Methanol Interactions with Nopinone Surfaces during Phase Evolution

Organic-organic interactions play important roles in the secondary organic aerosol formation, but the interactions are complex and poorly understood. Here we use environmental molecular beam experiments combined with molecular dynamics simulations to investigate the interactions between methanol and nopinone, as atmospheric organic proxies. In the experiments, methanol monomers and clusters are sent to collide with three types of surfaces, i.e., graphite, thin nopinone coating on graphite and multilayer surfaces, at temperatures between 140 K and 230 K. Methanol monomers are efficiently scattered from the graphite surface, whereas the scattering is substantially suppressed from nopinone surfaces. The desorption from the three surfaces is similar, suggesting that all the surfaces have weak or similar influences on the methanol desorption. The molecular dynamics results show that upon collisions the methanol clusters shatter, and the shattered fragments quickly diffuse and recombine to clusters. The desorption involves a series of processes, including detaching from clusters and desorbing as monomers. The experimental results also show that all trapped methanol molecules completely desorb within a short experimental time scale at temperatures of 180 K and above. At lower temperatures, the desorption rate decreases, and a long experimental time scale is used to resolve the desorption, where three desorption components are identified. The fast component is beyond the experimental detection limit. The intermediate component exhibits multi-step desorption character and has an activation energy of Ea = 0.18 ± 0.03 eV, in good agreement with simulation results. The slow desorption component is related to diffusion processes due to the weak temperature dependence.

Achilles: A Tool for Contact Angle Estimation from Molecular Dynamics Simulations

In this work, a tool for estimating the contact angle from the molecular dynamics simulations is developed and presented. The tool (Achilles) can detect water droplet on hydrophobic and hydrophilic surfaces. The tool can reconstruct the droplets broken across the periodic boundaries. Further a neighbor density based accurate filter is used to find the droplet liquid vapor interface and a circle is fitted using it after removing the dense layers of water next to solid surface. This fitted circle is solved for contact angle and results are outputted in the form of graphical images and text. The entire content of the internal computations of the tool is broken down into 4 phases and users can monitor the outcomes at every phase through output images. The tool is tested using sample molecular dynamics results of water droplet on hydrophobic and hydrophilic surfaces. We believe this tool can be a good addition to the molecular dynamics simulation community who work on the interfacial physics, droplet evaporation, super hydrophobic surfaces, and wettability etc.

Relative entropy of freely cooling granular gases. A molecular dynamics study

Whereas the original Boltzmann’s H-theorem applies to elastic collisions, its rigorous generalization to the inelastic case is still lacking. Nonetheless, it has been conjectured in the literature that the relative entropy of the velocity distribution function with respect to the homogeneous cooling state (HCS) represents an adequate nonequilibrium entropy-like functional for an isolated freely cooling granular gas. In this work, we present molecular dynamics results reinforcing this conjecture and rejecting the choice of the Maxwellian over the HCS as a reference distribution. These results are qualitatively predicted by a simplified theoretical toy model. Additionally, a Maxwell-demon-like velocity-inversion simulation experiment highlights the microscopic irreversibility of the granular gas dynamics, monitored by the relative entropy, where a short “anti-kinetic” transient regime appears for nearly elastic collisions only.

Secondary Metabolites from Caulerpa Cylindracea (Sonder) Could Be Alternative Natural Antiviral Compounds for COVID-19: A Further in Silico Proof

<p>SARS-CoV-2 has been exhibiting extremely spreading property all around the world since its existence from Wuhan-China in December-2019. Although it has caused a death toll of over than 1.3 M people, no validated vaccine has been proposed yet. On the other hand, very dense studies on the vaccine development have been carrying out in some countries such as the US, Germany, UK, China and Russia. Due to side effects of current antiviral agents used in the therapy of COVID-19, there is a great need for the development of alternative compounds for this disease. Caulerpin (CPN) and caulerpenyne (CYN), predominant natural secondary metabolites from invasive marine green algae <i>Caulerpa cylindracea,</i>are proposed to neutralize the virus from two targets: spike protein (5XLR) and main protease (6YB7) in this study. The results show that the binding energies related to CPN-6YB7 and CYN-6YB7 interactions are found to be -8.02 kcal/mol and -6.83 kcal/mol, respectively. The binding energies were -9.68 kcal/mol and -7.53 kcal/mol, respectively, for CPN-5XLR and CYN-5XLR. In the molecular dynamics results, RMSD values show that CPN and CYN can form stable complexes with the proteins where CYN is more stable with 6YB7 and CPN interacts better with 5XLR. These differences seem to be based on the type of interactions of the complexes. In conclusion, caulerpin and caulerpenyne can further be investigated experimentally for their anti-SARS-CoV-2 efficiency. </p>

Secondary Metabolites from Caulerpa Cylindracea (Sonder) Could Be Alternative Natural Antiviral Compounds for COVID-19: A Further in Silico Proof

<p>SARS-CoV-2 has been exhibiting extremely spreading property all around the world since its existence from Wuhan-China in December-2019. Although it has caused a death toll of over than 1.3 M people, no validated vaccine has been proposed yet. On the other hand, very dense studies on the vaccine development have been carrying out in some countries such as the US, Germany, UK, China and Russia. Due to side effects of current antiviral agents used in the therapy of COVID-19, there is a great need for the development of alternative compounds for this disease. Caulerpin (CPN) and caulerpenyne (CYN), predominant natural secondary metabolites from invasive marine green algae <i>Caulerpa cylindracea,</i>are proposed to neutralize the virus from two targets: spike protein (5XLR) and main protease (6YB7) in this study. The results show that the binding energies related to CPN-6YB7 and CYN-6YB7 interactions are found to be -8.02 kcal/mol and -6.83 kcal/mol, respectively. The binding energies were -9.68 kcal/mol and -7.53 kcal/mol, respectively, for CPN-5XLR and CYN-5XLR. In the molecular dynamics results, RMSD values show that CPN and CYN can form stable complexes with the proteins where CYN is more stable with 6YB7 and CPN interacts better with 5XLR. These differences seem to be based on the type of interactions of the complexes. In conclusion, caulerpin and caulerpenyne can further be investigated experimentally for their anti-SARS-CoV-2 efficiency. </p>

