Organic Chemistry Flashcards PDF

 1.1 IUPAC Naming Conventions 30 Day MCAT CHAPTER 1 - NOMENCLATURE Step 1: Find the parent chain, the longest carbon chain that contains the highest-priority functional group. Step 2: Number the chain in such...

 1.1 IUPAC Naming Conventions 30 Day MCAT CHAPTER 1 - NOMENCLATURE Step 1: Find the parent chain, the longest carbon chain that contains the highest-priority functional group. Step 2: Number the chain in such a way that the highest-priority functional group receives the lowest possible number. Step 3: Name the substituents with a prefix. Multiples of the same type receive (di-, tri-, tetra-, etc.). Step 4: Assign a number to each substituent depending on the carbon to which it is bonded. Step 5: Alphabetize substituents and separate numbers from each other by commas and from words by hyphens.  1.2 Hydrocarbons and Alcohols 30 Day MCAT CHAPTER 1 - NOMENCLATURE Alkane: Hydrocarbon with no double or triple bonds. Alkane = CnH (2n+2) Naming: Alkanes are named according to the number of carbons present followed by the suffix – ane. Alkene: Contains a double bond. Use suffix -ene. Alkyne: Contains a triple bond. Use suffix –yne. Alcohol: Contains a –OH group. Use suffix –ol or prefix hydroxy-. Alcohols have higher priority than double or triple bonds. Diol: Contains 2 hydroxyl groups. Geminal: If on same carbon Vicinal: If on adjacent carbons  1.3 Aldehydes and Ketones 30 Day MCAT CHAPTER 1 - NOMENCLATURE Carbonyl Group: C=O. Aldehydes and ketones both have a carbonyl group. Aldehyde: Carbonyl group on terminal C. Ketone: Carbonyl group on nonterminal C.  1.4 Carboxylic Acid and Derivatives 30 Day MCAT CHAPTER 1 - NOMENCLATURE Carboxylic Acid: The highest priority functional Ester: Carboxylic Acid derivative where –OH is group because it contains 3 bonds to oxygen. replaced with -OR. Naming: Suffix –oic acid. Anhydrides: The word acid is replaced with anhydride. For a mixed anhydride, name both Amide: Replace the –OH group of a carboxylic acids. acid with an amino group that may or may not be substituted.  2.1 Structural Isomers 30 Day MCAT CHAPTER 2 - ISOMERS Steroids: Cholesterol, ergosterol, etc., with distinct roles. Ring Forms: Glucose pyranose/furanose forms. Cyclic Sugars: α/β-glucose with varying hydroxyl group orientation. Enzymes: Isomer shapes affect enzyme interactions and reactions. Carbohydrates: Glucose/fructose have same C6H12O6 formula, differ in arrangement. Amino Acids: L/D configurations, L-amino acids in proteins. Fatty Acids: Cis/trans isomers with double bond arrangements. Nucleotides: Purine (A/G) and pyrimidine (C/T or U) isomers.  2.2 Stereoisomers 30 Day MCAT CHAPTER 2 - ISOMERS Compounds with atoms connected in the same order but differing in 3D orientation. Chiral Center: Four different groups attached to a central carbon. 2n Rule: n = # of chiral centers # of stereoisomers = 23 Conformational Isomers Differ by rotation around a single (s) bond Racemic Mixture: 50:50 mixture of two enantiomers. Cyclohexane. Equatorial: In the plane of the molecule. Not optically active because the rotations cancel out. Substituents. Axial: Sticking up/down from the molecule’s plane. Meso Compounds: Have an internal plane of symmetry, will also be Configurational Isomers optically inactive because the two sides of the molecule cancel each other out. Enantiomers: Nonsuperimposable mirror images. Opposite stereochemistry at every chiral carbon. Same Diastereomers: Stereoisomers that are NOT mirror chemical and physical properties, except for image. rotation of plane polarized light. Cis-Trans: A subtype of diastereomers. They differ at Optical Activity: The ability of a molecule to rotate plane- some, polarized but not all, chiral centers. Different chemical and light: d- or (+) = RIGHT, l- or (-) = LEFT. physical properties.  