Structural heterogeneity in a parent ground-state structure of AnPixJg2 revealed by theory and spectroscopy

2017 ◽  
Vol 19 (21) ◽  
pp. 13882-13894 ◽  
Author(s):  
Laura Katharina Scarbath-Evers ◽  
Sascha Jähnigen ◽  
Hossam Elgabarty ◽  
Chen Song ◽  
Rei Narikawa ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Ground State ◽  
Spectroscopic Properties ◽  
Structural Heterogeneity ◽  
Ground State Structure ◽  
State Structure ◽  
Dynamics Simulations

Extensive molecular dynamics simulations reveal two distinct isoforms of the cyanobacteriochrome AnPixJg2 (in its Pr state) with different chromophore conformations, yielding implications for spectroscopic properties.

Mechanistic analysis of light-driven overcrowded alkene-based molecular motors by multiscale molecular simulations

2021 ◽  
Vol 23 (14) ◽  
pp. 8525-8540
Author(s):  
Mudong Feng ◽  
Michael K. Gilson
Keyword(s):  
Molecular Dynamics ◽  
Excited State ◽  
Molecular Dynamics Simulations ◽  
Ground State ◽  
Molecular Motors ◽  
Motor Performance ◽  
Molecular Simulations ◽  
Mechanistic Analysis ◽  
Dynamics Simulations ◽  
Shed Light

Ground-state and excited-state molecular dynamics simulations shed light on the rotation mechanism of small, light-driven molecular motors and predict motor performance. How fast can they rotate; how much torque and power can they generate?

A density functional study of Rh13

2013 ◽  
Vol 91 (7) ◽  
pp. 591-597 ◽  
Author(s):  
Patrizia Calaminici ◽  
José M. Vásquez-Pérez ◽  
Diego A. Espíndola Velasco
Keyword(s):  
Molecular Dynamics ◽  
Ground State ◽  
Density Functional ◽  
Local Density ◽  
Structural Parameters ◽  
Functional Study ◽  
Ground State Structure ◽  
State Structure ◽  
Generalized Gradient ◽  
Density Functional Study

A density functional study was performed for the Rh13 cluster using the linear combination of Gaussian-type orbitals density functional theory (LCGTO-DFT) approach. The calculations employed both the local density approximation (LDA) as well as the generalized gradient approximation (GGA) in combination with a quasi-relativistic effective core potential (QECP). Initial structures for the geometry optimization were taken along Born–Oppenheimer molecular dynamics (BOMD) trajectories. The BOMD trajectories were performed at different temperatures and considered different potential energy surfaces (PES). As a result, several hundred isomers of the Rh13 cluster in different spin multiplicities were optimized with the aim to determine the lowest energy structures. All geometry optimizations were performed without any symmetry restriction. A vibrational analysis was performed to characterize these isomers. Structural parameters, relative stability energy, harmonic frequencies, binding energy, and most relevant Kohn–Sham (KS) molecular orbitals are reported. The obtained results are compared with available data from the literature. This study predicts a low symmetry biplanarlike structure as the ground-state structure of Rh13 with 11 unpaired electrons. This isomer was first noticed by inspection of first-principle Born–Oppenheimer molecular dynamics (BOMD) simulations between 300 and 600 K. This represents the most extensive theoretical study on the ground-state structure of the Rh13 cluster and underlines the importance of BOMD simulations to fully explore the PES landscapes of complicated systems.

Ab Initio Molecular Dynamics of Column IV Microclusters

1990 ◽  
Vol 193 ◽  
Author(s):  
David A. Drabold ◽  
Stefan Klemm ◽  
Otto F. Sankey
Keyword(s):  
Molecular Dynamics ◽  
Ab Initio ◽  
Molecular Dynamics Simulations ◽  
Vibrational Spectra ◽  
Ground State ◽  
Spectral Estimation ◽  
Ab Initio Molecular Dynamics ◽  
Estimation Technique ◽  
Dynamics Simulations ◽  
Small Clusters

ABSTRACTWe report the results of ab-initio molecular dynamics simulations for small clusters of Si and C atoms. Ground-state geometries and vibrational spectra are presented. We also describe a Bayesian spectral estimation technique which we have found to be useful in analyzing molecular dynamics trajectories.

scholarly journals Cavity molecular dynamics simulations of liquid water under vibrational ultrastrong coupling

2020 ◽  
Vol 117 (31) ◽  
pp. 18324-18331 ◽  
Author(s):  
Tao E. Li ◽  
Joseph E. Subotnik ◽  
Abraham Nitzan
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Liquid Water ◽  
Ground State ◽  
Cavity Mode ◽  
Translational Diffusion ◽  
Static Properties ◽  
Cavity Modes ◽  
Stretch Mode ◽  
Dynamics Simulations

We simulate vibrational strong coupling (VSC) and vibrational ultrastrong coupling (V-USC) for liquid water with classical molecular dynamics simulations. When the cavity modes are resonantly coupled to the O−H stretch mode of liquid water, the infrared spectrum shows asymmetric Rabi splitting. The lower polariton (LP) may be suppressed or enhanced relative to the upper polariton (UP) depending on the frequency of the cavity mode. Moreover, although the static properties and the translational diffusion of water are not changed under VSC or V-USC, we do find the modification of the orientational autocorrelation function of H2O molecules especially under V-USC, which could play a role in ground-state chemistry.

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