[konstantine.lg]

Hi guys! I study medicine and now I am havin some problems with chemistry as I try to make my experiment for university.
Well I have 2 questions, which I would like to make clear. First is about orbitals:
1. As far as I understand orbital is just a function and how we can see from its radial distribution function graphic,  some orbitals may overlap. So we dont have a certain pathway for electron, we can only see a probability of electron's being in a certain place. Furthemore this probailities can overlap. The qustion is: when an orbital has only a certain energy value and we have to add a difference of energy to make electron "jump" to another level, does it means that it makes some kind of "teleportation" on another energy level? Sorry if this qustion may sound silly but that is what I really cannot get from out teacher in the university.

And the second qustion is relating to Bond-dissociation energy. When an ion comes throw the ion channel in membran of axon, it has to get off his water-molecules which make a water-cover because of positive-charged ion and dipol-features of H2O. This will be stimulated throw very polar rests of aminoacids, because (how it is explaned in the book) its energeticly more benefitial. And now I have a qustion: why its energeticly more favourable for ion to bind with very polar rests of amino-acids than with water-dipols?

[Corribus]

Hi guys! I study medicine and now I am havin some problems with chemistry as I try to make my experiment for university.
Well I have 2 questions, which I would like to make clear. First is about orbitals:
1. As far as I understand orbital is just a function and how we can see from its radial distribution function graphic,  some orbitals may overlap. So we dont have a certain pathway for electron, we can only see a probability of electron's being in a certain place. Furthemore this probailities can overlap. The qustion is: when an orbital has only a certain energy value and we have to add a difference of energy to make electron "jump" to another level, does it means that it makes some kind of "teleportation" on another energy level? Sorry if this qustion may sound silly but that is what I really cannot get from out teacher in the university.

There is a spatial context to whether an electronic (or any quantum state) transition can occur. It's not "teleportation", in that the electron goes from one location instantly to another. Because the position of an electron cannot be defined with infinite precision, the overlap of time averaged product distribution functions (products of wavefunctions) are utilized (often called an overlap integral).  But for orbitals co-located at a single origin, other selection rules usually dominate the probability of a transition occurring (e.g., angular momentum and spin conservation rules).

Spatial considerations become much more relevant for the electron transitions of molecules, in which the vibrational wavefunction overlap is a critical parameter for determining whether a transition can occur. This is known as the Franck-Condon factor.

And the second qustion is relating to Bond-dissociation energy. When an ion comes throw the ion channel in membran of axon, it has to get off his water-molecules which make a water-cover because of positive-charged ion and dipol-features of H2O. This will be stimulated throw very polar rests of aminoacids, because (how it is explaned in the book) its energeticly more benefitial. And now I have a qustion: why its energeticly more favourable for ion to bind with very polar rests of amino-acids than with water-dipols?

Sadly, I'm having trouble following the English. Maybe you could clarify?

[konstantine.lg]

And the second qustion is relating to Bond-dissociation energy. When an ion comes throw the ion channel in membran of axon, it has to get off his water-molecules which make a water-cover because of positive-charged ion and dipol-features of H2O. This will be stimulated throw very polar rests of aminoacids, because (how it is explaned in the book) its energeticly more benefitial. And now I have a qustion: why its energeticly more favourable for ion to bind with very polar rests of amino-acids than with water-dipols?

Sadly, I'm having trouble following the English. Maybe you could clarify?

Well I will try one more time
As the ion is positiv-charged and water molecules are dipoles, they will surround the ion in extracellular matrix due to electrostatic force, right? Different ions have different diameter and different distance from outer orbital to protons, so that depending on nuclear charge and distance to it, different  atoms will have different electrostatic interaction with water molecules. K-ion will have more water dipols arround him then Na-ion, because the first one has less distance to nuclear and will attract water more than Na (as experiments show the distance is here more important that nuclear charge).
Now about selectivity of ion-channels in cellular membran of axon: the selectivity filter, which consists of strongly polar amino acid residues, will replace with this residues the hydration water of ion. So depending on residues of filter it can replace only certain water hydration. And because removing of this hydration water is for ion unfavorable, it will only than removed, when binding to amino acid residuces of selectivity filter will energetically more advantageous. So the question is: on what is this based? I mean why is binding to residues is more favorable  for ion then to water?

[konstantine.lg]

Does anybody have any idea about that stuff?

[Enthalpy]

Some elements of answer...

Rather than "the probability of being at a place", I prefer something like "the chances one would have to find it around a place IF he decided to use some method that permits a more accurate localization", because

• If you localize the electron better than it was, then it's not that orbital any more
• Particle interactions do not happen at points. They happen over the common volume of the involved particles, which can be much bigger than an atom, for instance at a dye molecule or in a  semiconductor component.

Orbitals overlap very much. Since they are orthogonal to an other, that is, the integral of their product is zero, it is necessary: at least one orbital must change its sign in the overlapping volume.

During the absorption or emission of a photon, the electron's wavefunction is a linear combination of both orbitals. Schrö's equation being linear, this is still a solution, but this solution isn't stationary (=not an orbital): it evolves over time.

