scholarly journals Water structure as a function of temperature from X-ray scattering experiments and ab initio molecular dynamics

2003 ◽  
Vol 5 (10) ◽  
pp. 1981 ◽  
Author(s):  
Greg Hura ◽  
Daniela Russo ◽  
Robert M. Glaeser ◽  
Teresa Head-Gordon ◽  
Matthias Krack ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Ab Initio ◽  
Water Structure ◽  
Ab Initio Molecular Dynamics ◽  
X Ray ◽  
X Ray Scattering ◽  
Ray Scattering

Liquid Structure of 1-Ethyl-3-methylimidazolium Alkyl Sulfates by X-ray Scattering and Molecular Dynamics

2012 ◽  
Vol 116 (45) ◽  
pp. 13448-13458 ◽  
Author(s):  
Marina Macchiagodena ◽  
Fabio Ramondo ◽  
Alessandro Triolo ◽  
Lorenzo Gontrani ◽  
Ruggero Caminiti
Keyword(s):  
Molecular Dynamics ◽  
Liquid Structure ◽  
X Ray ◽  
X Ray Scattering ◽  
Alkyl Sulfates ◽  
Ray Scattering

Structural refinement by restrained molecular-dynamics algorithm with small-angle X-ray scattering constraints for a biomolecule

2004 ◽  
Vol 37 (1) ◽  
pp. 103-109 ◽  
Author(s):  
Masaki Kojima ◽  
Alexander A. Timchenko ◽  
Junichi Higo ◽  
Kazuki Ito ◽  
Hiroshi Kihara ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Molecular Dynamics ◽  
Small Angle ◽  
Protein Structures ◽  
Saxs Data ◽  
X Ray ◽  
X Ray Scattering ◽  
Saxs Curve ◽  
Restrained Molecular Dynamics ◽  
Ray Scattering

A new algorithm to refine protein structures in solution from small-angle X-ray scattering (SAXS) data was developed based on restrained molecular dynamics (MD). In the method, the sum of squared differences between calculated and observed SAXS intensities was used as a constraint energy function, and the calculation was started from given atomic coordinates, such as those of the crystal. In order to reduce the contribution of the hydration effect to the deviation from the experimental (objective) curve during the dynamics, and purely as an estimate of the efficiency of the algorithm, the calculation was first performed assuming the SAXS curve corresponding to the crystal structure as the objective curve. Next, the calculation was carried out with `real' experimental data, which yielded a structure that satisfied the experimental SAXS curve well. The SAXS data for ribonuclease T1, a single-chain globular protein, were used for the calculation, along with its crystal structure. The results showed that the present algorithm was very effective in the refinement and adjustment of the initial structure so that it could satisfy the objective SAXS data.

Combined Experimental and Ab Initio Multireference Configuration Interaction Study of the Resonant Inelastic X-ray Scattering Spectrum of CO2

2014 ◽  
Vol 118 (35) ◽  
pp. 20163-20175 ◽  
Author(s):  
Dimitrios Maganas ◽  
Paw Kristiansen ◽  
Laurent-Claudius Duda ◽  
Axel Knop-Gericke ◽  
Serena DeBeer ◽  
...  
Keyword(s):  
Ab Initio ◽  
Configuration Interaction ◽  
Interaction Study ◽  
X Ray ◽  
X Ray Scattering ◽  
Scattering Spectrum ◽  
Ray Scattering

scholarly journals Study of High-Temperature Behaviour of ZnO by Ab Initio Molecular Dynamics Simulations and X-ray Absorption Spectroscopy

Materials ◽  
2021 ◽  
Vol 14 (18) ◽  
pp. 5206
Author(s):  
Dmitry Bocharov ◽  
Inga Pudza ◽  
Konstantin Klementiev ◽  
Matthias Krack ◽  
Alexei Kuzmin
Keyword(s):  
Molecular Dynamics ◽  
High Temperature ◽  
Ab Initio ◽  
Ab Initio Molecular Dynamics ◽  
Mean Square ◽  
Structural Anisotropy ◽  
X Ray ◽  
Temperature Dependences ◽  
Dynamics Simulations ◽  
X Ray Absorption

Wurtzite-type zinc oxide (w-ZnO) is a widely used material with a pronounced structural anisotropy along the c axis, which affects its lattice dynamics and represents a difficulty for its accurate description using classical models of interatomic interactions. In this study, ab initio molecular dynamics (AIMD) was employed to simulate a bulk w-ZnO phase in the NpT ensemble in the high-temperature range from 300 K to 1200 K. The results of the simulations were validated by comparison with the experimental Zn K-edge extended X-ray absorption fine structure (EXAFS) spectra and known diffraction data. AIMD NpT simulations reproduced well the thermal expansion of the lattice, and the pronounced anharmonicity of Zn–O bonding was observed above 600 K. The values of mean-square relative displacements and mean-square displacements for Zn–O and Zn–Zn atom pairs were obtained as a function of interatomic distance and temperature. They were used to calculate the characteristic Einstein temperatures. The temperature dependences of the O–Zn–O and Zn–O–Zn bond angle distributions were also determined.

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