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CHM 221: Final Study Guide + Notes

by: Reema Saribala

CHM 221: Final Study Guide + Notes CHM 221

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Reema Saribala

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Notes covering every powerpoint used by professor in class + important details and information highlighted by the professor. Specific annotations of what's most important along with tips/hints spec...
Chemistry For The Biosciences II
Dr. Leslie Knecht
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This 63 page Bundle was uploaded by Reema Saribala on Wednesday August 10, 2016. The Bundle belongs to CHM 221 at University of Miami taught by Dr. Leslie Knecht in Spring 2016. Since its upload, it has received 15 views. For similar materials see Chemistry For The Biosciences II in Chemistry at University of Miami.

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Date Created: 08/10/16
Klein Chapter 26 Lipids • Unlike other organic molecules, lipids are defined by a physical property: solubility. • Complex lipids can be hydrolyzed with acid or base to give smaller fragments. • Simple lipids cannot be hydrolyzed. Complex lipids: • Waxes - Waxes are high molar mass esters. - Other waxes only differ in the length of the carbon chains on either side of the ester. - Very high melting points because they have a lot of carbons. - Not expected to know how to name them. • Triglycerides - Triesters formed from glycerol and long chain carboxylic axis or fatty acids. - Twice as efficient at storing energy than carbohydrates and proteins. - Hydrolyzed triglycerides yield fatty acids 12 to 20 carbons in length. Some are saturated (no rings or double bonds) and some have one or more sites of unsaturation. - Unsaturated fatty acids have kinks in them. - Melting points of saturated triglycerides are much higher than those of unsaturated triglycerides because the kinks don’t allow a lot of intermolecular forces holding them together. - Saturated fatty acids increase melting point with increasing molecular weight. - Cis double bonds cause a decrease in the melting point. - Soap is made from carboxylate slats resulting from triglyceride hydrolysis. - In aqueous solutions, soap molecules self assemble into micelles. • Phospholipids - Ester-like derivatives of phosphoric acid - Most are phosphoglycerides. Two of the most common phosphoglycerides are cephalins and lecithins. Don’t need to know the exact structure but should be able to recognize that it is a phospholipid. - - In water and at the right concentrations, phosphoglycerides form bilayers - To form a vesicle, the non polar groups must be able to pack together closely to maximize London forces. - The fluid nature of the non polar region of the bilayer is critical to give cells flexibility. • Steroids - generally function as chemical messengers - have a basic chemical structure that consists of 4 fused rings. - fused cyclohexane rings can connect through cis or trans structures - Trans fused rings cannot undergo ring flipping. Therefore occurring steroids are almost always fused with trans connections.As a result, most steroids have very rigid structures. - Sex hormones are steroids that regulate tissue growth and reproduction processes. Male hormones are androgens (testosterone and androsterone). Female hormones are estrogens and progrestins.All three types of hormones are found in both women and men but concentrations differ. • Prostaglandins - Found in all body tissues and fluids - regulate many different functions including blood pressure, clotting, inflammation, kidney function, etc. - many different kinds of molecules. don’t need to memorize them but know the general structure. • Terpenes- diverse group of compounds that are made of isoprene units. The number of carbon atoms must be a multiple of five. Can have functional groups attached but probably won’t be on the exam. Could give a structure like beta Carotene and say “circle all the terpene units” Klein Chapter 15 Spectroscopy • How do we characterize molecules? - Properties - Size - Functional Groups • Spectroscopy involves an interaction between matter and light (electromagnetic radiation). • When light interacts with molecules, the effect depends on the wavelength of light used. • IR Spectroscopy - Molecular bonds can vibrate by stretching or by bending in a number of ways (a stretching vibration, an in-plane bending vibration, an out-of-plane bending vibration or twisting) - This chapter will focus mostly on stretching frequencies. - The energy necessary to vibration depends on the type of bond. - Characteristic peaks are created depending on how much energy is released when an electron relaxes from a higher to lower energy level. In a C-H bond, an electron needs to relax a larger gap than in the C-O bond. - Example Spectra: Called the absorption spectrum. Notice all bands point down. The unit is wavenumbers (cm ). The energy increases as the wavenumber increases because the frequency increases and they are directly proportional. - Asignal on the IR spectrum has three important characteristics: wavenumber, intensity (how deep is that peak? things like electronegativity differences affect this) and shape. - The wavenumber for a stretching vibration depends on the bond strength and the mass of the atoms bonded together. - Bonds between heavier atoms require a lower wavenumber IR light to stretch. - Anytime you see a ‘D’just remember that it is basically a hydrogen but one unit heavier. - The first thing to do when given an IR spectrum is draw a line straight up from 3000 wavenumbers. This can give information about the hybridization and bonding. - In alkanes, the peaks show up right below 3000 wavenumbers. That is because of the sp3 carbon C-H bonds. - In alkenes, the peaks show up right above the 3000 wavenumbers (around 3100). That is because of the sp2 carbon C-H bonds. - If it shifts a little higher, closer to 3200, then you have an sp C-H bond of alkynes. - Carbonyl’s typically have a signal around 1700 wavenumbers. - Resonance can affect the wavenumber of a stretching signal. - Double bonds are typically stronger but this does not apply with resonance; the molecules are getting weaker and weaker as you apply resonance.As you add resonance in, it makes the molecule weaker because it’s existing as single bonds some of the times. - When a bond undergoes a stretching vibration, its dipole moment also oscillates. - The oscillating dipole moment creates an electrical field surrounding the bond. - That difference in oscillation causes the strength of IR signals to vary. - Abroad single (the shape of the peak) results an O-H bonds (3400) change what they bond to; sometimes they’ll stay alone and sometimes they’ll bond with other things. The hydrogen bonding weakens the O-H bond -> broader. - When would the O-H peak be narrow? When it is not participating in hydrogen bonding. - The O-H stretch for a carboxylic acid broad. It shows up around 3000 rather than the typical 3400 for O-H. This is because other than resonance, it forms two hydrogen bonds which makes it weaker. You’re going to see a peak around 1700 because of the ketone functional group (C=O) in the carboxylic acid and a broad O-H peak around 3000. That broad peak is going to mask any C-H bonds. - Primary amine: attached to one carbon. tend to have two Hs on