2.3 Relative and Absolute Configurations 30 Day MCAT CHAPTER 2 - ISOMERS (Z) and (E) for Alkenes: (Z): Highest priority on same side. (E): Highest priority on opposite sides. (R) and (S) for Stereocenters: A stereocenter’s configuration is determined by putting the lowest priority group in the back and drawing a circle from group 1-2-3. (R): Clockwise (S): Counterclockwise Fischer Projection: Vertical lines go to back of page (dashes); Relative Configuration: Gives the stereochemistry of horizontal lines come out of the page (wedges). a compound in comparison to another compound. E.g. D and L. Altering Fischer Projection: Switching 1 pair of substituents inverts the stereochemistry; switching Absolute Configuration: Gives the stereochemistry 2 pairs retains of a compound without having to compare to other stereochemistry. Rotating entire diagram 90° inverts compounds. the stereochemistry; rotating 180° retains E.g. S and R. stereochemistry. Cahn-Ingold-Prelog Priority Rules: Priority is given by looking at atoms connected to the chiral carbon or double-bonded carbons; whichever has the highest atomic # gets highest priority.  3.1 Atomic Orbitals and Quantum Numbers 30 Day MCAT CHAPTER 3 - BONDING Quantum Numbers: Describe the size, shape, orientation, and number of atomic orbitals in an element Maximum e- in terms of n = 2n2 Maximum e- in subshell = 4l + 2  3.2 Molecular Orbitals 30 Day MCAT CHAPTER 3 - BONDING Bonding Orbitals: Created by head-to-head or tail-to-tail overlap of atomic orbitals of the same sign. energy ­stable Antibonding Orbitals: Created by head-to-head or tail-to-tail overlap of atomic orbitals of opposite signs. ­energy stable Single Bonds: 1 s bond, contains 2 electrons Double Bonds: 1 s + 1 p Pi bonds are created by sharing of electrons between two unhybridized p-orbitals that align side-by-side Triple Bonds: 1 s + 2 p Multiple bonds are less flexible than single bonds because rotation is not permitted in the presence of a p bond. Multiple bonds are shorter and stronger than single bonds, although individual p are weaker than s bonds  3.3 Hybridization 30 Day MCAT CHAPTER 3 - BONDING Resonance: Describes the delocalization of electrons in molecules that have conjugated bonds Conjugation: Occurs when single and multiple bonds alternate, creating a system of unhybridized p orbitals down the backbone of the molecule through which p electrons can delocalize sp3: 25% s character and 75% p character Tetrahedral geometry with 109.5° bond angles sp2: 33% s character and 67% p character Trigonal planar geometry with 120° bond angles sp: 50% s character and 50% p character Linear geometry with 180° bond angles  4.1 Acids and Bases 30 Day MCAT CHAPTER 4 - ANALYZING ORGANIC REACTIONS Acids: Bronsted-Lowry Definition: Acids are substances Lewis Definition: Bases are substances that can that donate protons (H+ ions) to other molecules donate an electron pair. This definition is broader and or ions. They act as proton donors. encompasses compounds that can donate electron Lewis Definition: Acids are substances that can pairs even if no protons are involved. accept an electron pair. This definition is broader Basicity: Basicity is the ability of a substance to and includes compounds that can accept accept protons. Bases increase the concentration of electron pairs even if no protons are involved. hydroxide ions (OH-) in water, leading to a higher pH. pH: Acidity is often measured using the pH scale, Strong vs. Weak Bases: Similar to acids, strong which ranges from 0 to 14. A lower pH indicates bases completely dissociate in water, while weak higher acidity, while a higher pH indicates higher bases only partially dissociate. basicity. Common Organic Bases: Amines (both primary, Strong vs. Weak Acids: Strong acids completely secondary, and tertiary), and alkoxides are common dissociate in water, releasing all their protons. organic bases. Weak acids only partially dissociate, establishing an equilibrium between the undissociated acid Acid-Base Reactions: and its ions. Neutralization forms water and a salt. Common Organic Acids: Carboxylic acids (e.g., pKa indicates acid/base strength. acetic acid), phenols, and sulfonic acids are Conjugate pairs switch protons. examples of common organic acids. Some molecules can act as both acids and bases. Bases: Bronsted-Lowry Definition: Bases are substances that accept protons (H+ ions) from other molecules or ions. They act as proton acceptors.  