Pub Date : 2023-10-16DOI: 10.1080/00268976.2023.2268191
Zhengyi Zhang, Hua Fang
ABSTRACTThe excited-state intramolecular proton transfer (ESIPT) mechanism and photophysical properties of three –CN-substituted (2-(4-(diethylamino)phenyl)- 3-mercapto-4H-chromen-4-one (3-NTF) compounds (3NTF-1, 3NTF-2, 3NTF-3) have been studied systematically based on density functional theory (DFT) and time-dependent DFT (TD-DFT) methods. We analysed the structural parameters, infrared frequencies and electron densities of the studied compounds, and found that the intramolecular hydrogen bonds (IHBs) at tautomer form are weakened in the excited (S1) state. The weaker IHB at tautomer form is beneficial to ESIPT process. The potential energy curves (PECs) were established and showed that the ESIPT processes of 3NTF-1 and 3NTF-2 are barrierless. The ESIPT process of 3NTF-3 needs to overcome a very low energy barrier. The electron-withdrawing group (–CN) increases the energy barrier of ground state intramolecular proton transfer (GSIPT) process in 3NTF. The order of GSIPT barrier is consistent with the order of their IHB strengths of normal forms. When the electron-withdrawing group (–CN) was introduced, the absorption and fluorescence peaks red-shifted. Two –CN groups resulted in the fluorescence peak of 3NTF red-shift more than one –CN group did.KEYWORDS: Excited state intramolecular proton transfer (ESIPT)time-dependent density functional theoryphotophysical propertypush–pull Disclosure statementNo potential conflict of interest was reported by the author(s).
{"title":"Effect of push–Pull functional group on the ESIPT behaviour and photophysical property of thiolflavone-based compound: a TD-DFT investigation","authors":"Zhengyi Zhang, Hua Fang","doi":"10.1080/00268976.2023.2268191","DOIUrl":"https://doi.org/10.1080/00268976.2023.2268191","url":null,"abstract":"ABSTRACTThe excited-state intramolecular proton transfer (ESIPT) mechanism and photophysical properties of three –CN-substituted (2-(4-(diethylamino)phenyl)- 3-mercapto-4H-chromen-4-one (3-NTF) compounds (3NTF-1, 3NTF-2, 3NTF-3) have been studied systematically based on density functional theory (DFT) and time-dependent DFT (TD-DFT) methods. We analysed the structural parameters, infrared frequencies and electron densities of the studied compounds, and found that the intramolecular hydrogen bonds (IHBs) at tautomer form are weakened in the excited (S1) state. The weaker IHB at tautomer form is beneficial to ESIPT process. The potential energy curves (PECs) were established and showed that the ESIPT processes of 3NTF-1 and 3NTF-2 are barrierless. The ESIPT process of 3NTF-3 needs to overcome a very low energy barrier. The electron-withdrawing group (–CN) increases the energy barrier of ground state intramolecular proton transfer (GSIPT) process in 3NTF. The order of GSIPT barrier is consistent with the order of their IHB strengths of normal forms. When the electron-withdrawing group (–CN) was introduced, the absorption and fluorescence peaks red-shifted. Two –CN groups resulted in the fluorescence peak of 3NTF red-shift more than one –CN group did.KEYWORDS: Excited state intramolecular proton transfer (ESIPT)time-dependent density functional theoryphotophysical propertypush–pull Disclosure statementNo potential conflict of interest was reported by the author(s).","PeriodicalId":18817,"journal":{"name":"Molecular Physics","volume":"77 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-10-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"136115366","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 : 2023-10-16DOI: 10.1080/00268976.2023.2268745
Ye-Xuan Li, Zhong-Min Su, Hong-Liang Xu
AbstractThe helical structure is a classical framework to design high-performance organic electro-optical materials. In this work, the structure-property’s relationships of helical tetraspirobenzene (1) and its oxidation (12+) and reduction (12–) products are explored. The results show that the redox brings some distinctive changes in their geometric structure and electronic property, which regulate the first hyperpolarisability (βtot). Among these structures, the 12– has the largest βtot value of 4.2 × 104, which is greatly larger than 2.0 × 102 a.u. of. 12+. Therefore, the reduction effect is more obvious than the oxidation effect. Furthermore, the UV-Vis absorption spectrum also proves this phenomenon: the oxidation product has a new red-shifted absorption peak (571 nm) and the reduction product has two new red-shifted absorption peaks (577 and 797 nm). We hope the present work can provide theoretical guidance for the search for high-performance nonlinear optical materials by using the redox effect.KEYWORDS: TetraspirobenzeneRedoxNLO property AcknowledgementsYe-Xuan Li: Data curation, Writing – original draft, Writing – review & editing. Hong-Liang Xu: Conceptualisation, Methodology, Writing – review & editing. Zhong-Min Su: Supervision.Disclosure statementNo potential conflict of interest was reported by the author(s).Data availability statementData will be made available on request.Additional informationFundingWe gratefully acknowledge the Natural Science Foundation of Science and Technology Department of Jilin Province [20230101043JC].
