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Article ; Online: Hollow polyhedral structures and properties of Ag2n-1Sn− (n = 2–11) clusters: A theoretical study

Tian, Zhimei / Song, Chongfu / Wang, Chang / Wu, Hai

J Mol Model. 2023 Apr., v. 29, no. 4 p.105-105

2023

Abstract: CONTEXT: The structures of Ag₂ₙ₋₁Sₙ⁻ (n = 2–11) clusters are obtained by the combination of genetic algorithm (GA) and density functional theory (DFT). All the global minimum structures prefer hollow polyhedral structures, in which S–Ag-S element, ... ...

Abstract	CONTEXT: The structures of Ag₂ₙ₋₁Sₙ⁻ (n = 2–11) clusters are obtained by the combination of genetic algorithm (GA) and density functional theory (DFT). All the global minimum structures prefer hollow polyhedral structures, in which S–Ag-S element, triangular Ag₃S₃ and tetragonal Ag₄S₄ units present to stabilize the structures. The S atoms in the structures appear in μ₃-S or μ₄-S form. Adiabatic and vertical electron affinities of the clusters have been obtained, which reveals that they increases as cluster size. Stability analysis shows that Ag₉S₅⁻ and Ag₁₉S₁₀⁻ have special stability. The HOMO, LUMO orbitals of the clusters are obtained and the orbital components of them are calculated. The HOMO orbitals are mainly from the p orbitals of S atoms, whereas the s, p and d orbitals of Ag atoms contribute much bigger than the p orbitals of S atoms for LUMO orbitals. The orbital delocalization indexes (ODI) of the HOMOs and LUMOs are calculated, and the small ODIs of the HOMOs and LUMOs for n = 4–10 reveal that these orbitals are highly delocalized. By studying the projected density of states and molecular orbitals of Ag₉S₅⁻ and Ag₁₉S₁₀⁻ clusters, it is found that their molecular orbitals have superatomic properties. Superatomic properties play an important role in stabilizing clusters. METHODS: This work used combined genetic algorithm and density functional theory (GA-DFT), and PBE0/Lanl2tz(Ag)/6-311G(d,p)(S) method to optimize the structures. Gaussian 16 program, Gauss view 6.0.16 program and Multiwfn 3.8 code are the softwares used.
Keywords	algorithms ; density functional theory ; models
Language	English
Dates of publication	2023-04
Size	p. 105.
Publishing place	Springer Berlin Heidelberg
Document type	Article ; Online
ZDB-ID	1284729-X
ISSN	0948-5023 ; 1610-2940
ISSN (online)	0948-5023
ISSN	1610-2940
DOI	10.1007/s00894-023-05524-5
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: Density Functional Study to Investigate the Ability of (ZnS)

Tian, Zhimei / Song, Chongfu / Wu, Hai

Molecules (Basel, Switzerland)

2023 Volume 28, Issue 3

Abstract: In this study, the density functional theory is used to study the ability of (ZnS) ...

Abstract	In this study, the density functional theory is used to study the ability of (ZnS)
Language	English
Publishing date	2023-01-26
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	1413402-0
ISSN	1420-3049 ; 1431-5165 ; 1420-3049
ISSN (online)	1420-3049
ISSN	1431-5165 ; 1420-3049
DOI	10.3390/molecules28031214
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Article ; Online: Hollow polyhedral structures and properties of Ag

Tian, Zhimei / Song, Chongfu / Wang, Chang / Wu, Hai

Journal of molecular modeling

2023 Volume 29, Issue 4, Page(s) 105

Abstract: Context: The structures of Ag: Methods: This work used combined genetic algorithm and density functional theory (GA-DFT), and PBE0/Lanl2tz(Ag)/6-311G(d,p)(S) method to optimize the structures. Gaussian 16 program, Gauss view 6.0.16 program and ... ...

