atoms within molecules

[lemur]

Are the atoms in molecules locked in a fixed position so that the molecule has a constant shape? Or do the nuclei and electrons swarm around each other in patterned (or random) ways?

 

edit: "atomic" in the thread title should be "atoms" - sorry.

Edited April 29, 2011 by lemur

[mississippichem]

Are the atoms in molecules locked in a fixed position so that the molecule has a constant shape? Or do the nuclei and electrons swarm around each other in patterned (or random) ways?

 

edit: "atomic" in the thread title should be "atoms" - sorry.

 

Chemical bonds are not at all rigid. In fact they act somewhat spring-like, a spring constant can even be calculated for a given bond. Atoms on the ends of bonds can rotate, vibrate, bend, or undergo translational motion. The vibration is quantized much like the energy levels of electrons [except these vibrational levels are very close together]. Bonds can even be broken by exciting them to very high vibrational levels.

 

We can use spectroscopy like Fourier-Transform Infrared or Raman Spectroscopy to study the various vibrations, translations, rotations, and bends as we can excite molecules to different vibrational levels by firing radiation at them and observing which frequencies they absorb.

 

The shape of molecules is always changing with this motion, but the average bond angles and connectivity remain the same.

Edited April 29, 2011 by mississippichem

[lemur]

Chemical bonds are not at all rigid. In fact they act somewhat spring-like, a spring constant can even be calculated for a given bond. Atoms on the ends of bonds can rotate, vibrate, bend, or undergo translational motion. The vibration is quantized much like the energy levels of electrons [except these vibrational levels are very close together]. Bonds can even be broken by exciting them to very high vibrational levels.

 

We can use spectroscopy like Fourier-Transform Infrared or Raman Spectroscopy to study the various vibrations, translations, rotations, and bends as we can excite molecules to different vibrational levels by firing radiation at them and observing which frequencies they absorb.

 

The shape of molecules is always changing with this motion, but the average bond angles and connectivity remain the same.

The spring explanation makes it sound like the atoms are more or less fixed relative to each other at certain angles, i.e. that they don't circulate/swarm around each other. On the other hand, is it possible that they are moving and that the motion still averages out to the same bond angles, the way a race car could take different paths around a track and still average out to the same force changes on the turns? It doesn't make sense to me that bonds would be fixed at certain positions on the atoms since they are constituted from particles moving around in attractive/repellant fields.

[swansont]

The spring explanation makes it sound like the atoms are more or less fixed relative to each other at certain angles, i.e. that they don't circulate/swarm around each other. On the other hand, is it possible that they are moving and that the motion still averages out to the same bond angles, the way a race car could take different paths around a track and still average out to the same force changes on the turns? It doesn't make sense to me that bonds would be fixed at certain positions on the atoms since they are constituted from particles moving around in attractive/repellant fields.

 

But they aren't "particles moving around" in the classical sense. Solids wouldn't have structural integrity if the constituent atoms were free to move as you propose.

[lemur]

But they aren't "particles moving around" in the classical sense. Solids wouldn't have structural integrity if the constituent atoms were free to move as you propose.

Why not? Wouldn't it depend on the shape-maleability of the molecule at a given energy-level? E.g. if a water molecule is compressed against others to its minimum volume, it would be a liquid, but if the repelling-energy among the molecules decreased to a level where the shape-maleability and overall average vibrational energy wasn't sufficient for them to slide around each other, they would crystalize into a solid.

 

Idk, what basis is there for saying the atoms are in fixed positions relative to each other? What determines the position of their bond-connections?

 

 

[mississippichem]

Idk, what basis is there for saying the atoms are in fixed positions relative to each other? What determines the position of their bond-connections?

 

All those types of spectroscopy that I mentioned above. They wouldn't work in the way they do without spring-like, fixed connectivity bonds. This is why ionic solids don't show up on FTIR for the most part.

 

What determines the position of their bond-connections?

 

Do you mean in reference to average bonds angles or connectivity? Both answers are lengthy and probably require a new thread. I can tell you that we confirm molecular structures precisely by growing crystals and subjecting them to neutron, electron, and x-ray diffraction experiments.

