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Week3 Tasks - Info for Cobalt(II) Cyanide

Properties of Cobalt(II) Cyanide

• Molecular Formula: Co(CN)₂
• Molar Mass: 110.97 g/mol
• m.p: N/A
• b.p: N/A
• Solubility in water: N/A

Cobalt(II) Cyanide

Cobalt(II) Cyanide

Inorganic compound

Cobalt(II) cyanide | Co(CN)2 - PubChem (nih.gov)

Cobalt(II) cyanide | PubChem

Nitrogenase

Nitrogenase: A Draft Mechanism

Structural Enzymology of Nitrogenase Enzymes

Practice Uploading a PDB Structure Image

Critique of Carbonic Anhydrase Mechanism Figure

Arrows in the figure directing the reaction are too big compared to the molecules.

The arrow, during hydrolysis, does not properly indicate the addition of water.

Inconsistent shapes for carboxylic acids through out the mechanism does not follow VSEPR.

There is no arrow showing water attacking or leaving the metal center.

Practice making a table

Properties	Data
Molecular Formula	Co(CN)2
Molar Mass	110.97 g/mol
m.p	N/A
b.p	N/A

Practice entering a formula

$Y_{2}={X^{2} \over 2}$

Practice making a chemical information box

Cobalt(II) cyanide

Names
IUPAC names cobalt(2+);dicyanide
Properties
Chemical formula	Co(CN)2
Molar mass	110.97 g/mol
Melting point	N/A
Boiling point	N/A
Solubility in water	N/A
Except where otherwise noted, data are given for materials in their standard state (at 25 °C [77 °F], 100 kPa).

Practice Using History Pages, Talk pages, Article ratings and Watchlists

Smokefoot made the edits to remove parts of the page that resembled a school essay. This was necessary because the information should be presented as facts instead of opinions. The statistics (-3,296), and (-1,805) indicate the net change in bytes removed from the article.

Wikipedia “Iron–sulfur cluster” article: Talk page discussion of Dec 4th / 5th 2018 edits

Hello,

I hoping to contribute, my knowledge to this article by discussing the strength, covalency and electron transfer effects. Ninja Recs (talk) 01:00, 12 October 2018 (UTC)

You are writing at a level that indicates that your teacher is needed. Please ask your teacher to read some Wikipedia articles first. --Smokefoot (talk) 01:20, 5 December 2018 (UTC)

Ninja Recs's Instructor gave 58 revisions to make to this contribution before moving to the live article however, regrettably, none of them were made --Kcsunshine999 (talk) 22:46, 5 September 2021 (UTC)

The main purpose of Smokefoot's edits in the carbonic anhydrase page was to remove redundancies, further explain the mechanism and remove a duplicate reference. The statistics (-642), (-607) and (-140) indicate the net change in bytes removed from the article.

Smokefoot's edit to the line 26 second box removes most of Bilal.bhatti96's sentences and rephrases them. In my opinion, this change was necessary to more clearly state the facts and remove opinion statements such as "the most important functions". However, the new edit also contained grammatical errors that should be corrected.

Bilal.bhatti96's edit adds additional information about the bohr effect to the carbonic anhydrase page. In my opinion, though this information related back to carbonic anhydrase this information was unnecessary to the article as an internal link to the bohr effect would more clearly explain the concept. This paragraph is still in the current version of the carbonic anhydrase page.

In the carbonic anhydrase talk page most of the conversations are constructive information such as improvements on images and clarifications. Therefore, this talk page was useful for improving the carbonic anhydrase article.

This article has been rated as Low-importance on the project's importance scale.

C This article has been rated as C-Class on the project's quality scale.

Low This article has been rated as Low-importance on the project's importance scale.

Protein Mechanism and Effects (First 250 Contribution)

The electron transfer reaction of rubredoxin is primarily facilitated by the reduction of Fe³⁺ to Fe²⁺, as well as a gating mechanism caused by the conformational changes in Leu 41.

