Noncovalent Systems Research Articles

Non-covalent self-assembly of substituted phthalocyanine with C60, C70, and 9-phenylanthracene: Spectroscopic insights and DFT calculations

Self-assembly of non-covalent donor-acceptor systems based on (octakis-3,5-di-tert-butylphenoxy)phthalocyanine (H2Pc(3,5-tBuPhO)8) and С60, С70 or 9-phenylanthracene (PhAn) is observed and described using the UV–vis and steady-state/time-resolved fluorescence methods. The 1:1 stoichiometry of the H2Pc(3,5-tBuPhO)8 - С60/С70/PhAn supramolecule was established by Job's method. The fluorescence quenching of phthalocyanine in the mentioned systems in toluene, indicating close bonding between a donor and an acceptor, was observed. The bonding constants are 1.2 × 104 M−1, 2.4 × 104 M−1, and 3.9 × 102 M−1 for the C60, C70, and PhAn derivatives, respectively. Using time-resolved fluorescence measurements, the static mechanism of quenching was established. The H2Pc(3,5-tBuPhO)8 fluorescence lifetimes in the absence and presence of С60/С70/PhAn, the charge separation rate constant (kCS) and the charge-separated state quantum yield (ΦCS) of donor-acceptor systems were calculated. (С70)H2Pc(3,5-tBuPhO)8 displays the highest kCS and ΦCS in good agreement with its stability parameter. Quantum-chemical calculations of the molecular spatial/electronic structure and the HOMO/LUMO composition that were revealed by DFT and TD DFT methods point to the H2Pc(3,5-tBuPhO)8 → fullerenes redistribution of the electron density and to the opposite one in the PhAn complex.

Exploring the Reactivity of Donor-Acceptor Systems through a Combined Conceptual and Constrained DFT Approach.

In the context of the conceptual density functional theory (cDFT) and based on the computational efficiency of the constrained DFT (CDFT), we demonstrate that chemical reactivity can be governed by the difference between the local interacting chemical potentials of the reactants (referred as Edual), in agreement with Sanderson's equalization principle. In a proof-of-concept study, we investigated illustrative examples involving typical non-covalent donor-acceptor systems and reactive systems are provided. For the selected systems, our approach reveals significant mimicking between Edual and the DFT-computed intermolecular interaction energy profiles. We further evaluate the influence of the Coulomb and exchange-correlation contributions in Edual. These latter results suggest that numerous potential energy surfaces of clusters can be explored using a Sanderson-like model only based on classical interactions between molecular orbitals domains. To conclude, this study achieved a deeper understanding of the principles of cDFT and assessed, in a wider context, its efficiency in predicting the chemical reactivity.

Balance between Physical Interpretability and Energetic Predictability in Widely Used Dispersion-Corrected Density Functionals.

We assess the performance of different dispersion models for several popular density functionals across a diverse set of noncovalent systems, ranging from the benzene dimer to molecular crystals. By analyzing the interaction energies and their individual components, we demonstrate that there exists variability across different systems for empirical dispersion models, which are calibrated for reproducing the interaction energies of specific systems. Thus, parameter fitting may undermine the underlying physics, as dispersion models rely on error compensation among the different components of the interaction energy. Energy decomposition analyses reveal that, the accuracy of revPBE-D3 for some aqueous systems originates from significant compensation between dispersion and charge transfer energies. However, revPBE-D3 is less accurate in describing systems where error compensation is incomplete, such as the benzene dimer. Such cases highlight the propensity for unpredictable behavior in various dispersion-corrected density functionals across a wide range of molecular systems, akin to the behavior of force fields. On the other hand, we find that SCAN-rVV10, a targeted-dispersion approach, affords significant reductions in errors associated with the lattice energies of molecular crystals, while it has limited accuracy in reproducing structural properties. Given the ubiquitous nature of noncovalent interactions and the key role of density functional theory in computational sciences, the future development of dispersion models should prioritize the faithful description of the dispersion energy, a shift that promises greater accuracy in capturing the underlying physics across diverse molecular and extended systems.