4.2 Oxidation/Reduction Reactions 30 Day MCAT CHAPTER 4 - ANALYZING ORGANIC REACTIONS Oxidation: Loss of Electrons: Oxidation involves the loss of electrons from a molecule. Increase in Oxidation State: The oxidation state of an atom increases during oxidation. Common Oxidizing Agents: Reagents that commonly bring about oxidation include KMnO4, K2Cr2O7, PCC (pyridinium chlorochromate), and O3 (ozone). Functional Group Changes: Oxidation can convert primary alcohols to aldehydes or carboxylic acids, secondary alcohols to ketones, and hydrocarbons to alcohols or other functional groups. Reduction: Gain of Electrons: Reduction involves the gain of electrons by a molecule. Decrease in Oxidation State: The oxidation state of an atom decreases during reduction. Common Reducing Agents: Reagents that Oxidation-Reduction: commonly bring about reduction include NaBH4 Redox reactions involve electron transfer. (sodium borohydride) and LiAlH4 (lithium Balancing includes electrons. aluminum hydride). Reducing agent gives electrons, oxidizing agent Functional Group Changes: Reduction can receives. convert aldehydes to primary alcohols, ketones to secondary alcohols, and nitro groups to amines.  4.3 Nucleophiles, Electrophiles, and Leaving Groups 30 Day MCAT CHAPTER 4 - ANALYZING ORGANIC REACTIONS Nucleophiles: Definition: Nucleophiles are electron-rich species that donate or share electrons by attacking electron- deficient sites. Role: Nucleophiles participate in bond formation during reactions. Examples: Alkoxides, amines, halide ions. Properties: High electron density, lone pairs, often negatively charged. Electrophiles: Definition: Electrophiles are electron-deficient species that accept or react with electrons from nucleophiles. Role: Electrophiles are targets for nucleophilic attacks. Examples: Carbocations, carbonyl compounds (aldehydes, ketones), positively charged species. Properties: Electron-poor, often positively charged or polarized. Leaving Groups: Depart with electrons, stabilize transition states.  4.4 Chemoselectivity 30 Day MCAT CHAPTER 4 - ANALYZING ORGANIC REACTIONS Methods to Achieve Chemoselectivity: Protecting Groups: Temporarily mask reactive groups to prevent unwanted reactions. Choice of Reagents: Specific reagents can target desired functional groups. Reaction Conditions: Reaction conditions can favor one reaction pathway over others. Benefits: Efficiency: Chemoselectivity streamlines synthesis and minimizes waste. Precision: Enables construction of intricate molecules with specific modifications. Chemoselectivity: Definition: Chemoselectivity involves choosing a specific chemical reaction to occur at one functional group or site in the presence of other reactive groups. Factors Influencing Chemoselectivity: Reactivity: Different functional groups have varying reactivities toward specific reagents. Steric Effects: Bulky groups may hinder access to certain sites. Electronic Effects: Electron-rich or electron-poor groups can influence reactivity. Applications: Multistep Synthesis: Chemoselectivity allows controlled sequential transformations. Natural Product Synthesis: Selective modifications in complex molecules.  5.1 Description and Properties 30 Day MCAT CHAPTER 5 - ALCOHOL Alcohols: Definition: Alcohols are organic compounds containing a hydroxyl (-OH) group bonded to a carbon atom. Nomenclature: Named by replacing the -e ending of the corresponding alkane with -ol. Primary, Secondary, Tertiary: Based on the number of carbon atoms directly bonded to the carbon bearing the -OH group. Chemical Properties: Physical Properties: Acidic Nature: Alcohols can act as weak acids, Solubility: Small alcohols are generally soluble donating a proton from the -OH group. in water due to hydrogen bonding. Nucleophilic Reactions: Alcohols can participate Boiling Points: Alcohols have higher boiling in nucleophilic substitution reactions. points compared to hydrocarbons of similar Oxidation: Primary alcohols can be oxidized to size due to hydrogen bonding. aldehydes and then to carboxylic acids. Secondary alcohols can be oxidized to ketones. Dehydration: Alcohols can undergo dehydration to form alkenes under acidic conditions. Ether Formation: Alcohols can react with acids to form ethers. Uses: Solvents: Many alcohols are used as solvents in various industries. Biomolecules: Alcohols are found in various biomolecules, including sugars and amino acids. Fuels: Ethanol is used as a biofuel and fuel additive. 