1</b> and <b>B2</b> increase the activation barrier, while electron-withdrawing groups (EWGs) decrease the activation barrier. EDGs and EWGs at the meta position of Ar¹ and Ar² decrease the activation barrier. The rate constant for the preferred pathway (formation of intermediate, <b>INT1A</b>) in the 32CA of <b>B1</b> (Ar¹ = Ph) and B2 (Ar² = Ph) in benzene is 2.98 × 10^–6 s⁻¹, which is about 126 times faster than the non-competing channel, leading to the formation of <b>P4A</b> (2.35 × 10^–8 s⁻¹) through <b>TS2A</b>. Results from the analysis of the global reactivity indices at the ground state of the reactants show that <b>B1</b> (Ar¹ = Ph) acts as the nucleophile with chemical potential of −3.73 eV and <b>B2</b> (Ar² = Ph) acts as the electrophile with chemical potential of −3.83 eV. GEDT analysis infers that the 32CA reaction between <b>B1</b> and <b>B2</b> is one of a nonpolar character.</p>","PeriodicalId":23045,"journal":{"name":"Theoretical Chemistry Accounts","volume":null,"pages":null},"PeriodicalIF":1.7,"publicationDate":"2024-05-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141194569","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}