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Week 3 Tasks - Info for [Ni(cyclam)](ClO4)2

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Chemical Structure for [Ni(cyclam)](ClO4)2

1.1Properties of [Ni(cyclam)](ClO4)2

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  • Molecular Formula: C10H24Cl2N4NiO8
  • Molar Mass: 457.915 g/mol
  • Melting Point: 185-186°C (Nicyclam_p3)
  • Boiling Point: 138-148°C (at 2 Torr) (Nicyclam_p2)
  • Solubility (in Water): 0.1368 g/mLwater (Nicyclam_p2)

1.2Bold Text: [Ni(cyclam)](ClO4)2

Italicized Text: [Ni(cyclam)](ClO4)2

1.3 Internal Link: Nickel

1.4 External Link: [1]

1.5

Water-Splitting Chemistry of Photosystem II[1]

[Ni(cyclam)](ClO4)2
 
Names
IUPAC name
nickel(2+);1,4,8,11-tetrazacyclotetradecane;diperchlorate
Other names
Nickel(cyclam) Diperchlorate
Identifiers
Abbreviations [Ni(cyclam)](ClO4)2
ChemSpider
Properties
C10H24Cl2N4NiO8
Molar mass 457.915 g/mol
Appearance N/A
Odor N/A
Density n/A
Melting point 185–186 °C (365–367 °F; 458–459 K)
Boiling point 138–148 °C (280–298 °F; 411–421 K)
0.1368 g/mLwater (Nicyclam_p2)
Solubility in other solvents N/A
Vapor pressure N/A
Viscosity N/A
Except where otherwise noted, data are given for materials in their standard state (at 25 °C [77 °F], 100 kPa).
 Y verify (what is  Y N ?)

Photosystem II Asembly: From Cyanobacteria to Plants[2]

Light Harvesting in Photosystem II[3]

References

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  1. ^ McEvoy, James P., and Gary W. Brudvig. "Water-Splitting Chemistry of Photosystem II."Chemical Reviews, vol. 106, no. 11, 2006, pp. 4455-4483.
  2. ^ Nickelsen, Jörg; Rengstl, Birgit (2013-04-29). "Photosystem II Assembly: From Cyanobacteria to Plants". Annual Review of Plant Biology. 64 (1): 609–635. doi:10.1146/annurev-arplant-050312-120124. ISSN 1543-5008.
  3. ^ van Amerongen, Herbert, and Roberta Croce. "Light Harvesting in Photosystem II."Photosynthesis Research, vol. 116, no. 2-3, 2013, pp. 251-66. ProQuest, http://search.proquest.com.uproxy.library.dc-uoit.ca/docview/1442928936?accountid=14694, doi:http://dx.doi.org.uproxy.library.dc-uoit.ca/10.1007/s11120-013-9824-3.

1.6 Figure Added

1.7

Chemical Properties
Property Values
IR Stretching Frequency N-H (3280 and 3200 cm-1
pKa 10.76, 10.18, 3.54, 2.67

1.8  

1.9

Topics/Subtopics for Assignment

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  • Iron-Sulfur Clusters - there is little information of the topic of Iron-Sulfur Clusters, I aim to find more information and add/expand on the article
    • Find specific enzymes/proteins that contain Iron-Sulfur clusters
    • Add internal Wikilinks to other wiki articles for related topics
    • Explore possible biochemical processes
    • Find/Create new figures that show different structure or interactions with other compounds/systems

Article providing info on structure, function, formation of Fe-S Clusters

Article Title: Structure, Function, and Formation of Biological Iron-Sulfur Clusters

Subtopic: Occurrences of Iron-Sulfur Clusters In Biology

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Notes (Not To Be Marked):

