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| equal to the number of protons in the nucleus of an aom of a given element. | ||
| the sum of neutrons and protons | ||
| Atoms with the same atomic number but different mass numbers. | ||
| when electrons occupy the lowest energy level available to them. | ||
| orbitals of equal energy | ||
| 2 electrons in the same orbital must have an opposite spin | ||
| each additional electron goes into the lowest energy subshell available to it. | ||
| electron in the outermost shell | ||
| A compound that has a COOH terminal group. Carboxylic acids are named by replacing the -e with oic acid | ||
| A compound that has a COOR group. Named as alkyl or aryl alkanoates | ||
| A compound that has an oxygen attached to two alkyl groups (R-O-R'). The compound can be named either as an alkoxyalkane or as an alkyl ether | ||
| alkanes with a halogen constituent | ||
| a compound that has carbon double bonded to nitrogen | ||
| a compound that has a nonterminal carbonyl group. Ketones are named by replacing the -e in the corresponding alkane with -one | ||
| A molecue that is not superimposable upon its mirror image. In order for a molecule to be chiral it must at least one chiral center | ||
| stereoisomers that differ by rotation about one or more single bonds, usually represented using newmman projections. | ||
| stereoisomers that are not mirror images of each other. Differ in configuration in at least one chiral center and share the same configuration in at least one chiral center. | ||
| Isomers that differ in configuration at only one sterogenic center | ||
| The bond that forms when the hemiacetal group of one sugar reacts with a hydroxyl group on another sugar to form an acetal group in between the two sugars. | ||
| Sugar that contains a ketone group | ||
| The smallest carbohydrate unit | ||
| The conversion of an alpha anomer to a beta | ||
| Proteins that require covanlently bonded prosthetic group to function properly. Hemoglobin is an example of such a protein. | ||
| The point in which a compound is electrically neutral. | ||
| the process in which a solid changes directly into a gas | ||
| Sequence of amino acids in a polypeptide, read from N-Terminus to the C-Terminus. | ||
| Different polypeptide chains, each referred to as a subunit, associate together to form a functional protein. | ||
| Regularly repeating local structures such as α-Helices and ß-pleated sheets often formed by hydrogen bonds between residues nearby on the chain. | ||
| A compound in which a carbon atom is bonded to a nitrogen atom with a single bond. Named by replacing the -e in the corresponding alkane with -amine. are derivatives of ammonia, wherein one or more hydrogen atoms have been replaced by a substituent such as an alkyl or aryl group | ||
| Amphoteric (reacts as acid or base) compound with no net electric charge. | ||
| A compound containg an -OH GROUP, the compound is named by replacing the -e in the corresponding alkane with -ol. | ||
| A compound tht has a HC=O as a terminal group. They are named by replacing the -e in the corresponding alkane with -al. | ||
| A compound consisting of only carbons and hydrogens bonded with sigma bonds. As chain length increases, boiling point, melting point, and density increase. | ||
| a carbon compound with a carbon-carbon double bond. | ||
| a carbon compound with a carbon-carbon triple bond. | ||
| A compound that has a carbonyl group bonded to nitrogen. They are named by dropping the -oic acid and adding -amide. | ||
| molecules that are mirror images of each other | ||
| Isomers that differ in the arrangement of substituents around a double bond. they are often differentiated using either the cis/trans notation for simple compounds or Z/E notation for more complex compounds, and can differ in their physical and chemical properties. | ||
| A stereoisomer with an internal plane of symmetry. they are optically inactive. | ||
| A mixture that contains equal amounts of the (+) and (-) enantiomers.they are not optically active. | ||
| molecules that have the same structural formulas and bonding patterns but different arrangements of atoms in space | ||
| compounds that have the same molecular formula but differ in the covalent arrangements of their atoms. | ||
| The first carbon atom adjacent to the carbon attached to the targeted functional group. | ||
| Atoms that can dissociate to form a stable species after accepting electron pairs. Weak bases tend to be good ____________. | ||
