On the interface of organic aerosols: molecular level understanding of surface melting, mixing and water adsorption/desorption dynamics

Author(s):  
Josip Lovrić ◽  
Xiangrui Kong ◽  
Sofia M. Johansson ◽  
Erik S. Thomson ◽  
Jan B. C. Pettersson

<p>The detailed description of organic aerosols surfaces in the atmosphere remains an open issue, which limits our ability to understand and predict environmental change. Important research questions concern the hydrophobic/hydrophilic character of fresh and aged aerosols and the related influence on water uptake in solid, liquid as well in intermediate state.  Also, surface characterization remains big challenge but we find it reachable by conjunction of Molecular Dynamics (MD) simulations and the environmental molecular beam (EMB) experimental method.  A  picture of the detailed molecular-level behavior of water molecules on organic surfaces is beginning to rise based on detailed experimental and theoretical studies; one example is a recent study that investigates water interactions with solid and liquid n-butanol near the melting point [1], another example focus on interaction of water with solid nopinone [2]. From the other side, in order to characterize surface properties during and before melting we employ MD simulations of n-butanol, nopinone and valeric acid. Nopinone (C<sub>9</sub>H<sub>14</sub>O) is a reaction product formed during oxidation of β-pinene and has been found in both the gas and particle phases of atmospheric aerosol. n-butanol (C<sub>4</sub>H<sub>9</sub>OH) is primary alcohol, naturally occurs scarcely and here serves as good representative for alcohols. In the same way valeric acid (CH<sub>3</sub>(CH<sub>2</sub>)<sub>3</sub>COOH) serves as a good representative for a family of carboxylic acids. Valeric acid is, as n-butanol, straight-chain molecule. We show that a classical force field for organic material is able to model crystal and liquid structures. The surface properties near the melting point of the condensed phase are reported, and the hydrophobic and hydrophilic character of the surface layer is discussed.  Overall surface melting dynamic is presented and quantified in the terms of structural and geometrical properties. Mixing of a methanol with the solid nopinone surface is examined and hereby presented.</p><p><strong>References</strong></p><p>[1] Johansson, S. M., Lovrić, J., Kong, X., Thomson, E. S., Papagiannakopoulos, P., Briquez, S., Toubin, C, Pettersson, J. B. C. (2019). Understanding water interactions with organic surfaces: environmental molecular beam and molecular dynamics studies of the water–butanol system. Physical Chemistry Chemical Physics. https://doi.org/10.1039/C8CP04151B   </p><p>[2] Johansson, S. M., Lovrić, J., Kong, X., Thomson, E. S., Hallquist, M., & Pettersson, J. B. C. (2020). Experimental and Computational Study of Molecular Water Interactions with Condensed Nopinone Surfaces Under Atmospherically Relevant Conditions. The Journal of Physical Chemistry A, acs.jpca.9b10970. https://doi.org/10.1021/acs.jpca.9b10970</p><p>Keywords: Molecular Dynamics, organic crystal, organic aerosols, water uptake, surface procesess, molecular level</p>

Author(s):  
Van P. Carey

Nanoscale aspects of interfacial phenomena can be critically import in convective vaporization and condensation in nanochannels or microchannels. Molecular dynamics (MD) simulations have been extensively used to model and explore the physics of interfacial phenomena at the molecular level. Efforts to improve MD simulations have often focused on development of more physically realistic interaction potentials used to model intermolecular force interactions, or on development of more efficient computing strategies. An important, and often overlooked aspect of MD simulations is the role that theoretical models from statistical thermodynamics can play in MD simulations. This paper argues that use of alternate statistical thermodynamics models, and unconventional strategies for using them, can be effective ways of enhancing MD simulations. The advantages of these types of approaches are explored in the context of three recent MD simulation studies of interfacial region thermophysics that have made use of statistical thermodynamics theory in novel ways. Examples considered include studies of the interfacial region between bulk liquid and vapor phases, thin liquid films on solid surfaces, and stability free thin liquid films. These examples illustrate ways that MD simulations can be combined with other models to enhance computational efficiency or extract more information from the MD simulation results. Successful strategies for implementing these types of scheme are examined, and their general applicability is assessed.


