CHEM 203 – Organic Chemistry Fall 2017 Molecular Formulas Elemental Analysis Molecular Mass Determination Structural inference from Rule of Thirteen Preview of HRMS CHEM 203 – Organic Chemistry

Molecular Formulas – What can be learned from them Importance: Organic molecules exist as discrete sets of covalent bonds based on the valence of the elements that comprise them i.e. hydrogen is monovalent, oxygen divalent and carbon tetravalent… If a molecular formula is known: Functional groups can be implied or ruled out Obvious, but often overlooked tool The number of times valence rules for elements are violated is implied Most commonly for carbon, which is called the index of unsaturation or hydrogen deficiency index (HDI), less commonly for elements such as oxygen and nitrogen that may be involved in acid-base chemistry

Molecular Formulas – What can be learned from them Hydrogen Deficiency Index For simple straight chain or branched hydrocarbons, there is always a certain ratio of hydrogen to carbon necessary to make the entire structure saturated: We say these molecules are not hydrogen deficient, and set the index at zero

Molecular Formulas – What can be learned from them Hydrogen Deficiency Index If we add a double bond anywhere in the structure, two hydrogens must be removed for each double bond We say these molecules are hydrogen deficient, and the index increases by one for each double bond added, for the first structure, the index is one, for the second the index is two

Molecular Formulas – What can be learned from them Hydrogen Deficiency Index A ring closure, like a double bond requires the “sacrifice” of two hydrogens from the formula, increasing the index by one for each closed ring in the compound Triple bonds act as two double bonds increasing the index by two for each one in a molecule Hence, the first structure has an index of one, the second an index of two

Molecular Formulas – What can be learned from them Hydrogen Deficiency Index– other elements Nitrogen is usually assumed to be trivalent; obviously ammonium salts and nitro compounds violate this. Assume nitrogen is trivalent, and therefore, for every nitrogen in a structure, one less hydrogen is needed to “fill” its valence requirement than carbon Halogens (normally monovalent) merely replace hydrogen in a like-indexed formula

Molecular Formulas – What can be learned from them Hydrogen Deficiency Index– the equation! Elements such as carbon and hydrogen never violate their index rules Elements such as oxygen rarely violate their index rules Elements such as nitrogen and the halogens may violate their index rules Higher elements, found commonly in biologically interesting organic compounds, such as sulfur and phosphorus exist in almost equal populations in the various valences they are capable of and are typically not considered by this method directly Furthermore, it is tedious to go through a structural analysis to get the index of unsaturation. It can be algebraically expressed by combining the effects of each of the common elements. For an organic compound of formula CxHyNzO the index of hydrogen deficiency becomes: HDI = x - y/2 + z/2 + 1 Remember to count halogens in the number of hydrogens and to omit oxygen

Molecular Formulas – What can be learned from them Hydrogen Deficiency Index Let’s test the equation: HDI = x - y/2 + z/2 + 1 C7H12 C5H5N C14H10 C60 C6H12O6 C6H8O

Molecular Formulas – What can be learned from them Hydrogen Deficiency Index Let’s test the equation: HDI = x - y/2 + z/2 + 1 C7H12 C5H5N C14H10 C60 C6H12O6 C6H8O

Molecular Formulas – What can be learned from them The Rule of Thirteen – Molecular Formulas from Molecular Mass For the formula “connoisseur” there is another algebraic treatment of molecular mass that can lead to possible molecular formulas When a molecular mass, M, is known, a base formula can be generated from the following equation: M = n + r 13 13 the base formula being: CnHn + r For this formula, the HDI can be calculated from the following formula: HDI = ( n – r + 2 ) 2

Molecular Formulas – What can be learned from them The Rule of Thirteen When a formula containing other elements than carbon and hydrogen are considered, the appropriate adjustment must be made. If we wish to consider that the base formula also includes oxygen, with atomic mass 16, one carbon (12) and four hydrogens (4 x 1) must be removed to give the same molecular mass Likewise, an adjustment to hydrogen deficiency must be made. The following table gives the carbon-hydrogen equivalents and change in HDI for elements also commonly found in organic compounds: Element added Subtract: D HDI (DU in text) C H12 7 35Cl C2H11 3 -7 79Br C6H7 -3 O CH4 1 F CH7 2 N CH2 1/2 Si C2H4 S C2H8 P C2H7 I C9H19

Molecular Formulas – What can be learned from them The Rule of Thirteen Possible molecular weights can only generate real formulas; if the assumption you made is incorrect fractional elements or HDI indices appear, or sub-zero HDI. Some examples: We experimentally determine the molecular mass to be 98 From the rule of thirteen a base formula is generated: 98 / 13 = n + r / 13 = 7 + 7 / 13 Base formula = C7 H7 + 7 = C7H14 and HDI (U) = (7 – 7 + 2)/2 = 1 Remember, this is only the first of several possible formulas that give a molecular mass of 98!

