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Resonance and Hybrid Structures02:16

Resonance and Hybrid Structures

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According to the theory of resonance, if two or more Lewis structures with the same arrangement of atoms can be written for a molecule, ion, or radical, the actual distribution of electrons is an average of that shown by the various Lewis structures.
Resonance Structures and Resonance Hybrids
The Lewis structure of a nitrite anion (NO2−) may actually be drawn in two different ways, distinguished by the locations of the N–O and N=O bonds.
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Ions as Acids and Bases02:54

Ions as Acids and Bases

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Salts with Acidic Ions
Salts are ionic compounds composed of cations and anions, either of which may be capable of undergoing an acid or base ionization reaction with water. Aqueous salt solutions, therefore, may be acidic, basic, or neutral, depending on the relative acid-base strengths of the salt’s constituent ions. For example, dissolving the ammonium chloride in water results in its dissociation, as described by the equation:
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Determining the pH of Salt Solutions04:08

Determining the pH of Salt Solutions

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The pH of a salt solution is determined by its component anions and cations. Salts that contain pH-neutral anions and the hydronium ion-producing cations form a solution with a pH less than 7. For example, in ammonium nitrate (NH4NO3) solution, NO3− ions do not react with water whereas NH4+ ions produce the hydronium ions resulting in the acidic solution.  In contrast, salts that contain pH-neutral cations and the hydroxide ion-producing anions form a solution with a pH greater than 7. For...
49.9K
Resonance02:52

Resonance

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The Lewis structure of a nitrite anion (NO2−) may actually be drawn in two different ways, distinguished by the locations of the N-O and N=O bonds.
71.0K
Ionic Bonding and Electron Transfer02:48

Ionic Bonding and Electron Transfer

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Ions are atoms or molecules bearing an electrical charge. A cation (a positive ion) forms when a neutral atom loses one or more electrons from its valence shell, and an anion (a negative ion) forms when a neutral atom gains one or more electrons in its valence shell. Compounds composed of ions are called ionic compounds (or salts), and their constituent ions are held together by ionic bonds: electrostatic forces of attraction between oppositely charged cations and anions. 
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Overview of VSEPR Theory
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A Micro-agar Salt Bridge Electrode for Analyzing the Proton Turnover Rate of Recombinant Membrane Proteins
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Salt Bridge Builder: Using Residue Distances to Predict Salt Bridge Formation.

Jason Sanchez1, Wenhan Guo2, Yuan Gao3

  • 1Department of Pharmaceutical Sciences, School of Pharmacy, The University of Texas at El Paso, 1101 N Campbell St, El Paso, Texas 79902, United States.

Journal of Chemical Information and Modeling
|April 6, 2026
PubMed
Summary
This summary is machine-generated.

We developed Salt Bridge Builder (SBB), a new software tool to engineer stabilizing salt bridges at protein interfaces. SBB uses residue distance heuristics to identify mutation sites, aiding protein design and stability prediction.

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Area of Science:

  • Protein engineering
  • Computational biology
  • Biophysics

Background:

  • Salt bridges are crucial for protein stability and interactions.
  • Existing tools focus on removing salt bridges, not creating them.
  • Systematic methods for engineering new salt bridges are limited.

Purpose of the Study:

  • Introduce Salt Bridge Builder (SBB), a software for engineering interprotein salt bridges.
  • Validate the stabilizing role of salt bridges at protein interfaces.
  • Develop an efficient algorithm for predicting salt bridge formation.

Main Methods:

  • Utilized residue distance heuristics from structural data.
  • Analyzed the SKEMPI v2 database for mutation effects.
  • Benchmarked six residue distance metrics, selecting side-chain centroid distance (SCCD).
  • Applied SBB to kinesin-5 and microtubule interactions.
  • Employed molecular dynamics simulations and principal component analysis.

Main Results:

  • SBB identifies candidate sites for novel interprotein salt bridges.
  • Disrupting salt bridges significantly reduces binding free energy.
  • SCCD offers optimal predictive performance and computational efficiency.
  • Kinesin-5 shows enrichment in potential salt bridge sites at the microtubule interface.
  • Local microenvironments influence engineered salt bridge stability.

Conclusions:

  • Residue-distance-based salt bridge engineering is a viable protein engineering strategy.
  • SBB provides a foundation for predicting engineered salt bridge stability.
  • Future SBB extensions will incorporate microenvironment-aware stability prediction.