Pub Date : 2025-02-01DOI: 10.1016/j.comptc.2025.115068
Eddy S. William , Samuel O. Inyang , Ituen B. Okon , Olusegun A. Akinde , Etido P. Inyang , Mfoniso U. Aka , Clement A. Onate , Okpo O. Ekerenam
Using the Nikiforov-Uvarov functional analysis (NUFA) method, we determined the energy eigenvalues and corresponding normalized eigenfunctions for a newly proposed shifted Deng-Fan-Hellmann potential in the presence of external magnetic and Aharonov-Bohm (AB) flux fields for H2, HCl, and CO molecules. Furthermore, we investigated the combined effect of magnetic and AB flux fields on the energy spectrum’s degeneracy. We have also obtained the energy eigenvalues for the special cases and cross-referenced them with findings from other studies to validate the accuracy of our analytical calculations. Using the Hellman-Feynman theorem, we derived expressions for the expectation values of the square of the inverse of position , kinetic energy , and square of momentum , along with their respective numerical values for the selected molecules. Additionally, we have obtained the thermomagnetic properties for the molecules using the energy eigenvalues. Our results are in line with the findings documented in the existing literature.
{"title":"Theoretical computation of eigenenergies, expectation values and thermodynamic functions of shifted Deng-Fan-Hellmann potential in external fields","authors":"Eddy S. William , Samuel O. Inyang , Ituen B. Okon , Olusegun A. Akinde , Etido P. Inyang , Mfoniso U. Aka , Clement A. Onate , Okpo O. Ekerenam","doi":"10.1016/j.comptc.2025.115068","DOIUrl":"10.1016/j.comptc.2025.115068","url":null,"abstract":"<div><div>Using the Nikiforov-Uvarov functional analysis (NUFA) method, we determined the energy eigenvalues and corresponding normalized eigenfunctions for a newly proposed shifted Deng-Fan-Hellmann potential in the presence of external magnetic and Aharonov-Bohm (AB) flux fields for H<sub>2</sub>, HCl, and CO molecules. Furthermore, we investigated the combined effect of magnetic and AB flux fields on the energy spectrum’s degeneracy. We have also obtained the energy eigenvalues for the special cases and cross-referenced them with findings from other studies to validate the accuracy of our analytical calculations. Using the Hellman-Feynman theorem, we derived expressions for the expectation values of the square of the inverse of position <span><math><mrow><mfenced><mrow><msup><mi>r</mi><mrow><mo>-</mo><mn>2</mn></mrow></msup></mrow></mfenced></mrow></math></span>, kinetic energy <span><math><mrow><mfenced><mrow><mi>T</mi></mrow></mfenced></mrow></math></span>, and square of momentum <span><math><mrow><mfenced><mrow><msup><mi>P</mi><mn>2</mn></msup></mrow></mfenced></mrow></math></span>, along with their respective numerical values for the selected molecules. Additionally, we have obtained the thermomagnetic properties for the molecules using the energy eigenvalues. Our results are in line with the findings documented in the existing literature.</div></div>","PeriodicalId":284,"journal":{"name":"Computational and Theoretical Chemistry","volume":"1244 ","pages":"Article 115068"},"PeriodicalIF":3.0,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143160050","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}
Pub Date : 2025-02-01DOI: 10.1016/j.comptc.2025.115071
Yi-Jia Wang , Lei Hu , Lei Hua , Ren-Zhong Li , Hong-Guang Xu , Wei-Jun Zheng
The interactions of methionine (Met) and heavy metal cations (Pb2+, Hg2+, and As3+) in both gas phase and aqueous solution were studied by theoretical calculations. The Met-Metal complex structures show that their most stable conformations in the gas phase are neutrals. In aqueous solution, Met-Pb2+ and Met-As3+ maintain neutrality, whereas Met-Hg2+ adopts a zwitterionic form. The proton transfer mechanism suggests that, for Met-Pb2+ and Met-Hg2+, the highest energy barrier of reaction is lower in aqueous solution compared to the gas phase, whereas for the Met-As3+ system, the opposite trend is observed. Additionally, the interaction energy, bond dissociation energy, atomic charge, interaction region indicator function, and atoms in molecules of key structures of the rate determining step in the proton transfer process were analyzed. The results will facilitate a deeper understanding of the mechanism underlying the complexation between amino acids and heavy metals.