| A species that tends to donate electrons to another atom. They are attracted to positive charge, a nucleus, (protons and neutrons). In protic solvents and situations with different attacking atoms, its strength correlates to size. In aprotic solvents with the same attacking atom, its strength corresponds to basicity. | ||
| Carbon atom bonded to two other carbon atoms. | ||
| Unimolecular nucleophilic substitution reactions. Leaving group leaves, forming a carbocation that then reacts with a nucleophile. Reactivity increases from methyl to primary to secondary to tertiary with increasing carbocation stability. | ||
| Bimolecular nucleophilic substitution reactions occur through a concerted mechanism where the nucleophile attacks as the leaving group starts to leave. Reactivity increases from tertiary to secondary to primary with decreasing steric effects. | ||
| are electron-donating substituents already attached to the aromatic ring. They increase the ring's potential to react with other species. Activating species are ortho/para directing. | ||
| Cyclic, fully conjugated planar compound with 4n+2TT electrons. Each atom in the compound must possess a p orbital in order to allow for maximum conjugation. | ||
| The term used to describe toluene substituted at the methyl position when it is used as a substituent. | ||
| Electron-withdrawing substituents already attached to the aromatic ring. They decrease the ring's potential to react with other species. These are meta-directing, except ortho/para directing halogens. | ||
| The rule that staes in order for a ring to be aromatic.planar, fully conjugated, cyclic polyene, 4n+2. | ||
| Term used to describe benzene when it is used as a substituent. | ||
| describe a situation where the atomic connectivity remains unchanged while the electron distribution between the atom changes. | ||
| An amine where the nitrogen atom is attached to two alkyl chains (HNR₂). | ||
| Type of Chromatography, used to separate nucleic acids based on size/length of chain. The media serves as the stationary phase and the nucleic acid as the mobile phase. Negatively charged nucleic acids travel toward the anode (positive end). Smaller strands travel faster than larger chains. | ||
| Separation technique used to separate particles according to mass, shape and density. Greater mass and density settle near the bottom while lighter compounds remain on top. This is meant to simulate a gravitational pull. | ||
| A TECHNIQUE THAT IS USED TO SEPARATE THE COMPONENTS OF A MIXTURE BASED ON THE TENDENCY OF EACH COMPONENT TO TRAVEL OR BE DRAWN ACROSS THE SURFACE OF ANOTHER MATERIAL | ||
| Process that can separate two substances in a mixture by evaporating a liquid and recondensing its vapor. | ||
| Separation method exploiting solubility properties. Two solvents are usually used, one aqueous and one organic, and teh component of interest will be soluble in one phase while the impurities will be soluble in the other solvent. | ||
| a process that separates a solid from the liquid in a heterogenous mixture | ||
| Type of chromatography used to separate proteins based on charge. Stationary gel has an established pH gradient and the mobile phase proteins will travel to the point where the pH equals their isoelectric point. | ||
| A seperation technique used to purify the particles of interest from a mixture of solids | ||
| proteins separated by size, large have biggest resistance. | ||
| a monosaccharide sugar that contains the aldehyde group or is hemiacetal | ||
| the intermolecular force occurring when a hydrogen atom that is bonded to a highly electronegative atom of one molecule is attracted to two unshared electrons of another molecule | ||
| Process by which the carbonyl oxygen of a ketone gets protonated to form an enol. | ||
| Isomers that can interconvert by exchanging the location of a proton. | ||
| An alkyl magnesium halide used to make carbon-carbon bonds. Alkyl group in a Grignard reagent has a negative charge and acts as a nucleophile attacking electrophilic carbons. | ||
| Nitrogen triple-bonded to a carbon. | ||
| An amine where the nitrogen atom is attached to one alkyl chain (H₂NR). | ||
| An amino group attached to a carbon in a carbon-carbon double bond. | ||
| Cyclic stereoisomers differing in configuration at the hemiacetal carbon (C1). In a 6-membered ring, if the hydroxy group attached to C1 and the substituent attached to C5 are trans, the molecule is referred to as the α anomer. If both groups are cis, the molecule is reffered to as ß anomer. C1 and C5 are carbons adjacent to the oxygen in the ring. | ||
