Organic Chemistry Chapter 13 Textbook Notes PDF

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Mass Spectrometry & IR Spectum. Organic Chemistry I with Dr. Snover. ...

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Organic Chemistry: Chapter 13 Textbook Notes: 13.3: Using the m/z value of the molecular ion to calculate the molecular formula - m/z value of the molecular ion gives the molecular mass of the compound - The rule of 13: permits us to use the m/z value of the molecular ion to determine the compound’s molecular formula. Steps on how to find the molecular formula: 1) Find the base value - Divide value by 13. * This gives you the number of carbons. * The number left over + the number of carbons gives you the number of hydrogens. Ex) 142= m/z value 142/13= 10 —-carbons 10*13= 130 142-130=12—-hydrogens 2) If the compound has one oxygen… Then subtract 1 carbon and 4 hydrogens are subtracted. If the compound has 2 oxygens…. Then repeat the process above( 2 Carbons and 8 hydrogens are removed) Working Example) Possible Structures for an ester with a molecular ion with an m/z value of 74: 74/13= 5 with 9 left over. 13.4: Isotopes in Mass Spectrometry M+1 Peak: represents the ion that is one unit heavier than the molecular ion being observed. Will be a tiny peak above the m/z value • This all is a result of the fact that there are two naturally occurring isotopes of carbon: 12C and 13C. So whichever molecules contain the 13C will showcase that M+ 1 peak. M+ 2 Peak: Results due to the presence of an 18O or having two heavy isotopes in the same molecule. Generally very small. Typically only show up in Bromine or Chlorine. Identification between bromine and chlorine: If M+2 peak is 1/3 the height of the M peak, Then it contains a chlorine atoms If M+2 peak and the M peak are nearly the same height, Then it contains a bromine atom. When calculating m/z values, use the atomic mass of a single isotope, NOT the atomic masses which are on the periodic tables.

13.5: High Resolution Mass Spectrometry can Reveal Molecular Formulas Low resolution mass spectrometer shows the m/z values of a fragment to the nearest whole number. High resolution mass spectrometer shows the exact molecular mass of a fragment to a precision of 0.0001 amu. 13.6: The Fragmentation Patterns of Functional Groups • Alkyl Halides: Ex) 1-bromopropane: C-Br bond is the weakest and therefore it cleaves heterolytically producing a propyl cation and two bromine atoms. Ex) 2-Chloropropane: C-Cl and C-C bond are similar in strength and therefore will both potentially break. Note: Result of hemolytic cleave( also called alpha cleavage- carbon bonded to the chlorine) And this results because it leads to a cation that is relatively stable because all its atoms have complete octets. **Alpha cleavage is UNLIKELY to occur in alkyl bromides because the C-C bond is much stronger than the C-Br bond. • Ethers: Ex) 2-isopropoxybutane: the C-O bond cleaves heterolytically while the C-C bond is cleaved homolytically. - The alkyl group most easily cleaved is the one that forms the most stable radical. (Look at the radical product of these reactions and use them to evaluate the stability of the bonds and determine which C=C will break) • Alcohols: Note: shows a SMALL molecular peak Note: In the case of alcohols, two bonds are broken because a stable WATER molecule is formed as a result of the fragmentation. Loss of the water molecule results in a fragmentation peak at m/z = M-18. ( The OH and the gamma H unite) • Ketones: - Generally has an intense molecular peak that is formed by knocking out a lone-pair electron. McLafferty Rearrangement: Occurs if one of the alkyl groups attached to a carbonyl carbon has a gamma hydrogen and a cleavage can have a fa-

vorable 6 membered transition state. Results in two bonds breaking.