Recent Progress in the Field of Intrinsic Self-Healing Elastomers

Self-healing elastomers refer to a class of synthetic polymers that possess the unique ability to autonomously repair from internal and external damages. In recent years, significant progress has been made in the field of self-healing elastomers. In particular, intrinsic self-healing elastomers have garnered a great deal of attention. This mini-review outlines recent advancements in the mechanisms, preparation methods, and properties of various intrinsic self-healing elastomers based on non-covalent bond systems, reversible covalent bond systems, and multiple dynamic bond composite systems. We hope that this review will prove valuable to researchers in order to facilitate the development of novel strategies and technologies for preparing high-performance self-healing elastomers for advanced applications.

Post-Kohn-Sham Random-Phase Approximation and Correction Terms in the Expectation-Value Coupled-Cluster Formulation.

Using expectation-value coupled-cluster theory and many-body perturbation theory (MBPT), we formulate a series of corrections to the post-Kohn-Sham (post-KS) random-phase approximation (RPA) energy. The beyond-RPA terms are of two types: those accounting for the non-Hartree-Fock reference and those introducing the coupled-cluster doubles non-ring contractions. The contributions of the former type, introduced via the semicanonical orbital basis, drastically reduce the binding strength in noncovalent systems. The good accuracy is recovered by the attractive third-order doubles correction referred to as Ec2g. The existing RPA approaches based on KS orbitals neglect most of the proposed corrections but can perform well thanks to error cancellation. The proposed method accounts for every contribution in the state-of-the-art renormalized second-order perturbation theory (rPT2) approach but adds additional terms which initially contribute in the third order of MBPT. The cost of energy evaluation scales as noniterative in the implementation with low-rank tensor decomposition. The numerical tests of the proposed approach demonstrate accurate results for noncovalent dimers of polar molecules and for the challenging many-body noncovalent cluster of CH4···(H2O)20.

Dynamic Covalent Self-sorting in Molecular and Polymeric Architectures Enabled by Spiroborate Bond Exchange.

Self-sorting is commonly observed in complex reaction systems, which has been utilized to guide the formation of single major by-design molecules. However, most studies have been focused on non-covalent systems, and using self-sorting to achieve covalently bonded architectures is still relatively less explored. Herein, we first demonstrated the dynamic nature of spiroborate linkage and systematically studied the self-sorting behavior observed in the transformation between spiroborate-linked well-defined polymeric and molecular architectures, which is enabled by spiroborate bond exchange. The scrambling between a macrocycle and a 1D helical covalent polymer led to the formation of a molecular cage, whose structures are all unambiguously elucidated by single-crystal X-ray diffraction. The results indicate that the molecular cage is the thermodynamically favored product in this multi-component reaction system. This work represents the first example of a 1D polymeric architecture transforming into a shape-persistent molecular cage, driven by dynamic covalent self-sorting. This study will further guide the design of spiroborate-based materials and open the possibilities for the development of novel complex yet responsive dynamic covalent molecular or polymeric systems.

Strengths and limitations of the adiabatic exact-exchange kernel for total energy calculations.

We investigate the adiabatic approximation to the exact-exchange kernel for calculating correlation energies within the adiabatic-connection fluctuation-dissipation framework of time-dependent density functional theory. A numerical study is performed on a set of systems having bonds of different character (H2 and N2 molecules, H-chain, H2-dimer, solid-Ar, and the H2O-dimer). We find that the adiabatic kernel can be sufficient in strongly bound covalent systems, yielding similar bond lengths and binding energies. However, for non-covalent systems, the adiabatic kernel introduces significant errors around equilibrium geometry, systematically overestimating the interaction energy. The origin of this behavior is investigated by studying a model dimer composed of one-dimensional, closed-shell atoms, interacting via soft-Coulomb potentials. The kernel is shown to exhibit a strong frequency dependence at small to intermediate atomic separation that affects both the low-energy spectrum and the exchange-correlation hole obtained from the corresponding diagonal of the two-particle density matrix.