{"title":"Structures and proton transfer processes of methionine effected by heavy metal cations (Pb2+, Hg2+, and As3+) in the gas phase and aqueous solution","authors":"Yi-Jia Wang , Lei Hu , Lei Hua , Ren-Zhong Li , Hong-Guang Xu , Wei-Jun Zheng","doi":"10.1016/j.comptc.2025.115071","DOIUrl":"10.1016/j.comptc.2025.115071","url":null,"abstract":"<div><div>The interactions of methionine (Met) and heavy metal cations (Pb<sup>2+</sup>, Hg<sup>2+</sup>, and As<sup>3+</sup>) in both gas phase and aqueous solution were studied by theoretical calculations. The Met-Metal complex structures show that their most stable conformations in the gas phase are neutrals. In aqueous solution, Met-Pb<sup>2+</sup> and Met-As<sup>3+</sup> maintain neutrality, whereas Met-Hg<sup>2+</sup> adopts a zwitterionic form. The proton transfer mechanism suggests that, for Met-Pb<sup>2+</sup> and Met-Hg<sup>2+</sup>, the highest energy barrier of reaction is lower in aqueous solution compared to the gas phase, whereas for the Met-As<sup>3+</sup> system, the opposite trend is observed. Additionally, the interaction energy, bond dissociation energy, atomic charge, interaction region indicator function, and atoms in molecules of key structures of the rate determining step in the proton transfer process were analyzed. The results will facilitate a deeper understanding of the mechanism underlying the complexation between amino acids and heavy metals.</div></div>","PeriodicalId":284,"journal":{"name":"Computational and Theoretical Chemistry","volume":"1244 ","pages":"Article 115071"},"PeriodicalIF":3.0,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143160057","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}
Pub Date : 2025-02-01DOI: 10.1016/j.comptc.2025.115069
E. Suárez, O. Guzmán-Juárez, R. Lemus
A general local algebraic model is proposed to describe the vibrational spectroscopy of molecules, including systems with normal mode behavior. The approach is based on the anharmonization of the algebraic representation of the normal modes at the local level without analogue in configuration space, albeit keeping the connection with it. An algebraic representation is obtained by introducing the bosonic realization associated with the normal modes. Latter on, a canonical transformation to pseudo local operators is proposed, which in turn are mapped to -operators associated with Morse ladder operators. The principal isotopologue of FCN is taken as an example. The vibrational description was carried out including 159 experimental energies with cm. A description of the isotopologues is described with similar quality. It is shown that the estimation of the force constants allows the correct wave functions to be obtained.
{"title":"A general local algebraic approach for molecules with normal mode behavior: Application to FCN","authors":"E. Suárez, O. Guzmán-Juárez, R. Lemus","doi":"10.1016/j.comptc.2025.115069","DOIUrl":"10.1016/j.comptc.2025.115069","url":null,"abstract":"<div><div>A general local algebraic model is proposed to describe the vibrational spectroscopy of molecules, including systems with normal mode behavior. The approach is based on the anharmonization of the algebraic representation of the normal modes at the local level without analogue in configuration space, albeit keeping the connection with it. An algebraic representation is obtained by introducing the bosonic realization associated with the normal modes. Latter on, a canonical transformation to pseudo local operators is proposed, which in turn are mapped to <span><math><mrow><mi>s</mi><mi>u</mi><mrow><mo>(</mo><mn>2</mn><mo>)</mo></mrow></mrow></math></span>-operators associated with Morse ladder operators. The principal isotopologue of FCN is taken as an example. The vibrational description was carried out including 159 experimental energies with <span><math><mrow><mi>rm</mi><mi>s</mi><mo>=</mo><mn>0</mn><mo>.</mo><mn>25</mn><mspace></mspace></mrow></math></span> cm<span><math><msup><mrow></mrow><mrow><mtext>-1</mtext></mrow></msup></math></span>. A description of the isotopologues is described with similar quality. It is shown that the estimation of the force constants allows the correct wave functions to be obtained.</div></div>","PeriodicalId":284,"journal":{"name":"Computational and Theoretical Chemistry","volume":"1244 ","pages":"Article 115069"},"PeriodicalIF":3.0,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143160058","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}