13.7: Other Ionization Methods CI-MS: sample is sprayed with a pre-ionized gas such as methane or ammonia and this causes the sample to ionize by electron transfer but is less likely to undergo fragmentation. Note: Both CI-MS and EI-MS require the sample to be vaporized before it is ionized. Hence techniques only used for sample with low molecular masses. DI(Desorption ionization): used for larger samples 13.8:Gas Chromatography-Mass Spectrometry - Mixture of compounds is injected into a gas chromatograph and different compounds travel through it differently based on boiling points. Low boiling point leaves first. And as they leave they enter the mass spectrometer where it is ionized. 13.9: Spectrometry & the Electromagnetic Spectrum Spectroscopy: the study of the interaction of matter and electromagnetic radiation. Different Types of Rays: - Cosmic Rays: discharged by the sun. Have the highest energy - Gamma Rays: emitted by the nuclei of certain radioactive elements - X-rays: used to examine internal structures - UV: component of sunlight - Visible: electromagnetic radiation we see - IR: is felt as heat - Microwaves: used to cook food - Radio waves: have the lowest energy of the various kinds of radiation. Used for radio and tv communication. Definitions: Frequency: the number of wave crests that pass by a given point in one second. Unit of Hertz Wavelength: the distance from any point on one wave to the corresponding point on the next wave. Units: 1nm Energy formula: E= hc= hc/wavelength - Wave number is used to describe the frequency of the radiation is by using the wavenumber. 13.10: Infrared Spectroscopy - A bond is always vibrating with both stretching and bending motions: • Stretch: a vibration that occurs along the line of the bond. Changes the bond length • Bend: a vibration that does NOT occur along the line of the bond. Changes the bond angle Note: Diatomic molecules ONLY undergo stretching vibrations

When there are three or more atoms in play then different case are possible: ( symmetric, unsymmetric, in-plane, out-of plane) Bending vibrations include: rock, scissor, way and twist. Infrared Radiation: Has range of frequencies: 4000 to 600 cm^-1 (has lower energy than visible light) - The frequency which the compound absorbs is where you see the peak in IR Definition: Infrared Spectrum: obtained by passing IR through a sample of compound is a plot of the percent transmission of radiation versus the wavenumber of the radiation transmitted. * 100% transmission means that all energy just passed through the molecule. Functional Group region: ( 4000-1400cm^-1) Where most functional groups show their absorption bands Fingerprint Region: (1400-600cm^-1) Characteristic of the compound

as a whole. Showcases the varying environments through the patterns of the absorption bands.

*Note: use fingerprint regions to compare different groups that may have the same functional group 13.11:Characteristic Infrared Absorption Bands Stretching vibrations require more energy and are therefore found in the functional group regions. 13.12: Intensity of Absorption Bands Intensity of the absorption band depends on the size of the change in the dipole moment when a molecule stretches. 1)The greater the dipole, the more intense the absorption! 2)The more polar the bond, the more intense the absorption! 3) Greater number of bonds responsible for absorption, more intense the absorption! 4) More concentrated samples have more intense absorption! 13.13: Position of Absorption Bands D

epends on the strength of the bond and the masses of the bonded atoms. * The stronger the bond, the more energy required to stretch it. Equation which describes the motion of a vibrating spring: *Shows that strong bonds and lighter atoms give absorption bands with higher frequencies

Bond order also affects the strength and therefore the position of the absorption bands. *Triple bond is stronger than double which is stronger than single. 13.14: Position and Shape of an Absorption Band is affected by Electron Delocalization and Hydrogen bonding When a compound has more SINGLE-BOND character, then it’s frequency decreases as a single bond is weaker than a double bond. Ex) 2-pentanone(1700cm^-1) vs. 2-cyclohexenone(1680 cm^-1) *So here localization is good for the compound