them. - Secondary amines:have two R groups (sets of carbons) attached to them - Tertiary amine: attached to 3 R groups (no hydrogens) - Primary and secondary amines exhibit N-H stretching signals. Tertiary amines don’t because they don’t have Hs. - Two peaks on primary amines (2 Hs) and one peak on a secondary amine (1 H). The appearance of two N-H signals for the primary amine is not simply the result of each N- H bond giving a different signal. Instead, the two N-H bonds vibrate together in two different ways. - Asingle molecule can only vibrate symmetrically or asymmetrically at any given point in time. • Analyzing an IR Spectrum (focus on the diagnostic region; above 1500 wavenumbers) - 1600-1850, check for double bonds - 2100-2300, check for triple bonds - 2700-4000, check for X-H bonds - Analyze wavenumber, intensity and shape for each signal Mass Spectrometry • Used primarily to determine the molar mass and formula for a compound. - Acompound is vaporized and then ionized. - The masses of the ions are detected and graphed. - If the radical cation (M ) remains intact, it is known as the molecular ion or parent ion. - The base peak is the tallest peak (highest intensity) in the spectrum and represents the most stable radical ion. For methane, the base peak represents the M or the parent ion. The base peak occurs at the molar mass of the parent ion. - However sometimes the parent ion is not always observed and that occurs when the ion is not stable (however this will not be included in this class). - Peaks with a mass of less than the radical represent fragments. This can be done by taking Hs off. - +. In the mass spec for benze, the M peak is the base peak. This peak does not easily fragment because it is an aromatic and is hence very stable. - Like most compounds, the M peak for pentane is not the base peak. The M peak +. fragments easily. When you look at your spectra, look all the way to the right and the one right before the last is the base peak. +. • The first step in analyzing a mass sep is to identify the M peak - It will tell you the molar mass of the compound. +. - An odd massed M peak MAY indicate an odd number of N atoms in the molecule. - An even massed M peak MAY indicate an even number of N atoms or zero N atoms in the molecule. • The (M+1) peak results from the presence of Carbon 13 in the sample. • It should be 1.1% of the parent peak. You can use this ratio to find the number of carbons in your compound. • • (intensity of (M+1) )/ (intensity M )= (# /1.1) (100) = number of carbons in the compound • 1.1 is the percent of the C-13 isotope and the M+1 peak is only there because of the C-13. • Step 1: Determine the number of carbon atoms by comparing the M+1 peak to the parent peak. Remember each carbon atom contributes to 1.1% of the height of the M+1 peak. Determine if any heteroatom are presents (nitrogen, oxygen or hydrogen). 79 81 +• • Br=51% and Br=49%, so molecules with bromine often have equally strong (M) and (M +2) peaks. In chlorines, on peak is about 1/3 the height. They are very recognizable because not many spectra have these characteristics. • High resolution mass spec - GC-MS gives two main forms of information: 1. The chromatogram gives the retention time 2. The mass spectrogram (low res or high res) - GC-MS is a great technique for detecting compounds such as drugs ins solutions like blood or urine. • Mass spec can often be used to determine the formula for an organic compound. • IR can often determine the functional groups present. • alkanes follow the formula below, because they are saturated. • Alkanes follow the formula below because they are saturated: C H n 2n+2 • If they are saturated, there must be a degree of unsaturation. Degrees of Unsaturation = [2 + (2 x #Carbons) + #Nitrogens - #Hydrogens - #Halogens]/2x Explain why a completely non polar bond will not give a stretching signal in the IR spectra. Wen the bond is nonpolar, the stretching does not cause an oscillating electric field so there is nothing for the IR light to interact with and no signal is seen. For C-H stretching in a non polar molecule though, because the individual bond has some slight polarity upon stretching, it will produce an oscillating electric field to interact with IR radiatiion giving a signal in the IR. Thus non polar bonds will be invisible by IR but polar bonds within non polar molecules will give an IR signal. Klein Chapter 16 NMR Spectroscopy Nuclear Magnetic Resonance spectroscopy may be the most powerful method of gaining • structural information about organic compounds.It involves an interaction between electromagnetic radiation and the nucleus of an atom. • Protons and neutrons in a nucleus behave as if they are spinning. The spinning charge in the nucleus creates a magnetic moment. • • Like a bar magnet, a magnetic moment exists perpendicular to the axis of nuclear spin. • If the normally disordered magnetic moments of atoms are exposed to an external magnetic field, their magnetic moments will align. • The aligned magnetic moments can either be with (alpha spin) or against (beta spin) the external magnetic field. • The alpha and beta spin states are not equal in energy. • The beta spin is higher in energy because it is going against the magnetic field. • When an atom with an alpha spin state is exposed to radio waves of just the right energy, it can be flipped to a beta spin state. • The stronger the magnetic field, the greater the energy gap is going to be. • The magnetic moment of the electrons surrounding the nucleus generally reduces the affect of the external field (because they have a charge and can shield the nucleus from the magnetic field) This is called shielding. This causes the alpha-beta gap to become smaller.The more shielded a nucleus is with electron density, the smaller the gap. • NMR requires a strong magnetic field and radio wave energy. • The strength of the magnetic field affects the energy gap. • In most current NMR instruments, a brief pulse of radio energy is used to excite the sample. Each of the atoms is excited and then relaxes, emitting energy that is recorded as free induction decay. • chloroform-d is used in proton NMR as a solvent so that it doesn’t show up on the NMR unlike regular chloroform which has an H (because the solvent is in excess and we would not want it to interfere with our results). • Characteristics of a proton NMR Spectrum - Number of signals - Signal location-shift - Signal area-integration - Signal shape-splitting pattern • Number of signals - Protons with different electronic environments will give different signals because NMR is based on electric fields. - Protons are homotopic if the molecule has an axis of rotational symmetry that allows one proton to be rotated onto the other without changing the molecule. Homotopic does not have different electronic environments so on the NMR you would only see one signal. - Another test for homotopic protons is to replace the protons one at a time with another atom. If the resulting compounds are identical, then the protons that you replaced are homotopic. - Protons that are enantiotopic will also have perfectly overlapping signals. Protons are enantiotopic if the molecule has a plane of reflection that makes one proton the mirror image of the other. The replacement test can be used here as well. - If the resulting compounds are enantiomers, then the protons that you replaced