Search research articles

ABOUT JoVE

Overview Leadership Blog JoVE Help Center

AUTHORS

Publishing Process Editorial Board Scope & Policies Peer Review FAQ Submit

LIBRARIANS

Testimonials Subscriptions Access Resources Library Advisory Board FAQ

RESEARCH

JoVE Journal Methods Collections JoVE Encyclopedia of Experiments Archive

EDUCATION

JoVE Core JoVE Business JoVE Science Education JoVE Lab Manual Faculty Resource Center Faculty Site

Terms & Conditions of Use

Related Concept Videos

Buffers

Buffers

A solution containing appreciable amounts of a weak conjugate acid-base pair is called a buffer solution, or a buffer. Buffer solutions resist a change in pH when small amounts of a strong acid or a strong base are added. A solution of acetic acid and sodium acetate is an example of a buffer that consists of a weak acid and its salt: CH3COOH (aq) + CH3COONa (aq). An example of a buffer that consists of a weak base and its salt is a solution of ammonia and ammonium chloride: NH3 (aq) + NH4Cl...

Phosphate Buffer

Phosphate Buffer

The phosphate buffer system is a critical biological mechanism for maintaining pH stability in the body. This system operates primarily through two components: sodium dihydrogen phosphate (NaH2PO4), which acts as a weak acid, and sodium hydrogen phosphate (Na2HPO4), which serves as a weak base.
Sodium dihydrogen phosphate does not fully dissociate in neutral or acidic solutions. When a strong base, such as sodium hydroxide (NaOH), is introduced into the solution, sodium dihydrogen phosphate...

Buffer Effectiveness

Buffer Effectiveness

Buffer solutions do not have an unlimited capacity to keep the pH relatively constant . Instead, the ability of a buffer solution to resist changes in pH relies on the presence of appreciable amounts of its conjugate weak acid-base pair. When enough strong acid or base is added to substantially lower the concentration of either member of the buffer pair, the buffering action within the solution is compromised.
The buffer capacity is the amount of acid or base that can be added to a given volume...

Calculating pH Changes in a Buffer Solution

Calculating pH Changes in a Buffer Solution

A buffer can prevent a sudden drop or increase in the pH of a solution after the addition of a strong acid or base up to its buffering capacity; however, such addition of a strong acid or base does result in the slight pH change of the solution. The small pH change can be calculated by determining the resulting change in the concentration of buffer components, i.e., a weak acid and its conjugate base or vice versa. The concentrations obtained using these stoichiometric calculations can be used...

Extraction: Effects of pH

Extraction: Effects of pH

Consider a neutral form of an amine, B, with a partition coefficient, K, in a liquid mixture containing organic and aqueous phases. The pH of the aqueous phase affects the charge on acidic and basic solutes, and the charged form is usually more soluble in the aqueous phase. Suppose the conjugate acid form of the amine is soluble only in the aqueous phase while the base form is soluble in both phases. Then the distribution coefficient, D, can be given as the ratio of amine concentration in the...

Buffers: Overview

Buffers: Overview

Buffers play a crucial role in stabilizing the pH of a solution by mitigating the effects of small amounts of added acid or base. They consist of a weak acid and its conjugate base or a weak base and its conjugate acid. A solution of acetic acid and sodium acetate is an example of a buffer that consists of a weak acid and its salt: CH3COOH (aq) + CH3COONa (aq). An example of a buffer that consists of a weak base and its salt is a solution of ammonia and ammonium chloride: NH3 (aq) + NH4Cl (aq).

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by

Same author

A minimal chemo-mechanical Markov model for rotary catalysis of F<sub>1</sub>-ATPase.

Nature communications·2026

Same author

Quantifying the Number of Dark, Gray, and Bright States as a Function of the Spectral Overlap in Polaritonic Systems.

Nano letters·2026

Same author

Hierarchical multi-timescale structural dynamics of the disordered N-terminal of p53.

Nature communications·2026

Same author

Diverse mechanisms of translation arrest by a Clostridia ribosome stalling peptide CliM.

Nature communications·2026

Same author

Bimodal Peptide Collision Cross Section Distribution Reflects Two Stable Conformations in the Gas Phase.

Journal of proteome research·2026

Same author

Improving Conformational Ensembles of Folded Proteins in Go̅Martini.

Journal of chemical theory and computation·2026

Search research articles

Related Experiment Video

Updated: Mar 25, 2026

Sedimentation Equilibrium of a Small Oligomer-forming Membrane Protein: Effect of Histidine Protonation on Pentameric Stability

Sedimentation Equilibrium of a Small Oligomer-forming Membrane Protein: Effect of Histidine Protonation on Pentameric Stability

Published on: April 2, 2015

Charge-Neutral Constant pH Molecular Dynamics Simulations Using a Parsimonious Proton Buffer.

Serena Donnini¹, R Thomas Ullmann², Gerrit Groenhof³

¹Nanoscience Center and Department of Biological and Environmental Sciences, University of Jyväskylä , P. O. Box 35, 40014 Jyväskylä, Finland.

Journal of Chemical Theory and Computation

|February 17, 2016

Summary

Constant pH molecular dynamics simulations can now maintain system neutrality using a novel proton buffer. This approach accurately captures biomolecular charge fluctuations while improving simulation efficiency.

More Related Videos

Deciphering the Structural Effects of Activating EGFR Somatic Mutations with Molecular Dynamics Simulation

Deciphering the Structural Effects of Activating EGFR Somatic Mutations with Molecular Dynamics Simulation

Published on: May 20, 2020

Rapid in-silico Battery Electrolyte Electrochemical Reaction Generation using 3T-VASP Multi-Scale Energy Minimization

Rapid in-silico Battery Electrolyte Electrochemical Reaction Generation using 3T-VASP Multi-Scale Energy Minimization

Published on: August 22, 2025

Related Experiment Videos

Last Updated: Mar 25, 2026

Sedimentation Equilibrium of a Small Oligomer-forming Membrane Protein: Effect of Histidine Protonation on Pentameric Stability

Sedimentation Equilibrium of a Small Oligomer-forming Membrane Protein: Effect of Histidine Protonation on Pentameric Stability

Published on: April 2, 2015

Deciphering the Structural Effects of Activating EGFR Somatic Mutations with Molecular Dynamics Simulation

Deciphering the Structural Effects of Activating EGFR Somatic Mutations with Molecular Dynamics Simulation

Published on: May 20, 2020

Rapid in-silico Battery Electrolyte Electrochemical Reaction Generation using 3T-VASP Multi-Scale Energy Minimization

Rapid in-silico Battery Electrolyte Electrochemical Reaction Generation using 3T-VASP Multi-Scale Energy Minimization

Published on: August 22, 2025

Area of Science:

Biophysics
Computational Chemistry
Biochemistry

Background:

Constant pH molecular dynamics (MD) simulations allow titratable sites to respond to pH and electrostatic changes.
Biomolecular charge fluctuates during simulations, potentially causing artifacts in non-neutral systems.

Purpose of the Study:

Introduce a method to maintain simulation box neutrality in constant pH MD simulations.
Accurately describe protonation fluctuations without artifacts.

Main Methods:

Developed a proton buffer system that exchanges protons with the biomolecule.
Coupled buffer proton exchange to biomolecular titration to maintain overall system charge neutrality.

Main Results:

The proton buffer effectively maintains system neutrality while allowing biomolecular charge fluctuations.
Required buffer sites are fewer than titratable sites, enhancing simulation efficiency.

Conclusions:

The proton buffer method ensures accurate and artifact-free constant pH MD simulations.
This approach significantly improves simulation and sampling efficiency for biomolecular systems.