Molecular orbital

IPC Friedrich-Schiller-Universität Jena1

Molecular orbital

Electronic configuration

Electronic states

UV/Vis-absorption spectrum

4. Molecular many electron systems: electronic & nuclear movement

* : antibinding



J = 0

J = 1

J = 2

J = 3

J = 4

Rot

atio

nal l

evel

s

v = 0

v = 1

v = 0

v = 1

v = 3

v = 4

Vib

ratio

nal l

evel

s

Exc

itatio

n [1

0-15

s]

Internal conversion[10-14 s]

Fluorescence[10-9 s]

Intersystem crossing

Phosphorescence[10-3 s]

S0

S1

S2

S3

S4

T1

Tn

IR- & NIR-spectroscopy

UV-VIS-spectroscopyMicrowave-spectroscopy

4. Molecular many electron systems: electronic & nuclear movement Jablonski-Scheme


Interpret electronic absorption spectra based on ||2 of the vibrational levels

electronic transitions (~10-16s) are much faster than the vibrational period (~10-13s) of a given molecule

thus nuclear coordinates do not change during transition

5.1 Franck-Condon principle

5. UV-Vis-Absorption


= degree of redistribution of electron density during transition

= degree of similarity of nuclear configuration between vibrational wavefunctions of initial and final states.

Transition probability is proportional to the square modulus of the overlap integral between vibrational wavefunctions of the two electronic states = Franck-Condon-Factor:




|i

|f|i|f




5.2 Molecular electronic transitions


Molecular electronic transitions: valence electrons are excited from one energy level to a higher energy level.

Electrons residing in the HOMO of a sigma bond can get excited to the LUMO of that bond: σ → σ* transition.

Promotion of an electron from a π-bonding orbital to an antibonding π* orbital: π → π* transition.

Auxochromes with free electron pairs denoted as n have their own transitions, as do aromatic pi bond transitions.

The following molecular electronic transitions exist:σ → σ* π → π* n → σ* n → π* aromatic π → aromatic π*

* n* n*

(C=C, C=O) (C=O, C=N, C=S) (–Hal, -S-, -Se- etc.)


5.2 Transition metal complexes

A biologically very important group of metal complex bonds are the porphyrin pigments such as:

Hemoglobin (pigment of the blood, central ion Fe2+)

Cytochromes of respiratory chain

Chlorophyll (green molecules in leaves, central atom Mg)


octahedron structure motive

The four ligand positions of the base of the pyramid are occupied by the lone electron pairs of nitrogen atoms of the plane porphyrin ring system

The two corners of the pyramid are occupied by specific amino acids (histidine) and/or by an oxygen molecule (hemoglobin)

Heme-group


Cytochrome C:

Pyramid corners of heme unit are occupied by N-atom of a histidine residue and S-atom of a mezhionine residue

Redox change of cytochromes predominatly occurs at the central iron atom [(Fe2+) ↔ (Fe3+)]

-Peaks= sensitive for redox change(analysis of mitochondria)





Hemoglobin (iron is always found as Fe2+)Arterial oxygen-loaded blood = light redBlood in veines free of oxygen = deep red

Desoxy Hemoglobin(Fe2+ / 92 pm / high spin)

End-on coordination of O2

(Fe2+ / 75 pm / low spin)

0,4 A°

B



Fundamental terms:

Polarimetry, optical rotation, circular birefringence: turning of the plane of linearly polarized light

Optically active molecules exhibit different refractive indices for right nR and left nL polarized light nR ≠ nL

Optical rotatory dispersion (ORD):Wavelength dependency of rotation

Allows determination of absolute configuration of chiral molecules

Circular dichroism:linearly polarized light is transformed into elliptically polarized light upon traveling through matter

Different absorption coefficients for left and right circular polarized light (R ≠ L ).

5.3 Polarimetry & Optical rotatory dispersion & Circular dichroism



Polarimetry What happens if light interacts with chiral molecules?

Enantiomeric molecules interact differently with circular polarized light. Polarizability depends on direction of rotation of incoming circular polarized light Optically active substances exhibit different refractive indices for right nR and left

nL polarized light nR ≠ nL




Polarimetry: Linearly polarized light Different refractive index for its left and right circular constituents Relative phase shift between left and rightVector addition yields again linear polarized light with rotated polarization plane



Sample cell

Incoming light

Transmitted light

phaseshift

Ey

Ex


Polarimetry:

For follows:

Na-D line = 589 nm

2-Butanol = 11.2° (Messwert)

T = 20°C

l = 1dm

Difference is rather small!

Due to the different refractive indices a phase difference = L –R

builds up in the active medium which is proportional to the path length l.

When exiting the medium linear polarized light where the oscillation plane is rotated by /2 arises

It follows:

l



l

nn RL )(

79

1066.31.0deg180

10589deg2.11)(

m

mnn RL


Polarimetry

The measured angle-of-rotation results in:

Specific rotation is a substance specific constant (dependent on temperature and wavelength) and is a measure for the optical activity of this particular substance.

