Elements

[Soter Salem]

In an effort to understand how little I understand, I must ask a question which is in all likelihood extremely foolish.

 

The defining difference between elements on the periodic table is the number of protons in each atom, and my question is how does the number of protons, neutrons, and electrons translate to physical properties such as 'wetness', durability, and structural integrity?

[lawljj]

In essence....they don't. It's the bonds that truly determine those things, and like you said, because of the different number of protons,electrons, and neutrons each element bonds in a unique way

[Soter Salem]

Okay then in that case, what is it about the hydrogen bond that gives water it's 'wetness'?

[spin-1/2-nuclei]

Okay then in that case, what is it about the hydrogen bond that gives water it's 'wetness'?

 

Hello the kinetic molecular theory of matter can explain this. The following is not all inclusive but:

 

Basically atoms and molecules move, and although we cannot observe this motion it gives rise to the different states of matter. The energy of these movements corresponds to the temperature of the substance. The higher the energy the more movement you will have. Moreover, the amount of energy atoms and molecules have determines how they interact with other molecules and atoms and with themselves.

 

At the atomic level, the subatomic particles play an important role in determining how hard/soft and atom is, how it will bond, and the geometries those bonds can adopt. At the molecular level, things like sterics (the size of the bond), hybridization (the number of bonds between two neighboring atoms), intermolecular forces (hydrogen bonds, van der waals, pi-stacking, etc), and other things like the identity of neighboring atoms (i.e. functional groups) in a molecule, and their connectivity (which determine pockets of electron density and deficiency), conjugated systems, pockets of rigidity, the list goes on and all of these things working together determine the physical and chemical properties of molecules like water.

 

Atoms with lower energy move less, thus they tend to be solids, whereas Atoms with high energies have a lot of movement and thus they typically form gasses, thus liquids are somewhere in between. This explains why freezing water turns it into a solid... the lowering of the temperature lowers the movement and therefore results in the formation of a solid (ice). Put another way, when the attractive forces between individual molecules are > the repulsive forces you get a solid. These solids are still moving (i.e. they have NOT obtained absolute zero - the temp at which all movement stops), there movement has just been restricted to vibrational movement.

 

In liquids like water, the intermolecular forces - such as hydrogen bonds - allow the molecules to move past one another but do not allow them to gain sufficient distance from one another to fully disperse and escape the intermolecular attractive forces.

 

When you have a gas the energy of the system is > all the attractive forces thus the individual gas molecules expand out as far as they can get from one another unless/until external factors are present.

 

hope this was helpful

Cheers

[math-helper]

Yes, these are the bonds but bonds are effected by the electronic configuration of elements.

[spin-1/2-nuclei]

Yes, these are the bonds but bonds are effected by the electronic configuration of elements.

 

 

Hello,

 

Yes, that is correct, but it is an oversimplification to say that the electronic configuration of atoms gives rise to the macroscale properties observed such as "wetness", or elasticity, or rigidity. Moreover, all macrosystems in the universe are almost infinitely composed of microsystems, and within these systems there is a constant struggle between external perturbations of "isolated" ares and the internal struggle of the "isolate" system to reach it's thermal equilibrium. That is to say that all systems strive to reach their lowest energy, but in reality this typically turns out to be a situation where some parts of the system are at higher energy than other parts, and when those higher energy/reactive parts of the system happen across other low energy parts of a different or within the same system that were previously isolated from the aforementioned higher energy parts, interaction to achieve the lowest possible energy between those two subsystems or macrosystem and macrosystem occur.

 

Objects in the macroscale, such as tennis balls or cubes of ice, are made up of systems of molecules, which are made up off systems of atoms, which are made up of systems of subatomic parts. The entire system is the sum of all it's parts. If you want to look at the properties of a supramolecular structure, the best way to do that is to look at the systems of molecules that make it up. Sure all of those molecules have atoms, which in turn have their own subatomic systems, as I said before - but knowing that a supramolecular structure is composed of hydrogen, oxygen, carbon, sulfur, and nitrogen atoms does not tell us anything about how that suparmolecular structure will look or even behave. Even knowing that supramolecular structure is composed of certain molecules like for example the amino acids is not going to tell us much about how that supramolecular structure will look or behave. (see the protein folding problem and enzyme activity)

 

For any given protein sequence - you cannot from that infer what the structure or reactivity of the protein is - what makes the protein the protein on the macroscale (i.e. the scale most relevant to us) is the sum of all it's parts, the atoms that make up the molecules that make up the sequence, which has a specific connectivity, which gives rise to the geometry, which gives rise to the structure, which gives rise the function.

 

Another way to look at this is to simply say - not all hydrogen atoms in a molecule or a system are the same. On both the molecular and supramolecular level the environment that the hydrogen is in will have a huge impact on what that hydrogen does.

