BrainChildren Chemistry
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Glossary
Glossary I
Ionic bonding
Solubility in Water
Factors affecting solubility
PH Level
Acidic Conditions
Protonation
Attachments
Protonation - Wikipedia
Parents
Acid-Base Properties
Acid-Base Reactions
Acid-catalyzed
Acidic Conditions
Activation Step
Basicity of Enol Oxygen
Glossary P
Grignard Reaction
Hydrogen ions
Initiation
Mechanism
Mechanism of Action
Mechanism Steps
Mechanisms, Superacid
Nucleophilic Addition
Preparation Methods
Proton
Reaction Mechanisms
Reactivity
Stepwise Mechanism
Termination
Children
1019. On the state of chromophore protonation in rhodopsin: implication for primary photochemistry in visual pigments
1296. Selective Protonation of Acidic Residues Triggers Opsin Activation
1430. Coupling of protonation switches during rhodopsin activation
1506. Thr94 and Wat2b effect protonation of the retinal chromophore in rhodopsin
1694. Asp83, Glu113 and Glu134 are not specifically involved in Schiff base protonation or wavelength regulation in bovine rhodopsin
176 On the state of chromophore protonation in rhodopsin: implication for primary photochemistry in visual pigments
184. Selective protonation of acidic residues triggers opsin activation
427. Coupling of protonation switches during rhodopsin activation
464. Conformational Changes in the Photocycle of Anabaena Sensory Rhodopsin: Absence of the Schiff base counterion protonation signal
567. Thr94 and Wat2b effect protonation of the retinal chromophore in rhodopsin
84 Protonation of the Schiff base chromophore in Rhodopsins
886. FTIR study of the protonation of a Schiff base in chloroform-methanol mixtures
887. Asp83, Glu113 and Glu134 are not specifically involved in Schiff base protonation or wavelength regulation in bovine rhodopsin
925. A carbon-13 and nitrogen-15 nuclear magnetic resonance study of the protonation of a retinal Schiff base by acids of different pKa's and in solvents of different polarities
939. Two-photon, carbon-13 and two-dimensional proton NMR spectroscopic studies of retinyl Schiff bases, protonated Schiff bases and Schiff base salts: evidence for a protonation induced ππ* excited state level ordering reversal
Acid Catalysis
Activation
Activation of Substrates
Activation of the carbonyl group by protonation: introduction
Alcohol Deprotonation
Alcohol Protonation
Aldehyde
Amide Protonation Constants
Amine Protonation
Amino acid deprotonation in enzyme catalysis
Applications of Protonation
Aromatic Protonation
Asymmetric Protonation Reactions
Base-catalyzed deprotonation
Base-catalyzed deprotonation reactions
Basics of protonation and deprotonation
Carbocations from Alkene Protonation
Carboxylic Acid Protonation
Concerted metallation-deprotonation
Definition and concept, Definition and Concepts
Deprotonation and Rearrangement Steps
Deprotonation and Restoration of Aromaticity
Deprotonation followed by rearrangement
Deprotonation of acids
Deprotonation of Alcohol
Deprotonation of Alcohols
Deprotonation of aldehydes for enolate formation
Deprotonation of aldehydes in acidic conditions
Deprotonation of aldehydes with strong bases
Deprotonation of aldehydes with weak bases
Deprotonation of Allylic Alcohols
Deprotonation of Allylic Amines
Deprotonation of Allylic Compounds
Deprotonation of Allylic Esters
Deprotonation of amine groups
Deprotonation of amines
Deprotonation of amino acids by proteases
Deprotonation of amphoteric species
Deprotonation of basic functional groups
Deprotonation of carbon acids
Deprotonation of carbonyl compounds
Deprotonation of carboxylic acid groups
Deprotonation of carboxylic acids
Deprotonation of DNA bases by DNA polymerases
Deprotonation of esters in acidic conditions
Deprotonation of esters with strong bases
Deprotonation of esters with weak bases
Deprotonation of hydroxyl groups
Deprotonation of ketones for enolate formation
Deprotonation of ketones in acidic conditions
Deprotonation of ketones with strong bases
Deprotonation of ketones with weak bases
Deprotonation of nitrogen acids
Deprotonation of Oxonium Ion
Deprotonation of oxygen acids
Deprotonation of phenols
Deprotonation of primary amines in acidic conditions
Deprotonation of primary amines with strong bases
Deprotonation of primary amines with weak bases
Deprotonation of secondary amines in acidic conditions
Deprotonation of secondary amines with strong bases
Deprotonation of secondary amines with weak bases
Deprotonation of specific functional groups
Deprotonation of substrates
Deprotonation of Terminal Alkynes
Deprotonation of tertiary amines in acidic conditions
Deprotonation of tertiary amines with strong bases
Deprotonation of tertiary amines with weak bases
Deprotonation of Water
Deprotonation reaction in the synthesis of acetoacetic ester
Deprotonation reactions
Deprotonation Step
Deprotonation to form Alkene
Deprotonation under high-temperature conditions
Deprotonation videos
Deprotonation videos
Deprotonation with alkali metal hydroxides
Deprotonation with alkoxides
Deprotonation with amines
Effect of heating on deprotonation rates
Effect of protonation on basicity
Effect of reactant concentration on deprotonation