| Three-dimensional structure of a peptide, results from hydrophobic and hydrophilic interactions between residues far apart on the chain. Disulfide bonds and hydrogen bonds can also add to the tertiary structure of the protein. | ||
| Primary alcohols can be oxidized to aldehydes using PCC and further oxidized to carboxylic acids using KMnO₄, Na₂Cr₂O₇, or CrO₃. Secondary alcohols can be oxidized to ketones using any of these oxidants. | ||
| shows the bonds between atoms but does not showthe three dimensional structure of the molecule. | ||
| a formula that shows all of the atoms in a molecule and places them in sequential arrangement that details which atoms are bonded to each other; the bonds themselves are not shown. | ||
| The skeletal formula of an organic compound is a shorthand representation of its molecular structure. Skeletal formulae are ubiquitous in organic chemistry because they show complicated structures clearly and they are quick and simple to draw. | ||
| a standard means of representing stereochemistry at chirality centers, particularly in carbohydrate chemistry. | ||
| a means of indicating sterochemical relationships between substituent groups on neighboring carbons | ||
| the number of pairs of hydrogens a compound requires in order to become a saturated alkane.formula is used in organic chemistry to help draw chemical structures. The formula lets the user determine how many rings, double bonds, and triple bonds are present in the compound to be drawn. It does not give the exact number of rings or double or triple bonds, but rather the sum of the number of rings and double bonds plus twice the number of triple bonds. The final structure is verified with use of NMR, mass and IR spectroscopy, as well as inspection. | ||
| aldehyde + alcohol, an organic compound usually formed as an intermediate product in the preparation of acetals from aldehydes or ketones | ||
| any of a series of univalent groups of the general formula CnH2n+1 derived from aliphatic hydrocarbons | ||
| a highly reactive species w/only 2 bonds to an uncharged C atom and w/a nonbonding pair of e-. ( :CH₂ ), R2C; neutral molecule containing a divalent carbon with only six valence electrons | ||
| ketone + alcohol, "carbon tetrahedral with R, R, OR, OH" | ||
| Ethers: IUPAC --> __ group attached to a large chain is named as an alkane | ||
| a compound formed from one or more other compounds in a reaction resulting in removal of water, carbonyls attached by oxygen | ||
| Compound with a carbon double-bonded to nitrogen (C=N).is a functional group or chemical compound containing a carbon-nitrogen double bond, with the nitrogen attached to a hydrogen atom (H) or a hydrocarbyl. The carbon has two additional single bonds. [1] [2] It may be regarded as an ammonia (NH3) molecule in which two hydrogen atoms have been replaced by a group, attached through a carbon atom with formation of a double bond. | ||
| N2H4, a colorless fuming corrosive liquidis an inorganic chemical compound with the formula N2H4. It is a colourless liquid with an ammonia-like odor and is derived from the same industrial chemistry processes that manufacture ammonia | ||
| any compound containing the group -C=NOH is one in a class of chemical compounds with the general formula R1R2C=NOH, where R1 is an organic side chain and R2 is either hydrogen, forming an aldoxime, or another organic group, forming a ketoxime. are usually generated by the reaction of hydroxylamine and aldehydes or ketones | ||
| is an off-white solid with the chemical formula of C6H5CONH2. It is a derivative of benzoic acid. It is slightly soluble in water, and soluble in many organic solvents. | ||
| a bond formed when two atomic orbitals combine to form a molecular orbital that is symmetrical around the axis connecting the two atomic nuclei, less reactive than pI bonds. | ||
| a covalent bond in which one atom contributes both bonding electrons. | ||
| Ususally P orbitals Side to side covalent chemical bond are covalent chemical bonds where two lobes of one involved electron orbital overlap two lobes of the other involved electron orbital. Only one of the orbital's nodal planes passes through both of the involved nuclei. weaker than sigma bonds | ||
| the regions around the nucleus within which the electrons have the highest probability of being found | ||