5.2 Reactions of Alcohols 30 Day MCAT CHAPTER 5 - ALCOHOL Reactions of Alcohols: Dehydration: Form alkenes under acid catalyst. Oxidation: Primary → aldehydes/ketones. Secondary → ketones. Substitution: React with HX to form alkyl halides (acid catalyst). Ether Formation: React with acids to form ethers. PBr3, SOCl2: Convert to alkyl halides. Protection: Convert to stable groups to prevent reactions. Lucas Test: Distinguish primary/secondary/tertiary alcohols. Williamson Synthesis: Form ethers with alkyl halides. Fischer Esterification: Form esters with carboxylic acids. Alcohol + Grignard: React with Grignard reagents for new bonds.  5.3 Reactions of Phenols 30 Day MCAT CHAPTER 5 - ALCOHOL Oxidation: Phenols can be oxidized using reagents like chromic acid (H2CrO4) to form quinones, which are important in various biological processes. Kolbe-Schmitt Reaction: Phenolate ions react with carbon dioxide under basic conditions to form salicylates, which are used in the synthesis of aspirin. Ether Formation: Phenols can react with alkyl halides to form ethers under basic conditions. Reimer-Tiemann Reaction: Phenols can be converted into salicylaldehydes by reacting with chloroform (CHCl3) and a strong base. Phenol + Acyl Chloride/Anhydride: React with Reactions of Phenols: acyl chlorides or anhydrides to form esters (Fisher esterification). Acidity: Phenols are weak acids and can donate a Phenol + Diazonium Salt: Reaction with diazonium proton from the hydroxyl group. They react with strong salts leads to the formation of aromatic bases to form phenoxide ions. compounds, such as azo dyes. Electrophilic Aromatic Substitution (EAS): Phenols Phenol + Nitrous Acid: React with nitrous acid to undergo EAS reactions due to the electron-donating form phenol diazonium salts, which can further nature of the -OH group. Examples include react to form phenol ethers or phenols with halogenation, nitration, sulfonation, and Friedel-Crafts halides or nucleophiles. acylation/alkylation.  6.1 Description and Properties 30 Day MCAT CHAPTER 6 - ALDEHYDES AND KETONES 1: ELECTROPHILICITY AND OXIDATION / REDUCTION Description and Properties Electrophilicity: Both aldehydes and ketones contain a carbonyl group (C=O), making the carbon atom electrophilic. Oxidation: Aldehydes can be oxidized to carboxylic acids. Common oxidizing agents include potassium dichromate (K2Cr2O7) and chromic acid (H2CrO4). Reduction: Aldehydes and ketones can be reduced to primary and secondary alcohols, respectively. Boiling Points: Higher than hydrocarbons due to C=O polarity and potential hydrogen bonding. Solubility: Small ones soluble in water due to hydrogen bonding. Reactivity: Carbonyl group allows nucleophilic additions and aldol reactions. Tautomerism: α-Hydrogens allow keto-enol tautomerism. Nucleophilic Addition: React with water, alcohols, amines in nucleophilic addition reactions.  6.2 Oxidation/Reduction Reactions 30 Day MCAT CHAPTER 6 - ALDEHYDES AND KETONES 1: ELECTROPHILICITY AND OXIDATION / REDUCTION Oxidation/Reduction Reactions in Organic Chemistry: Oxidation: Involves loss of electrons or increase in oxidation state. Reduction: Involves gain of electrons or decrease in oxidation state. Key Points Oxidizing Agents: Substances causing oxidation, e.g., KMnO4, K2Cr2O7. Reducing Agents: Substances causing reduction, e.g., NaBH4, LiAlH4. Oxidation State: Tracks electron transfer; increases in oxidation state indicate oxidation, and vice versa. Functional Group Changes: Alcohols → Aldehydes/Ketones → Carboxylic Acids. Dehydrogenation: Loss of hydrogen, e.g., alcohols to ketones. Hydrogenation: Gain of hydrogen, e.g., alkenes to alkanes. Redox in Biological Systems: Essential in metabolism, energy production, and many biochemical processes.  