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Article ; Online: Na

Wang, Likuo / Song, Zhenyou / Lou, Xiaobing / Chen, Yuwei / Wang, Tengrui / Wang, Zhongqiang / Chen, Huaican / Yin, Wen / Avdeev, Maxim / Kan, Wang Hay / Hu, Bingwen / Luo, Wei

Small (Weinheim an der Bergstrasse, Germany)

2024 , Page(s) e2400195

Abstract: ... counterparts are less studied. Herein, a new sodium-ion conductor with a chemical formula of Na ...

Abstract	All-solid-state batteries employing solid electrolytes (SEs) have received widespread attention due to their high safety. Recently, lithium halides are intensively investigated as promising SEs while their sodium counterparts are less studied. Herein, a new sodium-ion conductor with a chemical formula of Na
Language	English
Publishing date	2024-02-02
Publishing country	Germany
Document type	Journal Article
ZDB-ID	2168935-0
ISSN	1613-6829 ; 1613-6810
ISSN (online)	1613-6829
ISSN	1613-6810
DOI	10.1002/smll.202400195
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Article ; Online: Na

Song, Huimin / Jiang, Dequan / Wang, Naizheng / Xing, Wenhao / Guo, Ruixin / Lin, Zheshuai / Yao, Jiyong / Wang, Yonggang / Tu, Heng / Zhang, Guochun

Inorganic chemistry

2021 Volume 60, Issue 5, Page(s) 2893–2898

Abstract: An alkali-metal bismuth iodate, Na ...

Abstract	An alkali-metal bismuth iodate, Na
Language	English
Publishing date	2021-02-11
Publishing country	United States
Document type	Journal Article
ZDB-ID	1484438-2
ISSN	1520-510X ; 0020-1669
ISSN (online)	1520-510X
ISSN	0020-1669
DOI	10.1021/acs.inorgchem.0c03697
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Article ; Online: Na

Liu, Yang / Zhen, Wenyao / Wang, Yinghui / Song, Shuyan / Zhang, Hongjie

Journal of the American Chemical Society

2020 Volume 142, Issue 52, Page(s) 21751–21757

Abstract: Although more attention has been attracted to the therapy based on reactive oxygen species (ROS) for tumor therapy in recent years, such as photodynamic therapy and chemodynamic therapy, the limited ROS production rate leads to their poor treatment ... ...

Abstract	Although more attention has been attracted to the therapy based on reactive oxygen species (ROS) for tumor therapy in recent years, such as photodynamic therapy and chemodynamic therapy, the limited ROS production rate leads to their poor treatment effect owing to the relatively low content of O
MeSH term(s)	Cell Line, Tumor ; Endocytosis/drug effects ; Humans ; Hydrogen-Ion Concentration ; Immunotherapy/methods ; Nanoparticles/chemistry ; Osmolar Concentration ; Phospholipids/chemistry ; Reactive Oxygen Species/metabolism ; Sodium Compounds/chemistry ; Sodium Compounds/pharmacology ; Sulfates/chemistry ; Sulfates/pharmacology ; Tumor Microenvironment/drug effects ; Tumor Microenvironment/immunology
Chemical Substances	Phospholipids ; Reactive Oxygen Species ; Sodium Compounds ; Sulfates ; sodium persulfate (J49FYF16JE)
Language	English
Publishing date	2020-12-18
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	3155-0
ISSN	1520-5126 ; 0002-7863
ISSN (online)	1520-5126
ISSN	0002-7863
DOI	10.1021/jacs.0c09482
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Article ; Online: Na

Zhu, Mengyuan / Cao, Lei / Xiong, Siping / Sun, Haijian / Wu, Zhiyuan / Bian, Jin-Song

