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Related Concept Videos

Calculating Standard Free Energy Changes02:49

Calculating Standard Free Energy Changes

20.6K
The free energy change for a reaction that occurs under the standard conditions of 1 bar pressure and at 298 K is called the standard free energy change. Since free energy is a state function, its value depends only on the conditions of the initial and final states of the system. A convenient and common approach to the calculation of free energy changes for physical and chemical reactions is by use of widely available compilations of standard state thermodynamic data. One method involves the...
20.6K
Gibbs Free Energy and Thermodynamic Favorability02:23

Gibbs Free Energy and Thermodynamic Favorability

6.7K
The spontaneity of a process depends upon the temperature of the system. Phase transitions, for example, will proceed spontaneously in one direction or the other depending upon the temperature of the substance in question. Likewise, some chemical reactions can also exhibit temperature-dependent spontaneities. To illustrate this concept, the equation relating free energy change to the enthalpy and entropy changes for the process is considered:
6.7K
Gibbs Free Energy02:39

Gibbs Free Energy

32.6K
One of the challenges of using the second law of thermodynamics to determine if a process is spontaneous is that it requires measurements of the entropy change for the system and the entropy change for the surroundings. An alternative approach involving a new thermodynamic property defined in terms of system properties only was introduced in the late nineteenth century by American mathematician Josiah Willard Gibbs. This new property is called the Gibbs free energy (G) (or simply the free...
32.6K
Energy Diagrams, Transition States, and Intermediates02:13

Energy Diagrams, Transition States, and Intermediates

16.0K
Free-energy diagrams, or reaction coordinate diagrams, are graphs showing the energy changes that occur during a chemical reaction. The reaction coordinate represented on the horizontal axis shows how far the reaction has progressed structurally. Positions along the x-axis close to the reactants have structures resembling the reactants, while positions close to the products resemble the products.  Peaks on the energy diagram represent stable structures with measurable lifetimes, while...
16.0K
Free Energy Changes for Nonstandard States03:25

Free Energy Changes for Nonstandard States

10.8K
The free energy change for a process taking place with reactants and products present under nonstandard conditions (pressures other than 1 bar; concentrations other than 1 M) is related to the standard free energy change according to this equation:
 
where R is the gas constant (8.314 J/K·mol), T is the absolute temperature in kelvin, and Q is the reaction quotient. This equation may be used to predict the spontaneity of a process under any given set of conditions.
Reaction Quotient...
10.8K
¹H NMR: Complex Splitting01:13

¹H NMR: Complex Splitting

1.2K
A proton M that is coupled to a proton X results in doublet signals for M. However, NMR-active nuclei can be simultaneously coupled to more than one nonequivalent nucleus. When M is coupled to a second proton A, such as in styrene oxide, each peak in the doublet is split into another doublet.
Splitting diagrams or splitting tree diagrams are routinely used to depict such complex couplings. While drawing splitting diagrams, the splitting with the larger coupling constant is usually applied...
1.2K

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Using Three-color Single-molecule FRET to Study the Correlation of Protein Interactions
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Evaluating multi-state free energy profiles from splitting probability.

Rohan Singh1, Parbati Biswas1

  • 1Department of Chemistry, University of Delhi, Delhi 110007, India.

The Journal of Chemical Physics
|February 7, 2025
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Summary
This summary is machine-generated.

This study presents a new analytical model for analyzing DNA hairpin fold-unfold transitions. The model accurately predicts biomolecular dynamics and free energy profiles, aiding in understanding complex cellular environments.

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Area of Science:

  • Biophysics
  • Computational Biology
  • Molecular Dynamics

Background:

  • Single-molecule experiments are crucial for studying biomolecular structural transitions under mechanical force.
  • The committor function is key to determining the activation barrier for these transitions.
  • Understanding DNA hairpin dynamics in cellular environments is essential for molecular biology.

Purpose of the Study:

  • To develop an analytical model for committor analysis of multi-state DNA hairpin dynamics.
  • To investigate DNA hairpin conformational changes within a complex cellular environment.
  • To accurately model fold-unfold transitions using a generalized Langevin equation.

Main Methods:

  • Utilized a generalized Langevin equation with a general asymmetric bistable potential and power-law frictional memory kernel.
  • Derived exact analytical expressions for probability density function, first passage time distribution, and committor.
  • Compared model results with steered molecular dynamics simulations and experimental data.

Main Results:

  • The analytical model successfully captures the fold-unfold dynamics of DNA hairpins.
  • The model reproduces multi-state free energy profiles with asymmetric energy barriers.
  • Investigated the influence of linker stiffness, barrier height, and potential asymmetry on committor profiles.

Conclusions:

  • The proposed analytical model provides accurate insights into DNA hairpin conformational dynamics.
  • This approach enhances the understanding of biomolecular transitions in complex cellular settings.
  • The model's ability to reproduce experimental and simulation data validates its utility.