 

They short, psuedo-classical answer on bond angles is that electron pairs repel each other, and will seek a geometry that minimizes their repulsion interaction. The good answer involves group theory, and symmetry considerations and requires a new thread.

[lemur]

I can tell you that we confirm molecular structures precisely by growing crystals and subjecting them to neutron, electron, and x-ray diffraction experiments.

What about liquids and metals? How do you know that the molecules' shape isn't just fixed within the lattice of the crystal/solid because of interactive force?

 

They short, psuedo-classical answer on bond angles is that electron pairs repel each other, and will seek a geometry that minimizes their repulsion interaction. The good answer involves group theory, and symmetry considerations and requires a new thread.

the geometry of minimum repulsion interaction sounds logical. That implies that they would have the potential to swarm around due to their attraction and freedom of motion but they don't because they get locked into relative positions due to force geometry. In a planetary model, you would expect a trapped satellite to fall into the gravity-well, but with atoms/molecules, something prevents that right? It sounds almost as if the electrons get sandwiched between blockades and they oscillate between those. Sorry that I have to try to comprehend this on what must seem like a vague "pseudo-classical" level to you. It's just hard to imagine why free particles bound by attractive force would not be in dynamic motion relative to each other. Another way to describe it would be that I would think any and all force interactions, even at the molecular level, would result in the formation of geodesic paths where particles move freely due to their inertia. If they stop doing this at some level of miniscule-ness, it would be good to know why. Does inertia exist within molecules, among their atoms, or only among molecules themselves, with other forces governing the behavior of the atoms within the molecules?

 

 

[mississippichem]

What about liquids and metals? How do you know that the molecules' shape isn't just fixed within the lattice of the crystal/solid because of interactive force?

 

For that we have molecular dynamics, density functional theory (DFT), and a host of other molecular modeling techniques. We can also observe the structures of molecules with pretty much any kind of spectroscopy. We chemists have gotten really good (shameless self glorification ) at that since the advent of COSY 2-dimensional nuclear magnetic resonance spectroscopy.

 

the geometry of minimum repulsion interaction sounds logical. That implies that they would have the potential to swarm around due to their attraction and freedom of motion but they don't because they get locked into relative positions due to force geometry. In a planetary model, you would expect a trapped satellite to fall into the gravity-well, but with atoms/molecules, something prevents that right? It sounds almost as if the electrons get sandwiched between blockades and they oscillate between those. Sorry that I have to try to comprehend this on what must seem like a vague "pseudo-classical" level to you. It's just hard to imagine why free particles bound by attractive force would not be in dynamic motion relative to each other. Another way to describe it would be that I would think any and all force interactions, even at the molecular level, would result in the formation of geodesic paths where particles move freely due to their inertia. If they stop doing this at some level of miniscule-ness, it would be good to know why. Does inertia exist within molecules, among their atoms, or only among molecules themselves, with other forces governing the behavior of the atoms within the molecules?

 

Molecules most definitely have moments of inertia. As they have mass and can undergo rotational motion. The entire molecule can rotate or an atom or group of atoms can rotate about the axis of a bond. Just like in physics, in chemistry we can interchange classical and quantum treatments for systems. it just depends on what we are interested in, what degree of approximation we are willing to accept, and what the scale of the system is. A one molecule system gets treated very differently than [math] 10^23 [/math] molecules.

 

Some people even treat a single protein as a classical object because some of them have molecular weights in the 100,000's. I don't think we have to worry about an enormous hemoglobin molecule tunneling through a cell membrane. But we do have to worry about an electron pair tunneling through the nitrogen nucleus in an ammonia molecule, if we are interested in molecular geometry.

[lemur]

For that we have molecular dynamics, density functional theory (DFT), and a host of other molecular modeling techniques. We can also observe the structures of molecules with pretty much any kind of spectroscopy. We chemists have gotten really good (shameless self glorification ) at that since the advent of COSY 2-dimensional nuclear magnetic resonance spectroscopy.

Meaning you can make photos and/or videos of individual molecules? Down to what scale?