6.3 Nucleophilic Addition Reactions 30 Day MCAT CHAPTER 6 - ALDEHYDES AND KETONES 1: ELECTROPHILICITY AND OXIDATION / REDUCTION 7.1 General Principles 30 Day MCAT CHAPTER 7 - ALDEHYDE AND KETONES 2: ENLOE'S Functional Group: Aldehydes and ketones have a carbonyl group (C=O). Naming: Aldehydes end in -al, ketones end in - one. Structure: Aldehydes have C=O at the end, ketones within the chain. Reactivity: Aldehydes are more reactive; ketones are less reactive due to bulky groups. Oxidation: Aldehydes oxidize to acids; ketones resist oxidation. Reduction: Both can be reduced to alcohols. Nucleophilic Addition: Both undergo addition reactions. Tautomerism: Can shift between keto and enol forms. Aldol Condensation: Forms new C-C bonds. Imine/Enamine: React with amines to form imines/enamines. 7.2 Enolate Chemistry 30 Day MCAT CHAPTER 7 - ALDEHYDE AND KETONES 2: ENLOE'S Enolate Formation: Generated by deprotonating α-carbon of carbonyls. Nucleophilic: Strong nucleophiles due to α-carbon negative charge. Reactions: Alkylation, acylation, aldol, Claisen, Michael. Equilibrium: Enolates ↔ keto forms (tautomerism). Synthesis: Used in malonic ester, β-keto ester syntheses. Protecting Groups: Silyl ethers for enolate protection. Kinetic vs. Thermodynamic: Different enolates form under varying conditions. Stereochemistry: Enolate reactions offer stereoselectivity. 7.3 Aldol Condensation 30 Day MCAT CHAPTER 7 - ALDEHYDE AND KETONES 2: ENLOE'S Reaction Type: Combines carbonyl compounds to form β-hydroxy carbonyls. Base-Catalyzed: Involves enolate formation as nucleophile. Bond Formation: Enolate adds to carbonyl carbon. β-Hydroxy Carbonyl: Product has -OH at β-carbon. Condensation Step: Water elimination forms new C-C bond. Crossed/Self-Condensation: Within or between molecules. Synthetic Use: Builds C-C bonds, introduces functional groups. Stereochemistry: Can be stereoselective. α,β-Unsaturated Compounds: Dehydration leads to enones. Applications: Valuable in complex molecule synthesis. 8.1 Description and Properties 30 Day MCAT CHAPTER 8 - CARBOXYLIC ACIDS  8.2 Carboxylic Acid Synthesis 30 Day MCAT CHAPTER 8 - CARBOXYLIC ACIDS Hydrolysis of Amides: Amides can be hydrolyzed under acidic or basic conditions to yield carboxylic acids and amines. Grignard Reaction: Alkyl or aryl magnesium halides (Grignard reagents) react with carbon dioxide (CO2) to produce carboxylic acids. Malonic Ester Synthesis: Diethyl malonate reacts with alkyl halides in a base-catalyzed reaction, followed by hydrolysis, yielding substituted carboxylic acids. Oxidation of Primary Alcohols: Primary alcohols can be oxidized to carboxylic acids using strong Acyl Chloride Reaction: Acyl chlorides (acid oxidizing agents like potassium permanganate chlorides) react with water to form carboxylic acids (KMnO4) or chromic acid (H2CrO4). and hydrogen chloride (HCl). Oxidation of Aldehydes: Aldehydes can be further Decarboxylation: Some carboxylic acids can undergo oxidized to carboxylic acids using the same decarboxylation under heat to produce carbon oxidizing agents mentioned above. dioxide and a hydrocarbon. Hydrolysis of Nitriles: Nitriles can be hydrolyzed From Alkenes: Alkenes can be oxidized to form under acidic conditions (H2O, H2SO4) to yield carboxylic acids through reaction with ozone carboxylic acids. (ozonolysis) followed by oxidative workup. Hydrolysis of Esters: Esters undergo hydrolysis in From Alkynes: Alkynes can be hydrolyzed and the presence of a strong acid (H2SO4) or base oxidized to produce carboxylic acids. (NaOH) to produce carboxylic acids and alcohols. 