Talk:Structural Biochemistry/Chemical Bonding

This page is sooo bad, that I do not even know where to start... It is a pretty good synopsis of all the misconceptions about chemical bonding I am fighting to prevent in my CH 101 classes (or CH331, 452, 433 or 711 for that matter. Gunmhoine (discuss • contribs) 01:55, 12 April 2015 (UTC)

Criticsm
Covalent bonds are another type of chemical bond used to achieve a noble gas configuration, or an octet of electrons. Covalent bonds are formed between nonmetals, usually from the Boron, Carbon, Nitrogen, Oxygen, and Halogen families.


 * They can just as well be formed between two metal atoms like Li-Li as long as the electronegativity is the same. But then that concept is not even mentioned

Metals are rarely involved in covalent bonds.


 * Total nonsense

Each covalent bond consists of two electrons, one usually from each atom involved in the bond. The atoms form enough covalent bonds that when the electrons in the bonds are added with the valence electrons, they will have an octet.


 * This is an ASSUMPTION made by Lewis, debunked many decades ago

The key difference between ionic and covalent bonds lies in how the electrons are distributed between the two atoms. In ionic bonds, the electrons are transferred from one atom to the other, giving the atoms effective +1 and -1 charges.


 * It is better not to speak of 'ionic bonds' but of 'ionic bonding' instead because it is seldom limited to one pair of atoms, usually a whole crystal is involved. Besides those charges can very well be 2+ and two of -1 or or or.

However, in covalent bonds, the valence electrons from both of the two atoms are shared between two atoms. Thus, neither atom is given a full positive or negative charge. Instead, the electrons shared between the two atoms - whether it be 2, 4, or 6 electrons - varies from molecule to molecule.

There are two types of covalent bonds: pure covalent bonds and polar covalent bonds. Pure covalent bonds exist when there is no difference between the two atoms sharing the electrons. The electronegativity of the two atoms is identical. Because the electronegativity values do not differ, they pull the electrons that are being shared between them with the same force.


 * The force is always the same, it is the electromagnetic force. In other words 'force' is not the word to use. In other words, first define what electronegativity is (it is not a force), then use it

Thus, the electrons are shared equally and none of the atoms bears a partial positive or negative charge. An example of a pure covalent bond is a Cl-Cl or a Br-Br bond. Pure covalent bonds rarely exist for bonds that are not between identical atoms. Another example would be the covalent bonds between the carbons in long alkane chains.


 * Oh, I can think of a bond between Au and Se, both electronegativity 2.54 that is pretty covalent, but yes you just said that metals can't produce covalent bond, right?

Polar covalent bonds are those that exist between atoms of different electronegativities. The electrons in the bond are still being shared, but not equally between the two atoms. Though the exact ratio of the electron density that each atom bears cannot be determined easily, it is very easy to determine which atom pulls more electron density towards itself. The more electronegative atom will pull the shared electrons more, causing it to now bear a slightly negative charge. Because charge has to be conserved, the less electronegative atom must now bear a slight positive charge, equal in magnitude to the negative charge.


 * Not necessarily no. Not if you have more than two atoms.

As an example, consider a bond between carbon and chlorine. Chlorine is much more electronegative than carbon, thus it pulls more of the electrons towards itself. This gives the chlorine a slightly negative charge and the carbon a slightly positive charge. If the difference between the two atoms is so great causing one of the two atoms to posess a lot of the electron density, the bond becomes increasingly ionic and less covalent. For this reason, though H-Cl is considered a covalent bond, it is classified as a very strong acid, meaning it dissociates completely.


 * No, it doesn't. It is quite happy to be a gas molecule. Oh, you mean in water? Is all chemistry in water then?

Because the electronegativity difference is so vast, the chlorine molecule pulls all the electron density towards itself, thereby dissociating into H+ and Cl- ions in the presence in water.


 * Ah now they tell me... And leave out the fact that that proton latches on to a water molecule, as if hydrogen bonding is not important for biochemistry....

However, it is important to note that a molecule that contains polar bonds can be nonpolar. For example, take the molecule carbon tetrachloride. This molecule has four polar C-Cl bonds. However, due to the orientation of the polar bonds, they cancel out and the molecule as a whole is nonpolar.


 * Better to say that it lacks an overall permanent dipole moment

Hydrogen Bonds Hydrogen-bonding-in-water-2D.png

A hydrogen bond is a bond created by the dipole-dipole interaction of a hydrogen atom and an electronegative atom such as an oxygen or nitrogen atom due to dipole dipole interactions.


 * Ehm. Pray tell what dipole a hydrogen atom possesses then... It doesn't neither does an oxygen of nitrogen atom. No, we don't quite understand what makes the hydrogen bond as strong as it is, but interactions between non-existent dipoles it surely is not.

A common example of this is water where the electronegativity of the oxygen allows it to have a slight negative charge while the two hydrogen atoms have a slight positive charge. The negative charge on the oxygen forms a weak bond with the slight positive charge of another water molecule's hydrogen.
 * Certainly, there is an interaction of the dipole of one molecule with that of the other, but that is not hydrogen bonding. Hydrogen bonding is an interaction that comes on top of the dipole-dipole interaction

This type of bonding is also present in organic fluorine compounds between C and F groups.


 * What do you mean with 'C and F' groups?? Certainly CF4 does not have hydrogen bonding. It does not even have hydrogen atoms...

This force is weaker than covalent bond and ionic bonds, but stronger than Van der Waals interactions.


 * That at least is true. Hydrogen bonding straddles the border between intermolecular ('physical') interactions and chemical bonding.

Intermolecular hydrogen bonding is responsible for the high boiling point of water (100 °C), or most of the solutions that use water as the solvent. This is because of the strong hydrogen bond, as opposed to other group 16 hydrides. Intramolecular hydrogen bonding is partly responsible for the secondary, tertiary, and quaternary structures of proteins and nucleic acids.


 * Which is why this page should not add to any confusion of the matter....(And it does)

Role of Noncovalent Interactions in Macromolecules

In macromolecules such as proteins, DNA, and RNA, noncovalent interactions are essential. Noncovalent interactions include hydrogen, ionic, hydrophobic, and Van Der Waals bonding.


 * ?? What is the difference between hydrophoic and Van der Waals interactions? I wouldn't know any...

These interactions are described in more specificity in the list that follows this group. When compared to covalent bonds, noncovalent bonds are weak and continuously form and break bonds.


 * Only at the temperatures that we live at. Forming and breaking bonds is not an absolute characteristic, but a relative one. It comes from the balance between the interaction energy and the thermal energy (RT).

However, when several noncovalent bonds are formed, there is a net increase in bond strength.


 * Unclear what you mean. Does that affect the strength of the covalent bonds? Don't think so..

Their combined participation in a macromolecule makes a difference (i.e. substrate binding to enzyme and the lipid bilayer's role in transport). With several hydrogen bonds, ionic, and hydrophobic interactions existent at the same time, it is unlikely that these several weak interactions will break the substrate and enzyme without external energy.


 * How can a substrate be 'broken'? If the interactions would be stronger would it break them?

This property is the reason why enzymes have specific catalytic power.


 * I doubt that anyone really knows the be-all-end-all of why enzymes have a specific catalytic power. There is still a lot we do not know about that

Protein folding and the unique properties and structures of proteins also depend on these noncovalent interactions.


 * On these interactions yes. But are they really so 'noncovalent'? Is hydrogen bonding noncovalent? I have seen people dub it a weak covalent asymmetric three center bond.

Gunmhoine (discuss • contribs) 02:33, 12 April 2015 (UTC)