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  • Have ability to delocalize electron density over Fe and S atoms, ideal for electron transport[1]
  • Major components in photosynthetic, respiratory electron transport chains, e- transport pathways of membrane bound enzymes, and redox-active centers in ferredoxins[1]
  • Found in Rubredoxin (electron transfer protein) (textbook)[2]
  • Found in the cytochrome bc1 complex III of electron transfer chain of animals
  • Found in Cytochrome b6f complex of photosynthetic electron transfer chains in plants, cyanobacteria, and green algae
  • Redox inactive 4Fe-4S clusters have structural roles in DNA repair enzymes[1][3]

Occurrences of Iron-Sulfur Clusters in Biology (250 Word Contribution) (REVISED)

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Iron-Sulfur clusters occur in many biological systems as part of electron transfer proteins and enzymes due to their ability to aid in the transport of electrons over large distances. This property of the Fe-S clusters plays a crucial role in the proteins as they are used for the transportation of electrons in many biological processes.[1]

The Rieske proteins contain Fe-S clusters that coordinate as a 2Fe-2S structure and can be found in the membrane bound cytochrome bc1 complex III in the mitochondria of animals and bacteria (eukaryotic cells). They are also a part of the proteins of the chloroplast such as the cytochrome b6f complex in photosynthetic organisms. These photosynthetic organisms include plants, cyanobacteria, and green algae (prokaryotic cells). Both are part of the electron transport chain of their respective organisms which is a crucial step in the energy harvesting for many organisms.[2]

High potential iron-sulfur proteins occur in photosynthetic anaerobic bacteria and contain Fe-S clusters that coordinate in a 4Fe-4S cuboidal structure within the protein. [2]

The ferredoxin protein is a protein that contain within it either a coordinated 2Fe-2S cluster or a coordinated 4Fe-4S cuboidal cluster. The ferredoxin proteins that have the 2Fe-2S cluster can be found naturally occurring in a wide variety of eukaryotic cells whereas the ones containing the 4Fe-4S coordinated clusters usually only occur in bacteria.[2]

There have also been some instances where proteins contain redox-inactive 4Fe-4S clusters and are proposed to have structural roles. Such enzymes as endonuclease III and MutY, which are important for repair of damaged DNA in many organisms, are said to contain these redox-inactive clusters that do not act toward catalytic properties but contribute to structure and positioning of the enzyme.[1][3]

  1. ^ a b c d e Johnson, D. C., Dean, D. R., Smith, A. D., & Johnson, M. K. (2005). Structure, function, and formation of biological iron-sulfur clusters. Annual Review of Biochemistry, 74(1), 247-281. doi:10.1146/annurev.biochem.74.082803.133518
  2. ^ a b c d BIOLOGICAL INORGANIC CHEMISTRY : structure and reactivity. [S.l.]: UNIVERSITY SCIENCE BOOKS. 2018. ISBN 193878796X. OCLC 1048090793.
  3. ^ a b Guan, Y.; Manuel, R. C.; Arvai, A. S.; Parikh, S. S.; Mol, C. D.; Miller, J. H.; Lloyd, S.; Tainer, J. A. (1998-12). "MutY catalytic core, mutant and bound adenine structures define specificity for DNA repair enzyme superfamily". Nature Structural Biology. 5 (12): 1058–1064. doi:10.1038/4168. ISSN 1072-8368. PMID 9846876. {{cite journal}}: Check date values in: |date= (help)

400 Word Equivalents Contribution

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Crystal Structure of Photosystem I showing 4Fe-4S clusters belonging to the Ferredoxin protein.[1]

https://commons.wikimedia.org/wiki/File:Photosystem_1_-_Crystal_Structure.png https://commons.wikimedia.org/wiki/File:Ferredoxin_4Fe-4S_Metal_Center_Coordination.png