Upon the reduction of Fe³⁺ to Fe²⁺, the four Fe-S bonds become elongated, while the S-Cys bonds become shortened. The reduced structure of rubredoxin results in better electrostatic stabilization of the negatively charged sulfur, leading to a lower reorganizational energy that allows faster electron transfer.

The gating mechanism in Leu 41 that arises from the conformation change of the non-polar side- chain allows access to the Cys 9 Sγ site. The Leu 41’s non-polar side chain controls access to the redox site by adopting either an open or closed conformation. In the open conformation, the Leu 41 side-chain faces away from Cys 9 Sγ, increasing the polarity of the redox environment and exposing Cys 9 Sγ. As a result, Cys 9 Sγ becomes an electronegative potential surface to attract water molecules. A higher electron density offers a stronger electronegative potential hole to attract water to the gate in the reduced state, producing an open conformation. In contrast, the oxidized state’s weaker electronegative potential does attract water, producing a closed conformation. Thus, the conformation of Leu 41 is determined by the presence of water and the oxidation state of rubredoxin. The proximity of water to the [Fe(S-Cys)₄] ^2-+ active site stabilizes the higher net negative charge of the reduced Fe²⁺ oxidation state. This shifts the reduction potential to a more positive E⁰ value, increasing the [Fe(S-Cys)₄]^2-+ active site’s affinity for electrons.

Protein Mechanism and Effects (250 Contribution Revision + Figure Contribution)

Fe-S and amide NH-S(Cys) bond lengths upon reduction

The electron transfer reaction of rubredoxin is carried out by a reversible Fe³⁺/Fe²⁺ redox coupling by the reduction of Fe³⁺ to Fe²⁺ and a gating mechanism caused by the conformational changes of Leu41.

Upon the reduction of Fe³⁺ to Fe²⁺, the four Fe-S bond lengths increase and the amide-NH H-bonding to the S(Cys) become shortened. The reduced Fe²⁺ structure of rubredoxin results in a small increase in electrostatic stabilization of the amide-NH H-bonding to the S-Cys, leading to a lower reorganizational energy that allows faster electron transfer.

Leu41 gating mechanism in open conformation

A gating mechanism involving the conformational change of the Leu41’s non-polar sidechain further stabilizes the Fe²⁺ oxidation state. A site-directed mutagenesis of Leu41 to Alanine shows a 50mV shift of the Fe^3+/2+redox potential. The substitution of the smaller CH₃ shows that the Leu41 side chain stabilizes the Fe²⁺ oxidation state more then the Fe³⁺ oxidation state. The X-ray structure in the reduced Fe²⁺ state shows the Leu41 side chain adopting two different conformations with 40% in a "open conformation" and 60% in a "closed conformation". The Leu41’s non-polar side chain controls access to the redox site by adopting either an open or closed conformation. In the reduced Fe²⁺ state, the Leu41 side-chain faces away from Cys 9 Sγ, exposing the Cys 9 Sγ and increasing the polarity of the Fe³⁺ /Fe²⁺ center. ^[1] The lower Fe²⁺ cation change of the reduced state leaves a higher negative charge on the Cys 9 Sγ-donor which attracts water strongly. As a result, water is able to penetrate and form H-bonds with the Cys 9 Sγ thiolate that blocks the gate from closing, resulting in a open conformation. In contrast, the oxidized Fe³⁺ state produces a less negatively charged Cys 9 Sγ-donor that does not attract the water strongly. Without H-bonding of the water to the Cys 9 Sγ, the gate remains closed. Thus, the conformation of Leu41 is determined by the presence of water and the oxidation state of rubredoxin. The proximity of water to the [Fe(S-Cys)₄] ^2- active site stabilizes the higher net negative charge of the Fe²⁺ oxidation state. The stabilization of the Fe²⁺ oxidation state shifts the reduction potential to a more positive E⁰ value.