are enantiotopic. You must flip so that the 4th priority group (H) is coming towards or away from you (on a wedge or dash). - If the protons are neither homotopic nor enantiotopic, then they are not chemically equivalent. - There are some signals you can take to identify how many signals you should see in the proton NMR: - 1. The 2 protons on a CH gr2up will be equivalent if there are NO chirality centers in the molecule. - 2. The 2 protons on a CH gr2up will NOT be equivalent if there is a chirality center in the molecule. - 3. The 3 protons on any methyl group will always be equivalent to each other. - 4. Multiple protons are equivalent if they can be interchanged through either a rotation or mirror plane. - Recall that cyclohexane chairs have 6 equatorial and 6 axial protons. You would only see 1 signal. This is because a flipped chair would not be any more or less energetically favorable. This is because the NMR is not fast enough to see the individual structures so the average is observed; for a NON substituted chair. • Chemical Shifts - Tetramethylsilane (TMS) is used as the standard for NMR chemical shift. - The shift for a proton signal is calculated as a comparison to the TMS. - Doesn’t matter what the strength of the instrument is, the chemical shift is exactly the same. Units for chemical shift are often given as ppm (y-axis). - There are two areas that we need to know: an upfield and a downfield. - Low field strength = downfield. The chemical shifts there are higher. - When it’s closer to the TMS standard, this is called upfield and it is lower ppm numbers. - (On the graph below, higher energy to the left and lower energy to the right) - Alkane protons generally give signals around 1-2 ppm. - Protons can be shifted downfield when nearby electronegative atoms cause deshielding. - As we add more substituents onto the carbon, it deshields it more and more. - Alphas are carbons directly attached to the group. - When electrons in a pi system are subjected to an external magnetic field, they circulate a great deal causing diamagnetic anisotropy (a deshielding effect). This means that different regions in space will have different magnetic strengths (Because of circulating pi electrons). Things that are outside of the ring are deshielded (downfield) while those on the inside are shielded because all the electron density is going into the ring.Aromatic protons show up most downfield of anything we are going to see (around 8). It is because of this toilet bowl flow of electrons. - The result of the diamagnetic anisotropy effect is similar to deshielding for aromatic protons (~7 ppm chemical shift) - When things are closer to aromatic rings or electronegative atoms, the more deshielded they are. - The result of the diamagnetic anisotropy effect is similar to shielding for protons that extend into the pi system. • Integration - area under the peak; quantifies the relative number of protons giving rise to a signal - a computer will calculate the area of each peak representing that area with a step curve - the computer operator sets one of the peaks to a whole number to let it represent a number of protons - the computer uses the integration ratios to se the values for the other peaks - the integrations are relative quantities rather than an absolute count of the number of protons - Following molecule: Because there is symmetry, there will only be two signals, one with an integration of 2 and one with an integration of 3. This just tells us there is a ratio of 2:3 but not the total number of protons. If the number of hydrogens from the mass spec doesn’t add up with this value of hydrogen, it suggests that there is symmetry in the molecule. • Multiplicity - When a signal is observed in the proton NMR, often it is split into multiple peaks. - You look at carbons adjacent to the carbon the proton is on. If there is one hydrogen on the neighbor, the splitting pattern is a doublet. The splitting pattern is typically one more than the number of adjacent hydrogens. - If they are both against the field, that would be deshielding. If they are both with the field, that would be shielding. - Splitting would still occur if it was an OH. - By analyzing the splitting pattern of a signal in the proton NMR, you can determine the number of equivalent protons on adjacent carbons. - Remember three key rules: 1. Equivalent protons can not split one another (no chiral centers) 2. To split each other, protons must be within a 2 or 3 bond distance. 3. The n+1 rule only applies to protons that are all equivalent. - If there is ever a singlet and there is an OH group from your IR spectra, you know that singlet is from that OH. Nothing splits an OH. - Exchangeable protons are those that can be replaced with D. It then becomes NMR inactive and so it disappears completely when the proton NMR sample is prepared. - When asked to distinguish between compounds, the first thing you should do is count the number of hydrogens. That would be the easiest way because there would be a different number of signals. Step 2 would be to find out the splitting patterns on each one. • Carbon 13 only accounts for about 1% of carbon atoms in nature so a sensitive receiver coil and/or concentrated NMR sample is needed. • In Carbon-13 NMR, only the number of signals and the shift will be considered. To elucidate the Carbon-13 spectrum and make it easier to determine the total number of • Carbon-13 signals, Carbon-13 NMR are generally decoupled. In the vast majority of Carbon-13 spectra, all of the signals are singlets. • • Carbon-13 spectra generally give singlets that do not provide information about the number of hydrogen atoms attached to each carbon. • Distrotionless Enhancement by Polarization Transfer (DEPT) carbon-13 NMR provides information about the number of hydrogen atoms attached to each carbon. • DEPT-90: Only CH signals appear. • DEPT-135: CH3 and CH give (+) signals and CH2 give (-) signals. Steps to analyze a proton NMR spectrum: 1. calculate the degree of unsaturation 2. consider the number of NMR signals and integration to look for symmetry in the molecule 3. analyze each signal and draw molecular fragments that match the shift, integration and multiplicity 4. assemble the fragment into a complete structure like puzzle pieces In the carbon 13 NMR, there should be as many signals as there are carbons if there is no symmetry. Klein Chapter 3 Acids and Bases - Bronsted-Lowry acid: donates portons - Bronsted-Lowry base: accepts protons - When bonds break and form, pairs of electrons move and we can show their movement with curved arrows. The curved arrow shows the mechanism. - QuantitativeAnalysis: • Lower pKa value, the stronger the acid • Strong acids have weak conjugate bases • An acid-base reaction will favor the side of the weakest acid/base. - Qualitative analysis- compare structural stability to determine which is a stronger acid - Formal charge can affect stability. The more effectively a reaction product can stabilize its formal charge, the more the equilibrium will favor a product. - Consider the following example: - When HCl donates its proton, the electrons go to Cl which is extremely electronegative (it’s stable). - When the second compound donates its proton, the electrons go to the nearest carbon, forming a carboanion which is not stable. Therefore HCl is more stable. - The more effectively the conjugate base can