Structural Chemistry最新文献_第7页

Analysis on the charge transfer and intermolecular interaction of the synthesized biological molecule bis(benzimidazolium) maleate: a comprehensive DFT approach 合成生物分子马来酸二苯并咪唑的电荷转移和分子间相互作用分析：综合DFT方法

IF 2.2 4区化学

Structural Chemistry Pub Date : 2025-01-08 DOI: 10.1007/s11224-024-02421-2

C. Dabora Vincy, G. Bagavathi Sankar, R. S. Bemina, S. Madhan Kumar, S. Sahaya Jude Dhas, A. Arun Kumar, Joselin Beaula T

{"title":"Analysis on the charge transfer and intermolecular interaction of the synthesized biological molecule bis(benzimidazolium) maleate: a comprehensive DFT approach","authors":"C. Dabora Vincy, G. Bagavathi Sankar, R. S. Bemina, S. Madhan Kumar, S. Sahaya Jude Dhas, A. Arun Kumar, Joselin Beaula T","doi":"10.1007/s11224-024-02421-2","DOIUrl":"10.1007/s11224-024-02421-2","url":null,"abstract":"<div>The FT-IR, FT-Raman, and UV–Vis spectra of bis(benzimidazolium) maleate (BM) were analysed. Quantum computations with the DFT methodology were used for finding the stable conformer and structural optimization deploying the Gaussian '09 software. An X-ray diffraction study on a single crystal revealed that the grown crystal is an orthorhombic system with a space group. To examine the numerous intra- and intermolecular interactions in a molecular system, natural bond orbital (NBO) analysis is performed. After completing normal coordinate analysis to identify the vibrational modes, PED assignments were established. According to vibrational analysis, the stretching wavenumber of hydrogen bond donor NH and hydrogen bond acceptor CO2 is red-shifted due to interaction. DOS spectral analysis is used to investigate the molecular orbital contributions. The HOMO–LUMO analysis is used to determine the studied compound’s conductivity, reactivity, and stability. The COO− groups are vulnerable to electrophilic attack, whereas the NH group in the benzimidazolium ring is probably nucleophilic, according to the MEP plot, Fukui function, and natural population analysis. The Kirby-Bauer disc diffusion technique was used to determine the antifungal activity of the BM against Candida albicans and Aspergillus niger fungal pathogens. Molecular docking studies were used to elucidate the interaction between ligands and proteins. According to ADME parameter analysis and the Lipinski rule for the BM molecule, the chemical possesses good drug-like qualities and could eventually be developed into an antifungal medication.</div>","PeriodicalId":780,"journal":{"name":"Structural Chemistry","volume":"36 4","pages":"1211 - 1227"},"PeriodicalIF":2.2,"publicationDate":"2025-01-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145163613","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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Molecular adsorption studies of dimethylamine and trimethylamine on beta antimonide phosphorus nanotube—a first-principles perspective 二甲胺和三甲胺在锑化磷纳米管上的分子吸附研究——第一性原理观点

IF 2.2 4区化学

Structural Chemistry Pub Date : 2025-01-03 DOI: 10.1007/s11224-024-02436-9

M. Vijay Balaji, R. Chandiramouli, V. Nagarajan

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The mechanism of the phosphine-catalyzed oxa-Michael reaction: a DFT investigation 膦催化oxa-Michael反应机理的DFT研究