| atomic orbital obtained when two or more nonequivalent orbitals of the same atom combine before covalent bond formation. | ||
| one s + one p = two sp = linear; comb. of one s orbital & one p orbital to form 2 eq. hybrid orbitals in linear (180°) structure | ||
| Formation of three trigonal sp2 orbitals from one s and two p orbitals. the 2s orbital is mixed with only two of the three available 2p orbitals | ||
| one electron in the 2s2 orbital becomes excited and fills the 2p2 orbital which provides 4 spots for covalent bonds. (109.5) | ||
| the first bond of double and triple bonds. | ||
| the second bond in a double bond, and both the second and the third bond in a triple bond. | ||
| not being fixed in position (that's why you "push" electrons when drawing resonance structures). | ||
| they are delocalized electrons. | ||
| mean the same thing. | ||
| "distribute" the charge around | ||
| aromatic rings and conjugated double bonds. | ||
| •its effect on bond length and bond energies ◦Multiple bonding decreases bond length. ◦Multiple bonding increases bond energy. •rigidity in molecular structure ◦Multiple bonding increases rigidity in molecular structure. ◦Single bonds can rotate, but double and triple bonds can't. ◦Even partial double bonds like those found in the peptide bond prevents free rotation | ||
| ◦Same molecular formula, different structural formula. ◦"Same in writing, different in drawing..." ■Structural isomers have the same molecular formula, but different connectivity. ■Positional isomers: structural isomers that have the same functional groups positioned differently. ■Constitutional isomers: structural isomers that have different functional groups. | ||
| ■Geometric isomers have the same molecular formula, same connectivity, but have different orientation across a double bond. ■When both sides of the double bond contains the same 2 groups, then cis and trans is used. ■Cis = same side, Trans = opposite sides. ■When different groups are attached to either side of Z and E is used. ■Z is when the higher priority groups (ranked according to the Cahn-Ingold-Prelog rules) are orientated on the same side across the double bond. Zusammen is the German word for together. ■E is when the higher priority groups are orientated on different sides across the double bond. Entgegen is the German word for opposed. | ||
| ■Stereoisomers have the same molecular formula, same connectivity, but have different 3-D arrangements across one or more asymmetric (chiral) centers. | ||
| ALL chiral centers in one enantiomer is reversed in the other. | ||
| any atom with 4 different entities attached to it | ||
| a chiral center. | ||
| more than one chiral center, inversion of stereochemistry on some but not all of its chiral centers. For examples, diastereomers would have stereochemistries of (R)-(R) vs (R)-(S). Another example of diastereomers would be (R)-(R)-(S)-(R) vs (R)-(R)-(R)-(R). | ||
| as a molecule, they are achiral and optically inactive. | ||
| stereoisomers | ||
| chemical properties. | ||
| physical properties. | ||
| different physical properties. | ||
| can rotate about a single bond to switch between different conformations. | ||
| you don't have to break any bonds to convert from one conformation to another. They are more accurately called conformers. | ||
| ■Eclipsed ■Syn-periplanar: highest torsional strain, most unstable, bulky groups eclipse each other. ■Anticlinal eclipsed: high torsional strain, unstable, bulky groups eclipse hydrogens. ■Staggered ■Gauche: low torsional strain, stable, bulky groups 60° staggered. ■Anti: lowest torsional strain, most stable, bulky groups 180° staggered. ■Single bonds will rotate such that it achieves the most stable conformation. | ||
| ■Chair: most stable, everything is staggered. ■Twist boat: less stable, things are not completely eclipsed. ■Boat: least stable, everything is eclipsed. ■Hexose rings will twist and turn to achieve the most stable conformation. | ||
| the strain due to eclipsing of groups across a single bond. | ||
| ■Axial: most unstable because the axial groups are orientated with a high degree of clashing. ■Equatorial: most stable because the equatorial groups are orientated away from one another. ■Bulky groups like to be in the equatorial position. | ||
| completely staggered (chair), with bulky groups in the equatorial position. | ||
| completely eclipsed (boat), with bulky groups in the axial position. | ||