stabilize its negative charge, the stronger the acid. - What factors affect the stability of a negative formal charge? - The type of Atom that carries the charge - Resonance - Induction - The type of Orbital where the charge resides - ARIO • A- the type of atom that carries the charge. More electronegative atoms are better at stabilizing negative charge. Below, when the H is taken from a butane, the carbon is left with the electrons whereas in propanol, the oxygen is left with the electrons. Since oxygen is more electronegative, that conjugate base is more stable. • R- resonance can greatly stabilize a formal negative charge by spreading it out into partial charges. In the example below,Acetic acid can take part in resonance because it has an allylic lone pair. Hence, it is more stable. • I- induction can also stabilize a formal negative charge by spreading it out. The chlorines in trichloroacetic acid are pulling electrons towards them (because the C-Cl bond is polar). Becomes a chain; every electron deficient atom tries to pull electrons until electrons are also being pulled from the oxygen on the end (which is highly electronegative). To compensate, it easily kicks off the H to gain electrons. Hence it is stronger. • O- the type of orbital also can affect the stability of a formal negative charge. sp (most s character) is more stable than sp2 which is more stable than sp3 (least s character); s orbitals are closer to the nucleus so the more likely electrons will want to go there. sp is most acidic. the more s character there is, the close it’ll be to the nucleus and the more stable it’ll be. Pay attention to diagrams!!!! If a carbon is sp hybridized, it may not have a hydrogen attached because it’ll already have 4 bonds. - Equilibrium favors the side of the reaction with the higher pKa. However if pKa values are not known, relative stability of conjugates should be used. - Larger atoms can handle charge better than smaller charge (for example, oxygen vs. sulfur) - The more stable base is the weaker base because it doesn’t want to go get protons; it is happy the way it is. Weaker bases have stronger acids. - The acid on the right is stronger than the acid on the left (because its conjugate base is more stable and hence weaker). Hence equilibrium lies to the left. - Choosing a reagent: If you want to protonate a base, you must find an acid with a lower pKa value. - Any acid with a higher pKa can deprotonate. - The Leveling Effect: • The solvent could participate in an acid/base reaction • Because water can act as an acid or a base, it has a leveling effect on strong acids and bases. - There is an excess of water because it is the solvent. The base in the above equation will pick off hydrogens from the water instead of the base it actually wants to deprotonate because there is more water so it encounters that more frequently. Essentially what happens is we are removing the reagent (it becomes an acid before it actually gets to the base; can’t do the job it’s supposed to do) - Because they are so so similar,ARIO can not be used to explain the pKa difference comparing ethanol and tert-Butanol. Hence, ethanol’s (which has the lower pKa) base must be stabilized in some way (because that’s what helps with creating a stronger acid). - tert-Butanol has a lot of steric bulk while ethanol doesn’t. Fewer solvent molecules can surround that oxygen. However by solvent molecules surrounding the oxygen, the negative charge is becoming stabilized which is why ethanol is more stable and can make a better acid than tert-Butanol. - Counterions are also known as spectator ions. - Alewis acid accepts and shares a pair of electrons.Alewis base donates and shares a pair of electrons. Klein Chapter 2 Representing Molecules - Constitutional isomer: Different connectivities but same molecular formula - Bond-line structures • Like Lewis structures, lines are drawn between atoms to show covalent bonds. • Carbons exist where points meet and also at the ends of lines. • Carbon-Hydrogen bonds and lone pairs are omitted. • Pay attention to triple bonds! They should never be zig-zag. - Represent the bond angles with zigzags. Follow VSEPR and spread out the electron pairs on a central atom. - Single bonds are axes of rotation so be aware that they can rotate. Double bonds cannot rotate because it consists of a pi bond which is made up of the parallel overlap of orbitals. - Heteroatoms (atoms other than C and H) should be labeled with all hydrogen atoms and lone pairs attached. - Degree of Unsaturation = [2 + (2 x #Carbons) + #Nitrogens - #Hydrogens - #Halogens] / 2 - Unsaturation means there is a pi bond or a ring in the structure. - 1 degree = 1 double bond or 1 ring - 2 degrees = 2 double bonds, 2 rings, 1 ring + 1 double bond or 1 triple bonds - Rotational conformations mean you’re just changing the rotation of the bonds (not the connectivity) Memorize functional groups: - Alkane- single bond,Alkene- double bond,Alkyne- triple bond (alphabetical, numerical order) - Aldehyde: all da way to da hydrogen - Ether (one oxygen) vs. Ester (like Easter) (two oxygens) - Formal charge affects the stability and reactivity of molecules. - We know something is a carbocation (positive) because we have to show the charge on the bond line structure. The carbon is making only 3 bonds and not 4. - Carbanions are negative. It is unstable because it has a negative formal charge. - Carbocations and carbanions are extremely reactive. - Always draw formal charges on a bond-line structure to eliminate confusion. - Oxygen: • 1 bond, 3 lone pairs, -1 charge 2 bonds, 2 lone pairs, no charge • • 3 bonds, 1 lone pair, +1 charge - Nitrogen: • 2 bonds, 2 lone pairs, -1 charge • 3 bonds, 1 lone pair, no charge • 4 bonds, 0 lone pairs, +1 charge - Wedged means coming towards me, dashed means going away from me The p orbitals in that structure are all parallel which means the electrons can move around within them; the double bond can shift. That is resonance. You never touch sigma bonds in resonance. - The pi electrons can exist on both sides of the molecule so we can use two resonance contributors to represent the structure. The overall charge always remains the same. - Resonance makes a molecular more stable by 1. delocalization of electrons 2. Delocalization of charge - Curved arrows generally show electron movement for pairs of electrons. • The arrow starts where the electrons are currently located • The arrow ends where the electrons will end up after the electron movement • An arrow should never start at a single bond. Do not break single bonds (because they are sigma bonds). • Never exceed an octet for a 2nd row element. • 2nd row elements (B,C,N,O,F) will rarely but sometimes have LESS than an octet. • When using curved arrows to show resonance, often structures will carry a formal charge that must be shown. Keep in mind that the overall charge for the resonance structure should be the same (in this case, it is 0). - Vinyl is directly bonded to the C=C double bond.Allyl is one atom away from a C=C double bond. - From a double bond, go one atom away on either side. On that atom, if there is a lone pair, it is an allylic lone pair. If there is no lone pair, it is a not allylic lone pair. - When drawing resonance structures, you can only move allylic lone pairs!!! If there aren’t any, move the double bond. - When dealing with allylic positive charges, only