Structural Chemistry最新文献_第10页

Theoretical study of the formation of pyrazole and indazole carbamic acids 吡唑和吲唑氨基甲酸形成的理论研究

IF 2.1 4区化学

Structural Chemistry Pub Date : 2024-02-14 DOI: 10.1007/s11224-024-02286-5

Maxime Ferrer, Ibon Alkorta, Jose Elguero

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Docking, DFT, and structural study of N-((1,5-dimethyl-3-oxo-2-phenyl-2,3-dihydro-1H-pyrazol-4-yl)carbamothioyl)benzamide N-((1,5-二甲基-3-氧代-2-苯基-2,3-二氢-1H-吡唑-4-基)氨基硫酰基)苯甲酰胺的对接、DFT 和结构研究

IF 2.1 4区化学

Structural Chemistry Pub Date : 2024-02-13 DOI: 10.1007/s11224-024-02278-5

Khalaf A. Jasim, Nazk Mohammed Aziz, Muhammad Ashfaq, Reza Behjatmanesh-Ardakani, Ahmed S. Faihan, Muhammad Nawaz Tahir, Ahmed S. Al-Janabi, Necmi Dege, Andre J. Gesquiere

{"title":"Docking, DFT, and structural study of N-((1,5-dimethyl-3-oxo-2-phenyl-2,3-dihydro-1H-pyrazol-4-yl)carbamothioyl)benzamide","authors":"Khalaf A. Jasim, Nazk Mohammed Aziz, Muhammad Ashfaq, Reza Behjatmanesh-Ardakani, Ahmed S. Faihan, Muhammad Nawaz Tahir, Ahmed S. Al-Janabi, Necmi Dege, Andre J. Gesquiere","doi":"10.1007/s11224-024-02278-5","DOIUrl":"10.1007/s11224-024-02278-5","url":null,"abstract":"<div>In the current work, we report the synthesis and characterization of N-((1,5-dimethyl-3-oxo-2-phenyl-2,3-dihydro-1H-pyrazol-4-yl)carbamothioyl)benzamide by reacting 4-aminoantipyrine and benzoylisothiocynate in equimolar ratio. Moreover, the compound was characterized by single crystal XRD analysis. The various intermolecular interactions stabilized the supramolecular assembly, including H-bonding and interaction involving π-ring. Hirshfeld surface analysis was performed in order to probe intermolecular interactions in detail. Interaction energy calculations were conducted to find the type of interaction energy prominent in stabilizing supramolecular assembly. The quantum parameters of the prepared compound were investigated by utilizing the Def2-SVPD basis set in conjunction with the hybrid method of B3LYP. The results revealed quite similarities between the experimental and theoretical calculations. In addition, the HOMO orbitals are located at the hetero atoms, while the LUMO orbitals are located at the benzene ring. In addition, the prepared compound was docked with Ampicillin-CTX-M-15. The results showed good binding interaction between the ligand and the targeted amino acids, with the best binding score of − 5.26 kcal/mol.</div>","PeriodicalId":780,"journal":{"name":"Structural Chemistry","volume":"35 5","pages":"1411 - 1425"},"PeriodicalIF":2.1,"publicationDate":"2024-02-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1007/s11224-024-02278-5.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139756434","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}

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Polyiodides of amino acids. l-proline triiodides 氨基酸的聚碘化物。

