1
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Zhang FX, Wang M, Ma JB. Conversion of Carbon Dioxide into a Series of CB xO y- Compounds Mediated by LaB 3,4O 2- Anions: Synergy of the Electron Transfer and Lewis Pair Mechanisms to Construct B-C Bonds. Inorg Chem 2024; 63:14206-14215. [PMID: 39012836 DOI: 10.1021/acs.inorgchem.4c02337] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/18/2024]
Abstract
Converting CO2 into value-added products containing B-C bonds is a great challenge, especially for multiple B-C bonds, which are versatile building blocks for organoborane chemistry. In the condensed phase, the B-C bond is typically formed through transition metal-catalyzed direct borylation of hydrocarbons via C-H bond activation or transition metal-catalyzed insertion of carbenes into B-H bonds. However, excessive amounts of powerful boryl reagents are required, and products containing B-C bonds are complex. Herein, a novel method to construct multiple B-C bonds at room temperature is proposed by the gas-phase reactions of CO2 with LaBmOn- (m = 1-4, n = 1 or 2). Mass spectrometry and density functional theory calculations are applied to investigate these reactions, and a series of new compounds, CB2O2-, CB3O3-, and CB3O2-, which possess B-C bonds, are generated in the reactions of LaB3,4O2- with CO2. When the number of B atoms in the clusters is reduced to 2 or 1, there is only CO-releasing channel, and no CBxOy- compounds are released. Two major factors are responsible for this quite intriguing reactivity: (1) Synergy of electron transfer and boron-boron Lewis acid-base pair mechanisms facilitates the rupture of C═O double bond in CO2. (2) The boron sites in the clusters can efficiently capture the newly formed CO units in the course of reactions, favoring the formation of B-C bonds. This finding may provide fundamental insights into the CO2 transformation driven by clusters containing lanthanide atoms and how to efficiently build B-C bonds under room temperature.
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Affiliation(s)
- Feng-Xiang Zhang
- Key Laboratory of Cluster Science of Ministry of Education, Beijing Key Laboratory of Photoelectronic/Electrophotonic Conversion Materials, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing 102488, China
| | - Ming Wang
- Key Laboratory of Cluster Science of Ministry of Education, Beijing Key Laboratory of Photoelectronic/Electrophotonic Conversion Materials, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing 102488, China
| | - Jia-Bi Ma
- Key Laboratory of Cluster Science of Ministry of Education, Beijing Key Laboratory of Photoelectronic/Electrophotonic Conversion Materials, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing 102488, China
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2
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Liu KW, Li JL, Xu XL, Xu HG, Ding KW, Zheng WJ. Pentacoordinated pyramidal structures and bonding properties of WN 10-/0: anion photoelectron spectroscopy and theoretical calculations. Phys Chem Chem Phys 2024. [PMID: 39051262 DOI: 10.1039/d4cp02262a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/27/2024]
Abstract
Anion photoelectron spectroscopy and theoretical calculations were used to investigate the structural and bonding properties of WN10-/0. The electron affinity of WN10 is measured to be 1.582 ± 0.030 eV. The frequency of the NN stretch in WN10 is measured to be 2170 ± 80 cm-1, which is red-shifted with respect to that of the dinitrogen molecule indicating that the NN bonds are weakened in WN10. The theoretical adiabatic detachment energy (ADE) and vertical detachment energy (VDE) of WN10- obtained by calculations at the CCSD(T)/CBS level agree well with experimental results. The structures of WN10-/0 are C4v symmetric pentacoordinated pyramidal structures with five end-on dinitrogen ligands. Our experiments show that the peak of WN10- is dominant in the mass spectrum of anionic WNn, whereas the mass peak of WN12+ is dominant in the mass spectrum of cationic WNn, implying that the stabilities of WNn clusters are strongly related to their charge states.
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Affiliation(s)
- Kai-Wen Liu
- Beijing National Laboratory for Molecular Sciences (BNLMS), State Key Laboratory of Molecular Reaction Dynamics, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China.
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jia-Le Li
- State Key Laboratory of Fluorine & Nitrogen Chemicals, Xi'an 710065, China.
- Xi'an Modern Chemistry Research Institute, Xi'an 710065, China
| | - Xi-Ling Xu
- Beijing National Laboratory for Molecular Sciences (BNLMS), State Key Laboratory of Molecular Reaction Dynamics, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China.
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Hong-Guang Xu
- Beijing National Laboratory for Molecular Sciences (BNLMS), State Key Laboratory of Molecular Reaction Dynamics, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China.
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ke-Wei Ding
- State Key Laboratory of Fluorine & Nitrogen Chemicals, Xi'an 710065, China.
- Xi'an Modern Chemistry Research Institute, Xi'an 710065, China
| | - Wei-Jun Zheng
- Beijing National Laboratory for Molecular Sciences (BNLMS), State Key Laboratory of Molecular Reaction Dynamics, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China.
- University of Chinese Academy of Sciences, Beijing 100049, China
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3
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Kumaravel A, Sengupta T, Sathiyamoorthy P, Jeong J, Kang SG, Hong SH. Cobalt Oxide Nanoparticle Synthesis by Cell-Surface-Engineered Recombinant Escherichia coli and Potential Application for Anticancer Treatment. ACS OMEGA 2024; 9:31373-31383. [PMID: 39072137 PMCID: PMC11270722 DOI: 10.1021/acsomega.3c10246] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Revised: 06/19/2024] [Accepted: 06/26/2024] [Indexed: 07/30/2024]
Abstract
Cell surface display engineering facilitated the development of a cobalt-binding hybrid Escherichia coli. OmpC served as the molecular anchor for showcasing the cobalt-binding peptides (CBPs), creating the structural model of the hybrid OmpC-CBPs (OmpC-CP, OmpC-CF). Subsequently, the recombinant peptide's cobalt adsorption and retrieval effectiveness were evaluated at various concentrations. When subjected to a pH of 7 and a concentration of 2 mM, OmpC-CF exhibited a significantly higher cobalt recovery rate (2183.87 mol/g DCW) than OmpC-CP. The strain with bioadsorbed cobalt underwent thermal treatment at varying temperatures (400 °C, 500 °C, 600 °C, and 700 °C) and morphological characterization of the thermally decomposed cobalt nanoparticle oxides using diverse spectroscopy techniques. The analysis showed that nanoparticles confined themselves to metal ions, and EDS mapping detected the presence of cobalt on the cell surface. Finally, the nanoparticles' anticancer potential was assessed by subjecting them to heating at 500 °C in a furnace; they demonstrated noteworthy cytotoxicity, as evidenced by IC50 values of 59 μg/mL. These findings suggest that these nanoparticles hold promise as potential anticancer agents. Overall, this study successfully engineered a recombinant E. coli capable of efficiently binding to cobalt, producing nanoparticles with anticancer properties. The results of this investigation could have significant implications for advancing novel cancer therapies.
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Affiliation(s)
- Ashokkumar Kumaravel
- Department
of Chemical Engineering, University of Ulsan, 93 Daehak-ro, Nam-gu, Ulsan 44610, Republic of Korea
| | - Turbasu Sengupta
- Department
of Chemical Engineering, University of Ulsan, 93 Daehak-ro, Nam-gu, Ulsan 44610, Republic of Korea
| | - Padmanaban Sathiyamoorthy
- Department
of Medical Nanotechnology, School of Chemical & Biotechnology, SASTRA Deemed University, Tamil Nadu 613401, India
| | - Jaehoon Jeong
- Department
of Chemical Engineering, University of Ulsan, 93 Daehak-ro, Nam-gu, Ulsan 44610, Republic of Korea
| | - Sung Gu Kang
- Department
of Chemical Engineering, University of Ulsan, 93 Daehak-ro, Nam-gu, Ulsan 44610, Republic of Korea
| | - Soon Ho Hong
- Department
of Chemical Engineering, University of Ulsan, 93 Daehak-ro, Nam-gu, Ulsan 44610, Republic of Korea
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4
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Engsvang M, Wu H, Elm J. Iodine Clusters in the Atmosphere I: Computational Benchmark and Dimer Formation of Oxyacids and Oxides. ACS OMEGA 2024; 9:31521-31532. [PMID: 39072118 PMCID: PMC11270685 DOI: 10.1021/acsomega.4c01235] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/07/2024] [Revised: 06/19/2024] [Accepted: 06/21/2024] [Indexed: 07/30/2024]
Abstract
The contribution of iodine-containing compounds to atmospheric new particle formation is still not fully understood, but iodic acid and iodous acid are thought to be significant contributors. While several quantum chemical studies have been carried out on clusters containing iodine, there is no comprehensive benchmark study quantifying the accuracy of the applied methods. Here, we present the first study in a series that investigate the role of iodine species in atmospheric cluster formation. In this work, we have studied the iodic acid, iodous acid, iodine tetroxide, and iodine pentoxide monomers and their dimers formed with common atmospheric precursors. We have tested the accuracy of commonly applied methods for calculating the geometry of the monomers, thermal corrections of monomers and dimers, the contribution of spin-orbit coupling to monomers and dimers, and finally, the accuracy of the electronic energy correction calculated at different levels of theory. We find that optimizing the structures either at the ωB97X-D3BJ/aug-cc-pVTZ-PP or the M06-2X/aug-cc-pVTZ-PP level achieves the best thermal contribution to the binding free energy. The electronic energy correction can then be calculated at the ZORA-DLPNO-CCSD(T0) level with the SARC-ZORA-TZVPP basis for iodine and ma-ZORA-def2-TZVPP for non-iodine atoms. We applied this methodology to calculate the binding free energies of iodine-containing dimer clusters, where we confirm the qualitative trends observed in previous studies. However, we identify that previous studies overestimate the stability of the clusters by several kcal/mol due to the neglect of relativistic effects. This means that their contributions to the currently studied nucleation pathways of new particle formation are likely overestimated.
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Affiliation(s)
- Morten Engsvang
- Department of Chemistry, Aarhus University, Langelandsgade 140, 8000 Aarhus C, Denmark
| | - Haide Wu
- Department of Chemistry, Aarhus University, Langelandsgade 140, 8000 Aarhus C, Denmark
| | - Jonas Elm
- Department of Chemistry, Aarhus University, Langelandsgade 140, 8000 Aarhus C, Denmark
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5
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Kakalejčíková S, Bazeľ Y, Le Thi VA, Fizer M. An Innovative Vortex-Assisted Liquid-Liquid Microextraction Approach Using Deep Eutectic Solvent: Application for the Spectrofluorometric Determination of Rhodamine B in Water, Food and Cosmetic Samples. Molecules 2024; 29:3397. [PMID: 39064976 PMCID: PMC11280433 DOI: 10.3390/molecules29143397] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2024] [Revised: 07/12/2024] [Accepted: 07/16/2024] [Indexed: 07/28/2024] Open
Abstract
A new green and highly sensitive method for the determination of rhodamine B (RhB) by deep eutectic solvent-based vortex-assisted liquid-liquid microextraction with fluorescence detection (DES-VALLME-FLD) was developed. The extraction efficiency of conventional solvents and different deep eutectic solvent (DES) systems composed of tetrabutylammonium bromide (TBAB) and an alcohol (hexanol, octanol, or decanol) in different ratios were compared. DFT calculations of intermolecular electrostatic and non-covalent interactions of the most stable RhB forms with DES and water explain the experimental DESs' extraction efficiency. Semiempirical PM7 computations were used to obtain Hansen solubility parameters, which supported the good solubility of the monocationic RhB form in selected DESs. The dependence of the linear calibration of microextraction into 100 µL DES was observed in the RhB calibration range from 0.2 to 10.0 µg L-1 with a correlation coefficient of R2 = 0.9991. The LOD value was calculated to be 0.023 µg L-1. The accuracy and precision of the proposed method were verified over two days with RSD values of 2.9 to 4.1% and recovery of 94.6 to 103.7%. The developed method was applied to the determination of RhB in real samples (tap water, energy drink, and lipstick).
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Affiliation(s)
- Sofia Kakalejčíková
- Department of Analytical Chemistry, Institute of Chemistry, Pavol Jozef Šafárik University in Košice, 040 01 Košice, Slovakia; (S.K.); (V.A.L.T.)
| | - Yaroslav Bazeľ
- Department of Analytical Chemistry, Institute of Chemistry, Pavol Jozef Šafárik University in Košice, 040 01 Košice, Slovakia; (S.K.); (V.A.L.T.)
| | - Van Anh Le Thi
- Department of Analytical Chemistry, Institute of Chemistry, Pavol Jozef Šafárik University in Košice, 040 01 Košice, Slovakia; (S.K.); (V.A.L.T.)
| | - Maksym Fizer
- Department of Chemistry, University of Nevada, Reno, 1664 N. Virginia Street, Reno, NV 89557-0216, USA;
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6
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Zhang YH, Wang HQ, Li HF, Zeng JK, Zheng H, Mei XJ, Zhang JM, Jiang KL, Zhang B, Wu WH. Probing the Structural and Electronic Properties of the Anionic and Neutral Tellurium-Doped Boron Clusters TeB nq ( n = 3-16, q = 0, -1). J Phys Chem A 2024; 128:5459-5472. [PMID: 38973649 DOI: 10.1021/acs.jpca.4c00907] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/09/2024]
Abstract
In this study, we employ density functional theory along with the artificial bee colony algorithm for cluster global optimization to explore the low-lying structures of TeBnq (n = 3-16, q = 0, -1). The primary focus is on reporting the structural properties of these clusters. The results reveal a consistent doping pattern of the tellurium atom onto the in-plane edges of planar or quasi-planar boron clusters in the most energetically stable isomers. Additionally, we simulate the photoelectron spectra of the cluster anions. Through relative stability analysis, we identify three clusters with magic numbers -TeB7-, TeB10, and TeB12. The aromaticity of these clusters is elucidated using adaptive natural density partitioning (AdNDP) and magnetic properties analysis. Notably, TeB7- exhibits a perfect σ-π doubly aromatic structure, while TeB12 demonstrates strong island aromaticity. These findings significantly contribute to our understanding of the structural and electronic properties of these clusters.