| ◦Light is an electromagnetic wave. ◦Electromagnetic waves are waves of electric and magnetic fields (in phase, but perpendicular to each other and also to the direction of propagation). ◦Normal light has the EM fields in all directions (in a 360° circle perpendicular to the direction of propagation). ◦Polarized light has EM fields all in one direction. ◦Specific rotation: chiral molecules containing a single enantiomer will rotate polarized light (to varying degrees) either to the left or to the right. This is why chiral molecules are said to be "optically active". ◦Left rotation: (-) or l or levorotatory. ◦Right rotation: (+) or d or dextrorotatory. ◦Caution: (+) or (-) does NOT correspond to R/S configurations. ◦Caution: d and l is NOT the same as D and L. The upper case letters denote absolute configurations in sugars. | ||
| the prime example of relative configuration | ||
| ■If only 1 chiral center ■(R/S)-molecule, where R/S is the absolute configuration and molecule is the name of the compound. ■For example, (R)-2-hydroxyl-propanal. ■If more than 1 chiral center ■(#R/S, #R/S)-molecule, where # is the carbon number (in ascending order), R/S is the absolute configuration, and molecule is the name of the compound. ■For example, (2R,3S)-2,3,4-hydroxyl-butanal. | ||
| ■If only 1 double bond ■(E/Z)-molecule, where E/Z is the geometric configuration across the double bond, and molecule is the name of the compound. ■For example, (Z)-2-chloro-2-butene. (see geometric isomer figure) ■If more than 1 double bond ■(#E/Z, #E/Z)-molecule, where # is the carbon number (the smaller one in the double bond, in ascending order), and molecule is the name of the compound. | ||
| ■Start with shell 1, which is the atoms directly bonded to the chiral carbon. ■The atom with the higher MW has greater priority. ■If atoms are the same, look at next shell. ■Shell 2, which are the atoms adjacent around shell 1 atoms. ■The atom with the higher MW has greater priority. ■If same atoms, the more # of the high MW species, or the more bonds to the high MW species wins. ■For example, -CHO will have higher priority than -CH2OH because the aldehyde has a double bond to oxygen. ■For example, -CH(OH)2 will have higher priority than -CH2OH because the diol has 2 oxygens while the alcohol only has 1. ■What about -CH(OH)2 vs. CH2F? Ans: It doesn't matter how many oxygens there are, because fluorine has greater molecular weight. So fluorine has higher priority. ■If by now, everything is still the same, go to shell 3 and repeat the procedure. | ||
| ◦Racemic mixtures contain equal amounts of both enantiomers. Another name for racemic mixtures is racemate. ◦Racemic mixtures do not rotate polarized light, so they are optically inactive. | ||
| ■Convert enantiomers to diastereomers. ■Separation of diastereomers. ■Convert diastereomers back to enantiomers | ||
| ■Enzymes are highly specific and can differentiate between enantiomers. For example, if an enzyme digests or modifies all L-amino acids, then you'd be able to use that enzyme to separate a D/L racemic mixture. ■In nature, all proteins are made up of L-amino acids. | ||
| ■Vibrations: bonds can stretch, compress and bend like a spring. It is this vibration that is measured in IR-spec. ■Rotations: molecules can rotate. Rotations produce waves mainly in the microwave region. However, part of the rotation spectra does overlap with the vibration spectra. | ||
| ■Transmittance increases as you go up the y-axis. ■Where transmittance dips down, that's a region of absorbance. ■Wavenumbers decrease from left to right. ■Wavenumbers are correlated to frequency. ■Peaks toward the left have higher frequency of vibration. | ||
| ■Anything around 3000 cm-1 involves a hydrogen atom, be it O-H, N-H, or C-H. ■Anything around 2000 cm-1 and below does not involve hydrogen, be it C=O, C=C, C-C, or C-O. ■With the same atoms, the higher the bond order, the faster it vibrates, and so the higher the wavenumber. ■1700 cm-1 is for the carbonyl group. Remember this. ■3300 cm-1 can be O-H, N-H, or alkyne C-H. OH is the broadest, N-H slightly sharper, alkyne C-H is very sharp. ■Broad peaks are due to hydrogen bonding (OH and NH). ■Below 1300 cm-1 is called the fingerprint region. ■Patterns in the fingerprint region are unique for each compound just like a fingerprint is unique for each person. | ||
| ◦absorption in visible region gives complementary color (e.g., carotene) ■There are primary colors of light and primary colors of pigment. | ||
| on the opposite side of the color wheel. For example, the complementary of red is cyan. | ||
| its complementary color | ||
