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X-ray Crystallography

X-ray Crystallography

The size of the unit cell and the arrangement of atoms in a crystal may be determined from measurements of the diffraction of X-rays by the crystal, termed X-ray crystallography.
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Related Experiment Video

Updated: Jan 11, 2026

Iterative Optimization of DNA Duplexes for Crystallization of SeqA-DNA Complexes

Iterative Optimization of DNA Duplexes for Crystallization of SeqA-DNA Complexes

Published on: November 1, 2012

Correlating the Crystal Structure and Optical Response of DNA-Stabilized Ag₁₆Cl₂ Clusters.

Maya Khatun¹, Sami Malola¹, Hannu Häkkinen^1,2

¹Department of Physics, Nanoscience Center, University of Jyväskylä, FI-40014 Jyväskylä, Finland.

The Journal of Physical Chemistry. C, Nanomaterials and Interfaces

|November 13, 2025

Summary

Computational modeling of DNA-stabilized silver clusters reveals sensitivity to environmental and theoretical approximations. Further development is needed for accurate prediction of hybrid bionano-material properties.

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Published on: March 22, 2019

Area of Science:

Computational chemistry
Materials science
Biophysics

Background:

DNA-stabilized silver clusters are hybrid bionano-materials with potential applications.
Experimental crystal data exists for (DNA)2-Ag16Cl2, featuring a mutated guanosine-inosine DNA structure protecting an inorganic core.

Purpose of the Study:

To investigate the electronic structure and optical response of the (DNA)2-Ag16Cl2 cluster.
To assess the impact of various computational approximations on the predicted properties.

Main Methods:

Density functional theory (DFT) in ground-state and linear-response forms.
Utilized experimental crystal data for the (DNA)2-Ag16Cl2 system.
Explored different models for the cluster's environment and exchange-correlation functionals.

Main Results:

Computed optical absorption spectra are highly sensitive to the chosen environmental model (implicit solvent vs. explicit water).
The selection of exchange-correlation functionals significantly influences the results.
Minor variations in crystal packing within the unit cell lead to noticeable differences in computed properties.

Conclusions:

Accurate computational modeling of hybrid bionano-materials like (DNA)2-Ag16Cl2 presents significant challenges.
Further development of computational methods, particularly for sampling dynamical behavior, is crucial for correlating computed and measured properties.