Pub Date : 2025-02-01DOI: 10.1016/j.comptc.2025.115070
Xing Jin , Xiaodong Tang , Wanfen Pu , Renbao Liu , Yu Yang
Heavy oil is a crucial energy resource, and in-situ combustion (ISC) is regarded as one of the most efficient technologies for its recovery. Low temperature oxidation (LTO) is a critical process in enabling ISC technology. The Reactive Force Field (ReaxFF) method was employed to investigate the low-temperature oxidation (LTO) of heavy oil. The simulation results closely align with experimental data, validating the accuracy of the heavy oil model. The study reveals that LTO initiates with the decomposition of long carbon chains, resulting in the formation of alkylperoxy radicals, while CO2 is produced from the oxidation of smaller carbon fragments. The residual products of LTO include polycyclic aromatic hydrocarbons and aromatic compounds. These molecular-level insights into the LTO mechanisms offer valuable guidance for optimizing the process of in-situ combustion (ISC).
{"title":"Study on the characteristics and mechanism of low-temperature oxidation of heavy oil using ReaxFF molecular dynamics simulation","authors":"Xing Jin , Xiaodong Tang , Wanfen Pu , Renbao Liu , Yu Yang","doi":"10.1016/j.comptc.2025.115070","DOIUrl":"10.1016/j.comptc.2025.115070","url":null,"abstract":"<div><div>Heavy oil is a crucial energy resource, and in-situ combustion (ISC) is regarded as one of the most efficient technologies for its recovery. Low temperature oxidation (LTO) is a critical process in enabling ISC technology. The Reactive Force Field (ReaxFF) method was employed to investigate the low-temperature oxidation (LTO) of heavy oil. The simulation results closely align with experimental data, validating the accuracy of the heavy oil model. The study reveals that LTO initiates with the decomposition of long carbon chains, resulting in the formation of alkylperoxy radicals, while CO<sub>2</sub> is produced from the oxidation of smaller carbon fragments. The residual products of LTO include polycyclic aromatic hydrocarbons and aromatic compounds. These molecular-level insights into the LTO mechanisms offer valuable guidance for optimizing the process of in-situ combustion (ISC).</div></div>","PeriodicalId":284,"journal":{"name":"Computational and Theoretical Chemistry","volume":"1244 ","pages":"Article 115070"},"PeriodicalIF":3.0,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143160082","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}
Pub Date : 2025-02-01DOI: 10.1016/j.comptc.2024.115048
Rui Huang , Ze Wei , Jianhai Wang , Wenjing Ji , Junjie Zhu , Yuxuan Wang , Zhijun Wang , Xiaoyue Yao , Xinqun Wang , Hui Liu
Ferrous sulfide is one of sulfur corrosion products generated during the transportation and storage of petroleum. It possesses strong spontaneous combustion properties, potentially leading to fires or even explosions in the petrochemical industry. Ionic liquids, as a new class of green compounds, show promising potential for spontaneous combustion inhibition. In this paper, 60 common imidazolium-based ionic liquids are selected as inhibitors, and the inhibition effect and inhibition mechanism of ionic liquids are studied from the microscopic point of view. The results show that among the 60 imidazolium-based ionic liquids, those with the highest inhibition efficiency are [EMIM]C5H11BF3, [OMIM]CH3COO, and [C12MIM]BF4, and the inhibition efficiencies of the adsorbed molecules are in the following order: H2O > H2S > CH3SH > O2. An appropriate increase in the length of the alkyl chains on the imidazole ring of ionic liquids, as well as the introduction of substituents, can enhance the activity of the molecules, thereby improving their inhibition efficiency. Based on the structural properties and inhibition effect of ionic liquids, a quantitative structure–activity relationship (QSAR) method using quantum chemical descriptors to predict the inhibition effect of ionic liquids is proposed. Five descriptors are identified as the key factors influencing the inhibition efficiency of ionic liquids, with the prediction effect for O2 being the most accurate. The results are of great significance for revealing the mechanism of ferrous sulfide spontaneous combustion inhibited and the prevention and control of spontaneous combustion hazards.
