Multiscale modeling of reaction rates: application to archetypal SN2 nucleophilic substitutions

We propose an approach to the evaluation of kinetic rates of elementary chemical reactions within Kramers\u2019 theory based on the definition of the reaction coordinate as a linear combination of natural, pseudo Z-matrix, internal coordinates of the system. The element of novelty is the possibility to evaluate the friction along the reaction coordinate, within a hydrodynamic framework developed recently [J. Campeggio et al., J. Comput. Chem. 2019, 40, 679\u2013705]. This, in turn, allows to keep into account barrier recrossing, i.e. the transmission coefficient that is employed in correcting transition state theory evaluations. To test the capabilities and the flaws of the approach we use as case studies two archetypal SN2 reactions. First, we consider to the standard substitution of chloride ion to bromomethane. The rate constant at 295.15 K is evaluated to k/c 96 = 2.7 7 10 126 s 121 (with c 96 = 1 M), which compares well to the experimental value of 3.3 7 10 126 s 121 [R. H. Bathgate and E. A. Melwyn-Hughes, J. Chem. Soc 1959, 2642\u20132648]. Then, the method is applied to the SN2 reaction of methylthiolate to dimethyl disulfide in water. In biology, such an interconversion of thiols and disulfides is an important metabolic topic still not entirely rationalized. The predicted rate constant is k/c 96 = 7.7 7 103 s 121. No experimental data is available for such a reaction, but it is in accord with the fact that the alkyl thiolates to dialkyl disulfides substitutions in water have been found to be fast reactions [S. M. Bachrach, J. M. Hayes, T. Dao and J. L. Mynar, Theor. Chem. Acc. 2002, 107, 266\u2013271]

Changes in the fraction of strongly attached cross bridges in mouse atrophic and hypertrophic muscles as revealed by continuous wave electron paramagnetic resonance.

Electron paramagnetic resonance (EPR), coupled with site-directed spin labeling, has been proven to be a particularly suitable technique to extract information on the fraction of myosin heads strongly bound to actin upon muscle contraction. The approach can be used to investigate possible structural changes occurring in myosin of fiber s altered by diseases and aging. In this work, we labeled myosin at position Cys707, located in the SH1-SH2 helix in the myosin head cleft, with iodoacetamide spin label, a spin label that is sensitive to the reorientational motion of this protein during the ATPase cycle and characterized the biochemical states of the labeled myosin head by means of continuous wave EPR. After checking the sensitivity and the power of the technique on different muscles and species, we investigated whether changes in the fraction of strongly bound myosin heads might explain the contractile alterations observed in atrophic and hypertrophic murine muscles. In both conditions, the difference in contractile force could not be justified simply by the difference in muscle mass. Our results showed that in atrophic muscles the decrease in force generation was attributable to a lower fraction of strongly bound cross bridges during maximal activation. In contrast in hypertrophic muscles, the increase in force generation was likely due to several factors, as pointed out by the comparison of the EPR experiments with the tension measurements on single skinned fibers

Room temperature polariton condensation from Whispering gallery modes in CsPbBr3 microplatelets

Room temperature (RT) polariton condensate holds exceptional promise for revolutionizing various fields of science and technology, encompassing optoelectronics devices to quantum information processing. Using perovskite materials like all-inorganic CsPbBr3 single crystal provides additional advantages, such as ease of synthesis, cost-effectiveness, and compatibility with existing semiconductor technologies. In this work, we show the formation of whispering gallery modes (WGM) in CsPbBr3 single crystals with controlled geometry, synthesized using a lowcost and efficient capillary bridge method. Through the implementation of microplatelets geometry, we achieve enhanced optical properties and performance thanks to the presence of sharp edges and a uniform surface, effectively avoiding non-radiative scattering losses caused by defects. This allows us not only to observe strong light matter coupling and formation of whispering gallery polaritons, but also to demonstrate the onset of polariton condensation at RT. This investigation not only contributes to the advancement of our knowledge concerning the exceptional optical properties of perovskite-based polariton systems, but also unveils prospects for the exploration of WGM polariton condensation within the framework of a 3D perovskite-based platform, working at RT. The unique characteristics of polariton condensate, including low excitation thresholds and ultrafast dynamics, open up unique opportunities for advancements in photonics and optoelectronics devices

