A computational study of a light-driven artificial device: a third generation rotational photo-molecular motor in dilute solutions

A third-generation artificial photo-molecular motor, featuring two photo-switchable rotating moieties in connection with a pseudoasymmetric molecular centre, is investigated by combining quantum-mechanics (QM) algorithms with classical molecular dynamics (MD) propagators. In particular, in the present contribution we have addressed such a molecular motor in different rotational isomers following the experimental observations arising from the application of multiple spectroscopic techniques in dilute solutions. At first, we focused our attention on the reproduction of the UV/Vis absorption spectrum in two solvents (acetonitrile and cyclohexane) with different gradient-corrected density functional theory (B3LYP, Cam-B3LYP, PBE, PBE0) functionals in conjunction with the conductor-like and polarizable continuum model (C-PCM). Furthermore, we refined the absorption signals by combining a classical MD sampling at room-temperature with DFT-based electronic degrees of freedom to compute perturbed excitation wavelengths driven by thermal fluctuation and solvation effects. In this respect, we have modelled the investigated artificial motor within solution nanodroplets with solvent molecules treated contextually at atomistic level and via a dielectric and polarizable continuum model.

Into the dynamics of rotaxanes at atomistic resolution

Mechanically-interlocked molecules (MIMs) are at the basis of artificial molecular machines and are attracting increasing interest for various applications, from catalysis to drug delivery and nanoelectronics. MIMs are composed of mechanically-interconnected molecular sub-parts that can move with respect to each other, imparting these systems innately dynamical behaviors and interesting stimuli-responsive properties. The rational design of MIMs with desired functionalities requires studying their dynamics at sub-molecular resolution and on relevant timescales, which is challenging experimentally and computationally. Here, we combine molecular dynamics and metadynamics simulations to reconstruct the thermodynamics and kinetics of different types of MIMs at atomistic resolution under different conditions. As representative case studies, we use rotaxanes and molecular shuttles substantially differing in structure, architecture, and dynamical behavior. Our computational approach provides results in agreement with the available experimental evidence and a direct demonstration of the critical effect of the solvent on the dynamics of the MIMs. At the same time, our simulations unveil key factors controlling the dynamics of these systems, providing submolecular-level insights into the mechanisms and kinetics of shuttling. Reconstruction of the free-energy profiles from the simulations reveals details of the conformations of macrocycles on the binding site that are difficult to access via routine experiments and precious for understanding the MIMs' behavior, while their decomposition in enthalpic and entropic contributions unveils the mechanisms and key transitions ruling the intermolecular movements between metastable states within them. The computational framework presented herein is flexible and can be used, in principle, to study a variety of mechanically-interlocked systems.

Rotaxane nanomachines in future molecular electronics

As the electronics industry is integrating more and more new molecules to utilize them in logic circuits and memories to achieve ultra-high efficiency and device density, many organic structures emerged as promising candidates either in conjunction with or as an alternative to conventional semiconducting materials such as but not limited to silicon. Owing to rotaxane's mechanically interlocked molecular structure consisting of a dumbbell-shaped molecule threaded through a macrocycle, they could be excellent nanomachines in molecular switches and memory applications. As a nanomachine, the macrocycle of rotaxane can move reversibly between two stations along its axis under external stimuli, resulting in two stable molecular configurations known as "ON" and "OFF" states of the controllable switch with distinct resistance. There are excellent reports on rotaxane's structure, properties, and function relationship and its application to molecular electronics (Ogino, et al., 1984; Wu, et al., 1991; Bissell, et al., 1994; Collier, et al., 1999; Pease, et al., 2001; Chen, et al., 2003; Green, et al., 2007; Jia, et al., 2016). This comprehensive review summarizes [2]rotaxane and its application to molecular electronics. This review sorts the major research work into a multi-level pyramid structure and presents the challenges of [2]rotaxane's application to molecular electronics at three levels in developing molecular circuits and systems. First, we investigate [2]rotaxane's electrical characteristics with different driving methods and discuss the design considerations and roles based on voltage-driven [2]rotaxane switches that promise the best performance and compatibility with existing solid-state circuits. Second, we examine the solutions for integrating [2]rotaxane molecules into circuits and the limitations learned from these devices keep [2]rotaxane active as a molecular switch. Finally, applying a sandwiched crossbar structure and architecture to [2]rotaxane circuits reduces the fabrication difficulty and extends the possibility of reprogrammable [2]rotaxane arrays, especially at a system level, which eventually promotes the further realization of [2]rotaxane circuits.

