Pub Date : 2024-09-11DOI: 10.1007/s00214-024-03144-7
Yakov D. Samuilov, Alexander Ya. Samuilov
The detailed analysis of the mechanism of metathesis of N-methylformamide with dimethyl carbonate leading to the formation of N, O-dimethylcarbamate was carried out using the B3LYP/6-311++G(df,p), B3LYP-D3(BJ)/6-311++G(df,p) and ωB97XD/6-311++G(df,p) density functional methods. The reactions proceed in three stages. The first step consists in the tautomeric conversion of N-methylformamide to iminol. The second stage, which is the rate-limiting step, involves the addition of dimethyl carbonate via the N=C π-bond of iminol. The third stage of the reaction is the cleavage of the methyl formate molecule from N-methyl-N-[(hydroxy)(methoxy)methyl]-O-methylcarbamate. This conversion results in the formation of N, O-dimethylcarbamate. All stages of the reactions are catalyzed by associates of alcohols, which lead to a strong decrease in activation enthalpies.
{"title":"Reaction of N-methylformamide with dimethyl carbonate: a DFT study","authors":"Yakov D. Samuilov, Alexander Ya. Samuilov","doi":"10.1007/s00214-024-03144-7","DOIUrl":"https://doi.org/10.1007/s00214-024-03144-7","url":null,"abstract":"<p>The detailed analysis of the mechanism of metathesis of <i>N</i>-methylformamide with dimethyl carbonate leading to the formation of N, O-dimethylcarbamate was carried out using the B3LYP/6-311++G(df,p), B3LYP-D3(BJ)/6-311++G(df,p) and ωB97XD/6-311++G(df,p) density functional methods. The reactions proceed in three stages. The first step consists in the tautomeric conversion of <i>N</i>-methylformamide to iminol. The second stage, which is the rate-limiting step, involves the addition of dimethyl carbonate via the N=C π-bond of iminol. The third stage of the reaction is the cleavage of the methyl formate molecule from <i>N</i>-methyl-<i>N</i>-[(hydroxy)(methoxy)methyl]-O-methylcarbamate. This conversion results in the formation of <i>N</i>, O-dimethylcarbamate. All stages of the reactions are catalyzed by associates of alcohols, which lead to a strong decrease in activation enthalpies.</p>","PeriodicalId":23045,"journal":{"name":"Theoretical Chemistry Accounts","volume":"41 1","pages":""},"PeriodicalIF":1.7,"publicationDate":"2024-09-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142201996","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}
In this paper, we investigate two model reactions (an electrocyclic ring closure and a tautomerism equilibrium) in different sized fullerene cages to explore the intricate details of the confinement effect in chemistry and in chemical reactivity. Fullerene cages offers, with their unique geometry and electronic properties, an ideal theoretical model to explore confinement-induced alterations in reaction pathways and energy barriers. Computational results demonstrate that the induced confinement may significantly influence the thermodynamics and kinetics of the chemical processes under study through a comparative investigation of reactions in various fullerene cage sizes and their occurrence in gas phase. This theoretical investigation intends to improve our knowledge of molecular confinement events, while also highlighting the potential use of fullerene cages as adjustable nanoreactors for regulating and improving chemical reactivity.
{"title":"Chemical reactivity inside carbon cages: theoretical insights from a fullerene confinement","authors":"Christophe Morell, Yanis Abid Charef, Guillaume Hoffmann","doi":"10.1007/s00214-024-03141-w","DOIUrl":"https://doi.org/10.1007/s00214-024-03141-w","url":null,"abstract":"<p>In this paper, we investigate two model reactions (an electrocyclic ring closure and a tautomerism equilibrium) in different sized fullerene cages to explore the intricate details of the confinement effect in chemistry and in chemical reactivity. Fullerene cages offers, with their unique geometry and electronic properties, an ideal theoretical model to explore confinement-induced alterations in reaction pathways and energy barriers. Computational results demonstrate that the induced confinement may significantly influence the thermodynamics and kinetics of the chemical processes under study through a comparative investigation of reactions in various fullerene cage sizes and their occurrence in gas phase. This theoretical investigation intends to improve our knowledge of molecular confinement events, while also highlighting the potential use of fullerene cages as adjustable nanoreactors for regulating and improving chemical reactivity.</p>","PeriodicalId":23045,"journal":{"name":"Theoretical Chemistry Accounts","volume":"17 1","pages":""},"PeriodicalIF":1.7,"publicationDate":"2024-08-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142202002","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}
Pub Date : 2024-08-09DOI: 10.1007/s00214-024-03140-x
Wise Herowati, Wahyu Aji Eko Prabowo, Muhamad Akrom, Noor Ageng Setiyanto, Achmad Wahid Kurniawan, Novianto Nur Hidayat, Totok Sutojo, Supriadi Rustad
Machine learning (ML) approaches have been developed to predict materials’ corrosion inhibition efficiency, particularly pyrimidine compounds. Notably, the virtual sample generation (VSG) technique enhances prediction accuracy, a novel approach for handling small datasets in this context. The random forest model, the best-performing nonlinear algorithm, showed substantial accuracy improvement based on the increase in R2 value from 0.05 to 0.99 and the decrease in RMSE value from 5.60 to 0.42, after applying VSG. These results underscore the efficacy of the VSG technique in boosting the predictive performance of ML models, particularly in scenarios constrained by limited data availability.