Abstract	Context: The structures of Ag Methods: This work used combined genetic algorithm and density functional theory (GA-DFT), and PBE0/Lanl2tz(Ag)/6-311G(d,p)(S) method to optimize the structures. Gaussian 16 program, Gauss view 6.0.16 program and Multiwfn 3.8 code are the softwares used.
Language	English
Publishing date	2023-03-22
Publishing country	Germany
Document type	Journal Article
ZDB-ID	1284729-X
ISSN	0948-5023 ; 1610-2940
ISSN (online)	0948-5023
ISSN	1610-2940
DOI	10.1007/s00894-023-05524-5
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Article ; Online: Systematic study on the structures and properties of (Ag

Song, Chongfu / Tian, Zhimei

Journal of molecular modeling

2019 Volume 25, Issue 10, Page(s) 310

Abstract: Silver sulfide is a famous semiconductor, which can be used in many areas. Understanding the size evolution of silver sulfide clusters is useful in controlling their size to improve their properties in applications. The structures of ( ... ...

Abstract	Silver sulfide is a famous semiconductor, which can be used in many areas. Understanding the size evolution of silver sulfide clusters is useful in controlling their size to improve their properties in applications. The structures of (Ag
Language	English
Publishing date	2019-09-10
Publishing country	Germany
Document type	Journal Article
ZDB-ID	1284729-X
ISSN	0948-5023 ; 1610-2940
ISSN (online)	0948-5023
ISSN	1610-2940
DOI	10.1007/s00894-019-4191-4
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Article: Characterization of the interaction between superoxide dismutase and 2-oxoisovalerate dehydrogenase

Song, Chongfu / Hebin Li / Liangquan Sheng / Xiaobo Zhang

Gene. 2015 Aug. 15, v. 568

2015

Abstract: Thermophiles are attractive microorganisms to study the adaptation of life in high temperature environment. It is revealed that superoxide dismutase (SOD) is essential for thermoadaptation of thermophiles. However, the SOD-mediated pathway of ... ...

Abstract	Thermophiles are attractive microorganisms to study the adaptation of life in high temperature environment. It is revealed that superoxide dismutase (SOD) is essential for thermoadaptation of thermophiles. However, the SOD-mediated pathway of thermoadaptation remains unclear. To address this issue, the proteins interacted with SOD were characterized in Thermus thermophilus in this study. Based on co-immunoprecipitation and Western blot analyses, the results showed that 2-oxoisovalerate dehydrogenase Î± subunit was bound to SOD. The isothermal titration calorimetry analysis showed the existence of the interaction between SOD and 2-oxoisovalerate dehydrogenase Î± subunit. The bacterial two-hybrid data indicated that SOD was directly interacted with 2-oxoisovalerate dehydrogenase Î± subunit. Gene site-directed mutagenesis analysis revealed that the intracellular interaction between SOD and 2-oxoisovalerate dehydrogenase Î± subunit was dependent on their whole molecules. Therefore our study presented a novel aspect of SOD in the thermoadaptation of thermophiles by interaction with dehydrogenase, a key enzyme of tricarboxylic acid cycle.
Keywords	ambient temperature ; calorimetry ; genes ; precipitin tests ; proteins ; site-directed mutagenesis ; superoxide dismutase ; thermophilic microorganisms ; Thermus thermophilus ; titration ; tricarboxylic acid cycle ; Western blotting
Language	English
Dates of publication	2015-0815
Size	p. 1-7.
Publishing place	Elsevier B.V.
Document type	Article
ZDB-ID	391792-7
ISSN	1879-0038 ; 0378-1119
ISSN (online)	1879-0038
ISSN	0378-1119
DOI	10.1016/j.gene.2015.05.008
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: Characterization of the interaction between superoxide dismutase and 2-oxoisovalerate dehydrogenase.