[2]Rotaxane as a switch for molecular electronic memory application: A molecular dynamics study

As VLSI technology is shifting from microelectronics to nanoelectronics era, bi-stable [2]rotaxane emerges as a promising candidate for molecular electronics. A typical voltage-driven [2]rotaxane consists of a cyclobis-(paraquat-p-phenylene) macrocycle encircling a dumbbell shape molecular chain and moving between two stations on the chain: tetrathiafulvalene (TTF) and 1,5-dioxynaphthalene (DNP). As a molecular switch, the macrocycle can move reversibly between two stations along its axis with appropriate driving voltage, resulting in two stable molecular conformational states with distinct high and low resistance. This makes it a well-suited candidate to represent binary states ("0" and "1") for digital electronics. In this work, we performed molecular simulation to investigate the switching mechanism of [2]rotaxane molecule. We used distance and angle variables to characterize the movement of the macrocycle along the chain, and compared the switching behavior of [2]rotaxane in water, ethanol, dimethyl ether and vacuum. The results show that the solvent environment plays an important role in the switching characteristics of [2]rotaxane molecule. The switching of [2]rotaxane is stable, controllable, reversible and repeatable. We also looked into potential failure mechanism of the [2]rotaxane, which could shed light on the fault model, testing and reliability enhancement of [2]rotaxane based molecular electronics. Our simulation results support that [2]rotaxane molecules possess potential to be used for molecular memory and logic applications.

Pseudorotaxane formation affected by stereo-electronic effects. A theoretical and experimental study

We report a theoretical and experimental study on different complexes of pseudorotaxanes possessing pyridine axles. In order to evaluate the stereo-electronic effects of the methyl substituents in the pyridine ring, complexes with different substitution patterns were synthesized. In this way, it was possible to analyze the different behaviors of these complexes according to the positions of their methyl substituents. Combined techniques of molecular dynamics and quantum mechanical calculations with the help of molecular electrostatic potentials for a simpler visualization of the electronic effects were employed. We have sought experimental support of NMR spectroscopy analysis to corroborate the conclusions obtained from the molecular simulations. Our results not only clearly demonstrate that both electronic and steric effects play key roles in the feasibility of the formation of such complexes, but also the simulations reported here might predict the degree of difficulty of their formation. The combination of computational techniques employed here seems to be an excellent approach to be able to predict whether or not a complex can be formed and with what degree of difficulty. In addition, our experimental and theoretical results have allowed us to visualize the formation of external complexes in the rotaxanes reported here. In this case, the use of bolaforms with trimethylammonium groups at both ends was very useful to evaluate in detail the formation of the so-called external complexes in these systems.

Interactome of Glyceraldehyde-3-Phosphate Dehydrogenase Points to the Existence of Metabolons in Paracoccidioides lutzii

Paracoccidioides is a dimorphic fungus, the causative agent of paracoccidioidomycosis. The disease is endemic within Latin America and prevalent in Brazil. The treatment is based on azoles, sulfonamides and amphotericin B. The seeking for new treatment approaches is a real necessity for neglected infections. Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) is an essential glycolytic enzyme, well known for its multitude of functions within cells, therefore categorized as a moonlight protein. To our knowledge, this is the first approach performed on the Paracoccidioides genus regarding the description of PPIs having GAPDH as a target. Here, we show an overview of experimental GAPDH interactome in different phases of Paracoccidioides lutzii and an in silico analysis of 18 proteins partners. GAPDH interacted with 207 proteins in P. lutzii. Several proteins bound to GAPDH in mycelium, transition and yeast phases are common to important pathways such as glycolysis and TCA. We performed a co-immunoprecipitation assay to validate the complex formed by GAPDH with triose phosphate isomerase, enolase, isocitrate lyase and 2-methylcitrate synthase. We found GAPDH participating in complexes with proteins of specific pathways, indicating the existence of a glycolytic and a TCA metabolon in P. lutzii. GAPDH interacted with several proteins that undergoes regulation by nitrosylation. In addition, we modeled the GAPDH 3-D structure, performed molecular dynamics and molecular docking in order to identify the interacting interface between GAPDH and the interacting proteins. Despite the large number of interacting proteins, GAPDH has only four main regions of contact with interacting proteins, reflecting its ancestrality and conservation over evolution.

Light triggers molecular shuttling in rotaxanes: control over proximity and charge recombination

The lifetime of a charge separated state is enhanced by the effects of solvent polarity and the coordination controlled shuttling of a dumbbell in a porphyrin/fullerene rotaxane.

We present the synthesis of novel rotaxanes based on mechanically interlocked porphyrins and fullerene and their advanced investigations by means of photophysical measurements. To this end, a fullerene-capped dumbbell-type axle containing a central triazole was threaded through strapped (metallo)porphyrins—either a free-base or a zinc porphyrin. Femtosecond-resolved transient absorption measurements revealed charge-separation between the porphyrin and fullerene upon light excitation. Solvent polarity and solvent coordination effects induced molecular motion of the rotaxanes upon charge separation and enabled, for the first time, subtle control over the charge recombination by enabling and controlling the directionality of shuttling.