IF 2.2 4区化学

Structural Chemistry Pub Date : 2025-01-03 DOI: 10.1007/s11224-024-02431-0

Priyanka Suthar, Ruchi Singh, Raj K. Bansal

{"title":"The mechanism of the phosphine-catalyzed oxa-Michael reaction: a DFT investigation","authors":"Priyanka Suthar, Ruchi Singh, Raj K. Bansal","doi":"10.1007/s11224-024-02431-0","DOIUrl":"10.1007/s11224-024-02431-0","url":null,"abstract":"<div>Two possible model reaction mechanisms of trimethylphosphine-catalyzed oxa-Michael addition of phenol and methanol to acrolein, one in which trimethylphosphine acts as a nuclephile and adds to acrolein to generate the enolate anion (mechanism 1) and the other in which trimethylphosphine acts as a base and reacts with the hydroxyl compound to generate PhO− /MeO− anion (mechanism 2), were computed in the gas phase using the B3LYP functional and the ωB97XD functional which incorporates dispersion correction, with the same basis set, 6–31 + G(d). In mechanism 1, the third step involving the attack of PhO− or MeO− on the intermediate, Int.2 accompanied by the loss of Me3P occurring through TS3 is the rate-determining step. In this case, however, the activation free energy for the attack of PhO− is found to be smaller than for MeO−, which is contrary to the experimental results wherein methanol is reported to react faster than phenol. In mechanism 2, the second step involving nucleophilic attack of the PhO− or MeO− anion on C3 of acrolein via TS2’ is the rate-differentiating step vis-à-vis the reactions of phenol and methanol with acrolein. In this case, the activation free energy barrier for PhO− is much higher than for MeO−; in fact, the reaction with latter is found to be barrierless. It is in perfect compliance with the experimental results. These results indicate that trimethylphosphine-catalyzed oxa-Michael addition of phenol and methanol with acrolein occurs via the mechanism in which phosphine acts as a base. Acetonitrile is found to lower the activation energies.</div>","PeriodicalId":780,"journal":{"name":"Structural Chemistry","volume":"36 4","pages":"1187 - 1199"},"PeriodicalIF":2.2,"publicationDate":"2025-01-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145161201","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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Theoretical investigation of structural and electronic properties and water splitting electrocatalytic performance of TM-decorated (TM = Mn, Fe, Co, and Ni) biphenylene monolayers TM修饰（TM = Mn, Fe, Co, and Ni）联苯单分子膜结构、电子性能及水裂解电催化性能的理论研究

IF 2.2 4区化学

Structural Chemistry Pub Date : 2024-12-30 DOI: 10.1007/s11224-024-02444-9

Seifollah Jalili, Faezeh Taravat, Atena Pakzadiyan

{"title":"Theoretical investigation of structural and electronic properties and water splitting electrocatalytic performance of TM-decorated (TM = Mn, Fe, Co, and Ni) biphenylene monolayers","authors":"Seifollah Jalili, Faezeh Taravat, Atena Pakzadiyan","doi":"10.1007/s11224-024-02444-9","DOIUrl":"10.1007/s11224-024-02444-9","url":null,"abstract":"<div>Searching for novel materials with high efficiency as electrocatalysts in the field of water splitting is one of the most effective approaches to mitigate energy problems. In this study, we present the impact of transition metal (TM = Mn, Fe, Co, and Ni) decoration on the potential of biphenylene (BP) as a water-splitting electrocatalyst using density functional theory. We first present the structural and electronic properties of the TM-decorated BP monolayers. Our results show that TM decoration can influence the frontier orbitals of pristine BP, leading to a reduced energy gap due to charge transfer from TM to the BP surface. In the hydrogen evolution reaction (HER) section, the lowest ΔG for hydrogen adsorption as an intermediate was obtained for Co@BP at 0.26 eV, which is lower than that of pristine BP and graphene reported in previous studies. On the other hand, evaluating the oxygen evolution reaction (OER) electrocatalytic activity of TM-decorated BP monolayers reveals that Mn decoration is an efficient approach, among the selected transition metals, to improve the catalytic performance of BP. Our study introduces a procedure for the rational design of high-performance single-atom catalyst (SAC) materials.</div>","PeriodicalId":780,"journal":{"name":"Structural Chemistry","volume":"36 4","pages":"1173 - 1185"},"PeriodicalIF":2.2,"publicationDate":"2024-12-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145170602","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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Towards the computational design of organic molecules with specified properties 面向具有特定性质的有机分子的计算设计

IF 2.1 4区化学

Structural Chemistry Pub Date : 2024-12-26 DOI: 10.1007/s11224-024-02441-y

Anton B. Zakharov, Mariia Kyrpa, Alexander V. Kyrychenko, Sergiy M. Kovalenko, Oleg N. Kalugin, Volodymyr V. Ivanov, Ludwik Adamowicz

