[dillydoo]

Hello,
forgive me if I fail to use the correct chemistry terms as English isn't my native tongue or language that I'm studying in - correct me if I do. Also, I'm really sorry if this has been asked before. If you think I might compromise anyones time, I would be more than grateful if you would re-direct me to a similar thread or ask me to find one, thank you kindly!

I'm confused regarding the difference between an ion and a molecule because they seem to be able to have similar structures. Even molecules seem to consist of sometimes polyatomic ions that are charged. (Or am I wrong?)

I know of these structures:
(As I said before, please correct me if I'm wrong in anything!)

Monoatomic Ion	Ion with one charged atom of one element. (Having released or received a valency-e)
Polyatomic Ion	Ion with two or more charged atoms of the same or differing elements, attracted to each others for neutrality.
Diatomic Molecule	The simplest form of a molecule, consisting of two atoms with the same or different elements finding neutrality in the other.
Molecule	Can be a large bond of many atoms, even charged ions of any element.

...and the terms for these bonds:

• Sigma
• Pi
• Double bond
• (Nonpolar)Pure covalent bond
• Polar covalent bond
• Dative covalent bond (outdated?)
• Coordinate covalent bond

Now the humongous confusion:

• What is the cloud of electrons and why does it not constitute a compound? They share electrons between each others, instead of giving or taking valency but to me, it just sounds similar. Is it because they require different separation methods? Or does it have something to do with what the orbits look like? My teacher keeps talking about it like we're kids by using symbolics and metaphors, but I find it more confusing without a definite explanation.
•      (Because of this:)
  -Per rule of definition, a molecule cannot constitute of just a single atom and will always have two or more.
  -An atom that has become charged in one way or another, broken down by itself, is an Ion and can exist by itself.
  -A diatomic molecule consists of two atoms of the same or different elements. (Homonuclear/Heteronuclear)
  -A polyatomic ion consists of two or more ions but it's not a molecule.
       (I'm confused regarding:)
  A nonpolar covalent bond can exist in molecules, diamolecules and polyatomic ions, making them completely neutral. What's the difference then? Polar covalent bonds is the sae, they exist in all - but the atoms have a similar way of interacting as with an ion compound. The electron variations will attract them to one another which is similar to the ions charges. So why can a molecule or diatomic molecule still be called a molecule and not a polyatomic ion? Both polyatomic ions and the molecules seem to have found perfect neutrality by the exchange or sharing of electrons between atom pairs/bonds of polar charges.
  
• Dative bonds, I hear, is an outdated theory as it's more like a directive for the sharing of two or more electrons between atoms. What is a coordinate covalent bond then? Is it just the term for when there's a large chain of atoms that can intersect one another?
  
• A sigma, pi and double bond are all varieties of structures within the structures of covalent bonds... that's about all I understood? Something about intersecting orbitals, where the further out the bond happens, the more unstable it is and vice versa?
  
• Finally: Just what is the difference between a molecule and an ion?! I'm going nuts... And I don't like the simplified explanation that polyatomic ions can have a differing amount of electrons in comparison to their protons and molecules can not. I don't understand this explanation because molecules can consist of polyatomic ions?
  

Sorry if the questions are unclear or if my text was too long, I'm just so confused...

[Corribus]

Finally: Just what is the difference between a molecule and an ion?! I'm going nuts... And I don't like the simplified explanation that polyatomic ions can have a differing amount of electrons in comparison to their protons and molecules can not. I don't understand this explanation because molecules can consist of polyatomic ions?

Some of your definitions aren't very good.

Atoms and molecules: electrically neutral.
Ions: electrically charged.

A polyatomic ion is exactly like it sounds: basically a molecule that has an overall charge may be considered a polyatomic (more than one atom) ion. The simplest ions consist of a single atom where the charge of the nucleus either exceeds or is exceeded by the total charge of the surrounding electrons. In chloride, Cl-, for example, the nucleus has 17 protons and there are 18 electrons surrounding it, for an over all charge of -1. In the chlorine atom, the 17 protons in the nucleus are balanced by 17 electrons, for an overall charge of 0. An example of a polyatomic ion is nitrate, NO₃^-. This ion consists of three oxygen atoms and nitrogen bound together, but the structure has one more electron than the total number of protons in the system, for an overall charge of -1. This charge is not necessarily totally located near one atom; rather it may be spread over the entire ion.

Because polyatomic ions are charged, their properties are quite a bit different than those of molecules, which are electrically neutral. Also, ions are always accompanied by another ion with an opposite charge, as in sodium (Na⁺) nitrate (NO₃^-). In this case, the sodium ion is a simple cation, whereas the nitrate anion is polyatomic.

[dillydoo]

Yeah, I think it's my general confusion muddling my definitions which is the actual problem.

I don't know how to perfectly define one from the other. I guess my post was also a bit confusing to read - I tried to give a brief introduction to what I already knew. I understand each rule standalone, monoatomic, diatomic, polyatomic etc whether its molecules or ions and their general rule of thumb in what category they fall into but I can't tell what the difference in the relationship is.

Is this another one of those - for lack of other words - trigonometric function to define relationships in words?

The statements being:
Polyatomic ion is a molecule but molecules are not polyatomic (Edit:Ions) if...
(But) Polyatomic ion is a molecule when...

And the variables of your explanation tells me: 
Polyatomic ions are charged and therefore different than a molecule, but it is a molecule.

So what is it? Is it a question of hierarchy for the definition?

[Corribus]

Definitions vary. Personally, I don't view polyatomic ions as being molecules, as I consider electrical neutrality to be a defining characteristics of this class. I would guess that most chemists would agree, but some subdisciplines of chemistry have a broader viewpoint. Nevertheless, I think in common parlance, and certainly at the high school or undergraduate level, it is understood that molecules are two or more bound nuclei having no formal charge, and polyatomic ions are two or more bound nuclei having a net formal charge.

[dillydoo]

Definitions vary. Personally, I don't view polyatomic ions as being molecules, as I consider electrical neutrality to be a defining characteristics of this class. I would guess that most chemists would agree, but some subdisciplines of chemistry have a broader viewpoint. Nevertheless, I think in common parlance, and certainly at the high school or undergraduate level, it is understood that molecules are two or more bound nuclei having no formal charge, and polyatomic ions are two or more bound nuclei having a net formal charge.

Thank you so very much! I think I was looking for this answer, in all of the chaos I brought down on you. A standard perspectives to it, I suppose.