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Naskar P, Talukder S. Energetics and spectroscopic studies of CNO (-) (H 2 O) n $$ {\mathbf{CNO}}^{\left(\hbox{-} \right)}{\left({\mathbf{H}}_{\mathbf{2}}\mathbf{O}\right)}_{\mathbf{n}} $$ clusters and the temperature dependencies of the isomers: An approach based on a combined recipe of parallel tempering and quantum chemical methods. J Comput Chem 2024. [PMID: 39151062 DOI: 10.1002/jcc.27480] [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: 04/19/2024] [Revised: 07/22/2024] [Accepted: 07/30/2024] [Indexed: 08/18/2024]
Abstract
A system associated with several number of weak interactions supports numerous number of stable structures within a narrow range of energy. Often, a deterministic search method fails to locate the global minimum geometry as well as important local minimum isomers for such systems. Therefore, in this work, the stochastic search technique, namely parallel tempering, has been executed on the quantum chemical surface of theCNO (-) (H 2 O) n $$ {\mathrm{CNO}}^{\left(\hbox{-} \right)}{\left({\mathrm{H}}_2\mathrm{O}\right)}_n $$ system forn = 1 $$ n=1 $$ -8 to generate global minimum as well as several number of local minimum isomers. IR spectrum can act as the fingerprint property for such system to be identified. Thus, IR spectroscopic features have also been included in this work. Vertical detachment energy has also been calculated to obtain clear information about number of water molecules in several spheres around the central anion. In addition, in a real experimental scenario, not only the global but also the local minimum isomers play an important role in determining the average value of a particular physically observable property. Therefore, the relative conformational populations have been determined for all the evaluated structures for the temperature range between 20K and 400K. Further to understand the phase change behavior, the configurational heat capacities have also been calculated for different sizes.
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Affiliation(s)
- Pulak Naskar
- Department of Chemistry, Mrinalini Datta Mahavidyapith, Kolkata, India
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2
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Al-Shuaeeb RAA, Abd El-Mageed HR, Ahmed SA, Mohamed HS, Hamza ZS, Rafi MO, Rahman MS. Identification of potent COVID-19 main protease inhibitors by loading of favipiravir on Mg 12O 12 and Zn 12O 12 nanoclusters: an in silico strategy for COVID-19 treatment. J Biomol Struct Dyn 2023; 41:11437-11449. [PMID: 36591698 DOI: 10.1080/07391102.2022.2162967] [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: 11/11/2022] [Accepted: 12/18/2022] [Indexed: 01/03/2023]
Abstract
Pandemic new severe acute respiratory syndrome coronavirus (SARS-CoV-2) virus has increased throughout the world. There is no effective treatment against this virus until now. Since its appearance in Wuhan, China in December 2019, SARS-CoV-2 becomes the largest challenge the world is opposite today, including the discovery of an antiviral drug for this virus. Several viral proteins have been prioritized as SARS-CoV-2 antiviral drug targets, among them the papain-like protease (PLpro) and the main protease (Mpro). Inhibition of these proteases would target viral replication, viral maturation and suppression of host innate immune responses. Potential candidates have been identified to show inhibitory effects against Mpro, both in biochemical assays and viral replication in cells. There are different molecules such as lopinavir and favipiravir considerably inhibit the activity of Mpro in vitro. Different studies have shown that structurally improved favipiravir and other similar compounds can inhibit SARS-CoV-2 main protease. In this work, we study the interactions between favipiravir with Mg12O12 and Zn12O12 nanoclusters by density functional theory (DFT) and quantum mechanics atoms in molecules (QMAIM) methods to summarize the ability to load favipiravir onto Mg12O12 and Zn12O12 nanoclusters. Favipiravir-Mg12O12 and favipiravir-Zn12O12 lowest structures complexes were chosen to dock inside the SARS-CoV-2 main protease by molecular docking study. The molecular docking analysis revealed that the binding affinity of Mg12O12 and Zn12O12 nanoclusters inside the Mpro receptor is larger than that of favipiravir. Also, the loading of favipiravir on the surface of Mg12O12 and Zn12O12 nanoclusters increased the binding affinity against the Mpro receptor. Subsequently, 100 ns molecular dynamics simulation of the favipiravir-Mg12O12, and favipiravir-Zn12O12 docked inside the Mpro complexes established that favipiravir-Mg12O12, forms the most stable complex with the Mpro. Further molecular mechanics Poisson Boltzmann surface area (MMPBSA) analyses using the MD trajectories also demonstrated the higher binding affinity of favipiravir-Mg12O12 inside the Mpro. In summary, this study demonstrates a new way to characterize leads for novel anti-viral drugs against SARS-CoV-2, by improving the drug ability of favipiravir via loading it on Mg12O12 and Zn12O12 nanoclusters.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
| | - H R Abd El-Mageed
- Micro-analysis and Environmental Research and Community Services Center, Faculty of Science, Beni-Suef University, Beni-Suef City, Egypt
| | - Shimaa A Ahmed
- Department of Chemistry, Faculty of Science, Beni-Suef University, Beni-Suef, Egypt
| | - Hussein S Mohamed
- Chemistry of Medicinal and Aromatic Plants Department, Research institute of medicinal and aromatic plants (RIMAP), Beni-Suef University, Beni-Suef, Egypt
| | - Zeinab S Hamza
- Chemistry of Medicinal and Aromatic Plants Department, Research institute of medicinal and aromatic plants (RIMAP), Beni-Suef University, Beni-Suef, Egypt
| | - Md Oliullah Rafi
- Department of Genetic Engineering and Biotechnology, Jashore University of Science and Technology, Jessore Sadar Upazila, Bangladesh
| | - Md Shahedur Rahman
- Department of Genetic Engineering and Biotechnology, Jashore University of Science and Technology, Jessore Sadar Upazila, Bangladesh
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3
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Theoretical study of the side reactions of ethanol-to-butadiene conversion on MgO catalyst: formation of diethyl ether, ethyl acetal, 1,3-butanediol, methyl ethyl ketone, n-butanol, butanal, and acetone. Theor Chem Acc 2022. [DOI: 10.1007/s00214-022-02927-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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4
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Fonseca GV, Fernandes GFS, Machado FBC, Ferrão LFA. Electronic structure and physicochemical properties of the metal and semimetal oxide nanoclusters. J Mol Model 2022; 28:307. [PMID: 36087161 DOI: 10.1007/s00894-022-05308-3] [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: 04/17/2022] [Accepted: 08/30/2022] [Indexed: 11/25/2022]
Abstract
Clusters are physical entities composed of a few to thousands of atoms with capabilities to develop novel materials, like cluster-assembled materials. In this sense, knowing the electronic structure and physicochemical properties of the isolated clusters can be useful to understand how they interact with other chemical species by intermolecular forces, as free, embedded, and saturated clusters, and by intramolecular forces, acting as support clusters. In this way, in the present work, the electronic structure and physicochemical properties of metal oxide nanoclusters (MgO, Al2O3, SiO2, and TiO2) were studied by highly correlated molecular quantum chemistry methods. Through the electronic state's characterization, a semiconductor aspect was found for the titania oxide nanocluster (Te < 0.8 eV) while the other agglomerates showed a characteristic of insulating material (Te > 3.3 eV). From the stability index, the following stability order can be characterized: (SiO2)4 > (Al2O3)4 > (MgO)4 > (TiO2)3. Initial information of intermolecular and intramolecular forces caused by the studied clusters was calculated through the relative electrophilicity index, which classified the (MgO)4 and (TiO2)3 clusters as the more reactive ones, in which the (MgO)4 cluster was identified as a nucleophilic species, while the (TiO2)3 cluster as an electrophilic molecule.