- When we put another atom other than carbon next to the carbonyl group then the effect on frequency is evaluated by looking at its electronegativity and whether is donates or withdraws electrons. **Donating is bad! Inductive is good! - Amides require more energy to stretch than do esters. C-O Range: (1050-1250 cm^-1) * If this bond is in an ether or alcohol then it will be closer to the lower end of the spectrum. (Has pure single bond character) * If the bond is in a carboxylic acid it will be at the higher end of the range. (Has double bond character due to electron delocalization) * If the bond is an ester, it will show stretches at both ends. ( One single and one double bonds) Hydrogen Bonding: A) Are typically broad B) Carboxylic acids exist as hydrogen bonded dimers and occur at lower frequencies and tend to be broader(3300-2500cm^-1) C) Alcohol O-H bands tend to be around (3500-3200cm^-1) D) Hydrogen bonding and concentration of the solution influences the position and breadth of the OH stretch. - In a concentrated solution, there is more hydrogen bonding and the frequency for alcohols will be 3500-3200cm^-1 but if it is a dilute solution then there will be little hydrogen bonding and it will occur at a higher frequency(3650-3590cm^-1) * In comparison, the N-H bonds are less polar and therefore the bands are less intense. 13.15: C-H Absorption Bands * The hybridization of the carbon influences the strength of the C-H bond. The greater the s character, the stronger the bond. * Absorption band is around 3300cm^-1 for sp • Benzene vs Alkene: A benzene ring is indicated by two sharp absorption bands, one at ~1600 cm-1 and one at 1500-1430 cm-1, whereas an alkene is indicated by a band only at ~1600 cm-1 **But be careful because N-H bend is also around that area. However that band in comparison to this is stronger as it is more polar and is influenced by hydrogen bonding. And the N-H bend around 1600cm^-1 is supplemented by the N-H stretch around 3500-3300 cm-1 - Aldehydes: - The stretch of the C¬H bond of an aldehyde group shows two absorption bands—one at ~2820 cm-1 and the other at ~2720 cm-1 Bending Vibrations:

- If a compound has a sp^3 Carbon, then look around 1400cm^-1. Those hydrogens will result in a band to the left of that value. And if there is a methyl group present then it will show up to the right, therefore showing peaks around both sides of 1400. - If a compound has a sp^2 Carbon, then look around the 1000-600 cm^-1 region. If there are more than 4 adjacent CH3 groups, then there will be an absorption band around 720cm^-1. * The bending vibrations for an alkene depend on the number of alkyl groups bonded to the sp^-2 Carbon.

13.19: UV and Visible Spectroscopy UV and Visible Spectroscopy: (Definition)- provide information about compounds that have conjugated double bonds. Have just the right amount of energy to promote an electron from one molecular orbit to the another. UV Spectrum~ 180 to 400nm Visible Spectrum~400 to 780 nm *UV had greater energy than visible light Electronic Transition: (Definition)- When a molecule absorbs light with sufcient energy and it is able to promote an electron from ground state to an excited state. ***IMPORTANT: Only compounds with PI bonds can produce UV/VIs spectra Note: And when the electron is promoted, then the spin does NOT CHANGE.

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UV/Vis absorption bands are broad because each electronic state has vibrational sublevels. Chromophore: (Definition) - The part of a molecule that absorbs UV or visible light.

13.20: the Beer-Lambert Law Generally the law states, that the absorbance of a sample at a given wavelength depends on the amount of absorbing species that the light encounters as it passes through a solution of the sample. Simply, the CONCENTRATION OF THE SAMPLE & the LENGTH OF THE LIGHT PATH are important in determining absorbance.

Beer-Lambert Formula:

Molar Absorptivity: (Definition)- a constant that is characteristic of the compound at a particular wavelength. **IMPORTANT: Both the lambda max and the molar absorptivity increase as the number of conjugated double bonds increase. Auxochrome:(Definition)- a substituent that when attached to a chromophore alters both the lamda max and the intensity of the absorption[typically increasing it] Ex) OH and NH2 Phenolate ion has the longest wavelength and benzene has the shortest. 13.22: The Visible Spectrum and Color When a substance absorbs… Red ———— appears green Violet ———— appears yellow blue—————-appears orange When two complementary colors are absorbed, then a whitish color is seen. 13.23: Some uses of UV/Vis Spectroscopy Roles: - used to measure reaction rates( set graph for absorbance at a given wavelength as a function of time) - Determine the pKa of a compound( measure absorbance as a function of pH) [ half way point which is the pH will equal the pKa] - Estimate the nucleotide composition of DNA( sDNA has greater absorbance than dsDNA) [Plot absorbance as function of temperature] The melting temperature will be the midpoint of this plot....