Related Experiment Video
Updated: Jul 18, 2026
06:44
From Molecules to Materials: Engineering New Ionic Liquid Crystals Through Halogen Bonding
Published on: March 24, 2018
Charge structure and counterion distribution in hexagonal DNA liquid crystal
Liang Dai1, Yuguang Mu, Lars Nordenskiöld
1National University of Singapore, Department of Physics, Singapore.
Biophysical Journal
|November 14, 2006
Summary
Small-angle neutron scattering and simulations reveal DNA liquid crystal structure. Tetramethylammonium counterions show ordering between DNA fragments, with limited groove penetration, contrasting with molecular dynamics predictions.
Area of Science:
- Biophysics
- Materials Science
- Computational Chemistry
Background:
- DNA fragments can form liquid crystalline phases.
- Counterion distribution is crucial for understanding DNA structure and interactions.
- Small-angle neutron scattering (SANS) and computer simulations are powerful tools for nanoscale investigations.
Purpose of the Study:
- To investigate the structure of hexagonal DNA liquid crystals with tetramethylammonium (TMA) counterions.
- To compare experimental SANS data with molecular dynamics (MD) and Monte Carlo (MC) simulations.
- To elucidate the role of TMA counterions in DNA liquid crystal organization.
Main Methods:
- Small-angle neutron scattering (SANS) was used to obtain structure factors.
- Molecular dynamics (MD) simulations were performed on hexagonal DNA assemblies.
- Monte Carlo (MC) simulations were used for hexagonal arrays of charged rods.
Main Results:
- SANS revealed strong ordering of TMA counterions between DNA fragments.
- MD simulations showed inter-DNA distance fluctuations but minimal impact on radial counterion profiles.
- Discrepancy observed between MD simulations (significant groove penetration) and SANS/MC results (limited penetration) for TMA.
- Experimental data showed best agreement with Poisson-Boltzmann equation and/or MC simulation predictions.
Conclusions:
- TMA counterions strongly order between DNA molecules in hexagonal liquid crystals.
- The size of TMA limits its penetration into DNA grooves, contrary to some simulation predictions.
- Combined SANS and simulation approaches provide a comprehensive understanding of DNA-counterion interactions.
Related Concept Videos
02:42Ionic Crystal Structures
Ionic crystals consist of two or more different kinds of ions that usually have different sizes. The packing of these ions into a crystal structure is more complex than the packing of metal atoms that are the same size.
Most monatomic ions behave as charged spheres, and their attraction for ions of opposite charge is the same in every direction. Consequently, stable structures for ionic compounds result (1) when ions of one charge are surrounded by as many ions as possible of the opposite...
Most monatomic ions behave as charged spheres, and their attraction for ions of opposite charge is the same in every direction. Consequently, stable structures for ionic compounds result (1) when ions of one charge are surrounded by as many ions as possible of the opposite...
02:58Crystal Field Theory - Octahedral Complexes
Crystal Field Theory
To explain the observed behavior of transition metal complexes (such as colors), a model involving electrostatic interactions between the electrons from the ligands and the electrons in the unhybridized d orbitals of the central metal atom has been developed. This electrostatic model is crystal field theory (CFT). It helps to understand, interpret, and predict the colors, magnetic behavior, and some structures of coordination compounds of transition metals.
CFT focuses on...
To explain the observed behavior of transition metal complexes (such as colors), a model involving electrostatic interactions between the electrons from the ligands and the electrons in the unhybridized d orbitals of the central metal atom has been developed. This electrostatic model is crystal field theory (CFT). It helps to understand, interpret, and predict the colors, magnetic behavior, and some structures of coordination compounds of transition metals.
CFT focuses on...
02:46Crystal Field Theory - Tetrahedral and Square Planar Complexes
Tetrahedral Complexes
Crystal field theory (CFT) is applicable to molecules in geometries other than octahedral. In octahedral complexes, the lobes of the dx2−y2 and dz2 orbitals point directly at the ligands. For tetrahedral complexes, the d orbitals remain in place, but with only four ligands located between the axes. None of the orbitals points directly at the tetrahedral ligands. However, the dx2−y2 and dz2 orbitals (along the Cartesian axes) overlap with the ligands less than the dxy,...
Crystal field theory (CFT) is applicable to molecules in geometries other than octahedral. In octahedral complexes, the lobes of the dx2−y2 and dz2 orbitals point directly at the ligands. For tetrahedral complexes, the d orbitals remain in place, but with only four ligands located between the axes. None of the orbitals points directly at the tetrahedral ligands. However, the dx2−y2 and dz2 orbitals (along the Cartesian axes) overlap with the ligands less than the dxy,...
02:22Structures of Solids
Solids in which the atoms, ions, or molecules are arranged in a definite repeating pattern are known as crystalline solids. Metals and ionic compounds typically form ordered, crystalline solids. A crystalline solid has a precise melting temperature because each atom or molecule of the same type is held in place with the same forces or energy. Amorphous solids or non-crystalline solids (or, sometimes, glasses) which lack an ordered internal structure and are randomly arranged. Substances that...
01:18Unit Cells
A crystal's internal structure is an orderly array of atoms, ions, or molecules, and the details of this array significantly influence the solid's properties. In a crystal, periodically repeating 'structural motifs' - which could be atoms, molecules, or groups thereof - create a 'space lattice.' This is essentially a three-dimensional, infinite array of points, each surrounded by its neighbors in an identical way, forming the basic structure of the crystal.A 'unit cell' is a theoretical...
02:37Metallic Solids
Metallic solids such as crystals of copper, aluminum, and iron are formed by metal atoms. The structure of metallic crystals is often described as a uniform distribution of atomic nuclei within a “sea” of delocalized electrons. The atoms within such a metallic solid are held together by a unique force known as metallic bonding that gives rise to many useful and varied bulk properties.
All metallic solids exhibit high thermal and electrical conductivity, metallic luster, and malleability. Many...
All metallic solids exhibit high thermal and electrical conductivity, metallic luster, and malleability. Many...