2019 ◽  
Vol 116 (7) ◽  
pp. 2452-2457 ◽  
Author(s):  
Liang Zhang ◽  
Jean-François Lemonnier ◽  
Angela Acocella ◽  
Matteo Calvaresi ◽  
Francesco Zerbetto ◽  
...  

Three 819 knots in closed-loop strands of different lengths (∼20, 23, and 26 nm) were used to experimentally assess the consequences of knot tightness at the molecular level. Through the use of 1H NMR, diffusion-ordered spectroscopy (DOSY), circular dichroism (CD), collision-induced dissociation mass spectrometry (CID-MS) and molecular dynamics (MD) simulations on the different-sized knots, we find that the structure, dynamics, and reactivity of the molecular chains are dramatically affected by the tightness of the knotting. The tautness of entanglement causes differences in conformation, enhances the expression of topological chirality, weakens covalent bonds, inhibits decomplexation events, and changes absorption properties. Understanding the effects of tightening nanoscale knots may usefully inform the design of knotted and entangled molecular materials.


2019 ◽  
Vol 12 (608) ◽  
pp. eaax3194 ◽  
Author(s):  
Romana Schober ◽  
Daniel Bonhenry ◽  
Victoria Lunz ◽  
Jinhui Zhu ◽  
Adela Krizova ◽  
...  

The stromal interaction molecule 1 (STIM1) has two important functions, Ca2+ sensing within the endoplasmic reticulum and activation of the store-operated Ca2+ channel Orai1, enabling plasma-membrane Ca2+ influx. We combined molecular dynamics (MD) simulations with live-cell recordings and determined the sequential Ca2+-dependent conformations of the luminal STIM1 domain upon activation. Furthermore, we identified the residues within the canonical and noncanonical EF-hand domains that can bind to multiple Ca2+ ions. In MD simulations, a single Ca2+ ion was sufficient to stabilize the luminal STIM1 complex. Ca2+ store depletion destabilized the two EF hands, triggering disassembly of the hydrophobic cleft that they form together with the stable SAM domain. Point mutations associated with tubular aggregate myopathy or cancer that targeted the canonical EF hand, and the hydrophobic cleft yielded constitutively clustered STIM1, which was associated with activation of Ca2+ entry through Orai1 channels. On the basis of our results, we present a model of STIM1 Ca2+ binding and refine the currently known initial steps of STIM1 activation on a molecular level.


Author(s):  
Inkook Jang ◽  
Pamela L. Dickrell ◽  
David L. Burris ◽  
W. Gregory Sawyer ◽  
Simon R. Phillpot ◽  
...  

Polytetrafluoroethylene (PTFE) is a well known solid lubricant and polymer nanocomposites based on PTFE are considered to be promising materials for tribological applications in space. Like other polymer materials, many properties of PTFE depend on morphology. In this study, molecular dynamics (MD) simulations are performed to examine the effect of chain configuration on the frictional behavior of PTFE at the molecular level and compared to microtribological studies on aligned transfer films of PTFE.


2000 ◽  
Vol 653 ◽  
Author(s):  
Celeste Sagui ◽  
Thoma Darden

AbstractFixed and induced point dipoles have been implemented in the Ewald and Particle-Mesh Ewald (PME) formalisms. During molecular dynamics (MD) the induced dipoles can be propagated along with the atomic positions either by interation to self-consistency at each time step, or by a Car-Parrinello (CP) technique using an extended Lagrangian formalism. The use of PME for electrostatics of fixed charges and induced dipoles together with a CP treatment of dipole propagation in MD simulations leads to a cost overhead of only 33% above that of MD simulations using standard PME with fixed charges, allowing the study of polarizability in largemacromolecular systems.


