Diffusion coefficients and viscosities of organic aerosol components through equilibrium and non-equilibrium molecular dynamics simulations

Author(s):  
Katerina S. Karadima ◽  
Vlasis G. Mavrantzas ◽  
Spyros N. Pandis

<p>Organic aerosols have been typically considered to be liquid, with equilibration between gas and aerosol phase assumed to be reached within seconds. However, Virtanen et al. (Nature, 2010) suggested that particles in amorphous solid state may also occur in the atmosphere implying that mass transfer between the atmospheric particulate and gas phases may be much slower than initially thought. Experimentally, the direct measurement of the diffusion coefficients of different compounds inside atmospheric organic particles is challenging. Thus, an indirect approach is usually employed, involving viscosity measurements and then estimation of diffusion coefficients via the Stokes-Einstein equation, according to which the diffusion coefficient is inversely proportional to the medium viscosity. However, the corresponding diffusion estimates are highly uncertain, especially for highly viscous aerosols which is the most important case. Molecular simulation methods, such as molecular dynamics (MD), can be an alternative method to determine directly the diffusion rates and the viscosity of the constituents of atmospheric organic particles. MD also provides detailed information of the exact dynamics and motion of the molecules, thus offering a deeper understanding on the underlying mechanisms and interactions.</p><p>In the present work, we use equilibrium and non-equilibrium MD simulations to estimate the viscosity and diffusion coefficients of bulk systems of representative organic compounds with different chemical structures and physicochemical characteristics. Hydrophilic and hydrophobic compounds representative of primary and secondary oxidized organic products and of primary organic compounds emitted by various sources are considered. The viscosity and self-diffusion coefficients calculated by our simulations are in good agreement with available experimentally measured values. Our results confirm that the presence of carboxyl and hydroxyl groups in the molecule increases the viscosity. The number of carboxyl and hydroxyl groups, in particular, seems to have a good effect on diffusivity (the diffusivity decreases as the number of these functional groups increase), and to a lesser extent on the viscosity. We also discuss the role of the hydrogen bonds formed between these functional groups.</p>

Molecules ◽  
2020 ◽  
Vol 25 (17) ◽  
pp. 4030
Author(s):  
He Zhang ◽  
Peng Xi ◽  
Qiming Zhuo ◽  
Wenli Liu

To study the effects of different oxygen functional groups on the quality of flotation clean low-rank coal, two kinds of collectors with different oxygen-containing functional groups, methyl laurate, and dodecanol, were selected and their flotation behaviors were investigated. The Bulianta coal was the typical sub-bituminous coal in China, and the coal molecular model of which was constructed based on proximate analysis, ultimate analysis, 13C-NMR, and XPS. The chemical structure model of the coal molecule was optimized, and the periodic boundary condition was added via the method of molecular dynamics methods. The different combined systems formed by collectors, water, and a model surface of Bulianta coal have been studied using molecular dynamics simulation. The simulation results of dodecanol and methyl laurate on the surface of Bulianta coal show that dodecanol molecules are not evenly adsorbed on the surface of coal, and have higher adsorption capacity near carboxyl and hydroxyl groups, but less adsorption capacity near carbonyl and ether bonds. Methyl laurate can completely cover the oxygen-containing functional groups on the coal surface. Compared with dodecanol, methyl laurate can effectively improve the hydrophobicity of the Bulianta coal surface, which is consistent with the results of the XPS test and the flotation test.


Pharmaceutics ◽  
2021 ◽  
Vol 13 (5) ◽  
pp. 734
Author(s):  
Aija Trimdale ◽  
Anatoly Mishnev ◽  
Agris Bērziņš

The arrangement of hydroxyl groups in the benzene ring has a significant effect on the propensity of dihydroxybenzoic acids (diOHBAs) to form different solid phases when crystallized from solution. All six diOHBAs were categorized into distinctive groups according to the solid phases obtained when crystallized from selected solvents. A combined study using crystal structure and molecule electrostatic potential surface analysis, as well as an exploration of molecular association in solution using spectroscopic methods and molecular dynamics simulations were used to determine the possible mechanism of how the location of the phenolic hydroxyl groups affect the diversity of solid phases formed by the diOHBAs. The crystal structure analysis showed that classical carboxylic acid homodimers and ring-like hydrogen bond motifs consisting of six diOHBA molecules are prominently present in almost all analyzed crystal structures. Both experimental spectroscopic investigations and molecular dynamics simulations indicated that the extent of intramolecular bonding between carboxyl and hydroxyl groups in solution has the most significant impact on the solid phases formed by the diOHBAs. Additionally, the extent of hydrogen bonding with solvent molecules and the mean lifetime of solute–solvent associates formed by diOHBAs and 2-propanol were also investigated.


Symmetry ◽  
2021 ◽  
Vol 13 (4) ◽  
pp. 720
Author(s):  
Satomi Niwayama

Symmetric organic compounds are generally obtained inexpensively, and therefore they can be attractive building blocks for the total synthesis of various pharmaceuticals and natural products. The drawback is that discriminating the identical functional groups in the symmetric compounds is difficult. Water is the most environmentally benign and inexpensive solvent. However, successful organic reactions in water are rather limited due to the hydrophobicity of organic compounds in general. Therefore, desymmetrization reactions in aqueous media are expected to offer versatile strategies for the synthesis of a variety of significant organic compounds. This review focuses on the recent progress of desymmetrization reactions of symmetric organic compounds in aqueous media without utilizing enzymes.


Crystals ◽  
2021 ◽  
Vol 11 (1) ◽  
pp. 62
Author(s):  
Xu Xu ◽  
Zeping Zhang ◽  
Wenjuan Yao

Graphene and graphene oxide (GO) usually have grain boundaries (GBs) in the process of synthesis and preparation. Here, we “attach” GBs into GO, a new molecular configuration i.e., polycrystalline graphene oxide (PGO) is proposed. This paper aims to provide an insight into the stability and mechanical properties of PGO by using the molecular dynamics method. For this purpose, the “bottom-up” multi-structure-spatial design performance of PGO and the physical mechanism associated with the spatial structure in mixed dimensions (combination of sp2 and sp3) were studied. Also, the effect of defect coupling (GBs and functional groups) on the mechanical properties was revealed. Our results demonstrate that the existence of the GBs reduces the mechanical properties of PGO and show an “induction” role during the tensile fracture process. The presence of functional groups converts in-plane sp2 carbon atoms into out-of-plane sp3 hybrid carbons, causing uneven stress distribution. Moreover, the mechanical characteristics of PGO are very sensitive to the oxygen content of functional groups, which decrease with the increase of oxygen content. The weakening degree of epoxy groups is slightly greater than that of hydroxyl groups. Finally, we find that the mechanical properties of PGO will fall to the lowest values due to the defect coupling amplification mechanism when the functional groups are distributed at GBs.


Molecules ◽  
2021 ◽  
Vol 26 (6) ◽  
pp. 1711
Author(s):  
Mohamed Ahmed Khaireh ◽  
Marie Angot ◽  
Clara Cilindre ◽  
Gérard Liger-Belair ◽  
David A. Bonhommeau

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.


Sign in / Sign up

Export Citation Format

Share Document