| complementary colors of the primary colors of light. This is because pigments absorb a certain color of light and reflect the rest back into your eyes. | ||
| ■Changes to chemical structure can lead to changes in absorption. ■H-indicator <--> H+ + Indicator- ■H-indicator absorbs at a certain wavelength and is of one color. ■Indicator- absorbs at a different wavelength so is of a different color. ■At low pH, high [H+], H-indicator and its color will predominate. ■At high pH, low [H+], indicator- and its color will predominate. ■At neutral pH, both H-indicator and indicator- will co-exist in an equilibrium, so the color will be a mixture of the two. | ||
| ■Red: very acidic ■Orange: acidic ■Yellow: weakly acidic ■Green: neutral ■Blue: basic ■Purple: very basic | ||
| ■Every time you have a bond, the atoms in a bond have their atomic orbitals merged together to form molecular orbitals. ■Every time you have a molecular orbitals, you get bonding molecular orbitals and non-bonding and/or anti-bonding orbitals. ■Normally, electrons sit in their bonding orbitals because it is the most stable there. If bonding orbitals are full, then non-bonding orbitals are occupied. ■Given enough energy (as in absorption), the electrons transition from the bonding or non-bonding orbitals to the anti-bonding orbitals. ■If too much energy is absorbed, enough electrons escape the bonding orbitals / enter the anti-bonding orbitals to break the bond completely. ■For UV absorption, we're not worried about breaking bonds. We're only interested in the pi-electrons of double bonds because their molecular orbital transitions result in UV absorption. ■Double bonds absorb UV because the pi electrons transition from the bonding and non-bonding molecular orbitals to the anti-bonding orbitals. | ||
| ■Conjugated systems decreases the energy of electromagnetic radiation that is absorbed. ■The more conjugated double bonds there are, the longer the wavelengths of absorbed radiation. ■If there are enough conjugated double bonds, the molecule will start to absorb in the visible region. | ||
| bombard a molecule with electrons. | ||
| Ans: this "molecular ion" will be detected as the parent peak, also called the molecular ion peak. | ||
| Ans: all the fragmented ions will be detected and plotted in the mass spectra. | ||
| the more fragmentation. ◦The more fragmentation, the smaller the molecular ion peak. | ||
| they can be individually detected and plotted on a spectrum. | ||
| the peak that depicts the ion of the molecule without fragmentation. It has the highest m/z ratio. •Peaks clustered really close to one another depicts isotopes. •The base peak is the tallest peak (most abundant species). | ||
| ◦Measuring the molecular weight of a molecule. ◦Identify the molecule by fragmentation patterns. ◦Identity heteroatoms by their characteristic isotope ratios. | ||
| ◦Protons have spins of up or down (+½ or -½, counterclockwise or clockwise. The detailed vectors are not important here, so simply up or down is fine). ◦With an even number of protons, the spins pair up and the up and down spins of all the protons cancel each other out. ◦With an odd number of protons, there is a net spin of up or down. ◦Normally, both up or down spins are equal in energy (they are degenerate). So, either way goes. ◦In the presence of a magnetic field, the spin that lines up with the magnetic field gets the lower energy. If the external magnetic field is up, then you better spin up. If the magnetic field is down, then you better spin down. ◦If we were to give the protons some energy (by radio wave absorption), then the protons can be promoted (flipped) to the higher energy spin, which is opposite to the direction of the external magnetic field. This absorption is called resonance. The resonance frequency is the frequency of the radio wave that's needed to cause a flip in spin. | ||
| the chemical shift. | ||
| resonance frequencies. | ||
| resonance frequencies. | ||
| TMS (tetramethylsilane) in unit of ppm. | ||
| the farther their chemical shifts | ||
| the degree of electron shielding or deshielding. | ||
| carbon is not so electronegative. | ||
| smaller and they have small chemical shifts and appear upfield (to the right). ■When things are deshielded, the magnetic field is larger and they have large chemical shifts and appear downfield (to the left). | ||
| the nuclear stands for protons; magnetic stands for the external magnetic field; the resonance stands for the absorption of radio waves. | ||