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Affiliation(s)
- Giovana V Fonseca
- Instituto de Ciência e Tecnologia da UNIFESP, São José dos Campos, Brazil
| | - Gabriel F S Fernandes
- Departamento de Química, Instituto Tecnológico de Aeronáutica, São José dos Campos, SP, 12228-900, Brazil
| | - Francisco B C Machado
- Departamento de Química, Instituto Tecnológico de Aeronáutica, São José dos Campos, SP, 12228-900, Brazil
| | - Luiz F A Ferrão
- Departamento de Química, Instituto Tecnológico de Aeronáutica, São José dos Campos, SP, 12228-900, Brazil.
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5
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Kadhim MM, Taban TZ, Obaid RF, Almashhadani HA, Shadhar MH, Bustani GS, Rheima AM, Mohamadi A. A computational study on the potential application of Ca12O12 cluster for sensing of fungicide molecule. BRAZILIAN JOURNAL OF CHEMICAL ENGINEERING 2022. [DOI: 10.1007/s43153-022-00262-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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6
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Kartika R, Alsultany FH, Turki Jalil A, Mahmoud MZ, Fenjan MN, Rajabzadeh H. Ca12O12 nanocluster as highly sensitive material for the detection of hazardous mustard gas: Density-functional theory. INORG CHEM COMMUN 2022. [DOI: 10.1016/j.inoche.2021.109174] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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7
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Gao Y, Xu F, Wu J, Zhao H, Ebadi AG. Detection and adsorption of cathinone drug by magnesium oxide nanostructure: DFT study. COMPUT THEOR CHEM 2022. [DOI: 10.1016/j.comptc.2021.113507] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/07/2022]
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8
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Ma S, Yi L, Wu Z. Metal oxide (BeO-MgO-ZnO) nanoclusters as drug delivery systems for isoniazid anticancer drug: a DFT study. Mol Phys 2021. [DOI: 10.1080/00268976.2021.1986162] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
- Songhe Ma
- General Surgery Department of Qichun People's Hospital, Qichun, Hubei, China
| | - Le Yi
- General Surgery Department of Qichun People's Hospital, Qichun, Hubei, China
| | - Zhiquan Wu
- Department of Oncology, Qichun People's Hospital, Qichun, Hubei, China
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9
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Mafuné F, Bakker JM, Kudoh S. Dissociative adsorption of NO introduces flexibility in gas phase Rh6+ clusters leading to a rich isomeric distribution. Chem Phys Lett 2021. [DOI: 10.1016/j.cplett.2021.138937] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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10
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Hussain S, Chatha SAS, Hussain AI, Hussain R, Yasir Mehboob M, Mansha A, Shahzad N, Ayub K. A Theoretical Framework of Zinc-Decorated Inorganic Mg 12O 12 Nanoclusters for Efficient COCl 2 Adsorption: A Step Forward toward the Development of COCl 2 Sensing Materials. ACS OMEGA 2021; 6:19435-19444. [PMID: 34368531 PMCID: PMC8340102 DOI: 10.1021/acsomega.1c01473] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Accepted: 07/12/2021] [Indexed: 05/09/2023]
Abstract
Gas sensors are widely explored due to their remarkable detection efficiency for pollutants. Phosgene is a toxic gas and its high concentration in the environment causes some serious health problems like swollen throat, a change in voice, late response of nervous systems, and many more. Therefore, the development of sensors for quick monitoring of COCl2 in the environment is the need of the time. In this aspect, we have explored the adsorption behavior of late transition metal-decorated Mg12O12 nanoclusters for COCl2. Density functional theory at the B3LYP/6-31G(d,p) level is used for optimization, frontier molecular orbital analysis, dipole moment, natural bonding orbitals, bond lengths, adsorption energies, and global reactivity descriptor analysis. Decoration of Zn on pure Mg12O12 delivered two geometries named as Y1 and Y2 with adsorption energy values of -388.91 and -403.11 kJ/mol, respectively. Adsorption of COCl2 on pure Mg12O12 also delivered two geometries (X1 and X2) with different orientations of COCl2. The computed adsorption energy values of X1 and X2 are -44.92 and -71.32 kJ/mol. However, adsorption of COCl2 on Zn-decorated Mg12O12 offered two geometries named as Z1 and Z2 with adsorption energy values of -455.22 and -419.04 kJ/mol, respectively. These adsorption energy values suggested that Zn decoration significantly enhances the adsorption capability of COCl2 gas. Further, the narrow band gap and large dipole moment values of COCl2-adsorbed Zn-decorated Mg12O12 nanoclusters suggested that designed systems are efficient candidates for COCl2 adsorption. Global reactivity indices unveil the great natural stability and least reactivity of designed systems. Results of all analyses suggested that Zn-decorated Mg12O12 nanoclusters are efficient aspirants for the development of high-performance COCl2 sensing materials.
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Affiliation(s)
- Shahid Hussain
- Department
of Applied Chemistry, Government College
University, Faisalabad 38000, Pakistan
| | | | - Abdullah Ijaz Hussain
- Department
of Applied Chemistry, Government College
University, Faisalabad 38000, Pakistan
| | - Riaz Hussain
- Department
of Chemistry, University of Okara, Okara 56300, Punjab, Pakistan
| | | | - Asim Mansha
- Department
of Chemistry, Government College University, Faisalabad 38000, Pakistan
| | - Nabeel Shahzad
- Department
of Chemistry, Government College University, Faisalabad 38000, Pakistan
| | - Khurshid Ayub
- Department
of Chemistry, COMSATS University, Abbottabad Campus, Abbottabad 22060, Pakistan
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11
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Hussain S, Chatha SAS, Hussain AI, Hussain R, Yasir Mehboob M, Mansha A, Shahzad N, Ayub K. In Silico Designing of Mg12O12 Nanoclusters with a Late Transition Metal for NO 2 Adsorption: An Efficient Approach toward the Development of NO 2 Sensing Materials. ACS OMEGA 2021; 6:14191-14199. [PMID: 34124442 PMCID: PMC8190788 DOI: 10.1021/acsomega.1c00850] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Accepted: 03/18/2021] [Indexed: 05/09/2023]
Abstract
Gas sensors are widely used for detection of environmental pollution caused by various environmental factors such as road traffic and combustion of fossil fuels. Nitrogen dioxide (NO2) is one of the leading pollutants of the present age, which causes a number of serious health issues including acute bronchitis, cough, and phlegm, particularly in children. Nowadays, researchers are focused on designing new sensor materials for detection and removal of NO2 from the environment. In this line, we have made an attempt to design NO2 sensing materials by using theoretical techniques. Here, we have reported decoration of Mg12O12 nanoclusters with a late transition metal (Cu) by employing density functional theory at the B3LYP/6-31G(d,p) basis set. The decoration of metal on Mg12O12 gives two geometries (M1 and M2) with adsorption energies of -363.81 and -384.09 kJ/mol, respectively. Adsorption of NO2 on pristine Mg12O12 expressed an adsorption energy value of -62.36 kJ/mol. Adsorption of NO2 on Cu-decorated Mg12O12 nanocages delivered two geometries (N1 and N2) with adsorption energies of -442.56 and -447.64 kJ/mol. Metal-decorated Mg12O12 nanoclusters offer better adsorption of NO2 as compared to pristine Mg12O12 . Adsorption of NO2 on Cu-Mg12O12 nanoclusters also causes narrowing of band gap of magnesium oxide nanoclusters. Large dipole moment, high Q NBO with large electrophilic index in NO2-Cu-Mg12O12 nanoclusters suggested that metal-decorated Mg12O12 nanoclusters are efficient candidates for NO2 adsorption. Different geometric parameters and results of global reactivity descriptors show that NO2-Cu-Mg12O12 nanoclusters are quite stable in nature with least reactivity. Thus, conceptualized systems are potential candidates for applications in NO2 sensing materials.
