Influence of non-protein amino-acid mimosine in peptide conformational propensities from novel Amber force field parameters

Mimosine is a non-protein amino acid derived from plants known for its ability to bind to divalent or trivalent metal cations such as Zn$^{2+}$, Ni$^{2+}$, Fe$^{2+}$ or Al$^{3+}$. This results in interesting antimicrobial and anti-cancer properties, which make mimosine a promising candidate for therapeutic applications. One possibility is to incorporate mimosine into synthetic short peptide drugs. However, our understanding of how this amino acid affects peptide structure is still limited, reducing our ability to design effective therapeutic compounds. In this work, we used computer simulations to understand this question. We first build parameters for the mimosine residue to be used in combination with two classical force fields of the Amber family. Then, we used atomistic molecular dynamics simulations with the resulting parameter sets to evaluate the influence of mimosine in the structural propensities for this amino acid. We compared the results of these simulations with identical peptides where mimosine is replaced by either phenylalanine or tyrosine. We found that the strong dipole in mimosine induces a preference for conformations where the amino acid rings are stacked over more traditional conformations. We validated our results using quantum mechanical calculations, which provide a robust foundation to the outcome of our classical simulations.

Crystalline Forms of Trazodone Dihydrates

In this study, treatment of anhydrous trazodone powder with ammonium carbamate in warm water crystallised two new polymorphs or dihydrates of trazodone after 5 h, whose structures were determined by X-ray single crystal diffraction. Each dihydrate contains infinite zigzag hydrogen-bonded chains of water molecules, which are stabilised by the N4 acceptor atom of the piperazine ring and the pendant carbonyl O1 atom of the triazole ring, as well as other water molecules. The strong dipole moment expected for the O1 atom makes it a good hydrogen bond acceptor for stabilising the chains of water molecules. Each molecule of trazodone has a similar conformation in both hydrates, except for the propyl chains, which adopt different conformations: anti-gauche in the β hydrate (triazole N-C-C-C and C-C-C-piperazine N) and anti-anti in the γ hydrate. Both piperazine rings adopt chair conformations, and the exocyclic N-C bonds are in equatorial orientations. The Hirshfeld surfaces and two-dimensional fingerprint plots for the polymorphs were calculated using CrystalExplorer17, which indicated contacts significantly shorter than the sum of the van der Waals radii in the vicinity of the piperazine N4 and triazole O1 atoms corresponding to the strong hydrogen bonds accepted by these atoms.

Strong Dipole–Quadrupole–Exciton Coupling Realized in a Gold Nanorod Dimer Placed on a Two-Dimensional Material

Simple systems in which strong coupling of different excitations can be easily realized are highly important, not only for fundamental research but also for practical applications. Here, we proposed a T-shaped gold nanorod (GNR) dimer composed of a long GNR and a short GNR perpendicular to each other and revealed that the dark quadrupole mode of the long GNR can be activated by utilizing the dipole mode excited in the short GNR. It was found that the strong coupling between the dipole and quadrupole modes can be achieved by exciting the T-shaped GNR dimer with a plane wave. Then, we demonstrated the realization of strong dipole–quadrupole–exciton coupling by placing a T-shaped GNR on a tungsten disulfide (WS2) monolayer, which leads to a Rabi splitting as large as ~299 meV. It was confirmed that the simulation results can be well fitted by using a Hamiltonian based on the coupled harmonic oscillator model and the coupling strengths for dipole–quadrupole, dipole–exciton and quadrupole–exciton can be extracted from the fitting results. Our findings open new horizons for realizing strong plasmon–exciton coupling in simple systems and pave the way for constructing novel plasmonic devices for practical applications.

SPECTROSCOPY OF A NON-L TROSCOPY OF A NON-LUMINESCEN UMINESCENT ASSOCI T ASSOCIATE OF INDIGO CARMINE IN SOLUTIONS

Introduction. The food dye Indigo Carmine (E-132) was subjected to spectroscopic studies. It is shown that conditions for their participation in Association processes are created in aqueous and binary mixtures of solvents. The absorption bands against the background of the hypochromic effect in their electronic spectra are determined. Experimentally and by quantum chemical calculations, it is established that the dipole moments of the Indigo Carmine dye in the excited state increase up to 40 % and they contribute to the appearance of a strong dipole-dipole interaction, which results in the unification of Monomeric molecules into an associate. The interaction force (van der Waals) leads to resonant splitting of electronic States and changes in the probability of electron transition from the main excited levels of dye molecules. Research methods. The choice of binary mixtures of solvents was due to the fact that in one of the components of the solvents the dyes under study dissolved well, in the other they practically did not dissolve

A Review of Many-Body Interactions in Linear and Nonlinear Plasmonic Nanohybrids

In this review article, we discuss the many-body interactions in plasmonic nanohybrids made of an ensemble of quantum emitters and metallic nanoparticles. A theory of the linear and nonlinear optical emission intensity was developed by using the many-body quantum mechanical density matrix method. The ensemble of quantum emitters and metallic nanoparticles interact with each other via the dipole-dipole interaction. Surfaces plasmon polaritons are located near to the surface of the metallic nanoparticles. We showed that the nonlinear Kerr intensity enhances due to the weak dipole-dipole coupling limits. On the other hand, in the strong dipole-dipole coupling limit, the single peak in the Kerr intensity splits into two peaks. The splitting of the Kerr spectrum is due to the creation of dressed states in the plasmonic nanohybrids within the strong dipole-dipole interaction. Further, we found that the Kerr nonlinearity is also enhanced due to the interaction between the surface plasmon polaritons and excitons of the quantum emitters. Next, we predicted the spontaneous decay rates are enhanced due to the dipole-dipole coupling. The enhancement of the Kerr intensity due to the surface plasmon polaritons can be used to fabricate nanosensors. The splitting of one peak (ON) two peaks (OFF) can be used to fabricate the nanoswitches for nanotechnology and nanomedical applications.

Entanglement via rotational blockade of MgF molecules in a magic potential

Rotations of MgF molecules can be entangled via strong dipole–dipole interactions when trapped in optical tweezers with a magic polarization angle.

KINETICS OF THE SPONTANEOUS DECAY IN COLD ATOMIC SYSTEMS

We discuss the spontaneous decay in a system of cold identical two-level atoms when, due to the strong dipole-dipole interaction, the collision-induced spontaneous decay plays the leading role in the process. We show that the time profile of the spontaneous transition is essentially non-exponential. Also, we argue that at a low initial temperature of the atomic system the spontaneous decay is accompanied by a strong heating caused by the inelastic atom-atom collisions. We show that the spontaneous emission spectrum is asymmetric. In addition, the width of the emission spectrum is a function of time. While atoms decay the emission spectrum becomes broader. The spectrum’s asymmetry and the atomic system’s heating have the same physical origin coming from the peculiarities of the atoms distribution function.