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Affiliation(s)
- Yong-Hang Zhang
- College of Information Science and Engineering, Huaqiao University, Xiamen 361021, China
| | - Huai-Qian Wang
- College of Information Science and Engineering, Huaqiao University, Xiamen 361021, China
- College of Engineering, Huaqiao University, Quanzhou 362021, China
| | - Hui-Fang Li
- College of Engineering, Huaqiao University, Quanzhou 362021, China
| | - Jin-Kun Zeng
- College of Information Science and Engineering, Huaqiao University, Xiamen 361021, China
| | - Hao Zheng
- College of Information Science and Engineering, Huaqiao University, Xiamen 361021, China
| | - Xun-Jie Mei
- College of Engineering, Huaqiao University, Quanzhou 362021, China
| | - Jia-Ming Zhang
- College of Information Science and Engineering, Huaqiao University, Xiamen 361021, China
| | - Kai-Le Jiang
- College of Information Science and Engineering, Huaqiao University, Xiamen 361021, China
| | - Bo Zhang
- College of Information Science and Engineering, Huaqiao University, Xiamen 361021, China
| | - Wen-Hai Wu
- College of Engineering, Huaqiao University, Quanzhou 362021, China
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7
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Marcos PA, Aguilar N, Rozas S, Martel S, Bol A, Aparicio S. Manganese-rhodium nanoparticles: Adsorption on titanium oxide surfaces and catalyst for syngas reactions. J Chem Phys 2024; 161:024113. [PMID: 38990117 DOI: 10.1063/5.0215450] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2024] [Accepted: 06/15/2024] [Indexed: 07/12/2024] Open
Abstract
Manganese-rhodium (Mn-Rh) nanoparticles have emerged as a promising candidate for catalytic applications in the production of syngas, a critical precursor for a wide range of industrial processes. This study employs a comprehensive, theoretical, and computational approach to investigate the structural and electronic properties of Mn-Rh nanoparticles, with a specific focus on their interaction with titanium oxide (TiO2) surfaces and their potential as catalysts for syngas reactions. The density functional theory calculations are employed to explore the adsorption behavior of Mn-Rh nanoparticles on TiO2 surfaces. By analyzing the adsorption energies, geometries, and electronic structure at the nanoscale interface, we provide valuable insights into the stability and reactivity of Mn-Rh nanoparticles when immobilized on TiO2 supports. Furthermore, the catalytic performance of Mn-Rh nanoparticles in syngas production is thoroughly examined. Through detailed reaction mechanism studies and kinetic analysis, we elucidate the role of Mn and Rh in promoting syngas generation via carbon dioxide reforming and partial oxidation reactions. The findings demonstrate the potential of Mn-Rh nanoparticles as efficient catalysts for these crucial syngas reactions. This research work not only enhances our understanding of the fundamental properties of Mn-Rh nanoparticles but also highlights their application as catalysts for sustainable and industrially significant syngas production.
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Affiliation(s)
- P A Marcos
- Department of Physics, University of Burgos, 09001 Burgos, Spain
| | - N Aguilar
- Department of Chemistry, University of Burgos, 09001 Burgos, Spain
| | - S Rozas
- Department of Chemistry, University of Burgos, 09001 Burgos, Spain
| | - S Martel
- International Research Center in Critical Raw Materials for Advanced Industrial Technologies (ICCRAM), University of Burgos, 09001 Burgos, Spain
| | - A Bol
- Department of Physics, University of Burgos, 09001 Burgos, Spain
- International Research Center in Critical Raw Materials for Advanced Industrial Technologies (ICCRAM), University of Burgos, 09001 Burgos, Spain
| | - S Aparicio
- Department of Chemistry, University of Burgos, 09001 Burgos, Spain
- International Research Center in Critical Raw Materials for Advanced Industrial Technologies (ICCRAM), University of Burgos, 09001 Burgos, Spain
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8
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Zhang Y, Yang J, Dong C, Li X. Introducing hafnium to atomically small- and medium-sized tin clusters (HfSn n0/-/2- (n = 4-17)): A computational investigation of geometrical and growth behavior, spectral properties, electronic configuration and thermochemistry. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2024; 315:124277. [PMID: 38636426 DOI: 10.1016/j.saa.2024.124277] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2024] [Revised: 03/30/2024] [Accepted: 04/11/2024] [Indexed: 04/20/2024]
Abstract
The global and local minimum configurations of single Hf atom doped Sn clusters are conducted via density function theory (DFT) combined with artificial bee colony algorithm (ABCluster). Furthermore, DFT method is also used to systematically investigate on their structural growth evolution, spectral and electronic information, thermochemical properties following the size of tin clusters doped Hf atom. Structurally, the ground-state geometries of neutral, anion and di-anion are discovered that, from n = 4, the number of Sn atoms in cluster, HfSnn0/-/2- adsorb additional Sn atom on the prior architecture one by one until forming n = 17 for HfSnn-10/-, as well as forming n = 16 for HfSnn-12-. And for the HfSn110/- and HfSn102- as beginning the species veritably develop sealed architectures. The strongest vibrational modes of sealed nanoclusters are stretching modes of Hf atom with infrared actives and breathing modes of the Sn cage framework with Raman actives, respectively. The natural population analysis (NPA) elucidates the stronger relationship between the Hf atoms and the tin frameworks in sealed clusters than that in unsealed clusters. The results of thermochemical properties, molecular orbital shell (MOs), adaptive natural density partitioning (AdNDP) and ultraviolet visible absorption spectrum (UV-Vis) indicate that, the HfSn16 with high symmetry of Td exhibits thermochemical stability and optoelectronic properties, which is utilized potentially as zero-dimensional unit of self-assembling fluorescent nanomaterials.
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Affiliation(s)
- Yanpeng Zhang
- College of Chemical Engineering, Inner Mongolia University of Technology, and Inner Mongolia Key Laboratory of Theoretical and Computational Chemistry Simulation, Hohhot 010051, People's Republic of China
| | - Jucai Yang
- College of Chemical Engineering, Inner Mongolia University of Technology, and Inner Mongolia Key Laboratory of Theoretical and Computational Chemistry Simulation, Hohhot 010051, People's Republic of China; College of Resources and Environmental Engineering, Inner Mongolia University of Technology, Hohhot 010051, People's Republic of China
| | - Caixia Dong
- College of Resources and Environmental Engineering, Inner Mongolia University of Technology, Hohhot 010051, People's Republic of China.
| | - Xiaojun Li
- College of Science, Xi'an University of Posts and Telecommunications, Xi'an 710121, Shaanxi, People's Republic of China.
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Tang Z, Zhu H, Pan Z, Gao J, Zhang J. A many-body energy decomposition analysis (MB-EDA) scheme based on a target state optimization self-consistent field (TSO-SCF) method. Phys Chem Chem Phys 2024; 26:17549-17560. [PMID: 38884195 DOI: 10.1039/d4cp01259c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/18/2024]
Abstract
In this paper, we combine an energy decomposition analysis (EDA) scheme with many-body expansion (MBE) to develop a MB-EDA method to study the cooperative and anti-cooperative effects in molecular cluster systems. Based on the target state optimization self-consistent field (TSO-SCF) method, the intermolecular interaction energy can be decomposed into five chemically meaningful terms, i.e., electrostatic, exchange, polarization, charge transfer and dispersion interaction energies. MB-EDA can decompose each of these terms in MBE. This MB-EDA has been applied to 3 different cluster systems: water clusters, ionic liquid clusters, and acetonitrile-methane clusters. This reveals that electrostatic, exchange, and dispersion interactions are highly pairwise additive in all systems. In water and ionic liquid clusters, the many-body effects are significant in both polarization and charge transfer interactions, but are cooperative and anti-cooperative, respectively. For acetonitrile-methane clusters, which do not involve hydrogen bonds or charge-charge Coulombic interactions, the many-body effects are quite small. The chemical origins of different many-body effects are deeply analyzed. The MB-EDA method has been implemented in Qbics (https://qbics.info) and can be a useful tool for understanding the many-body behavior in molecular aggregates at the quantum chemical level of theory.
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Affiliation(s)
- Zhen Tang
- Peking University Shenzhen Graduate School, Shenzhen, Guangdong 518055, People's Republic of China.
- Institute of Systems and Physical Biology, Shenzhen Bay Laboratory, Shenzhen, Guangdong 518055, People's Republic of China.
| | - Hong Zhu
- Peking University Shenzhen Graduate School, Shenzhen, Guangdong 518055, People's Republic of China.
- Institute of Systems and Physical Biology, Shenzhen Bay Laboratory, Shenzhen, Guangdong 518055, People's Republic of China.
| | - Zhijun Pan
- Institute of Systems and Physical Biology, Shenzhen Bay Laboratory, Shenzhen, Guangdong 518055, People's Republic of China.
| | - Jiali Gao
- Peking University Shenzhen Graduate School, Shenzhen, Guangdong 518055, People's Republic of China.
- Institute of Systems and Physical Biology, Shenzhen Bay Laboratory, Shenzhen, Guangdong 518055, People's Republic of China.
- Department of Chemistry and Supercomputing Institute, University of Minnesota, Minneapolis, MN 55455, USA
| | - Jun Zhang
- Institute of Systems and Physical Biology, Shenzhen Bay Laboratory, Shenzhen, Guangdong 518055, People's Republic of China.
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10
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Knattrup Y, Kubečka J, Wu H, Jensen F, Elm J. Reparameterization of GFN1-xTB for atmospheric molecular clusters: applications to multi-acid-multi-base systems. RSC Adv 2024; 14:20048-20055. [PMID: 38911834 PMCID: PMC11191700 DOI: 10.1039/d4ra03021d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2024] [Accepted: 06/16/2024] [Indexed: 06/25/2024] Open
Abstract
Atmospheric molecular clusters, the onset of secondary aerosol formation, are a major part of the current uncertainty in modern climate models. Quantum chemical (QC) methods are usually employed in a funneling approach to identify the lowest free energy cluster structures. However, the funneling approach highly depends on the accuracy of low-cost methods to ensure that important low-lying minima are not missed. Here we present a reparameterized GFN1-xTB model based on the clusteromics I-V datasets for studying atmospheric molecular clusters (AMC), denoted AMC-xTB. The AMC-xTB model reduces the mean of electronic binding energy errors from 7-11.8 kcal mol-1 to roughly 0 kcal mol-1 and the root mean square deviation from 7.6-12.3 kcal mol-1 to 0.81-1.45 kcal mol-1. In addition, the minimum structures obtained with AMC-xTB are closer to the ωB97X-D/6-31++G(d,p) level of theory compared to GFN1-xTB. We employ the new parameterization in two new configurational sampling workflows that include an additional meta-dynamics sampling step using CREST with the AMC-xTB model. The first workflow, denoted the "independent workflow", is a commonly used funneling approach with an additional CREST step, and the second, the "improvement workflow", is where the best configuration currently known in the literature is improved with a CREST + AMC-xTB step. Testing the new workflow we find configurations lower in free energy for all the literature clusters with the largest improvement being up to 21 kcal mol-1. Lastly, by employing the improvement workflow we massively screened 288 new multi-acid-multi-base clusters containing up to 8 different species. For these new multi-acid-multi-base cluster systems we observe that the improvement workflow finds configurations lower in free energy for 245 out of 288 (85.1%) cluster structures. Most of the improvements are within 2 kcal mol-1, but we see improvements up to 8.3 kcal mol-1. Hence, we can recommend this new workflow based on the AMC-xTB model for future studies on atmospheric molecular clusters.
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Affiliation(s)
- Yosef Knattrup
- Department of Chemistry, Aarhus University Langelandsgade 140, Aarhus C 8000 Denmark +45 28938085
| | - Jakub Kubečka
- Department of Chemistry, Aarhus University Langelandsgade 140, Aarhus C 8000 Denmark +45 28938085
| | - Haide Wu
- Department of Chemistry, Aarhus University Langelandsgade 140, Aarhus C 8000 Denmark +45 28938085
| | - Frank Jensen
- Department of Chemistry, Aarhus University Langelandsgade 140, Aarhus C 8000 Denmark +45 28938085
| | - Jonas Elm
- Department of Chemistry, Aarhus University Langelandsgade 140, Aarhus C 8000 Denmark +45 28938085
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11
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Venkataramanan NS, Suvitha A, Sahara R. Unveiling the Intermolecular Interactions between Drug 5-Fluorouracil and Watson-Crick/Hoogsteen Base Pairs: A Computational Analysis. ACS OMEGA 2024; 9:24831-24844. [PMID: 38882136 PMCID: PMC11170692 DOI: 10.1021/acsomega.4c01545] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/18/2024] [Revised: 05/09/2024] [Accepted: 05/14/2024] [Indexed: 06/18/2024]
Abstract
The adsorption of 5-fluorouracil (5FU) on Watson-Crick (WC) base pairs and Hoogsteen (HT) base pairs has been studied using the dispersion-corrected density functional theory (DFT). The adsorption, binding energy, and thermochemistry for the drug 5FU on the WC and HT base pairs were determined. The most stable geometries were near planar geometry, and 5FU has a higher preference for WC than HT base pairs. The adsorption energies of 5FU on nucleobase pairs are consistently higher than pristine nucleobase pairs, indicating that nucleobase pair cleavage is less likely during the adsorption of the 5FU drug. The enthalpy change for the formation of 5FU-DNA base pairs is higher than that for the formation of 5FU-nucleobases and is enthalpy-driven. The E gap of AT base pairs is higher, suggesting that their chemical reactivity toward further reaction would be less than that of GC base pairs. The electron density difference (EDD) analysis shows a significant decrease in electron density in aromatic regions on the purine bases (adenine/guanine) compared to the pyrimidine bases. The MESP diagram of the stable 5FU-nucleobase pair complexes shows a directional interaction, with the positive regions in a molecule interacting with the negative region of other molecules. The atoms in molecule analysis show that the ρ(r) values of C=O···H-N are higher than those of N···H/N-H···O. The N···H intermolecular bonds between the base pair/drug and nucleobases are weak, closed shell interactions and are electrostatic in nature. The noncovalent interaction analysis shows that several new spikes are engendered along with an increase in their strength, which indicates that the H-bonding interactions are stronger and play a dominant role in stabilizing the complexes. Energy decomposition analysis shows that the drug-nucleobase pair complex has a marginal increase in the electrostatic contributions compared to nucleobase pair complexes.
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Affiliation(s)
| | | | - Ryoji Sahara
- Research Center for Structural Materials, National Institute for Materials Science (NIMS), 1-2-1 Sengen, Tsukuba 305-0047, Japan
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12
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Domingos SR, Tikhonov DS, Steber AL, Eschenbach P, Gruet S, Hrodmarsson HR, Martin K, Garcia GA, Nahon L, Neugebauer J, Avarvari N, Schnell M. Evolution of the ionisation energy with the stepwise growth of chiral clusters of [4]helicene. Nat Commun 2024; 15:4928. [PMID: 38858352 PMCID: PMC11164862 DOI: 10.1038/s41467-024-48778-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Accepted: 05/13/2024] [Indexed: 06/12/2024] Open
Abstract
Polycyclic aromatic hydrocarbons (PAHs) are widely established as ubiquitous in the interstellar medium (ISM), but considering their prevalence in harsh vacuum environments, the role of ionisation in the formation of PAH clusters is poorly understood, particularly if a chirality-dependent aggregation route is considered. Here we report on photoelectron spectroscopy experiments on [4]helicene clusters performed with a vacuum ultraviolet synchrotron beamline. Aggregates (up to the heptamer) of [4]helicene, the smallest PAH with helical chirality, were produced and investigated with a combined experimental and theoretical approach using several state-of-the-art quantum-chemical methodologies. The ionisation onsets are extracted for each cluster size from the mass-selected photoelectron spectra and compared with calculations of vertical ionisation energies. We explore the complex aggregation topologies emerging from the multitude of isomers formed through clustering of P and M, the two enantiomers of [4]helicene. The very satisfactory benchmarking between experimental ionisation onsets vs. predicted ionisation energies allows the identification of theoretically predicted potential aggregation motifs and corresponding energetic ordering of chiral clusters. Our structural models suggest that a homochiral aggregation route is energetically favoured over heterochiral arrangements with increasing cluster size, hinting at potential symmetry breaking in PAH cluster formation at the scale of small grains.
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Affiliation(s)
- Sérgio R Domingos
- Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607, Hamburg, Germany.
- CFisUC, Department of Physics, University of Coimbra, 3004-516, Coimbra, Portugal.
| | - Denis S Tikhonov
- Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607, Hamburg, Germany.
| | - Amanda L Steber
- Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607, Hamburg, Germany.