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Affiliation(s)
- Shahid Hussain
- Department
of Applied Chemistry, Government College
University, Faisalabad 38000, Pakistan
| | | | - Abdullah Ijaz Hussain
- Department
of Applied Chemistry, Government College
University, Faisalabad 38000, Pakistan
| | - Riaz Hussain
- Department
of Chemistry, University of Okara, Okara, Punjab 56300, Pakistan
| | | | - Asim Mansha
- Department
of Chemistry, Government College University, Faisalabad 38000, Pakistan
| | - Nabeel Shahzad
- Department
of Chemistry, Government College University, Faisalabad 38000, Pakistan
| | - Khurshid Ayub
- Department
of Chemistry, COMSATS University Islamabad, Abbottabad Campus, Abbottabad 22060, Pakistan
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12
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Morales‐García Á, Viñes F, Gomes JRB, Illas F. Concepts, models, and methods in computational heterogeneous catalysis illustrated through
CO
2
conversion. WIRES COMPUTATIONAL MOLECULAR SCIENCE 2021. [DOI: 10.1002/wcms.1530] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Ángel Morales‐García
- Departament de Ciència de Materials i Química Física & Institut de Química Teòrica i Computacional (IQTCUB) Universitat de Barcelona Barcelona Spain
| | - Francesc Viñes
- Departament de Ciència de Materials i Química Física & Institut de Química Teòrica i Computacional (IQTCUB) Universitat de Barcelona Barcelona Spain
| | - José R. B. Gomes
- CICECO—Aveiro Institute of Materials, Department of Chemistry University of Aveiro Aveiro Portugal
| | - Francesc Illas
- Departament de Ciència de Materials i Química Física & Institut de Química Teòrica i Computacional (IQTCUB) Universitat de Barcelona Barcelona Spain
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13
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Sholokhova AY, Malkin AI, Buryak AK. Mass Spectrometric Study of Teflon Degradation Products after Mechanochemical Activation via Surface-Activated Laser Desorption/Ionization. RUSSIAN JOURNAL OF PHYSICAL CHEMISTRY A 2021. [DOI: 10.1134/s0036024421040245] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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14
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Mirdha RH, Naskar P, Chaudhury P. Structural transformation in $$(\hbox {MgO})_{{{n}}}$$ clusters using a gradient-only strategy and its comparison with a full Hessian-based calculation. INDIAN JOURNAL OF PHYSICS 2021; 95:561-570. [DOI: 10.1007/s12648-020-01724-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Accepted: 11/25/2019] [Indexed: 07/19/2023]
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15
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16
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Kayanuma M, Shinke Y, Miyazawa T, Fujitani T, Choe YK. Theoretical study of the side reactions of the catalytic conversion of ethanol to butadiene on metal oxide catalysts. CATAL COMMUN 2021. [DOI: 10.1016/j.catcom.2020.106239] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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17
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Ghosh K, Sharma R, Chaudhury P. Structure elucidation and construction of isomerisation pathways in small to moderate-sized (6-27) MgO nanoclusters: an adaptive mutation simulated annealing based analysis with quantum chemical calculations. Phys Chem Chem Phys 2020; 22:9616-9629. [PMID: 32324181 DOI: 10.1039/c9cp06947j] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Determination of global minimum structures and elucidation of reaction paths or minimum energy paths between low-lying minima are of great chemical importance. To that end, we have used our own Adaptive Mutation Simulated Annealing method to determine the global minimum and the minimum energy paths for various isomerisation reactions for small to moderate-sized (MgO)n (n = 6-27) clusters, using the Born-Mayer potential with suitable parameter values. The minimum energy structures obtained by us match well with previously reported data and are used as guess structures for further optimisation at the DFT level (using the B3LYP functional and DGDZVP basis set). Our optimised structures are found to match very well with the further DFT optimised structures, where the comparison is done by determining the root mean square deviation values as well as the radial distribution function profiles. A scheme is proposed to determine the minimum energy paths for isomerisation reactions for some cluster sizes where the transition state/s obtained by us, at very low computational cost, match well with those obtained from further optimisation using DFT calculations. We have shown the efficacy of our method in determining the reaction pathways, even for cases that involve multi-step reactions.
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Affiliation(s)
- Kuntal Ghosh
- Department of Chemistry, St. Xavier's College, 30 Mother Teresa Sarani, Kolkata - 700016, India.
| | - Rahul Sharma
- Department of Chemistry, St. Xavier's College, 30 Mother Teresa Sarani, Kolkata - 700016, India.
| | - Pinaki Chaudhury
- Department of Chemistry, University of Calcutta, Kolkata - 700009, India.