 

Some people even treat a single protein as a classical object because some of them have molecular weights in the 100,000's. I don't think we have to worry about an enormous hemoglobin molecule tunneling through a cell membrane. But we do have to worry about an electron pair tunneling through the nitrogen nucleus in an ammonia molecule, if we are interested in molecular geometry.

Why does it matter if an electron pair tunnels through the nucleus? Does that change the shape/orientation of the molecule?

 

 

[swansont]

Why not? Wouldn't it depend on the shape-maleability of the molecule at a given energy-level? E.g. if a water molecule is compressed against others to its minimum volume, it would be a liquid, but if the repelling-energy among the molecules decreased to a level where the shape-maleability and overall average vibrational energy wasn't sufficient for them to slide around each other, they would crystalize into a solid.

 

Idk, what basis is there for saying the atoms are in fixed positions relative to each other? What determines the position of their bond-connections?

 

It can't for a solid, because it can't. The atoms have to be in nominally fixed positions. If they weren't, it wouldn't be a solid.

 

For an individual molecule, you have to look at the forces involved. Systems tend to their minimum energy, based on the orbitals present, which is what dictates the bond angles they have. One bond that shares electrons modifies the shape of the orbitals involved, and the other orbitals are also modified because the electrons repel. If you change the bond angle, it requires that you have more energy, because you have to do work. The amount of work/energy is related to the size of the change. Significant changes in the angle require energies similar to the binding energy, so if you added the amount of energy to get that kind of motion, you would rip the molecule apart.

[mississippichem]

One bond that shares electrons modifies the shape of the orbitals involved, and the other orbitals are also modified because the electrons repel.

 

I'm glad you mentioned this. I think people have trouble understanding that bonds are not confined and the orbitals of a molecule exist as a dynamic, interdependent set. You can't just excite one without exciting the whole set. Many of these folks are victims of the "solar system" atomic model which also doesn't lend itself to any kind of intuition about bond angles. Bah humbug.

 

Lemur: this answers your question about the tunneling of electrons through the nucleus and why it matters.

[lemur]

It can't for a solid, because it can't. The atoms have to be in nominally fixed positions. If they weren't, it wouldn't be a solid.

But how would you know whether the nominal fixity was due to interaction among the molecules of the solid or their internal configuration independent of how they are arranged vis-a-vis other molecules?

 

For an individual molecule, you have to look at the forces involved. Systems tend to their minimum energy, based on the orbitals present, which is what dictates the bond angles they have. One bond that shares electrons modifies the shape of the orbitals involved, and the other orbitals are also modified because the electrons repel. If you change the bond angle, it requires that you have more energy, because you have to do work. The amount of work/energy is related to the size of the change. Significant changes in the angle require energies similar to the binding energy, so if you added the amount of energy to get that kind of motion, you would rip the molecule apart.

I understand the ripping apart within a solid, because there are other molecules fixed in position to create friction for the moving molecule, just like pulling a plastic sack full of billiard balls out from the middle of a pile of such sacks would tear the sack. But if molecules in a liquid can "roll around" past each other, why couldn't their atomic-parts also be "rolling around" and shape-changing according to the flexibility of the bonding energy that holds the nuclei together? I realize that this is hypothetical in light of mississippichem's claims about 2D spectroscopy photography/video, but it still seems plausible to me that if molecular bonding occurs through the sharing of electrons that generally circulate around their nuclei, that the bonds themselves and the bonded nuclei could be in relative dynamic motion until fixed by external constraints.

 

 

[swansont]

But how would you know whether the nominal fixity was due to interaction among the molecules of the solid or their internal configuration independent of how they are arranged vis-a-vis other molecules?

 

 

I understand the ripping apart within a solid, because there are other molecules fixed in position to create friction for the moving molecule, just like pulling a plastic sack full of billiard balls out from the middle of a pile of such sacks would tear the sack. But if molecules in a liquid can "roll around" past each other, why couldn't their atomic-parts also be "rolling around" and shape-changing according to the flexibility of the bonding energy that holds the nuclei together? I realize that this is hypothetical in light of mississippichem's claims about 2D spectroscopy photography/video, but it still seems plausible to me that if molecular bonding occurs through the sharing of electrons that generally circulate around their nuclei, that the bonds themselves and the bonded nuclei could be in relative dynamic motion until fixed by external constraints.

