Probing Intermolecular Interactions of Amyloidogenic Fragments of SOD1 by Site-Specific Tryptophan and Its Noncanonical Derivative

Transient amyloid intermediates are likely to be cytotoxic and play an essential role in amyloid-associated neurodegenerative diseases. Characterization of their structural and dynamic evolution is the key to elucidating the molecular mechanism of amyloid formation. Here, combining circular dichroism (CD), exciton couplet theory, and Fourier transform infrared spectroscopy with site-specific tryptophan (Trp) and its noncanonical derivative 5-cyano-tryptochan (Trp_5CN), we developed a method to monitor strand-to-strand tertiary and sheet-to-sheet quaternary interactions in the aggregation cascades of an amyloidogenic fragment from protein SOD1_28-38 (with the sequence KVKVWGSIKGL). We found that the exciton couplet generated from the B_b band of Trp can be used as a probe for side chain interactions. Its sensitivity can be further improved by four times with the incorporation of Trp_5CN. We further observed a red-shift of ∼2 cm^-1 and a broadening of ∼2 cm^-1 in the IR band generated from the CN stretch during the aggregation, which we attributed to the transition from a corkscrew-like structure to a cross-linked intermediate phase. We show here that the integration of optical methods with unique aromatic side chain-related probes is able to elucidate amyloid intermolecular interactions and even capture elusive transient intermediates on and off the amyloid assembling pathway.

Chiroptical Properties in Thin Films of π-Conjugated Systems

Chiral π-conjugated molecules provide new materials with outstanding features for current and perspective applications, especially in the field of optoelectronic devices. In thin films, processes such as charge conduction, light absorption, and emission are governed not only by the structure of the individual molecules but also by their supramolecular structures and intermolecular interactions to a large extent. Electronic circular dichroism, ECD, and its emission counterpart, circularly polarized luminescence, CPL, provide tools for studying aggregated states and the key properties to be sought for designing innovative devices. In this review, we shall present a comprehensive coverage of chiroptical properties measured on thin films of organic π-conjugated molecules. In the first part, we shall discuss some general concepts of ECD, CPL, and other chiroptical spectroscopies, with a focus on their applications to thin film samples. In the following, we will overview the existing literature on chiral π-conjugated systems whose thin films have been characterized by ECD and/or CPL, as well other chiroptical spectroscopies. Special emphasis will be put on systems with large dissymmetry factors (g_abs and g_lum) and on the application of ECD and CPL to derive structural information on aggregated states.

Steering the Self-Assembly Outcome of a Single NDI Monomer into Three Morphologically Distinct Supramolecular Assemblies, with Concomitant Change in Supramolecular Polymerization Mechanism

Noncovalent self-assembly creates an effective route to highly sophisticated supramolecular polymers with tunable properties. However, the outcome of this assembly process is highly dependent on external conditions. In this work, a monomeric naphthalene diimide (NDI), designed to allow solubility in a wide range of solvents, can assemble into three distinct noncovalent supramolecular species depending on solvent composition and temperature. Namely, while the self-assembly in chlorinated solvents yields relatively short, hydrogen-bonded nanotubes, the reduction of solvent polarity changes the assembly outcome, yielding π-π stacking polymers, which can further bundle into a more complex aggregate. The obtained polymers differ not only in their global morphology but-more strikingly-also in the thermodynamics and kinetics of their supramolecular self-assembly, involving isodesmic or two-stage cooperative assembly with kinetic hysteresis, respectively. Ultimately, three distinct assembly states can be accessed in a single experiment.

Quantitative first principles calculations of protein circular dichroism in the near-ultraviolet

Vibrational structure in the near-UV circular dichroism (CD) spectra of proteins is an important source of information on protein conformation and can be exploited to study structure and folding. A fully quantitative theory of the relationship between protein conformation and optical spectroscopy would facilitate deeper interpretation of and insight into biophysical and simulation studies of protein dynamics and folding. We have developed new models of the aromatic side chain chromophores toluene, p-cresol and 3-methylindole, which incorporate ab initio calculations of the Franck-Condon effect into first principles calculations of CD using an exciton approach. The near-UV CD spectra of 40 proteins are calculated with the new parameter set and the correlation between the computed and the experimental intensity from 270 to 290 nm is much improved. The contribution of individual chromophores to the CD spectra has been calculated for several mutants and in many cases helps rationalize changes in their experimental spectra. Considering conformational flexibility by using families of NMR structures leads to further improvements for some proteins and illustrates an informative level of sensitivity to side chain conformation. In several cases, the near-UV CD calculations can distinguish the native protein structure from a set of computer-generated misfolded decoy structures.