IF 2.1 4区化学

Structural Chemistry Pub Date : 2024-02-09 DOI: 10.1007/s11224-024-02291-8

Gerald Giester, Vahram V. Ghazaryan, Ashkhen L. Zatikyan, Aram M. Petrosyan

{"title":"Polyiodides of amino acids. l-proline triiodides","authors":"Gerald Giester, Vahram V. Ghazaryan, Ashkhen L. Zatikyan, Aram M. Petrosyan","doi":"10.1007/s11224-024-02291-8","DOIUrl":"10.1007/s11224-024-02291-8","url":null,"abstract":"<div>Two new salts of l-proline containing triiodide anions were obtained and investigated: (l-ProH···l-Pro)(I3) (I) and [(l-ProH)3(l-Pro)](I3)3 (II). Both compounds crystallize in the polar monoclinic space group P21. Crystal structure determinations showed that (I) contains a dimeric cation formed by an O-H···O hydrogen bond with an O···O distance of 2.458(4) Å, while (II) features a peculiar tetrameric cation [l-ProH···(l-Pro-H-l-Pro)···l-ProH], where (l-Pro-H-l-Pro) is a pseudocentrosymmetric dimer with a very short hydrogen bond with an O···O distance of 2.427 Å. Infrared spectra of both crystals were registered and interpreted based on their structures. Electronic band structures were determined by quantum chemical calculations. The CASTEP code was used to calculate the band structures, total and partial density of states (TDOS, PDOS). Bandgaps were also measured by the diffuse reflectance method.</div>","PeriodicalId":780,"journal":{"name":"Structural Chemistry","volume":"35 5","pages":"1399 - 1409"},"PeriodicalIF":2.1,"publicationDate":"2024-02-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1007/s11224-024-02291-8.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139756915","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}

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Adsorption attributes of methyl naphthalene and naphthalene on P-Germanane sheets–a DFT outlook 甲基萘和萘在 P-锗烷薄片上的吸附属性--DFT 展望

IF 2.1 4区化学

Structural Chemistry Pub Date : 2024-02-07 DOI: 10.1007/s11224-024-02285-6

M. S. Jyothi, V. Nagarajan, R. Chandiramouli

{"title":"Adsorption attributes of methyl naphthalene and naphthalene on P-Germanane sheets–a DFT outlook","authors":"M. S. Jyothi, V. Nagarajan, R. Chandiramouli","doi":"10.1007/s11224-024-02285-6","DOIUrl":"10.1007/s11224-024-02285-6","url":null,"abstract":"<div>The adsorption attributes of methyl naphthalene and naphthalene molecules on P-Germanane sheets are explored based on the density functional theory method. The novel P-Germanane stability is established based on formation energy and phonon band spectrum. The stable P-Germanane exhibits a band gap of 3.944 eV. The calculated adsorption energy infers that methyl naphthalene and naphthalene are physisorbed on P-Germanane sheets. The charge transfer reveals that P-Germanane sheets behave as donors of electrons and target molecules behave as acceptors. The electronic attributes of P-Germanane sheets get altered owing to methyl naphthalene and naphthalene adsorption inferred from the band structure, PDOS spectrum, and electron density difference diagrams. We identified global minima position upon adsorption of 1-methylnaphthalene, and naphthalene on P-Germanane, which are named as bridge, octal, and tetra sites and adsorption attributes are explored in these sites. The adsorption energy and relative energy gap variation are noticed to be maximum for tetra site orientation of naphthalene on P-Germanane. The outcome exposes that P-Germanane sheets can be used as adsorption substrates for the detection of methyl naphthalene and naphthalene molecules.</div>","PeriodicalId":780,"journal":{"name":"Structural Chemistry","volume":"35 5","pages":"1387 - 1397"},"PeriodicalIF":2.1,"publicationDate":"2024-02-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139756430","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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Arno Penzias—Nobel laureate—Co-discoverer of the cosmic microwave background radiation and researcher of the chemistry of the sky 阿诺-彭齐亚斯--诺贝尔奖获得者--宇宙微波背景辐射的共同发现者和天空化学研究者

IF 2.1 4区化学

Structural Chemistry Pub Date : 2024-02-07 DOI: 10.1007/s11224-024-02289-2

Istvan Hargittai

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Oxidation process of 1,4-dihydropyridine, 1,4-dihydropyrimidine, and pyrrolo-1,4-dihydropyrimidine: quantum chemical study 1,4-二氢吡啶、1,4-二氢嘧啶和吡咯-1,4-二氢嘧啶的氧化过程：量子化学研究