- Department of Physical Chemistry, Faculty of Science, University of Valladolid, 47011, Valladolid, Spain.
| | - Patrick Eschenbach
- Organisch-Chemisches Institut, University of Münster, 48149, Münster, Germany
- Center for Multiscale Theory and Computation (CMTC), University of Münster, 48149, Münster, Germany
| | - Sebastien Gruet
- Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607, Hamburg, Germany
| | - Helgi R Hrodmarsson
- Synchrotron SOLEIL, L'Orme des Merisiers, 91192, Gif sur Yvette, Cedex, France
- LISA UMR 7583 Université Paris-Est Créteil and Université de Paris, Institut Pierre et Simon Laplace, 61 Avenue du Général de Gaulle, 94010, Créteil, France
| | - Kévin Martin
- Univ Angers, CNRS, MOLTECH-Anjou, SFR MATRIX, 49000, Angers, France
| | - Gustavo A Garcia
- Synchrotron SOLEIL, L'Orme des Merisiers, 91192, Gif sur Yvette, Cedex, France
| | - Laurent Nahon
- Synchrotron SOLEIL, L'Orme des Merisiers, 91192, Gif sur Yvette, Cedex, France
| | - Johannes Neugebauer
- Organisch-Chemisches Institut, University of Münster, 48149, Münster, Germany
- Center for Multiscale Theory and Computation (CMTC), University of Münster, 48149, Münster, Germany
| | - Narcis Avarvari
- Univ Angers, CNRS, MOLTECH-Anjou, SFR MATRIX, 49000, Angers, France
| | - Melanie Schnell
- Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607, Hamburg, Germany.
- Institut für Physikalische Chemie, Christian-Albrechts-Universität zu Kiel, Max-Eyth-Str. 1, 24118, Kiel, Germany.
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13
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Mu L, Shi G, Fang H. Hydrated cation-π interactions of π-electrons with hydrated Mg2+ and Ca2+ cations. J Chem Phys 2024; 160:214712. [PMID: 38842493 DOI: 10.1063/5.0210995] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2024] [Accepted: 05/23/2024] [Indexed: 06/07/2024] Open
Abstract
Hydrated cation-π interactions at liquid-solid interfaces between hydrated cations and aromatic ring structures of carbon-based materials are pivotal in many material, biological, and chemical processes, and water serves as a crucial mediator in these interactions. However, a full understanding of the hydrated cation-π interactions between hydrated alkaline earth cations and aromatic ring structures, such as graphene remains elusive. Here, we present a molecular picture of hydrated cation-π interactions for Mg2+ and Ca2+ by using the density functional theory methods. Theoretical results show that the graphene sheet can distort the hydration shell of the hydrated Ca2+ to interact with Ca2+ directly, which is water-cation-π interactions. In contrast, the hydration shell of the hydrated Mg2+ is quite stable and the graphene sheet interacts with Mg2+ indirectly, mediated by water molecules, which is the cation-water-π interactions. These results lead to the anomalous order of adsorption energies for these alkaline earth cations, with hydrated Mg2+-π < hydrated Ca2+-π when the number of water molecules is large (n ≥ 6), contrary to the order observed for cation-π interactions in the absence of water molecules (n = 0). The behavior of hydrated alkaline earth cations adsorbed on a graphene surface is mainly attributed to the competition between the cation-π interactions and hydration effects. These findings provide valuable details of the structures and the adsorption energy of hydrated alkaline earth cations adsorbed onto the graphene surface.
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Affiliation(s)
- Liuhua Mu
- Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou, Zhejiang 325001, China
- School of Physical Science, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Guosheng Shi
- Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou, Zhejiang 325001, China
- Shanghai Applied Radiation Institute, State Key Laboratory Advanced Special Steel, Shanghai University, Shanghai 201800, China
| | - Haiping Fang
- School of Physics, East China University of Science and Technology, Shanghai 200237, China
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14
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Li W, Feng H, Shang R. First Principle Study on Structural, Electronic, Magnetic, and Optical Properties of Co-Doped Middle Size Silver Clusters. Molecules 2024; 29:2670. [PMID: 38893544 PMCID: PMC11173722 DOI: 10.3390/molecules29112670] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2024] [Revised: 05/31/2024] [Accepted: 06/02/2024] [Indexed: 06/21/2024] Open
Abstract
The structural, electronic, magnetic, and optical properties of Co-doped 10-20-atom silver clusters are investigated by GGA/PBE via the density functional theory. The Ag-Co clusters form core-shell structures with a Co atom in the center. Co atom doping modulates electronic properties like energy gap, molecular softness, global hardness, electronegativity, and electrophilicity index. For the optical spectra of the Ag-Co clusters, the energy of their spectra overall exhibits little change with increasing numbers of atoms; the strongest peaks are roughly distributed at 3.5 eV, and the intensity of their spectra overall is strengthened. Raman and vibrational spectra reflect structural changes with Co atom addition. The addition of the Co atom alters magnetic moments of specific Ag-Co clusters, while others remain unchanged.
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Affiliation(s)
- Weiyin Li
- School of Electrical and Information Engineering, North Minzu University, Yinchuan 750021, China; (H.F.); (R.S.)
- Key Laboratory of Physics and Photoelectric Information Functional Materials, North Minzu University, Yinchuan 750021, China
- Microelectronics and Solid-State Electronics Device Research Center, North Minzu University, Yinchuan 750021, China
| | - Hao Feng
- School of Electrical and Information Engineering, North Minzu University, Yinchuan 750021, China; (H.F.); (R.S.)
- Key Laboratory of Physics and Photoelectric Information Functional Materials, North Minzu University, Yinchuan 750021, China
- Microelectronics and Solid-State Electronics Device Research Center, North Minzu University, Yinchuan 750021, China
| | - Ruiyong Shang
- School of Electrical and Information Engineering, North Minzu University, Yinchuan 750021, China; (H.F.); (R.S.)
- Key Laboratory of Physics and Photoelectric Information Functional Materials, North Minzu University, Yinchuan 750021, China
- Microelectronics and Solid-State Electronics Device Research Center, North Minzu University, Yinchuan 750021, China
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15
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Maya J, Malloum A, Fifen JJ, Dhaouadi Z, Fouda HPE, Conradie J. Quantum cluster equilibrium theory applied to liquid ammonia. J Comput Chem 2024; 45:1279-1288. [PMID: 38353541 DOI: 10.1002/jcc.27327] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Revised: 01/21/2024] [Accepted: 01/29/2024] [Indexed: 04/19/2024]
Abstract
Through this paper, the authors propose using the quantum cluster equilibrium (QCE) theory to reinvestigate ammonia clusters in the liquid phase. The ammonia clusters from size monomer to hexadecamer were considered to simulate the liquid ammonia in this approach. The clusterset used to model the liquid ammonia is an ensemble of different structures of ammonia clusters. After studious research of the representative configurations of ammonia clusters through the cluster research program ABCluster, the configurations have been optimized at the MN15/6-31++G(d,p) level of theory. These optimizations lead to geometries and frequencies as inputs for the Peacemaker code. The QCE study of this molecular system permits us to get the liquid phase populations in a temperature range of 190-260 K, covering the temperatures from the melting point to the boiling point. The results show that the population of liquid ammonia comprises mainly the ammonia hexadecamer followed by pentadecamer, tetradecamer, and tridecamer. We noted that the small-sized ammonia clusters do not contribute to the population of liquid ammonia. In addition, the thermodynamic properties, such as heat of vaporization, heat capacity, entropy, enthalpy, and free energies, obtained by the QCE theory have been compared to the experiment given some relatively good agreements in the gas phase and show considerable discrepancies in liquid phase except the density. Finally, based on the predicted population, we calculated the infrared spectrum of liquid ammonia at 215 K temperature. It comes out that the calculated infrared spectrum qualitatively agrees with the experiment.
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Affiliation(s)
- Josué Maya
- Department of Physics, Faculty of Science, University of Ngaoundere, Ngaoundere, Cameroon
- National Radiation Protection Agency, Yaounde, Cameroon
| | - Alhadji Malloum
- Department of Physics, Faculty of Science, University of Maroua, Maroua, Cameroon
- Department of Chemistry, University of the Free State, Bloemfontein, South Africa
| | - Jean Jules Fifen
- Department of Physics, Faculty of Science, University of Ngaoundere, Ngaoundere, Cameroon
| | - Zoubeida Dhaouadi
- Laboratoire de Spectroscopie Atomique Moléculaire et Application, Université de Tunis El Manar, Tunis, Tunisie
| | | | - Jeanet Conradie
- Department of Chemistry, University of the Free State, Bloemfontein, South Africa
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16
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Du W, Wang Y, Yang J, Chen J. Two rhombic ice phases from aqueous salt solutions under graphene confinement. Phys Rev E 2024; 109:L062103. [PMID: 39020996 DOI: 10.1103/physreve.109.l062103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2023] [Accepted: 05/03/2024] [Indexed: 07/20/2024]
Abstract
Water exhibits rich ice phases depending upon its respective formation conditions, and in particular, the two-dimensional ice with nonhexagonal symmetry adsorbed on solids relates to the exceptional arrangement of water molecules. Despite extensive reporting of two-dimensional ice on various solid surfaces, the geometry and thermodynamics of ice formation from an aqueous salt solution are still unknown. In this Letter, we show the formation of single- and two-phase mixed two-dimensional rhombic ice from aqueous salt solutions with different concentrations under strong compressed confinement of graphene at ambient temperature by using classical molecular dynamics simulations and first-principles calculations. The two rhombic ice phases exhibit identical geometry and thermodynamic properties, but different projections of the oxygen atoms against solid surface symmetry, where they relate to the stable and metastable arrangements of water molecules confined between two graphene layers. A single-phase rhombic ice would grow from the confined saturated aqueous solutions since the previously stable rhombic molecular arrangement becomes an unstable high-energy state by introducing salt ions nearby. Our result reveals different rhombic ice phases growing from pure water and aqueous solutions, highlighting the deciding role of salt ions in the ice formation process due to their common presence in liquids.
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17
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Zhang JM, Wang HQ, Li HF, Mei XJ, Zeng JK, Qin LX, Zheng H, Zhang YH, Jiang KL, Zhang B, Wu WH. Aromatic and magnetic properties in a series of heavy rare earth-doped Ge 6 cluster anions. J Comput Chem 2024; 45:1087-1097. [PMID: 38243618 DOI: 10.1002/jcc.27317] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Revised: 01/03/2024] [Accepted: 01/10/2024] [Indexed: 01/21/2024]
Abstract
A series of pentagonal bipyramidal anionic germanium clusters doped with heavy rare earth elements,REGe 6 - (RE = Gd, Tb, Dy, Ho, Er, Tm, Yb, and Lu), have been identified at the PBE0/def2-TZVP level using density functional theory (DFT). Our findings reveal that the centrally doped pentagonal ring structure demonstrates enhanced stability and heightened aromaticity due to its uniform bonding characteristics and a larger charge transfer region. Through natural population analysis and spin density diagrams, we observed a monotonic decrease in the magnetic moment from Gd to Yb. This is attributed to the decreasing number of unpaired electrons in the 4f orbitals of the heavy rare earth atoms. Interestingly, the system doped with Er atoms showed lower stability and anti-aromaticity, likely due to the involvement of the 4f orbitals in bonding. Conversely, the systems doped with Gd and Tb atoms stood out for their high magnetism and stability, making them potential building blocks for rare earth-doped semiconductor materials.
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Affiliation(s)
- Jia-Ming Zhang
- College of Information Science and Engineering, Huaqiao University, Xiamen, China
| | - Huai-Qian Wang
- College of Information Science and Engineering, Huaqiao University, Xiamen, China
- College of engineering, Huaqiao University, Quanzhou, China
| | - Hui-Fang Li
- College of engineering, Huaqiao University, Quanzhou, China
| | - Xun-Jie Mei
- College of engineering, Huaqiao University, Quanzhou, China
| | - Jin-Kun Zeng
- College of Information Science and Engineering, Huaqiao University, Xiamen, China
| | - Lan-Xin Qin
- College of engineering, Huaqiao University, Quanzhou, China
| | - Hao Zheng
- College of Information Science and Engineering, Huaqiao University, Xiamen, China
| | - Yong-Hang Zhang
- College of Information Science and Engineering, Huaqiao University, Xiamen, China
| | - Kai-Le Jiang
- College of Information Science and Engineering, Huaqiao University, Xiamen, China
| | - Bo Zhang
- College of Information Science and Engineering, Huaqiao University, Xiamen, China
| | - Wen-Hai Wu
- College of engineering, Huaqiao University, Quanzhou, China
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18
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Qian Q, Chen J, Qin M, Pei Y, Chen C, Tang D, Makvandi P, Du W, Yang G, Fang H, Zhou Y. Enhancing antibacterial properties by regulating valence configurations of copper: a focus on Cu-carboxyl chelates. J Mater Chem B 2024; 12:5128-5139. [PMID: 38699827 DOI: 10.1039/d4tb00370e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/05/2024]
Abstract
Optimizing the antibacterial effectiveness of copper ions while reducing environmental and cellular toxicity is essential for public health. A copper chelate, named PAI-Cu, is skillfully created using a specially designed carboxyl copolymer (a combination of acrylic and itaconic acids) with copper ions. PAI-Cu demonstrates a broad-spectrum antibacterial capability both in vitro and in vivo, without causing obvious cytotoxic effects. When compared to free copper ions, PAI-Cu displays markedly enhanced antibacterial potency, being about 35 times more effective against Escherichia coli and 16 times more effective against Staphylococcus aureus. Moreover, Gaussian and ab initio molecular dynamics (AIMD) analyses reveal that Cu+ ions can remain stable in the carboxyl compound's aqueous environment. Thus, the superior antibacterial performance of PAI-Cu largely stems from its modulation of copper ions between mono- and divalent states within the Cu-carboxyl chelates, especially via the carboxyl ligand. This modulation leads to the generation of reactive oxygen species (˙OH), which is pivotal in bacterial eradication. This research offers a cost-effective strategy for amplifying the antibacterial properties of Cu ions, paving new paths for utilizing copper ions in advanced antibacterial applications.
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Affiliation(s)
- Qiuping Qian
- Joint Center of Translational Medicine, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou 325000, Zhejiang, China.
- Zhejiang Engineering Research Center for Tissue Repair Materials, Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou 325000, China.
| | - Jige Chen
- Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201210, China
- Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Mingming Qin
- Zhejiang Engineering Research Center for Tissue Repair Materials, Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou 325000, China.
| | - Yu Pei
- Joint Center of Translational Medicine, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou 325000, Zhejiang, China.
| | - Chunxiu Chen
- Joint Center of Translational Medicine, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou 325000, Zhejiang, China.
| | - Dongping Tang
- Zhejiang Engineering Research Center for Tissue Repair Materials, Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou 325000, China.
| | - Pooyan Makvandi
- The Quzhou Affiliated Hospital of Wenzhou Medical University, Quzhou People's Hospital Quzhou, Zhejiang 324000, China
| | - Wei Du
- Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Guoqiang Yang
- Joint Center of Translational Medicine, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou 325000, Zhejiang, China.
- Zhejiang Engineering Research Center for Tissue Repair Materials, Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou 325000, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Haiping Fang
- School of Physics and National Engineering Research Center of Industrial Wastewater Detoxication and Resource Recovery, East China University of Science and Technology, Shanghai, 200237, China.
- Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
| | - Yunlong Zhou
- Joint Center of Translational Medicine, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou 325000, Zhejiang, China.