one arrow is needed in the resonance mechanism. - Alone pair adjacent to a positive charge: - Api bond between atoms of different electronegativity: oxygen is more electronegative than carbon so it would prefer electrons more than carbon. Hence, we can create a resonance structure. - Conjugated pi bonds in a ring: Each atom in the ring MUST have an un-hybridized p orbital that can overlap with its neighbors. Summary: - Formal charge generally decreases stability, especially a +1 charge on an electronegative atom or -1 on a low electronegativity atom. Complete octets increase stability. - Localized electrons are NOT in resonance. - Delocalized electronsARE in resonance. - There are a couple ways to recognize electrons that are delocalized through resonance. - To be delocalized, electrons must exist in an unhybridized p orbital that can overlap with p orbitals on neighboring atoms. - To be delocalized, electrons must be on an sp or sp2 hybridized atom. - When determining geometry, you do not include a lone pair if it is an allylic lone pair (because that means it’s involved in resonance. - If a lone pair is on an atom involved in a double bond, it is a localized lone pair (even if it is an allylic lone pair on the other side) Klein Chapter 1 Organic Chemistry - Condensed formulas only tell us how many atoms exist, not connectivity. - Molecules with the same molecular formula but differ in the way atoms are connected are called constitutional isomers. - Atoms that are most commonly bonded to carbon include N, O, H and halides (F, Cl, Br, I). - With some exceptions, each element generally forms a specific number of bonds with other atoms. - The number of bonds is generally equivalent to the valence electrons of the atom. - The potential energy of the bonded species is lower than the potential energy of the species by itself. That is why bonding happens. - Bonding happens if the potential energy of the bonded thing is lower than the potential energy of the individual components. - Anything that is not a carbon is a heteroatom and they must be drawn on the carbon skeleton structure like below: - There are 6 carbons in the structure below. - Oxygen, one bond, -1. - Oxygen, two bonds, 0. - Oxygen, three bonds, +1. - Nitrogen, three bonds, 0. - Nitrogen, four bonds, +1. - Nitrogen, two bonds, -1. - Acovalent bond can be polar or non-polar. - Polar covalent bonds occur when there is an electronegativity difference between two bonded atoms. - Non-polar covalent bonds when there is not a difference in electronegativity. - Electrons tend to shift away from lower electronegativity atoms to higher electronegativity atoms. - The greater the difference in electronegativity, the more polar the bond. - Previously, we learned that there is a mathematical term to describe the probability of finding an electron in a particular location. - This location or space is referred to as atomic orbitals. - An electron’s wave function can be (+), (-) or zero. - Abond occurs when atomic orbitals overlap. Overlapping orbitals is like overlapping waves. - Only constructive interference results in a bond and destructive interference doesn’t (Valence Bond Theory). - The bond for H m2lecule results from constructive interference. - The bonded electrons spend most of their time in the center. - Molecular Orbital Theory • Focuses on the entire molecule • MOs are a more complete analysis of bonds because they include both constructive and destructive interference. • The number of MOs created must be equal to the number ofAtomic orbitals that were used. - When the bonding and anti bonding have the same number of electrons, they cancel each other out and a bond doesn’t form. (This is why we’ve never seen a He ) 2 - Bonding and anti-bonding are molecular orbitals, which are different from atomic orbitals. Pay attention to wording! - The higher the bond order, the stronger the bond. - Four degenerate sp orbitals are created (because the 2s orbital is of lower energy as the 2p orbitals; the 4th hydrogen wouldn’t want to go to a lower energy level so 4 orbitals of equal energy are created instead; there are no differences between each H, they all want to share electrons with the carbon but don’t want to be of different energies). - The hybrid orbital has more characteristics of a p orbital than the s orbital. The hybrid orbital is a mixture of s and p but it looks more like a p (it has lopsided lobes). - The hybrid orbital averages the energies of one s orbital and 3 p orbitals. It’s not as high as a p and not as low as an s. 3 - To make CH , t4e 1s atomic orbitals of four H atoms will overlap with four sp hybrid atomic orbitals of C. **Know how to draw this*** - All double and triple bonds are made because of the overlap of p orbitals. - Sigma bonds (which are the result of hybrid orbital overlap) are all single bonds. Even double and triple bonds have one sigma bond (the other bonds are pi bonds). The other type of bond is a pi bond (side-by-side) (which is the result of the overlap of p orbitals). - The double bond above indicates that there is a pi bond which is the result of the overlap of p orbitals. That is why there must be an available p orbital to overlap in the first place (Hence the third 2p orbital does not get hybridized). - An sp hybridized carbon will have three equal-energy sp orbitals and one unhybridized p orbital. - 2 The sp orbital is lower in energy than the p. - The sp orbital is lower in energy than the sp orbital. - The unhybridized p orbitals gives both constructive and destructive interference. 2 2 - Sp hybridization is not appropriate for methane because we need four bonds but with sp , we are only making 3 hybrid orbitals and that’s not enough. - If there are no double bonds and no lone pairs, there should be no p orbitals. - You need as many p bonds on the atom as you have p orbitals on the atom. - Asigma bond is stronger than a pi bond because there is much more overlap in the sigma bond unlike the pi bond where there is more distance. 3 3 - sp -sp sigma bond is weaker (has more p characteristics) and hence is a longer bond than an sp-sp sigma bond. - Determining Molecular Geometry 1. Determine the steric number (# of steric bonds + # of lone pairs) 2. Predict the hybridization of the central atom 3 • If the steric number is 4, then it is sp • If the steric number is 3, then it is sp • If the steric number is 2 then it is sp 3 - For any sp hybridized atom, the 4 valence electron pairs will form a tetrahedral electron group geometry. - Lone pairs make the electron group geometry (solely based on steric number) different from the molecular geometry (also bringing in interactions between lone pairs and bonded pairs). - Electron pairs that are located in sp2 hybridized orbitals will form a trigonal planar electron group geometry. - Electron pairs that are located in sp hybridized orbitals will form a linear electron group geometry. - Electronegativity differences cause shifting of electrons within their orbitals (also called induction). This results in a dipole moment. - For molecules with multiple polar bonds, the dipole moment is the vector sum of all of the individual bond dipoles. - Determine a molecule’s geometry first before analyzing its polarity. - If an atom is symmetrical and has no lone pairs, it is non-polar. - Intermolecular forces are responsible for many properties such as solubility, boiling