Structural Chemistry最新文献

Stabilization of cyclo-N6 by insertion into [18]-annulene: a DFT study 通过插入 [18]-annulene 稳定环-N6：DFT 研究

IF 2.1 4区化学

Structural Chemistry Pub Date : 2024-10-18 DOI: 10.1007/s11224-024-02394-2

Fabio Pichierri

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Theoretical study of novel antipyrine derivatives as promising corrosion inhibitors for mild steel in an acidic environment 新型抗吡啶衍生物作为酸性环境中低碳钢腐蚀抑制剂的理论研究

IF 1.7 4区化学

Structural Chemistry Pub Date : 2024-09-11 DOI: 10.1007/s11224-024-02368-4

Christopher Ikechukwu Ekeocha, Ikechukwu Nelson Uzochukwu, Ikenna Benedict Onyeachu, Ini-Ibehe Nabuk Etim, Emeka Emmanuel Oguzie

{"title":"Theoretical study of novel antipyrine derivatives as promising corrosion inhibitors for mild steel in an acidic environment","authors":"Christopher Ikechukwu Ekeocha, Ikechukwu Nelson Uzochukwu, Ikenna Benedict Onyeachu, Ini-Ibehe Nabuk Etim, Emeka Emmanuel Oguzie","doi":"10.1007/s11224-024-02368-4","DOIUrl":"https://doi.org/10.1007/s11224-024-02368-4","url":null,"abstract":"The research delved into studying the anti-corrosive capabilities of newly developed antipyrine derivatives for mild steel in an acidic environment through density functional theory (DFT) and molecular dynamic (MD) simulation. The results of DFT calculations indicated that the newly designed antipyrine molecules exhibited high EHOMO (− 4.788, − 4.908, and − 4.942) and low ELUMO (− 2.339, − 3.109, and − 3.101) and energy gap (2.449, 1.799, and 1.841) for compound A1, A2, and A3, respectively. This suggests their propensity to transfer and accept electrons during molecular interaction with the alloy surface, promoting adsorption and corrosion protection. The antipyrine molecules were also noted to contain numerous electron-rich sites around the heteroatoms, functional groups, and inherent aromatic rings within their structures which helps in facilitating molecular interaction with the metal, leading to the adsorption, and formation of a protective layer for effective corrosion protection. High AlogP values (3.74 to 5.00) strongly indicate the molecules' hydrophilic nature, coating ability, and propensity to disperse water molecules and chloride ions in the corrosive system. The MD simulations also revealed high energy of adsorption, which follows a decreasing trend of A2 (− 161.00 kcal⋅mol−1) > A1 (− 157.15 kcal⋅mol−1) > A3 (− 107.93 kcal⋅mol−1) indicating strong and spontaneous adsorption with a flat orientation on the Fe(110) surface. The radial distribution function (RDF) results further supported the chemosorption nature of the inhibitor molecule, and the formation of robust bonds with Fe(110) with all calculated RDF values falling below 3.5 Å. Inclusively, the investigated antipyrine compounds exhibited strong anti-corrosive properties, positioning them as promising corrosion inhibitors for mild steel deployed in acidic environments.","PeriodicalId":780,"journal":{"name":"Structural Chemistry","volume":"35 1","pages":""},"PeriodicalIF":1.7,"publicationDate":"2024-09-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142215618","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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An analogous Twisted Little Tale on the significance of unusual infrared frequencies 关于不寻常红外频率意义的类似扭曲小故事

IF 2.1 4区化学

Structural Chemistry Pub Date : 2024-09-09 DOI: 10.1007/s11224-024-02376-4

Israel Agranat

{"title":"An analogous Twisted Little Tale on the significance of unusual infrared frequencies","authors":"Israel Agranat","doi":"10.1007/s11224-024-02376-4","DOIUrl":"10.1007/s11224-024-02376-4","url":null,"abstract":"<div>The autobiographical 2024 Brief Report published in Structural Chemistry by the heterocyclic chemist Professor José Elguero prompted the author to describe his recollections of a similar yet twisted little tale of an incident occurred in 1964 during his Organic Chemistry Ph.D. period at The Hebrew University of Jerusalem. The trait d’union between the two tales is the significance of unusual infrared frequencies in the characterization of newly synthesized organic compounds. The absence of an infrared band at the 1800–1900 cm−1 region was a sufficient condition for ruling out a cyclopropanone structure (Elguero’s little tale). The presence of such an infrared band was a necessary condition for the presence of a triafulvene and triapentafulvalene systems (author’s twisted little tale). The related experience in the publication of Communications to the Editor articles in the Journal of the American Chemical Society is also described. A further teaching of the author’s tale is the importance of early learning of ethics and integrity in the scientific publication process.</div>","PeriodicalId":780,"journal":{"name":"Structural Chemistry","volume":"35 6","pages":"1937 - 1941"},"PeriodicalIF":2.1,"publicationDate":"2024-09-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1007/s11224-024-02376-4.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142215620","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Density functional theory studies the interaction of neopentane with functionalized porous graphene 密度泛函理论研究新戊烷与功能化多孔石墨烯的相互作用