- Zhejiang Engineering Research Center for Tissue Repair Materials, Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou 325000, China.
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19
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Doust Mohammadi M, Bhowmick S, Maisser A, Schmidt-Ott A, Biskos G. Electronic properties and collision cross sections of AgO kH m± ( k, m = 1-4) aerosol ionic clusters. Phys Chem Chem Phys 2024; 26:14547-14560. [PMID: 38721799 DOI: 10.1039/d3cp05499c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/23/2024]
Abstract
Experimental evidence shows that hydroxylated metal ions are often produced during cluster synthesis by atmospheric pressure spark ablation. In this work, we predict the ground state equilibrium structures of AgOkHm± clusters (k and m = 1-4), which are readily produced when spark ablating Ag, using the coupled cluster with singles and doubles (CCSD) method. The stabilization energy of these clusters is calculated with respect to the dissociation channel having the lowest energy, by accounting perturbative triples corrections to the CCSD method. The interatomic interactions in each of the systems have been investigated using the frontier molecular orbital (FMO), natural bond orbital (NBO) and quantum theory of atoms in molecules (QTAIM) methods. Many of the ground states of these ionic clusters are found to be stable, corroborating experimental observations. We find that clusters having singlet spin states are more stable in terms of dissociation than the clusters that have doublet or triplet spin states. Our calculations also indicate a strong affinity of the ionic and neutral Ag atom towards water and hydroxyl radicals or ions. Many 3-center, 4-electron (3c/4e) hyperbonds giving rise to more than one resonance structure are identified primarily for the anionic clusters. The QTAIM analysis shows that the O-H and O-Ag bonds in the clusters of both polarities are respectively covalent and ionic. The FMO analysis indicates that the anionic clusters are more reactive than the cationic ones. Using the cluster structures predicted by the CCSD method, we calculate the collision cross sections of the AgOkHm± family, with k and m ranging from 1 to 4, by the trajectory method. In turn, we predict the electrical mobilities of these clusters when suspended in helium at atmospheric pressure and compare them with experimental measurements.
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Affiliation(s)
- Mohsen Doust Mohammadi
- Climate & Atmosphere Research Centre, The Cyprus Institute, 20 Konstantinou Kavafi Street, Nicosia 2121, Cyprus.
| | - Somnath Bhowmick
- Climate & Atmosphere Research Centre, The Cyprus Institute, 20 Konstantinou Kavafi Street, Nicosia 2121, Cyprus.
| | - Anne Maisser
- Climate & Atmosphere Research Centre, The Cyprus Institute, 20 Konstantinou Kavafi Street, Nicosia 2121, Cyprus.
| | - Andreas Schmidt-Ott
- Climate & Atmosphere Research Centre, The Cyprus Institute, 20 Konstantinou Kavafi Street, Nicosia 2121, Cyprus.
- Faculty of Applied Sciences, Delft University of Technology, Delft, 2629 HZ, The Netherlands
| | - George Biskos
- Climate & Atmosphere Research Centre, The Cyprus Institute, 20 Konstantinou Kavafi Street, Nicosia 2121, Cyprus.
- Faculty of Civil Engineering and Geosciences, Delft University of Technology, Delft, 2628 CN, The Netherlands
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20
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Sarmah K, Guha AK. Quest for Double Möbius Aromaticity. Chemistry 2024; 30:e202400395. [PMID: 38451013 DOI: 10.1002/chem.202400395] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Revised: 03/06/2024] [Accepted: 03/07/2024] [Indexed: 03/08/2024]
Abstract
Neutral four-membered rings with 4n electrons are generally Hückel antiaromatic. On the other hand, 4n electron system can also be Möbius aromatic, although identification has escaped so far. A recent study of double Möbius aromaticity has been put forwarded in the D2h symmetric singlet ground state of four member Pa2B2 ring. Although interesting, but the synthesis possesses a significant challenge as Pa is rare, highly radioactive and toxic. Herein, a synthetically viable four membered Rh2B2 cluster is proposed which contains double Möbius aromaticity. Interestingly, the three membered RhB2 - cluster also possess Möbius aromaticity and is the smallest ring to show such phenomenon.
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Affiliation(s)
- Kangkan Sarmah
- Advanced Computational Chemistry Centre, Department of Chemistry, Cotton University, Panbazar, Guwahati, Assam, INDIA-, 781001
| | - Ankur K Guha
- Advanced Computational Chemistry Centre, Department of Chemistry, Cotton University, Panbazar, Guwahati, Assam, INDIA-, 781001
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21
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Jiang L, Zhou Y, Jiang Y, Zhang Z, Li Z, Zhao X, Wu J. Unique solvation structure induced by anionic Cl in aqueous zinc ion batteries. Heliyon 2024; 10:e30592. [PMID: 38765152 PMCID: PMC11098851 DOI: 10.1016/j.heliyon.2024.e30592] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Revised: 04/23/2024] [Accepted: 04/30/2024] [Indexed: 05/21/2024] Open
Abstract
Aqueous zinc ion batteries (AZIBs) have garnered significant attention in large-scale static energy storage battery systems due to their low cost, high safety and environmental friendliness. However, it has some inherent problems during operation, such as the occurrence of side reactions (hydrogen evolution reaction, HER) and anode corrosion, formation of by-products and growth of metal dendrites. To analyze the mechanism of generation from aspect of the electrolyte solvation structure and make cell efficiency further improvements based on it, so we use DFT calculations to find the most stable solvation structure in AZIBs with ZnCl2 as the electrolyte and analyze it. We define the relative concentration C r , and calculate different groups metal cation cluster structures such as [ Zn ( H 2 O ) n ] 2 + , [ ZnCl ( H 2 O ) n ] + , [ ZnCl 2 ( H 2 O ) n ] and [ ZnCl 3 ( H 2 O ) n ] - that exist at different C r . We discuss the effect of different clusters formed due to the C r variations on the battery performance in terms of three aspects: the structural conformation, the cluster characteristics (including the hydrogen bonding network, bond lengths, bond angles, as well as the electrostatic potential ESP) and the cluster performance (including the adsorption energy Ea, binding energy Eb, and desolvation energy Edes). The results shows that the electrolyte metal cation Zn2+ can be coordinated with up to six H2O molecules in first shell, and this metal cation solvation structure contributes to the occurrence and formation of side reactions and by-products, which reduces the battery efficiency. Increasing the electrolyte anion Cl- concentration by appropriately increasing the C r helps to desolvate the metal cation cluster structure, which greatly improves the battery efficiency and suppresses the side reactions and by-products. Yet the improvement effect was not obviously further improved by further increasing the Cl- concentration.
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Affiliation(s)
- Liyuan Jiang
- School of Mathematics, Physics and Statistics, Shanghai University of Engineering Science, 333 Longteng Road, Shanghai, 201620, China
| | - Yulin Zhou
- School of Mathematics, Physics and Statistics, Shanghai University of Engineering Science, 333 Longteng Road, Shanghai, 201620, China
| | - Yan Jiang
- School of Mathematics, Physics and Statistics, Shanghai University of Engineering Science, 333 Longteng Road, Shanghai, 201620, China
| | - Zongyao Zhang
- School of Mathematics, Physics and Statistics, Shanghai University of Engineering Science, 333 Longteng Road, Shanghai, 201620, China
| | - Zhengdao Li
- School of Mathematics, Physics and Statistics, Shanghai University of Engineering Science, 333 Longteng Road, Shanghai, 201620, China
| | - Xinxin Zhao
- School of Mathematics, Physics and Statistics, Shanghai University of Engineering Science, 333 Longteng Road, Shanghai, 201620, China
| | - Jianbao Wu
- School of Mathematics, Physics and Statistics, Shanghai University of Engineering Science, 333 Longteng Road, Shanghai, 201620, China
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Chakraborty B, Pal R, Pratihar DK, Chattaraj PK. Bonobo Optimizer: A New Tool Toward the Global Optimization of Small Atomic Clusters. J Phys Chem A 2024. [PMID: 38696762 DOI: 10.1021/acs.jpca.4c02024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/04/2024]
Abstract
In the realm of structural and bonding investigations within chemical systems, elucidating global minimum energy configurations stands as a paramount goal. As the systems increase in size and complexity, this pursuit becomes progressively challenging. Herein, we introduce Bonobo optimizer (BO), a metaheuristic algorithm inspired by the social and reproductive behaviors of bonobos, to the domain of chemical problem solving. Focusing on small carbon clusters, this study systematically evaluates BO's performance, showcasing its robustness and efficiency. Parametric studies highlight the algorithm's adaptability, consistently converging to global minimum structures. Rigorous statistical validation supports the results, and a comparative analysis against established global optimization algorithms underlines BO's superior efficiency. This exploration extends the applicability of BO to the optimization of atomic clusters, providing a promising avenue for future advancements in computational chemistry.
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Affiliation(s)
- Bhrigu Chakraborty
- Department of Chemistry, Indian Institute of Technology Kharagpur, Kharagpur 721302, India
| | - Ranita Pal
- Advanced Technology Development Centre, Indian Institute of Technology Kharagpur, Kharagpur 721302, India
| | - Dilip Kumar Pratihar
- Department of Mechanical Engineering, Indian Institute of Technology Kharagpur, Kharagpur 721302, India
| | - Pratim Kumar Chattaraj
- Department of Chemistry, Birla Institute of Technology, Mesra, Ranchi, Jharkhand 835215, India
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23
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Ren RQ, Long ZW, Li SX, Gao CG. Size effects and electronic properties of zinc-doped boron clusters Zn B n (n = 1-15). J Mol Model 2024; 30:123. [PMID: 38573432 DOI: 10.1007/s00894-024-05906-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Accepted: 03/15/2024] [Indexed: 04/05/2024]
Abstract
CONTEXT To gain a deeper understanding of zinc-doped boron clusters, theoretical calculations were performed to investigate the size effects and electronic properties of zinc-doped boron clusters. The study of the electronic properties, spectral characteristics, and geometric structures of Zn B n (n = 1-15) is of great significance in the fields of semiconductor materials science, material detection, and improving catalytic efficiency. The results indicate that Zn B n (n = 1-15) clusters predominantly exhibit planar or quasi-planar structures, with the Zn atom positioned in the outer regions of the B n framework. The second stable structure of Zn B 3 is a three-dimensional configuration, indicating that the structures of zinc-doped boron clusters begin to convert from the planar or quasi-planar structures to the 3D configurations. The second low-energy structure of Zn B 15 is a novel configuration. Relative stability analyses show that the Zn B 12 has better chemical stability than other clusters with a HOMO-LUMO gap of 2.79 eV. Electric charge analysis shows that part electrons on zinc atoms are transferred to boron atoms, and electrons prefer to cluster near the B n framework. According to the electron localization function, it gets harder to localize electrons as the equivalent face value drops, and it's challenging to see covalent bond formation between zinc and boron atoms. The spectrograms of Zn B n (n = 1-15) exhibit distinct properties and notable spectral features, which can be used as a theoretical basis for the identification and confirmation of boron clusters doped with single-atom transition metals. METHODS The calculations were performed using the ABCluster global search technique combined with density functional theory (DFT) methods. The selected low-energy structures were subjected to geometric optimization and frequency calculations at the PBE0/6-311 + G(d) level to ensure structural stability and eliminate any imaginary frequencies. To acquire more precise relative energies, we performed single-point energies calculations for the low-lying isomers of Zn B n (n = 1-15) at the CCSD(T)/6-311 + G(d)//PBE0/6-311 + G(d) level of theory. All calculations were performed using Gaussian 09 software. To facilitate analysis, we utilized software tools such as Multiwfn, and VMD.
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Affiliation(s)
- Rong-Qin Ren
- Department of Physics, Guizhou University, Guiyang, 550025, China
| | - Zheng-Wen Long
- Department of Physics, Guizhou University, Guiyang, 550025, China.
| | - Shi-Xiong Li
- School of Physics and Electronic Science, Guizhou Education University, Guiyang, 550018, China
| | - Cheng-Gui Gao
- School of Physics and Electronic Science, Guizhou Education University, Guiyang, 550018, China
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24
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Laraib SR, Liu J, Xia YG, Wu YW, Mohammadi MD, Noor NF, Lu Q. Assessing the efficacy of aluminum metal clusters Al 13 and Al 15 in mitigating NO 2 and SO 2 pollutants: a DFT investigation. RSC Adv 2024; 14:11217-11231. [PMID: 38590351 PMCID: PMC11000095 DOI: 10.1039/d4ra00708e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2024] [Accepted: 03/20/2024] [Indexed: 04/10/2024] Open
Abstract
The present investigation delves into the adverse environmental impact of atmospheric pollutant gases, specifically nitrogen dioxide (NO2) and sulfur dioxide (SO2), which necessitates the identification and implementation of effective control measures. The central objective of this study is to explore the eradication of these pollutants through the utilization of aluminum Al13 and Al15 metal clusters, distinguished by their unique properties. The comprehensive evaluation of gas/cluster interactions is undertaken employing density functional theory (DFT). Geometric optimization calculations for all structures are executed using the ωB97XD functional and the Def2-svp basis set. To probe various interaction modalities, gas molecule distribution around the metal clusters is sampled using the bee colony algorithm. Frequency calculations employing identical model chemistry validate the precision of the optimization calculations. The quantum theory of atoms in molecules (QTAIM) and natural bond orbital (NBO) methodologies are applied for the analysis of intermolecular interactions. This research establishes the robust formation of van der Waals attractions between the investigated gas molecules, affirming aluminum metal clusters as viable candidates for the removal and control of these gases.
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Affiliation(s)
- Sajida Riffat Laraib
- National Engineering Research Center of New Energy Power Generation, North China Electric Power University Beijing 102206 China
| | - Ji Liu
- National Engineering Research Center of New Energy Power Generation, North China Electric Power University Beijing 102206 China
| | - Yuan-Gu Xia
- National Engineering Research Center of New Energy Power Generation, North China Electric Power University Beijing 102206 China
| | - Yang-Wen Wu
- National Engineering Research Center of New Energy Power Generation, North China Electric Power University Beijing 102206 China
| | | | - Nayab Fatima Noor
- Military College of Signals, National University of Science and Technology Rawalpindi Pakistan
| | - Qiang Lu
- National Engineering Research Center of New Energy Power Generation, North China Electric Power University Beijing 102206 China
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25
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Aswathi J, Janardanan D. Generation of 3-aminopropanamide and its cluster formation with nucleation precursors- a theoretical exploration. CHEMOSPHERE 2024; 354:141630. [PMID: 38462185 DOI: 10.1016/j.chemosphere.2024.141630] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2023] [Revised: 02/05/2024] [Accepted: 03/01/2024] [Indexed: 03/12/2024]
Abstract
Aminoamides are formed in the atmospheric environments by the auto-oxidation of the parent diamines. In this work, the oxidation chemistry of diamine (1,3-Diaminopropane, Dap) to the amino amide (3- aminopropanamide, 3-APA) and its new particle formation potential with small atmospheric molecules such as NH3 (A), H2O (W) and H2SO4 (SA) are theoretically investigated using the M062X/6-311++G** theory. The bimolecular rate coefficient of the ·OH initiated H-atom abstraction is computed to be 1.01 × 10-11 cm3 molecule-1 s-1. Further reaction of the peroxy radical intermediate indicates that the pathway involving γ H- shift of the initially formed radical intermediates to be more favourable on kinetic grounds with the effective bimolecular rate coefficient of 3.87 × 10-14 cm3 molecule-1s-1. The thermodynamic barrier associated with the H-shifts involved in this pathway is in the range of 13-20 kcal/mol. The cluster formation of APA with SA is more favourable than the clusters with W and A, wherein the free energy of formation of (APA)(SA) and (APA)(SA)2 are -11.3 and -22.6 kcal/mol, respectively. However, the feasibility of cluster formation with W and A increases with the altitude and becomes spontaneous in the case of water at an altitude of 12 km. The present work indicates that aminoamides like 3-APA can participate in the initial stages of new particle formation events by forming clusters with SA molecules. The scattering parameters and topological analysis of different (Amide)(SA) clusters indicate more scattering properties for the (APA)(SA) cluster, which has an adverse effect on the atmosphere. Furthermore, topological analysis indicates that H-bond formation is more prominent in the (APA)(SA) cluster.
