Grid Calculation Tools for Massive Applications of Collision Dynamics Simulations: Carbon Dioxide Energy Transfer

2014 ◽  
pp. 627-639 ◽  
Author(s):  
Andrea Lombardi ◽  
Noelia Faginas-Lago ◽  
Antonio Laganà
Keyword(s):  
Carbon Dioxide ◽  
Energy Transfer ◽  
Collision Dynamics ◽  
Dynamics Simulations

Atom Condensed Fukui Function for Condensed Phases and Biological Systems and Its Application to Enzymatic Fixation of Carbon Dioxide

2019 ◽  
Author(s):  
Javier Oller ◽  
David A. Sáez ◽  
Esteban Vöhringer-Martinez
Keyword(s):  
Carbon Dioxide ◽  
Aqueous Solution ◽  
Molecular System ◽  
Chemical Reactivity ◽  
Nucleophilic Attack ◽  
Stable Conformation ◽  
Fukui Functions ◽  
Reactivity Descriptors ◽  
Dynamics Simulations ◽  
Fixation Of Carbon Dioxide

<div><div><div><p>Local reactivity descriptors such as atom condensed Fukui functions are promising computational tools to study chemical reactivity at specific sites within a molecule. Their applications have been mainly focused on isolated molecules in their most stable conformation without considering the effects of the surroundings. Here, we propose to combine QM/MM Born-Oppenheimer molecular dynamics simulations to obtain the microstates (configurations) of a molecular system using different representations of the molecular environment and calculate Boltzmann weighted atom condensed local reac- tivity descriptors based on conceptual DFT. Our approach takes the conformational fluctuations of the molecular system and the polarization of its electron density by the environment into account allowing us to analyze the effect of changes in the molecular environment on reactivity. In this contribution, we apply the method mentioned above to the catalytic fixation of carbon dioxide by crotonyl-CoA carboxylase/reductase and study if the enzyme alters the reactivity of its substrate compared to an aqueous solution. Our main result is that the protein en- vironment activates the substrate by the elimination of solute-solvent hydrogen bonds from aqueous solution in the two elementary steps of the reaction mechanism: the nucleophilic attack of a hydride anion from NADPH on the α, β unsaturated thioester and the electrophilic attack of carbon dioxide on the formed enolate species.</p></div></div></div>

scholarly journals Unveiling Carbon Dioxide and Ethanol Diffusion in Carbonated Water-Ethanol Mixtures by Molecular Dynamics Simulations

Molecules ◽  
2021 ◽  
Vol 26 (6) ◽  
pp. 1711
Author(s):  
Mohamed Ahmed Khaireh ◽  
Marie Angot ◽  
Clara Cilindre ◽  
Gérard Liger-Belair ◽  
David A. Bonhommeau
Keyword(s):  
Carbon Dioxide ◽  
Molecular Dynamics ◽  
Diffusion Coefficients ◽  
Hydrodynamic Radius ◽  
Md Simulations ◽  
Molecular Models ◽  
Experimental Values ◽  
Carbon Dioxide Co2 ◽  
Dynamics Simulations ◽  
Apparent Disagreement

The diffusion of carbon dioxide (CO2) and ethanol (EtOH) is a fundamental transport process behind the formation and growth of CO2 bubbles in sparkling beverages and the release of organoleptic compounds at the liquid free surface. In the present study, CO2 and EtOH diffusion coefficients are computed from molecular dynamics (MD) simulations and compared with experimental values derived from the Stokes-Einstein (SE) relation on the basis of viscometry experiments and hydrodynamic radii deduced from former nuclear magnetic resonance (NMR) measurements. These diffusion coefficients steadily increase with temperature and decrease as the concentration of ethanol rises. The agreement between theory and experiment is suitable for CO2. Theoretical EtOH diffusion coefficients tend to overestimate slightly experimental values, although the agreement can be improved by changing the hydrodynamic radius used to evaluate experimental diffusion coefficients. This apparent disagreement should not rely on limitations of the MD simulations nor on the approximations made to evaluate theoretical diffusion coefficients. Improvement of the molecular models, as well as additional NMR measurements on sparkling beverages at several temperatures and ethanol concentrations, would help solve this issue.

scholarly journals Local structure and distortions of mixed methane-carbon dioxide hydrates

2021 ◽  
Vol 4 (1) ◽  
Author(s):  
Bernadette R. Cladek ◽  
S. Michelle Everett ◽  
Marshall T. McDonnell ◽  
Matthew G. Tucker ◽  
David J. Keffer ◽  
...  
Keyword(s):  
Carbon Dioxide ◽  
Exchange Process ◽  
Carbon Dioxide Sequestration ◽  
Distribution Functions ◽  
Atomic Scale ◽  
Mixed Gas ◽  
Pure Compounds ◽  
Dynamics Simulations ◽  
Pair Distribution Functions ◽  
Methane Carbon

AbstractA vast source of methane is found in gas hydrate deposits, which form naturally dispersed throughout ocean sediments and arctic permafrost. Methane may be obtained from hydrates by exchange with hydrocarbon byproduct carbon dioxide. It is imperative for the development of safe methane extraction and carbon dioxide sequestration to understand how methane and carbon dioxide co-occupy the same hydrate structure. Pair distribution functions (PDFs) provide atomic-scale structural insight into intermolecular interactions in methane and carbon dioxide hydrates. We present experimental neutron PDFs of methane, carbon dioxide and mixed methane-carbon dioxide hydrates at 10 K analyzed with complementing classical molecular dynamics simulations and Reverse Monte Carlo fitting. Mixed hydrate, which forms during the exchange process, is more locally disordered than methane or carbon dioxide hydrates. The behavior of mixed gas species cannot be interpolated from properties of pure compounds, and PDF measurements provide important understanding of how the guest composition impacts overall order in the hydrate structure.

CARS (coherent anti-Stokes Raman scattering) investigations of the intermolecular vibrational energy transfer between nitrogen and carbon dioxide molecules

1993 ◽  
Vol 71 (3-4) ◽  
pp. 142-146 ◽  
Author(s):  
L. Wang ◽  
J. R. Xu ◽  
W. E. Jones
Keyword(s):  
Carbon Dioxide ◽  
Energy Transfer ◽  
Raman Scattering ◽  
Rate Constants ◽  
Transfer Rate ◽  
Vibrational Energy ◽  
Vibrational Energy Transfer ◽  
Scattering Technique ◽  
Anti Stokes ◽  
First Time

The CARS (coherent anti-Stokes Raman scattering) technique has been used for the first time to observe directly the vibrational energy transfer between nitrogen N2 (X1Σ, ν = 1, 2) and carbon dioxide. The transfer-rate constants were determined as (1.0 ± 0.1) × 1011 cm3 mol−1 s−1 and (1.7 ± 0.4) × 1011 cm3 mol−1 s−1 for N2(ν = 1) and N2(ν = 2), respectively.

scholarly journals Thermostat for nonequilibrium multiparticle-collision-dynamics simulations

2015 ◽  
Vol 91 (1) ◽  
Author(s):  
Chien-Cheng Huang ◽  
Anoop Varghese ◽  
Gerhard Gompper ◽  
Roland G. Winkler
Keyword(s):  
Collision Dynamics ◽  
Multiparticle Collision Dynamics ◽  
Dynamics Simulations
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