{"title":"Probing the REDOX effect of helical tetraspirobenzene on nonlinear optical properties","authors":"Ye-Xuan Li, Zhong-Min Su, Hong-Liang Xu","doi":"10.1080/00268976.2023.2268745","DOIUrl":"https://doi.org/10.1080/00268976.2023.2268745","url":null,"abstract":"AbstractThe helical structure is a classical framework to design high-performance organic electro-optical materials. In this work, the structure-property’s relationships of helical tetraspirobenzene (1) and its oxidation (12+) and reduction (12–) products are explored. The results show that the redox brings some distinctive changes in their geometric structure and electronic property, which regulate the first hyperpolarisability (βtot). Among these structures, the 12– has the largest βtot value of 4.2 × 104, which is greatly larger than 2.0 × 102 a.u. of. 12+. Therefore, the reduction effect is more obvious than the oxidation effect. Furthermore, the UV-Vis absorption spectrum also proves this phenomenon: the oxidation product has a new red-shifted absorption peak (571 nm) and the reduction product has two new red-shifted absorption peaks (577 and 797 nm). We hope the present work can provide theoretical guidance for the search for high-performance nonlinear optical materials by using the redox effect.KEYWORDS: TetraspirobenzeneRedoxNLO property AcknowledgementsYe-Xuan Li: Data curation, Writing – original draft, Writing – review & editing. Hong-Liang Xu: Conceptualisation, Methodology, Writing – review & editing. Zhong-Min Su: Supervision.Disclosure statementNo potential conflict of interest was reported by the author(s).Data availability statementData will be made available on request.Additional informationFundingWe gratefully acknowledge the Natural Science Foundation of Science and Technology Department of Jilin Province [20230101043JC].","PeriodicalId":18817,"journal":{"name":"Molecular Physics","volume":"81 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-10-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"136115003","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 : 2023-10-11DOI: 10.1080/00268976.2023.2267694
José A. Vélez-Pérez, Luis Olivares-Quiroz
AbstractWe analyse the role of single-point mutations on the translocation of heteropolymer protein chains with helical folding. We propose a statistical mechanics model that computes the equilibrium partition function of a given protein by incorporating experimental helix propensities of amino acids. From that we evaluate the free energy barrier for translocation and the average translocation time for single-point protein mutants and compared with wild-type proteins used as reference. In our calculations, single-point mutations that increase energy of the folded state in 5kJ/mol increase the energy barrier for translocation up to 50%, ∼0.75kBT, in consequence, the translocation time undergoes variations between 10% and 150% with the largest variations associated to substitutions of amino acids glycine and proline by alanine. In fact, substitutions of amino acids with the lowest helix propensities by amino acids with the largest helix propensities induced the largest mutational effects. These results indicate that effects of single-point mutations become evident when mutations increase energy of the folded state at least in ∼5kJ/mol. Our model predicts translocation time delays for proline to alanine single-point mutations which agree with deficiencies of protein translocation observed recently in experiments.Keywords: Statistical physicsfirst passage timepartition function AcknowledgmentsJosé Antonio Vélez-Pérez thanks Sistema Nacional de Investigadores (SNI) CONAHCyT for their support. Luis Olivares-Quiroz would like to acknowledge support from Sistema Nacional de Investigadores (SNI-CONAHCyT) and Colegio de Ciencia y Tecnología (CyT) Universidad Autónoma de la Ciudad de México UACM.Disclosure statementNo potential conflict of interest was reported by the author(s).