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Affiliation(s)
- J Aswathi
- Computational Chemistry Laboratory, Department of Chemistry, School of Physical Sciences, Central University of Kerala, Kasaragod, Kerala, 671320, India
| | - Deepa Janardanan
- Computational Chemistry Laboratory, Department of Chemistry, School of Physical Sciences, Central University of Kerala, Kasaragod, Kerala, 671320, India.
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26
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Sarmah K, Kalita AJ, Purkayastha SK, Guha AK. Pushing The Extreme of Multicentre Bonding: Planar Pentacoordinate Hydride. Angew Chem Int Ed Engl 2024; 63:e202318741. [PMID: 38298097 DOI: 10.1002/anie.202318741] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Revised: 01/05/2024] [Accepted: 01/31/2024] [Indexed: 02/02/2024]
Abstract
Planar hypercoordination has sparkled interest among the researchers from last few decades. Most of the elements in the Periodic Table have shown this remarkable structural feature. However, the smallest element, hydrogen, is missing in the list. No evidence is there in the literature. Herein, we introduce the first planar pentacoordinate hydrogen atom (ppH) in the global minimum geometry of Li5 H6 - cluster. Bonding analysis indicates that the central hydrogen atom is stabilized by multicentre bonding with five surrounding Li atoms. Natural charge analysis reveals that the central hydrogen is acting like a hydride which is strongly attracted by the positively charged surrounding lithium centres. The ppH structure is stabilized by strong electrostatic attraction as well as extensive multicentre bonding. Aromaticity has no role to play here. The cluster is dynamically stable and is expected to be detected in gas phase.
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Affiliation(s)
- Kangkan Sarmah
- Advanced Computational Chemistry Centre, Cotton University Panbazar, Guwahati, Assam, INDIA-, 781001
| | - Amlan J Kalita
- Advanced Computational Chemistry Centre, Cotton University Panbazar, Guwahati, Assam, INDIA-, 781001
| | - Siddhartha K Purkayastha
- Advanced Computational Chemistry Centre, Cotton University Panbazar, Guwahati, Assam, INDIA-, 781001
| | - Ankur K Guha
- Advanced Computational Chemistry Centre, Cotton University Panbazar, Guwahati, Assam, INDIA-, 781001
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27
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Jiang X, Zhang P, Jiang L, Zhao X, Wu J. Theoretical study on the role of magnesium chloride complexes induced by different magnesium-to-chlorine ratios in magnesium-sulfur batteries. RSC Adv 2024; 14:9668-9677. [PMID: 38525063 PMCID: PMC10958330 DOI: 10.1039/d4ra00950a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2024] [Accepted: 03/11/2024] [Indexed: 03/26/2024] Open
Abstract
In magnesium-sulfur batteries, electrolyte exploration is vital for developing high-energy-density, safe, and reliable batteries. This study focused on cyclic THF and chain DME, representative solvents in ether electrolytes. MgCl2, an ideal anionic salt, forms mono-nuclear (MgCl2(DME)2), bi-nuclear ([Mg2(μ-Cl)2(DME)4]2+), and tri-nuclear ([Mg3(μ-Cl)4(DME)5]2+) complexes in DME. With increasing salt concentration, these complexes sequentially form. Under lower salt concentrations, THF and MgCl2 form mono-nuclear complexes ([MgCl2(THF)4]) and continue to form bi-nuclear complexes ([Mg2(μ-Cl)3(THF)6]+). However, at higher salt concentrations, bi-nuclear complexes ([Mg2(μ-Cl)3(THF)6]+) directly form in THF. Comparing HOMO-LUMO values, [Mg(DME)3]2+ is easily oxidized. Energy gaps decrease with Cl- ion addition, enhancing solution conductivity. Ratios of Mg2+ and Cl- in S-reduction complexes differ, suggesting DME is better at a low Mg/Cl ratio, and THF at a high Mg/Cl ratio. This study contributes to understanding complexes and enhancing Mg-S battery performance.
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Affiliation(s)
- Xiaoli Jiang
- School of Mathematics, Physics and Statistics, Shanghai University of Engineering Science 333 Longteng Road Shanghai 201620 China
| | - Panyu Zhang
- School of Mathematics, Physics and Statistics, Shanghai University of Engineering Science 333 Longteng Road Shanghai 201620 China
| | - Liyuan Jiang
- School of Mathematics, Physics and Statistics, Shanghai University of Engineering Science 333 Longteng Road Shanghai 201620 China
| | - Xinxin Zhao
- School of Mathematics, Physics and Statistics, Shanghai University of Engineering Science 333 Longteng Road Shanghai 201620 China
| | - Jianbao Wu
- School of Mathematics, Physics and Statistics, Shanghai University of Engineering Science 333 Longteng Road Shanghai 201620 China
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28
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Peng X, Li J, Dang J, Yin S, Zheng H, Wang C, Mo Y. Conformational Preference of Lithium Polysulfide Clusters Li 2S x ( x = 4-8) in Lithium-Sulfur Batteries. Inorg Chem 2024; 63:4716-4724. [PMID: 38417153 PMCID: PMC10934799 DOI: 10.1021/acs.inorgchem.3c04537] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Revised: 02/09/2024] [Accepted: 02/19/2024] [Indexed: 03/01/2024]
Abstract
Structures are of fundamental importance for diverse studies of lithium polysulfide clusters, which govern the performance of lithium-sulfur batteries. The ring-like geometries were regarded as the most stable structures, but their physical origin remains elusive. In this work, we systematically explored the minimal structures of Li2Sx (x = 4-8) clusters to uncover the driving force for their conformational preferences. All low-lying isomers were generated by performing global searches using the ABCluster program, and the ionic nature of the Li···S interactions was evidenced with the energy decomposition analysis based on the block-localized wave function (BLW-ED) approach and further confirmed with the quantum theory of atoms in molecule (QTAIM). By analysis of the contributions of various energy components to the relative stability with the references of the lowest-lying isomers, the controlling factor for isomer preferences was found to be the polarization interaction. Notably, although the electrostatic interaction dominates the binding energies, it contributes favorably to the relative stabilities of most isomers. The Li+···Li+ distance is identified as the key geometrical parameter that correlates with the strength of the polarization of the Sx2- fragment imposed by the Li+ cations. Further BLW-ED analyses reveal that the cooperativity of the Li+ cations primarily determines the relative strength of the polarization.
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Affiliation(s)
- Xinru Peng
- Key
Laboratory for Macromolecular Science of Shaanxi Province, School
of Chemistry & Chemical Engineering, Shaanxi Normal University, Xi’an 710119, China
| | - Jiayao Li
- Key
Laboratory for Macromolecular Science of Shaanxi Province, School
of Chemistry & Chemical Engineering, Shaanxi Normal University, Xi’an 710119, China
| | - Jingshuang Dang
- Key
Laboratory for Macromolecular Science of Shaanxi Province, School
of Chemistry & Chemical Engineering, Shaanxi Normal University, Xi’an 710119, China
| | - Shiwei Yin
- Key
Laboratory for Macromolecular Science of Shaanxi Province, School
of Chemistry & Chemical Engineering, Shaanxi Normal University, Xi’an 710119, China
| | - Hengyan Zheng
- Key
Laboratory for Macromolecular Science of Shaanxi Province, School
of Chemistry & Chemical Engineering, Shaanxi Normal University, Xi’an 710119, China
| | - Changwei Wang
- Key
Laboratory for Macromolecular Science of Shaanxi Province, School
of Chemistry & Chemical Engineering, Shaanxi Normal University, Xi’an 710119, China
| | - Yirong Mo
- Department
of Nanoscience, Joint School of Nanoscience and Nanoengineering, University of North Carolina at Greensboro, Greensboro, North Carolina 27401, United States
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29
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Sarmah K, Kalita AJ, Guha AK. Planar tetracoordinate fluorine atom: global minimum with viable possibility. Phys Chem Chem Phys 2024; 26:6678-6682. [PMID: 38273813 DOI: 10.1039/d3cp06017a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2024]
Abstract
Planar hypercoordinate structures are emerging tremendously. Most of the second-row elements from the periodic table exhibit this remarkable structural feature. Planar tetracoordinate fluorine (ptF) atoms were also predicted in group 13 supported clusters. However, high-level ab initio calculations nullified the fact and established that all these ptFs were not minimum energy structures on the potential energy surface. Thus, a true ptF is still scarce in the literature. Herein, we propose the unprecedented ptF as the global minimum of the C2V symmetric H3Li4F- cluster. Heavier alkali metals (Na and K) showed similar results. Both density functional theory (DFT) and ab initio calculations revealed that the ptF structure is a real minimum and indeed, the global minimum. Bonding analysis indicates that the central fluorine atom is stabilized by multicentre bonding with four surrounding Li atoms. Natural charge analysis reveals that the fluorine atom is negatively charged, which is strongly attracted by the positively charged surrounding lithium centres, thereby imparting significant electrostatic attraction. Aromaticity has no role to play here. The cluster is dynamically stable and is expected to be detected in the gas phase.
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Affiliation(s)
- Kangkan Sarmah
- Advanced Computational Chemistry Centre, Cotton University, Panbazar, Guwahati, Assam 781001, India.
| | - Amlan J Kalita
- Advanced Computational Chemistry Centre, Cotton University, Panbazar, Guwahati, Assam 781001, India.
| | - Ankur Kanti Guha
- Advanced Computational Chemistry Centre, Cotton University, Panbazar, Guwahati, Assam 781001, India.
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30
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Zhang Y, Zhang Y, Yang J, Dong C, Li X. Theoretical study on structural evolution, photoelectron and vibrational spectra, and thermochemistry properties of neutral, anionic and di-anionic titanium-doped tin (TiSn n0/-/2- (n = 4-17)) nanoalloy clusters. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2024; 306:123593. [PMID: 37925959 DOI: 10.1016/j.saa.2023.123593] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Revised: 09/28/2023] [Accepted: 10/29/2023] [Indexed: 11/07/2023]
Abstract
The structural evolution, chemical stability, electronic and vibrational properties, as well as charge transfer and bonding character of TiSnn0/-/2- (n = 4-17) clusters have been performed with density functional theory calculations using ABCluster search technique. Structurally, it is found that the growth patterns prefer three kinds of absorbed stages from polygonal bipyramidal configuration for n = 4-6, to absorbing additional Sn on the adjacent surfaces of pentagonal bipyramid unit from n = 7-12, and finally to the TiSn130/-/2- cluster as the first foundational architectures, of which the encapsulated cage structure is formed when n = 11. The simulated PES spectra agree with available experiments. More interestingly, the neutral TiSn16 cluster not only possesses the high thermodynamic and relative stability but also preferable photochemical reactivity, that can be further explained by superatom features and delocalized multi-center bonds (AdNDP), while the strong p-d hybridization between Ti atom and Sn unit plays an important role in the stabilities of clusters, making it as the most suitable building units. In addition, the UV-Vis absorption spectra of TiSn16 are discussed, and the main transitions of crucial excited states are analyzed in detail. The Infrared and Raman vibrational characteristic peaks of all these neutral and charged species are properly assigned, of which the TiSnn0/-/2- (n = 10-17) clusters possess degenerating deformation mode of Ti atom wagging in Sn cage framework (Infrared active) and breathing mode of Sn cage framework (Raman active). All these findings will provide a further understanding for the nanoalloy cluster as the most suitable building block with further development as a potential optoelectronic material.
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Affiliation(s)
- Yanpeng Zhang
- College of Chemical Engineering, Inner Mongolia University of Technology, and Inner Mongolia Key Laboratory of Theoretical and Computational Chemistry Simulation, Hohhot 010051, People's Republic of China
| | - Yousuo Zhang
- China Communications Construction Company (Suzhou) of Urban Development & Construction Limited Company, Shihu Jinling Plaza, Yuexi Street, Wuzhong District, Suzhou City 215100, People's Republic of China
| | - Jucai Yang
- College of Chemical Engineering, Inner Mongolia University of Technology, and Inner Mongolia Key Laboratory of Theoretical and Computational Chemistry Simulation, Hohhot 010051, People's Republic of China; College of Resources and Environmental Engineering, Inner Mongolia University of Technology, Hohhot 010051, People's Republic of China
| | - Caixia Dong
- College of Resources and Environmental Engineering, Inner Mongolia University of Technology, Hohhot 010051, People's Republic of China.
| | - Xiaojun Li
- College of Science, Xi'an University of Posts and Telecommunications, Xi'an 710121, Shaanxi, People's Republic of China.
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31
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Zhang Y, Yang J, Dong C. Structural Growth Pattern, Electronic Configurations, and Spectral and Thermochemistry Properties of ZrSn n0/-/2- ( n = 4-17) Nanoscale Compounds: A Systematic Study Using Density Functional Theory. ACS OMEGA 2024; 9:3675-3690. [PMID: 38284033 PMCID: PMC10809232 DOI: 10.1021/acsomega.3c07674] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Revised: 11/29/2023] [Accepted: 12/27/2023] [Indexed: 01/30/2024]
Abstract
By performing density functional theory (DFT) calculations for geometric optimization in conjunction with the artificial bee colony algorithm for cluster (ABCluster) global search approach, the ground-state structures of the neutral, anionic, and dianionic ZrSnn0/-/2- (n = 4-17) nanoscale compounds are obtained. Their structural growth evolution, spectral information, and electronic and thermochemical properties are investigated. Regarding the architectural evolution of the neutral, anion, and dianionic species, ZrSnn0/-/2- (n = 4-17) compounds possess two different stages of adsorption patterns in which, when n = 4-7 and n = 8-17, ZrSn40/-/2- and ZrSn80/-/2- compounds as the basic motif adsorb Sn atoms to become the larger clusters, respectively. The simulated photoelectron spectra (PES) of anionic compounds are in good agreement with the available experimental PES. The infrared and Raman spectra can be summarized as follows: under infrared vibrational modes, the sealed cages of ZrSnn0/-/2- compounds belong to the deformation mode, and under Raman vibrational modes, they belong to the breathing mode of the Sn cage framework. The density of states (DOS) spectra and natural population analysis (NPA) indicate that the interaction between the Zr atom and Snn frameworks of capsulated compounds has been developing stronger than for unsealed compounds. The results of thermochemical properties, molecular orbital shell (MOs) analysis, and ultraviolet-visible (UV-vis) absorption spectrum indicate that the neutral ZrSn16 nanoscale compound possesses not only both thermodynamic and chemical stability but also far-infrared sensing and optoelectronic properties and hence, is the best building block motif for new multipurpose nanoscale materials.