 

For example CH4 has four hydrogens that in most cases aren't going to be very reactive. On the other hand H3C-(C=0)-OH has four hydrogens as well, but because of the environment of those hydrogens 1 of them (the carboxyllic acid hydrogen) is going to be relatively reactive. In yet another example, we have H3C-CH2-OH, in this case the hydrogen of the alcohol is going to be the most reactive relative to the other H atoms in ethanol. But if you compare the three, by an acidity measurement called pka, you will see that despite being comprised of mostly the same atoms (hydrogen, oxygen, carbon) these systems of atoms - i.e. molecules - are not the same. Methane is the least reactive, followed by ethanol, and then acetic acid.

 

Methane has a pka of 50

Alcohol has a pka of 16

Acetic Acid has a pka of 5

 

So even though every hydrogen in the example above has the same electronic configuration, the reactivity of the hydrogen atom in each situation is not the same.

The same can be said for the carbon, and oxygen.

 

So for example, carbon's electronic ground state configuration is [He]2s^2 2p^2 - meaning that carbon's valence electrons allow for carbon to have 4 bonds. When you calculate the formal charge of an atom in a molecule: FC = [Valence electrons] - [# of lone pair electrons] -[# of bonds]. For carbon you will see that in all the examples above this is 4 - 0 - 4 = 0 therefore the carbon is neutral in those molecules.

 

Now, if we consider a carbon atom during an SN1 reaction, where the carbon of the reaction center - having just lost a bond via the loss of a leaving group - we can see that in this case the carbon has a formal charge of +1

 

R3-C+, where R stands for other systems of atoms covalently bound to the carbon.

 

You have: FC = 4 - 0 - 3 = +1

 

So now that we know that atoms within molecular systems can have charge, it is important to note that it is the environment those atoms are in that determines whether or not the atom can hold the charge that is being proposed.

 

the more electronegative atom "prefers" to have the negative charge, the less electronegative atom "prefers" to have the positive charge, but this is only if charge separation cannot be avoided.

 

A good way to understand this is to take a look at what we call resonance structures.

 

if I have

 

H2C=CH-HC=CH-CH=CH2, from right to left carbon(s) 1 - 6

 

In a resonance structure we can move sources of electron density, but we cannot make or break bonds (there are many other rules as well, but they are not overly relevant to the large picture here so I will skip those for now)

 

So step 1, I move electron density from carbons 1 and 2 to carbons 2 and 3, and (so that I do not violate the octet rule) I also have to move electron density from carbon 2 and 3 to 4 and 5 and the final double bond to carbon 6 in the form of a lone pair/negative charge. This leaves a positive charge on carbon 1, which is a primary center. A primary center, simply means that the carbon has only 1 out of the 4 bonds possible being a non-hydrogen bond, and a negative charge on carbon 6.

 

It's important to note that moving double and triple bonds is consider moving electron density, but once you get down to the final single bond between two atoms - you cannot move that bond - when you are drawing resonance structures.

 

Now we have:

 

H2C=CH-HC=CH-CH=CH2 <--------> H2C(+)-CH=CH-CH=CH-CH2(-)

 

So now we understand that within a molecular system, depending on the environment/conditions, different atoms can have different charges. This leads to different reactivity of the same atom. *it's important to note that the overal energy in the system will not change. That is to say conservation of energy must be obeyed, and that is why if you add of the charges on both sides of the arrows above you will see that there was no net loss or gain on the energy of the system, but there was a significant change in the energy of each of the charged carbon atoms.

 

So while the net energy of the system is not changed the stability of the system is changed. In real life all molecules exist as an average of all of their possible resonance structures, those that are neutral - i.e. - more stable are weighted more because the molecules spend more time in the more stable configurations.

 

This is just scratching the surface of how atoms behave within molecular systems. I don't have time or space to go in to them all, but hopefully this gives you a pretty good idea of the complexity involved in these concepts.

 

Systems of molecules have similar behaviors.

Even though most supramolecular biological compounds are made up of systems of amino acids, the arrangement of those amino acids greatly determines the structure.

 

inherent chirality, hydrogen bonds, pi stacking, hydrophobic/hydrophillic interactions, blocking/encouraging rotations and vibrations of pockets of molecules in the supramolecular system, sterics, etc, etc all determine the structure and function of those proteins and they function in a way similar to what has been described for atoms in their molecular systems. The amount of contribution made from one or the other depends greatly on the environment.

 

Molecules in their supramolecular systems will align themselves in such a way that electron density is shared for the benefit of the entire system, as much as can be achieved. Because as I said before, all systems are looking to achieve the lowest energy possible, i.e. they all want to become the most stable.

 

This post was not all inclusive by any means, but it should give you a good understanding of the very basic aspects of this so that you can now know where to start to research this further, if you so desire..

 

Hopefully this was helpful.

Cheers

Edited August 20, 2011 by spin-1/2-nuclei