Signal transduction and targeted therapy

2020 Volume 5, Issue 1, Page(s) 55

MeSH term(s)	Animals ; Autophagy ; Brain/enzymology ; Brain/pathology ; Brain Ischemia/enzymology ; Brain Ischemia/genetics ; Brain Ischemia/pathology ; Brain Ischemia/prevention & control ; Mice ; Mice, Knockout ; Sodium-Potassium-Exchanging ATPase/genetics ; Sodium-Potassium-Exchanging ATPase/metabolism
Chemical Substances	Sodium-Potassium-Exchanging ATPase (EC 7.2.2.13)
Language	English
Publishing date	2020-05-20
Publishing country	England
Document type	Letter ; Research Support, Non-U.S. Gov't
ZDB-ID	2886872-9
ISSN	2059-3635 ; 2095-9907
ISSN (online)	2059-3635
ISSN	2095-9907
DOI	10.1038/s41392-020-0153-7
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Article ; Online: Na

Jiang, Ming / Kuang, Su-Fang / Lai, Shi-Shi / Zhang, Song / Yang, Jun / Peng, Bo / Peng, Xuan-Xian / Chen, Zhuang-Gui / Li, Hui

mBio

2020 Volume 11, Issue 6

Abstract: Sodium-translocating NADH:quinone oxidoreductase ( ... ...

Abstract	Sodium-translocating NADH:quinone oxidoreductase (Na
MeSH term(s)	Alanine/metabolism ; Aminoglycosides/pharmacology ; Anti-Bacterial Agents/analysis ; Anti-Bacterial Agents/pharmacology ; Aspartic Acid/metabolism ; Bacterial Proteins/genetics ; Bacterial Proteins/metabolism ; Biological Transport ; Drug Resistance, Bacterial ; Gentamicins/analysis ; Gentamicins/pharmacology ; Glutamic Acid/metabolism ; Membrane Potentials/drug effects ; Metabolome ; Metabolomics ; Oxidation-Reduction ; Sequence Deletion ; Sodium-Potassium-Exchanging ATPase/genetics ; Sodium-Potassium-Exchanging ATPase/metabolism ; Vibrio alginolyticus/drug effects ; Vibrio alginolyticus/genetics ; Vibrio alginolyticus/growth & development
Chemical Substances	Aminoglycosides ; Anti-Bacterial Agents ; Bacterial Proteins ; Gentamicins ; Aspartic Acid (30KYC7MIAI) ; Glutamic Acid (3KX376GY7L) ; Sodium-Potassium-Exchanging ATPase (EC 7.2.2.13) ; Alanine (OF5P57N2ZX)
Language	English
Publishing date	2020-11-17
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2557172-2
ISSN	2150-7511 ; 2161-2129
ISSN (online)	2150-7511
ISSN	2161-2129
DOI	10.1128/mBio.02086-20
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Article ; Online: Na

Suo, Jinwei / Zhang, Heng / Zhao, Qi / Zhang, Nan / Zhang, Yongxue / Li, Ying / Song, Baohua / Yu, Juanjuan / Cao, Jianguo / Wang, Tai / Luo, Ji / Guo, Lihai / Ma, Jun / Zhang, Xumin / She, Yimin / Peng, Lianwei / Ma, Weimin / Guo, Siyi / Miao, Yuchen /

Chen, Sixue / Qin, Zhi / Dai, Shaojun

Genomics, proteomics & bioinformatics

2020 Volume 18, Issue 3, Page(s) 271–288

Abstract: ... Puccinellia tenuiflora) under Na ...

Abstract	Alkali-salinity exerts severe osmotic, ionic, and high-pH stresses to plants. To understand the alkali-salinity responsive mechanisms underlying photosynthetic modulation and reactive oxygen species (ROS) homeostasis, physiological and diverse quantitative proteomics analyses of alkaligrass (Puccinellia tenuiflora) under Na
MeSH term(s)	Carbamates/pharmacology ; Chloroplasts/drug effects ; Chloroplasts/metabolism ; Phosphoproteins/analysis ; Phosphoproteins/metabolism ; Photosynthesis ; Plant Leaves/drug effects ; Plant Leaves/metabolism ; Plant Proteins/metabolism ; Poaceae/drug effects ; Poaceae/metabolism ; Proteome/analysis ; Proteome/metabolism ; Reactive Oxygen Species/metabolism ; Salinity
Chemical Substances	Carbamates ; Phosphoproteins ; Plant Proteins ; Proteome ; Reactive Oxygen Species ; carbamic acid (O0UC6XOS4H)
Language	English
Publishing date	2020-07-16
Publishing country	China
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2240213-5
ISSN	2210-3244 ; 1672-0229
ISSN (online)	2210-3244
ISSN	1672-0229
DOI	10.1016/j.gpb.2018.10.011
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ab Jg. 2022: Lesesaal (EG)

