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Wang ZF, Jia LP, Fang LC, Wang ZH, Liu FJ, Li SX, Huang XG. Thalassiosira weissflogii grown in various Zn levels shows different ecophysiological responses to seawater acidification. Mar Pollut Bull 2022; 185:114327. [PMID: 36356339 DOI: 10.1016/j.marpolbul.2022.114327] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2022] [Revised: 10/25/2022] [Accepted: 10/28/2022] [Indexed: 06/16/2023]
Abstract
The presence of zinc (Zn), a vital element for algal physiological functions, coupled with the silicification of diatoms implies that it plays an integral role in the carbon and silicon cycles of the sea. In this study, we examined the effects of different pCO2 and Zn levels on growth rate, elemental compositions and silicification by Thalassiosira weissflogii. The results showed that under normal pCO2 (400 μatm), cultures of T. weissflogii were depressed for growth rate and silica incorporation rate, but encouraged for cellular silicon content, Si/C, Si/N, and sinking rate when Zn deficient (0.3 pmol L-1). However, cellular silicon and sinking rate of Zn-deficient and Zn-replete (25 pmol L-1) T. weissflogii were decreased and increased at higher pCO2 (800 μatm), respectively. Thus, acidification may affect diatoms significantly differently depending on the Zn levels of the ocean and then alter the biochemical cycling of carbon and silica.
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Affiliation(s)
- Zhao-Fei Wang
- Fujian Province University Key Laboratory of Pollution Monitoring and Control, Minnan Normal University, Zhangzhou 36300, China
| | - Li-Ping Jia
- Fujian Province University Key Laboratory of Pollution Monitoring and Control, Minnan Normal University, Zhangzhou 36300, China; Fujian Province Key of Modern Analytical Science and Separation Technology, Minnan Normal University, Zhangzhou 363000, China
| | - Ling-Chuan Fang
- Status Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, Institute of Soil and Water Conservation, Northwest A&F University, Yangling 712100, China
| | - Zhen-Hong Wang
- Fujian Province University Key Laboratory of Pollution Monitoring and Control, Minnan Normal University, Zhangzhou 36300, China; Fujian Province Key of Modern Analytical Science and Separation Technology, Minnan Normal University, Zhangzhou 363000, China
| | - Feng-Jiao Liu
- Fujian Province University Key Laboratory of Pollution Monitoring and Control, Minnan Normal University, Zhangzhou 36300, China; Fujian Province Key of Modern Analytical Science and Separation Technology, Minnan Normal University, Zhangzhou 363000, China
| | - Shun-Xing Li
- Fujian Province University Key Laboratory of Pollution Monitoring and Control, Minnan Normal University, Zhangzhou 36300, China; Fujian Province Key of Modern Analytical Science and Separation Technology, Minnan Normal University, Zhangzhou 363000, China
| | - Xu-Guang Huang
- Fujian Province University Key Laboratory of Pollution Monitoring and Control, Minnan Normal University, Zhangzhou 36300, China; Fujian Province Key of Modern Analytical Science and Separation Technology, Minnan Normal University, Zhangzhou 363000, China.
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Bauzá A, Frontera A. Noncovalent Interactions Involving Group 6 in Biological Systems: The Case of Molybdopterin and Tungstopterin Cofactors. Chemistry 2022; 28:e202201660. [PMID: 35670547 PMCID: PMC9545818 DOI: 10.1002/chem.202201660] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Indexed: 12/14/2022]
Abstract
In this study we propose to coin the term Wolfium bond (WfB) to refer to a net attractive force (noncovalent interaction) between any element of group 6 and electron donor atoms (neutral molecules or anions) and to differentiate it from a coordination bond (metal‐ligand interaction). We provide evidence of the existence of this interaction by inspecting the X‐ray crystal structure of proteins containing Molybdopterin and Tungstopterin cofactors from the Protein Data Bank (PDB). The plausible biological role of the interaction as well as its physical nature (antibonding Wf‐Ligand orbital involved) are also analyzed by means of ab initio calculations (RI‐MP2/def2‐TZVP level of theory), Atoms in Molecules (AIM), Natural Bond Orbital (NBO) and Noncovalent Interactions plot (NCIplot) analyses.