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18
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Rezaei-Sameti M, Abdoli S. The capability of the pristine and (Sc, Ti) doped Be12O12 nanocluster to detect and adsorb of Mercaptopyridine molecule: A first principle study. J Mol Struct 2020. [DOI: 10.1016/j.molstruc.2019.127593] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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19
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Ji X, Jameh-Bozorghi S. Metal oxide nanoclusters as drug delivery systems for an anticancer drug: a theoretical study. Mol Phys 2020. [DOI: 10.1080/00268976.2020.1738581] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Affiliation(s)
- Xue Ji
- Department of Health Nursing, Yunnan Open University, Kunming, Yunnan, People’s Republic of China
| | - Saeed Jameh-Bozorghi
- Department of Chemistry, Faculty of Science, Hamedan Branch, Islamic Azad University, Hamedan, Iran
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20
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Nakano M, Hebiguchi D, Azuma S, Moriyama R, Ohshimo K, Misaizu F. Structures of Magnesium Oxide Cluster Cations Studied Using Ion Mobility Mass Spectrometry. J Phys Chem A 2020; 124:101-107. [DOI: 10.1021/acs.jpca.9b08930] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Motoyoshi Nakano
- Department of Chemistry, Graduate School of Science, Tohoku University, 6-3 Aoba, Aramaki, Aoba-ku, Sendai, 980-8578, Japan
| | - Daiki Hebiguchi
- Department of Chemistry, Graduate School of Science, Tohoku University, 6-3 Aoba, Aramaki, Aoba-ku, Sendai, 980-8578, Japan
| | - Shohei Azuma
- Department of Chemistry, Graduate School of Science, Tohoku University, 6-3 Aoba, Aramaki, Aoba-ku, Sendai, 980-8578, Japan
| | - Ryoichi Moriyama
- Department of Chemistry, Graduate School of Science, Tohoku University, 6-3 Aoba, Aramaki, Aoba-ku, Sendai, 980-8578, Japan
| | - Keijiro Ohshimo
- Department of Chemistry, Graduate School of Science, Tohoku University, 6-3 Aoba, Aramaki, Aoba-ku, Sendai, 980-8578, Japan
| | - Fuminori Misaizu
- Department of Chemistry, Graduate School of Science, Tohoku University, 6-3 Aoba, Aramaki, Aoba-ku, Sendai, 980-8578, Japan
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21
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Chen X, Sun Z, Zhang H, Onsori S. Effect of metal atoms on the electronic properties of metal oxide nanoclusters for use in drug delivery applications: a density functional theory study. Mol Phys 2019. [DOI: 10.1080/00268976.2019.1692150] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Affiliation(s)
- Xiaoying Chen
- Department of Emergency Medicine, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Institute of Emergency Medicine, Zhejiang University, Zhejiang, China
| | - Zhangping Sun
- Intensive Care Unit, The Central Hospital of Yingkou, Liaoning, China
| | - Huanran Zhang
- Department of Emergency Medicine, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Saeid Onsori
- Department of Chemistry, Central Tehran Branch, Islamic Azad University, Tehran, Iran
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Escatllar AM, Lazaukas T, Woodley SM, Bromley ST. Structure and Properties of Nanosilicates with Olivine (Mg 2SiO 4) N and Pyroxene (MgSiO 3) N Compositions. ACS EARTH & SPACE CHEMISTRY 2019; 3:2390-2403. [PMID: 32055761 PMCID: PMC7009040 DOI: 10.1021/acsearthspacechem.9b00139] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2019] [Revised: 06/25/2019] [Accepted: 07/18/2019] [Indexed: 05/26/2023]
Abstract
Magnesium-rich silicates are ubiquitous both terrestrially and astronomically, where they are often present as small particles. Nanosized Mg-rich silicate particles are likely to be particularly important for understanding the formation, processing, and properties of cosmic dust grains. Although astronomical observations and laboratory studies have revealed much about such silicate dust, our knowledge of this hugely important class of nanosolids largely rests on top-down comparisons with the properties of bulk silicates. Herein, we provide a foundational bottom-up study of the structure and properties of Mg-rich nanosilicates based on carefully procured atomistic models. Specifically, we employ state-of-the-art global optimization methods to search for the most stable structures of silicate nanoclusters with olivine (Mg2SiO4) N and pyroxene (MgSiO3) N compositions with N = 1-10. To ensure the reliability of our searches, we develop a new interatomic potential that has been especially tuned for nanosilicates. Subsequently, we refine these searches and calculate a range of physicochemical properties of the most stable nanoclusters using accurate density functional theory based electronic structure calculations. We report a detailed analysis of structural and energy properties, charge distributions, and infrared vibrational spectra, where in all cases we compare our finding for nanosilicates with those of the corresponding bulk silicate crystals. For most properties considered, we find large differences with respect to the bulk limit, underlining the limitations of a top-down approach for describing these species. Overall, our work provides a new platform for an accurate and detailed understanding of nanoscale silicates.
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Affiliation(s)
- Antoni Macià Escatllar
- Departament
de Ciència de Materials i Química Física &
Institut de Química Teòrica i Computacional (IQTCUB), Universitat de Barcelona, E-08028 Barcelona, Spain
| | - Tomas Lazaukas
- Department
of Chemistry, University College, London WC1H 0AJ, U.K.
| | - Scott M. Woodley
- Department
of Chemistry, University College, London WC1H 0AJ, U.K.
| | - Stefan T. Bromley
- Departament
de Ciència de Materials i Química Física &
Institut de Química Teòrica i Computacional (IQTCUB), Universitat de Barcelona, E-08028 Barcelona, Spain
- Institució
Catalana de Recerca i Estudis Avançats (ICREA), E-08010 Barcelona, Spain
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23
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Effect of B, Al and Ga atoms on structures, electrical and optical properties of BeO nanotube. ChemistrySelect 2019. [DOI: 10.1002/slct.201900989] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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24
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Naskar P. Structural and spectroscopic aspects of SCN (-)(H 2O) n clusters and the temperature dependency of the isomers: a parallel tempering based approach. Mol Phys 2019. [DOI: 10.1080/00268976.2018.1528395] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Affiliation(s)
- Pulak Naskar
- Department of Chemistry, University of Calcutta, Kolkata, India
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25
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Thermodynamic Modelling on Nanoscale Growth of Magnesia Inclusion in Fe-O-Mg Melt. METALS 2019. [DOI: 10.3390/met9020174] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Nano-magnesia is the intermediate product during the growth of magnesia inclusion in Mg-deoxidized steel. Understanding the thermodynamics on nano-magnesia is important to explore the relationship between magnesia product size and deoxidation reaction in molten steel. In this work, a thermodynamic modeling is developed to study the Mg-deoxidation reaction between nano-magnesia inclusions and liquid iron. The thermodynamic results based on the first principle method show that the Gibbs free energy change for the forming magnesia product decrease gradually with the increasing nano-magnesia size in liquid iron. The published experimental data about Mg-deoxidation equilibria in liquid iron are scattered across the region between the thermodynamic curves of 2 nm magnesia and bulk-magnesia. It is suggested that these scattered experimental data of Mg-deoxidized liquid iron are in different thermodynamic states. Some of these experiments are in equilibrium with bulk-magnesia, while most of these experiments do not reach the equilibrium state between bulk magnesia and liquid iron, but in quasi-equilibria between nano-magnesia and liquid iron. This is the reason that different researchers gave different equilibrium constants. Furthermore, the behavior of the metastable magnesia is one of the most important reasons for the supersaturation ratio or the excess oxygen for MgO formation in liquid iron.
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26
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Mojica-Sánchez JP, Zarate-López TI, Flores-Álvarez JM, Reyes-Gómez J, Pineda-Urbina K, Gómez-Sandoval Z. Magnesium oxide clusters as promising candidates for hydrogen storage. Phys Chem Chem Phys 2019; 21:23102-23110. [DOI: 10.1039/c9cp05075b] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
A magnesium oxide candidate for hydrogen storage is identified through Born–Oppenheimer molecular dynamics.
