As I recall from high school chemistry, when atoms come together to form a molecule, they’re arrange themselves into a certain shape. For instance, if I recall correctly, H[sub]2[/sub]O is shaped like a V with the oxygen at the point and the two hydrogens at the end of either arm.
Is this inviolate? If I have some super complex molecule with 40 different elements, is there only one way to put them together?
Any layperson-level explanation for why molecules do seem to shape up in certain ways?
Well, there’s always isomers: the same atoms, just put together in different ways.
It’s all about the electrons, baby. Take water. One oxygen atom and two hydrogen atoms. The nucleus of the atom exerts a pull that keeps 2 of oxygen’s electrons locked down, as it were, but 6 of them are free to roam around the nucleus(These are called valence electrons.) Hydrogen has one valence electron. Oxygen really wants 8 valence electrons and hydrogen really wants 2. So one hydrogen atom shares an electron with oxygen and vice versa so that hydrogen has 2 valence electrons and oxygen has seven and then the other hydrogen does the same thing. Everyone is happy and their outer shells are filled. This is known as covalent bonding. But the hydrogen atoms are now feeling the effects of another electron and they only have one proton each so they become slightly negative. And the oxygen atom now has two more electrons than protons so it become negative. They aren’t negative enough to break the covalent bonds but it is enough to force the molecule to assume a bent shape as each negative center tries to create the maximum distance between itself and the other negative centers.
Not necessarily. It depends on the bonds. One molecule might have one element triply bonded with one element and singly bonded with another. A different molecule may have that element doubly bonded with two other elements. It depends on their valence electrons and the electronegativity of the atoms. In any case, what you would have are isomers. And they are why molecular formulas are written with elements repeated. For example, the molecular formula for acetic acid is CH[sub]3[/sub]COOH. C[sub]2[/sub]H[sub]4[/sub]O[sub]2[/sub] could mean any of a number of molecules that may have differing properties than acetic acid. CH[sub]3[/sub]COOH gives you a general idea of the molecular shape if you wanted to map it out. (3 hydrogens bonded to one carbon and two oxygens and a hydrogen on the other.) There are also chiral molecules that are exactly the same but reversed. And their properties can differ as well.
Now, let’s sit back and wait while an actual chemist explains why I’m completely wrong.
Molecular shape is a fundamental question in chemistry, understanding it is at the heart of understanding chemistry in some ways, as the shape or structure of a molecule is deeply connected with its function. Inner Stickler is right, it really is all about the electrons, baby. The shape of simple molecules is well understood in these terms, such that chemistry students can look at a formula like SF4, or BF3, and tell you what the 3-dimensional shape will be.
The shape of large molecules like proteins is far more complicated, and working this out experimentally is a huge part of current research in chemistry and biology. How the atoms are connected in proteins is not complicated, the shape of a single amino acid is well understood. Join 500 of them together to make a protein, though, and it becomes more difficult to say how each part of the structure interacts with other parts.
For the simple molecules, there is a theory called VSEPR (valence shell electron pair repulsion) used for thinking about shape. Inner Stickler has verbalised this for the water example, in a nutshell it says that electron pairs repel one another. By counting the number of electron pairs in covalent bonds, and the number of electron pairs not in bonds (lone pairs), we can work out what the shape of a molecule will be. I remember being taught this in high school, so it’s an elementary but important idea.
This link sets out the idea, and you can see some nice animations of molecules like water, methane, ammonia etc.
The conditions under which a molecule is formed can also affect the shape. Carbon molecules have a number of different shapes that they can take and often have different characteristics depending upon the shape.
I’ll repeat this point that other posters have touched on - for a complex formula, (even one with only 2 or 3 different elements but lots of each,) there can be many different ways to put a molecule together, lots of different final ‘shapes’ you could end up with. Each shape really is a different type of molecule with different properties - glucose and fructose, the two most common symple sugars, (which when joined together form the common table sugar, sucrose, a compond sugar,) are both C[sub]6[/sub]H[sub]12[/sub]O[sub]6[/sub], but arranged into slightly different shapes.
It’s the shape that defines a molecule, essentially. Listing the parts that it can be broken down into is just a vastly simplified way of categorizing it - like describing a piece of furniture or a house by its component pieces.
(I am not a chemist, just an interested lay person. The above was accurate to the best of my abilities at this present moment.)
No covalent bonds have been harmed in the making of this movie.
Be aware in that the animation in Squinks link the little balls don’t represent atoms they represent amino acids.
I can’t add anything without being repetative.
I’d also add that even once a molecule is assembled, there is some flexibility where the molecule is prone to flip between one shape and another. The most common illustration is cyclohexane, which can flip between a chair-shaped conformation and a boat-shaped conformation without even changing its bonds. I’m trying to think of a good commonsense example… maybe the “clicker top” of a gatorade bottle is a good example. When there is a vacuum inside the bottom, it’s convex, but once that energy is equalized it becomes concave. It’s still the same cap, it’s just that its shape depends on its potential energy.
I don’t quite follow. Surely the best separation of negative centres would be if they were arranged in series?
The bent shape implies perhaps that the hydrogen atoms are still sorta, kinda in their H2 molecule. But why, when they’re nicely paired up with an electron from the oxygen atom?
Is it something to do with orbitals perhaps?
Think of the oxygen as tetrahedral where two of the positions are taken up with the electron pairs. that leaves the hydrogens in a bent configuration.