Surface Plasmon Resonance Allows to Correlate Molecular Properties With Diffusion Coefficients of Linear Chain Alcohols.

Every biological and physicochemical process occurring in a fluid phase depends on the diffusion coefficient (D) of the species in solution. In the present work, a model to describe and fit the behaviour of D ${D}$ as a function of structure and extensive thermodynamics parameters in binary solutions of linear chain organic molecules is developed. Supporting experimental and computational evidences for this model are obtained by measuring D ${D}$ for a series of n ${n}$ -alcohols through a novel surface plasmon resonance method and molecular dynamics simulations. This allows to propose a kind of combined analysis to explain the dependence of D ${D}$ on various thermodynamic and structural parameters. The results suggest that for small linear systems in the range from 0 to 200 g mol-1 and under the assumption that the diffusive activation energy is a linear function of mass, D ${D}$ is strictly dependent on the molecular shape and on the relative strength of the solute-solvent intermolecular forces represented by a parameter named R. The newly proposed approach can be utilized to characterize and monitor progressive changes in physicochemical properties for any investigated species upon increasing the dimension of the aggregate/molecule along a certain direction.

Molecular ordering-enhanced circularly polarized luminescence of chiral 1,10-phenanthroline derivatives.

2,9-Bis((1R,2S,5R)-2-isopropyl-5-methylcyclohexanoxy)-1,10-phenanthroline [2,9-di-L-menthoxy-1,10-phenanthroline] (Men2Phen) and 2,9-bis(2-(S)-methylbutoxy)-1,10-phenanthroline (MB2Phen) were synthesized as chiral derivatives of 1,10-phenanthroline (Phen). Differences in rigidity and bulkiness of the chiral substituents at the 2- and 9-positions of the Phen backbone led to distinctive molecular dissymmetry in the ground state resulting in remarkable differences in circular dichroism. Men2Phen exhibited efficient circularly polarized luminescence (CPLm) at an anisotropy factor of 10-2 in the solid state based on molecular ordering disclosed by X-ray crystal analysis, while it showed much lower anisotropy factor in solution. MB2Phen, which was rather amorphous and did not afford good crystals, showed only negligible CPLm both in the solid state and in solution.

Unraveling Copper Exchange in the Atox1-Cu(I)-Mnk1 Heterodimer: A Simulation Approach.

Copper, an essential metal for various cellular processes, requires tight regulation to prevent cytotoxicity. Intracellular pathways crucial for maintaining optimal copper levels involve soluble and membrane transporters, namely, metallochaperones and P-type ATPases, respectively. In this study, we used a simulation workflow based on free-energy perturbation (FEP) theory and parallel bias metadynamics (PBMetaD) to predict the Cu(I) exchange mechanism between the human Cu(I) chaperone, Atox1, and one of its two physiological partners, ATP7A. ATP7A, also known as the Menkes disease protein, is a transmembrane protein and one of the main copper-transporting ATPases. It pumps copper into the trans-Golgi network for the maturation of cuproenzymes and is also essential for the efflux of excess copper across the plasma membrane. In this analysis, we utilized the nuclear magnetic resonance (NMR) structure of the Cu(I)-mediated complex between Atox1 and the first soluble domain of the Menkes protein (Mnk1) as a starting point. Independent free-energy simulations were conducted to investigate the dissociation of both Atox1 and Mnk1. The calculations revealed that the two dissociations require free energy values of 6.3 and 6.2 kcal/mol, respectively, following a stepwise dissociation mechanism.

Distinctive Chiral Conformations Induced to Poly (naphthalene-1,4-diyl) by Helix-sense-selective Polymerization and Circularly Polarized Light Irradiation.