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Article ; Online: Na

Bao, Song-Song / Wang, Di / Huang, Xin-Da / Etter, Martin / Cai, Zhong-Sheng / Wan, Xiangang / Dinnebier, Robert E / Zheng, Li-Min

Inorganic chemistry

2018 Volume 57, Issue 21, Page(s) 13252–13258

Abstract: Iridium(IV) oxides have gained increased attention in recent years owing to the presence of competing spin-orbit coupling and Coulomb interactions, which facilitate the emergence of novel quantum phenomena. In contrast, the electronic structure and ... ...

Abstract	Iridium(IV) oxides have gained increased attention in recent years owing to the presence of competing spin-orbit coupling and Coulomb interactions, which facilitate the emergence of novel quantum phenomena. In contrast, the electronic structure and magnetic properties of Ir
Language	English
Publishing date	2018-10-19
Publishing country	United States
Document type	Journal Article
ZDB-ID	1484438-2
ISSN	1520-510X ; 0020-1669
ISSN (online)	1520-510X
ISSN	0020-1669
DOI	10.1021/acs.inorgchem.8b01753
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Article ; Online: Na

Tang, Changcheng / Jiang, XingXing / Yin, Wenlong / Liu, Lijuan / Xia, Mingjun / Huang, Qian / Song, Gaomin / Wang, Xiaoyang / Lin, Zheshuai / Chen, Chuangtian

Dalton transactions (Cambridge, England : 2003)

2018 Volume 48, Issue 1, Page(s) 21–24

Abstract: A new sodium-rich fluorooxoborate Na3B7O11F2 features a novel large [B14O24F4] ring formed by two corner-shared [B7O13F2] groups, each containing two [B3O7] anionic units linked by a [BO2F2] group. The band gap of the title compound calculated by using ... ...

Abstract	A new sodium-rich fluorooxoborate Na3B7O11F2 features a novel large [B14O24F4] ring formed by two corner-shared [B7O13F2] groups, each containing two [B3O7] anionic units linked by a [BO2F2] group. The band gap of the title compound calculated by using first-principles calculations is 7.69 eV (∼161 nm) and the birefringence refractive index is 0.083 at 193 nm. The results show that it is potentially an excellent deep-ultraviolet (DUV) birefringence crystal.
Language	English
Publishing date	2018-12-10
Publishing country	England
Document type	Journal Article
ZDB-ID	1472887-4
ISSN	1477-9234 ; 1364-5447 ; 0300-9246 ; 1477-9226
ISSN (online)	1477-9234 ; 1364-5447
ISSN	0300-9246 ; 1477-9226
DOI	10.1039/c8dt03348j
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Article ; Online: Towards a free energy-based elastic network model and its application to the SARS-COV2 binding to ACE2.

Na, Hyuntae / Song, Guang

Physical biology

2023 Volume 20, Issue 4

Abstract: Classical normal mode analysis (cNMA) is a standard method for studying the equilibrium vibrations of macromolecules. A major limitation of cNMA is that it requires a cumbersome step of energy minimization that also alters the input structure ... ...