point, density, state of matter, melting point, etc. - The more intermolecular forces you have, the higher the boiling point is going to be. - Neutral molecules (polar or non-polar) are attracted to one other by: • dipole-dipole interactions; result when polar molecules line up their opposite charges. • hydrogen bonding (strongest IMF force); an especially strong type of dipole-dipole attraction. Only when a hydrogen shares electrons with a highly electronegative FON atom (oxygen, nitrogen, fluorine); it then carries a large partial positive charge. Even with large partial changes, H-bonds are still about 20 times weaker than covalent bonds. (protic: capable of hydrogen bonding). H-bonds are among the forces that cause DNAto form a double helix and some proteins to fold into an alpha-helix. • dispersion forces (or London forces or fleeting dipole-diode forces); the constant random motion of the electrons in the molecule will sometimes produce an electron distribution that is not evenly balanced with the positive charge of the nuclei. The greater the surface area of a molecule, the more temporary dipole attractions are possible. Consider the feet of Gecko. They have many flexible hairs on their feet that maximize surface contact. - The more branching, the less the surface area and the less the boiling point. - Solubility: like dissolves like - Polar compounds generally mix well with other polar compounds. - Non polar compounds generally mix well with other non polar compounds. - Soap molecules organize into micelles in water which form a non polar interior to carry dirt. Klein Chapter 4 Alkanes and Cycloalkanes - Hydrocarbons are compounds that are only composed of hydrogen and carbon. - Alkane: saturated hydrocarbon; no double or triple bonds - IUPAC system: International Union of Pure andApplied Chemistry - Naming compounds: 1. Find the parent chain; longest consecutive chain of carbons • If there is more than one possible parent chain, choose the one with the most substituents attached. • If the parent chain is cyclic (a ring of carbons), add the prefix “cyclo” to the beginning of the parent name. • The parent name may not include carbons that are both in a ring and outside a ring. • meth, eth, prop, but, pent, hex, hept, oct, non, dec 2. Identifying the substituents • Count the number of carbons in each side group and use the terms from table 4.2 to name the substituents. • The terms in table 4.2 are the same as those in 4.1 except that they end with -yl instead of ane. A. Number the longest carbon chain within the substituent.Start with the carbon directly attached to the main chain. B. Name the substituent. C. Name and number the substituent’s side group. - To assemble the complete name, assign a locant to each substituent and list them before the parent chan name in alphabetical order. - Aprefix is used if multiple substituents are identical. - Summary: • Identify the parent chain. • Identify the name the substituents. • Number the parent chain and assign a locant to each substituent. (Give the first substituent the lowest number possible). • List the numbered substituents before the parent name in alphabetical order. • Ignore all prefixes except iso. - Constitutional isomers have no pi bonds so no degree of saturation. - Relative stability of isomers: stable= low potential energy= low reactivity = little energy will be released upon reacting. Branching makes an alkane more stable. - Sources and Uses ofAlkanes: • small alkanes with 1-4 carbons are gases • medium size alkanes with 5-12 carbons are liquids (gasoline) • Alkanes only have dispersion! • Large alkanes with 13-20 carbons are oils. Extra large alkanes with 20-100 carbons are solids like tar and wax. • • Super-sized alkanes called polymers can have thousands or millions of carbon atoms in each molecule. • The more carbons you have, the more solid it is. - Newman Projections • Different rotational states are called conformations. • Wedge and dash, sawhorse, Newman projection • Look directly down the C-C single bond axis. • The front carbon should eclipse the single bond and the carbon behind it. • Show the front carbon as a point and the back carbon as a large circle behind it. - Rotational Conformations • The angle between H atoms on adjacent carbons is called dihedral or torsional angle. It’s 60 degrees in the molecules to the right. • Staggered conformation- lowest energy • Maximum possible angle between the two atoms • If ethane were to rotate 60 degrees about the C-C bond, the H atoms on adjacent carbons eclipse one another. • Eclipsed conformation- highest in energy • The difference in energy between the staggered and eclipsed conformations is called torsional strain. In the staggered conformation, the bonding and anti bonding MOs of neighboring carbons overlap. - Butane’s Conformation The analysis of torsional strain for butane shows more variation. • • Anti: methyl groups are the farthest apart • Gauche: methyl groups experience a gauche interaction (two substituents are 60 degrees away from each other. - CyclicAlkanes • Carbon atoms in alkanes are sp3 hybridized. • To optimize the bond angles, most cycloalkanes are NOT flat in their most stable conformation. - Cyclobutane • Angle strain results from bond angles of 88 degrees, although it is not as severe as the 60 degree angle in cyclopropane. • Slight torsional strain results because adjacent C-H bonds are neither fully eclipsed nor fully staggered. - Cyclopentane • Angles are close to the optimal value. • Identify the minimal but significant torsional strain in the structure. - Cyclohexane • Considered to have zero ring strain in its optimal conformation, the chair. • Know how to draw newman structure for it. No angle strain- angle must be 109.5 degrees. No torsional strain- all adjacent C-H bonds must be staggered. Other conformations of hexane exist but are a bit less stable; the boat - Drawing Chairs • Use 3 sets of parallel lines. • Draw 2 parallel lines that are staggered. • Above and to the left of both lines make a dot. • Below and to the right of both lines, make a mother dot. • Connect the dots and lines. • Right top corner, draw a substituent group going straight up. • Bottom right corner, draw a substituent group going straight down. • Middle bottom corner, draw one straight up. • Bottom left corner, draw one straight down. • Top left, draw one straight up. • Middle top, draw ones straight up. • Up/down alternate • Each carbon must have a substituent pointed up and down so draw an equatorial substituent pointed the other way, not straight, but “upwards” or “downwards” - Monosubstituted Cyclohexane • Instead of an H, one is a methyl or halogen, etc. • Substituent in axial position is higher in energy. • It’s always better for the substituents to be equatorial if possible because you don’t have the torsional strain. • The axial substituent causes additional steric strain. An UP substituent could be axial or equatorial depending on how the ring is flipped. • • Wedged means up, Hashed means down. • If you can’t put all in the equatorial position (if they are both wedged), then the bigger atom would be in the equatorial position. - Lowest in energy to have a substituent in an equatorial position - Flipping the Chair • Number the carbons in your drawing. • Draw your first chair. • Draw your first ‘up’bond. Note that these are at your points on the initial chair you