摘要分析了单点突变对螺旋折叠异聚蛋白链易位的影响。我们提出了一个统计力学模型，通过结合氨基酸的实验螺旋倾向来计算给定蛋白质的平衡配分函数。以此计算了单点蛋白突变体易位的自由能垒和平均易位时间，并与野生型蛋白进行了比较。在我们的计算中，单点突变增加5kJ/mol折叠态的能量，使易位的能量势垒增加50%，约0.75kBT，因此，易位时间的变化在10%到150%之间，其中最大的变化与氨基酸甘氨酸和脯氨酸被丙氨酸取代有关。事实上，螺旋倾向最小的氨基酸被螺旋倾向最大的氨基酸取代会引起最大的突变效应。这些结果表明，当突变增加折叠态的能量至少在~ 5kJ/mol时，单点突变的影响变得明显。我们的模型预测了脯氨酸到丙氨酸单点突变的易位时间延迟，这与最近在实验中观察到的蛋白质易位缺陷一致。关键词:统计物理第一次穿越时间划分函数致谢jossjosantonio vsamez - psamez感谢Sistema Nacional de Investigadores (SNI) CONAHCyT的支持。Luis Olivares-Quiroz在此感谢国家调查系统(SNI-CONAHCyT)和Tecnología科学学院(CyT) Autónoma墨西哥墨西哥大学(UACM)的支持。披露声明作者未报告潜在的利益冲突。
{"title":"Effects of single-point mutations on translocation of non-interacting heteropolymer protein chains","authors":"José A. Vélez-Pérez, Luis Olivares-Quiroz","doi":"10.1080/00268976.2023.2267694","DOIUrl":"https://doi.org/10.1080/00268976.2023.2267694","url":null,"abstract":"AbstractWe analyse the role of single-point mutations on the translocation of heteropolymer protein chains with helical folding. We propose a statistical mechanics model that computes the equilibrium partition function of a given protein by incorporating experimental helix propensities of amino acids. From that we evaluate the free energy barrier for translocation and the average translocation time for single-point protein mutants and compared with wild-type proteins used as reference. In our calculations, single-point mutations that increase energy of the folded state in 5kJ/mol increase the energy barrier for translocation up to 50%, ∼0.75kBT, in consequence, the translocation time undergoes variations between 10% and 150% with the largest variations associated to substitutions of amino acids glycine and proline by alanine. In fact, substitutions of amino acids with the lowest helix propensities by amino acids with the largest helix propensities induced the largest mutational effects. These results indicate that effects of single-point mutations become evident when mutations increase energy of the folded state at least in ∼5kJ/mol. Our model predicts translocation time delays for proline to alanine single-point mutations which agree with deficiencies of protein translocation observed recently in experiments.Keywords: Statistical physicsfirst passage timepartition function AcknowledgmentsJosé Antonio Vélez-Pérez thanks Sistema Nacional de Investigadores (SNI) CONAHCyT for their support. Luis Olivares-Quiroz would like to acknowledge support from Sistema Nacional de Investigadores (SNI-CONAHCyT) and Colegio de Ciencia y Tecnología (CyT) Universidad Autónoma de la Ciudad de México UACM.Disclosure statementNo potential conflict of interest was reported by the author(s).","PeriodicalId":18817,"journal":{"name":"Molecular Physics","volume":"49 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-10-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"136211016","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 : 2023-10-10DOI: 10.1080/00268976.2023.2266069
Md Anamul Haque Shumon, Md. Masud Alam, Farah Khan, Sharmin Sultana, Mohammad K. Islam, Abdallah A. A. Mohammed, Salman A. Khan, Md. Anamul Hoque, Shariff E. Kabir
AbstractHerein, the phase separation of triton X-100 (TNX-100) and cephradine monohydrate (CPM) drug (a first-generation cephalosporin family drug) mixture was studied in aqueous and in various aq. electrolytes (Na and K-based salts) media. As compared to the water environment, TNX 100 + CPM system demonstrated lower magnitudes of CP values in electrolytes solution. The outcomes exhibited dwindling CP values are: MCl < M2CO3 < M2SO4; (M = Na, K). Moreover, the ΔHc0 (enthalpy change), ΔGc0 (free energy change) and ΔSc0 (entropy change), compensation temperature (Tc) and intrinsic enthalpy gain (ΔHc0,∗) were also computed in the circumstances of TNX 100 + CPM mixture in water and aq. electrolytes media. The values of ΔGc0 were obtained to be positive demonstrating the non-spontaneity of the process. The ΔHc0 and ΔSc0 values were positive in aq. medium and negative in aq. salts solutions where the magnitudes ΔHc0 and ΔSc0 values decreased with the growing contents of TNX 100/salts. The results suggest that the interaction forces between TNX 100 and CPM in a water environment are hydrophobic in nature with π–π interactions whereas in aq. salts media the recommended forces are hydrophobic and exothermic forces along with π–π interactions.KEYWORDS: TNX 100cephradine monohydrateelectrolytesphase separationthermodynamics Disclosure statementNo potential conflict of interest was reported by the author(s).Additional informationFundingThis work was funded by the Researchers Supporting Project Number [RSPD2023R766] King Saud University, Riyadh, Saudi Arabia. Md. Masud Alam would like to acknowledge Mawlana Bhashani Science and Technology University, Bangladesh for providing financial support (Year 2021) to carry out a part of the research work.