8.3 Reactions of Carboxylic Acids 30 Day MCAT CHAPTER 8 - CARBOXYLIC ACIDS 9.1 Amides, Esters and Anhydrides 30 Day MCAT CHAPTER 9 - CARBOXYLIC ACID DERIVATIVES 9.2 Reactivity Principles 30 Day MCAT CHAPTER 9 - CARBOXYLIC ACID DERIVATIVES Electrophiles/Nucleophiles: Interaction of electron- deficient (E) and electron-rich (N) species. Lewis Acids/Bases: Acid-base interactions, Lewis acids accept, bases donate electrons. Substituent Effects: Electron-donating/withdrawing groups influence reactivity. Steric Hindrance: Bulky groups affect reaction pathways and rates. Aromaticity: Aromatic compounds are stable due to resonance. Resonance/Polarity: Delocalization and polarity impact stability and mechanisms. Mechanisms: Understand step-by-step reaction paths. Conditions: Temperature, solvent, pressure affect reactions. Stereochemistry/Catalysis: Chiral outcomes, catalysts accelerate. Substitution/Elimination: SN and E reactions depend on structure. Addition/Redox: Alkenes/alkynes undergo addition, redox involves electrons. Energetics/Kinetics: Gibbs energy, rates determine feasibility. Reaction Types: Identify condensation, hydrolysis, rearrangements.  9.3 Nucleophilic Acyl Substitution Reactions 30 Day MCAT CHAPTER 9 - CARBOXYLIC ACID DERIVATIVES All carboxylic acid derivatives can undergo nucleophilic substitution reactions. The rates at which they do so is determined by their relative reactivities. Cleavage: Anhydrides can be cleaved by the addition of a nucleophile. Addition of ammonia or an amine results in an amide and a carboxylic acid. Addition of an alcohol results in an ester and a carboxylic acid. Addition of water results in two carboxylic acids Transesterification: The exchange of one esterifying group for another on an ester. The attacking nucleophile is an alcohol. Amides: Can be hydrolyzed to carboxylic acids under strongly acidic or basic conditions. The attacking nucleophile is water or the hydroxide anion.  10.1 Amino Acids, Peptides, and Proteins 30 Day MCAT CHAPTER 10 - NITROGEN AND PHOSPHORUS CONTAINING COMPOUNDS Amino Acid: The a-carbon of an amino acid is attached to four groups: an amino group, a carboxyl group, a hydrogen atom, and an R group. It is chiral in all amino acids except glycine. All amino acids in eukaryotes are L-amino acids. They all have (S) stereochemistry except cysteine, which is (R). Amphoteric: Amino acids are amphoteric, meaning they can act as acids or bases. Amino acids get their acidic characteristics from carboxylic acids and their basic characteristics from amino groups. In neutral solution, amino acids tend to exist as zwitterions (dipolar ions). Aliphatic: Non-aromatic. Side chain contains only C and H. Gly, Ala, Val, Leu, Ile, Pro. Met can also be considered aliphatic. Peptide Bonds: Form by condensation reactions and can be cleaved hydrolytically. Resonance of peptide bonds restricts motion about the C-N bond, which takes on partial double bond character. A strong acid or base is needed to cleave a peptide bond. Formed when the N-terminus of an AA nucleophilically attacks the C- terminus of another AA. Polypeptides: Made up of multiple amino acids linked by peptide bonds. Proteins are large, folded, functional polypeptides.  10.2 Synthesis of Amino Acids 30 Day MCAT CHAPTER 10 - NITROGEN AND PHOSPHORUS CONTAINING COMPOUNDS Biologically, amino acids are synthesized in many ways. In the lab, certain standardized mechanisms are used. Strecker Synthesis: Generates an amino acid from an aldehyde. An aldeyhyde is mixed with ammonium chloride (NH4Cl) and potassium cyanide. The ammonia attacks the carbonyl carbon, generating an imine. The imine is then attacked by the cyanide, generating an aminonitrile. The aminonitrile is hydrolyzed by two equivalents of water, generating an amino acid. Gabriel Synthesis: Generates an amino acid from potassium phthalimide, diethyl bromomalonate, and an alkyl halide. Phthalimide attacks the diethyl bromomalonate, generating a phthalimidomalonic ester. The phthalimidomalonic ester attacks an alkyl halide, adding an alkyl group to the ester. The product is hydrolyzed, creating phthalic acid (with two carboxyl groups) and converting the esters into carboxylic acids. One carboxylic acid of the resulting 1,3-dicarbonyl is removed by decarboxylation.  