Accuracy of Noncovalent Interactions Involving d-Elements by the 1-Determinant Fixed-Node Diffusion Monte Carlo Method with Effective Core Potentials.

A critical assessment of effective core potential (ECP)-based single-determinant (SD) fixed-node diffusion quantum Monte Carlo (FNDMC) accuracy in prototypical noncovalent closed-shell systems involving d-elements is presented. Careful analysis of biases and elimination of possible bias sources leads to two findings of practical importance for SD FNDMC in these systems. First, in some systems (HCu:HCu, HCu:CuH), SD FNDMC reveals large biases of interaction energy differences (significantly exceeding the target 2% relative error) vs a reliable coupled-cluster CCSD(T)/CBS (complete basis set) reference. Second, the leading error of SD FNDMC with ECPs was attributed to a higher nuclear charge Z of d-group (pseudo) atoms, when compared to sp elements, in line with a previously reported finding that aggregate SD FNDMC bias tends to increase in systems with higher electronic densities. Therefore, SD FNDMC should only be used with caution in systems with a large Z.

Novel MXene sensors based on fast healing vitrimers

Soft matter containing Ti3C2Tx MXenes exhibits promising potential in electromechanical sensor development. Current systems suffer from a decrease in sensibility up to complete breakdown due to small structural defects that will be generated during their longtime practical service. Various non-covalent hydrogel systems, based on hydrogen bonding and ionic coupling, have been employed to improve their durability related to their repairability. However, Ti3C2Tx MXenes are not stable in those networks, since they will be irreversibly oxidized in high humidity environment during practical application. Here, we report the use of a novel dynamic covalent bond based network – a MXene acrylate vitrimer network (MAVIN) with a low glass transition temperature, which can not only be repaired fast with high efficiency but also protects the MXenes in sensor applications from oxidation under working conditions. In addition, owing to the strong microwave absorptivity of Ti3C2Tx and of the flexible dynamic covalent bond network, a damaged MAVIN sensor can be repaired by microwave radiation with a high healing efficiency of 92.4% within 1 minute, which is as good as the best healing efficiency reported in literature so far but 30 times faster. With stability at a voltage of 3 V and fast healing demonstrated, MAVIN promises potential usage in reliable and sustainable strain sensors.

Microflow size exclusion chromatography to preserve micromolar affinity complexes and achieve subunit separations for native state mass spectrometry

For high throughput native mass spectrometry (MS) protein characterization, it is advantageous to desalt and separate proteins by size exclusion chromatography (SEC). Sensitivity, resolution, and speed in these methods remain limited by standard SEC columns. Moreover, the efficient packing of small bore columns is notoriously difficult. SEC sensitivity is inherently limited because solutes are not focused into concentrated bands and low affinity native complexes may dissociate on column. Recent work evaluated the suitability of crosslinked gel media in small bore formats for online desalting. Here, small bore format online SEC for native MS studies is again investigated but with alternative materials. We systematically studied the utility of diol and hydroxy terminated polyethylene oxide (PEO) bonded 1.7 µm organosilica particles as packed into 1 mm ID stainless steel (SS) hardware and hardware treated with hydrophilic hybrid surface technology (h-HST). For the equivalent diol-bonded particle and hardware, UV limits of detection (LODs) were reduced 32 to 89% with a microflow separation (15 µL/min) on a 1 × 50 mm column as compared to a 4.6 × 150 mm high-flow separation (300 µL/min) at the same linear velocity. Run times were also shortened by 45%. A switch from SS to h-HST hardware led to a significant reduction in secondary interactions and a corresponding improvement in detection limits for trastuzumab, myoglobin, IgG and albumin for both UV and MS. Coupling of the small bore columns to multichannel microflow emitters resulted in 10 to 100-fold gains in MS sensitivity, depending on the analyte. MS LOD values were significantly reduced into the low attomole ranges. Columns were then evaluated for their effects on the preservation of complexes, including concanavalin A, in its apo and ligand-bound states, and three therapeutically relevant noncovalent systems previously undetected on large column formats. The results suggest that the detection of large complexes by SEC is not just a function of sensitivity but is directly affected by chemical secondary interactions. The ability to detect 0.1 to 1 MDa complexes, with between 1 and 40 micromolar dissociation constants, represents a critical advancement for high-throughput native MS workflows as applied to the analysis of therapeutics.