{"title":"Quantitative structure–activity relationship and mechanism of ionic liquids inhibiting spontaneous combustion of ferrous sulfide","authors":"Rui Huang , Ze Wei , Jianhai Wang , Wenjing Ji , Junjie Zhu , Yuxuan Wang , Zhijun Wang , Xiaoyue Yao , Xinqun Wang , Hui Liu","doi":"10.1016/j.comptc.2024.115048","DOIUrl":"10.1016/j.comptc.2024.115048","url":null,"abstract":"<div><div>Ferrous sulfide is one of sulfur corrosion products generated during the transportation and storage of petroleum. It possesses strong spontaneous combustion properties, potentially leading to fires or even explosions in the petrochemical industry. Ionic liquids, as a new class of green compounds, show promising potential for spontaneous combustion inhibition. In this paper, 60 common imidazolium-based ionic liquids are selected as inhibitors, and the inhibition effect and inhibition mechanism of ionic liquids are studied from the microscopic point of view. The results show that among the 60 imidazolium-based ionic liquids, those with the highest inhibition efficiency are [EMIM]C<sub>5</sub>H<sub>11</sub>BF<sub>3</sub>, [OMIM]CH<sub>3</sub>COO, and [C<sub>12</sub>MIM]BF<sub>4</sub>, and the inhibition efficiencies of the adsorbed molecules are in the following order: H<sub>2</sub>O > H<sub>2</sub>S > CH<sub>3</sub>SH > O<sub>2</sub>. An appropriate increase in the length of the alkyl chains on the imidazole ring of ionic liquids, as well as the introduction of substituents, can enhance the activity of the molecules, thereby improving their inhibition efficiency. Based on the structural properties and inhibition effect of ionic liquids, a quantitative structure–activity relationship (QSAR) method using quantum chemical descriptors to predict the inhibition effect of ionic liquids is proposed. Five descriptors are identified as the key factors influencing the inhibition efficiency of ionic liquids, with the prediction effect for O<sub>2</sub> being the most accurate. The results are of great significance for revealing the mechanism of ferrous sulfide spontaneous combustion inhibited and the prevention and control of spontaneous combustion hazards.</div></div>","PeriodicalId":284,"journal":{"name":"Computational and Theoretical Chemistry","volume":"1244 ","pages":"Article 115048"},"PeriodicalIF":3.0,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143160642","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}
Pub Date : 2025-02-01DOI: 10.1016/j.comptc.2024.115042
Jalloul Trabelsi , Mounir Esboui , Sahbi Essid
Structures, optical properties and circular dichroism of chiral smectic liquid crystals, specifically denoted as CnF2(COO), CnF2(COS), and CnF2(CO Se) with n ranging from 7 to 12, were investigated using density functional theory (DFT). Based on the optimized molecular geometries of these compounds, we report the UV–Vis absorption spectra, optical properties, circular dichroism, and involving ππ* and nπ*electronic transitions. Our analysis delves into the influence of the alkyl chain length and substituents on optical properties, circular dichroism, as well as the highest occupied molecular orbital (HOMO), lowest unoccupied molecular orbital (LUMO), and the energy gap. Notably, the substituents lead to shifts in the UV–Vis absorption spectra. In addition, we explore the changes in polarizability associated with the alkyl chain length of these different substitutions. The interaction between an external electric field and liquid crystals is reconsidered, by studying its effect on polarizabilities and on the dipole moment. We note significant changes in the dipole moment and polarizability occurring at an electric field of about 4.5 V/nm for C7F2(COO), 5 V/nm for C7F2(COS) and 5.5 V/nm for C7F2(COSe).
