Ultraviolet-Visible (UV-VIS) Spectroscopy Gives information about conjugated p electron systems 1

Transitions between electron energy states gaps between electron energy levels are greater than those between vibrational levels gap corresponds to wavelengths between 200 and 800 nm DE = hn 2

X-axis is wavelength in nm (high energy at left, low energy at right) Conventions in UV-VIS X-axis is wavelength in nm (high energy at left, low energy at right) lmax is the wavelength of maximum absorption and is related to electronic makeup of molecule— especially p electron system Y axis is a measure of absorption of electromagnetic radiation expressed as Absorbance or molar absorptivity (e) 3

UV and Visible light cause only two kinds of electronic transitions Only organic compounds with p electrons can absorb energy in the UV/Visible region A visible spectrum is obtained if visible light is absorbed A UV spectrum is obtained if UV light is absorbed

pp* Transition in cis,trans-1,3-cyclooctadiene LUMO y3* DE = hn y2 HOMO y1 Most stable p-electron configuration p-Electron configuration of excited state 5

pp* Transition in Alkenes HOMO-LUMO energy gap is affected by substituents on double bond as HOMO-LUMO energy difference decreases (smaller DE), lmax shifts to longer wavelengths 5

Methyl groups on double bond cause lmax to shift to longer wavelengths Substituent Effects Methyl groups on double bond cause lmax to shift to longer wavelengths H H H CH3 C C H CH3 H H lmax 170 nm lmax 188 nm 5

A chromophore is the part of a molecule which absorbs UV or visible light

Effect of Conjugation on lmax

Substituent Effects Extending conjugation has a larger effect on lmax; shift is again to longer wavelengths H H H H C C H C H H H H H lmax 170 nm lmax 217 nm 5

236 nm What is carvone’s max?

The Beer–Lambert Law A = cle A = log(I / I0) c = concentration of substance in solution l = length of the cell in cm e = molar absorptivity The molar absorptivity of a compound is a constant that is characteristic of the compound at a particular wavelength

UV Spectrum of cis,trans-1,3-cyclooctadiene 2000 Molar absorptivity (e) lmax 230 nm emax 2630 1000 200 220 240 260 280 Wavelength, nm 4

lmax 217 nm (conjugated diene) Substituent Effects H C lmax 217 nm (conjugated diene) C H CH3 H3C lmax 263 nm conjugated triene plus two methyl groups 5

Both the lmax and e increase as the number of conjugated double bonds increases

An auxochrome is a substituent in a chromphore that alters the lmax and the intensity of the absorption

Uses of UV/Vis Spectroscopy Measure the rates of a reaction Determine the pKa of a compound Estimate the nucleotide composition of DNA

Figure Number: 08-08 Title: Figure 8.8 Caption: Nitroethane anion formation can be monitored by UV at 240 nm. Notes: The rate of proton removal from nitroethane can be measured by monitoring the nitroethane anion formed by the reaction.

Figure Number: 08-09 Title: Figure 8.9 Caption: Pyruvate concentration can be monitored by UV at 340 nm. Notes: The rate of reduction of pyruvate by NADH can be measured by monitoring pyruvate disappearance at 340 nm.

Figure Number: 08-10 Title: Figure 8.10 Caption: The absorbance of an aqueous solution of phenol at 287 nm as a function of pH. Notes: The absorption at 287 nm is due to the presence of phenoxide ion (the conjugate base of phenol). When half of the phenol has been converted into phenoxide, the concentrations of phenol and phenoxide are equal. At this point, pH = pKa.

Figure Number: 08-11 Title: Figure 8.11 Caption: The absorbance of a solution of DNA at 260 nm as a function of the temperature of the solution. Notes: Single-stranded DNA absorbs at 260 nm because nonbonding electrons on nitrogen atoms, which are normally tied up in hydrogen bonding together complementary strands of DNA, are free to undergo n --> p* transitions in single-stranded DNA. When the temperature has risen to the point that half of the DNA is single-stranded, DNA is said to be at its "melting" temperature, Tm.

