Computational Insights into the Allosteric Effect and Dynamic Structural Features of the SARS-COV-2 Spike Protein

COVID-19 caused by SARS-COV-2 is continuing to surge globally. The spike (S) protein is the key protein of SARS-COV-2 that recognizes and binds to the host target ACE2. In this study, molecular dynamics simulation was used to elucidate the allosteric effect of the S protein. Binding of ACE2 caused a centripetal movement of the receptor-binding domain of the S protein. The dihedral changes in Phe329 and Phe515 played a key role in this process. Two potential cleavage sites S1/S2 and S2′ were exposed on the surface after the binding of ACE2. The binding affinity of SARS-COV-2 S protein and ACE2 was higher than that of SARS-COV. This was mainly due to the mutation of Asp480 in SARS-COV to Ser494 in SARS-COV-2, which greatly weakened the electrostatic repulsion. The result provides a theoretical basis for the SARS-COV-2 infection and aids the development of biosensors and detection reagents.     

Cycloparaphenylene and their radicals anchored to a metal−organic framework

Cycloparaphenylene (CPP) shows modulated photophysical and electronic properties due to its strained structure and radially oriented π-electron system. Incorporation of CPP into metal-organic frameworks (MOFs) could transfer its extensive properties in solution to porous solids. Moreover, with the unique arrangement of the macrocycles and their interactions with the framework, emerging characteristics are anticipated. As an example of “robust dynamics”, we synthesized the first MOF structure (FDM-1001) with CPP precisely anchored to the ordered framework by employing a [8]CPP-containing linear dicarboxylate linker. Metric relationship between the dynamic macrocycles and the robust backbone creates ideal π-π interactions between them, which leads to an essentially directional arrangement of [8]CPP in the three-dimensional space. Furthermore, the MOF with [8]CPP could be successfully oxidized to generate an infinite array of radicals that show enhanced air stability compared to its molecular analogue.     

Molecular dynamic study of dielectric polarization and ferroelectricity in a model polar polymer

Molecular dynamics simulations are used to explore the polarization response of a lamellar crystal consisting of folded chains of a highly simplified model polar polymer. The system is based on a united atom model of polyethylene with constrained bond lengths and bond angles, and it is endowed with artificial partial charges placed on the united atoms to give it a simple polar character. Simulations performed with various temperatures, electric field directions, and electric field application histories reveal a complicated sequence of reorientation processes, including pronounced ferroelectric behavior. The sequence includes a weak, temperature‐independent prompt response, and a slow‐rising delay regime with stretched exponential behavior and thermally‐activated reorientation parameters consistent with trans‐gauche (TG) barrier crossings in the amorphous phase. When the delay regime has progressed sufficiently, a primary large‐amplitude response due to organized rotation of large subsegments in the crystalline phase occurs in a rapid manner that requires relatively few TG barrier crossings. A final, extremely slow rise in residual polarization completes the sequence. © 2015 Wiley Periodicals, Inc. J. Polym. Sci., Part B: Polym. Phys. 2015 , 53, 740–759     

Composition-dependent melting behaviour of NaxK55–x core–shell nanoalloys

Molecular dynamics simulations at constant temperature are performed to investigate melting-like transition in Na₁₃K₄₂, Na₁₉K₃₆ and Na₂₆K₂₉ nanoalloys using a second-moment-approximation tight-binding analytic potential to calculate the forces on the constituent atoms. A weighted histogram analysis method is employed to remove non-ergodicity issues due to the complex potential energy surface of these nanoalloys. The heat capacity shows three distinctive steps in melting for Na₁₃K₄₂, while Na₂₆K₂₉ and Na₁₉K₃₆ have two-step and one-step melting transition, respectively. The steepest descent method is used to quench the configurations in a given interval during the simulation and also study the isomerisation processes occurring at different temperatures. Analysing the configuration energies of quenched structures for the entire nanoalloy and the core atoms separately gives more details about the melting mechanism. The Lindemann parameter is also calculated at several temperatures during the simulation which shows a gradual increase for Na₁₃K₄₂ and Na₂₆K₂₉ while a sharp change is observed for Na₁₉K₃₆. These findings are in agreement with the multi-step nature of the phase transition in Na₁₃K₄₂ and Na₂₆K₂₉ and one-step melting of the Na₁₉K₃₆ magic composition.     

