The reactions between SO.sub.3 and atmospheric acids are indispensable in improving the formation of aerosol particles. However, relative to those of SO.sub.3 with organic acids, the reaction of ...SO.sub.3 with inorganic acids has not received much attention. Here, we explore the atmospheric reaction between SO.sub.3 and H.sub.2 SO.sub.4, a typical inorganic acid, in the gas phase and at the air-water interface using quantum chemical (QC) calculations and Born-Oppenheimer molecular dynamics simulations. We also report the effect of H.sub.2 S.sub.2 O.sub.7, the product of the reaction between SO.sub.3 and H.sub.2 SO.sub.4, on new particle formation (NPF) in various environments using the Atmospheric Cluster Dynamics Code (ACDC) kinetic model and QC calculations. The present findings show that the gas-phase reactions of SO.sub.3 + H.sub.2 SO.sub.4 without and with water molecules are both low-energy-barrier processes. With the involvement of interfacial water molecules, H.sub.2 O induced the formation of the S2O72-â¯H3O+ ion pair, HSO4- mediated the formation of the HSO4-â¯H3O+ ion pair, and the deprotonation of H.sub.2 S.sub.2 O.sub.7 was observed and proceeded on the picosecond timescale. The present findings suggest the potential contribution of the SO.sub.3 -H.sub.2 SO.sub.4 reaction to NPF and aerosol particle growth, showing that (i) although H.sub.2 S.sub.2 O.sub.7 is easily hydrolyzed with water to form H.sub.2 SO.sub.4, it can directly participate in H.sub.2 SO.sub.4 -NH.sub.3 -based cluster formation and can present a more obvious enhancement effect on SA-A-based cluster formation, and (ii) the formed interfacial S2O72- can attract candidate species from the gas phase to the water surface and, thus, accelerate particle growth.
The relationship between structure and reactivity plays a dominant role in water dissociation on the various TiOsub.2 crystallines. To observe the adsorption and dissociation behavior of Hsub.2O, the ...reaction force field (ReaxFF) is used to investigate the dynamic behavior of Hsub.2O on rutile (110) and anatase (101) surfaces in an aqueous environment. Simulation results show that there is a direct proton transfer between the adsorbed Hsub.2O (Hsub.2Osub.ad) and the bridging oxygen (Osub.br) on the rutile (110) surface. Compared with that on the rutile (110) surface, an indirect proton transfer occurs on the anatase (101) surface along the H-bond network from the second layer of water. This different mechanism of water dissociation is determined by the distance between the 5-fold coordinated Ti (Tisub.5c) and Osub.br of the rutile and anatase TiOsub.2 surfaces, resulting in the direct or indirect proton transfer. Additionally, the hydrogen bond (H-bond) network plays a crucial role in the adsorption and dissociation of Hsub.2O on the TiOsub.2 surface. To describe interfacial water structures between TiOsub.2 and bulk water, the double-layer model is proposed. The first layer is the dissociated Hsub.2O on the rutile (110) and anatase (101) surfaces. The second layer forms an ordered water structure adsorbed to the surface Osub.br or terminal OH group through strong hydrogen bonding (H-bonding). Affected by the H-bond network, the Hsub.2O dissociation on the rutile (110) surface is inhibited but that on the anatase (101) surface is promoted.
Featured Cover Vlassis, Nikolaos N.; Zhao, Puhan; Ma, Ran ...
International journal for numerical methods in engineering,
09/2022, Letnik:
123, Številka:
17
Journal Article
Recenzirano
Odprti dostop
The cover image is based on the Original Article Molecular dynamics inferred transfer learning models for finite‐strain hyperelasticity of monoclinic crystals: Sobolev training and validations ...against physical constraints by Nikolaos Vlassis et al., https://doi.org/10.1002/nme.6992.