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Affiliation(s)
- Juan Pablo Mojica-Sánchez
- Instituto Tecnológico José Mario Molina Pasquel y Henríquez Campus Tamazula de Gordiano
- Tamazula de Gordiano
- Mexico
- Facultad de Ciencias Químicas
- Universidad de Colima
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27
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Behzadi E, Sarsharzadeh R, Nouri M, Attar F, Akhtari K, Shahpasand K, Falahati M. Albumin binding and anticancer effect of magnesium oxide nanoparticles. Int J Nanomedicine 2018; 14:257-270. [PMID: 30643405 PMCID: PMC6312066 DOI: 10.2147/ijn.s186428] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
BACKGROUND Recently, nanomaterials have moved into biological and medicinal implementations like cancer therapy. Therefore, before clinical trials, their binding to plasma proteins like human serum albumin (HSA) and their cytotoxic effects against normal and cancer cell lines should be addressed. METHODS Herein, the interaction of magnesium oxide nanoparticles (MgO NPs) with HSA was studied by means of fluorescence spectroscopy, circular dichroism (CD) spectroscopy, and docking studies. Afterwards, the cytotoxic impacts of MgO NPs on human leukemia cell line (K562) and peripheral blood mononucleated cells (PBMCs) were evaluated by MTT and flow cytometry assays to quantify reactive oxygen species (ROS) generation and apoptosis. RESULTS It was demonstrated that MgO NPs spontaneously form a static complex with HSA molecules through hydrophobic interactions. Docking study based on the size of NPs demonstrated that different linkages can be established between MgO NPs and HSA. The CD investigation explored that MgO NPs did not alter the secondary structure of HSA. Cellular studies revealed that MgO NPs induced cytotoxicity against K562 cell lines, whereas no adverse effects were detected on PBMCs up to optimum applied concentration of MgO NPs. It was exhibited that ROS production mediated by IC50 concentrations of MgO NPs caused apoptosis-associated cell death. The pre-incubation of K562 with ROS scavenger (curcumin) inhibited the impact of MgO NPs -based apoptosis on cell fate, revealing the upstream effect of ROS in our system. CONCLUSION In summary, MgO NPs may exhibit strong plasma distribution and mediate apoptosis by ROS induction in the cancer cell lines. These data demonstrate a safe aspect of MgO NPs on the proteins and normal cells and their application as a distinctive therapeutic approach in the cancer treatment.
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Affiliation(s)
- Elham Behzadi
- Department of Cellular and Molecular Biology, Faculty of Advanced Science and Technology, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran
| | - Rozhin Sarsharzadeh
- Department of Cellular and Molecular Biology, Faculty of Advanced Science and Technology, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran
| | - Mina Nouri
- Department of Cellular and Molecular Biology, Faculty of Advanced Science and Technology, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran
| | - Farnoosh Attar
- Department of Biology, Faculty of Food Industry and Agriculture, Standard Research Institute (SRI), Karaj, Iran
| | - Keivan Akhtari
- Department of Physics, University of Kurdistan, Sanandaj, Iran
| | - Koorosh Shahpasand
- Department of Brain and Cognitive Sciences, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran
| | - Mojtaba Falahati
- Department of Nanotechnology, Faculty of Advanced Science and Technology, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran,
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28
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Bakker JM, Jalink J, Dieleman D, Kirilyuk A. Structural determination of neutral Co n clusters (n = 4-10,13) through IR-UV two-color vibrational spectroscopy and DFT calculations. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2018; 30:494003. [PMID: 30451159 DOI: 10.1088/1361-648x/aaebf3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
We recorded IR spectra for neutral cobalt clusters via two-color IR-UV ionization, using the Free Electron Laser for intracavity experiments (FELICE). Well-resolved IR spectra are presented for [Formula: see text] (n = 4-10, 13) and analyzed with the help of Density Functional Theory calculations using two different correlation exchange functionals: the revisited Tao-Perdew-Staroverov-Scuseria (revTPSS) and the frequently used Perdew-Burke-Ernzerhof (PBE) approaches. Although we have not performed an extensive structure search, we tentatively assign the spectra for all cluster sizes except for n = 7, and n = 10. We find that neither of the two functionals chosen clearly outperforms the other in predicting IR spectra, and that relatively low scaling factors of 0.82 (PBE) and 0.8 (revTPSS) are required. In contrast to the magnetic moments, the calculated electric dipole moments fluctuate strongly as a function of cluster size and could therefore be used as an indirect probe to the cluster structure.
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Affiliation(s)
- J M Bakker
- Radboud University, Institute for Molecules and Materials, FELIX Laboratory, Toernooiveld 7c, 6525 ED Nijmegen, Netherlands
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29
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Xiao Y, Lei H, Yang B, Wang G, Wang Q, Jin W. Nucleation and growth for magnesia inclusion in Fe-O-Mg melt. RSC Adv 2018; 8:38336-38345. [PMID: 35559083 PMCID: PMC9089909 DOI: 10.1039/c8ra07728b] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2018] [Accepted: 11/07/2018] [Indexed: 01/01/2023] Open
Abstract
The crystallization process of magnesia in iron melt begins with nucleation, which determines the structure and size of magnesia inclusions. Thus, it is necessary to have a deep insight into the crystallization of magnesia by two-step nucleation mechanisms. In this work, the two-step nucleation method was used to investigate the behavior during the early stages of magnesia inclusions crystallization. A first principles method was applied to calculate the thermodynamic properties of magnesia crystal from various cluster structures for the formation of magnesia inclusions. Based on the numerical results, the nucleation mechanism of magnesia in liquid iron has been discussed. The magnesia clusters appear as the structural units for Mg-deoxidation reaction in the liquid iron, and the residual magnesia clusters are the reason for the supersaturation ratio or the excess oxygen for MgO formation in the liquid iron. Based on the comparison between Mg-deoxidation equilibrium experiments and numerical results, the previous experiments may be in a different thermodynamic state. The equilibrium reaction product should be not only magnesia clusters but also bulk-magnesia in those equilibrium experiments. The crystallization process of magnesia involves two steps.![]()
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Affiliation(s)
- Yuanyou Xiao
- Key Laboratory of Electromagnetic Processing of Materials, Ministry of Education, Northeastern University Shenyang Liaoning Province 110819 P. R. China .,School of Materials and Metallurgy, Northeastern University Shenyang Liaoning Province 110819 P. R. China.,Key Laboratory of Chemical Metallurgy Engineering Liaoning Province, University of Science and Technology Liaoning Anshan Liaoning Province 114051 P. R China
| | - Hong Lei