Generation of a Multicomponent Library of Disulfide Donor-Acceptor Architectures Using Dynamic Combinatorial Chemistry

We describe here the generation of new donor-acceptor disulfide architectures obtained in aqueous solution at physiological pH. The application of a dynamic combinatorial chemistry approach allowed us to generate a large number of new disulfide macrocyclic architectures together with a new type of [2]catenanes consisting of four distinct components. Up to fifteen types of structurally-distinct dynamic architectures have been generated through one-pot disulfide exchange reactions between four thiol-functionalized aqueous components. The distribution of disulfide products formed was found to be strongly dependent on the structural features of the thiol components employed. This work not only constitutes a success in the synthesis of topologically- and morphologically-complex targets, but it may also open new horizons for the use of this methodology in the construction of molecular machines.

Charge-transfer complexation between naphthalene diimides and aromatic solvents

Naphthalene diimides (NDIs) form emissive ground-state charge-transfer (CT) complexes with various electron rich aromatic solvents like benzene, o-xylene and mesitylene. TD-DFT calculation of the complexes suggests CT interaction and accounts for the observed ground-state changes.

Vibronic structure in the far-UV electronic circular dichroism spectra of proteins

The Franck–Condon effect is considered and the vibrational structure of the π_nbπ* transition of the peptide backbone is incorporated into matrix method calculations of the electronic circular dichroism (CD) spectra of proteins in the far-ultraviolet. We employ the state-averaged CASPT2 method to calculate the ground and π_nbπ* excited state geometries and frequencies of N-methylacetamide (NMA), which represents the peptide chromophore. The results of these calculations are used to incorporate vibronic levels of the excited states into the matrix method calculation. The CD spectra of a set of 49 proteins, comprising a range of structural types, are calculated to assess the influence of the vibrational structure. The calculated spectra of α-helical proteins are better resolved using the vibronic parameters and correlation between the experimental and the calculated intensity of less regular β structure proteins improves over most wavelengths in the far-UV. No obvious improvement is observed in the calculated spectra of regular β-sheet proteins. Our high-level ab initio calculations of the vibronic structure of the π_nbπ* transition in NMA have provided some further insight into the physical origins of the nature of protein CD spectra in the far-UV.

Biomimetic molecular organization of naphthalene diimide in the solid state: tunable (chiro-) optical, viscoelastic and nanoscale properties

Biomimetic molecular organization of naphthalene diimide in the solid state: tunable (chiro-) optical, viscoelastic and nanoscale properties.

Amino acid derivatized arylenediimides: a versatile modular approach for functional molecular materials

Nature's elegant molecular designs and their assemblies with specific structure-property correlations have inspired researchers to design and develop bio-mimics for advanced functional applications. To realize such advanced molecular materials, naturally evolved amino acids are arguably the ideal auxiliaries due to their remarkable molecular/chiral recognition and distinctive sequence specific self-assembling properties. Over the years, this modular approach of derivatizing naphthalenediimides (NDIs) and perylenediimides (PDIs) with amino acids and peptides have resulted in several hitherto unknown molecular assemblies with phenomenal impact on their performance. Derivatization with versatile arylenediimides is especially interesting due to their wide spread applications in fields ranging from biomedicine to electronics. Herein some of these seminal reports of this rapidly emerging field and the design principles embraced are discussed.

Helical assembly induced by hydrogen bonding from chiral carboxylic acids based on perylene bisimides

The control over self-assembly behavior becomes absolutely critical because it is dependent on the orientation and morphology. The motivation is focused on borrowing the help of O-H···O hydrogen bonding interactions to realize the control in chiral self-assembly. A series of perylene bisimide (PBI) dyes 3a-3d bearing chiral amino acid derivatives on the imide N atoms and four phenoxy-type substituents at the bay positions of the perylene core were synthesized. Optical properties and aggregation behavior of PBIs were investigated by absorption, fluorescence, circular dichroism (CD), and (1)H NMR spectroscopy. Except for the chiral ester 3c and achiral 3d, chiral dyes 3a and 3b show bisignated CD signals, indicating that the chiral carboxylic acid-functionalized PBI systems are found to be spontaneously self-assembled into supramolecular helices via intermolecular hydrogen bonding rather than π-π stacking. Furthermore, the chirality-controlled helical superstructures are strongly dependent on several factors, such as solvent polarity, concentration, and temperature. The supramolecular helical chirality can be well-controlled by the chiral amino acid residues in the PBI system; that is, the assembled clockwise (plus, P) or anticlockwise (minus, M) helices can be induced by L- or D-isomers, respectively.