Effect of solvent on deprotonation
Effect of temperature on deprotonation
Effect on Protonation
Enantioselective Deprotonation
Enantioselective Protonation
Enolate Formation via Deprotonation of Carbonyl Compounds
Enzymatic Protonation Mechanisms
Enzyme-catalyzed deprotonation reactions
Examples of enzyme-catalyzed deprotonation reactions
FEBS letters (1990), 260(1), 113-8, 1694. Asp83, Glu113 and Glu134 are not specifically involved in Schiff base protonation or wavelength regulation in bovine rhodopsin
Formation of Carbocations
Initial Deprotonation
Intermediate Formation
Investigation of factors influencing deprotonation rates
Ketone
Lewis Acids
Mechanistic Pathways
Molecular dynamics simulations of deprotonation
Monomer activation
Multiple protonation sites
Nucleophilic Attack
pH and protonation/deprotonation
Phenol Protonation
Photochemistry and photobiology (1980), 32(2), 273-6, 176 On the state of chromophore protonation in rhodopsin: implication for primary photochemistry in visual pigments
Practice Problem: Site of Protonation on a Weak Base
Protein-Protonation Interactions
Protic Superacids
Protonation and Conductivity
Protonation and Deprotonation
Protonation and deprotonation as acid-base reactions
Protonation and deprotonation as redox reactions
Protonation and deprotonation in chemical reactions
Protonation and deprotonation of amines
Protonation and deprotonation reactions
Protonation and pH Regulation
Protonation and Solubility
Protonation at Carbonyl Oxygen
Protonation at Nucleophile
Protonation in Acid-Base Equilibria
Protonation in Battery Systems
Protonation in Biochemistry
Protonation in Chemical Analysis
Protonation in Chromatography
Protonation in Coordination Chemistry
Protonation in Drug Design
Protonation in Electrochemistry
Protonation in Electrophoresis
Protonation in Environmental Chemistry
Protonation in Enzyme Catalysis
Protonation in Enzyme Reactions
Protonation in Fuel Cells
Protonation in Infrared Spectroscopy
Protonation in Inorganic Chemistry
Protonation in Inorganic Synthesis
Protonation in Mass Spectrometry
Protonation in Metal-Ligand Bonding
Protonation in Metal-Oxide Reactions
Protonation in Nuclear Magnetic Resonance
Protonation in Organic Chemistry
Protonation in Physical Chemistry
Protonation in Polymerization Reactions
Protonation in Protein Folding
Protonation in Redox Reactions
Protonation in Transition Metal Catalysis
Protonation in UV-Vis Spectroscopy
Protonation in Water Treatment
Protonation of acidic functional groups
Protonation of Alcohol
Protonation of Alkene
Protonation of Alkenes
Protonation of Amide
Protonation of Amide Nitrogen
Protonation of Amide Oxygen
Protonation of Amino Acids
Protonation of amphoteric species
Protonation of Aromatic Rings
Protonation of Benzothiazole
Protonation of Carbon-Carbon Double Bonds
Protonation of carbonyl
Protonation of Carbonyl Group
Protonation of Carbonyl Oxygen
Protonation of enolates
Protonation of Metal Complexes
Protonation of neutral molecules
Protonation of Other Molecules
Protonation of oxime
Protonation of Phosphate Oxygen
Protonation of Reactants
Protonation of the Alkene
Protonation of the Carbonyl Oxygen
Protonation of the Reactant
Protonation of water
Protonation of Water Molecules
Protonation or deprotonation reactions
Protonation reactions
Protonation reactions in synthesis
Protonation state
Protonation State of Active Site
Protonation States
Protonation states and pKa calculations
Protonation Step
Protonation Steps
Protonation to Alcohol
Quantum mechanics/molecular mechanics simulations of deprotonation
Rearrangement reactions after deprotonation
Reductive Protonation
Role of enzymes in deprotonation reactions
Role of strong bases in the deprotonation step
Solvent Protonation and Deprotonation
Step 1: Deprotonation of Acetoacetic Ester
Step 2: Deprotonation
Step 2: Protonation
Step 3: Deprotonation
Step 4: Protonation and Keto-Enol Tautomerism
Strong Acid
Strong Acidity
The Automatic Rhodopsin Modeling (ARM) protocol, has recently been proposed as a tool for the fast and parallel generation of basic hybrid quantum mechanics/mol. mechanics (QM/MM) models of wild-type and mutant rhodopsins. However, in its present version, the input prepn. requires a few hour long user's manipulation of the template protein structure which also impairs the reproducibility of the generated models. This limitation, which makes the model building semi-automatic rather than fully automatic, comprises four tasks: the definition of the retinal chromophore cavity, the assignment of the protonation states of the ionizable residues, the neutralization of the protein with external counter-ions and, finally, the congruous generation of single or multiple mutations. In this work, the authors show that the automation of the original ARM protocol can be extended to a level suitable for performing the above tasks without user's manipulation and with an input prepn. time of minutes. The new protocol, call
Theoretical studies on deprotonation reactions
Video 1: Deprotonation of amines explained
Video 2: Deprotonation of carbonyl compounds in action
Weak Acid
Jumps
Deprotonation