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Related Concept Videos

Colors and Magnetism03:02

Colors and Magnetism

Color in Coordination Complexes
When atoms or molecules absorb light at the proper frequency, their electrons are excited to higher-energy orbitals. For many main group atoms and molecules, the absorbed photons are in the ultraviolet range of the electromagnetic spectrum, which cannot be detected by the human eye. For coordination compounds, the energy difference between the d orbitals often allows photons in the visible range to be absorbed and emitted, which is seen as colors by the human eye.
Crystal Field Theory - Octahedral Complexes02:58

Crystal 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...
Valence Bond Theory02:42

Valence Bond Theory

Coordination compounds and complexes exhibit different colors, geometries, and magnetic behavior, depending on the metal atom/ion and ligands from which they are composed. In an attempt to explain the bonding and structure of coordination complexes, Linus Pauling proposed the valence bond theory, or VBT, using the concepts of hybridization and the overlapping of the atomic orbitals. According to VBT, the central metal atom or ion (Lewis acid) hybridizes to provide empty orbitals of suitable...
Single-Strand DNA Binding Proteins01:03

Single-Strand DNA Binding Proteins

For successful DNA replication, the unwinding of double-stranded DNA must be accompanied by stabilization and protection of the separated single strands of the DNA. This crucial task is performed by single-strand DNA-binding (SSB) proteins. They bind to the DNA in a sequence-independent manner, which means that the nitrogenous bases of the DNA need not be present in a specific order for binding of SSB proteins to it. The binding of SSB proteins straightens single-stranded DNA (ssDNA) and makes...
Crystal Field Theory - Tetrahedral and Square Planar Complexes02:46

Crystal 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,...
Extraction: Advanced Methods00:56

Extraction: Advanced Methods

Metal ions can be separated from one another by complexation with organic ligands–the chelating agent– to form uncharged chelates. Here, the chelating agent must contain hydrophobic groups and behave as a weak acid, losing a proton to bind with the metal. Since most organic ligands used in this process are insoluble or undergo oxidation in the aqueous phase, the chelating agent is initially added to the organic phase and extracted into the aqueous phase. The metal-ligand complex is formed in...

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Related Experiment Video

Updated: Jun 24, 2026

Structure and Coordination Determination of Peptide-metal Complexes Using 1D and 2D 1H NMR
14:44

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Published on: December 16, 2013

Structural origin of copper ion containing artificial DNA: a density functional study.

Toru Matsui1, Hideaki Miyachi, Takeshi Sato

  • 1Department of Applied Chemistry, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan.

The Journal of Physical Chemistry. B
|April 16, 2009
PubMed
Summary

Structural stability in copper-containing artificial DNA originates from van der Waals interactions, not spin-spin forces. This finding impacts understanding DNA base-pair stacking and stability.

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Area of Science:

  • Computational chemistry
  • Biophysics
  • Materials science

Background:

  • Copper ions can be incorporated into artificial DNA structures.
  • Understanding the forces governing the stability of these modified DNA structures is crucial for their potential applications.
  • Previous hypotheses suggested spin-spin interactions were dominant in copper-containing DNA.

Purpose of the Study:

  • To investigate the origin of structural stability in artificial DNA containing copper ions.
  • To evaluate the stacking energy of a hydroxypyridone-copper dimer using computational methods.
  • To compare the interactions in copper-containing DNA with natural B-DNA.

Main Methods:

  • Density functional theory (DFT) calculations were employed.
  • An Anderson-Langreth-Lindqvist van der Waals (vdW) functional was utilized.
  • Open-shell DFT was used to analyze spin states (singlet and triplet).

Main Results:

  • The calculated copper-copper distance (3.6 angstroms) aligns with experimental data.
  • The stacking energy was found to be 8-10 kcal/mol, comparable to natural B-DNA base pairs.
  • Van der Waals interactions were identified as the dominant force in inter-base-pair interactions, contradicting prior conjectures.
  • Antiferromagnetic and ferromagnetic states were nearly degenerate under specific structural conditions.

Conclusions:

  • Van der Waals interactions play a dominant role in the structural stability of copper-containing artificial DNA.
  • The findings challenge previous assumptions about the primary interactions governing these systems.
  • Computational modeling provides valuable insights into the fundamental properties of modified nucleic acids.