So the electron does not have to hop between the orbitals, and takes its time to change its shape. It's called the fluorescence time, and defines the duration of the emitted photon when nothing else (collisions, resonant cavity...) shortens the process, and as a consequence, it defines the spectral width of the transition.

By the way, "teleportation" has a different meaning in QM, which hasn't well chosen the word.

If the initial and final orbitals have the proper relationship (difference between the momenta = 1) then the electron can change from being one orbital to being the other by absorbing or emitting a photon. With that unit difference, the weighed sum of both orbitals shows an eccentric bulge that moves over time (it has a classical position, speed, acceleration) at the frequency of the photon, and the electron's charge makes the rest.

I've paraphrased here other discussions...
http://www.chemicalforums.com/index.php?topic=76309.0
http://www.scienceforums.net/topic/70011-absorption-spectra/
http://www.scienceforums.net/topic/82768-do-photons-influence-the-leap-of-an-electron/
http://www.scienceforums.net/topic/81151-between-the-quantum-orbitals/

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I don't know axons well enough, but it's perfectly normal that an ion sticks sometimes to water molecules and sometimes to other molecules. It depends on how "sticky" the molecules are, and even less favourable molecules can get a share of the available ions just because the ambient heat provides the energy difference - we're speaking here of small "sticking" energies, similar to the energy of ambient heat, and these effects are reversible and temporary.

Where at the other molecule: I imagine that for instance a K⁺ can leave the oxygen of water to stick at an oxygen or nitrogen atom from an amide function. Other people here know it better than I.

[konstantine.lg]

Thank you very much! I've explained it pretty nice. I would like you to clarify your words here:

Schrö's equation being linear, this is still a solution, but this solution isn't stationary (=not an orbital): it evolves over time.

[Enthalpy]

With Schrö(dinger), I meant old Erwin.

The wavefunction of an electron depends on 3 spatial dimension and the time - depending on what you're interested in, you can aggregate the spin to that, and it should be all unless I make a blunder.

Some wavefunctions are "stationary", that is, only their phase varies like exp(2iπEt/h) where E is a definite energy, and their amplitude depends only on x, y, z but not t. So for instance the probability |ψ|² to find the electron around a location does not depend on the time, hence "stationary".

When the electron is trapped in an atom, that is, is has too little energy to escape, stationary wavefunctions are called "orbitals". These are especially interesting because their energies are well spaced, so usual heat doesn't send the electron from one orbital to the other; as a consequence, at equilibrium, the electrons fill the deepest available orbitals. That's simple (...except that electrons interact, so the filling depends an all electrons, and the orbitals aren't exactly the relatively simple ones we know for a hydrogen atom).

The orbitals are centered on the nucleus and don't move, that is, |ψ|² is static. This is why the electron doesn't radiate in an atom at rest. That's why QM was needed historically , and it solves it brilliantly.

Though, the stationary solutions are not the only ones. ψ₁ and ψ₂ being solutions, any a₁*ψ₁ + a₂*ψ₂ is a solution too. While orbitals have definite energies, their linear combinations have no definite energy as they can't be written as ψ(x,y,z)*exp(2iπEt/h), and they evolve over time.

Take a weighed sum of 1s and 2p orbitals. 1s is spherical, so apart from the exp(2iπE_1St/h) phase, it has the same phase and sign all around the nucleus. 2p is a peacock, with one side + and the other -, all multiplied by its exp(2iπE_2Pt/h).
http://winter.group.shef.ac.uk/orbitron/ (choose in the left margin)
Now, because E_1S ≠ E_2P, and since the exp(...t) combine with the + and - to define the phase, at some t the 1s and 2p orbitals will be in phase at the right side and |ψ|² increases there and decreases at the left side, while at other t, |ψ|² increases at left. This is an eccentric position that moves over time, with a speed and acceleration.

The bulge in |ψ|² makes a complete cycle around the nucleus at the frequency (E_2P - E_1S)/h, and because the charge accelerates, it radiates light with that frequency, or a photon energy E_2P - E_1S.

By the way, peacocks are not the only solution for the 2p orbitals. Doughnuts are just as good and as fundamental; peacocks are linear combinations of doughnuts and vice versa. Other linear combinations give elliptic orbitals. And if you combine a doughnut 2p with a 1s, then the bulge in |ψ|² orbits the nucleus instead of wobbling between right and left of the nucleus. Correspondingly, the emitted photon is polarized circularly, while it's linear with a peacock 2p.

2p and 1s differ by the adequate amount, so |ψ|²'s bulge moves properly. As opposed, 2s and 1s still make a pulsating linear combination, but this pulsation is spherical, so it doesn't radiate light, as light is polarized as a vector (the photon's spin is 1, in other terms). While such linear combinations are possible, there is no radiative transition between 2s and 1s: this is a "forbidden transition". The same happens between 3d and 1s: their linear combination has two bulges orbiting the nucleus at 180° or, depending on the 3d you choose, wobbling between right and left simultaneously and both at the centre. This makes no electric dipole but a quadripole instead, which doesn't radiate efficiently an electromagnetic field, so that transition too is forbidden.