Abstract	Classical normal mode analysis (cNMA) is a standard method for studying the equilibrium vibrations of macromolecules. A major limitation of cNMA is that it requires a cumbersome step of energy minimization that also alters the input structure significantly. Variants of normal mode analysis (NMA) exist that perform NMA directly on PDB structures without energy minimization, while maintaining most of the accuracy of cNMA. Spring-based NMA (sbNMA) is such a model. sbNMA uses an all-atom force field as cNMA does, which includes bonded terms such as bond stretching, bond angle bending, torsional, improper, and non-bonded terms such as van der Waals interactions. Electrostatics was not included in sbNMA because it introduced negative spring constants. In this work, we present a way to incorporate most of the electrostatic contributions in normal mode computations, which marks another significant step toward a free-energy-based elastic network model (ENM) for NMA. The vast majority of ENMs are entropy models. One significance of having a free energy-based model for NMA is that it allows one to study the contributions of both entropy and enthalpy. As an application, we apply this model to study the binding stability between SARS-COV2 and angiotensin converting enzyme 2 (or ACE2). Our results show that the stability at the binding interface is contributed nearly equally by hydrophobic interactions and hydrogen bonds.
MeSH term(s)	Humans ; Angiotensin-Converting Enzyme 2 ; COVID-19 ; Entropy ; RNA, Viral ; SARS-CoV-2
Chemical Substances	Angiotensin-Converting Enzyme 2 (EC 3.4.17.23) ; RNA, Viral ; ACE2 protein, human (EC 3.4.17.23)
Language	English
Publishing date	2023-05-30
Publishing country	England
Document type	Journal Article
ZDB-ID	2133216-2
ISSN	1478-3975 ; 1478-3967
ISSN (online)	1478-3975
ISSN	1478-3967
DOI	10.1088/1478-3975/acd6cd
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Article ; Online: Coarse-Graining Waters: Unveiling The Effective Hydrophilicity/Hydrophobicity of Individual Protein Atoms and The Roles of Waters' Hydrogens.

Na, Hyuntae / Song, Guang

Journal of chemical theory and computation

2023 Volume 19, Issue 20, Page(s) 7307–7323

Abstract: There have been many coarse-graining methods developed that aim to reduce the sizes of simulated systems and their computational costs. In this work, we develop a new coarse-graining method, called coarse-graining-delta (or δ-CG in short), that reduces ... ...

Abstract	There have been many coarse-graining methods developed that aim to reduce the sizes of simulated systems and their computational costs. In this work, we develop a new coarse-graining method, called coarse-graining-delta (or δ-CG in short), that reduces the degrees of freedom of the potential energy surface by coarse-graining relative locations of atoms from their unit centers. Our method extends and generalizes the methods used in the coarse-grained normal mode analysis and enables us to study the roles of the individual removed atoms in a system, which have been difficult to study in molecular dynamics simulations. By applying δ-CG to coarse-grain three-point water molecules into single-point solvent particles, we successfully identify the effective hydrophilicity and hydrophobicity of all the individual protein atom types, which collectively correlate well with the known hydrophilic, hydrophobic, and amphipathic characteristics of amino acids. Moreover, our investigation shows that water's hydrogens have two roles in interacting with protein atoms. First, water molecules adjust their poses around different amino acids and their atoms, and the statistical preferences of the hydrogen poses near the atoms determine the effective hydrophilicity and hydrophobicity of the atoms, which have not been successfully addressed before. Second, the collective dynamics of the hydrogens assist the water molecules in escaping from the potential energy wells of the hydrophilic atoms. Our method also shows that coarse-graining a system mathematically leads to breaking antisymmetry of the nonbonded interactions; as a result, two interacting coarse-grained units exert different forces on each other. Our study indicates that the accuracy of coarse-grained force fields, such as the MARTINI force field and the UNRES force field, can be improved in two ways: (i) refining their potential energy functions and coefficients by analyzing the coarse-grained potential energy surface using δ-CG, and (ii) introducing non-antisymmetric interactions.
MeSH term(s)	Proteins/chemistry ; Molecular Dynamics Simulation ; Water/chemistry ; Amino Acids ; Hydrophobic and Hydrophilic Interactions
Chemical Substances	Proteins ; Water (059QF0KO0R) ; Amino Acids
Language	English
Publishing date	2023-10-02
Publishing country	United States
Document type	Journal Article
ISSN	1549-9626
ISSN (online)	1549-9626
DOI	10.1021/acs.jctc.3c00700
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