How Accurate Are Approximate Density Functionals for Noncovalent Interaction of Very Large Molecular Systems?

Noncovalent intermolecular interactions are very important in many research areas. Therefore, it is vital to understand the extent to which approximate density functionals give a proper description of noncovalent interactions. Previous research has demonstrated that some approximate density functionals can predict usefully accurate interaction energies for many noncovalent systems; however, most of that work is limited to small and moderate-sized molecules. Very recently though, accurate benchmarks have become available for some very large molecules. The present work applies 21 approximate density functionals to compute the binding energies of seven large molecular systems that have a number of atoms ranging from 200 to 910. The results are judged by comparison to the recently published CIM-DLPNO-CCSD(T) results, which are assumed to provide a reliable benchmark. The five most accurate methods among those tested are found to be PW6B95-D4, PW6B95-D3(BJ), revM11, M06-L, and MN15.

DFT Investigation of Porphyrin Aggregates

Owing the attractive potential applications of porphyrin assemblies in photocatalysis, sensors and material science, nowadays studies concerning porphyrin aggregation are largely diffused. These chromophores can organize in elaborated architectures by an assorted set of non-covalent interactions (i.e. π–π stacking, H-bonding, metal coordination, hydrophobic effect, and electrostatic forces) between the tetrapyrrolic macrocycles, mostly in J-or H-aggregated species, where the aromatic platforms are stacked side by side and face to face, respectively. UV-vis spectroscopy allows the identification of the porphyrin arrangement within the aggregates, through the modified spectral features of the porphyrin monomer following the interaction among the porphyrin units. Despite plenty of experimental investigations dealing with the self-organization of porphyrin both in solution and at the solid state, computational studies are still limited.In this communication, a computational examination of the different porphyrin aggregation approaches will be presented, taking into account the amphiphilic [5-{4-(3-trimethylammonium)propyloxyphenyl}-10,15,20-triphenylporphyrin] chloride, whose aggregation behavior has been previously experimentally investigated. In particular, the definition of appropriate functionals to study and characterize porphyrin aggregates, to get more insights on the kind of the interactions responsible for the formation of the specific noncovalent systems (J-, H-, T- or cation-π aggregates) experimentally observed will be proposed.Fig. 1. Optimized geometry of H-type (left) and cation-π (right) dimers of [5-{4-(3-trimethylammonium)propyloxyphenyl}-10,15,20-triphenylporphyrin] chloride in water, with WB97XD functional and 6-31G(d) basis set. Figure 1

Covalent and non-covalent systems based on s-, p-, and d-metal macroheterocyclic complexes and fullerenes

The review summarizes various systems containing macroheterocyclic donor platforms and fullerenes. The specific features of the chemical structure and spectral properties of such molecular systems, charge transfer processes in complexes and mechanisms of their formation, and potential fields of their practical application are considered. Special attention is given to supra-molecular systems, in which metal-containing porphyrins/phthalocyanines bearing a complex-forming cation other than zinc act as electron donors.

Poly(2-oxazoline)- and Poly(2-oxazine)-Based Self-Assemblies, Polyplexes, and Drug Nanoformulations-An Update.

