Unconventional Secondary Structure Mimics: Ladder-Rungs

Secondary structures tend to be recognizable because they have repeating structural motifs, but mimicry of these does not have to follow such well-defined patterns. Bioinformatics studies to match side-chain orientations of a novel hydantoin triazole chemotype ( 1 ) to protein-protein interfaces revealed it tends to align well across parallel and antiparallel sheets, like rungs on a ladder. One set of these overlays was observed for the protein-protein interaction uPA⋅uPAR. Consequently, chemotype 1 was made with appropriate side-chains to mimic uPA at this interface. Biophysical assays indicate these compounds did in fact bind uPAR, and elicit cellular responses that affected invasion, migration, and wound healing.     

Identifying aspirin polymorphs from combined DFT-based crystal structure prediction and solid-state NMR

A combined experimental and computational approach was used to distinguish between different polymorphs of the pharmaceutical drug aspirin. This method involves the use of ab initio random structure searching (AIRSS), a density functional theory (DFT)-based crystal structure prediction method for the high-accuracy prediction of polymorphic structures, with DFT calculations of nuclear magnetic resonance (NMR) parameters and solid-state NMR experiments at natural abundance. AIRSS was used to predict the crystal structures of form-I and form-II of aspirin. The root-mean-square deviation between experimental and calculated ¹H chemical shifts was used to identify form-I as the polymorph present in the experimental sample, the selection being successful despite the large similarities between the molecular environments in the crystals of the two polymorphs.     

Study of Endogen Substrates,Drug Substrates and Inhibitors Binding Conformations on MRP4 and Its Variants by Molecular Docking and Molecular Dynamics

Multidrug resistance protein-4 (MRP4) belongs to the ABC transporter superfamily and promotes the transport of xenobiotics including drugs. A non-synonymous single nucleotide polymorphisms (nsSNPs) in the ABCC4 gene can promote changes in the structure and function of MRP4. In this work, the interaction of certain endogen substrates, drug substrates, and inhibitors with wild type-MRP4 (WT-MRP4) and its variants G187W and Y556C were studied to determine differences in the intermolecular interactions and affinity related to SNPs using protein threading modeling, molecular docking, all-atom, coarse grained, and umbrella sampling molecular dynamics simulations (AA-MDS and CG-MDS, respectively). The results showed that the three MRP4 structures had significantly different conformations at given sites, leading to differences in the docking scores (DS) and binding sites of three different groups of molecules. Folic acid (FA) had the highest variation in DS on G187W concerning WT-MRP4. WT-MRP4, G187W, Y556C, and FA had different conformations through 25 ns AA-MD. Umbrella sampling simulations indicated that the Y556C-FA complex was the most stable one with or without ATP. In Y556C, the cyclic adenosine monophosphate (cAMP) and ceefourin-1 binding sites are located out of the entrance of the inner cavity, which suggests that both cAMP and ceefourin-1 may not be transported. The binding site for cAMP and ceefourin-1 is quite similar and the affinity (binding energy) of ceefourin-1 to WT-MRP4, G187W, and Y556C is greater than the affinity of cAMP, which may suggest that ceefourin-1 works as a competitive inhibitor. In conclusion, the nsSNPs G187W and Y556C lead to changes in protein conformation, which modifies the ligand binding site, DS, and binding energy.     

Doxorubicin Encapsulation in Carbon Nanotubes Having Haeckelite or Stone–Wales Defects as Drug Carriers: A Molecular Dynamics Approach

Doxorubicin (DOX), a recognized anticancer drug, forms stable associations with carbon nanotubes (CNTs). CNTs when properly functionalized have the ability to anchor directly in cancerous tumors where the release of the drug occurs thanks to the tumor slightly acidic pH. Herein, we study the armchair and zigzag CNTs with Stone–Wales (SW) defects to rank their ability to encapsulate DOX by determining the DOX-CNT binding free energies using the MM/PBSA and MM/GBSA methods implemented in AMBER16. We investigate also the chiral CNTs with haeckelite defects. Each haeckelite defect consists of a pair of square and octagonal rings. The armchair and zigzag CNT with SW defects and chiral nanotubes with haeckelite defects predict DOX-CNT interactions that depend on the length of the nanotube, the number of present defects and nitrogen doping. Chiral nanotubes having two haeckelite defects reveal a clear dependence on the nitrogen content with DOX-CNT interaction forces decreasing in the order 0N > 4N > 8N. These results contribute to a further understanding of drug-nanotube interactions and to the design of new drug delivery systems based on CNTs.     

Synthesis,Electronic Properties and WOLED Devices of Planar Phosphorus‐Containing Polycyclic Aromatic Hydrocarbons

We describe the synthesis and the physical properties of polyaromatic hydrocarbons (PAHs) containing a phosphorus atom at the edge. In particular, the impact of the successive addition of aromatic rings on the electronic properties was investigated by experimental (UV/Vis absorption, fluorescence, cyclic voltammetry) and theoretical studies (DFT). The physical properties recorded in solution and in the solid state showed that the P‐containing PAHs exhibit properties expected for an emitter in white organic light‐emitting diodes (WOLEDs).     

Second-order random wave solutions for interfacial internal waves in N-layer density-stratified fluid

This paper studies the random internal wave equations describing the density interface displacements and the velocity potentials of N-layer stratified fluid contained between two rigid walls at the top and bottom. The density interface displacements and the velocity potentials were solved to the second-order by an expansion approach used by Longuet-Higgins （1963） and Dean （1979） in the study of random surface waves and by Song （2004） in the study of second- order random wave solutions for internal waves in a two-layer fluid. The obtained results indicate that the first-order solutions are a linear superposition of many wave components with different amplitudes, wave numbers and frequencies, and that the amplitudes of first-order wave components with the same wave numbers and frequencies between the adjacent density interfaces are modulated by each other. They also show that the second-order solutions consist of two parts： the first one is the first-order solutions, and the second one is the solutions of the second-order asymptotic equations, which describe the second-order nonlinear modification and the second-order wave-wave interactions not only among the wave components on same density interfaces but also among the wave components between the adjacent density interfaces. Both the first-order and second-order solutions depend on the density and depth of each layer. It is also deduced that the results of the present work include those derived by Song （2004） for second-order random wave solutions for internal waves in a two-layer fluid as a particular case.     

On a stochastic nonlinear equation in one-dimensional viscoelasticity

In this paper we discuss an initial-boundary value problem for a stochastic nonlinear equation arising in one-dimensional viscoelasticity. We propose to use a new direct method to obtain a solution. This method is expected to be applicable to a broad class of nonlinear stochastic partial differential equations.

     

Zone specificity in low energy electron stimulated desorption of Cl from reconstructed Si(1 1 1)-7 × 7:Cl surfaces

Diffraction in electron stimulated desorption has revealed a propensity for Cl⁺ desorption from rest atom vs. adatom areas and unfaulted vs. faulted zones of Cl-terminated Si(1 1 1)-(7 × 7) surfaces. We associate the 15 eV ± 1 eV threshold with ionization of Si-Cl σ-bonding surface states and formation of screened two-hole states with Si 3s character. Similar specificity is observed from A and B reconstructions. This can be due to reduced screening in unfaulted regions and increased hole localization in Si back-bonds within faulted regions.