Optically active poly(naphthalene-1,4-diyl) was prepared through helix-sense-selective polymerization of the corresponding monomers and also through circularly polarized light (CPL) irradiation, resulting in distinctive circular dichroism (CD) spectral patterns. Chirality of the helix-sense-selective polymerization -based polymer is ascribed to preferred-handed helicity while that of the CPL-based polymer to a non-helical, chiral conformation ('biased-dihedral conformation') with preferred-handedness which was stable only in the solid state. The helix of the helix-sense-selective polymerization-based polymer gradually racemized in tetrahydrofuran while it was stabilized by aggregate formation in a hexane-dichloromethane solution. Both helix-sense-selective polymerization- and CPL-based polymers exhibited efficient circularly polarized luminescence.

BDNF- and VEGF-Responsive Stimulus to an NGF Mimic Cyclic Peptide with Copper Ionophore Capability and Ctr1/CCS-Driven Signaling.

Neurotrophins are a family of growth factors that play a key role in the development and regulation of the functioning of the central nervous system. Their use as drugs is made difficult by their poor stability, cellular permeability, and side effects. Continuing our effort to use peptides that mimic the neurotrophic growth factor (NGF), the family model protein, and specifically the N-terminus of the protein, here we report on the spectroscopic characterization and resistance to hydrolysis of the 14-membered cyclic peptide reproducing the N-terminus sequence (SSSHPIFHRGEFSV (c-NGF(1-14)). Far-UV CD spectra and a computational study show that this peptide has a rigid conformation and left-handed chirality typical of polyproline II that favors its interaction with the D5 domain of the NGF receptor TrkA. c-NGF(1-14) is able to bind Cu2+ with good affinity; the resulting complexes have been characterized by potentiometric and spectroscopic measurements. Experiments on PC12 cells show that c-NGF(1-14) acts as an ionophore, influencing the degree and the localization of both the membrane transporter (Ctr1) and the copper intracellular transporter (CCS). c-NGF(1-14) induces PC12 differentiation, mimics the protein in TrkA phosphorylation, and activates the kinase cascade, inducing Erk1/2 phosphorylation. c-NGF(1-14) biological activities are enhanced when the peptide interacts with Cu2+ even with the submicromolar quantities present in the culture media as demonstrated by ICP-OES measurements. Finally, c-NGF(1-14) and Cu2+ concur to activate the cAMP response element-binding protein CREB that, in turn, induces the brain-derived neurotrophic factor (BDNF) and the vascular endothelial growth factor (VEGF) release.

Amplified Chirality Transfer to Aromatic Molecules through Non-specific Inclusion by Amorphous, Hyperbranched Poly(fluorenevinylene) Derivatives.

Optically active, hyperbranched, poly(fluorene-2,4,7-triylethene-1,2-diyl) [poly(fluorenevinylene)] derivatives bearing a neomenthyl group and a pentyl group at the 9-position of the fluorene backbone at various ratios acted as a chirality donor (host polymers) efficiently included naphthalene, anthracene, pyrene, 9-phenylanthracene, and 9,10-diphenyanthracene as a chirality acceptor (guest molecules) in their interior space in film as well as in solution, with the guest molecules exhibiting intense circular dichroism through chirality transfer with chirality amplification. The efficiency of the chirality transfer was much higher with higher-molar-mass polymers than lower-molar-mass ones as well as with hyperbranched polymers compared to the analogous linear ones. The hyperbranched polymers include the small molecules in their complex structure without any specific interactions at various stoichiometries. The included molecules may have ordered intermolecular arrangement that may be somewhat similar to those of liquid crystals. Naphthalene, anthracene, and pyrene included in the polymer exhibited efficient circularly polarized luminescence, where the chirality was remarkably amplified in excited states, and anthracene exhibited especially high anisotropies in the emission on the order of 10-2 .

Simulation workflows to predict the circular dichroism and circularly polarized luminescence of chiral materials.

Chiral materials are attracting considerable interest in various fields in view of their unique properties and optical activity. Indeed, the peculiar features of chiral materials to absorb and emit circularly polarized light enable their use in an extensive range of applications. Motivated by the interest in boosting the development of chiral materials characterized by enhanced chiroptical properties such as circular dichroism (CD) and circular polarized luminescence (CPL), we herein illustrate in this tutorial how theoretical simulations can be used for the predictions and interpretations of chiroptical data and for the identification of chiral geometries. We are focusing on computational frameworks that can be used to investigate the theoretical aspects of chiral materials' photophysical and conformational characteristics. We will then illustrate ab initio methods based on density functional theory (DFT) and its time-dependent extension (TD-DFT) to simulate CD and CPL signals, and we will exemplify a variety of enhanced sampling techniques useful for an adequate sampling of the configurational space for chiral systems.