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Affiliation(s)
- Antonio Bauzá
- Departament de Química, Universitat de les Illes Balears, Ctra. de Valldemossa km 7.5, 07122, Palma de Mallorca (Baleares), Spain
| | - Antonio Frontera
- Departament de Química, Universitat de les Illes Balears, Ctra. de Valldemossa km 7.5, 07122, Palma de Mallorca (Baleares), Spain
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Jena S, Dutta J, Tulsiyan KD, Sahu AK, Choudhury SS, Biswal HS. Noncovalent interactions in proteins and nucleic acids: beyond hydrogen bonding and π-stacking. Chem Soc Rev 2022; 51:4261-4286. [PMID: 35560317 DOI: 10.1039/d2cs00133k] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Understanding the noncovalent interactions (NCIs) among the residues of proteins and nucleic acids, and between drugs and proteins/nucleic acids, etc., has extraordinary relevance in biomolecular structure and function. It helps in interpreting the dynamics of complex biological systems and enzymatic activity, which is esential for new drug design and efficient drug delivery. NCIs like hydrogen bonding (H-bonding) and π-stacking have been researchers' delight for a long time. Prominent among the recently discovered NCIs are halogen, chalcogen, pnictogen, tetrel, carbo-hydrogen, and spodium bonding, and n → π* interaction. These NCIs have caught the imaginations of various research groups in recent years while explaining several chemical and biological processes. At this stage, a holistic view of these new ideas and findings lying scattered can undoubtedly trigger our minds to explore more. The present review attempts to address NCIs beyond H-bonding and π-stacking, which are mainly n → σ*, n → π* and σ → σ* type interactions. Five of the seven NCIs mentioned earlier are linked to five non-inert end groups of the modern periodic table. Halogen (group-17) bonding is one of the oldest and most explored NCIs, which finds its relevance in biomolecules due to the phase correction and inhibitory properties of halogens. Chalcogen (group 16) bonding serves as a redox-active functional group of different active sites of enzymes and acts as a nucleophile in proteases and phosphates. Pnictogen (group 15), tetrel (group 14), triel (group 13) and spodium (group 12) bonding does exist in biomolecules. The n → π* interactions are linked to backbone carbonyl groups and protein side chains. Thus, they are crucial in determining the conformational stability of the secondary structures in proteins. In addition, a more recently discovered to and fro σ → σ* type interaction, namely carbo-hydrogen bonding, is also present in protein-ligand systems. This review summarizes these grand epiphanies routinely used to elucidate the structure and dynamics of biomolecules, their enzymatic activities, and their application in drug discovery. It also briefs about the future perspectives and challenges posed to the spectroscopists and theoreticians.
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Affiliation(s)
- Subhrakant Jena
- School of Chemical Sciences, National Institute of Science Education and Research (NISER), PO- Bhimpur-Padanpur, Via-Jatni, District- Khurda, PIN - 752050, Bhubaneswar, India.,Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai, 400094, India.
| | - Juhi Dutta
- School of Chemical Sciences, National Institute of Science Education and Research (NISER), PO- Bhimpur-Padanpur, Via-Jatni, District- Khurda, PIN - 752050, Bhubaneswar, India.,Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai, 400094, India.
| | - Kiran Devi Tulsiyan
- School of Chemical Sciences, National Institute of Science Education and Research (NISER), PO- Bhimpur-Padanpur, Via-Jatni, District- Khurda, PIN - 752050, Bhubaneswar, India.,Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai, 400094, India.
| | - Akshay Kumar Sahu
- School of Chemical Sciences, National Institute of Science Education and Research (NISER), PO- Bhimpur-Padanpur, Via-Jatni, District- Khurda, PIN - 752050, Bhubaneswar, India.,Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai, 400094, India.
| | - Shubhranshu Shekhar Choudhury
- School of Chemical Sciences, National Institute of Science Education and Research (NISER), PO- Bhimpur-Padanpur, Via-Jatni, District- Khurda, PIN - 752050, Bhubaneswar, India.,Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai, 400094, India.
| | - Himansu S Biswal
- School of Chemical Sciences, National Institute of Science Education and Research (NISER), PO- Bhimpur-Padanpur, Via-Jatni, District- Khurda, PIN - 752050, Bhubaneswar, India.,Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai, 400094, India.