Song, Chongfu / Li, Hebin / Sheng, Liangquan / Zhang, Xiaobo

Gene

2015 Volume 568, Issue 1, Page(s) 1–7

Abstract	Thermophiles are attractive microorganisms to study the adaptation of life in high temperature environment. It is revealed that superoxide dismutase (SOD) is essential for thermoadaptation of thermophiles. However, the SOD-mediated pathway of thermoadaptation remains unclear. To address this issue, the proteins interacted with SOD were characterized in Thermus thermophilus in this study. Based on co-immunoprecipitation and Western blot analyses, the results showed that 2-oxoisovalerate dehydrogenase α subunit was bound to SOD. The isothermal titration calorimetry analysis showed the existence of the interaction between SOD and 2-oxoisovalerate dehydrogenase α subunit. The bacterial two-hybrid data indicated that SOD was directly interacted with 2-oxoisovalerate dehydrogenase α subunit. Gene site-directed mutagenesis analysis revealed that the intracellular interaction between SOD and 2-oxoisovalerate dehydrogenase α subunit was dependent on their whole molecules. Therefore our study presented a novel aspect of SOD in the thermoadaptation of thermophiles by interaction with dehydrogenase, a key enzyme of tricarboxylic acid cycle.
MeSH term(s)	2-Oxoisovalerate Dehydrogenase (Acylating)/chemistry ; 2-Oxoisovalerate Dehydrogenase (Acylating)/metabolism ; Adaptation, Physiological ; Amino Acid Sequence ; Bacterial Proteins/chemistry ; Bacterial Proteins/metabolism ; Molecular Sequence Data ; Protein Binding ; Protein Interaction Domains and Motifs ; Protein Interaction Mapping ; Superoxide Dismutase/chemistry ; Superoxide Dismutase/metabolism ; Thermodynamics ; Thermus thermophilus/enzymology
Chemical Substances	Bacterial Proteins ; Superoxide Dismutase (EC 1.15.1.1) ; 2-Oxoisovalerate Dehydrogenase (Acylating) (EC 1.2.1.25)
Language	English
Publishing date	2015-08-15
Publishing country	Netherlands
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	391792-7
ISSN	1879-0038 ; 0378-1119
ISSN (online)	1879-0038
ISSN	0378-1119
DOI	10.1016/j.gene.2015.05.008
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article: Immobilization and Characterization of a Thermostable Lipase

Song, Chongfu / Sheng, Liangquan / Zhang, Xiaobo

Marine biotechnology. 2013 Dec., v. 15, no. 6

2013

Abstract: Lipases have found a number of commercial applications. However, thermostable lipase immobilized on nanoparticle is not extensively characterized. In this study, a recombinant thermostable lipase (designated as TtL) from Thermus thermophilus WL was ... ...

Abstract	Lipases have found a number of commercial applications. However, thermostable lipase immobilized on nanoparticle is not extensively characterized. In this study, a recombinant thermostable lipase (designated as TtL) from Thermus thermophilus WL was expressed in Escherichia coli and immobilized onto 3-APTES-modified Fe₃O₄@SiO₂ supermagnetic nanoparticles. Based on analyses with tricine–sodium dodecyl sulfate–polyacrylamide gel electrophoresis, X-ray diffraction, transmission electron microscopy, and vibrating sample magnetometer observation, the diameter of immobilized lipase nanoparticle was 18.4 (±2.4) nm, and its saturation magnetization value was 52.3� emu/g. The immobilized lipase could be separated from the reaction medium rapidly and easily in a magnetic field. The biochemical characterizations revealed that, comparing with the free one, the immobilized lipase exhibited better resistance to temperature, pH, metal ions, enzyme inhibitors, and detergents. The K ₘ value for the immobilized TtL (2.56� mg/mL) was found to be lower than that of the free one (3.74� mg/mL), showing that the immobilization improved the affinity of lipase for its substrate. In addition, the immobilized TtL exhibited good reusability. It retained more than 79.5� % of its initial activity after reusing for 10� cycles. Therefore, our study presented that the possibility of the efficient reuse of the thermostable lipase immobilized on supermagnetic nanoparticles made it attractive from the viewpoint of practical application.
Keywords	Escherichia coli ; Thermus thermophilus ; X-ray diffraction ; enzyme inhibitors ; gel electrophoresis ; magnetic fields ; metal ions ; nanoparticles ; thermal stability ; transmission electron microscopy ; triacylglycerol lipase
Language	English
Dates of publication	2013-12
Size	p. 659-667.
Publishing place	Springer-Verlag
Document type	Article
ZDB-ID	1479877-3
ISSN	1436-2236 ; 1436-2228
ISSN (online)	1436-2236
ISSN	1436-2228
DOI	10.1007/s10126-013-9515-2
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Article ; Online: Immobilization and characterization of a thermostable lipase.