{"title":"DFT study of the effect of substitution and of the alkyl chain length on optical properties and polarizabilities of CnF2(COX) (X = O, S, Se)","authors":"Jalloul Trabelsi , Mounir Esboui , Sahbi Essid","doi":"10.1016/j.comptc.2024.115042","DOIUrl":"10.1016/j.comptc.2024.115042","url":null,"abstract":"<div><div>Structures, optical properties and circular dichroism of chiral smectic liquid crystals, specifically denoted as C<em><sub>n</sub></em>F<sub>2</sub>(COO), C<em><sub>n</sub></em>F<sub>2</sub>(COS), and C<em><sub>n</sub></em>F<sub>2</sub>(CO Se) with <em>n</em> ranging from 7 to 12, were investigated using density functional theory (DFT). Based on the optimized molecular geometries of these compounds, we report the UV–Vis absorption spectra, optical properties, circular dichroism, and involving ππ* and nπ*electronic transitions. Our analysis delves into the influence of the alkyl chain length and substituents on optical properties, circular dichroism, as well as the highest occupied molecular orbital (HOMO), lowest unoccupied molecular orbital (LUMO), and the energy gap. Notably, the substituents lead to shifts in the UV–Vis absorption spectra. In addition, we explore the changes in polarizability associated with the alkyl chain length of these different substitutions. The interaction between an external electric field and liquid crystals is reconsidered, by studying its effect on polarizabilities and on the dipole moment. We note significant changes in the dipole moment and polarizability occurring at an electric field of about 4.5 V/nm for C<sub>7</sub>F<sub>2</sub>(COO), 5 V/nm for C<sub>7</sub>F<sub>2</sub>(COS) and 5.5 V/nm for C<sub>7</sub>F<sub>2</sub>(COSe).</div></div>","PeriodicalId":284,"journal":{"name":"Computational and Theoretical Chemistry","volume":"1244 ","pages":"Article 115042"},"PeriodicalIF":3.0,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143160645","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}
Pub Date : 2025-02-01DOI: 10.1016/j.comptc.2024.115019
I.K. Petrushenko
Interactions of a benzene molecule with four different silica clusters decorated with mono- and divalent cations (Li+, Na+, Mg2+) have been theoretically studied. By means of SAPT0 calculations, we have analyzed the changes in the energy components in dependence of hydrophobic or hydrophilic positions of adsorption, the size of the cluster studied or the cation used for the ’decoration’. It was found that adsorption of benzene on pristine silica clusters is mainly driven by electrostatic (∼37–43 %) and dispersion (∼37–55 %) forces. At the same time, cation–π interactions can be accounted for by significant electrostatic (∼20–50 %) and induction (∼24–54 %) energy terms. IGM analysis reveals the existence of cation–π and van der Waals interactions. The significant binding of benzene to the decorated silica surface (up to ∼ − 19.97, −29.63, − 93.82 kcal/mol for Na+, Li+, Mg2+, respectively) can pave a way for the sorption of a typical organic contaminant.