Neurotrophic Activity and Its Modulation by Zinc Ion of a Dimeric Peptide Mimicking the Brain-Derived Neurotrophic Factor N-Terminal Region.

Brain-derived neurotrophic factor (BDNF) is a neurotrophin (NT) essential for neuronal development and synaptic plasticity. Dysregulation of BDNF signaling is implicated in different neurological disorders. The direct NT administration as therapeutics has revealed to be challenging. This has prompted the design of peptides mimicking different regions of the BDNF structure. Although loops 2 and 4 have been thoroughly investigated, less is known regarding the BDNF N-terminal region, which is involved in the selective recognition of the TrkB receptor. Herein, a dimeric form of the linear peptide encompassing the 1-12 residues of the BDNF N-terminal (d-bdnf) was synthesized. It demonstrated to act as an agonist promoting specific phosphorylation of TrkB and downstream ERK and AKT effectors. The ability to promote TrkB dimerization was investigated by advanced fluorescence microscopy and molecular dynamics (MD) simulations, finding activation modes shared with BDNF. Furthermore, d-bdnf was able to sustain neurite outgrowth and increase the expression of differentiation (NEFM, LAMC1) and polarization markers (MAP2, MAPT) demonstrating its neurotrophic activity. As TrkB activity is affected by zinc ions in the synaptic cleft, we first verified the ability of d-bdnf to coordinate zinc and then the effect of such complexation on its activity. The d-bdnf neurotrophic activity was reduced by zinc complexation, demonstrating the role of the latter in tuning the activity of the new peptido-mimetic. Taken together our data uncover the neurotrophic properties of a novel BDNF mimetic peptide and pave the way for future studies to understand the pharmacological basis of d-bdnf action and develop novel BDNF-based therapeutic strategies.

Non-uniform Self-folding of Helical Poly(fluorenevinylene) Derivatives in the Solid State Leading to Amplified Circular Dichroism and Circularly Polarized Light Emission.

An unprecedented non-uniform self-folding of artificial polymer chains composed of turn moieties and stretched segments is presented through the design of a set of optically active poly(fluorene-2,7-diylethene-1,2-diyl) (poly(fluorenevinylene)) derivatives bearing a neomenthyl group and a pentyl group attached at the 9-position of fluorene backbone at various ratios. The folded structure is formed and stabilized through inter-chain interactions in the solid state, leading to remarkably enhanced chiroptical properties (chirality amplification) in terms of circular dichroism (CD) and circularly polarized light (CPL) emission. This phenomenon is rationalized by experimental and theoretical CD and CPL spectral analyses. The polymer arrangements in the solid state were further assessed through transmission electron microscopic observations combined with enhanced sampling molecular dynamics simulations in the solid state revealing the thin film organizations.

Multinuclear Metal-Binding Ability of the N-Terminal Region of Human Copper Transporter Ctr1: Dependence Upon pH and Metal Oxidation State.