{"title":"Machine learning for pyrimidine corrosion inhibitor small dataset","authors":"Wise Herowati, Wahyu Aji Eko Prabowo, Muhamad Akrom, Noor Ageng Setiyanto, Achmad Wahid Kurniawan, Novianto Nur Hidayat, Totok Sutojo, Supriadi Rustad","doi":"10.1007/s00214-024-03140-x","DOIUrl":"https://doi.org/10.1007/s00214-024-03140-x","url":null,"abstract":"<p>Machine learning (ML) approaches have been developed to predict materials’ corrosion inhibition efficiency, particularly pyrimidine compounds. Notably, the virtual sample generation (VSG) technique enhances prediction accuracy, a novel approach for handling small datasets in this context. The random forest model, the best-performing nonlinear algorithm, showed substantial accuracy improvement based on the increase in <i>R</i><sup>2</sup> value from 0.05 to 0.99 and the decrease in RMSE value from 5.60 to 0.42, after applying VSG. These results underscore the efficacy of the VSG technique in boosting the predictive performance of ML models, particularly in scenarios constrained by limited data availability.</p>","PeriodicalId":23045,"journal":{"name":"Theoretical Chemistry Accounts","volume":"10 1","pages":""},"PeriodicalIF":1.7,"publicationDate":"2024-08-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141943359","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}
Pub Date : 2024-08-03DOI: 10.1007/s00214-024-03139-4
Peixian Wang, Bin Song, Gaoling Zhao
Based on the first-principles calculations, we systematically studied and fully characterized the electronic structure and optical properties of four novel ZnO phases assembled by Zn12O12 clusters and compared them with the results of wurtzite (WZ) ZnO. The results show that the density of states of the four cluster-assembled materials is similar to that of WZ-ZnO, but the bandgap is larger than that of the latter. Among them, FAU-ZnO, LTA-ZnO, and SOD-ZnO are direct bandgap semiconductors. The calculation of the optical properties of SOD-ZnO is most similar to those of WZ-ZnO, but R-ZnO has higher static permittivity, reflection, and refraction coefficients. Considering that the presence of cage-like voids in cluster-assembled materials is more conducive to doping of various elements, cluster-assembled materials are more likely to change the bandgap and corresponding electronic structure through doping than WZ-ZnO. From this perspective, these two materials have great potential for photocatalytic and optoelectronic device applications.
{"title":"Electronic and optical properties of several cluster-assembled materials based on Zn12O12: a first-principles study","authors":"Peixian Wang, Bin Song, Gaoling Zhao","doi":"10.1007/s00214-024-03139-4","DOIUrl":"https://doi.org/10.1007/s00214-024-03139-4","url":null,"abstract":"<p>Based on the first-principles calculations, we systematically studied and fully characterized the electronic structure and optical properties of four novel ZnO phases assembled by Zn<sub>12</sub>O<sub>12</sub> clusters and compared them with the results of wurtzite (WZ) ZnO. The results show that the density of states of the four cluster-assembled materials is similar to that of WZ-ZnO, but the bandgap is larger than that of the latter. Among them, FAU-ZnO, LTA-ZnO, and SOD-ZnO are direct bandgap semiconductors. The calculation of the optical properties of SOD-ZnO is most similar to those of WZ-ZnO, but R-ZnO has higher static permittivity, reflection, and refraction coefficients. Considering that the presence of cage-like voids in cluster-assembled materials is more conducive to doping of various elements, cluster-assembled materials are more likely to change the bandgap and corresponding electronic structure through doping than WZ-ZnO. From this perspective, these two materials have great potential for photocatalytic and optoelectronic device applications.</p>","PeriodicalId":23045,"journal":{"name":"Theoretical Chemistry Accounts","volume":"3 1","pages":""},"PeriodicalIF":1.7,"publicationDate":"2024-08-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141943360","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}
Pub Date : 2024-07-25DOI: 10.1007/s00214-024-03137-6
Yasin Gholiee