{"title":"Physisorption of benzene on cation/silica clusters via cation–π interactions: Theoretical study","authors":"I.K. Petrushenko","doi":"10.1016/j.comptc.2024.115019","DOIUrl":"10.1016/j.comptc.2024.115019","url":null,"abstract":"<div><div>Interactions of a benzene molecule with four different silica clusters decorated with mono- and divalent cations (Li<sup>+</sup>, Na<sup>+</sup>, Mg<sup>2+</sup>) have been theoretically studied. By means of SAPT0 calculations, we have analyzed the changes in the energy components in dependence of hydrophobic or hydrophilic positions of adsorption, the size of the cluster studied or the cation used for the ’decoration’. It was found that adsorption of benzene on pristine silica clusters is mainly driven by electrostatic (∼37–43 %) and dispersion (∼37–55 %) forces. At the same time, cation–π interactions can be accounted for by significant electrostatic (∼20–50 %) and induction (∼24–54 %) energy terms. IGM analysis reveals the existence of cation–π and van der Waals interactions. The significant binding of benzene to the decorated silica surface (up to ∼ − 19.97, −29.63, − 93.82 kcal/mol for Na<sup>+</sup>, Li<sup>+</sup>, Mg<sup>2+</sup>, respectively) can pave a way for the sorption of a typical organic contaminant.</div></div>","PeriodicalId":284,"journal":{"name":"Computational and Theoretical Chemistry","volume":"1244 ","pages":"Article 115019"},"PeriodicalIF":3.0,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143161369","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}
Pub Date : 2025-02-01DOI: 10.1016/j.comptc.2024.115043
Mohammed I. Alomari , Taher S. Ababneh , Jamal N. Dawoud
The adsorption characteristics and structural dynamics of CO2 within the cavities of three cucurbiturils—CB[4], CB[5], and CB[6]—have been examined using DFT calculations, specifically APF-D and ωB97XD functionals with the 6-31+G(d) and aug-cc-pVTZ basis sets. The CO2 adsorption configurations reveal two minimal-energy poses: a vertical alignment at the entrance and a horizontal alignment at the center of the host molecule. The quantum chemical results suggest a stronger affinity for CO2 adsorption in the larger cucurbiturils compared to their smaller counterparts. The strongest interaction energy among all binding sites is observed for CO2 located at the portal of CB[5], with an interaction energy of approximately −40 kJ/mol. At the center of host molecules, CB[6] demonstrates the strongest attractive energy toward CO2 and achieves the highest adsorption rate. Conversely, CO2 capture in smaller cucurbiturils, such as CB[4], is less effective due to their smaller cavity size. The encapsulation efficiency follows the trend CB[6] > CB[5] > CB[4]. The interaction between the host and guest is identified as van der Waals, as indicated by natural bond orbital (NBO) analysis.
{"title":"Structural, thermodynamic, and kinetic analysis of CO2 binding with cucurbiturils (CB[4], CB[5], CB[6]): A DFT computational study","authors":"Mohammed I. Alomari , Taher S. Ababneh , Jamal N. Dawoud","doi":"10.1016/j.comptc.2024.115043","DOIUrl":"10.1016/j.comptc.2024.115043","url":null,"abstract":"<div><div>The adsorption characteristics and structural dynamics of CO<sub>2</sub> within the cavities of three cucurbiturils—CB[4], CB[5], and CB[6]—have been examined using DFT calculations, specifically APF-D and ωB97XD functionals with the 6-31+G(d) and aug-cc-pVTZ basis sets. The CO<sub>2</sub> adsorption configurations reveal two minimal-energy poses: a vertical alignment at the entrance and a horizontal alignment at the center of the host molecule. The quantum chemical results suggest a stronger affinity for CO<sub>2</sub> adsorption in the larger cucurbiturils compared to their smaller counterparts. The strongest interaction energy among all binding sites is observed for CO<sub>2</sub> located at the portal of CB[5], with an interaction energy of approximately −40 kJ/mol. At the center of host molecules, CB[6] demonstrates the strongest attractive energy toward CO<sub>2</sub> and achieves the highest adsorption rate. Conversely, CO<sub>2</sub> capture in smaller cucurbiturils, such as CB[4], is less effective due to their smaller cavity size. The encapsulation efficiency follows the trend CB[6] > CB[5] > CB[4]. The interaction between the host and guest is identified as van der Waals, as indicated by natural bond orbital (NBO) analysis.</div></div>","PeriodicalId":284,"journal":{"name":"Computational and Theoretical Chemistry","volume":"1244 ","pages":"Article 115043"},"PeriodicalIF":3.0,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143161373","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}
Pub Date : 2025-02-01DOI: 10.1016/j.comptc.2024.115039
Mengguo Chen , Fanru Yuan , Huijian Zhao , Zhili Yin , Shaohui Liu , Hongmin Liu , Longhua Yang
Three newly identified pathological mutations (Glu379Lys, Asp556Gly, Tyr761His) in histone lysine-specific demethylase 1 (LSD1) are associated with a novel genetic disorder. To understand how they affect the properties of this chromatin-associated enzyme at the atomic level, this study investigated the interaction mechanisms of wild-type and mutated LSD1 with histone H3 and non-histone Snail1 substrates using a combination of virtual mutations, molecular dynamics simulations, and free energy calculations. Results show Glu379Lys causes the most significant decrease in binding affinity and catalytic ability due to charge reversal, with effects varying at different terminals for different substrates. Asp556Gly’s impact is minimized by compensation from adjacent Asp555 and Asp553. Tyr761His affects binding and catalytic abilities through altered relative positions of Tyr761/Tyr761His, Met4/Phe4, and FAD. This research establishes a theoretical foundation for investigating the pathological mechanism in patients with these separate mutations, and holds value for further designing specific LSD1 inhibitors for their treatment.