Secondary Metabolites from Caulerpa Cylindracea (Sonder) Could Be Alternative Natural Antiviral Compounds for COVID-19: A Further in Silico Proof

<p>SARS-CoV-2 has been exhibiting extremely spreading property all around the world since its existence from Wuhan-China in December-2019. Although it has caused a death toll of over than 1.3 M people, no validated vaccine has been proposed yet. On the other hand, very dense studies on the vaccine development have been carrying out in some countries such as the US, Germany, UK, China and Russia. Due to side effects of current antiviral agents used in the therapy of COVID-19, there is a great need for the development of alternative compounds for this disease. Caulerpin (CPN) and caulerpenyne (CYN), predominant natural secondary metabolites from invasive marine green algae <i>Caulerpa cylindracea,</i>are proposed to neutralize the virus from two targets: spike protein (5XLR) and main protease (6YB7) in this study. The results show that the binding energies related to CPN-6YB7 and CYN-6YB7 interactions are found to be -8.02 kcal/mol and -6.83 kcal/mol, respectively. The binding energies were -9.68 kcal/mol and -7.53 kcal/mol, respectively, for CPN-5XLR and CYN-5XLR. In the molecular dynamics results, RMSD values show that CPN and CYN can form stable complexes with the proteins where CYN is more stable with 6YB7 and CPN interacts better with 5XLR. These differences seem to be based on the type of interactions of the complexes. In conclusion, caulerpin and caulerpenyne can further be investigated experimentally for their anti-SARS-CoV-2 efficiency. </p>

Enhanced heterogenous hydration of SO 2 through immobilization of pyridinic-N on carbon materials

Carbon materials doped with nitrogen have long been used for SO 2 removal from flue gases for the benefits of the environment. The role of water is generally regarded as hydration of SO 3 which is formed through the oxidization of SO 2 . However, the hydration of SO 2 , especially on the surface of N-doped carbon materials, was almost ignored. In this study, the hydration of SO 2 was investigated in detail on the pyridinic nitrogen (PyN)-doped graphene (GP) surfaces. It is found that, compared with the homogeneous hydration of SO 2 assisted with NH 3 in gas phase, the heterogeneous hydration is much more thermodynamically and kinetically favourable. Specifically, when a single H 2 O molecule is involved, the energy barrier for SO 2 hydration is as low as 0.15 eV, with 0.59 eV released, indicating the hydration of SO 2 can occur at rather low water concentration and temperature. Thermodynamic integration molecular dynamics results show the feasibility of the hydrogenated substrate recovery and the immobilized N acting as a catalytic site for SO 2 hydration. Our findings show that the heterogeneous hydration of SO 2 should be universal and potentially uncover the puzzling reaction mechanism for SO 2 catalytic oxidation at low temperature by N-doped carbon materials.

How machine learning can assist the interpretation of ab initio molecular dynamics simulations and conceptual understanding of chemistry

Machine learning models, trained to reproduce molecular dynamics results, help interpreting simulations and extracting new understanding of chemistry.

Размерная зависимость температуры плавления наночастиц кремния: молекулярно-динамическое и термодинамическое моделирование

Size dependence of the melting temperature of Si nanoparticles has been investigated combining molecular dynamics and thermodynamic simulation based on Thomson’s formula. The results of the atomistic simulation obtained by using the Stillinger-Weber potential agree with the results of other authors and with the thermodynamic simulation results predicting that the melting temperature T_m of Si nanoparticles diminishes under increasing their reciprocal radius R^(-1) following to the linear law. The available experimental data predict much lower values of T_m, including underestimated values of the limiting value T_m^((∞)) found by means of the linear extrapolation of experimental dots to R^(-1)→0 (i.e. to the particle radius R→∞), and the underestimation of T_m^((∞)) ranges from 200 to 300 K in comparison with the melting point 1688 K of the bulk crystalline Si. Taking into account the results obtained and their comparison with available results of other authors, a conclusion is made that molecular dynamics results, obtained by using the Stillinger-Weber potential, should be more adequate than the available experimental data on the melting temperature of Si nanoparticles.

Flavonoids as Putative epi-modulators: Insights into their Binding Mode with BRD4 Bromodomain using Molecular Docking and Dynamics.

Flavonoids are widely recognized as natural polydrugs, given their anti-inflammatory, antioxidant, sedative and antineoplastic activities. Recently, different studies have shown that flavonoid have the potential to inhibit BET bromodomains. Previous reports suggest that flavonoids are putative inhibitors of the ZA channel due to their orientation and interactions with P86, V87, L92, L94 and N140. Herein, a comprehensive characterization of the binding mode of the biflavonoid amentoflavone and fisetin is discussed. To this end, both compounds were docked with BRD4 using four docking programs. Results were post-processed with protein-ligand interaction fingerprints. To gain further insights into the binding mode of the two natural products, docking results were further analyzed with molecular dynamics. Results showed that amentoflavone makes numerous contacts in the ZA channel, as previously described for flavonoids and kinase inhibitors. It was also found that amentoflavone can potentially make contacts with non-canonical residues for BET inhibition. Most of these contacts were not observed with fisetin. Based on these results, amentoflavone was tested for BRD4 inhibition, showing activity in the micromolar range. This work may serve as basis for scaffold optimization and further characterization of flavonoids as BET inhibitors.