drew. • Alternate your up and down bonds on each carbon. • Pick a single carbon and identify its equatorial substituent. Do not draw these bonds straight in the x or y plane. • Number the carbons in your chair • Add substituents to your chair on the properly numbered carbon. Wedged means pointing up, hashed means going down. • To do a proper flip, just ignore your first chair and draw a second chair with your green dots on the opposite side. • (the dots stay the same number of carbon as in the first chair) - Polycyclic Systems: There are many biologically important steroids, all of which involve fusing cycloalkanes as part of their structure. Klein Chapter 5 Stereochemistry - Isomers are molecules that have the same formula but are not identical: • Constitutional isomers: Same molecular formula but different constitution • Stereoisomers: Same molecular formula and constitution but different spatial arrangement of atoms; you change that 3-D spatial arrangement - With rings and double bonds, cis-trans notation is used to distinguish between stereoisomers. - Cis- identical groups are positioned on the SAME side of a ring or of a double bond - Trans- identical groups are positioned on OPPOSITE sides of a ring - If we are asked to name a compound with rings or double bonds and we do not say cis or trans, the answer is WRONG! - To maintain orbital overlap in the pi bond, double bonds cannot rotate freely. - Although the two molecules below have the same connectivity, they are NOT identical because we can’t rotate from one to the other; the bond is stuck in place. - *Hint: Use degree of saturation when trying to determine whether two compounds are constitutional isomers, stereoisomers or neither. - If one carbon in a double has 2 of the same groups coming off, it cannot be cis or trans. - Cis-trans are not the only types of stereoisomers. You also have chirality to consider. - Achiral object is not identical to its mirror image. - You can test whether two objects are identical by seeing if they are superimposable. - Things that are chiral are not superimposable. - Chirality most often results when a carbon atom is bonded to 4 unique groups of atoms. - When an atom such as carbon forms a tetrahedral center with 4 different groups attached to it, it is called a chirality center (aka stereo center or stereogenic center) - Only sp3 carbons can be chiral centers. - Enantiomers are two molecules that are mirror images but are not identical and non-superimposable. - Naming enantiomers Chapter 7 The Quantum-Mechanical Model of theAtom -Electrons are incredibly small -Electron behavior determines much of the behavior of atoms. -Directly observing electrons in the atom is impossible; the electron is so small that observing it changes its behavior. -Electrons dictate reactivity. -The quantum-mechanical model helps us explain the behavior of electrons. -Electrons have very similar properties to light; light can be used as a model to understand how electrons work. Light is a form of electromagnetic radiation (electric field component + magnetic field component). They oscillate, travel along a plane and move through space at the same speed in a vacuum (3.00 × 10 m/s) -Distance between one crest of the wave to the next is a wavelength. This dictates what color we see. -Amplitude is how high the wave goes. It dictates brightness/intensity. -Shorter wavelength, higher frequency, higher in energy. (purple is the most harmful color for you) -Speed (c)= frequency (f) × wavelength (λ) (remember to always convert units to meters) -Frequency is the number of waves that pass through a point in a given period of time. (unit: hertz, Hz, or cycles/s, s ). -Waves in phase/in sync (same frequency and wavelength as each other) have an additive effect and amplify each other; this is a result of constructive interference. -Waves out of phase result in destructive interference. -If you have a wave and want it to cause a diffraction pattern, it will come out of the opening in waves.Alaser beam on the other hand may just go and shoot straight through the slit. That is particle behavior. -Electrons have a wave like behavior, much like light does. -Einstein, 1905, Photoelectric Effect. He took a metal surface and bombarded that surface with light; the light has a certain amount of energy associated with it and if the energy was high enough, an electron would be ejected from the metal. Einstein said that light not only has a wave nature but also has a particle nature. -Part of what the photoelectric effect showed was that it didn’t matter how intense or bright the light was; if it was not the right frequency, no electrons would be ejected. It doesn’t matter what the amplitude is, it matters what the frequency is because it is the frequency that is associated with energy. -High frequency light from a dim source caused electron emission without any lag time. -Einstein’s Explanation: Light energy was delivered to the atoms in packets called photons. The energy of a photon of light is directly proportional to its frequency. The proportionality constant is called Planck’s constant (h). Its value is 6.63 × 10 -34J/s. -E = hf = (h × c) / λ This is the energy of a photon; a single photon. There are anAvogadro’s number of photons in 1 mole of photons. Pay attention to the wording of a problem! -Bohr’s model of the atom: -electrons can only have specific/quantized energy values; there is no in between -as an electron moves from a higher to lower energy level, energy is emitted in the form of light - En= -R H 1 / n ) -18 - RH(Rydberg constant) = 2.18 × 10 J -n (principal quantum number) = 1,2,3,…… - Ephoton= ΔE = E - f i 2 - E f -R ( H / n ) f - I -R ( H / n ) I -Wave behavior of electrons; Louis de Broglie -particles could have wave-like character -the wavelength of a particle is inversely proportional to its momentum - λ = h/mv -v = velocity of e (m/s) -m = mass of e (kg)= 9.11 × 10 -31kg -pay attention to units! know unit conversions. -Schrodinger Wave Equation -describes both the particle and wave nature of electrons -the wave function describes: 1. Energy of an electron with a given Ψ 2. probability of finding an electron in a volume of space -can only be solved exactly for the hydrogen atom because it contains only one electron. must approximate its solution for multi-electron systems -Heisenberg uncertainty principal: it’s impossible to know simultaneously both the momentum and position of a particle with certainty. -ΔxΔp ≥ h/4π (x is position, p is momentum, h is planck’s constant) -Solutions to the wave function, Ψ -size, shape and orientation in space of an orbital are determined to be 3 integer terms in the wave function -These integers are called: -principal quantum number, n -angular momentum quantum number, l -magnetic quantum number, m l -Principal quantum number (n), always a whole number greater than 0, is the distance of an electron from the nucleus. -Electron density falls off rapidly as distance from nucleus increases (because electrons want to be close to the nucleus which has a net positive charge from the protons). -The number of the row in the periodic table corresponds to the principal quantum number (number of shells). -Angular momentum quantum number (l) = 0, 1, 2, 3, ….. , (n-1); tells us the volume of space that an electron occupies n = 1, l = 0 n = 2, l = 0 or 1 n = 3, l = 0, 1, or 2 Example, for 3s, n=3 but l=0. - l = 0, s orbital. lowest energy orbital in a principal energy state. spherical. number of nodes = (n-1).Anode is the place where there is a zero probability of finding an electron. -l = 1, p orbital. shape is a figure 8. node is where the line meets. -l = 2, d orbital. don’t need to know the shape. nodes exist. -l = 3, f orbital - the blocks in the periodic table correspond to the l value- tells us whether they are s, p, d or f block elements. -Magnetic quantum number, m The numberl.f these tells you how many orientations there are. - for a given value of l m =l-l, …., 0, …. +l - if l = 1 (p orbital), m = l1, 0, or 1 if l = 2 (d orbital), m = l2, -1, 0, 1, or 2 -Spin quantum number, m . s -m = +½ or -½ s - the positive half represents the up spin and the negative spin represents the down spin. -Schrodinger Wave Equation: Ψ = fn(n, l, m, m ) l s -Existence (and energy) of electron in atom is described by its unique wave function Y. The wave function must have 4 different values. -Pauli exclusion principle- no two electrons in an atom can have the same 4 quantum numbers. -Shell: electrons with the same value of n -Subshell: electrons with the same value of n and l -Orbital: electrons with the same values of n, l, and m l -Orbitals are determined from mathematical wave functions that have positive or negative values. The sign of the wave function is called its phase. For a bond to be created, phases need to line up/ have to overlap. Chemistry Chapter 8 Periodic Properties of the Elements -Adescription of the orbitals occupied by electrons is called an electron configuration. -In every orbital, a spin must be paired. Only two electrons can fit in a single orbital. If two electrons are in the same orbital, one must have a + m and one must have a - m (they must have s s opposite spins) Energy of electrons in a single-electron atom: Energy of electrons in a multi-electron atom: -Fill up electrons in the lowest energy orbitals first (Aufbau Principle) -The most stable arrangement of electrons in sub-shells is the one with the greatest number of parallel spins (Hund’s rule) Order of filling up orbitals in multi-electron systems: 1s < 2s < 2p < 3s < 3p < 4s < 3d < 4p < 5s < 4d < 5p < 6s -copper, silver, and gold are exceptions to the typical electronic configuration (follow the d and 9 4 9 4 d rule; should never have d and d in the ground state but can have them in the charged state) -The electrons in all the sub levels with the highest principal energy are called the valence electrons. Noble gases have 8 valence electrons (the most) while the other elements have less. -Electrons in lower energy shells are called core electrons. -Valence electrons dictate a lot of the properties and reactivities of the elements. -For the 5s electron in Rb the set of quantum numbers is n=5, l=0, m=0, m =+1/2 l s -For an electron in the 2p sub level, the set of quantum numbers is n=2, l=1, m=-1 or (0,+1l, and m s -1/2 or + 1/2 -Atoms lose electrons so that cation has a noble-gas outer electron configuration. -Atoms gain electrons so that anion has a noble-gas outer electron configuration. -Isoelectronic- atoms that have the same electron configuration -When a cation is formed from an atom of a transition metal, electrons are always removed first from the ns orbital and then from the (n-1)d orbitals. -Metal ions behave differently from their neutral atoms; the (n-1)d orbital is more stable than the ns orbital. -Transition metals can form many different cations that are NOT isoelectronic with a noble gas. Trends inAtomic Radius: -Atomic radius increases down the group and decreases across a period. -Outer electrons are shielded from the nucleus by the core electrons, which causes the outer electrons to not experience the full strength of the nuclear charge. Instead, it feels the effective nuclear charge (Z = Z (nuclear charge/number of protons) - S (number of core or inner electrons)); net eff positive charge that is attracting a particular electron. -The effective nuclear charge increases as you go across a period; the outer electrons feel a stronger attraction to the nucleus and hence the radius decreases. -Even one unpaired electron makes it paramagnetic. -Cations tend to be smaller than their neutral counterpart. -Anions tend to be larger than their neutral counterpart. -For isoelectronic species, the more negative the charge the larger the atom/ion. -Ionization energy is the minimum energy (kJ/mol) required to remove an electron from a gaseous atom in its ground state. -The higher the positive charge of the ion, the more energy it takes to remove an electron I 1< I 2 I 3 -It is much harder to remove an electron from a cation. -Electron affinity is the energy change that occurs when an electron is accepted by an atom in the gaseous state to form an anion. -The more negative the value, the more likely it is to pick up an electron -In general, as we go from left to right, the electron affinity gets more negative. -Metallic character decreases as you go left to right and increases as you go from top to bottom. Chemistry Chapter 9 Chemical Bonding I: Lewis Theory - One of the simplest bonding theories is called Lewis Theory. - It emphasizes valence electrons to explain bonding. - Using Lewis theory, we can draw models called Lewis structures (or Electron Dot Structures). - Lewis structures allow us to predict many properties of molecules (such as molecular stability, shape, size and polarity). - Chemical bonds form because they lower the potential energy between the charged particles that compose atoms. - Achemical bond forms when the potential energy of the bonded atoms is less than the potential energy of the separate atoms. - Metals to nonmetals, Ionic bond, Electrons transferred. Most of the time, ionic bonds form solids/ crystalline structures. - Nonmetals to nonmetals, Covalent bond, Electrons shared - When a metal atom loses electron, it becomes a cation (metals have low ionization energy). - When a nonmetal atom gains electrons it becomes an anion (non metals have high electron affinities). - Oppositely charged ions from an ionic bond. - Nonmetal atoms have high ionization energies, so it is difficult to remove electrons from them. - When nonmetals bond together, it is better to share valence electrons. - Shared electrons hold the atoms together by attracting the nuclei of both atoms. - The column number on the Periodic Table will tell you how many valence electrons a main group atom has. - Valence electrons are the outer shell electrons of an atom. The valence electrons are the electrons that participate in chemical bonding. - Metals form cations by losing enough electrons to get the same electron configuration as the previous noble gas. - Nonmetals form anions by gaining enough electrons to get the same electron configuration as the next noble gas. - The noble gas electron configuration must be very stable. - An ionic bond is the electrostatic force that holds ions together in an ionic compound. - The opposite charges of cations and anions form the actual ionic bond. - No anion-cation pair exists in a crystalline solid because the charge is distributed over the whole thing; results in the formation of a crystal lattice. The chemical formula is the empirical formula. - Lattice energy (E) is the energy required to completely separate one mole of a solid ionic co


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