10.3 Phosphorus Containing Compounds 30 Day MCAT CHAPTER 10 - NITROGEN AND PHOSPHORUS CONTAINING COMPOUNDS Phosphoric Acid: Sometimes referred to as a phosphate group or inorganic phosphate, denoted Pi. At physiological pH, inorganic phosphate includes molecules of both hydrogen phosphate (HPO4 2-) and dihydrogen phosphate (H2PO4 - ). Phosphoric Acid Structure: Contains 3 hydrogens, each with a unique pKa. The wide variety in pKa values allows phosphoric acid to act as a buffer over a large range of pH values. Phosphodiester Bonds: Phosphorus is found in the backbone of DNA, which uses phosphodiester bonds. In forming these bonds, a pyrophosphate (PPi, P2O7 4-) is released. Pyrophosphate can then be hydrolyzed to two inorganic phosphates. Phosphate bonds are high energy because of large negative charges in adjacent phosphate groups and resonance stabilization of phosphates Organic Phosphates: Carbon containing compounds that also have phosphate groups. The most notable examples are nucleotide triphosphates (such as ATP or GTP) and DNA. 11.1 Infrared Spectroscopy 30 Day MCAT CHAPTER 11 - SPECTROSCOPY  11.2 Ultraviolet Spectroscopy 30 Day MCAT CHAPTER 11 - SPECTROSCOPY UV spectroscopy is most useful for studying Electronic Transitions: UV spectroscopy studies compounds containing double bonds and/or electronic transitions, focusing on π-electron systems. heteroatoms with lone pairs that create conjugated systems. Absorption of UV Light: Molecules absorb UV light when electrons move from lower-energy π-orbitals to Measures the absorption of UV light, which causes higher-energy π*-orbitals. movement of electrons between molecular orbitals. UV spectra are generally plotted as percent Conjugation: Extended conjugation increases transmittance or absorbance vs. Wavelength. absorption. More conjugated systems shift absorption to longer wavelengths. HOMO & LUMO: To appear on a UV spectrum, a molecule must have a small enough energy Chromophores: Chromophores are groups responsible difference between its HOMO and LUMO to permit an for UV absorption (e.g., double bonds, aromatic rings). electron to move from one orbital to the other. The smaller the difference between HOMO and LUMO, λ-max: λ-max is the wavelength of maximum the longer the wavelengths a molecule can absorb. absorption, indicating the type of chromophore present. Solvent Effects: Solvent polarity shifts absorption. Quantitative Analysis: Measures concentration. Applications: Identifies groups, monitors reactions Limitations: Limited structural info. Complementary: Used with other techniques.  11.3 Nuclear Magnetic Resonance Spectroscopy 30 Day MCAT CHAPTER 11 - SPECTROSCOPY NMR spectroscopy measures alignment of nuclear Upfield: RIGHT. More shielded, by EDG or less EN spin with an applied magnetic field, which depends atom nearby. on the magnetic environment of the nucleus itself. It is useful for determining the structure (connectivity) Spin-Spin Coupling: When hydrogens are on of a compound, including functional groups. adjacent atoms, they interfere with each other’s magnetic environment, causing spin-spin coupling Generally plotted as frequency vs. absorption energy. (splitting). A proton’s (or a group of protons’) peak They are standardized by using chemical shift (d), is split into n+ 1 subpeaks, where n is the number of measured in parts per million (ppm) of protons that are three bonds away from the proton spectrophotometer frequency. of interest. Splitting patterns include doublets, triplets, and multiplets. TMS: NMR spectra are calibrated using tetramethylsilane (TMS), which has a chemical shift of 0 ppm Integration: Area under the curve. Proportional to the number of protons contained under the peak. Deshielding: Occurs when electron-withdrawing groups pull electron density away from the proton’s nucleus, allowing it to be more easily affected by the magnetic field. Deshielding moves a peak further downfield Downfield: LEFT. Deshielded by EWG or EN atom nearby.  