{"title":"Phase separation and physico-chemical variables of triton X-100 and cephradine monohydrate drug mixture: investigation of the impacts of nature of electrolytes and compositions","authors":"Md Anamul Haque Shumon, Md. Masud Alam, Farah Khan, Sharmin Sultana, Mohammad K. Islam, Abdallah A. A. Mohammed, Salman A. Khan, Md. Anamul Hoque, Shariff E. Kabir","doi":"10.1080/00268976.2023.2266069","DOIUrl":"https://doi.org/10.1080/00268976.2023.2266069","url":null,"abstract":"AbstractHerein, the phase separation of triton X-100 (TNX-100) and cephradine monohydrate (CPM) drug (a first-generation cephalosporin family drug) mixture was studied in aqueous and in various aq. electrolytes (Na and K-based salts) media. As compared to the water environment, TNX 100 + CPM system demonstrated lower magnitudes of CP values in electrolytes solution. The outcomes exhibited dwindling CP values are: MCl < M2CO3 < M2SO4; (M = Na, K). Moreover, the ΔHc0 (enthalpy change), ΔGc0 (free energy change) and ΔSc0 (entropy change), compensation temperature (Tc) and intrinsic enthalpy gain (ΔHc0,∗) were also computed in the circumstances of TNX 100 + CPM mixture in water and aq. electrolytes media. The values of ΔGc0 were obtained to be positive demonstrating the non-spontaneity of the process. The ΔHc0 and ΔSc0 values were positive in aq. medium and negative in aq. salts solutions where the magnitudes ΔHc0 and ΔSc0 values decreased with the growing contents of TNX 100/salts. The results suggest that the interaction forces between TNX 100 and CPM in a water environment are hydrophobic in nature with π–π interactions whereas in aq. salts media the recommended forces are hydrophobic and exothermic forces along with π–π interactions.KEYWORDS: TNX 100cephradine monohydrateelectrolytesphase separationthermodynamics Disclosure statementNo potential conflict of interest was reported by the author(s).Additional informationFundingThis work was funded by the Researchers Supporting Project Number [RSPD2023R766] King Saud University, Riyadh, Saudi Arabia. Md. Masud Alam would like to acknowledge Mawlana Bhashani Science and Technology University, Bangladesh for providing financial support (Year 2021) to carry out a part of the research work.","PeriodicalId":18817,"journal":{"name":"Molecular Physics","volume":"246 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-10-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"136295221","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 : 2023-10-10DOI: 10.1080/00268976.2023.2264399
M. Lawrence, P. Rajesh, M. Vimala, R. Girija, S. Sahaya Jude Dhas
AbstractThe present work deals with the understanding of the integrated experimental and theoretical study of the molecular structure and vibrational spectra of N-allyl-N-ethylformamide (NAEF). Density functional theory (DFT) calculations were used to study the subject molecule, N-allyl-N-ethylformamide (NAEF), utilising the B3LYP method and the basis set 6-311++G (d,p). Geometrical parameters and the structure of NAEF were computed such that global descriptors and reactive sites were obtained. Frontier’s analysis of molecular orbital energy demonstrates that the molecule’s charge exchange is considerably high. Non-linear optical properties of N-allyl-N-ethylformamide (NAEF) were computed and compared with the standard material of urea. The vibrational assignments were analysed for the existence of the probable functional groups and tabulated. The thermodynamic functions were computed at different temperatures and listed accordingly. NMR spectroscopy and quantum computational chemistry methods have been employed for the understanding of the structures of NAEF. Moreover, different techniques such as topological analysis and drug-likeness were utilised to determine the structure and other properties of NAEF. The molecular docking study could determine the residue with the highest docking score (lowest binding energy) and the most non-covalent interactions.KEYWORDS: Density functional theorymolecular dockingnatural bond orbitalchromatographyhyperpolarisability CRediT authorship contribution statementM. Lawrence: Conceptualisation, Methodology, Validation, Formal analysis, Writing – original draft, Writing – review & editing, Visualisation. P. Rajesh: Investigation, Supervision, Project administration, review & editing. M. Vimala: Conceptualisation, Software, Resources, Project administration, Writing – review & editing. R. Girija: Validation, Methodology, Resources & writing. S. Sahaya Jude Dhas: Conceptualisation, Software, Investigation, Project administration, Writing – review & editing.Disclosure statementNo potential conflict of interest was reported by the author(s).Data availability statementData will be made available on request.
