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Related Concept Videos

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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Aromatic Hydrocarbon Cations: Structural Overview01:18

Aromatic Hydrocarbon Cations: Structural Overview

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Cycloheptatriene is a neutral monocyclic unsaturated hydrocarbon that consists of an odd number of carbon atoms and an intervening sp3 carbon in the ring. The three double bonds in the ring correspond to 6 π electrons, which is a Huckel number, and therefore satisfies the criteria of 4n + 2 π electrons. However, the intervening sp3 carbon disrupts the continuous overlap of p orbitals. As a result, cycloheptatriene is not aromatic.
Removing one hydrogen from the intervening CH2 group...
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Molecular Orbital Theory II03:51

Molecular Orbital Theory II

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Molecular Orbital Energy Diagrams
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Aromatic Hydrocarbon Anions: Structural Overview01:18

Aromatic Hydrocarbon Anions: Structural Overview

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Neutral hydrocarbons like cyclopentadiene with an odd number of carbon atoms and one intervening CH2 group in the ring are not aromatic. Cyclopentadiene with 4 π electrons does not satisfy the 4n + 2 π electron rule. Additionally, the intervening CH2 group is sp3 hybridized and lacks a vacant p orbital, thereby interrupting the overlap of p orbitals in a continuous manner and preventing the delocalization of π electrons throughout the ring.
Due to the absence of continuous...
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Lewis Structures of Molecular Compounds and Polyatomic Ions02:54

Lewis Structures of Molecular Compounds and Polyatomic Ions

37.2K
To draw Lewis structures for complicated molecules and molecular ions, it is helpful to follow a step-by-step procedure as outlined:
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Acid Strength and Molecular Structure03:05

Acid Strength and Molecular Structure

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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...
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Updated: Sep 12, 2025

Analyzing Protein Architectures and Protein-Ligand Complexes by Integrative Structural Mass Spectrometry
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Analyzing Protein Architectures and Protein-Ligand Complexes by Integrative Structural Mass Spectrometry

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RNA Structural Complexity Dictates Its Ion Atmosphere.

Hiranmay Maity1, Heyang Zhang1, D Thirumalai2

  • 1Department of Chemistry, The State University of New York at Buffalo, Buffalo, New York 14260, United States.

The Journal of Physical Chemistry Letters
|August 7, 2025
PubMed
Summary
This summary is machine-generated.

RNA flexibility dictates how ions interact, influencing its behavior. Unstructured RNAs show diffuse ion clouds, while folded RNAs have compact ones, impacting electrostatic interactions.

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Structure and Coordination Determination of Peptide-metal Complexes Using 1D and 2D 1H NMR
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Area of Science:

  • Biophysics
  • Computational Biology
  • Molecular Biology

Background:

  • Electrostatic interactions and ion binding are crucial for RNA function.
  • The behavior of flexible RNAs in solution remains less understood compared to structured RNAs.

Purpose of the Study:

  • To investigate the influence of RNA structural flexibility on ion atmospheres using molecular dynamics simulations.
  • To compare the electrostatic interactions of magnesium (Mg2+) and calcium (Ca2+) ions with RNAs of varying flexibility.

Main Methods:

  • Molecular dynamics simulations were employed to model three distinct RNA structures: an unstructured polyuridylic tract (rU30), a semiflexible (CAG) repeat, and a folded pseudoknot.
  • Analysis focused on the spatial distribution and dynamics of Mg2+ and Ca2+ ion atmospheres around each RNA.

Main Results:

  • Unstructured RNA (rU30) attracted diffuse Mg2+ clouds, whereas the CAG repeat and pseudoknot exhibited more compact Mg2+ binding.
  • Ca2+ consistently formed inner-sphere contacts with all tested RNA structures.
  • Ion atmospheres extended farther for unstructured RNAs, increasing their electrostatic influence, yet ion exchange kinetics remained similar across structures.

Conclusions:

  • RNA structural flexibility significantly modulates ionic screening and the electrostatic sphere of influence.
  • A decoupling exists between the spatial distribution of ions and their exchange dynamics.
  • Findings have implications for understanding RNA-based biomolecular recognition, phase separation, and RNA condensates.