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- https://chem.libretexts.org/Courses/Smith_College/Organic_Chemistry_(LibreTexts)/01%3A_Structure_and_Bonding/1.07%3A_sp_Hybrid_Orbitals_and_the_Structure_of_MethaneThe four identical C-H single bonds in methane form as the result of sigma bond overlap between the sp3 hybrid orbitals of carbon and the s orbital of each hydrogen.
- https://chem.libretexts.org/Courses/Smith_College/Organic_Chemistry_(LibreTexts)/02%3A_Polar_Covalent_Bonds_Acids_and_Bases/2.12%3A_Noncovalent_Interactions_Between_MoleculesIn contrast to intramolecular forces, such as the covalent bonds that hold atoms together in molecules and polyatomic ions, intermolecular forces hold molecules together in a liquid or solid. Intermol...In contrast to intramolecular forces, such as the covalent bonds that hold atoms together in molecules and polyatomic ions, intermolecular forces hold molecules together in a liquid or solid. Intermolecular forces are generally much weaker than covalent bonds. The most common intermolecular forces in organic chemistry are from strongest to weakest are hydrogen bonds, dipole-dipole interactions, and London Dispersion (van der Waals) forces.
- https://chem.libretexts.org/Courses/Smith_College/Organic_Chemistry_(LibreTexts)/26%3A_Biomolecules-_Amino_Acids_Peptides_and_Proteins/26.13%3A_How_do_Enzymes_Work_Citrate_SynthaseThe carboxylate group of an aspartic acid (B:) on citrate synthase removes the acidic alpha proton on acetyl CoA, while a histidine site (H-A) donates a proton to form the enol. Then a second histidin...The carboxylate group of an aspartic acid (B:) on citrate synthase removes the acidic alpha proton on acetyl CoA, while a histidine site (H-A) donates a proton to form the enol. Then a second histidine site (H-A) protonates the carbonyl oxygen of oxaloacetate, while the carbon of the carbonyl is attacked by the enol. The acyl group of a thioester of (S)-citryl CoA can be transferred to a water molecule in a hydrolysis reaction to converting (S)-citryl CoA to citrate.
- https://chem.libretexts.org/Courses/Martin_Luther_College/Organic_Chemistry_-_MLC/05%3A_Biomolecules/5.02%3A_Biomolecules-_Amino_Acids_Peptides_and_Proteins/5.2.05%3A_Peptides_and_ProteinsCritical to the structure of proteins is the fact that, although it is conventionally drawn as a single bond, the C-N bond in a peptide linkage has a significant barrier to rotation, almost as if it w...Critical to the structure of proteins is the fact that, although it is conventionally drawn as a single bond, the C-N bond in a peptide linkage has a significant barrier to rotation, almost as if it were a double bond. The structure of a peptide can be written fairly easily without showing the complete amide synthesis reaction by learning the structure of the "backbone" for peptides and proteins.
- https://chem.libretexts.org/Courses/Smith_College/Organic_Chemistry_(LibreTexts)/12%3A_Structure_Determination_-_Mass_Spectrometry_and_Infrared_Spectroscopy/12.04%3A_Mass_Spectrometry_of_Some_Common_Functional_GroupsDetailed analysis of the typical fragmentation patterns of different functional groups is beyond the scope of this text, but it is worthwhile to see a few representative examples, even if we don’t att...Detailed analysis of the typical fragmentation patterns of different functional groups is beyond the scope of this text, but it is worthwhile to see a few representative examples, even if we don’t attempt to understand the exact process by which the fragmentation occurs.
- https://chem.libretexts.org/Courses/Smith_College/Organic_Chemistry_(LibreTexts)/21%3A_Carboxylic_Acid_Derivatives-_Nucleophilic_Acyl_Substitution_Reactions/21.02%3A_Naming_Carboxylic_Acid_DerivativesIf the corresponding carboxylic acid has an –oic acid or –ic acid ending it is removed and replaced with the ending -oyl followed by the first syllable of the name of the halogen along with an –ide en...If the corresponding carboxylic acid has an –oic acid or –ic acid ending it is removed and replaced with the ending -oyl followed by the first syllable of the name of the halogen along with an –ide ending. The acid halide functional group is assumed to be on the end of the parent chain, so it is not necessary to include the functional group location number in the name.
- https://chem.libretexts.org/Courses/Smith_College/Organic_Chemistry_(LibreTexts)/04%3A_Organic_Compounds_-_Cycloalkanes_and_their_Stereochemistry/4.07%3A_Axial_and_Equatorial_Bonds_in_CyclohexaneThe hydrogens of cyclohexane exist in two distinct locations - axial and equatorial. The two chair conformations of cyclohexane rapidly interconverts through a process called ring flip.
- https://chem.libretexts.org/Courses/Smith_College/Organic_Chemistry_(LibreTexts)/06%3A_An_Overview_of_Organic_Reactions/6.12%3A_A_Comparison_between_Biological_Reactions_and_Laboratory_ReactionsA critical element in the three-dimensional structure of any enzyme is the presence of an ‘active site’, which is a pocket, usually located in the interior of the protein, that serves as a docking poi...A critical element in the three-dimensional structure of any enzyme is the presence of an ‘active site’, which is a pocket, usually located in the interior of the protein, that serves as a docking point for the enzyme’s substrate(s) (‘substrate’ is the term that biochemists use for a reactant molecule in an enzyme-catalyzed reaction).
- https://chem.libretexts.org/Courses/University_of_Alberta_Augustana_Campus/AUCHE_250%3A_Organic_Chemistry_I/06%3A_Substitutions/6.02%3A_Characteristics_of_the_SN2_ReactionIf each of the three substituents were hydrogen atoms, as illustrated in the first example below, there would be little steric repulsion created in the planar portion of the transition state thereby i...If each of the three substituents were hydrogen atoms, as illustrated in the first example below, there would be little steric repulsion created in the planar portion of the transition state thereby increasing the ease at which the nucleophilic substitution reaction occurs. As Size Increases, Basicity Decreases: In general, if we move from the top of the periodic table to the bottom of the periodic table as shown in the diagram below, the size of an atom will increase.
- https://chem.libretexts.org/Bookshelves/Organic_Chemistry/Organic_Chemistry_II_(Morsch_et_al.)/15%3A_Benzene_and_Aromaticity/15.05%3A_Aromatic_Heterocycles_-_Pyridine_and_PyrroleThe lone pair electrons on pyridine's nitrogen are contained in a sp 2 orbital that lies in the same plane as the ring and does not overlap with the p orbitals of the ring. When looking at the electro...The lone pair electrons on pyridine's nitrogen are contained in a sp 2 orbital that lies in the same plane as the ring and does not overlap with the p orbitals of the ring. When looking at the electrostatic potential map of imidazole, the lone pair electrons on the pyrrole-like nitrogen are distributed around the ring while the lone pair electrons on the pyridine-like nitrogen are non-conjugated and locked into place.
- https://chem.libretexts.org/Bookshelves/Organic_Chemistry/Organic_Chemistry_III_(Morsch_et_al.)/24%3A_Amines_and_Heterocycles/24.04%3A_Basicity_of_ArylaminesIn the case of para-methoxyaniline, the lone pair on the methoxy group donates electron density to the aromatic system, and a resonance contributor can be drawn in which a negative charge is placed on...In the case of para-methoxyaniline, the lone pair on the methoxy group donates electron density to the aromatic system, and a resonance contributor can be drawn in which a negative charge is placed on the carbon adjacent to the nitrogen, which makes the substituted arylamine more basic than aniline.