| ◦Magnetic fields produced by neighboring protons cause spin-spin splitting. ◦Neighboring is defined as 3 bonds away, which is the same thing as hydrogens attached to adjacent atoms. ◦Things are split into n+1 peaks, where n is the number of neighboring protons. ◦Aromatic protons can split over 3 bonds, which is why the NMR spectra for the aromatic region is a mess. ◦The J value defines how far apart things get split. ◦Protons across single and aromatic bonds get split approximately the same. ◦Protons across double bonds get split farther apart. | ||
| •Separates liquids based on boiling point. The stuff with the lower boiling point is boiled off and collected; the higher boiling point stuff remains behind. •Simple distillation = done with a normal column = can separate two liquids if the difference in boiling point is large. •Fractional distillation = done with a fractionating column = can separate two liquids with smaller differences in boiling point. •Vacuum distillation = done under lower pressure (vacuum) = lowers the boiling point for all liquid components so you don't have to crank up the temperature so high (chemical might decompose). | ||
| Mobile phase flow-----> Faster attracted to mobile phase repelled by stationary phase spends more time in mobile phase | ||
| An analytical technique which separates mixtures based on their distribution between a stationary liquid phase and a moving gas phase. | ||
| The mobile phase in HPLC refers to the solvent being continuously applied to the column, or stationary phase. The mobile phase acts as a carrier for the sample solution. A sample solution is injected into the mobile phase of an assay through the injector port. | ||
| The part of the chromatographic system though which the mobile phase flows where distribution of the solutes between the phases occurs | ||
| A method of separating the colors in a mixture based on the different weights of the molecules that make up the different pigments in the mixture. ◦Classically used to separate pigments in dyes. ◦Solvent = mobile phase. Paper = stationary phase. ◦Pigments in dyes stick to paper, solvent tries to wash them along, those with greater affinity to paper stays behind, those with greater affinity to solvent gets washed along. ◦Rf value = distance traveled by pigment / distance of solvent front. ◦Rf = 0 means that pigment has not moved. ◦Rf = 1 means that pigment moved as far as the solvent front. | ||
| procedure which is used to separate a mixture of substances into its individual components, based upon relative soluability ◦Thin-layer chromatography = advanced paper chromatography. ◦Instead of paper, you have a plate coated with a specific stationary phase of your choosing. ◦Rf value used in the same way as paper chromatography. | ||
| ◦Good if analyte can be promoted to gas phase. ◦Gas-liquid chromatography (GLC) is the same thing as gas chromatography (GC). ◦The gas part is the mobile phase, the liquid part is the stationary phase coated to the inside walls of the column. ◦Substrate equilibrates between mobile (gas) and stationary (liquid coat) phase. ◦Those with greater affinity for the stationary phase comes out of the column slower. Polar substrate has more affinity for polar stationary phase, and hydrophobic substrate has more affinity for hydrophobic stationary phase. | ||
| •Recrystalization = barely dissolving your compound, then let it recrystalize out of solution = compound ends up being more pure. •Barely dissolving = use just enough to fully dissolve your compound under warm temperature = saturated solution. •Recrystalize = solution cools, solubility decreases, compound comes out of solution. •Solvent choice = choose a solvent in which your compound is soluble in at warm temperature, but not at cool temperature. Also, choose a solvent in which impurities are highly soluble. •Impurities should remain dissolved in the solvent even your compound recrystalizes out. | ||
| ◦nomenclature ■# C atoms Name for straight chain alkane Name for cyclic alkane 1 Methane N/A 2 Ethane N/A 3 Propane Cyclopropane 4 Butane Cyclobutane 5 Pentane Cyclopentane 6 Hexane Cyclohexane 7 Heptane Cycloheptane 8 Octane Cyclooctane 9 Nonane Cyclononane 10 Decane Cyclodecane | ||
| ■Hydrophobic. ■London Dispersion Forces present only. ■Lower boiling points than compounds the same size but with functional groups. ■Very long alkanes can have very high boiling points due to the sum of all the dispersion forces. A useful reference is that heptane, the 7 membered alkane, has the same boiling point as water. | ||