Molar rotation is defined as follows:

in angular degree, length in decimeter(!) and c in g ml-1.




Optical rotatory dispersion(ORD)

ORD measures molar rotation [] as function of the wavelength!

If the substance to be investigated has no electronic absorption within the investigated spectral region the following ORD spectra are obtained

Reason: refractive indices for left and right polarized light change differently with wavelength (rotatory dispersion is proportional to refractive index difference).

ORD-spectra of 17ß- and 17-

hydroxy-5-androstan




Optical rotatory dispersion(ORD)

Refractive indices for left and right polarized light exhibit anomalous dispersion in the range of an absorption band

Cotton effect

Positiv negativ Cotton effect




Optical rotatory dispersion(ORD) Quantitative theoretical correlations between

molecular structure and ORD (Cotton effect) are difficult to derive;

Empirical investigation are important: ORD has been successfully applied for constitution elucidation e.g. to position carbonyl groups in complex optically active molecules.

By comparing ORD curves for structurally isomeric ketons (reference material needed!) the keto group can be localized.

ORD curve of molecule (2) is a superposition of a negative curve i.e. molecular skeleton without a chromophore (background curve) and a positive Cotton curve (C=O chromophore).

ORD-Spektren von 5-Spirostan und 5-

Spirostan-3-on


5.3 Polarimety & Optical rotatory dispersion & Circular dichroism


Circular Dichroism (CD)

Enantiomeric molecules exhibit besides different refractive indices for left and right circular polarized light also different absorption coefficients:

It follows:

left and right circular components ORD : different retardation CD also different absorption

Transmitted light is elliptically polarized.

Circular Dichroism



Ey

Ex



[10-1 × deg × cm2 × g-1]

[10 × deg × cm2 × mol-1]

The ratio between short and the long elliptical axis is defined as tangent of an angle , the so called ellipticity (tan = b/a):

a = ER + EL

b = ER - EL

The specific ellipticity is defined as:

where 0bs is the experimentally determined

ellipticity.

The molar ellipticity is defined as:





Signal heights are displayed either as absorption difference or as ellipticity [].

Molar ellipticity and circular dichroism can be interconverted:

Correlation between ORD and CD:

ORD is based on the different refractive indices of left and right circular polarized light (nR ≠ nL )

CD results from the different absorption behavior for left and right circular polarized light (R ≠ L)

Connection of both phenomena via Kronig-Kramer relationship:

This relation allows the calculation of an ORD value for a particular wavelength from the corresponding CD spectrum

grad cm2 dmol-1


5.3 Polarimety & Optical rotatory dispersion & Circular dichroism


Circular Dichroismus (CD) Simple model:

For an electronic transition to be CD active the following must be true:µe is the electronic transition dipole moment

(= linear displacement of electrons upon transition into an excited state) µm is the magnetic transition moment

(= radial displacement of electrons upon excited state transition)

Scalar product is characterized by a helical electron displacement.

Depending on the chirality of the helix preferably more right or left circular polarized light will be absorbed, respectively.

Electronic transition Magnetic transition Optical activity




Circular Dichroism (CD) Application field:

-sheet

random coil

-helix




Circular Dichroism (CD) Application field:

Typical reference CD spectra:

Poly-L-Lysine in different conformations:

-Helix, -sheet and random coil.

Temperature

dependent CD spectra

of insuline:

For increasing

temperature the

molecule changes

form -helix into the

denaturated random

coil form with ß-sheet

contributions.




Vibrational transitions in the IR and NIR

VCD monitors difference in absorption between left and right circular polarized light

Vibrational-Circular-Dichroism (VCD)

v=0

v=1




Determination of the absoluteconfiguration

Vibrational-Circular-Dichroism (VCD) ()-Mirtazapine

Advantages VCD vs. CD

Electronic chromophore is not necessary

VCD exhibits more characterisitic bands




6. Fluorescence Spectroscopy


J = 0

J = 1

J = 2

J = 3

J = 4

Rot

atio

nal l

evel

s

v = 0

v = 1

v = 0

v = 1

v = 3

v = 4

Vib

ratio

nal l

evel

s

Exc

itatio

n [1

0-15

s]

Internal conversion[10-14 s]

Fluorescence[10-9 s]

Intersystem crossing

Phosphorescence[10-3 s]

S0

S1

S2

S3

S4

T1

Tn

IR- & NIR-spectroscopy

UV-VIS-spectroscopyMicrowave-spectroscopy

6. Basic concepts in fluorescence spectroscopy


Energy differences between vibrational states which determine vibronic band intensities are very often the same for ground and electronic excited state

Emission spectrum = mirror image of absorption spectrum

Emission bands are shifted bathochromically i.e. to higher wavelengths

= Stokes-Shift due to vibrational energy

relaxation within electronic excited state

6.1 Stokes-Shift

6. Basic concepts in fluorescence spectroscopy

Molecular orbital

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