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Affiliation(s)
- Yanpeng Zhang
- College
of Chemical Engineering, Inner Mongolia
University of Technology, and Inner Mongolia Key Laboratory of Theoretical
and Computational Chemistry Simulation, Hohhot 010051, People’s Republic of China
| | - Jucai Yang
- College
of Chemical Engineering, Inner Mongolia
University of Technology, and Inner Mongolia Key Laboratory of Theoretical
and Computational Chemistry Simulation, Hohhot 010051, People’s Republic of China
- College
of Resources and Environmental Engineering, Inner Mongolia University of Technology, Hohhot 010051, People’s Republic of China
| | - Caixia Dong
- College
of Resources and Environmental Engineering, Inner Mongolia University of Technology, Hohhot 010051, People’s Republic of China
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32
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Kalita AJ, Rohman SS, Sahu PP, Guha AK. Planar Tetracoordinate Hydrogen: Pushing the Limit of Multicentre Bonding. Angew Chem Int Ed Engl 2024; 63:e202317312. [PMID: 38010906 DOI: 10.1002/anie.202317312] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Revised: 11/22/2023] [Accepted: 11/24/2023] [Indexed: 11/29/2023]
Abstract
Among the list of planar tetracoordinate atoms, the smallest element hydrogen is missing. No experimental and theoretical evidence have ever been put forwarded. Herein, we introduce the first planar tetracoordinate hydrogen atom (ptH) in the global minimum geometry of In4 H+ cluster. Bonding analysis indicates that the central hydrogen atom is acting like a proton and significant charge transfer from the surrounding In4 framework results in a negative charge of the central hydrogen atom. The proposed global minimum geometry possesses σ-aromaticity and the central hydrogen atom forms unusual multicentre bond with more than three centres.
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Affiliation(s)
- Amlan J Kalita
- Advanced Computational Chemistry Centre, Cotton University Panbazar, Guwahati, Assam, 781001, India
| | - Shahnaz S Rohman
- Department of Chemistry, National Institute of Technology, Calicut, Kerala, 673601, India
| | - Prem P Sahu
- Department of Chemistry, Indian Institute of Technology Hyderabad Kandi, Sangareddy, Telangana, 502284, India
- Department of Chemistry "Ugo Schiff", University of Florence, Via della Lastruccia 3, 50019, Sesto Fiorentino, Italy
| | - Ankur Kanti Guha
- Advanced Computational Chemistry Centre, Cotton University Panbazar, Guwahati, Assam, 781001, India
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33
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Anni D, Amika Mbema JC, Malloum A, Conradie J. Hydration of [Formula: see text]aminobenzoic acid: structures and non-covalent bondings of aminobenzoic acid-water clusters. J Mol Model 2024; 30:38. [PMID: 38214749 PMCID: PMC10786749 DOI: 10.1007/s00894-023-05810-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2023] [Accepted: 12/12/2023] [Indexed: 01/13/2024]
Abstract
CONTEXT Micro-hydration of the aminobenzoic acid is essential to understand its interaction with surrounding water molecules. Understanding the micro-hydration of the aminobenzoic acid is also essential to study its remediation from wastewater. Therefore, we explored the potential energy surfaces (PESs) of the para-aminobenzoic acid-water clusters, ABW[Formula: see text], [Formula: see text], to study the microsolvation of the aminobenzoic acid in water. In addition, we performed a quantum theory of atoms in molecules (QTAIM) analysis to identify the nature of non-covalent bondings in the aminobenzoic acid-water clusters. Furthermore, temperature effects on the stability of the located isomers have been examined. The located structures have been used to calculate the hydration free energy and the hydration enthalpy of the aminobenzoic acid using the cluster continuum solvation model. The hydration free energy and the hydration enthalpy of the aminobenzoic acid at room temperature are evaluated to be -7.0 kcal/mol and -18.1 kcal/mol, respectively. The hydration enthalpy is in perfect agreement with a previous experimental estimate. Besides, temperature effects on the calculated hydration enthalpy and free energy are reported. Finally, we calculated the gas phase binding energies of the most stable structures of the ABW[Formula: see text] clusters using twelve functionals of density functional theory (DFT), including empirical dispersion. The DFT functionals are benchmarked against the DLPNO-CCSD(T)/CBS. We have found that the three most suitable DFT functionals are classified in the following order: PW6B95D3 > MN15 > [Formula: see text]B97XD. Therefore, the PW6B95D3 functional is recommended for further study of the aminobenzoic acid-water clusters and similar systems. METHODS The exploration started with classical molecular dynamics simulations followed by complete optimization at the PW6B95D3/def2-TZVP level of theory. Optimizations are performed using Gaussian 16 suite of codes. QTAIM analysis is performed using the AIMAll program.
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Affiliation(s)
- Diane Anni
- Department of Physics, Faculty of Science, University of Maroua, PO BOX 46, Maroua, Cameroon
| | - Jean Claude Amika Mbema
- Department of Physics, Faculty of Science, University of Maroua, PO BOX 46, Maroua, Cameroon
| | - Alhadji Malloum
- Department of Physics, Faculty of Science, University of Maroua, PO BOX 46, Maroua, Cameroon.
- Department of Chemistry, University of the Free State, PO BOX 339, Bloemfontein, 9300, South Africa.
| | - Jeanet Conradie
- Department of Chemistry, University of the Free State, PO BOX 339, Bloemfontein, 9300, South Africa
- Department of Chemistry, UiT - The Arctic University of Norway, N-9037, Tromsø, Norway
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34
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Roth M, Toker Y, Major DT. Monte Carlo-Simulated Annealing and Machine Learning-Based Funneled Approach for Finding the Global Minimum Structure of Molecular Clusters. ACS OMEGA 2024; 9:1298-1309. [PMID: 38222530 PMCID: PMC10785639 DOI: 10.1021/acsomega.3c07600] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/01/2023] [Revised: 11/09/2023] [Accepted: 11/15/2023] [Indexed: 01/16/2024]
Abstract
Understanding the physical underpinnings and geometry of molecular clusters is of great importance in many fields, ranging from studying the beginning of the universe to the formation of atmospheric particles. To this end, several approaches have been suggested, yet identifying the most stable cluster geometry (i.e., global potential energy minimum) remains a challenge, especially for highly symmetric clusters. Here, we suggest a new funneled Monte Carlo-based simulated annealing (SA) approach, which includes two key steps: generation of symmetrical clusters and classification of the clusters according to their geometry using machine learning (MCSA-ML). We demonstrate the merits of the MCSA-ML method in comparison to other approaches on several Lennard-Jones (LJ) clusters and four molecular clusters-Ser8(Cl-)2, H+(H2O)6, Ag+(CO2)8, and Bet4Cl-. For the latter of these clusters, the correct structure is unknown, and hence, we compare the experimental and simulated fragmentation patterns, and the fragmentation of the proposed global minimum matches experiments closely. Additionally, based on the fragmentation of the predicted betaine cluster, we were able to identify hitherto unknown neutral fragmentation channels. In comparison to results obtained with other methods, we demonstrated a superior ability of MCSA-ML to predict clusters with high symmetry and similar abilities to predict clusters with asymmetrical structures.
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Affiliation(s)
- Michal Roth
- Department
of Physics, Bar-Ilan University, Ramat-Gan 5290002, Israel
- Institute
of Nanotechnology and Advanced Materials, Bar-Ilan University, Ramat-Gan 5290002, Israel
| | - Yoni Toker
- Department
of Physics, Bar-Ilan University, Ramat-Gan 5290002, Israel
- Institute
of Nanotechnology and Advanced Materials, Bar-Ilan University, Ramat-Gan 5290002, Israel
| | - Dan T. Major
- Institute
of Nanotechnology and Advanced Materials, Bar-Ilan University, Ramat-Gan 5290002, Israel
- Department
of Chemistry, Bar-Ilan University, Ramat-Gan 5290002, Israel
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35
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Malloum A, Conradie J. Structures of DMSO clusters and quantum cluster equilibrium (QCE). J Mol Graph Model 2024; 126:108661. [PMID: 37913567 DOI: 10.1016/j.jmgm.2023.108661] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Revised: 10/25/2023] [Accepted: 10/26/2023] [Indexed: 11/03/2023]
Abstract
Dimethylsulfoxide (DMSO) clusters are crucial for understanding processes in liquid DMSO. Despite its importance, DMSO clusters have received negligible attention due to the complexity of their potential energy surfaces (PESs). In this work, we explored the PESs of the DMSO clusters from dimer to decamer, starting with classical molecular dynamics, followed by full optimizations at the PW6B95-D3/def2-TZVP level of theory. In addition, the binding energies, the binding enthalpy per DMSO, and the quantum theory of atoms in molecules (QTAIM) analysis of the most stable isomers are reported. Temperature effects on the stability of the isomers have also been assessed. After thoroughly exploring the PESs of the DMSO clusters, 159 configurations have been used to apply the quantum cluster equilibrium (QCE) theory to liquid DMSO. The quantum cluster equilibrium theory has been applied to determine the liquid properties of DMSO from DMSO clusters. Thus, using the QCE, the population of the liquid DMSO, its infrared spectrum, and some thermodynamic properties of the liquid DMSO are predicted. The QCE results show that the population of the liquid DMSO is mainly dominated by the DMSO dimer and decamer, with the contribution in trace of the DMSO monomer, trimer, tetramer, pentamer, and octamer. More interestingly, the predicted infrared spectrum of liquid DMSO is in qualitative agreement with the experiment.
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Affiliation(s)
- Alhadji Malloum
- Department of Chemistry, University of the Free State, PO BOX 339, Bloemfontein 9300, South Africa; Department of Physics, Faculty of Science, University of Maroua, PO BOX 46, Maroua, Cameroon.
| | - Jeanet Conradie
- Department of Chemistry, University of the Free State, PO BOX 339, Bloemfontein 9300, South Africa; Department of Chemistry, UiT - The Arctic University of Norway, N-9037 Tromsø, Norway
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36
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Abstract
Despite the long list of planar tetracoordinate atoms, hydrogen is elusive. This is especially due to the inherent ability of hydrogen to form multicenter bonds with other centers. Herein, we introduce the first planar tetracoordinate hydrogen atom (ptH) in the global minimum geometry of a C2v symmetric Li4H4- cluster. Bonding analysis indicates that the central hydrogen atom is stabilized by multicenter bonding with four surrounding Li atoms. Natural charge analysis reveals that the central hydrogen is acting like a hydride, which is strongly attracted by the positively charged surrounding lithium centers. The ptH structure is stabilized by strong electrostatic attraction as well as extensive multicenter bonding. Aromaticity has no role to play here. The cluster is dynamically stable and is expected to be detected in the gas phase. Introduction of a heavier alkali metal such as sodium makes the planar C2v cluster a local minimum with slightly higher energy than the linear global minimum geometry.
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Affiliation(s)
- Kangkan Sarmah
- Advanced Computational Chemistry Centre, Cotton University, Panbazar, Guwahati, Assam, India 781001
| | - Amlan Jyoti Kalita
- Advanced Computational Chemistry Centre, Cotton University, Panbazar, Guwahati, Assam, India 781001
| | - Ankur K Guha
- Advanced Computational Chemistry Centre, Cotton University, Panbazar, Guwahati, Assam, India 781001
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37
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Radael GN, Oliveira GG, Pontes RM. A DFT study of ethanol interaction with the bimetallic clusters of PtSn and its implications on reactivity. J Mol Graph Model 2023; 125:108621. [PMID: 37689026 DOI: 10.1016/j.jmgm.2023.108621] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 08/28/2023] [Accepted: 08/30/2023] [Indexed: 09/11/2023]
Abstract
The comprehension of the factors affecting the adsorption of ethanol over metals and metal alloys is a crucial step for the rational development of new catalysts for hydrogen production through ethanol reforming. In this work, we analyze the effect of combining Pt and Sn on a metal cluster on the complexation energy and reactivity for OH dehydrogenation of ethanol. Metal clusters of Pt10, Sn10 and Pt5Sn5 had their putative minimum located with the help of the artificial bee colony algorithm. Whereas the isolated Pt cluster shows a high degree of polarization (ESP surface), the Sn cluster shows a quite uniform electron density surface. The PtSn cluster is strongly polarized, with Pt atoms withdrawing electron density of Sn atoms. Complexation occurs with the oxygen atom of ethanol directed towards the point of highest electron potential in the ESP surface. Pt presents the highest complexation energy, -20.90 kcal/mol, against only -7.83 kcal/mol (at the B97-3c level). For the PtSn cluster, the value is intermediate, namely -12.39 kcal/mol. The more malleable electron density of Pt and its electron affinity are responsible for its highest complexation energy. These characteristics are partially transferred to the PtSn cluster. QTAIM results show that, for the PtSn cluster, the O-H bond in ethanol is somewhat weaker than for pure Pt and Sn. As a consequence, the energy barrier for the O-H dehydrogenation has its lowest value for the PtSn cluster, which shows that the alloying of two metals can lead to quite quite unexpected results opening the perspective for a more rational fine tuning of catalysts properties.
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Affiliation(s)
- Graziela N Radael
- Departamento de Química, Universidade Estadual de Maringá, Av. Colombo, 5790, Maringá, Paraná, CEP 87900-020, Brazil
| | - Gabriel G Oliveira
- Departamento de Química, Universidade Estadual de Maringá, Av. Colombo, 5790, Maringá, Paraná, CEP 87900-020, Brazil
| | - Rodrigo M Pontes
- Departamento de Química, Universidade Estadual de Maringá, Av. Colombo, 5790, Maringá, Paraná, CEP 87900-020, Brazil.
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38
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Chamba G, Rissanen M, Barthelmeß T, Saiz-Lopez A, Rose C, Iyer S, Saint-Macary A, Rocco M, Safi K, Deppeler S, Barr N, Harvey M, Engel A, Dunne E, Law CS, Sellegri K. Evidence of nitrate-based nighttime atmospheric nucleation driven by marine microorganisms in the South Pacific. Proc Natl Acad Sci U S A 2023; 120:e2308696120. [PMID: 37991941 PMCID: PMC10691324 DOI: 10.1073/pnas.2308696120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Accepted: 10/04/2023] [Indexed: 11/24/2023] Open
Abstract
Our understanding of ocean-cloud interactions and their effect on climate lacks insight into a key pathway: do biogenic marine emissions form new particles in the open ocean atmosphere? Using measurements collected in ship-borne air-sea interface tanks deployed in the Southwestern Pacific Ocean, we identified new particle formation (NPF) during nighttime that was related to plankton community composition. We show that nitrate ions are the only species for which abundance could support NPF rates in our semicontrolled experiments. Nitrate ions also prevailed in the natural pristine marine atmosphere and were elevated under higher sub-10 nm particle concentrations. We hypothesize that these nucleation events were fueled by complex, short-term biogeochemical cycling involving the microbial loop. These findings suggest a new perspective with a previously unidentified role of nitrate of marine biogeochemical origin in aerosol nucleation.
