# Molecular Orbital & Normal Modes

1. Feb 17, 2015

### lucas_

I'd like to ask a couple of questions.
As a solid object gets bigger, the molecular orbital (combinations of all single atom orbitals) has greater size too? For a one inch square object (of closely packed molecules like crystals), what is its molecular orbital size compared to a one foot square crystal object?

Second. When photons hit an object and the molecules. They are absorbed as molecular vibrations and redistribution into normal modes. The molecular orbital is not affected because you need much higher energy photons to affect the electronic orbitals. So what is the connection of molecular orbital to molecular vibrations?

2. Feb 18, 2015

### DrDu

Yes, you may think of the molecular wavefunctions to extend over the whole crystal, although this has hardly observable consequences. I.e., you could also assume that they extend only over say 1 $\mu$m. Remember that molecular orbitals are rather a theoretical construct than a physical reality. For many types of solids, e.g. isolators, you could use alternative descriptions, like Valence Bond theory which use atomic orbitals and get equal results.

Second: In the Born Oppenheimer approximation, the molecular orbitals depend parametrically on the position on the nuclei and this is also the mechanism they generate a potential for the motion of the nuclei.

3. Feb 18, 2015

### lucas_

Raman and IR Spectroscopy deal directly with the molecular vibrations. I was asking what is the use of knowing the molecular orbital.. would these affect intermolecular bonding? is there some spectroscopy that deal with them?

4. Feb 18, 2015

### hokhani

Do you mean by the statement above:
In each instant of time, the electronic energy depends on the instantaneous positions of nuclei and also this electronic energy is a potential term for nuclear Hamiltonian?

5. Feb 18, 2015

### DrDu

Yes, exactly.

6. Feb 18, 2015

### lucas_

So understanding molecular orbits is sort of making bookkeeping of he nucleus positions. But what happens when you introduced energy to it in the form of photons. Do we need solely gamma rays to affect the molecular orbital or do low frequency IR can affect it too. What is the relationship between thermal properties of the molecules with reference to the molecular orbital? Can you store energy in the molecular orbitals and transfer these thermal energy to the molecular vibrations?

7. Feb 18, 2015

### DrDu

IR won't induce transirions between electronic states, but visible or UV light may.
Why don't you read an introductory text on spectroscopy?

8. Feb 18, 2015

### lucas_

I was familiar with spectroscopy as it relates to vibrational modes of the molecules. But I'm not familiar with spectroscopy that deals with molecular orbitals. What are the ways to turn Bonding orbital into Antibonding orbital disentangling the molecules (or reforming them at other configurations)? Do we study Molecular Orbitals to understand bonding solely or is it active such that we can send photons to them manipulating the nuclei?

9. Feb 19, 2015

### DrDu

[QUOTE="lucas_, post: 5014565, member: ]Do we study Molecular Orbitals to understand bonding solely or is it active such that we can send photons to them manipulating the nuclei?[/QUOTE]
Yes, look up photochemistry and pump probe spectroscopy.

10. Feb 19, 2015

### lucas_

Dr.Du I studied all your recommendations and I came across Vibronic Coupling and have a couple of questions (I have studied it too).

Most molecules can be analyzed via the Bohr-Oppenheimer Approximations. Does it mean Vibronic Coupling is active in all molecules and we just ignore it mostly? or do the latter only exist for certain molecular combinations? Can you give a more everyday example such as NaCl? Do all objects have vibronic coupling? How do you distinguish what objects have it or not? Most of what I read about it is that vibronic coupling is difficult to analyze hence ignored.

11. Feb 20, 2015

### DrDu

Vibronic coupling definitely is important in spectroscopy. I would distinguish at least two different kinds: In the first one, the nuclear coordinate dependence of the Born-Oppenheimer wavefunction plays a role. Specifically, the wavefunction can be expanded around the equilibrium position $R_0$: $\psi(R,r)=\psi(R_0,r)+(R-R_0)\psi'(R_0,r)+\cdots$. The dependence on the nuclear coordinate $R-R_0$ can make an otherwise electronically forbidden transition allowed. This is common in d-d transitions and responsible for the bluish colour of copper sulphate or rose colour of manganum (II) salts.
The second kind of effect corresponds to non-adiabatic coupling beyond the Born Oppenheimer approximation. This is usually not so important for the ground state but of high importance for excited states. Namely it leads to the very fast radiationless decay of electronically excited states back to the ground state. In this process the electronic excitation energy is converted into vibrational quanta and so into heat, at the end.
This coupling is responsible for the fact that there are only few strongly fluorescent substances.

