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Related Concept Videos

Cooperative Allosteric Transitions01:58

Cooperative Allosteric Transitions

Cooperative allosteric transitions can occur in multimeric proteins, where each subunit of the protein has its own ligand-binding site. When a ligand binds to any of these subunits, it triggers a conformational change that affects the binding sites in the other subunits; this can change the affinity of the other sites for their respective ligands. The ability of the protein to change the shape of its binding site is attributed to the presence of a mix of flexible and stable segments in the...
Cooperative Allosteric Transitions01:58

Cooperative Allosteric Transitions

Cooperative allosteric transitions can occur in multimeric proteins, where each subunit of the protein has its own ligand-binding site. When a ligand binds to any of these subunits, it triggers a conformational change that affects the binding sites in the other subunits; this can change the affinity of the other sites for their respective ligands. The ability of the protein to change the shape of its binding site is attributed to the presence of a mix of flexible and stable segments in the...
Cooperative Allosteric Transitions01:58

Cooperative Allosteric Transitions

Cooperative allosteric transitions can occur in multimeric proteins, where each subunit of the protein has its own ligand-binding site. When a ligand binds to any of these subunits, it triggers a conformational change that affects the binding sites in the other subunits; this can change the affinity of the other sites for their respective ligands. The ability of the protein to change the shape of its binding site is attributed to the presence of a mix of flexible and stable segments in the...
Reactivity of Enolate Ions01:23

Reactivity of Enolate Ions

Enolate ions are formed by the acid–base reaction of a carbonyl compound with a base. This leads to deprotonation of the α hydrogen atom, leading to a resonance-stabilized enolate ion where one of the contributing structures is an oxyanion, which imparts additional stability. Therefore, the proton on the α carbon is more acidic in nature than that of other sp3-hybridized C–H bonds but less acidic than those in O–H bonds where the negative charge in the conjugate base is localized on the oxygen...
Phase II Reactions: Glutathione Conjugation and Mercapturic Acid Formation01:22

Phase II Reactions: Glutathione Conjugation and Mercapturic Acid Formation

Glutathione, a tripeptide made up of glutamate, cysteine, and glycine, is a critical player in the detoxification of drugs and xenobiotics via a process known as glutathione conjugation or mercapturic acid formation. This phase II biotransformation reaction involves the covalent binding of glutathione to a drug or its metabolite, enhancing the compound's water solubility and enabling its excretion.
Several distinctive characteristics distinguish glutathione conjugation from other phase II...
Phase II Reactions: Sulfation and Conjugation with α-Amino Acids01:19

Phase II Reactions: Sulfation and Conjugation with α-Amino Acids

Sulfation and α-amino acid conjugation are two critical biotransformation reactions in drug metabolism. Sulfation, a phase II biotransformation reaction, involves adding a polar sulfate group to a drug, enhancing its water solubility and promoting excretion. This process can either co-occur with or occur independently of glucuronidation. Nonmicrosomal sulfotransferase enzymes catalyze the process. The reaction involves 3'-phosphoadenosine-5'-phosphosulfate or PAPS coenzyme activation, sulfur...

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Genetically-encoded Molecular Probes to Study G Protein-coupled Receptors
16:16

Genetically-encoded Molecular Probes to Study G Protein-coupled Receptors

Published on: September 13, 2013

Optimized GGA functional for proton transfer reactions.

Vincent Tognetti1, Carlo Adamo

  • 1Laboratoire d'Electrochimie, Chimie des Interfaces et Modélisation pour l'Energie, UMR CNRS 7575, Ecole Nationale Supérieure de Chimie de Paris Chimie-ParisTech, 11 rue P. et M. Curie, F-75231 Paris Cedex 05, France.

The Journal of Physical Chemistry. A
|June 13, 2009
PubMed
Summary
This summary is machine-generated.

A new modified BP86 (mBP86) functional improves calculations for proton transfer reactions, offering better accuracy than standard methods. This development provides a reliable and cost-effective alternative for large-scale simulations.

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Area of Science:

  • Computational Chemistry
  • Quantum Chemistry
  • Theoretical Chemistry

Background:

  • Standard Generalized Gradient Approximation (GGA) methods often underestimate activation barriers for proton transfer reactions.
  • Accurate simulation of proton transfer is crucial for understanding various chemical and biological processes.

Purpose of the Study:

  • To introduce a modified gradient-corrected BP86 functional (mBP86) for improved accuracy in calculating proton transfer reaction barriers.
  • To evaluate the performance of mBP86 for chemical properties and large-scale simulations.

Main Methods:

  • Reparameterization of the Becke's 1988 exchange functional using activation barriers of proton transfer reactions.
  • First-principles molecular dynamics simulations of proton transfer in malonaldehyde and protonated imidazole dimer using the mBP86 functional.

Main Results:

  • The mBP86 functional significantly improves the underestimation of activation barriers by standard GGA methods.
  • mBP86 shows better accuracy for atomization and reaction energies compared to the parent BP86 functional.
  • Simulations using mBP86 yield energy and structure evolution comparable to the widely used B3LYP functional.

Conclusions:

  • The mBP86 functional represents a general improvement over the BP86 functional for various chemical properties.
  • mBP86 offers a cost-effective and reliable alternative to hybrid functionals for large-scale proton transfer simulations.