- Key Laboratory of Electromagnetic Processing of Materials, Ministry of Education, Northeastern University Shenyang Liaoning Province 110819 P. R. China .,School of Materials and Metallurgy, Northeastern University Shenyang Liaoning Province 110819 P. R. China
| | - Bin Yang
- Key Laboratory of Electromagnetic Processing of Materials, Ministry of Education, Northeastern University Shenyang Liaoning Province 110819 P. R. China .,School of Materials and Metallurgy, Northeastern University Shenyang Liaoning Province 110819 P. R. China
| | - Guocheng Wang
- Key Laboratory of Chemical Metallurgy Engineering Liaoning Province, University of Science and Technology Liaoning Anshan Liaoning Province 114051 P. R China
| | - Qi Wang
- Key Laboratory of Chemical Metallurgy Engineering Liaoning Province, University of Science and Technology Liaoning Anshan Liaoning Province 114051 P. R China
| | - Wei Jin
- Key Laboratory of Synthetic and Biological Colloids, Ministry of Education, School of Chemical and Material Engineering, Jiangnan University Wuxi Jiangsu Province 214122 P. R. China
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30
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Masuzaki D, Takehashi Y, Mafuné F. Stability and Effect of Hydration on Calcium Oxide Cluster Ions, CanOm+, in the Gas Phase. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2018. [DOI: 10.1246/bcsj.20180149] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Daigo Masuzaki
- Department of Basic Science, School of Arts and Sciences, The University of Tokyo, Komaba, Meguro, Tokyo 153-8902, Japan
| | - Yuma Takehashi
- Department of Basic Science, School of Arts and Sciences, The University of Tokyo, Komaba, Meguro, Tokyo 153-8902, Japan
| | - Fumitaka Mafuné
- Department of Basic Science, School of Arts and Sciences, The University of Tokyo, Komaba, Meguro, Tokyo 153-8902, Japan
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31
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Rad AS, Ayub K. Nonlinear optical, IR and orbital properties of Ni doped MgO nanoclusters: A DFT investigation. COMPUT THEOR CHEM 2018. [DOI: 10.1016/j.comptc.2018.06.003] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
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32
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DFT and TD-DFT study of the adsorption and detection of sulfur mustard chemical warfare agent by the C 24 , C 12 Si 12 , Al 12 N 12 , Al 12 P 12 , Be 12 O 12 , B 12 N 12 and Mg 12 O 12 nanocages. J Mol Struct 2018. [DOI: 10.1016/j.molstruc.2018.03.051] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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33
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Abstract
Knowing the possible structures of individual clusters in nanostructured materials is an important first step in their design. With previous structure prediction data for BaO nanoclusters as a basis, data mining techniques were used to investigate candidate structures for magnesium oxide, calcium oxide and strontium oxide clusters. The lowest-energy structures and analysis of some of their structural properties are presented here. Clusters that are predicted to be ideal targets for synthesis, based on being both the only thermally accessible minimum for their size, and a size that is thermally accessible with respect to neighbouring sizes, include global minima for: sizes
n
=
9
,
15
,
16
,
18
and 24 for (MgO)
n
; sizes
n
=
8
,
9
,
12
,
16
,
18
and 24 for (CaO)
n
; the greatest number of sizes of (SrO)
n
clusters (
n
=
8
,
9
,
10
,
12
,
13
,
15
,
16
,
18
and 24); and for (BaO)
n
sizes of
n
=
8
,
10
and 16.
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34
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Bromley ST, Gómez Martín JC, Plane JMC. Under what conditions does (SiO) N nucleation occur? A bottom-up kinetic modelling evaluation. Phys Chem Chem Phys 2018; 18:26913-26922. [PMID: 27722645 DOI: 10.1039/c6cp03629e] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Silicon monoxide (SiO) is a structurally complex compound exhibiting differentiated oxide-rich and silicon-rich nano-phases at length scales covering nanoclusters to the bulk. Although nano-sized and nano-segregated SiO has great technological potential (e.g. nano-silicon for optical applications) and is of enormous astronomical interest (e.g. formation of silicate cosmic dust) an accurate general description of SiO nucleation is lacking. Avoiding the deficiencies of a bulk-averaged approach typified by classical nucleation theory (CNT) we employ a bottom-up kinetic model which fully takes into account the atomistic details involved in segregation. Specifically, we derive a new low energy benchmark set of segregated (SiO)N cluster ground state candidates for N ≤ 20 and use the accurately calculated properties of these isomers to calculate SiO nucleation rates. We thus provide a state-of-the art evaluation of the range of pressure and temperature conditions for which formation of SiO will or will not proceed. Our results, which match with available experiment, reveal significant deficiencies with CNT approaches. We employ our model to shed light on controversial issue of circumstellar silicate dust formation showing that, at variance with the predictions from CNT-based calculations, pure SiO nucleation under such conditions is not viable.
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Affiliation(s)
- Stefan T Bromley
- Departament de Ciència de Materials i Química Física & Institut de Química Teòrica i Computacional (IQTCUB), Universitat de Barcelona, C/ Martí i Franquès 1, E-08028 Barcelona, Spain. and Institució Catalana de Recerca i Estudis Avançats (ICREA), 08010 Barcelona, Spain
| | | | - John M C Plane
- School of Chemistry, University of Leeds, Leeds, LS2 9JT, UK.
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35
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Mirdha RH, Naskar P, Chaudhury P. Mapping out reaction paths for conformational changes in (M
g
O)
n
clusters: a study based on a stochastic procedure. Struct Chem 2017. [DOI: 10.1007/s11224-017-1049-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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36
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Feitoza L, Castro MA, Leão SA, Fonseca TL. Electronic and vibrational second hyperpolarizabilities of (MgO) n clusters. J Chem Phys 2017; 146:144309. [PMID: 28411612 DOI: 10.1063/1.4979910] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
In this work, we report results for the static second hyperpolarizability of magnesium oxide clusters including electronic and vibrational contributions. The comparison between second-order Møller-Plesset (MP2) perturbation theory and coupled cluster results to the electronic contribution points out that MP2 is a suitable method to compute this property. When computed at the MP2 level, the electronic contribution per atom converges to approximately 5000 a.u. Vibrational corrections were computed at the MP2 level through the perturbation theoretical method of Bishop and Kirtman. Results obtained showed that the term [α2]0,0 represents around 20% of the electronic counterpart while the term [μβ]0,0 is comparable to it. Modes that contribute significantly to [α2]0,0 are those in which all or part of the bond lengths simultaneously increase and decrease, leading to large polarizability derivatives. In turn, modes that provide relevant contributions to [μβ]0,0 are those in which oxygen anions move in opposite directions to the magnesium cations yielding large derivatives of the dipole moment and first hyperpolarizability.