Molecular Formulas – What can be learned from them The Rule of Thirteen From this starting point, we can infer the isomeric alkenes (HDI = 1) of molecular formula C7H14: Or we can infer the various aliphatic ring compounds, C7H14: Observe how, with the knowledge of molecular mass, we can whittle the infinity of possible organic compounds to two families of closely related isomers, and even begin to know something about the chemistry of the unknown Remember, off of the base formula we can begin to add other elements to see what other possibilities give a molecular mass of 98…

Molecular Formulas – What can be learned from them The Rule of Thirteen If we now assume the unknown has a single oxygen: Base formula: C7H14 Add oxygen: C7H14O (mol. mass now 114) Subtract CH4: C6H10O (mol. mass now correct at 98) HDI correction: 1 + 1 = 2 (originally 1, add one for O) (you can check the HDI vs. the new formula as well) We can now picture compounds that have the formula C6H10O with a HDI of 2: Quickly, we can add other elements, such as nitrogen, halogen and sulfur. See how for a low molecular mass the inference of big elements greatly simplifies the number of possible structures

Molecular Formulas – What can be learned from them The Rule of Thirteen Quickly, we can add other elements, such as nitrogen, halogen and sulfur. See how for a low molecular mass the inference of big elements greatly simplifies the number of possible structures: Base formula: C7H14 Add Nitrogen: C6H12N (sub. CH2) HDI: 1.5 Probably an incorrect formula, it is unlikely this compound has nitrogen Add Sulfur: C5H6S (sub. C2H8) HDI: 3 Very few possibilities with only 6 hydrogens and an HDI of 3 Add Bromine: CH7Br (sub. C6H7) HDI: -2 Impossible structure

Molecular Formulas – Where we are Importance of Molecular Formula in Structure Determination HDI HDI calc. HDI calc. Molecular Formula Molecular Mass Functional group inference Rule of 13 Now we see the experimental need to get this information

Mass Spectrometry Introduction Mass spectrometry is a technique used for measuring the molecular weight and determining the molecular formula of an organic compound. In a mass spectrometer, a molecule is vaporized and ionized by bombardment with a beam of high-energy electrons. The energy of the electrons is ~ 1600 kcal (or 70 eV). Since it takes ~100 kcal of energy to cleave a typical s bond, 1600 kcal is an enormous amount of energy to come into contact with a molecule. The electron beam ionizes the molecule by causing it to eject an electron.

Mass Spectrometry Introduction

Mass Spectrometry Introduction When the electron beam ionizes the molecule, the species that is formed is called a radical cation, and symbolized as M+• The radical cation M+• is called the molecular ion or parent ion. The mass of M+• represents the molecular weight of M Because M is unstable, it decomposes to form fragments of radicals and cations that have a lower molecular weight than M+• The mass spectrometer analyzes the masses of cations A mass spectrum is a plot of the amount of each cation (its relative abundance) versus its mass to charge ratio (m/z, where m is mass, and z is charge) Since z is almost always +1, m/z actually measures the mass (m) of the individual ions.

Mass Spectrometry Introduction Consider the mass spectrum of CH4 below: The tallest peak in the mass spectrum is called the base peak The base peak is also the M peak, although this may not always be the case Though most C atoms have an atomic mass of 12, 1.1% have a mass of 13. Thus, 13CH4 is responsible for the peak at m/z = 17. This is called the M + 1 peak.

Mass Spectrometry Introduction The mass spectrum of CH4 consists of more peaks than just the M peak Since the molecular ion is unstable, it fragments into other cations and radical cations containing one, two, three, or four fewer hydrogen atoms than methane itself Thus, the peaks at m/z 15, 14, 13 and 12 are due to these lower molecular weight fragments.

Mass Spectrometry Introduction

Mass Spectrometry Alkyl Halides and the M + 2 Peak Most elements have one major isotope. Chlorine has two common isotopes, 35Cl and 37Cl, which occur naturally in a 3:1 ratio Thus, there are two peaks in a 3:1 ratio for the molecular ion of an alkyl chloride The larger peak, the M peak, corresponds to the compound containing the 35Cl. The smaller peak, the M + 2 peak, corresponds to the compound containing 37Cl Thus, when the molecular ion consists of two peaks (M and M + 2) in a 3:1 ratio, a Cl atom is present Br has two isotopes—79Br and 81Br, in a ratio of ~1:1. Thus, when the molecular ion consists of two peaks (M and M + 2) in a 1:1 ratio, a Br atom is present.