摘要本文对n -烯丙基- n -乙基甲酰胺(NAEF)的分子结构和振动谱进行了实验和理论的综合研究。利用B3LYP方法和基集6-311++G (d,p)，利用密度泛函理论(DFT)计算研究了目标分子n -烯丙基- n -乙基甲酰胺(NAEF)。计算了NAEF的几何参数和结构，得到了全局描述符和反应位点。Frontier对分子轨道能量的分析表明，分子的电荷交换相当高。计算了n-烯丙基- n-乙基甲酰胺(NAEF)的非线性光学性质，并与标准材料尿素进行了比较。分析了可能存在的官能团的振动赋值，并将其制表。计算了不同温度下的热力学函数，并列出了相应的表。核磁共振波谱和量子计算化学方法已被用于了解NAEF的结构。此外，不同的技术，如拓扑分析和药物相似性被用来确定NAEF的结构和其他性质。分子对接研究可以确定对接分数最高(结合能最低)和非共价相互作用最多的残基。关键词:密度泛函理论;分子对接;自然键轨道;劳伦斯:概念化，方法论，验证，形式分析，写作-原稿，写作-审查和编辑，可视化。P. Rajesh:调查，监督，项目管理，审查和编辑。M. Vimala:概念化，软件，资源，项目管理，写作-审查和编辑。R. Girija:验证、方法论、资源和写作。S. Sahaya Jude Dhas:概念化，软件，调查，项目管理，写作-审查和编辑。披露声明作者未报告潜在的利益冲突。数据可用性声明数据可应要求提供。
{"title":"Synthesis and spectroscopic investigation of N-allyl-N-ethylformamide: computational aspects of DFT, molecular docking and drug-likeness analyses","authors":"M. Lawrence, P. Rajesh, M. Vimala, R. Girija, S. Sahaya Jude Dhas","doi":"10.1080/00268976.2023.2264399","DOIUrl":"https://doi.org/10.1080/00268976.2023.2264399","url":null,"abstract":"AbstractThe present work deals with the understanding of the integrated experimental and theoretical study of the molecular structure and vibrational spectra of N-allyl-N-ethylformamide (NAEF). Density functional theory (DFT) calculations were used to study the subject molecule, N-allyl-N-ethylformamide (NAEF), utilising the B3LYP method and the basis set 6-311++G (d,p). Geometrical parameters and the structure of NAEF were computed such that global descriptors and reactive sites were obtained. Frontier’s analysis of molecular orbital energy demonstrates that the molecule’s charge exchange is considerably high. Non-linear optical properties of N-allyl-N-ethylformamide (NAEF) were computed and compared with the standard material of urea. The vibrational assignments were analysed for the existence of the probable functional groups and tabulated. The thermodynamic functions were computed at different temperatures and listed accordingly. NMR spectroscopy and quantum computational chemistry methods have been employed for the understanding of the structures of NAEF. Moreover, different techniques such as topological analysis and drug-likeness were utilised to determine the structure and other properties of NAEF. The molecular docking study could determine the residue with the highest docking score (lowest binding energy) and the most non-covalent interactions.KEYWORDS: Density functional theorymolecular dockingnatural bond orbitalchromatographyhyperpolarisability CRediT authorship contribution statementM. Lawrence: Conceptualisation, Methodology, Validation, Formal analysis, Writing – original draft, Writing – review & editing, Visualisation. P. Rajesh: Investigation, Supervision, Project administration, review & editing. M. Vimala: Conceptualisation, Software, Resources, Project administration, Writing – review & editing. R. Girija: Validation, Methodology, Resources & writing. S. Sahaya Jude Dhas: Conceptualisation, Software, Investigation, Project administration, Writing – review & editing.Disclosure statementNo potential conflict of interest was reported by the author(s).Data availability statementData will be made available on request.","PeriodicalId":18817,"journal":{"name":"Molecular Physics","volume":"22 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-10-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"136293439","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 : 2023-10-10DOI: 10.1080/00268976.2023.2266512
Wentao Li, Yong Zhang
AbstractThe dynamic calculations of the C+ + HD (v0 = 0, j0 = 0) → D/H + CH+/CD+ reaction in the collision energy range of 0.001–1.80 eV are carried out by using a time-dependent wave packet. The intramolecular isotope effect of the C+ + HD reaction is discussed in detail. Some meaningful dynamic properties of the C+ + HD reaction are reported and compared with available theoretical and experimental results. The results indicated that present values are, in general, in better agreement with experimental data than previous theoretical reports. However, due to the lack of consideration of rotational excitation of reactant and non-adiabatic effect, the present results are always smaller than the experimental results. Differential cross-sections of the D + CH+ and H + CD+ product channels exhibit forward–backward symmetric behaviour, which indicates that the ‘complex-forming’ mechanism plays a dominant role in the reaction.Highlights The dynamic calculations of the C+ + HD (v0 = 0, j0 = 0) → D/H + CH+/CD+ reaction are performed using a time-dependent wave packet method based on the newly reported potential energy surface.The dynamicl properties, such as integral cross-sections, rate constants, etc., are calculated and compared with previous theoretical and experimental results.The rovibrational state distributions of the product are reported.KEYWORDS: Isotope effectreaction probabilityintegral cross-sectiondifferential cross-sectionrate constant Disclosure statementNo potential conflict of interest was reported by the author(s).Additional informationFundingThis work is supported by Key Projects of Science and Technology in the 13th Five Year Plan of Jilin Provincial Department of Education (grant number JJKH20200482KJ) and Jilin Province Science and Technology Department Program (grant number 20220101024JC).