IF 2.1 4区化学

Structural Chemistry Pub Date : 2024-02-07 DOI: 10.1007/s11224-024-02284-7

Mariia O. Shyshkina, Serhiy M. Desenko

{"title":"Oxidation process of 1,4-dihydropyridine, 1,4-dihydropyrimidine, and pyrrolo-1,4-dihydropyrimidine: quantum chemical study","authors":"Mariia O. Shyshkina, Serhiy M. Desenko","doi":"10.1007/s11224-024-02284-7","DOIUrl":"10.1007/s11224-024-02284-7","url":null,"abstract":"<div>Derivatives of 1,4-dihydropyridine, 1,4-dihydropyrimidine, and its azolo analogs possess a wide range of biological activity and are involved in cellular bioenergetics. Dihydrocycles can be oxidized up to corresponding aromatic ones due to two one-electron transfers. Mechanism of the oxidation process was modeled as a stepwise change of the 1,4-dihydropyridine, 1,4-dihydropyrimidine, and pyrrolo-1,4-dihydropyrimidine using different levels of theory (Hartree–Fock, MP2, DFT), basis sets, and models of environment (vacuum approximation, PCM model describing a non-specific influence of polarizing environment, or PCM model with an explicit water molecule describing both non-specific and specific influence of neighboring molecules). It is shown that the potential of the first one-electron transfer I1 depends on the level of theory and the model of an environment used in calculations. The potential of the second one-electron transfer I2 depends only on the model of an environment. The analysis of their differences calculated using different approaches has revealed the dependence only from the level of theory. Since DFT methods provide the geometric characteristics of 1,4-dihydroheterocycles closest to the experimental data, it seems reasonable to use these relatively cheap calculations to study the oxidation process.</div>","PeriodicalId":780,"journal":{"name":"Structural Chemistry","volume":"35 3","pages":"993 - 1002"},"PeriodicalIF":2.1,"publicationDate":"2024-02-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139756631","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

The prediction of crystal densities of a big data set using 1D and 2D structure features 利用一维和二维结构特征预测大数据集的晶体密度

IF 2.1 4区化学

Structural Chemistry Pub Date : 2024-02-06 DOI: 10.1007/s11224-024-02279-4

Xianlan Li, Dingling Kong, Yue Luan, Lili Guo, Yanhua Lu, Wei Li, Meng Tang, Qingyou Zhang, Aimin Pang

{"title":"The prediction of crystal densities of a big data set using 1D and 2D structure features","authors":"Xianlan Li, Dingling Kong, Yue Luan, Lili Guo, Yanhua Lu, Wei Li, Meng Tang, Qingyou Zhang, Aimin Pang","doi":"10.1007/s11224-024-02279-4","DOIUrl":"10.1007/s11224-024-02279-4","url":null,"abstract":"<div>A large data set of over 30 thousand organic compounds containing carbon, nitrogen, oxygen, fluorine, and hydrogen was collected, and the density of each compound was predicted by 1D descriptors derived from its molecular formula and 2D descriptors derived from its constitutional structural features. The 2D structural features are composed of Benson’s groups, corrected groups, and 2D structural features of the whole molecular structures. All the descriptors were extracted by an in-house program in Java with a function to ensure that each atom (or bond) of molecules is represented by Benson’s groups once for atom-based (or bond-based) descriptors. Partial least square (PLS) and random forest (RF) methods were used separately to build models to predict the density. Further, the variable selection of descriptors was performed by variable importance of RF. For partial least square, the combination of the models constructed by descriptors based on the atoms and the bonds achieved the best results in this paper: for the cross-validation of the training set, the Pearson correlation coefficient (R) = 0.9270, mean absolute error (MAE) = 0.0270 g·cm−3, and root mean squared error (RMSE) = 0.0426 g·cm−3; for the prediction of the test set, R = 0.9454, MAE = 0.0263 g·cm−3, and RMSE = 0.0375 g·cm−3.</div>","PeriodicalId":780,"journal":{"name":"Structural Chemistry","volume":"35 5","pages":"1375 - 1385"},"PeriodicalIF":2.1,"publicationDate":"2024-02-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139773050","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

The breakthrough in vaccination: Nobel Prize in Physiology or Medicine 2023 疫苗接种的突破2023 年诺贝尔生理学或医学奖