Since the first attempts at structure-based drug design about four decades ago, molecular modelling techniques for drug design have developed enormously, along with the increasing computational power ...and structural and biological information of active compounds and potential target molecules. Nowadays, molecular modeling can be considered to be an integral component of the modern drug discovery and development toolbox. Nevertheless, there are still many methodological challenges to be overcome in the application of molecular modeling approaches to drug discovery. The eight original research and five review articles collected in this book provide a snapshot of the state-of-the-art of molecular modeling in drug design, illustrating recent advances and critically discussing important challenges. The topics covered include virtual screening and pharmacophore modelling, chemoinformatic applications of artificial intelligence and machine learning, molecular dynamics simulation and enhanced sampling to investigate contributions of molecular flexibility to drug–receptor interactions, the modeling of drug–receptor solvation, hydrogen bonding and polarization, and drug design against protein–protein interfaces and membrane protein receptors.
The inclusion complexes of cucurbitnuril, CBn (n = 6–8), with poly aromatic hydrocarbon (PAH) Benzo(a)Pyrene (BaP), and fluoranthene (FLT) were investigated carefully in aqueous media. Fluorescence ...and sup.1H NMR spectroscopy were used to characterize and investigate the inclusion complexes that were prepared in the aqueous media. The most predominant complexes of both guests with hosts were the 1:1 guest: host complexes. Stability constants of 2322 ± 547 Msup.−1, 7281 ± 689 Msup.−1, 3566 ± 473 Msup.−1 were obtained for the complexes of BaP with CB6, CB7, and CB8, respectively. On the other hand, stability constants of 5900.270 ± 326 Msup.−1, 726.87 ± 78 Msup.−1, 3327.059 ± 153 Msup.−1 were obtained for the complexes of FLT with CB6, CB7, and CB8, respectively. Molecular dynamic (MD) simulations were used to study the mode and mechanism of the inclusion process and to monitor the stability of these complexes in aqueous media at an atomistic level. Analysis of MD trajectories has shown that both BaP and FLT form stable inclusion complexes with CB7 and CB8 in aqueous media throughout the simulation time, subsequently corroborating the experimental results. Nevertheless, the small size of CB6 prohibited the encapsulation of the two PAHs inside the cavity, but stable exclusion complex was observed between them. The main driving forces for the stability of these complexes are the hydrophobic forces, van der Waals interactions, electrostatic effect, the π····π and C–H···π interaction. These results suggest that BaP and FLT can form stable complexes with CBn (n = 6–8) in solution.
Ab initio molecular dynamics revolutionized the field of realistic computer simulation of complex molecular systems and processes, including chemical reactions, by unifying molecular dynamics and ...electronic structure theory. This book provides the first coherent presentation of this rapidly growing field, covering a vast range of methods and their applications, from basic theory to advanced methods. This fascinating text for graduate students and researchers contains systematic derivations of various ab initio molecular dynamics techniques to enable readers to understand and assess the merits and drawbacks of commonly used methods. It also discusses the special features of the widely used Car–Parrinello approach, correcting various misconceptions currently found in research literature. The book contains pseudo-code and program layout for typical plane wave electronic structure codes, allowing newcomers to the field to understand commonly used program packages and enabling developers to improve and add new features in their code.
How to fabricate large area controllable surface-enhanced Raman scattering (SERS) active nanostructure substrates has always been one of the important issues in the development of nanostructure ...devices. In this paper, nano-etching technology and magnetron sputtering technology are combined to prepare nanostructure substrate with evolvable structure, and Ag/TiOsub.2/Ag composites are introduced into the evolvable composite structure. The activity of SERS is further enhanced by the combination of TiOsub.2 and Ag and the electron transfer characteristics of TiOsub.2 itself. Deposition, plasma etching, and transfer are carried out on self-assembled 200 nm polystyrene (PS) colloidal sphere arrays. Due to the shadow effect between colloidal spheres and the size of metal particles introduced by deposition, a series of Ag/TiOsub.2/Ag nanostructure arrays with adjustable nanostructure substrates such as nano-cap (NC), nano cap-star (NCS), and nano particle-disk (NPD) can be obtained. These nanoarrays with rough surfaces and different evolutionary structures can uninterruptedly regulate optical plasmon resonance and reconstruct SERS hotspots over a large range, which has potential application value in surface science, chemical detection, nanometer photonics, and so on.