11.4 Mass Spectroscopy 30 Day MCAT CHAPTER 11 - SPECTROSCOPY Used to determine the molecular weight and aid in determining molecular structure. The charged molecule collides with an electron, resulting in the ejection of an electron from the molecule, making it a radical. Base Peak: Tallest peak (not always the intact molecule) Molecular Ion Peak: Peak that represents the molecule. M+1 Peak: Relative abundance of 13C. Found in relative abundance of 1.1%. So, if M+1 has an m/z value of 4.4, that means there are 4 carbons. 4.4/1.1 = 4. M+2 Peak: Relative abundance of either 81Br or 37Cl. Br has a 1:1 ratio relative to the M peak. Cl has a 3:1 ratio relative to the M peak.  12.1 Solubility-Based Methods 30 Day MCAT CHAPTER 12 - SEPARATIONS AND PURIFICATIONS Extraction: Combines two immiscible liquids, one of which easily dissolves the compound of interest. Nonpolar Layer: Organic layer, dissolves nonpolar compounds. Polar Layer: Aqueous (water) layer. Dissolves compounds with hydrogen bonding or polarity. Wash: The reverse of an extraction. A small amount of solvent that dissolves impurities is run over the compound of interest. Filtration: Isolates a solid (residue) from a liquid (filtrate) Gravity Filtration: Use when the product of interest is in the filtrate. Hot solvent is used to maintain solubility. Vacuum Filtration: Used when the product of interest is the solid. A vacuum is connected to the flask to pull the solvent through more quickly. Recrystallization: The product is dissolved in a minimum amount of hot solvent. If the impurities are more soluble, the crystals will reform while the flask cools, excluding the impurities.  12.2 Distillation 30 Day MCAT CHAPTER 12 - SEPARATIONS AND PURIFICATIONS Distillation: Separates liquids according to differences in their boiling points. The liquid with the lowest BP vaporizes first and is collected as the distillate. Simple Distillation: Can be used if the boiling points are under 150°C and are at least 25°C apart. Vacuum Distillation: Should be used if the boiling points are over 150°C to prevent degradation of the product. The vacuum lowers the air pressure, which decreases the temp the liquid must reach in order to boil. Fractional Distillation: Should be used if the boiling points are less than 25°C apart because it allows more refined separation of liquids by BP. Purification: Separates liquids by boiling points. Steam: Extracts volatile compounds. Azeotropes: Constant boiling point mixtures. Setup: Flask, heat, condenser, collection. Vaporization/Condensation: Heating, cooling process. Applications: Lab purification, isolation.  12.3 Chromatography 30 Day MCAT CHAPTER 12 - SEPARATIONS AND PURIFICATIONS Separates two or more molecules from a mixture. Includes liquid chromatography, gas chromatography, size-exclusion chromatography, ion-exchange chromatography, affinity chromatography, and thin- layer chromatography. All forms of chromatography use two phases to separate compounds based on physical or chemical properties stationary phase or adsorbent is usually a polar solid mobile phase runs through the stationary phase and is usually a liquid or gas this elutes the sample through the stationary phase Column chromatography utilizes polarity, size, or affinity to separate compounds based on their physical or chemical Thin-layer and paper chromatography are used to properties identify a sample in ion-exchange chromatography, the beads are the stationary phase is a polar material, either coated with charged substances to bind compounds silica, alumina, or paper with opposite charge the mobile phase is a nonpolar solvent, which in size-exclusion chromatography, the beads have climbs the card through capillary action small pores which trap smaller compounds and allow the card is spotted and developed; Rf values can larger compounds to travel through faster be calculated and compared to reference values in affinity chromatography, the column is made to have reverse-phase chromatography uses a nonpolar high affinity for a compound by coating the beads with card with a polar solvent a receptor or antibody to the compound