 

As I just said, it' a matter of energy. Rephrasing the question a little isn't going to change the answer.

 

The enthalpy of vaporization for water (which is large owing to the strong bonding) is 40.54 kJ/mol. If you divide by Avogadros number, this is less than 0.5 eV per molecule of total bonding to its neighbors (so individual pair bonding would be even smaller). That's why the molecules can roll around each other — those bonds are much weaker than the ones holding the molecule together. If they weren't, the molecules would always be falling apart.

[lemur]

As I just said, it' a matter of energy. Rephrasing the question a little isn't going to change the answer.

 

The enthalpy of vaporization for water (which is large owing to the strong bonding) is 40.54 kJ/mol. If you divide by Avogadros number, this is less than 0.5 eV per molecule of total bonding to its neighbors (so individual pair bonding would be even smaller). That's why the molecules can roll around each other — those bonds are much weaker than the ones holding the molecule together. If they weren't, the molecules would always be falling apart.

But that only describes the fixity between different molecules, not that between the atoms in each molecule. You make it sound like it is automatically the case that if bonds are strong enough to prevent detachment, they must also fix the positions of the atoms relative to each other. It's like a hammer thrower who doesn't let go - the chain need not be rigid for the relative configuration of hammer and thrower to remain basically fixed and move together as a moving system. Why couldn't electron bonds allow more intramolecular motion at one energy level and less at another? Metals get progressively softer as energy/temperature increases, and they're electron-rich.

[swansont]

But that only describes the fixity between different molecules, not that between the atoms in each molecule.

 

You asked the question about atoms sliding over each other. Now you complain that I answered it?

 

You make it sound like it is automatically the case that if bonds are strong enough to prevent detachment, they must also fix the positions of the atoms relative to each other. It's like a hammer thrower who doesn't let go - the chain need not be rigid for the relative configuration of hammer and thrower to remain basically fixed and move together as a moving system. Why couldn't electron bonds allow more intramolecular motion at one energy level and less at another? Metals get progressively softer as energy/temperature increases, and they're electron-rich.

 

It's a matter of the Energy

 

Hmmm. Answer still hasn't changed.

 

Electrons separated by 0.2 nm (water-molecule-scale size) have a potential energy of about 7 eV; this scales as 1/r. Thermal energy (kT) is about 0.025 eV at room temperature; this tells you how much energy is in vibrations and rotations. You can't move the electrons much with that amount of energy.

 

BTW, a solid getting softer is a matter of intermolecular forces, which you just got done implying wasn't the topic you wanted to discuss.

[John Cuthber]

Gas phase electron diffraction can tell you the shapes and sizes of molecules, You can then look at the solid phase by X ray diffraction.

The molecules are often pretty much the same in both cases.

[lemur]

You asked the question about atoms sliding over each other. Now you complain that I answered it?

Not complain but question your explanation.

 

Electrons separated by 0.2 nm (water-molecule-scale size) have a potential energy of about 7 eV; this scales as 1/r. Thermal energy (kT) is about 0.025 eV at room temperature; this tells you how much energy is in vibrations and rotations. You can't move the electrons much with that amount of energy.

If electrons are particles moving along geodesic paths, the energy wouldn't go into moving them but rather changing their relations relative to each other and the other particles they interact with, right?

 

BTW, a solid getting softer is a matter of intermolecular forces, which you just got done implying wasn't the topic you wanted to discuss.

It wasn't. I was just giving that as an easily recognizable examples of how electrons could become more fluid as energy increased. You make it very difficult to compare and contrast related phenomena when you problematize every comparison as being a separate topic.

 

 

[swansont]

Not complain but question your explanation.

 

No, not really. I gave an example of strong intermolecular forces and you didn't question it at all. You pointed out that it didn't answer some other question.

 

If electrons are particles moving along geodesic paths, the energy wouldn't go into moving them but rather changing their relations relative to each other and the other particles they interact with, right?

 

But electrons aren't moving along some geodesic path, which has been explained to you many times now.