{"title":"Computational simulation study of the mutation effects on the interaction mechanisms of LSD1 with histone H3 and non-histone Snail1 substrates","authors":"Mengguo Chen , Fanru Yuan , Huijian Zhao , Zhili Yin , Shaohui Liu , Hongmin Liu , Longhua Yang","doi":"10.1016/j.comptc.2024.115039","DOIUrl":"10.1016/j.comptc.2024.115039","url":null,"abstract":"<div><div>Three newly identified pathological mutations (Glu379Lys, Asp556Gly, Tyr761His) in histone lysine-specific demethylase 1 (LSD1) are associated with a novel genetic disorder. To understand how they affect the properties of this chromatin-associated enzyme at the atomic level, this study investigated the interaction mechanisms of wild-type and mutated LSD1 with histone H3 and non-histone Snail1 substrates using a combination of virtual mutations, molecular dynamics simulations, and free energy calculations. Results show Glu379Lys causes the most significant decrease in binding affinity and catalytic ability due to charge reversal, with effects varying at different terminals for different substrates. Asp556Gly’s impact is minimized by compensation from adjacent Asp555 and Asp553. Tyr761His affects binding and catalytic abilities through altered relative positions of Tyr761/Tyr761His, Met4/Phe4, and FAD. This research establishes a theoretical foundation for investigating the pathological mechanism in patients with these separate mutations, and holds value for further designing specific LSD1 inhibitors for their treatment.</div></div>","PeriodicalId":284,"journal":{"name":"Computational and Theoretical Chemistry","volume":"1244 ","pages":"Article 115039"},"PeriodicalIF":3.0,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143161378","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}
Pub Date : 2025-02-01DOI: 10.1016/j.comptc.2025.115108
Zhifeng Li , Xiao Ru , Zijing Lin
The properties of peptides are determined by their conformations, making it essential to obtain their conformational ensembles; however, this presents significant challenges when using computational methods. In this study, we propose a novel method for searching low-energy conformational ensembles of peptides. This method integrates a splicing-based approach with a workflow that employs potential energy surfaces of varying accuracy and computational efficiency. When applied to a set of short peptides, our method demonstrates superior capability in identifying low-energy structures and generating structurally diverse ensembles compared to existing state-of-the-art techniques. The results suggest that this method is a reliable and efficient tool for obtaining low-energy conformational ensembles of peptides, which is useful for many peptide researches.
{"title":"Peptide conformation search using fragment splicing and tiered energy models","authors":"Zhifeng Li , Xiao Ru , Zijing Lin","doi":"10.1016/j.comptc.2025.115108","DOIUrl":"10.1016/j.comptc.2025.115108","url":null,"abstract":"<div><div>The properties of peptides are determined by their conformations, making it essential to obtain their conformational ensembles; however, this presents significant challenges when using computational methods. In this study, we propose a novel method for searching low-energy conformational ensembles of peptides. This method integrates a splicing-based approach with a workflow that employs potential energy surfaces of varying accuracy and computational efficiency. When applied to a set of short peptides, our method demonstrates superior capability in identifying low-energy structures and generating structurally diverse ensembles compared to existing state-of-the-art techniques. The results suggest that this method is a reliable and efficient tool for obtaining low-energy conformational ensembles of peptides, which is useful for many peptide researches.</div></div>","PeriodicalId":284,"journal":{"name":"Computational and Theoretical Chemistry","volume":"1245 ","pages":"Article 115108"},"PeriodicalIF":3.0,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143143769","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}
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