IF 1.7 4区化学

Structural Chemistry Pub Date : 2024-09-09 DOI: 10.1007/s11224-024-02378-2

Liying Zhang, Wenda Yan, Dongning He, Yong Fang

{"title":"Density functional theory studies the interaction of neopentane with functionalized porous graphene","authors":"Liying Zhang, Wenda Yan, Dongning He, Yong Fang","doi":"10.1007/s11224-024-02378-2","DOIUrl":"https://doi.org/10.1007/s11224-024-02378-2","url":null,"abstract":"Porous graphenes are one of the ideal separation materials. The interaction between neopentane molecule and chemical groups N-, F-, and OH- functionalized single-layer porous graphene model (pore16) was investigated by using first-principles method. The pore size of pore16 modified by one N atom is almost the same (the difference is only 0.006 Å), while the difference of the energy barrier to neopentane is as high as 0.30 eV. For 2Npore16, the energy barrier varies by 0.88 eV, while for 4Npore16, it varies by 0.67 eV. It is evident that as the number of N atoms increases, the energy barrier widens, and this phenomenon is also found in the functionalization of F and OH. The same type and number of functional groups may have different pore sizes, which may result in very different separation properties. Interestingly, adding functionalization leads to the formation of hydrogen bonds in OHpore16, which affects the separation performance of molecule. This implies that not only pore size and shape are the main factors, but also the chemical functionalization of specific sites is the main factor. In general, this study emphasizes an important attraction might be encountered in both the design and modeling of two-dimensional membranes for separating purposes.","PeriodicalId":780,"journal":{"name":"Structural Chemistry","volume":"59 1","pages":""},"PeriodicalIF":1.7,"publicationDate":"2024-09-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142215619","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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Topological relations between crystal structures: a route to predicting inorganic materials 晶体结构之间的拓扑关系：预测无机材料的途径

IF 2.1 4区化学

Structural Chemistry Pub Date : 2024-09-09 DOI: 10.1007/s11224-024-02379-1

Natalia A. Kabanova, Ekaterina A. Grishina, Vladislav T. Osipov, Valeria E. Pavlova, Maria A. Solodovnikova, Artem A. Kabanov, Vladislav A. Blatov

{"title":"Topological relations between crystal structures: a route to predicting inorganic materials","authors":"Natalia A. Kabanova, Ekaterina A. Grishina, Vladislav T. Osipov, Valeria E. Pavlova, Maria A. Solodovnikova, Artem A. Kabanov, Vladislav A. Blatov","doi":"10.1007/s11224-024-02379-1","DOIUrl":"10.1007/s11224-024-02379-1","url":null,"abstract":"<div>We review topological approaches to the analysis of crystal structures of intermetallic compounds and to searching for structural relations between them as the relations between their underlying atomic nets. We introduce the concept of skeletal net to find the simplest system of interatomic contacts in intermetallic compounds, which supports the three-periodic crystal architecture. Using the observed approaches, we have revealed topological relations between crystal structures of binary MeX compounds (Me = Re, Ti or Rh; X = B, C, N, or Si) and found a key role of the body-centered cubic net in their topological hierarchy. We have explored the configuration space of the corresponding crystalline systems by generating all possible ‘subnet-supernet’ topological transformations, optimized the resulting topological motifs with DFT methods and found a new phase of RhB to be stable above 22 GPa. We discuss the role of topological representations in the prediction of new crystalline chemical substances.</div>","PeriodicalId":780,"journal":{"name":"Structural Chemistry","volume":"35 6","pages":"1793 - 1803"},"PeriodicalIF":2.1,"publicationDate":"2024-09-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142215639","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}

引用次数: 0

Elucidating the mechanism and selectivity of [3 + 2] cycloaddition: a DFT and molecular docking investigation of the reaction of 6-butoxy-5,6-dihydro-4H-1,2-oxazine 2-oxide with dimethyl maleate 阐明 [3 + 2] 环加成的机理和选择性：对 6-丁氧基-5,6-二氢-4H-1,2-恶嗪 2-氧化物与马来酸二甲酯反应的 DFT 和分子对接研究

IF 1.7 4区化学

Structural Chemistry Pub Date : 2024-09-04 DOI: 10.1007/s11224-024-02373-7

Haydar Mohammad-Salim, Jesus Vicente de Julián-Ortiz, Kholood A. Dahlous, Mohammad Shahidul Islam, Tahani Mazyad Almutairi, Sofiane Benmetir