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Affiliation(s)
- Guillaume Chamba
- Université Clermont Auvergne, CNRS, Laboratoire de Météorologie Physique, Clermont-FerrandF-63000, France
| | - Matti Rissanen
- Aerosol Physics Laboratory, Faculty of Engineering and Natural Sciences, University of Tampere, Tampere33720, Finland
- Chemistry Department, Molecular Research Unit, University of Helsinki, Helsinki00014, Finland
| | - Theresa Barthelmeß
- Research Center for Marine Geosciences, Helmholtz Centre for Ocean Research Kiel, Kiel24105, Germany
| | - Alfonso Saiz-Lopez
- Department of Atmospheric Chemistry and Climate, Institute of Physical Chemistry Blas Cabrera, Consejo Superior de Investigaciones Científicas, Madrid28006, Spain
| | - Clémence Rose
- Université Clermont Auvergne, CNRS, Laboratoire de Météorologie Physique, Clermont-FerrandF-63000, France
| | - Siddharth Iyer
- Aerosol Physics Laboratory, Faculty of Engineering and Natural Sciences, University of Tampere, Tampere33720, Finland
| | - Alexia Saint-Macary
- National Institute of Water and Atmospheric Research, Wellington6021, New Zealand
- Department of Marine Sciences, University of Otago, Dunedin9016, New Zealand
| | - Manon Rocco
- Université Clermont Auvergne, CNRS, Laboratoire de Météorologie Physique, Clermont-FerrandF-63000, France
| | - Karl Safi
- National Institute of Water and Atmospheric Research, Hamilton3216, New Zealand
| | - Stacy Deppeler
- National Institute of Water and Atmospheric Research, Wellington6021, New Zealand
| | - Neill Barr
- National Institute of Water and Atmospheric Research, Wellington6021, New Zealand
| | - Mike Harvey
- National Institute of Water and Atmospheric Research, Wellington6021, New Zealand
| | - Anja Engel
- Research Center for Marine Geosciences, Helmholtz Centre for Ocean Research Kiel, Kiel24105, Germany
| | - Erin Dunne
- Commonwealth Scientific and Industrial Research Organisation Environment, AspendaleVIC3195, Australia
| | - Cliff S. Law
- National Institute of Water and Atmospheric Research, Wellington6021, New Zealand
- Department of Marine Sciences, University of Otago, Dunedin9016, New Zealand
| | - Karine Sellegri
- Université Clermont Auvergne, CNRS, Laboratoire de Météorologie Physique, Clermont-FerrandF-63000, France
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39
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Kubečka J, Besel V, Neefjes I, Knattrup Y, Kurtén T, Vehkamäki H, Elm J. Computational Tools for Handling Molecular Clusters: Configurational Sampling, Storage, Analysis, and Machine Learning. ACS OMEGA 2023; 8:45115-45128. [PMID: 38046354 PMCID: PMC10688175 DOI: 10.1021/acsomega.3c07412] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Revised: 10/25/2023] [Accepted: 10/26/2023] [Indexed: 12/05/2023]
Abstract
Computational modeling of atmospheric molecular clusters requires a comprehensive understanding of their complex configurational spaces, interaction patterns, stabilities against fragmentation, and even dynamic behaviors. To address these needs, we introduce the Jammy Key framework, a collection of automated scripts that facilitate and streamline molecular cluster modeling workflows. Jammy Key handles file manipulations between varieties of integrated third-party programs. The framework is divided into three main functionalities: (1) Jammy Key for configurational sampling (JKCS) to perform systematic configurational sampling of molecular clusters, (2) Jammy Key for quantum chemistry (JKQC) to analyze commonly used quantum chemistry output files and facilitate database construction, handling, and analysis, and (3) Jammy Key for machine learning (JKML) to manage machine learning methods in optimizing molecular cluster modeling. This automation and machine learning utilization significantly reduces manual labor, greatly speeds up the search for molecular cluster configurations, and thus increases the number of systems that can be studied. Following the example of the Atmospheric Cluster Database (ACDB) of Elm (ACS Omega, 4, 10965-10984, 2019), the molecular clusters modeled in our group using the Jammy Key framework have been stored in an improved online GitHub repository named ACDB 2.0. In this work, we present the Jammy Key package alongside its assorted applications, which underline its versatility. Using several illustrative examples, we discuss how to choose appropriate combinations of methodologies for treating particular cluster types, including reactive, multicomponent, charged, or radical clusters, as well as clusters containing flexible or multiconformer monomers or heavy atoms. Finally, we present a detailed example of using the tools for atmospheric acid-base clusters.
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Affiliation(s)
- Jakub Kubečka
- Aarhus
University, Department of Chemistry, Langelandsgade 140, Aarhus 8000, Denmark
| | - Vitus Besel
- University
of Helsinki, Institute for Atmospheric and
Earth System Research/Physics, Faculty of Science, P.O. Box 64, Helsinki 00140, Finland
| | - Ivo Neefjes
- University
of Helsinki, Institute for Atmospheric and
Earth System Research/Physics, Faculty of Science, P.O. Box 64, Helsinki 00140, Finland
| | - Yosef Knattrup
- Aarhus
University, Department of Chemistry, Langelandsgade 140, Aarhus 8000, Denmark
| | - Theo Kurtén
- University
of Helsinki, Institute for Atmospheric and
Earth System Research/Chemistry, Faculty of Science, P.O. Box 64, Helsinki 00140, Finland
| | - Hanna Vehkamäki
- University
of Helsinki, Institute for Atmospheric and
Earth System Research/Physics, Faculty of Science, P.O. Box 64, Helsinki 00140, Finland
| | - Jonas Elm
- Aarhus
University, Department of Chemistry, Langelandsgade 140, Aarhus 8000, Denmark
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40
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Wu H, Engsvang M, Knattrup Y, Kubečka J, Elm J. Improved Configurational Sampling Protocol for Large Atmospheric Molecular Clusters. ACS OMEGA 2023; 8:45065-45077. [PMID: 38046341 PMCID: PMC10688134 DOI: 10.1021/acsomega.3c06794] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Revised: 10/12/2023] [Accepted: 10/17/2023] [Indexed: 12/05/2023]
Abstract
The nucleation process leading to the formation of new atmospheric particles plays a crucial role in aerosol research. Quantum chemical (QC) calculations can be used to model the early stages of aerosol formation, where atmospheric vapor molecules interact and form stable molecular clusters. However, QC calculations heavily depend on the chosen computational method, and when dealing with large systems, striking a balance between accuracy and computational cost becomes essential. We benchmarked the binding energies and structures and found the B97-3c method to be a good compromise between the accuracy and computational cost for studying large cluster systems. Further, we carefully assessed configurational sampling procedures for targeting large atmospheric molecular clusters containing up to 30 molecules (approximately 2 nm in diameter) and proposed a funneling approach with highly improved accuracy. We find that several parallel ABCluster explorations lead to better guesses for the cluster global energy minimum structures than one long exploration. This methodology allows us to bridge computational studies of molecular clusters, which typically reach only around 1 nm, with experimental studies that often measure particles larger than 2 nm. By employing this workflow, we searched for low-energy configurations of large sulfuric acid-ammonia and sulfuric acid-dimethylamine clusters. We find that the binding free energies of clusters containing dimethylamine are unequivocally more stable than those of the ammonia-containing clusters. Our improved configurational sampling protocol can in the future be applied to study the growth and dynamics of large clusters of arbitrary compositions.
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Affiliation(s)
- Haide Wu
- Department of Chemistry, Aarhus
University, Langelandsgade 140, 8000 Aarhus C, Denmark
| | - Morten Engsvang
- Department of Chemistry, Aarhus
University, Langelandsgade 140, 8000 Aarhus C, Denmark
| | - Yosef Knattrup
- Department of Chemistry, Aarhus
University, Langelandsgade 140, 8000 Aarhus C, Denmark
| | - Jakub Kubečka
- Department of Chemistry, Aarhus
University, Langelandsgade 140, 8000 Aarhus C, Denmark
| | - Jonas Elm
- Department of Chemistry, Aarhus
University, Langelandsgade 140, 8000 Aarhus C, Denmark
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41
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Guha AK. Identification of Global Minimum of HNBeCO Complex. J Phys Chem A 2023; 127:9743-9747. [PMID: 37938901 DOI: 10.1021/acs.jpca.3c05289] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2023]
Abstract
Multiple bonding has always excited chemists. Recently, triple bonding between beryllium and N atoms in the HNBeCO complex has been reported based on experimental infrared spectroscopy and theoretical calculations. However, the present work reports a different structure based on a detailed potential energy surface scan. The global minimum geometry features only a weak partial Be-N double bond. The global minimum geometry lies very deep in the potential energy surface with respect to the reported one. Isomerization kinetics reveals that the reported structure has to overcome a very small barrier (5.4 kcal/mol) to isomerize to the global one. Although the previously reported structure is a real minimum, the present study identifies a much lower energy structure. A re-examination of the experimental spectra might show that the global minimum has also been observed.
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Affiliation(s)
- Ankur K Guha
- Advanced Computational Chemistry Centre, Department of Chemistry, Cotton University, Panbazar, Guwahati, Assam 781001, India
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42
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Gao XF, Liu GH, Hu XK, Chen LL, Zhu BC, Zheng DS, Liao YH. DFT-Based Study of the Structure, Stability, and Spectral and Optical Properties of Gas-Phase NbMg n ( n = 2-12) Clusters. ACS OMEGA 2023; 8:41391-41401. [PMID: 37970033 PMCID: PMC10633863 DOI: 10.1021/acsomega.3c05113] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/16/2023] [Revised: 10/09/2023] [Accepted: 10/12/2023] [Indexed: 11/17/2023]
Abstract
Gas-phase NbMgn (n = 2-12) clusters were fully searched by CALYPSO software, and then the low-energy isomers were further optimized and calculated under DFT. It is shown that the three lowest energy isomers of NbMgn (n = 3-12) at each size are grown from two seed structures, i.e., tetrahedral and pentahedral structures, and the transition size occurs at the NbMg8 cluster. Interestingly, the relative stability calculations of the NbMg8 cluster ground-state isomer stand out under the examination of several parameters' calculations. The charge-transfer properties of the clusters of the ground-state isomers of various sizes had been comprehensively investigated. In order to be able to provide data guidance for future experimental probing of these ground-state clusters, this work also predicted infrared and Raman spectra at the same level of theoretical calculations. The results show that the multipeak nature of the IR and Raman spectra predicts that it is difficult to distinguish them directly. Finally, the optical properties of these clusters were investigated by calculating the static linear, second-order nonlinear, and third-order nonlinear coefficients. Importantly and interestingly, the NbMg8 cluster was shown to have superior nonlinear optical characteristics to all other clusters; thus, it is a powerful candidate for a potentially ultrasensitive nonlinear optical response device for some special purpose.
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Affiliation(s)
- Xiao-Feng Gao
- School
of Mathematics and Physics, Hubei Polytechnic
University, Huangshi 435003, People’s
Republic of China
- School
of Physics and Optoelectronic Engineering, Yangtze University, Jingzhou 434023, People’s
Republic of China
| | - Guang-Hui Liu
- Daye
Special Steel Co., LTD, Huangshi 435003, People’s
Republic of China
| | - Xian-Kai Hu
- School
of Mathematics and Physics, Hubei Polytechnic
University, Huangshi 435003, People’s
Republic of China
| | - Lan-Li Chen
- School
of Mathematics and Physics, Hubei Polytechnic
University, Huangshi 435003, People’s
Republic of China
| | - Ben-Chao Zhu
- School
of Public Health, Hubei University of Medicine, Shiyan 442000, People’s Republic of China
| | - Ding-Shan Zheng
- School
of Physics and Optoelectronic Engineering, Yangtze University, Jingzhou 434023, People’s
Republic of China
| | - Yan-Hua Liao
- School
of Mathematics and Physics, Hubei Polytechnic
University, Huangshi 435003, People’s
Republic of China
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43
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Dong Q, Zhang K, Huang Y, Feng X, Yu T, Li X, Qiu J, Zhou S. Subnano Te Cluster in Glass for Efficient Full-Spectrum Conversion. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2023; 10:e2303421. [PMID: 37822163 PMCID: PMC10667836 DOI: 10.1002/advs.202303421] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Revised: 07/31/2023] [Indexed: 10/13/2023]
Abstract
Broadband near-infrared (NIR) photonic materials have wide applications. Although extensive studies on rare-earth, transition-metal, and even semiconductor-activated materials have enabled the development of a rich NIR material pool, developing broadband and efficient photonic candidates covering the NIR I and II regions from 750 to 1500 nm has been met with limited success. Here, it is reported that a subnano Te cluster with a characteristic configuration different from that of the ion state may fill the aforementioned gap. Further, a strategy is proposed for the in situ generation and stabilization of Te clusters by tuning the cluster evolution in glass. A novel active photonic glass embedded with a Te cluster is fabricated; it exhibits intense and broadband short-wave NIR luminescence with a central wavelength at 1030 nm and a bandwidth exceeding 330 nm. Interestingly, the glass exhibited a full visible-spectrum conversion ability from 300 to 800 nm. The application of this unique broadband excitation feature for night vision and tissue penetration is demonstrated using a smartphone as the excitation source. These findings demonstrate a fundamental principle of cluster design in glass for creating new properties and provide a new direction for developing novel cluster-derived functional composite materials.
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Affiliation(s)
- Quan Dong
- State Key Laboratory of Luminescent Materials and DevicesSchool of Materials Science and EngineeringSouth China University of TechnologyGuangdong Provincial Key Laboratory of Fiber Laser Materials and Applied TechniquesGuangdong Engineering Technology Research and Development Center of Special Optical Fiber Materials and DevicesGuangzhou510640China
| | - Ke Zhang
- State Key Laboratory of Luminescent Materials and DevicesSchool of Materials Science and EngineeringSouth China University of TechnologyGuangdong Provincial Key Laboratory of Fiber Laser Materials and Applied TechniquesGuangdong Engineering Technology Research and Development Center of Special Optical Fiber Materials and DevicesGuangzhou510640China
| | - Yupeng Huang
- State Key Laboratory of Luminescent Materials and DevicesSchool of Materials Science and EngineeringSouth China University of TechnologyGuangdong Provincial Key Laboratory of Fiber Laser Materials and Applied TechniquesGuangdong Engineering Technology Research and Development Center of Special Optical Fiber Materials and DevicesGuangzhou510640China
| | - Xu Feng
- State Key Laboratory of Luminescent Materials and DevicesSchool of Materials Science and EngineeringSouth China University of TechnologyGuangdong Provincial Key Laboratory of Fiber Laser Materials and Applied TechniquesGuangdong Engineering Technology Research and Development Center of Special Optical Fiber Materials and DevicesGuangzhou510640China
| | - Tao Yu
- State Key Laboratory of Fluorine and Nitrogen ChemicalsXi'an Modern Chemistry Research InstituteXi'an710065China
| | - Xueliang Li
- State Key Laboratory of Luminescent Materials and DevicesSchool of Materials Science and EngineeringSouth China University of TechnologyGuangdong Provincial Key Laboratory of Fiber Laser Materials and Applied TechniquesGuangdong Engineering Technology Research and Development Center of Special Optical Fiber Materials and DevicesGuangzhou510640China
| | - Jianrong Qiu
- College of Optical Science and EngineeringState Key Laboratory of Modern Optical InstrumentationZhejiang UniversityHangzhou310027China
| | - Shifeng Zhou
- State Key Laboratory of Luminescent Materials and DevicesSchool of Materials Science and EngineeringSouth China University of TechnologyGuangdong Provincial Key Laboratory of Fiber Laser Materials and Applied TechniquesGuangdong Engineering Technology Research and Development Center of Special Optical Fiber Materials and DevicesGuangzhou510640China
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44
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Engsvang M, Kubečka J, Elm J. Toward Modeling the Growth of Large Atmospheric Sulfuric Acid-Ammonia Clusters. ACS OMEGA 2023; 8:34597-34609. [PMID: 37779982 PMCID: PMC10536041 DOI: 10.1021/acsomega.3c03521] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/20/2023] [Accepted: 08/30/2023] [Indexed: 10/03/2023]
Abstract
Studying large atmospheric molecular clusters is needed to understand the transition between clusters and aerosol particles. In this work, we studied the (SA)n(AM)n clusters with n up to 30 and the (SA)m(AM)m±2 clusters, with m = 6-20. The cluster configurations are sampled using the ABCluster program, and the cluster geometries and thermochemical parameters are calculated using GFN1-xTB. The cluster binding energies are calculated using B97-3c. We find that the addition of sulfuric acid is preferred to the addition of ammonia. The addition free energies were found to have large uncertainties, which could potentially be attributed to errors in the applied level of theory. Based on DLPNO-CCSD(T0)/aug-cc-pVTZ benchmarks of the binding energies of the large (SA)8-9(AM)10 and (SA)10(AM)10-11 clusters, we find that ωB97X-D3BJ with a large basis set is required to yield accurate binding and addition energies. However, based on recalculations of the single-point energy at r2SCAN-3c and ωB97X-D3BJ/6-311++G(3df,3pd), we show that the single-point energy contribution is not the primary source of error. We hypothesize that a larger source of error might be present in the form of insufficient configurational sampling. Finally, we train Δ machine learning model on (SA)n(AM)n clusters with n up to 5 and show that we can predict the binding energies of clusters up to sizes of (SA)30(AM)30 with a binding energy error below 0.6 %. This is an encouraging approach for accurately modeling the binding energies of large acid-base clusters in the future.