A computational study on the host–guest complexes of neutral bis(4-nitrophenyl)squaramide (SQ) and halide anions is reported. In the gas-phase, the calculated interaction and stabilization energies indicates a diminishing intrinsic affinity of SQ for anions from fluoride to iodide. The nature of interactions is investigated using Natural Bond Orbital (NBO), Quantum Theory of Atoms in Molecules (QTAIM) along with Energy Decomposition Analysis-Natural Orbitals for Chemical Valence (EDA-NOCV). While electrostatic interactions account for roughly 60% of the total, EDA-NOCV analysis demonstrated increasing contributions of orbital interactions from (left[ {{text{SQ}} cdots {text{I}}} right]^{ - }) to (left[ {{text{SQ}} cdots {text{F}}} right]^{ - }) complexes. In solution, thermodynamic cycle analyses and Gibbs free energy calculations reveal a propensity towards the formation of (left[ {{text{SQ}} cdots {text{F}}} right]^{ - }), taking into account the influence of solvation energies on the overall stability. The consistent trend observed in selectivity both in the gas phase and in solution suggests that changes in solvation energy do not significantly impact the stability of complexes. The findings were additionally supported by a significant correlation observed between the computed and experimental formation constants.
{"title":"Exploring host–guest interactions of bis(4-nitrophenyl)squaramide with halide anions: a computational investigation in the gas-phase and solution","authors":"Yasin Gholiee","doi":"10.1007/s00214-024-03137-6","DOIUrl":"https://doi.org/10.1007/s00214-024-03137-6","url":null,"abstract":"<p>A computational study on the host–guest complexes of neutral bis(4-nitrophenyl)squaramide (SQ) and halide anions is reported. In the gas-phase, the calculated interaction and stabilization energies indicates a diminishing intrinsic affinity of SQ for anions from fluoride to iodide. The nature of interactions is investigated using Natural Bond Orbital (NBO), Quantum Theory of Atoms in Molecules (QTAIM) along with Energy Decomposition Analysis-Natural Orbitals for Chemical Valence (EDA-NOCV). While electrostatic interactions account for roughly 60% of the total, EDA-NOCV analysis demonstrated increasing contributions of orbital interactions from <span>(left[ {{text{SQ}} cdots {text{I}}} right]^{ - })</span> to <span>(left[ {{text{SQ}} cdots {text{F}}} right]^{ - })</span> complexes. In solution, thermodynamic cycle analyses and Gibbs free energy calculations reveal a propensity towards the formation of <span>(left[ {{text{SQ}} cdots {text{F}}} right]^{ - })</span>, taking into account the influence of solvation energies on the overall stability. The consistent trend observed in selectivity both in the gas phase and in solution suggests that changes in solvation energy do not significantly impact the stability of complexes. The findings were additionally supported by a significant correlation observed between the computed and experimental formation constants.</p>","PeriodicalId":23045,"journal":{"name":"Theoretical Chemistry Accounts","volume":"66 1","pages":""},"PeriodicalIF":1.7,"publicationDate":"2024-07-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141772031","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}
Pub Date : 2024-07-12DOI: 10.1007/s00214-024-03133-w
Umair Umer, Syed Muhammad Usama, Hailin Zhao, Zhigang Sun
Efficient calculations of the quantum product state-resolved differential cross sections play a crucial role in unraveling the dynamics of a chemical reaction. Using hyperspherical coordinates, a stair-shaped grid-based time-dependent quantum wave packet method is proposed for efficiently calculating the product quantum state-resolved reactive scattering information. As numerical examples, quantum product state-resolved reaction probabilities for the reactions of O + O(_{2}) and Cl + H(_{2})((v_0)=1) with (J=0) are computed, which involve long-time resonance states extending over long-range grids and are difficult for obtaining accurate results using the time-dependent method. The results through calculations are being compared to those obtained using the reactant coordinate-based (RCB) method and the interaction-asymptotic decomposition method (IARD).