Mycobacterium abscessus subsp. massiliense mycma_0076 and mycma_0077 Genes Code for Ferritins That Are Modulated by Iron Concentration

Mycobacterium abscessus complex has been characterized in the last decade as part of a cluster of mycobacteria that evolved from an opportunistic to true human pathogen; however, the factors responsible for pathogenicity are still undefined. It appears that the success of mycobacterial infection is intrinsically related with the capacity of the bacteria to regulate intracellular iron levels, mostly using iron storage proteins. This study evaluated two potential M. abscessus subsp. massiliense genes involved in iron storage. Unlike other opportunist or pathogenic mycobacteria studied, M. abscessus complex has two genes similar to ferritins from M. tuberculosis (Rv3841), and in M. abscessus subsp. massiliense, those genes are annotated as mycma_0076 and mycma_0077. Molecular dynamic analysis of the predicted expressed proteins showed that they have a ferroxidase center. The expressions of mycma_0076 and mycma_0077 genes were modulated by the iron levels in both in vitro cultures as well as infected macrophages. Structural studies using size-exclusion chromatography, circular dichroism spectroscopy and dynamic light scattering showed that r0076 protein has a structure similar to those observed in the ferritin family. The r0076 forms oligomers in solution most likely composed of 24 subunits. Functional studies with recombinant proteins, obtained from heterologous expression of mycma_0076 and mycma_0077 genes in Escherichia coli, showed that both proteins were capable of oxidizing Fe2+ into Fe3+, demonstrating that these proteins have a functional ferroxidase center. In conclusion, two ferritins proteins were shown, for the first time, to be involved in iron storage in M. abscessus subsp. massiliense and their expressions were modulated by the iron levels.

Rational design of multifunctional star-shaped molecules with a 1,3,5-triazine core and different arms for application in organic light-emitting diodes and organic solar cells

A series of star-shaped 1,3,5-triazine derivatives for intended application in organic light-emitting diodes (OLEDs) and organic solar cells (OSCs) were investigated theoretically to explore their optical, electronic, and charge-transport properties. Analysis of their frontier molecular orbitals (FMOs) indicated that vertical electronic transitions associated with absorption and emission by these derivatives can be characterized as intramolecular charge-transfer (ICT) processes. The calculated results show that the optical, electronic, and charge-transport properties of the derivatives are influenced by the end groups and π-bridges present. Our results suggest that the molecules under investigation could serve as donor materials in OSCs and/or luminescent materials in OLEDs. In addition, all of the molecules are expected to be promising candidates for hole- and electron-transport materials. Based on our results, we were able to propose a rational method of designing multifunctional materials for application in OLEDs and OSCs. Graphical abstract A series of multifunctional star-shaped small molecules were investigated as charge-transport and luminescent materials for OLEDs as well as charge-transport and donor materials for OSCs.

A theoretical study on photophysical properties of triphenylamine-cored molecules with naphthalimide arms and different π-conjugated bridges as organic solar cell materials

Theoretical investigations show that star-shaped molecules are expected to be promising candidates for charge transfer and donor materials for OSCs.

Well-tempered metadynamics as a tool for characterizing multi-component, crystalline molecular machines

The well-tempered, smoothly converging form of the metadynamics algorithm has been implemented in classical molecular dynamics simulations and used to obtain an estimate of the free energy surface explored by the molecular rotations in the plastic crystal, octafluoronaphthalene. The biased simulations explore the full energy surface extremely efficiently, more than 4 orders of magnitude faster than unbiased molecular dynamics runs. The metadynamics collective variables used have also been expanded to include the simultaneous orientations of three neighboring octafluoronaphthalene molecules. Analysis of the resultant three-dimensional free energy surface, which is sampled to a very high degree despite its significant complexity, demonstrates that there are strong correlations between the molecular orientations. Although this correlated motion is of limited applicability in terms of exploiting dynamical motion in octafluoronaphthalene, the approach used is extremely well suited to the investigation of the function of crystalline molecular machines.

Degenerate molecular shuttles with flexible and rigid spacers

The preparation and dynamic behavior of degenerate rotaxane molecular shuttles are described in which a benzylic amide macrocycle moves back and forth between two naphthalimide-glycine units along a diphenylethyne spacer or an aliphatic spacer consisting of a C(9), C(12), or C(26) alkyl chain. Subtle differences in the (1)H NMR spectra of the rotaxanes can be related to the presence of conformers in which the macrocycle interacts simultaneously with both glycines, especially in the case of the C(9) spacer. The kinetic data of the shuttling behavior in the C(26) rotaxane were obtained from dynamic NMR spectroscopy. The Eyring activation parameters were found to be ΔH(‡) = 10 ± 1 kcal mol(-1), ΔS(‡) = -6.5 ± 2.0 cal mol(-1) K(-1), ΔG(‡)(298) = 11.9 ± 0.2 kcal mol(-1). For the systems with the shorter spacers, the shuttling rates were higher. Also in the diphenylethyne, rotaxane shuttling is rapid on the NMR time scale, indicating that the rigid unit does not impose a large barrier to the translocation of the macrocycle.