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Affiliation(s)
- Luan Feitoza
- Instituto de Física, Universidade Federal de Goiás, Campus Samambaia, 74690-900 Goiânia, Goias, Brazil
| | - Marcos A Castro
- Instituto de Física, Universidade Federal de Goiás, Campus Samambaia, 74690-900 Goiânia, Goias, Brazil
| | - Salviano A Leão
- Instituto de Física, Universidade Federal de Goiás, Campus Samambaia, 74690-900 Goiânia, Goias, Brazil
| | - Tertius L Fonseca
- Instituto de Física, Universidade Federal de Goiás, Campus Samambaia, 74690-900 Goiânia, Goias, Brazil
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37
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Shayeganfar F, Beheshtiyan J, Neek-Amal M, Shahsavari R. Electro- and opto-mutable properties of MgO nanoclusters adsorbed on mono- and double-layer graphene. NANOSCALE 2017; 9:4205-4218. [PMID: 28290570 DOI: 10.1039/c6nr08586e] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Inspired by recent experiments, the trapping of molecules in 2D materials has gained increasing attention due to the unique ability of the molecules to modulate the electronic and optical properties of 2D materials, which calls for fundamental understanding and predictive design strategies. Herein, we focus on mono- and double-layer graphene encapsulating various MgO clusters and explore their diverse electronic and optical properties using a number of high-level first-principles calculations. By correlating the stability of adsorption, geometry, charge transfer, band structures, optical absorption spectrum, and the van der Waals pressure, our results decode various synergies in electro- and opto-mutable properties of MgO/graphene systems. We found that 2D-MgO flakes on graphene layers exhibit surface polarization effects - in contrast to their isolated neutral flakes - and show a significant charge transfer from graphene to n-doped flakes, breaking the symmetry of graphene layers. We obtained a van der Waals pressure of ∼0.7 (0.9) GPa on bilayer graphene encapsulating MgO nanoclusters, which matches extremely well with experiment. While there is one quantum emission in the visible light region for a single MgO flake, a wide range of visible light is accessible for MgO on mono- and double-layer graphene. Overall, these findings provide new physical insights and design strategies to modulate 2D materials with several applications in optoelectronics while significantly broadening the spectrum of strategies for fabricating new hybrid 2D heterostructures by encapsulating external molecules.
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Affiliation(s)
- Farzaneh Shayeganfar
- Department of Civil and Environmental Engineering, Rice University, Houston, TX 77005, USA. and Institute for Advanced Technologies, Shahid Rajaee Teacher Training University, 16875-163, Lavizan, Tehran, Iran
| | - Javad Beheshtiyan
- Institute for Advanced Technologies, Shahid Rajaee Teacher Training University, 16875-163, Lavizan, Tehran, Iran and Department of Physics, University of Antwerp, Groenenborgerlaan 171, B-2020 Antwerpen, Belgium
| | - Mehdi Neek-Amal
- Institute for Advanced Technologies, Shahid Rajaee Teacher Training University, 16875-163, Lavizan, Tehran, Iran and Department of Physics, University of Antwerp, Groenenborgerlaan 171, B-2020 Antwerpen, Belgium
| | - Rouzbeh Shahsavari
- Department of Civil and Environmental Engineering, Rice University, Houston, TX 77005, USA. and Department of Material Science and NanoEngineering, Rice University, Houston, TX 77005, USA and Smalley Institute for Nanoscale Science and Technology, Rice University, Houston, TX 77005, USA
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38
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Lazauskas T, Sokol AA, Woodley SM. An efficient genetic algorithm for structure prediction at the nanoscale. NANOSCALE 2017; 9:3850-3864. [PMID: 28252128 DOI: 10.1039/c6nr09072a] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
We have developed and implemented a new global optimization technique based on a Lamarckian genetic algorithm with the focus on structure diversity. The key process in the efficient search on a given complex energy landscape proves to be the removal of duplicates that is achieved using a topological analysis of candidate structures. The careful geometrical prescreening of newly formed structures and the introduction of new mutation move classes improve the rate of success further. The power of the developed technique, implemented in the Knowledge Led Master Code, or KLMC, is demonstrated by its ability to locate and explore a challenging double funnel landscape of a Lennard-Jones 38 atom system (LJ38). We apply the redeveloped KLMC to investigate three chemically different systems: ionic semiconductor (ZnO)1-32, metallic Ni13 and covalently bonded C60. All four systems have been systematically explored on the energy landscape defined using interatomic potentials. The new developments allowed us to successfully locate the double funnels of LJ38, find new local and global minima for ZnO clusters, extensively explore the Ni13 and C60 (the buckminsterfullerene, or buckyball) potential energy surfaces.
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Affiliation(s)
- Tomas Lazauskas
- University College London, Kathleen Lonsdale Materials Chemistry, Department of Chemistry, 20 Gordon Street, London WC1H 0AJ, UK.
| | - Alexey A Sokol
- University College London, Kathleen Lonsdale Materials Chemistry, Department of Chemistry, 20 Gordon Street, London WC1H 0AJ, UK.
| | - Scott M Woodley
- University College London, Kathleen Lonsdale Materials Chemistry, Department of Chemistry, 20 Gordon Street, London WC1H 0AJ, UK.
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39
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The influence of Sc doping on structural, electronic and optical properties of Be 12O 12, Mg 12O 12 and Ca 12O 12 nanocages: a DFT study. J Mol Model 2017; 23:82. [PMID: 28213715 DOI: 10.1007/s00894-017-3243-x] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2016] [Accepted: 01/23/2017] [Indexed: 10/20/2022]
Abstract
Density functional theory (DFT) calculations were used to study the effect of scandium doping on the structural, energetic, electronic, linear and nonlinear optical (NLO) properties of Be12O12, Mg12O12 and Ca12O12 nanoclusters. Scandium (Sc) doping on nanoclusters leads to narrowing of their E g, which enhances their conductance greatly. Also, the polarizability (α) and first hyperpolarizability (β0) of nanoclusters were dramatically increased as Be, Mg or Ca atoms are substituted with a Sc atom. Among all clusters, α and β0 values for Sc-doped Ca12O12 were the largest. Consequently, the effect of the doping atom, as well as of cluster size, on electronic and optical properties was explored. Time dependent (TD)-DFT calculations were also carried out to confirm the β0 values; the results show that the higher value of first hyperpolarizability belongs to Sc-doped Ca12O12, which has the smallest transition energy (ΔEgn). The results obtained show that these clusters can be candidates for using in electronic devices and NLO materials in industry.
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40
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Density functional theory study on geometries, stability and electronic structures of CamMgn-mOn (m = 1–2, n = 2–10) clusters. COMPUT THEOR CHEM 2016. [DOI: 10.1016/j.comptc.2016.09.016] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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41
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Mohammadi Hesari A, Shamlouei HR, Raoof Toosi A. Effects of the adsorption of alkali metal oxides on the electronic, optical, and thermodynamic properties of the Mg12O12nanocage: a density functional theory study. J Mol Model 2016; 22:189. [DOI: 10.1007/s00894-016-3044-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2016] [Accepted: 06/20/2016] [Indexed: 12/01/2022]
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42
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Fournier R, Mohareb A. Optimizing molecular properties using a relative index of thermodynamic stability and global optimization techniques. J Chem Phys 2016; 144:024114. [PMID: 26772561 DOI: 10.1063/1.4939530] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We devised a global optimization (GO) strategy for optimizing molecular properties with respect to both geometry and chemical composition. A relative index of thermodynamic stability (RITS) is introduced to allow meaningful energy comparisons between different chemical species. We use the RITS by itself, or in combination with another calculated property, to create an objective function F to be minimized. Including the RITS in the definition of F ensures that the solutions have some degree of thermodynamic stability. We illustrate how the GO strategy works with three test applications, with F calculated in the framework of Kohn-Sham Density Functional Theory (KS-DFT) with the Perdew-Burke-Ernzerhof exchange-correlation. First, we searched the composition and configuration space of CmHnNpOq (m = 0-4, n = 0-10, p = 0-2, q = 0-2, and 2 ≤ m + n + p + q ≤ 12) for stable molecules. The GO discovered familiar molecules like N2, CO2, acetic acid, acetonitrile, ethane, and many others, after a small number (5000) of KS-DFT energy evaluations. Second, we carried out a GO of the geometry of CumSnn (+) (m = 1, 2 and n = 9-12). A single GO run produced the same low-energy structures found in an earlier study where each CumSnn (+) species had been optimized separately. Finally, we searched bimetallic clusters AmBn (3 ≤ m + n ≤ 6, A,B= Li, Na, Al, Cu, Ag, In, Sn, Pb) for species and configurations having a low RITS and large highest occupied Molecular Orbital (MO) to lowest unoccupied MO energy gap (Eg). We found seven bimetallic clusters with Eg > 1.5 eV.