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Gao M, Zhao Q, Yu H, Fu M, Li Q. Insight into Spodium–π Bonding Characteristics of the MX2···π (M = Zn, Cd and Hg; X = Cl, Br and I) Complexes—A Theoretical Study. Molecules 2022; 27:molecules27092885. [PMID: 35566234 PMCID: PMC9101229 DOI: 10.3390/molecules27092885] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Revised: 04/28/2022] [Accepted: 04/29/2022] [Indexed: 01/25/2023] Open
Abstract
The spodium–π bonding between MX2 (M = Zn, Cd, and Hg; X = Cl, Br, and I) acting as a Lewis acid, and C2H2/C2H4 acting as a Lewis base was studied by ab initio calculations. Two types of structures of cross (T) and parallel (P) forms are obtained. For the T form, the X–M–X axis adopts a cross configuration with the molecular axis of C≡C or C=C, but both of them are parallel in the P form. NCI, AIM, and electron density shifts analyses further, indicating that the spodium–π bonding exists in the binary complexes. Spodium–π bonding exhibits a partially covalent nature characterized with a negative energy density and large interaction energy. With the increase of electronegativity of the substituents on the Lewis acid or its decrease in the Lewis base, the interaction energies increase and vice versa. The spodium–π interaction is dominated by electrostatic interaction in most complexes, whereas dispersion and electrostatic energies are responsible for the stability of the MX2⋯C2F2 complexes. The spodium–π bonding further complements the concept of the spodium bond and provides a wider range of research on the adjustment of the strength of spodium bond.
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Affiliation(s)
- Meng Gao
- College of Chemical and Biological Engineering, Shandong University of Science and Technology, Qingdao 266590, China; (Q.Z.); (H.Y.); (M.F.)
- Correspondence: (M.G.); (Q.L.)
| | - Qibo Zhao
- College of Chemical and Biological Engineering, Shandong University of Science and Technology, Qingdao 266590, China; (Q.Z.); (H.Y.); (M.F.)
| | - Hao Yu
- College of Chemical and Biological Engineering, Shandong University of Science and Technology, Qingdao 266590, China; (Q.Z.); (H.Y.); (M.F.)
| | - Min Fu
- College of Chemical and Biological Engineering, Shandong University of Science and Technology, Qingdao 266590, China; (Q.Z.); (H.Y.); (M.F.)
| | - Qingzhong Li
- The Laboratory of Theoretical and Computational Chemistry, School of Chemistry and Chemical Engineering, Yantai University, Yantai 264005, China
- Correspondence: (M.G.); (Q.L.)
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Abstract
Two new d10-metal dithiophosphate complexes have been synthesized in purely aqueous media and characterized by elemental and spectral analyses. DFT calculations, QTAIM and NCI Plot index methods are preformed to differentiate the coordination and spodium bonds in the complexes.
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Affiliation(s)
- Pretam Kumar
- Post Graduate Department of Chemistry, University of Jammu, Baba Saheb Ambedkar Road, Jammu Tawi-180006, J&K, India
| | - Antonio Frontera
- Departament de Química, Universitat de les Illes Balears, Crta de Valldemossa km 7.5, 07122 Palma de Mallorca (Baleares), Spain
| | - Sushil K. Pandey
- Post Graduate Department of Chemistry, University of Jammu, Baba Saheb Ambedkar Road, Jammu Tawi-180006, J&K, India
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