The 14mer peptide corresponding to the N-terminal region of human copper transporter Ctr1 was used to investigate the intricate mechanism of metal binding to this plasma membrane permease responsible for copper import in eukaryotic cells. The peptide contains a high-affinity ATCUN Cu(II)/Ni(II)-selective motif, a methionine-only MxMxxM Cu(I)/Ag(I)-selective motif and a double histidine HH(M) motif, which can bind both Cu(II) and Cu(I)/Ag(I) ions. Using a combination of NMR spectroscopy and electrospray mass spectrometry, clear evidence was gained that the Ctr1 peptide, at neutral pH, can bind one or two metal ions in the same or different oxidation states. Addition of ascorbate to a neutral solution containing Ctr11-14 and Cu(II) in 1:1 ratio does not cause an appreciable reduction of Cu(II) to Cu(I), which is indicative of a tight binding of Cu(II) to the ATCUN motif. However, by lowering the pH to 3.5, the Cu(II) ion detaches from the peptide and becomes susceptible to reduction to Cu(I) by ascorbate. It is noteworthy that at low pH, unlike Cu(II), Cu(I) stably binds to methionines of the peptide. This redox reaction could take place in the lumen of acidic organelles after Ctr1 internalization. Unlike Ctr11-14-Cu(II), bimetallic Ctr11-14-2Cu(II) is susceptible to partial reduction by ascorbate at neutral pH, which is indicative of a lower binding affinity of the second Cu(II) ion. The reduced copper remains bound to the peptide, most likely to the HH(M) motif. By lowering the pH to 3.5, Cu(I) shifts from HH(M) to methionine-only coordination, an indication that only the pH-insensitive methionine motif is competent for metal binding at low pH. The easy interconversion of monovalent cations between different coordination modes was supported by DFT calculations.

Aggregation-induced chirality amplification of optically active fluorescent polyurethane and a cyclic dimer in the ground and excited states.

Optically active linear polyurethane and a cyclic dimer were synthesized from 2,7-diisocyanatofluorene and 2,2'-dihydroxy-1,1'-binaphthyl. The circular dichroism (CD) spectral intensity of the polymer was amplified at a higher concentration through aggregate formation, while circularly polarized light (CPL) emission was not enhanced. The cyclic dimer's CPL emission was largely amplified (glum 1.1 × 10-2) due to intermolecular excimer formation through aggregation, while the CD intensity was not affected.

Photo racemization of 2,2'-dihydroxy-1,1'-binaphthyl derivatives.

Photo racemization of 2,2'-dihydroxy-1,1'-binaphthyl (BINOL) and its monomethyl ether, monobutyl ether, and dimethyl ether was studied by means of circularly dichroism spectra, chiral HPLC, and theoretical calculations of rotation energy barriers. Racemization was fastest for BINOL and about one seventh as fast for the monomethyl and monobutyl ethers while it was too slow to be detected for the dimethyl ether under the present conditions.

Multi-replica biased sampling for photoswitchable π-conjugated polymers.

In recent years, π-conjugated polymers are attracting considerable interest in view of their light-dependent torsional reorganization around the π-conjugated backbone, which determines peculiar light-emitting properties. Motivated by the interest in designing conjugated polymers with tunable photoswitchable pathways, we devised a computational framework to enhance the sampling of the torsional conformational space and, at the same time, estimate ground- to excited-state free-energy differences. This scheme is based on a combination of Hamiltonian Replica Exchange Method (REM), parallel bias metadynamics, and free-energy perturbation theory. In our scheme, each REM samples an intermediate unphysical state between the ground and the first two excited states, which are characterized by time-dependent density functional theory simulations at the B3LYP/6-31G* level of theory. We applied the method to a 5-mer of 9,9-dioctylfluorene and found that upon irradiation, this system can undergo a dihedral inversion from -155° to 155°, crossing a barrier that decreases from 0.1 eV in the ground state (S0) to 0.05 eV and 0.04 eV in the first (S1) and second (S2) excited states. Furthermore, S1 and even more S2 were predicted to stabilize coplanar dihedrals, with a local free-energy minimum located at ±44°. The presence of a free-energy barrier of 0.08 eV for the S1 state and 0.12 eV for the S2 state can trap this conformation in a basin far from the global free-energy minimum located at 155°. The simulation results were compared with the experimental emission spectrum, showing a quantitative agreement with the predictions provided by our framework.

Blue circularly polarized luminescent amorphous molecules with single-handed propeller chirality induced by circularly polarized light irradiation.

Preferred-handed propeller conformation was induced by circularly polarized light irradiation to three amorphous molecules with trigonal symmetry, and the molecules with induced chirality efficiently exhibited blue circularly polarized luminescence. In both chirality induction and luminescence, chirality appeared to be amplified due to intermolecular interactions through π-stacking.