 

It wasn't. I was just giving that as an easily recognizable examples of how electrons could become more fluid as energy increased. You make it very difficult to compare and contrast related phenomena when you problematize every comparison as being a separate topic.

 

You were the one who implied they were unrelated phenomena.

 

 

You asked if molecules are fixed or if they "swarm." You got an answer (several, really) saying "closer to fixed." Your objection, though, is not that the answers lacked detail — you didn't ask for more detail. You didn't ask for numbers. You immediately challenged that, solely on the basis that it didn't make sense to you. And you continue to object to any answer you don't like.

 

The forum idea here is pretty simple:

 

— If you want science questions answered, there are people here who like to answer them and will do their best to do so. If you need clarification of an answer, ask for it.

 

— If you want to propose some other model of how things happen, you can present and defend it in speculations. Be prepared to answer challenges to it

 

What you really can't do is ask a question and then try and deconstruct the answer with your own model of how you think things should work. When an answer contradicts your personal model, you can't just assume that the answer is wrong, especially if there is no reason to say that your model is correct. "My model makes sense to me" is insufficient.

 

Pick a path.

[lemur]

No, not really. I gave an example of strong intermolecular forces and you didn't question it at all. You pointed out that it didn't answer some other question.

But that "other question" doesn't matter b/c it's not the one you want to deal with, right? And yet you criticize me for not accepting your answer as the pertinent one?

 

But electrons aren't moving along some geodesic path, which has been explained to you many times now.

But you're necessarily uncertain of what they're doing, aren't you? Isn't that why you plot probability curves and wave functions for them? When a free electron moves from A to B, it doesn't travel in a straight line? When it is affected by a positive electrostatic field, its path doesn't curve into the field?

 

You asked if molecules are fixed or if they "swarm." You got an answer (several, really) saying "closer to fixed." Your objection, though, is not that the answers lacked detail — you didn't ask for more detail. You didn't ask for numbers. You immediately challenged that, solely on the basis that it didn't make sense to you. And you continue to object to any answer you don't like.

Don't mistake that for rejection, though. I was and am interested in what you experts have to say about it, and I am certainly not dismissing anything you say. All I am voicing is my reasoning for why it makes more sense for particles to move freely relative to each other if there isn't some fixing mechanism that causes them to attach at specific points. Mississippichem's explanation that it has to do with the geometry of the charges made the most sense because it implied, as I understood it, that without limiting geometry, these particles would move geodesically. Yes, I understand electrons do weird things like tunnel and entangle, etc. but at some level atoms have to start following geodesic paths, so I was trying to figure out why they would or wouldn't do that at the intramolecular level and learn what experts know in the process.

 

— If you want science questions answered, there are people here who like to answer them and will do their best to do so. If you need clarification of an answer, ask for it.

That's a given, but maybe I should say so more explicitly instead of just expressing my response, which should show when I'm not getting something because it wasn't clear enough to me.

 

— If you want to propose some other model of how things happen, you can present and defend it in speculations. Be prepared to answer challenges to it

If I was doing that, I'd do it in speculations. All I was doing in this thread is expressing what is logical according to spatial reasoning. Yes, I know you are going to say that's classical mechanics and thus inapplicable but, as I said, I'm trying to figure out at what level classical mechanics applies. Since molecules are described as having "shapes," it seems reasonable to apply spatial reasoning to how those shapes are constituted and maintained, no?

 

What you really can't do is ask a question and then try and deconstruct the answer with your own model of how you think things should work. When an answer contradicts your personal model, you can't just assume that the answer is wrong, especially if there is no reason to say that your model is correct. "My model makes sense to me" is insufficient.

I actually immediately accepted Mississippichem's explanation of the bonds being like connective springs that oscillate and have angles, etc. as being legitimate. The reason I brought up my intuitive logic that it could happen another way is that I thought he or someone else might be able to give me an example of why it can't work that other way. That way I can exclude what I think not just on the basis that it's not standard knowledge but also because it has been thought of and falsified OR that it can be clearly falsified on the basis of known information. That is just clarification of why a theory works one way and not another - it's not speculating about new theories (yet), though I suppose it could evolve into that - but then I would repost it in speculations.