{"title":"Towards the computational design of organic molecules with specified properties","authors":"Anton B. Zakharov, Mariia Kyrpa, Alexander V. Kyrychenko, Sergiy M. Kovalenko, Oleg N. Kalugin, Volodymyr V. Ivanov, Ludwik Adamowicz","doi":"10.1007/s11224-024-02441-y","DOIUrl":"10.1007/s11224-024-02441-y","url":null,"abstract":"<div>In this work, we present and test a procedure for generating a chemical virtual library and its subsequent use to select molecular systems with desired properties. The library consists of molecular structures generated from a set of chemical fragments. As an example, we consider two tasks. The first one involves identifying structures with specific spectral properties, particularly concerning the UV–Vis region of the spectrum. To address this, the thiophene cycles with typical donor (dimethylamino) and acceptor (nitro) substituents are chosen as the molecular building blocks. First, the molecules from the derived virtual library are subject to computational screening using the semi-empirical tight binding density-functional method. The primary objective of the screening is to identify molecular structures that exhibit desired spectral properties, especially absorption in the long-wavelength region. Second, for the most promising structures identified in the initial screening, more accurate TD-DFT (B3LYP/cc-pVDZ) calculations are performed. Additionally, the advantage of the developed approach for library generation, aimed at further investigation of biological activity, is illustrated using an example involving papain-like protease (PLpro) inhibitors of the SARS-CoV-2 virus. The calculation scheme used in the considered examples is implemented in the Python program suite QUASAR.</div>","PeriodicalId":780,"journal":{"name":"Structural Chemistry","volume":"36 2","pages":"723 - 738"},"PeriodicalIF":2.1,"publicationDate":"2024-12-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143622276","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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Computational studies on transition metal and nitrogen atoms co-doped fullerene as an efficient electrocatalyst for nitrate reduction to ammonia 过渡金属与氮原子共掺杂富勒烯作为硝酸还原制氨高效电催化剂的计算研究

IF 2.2 4区化学

Structural Chemistry Pub Date : 2024-12-26 DOI: 10.1007/s11224-024-02443-w

Faiza Shafiq, Lei Yang, Weihua Zhu

{"title":"Computational studies on transition metal and nitrogen atoms co-doped fullerene as an efficient electrocatalyst for nitrate reduction to ammonia","authors":"Faiza Shafiq, Lei Yang, Weihua Zhu","doi":"10.1007/s11224-024-02443-w","DOIUrl":"10.1007/s11224-024-02443-w","url":null,"abstract":"<div>Persistent accumulation of nitrate in water causes an imbalance in the nitrogen cycle in the earth, posing a serious risk to human health and the ecosystem. The technique for electro catalyzing nitrate reduction has become widely employed due to the rapid development of efficient catalysts. Transition metal (TM)-based catalysts are highly sought due to their low cost and excellent catalytic activity. TM and nitrogen co-doped fullerene (TMN-C60) were constructed and investigated for nitrate reduction reaction (NO3RR) using DFT and AIMD. FeN-C60 has been discovered to have a low limiting potential of − 0.56 V based on typical hydrogen electrode model, making it a potential candidate for NO3RR. The analysis of PDOS demonstrates the considerable pd hybridization and the interactions between dopants and C60. FeN-C60 is stable over 400 K, confirming its sustainability in the electrocatalysis. Periodic spin-polarized DFT calculations were carried out using the DMol3 package, utilizing the GGA-PBE functional and DND basis set. The DSPP technique and Grimme correction were applied to address core electrons and accurately correct dispersion force, respectively. Thermal smearing was set to 5.0 × 10−3 Ha. AIMD simulations were implemented using NVT ensemble at 400 K. The total simulation time of 10 ps with 1 fs time step was used.</div>","PeriodicalId":780,"journal":{"name":"Structural Chemistry","volume":"36 4","pages":"1163 - 1171"},"PeriodicalIF":2.2,"publicationDate":"2024-12-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145169161","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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A combinatorial exploration of a very large set of azaboles 对一组非常大的偶氮代谢的组合探索

IF 2.1 4区化学

Structural Chemistry Pub Date : 2024-12-26 DOI: 10.1007/s11224-024-02422-1

Ibon Alkorta, Maxime Ferrer, Goar Sánchez-Sanz, Felipe Reviriego, José Elguero

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Different topology of mixed valence CoIICoIII complexes with SCN anions and hydrazone–pyridine-based ligands 与SCN阴离子和腙吡啶配体混合价CoIICoIII配合物的不同拓扑结构

IF 2.1 4区化学

Structural Chemistry Pub Date : 2024-12-24 DOI: 10.1007/s11224-024-02442-x

Ghodrat Mahmoudi, Alexander S. Novikov, Tomislav Balić, Ennio Zangrando, Jonathan M. White, Bagher Eftekhari-Sis