Zinc Interactions with a Soluble Mutated Rat Amylin to Mimic Whole Human Amylin: An Experimental and Simulation Approach to Understand Stoichiometry, Speciation and Coordination of the Metal Complexes.

Islet amyloid polypeptide (IAPP) is a hormone co-secreted with insulin and zinc from pancreatic ß-cells. To overcome the low solubility of human IAPP, we characterized zinc complexes species formed with 1) a mutated form of rat-IAPP(1-37; R18 H) able to mimic the human IAPP, 2) the r-IAPP(1-37) and the IAPP(1-8) fragment. Stoichiometry, speciation and coordination features of zinc(II) complexes were unveiled by ESI-MS, potentiometry and NMR measurements combined with DFT and free-energy simulations. Mononuclear species start to form around pH 6; Zn2+ binds both His18 and N-amino terminus in rat-IAPP(1-37; R18 H). The in silico study allows us to assess not only a structured turn compact domain in r-IAPP(1-37) and r-IAPP(1-37; R18 H) featured by a different free energy barrier for the transition from the compact to elongated conformation upon the coordination of Zn2+ , but also to bring into light a coordination shell further stabilized by noncovalent interactions.

Learning how planarization can affect dichroic patterns in polyfluorenes.

The circular dichroism spectra of a single chain of polyfluorene was predicted for a p-twisted helix conformation and local planarized polymer sections in the presence and in the absence of thermal vibrations. Under thermal vibrations at 300 K, the planarized section of polyfluorene affords a red-shifted positive dichroic band between 446 and 456 nm, preserving a degree of chirality. The S1 ← S0 excitation energy decreases from 3.29 eV, for the p-twisted helix to 2.77 or 2.71 eV, for planarized sections with one or two coplanar twists, respectively. Thermal vibrations and intramolecular rotations eventually affect the circular dichroism spectrum patterns, where planarized bent conformers induce a positive band towards 450 nm.

Synergistic Approach of Ultrafast Spectroscopy and Molecular Simulations in the Characterization of Intramolecular Charge Transfer in Push-Pull Molecules.

The comprehensive characterization of Intramolecular Charge Transfer (ICT) stemming in push-pull molecules with a delocalized π-system of electrons is noteworthy for a bespoke design of organic materials, spanning widespread applications from photovoltaics to nanomedicine imaging devices. Photo-induced ICT is characterized by structural reorganizations, which allows the molecule to adapt to the new electronic density distribution. Herein, we discuss recent photophysical advances combined with recent progresses in the computational chemistry of photoactive molecular ensembles. We focus the discussion on femtosecond Transient Absorption Spectroscopy (TAS) enabling us to follow the transition from a Locally Excited (LE) state to the ICT and to understand how the environment polarity influences radiative and non-radiative decay mechanisms. In many cases, the charge transfer transition is accompanied by structural rearrangements, such as the twisting or molecule planarization. The possibility of an accurate prediction of the charge-transfer occurring in complex molecules and molecular materials represents an enormous advantage in guiding new molecular and materials design. We briefly report on recent advances in ultrafast multidimensional spectroscopy, in particular, Two-Dimensional Electronic Spectroscopy (2DES), in unraveling the ICT nature of push-pull molecular systems. A theoretical description at the atomistic level of photo-induced molecular transitions can predict with reasonable accuracy the properties of photoactive molecules. In this framework, the review includes a discussion on the advances from simulation and modeling, which have provided, over the years, significant information on photoexcitation, emission, charge-transport, and decay pathways. Density Functional Theory (DFT) coupled with the Time-Dependent (TD) framework can describe electronic properties and dynamics for a limited system size. More recently, Machine Learning (ML) or deep learning approaches, as well as free-energy simulations containing excited state potentials, can speed up the calculations with transferable accuracy to more complex molecules with extended system size. A perspective on combining ultrafast spectroscopy with molecular simulations is foreseen for optimizing the design of photoactive compounds with tunable properties.