IF 2.1 4区化学

Structural Chemistry Pub Date : 2024-02-05 DOI: 10.1007/s11224-024-02281-w

Krisztina Hagymási

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Quantum chemical evaluation, ELF, LOL analysis, Fukui, herbicide-likeness and molecular docking studies of 4-methyl-phenoxyacetic acid, 4-acetyl-phenoxyacetic acid and 4-tert-butyl-phenoxyacetic acid – a comparative study 4-甲基苯氧乙酸、4-乙酰基苯氧乙酸和 4-叔丁基苯氧乙酸的量子化学评价、ELF、LOL 分析、Fukui、除草剂相似性和分子对接研究 - 对比研究

IF 2.1 4区化学

Structural Chemistry Pub Date : 2024-02-03 DOI: 10.1007/s11224-023-02271-4

Karpagavalli K, Daisy Magdaline J, Chithambarathanu T, Vijaya P, Amjesh R

{"title":"Quantum chemical evaluation, ELF, LOL analysis, Fukui, herbicide-likeness and molecular docking studies of 4-methyl-phenoxyacetic acid, 4-acetyl-phenoxyacetic acid and 4-tert-butyl-phenoxyacetic acid – a comparative study","authors":"Karpagavalli K, Daisy Magdaline J, Chithambarathanu T, Vijaya P, Amjesh R","doi":"10.1007/s11224-023-02271-4","DOIUrl":"10.1007/s11224-023-02271-4","url":null,"abstract":"<div>The phenoxyacetic acid and its derivatives have attracted considerable attention as they have proven to be excellent bioactive herbicides. The optimized molecular geometry and the fundamental vibrational frequencies of 4-methyl-phenoxyacetic acid (4MPA), 4-acetyl-phenoxyacetic acid (4APA) and 4-tert-butyl-phenoxyacetic acid (4TBPA) have computed using density functional theory (DFT) method with 6–311++G(d,p) basis set. The theoretically predicted wavenumbers are found to be in close agreement with the experimentally determined one. The band gap energy of HOMO and LUMO depicts the charge transfer interactions occurring within the molecules. Global reactivity descriptors have utilized to assess the chemical reactivity. It has been observed that 4APA exhibits good electrophilic properties with a higher electrophilicity index (ω = 2.993 eV) compared to other compounds such as 4TBPA and 4MPA. The molecular electrostatic potential surface (MESP) has been plotted over the optimized structure to estimate the reactive sites of electrophilic and nucleophilic attacks on the phenoxyacetic acid molecule. Fukui function is also used to analyze their electrophilic and nucleophilic descriptors with Hirshfeld charges. Electron localization function (ELF) and local orbital localizer (LOL) are discussed using the multifunction wavefunction (Multiwfn) analyzer. Using the HerbiPAD tool, the herbicide-likeness parameter has exposed the good herbicide-like behaviour of the title compounds. Additionally, the Tice rule and pKa are described, providing valuable insights into the herbicidal activity of phenoxyacetic acid compounds. The 4APA compound is highly effective, which exhibits more herbicidal activity when interacting with the auxin receptor TIR1. It demonstrates a strong binding affinity of -8.56 kcal/mol.</div>","PeriodicalId":780,"journal":{"name":"Structural Chemistry","volume":"35 4","pages":"1307 - 1333"},"PeriodicalIF":2.1,"publicationDate":"2024-02-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139679712","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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Synthesis, spectral characteristics and molecular structure of N-(1-(5-amino-1H-1,2,4-triazol-1-yl)-2,2,2-trichloroethyl)carboxamides N-(1-(5-氨基-1H-1,2,4-三唑-1-基)-2,2,2-三氯乙基)羧酰胺的合成、光谱特征和分子结构

IF 2.1 4区化学

Structural Chemistry Pub Date : 2024-02-02 DOI: 10.1007/s11224-024-02282-9

Valeriia V. Pavlova, Pavlo V. Zadorozhnii, Vadym V. Kiselev, Aleksandr V. Kharchenko

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