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Affiliation(s)
- René Fournier
- Department of Chemistry, York University, Toronto, Ontario M3J 1P3, Canada
| | - Amir Mohareb
- Department of Chemistry, York University, Toronto, Ontario M3J 1P3, Canada
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43
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Sandhya KS, Pukazhselvan D, Fagg DP, Koga N. Interaction of magnesium hydride clusters with Nb doped MgO additive studied by density functional calculations. RSC Adv 2016. [DOI: 10.1039/c6ra11281a] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
The hydrogen adsorption behaviour of MgO differs significantly to that of Nb doped MgO, draws new promising applications in hydrogen storage and catalysis.
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Affiliation(s)
- K. S. Sandhya
- Department of Complex Systems Science
- Graduate School of Information Science
- Nagoya University
- Japan
- Core Research for Evolutional Science and Technology
| | - D. Pukazhselvan
- Nanoengineering Research Group
- Centre for Mechanical Technology and Automation (TEMA)
- Department of Mechanical Engineering
- 3810-193 Aveiro
- Portugal
| | - Duncan Paul Fagg
- Nanoengineering Research Group
- Centre for Mechanical Technology and Automation (TEMA)
- Department of Mechanical Engineering
- 3810-193 Aveiro
- Portugal
| | - Nobuaki Koga
- Department of Complex Systems Science
- Graduate School of Information Science
- Nagoya University
- Japan
- Core Research for Evolutional Science and Technology
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Oschetzki D, Rauhut G. Pushing the limits in accurate vibrational structure calculations: anharmonic frequencies of lithium fluoride clusters (LiF)n, n = 2-10. Phys Chem Chem Phys 2015; 16:16426-35. [PMID: 24981078 DOI: 10.1039/c4cp02264e] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The vibrational spectra of a series of small lithium fluoride clusters, i.e. (LiF)n, n = 2-10, were studied by vibrational configuration interaction (VCI) calculations relying on potential energy surfaces including three-mode coupling terms and being obtained from explicitly correlated local coupled cluster calculations. Due to the account for anharmonicity effects, the simulated spectra allow for a direct comparison with experimental data and may thus help to identify clusters in the experiments. Even structurally closely related clusters can clearly be distinguished by infrared spectroscopy. The largest system in this study required more than 1000 basis functions in the electronic structure calculations and more than 10(7) configurations in the vibrational structure calculations and became computationally feasible only due to a combination of different approximations and highly parallelized algorithms.
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Affiliation(s)
- Dominik Oschetzki
- Institute of Theoretical Chemistry, University of Stuttgart, Pfaffenwaldring 55, Stuttgart D-70569, Germany.
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Srivastava AK, Misra N. Ab initioinvestigations on planar (MgO)nclusters (n = 1–5) and their hydrogen adsorption behaviour. MOLECULAR SIMULATION 2015. [DOI: 10.1080/08927022.2015.1032278] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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Jalink J, Bakker JM, Rasing T, Kirilyuk A. Channeling Vibrational Energy To Probe the Electronic Density of States in Metal Clusters. J Phys Chem Lett 2015; 6:750-754. [PMID: 26262498 DOI: 10.1021/jz502669s] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
We investigate the electronic density of states (DOS) of isolated neutral cobalt clusters by probing the temperature-modulated population of electronic states through UV photoionization. The temperature is controlled via resonant excitation of lattice vibrations using the free-electron laser FELICE, after which the vibrational and electronic systems equilibrate through the electron-phonon coupling, redistributing the population of electronic states. The data are analyzed by surface photoemission theory, modified to incorporate the realistic DOS.
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Affiliation(s)
- Jeroen Jalink
- †Radboud University, Institute for Molecules and Materials, Heyendaalseweg 135, 6525 AJ Nijmegen, Netherlands
| | - Joost M Bakker
- ‡Radboud University, Institute for Molecules and Materials, FELIX Laboratory, Toernooiveld 7c, 6525 ED Nijmegen, Netherlands
| | - Theo Rasing
- †Radboud University, Institute for Molecules and Materials, Heyendaalseweg 135, 6525 AJ Nijmegen, Netherlands
| | - Andrei Kirilyuk
- †Radboud University, Institute for Molecules and Materials, Heyendaalseweg 135, 6525 AJ Nijmegen, Netherlands
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48
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Abstract
A heterogeneous catalyst is a functional material that continually creates active sites with its reactants under reaction conditions. These sites change the rates of chemical reactions of the reactants localized on them without changing the thermodynamic equilibrium between the materials.
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Affiliation(s)
- Robert Schlögl
- Fritz Haber Institute of the Max Planck Society, Faradayweg 4-6, 14195 Berlin (Germany) http://www.fhi-berlin.mpg.de http://www.cec.mpg.de; Max Planck Institute for Chemical Energy Conversion, Stiftstrasse 34-36, 45470 Mülheim a.d. Ruhr (Germany).
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49
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Truong NX, Savoca M, Harding DJ, Fielicke A, Dopfer O. Vibrational spectra and structures of SinC clusters (n = 3–8). Phys Chem Chem Phys 2015; 17:18961-70. [DOI: 10.1039/c5cp02588e] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
The geometries of C-doped silicon clusters determined from infrared spectroscopy and computational chemistry reveal the stable Si3C unit as a common structural motif.
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Affiliation(s)
- Nguyen Xuan Truong
- Institut für Optik und Atomare Physik
- Technische Universität Berlin
- D-10623 Berlin
- Germany
| | - Marco Savoca
- Institut für Optik und Atomare Physik
- Technische Universität Berlin
- D-10623 Berlin
- Germany
| | - Dan J. Harding
- Institut für Physikalische Chemie
- Georg-August-Universität Göttingen
- D-37077 Göttingen
- Germany
- Department of Dynamics at Surfaces
| | - André Fielicke
- Institut für Optik und Atomare Physik
- Technische Universität Berlin
- D-10623 Berlin
- Germany
| | - Otto Dopfer
- Institut für Optik und Atomare Physik
- Technische Universität Berlin
- D-10623 Berlin
- Germany
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50
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Godino-Ojer M, López-Peinado AJ, Martín-Aranda RM, Przepiórski J, Pérez-Mayoral E, Soriano E. Eco-Friendly Catalytic Systems Based on Carbon-Supported Magnesium Oxide Materials for the Friedländer Condensation. ChemCatChem 2014. [DOI: 10.1002/cctc.201402602] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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