For many decades, poly(2-oxazoline)s and poly(2-oxazine)s, two closely related families of polymers, have led the life of a rather obscure research topic with only a few research groups world-wide working with them. This has changed in the last five to ten years, presumably triggered significantly by very promising clinical trials of the first poly(2-oxazoline)-based drug conjugate. The huge chemical and structural toolbox poly(2-oxazoline)s and poly(2-oxazine)s has been extended very significantly in the last few years, but their potential still remains largely untapped. Here, specifically, the developments in macromolecular self-assemblies and non-covalent drug delivery systems such as polyplexes and drug nanoformulations based on poly(2-oxazoline)s and poly(2-oxazine)s are reviewed. This highly dynamic field benefits particularly from the extensive synthetic toolbox poly(2-oxazoline)s and poly(2-oxazine)s offer and also may have the largest potential for a further development. It is expected that the research dynamics will remain high in the next few years, particularly as more about the safety and therapeutic potential of poly(2-oxazoline)s and poly(2-oxazine)s is learned.

Non-covalent supramolecular systems with photoinduced electron transfer based on zinc bis(dipyrromethenate)s and C60

In this paper, we continue the study of non-covalent supramolecular systems based on zinc bis(dipyrromethenate)s ([Zn2L2]) with fullerene C60 and present the results of study of [Zn2L2]s periphery methylation degree effect on their supramolecular complexation with C60. The structural organization and spectral properties of supramolecular systems based on [Zn2L2]s and C60 were studied by means of UV/vis, fluorescence, time-resolved fluorescence, elemental analysis, FT-IR, PXRD, 1H NMR, DOSY spectroscopy, and computer modeling. The revealed features and the photoelectrochemical characteristics (photocurrent density, IPCE) obtained by the amperometric method give evidence of potential usage of [Zn2L2]s-C60 supramolecular complexes with 1:4 stoichiometry as optoelectronics and photovoltaic devices components.

How Water in Aliphatic Solvents Directs the Interference of Chemical Reactivity in a Supramolecular System.

Water is typically considered to be insoluble in alkanes. Recently, however, monomerically dissolved water in alkanes has been shown to dramatically impact the structure of hydrogen-bonded supramolecular polymers. Here, we report that water in methylcyclohexane (MCH) also determines the outcome of combining a Michael reaction with a porphyrin-based supramolecular system. In dry conditions, the components of the reaction do not affect or destabilize the supramolecular polymer, whereas in ambient or wet conditions the polymers are rapidly destabilized. Although spectroscopic investigations show no effect of water on the molecular structure of the supramolecular polymer, light scattering and atomic force microscopy experiments show that water increases the flexibility of the supramolecular polymer and decreases the polymer length. Through a series of titrations, we show that a cooperative interaction, involving the coordination of the amine catalyst to the porphyrin and complexation of the substrates to the flexible polymers invokes the depolymerization of the aggregates. Water crucially stabilizes these cooperative interactions to cause complete depolymerization in humid conditions. Additionally, we show that the humidity-controlled interference in the polymer stability occurs with various substrates, indicating that water may play a ubiquitous role in supramolecular polymerizations in oils. By controlling the amount of water, the influence of a covalent chemical process on noncovalent aggregates can be mediated, which holds great potential to forge a connection between chemical reactivity and supramolecular material structure. Moreover, our findings highlight that understanding cooperative interactions in multicomponent noncovalent systems is crucial to design complex molecular systems.

Characterisation of pH dependent peptide nanostructures using small angle scattering

The development of adaptive nanomaterials that are responsive to changes in their surrounding environment would enable such materials to be used in wide range of applications such as drug delivery vehicles or biosensors. Reversible boronic ester chemistry, which is used in this work, has several advantages as a building block for making adaptive nanomaterials including the ease of preparation, high sensitivity to external stimuli such as pH, and relative stability especially when compared to other non-covalent reversible systems. Herein, by using small boronic acids as anchor and peptides as connectors, we report progress in the initial development of novel, peptidyl-based pH dependent adaptive nanomaterials using reversible boronic ester chemistry and its characterisation using small angle X-ray scattering.