 
Rubredoxin has an iron metal center that is coordinated to a sulfur atom for each of the four surrounding cysteine amino acids. In this diagram molecules in orange are iron, yellow are sulfur, red are oxygen, and blue are nitrogen.The bonds shown as purple dashes are metal-ligand coordination bonds between iron and sulfur of the amino acid cysteine. The blue dashes are representative of hydrogen bonding[1]

https://commons.wikimedia.org/wiki/File:Rubredoxin_from_Pyrococcus_Furiosus.png

 
The Rieske protein consisting of a 2Fe-2S complex coordinated to an aromatic nitrogen atom from each of two adjacent histidine amino acids and a sulfur atom from each of two adjacent cysteine amino acids. In this diagram molecules in orange are iron, yellow are sulfur, red are oxygen, and blue are nitrogen. The bonds shown as purple dashes are metal-ligand coordination bonds between iron and sulfur of the amino acid cysteine. The blue dashes are representative of hydrogen bonding.[1]

https://commons.wikimedia.org/wiki/File:Rieske_Protein_from_Cytochrome_BC1-Complex.png

https://commons.wikimedia.org/wiki/File:HiPIP_(Fe4S4)2%2B.png

Experimental pre-edge intensities and covalencies of Fe4S4 and related Fe2S2 model complexes.[2]
Cluster μ2/μ3 S2- Pre-edge Intensity Fe←μ-S2- %Covalency per Bond Cys-S- Pre-edge Intensity Fe←Cys-S- %Covalency per Bond
Fe2S2Cl42- 2.96 68% 1.07 15%
Fe2S2(SEt)42- 1.13 78% 0.45 25%
Fe4S4Cl42- 2.5 39% 1.03 15%
Fe4S4(SEt)42- 1.72 41% 0.7 41%
 
Ferredoxin containing High-Potential Iron-Sulfur Protein isolated from the phototrophic bacterium Rhodocyclus Tenuis.[1]

Iron-Sulfur Proteins - Second 250 Word Contribution

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Covalency of Iron-Sulfur Proteins (New Addition to Article)

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Experimental data shows that iron ions and sulfur ions have a tendency to form stable metal-ligand coordination bonds and have higher covalency. Being that Fe2+/3+ are considered a hard metal ion and a sulfur ion is considered a soft ligand one would not assume that the two ions would coordinate very well. When a molecule with a sulfur group coordinates to Fe2+/3+ ion, they have a high effective nuclear charge that increases the covalency of the iron sulfur bond. Data collected using X-ray Absorption Spectroscopy (XAS) shows that the covalency of an iron metal complex is greater when the metal is coordinated to sulfur ion as opposed to a chloride ion for both 2Fe-2S and 4Fe-4S complexes.[3] (Lecture e- transfer P2a)

Structural Motifs (Adding to Addition Information)

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The protein backbone provides a rigid structure that holds the iron and sulfur atoms at certain bond distances and bond angle that closely resemble some model complexes however, small differences in geometry help enforce an entatic state.[3]

4Fe-4S Clusters (Re-wording and Adding Additional Info to Article)

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The most stable form of the 4Fe-4S cluster contained within bacterial ferredoxin and HiPIP occur when the iron ions in the cluster are have two iron atoms in the 2+ oxidation state and two iron atoms in the 3+ oxidation state. In this state one electron is delocalized between the two mixed valence pair Fe2+ and Fe3+ ions making the resulting metal ions exist in an Fe2.5+ oxidation state.

For the bacterial ferredoxin, the [2Fe2+, 2Fe3+] cluster exists as the oxidized form and is reduced when an electron is added to one of the Fe3+ ions.

For the HiPIP, the [2Fe2+, 2Fe3+] cluster exists as the reduced form and is oxidized when an electron is removed from one of the Fe3+ ions.[3]

  1. ^ a b c d Image from the RCSB PDB (www.rcsb.org) of PDB ID 1BNA (H.R. Drew, R.M. Wing, T. Takano, C. Broka, S. Tanaka, K. Itakura, R.E.Dickerson) (1981) Structure of a B-DNA dodecamer: conformation and dynamics Proc.Natl.Acad.Sci.USA 78: 2179-2183).
  2. ^ Edward I. Solomon*† p. 118 Coord. Chem. Rev. 2005, 249(1-2), 97)
  3. ^ a b c Cite error: The named reference :1 was invoked but never defined (see the help page).
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