Mass Spectrometry Alkyl Halides and the M + 2 Peak

Mass Spectrometry Alkyl Halides and the M + 2 Peak

Mass Spectrometry High Resolution Mass Spectrometers Low resolution mass spectrometers report m/z values to the nearest whole number. Thus, the mass of a given molecular ion can correspond to many different masses High resolution mass spectrometers measure m/z ratios to four (or more) decimal places. This is valuable because except for 12C whose mass is defined as 12.0000, the masses of all other nuclei are very close—but not exactly—whole numbers Table 14.1 lists the exact mass values for a few common nuclei. Using these values it is possible to determine the single molecular formula that gives rise to a molecular ion.

Mass Spectrometry High-Resolution Mass Spectrometers Consider a compound having a molecular ion at m/z = 60 using a low-resolution mass spectrometer. The molecule could have any one of the following molecular formulas.

Mass Spectrometry Gas Chromatography-Mass Spectrometry (GC-MS)

Mass Spectrometry Gas Chromatography-Mass Spectrometry (GC-MS) To analyze a urine sample for tetrahydrocannabinol, (THC) the principle psychoactive component of marijuana, the organic compounds are extracted from urine, purified, concentrated and injected into the GC-MS THC appears as a GC peak, and gives a molecular ion at 314, its molecular weight

Wrapping it up – what can be done with mass spectra? Most powerful tool for determining molecular mass of small compounds Locate M+ ion Gives molecular mass If odd there is 1,3,5… nitrogens in compound If even there are 0,2,4… nitrogens in compound If large – aromatic ring is probably present If small or not-existent – alcohol, amine Use the rule of thirteen to generate possible molecular formulas Locate M+1 ion Divide intensity of M+1 by M+ and multiply by 100% Divide the result by 1.1 – this gives the rough number of carbons Locate M+2 ion If present indicates presence of silicon, sulfur, clorine or bromine If M+2 is ~4-5% the intensity of M+ sulfur or silicon is present If M+2 is 33% the intensity of M+ there is a chlorine present If M+2 is equal in intensity to M+ there is a bromine present

Conjugation, Resonance and Dienes Conjugated Dienes and Ultraviolet Light The absorption of ultraviolet (UV) light by a molecule can promote an electron from a lower electronic state to a higher one. Ultraviolet light has a slightly shorter wavelength (and thus higher frequency) than visible light. The most useful region of UV light for this purpose is 200-400 nm.

Conjugation, Resonance and Dienes Conjugated Dienes and Ultraviolet Light When electrons in a lower energy state (the ground state) absorb light having the appropriate energy, an electron is promoted to a higher electronic state (excited state). The energy difference between the two states depends on the location of the electron.

Conjugation, Resonance and Dienes Conjugated Dienes and Ultraviolet Light The promotion of electrons in  bonds and unconjugated  bonds requires light having a wavelength of < 200 nm; that is, a shorter wavelength and higher energy than light in the UV region of the electromagnetic spectrum. With conjugated dienes, the energy difference between the ground and excited states decreases, so longer wavelengths of light can be used to promote electrons. The wavelength of UV light absorbed by a compound is often referred to as its max.

Conjugation, Resonance and Dienes Conjugated Dienes and Ultraviolet Light As the number of conjugated  bonds increases, the energy difference between the ground and excited state decreases, shifting the absorption to longer wavelengths. With molecules having eight or more conjugated  bonds, the absorption shifts from the UV to the visible region, and the compound takes on the color of the light it does not absorb.

Conjugation, Resonance and Dienes Conjugated Dienes and Ultraviolet Light Lycopene absorbs visible light at max = 470 nm, in the blue-green region of the visible spectrum. Because it does not absorb light in the red region, lycopene appears bright red.

Conjugation, Resonance and Dienes Sunscreens UV radiation from the sun is high enough in energy to cleave bonds, forming radicals that can prematurely age skin and cause cancer. However, since much of this radiation is filtered out by the ozone layer, only UV light having wavelengths > 290 nm reaches the skin’s surface. Much of this UV light is absorbed by melanin, the highly conjugated colored pigment in the skin that serves as the body’s natural protection against the harmful effects of UV radiation.

Conjugation, Resonance and Dienes Sunscreens Prolonged exposure to the sun can allow more UV radiation to reach your skin than melanin can absorb. Commercial sunscreens can offer some protection, because they contain conjugated compounds that absorb UV light, thus shielding the skin (for a time) from the harmful effects of UV radiation. Commercial sunscreens are given an SPF rating (sun protection factor), according to the amount of sunscreen present. The higher the number, the greater the protection. Two sunscreens that have been used for this purpose are para-aminobenzoic acid (PABA) and padimate O.