Biological macromolecule binding and anticancer activity of synthetic alkyne-containing L-phenylalanine derivatives.

Herein, we described the synthesis of two L-phenylalanines α-derivatized with a terminal alkyne moiety whose structures differed by phenyl ring halogen substitution (two o-Cl in 1 vs. one p-Br in 2) and investigated their effect on biological macromolecules and living cells. We explored their interaction with quadruplex DNA (G4 DNA), using tel26 and c-myc as models, and bovine serum albumin (BSA). By CD spectroscopy, we found that 1 caused minor tel26 secondary structure changes, leading also to a slight thermal stabilization of this hybrid antiparallel/parallel G4 structure, while the c-myc parallel topology remained essentially unchanged upon 1 binding. Other CD evidences showed the ability of 1 to bind BSA, while molecular docking studies suggested that the same molecule could be housed into the hydrophobic cavity between sub-domains IIA, IIB, and IIIA of the protein. Furthermore, preliminary aggregation studies, based on concentration-dependent spectroscopic experiments, suggested the ability of 1 to aggregate forming noncovalent polymeric systems in aqueous solution. Differently from 1, the bromine-modified compound was able to bind Cu(II) ion, likely with the formation of a CuL2 complex, as found by UV spectroscopy. Finally, cell tests excluded anycytotoxic effect of both compounds toward normal cells, but showed slight antiproliferative effects of 2 on PC3 cancerous cells at 24h, and of 1 on both T98G and MDA-MB-231 cancer cells at 48h.

Kinetics of Adsorption and Desorption of Non-Covalent Self-Assembling Systems

Self-Assembling systems that rely on non-covalent forces to drive ordering are the subject of intense study. Of particular interest are redox active systems like porphyrins and phthalocyanines that can generate self-assembled monolayers (SAMs) at the solution-solid interface. These offer the potential of creating highly ordered films from the simple process of solution dipping. In recent years, it has become clear that kinetics plays a significant role in determining the structure of these films. However, very little is known about the rates and mechanisms of the formation and stability of these interesting surface layers. In this talk we will present new data and models for the adsorption and desorption kinetics of non-covalent SAMs on gold surfaces. As might be suspected, the adsorption and desorption rates do not follow simple Langmuir behavior. Also, the potential for multilayer growth must be considered.

DFT Investigation of Porphyrin Aggregates

Owing the attractive potential applications of porphyrin assemblies in photocatalysis, sensors and material science, nowadays studies concerning porphyrin aggregation are largely diffused. These chromophores can organize in elaborated architectures by an assorted set of non-covalent interactions (i.e. π–π stacking, H-bonding, metal coordination, hydrophobic effect, and electrostatic forces) between the tetrapyrrolic macrocycles, mostly in J-or H-aggregated species, where the aromatic platforms are stacked side by side and face to face, respectively. UV-vis spectroscopy allows the identification of the porphyrin arrangement within the aggregates, through the modified spectral features of the porphyrin monomer following the interaction among the porphyrin units. Despite plenty of experimental investigations dealing with the self-organization of porphyrin both in solution and at the solid state, computational studies are still limited.In this communication, a computational examination of the different porphyrin aggregation approaches will be presented, taking into account the amphiphilic [5-{4-(3-trimethylammonium)propyloxyphenyl}-10,15,20-triphenylporphyrin] chloride, whose aggregation behavior has been previously experimentally investigated. In particular, the definition of appropriate functionals to study and characterize porphyrin aggregates, to get more insights on the kind of the interactions responsible for the formation of the specific noncovalent systems (J-, H-, T- or cation-π aggregates) experimentally observed will be proposed.Fig. Calculated structures of J-type (left) and cation-π (right) dimers of [5-{4-(3-trimethylammonium)propyloxyphenyl}-10,15,20-triphenylporphyrin] chloride. Figure 1