Pyrazolones Activate the Proteasome by Gating Mechanisms and Protect Neuronal Cells from ß-Amyloid Toxicity.

Proteasome malfunction parallels abnormal amyloid accumulation in Alzheimer's Disease (AD). Here we scrutinize a small library of pyrazolones by assaying their ability to enhance proteasome activity and protect neuronal cells from amyloid toxicity. Tube tests evidenced that aminopyrine and nifenazone behave as 20S proteasome activators. Enzyme assays carried out on an "open gate" mutant (α3ΔN) proteasome demonstrated that aminopyrine activates proteasome through binding the α-ring surfaces and influencing gating dynamics. Docking studies coupled with STD-NMR experiments showed that H-bonds and π-π stacking interactions between pyrazolones and the enzyme play a key role in bridging α1 to α2 and, alternatively, α5 to α6 subunits of the outer α-ring. Aminopyrine and nifenazone exhibit neurotrophic properties and protect differentiated human neuroblastoma SH-SY5Y cells from ß-amyloid (Aß) toxicity. ESI-MS studies confirmed that aminopyrine enhances Aß degradation by proteasome in a dose-dependent manner. Our results suggest that some pyrazolones and, in particular, aminopyrine are promising compounds for the development of proteasome activators for AD treatment.

The curious case of opossum prion: a physicochemical study on copper(ii) binding to the bis-decarepeat fragment from the protein N-terminal domain.

The opossum is a peculiar model of immunity to prion diseases. Here we scrutinised the bis-decarepeat peptide sequence of the opossum prion (Op_bis-deca) protein by a multitechnique approach, with a combined experimental (potentiometry, UV-visible, circular dichroism, NMR and EPR spectroscopy, quartz crystal microbalance with dissipation monitoring and confocal microscopy) and simulation (DFT calculations) approach. Results showed that the macrochelate structures formed upon the binding to Cu(ii) by the analogous bis-octarepeat peptide sequence of human prion (Hu_bis-octa) are not found in the case of Op_bis-deca. At physiological pH and equimolar amount of copper ions, the [CuLH-2] is the major species formed by Op_bis-deca. In this species one imidazole and two amide nitrogen atoms are involved in metal coordination and its stability constant value is lower than that of the analogous species formed by Hu_bis-octa, due to the presence of an extra proline residue. Moreover, the study on the interaction of the peptides or the peptide/Cu(ii) complexes with the model cell membranes made of supported lipid bilayers disclosed different levels of interaction, monitored by the viscoelastic changes of the membranes, which exhibited a similar viscoelastic response at the interface of the two complexes, while in the absence of Cu(ii), the Hu_bis-octa/SLB interface was more viscoelastic than the Op_bis-deca one.

The Copper(II)-Assisted Connection between NGF and BDNF by Means of Nerve Growth Factor-Mimicking Short Peptides.

Nerve growth factor (NGF) is a protein necessary for development and maintenance of the sympathetic and sensory nervous systems. We have previously shown that the NGF N-terminus peptide NGF(1-14) is sufficient to activate TrkA signaling pathways essential for neuronal survival and to induce an increase in brain-derived neurotrophic factor (BDNF) expression. Cu2+ ions played a critical role in the modulation of the biological activity of NGF(1-14). Using computational, spectroscopic, and biochemical techniques, here we report on the ability of a newly synthesized peptide named d-NGF(1-15), which is the dimeric form of NGF(1-14), to interact with TrkA. We found that d-NGF(1-15) interacts with the TrkA-D5 domain and induces the activation of its signaling pathways. Copper binding to d-NGF(1-15) stabilizes the secondary structure of the peptides, suggesting a strengthening of the noncovalent interactions that allow for the molecular recognition of D5 domain of TrkA and the activation of the signaling pathways. Intriguingly, the signaling cascade induced by the NGF peptides ultimately involves cAMP response element-binding protein (CREB) activation and an increase in BDNF protein level, in keeping with our previous result showing an increase of BDNF mRNA. All these promising connections can pave the way for developing interesting novel drugs for neurodegenerative diseases.