The results of dielectric relaxation spectroscopy of the chiral liquid crystal 4′-butyl-4-(2-methylbutoxy)azoxybenzene in the crystal phase are presented. The scaling procedure showed complex ...molecular dynamics and allows one to decompose the observed relaxation process into two closely located relaxation processes around the short molecular axis. Temperature dependences of relaxation times characterizing flip-flop motions (rotation around the short molecular axis) and rotation around the long molecular axis are of the Arrhenius type.
Micro-Exon Genes are a widespread class of genes known for their high variability, widespread in the genome of parasitic trematodes such as Schistosoma mansoni. In this study, we present a strategy ...that allowed us to solve the structures of three alternatively spliced isoforms from the Schistoma mansoni MEG 2.1 family for the first time. All isoforms are hydrophobic, intrinsically disordered, and recalcitrant to be expressed in high yield in heterologous hosts. We resorted to the chemical synthesis of shorter pieces, before reconstructing the entire sequence. Here, we show that isoform 1 partially folds in a-helix in the presence of trifluoroethanol while isoform 2 features two rigid elbows, that maintain the peptide as disordered, preventing any structuring. Finally, isoform 3 is dominated by the signal peptide, which folds into a-helix. We demonstrated that combining biophysical techniques, like circular dichroism and nuclear magnetic resonance at natural abundance, with in silico molecular dynamics simulation for isoform 1 only, was the key to solve the structure of MEG 2.1. Our results provide a crucial piece to the puzzle of this elusive and highly variable class of proteins.
Molecular dynamics has emerged as an important research methodology covering systems to the level of millions of atoms. However, insufficient sampling often limits its application. The limitation is ...due to rough energy landscapes, with many local minima separated by high-energy barriers, which govern the biomolecular motion.
In the past few decades methods have been developed that address the sampling problem, such as replica-exchange molecular dynamics, metadynamics and simulated annealing. Here we present an overview over theses sampling methods in an attempt to shed light on which should be selected depending on the type of system property studied.
Enhanced sampling methods have been employed for a broad range of biological systems and the choice of a suitable method is connected to biological and physical characteristics of the system, in particular system size. While metadynamics and replica-exchange molecular dynamics are the most adopted sampling methods to study biomolecular dynamics, simulated annealing is well suited to characterize very flexible systems. The use of annealing methods for a long time was restricted to simulation of small proteins; however, a variant of the method, generalized simulated annealing, can be employed at a relatively low computational cost to large macromolecular complexes.
Molecular dynamics trajectories frequently do not reach all relevant conformational substates, for example those connected with biological function, a problem that can be addressed by employing enhanced sampling algorithms. This article is part of a Special Issue entitled Recent developments of molecular dynamics.
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•Insufficient conformational sampling often limits molecular dynamics applications.•REMD and metadynamics allow a broader exploration of the energy surface.•GSA can be employed for large flexible macromolecular complexes.•GSA shows that a flexible linker in the cellulosome allows two preferential conformations.
![Comparison of H[sub.2]O Ads...](http://api.summon.serialssolutions.com/2.0.0/image/issn/XR4PS5YY4K/1420-3049/small "Comparison of H[sub.2]O Adsorption and Dissociation Behaviors on Rutile Surfaces Based on ReaxFF Molecular Dynamics Simulation")
![Design of Ag/TiO[sub.2]/Ag ...](http://api.summon.serialssolutions.com/2.0.0/image/issn/XR4PS5YY4K/1996-1944/small "Design of Ag/TiO[sub.2]/Ag Composite Nano-Array Structure with Adjustable SERS-Activity")
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