Engineering Dion-Jacobson Perovskites in Polariton Waveguides

Hybrid two-dimensional perovskites hold considerable promise as semiconductors for a wide range of optoelectronic applications. Many efforts are addressed to exploit the potential of these materials by tailoring their characteristics. In this work, the optical properties and electronic band structure in three new Dion-Jacobson (DJ) perovskites (PVKs) are engineered by modulating their structural distortion. Two different interlayer cations: 1-6, Hexamethylendiammonium, HE, and 3-(Dimethylamino)-1-propylammonium, DMPA, have been selected to investigate the role of the cation length and the ammonium binding group on the crystalline structure. This study provides new insights into the understanding of the structure-property relationship in DJ perovskites and demonstrates that exciton characteristics can be easily modulated with the judicious design of the organic cations. DJ PVKs developed in this work were also grown as size-controlled single crystal microwires through a microfluidic-assisted synthesis technique and integrated in a nanophotonic device. The DJ PVK microwire acts as a waveguide exhibiting strong light-matter coupling between the crystal optical modes and DJ PVK exciton. Through the investigation of these polariton waveguides, the nature of the double peak emission, which is often observed in these materials and whose nature is largely debated in the literature, is demonstrated originating from the hybrid polariton state

Heuristic approaches to the optimization of acceptor systems in bulk heterojunction cells: a computational study

A computational protocol combining a heuristic search based on genetic algorithms (GAs) and quantum chemistry methods is implemented and applied to a family of acceptor compounds based on the 9,9'-bifluorenylidene backbone, to be coupled with the poly-3(hexylthiophene) polymer (donor) in a bulk heterojunction solar cell. Highly performing candidates are generated via GA from an initial generation, after a number of iterations (i.e., new generations), under the selective pressure of electronic constrains calculated at density functional theory level. The combination of heuristic search techniques and advanced electronic structure methodologies for characterization seems to be amenable to further applications in the field of molecular design

Dynamical regimes of nematic infinite planar samples

A computational treatment of Leslie-Ericksen constitutive equations of nematodynamics, is applied to an infinite planar sample, in the presence of mechanical stresses and magnetic torques. Dynamical regimes are explored in order to investigate the competing effects of magnetic and mechanical torques and backflow effects resulting from coupling of velocity and director fields and to understand the transient behaviour of the nematic director, when the magnetic field is parallel or perpendicular to the shear direction

Tuning charge transfer in model bio-inspired porphyrincarotenedyads

We present a computational study on model bio-inspired donor-acceptor (DA) dyads formed by a carotenoid (C) covalently linked to a tetraphenylporphyrin (TPP) at the ortho position of one of the TPP phenyl rings [1]. The mutual orientation of the components and their distance closely resembles the geometry of the dyad chlorophyll-peridinin in PCP [2]. Dyadic systems are intensively studied for potential application in the construction of organic solar cells and development of efficient photocatalytic systems for the solar energy conversion for the unique advantages they offer with regard to synthetic feasibility. The recent progress in computational methodologies, especially the development of DFT rooted methods suitable to describe charge transfer (CT) processes, allow to perform systematic investigations in silico of those molecular features which might be important to design high performance bio-inspired artificial devices. Focussed on CT process, this study aims (i) at better understanding the effect of slight chemical modifications on the absorption spectra, in particular on the lowest CT bands, as well as (ii) at gaining deeper insight on the role of H2O and hystidine (Hys) in the biological system. The coordination of H2O or Hys might occur in two different positions: it can be sandwiched between the carotene and the porphyrin ring or can be coordinated to the metal under the porphyrin plane. The effect of different metals of biological interest is also investigated to rationalize the fine tuning of the CT process