{"title":"The dynamic studies of the C <sup>+</sup> + HD reaction using the time-dependent wave packet method","authors":"Wentao Li, Yong Zhang","doi":"10.1080/00268976.2023.2266512","DOIUrl":"https://doi.org/10.1080/00268976.2023.2266512","url":null,"abstract":"AbstractThe dynamic calculations of the C+ + HD (v0 = 0, j0 = 0) → D/H + CH+/CD+ reaction in the collision energy range of 0.001–1.80 eV are carried out by using a time-dependent wave packet. The intramolecular isotope effect of the C+ + HD reaction is discussed in detail. Some meaningful dynamic properties of the C+ + HD reaction are reported and compared with available theoretical and experimental results. The results indicated that present values are, in general, in better agreement with experimental data than previous theoretical reports. However, due to the lack of consideration of rotational excitation of reactant and non-adiabatic effect, the present results are always smaller than the experimental results. Differential cross-sections of the D + CH+ and H + CD+ product channels exhibit forward–backward symmetric behaviour, which indicates that the ‘complex-forming’ mechanism plays a dominant role in the reaction.Highlights The dynamic calculations of the C+ + HD (v0 = 0, j0 = 0) → D/H + CH+/CD+ reaction are performed using a time-dependent wave packet method based on the newly reported potential energy surface.The dynamicl properties, such as integral cross-sections, rate constants, etc., are calculated and compared with previous theoretical and experimental results.The rovibrational state distributions of the product are reported.KEYWORDS: Isotope effectreaction probabilityintegral cross-sectiondifferential cross-sectionrate constant Disclosure statementNo potential conflict of interest was reported by the author(s).Additional informationFundingThis work is supported by Key Projects of Science and Technology in the 13th Five Year Plan of Jilin Provincial Department of Education (grant number JJKH20200482KJ) and Jilin Province Science and Technology Department Program (grant number 20220101024JC).","PeriodicalId":18817,"journal":{"name":"Molecular Physics","volume":"4 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-10-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"136294301","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 : 2023-10-09DOI: 10.1080/00268976.2023.2267687
Guokun Xie, Yinxing Li, Zheng Zhao, Ningning Wang
AbstractBimetallic sodium-doped magnesium cluster cations, NaMgn+(n= 2–12), have been investigated through a synergetic combination of the CALYPSO code and DFT calculations. The results reveal that the lowest-energy structures of NaMgn+ exhibit linear, planar, triangular pyramid, pentagonal pyramid, and triangular prism topologies. The structures can be described as a substituted geometry of pure Mg clusters at the small size. Starting from n = 9, the dominant structures transform into a triangular prism-based configuration. Like anionic and neutral NaMgn clusters, the Na atom prefers the peripheral regions of the Mgn framework. Stability studies indicate NaMg4+ and NaMg10+ to be the~most stable clusters, which may benefit from their closed-shell electron structures. Analysis of the bonding nature shows stronger Mg-Mg interaction than the Na-Mg interaction in the NaMg4+ and NaMg10+ clusters. The reason is that covalent bonds are formed in the Mg-Mg regions, while there is no aggregation of electron density in the Na-Mg regions.KEYWORDS: DFTCALYPSONaMgn+ clustersstructureselectronic properties Disclosure statementNo potential conflict of interest was reported by the author(s).Additional informationFundingThis work was supported by the Natural Science Basic Research Plan in Shaanxi Province of China (grant number 2023-JC-YB-464).
{"title":"Structural evolution, stability, electronic and bonding properties of sodium-doped magnesium cluster cations","authors":"Guokun Xie, Yinxing Li, Zheng Zhao, Ningning Wang","doi":"10.1080/00268976.2023.2267687","DOIUrl":"https://doi.org/10.1080/00268976.2023.2267687","url":null,"abstract":"AbstractBimetallic sodium-doped magnesium cluster cations, NaMgn+(n= 2–12), have been investigated through a synergetic combination of the CALYPSO code and DFT calculations. The results reveal that the lowest-energy structures of NaMgn+ exhibit linear, planar, triangular pyramid, pentagonal pyramid, and triangular prism topologies. The structures can be described as a substituted geometry of pure Mg clusters at the small size. Starting from n = 9, the dominant structures transform into a triangular prism-based configuration. Like anionic and neutral NaMgn clusters, the Na atom prefers the peripheral regions of the Mgn framework. Stability studies indicate NaMg4+ and NaMg10+ to be the~most stable clusters, which may benefit from their closed-shell electron structures. Analysis of the bonding nature shows stronger Mg-Mg interaction than the Na-Mg interaction in the NaMg4+ and NaMg10+ clusters. The reason is that covalent bonds are formed in the Mg-Mg regions, while there is no aggregation of electron density in the Na-Mg regions.KEYWORDS: DFTCALYPSONaMgn+ clustersstructureselectronic properties Disclosure statementNo potential conflict of interest was reported by the author(s).Additional informationFundingThis work was supported by the Natural Science Basic Research Plan in Shaanxi Province of China (grant number 2023-JC-YB-464).","PeriodicalId":18817,"journal":{"name":"Molecular Physics","volume":"23 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-10-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135093688","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 : 2023-10-06DOI: 10.1080/00268976.2023.2260905
Muhammad Aqib, Mehar Ali Malik, Hafiz Usman Afzal, Tahzeeb Fatima
AbstractTopological indices are the numerical parameters of molecular graphs that characterise their behaviour and are mathematical invariant that preserves chemical and material properties. In a QSAR/QSPR study, physico-chemical properties and topological indices are studied. In this research, we shall calculate forgotten topological, inverse sum, the general sum connectivity and the first multiplicative atom–bond connectivity indices of carbon nanotube TUC4C8[m,n] and C4C8[m,n] nanotorus. The main motivation here is the molecular graphs of the nano-chemical compound TUC4C8 nanotubes and C4C8 nanotorus. While the central and latest point of convergence of our discussion is to provide a ‘3D graphical trend and relative comparison’ of these derived topological descriptors of these materials that will make them more useful and comparative for chemists, nano and material scientists and would open a new 3D graphical horizon towards material sciences and chemical engineering.Keywords: Forgotten indexatom–bond connectivity indexTUC4C8 nanotubeC4C8 nanotorus Disclosure statementNo potential conflict of interest was reported by the author(s).