| ◦combustion ■Complete combustion of alkanes: alkane or cycloalkane + O2 → CO2 + H2O ■Complete combustion of anything: fuel + oxygen → carbon dioxide + water ◦substitution reactions with halogens, etc. ■Alkane + halogen + free radical initiator → alkyl halide ■Free radical initiators = hν (UV light) or peroxides. ■Substitution occurs via a free radical mechanism | ||
| ◦stability of free radicals; chain reaction mechanism; inhibition ■The more substituted the radical, the more stable it is. ■Stability: 3° > 2° > 1° > methyl. ■Substitution will occur preferentially at the more substituted carbon atom. | ||
| anything that inhibits free radicals will inhibit this reaction. One example is antioxidants, which eats up free radicals and therefore inhibits the free radical chain reaction. | ||
| ■Cyclopropane has the highest ring strain. ■Cyclobutane has the second highest ring strain. ■Cyclohexane has the lowest ring strain. ■Any ring with greater or equal to 14 carbon atoms has the next lowest ring strain. | ||
| deviation from the ideal sp3 tetrahedral bond angle of 109.5° | ||
| the molecule having eclipsed conformations instead of staggered ones | ||
| angle (Baeyer) strain and torsional strain. | ||
| angle (Baeyer) or torsional strain. | ||
| spiro bicyclics, which have similar ring strain as their monocyclic counterparts. | ||
| •nomenclature ◦Prefix: hydroxyl, hydroxy. ◦Suffix: -ol, alcohol. •physical properties ◦Hydrogen bonding. ◦Higher boiling point than the same compound without the alcohol group. ◦Water soluble as long as molecule does not contain a long hydrophobic region. •infrared absorption of OH group: 3300 cm-1 and broad due to hydrogen bonding. | ||
| •substitution reactions: SN1 or SN2, depending on alcohol and derived alkyl halide ◦R-OH + HX <--> R-X + H2O ◦Factors that favor sn1: stable carbocation, tertiary carbon center, protic solvent. ◦Factors that favor sn2: unstable carbocation, primary carbon center, aprotic (but polar) solvent. ◦All substitution reactions need a good leaving group. ◦SN1 = unimolecular reaction, intermediate carbocation formed. ◦SN2 = bimolecular reaction, passes through transition state. •oxidation ◦KMnO4 and CrO3 will oxidize primary alcohols to carboxylic acids, but PCC will only oxidize a primary ◦alcohol to the aldehyde. ◦Secondary alcohols always oxidize to the ketone. ◦Tertiary alcohols do not oxidize. | ||
| the best protecting group for alcohol is the trimethylsilyl group. ◦To protect, add Cl-SiMe3 to R-OH. ◦The alcohol gets "capped" into R-O-SiMe3. ◦To deprotect, add F-. | ||
| ◦R-OH + SOCl2 --> R-Cl (by products: SO2 + HCl) ◦R-OH + PBr3 --> R-Br (by products: H3PO3, R3PO3, HBr) | ||
| leaving groups. ◦The R can be: ■Methane, which makes methanesulfonate. ■Toluene, which makes tosylate. ■Trifluoromethane, which makes triflate. | ||
| an alcohol (R-OH) with mesyl chloride (MsCl). | ||
| an alcohol (R-OH) with tosyl chloride (TsCl). | ||
| acid + alcohol = ester , The reaction between an alcohol and a carboxylic acid yield and ester plus water | ||
| replace the carbon of esters with a different atoms. | ||
| involve inorganic esters. | ||
| the 5'-phosphate to form an inorganic ester linkage (phosphodiester linkage of DNA/RNA backbone). | ||
| •hydrogen bonding: hydrogen bonding in alcohols give them a higher boiling point than their corresponding alkanes. •acidity of alcohols compared to other classes of oxygen-containing compounds: lower pKa = more acidic. •Compound pKa COOH (carboxylic acids) 5 ArOH (phenols) 10 H2O (water) 16 ROH (alcohols) 15 -CH2(CO)-R (alpha hydrogen in aldehydes and ketones) 20 -CH2(CO)-OR (alpha hydrogen in esters) 25 •effect of chain branching on physical properties: more branching = molecules can not pack as well = more fluidity = harder to freeze = lower freezing/melting point. | ||
| Description •nomenclature ◦Aldehyde suffix: -al, -aldehyde. ◦Ketone prefix: keto-. ◦Ketone suffix: -one, ketone. •physical properties ◦C=O bond is polar, with the carbon partially positive and oxygen partially negative. ◦Dipole-dipole interactions give these molecules higher boiling points than their corresponding alkanes, but not as high as the corresponding alcohols or carboxylic acids. •infrared absorption of C=O bond: 1700 cm-1 | ||
| 1 equivalent of alcohols to make hemiacetals. ■Aldehydes and ketones react with 2 equivalent of alcohols to make acetals. | ||
| the starting compound must be a ketone and not an aldehyde. |