{"title":"Product state-resolved reactive scattering calculations using stair shaped grids in hyperspherical coordinates for the quantum wave packet method","authors":"Umair Umer, Syed Muhammad Usama, Hailin Zhao, Zhigang Sun","doi":"10.1007/s00214-024-03133-w","DOIUrl":"https://doi.org/10.1007/s00214-024-03133-w","url":null,"abstract":"<p>Efficient calculations of the quantum product state-resolved differential cross sections play a crucial role in unraveling the dynamics of a chemical reaction. Using hyperspherical coordinates, a stair-shaped grid-based time-dependent quantum wave packet method is proposed for efficiently calculating the product quantum state-resolved reactive scattering information. As numerical examples, quantum product state-resolved reaction probabilities for the reactions of O + O<span>(_{2})</span> and Cl + H<span>(_{2})</span>(<span>(v_0)</span>=1) with <span>(J=0)</span> are computed, which involve long-time resonance states extending over long-range grids and are difficult for obtaining accurate results using the time-dependent method. The results through calculations are being compared to those obtained using the reactant coordinate-based (RCB) method and the interaction-asymptotic decomposition method (IARD).</p>","PeriodicalId":23045,"journal":{"name":"Theoretical Chemistry Accounts","volume":"59 1","pages":""},"PeriodicalIF":1.7,"publicationDate":"2024-07-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141611972","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}
Quantum dots (QDs) have attracted significant interest because of their tunable bandgaps, which enable numerous applications in fields such as photovoltaics, biomedicine, and materials science. This study explores various core electron treatments in the density functional theory (DFT) analysis of II-VI semiconductor quantum dots and their bulk counterparts. We compared All-electron (AE), Effective Core Potential (ECP), All-Electron Relativistic (AER), and DFT-Semicore pseudopotential (DSPP) treatments. Our findings indicate that the AE treatment aligns closely with the experimental results for smaller QDs, whereas the accuracy of DSPP increases with larger QDs. DSPP provides an optimal balance between computational efficiency and accuracy, making it suitable for studying II-VI QDs. Notably, the bandgap behavior varies, being direct for zinc and cadmium chalcogenides, whereas mercury chalcogenides are zero-gap semiconductors (semimetals). The inner bonds of the QDs exhibit an ionic character, whereas the terminal bonds display a covalent character. This study enhances our understanding of the structural and electronic properties of II-VI quantum QDs, aiding their application in various technologies.
{"title":"Comparison of various core electron treatments for studying the properties of II-VI quantum dots and their bulk counterparts: a DFT study","authors":"Rakhi Thareja, Jyoti Singh, Pragati Malik, Rita Kakkar","doi":"10.1007/s00214-024-03134-9","DOIUrl":"https://doi.org/10.1007/s00214-024-03134-9","url":null,"abstract":"<p>Quantum dots (QDs) have attracted significant interest because of their tunable bandgaps, which enable numerous applications in fields such as photovoltaics, biomedicine, and materials science. This study explores various core electron treatments in the density functional theory (DFT) analysis of II-VI semiconductor quantum dots and their bulk counterparts. We compared All-electron (AE), Effective Core Potential (ECP), All-Electron Relativistic (AER), and DFT-Semicore pseudopotential (DSPP) treatments. Our findings indicate that the AE treatment aligns closely with the experimental results for smaller QDs, whereas the accuracy of DSPP increases with larger QDs. DSPP provides an optimal balance between computational efficiency and accuracy, making it suitable for studying II-VI QDs. Notably, the bandgap behavior varies, being direct for zinc and cadmium chalcogenides, whereas mercury chalcogenides are zero-gap semiconductors (semimetals). The inner bonds of the QDs exhibit an ionic character, whereas the terminal bonds display a covalent character. This study enhances our understanding of the structural and electronic properties of II-VI quantum QDs, aiding their application in various technologies.</p>","PeriodicalId":23045,"journal":{"name":"Theoretical Chemistry Accounts","volume":"1 1","pages":""},"PeriodicalIF":1.7,"publicationDate":"2024-07-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141551647","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}
Pub Date : 2024-07-03DOI: 10.1007/s00214-024-03136-7
Cui Liu, Yu Yang, Kui Tang, Feiyang Wu, Yuyang Liu, Zhi Yang, Yuxin Chai, Jianping Sun
In this study, the geometric and electronic properties of Ti2CO2 and Ti2CO2/G heterostructures as anode materials for sodium-ion batteries were systematically investigated using first-principles calculations. The storage mechanism and properties of sodium atoms on Ti2CO2 and Ti2CO2/G heterostructures were further studied. By comparing the adsorption energy (− 1.4 eV, − 1.26 eV), diffusion barrier (0.21 eV, 0.14 eV), storage capacity (478mAh/g, 528mAh/g), average open-circuit voltage (0.68 eV, 0.51 eV), and elastic modulus (161.40 N/m, 364.82 N/m) of sodium atoms on Ti2CO2 and Ti2CO2/G heterostructures, we found that Ti2CO2/G heterostructure exhibits superior structural stability, better electronic conductivity, higher storage capacity, lower average open-circuit voltage, lower diffusion barrier, and superior mechanical performance. Through this study, we explore the potential of Ti2CO2/G as an anode material for sodium-ion batteries and its sodium storage mechanism.