{"title":"Elucidating the mechanism and selectivity of [3 + 2] cycloaddition: a DFT and molecular docking investigation of the reaction of 6-butoxy-5,6-dihydro-4H-1,2-oxazine 2-oxide with dimethyl maleate","authors":"Haydar Mohammad-Salim, Jesus Vicente de Julián-Ortiz, Kholood A. Dahlous, Mohammad Shahidul Islam, Tahani Mazyad Almutairi, Sofiane Benmetir","doi":"10.1007/s11224-024-02373-7","DOIUrl":"https://doi.org/10.1007/s11224-024-02373-7","url":null,"abstract":"The [3 + 2] cycloaddition (32CA) reactions involving 6-butoxy-5,6-dihydro-4H-1,2-oxazine 2-oxide and dimethyl maleate are examined in this study. Molecular electron density theory (MEDT) is applied at the M06-2X/6-311G(d,p) level, coupled with the D3 dispersion correction. The nitronate 1 species are identified as zwitterionic entities through an analysis of the electron localization function (ELF). This 32CA reaction follows an asynchronous one-step mechanism. Conceptual DFT indices are utilized to classify dimethyl maleate as the electrophilic component and the nitronate as the nucleophilic counterpart. The [3 + 2] cycloaddition processes are predominantly governed by kinetic control, as indicated by activation free energies of − 23.6 and − 11.4 kcal.mol−1 for the exo and endo pathways, respectively, aligning with experimental findings. Despite the nucleophilic and electrophilic character of the reagents, the global electron density transfer at the TSs indicates rather polar 32CA reactions. The formation of a pseudoradical center initiates at carbon atoms C3 and C4. A subsequent docking analysis is conducted on cycloadducts 3 and 4 in relation to the main protease of SARS-CoV-2 (6LU7), alongside the co-crystal ligand. The results of this analysis reveal that cycloadducts 3 exhibit higher binding energy, while cycloadducts 4 display lower binding energy compared to the co-crystal ligand. The results confirm that the presence of isoxazolidine ring increases the affinity of the product 3.","PeriodicalId":780,"journal":{"name":"Structural Chemistry","volume":"5 1","pages":""},"PeriodicalIF":1.7,"publicationDate":"2024-09-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142215638","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}

引用次数: 0

Structure correlations among arylpyran pseudoacids and derivatives 芳基吡喃假酸及其衍生物的结构相关性

IF 1.7 4区化学

Structural Chemistry Pub Date : 2024-09-03 DOI: 10.1007/s11224-024-02364-8

Michael Nguyen, Marilyn Brooks, Emily O’Loughlin, Edward J. Valente

{"title":"Structure correlations among arylpyran pseudoacids and derivatives","authors":"Michael Nguyen, Marilyn Brooks, Emily O’Loughlin, Edward J. Valente","doi":"10.1007/s11224-024-02364-8","DOIUrl":"https://doi.org/10.1007/s11224-024-02364-8","url":null,"abstract":"Many 4- and 5-oxocarboxylic acids show open-cyclic solution racemization/tautomerism including the dehydration-resistant arylpyran pseudoacid 3-hydroxy-4,4-dimethylisobenzopyran-1-one. The crystal and molecular structures of nine α-anomeric derivatives (including 11 distinct molecular structures) of this pseudoacid (or close analogs) have been determined, including pseudoacyl chlorides, normal, pseudoanhydrides, a dipseudoanhydride, and a tertiary pseudoamide. The basicity of the implied exocyclic leaving groups span 40 pK units. Together with seven closely related pseudoacid molecular structures previously determined, a data set containing 18 compounds was generated. Exocyclic C–O bonds shortened as endocyclic C–O bonds lengthened in linear functions of exocyclic leaving group basicity with l(xC-O, Å) = 1.4426 − 0.00400 * pKa, N = 13, R2 = 0.969; l(nC-O, Å) = 1.4204 + 0.00205 * pKa, N = 18, R2 = 0.951. These correlations were compared with results for other α-anomeric pyranoid systems, tetrahydropyran and dihydropyran, and an arylfuran pseudoacyl system. Exocyclic substituents effectively modified endocyclic C–O bond polarities over a considerable range.","PeriodicalId":780,"journal":{"name":"Structural Chemistry","volume":"276 1","pages":""},"PeriodicalIF":1.7,"publicationDate":"2024-09-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142215621","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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On how scientists communicate with their peers 科学家如何与同行交流

IF 2.1 4区化学

Structural Chemistry Pub Date : 2024-09-03 DOI: 10.1007/s11224-024-02371-9

Istvan Hargittai

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A theoretical study on adsorption and sensing of SO2, CS2, CO2, CH2O, H2O, C2H2, and CF3H air pollutant gases by B3S monolayer B3S 单层对 SO2、CS2、CO2、CH2O、H2O、C2H2 和 CF3H 等大气污染气体的吸附和传感理论研究