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Affiliation(s)
- Morten Engsvang
- Department
of Chemistry, Aarhus University, Langelandsgade 140, 8000 Aarhus C, Denmark
| | - Jakub Kubečka
- Department
of Chemistry, Aarhus University, Langelandsgade 140, 8000 Aarhus C, Denmark
| | - Jonas Elm
- Department
of Chemistry, iClimate, Aarhus University, Langelandsgade 140, 8000 Aarhus C, Denmark
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45
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Gohain N, Bordoloi A, Kalita AJ, Guha AK. Rare Spin Avoided σ-σ Diradical Planar Tetracoordinate Boron Cluster: A Proto-Star for Planar Pentacoordination. Chemphyschem 2023; 24:e202300101. [PMID: 37409624 DOI: 10.1002/cphc.202300101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Revised: 04/11/2023] [Accepted: 07/06/2023] [Indexed: 07/07/2023]
Abstract
We report a global planar star-like cluster B3 Li3 featuring three planar tetracoordinate boron centres with a rare spin avoided σ-σ diradical character. The cluster was found to be stable towards dissociation into different fragments. The spin density was found to be localized solely on the three boron atoms in the molecular plane. This spin avoided σ-σ diradical character leads to the extension of the coordination number to yield a neutral B3 Li3 H3 and a cationic B3 Li3 H3 + cluster with three planar pentacoordinate boron centres in their global minimum structures. The planar geometry of the aninonic B3 Li3 H3 - cluster is slightly higher in energy. The planar global clusters were found to maintain planarity in their ligand protected benzene bound complexes, B3 Li3 (Bz)3 , B3 Li3 H3 (Bz)3 and B3 Li3 H3 (Bz)3 + with high ligand dissociation energies offering candidature for experimental detection.
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Affiliation(s)
- Namrata Gohain
- Advanced Computational Chemistry Centre, Cotton University, Panbazar, Guwahati, Assam, INDIA-, 781001
| | - Abhik Bordoloi
- Advanced Computational Chemistry Centre, Cotton University, Panbazar, Guwahati, Assam, INDIA-, 781001
| | - Amlan J Kalita
- Advanced Computational Chemistry Centre, Cotton University, Panbazar, Guwahati, Assam, INDIA-, 781001
| | - Ankur K Guha
- Advanced Computational Chemistry Centre, Cotton University, Panbazar, Guwahati, Assam, INDIA-, 781001
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Knattrup Y, Kubečka J, Elm J. Nitric Acid and Organic Acids Suppress the Role of Methanesulfonic Acid in Atmospheric New Particle Formation. J Phys Chem A 2023; 127:7568-7578. [PMID: 37651638 DOI: 10.1021/acs.jpca.3c04393] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/02/2023]
Abstract
Multicomponent atmospheric molecular clusters, typically comprising a combination of acids and bases, play a pivotal role in our climate system and contribute to the perplexing uncertainties embedded in modern climate models. Our understanding of cluster formation is limited by the lack of studies on complex mixed-acid-mixed-base systems. Here, we investigate multicomponent clusters consisting of mixtures of several acid and base molecules: sulfuric acid (SA), methanesulfonic acid (MSA), nitric acid (NA), formic acid (FA), along with methylamine (MA), dimethylamine (DMA), and trimethylamine (TMA). We calculated the binding free energies of a comprehensive set of 252 mixed-acid-mixed-base clusters at the DLPNO-CCSD(T0)/aug-cc-pVTZ//ωB97X-D/6-31++G(d,p) level of theory. Combined with the existing datasets, we simulated the new particle formation (NPF) rates using the Atmospheric Cluster Dynamics Code (ACDC). We find that the presence of NA and FA had a substantial impact, increasing the NPF rate by 60% at realistic conditions. Intriguingly, we find that NA and FA suppress the role of MSA in NPF. These findings suggest that even high concentration of MSA has a limited impact on NPF in polluted regions with high FA and NA. We outline a method for generating a lookup table that could potentially be used in climate models that sufficiently incorporates all the required chemistry. By unraveling the molecular mechanisms of mixed-acid-mixed-base clusters, we get one step closer to comprehending their implications for our global climate system.
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Affiliation(s)
- Yosef Knattrup
- Department of Chemistry, Aarhus University, Langelandsgade 140, 8000 Aarhus C, Denmark
| | - Jakub Kubečka
- Department of Chemistry, Aarhus University, Langelandsgade 140, 8000 Aarhus C, Denmark
| | - Jonas Elm
- Department of Chemistry, iClimate, Aarhus University, Langelandsgade 140, 8000 Aarhus C, Denmark
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Kalita AJ, Gohain N, Bordoloi A, Guha AK. Planar pentacoordinate carbon in a 16-electron neutral CCu 2Be 3H 4 cluster. Phys Chem Chem Phys 2023. [PMID: 37486198 DOI: 10.1039/d3cp00758h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/25/2023]
Abstract
Planar hypercoordination in carbon is a fascinating area, which departs from the usual view of coordination geometry in carbon. Herein, we propose a planar pentacoordinate carbon species in the global minimum of the CCu2Be3H4 cluster. The cluster is a 16-electron species that is thermodynamically and kinetically very stable. Bonding analyses reveal 2π/6σ double aromaticity in the cluster. A low-energy isomerization pathway also reveals that the cluster has a sufficient lifetime for its experimental detection.
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Affiliation(s)
- Amlan J Kalita
- Advanced Computational Chemistry Centre, Department of Chemistry, Cotton University, Panbazar, Guwahati, Assam, 781001, India.
| | - Namrata Gohain
- Advanced Computational Chemistry Centre, Department of Chemistry, Cotton University, Panbazar, Guwahati, Assam, 781001, India.
| | - Abhik Bordoloi
- Advanced Computational Chemistry Centre, Department of Chemistry, Cotton University, Panbazar, Guwahati, Assam, 781001, India.
| | - Ankur K Guha
- Advanced Computational Chemistry Centre, Department of Chemistry, Cotton University, Panbazar, Guwahati, Assam, 781001, India.
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Marshall MD, Leung HO. Molecular Structures and Microwave Spectra of the Gas-Phase Homodimers of 3-Fluoro-1,2-epoxypropane and 3,3-Difluoro-1,2-epoxypropane. J Phys Chem A 2023. [PMID: 37471074 DOI: 10.1021/acs.jpca.3c03643] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/21/2023]
Abstract
Molecular structures for the heterochiral and homochiral gas-phase homodimers of 3-fluoro-1,2-epoxypropane and 3,3-difluoro-1,2-epoxypropane are investigated using both ab initio and density functional quantum chemistry calculations. Although microwave spectra for the heterochiral dimers are not observed as the lowest-energy isomers lack an electric dipole moment and others are presumably too high in energy, rotational spectra are observed for the homochiral dimers of each molecule that are consistent with the lowest-energy isomers of each. The presence of hydrogen atoms in the fluoromethyl groups makes it possible for these groups to participate in the intermolecular interactions that stabilize these dimers, resulting in a distinctly different bonding motif than is observed in the homodimers of 3,3,3-trifluoro-1,2-epoxypropane where the lack of a hydrogen atom prevents this possibility. The rotational spectra and energy ordering of the dimers are sufficiently well predicted with modest calculational methods to enable straightforward assignment of the observed spectra and to identify the molecular carrier of an assigned spectrum.
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Affiliation(s)
- Mark D Marshall
- Department of Chemistry, Amherst College, P.O. Box 5000, Amherst, Massachusetts 01002-5000, United States
| | - Helen O Leung
- Department of Chemistry, Amherst College, P.O. Box 5000, Amherst, Massachusetts 01002-5000, United States
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Jiang X, Wu J, Zhang P, Jiang L, Lu S, Zhao X, Yin Z. First-principles investigation on multi-magnesium sulfide and magnesium sulfide clusters in magnesium-sulfide batteries. RSC Adv 2023; 13:20926-20933. [PMID: 37441038 PMCID: PMC10335111 DOI: 10.1039/d3ra03165a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Accepted: 07/05/2023] [Indexed: 07/15/2023] Open
Abstract
Because of the abundance of magnesium and sulfur and their low cost, the development of magnesium sulfur batteries is very promising. In particular, the battery performance of nanoscale (MgS)n clusters is much better than that of bulk sized MgS. However, the structures, stability, and properties of MgxSy and (MgS)n clusters, which are very important to improve the performance of Mg-S batteries, are still unexplored. Herein, the most stable structures of MgxSy (x = 1-8, y = 1-8) and (MgS)n (n = 1-10) are reliably determined using the structure search method and density functional theory to calculate. According to calculation results, MgS3 and Mg6S8 may not exist in the actual charging and discharging products of magnesium sulfide batteries. The (MgS)n (n ≥ 5) clusters exhibit intriguing cage-like structures, which are favorable for eliminating dangling bonds and enhancing structural stability. Compared to the MgS monomer, each sulfur atom in the clusters is coordinated with more magnesium atoms, thus lengthening the Mg-S bond length and decreasing the Mg-S bond activation energy. Notably, with the increase of dielectric constant of electrolyte solvent, compared to the DME (ε = 7.2), THF (ε = 7.6) and C2H4Cl2 (ε = 10.0), MgxSy and (MgS)n clusters are most stable in the environment of C3H6O (ε = 20.7). It can delay the transformation of magnesium polysulfide to the final product MgS, which is conducive to improving the performance of Mg-S batteries. The predicted characteristic peaks of infrared and Raman spectra provide useful information for in situ experimental investigation. Our work represents a significant step towards understanding (MgS)n clusters and improving the performance of Mg-S batteries.
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Affiliation(s)
- Xiaoli Jiang
- School of Mathematics, Physics and Statistics, Shanghai University of Engineering Science 333 Longteng Road Shanghai 201620 China
| | - Jianbao Wu
- School of Mathematics, Physics and Statistics, Shanghai University of Engineering Science 333 Longteng Road Shanghai 201620 China
| | - Panyu Zhang
- School of Mathematics, Physics and Statistics, Shanghai University of Engineering Science 333 Longteng Road Shanghai 201620 China
| | - Liyuan Jiang
- School of Mathematics, Physics and Statistics, Shanghai University of Engineering Science 333 Longteng Road Shanghai 201620 China
| | - Shuhan Lu
- School of Mathematics, Physics and Statistics, Shanghai University of Engineering Science 333 Longteng Road Shanghai 201620 China
| | - Xinxin Zhao
- School of Mathematics, Physics and Statistics, Shanghai University of Engineering Science 333 Longteng Road Shanghai 201620 China
| | - ZhiXiang Yin
- School of Mathematics, Physics and Statistics, Shanghai University of Engineering Science 333 Longteng Road Shanghai 201620 China
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50
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Doust Mohammadi M, Louis H, Chukwu UG, Bhowmick S, Rasaki ME, Biskos G. Gas-Phase Interaction of CO, CO 2, H 2S, NH 3, NO, NO 2, and SO 2 with Zn 12O 12 and Zn 24 Atomic Clusters. ACS OMEGA 2023; 8:20621-20633. [PMID: 37323380 PMCID: PMC10268014 DOI: 10.1021/acsomega.3c01177] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Accepted: 05/22/2023] [Indexed: 06/17/2023]
Abstract
Atmospheric pollutants pose a high risk to human health, and therefore it is necessary to capture and preferably remove them from ambient air. In this work, we investigate the intermolecular interaction between the pollutants such as CO, CO2, H2S, NH3, NO, NO2, and SO2 gases with the Zn24 and Zn12O12 atomic clusters, using the density functional theory (DFT) at the meta-hybrid functional TPSSh and LANl2Dz basis set. The adsorption energy of these gas molecules on the outer surfaces of both types of clusters has been calculated and found to have a negative value, indicating a strong molecular-cluster interaction. The largest adsorption energy has been observed between SO2 and the Zn24 cluster. In general, the Zn24 cluster appears to be more effective for adsorbing SO2, NO2, and NO than Zn12O12, whereas the latter is preferable for the adsorption of CO, CO2, H2S, and NH3. Frontier molecular orbital (FMO) analysis showed that Zn24 exhibits higher stability upon adsorption of NH3, NO, NO2, and SO2, with the adsorption energy falling within the chemisorption range. The Zn12O12 cluster shows a characteristic decrease in band gap upon adsorption of CO, H2S, NO, and NO2, suggesting an increase in electrical conductivity. Natural bond orbital (NBO) analysis also suggests the presence of strong intermolecular interactions between atomic clusters and the gases. This interaction was recognized to be strong and noncovalent, as determined by noncovalent interaction (NCI) and quantum theory of atoms in molecules (QTAIM) analyses. Overall, our results suggest that both Zn24 and Zn12O12 clusters are good candidate species for promoting adsorption and, thus, can be employed in different materials and/or systems for enhancing interaction with CO, H2S, NO, or NO2.
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Affiliation(s)
| | - Hitler Louis
- Computational
and Bio-Simulation Research Group, University
of Calabar, Calabar 540221, Nigeria
| | - Udochukwu G. Chukwu
- Computational
and Bio-Simulation Research Group, University
of Calabar, Calabar 540221, Nigeria
| | - Somnath Bhowmick
- Climate
and Atmosphere Research Centre, The Cyprus
Institute, Nicosia 2121, Cyprus
| | - Michael E. Rasaki
- Computational
and Bio-Simulation Research Group, University
of Calabar, Calabar 540221, Nigeria
| | - George Biskos
- Climate
and Atmosphere Research Centre, The Cyprus
Institute, Nicosia 2121, Cyprus
- Faculty
of Civil Engineering and Geosciences, Delft
University of Technology, Delft 2628CN, The Netherlands
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