{"title":"Structural characterization of nanomaterials C <sub>4</sub> C <sub>8</sub>","authors":"Muhammad Aqib, Mehar Ali Malik, Hafiz Usman Afzal, Tahzeeb Fatima","doi":"10.1080/00268976.2023.2260905","DOIUrl":"https://doi.org/10.1080/00268976.2023.2260905","url":null,"abstract":"AbstractTopological indices are the numerical parameters of molecular graphs that characterise their behaviour and are mathematical invariant that preserves chemical and material properties. In a QSAR/QSPR study, physico-chemical properties and topological indices are studied. In this research, we shall calculate forgotten topological, inverse sum, the general sum connectivity and the first multiplicative atom–bond connectivity indices of carbon nanotube TUC4C8[m,n] and C4C8[m,n] nanotorus. The main motivation here is the molecular graphs of the nano-chemical compound TUC4C8 nanotubes and C4C8 nanotorus. While the central and latest point of convergence of our discussion is to provide a ‘3D graphical trend and relative comparison’ of these derived topological descriptors of these materials that will make them more useful and comparative for chemists, nano and material scientists and would open a new 3D graphical horizon towards material sciences and chemical engineering.Keywords: Forgotten indexatom–bond connectivity indexTUC4C8 nanotubeC4C8 nanotorus Disclosure statementNo potential conflict of interest was reported by the author(s).","PeriodicalId":18817,"journal":{"name":"Molecular Physics","volume":"18 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-10-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135351372","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 : 2023-10-05DOI: 10.1080/00268976.2023.2266064
Di Liu, Xinyu Li, Lulu Li, Bing Yan
AbstractSpectroscopic properties and potential energy curves of alkali metal (M = Na and K) – rare gas (Rg = He, Ne, Ar, Kr, Xe and Rn) van der Waals molecules in their ground states have been studied in detail using spin-restricted open-shell coupled cluster with single and double excitations and perturbative contribution of connected triple excitations (RCCSD(T)) methods. The core-valence correlation (CV) effect was found to be crucial for M-RG molecules containing heavy rare gas atoms. The electronic energies were corrected for the basis set superposition error (BSSE) using the counterpoise method. Energies were extrapolated to the complete basis set (CBS) limit using a two-point scheme. The permanent electric dipole moments, static electric dipole polarizabilities and long-range dispersion coefficients were also calculated. The computed spectroscopic constants, vibrational levels and rotational constants were reported for M-RG and good agreement with the available experimental and theoretical values were found.KEYWORDS: Van der Waals systemsopen-shell coupled clusterspectroscopic constants AcknowledgementsDi Liu: Conceptualisation, Data curation, Writing – original draft, Writing – review & editing. Xinyu Li: Software, Methodology, Writing – review & editing. Lulu Li: Review. Bing Yan: Supervision, Validation. Data availability Data will be made available on request.Disclosure statementNo potential conflict of interest was reported by the author(s).Additional informationFundingThis work was supported by the National Natural Science Foundation of China (grant number 11874177, 12274178, and 11574114), the High Performance Computing Center (HPCC) of Jilin University and high performance computing cluster Tiger@ IAMP.