{"title":"Different topology of mixed valence CoIICoIII complexes with SCN anions and hydrazone–pyridine-based ligands","authors":"Ghodrat Mahmoudi, Alexander S. Novikov, Tomislav Balić, Ennio Zangrando, Jonathan M. White, Bagher Eftekhari-Sis","doi":"10.1007/s11224-024-02442-x","DOIUrl":"10.1007/s11224-024-02442-x","url":null,"abstract":"<div>Two novel mixed valence CoIICoIII complexes [Co4II(SCN)12(EtOH)2Co4III(L1)8] (1) and [CoII(SCN)2Co2III(L2)4]n (2) (HL1 = N’-(1-(pyridin-2-yl)ethylidene)nicotinohydrazide and HL2 = N’-(phenyl(pyridin-2-yl)methylene)isonicotinohydrazide) have been synthesized and structurally characterized by the single crystal X-ray crystallography. In both cases, the deprotonated ligands HL1 and HL2 behave as chelating species toward CoIII, further connecting CoII fragments through the nicotine pyridine donors. A different topology is observed in the solid state of these complexes, complex 1 being an octanuclear cyclic species, while 2 is a 1D coordination polymer. The DFT calculations followed by the topological analysis of the electron density distribution have shown the existence of interesting non-covalent S···π-system interactions in 1. The CSD database search for similar supramolecular motif involving NCS anion has shown that the number and strength of S···π interactions depend both on acidity of metal cation and number aromatic systems in the molecular structure of ligand.</div>","PeriodicalId":780,"journal":{"name":"Structural Chemistry","volume":"36 3","pages":"1105 - 1113"},"PeriodicalIF":2.1,"publicationDate":"2024-12-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143904830","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, spectroscopic and structural characterization of cyclometallated rhodium(III) complexes with 1-phenyl-1H-pyrazole and α-diimines ligands, comparison with their iridium(III) analogues 1-苯基- 1h -吡唑和α-二亚胺环金属化铑（III）配合物的合成、光谱和结构表征及其与铱（III）类似物的比较

IF 2.1 4区化学

Structural Chemistry Pub Date : 2024-12-23 DOI: 10.1007/s11224-024-02439-6

Anna Kamecka, Andrzej Kapturkiewicz, Patryk Wójcik, Kinga Suwińska, Joanna Masternak, Natalia Barbarczyk

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Geometrical and thermodynamical stability of the adducts of the phytochemicals of Swertia chirayita (Roxb. Ex Fleming) with a protein of Plasmodium falciparum 獐牙菜属植物化学物质加合物的几何和热力学稳定性。（原弗莱明）含有一种恶性疟原虫蛋白

IF 2.1 4区化学

Structural Chemistry Pub Date : 2024-12-23 DOI: 10.1007/s11224-024-02415-0

Ram Lal Swagat Shrestha, Bishnu Prasad Marasini, Jhashanath Adhikari Subin

{"title":"Geometrical and thermodynamical stability of the adducts of the phytochemicals of Swertia chirayita (Roxb. Ex Fleming) with a protein of Plasmodium falciparum","authors":"Ram Lal Swagat Shrestha, Bishnu Prasad Marasini, Jhashanath Adhikari Subin","doi":"10.1007/s11224-024-02415-0","DOIUrl":"10.1007/s11224-024-02415-0","url":null,"abstract":"<div>The global economic burden of malaria is rising due to climate change, and the search for effective and specific drugs against it that are affordable has become essential. The phytochemicals with ethnobotanical values are relatively safer and are a viable option for their use as therapeutics. The chemical components of a plant, Swertia chirayita (Roxb. Ex Fleming), showed strong binding potential against the parasite membrane protein of Plasmodium falciparum (PDB ID: 5K8S), a causative agent of the disease, as determined from computational methods. The docking scores of the top two candidates, amarogentin and swertinin, were determined to be − 10.064 kcal/mol and − 9.904 kcal/mol, respectively, with the native ligand possessing a higher value of − 8.395 kcal/mol. The protein–ligand complexes formed by these top two ligands were geometrically and thermodynamically stable, as revealed by several parameters extracted from the molecular dynamics simulations. Especially, the smooth nature of ligand RMSD curves denoted the attainment of equilibrium and binding free energy changes; ΔGBFE < 0 predicted the sustained thermodynamical spontaneity of the complex formation reaction. The preliminary results suggest that the hit phytochemicals could inhibit the normal functioning of the target protein and are recommended for further experimental trials. The traditional knowledge of the plants with therapeutic values could be extended to modern medicines with molecular-level understanding and be used in the drug design process in a low-resource setting.</div>","PeriodicalId":780,"journal":{"name":"Structural Chemistry","volume":"36 3","pages":"1091 - 1104"},"PeriodicalIF":2.1,"publicationDate":"2024-12-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143904823","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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