{"title":"Properties of Ti2CO2 and Ti2CO2/G heterostructures as anodes of sodium-ion batteries by first-principles study","authors":"Cui Liu, Yu Yang, Kui Tang, Feiyang Wu, Yuyang Liu, Zhi Yang, Yuxin Chai, Jianping Sun","doi":"10.1007/s00214-024-03136-7","DOIUrl":"https://doi.org/10.1007/s00214-024-03136-7","url":null,"abstract":"<p>In this study, the geometric and electronic properties of Ti2CO2 and Ti2CO2/G heterostructures as anode materials for sodium-ion batteries were systematically investigated using first-principles calculations. The storage mechanism and properties of sodium atoms on Ti<sub>2</sub>CO<sub>2</sub> and Ti<sub>2</sub>CO<sub>2</sub>/G heterostructures were further studied. By comparing the adsorption energy (− 1.4 eV, − 1.26 eV), diffusion barrier (0.21 eV, 0.14 eV), storage capacity (478mAh/g, 528mAh/g), average open-circuit voltage (0.68 eV, 0.51 eV), and elastic modulus (161.40 N/m, 364.82 N/m) of sodium atoms on Ti<sub>2</sub>CO<sub>2</sub> and Ti<sub>2</sub>CO<sub>2</sub>/G heterostructures, we found that Ti<sub>2</sub>CO<sub>2</sub>/G heterostructure exhibits superior structural stability, better electronic conductivity, higher storage capacity, lower average open-circuit voltage, lower diffusion barrier, and superior mechanical performance. Through this study, we explore the potential of Ti<sub>2</sub>CO<sub>2</sub>/G as an anode material for sodium-ion batteries and its sodium storage mechanism.</p>","PeriodicalId":23045,"journal":{"name":"Theoretical Chemistry Accounts","volume":"2015 1","pages":""},"PeriodicalIF":1.7,"publicationDate":"2024-07-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141551646","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}
Pub Date : 2024-06-22DOI: 10.1007/s00214-024-03132-x
Juan Ferrer, Emilio San-Fabián
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 Magnetococcus marinus. 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 ab initio 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 (ab initio) methods giving us the key to the distribution of the interaction energies and therefore how dehydration occurs.
钠通道的选择性一直是众多实验和理论研究的主题。在这项研究中,我们从理论角度出发,根据海洋磁球菌(Magnetococcus marinus)电压激活通道开放结构的选择性过滤器(SF)建立了一个模型。通过这种方法,我们可以计算出系统(阳离子-水-SF-片段)中钠离子和钾离子的相互作用能量。结果凸显了阳离子差分脱水的重要性以及发生脱水的环境。半经验和 ab initio 方法被用于分析和量化阳离子在钠通道 SF 中的相互作用能,其中 DFT(ab initio)方法为我们提供了相互作用能分布的关键,因此也为我们提供了脱水发生的方式。
{"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":"24 1","pages":""},"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}
Pub Date : 2024-06-19DOI: 10.1007/s00214-024-03130-z
André G. H. Barbosa
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 D5h 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.
众所周知,环戊二烯阴离子的自旋耦合(SC)描述存在问题。对该阴离子的六轨道六电子自旋耦合计算打破了 D5h 电子密度空间对称性,将六个 pi 单占轨道中的两个近似定位在一个碳上。对同样的六个轨道上的六个 pi 电子进行的完全活性空间价键(CASVB)计算并没有打破对称性,在五个碳上产生了五个等效的 pi 轨道和一个沿 C5 分子旋转轴具有高振幅的 pi 轨道。自旋耦合计算包括五个轨道中的六个电子,即 SC(6,5),在碳上产生五个等效的非正交 pi 轨道,每个轨道的电子占有率为 "1.2"(6/5)。在本文中,这些不同的解法与本文作者提出的解法进行了对比。在作者提出的解法中,完全配对对称破缺解法的五个空间不同但等价的构型被组合在一起,进行了 30 个轨道中六个电子的多构型自旋耦合计算。结论是,尽管这种计算很复杂,但其结果在性质上更类似于对环戊二烯阴离子共振 pi 系统的价键式描述。
{"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<sub>5h</sub> 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 C<sub>5</sub> 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":"1 1","pages":""},"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}