Song, Chongfu / Sheng, Liangquan / Zhang, Xiaobo

Marine biotechnology (New York, N.Y.)

2013 Volume 15, Issue 6, Page(s) 659–667

Abstract	Lipases have found a number of commercial applications. However, thermostable lipase immobilized on nanoparticle is not extensively characterized. In this study, a recombinant thermostable lipase (designated as TtL) from Thermus thermophilus WL was expressed in Escherichia coli and immobilized onto 3-APTES-modified Fe3O4@SiO2 supermagnetic nanoparticles. Based on analyses with tricine-sodium dodecyl sulfate-polyacrylamide gel electrophoresis, X-ray diffraction, transmission electron microscopy, and vibrating sample magnetometer observation, the diameter of immobilized lipase nanoparticle was 18.4 (± 2.4) nm, and its saturation magnetization value was 52.3 emu/g. The immobilized lipase could be separated from the reaction medium rapidly and easily in a magnetic field. The biochemical characterizations revealed that, comparing with the free one, the immobilized lipase exhibited better resistance to temperature, pH, metal ions, enzyme inhibitors, and detergents. The K m value for the immobilized TtL (2.56 mg/mL) was found to be lower than that of the free one (3.74 mg/mL), showing that the immobilization improved the affinity of lipase for its substrate. In addition, the immobilized TtL exhibited good reusability. It retained more than 79.5 % of its initial activity after reusing for 10 cycles. Therefore, our study presented that the possibility of the efficient reuse of the thermostable lipase immobilized on supermagnetic nanoparticles made it attractive from the viewpoint of practical application.
MeSH term(s)	Bacterial Proteins ; DNA Primers/genetics ; Electrophoresis, Polyacrylamide Gel ; Enzymes, Immobilized/chemistry ; Enzymes, Immobilized/isolation & purification ; Escherichia coli ; Lipase/chemistry ; Lipase/isolation & purification ; Lipase/metabolism ; Magnetometry ; Microscopy, Electron, Transmission ; Models, Molecular ; Nanoparticles/metabolism ; Particle Size ; Thermus thermophilus/enzymology ; X-Ray Diffraction
Chemical Substances	Bacterial Proteins ; DNA Primers ; Enzymes, Immobilized ; Lipase (EC 3.1.1.3) ; thermostable lipase (EC 3.1.1.3)
Language	English
Publishing date	2013-06-08
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	1479877-3
ISSN	1436-2236 ; 1436-2228
ISSN (online)	1436-2236
ISSN	1436-2228
DOI	10.1007/s10126-013-9515-2
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Article: Preparation and characterization of a thermostable enzyme (Mn-SOD) immobilized on supermagnetic nanoparticles

Song, Chongfu / Sheng, Liangquan / Zhang, Xiaobo

Applied microbiology and biotechnology.. 2012 Oct., v. 96, no. 1

2012

Abstract: Superoxide dismutase (SOD) has been widely applied in medical treatments, cosmetic, food, agriculture, and chemical industries. In industry, the immobilization of enzymes can offer better stability, feasible continuous operations, easy separation and ... ...