12. Feb 20, 2015

### lucas_

Which of the two kinds occur in daily common substance like silicon, carbon, hydrogen for instance? We commonly ignored electronic transition in the equipartitions of energy and just focus on vibrational, translational and rotational degrees of freedom. Does vibronic coupling entail that in ALL substances, there is a contribution of the electronic degrees of freedom in the heat capacity but just ignored due to the very tiny values? I want to know how to tell what substance (and how to tell which) Is sensitive to vibronic coupling if this is not present in all substances. Thank you.

13. Feb 21, 2015

### DrDu

Vibronic coupling has practically no influence on the thermodynamic properties of materials for several reasons:
1. The excited electronic states are energetically too high to be excitable by thermal energies.
2. The Born-Oppenheimer approximation is very good for the ground state.
3. Even for the thermodynamical properties of excited states, the vibronic coupling plays only a minor role due to some variant of the Bohr van Leeuven theorem.

The following article is the specialists reference on vibronic couplings:
Köppel, H., W. Domcke, and L. S. Cederbaum. "Multimode Molecular Dynamics Beyond the Born‐Oppenheimer Approximation." Advances in Chemical Physics, Volume 57 (2007): 59-246.

14. Feb 21, 2015

### lucas_

The above reference is not available but I tried to search other materials and topics like conical intersections and actually read it, and it seems there is not a lot of materials for laymen available. I think vibronic coupling is related to photochemistry since electron transition is sensitive to visible and UV light. In the human body and biochemistry what parts is sensitive to such vibronic coupling? What particular chemical reactions? Do you believe it can either suppress or accelerate chemical reactions? Can you give an obvious example. Thanks.

15. Feb 22, 2015

### DrDu

There are two important photochemical reactions in the body: the cis-trans isomerisations of retinal in the light receptors in the eye and vitamin D synthesis.

16. Feb 22, 2015

### lucas_

Are you saying vibronic coupling is not important for non photochemical applications? I read that any chemical reactions sensitive to conical interactions will be sensitive to vibronic coupling. Aren't there any chemical reactions in the body (like enzymes) that have conical interactions (ignoring photochemical stuff like retina or vitamin D)? From memory.. what chemical reactions can you give by rule of thumb that is sensitive to conical interactions (http://en.wikipedia.org/wiki/Conical_intersection)?
I'm still a bit confused how to distinguish.

Hope others like atty can assist too. Thanks.

17. Feb 22, 2015

### DrDu

I can't think of anyone. While there may be conical intersections between the ground and excited PES, these are not thermally accessible. The only case where CI's are of some importance for the ground state is in the case of the Jahn Teller effect although even there, the nuclear vibrations won't reach the CI.

18. Feb 22, 2015

### lucas_

DNA is sensitive to it. http://en.wikipedia.org/wiki/Conical_intersection

"For example, the stability of DNA with respect to the UV irradiation is due to such conical intersection.[1] The molecular wave packet excited to some electronic excited state by the UV photon follows the slope of the potential energy surface and reaches the conical intersection from above. At this point the very large vibronic coupling induces a non-radiative transition (surface-hopping) which leads the molecule back to its electronic ground state."

I don't like outdoors. So if our body needs to be exposed to natural sunlight and some UV to activate our DNA and genes. Then I need to make huge effort to go outdoor. Studying this would give me the motivation. Are you sure our DNA doesn't need constant exposure to light to be optimum? Why is our DNA sensitive to conical intersection?

19. Feb 22, 2015

### DrDu

But you were asking for non-photochemical reactions?

20. Feb 22, 2015

### lucas_

What? But DNA thing is a non-photochemical reaction. Do you consider it as photochemical? I seemed to read that many chemical reactions can have vibronic coupling. Are you saying only photochemistry reactions can support vibronic coupling? Or maybe there are many materials or substance that we don't know are photochemical active? (those with conical intersection)?

There seems many concept. Photochemical active vs non-photochemical active. Excited states and ground states. I'm including excited states in the conical intersection thing. So if they can be in excited states.. you include DNA as suppoting conical intersection? What other chemical reactions in the body have conical intersection in the *excited* state part?