High‐order ADER‐WENO ALE schemes on unstructured triangular meshes—application of several node solvers to hydrodynamics and magnetohydrodynamics

In this paper, we present a class of high‐order accurate cell‐centered arbitrary Lagrangian–Eulerian (ALE) one‐step ADER weighted essentially non‐oscillatory (WENO) finite volume schemes for the solution of nonlinear hyperbolic conservation laws on two‐dimensional unstructured triangular meshes. High order of accuracy in space is achieved by a WENO reconstruction algorithm, while a local space–time Galerkin predictor allows the schemes to be high order accurate also in time by using an element‐local weak formulation of the governing PDE on moving meshes. The mesh motion can be computed by choosing among three different node solvers, which are for the first time compared with each other in this article: the node velocity may be obtained either (i) as an arithmetic average among the states surrounding the node, as suggested by Cheng and Shu, or (ii) as a solution of multiple one‐dimensional half‐Riemann problems around a vertex, as suggested by Maire, or (iii) by solving approximately a multidimensional Riemann problem around each vertex of the mesh using the genuinely multidimensional Harten–Lax–van Leer Riemann solver recently proposed by Balsara et al. Once the vertex velocity and thus the new node location have been determined by the node solver, the local mesh motion is then constructed by straight edges connecting the vertex positions at the old time level tⁿ with the new ones at the next time level t^{n + 1}. If necessary, a rezoning step can be introduced here to overcome mesh tangling or highly deformed elements. The final ALE finite volume scheme is based directly on a space–time conservation formulation of the governing PDE system, which therefore makes an additional remapping stage unnecessary, as the ALE fluxes already properly take into account the rezoned geometry. In this sense, our scheme falls into the category of direct ALE methods. Furthermore, the geometric conservation law is satisfied by the scheme by construction. We apply the high‐order algorithm presented in this paper to the Euler equations of compressible gas dynamics as well as to the ideal classical and relativistic magnetohydrodynamic equations. We show numerical convergence results up to fifth order of accuracy in space and time together with some classical numerical test problems for each hyperbolic system under consideration. Copyright © 2014 John Wiley & Sons, Ltd.     

How Does Solvation Affect the Binding of Hydrophilic Amino Saccharides to Cucurbit[7]uril with Exceptional Anomeric Selectivity?

Cucurbit[7]uril (CB[7]) is known to bind strongly to hydrophilic amino saccharide guests with exceptional α‐anomer selectivities under aqueous conditions. Single‐crystal X‐ray crystallography and computational methods were used to elucidate the reason behind this interesting phenomenon. The crystal structures of protonated galactosamine (GalN) and glucosamine (GluN) complexes confirm the inclusion of α anomers inside CB[7] and disclose the details of the host–guest binding. Whereas computed gas‐phase structures agree with these crystal structures, gas‐phase binding free energies show preferences for the β‐anomer complexes over their α counterparts, in striking contrast to the experimental results under aqueous conditions. However, when the solvation effect is considered, the binding structures drastically change and the preference for the α anomers is recovered. The α anomers also tend to bind more tightly and leave less space in the CB[7] cavity toward inclusion of only one water molecule, whereas loosely bound β anomers leave more space toward accommodating two water molecules, with markedly different hydrogen‐bonding natures. Surprisingly, entropy seems to contribute significantly to both anomeric discrimination and binding. This suggests that of all the driving factors for the strong complexation of the hydrophilic amino saccharide guests, water mediation plays a crucial role in the anomer discrimination.     