Abstract	Superoxide dismutase (SOD) has been widely applied in medical treatments, cosmetic, food, agriculture, and chemical industries. In industry, the immobilization of enzymes can offer better stability, feasible continuous operations, easy separation and reusing, and significant decrease of the operation costs. However, little attention has focused on the immobilization of the SOD, as well as the immobilization of thermostable enzymes. In this study, the recombinant thermostable manganese superoxide dismutase (Mn-SOD) of Thermus thermophilus wl was purified and covalently immobilized onto supermagnetic 3-APTES-modified Fe3O4@SiO2 nanoparticles using glutaraldehyde method to prepare the Mn-SOD bound magnetic nanoparticles. The Mn-SOD nanoparticles were characterized by sodium dodecyl sulfate-polyacrylamide gel electrophoresis, X-ray diffraction, transmission electron microscopy, and vibrating sample magnetometer analysis. The results indicated that the diameter of Mn-SOD nanoparticles was 40 (± 5) nm, and its saturation magnetization value was 27.9 emu/g without remanence or coercivity. By comparison with the free Mn-SOD, it was found that the immobilized Mn-SOD on nanoparticles exhibited better resistance to temperature, pH, metal ions, enzyme inhibitors, and detergents. The results showed that the immobilized Mn-SOD on nanoparticles could be reused ten times without significant decrease of enzymatic activity. Therefore, our study presented a novel strategy for the immobilization of thermostable Mn-SOD and for the application of thermostable enzymes.
Keywords	Thermus thermophilus ; X-ray diffraction ; chemical industry ; enzyme activity ; enzyme inhibitors ; gel electrophoresis ; immobilized enzymes ; manganese ; medical treatment ; metal ions ; nanoparticles ; operating costs ; sodium ; superoxide dismutase ; temperature ; thermal stability ; transmission electron microscopy
Language	English
Dates of publication	2012-10
Size	p. 123-132.
Publishing place	Springer-Verlag
Document type	Article
ZDB-ID	392453-1
ISSN	1432-0614 ; 0171-1741 ; 0175-7598
ISSN (online)	1432-0614
ISSN	0171-1741 ; 0175-7598
DOI	10.1007/s00253-011-3835-9
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: Preparation and characterization of a thermostable enzyme (Mn-SOD) immobilized on supermagnetic nanoparticles.

Song, Chongfu / Sheng, Liangquan / Zhang, Xiaobo

Applied microbiology and biotechnology

2012 Volume 96, Issue 1, Page(s) 123–132

Abstract	Superoxide dismutase (SOD) has been widely applied in medical treatments, cosmetic, food, agriculture, and chemical industries. In industry, the immobilization of enzymes can offer better stability, feasible continuous operations, easy separation and reusing, and significant decrease of the operation costs. However, little attention has focused on the immobilization of the SOD, as well as the immobilization of thermostable enzymes. In this study, the recombinant thermostable manganese superoxide dismutase (Mn-SOD) of Thermus thermophilus wl was purified and covalently immobilized onto supermagnetic 3-APTES-modified Fe(3)O(4)@SiO(2) nanoparticles using glutaraldehyde method to prepare the Mn-SOD bound magnetic nanoparticles. The Mn-SOD nanoparticles were characterized by sodium dodecyl sulfate-polyacrylamide gel electrophoresis, X-ray diffraction, transmission electron microscopy, and vibrating sample magnetometer analysis. The results indicated that the diameter of Mn-SOD nanoparticles was 40 (± 5) nm, and its saturation magnetization value was 27.9 emu/g without remanence or coercivity. By comparison with the free Mn-SOD, it was found that the immobilized Mn-SOD on nanoparticles exhibited better resistance to temperature, pH, metal ions, enzyme inhibitors, and detergents. The results showed that the immobilized Mn-SOD on nanoparticles could be reused ten times without significant decrease of enzymatic activity. Therefore, our study presented a novel strategy for the immobilization of thermostable Mn-SOD and for the application of thermostable enzymes.
MeSH term(s)	Electrophoresis, Polyacrylamide Gel ; Enzyme Stability ; Enzymes, Immobilized/chemistry ; Enzymes, Immobilized/metabolism ; Hydrogen-Ion Concentration ; Magnetics ; Microscopy, Electron, Transmission ; Nanoparticles ; Superoxide Dismutase/chemistry ; Superoxide Dismutase/isolation & purification ; Superoxide Dismutase/metabolism ; Temperature ; Thermus thermophilus/enzymology ; X-Ray Diffraction
Chemical Substances	Enzymes, Immobilized ; Superoxide Dismutase (EC 1.15.1.1)
Language	English
Publishing date	2012-10
Publishing country	Germany
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	392453-1
ISSN	1432-0614 ; 0171-1741 ; 0175-7598
ISSN (online)	1432-0614
ISSN	0171-1741 ; 0175-7598
DOI	10.1007/s00253-011-3835-9
Database	MEDical Literature Analysis and Retrieval System OnLINE

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