The Visible Spectrum and Color

Biological / Physiological response Vision Biological / Physiological response to light stimuli 1

The Eye and Vision

The Eye and its Neurological Wiring

Vision: Receptive Field (RF) Definition: the area of the retina (or visual field) in which light signals evoke responses It’s a property of the cell, not a cell or a part of the cell It depends largely on the synaptic inputs to the cell and to some degree the biophysical property of the cell itself

Projection from retina to LGN fixation point Nasal RGC: axons crossover, project to contralateral LGN Temporal RGC: axons stay on the same side (ipsilateral) Left visual field: right LGN, right V1 Right visual field: left LGN, left V1 fovea

Visual pathway from retina to V1

Optical imaging of orientation map

Retinotopic map c b a a b c neighboring cells have neighboring RF retinotopic map is true in the retina, LGN and V1, but it gets fuzzy as you move on to higher visual areas c Project orderly to LGN and V1 b a a b c object retina

The Retina & Photoreceptive Cells

Different cells in the retina The Basic Retinal Circuit Back of eye 6. Pigment cells 1. Receptor Cells (Graded potential) (input) 2. Bipolar Cells 3. Ganglion Cells (action potential) (Output) 4. Horozontal Cells (Graded potential) 5. Amacrine Cells (Graded/action potential) Structure of the eye Front of eye 2

light Fovea: high spatial resolution Periphery: low spatial resolution

Direct pathway: Photo receptor  Bipolar  RGC +: excitatory synapse, preserve response direction -: inhibitory synapse, flip response direction Direct pathway is responsible to the RF center

Indirect pathway Indirect pathway mediated by horizontal is responsible to the RF surround There are other indirect pathway mediated by amacrine cells

Summary of retinal circuit Direct pathway Indirect pathway Pathways mediated by amacrine cells

The Nobel Prize in Physiology or Medicine 1981: Roger W.Sperry: for his discoveries concerning the functional specialization of the cerebral hemispheres David H. Hubel & Torsten N. Wiesel: for their discoveries concerning information processing in the visual system

Terpenes in Vision Can diet affect sight Terpenes in Vision Can diet affect sight?.....It might depend on what you’re looking at. Color vision vs. B&W: Rods vs. Cones The Photochemical Process Lycopenes Carotenes Vitamin A Retinol / Retinal Humans only see in B&W at night, but some animals like the nocturnal hawkmoth see color. Nature, 922-25, 2002

orange-red pigment in tomatoes Lycopene orange-red pigment in tomatoes lmax 505 nm 5

Cis-Trans Isomerization & Vision

B&W Chemistry Step One: Oxidation

B&W Chemistry Step Two: Trans -> Cis Isomerization

B&W Chemistry Step Three: “Hooked on Opsin”

B&W Chemistry Step Four: “Flash”

B&W Chemistry Step Five: “Repeat Process”

Vision exercise

Isoprene (2-methyl-1,3-butadiene) Terpenes Terpenes are natural products that form from a pyrophosphate and are structurally related to isoprene. H2C C CH3 CH CH2 Isoprene (2-methyl-1,3-butadiene)

The Isoprene Unit An isoprene unit is the carbon skeleton of isoprene (ignoring the double bonds) Two isoprene units:

The Isoprene Unit The isoprene units are joined "head-to-tail." head

Isoprene Links Heads or Tails?

Common Carbon Backbone

Terpenes Class Number of carbon atoms Monoterpene 10 Sesquiterpene 15 Classification of Terpenes Class Number of carbon atoms Monoterpene 10 Sesquiterpene 15 Diterpene 20 Sesterpene 25 Triterpene 30 Tetraterpene 40

a-Phellandrene (eucalyptus) Terpenes Representative Monoterpenes OH O H a-Phellandrene (eucalyptus) Menthol (peppermint) Citral (lemon grass)

a-Phellandrene (eucalyptus) Terpenes Representative Monoterpenes OH O H a-Phellandrene (eucalyptus) Menthol (peppermint) Citral (lemon grass)

a-Phellandrene (eucalyptus) Terpenes Representative Monoterpenes a-Phellandrene (eucalyptus) Menthol (peppermint) Citral (lemon grass)

Terpenes Representative Sesquiterpenes H a-Selinene (celery)

Terpenes Representative Sesquiterpenes H a-Selinene (celery)

Terpenes Representative Sesquiterpenes a-Selinene (celery)

Terpenes Representative Diterpenes OH Vitamin A

Terpenes Representative Diterpenes OH Vitamin A

Terpenes Representative Diterpenes Vitamin A

Common Terpenes

Limonene

Limonene