Molecular dynamics simulation of poly(3‐hexylthiophene) helical structure In Vacuo and in amorphous polymer surrounding

The stability of poly(3‐hexylthiophene) (P3HT) helical structure has been investigated in vacuo and in amorphous polymer surrounding via molecular dynamics‐based simulations at temperatures below and above the P3HT melting point. The results show that the helical chain remains stable at room temperature both in vacuo and in amorphous surrounding, and promptly loses its structure at elevated temperatures. However, the amorphous surrounding inhibits the destruction of the helix at higher temperatures. In addition, it is shown that the electrostatic interactions do not significantly affect the stability of the helical structure. © 2016 Wiley Periodicals, Inc. J. Polym. Sci., Part B: Polym. Phys. 2016 , 54, 2448–2456     

Capturing Transient Endoperoxide in the Singlet Oxygen Oxidation of Guanine

The chemistry of singlet O₂ toward the guanine base of DNA is highly relevant to DNA lesion, mutation, cell death, and pathological conditions. This oxidative damage is initiated by the formation of a transient endoperoxide through the Diels–Alder cycloaddition of singlet O₂ to the guanine imidazole ring. However, no endoperoxide formation was directly detected in native guanine or guanosine, even at ?100 °C. Herein, gas‐phase ion–molecule scattering mass spectrometry was utilized to capture unstable endoperoxides in the collisions of hydrated guanine ions (protonated or deprotonated) with singlet O₂ at ambient temperature. Corroborated by results from potential energy surface exploration, kinetic modeling, and dynamics simulations, various aspects of endoperoxide formation and transformation (including its dependence on guanine ionization and hydration states, as well as on collision energy) were determined. This work has pieced together reaction mechanisms, kinetics, and dynamics data concerning the early stage of singlet O₂ induced guanine oxidation, which is missing from conventional condensed‐phase studies.     

Molecular dynamics simulations of monodisperse/bidisperse polymer melt crystallization

We use large scale coarse‐grained molecular dynamics simulations to study the kinetics of polymer melt crystallization. For monodisperse polymer melts of several chain lengths under various cooling protocols, we show that short chains have a higher terminal crystallinity value compared to longer ones. They align at the early stages and then cease evolving. Long chains, however, align, fold into lamella structures and then slowly optimize their dangling ends for the remaining simulation time. We then identify the mechanism behind bidisperse blend crystallization. To this end, we introduce a new algorithm (called Individual Chain Crystallinity) that allows the calculation of the crystallinity separately for short and long chains in the blend. We find that, in general, bidispersity hinders crystallization significantly. At first the crystallinity of the long chain components exceeds that of the monodisperse melt, but subsequently falls below the corresponding monodisperse melt curve after a certain “crossover time.” The time of the crossover can be attributed to the time required for the full crystallization of the short chains. This indicates that at the early stages the short chains are helping long chains to crystallize. However, after all short chains have crystallized they start to hinder the crystallization of the long chains by obstructing their motion. Lastly, polymer crystallization upon various thermodynamic protocols is studied. Slower cooling is found to increase the crystallinity value. Upon an instantaneous deep quench and subsequent isothermal relaxation, the crystallinity grows rapidly with time at early stages and subsequently saturates. © 2016 Wiley Periodicals, Inc. J. Polym. Sci., Part B: Polym. Phys. 2016 , 54, 2318–2326     

Mechanical properties and thermal conductivity of the twisted graphene nanoribbons

Molecular dynamics method was used to simulate the twists of four GNRs (graphene nanoribbons), two AGNRs (armchair GNRs), and two ZGNRs (zigzag GNRs). Thermal conductivity of the length-fixing GNRs under torsion and at high temperature was calculated. It is found that the ZGNRs have better torsional rigidity than the AGNRs; under the torsional deformation of 34.2°/nm local buckling occurs in the length-fixing GNRs, and under the deformation of 22.8°/nm overall buckling occurs in the ones with free-length. In the range of investigated twist-angle and temperature, the thermal conductivity of the length-fixing GNRs decreases with the increase of torsional deformation and temperature. The wider GNRs have better anti-torsion capability and thermal conductivity.