IF 1.7 4区化学

Structural Chemistry Pub Date : 2024-08-30 DOI: 10.1007/s11224-024-02370-w

Mohamed J. Saadh, Nizomiddin Juraev, Mohammed Ahmed Mustafa, Anupam Yadav, Razan Nadhim Shaker, Karrar.R. Al-Shami, Ameer H. Al-Rubaye, Salima B. Alsaadi, Ahmed Elawady

{"title":"A theoretical study on adsorption and sensing of SO2, CS2, CO2, CH2O, H2O, C2H2, and CF3H air pollutant gases by B3S monolayer","authors":"Mohamed J. Saadh, Nizomiddin Juraev, Mohammed Ahmed Mustafa, Anupam Yadav, Razan Nadhim Shaker, Karrar.R. Al-Shami, Ameer H. Al-Rubaye, Salima B. Alsaadi, Ahmed Elawady","doi":"10.1007/s11224-024-02370-w","DOIUrl":"https://doi.org/10.1007/s11224-024-02370-w","url":null,"abstract":"In the present work, with the aid of the density functional theory (DFT) method, we have investigated the possibility of applying the B3S monolayer (B3SML) for sensing and adsorption of some air pollutants containing SO2, CS2, CO2, CH2O, H2O, C2H2, and CF3H from the gaseous environment. The results showed that after the adsorption of SO2, H2O, and C2H2 by B3SML, big changes took place which led to a decrease of the λmax of each complex down to 1598.5 nm, 1418.0 nm, and 1580.0 nm, respectively. Therefore, the frequencies of the mentioned adsorption complexes rise and strong blueshifts occur. Moreover, the outcomes of the band gap estimations reveal that the B3SML could selectively detect the existence of C2H2 with a clearer and stronger electronic signal compared to all other gases. In addition, this nanosheet is able to sense CS2, CH2O, SO2, and H2O with good signals. Hence, it could not recognize the difference between CH2O and SO2 gases. Also, the results of the thermodynamic calculations indicate that B3SML would selectively adsorb and destruct SO2, C2H2, and H2O gases. Moreover, this sorbent could adsorb CH2O and CS2 species, but it would approximately not adsorb CO2 and CF3H.","PeriodicalId":780,"journal":{"name":"Structural Chemistry","volume":"8 1","pages":""},"PeriodicalIF":1.7,"publicationDate":"2024-08-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142215641","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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Structures and electronic properties of the TMn@W12O36 (TM = Cu, Ag and Au, n = 1–4) clusters TMn@W12O36（TM = 铜、银和金，n = 1-4）团簇的结构和电子特性

IF 1.7 4区化学

Structural Chemistry Pub Date : 2024-08-22 DOI: 10.1007/s11224-024-02372-8

Shengxue Wang, Zhi Li, Yuhang Ba, Siyu Li, Zhihan Mu, Feiyang Li

{"title":"Structures and electronic properties of the TMn@W12O36 (TM = Cu, Ag and Au, n = 1–4) clusters","authors":"Shengxue Wang, Zhi Li, Yuhang Ba, Siyu Li, Zhihan Mu, Feiyang Li","doi":"10.1007/s11224-024-02372-8","DOIUrl":"https://doi.org/10.1007/s11224-024-02372-8","url":null,"abstract":"To determine the effect of the embedded Cu, Ag, and Au on the electronic properties of tungsten oxides, the structures, stability, and electronic properties of the TMn@W12O36 (TM = Cu, Ag and Au, n = 1–4) clusters have been investigated by using density functional theory. The results reveal that the embedded TMn clusters decrease the structural stability of the W12O36 cages. The Ag@W12O36 and Ag3@W12O36 clusters exhibit higher structural stability than other TM@W12O36 and TM3@W12O36 (TM = Cu and Au) clusters. The Cu3 clusters prefer to be embedded into the W12O36 clusters. The embedded TMn clusters increase obviously the chemical reactivity of the W12O36 cages. The chemical reactivity of the Ag2@W12O36 and Ag4@W12O36 clusters is similar to that of the Cu2@W12O36 and Cu4@W12O36 clusters. The Au@W12O36, Au2@W12O36, Ag3@W12O36 and Au4@W12O36 clusters display more chemical stability. The charge transfer amounts between the Ag and O atoms of the TMn@W12O36 clusters are larger than those between the Cu (Au) and O atoms of them.","PeriodicalId":780,"journal":{"name":"Structural Chemistry","volume":"42 1","pages":""},"PeriodicalIF":1.7,"publicationDate":"2024-08-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142215642","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}

引用次数: 0