{"title":"<i>Ab initio</i> interaction potentials of alkali metal (M = Na and K)–rare gas (Rg = He, Ne, Ar, Kr, Xe and Rn) complexes","authors":"Di Liu, Xinyu Li, Lulu Li, Bing Yan","doi":"10.1080/00268976.2023.2266064","DOIUrl":"https://doi.org/10.1080/00268976.2023.2266064","url":null,"abstract":"AbstractSpectroscopic properties and potential energy curves of alkali metal (M = Na and K) – rare gas (Rg = He, Ne, Ar, Kr, Xe and Rn) van der Waals molecules in their ground states have been studied in detail using spin-restricted open-shell coupled cluster with single and double excitations and perturbative contribution of connected triple excitations (RCCSD(T)) methods. The core-valence correlation (CV) effect was found to be crucial for M-RG molecules containing heavy rare gas atoms. The electronic energies were corrected for the basis set superposition error (BSSE) using the counterpoise method. Energies were extrapolated to the complete basis set (CBS) limit using a two-point scheme. The permanent electric dipole moments, static electric dipole polarizabilities and long-range dispersion coefficients were also calculated. The computed spectroscopic constants, vibrational levels and rotational constants were reported for M-RG and good agreement with the available experimental and theoretical values were found.KEYWORDS: Van der Waals systemsopen-shell coupled clusterspectroscopic constants AcknowledgementsDi Liu: Conceptualisation, Data curation, Writing – original draft, Writing – review & editing. Xinyu Li: Software, Methodology, Writing – review & editing. Lulu Li: Review. Bing Yan: Supervision, Validation. Data availability Data will be made available on request.Disclosure statementNo potential conflict of interest was reported by the author(s).Additional informationFundingThis work was supported by the National Natural Science Foundation of China (grant number 11874177, 12274178, and 11574114), the High Performance Computing Center (HPCC) of Jilin University and high performance computing cluster Tiger@ IAMP.","PeriodicalId":18817,"journal":{"name":"Molecular Physics","volume":"50 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-10-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"134947644","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 : 2023-09-29DOI: 10.1080/00268976.2023.2261568
Hamed Soleymanabadi, Sadeq Alshimaysawee
AbstractAn exploration into the electronic characteristics of graphene nanosheets (GDY) and its silicon-doped counterpart, SiGDY, was undertaken through the application of first-principle calculations. Analysis was conducted concerning the interaction between the ibuprofen (IBP) pharmaceutical and the surfaces of GDY and SiGDY sheet materials. This research undertook an evaluation of various factors like the energy of adsorption, transfer of charge, and alterations in electrical conductivity. The findings of this analysis revealed that the original GDY displayed minimal affinity towards IBP. Upon the attachment of IBP, there was a mere 8.92 percent marginal change observed in the energy range of the GDY surface. The interaction between SiGDY and IBP showcased an aqueous energy measurement of −49.11 kcal/mol, accompanied by a gaseous energy measurement of −20.09 kcal/mol. Utilising the pharmaceutical's solvation energy value, its solubility in the aqueous phase was determined. The profoundly positively charged SiGDY sheet and IBP underwent substantial charge transfer, engendering the essential binding energy for IBP adherence. The electrical conductivity of SiGDY underwent a noteworthy increase of roughly 26.41 percent upon the attachment of IBP.Display full sizeKEYWORDS: Ibuprofenconductivitysolubilityadsorption Disclosure statementNo potential conflict of interest was reported by the author(s).
{"title":"Evaluation of ibuprofen drug assay using silicon doped graphdiyne: insights from density functional theory","authors":"Hamed Soleymanabadi, Sadeq Alshimaysawee","doi":"10.1080/00268976.2023.2261568","DOIUrl":"https://doi.org/10.1080/00268976.2023.2261568","url":null,"abstract":"AbstractAn exploration into the electronic characteristics of graphene nanosheets (GDY) and its silicon-doped counterpart, SiGDY, was undertaken through the application of first-principle calculations. Analysis was conducted concerning the interaction between the ibuprofen (IBP) pharmaceutical and the surfaces of GDY and SiGDY sheet materials. This research undertook an evaluation of various factors like the energy of adsorption, transfer of charge, and alterations in electrical conductivity. The findings of this analysis revealed that the original GDY displayed minimal affinity towards IBP. Upon the attachment of IBP, there was a mere 8.92 percent marginal change observed in the energy range of the GDY surface. The interaction between SiGDY and IBP showcased an aqueous energy measurement of −49.11 kcal/mol, accompanied by a gaseous energy measurement of −20.09 kcal/mol. Utilising the pharmaceutical's solvation energy value, its solubility in the aqueous phase was determined. The profoundly positively charged SiGDY sheet and IBP underwent substantial charge transfer, engendering the essential binding energy for IBP adherence. The electrical conductivity of SiGDY underwent a noteworthy increase of roughly 26.41 percent upon the attachment of IBP.Display full sizeKEYWORDS: Ibuprofenconductivitysolubilityadsorption Disclosure statementNo potential conflict of interest was reported by the author(s).","PeriodicalId":18817,"journal":{"name":"Molecular Physics","volume":"78 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-09-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135132127","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}
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