2020 ◽  
Author(s):  
Matías R. Machado ◽  
Sergio Pantano

<p> Despite the relevance of properly setting ionic concentrations in Molecular Dynamics (MD) simulations, methods or practical rules to set ionic strength are scarce and rarely documented. Based on a recently proposed thermodynamics method we provide an accurate rule of thumb to define the electrolytic content in simulation boxes. Extending the use of good practices in setting up MD systems is promptly needed to ensure reproducibility and consistency in molecular simulations.</p>


2019 ◽  
Vol 16 (3) ◽  
pp. 291-300
Author(s):  
Saumya K. Patel ◽  
Mohd Athar ◽  
Prakash C. Jha ◽  
Vijay M. Khedkar ◽  
Yogesh Jasrai ◽  
...  

Background: Combined in-silico and in-vitro approaches were adopted to investigate the antiplasmodial activity of Catharanthus roseus and Tylophora indica plant extracts as well as their isolated components (vinblastine, vincristine and tylophorine). </P><P> Methods: We employed molecular docking to prioritize phytochemicals from a library of 26 compounds against Plasmodium falciparum multidrug-resistance protein 1 (PfMDR1). Furthermore, Molecular Dynamics (MD) simulations were performed for a duration of 10 ns to estimate the dynamical structural integrity of ligand-receptor complexes. </P><P> Results: The retrieved bioactive compounds viz. tylophorine, vinblastin and vincristine were found to exhibit significant interacting behaviour; as validated by in-vitro studies on chloroquine sensitive (3D7) as well as chloroquine resistant (RKL9) strain. Moreover, they also displayed stable trajectory (RMSD, RMSF) and molecular properties with consistent interaction profile in molecular dynamics simulations. </P><P> Conclusion: We anticipate that the retrieved phytochemicals can serve as the potential hits and presented findings would be helpful for the designing of malarial therapeutics.


Polymers ◽  
2020 ◽  
Vol 13 (1) ◽  
pp. 99
Author(s):  
Cristian Privat ◽  
Sergio Madurga ◽  
Francesc Mas ◽  
Jaime Rubio-Martínez

Solvent pH is an important property that defines the protonation state of the amino acids and, therefore, modulates the interactions and the conformational space of the biochemical systems. Generally, this thermodynamic variable is poorly considered in Molecular Dynamics (MD) simulations. Fortunately, this lack has been overcome by means of the Constant pH Molecular Dynamics (CPHMD) methods in the recent decades. Several studies have reported promising results from these approaches that include pH in simulations but focus on the prediction of the effective pKa of the amino acids. In this work, we want to shed some light on the CPHMD method and its implementation in the AMBER suitcase from a conformational point of view. To achieve this goal, we performed CPHMD and conventional MD (CMD) simulations of six protonatable amino acids in a blocked tripeptide structure to compare the conformational sampling and energy distributions of both methods. The results reveal strengths and weaknesses of the CPHMD method in the implementation of AMBER18 version. The change of the protonation state according to the chemical environment is presumably an improvement in the accuracy of the simulations. However, the simulations of the deprotonated forms are not consistent, which is related to an inaccurate assignment of the partial charges of the backbone atoms in the CPHMD residues. Therefore, we recommend the CPHMD methods of AMBER program but pointing out the need to compare structural properties with experimental data to bring reliability to the conformational sampling of the simulations.


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.


CrystEngComm ◽  
2021 ◽  
Author(s):  
Andrey Sarikov ◽  
Anna Marzegalli ◽  
Luca Barbisan ◽  
Massimo Zimbone ◽  
Corrado Bongiorno ◽  
...  

In this work, annihilation mechanism of stacking faults (SFs) in epitaxial 3C-SiC layers grown on Si(001) substrates is studied by molecular dynamics (MD) simulations. The evolution of SFs located in...


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