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Molecular Structure and Acidity

Molecular Structure and Acidity

An acid can be deprotonated to form a conjugate base or an anion. If the produced anion is more stable, then the acid is stronger. On the contrary, if the anion is unstable, then the acid is weaker. Hence, to determine the acidity of the compound, the stability of its conjugate base is studied using various factors.
The size effect explains the change in atomic size on acidity. When comparing the acids formed from elements that belong to the same column in the periodic table, their atomic sizes...

Acid Strength and Molecular Structure

Acid Strength and Molecular Structure

Binary Acids and Bases
In the absence of any leveling effect, the acid strength of binary compounds of hydrogen with nonmetals (A) increases as the H-A bond strength decreases down a group in the periodic table. For group 17, the order of increasing acidity is HF < HCl < HBr < HI. Likewise, for group 16, the order of increasing acid strength is H2O < H2S < H2Se < H2Te. Across a row in the periodic table, the acid strength of binary hydrogen compounds increases with increasing...

ortho–para-Directing Activators: –CH3, –OH, –&NoBreak;NH2, –OCH3

ortho–para-Directing Activators: –CH₃, –OH, –⁠NH₂, –OCH₃

All ortho–para directors, excluding halogens, are activating groups. These groups donate electrons to the ring, making the ring carbons electron-rich. Consequently, the reactivity of the aromatic ring towards electrophilic substitution increases. For instance, the nitration of anisole is about 10,000 times faster than the nitration of benzene. The electron-donating effect of the methoxy group in anisole activates the ortho and para positions on the ring and stabilizes the corresponding...

Lewis Structures of Molecular Compounds and Polyatomic Ions

Lewis Structures of Molecular Compounds and Polyatomic Ions

To draw Lewis structures for complicated molecules and molecular ions, it is helpful to follow a step-by-step procedure as outlined:

Structure of Benzene: Molecular Orbital Model

Structure of Benzene: Molecular Orbital Model

According to the molecular orbital (MO) model, benzene has a planar structure with a regular hexagon of six sp2 hybridized carbons. As shown in Figure 1, each carbon is bonded to three other atoms with C–C–C and H–C–C bond angles of 120°. The C–H bond length is 109 pm, and the C–C bond length is 139 pm which is midway between the single bond length of sp3 hybridized carbons (154 pm) and sp2 hybridized carbons (133 pm).

Molecular Models

Molecular Models

Physical models representing molecular architectures of chemical compounds play essential roles in understanding chemistry. The use of molecular models makes it easier to visualize the structures and shapes of atoms and molecules.

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Quantitative Structure-Activity Relationship, Activity Prediction, and Molecular Dynamics of Non-nucleotide Reverse Transcriptase Inhibitors

Quantitative Structure-Activity Relationship, Activity Prediction, and Molecular Dynamics of Non-nucleotide Reverse Transcriptase Inhibitors

Published on: May 9, 2025

Molecular dynamics simulations of structural changes during procaspase 3 activation.

Stefano Piana¹, Ursula Rothlisberger

¹Institute of Molecular and Biological Chemistry, Federal Institute of Technology, EPFL, Lausanne, Switzerland.

|May 18, 2004

Summary

Molecular dynamics simulations reveal how procaspase 3 activates. The study found the selectivity loop in free caspase 3 is preorganized for substrates, unlike in procaspase 3 dimers.

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Area of Science:

Biochemistry
Structural Biology
Computational Biology

Background:

Procaspase 3 is a key enzyme in apoptosis, but its activation mechanism remains incompletely understood.
Understanding procaspase activation is crucial for developing targeted therapies for diseases involving aberrant apoptosis.
Existing structural data on caspase zymogens is limited, with procaspase 7 being the only crystallized example.

Purpose of the Study:

To investigate the structural rearrangements during the activation pathway of procaspase 3 using molecular dynamics simulations.
To build and analyze a computational model of procaspase 3.
To compare the structural features of the procaspase 3 model with available experimental data, particularly procaspase 7.

Main Methods:

Utilized a retrostructural approach to construct procaspase 3 from mature caspase 3.
Performed molecular dynamics (MD) simulations to observe the reformation of the cleaved peptide bond and subsequent structural changes.
Analyzed key structural features and compared them with the X-ray structure of procaspase 7.

Main Results:

MD simulations successfully modeled the structural changes during procaspase 3 activation.
The flexible selectivity loop in free caspase 3 was found to be preorganized for substrate binding.
This preorganization of the selectivity loop was absent in monomeric caspase 3 and the procaspase 3 dimer.

Conclusions:

The structure of the selectivity loop is highly sensitive to perturbations and its preorganization is a key feature of the active caspase 3 conformation.
These findings provide insights into the activation mechanism of procaspase 3 and the role of the selectivity loop.
The study highlights the utility of MD simulations in understanding enzyme activation pathways and zymogen structural dynamics.